Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Qian Xu [aut, ctb],
Yongjuan Yang [aut, ctb],
Yanan Tian [aut, ctb],
Robert Chapkin [aut, ctb],
Jianhua Huang [aut, ctb],
James J. Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldKnk versions 1.0.1 dated 2021-01-22 and 1.0.3 dated 2026-01-25
DESCRIPTION | 33 +++---- MD5 | 22 ++-- NAMESPACE | 45 +++++---- R/dRegulation.R | 121 +++++++++++++------------ R/plotKO.R |only R/qFilter.R | 12 +- R/scQC.R | 69 +++++++------- R/scTenifoldKnk.R | 174 ++++++++++++++++++++++--------------- R/strictDirection.R | 14 +- README.md | 122 ++++++++++++++----------- inst/single-cell/example.csv | 202 +++++++++++++++++++++---------------------- man/plotKO.Rd |only man/scTenifoldKnk.Rd | 153 +++++++++++++++++--------------- 13 files changed, 519 insertions(+), 448 deletions(-)
Title: Mechanistic Metacommunity Simulator
Description: Flexible, mechanistic, and spatially explicit simulator of
metacommunities. It extends our previous package - 'rangr' (see
<https://github.com/ropensci/rangr>), which implemented a mechanistic
virtual species simulator integrating population dynamics and
dispersal. The 'mrangr' package adds the ability to simulate multiple
species interacting through an asymmetric matrix of pairwise
relationships, allowing users to model all types of biotic
interactions — competitive, facilitative, or neutral — within
spatially explicit virtual environments. This work was supported by
the National Science Centre, Poland, grant no. 2018/29/B/NZ8/00066 and
the Poznań Supercomputing and Networking Centre (grant no. pl0090-01).
Author: Katarzyna Markowska [aut, cre, cph],
Lechoslaw Kuczynski [aut, cph]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between mrangr versions 1.0.0 dated 2026-01-19 and 1.0.1 dated 2026-01-25
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Title: Missing Value Imputation in Parallel
Description: A framework that boosts the imputation of 'missForest' by Stekhoven, D.J. and Bühlmann, P. (2012) <doi:10.1093/bioinformatics/btr597> by harnessing parallel processing and through the fast Gradient Boosted Decision Trees (GBDT) implementation 'LightGBM' by Ke, Guolin et al.(2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>. 'misspi' has the following main advantages: 1. Allows embrassingly parallel imputation on large scale data. 2. Accepts a variety of machine learning models as methods with friendly user portal. 3. Supports multiple initializations methods. 4. Supports early stopping that prohibits unnecessary iterations.
Author: Zhongli Jiang [aut, cre]
Maintainer: Zhongli Jiang <happycatstat@gmail.com>
Diff between misspi versions 0.1.0 dated 2023-10-17 and 0.1.1 dated 2026-01-25
DESCRIPTION | 20 +++++++-------- MD5 | 18 ++++++++------ NEWS.md |only R/evaliq.R | 3 +- R/missar.R | 3 -- R/misspi-package.R |only R/misspi.R | 63 +++++++++++++++++++++++++++++++++++--------------- README.md |only man/evaliq.Rd | 3 +- man/missar.Rd | 3 -- man/misspi-package.Rd |only man/misspi.Rd | 6 ++-- 12 files changed, 74 insertions(+), 45 deletions(-)
Title: Data Sets from Mixed-Effects Models in S
Description: Data sets and sample analyses from Pinheiro and Bates,
"Mixed-effects Models in S and S-PLUS" (Springer, 2000).
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [cre, aut] ,
Steven Walker [aut]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
This is a re-admission after prior archival of version 0.9-3 dated 2019-02-08
Diff between MEMSS versions 0.9-3 dated 2019-02-08 and 0.9-4 dated 2026-01-25
DESCRIPTION | 31 +++++++++++++++++++++---------- MD5 | 4 ++-- man/Soybean.Rd | 4 ++-- 3 files changed, 25 insertions(+), 14 deletions(-)
Title: Matrix Computation Based Identification of Prime Implicants
Description: Computes the prime implicants or a minimal disjunctive normal form for a
logic expression presented by a truth table or a logic tree. Has been particularly
developed for logic expressions resulting from a logic regression analysis, i.e.
logic expressions typically consisting of up to 16 literals, where the prime implicants
are typically composed of a maximum of 4 or 5 literals.
Author: Holger Schwender [aut, cre]
Maintainer: Holger Schwender <holger.schw@gmx.de>
Diff between mcbiopi versions 1.1.6 dated 2018-10-06 and 1.1.7 dated 2026-01-25
DESCRIPTION | 12 +++++++----- MD5 | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-)
Title: Database Interface to 'Elasticsearch' and 'OpenSearch'
Description: Connect to 'Elasticsearch' and 'OpenSearch', 'NoSQL' databases
built on the 'Java' Virtual Machine and using the 'Apache' 'Lucene' library.
Interacts with the 'Elasticsearch' 'HTTP' API'
(<https://www.elastic.co/elasticsearch/>) and the
'OpenSearch' 'HTTP' 'API' (<https://opensearch.org/>).
Includes functions for setting connection details to 'Elasticsearch' and
'OpenSearch' instances, loading bulk data, searching for documents with
both 'HTTP' query variables and 'JSON' based body requests.
In addition, 'elastic' provides functions for interacting with APIs
for 'indices', documents, nodes, clusters, an interface to the cat API,
and more.
Author: Ralf Herold [cre] ,
Scott Chamberlain [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
This is a re-admission after prior archival of version 1.2.0 dated 2021-03-16
Diff between elastic versions 1.2.0 dated 2021-03-16 and 1.2.2 dated 2026-01-25
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| 33 elastic-1.2.2/elastic/R/docs_create.R | 2 elastic-1.2.2/elastic/R/docs_delete.R | 14 elastic-1.2.2/elastic/R/docs_delete_by_query.R | 82 elastic-1.2.2/elastic/R/docs_get.r | 24 elastic-1.2.2/elastic/R/docs_mget.r | 6 elastic-1.2.2/elastic/R/docs_update_by_query.R | 3 elastic-1.2.2/elastic/R/elastic-package.r | 14 elastic-1.2.2/elastic/R/explain.R | 4 elastic-1.2.2/elastic/R/field_caps.R | 16 elastic-1.2.2/elastic/R/field_stats.R | 46 elastic-1.2.2/elastic/R/fielddata.R | 56 elastic-1.2.2/elastic/R/index.R | 16 elastic-1.2.2/elastic/R/index_templates.R | 28 elastic-1.2.2/elastic/R/ingest.R | 32 elastic-1.2.2/elastic/R/mapping.R | 36 elastic-1.2.2/elastic/R/mtermvectors.R | 40 elastic-1.2.2/elastic/R/nodes.R | 6 elastic-1.2.2/elastic/R/parsers.r | 6 elastic-1.2.2/elastic/R/percolater.R | 56 elastic-1.2.2/elastic/R/reindex.R | 28 elastic-1.2.2/elastic/R/scroll.R | 16 elastic-1.2.2/elastic/R/search_shards.R | 24 elastic-1.2.2/elastic/R/search_template.R | 34 elastic-1.2.2/elastic/R/searchapis.R | 8 elastic-1.2.2/elastic/R/tasks.R | 24 elastic-1.2.2/elastic/R/termvectors.R | 10 elastic-1.2.2/elastic/R/tokenizer_set.R | 10 elastic-1.2.2/elastic/inst/WORDLIST |only elastic-1.2.2/elastic/inst/examples/bar.json | 12 elastic-1.2.2/elastic/inst/examples/foo.json | 12 elastic-1.2.2/elastic/inst/examples/gbif_data.json | 602 elastic-1.2.2/elastic/inst/examples/gbif_geo.json | 602 elastic-1.2.2/elastic/inst/examples/gbif_geopoint.json | 722 elastic-1.2.2/elastic/inst/examples/gbif_geoshape.json | 564 elastic-1.2.2/elastic/inst/examples/gbif_geosmall.json | 12 elastic-1.2.2/elastic/inst/examples/msearch_eg1.json | 4 elastic-1.2.2/elastic/inst/examples/msearch_eg2.json | 10 elastic-1.2.2/elastic/inst/examples/omdb.json | 358 elastic-1.2.2/elastic/inst/examples/plos_data.json | 2000 +- elastic-1.2.2/elastic/inst/examples/shakespeare_data.json |10000 +++++------ elastic-1.2.2/elastic/inst/examples/shakespeare_data_.json |10000 +++++------ elastic-1.2.2/elastic/inst/ignore/docs_bulk_plugins.R | 4 elastic-1.2.2/elastic/man/Search.Rd | 66 elastic-1.2.2/elastic/man/Search_template.Rd | 2 elastic-1.2.2/elastic/man/Search_uri.Rd | 4 elastic-1.2.2/elastic/man/alias.Rd | 6 elastic-1.2.2/elastic/man/cat.Rd | 2 elastic-1.2.2/elastic/man/count.Rd | 4 elastic-1.2.2/elastic/man/docs_bulk.Rd | 12 elastic-1.2.2/elastic/man/docs_bulk_create.Rd | 6 elastic-1.2.2/elastic/man/docs_bulk_delete.Rd | 9 elastic-1.2.2/elastic/man/docs_bulk_index.Rd | 10 elastic-1.2.2/elastic/man/docs_bulk_prep.Rd | 14 elastic-1.2.2/elastic/man/docs_bulk_update.Rd | 10 elastic-1.2.2/elastic/man/docs_create.Rd | 2 elastic-1.2.2/elastic/man/docs_delete.Rd | 4 elastic-1.2.2/elastic/man/docs_delete_by_query.Rd | 18 elastic-1.2.2/elastic/man/docs_get.Rd | 4 elastic-1.2.2/elastic/man/docs_mget.Rd | 2 elastic-1.2.2/elastic/man/docs_update_by_query.Rd | 5 elastic-1.2.2/elastic/man/elastic.Rd | 11 elastic-1.2.2/elastic/man/explain.Rd | 2 elastic-1.2.2/elastic/man/field_caps.Rd | 2 elastic-1.2.2/elastic/man/field_stats.Rd | 6 elastic-1.2.2/elastic/man/fielddata.Rd | 6 elastic-1.2.2/elastic/man/index_template.Rd | 2 elastic-1.2.2/elastic/man/indices.Rd | 10 elastic-1.2.2/elastic/man/ingest.Rd | 8 elastic-1.2.2/elastic/man/mapping.Rd | 14 elastic-1.2.2/elastic/man/mtermvectors.Rd | 4 elastic-1.2.2/elastic/man/nodes.Rd | 2 elastic-1.2.2/elastic/man/percolate.Rd | 6 elastic-1.2.2/elastic/man/reindex.Rd | 2 elastic-1.2.2/elastic/man/search_shards.Rd | 2 elastic-1.2.2/elastic/man/searchapis.Rd | 2 elastic-1.2.2/elastic/man/tasks.Rd | 2 elastic-1.2.2/elastic/man/termvectors.Rd | 2 elastic-1.2.2/elastic/man/tokenizer_set.Rd | 4 elastic-1.2.2/elastic/tests/test-all.R |only elastic-1.2.2/elastic/tests/testthat/teardown.R | 3 elastic-1.2.2/elastic/tests/testthat/test-alias.R | 6 elastic-1.2.2/elastic/tests/testthat/test-cat.R | 10 elastic-1.2.2/elastic/tests/testthat/test-count.R | 11 elastic-1.2.2/elastic/tests/testthat/test-docs.R | 38 elastic-1.2.2/elastic/tests/testthat/test-docs_bulk.R | 37 elastic-1.2.2/elastic/tests/testthat/test-docs_bulk_prep.R | 50 elastic-1.2.2/elastic/tests/testthat/test-docs_bulk_update.R | 22 elastic-1.2.2/elastic/tests/testthat/test-explain.R | 2 elastic-1.2.2/elastic/tests/testthat/test-indices.R | 24 elastic-1.2.2/elastic/tests/testthat/test-ingest.R | 20 elastic-1.2.2/elastic/tests/testthat/test-mappings.R | 33 elastic-1.2.2/elastic/tests/testthat/test-msearch.R | 6 elastic-1.2.2/elastic/tests/testthat/test-mtermvectors.R | 7 elastic-1.2.2/elastic/tests/testthat/test-nodes.R | 4 elastic-1.2.2/elastic/tests/testthat/test-scroll.R | 18 elastic-1.2.2/elastic/tests/testthat/test-search.r | 113 elastic-1.2.2/elastic/tests/testthat/test-search_template.R | 30 elastic-1.2.2/elastic/tests/testthat/test-search_uri.R | 28 elastic-1.2.2/elastic/tests/testthat/test-termvectors.R | 16 elastic-1.2.2/elastic/tests/testthat/test-type_remover.R | 15 elastic-1.2.2/elastic/tests/testthat/test-validate.R | 11 124 files changed, 13522 insertions(+), 13434 deletions(-)
Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through
an integrated workflow. Provides functions for image/video
organization and metadata extraction, species/individual
identification. Creates detection histories for occupancy and spatial
capture-recapture analyses, with support for multi-season studies.
Includes tools for fitting community occupancy models in JAGS and
NIMBLE, and an interactive dashboard for survey data visualization and
analysis. Features visualization of species distributions and activity
patterns, plus export capabilities for GIS and reports. Emphasizes
automation and reproducibility while maintaining flexibility for
different study designs.
Author: Juergen Niedballa [aut, cre] ,
Alexandre Courtiol [aut] ,
Rahel Sollmann [aut] ,
John Mathai [ctb],
Seth Timothy Wong [ctb] ,
An The Truong Nguyen [ctb] ,
Azlan bin Mohamed [ctb] ,
Andrew Tilker [ctb] ,
Roshan Guharajan [ctb] ,
Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 3.0.0 dated 2025-09-28 and 3.0.2 dated 2026-01-25
camtrapR-3.0.0/camtrapR/tests/testthat/test_surveyReport.R |only camtrapR-3.0.2/camtrapR/DESCRIPTION | 92 +- camtrapR-3.0.2/camtrapR/MD5 | 68 + camtrapR-3.0.2/camtrapR/NAMESPACE | 1 camtrapR-3.0.2/camtrapR/NEWS.md | 14 camtrapR-3.0.2/camtrapR/R/cameraOperation.R | 7 camtrapR-3.0.2/camtrapR/R/communityModel.R | 10 camtrapR-3.0.2/camtrapR/R/createCovariates.R | 14 camtrapR-3.0.2/camtrapR/R/detectionHistory.R | 7 camtrapR-3.0.2/camtrapR/R/detectionMaps.R | 2 camtrapR-3.0.2/camtrapR/R/filterRecordTable.R | 12 camtrapR-3.0.2/camtrapR/R/plot.R | 55 - camtrapR-3.0.2/camtrapR/R/recordTableIndividual.R | 15 camtrapR-3.0.2/camtrapR/R/surveyDashboard.R | 2 camtrapR-3.0.2/camtrapR/R/surveyReport.R | 21 camtrapR-3.0.2/camtrapR/R/variousOtherHelperFunctions.R | 401 +--------- camtrapR-3.0.2/camtrapR/README.md | 10 camtrapR-3.0.2/camtrapR/build/vignette.rds |binary camtrapR-3.0.2/camtrapR/inst/doc/camtrapr1.pdf |binary camtrapR-3.0.2/camtrapR/inst/doc/camtrapr2.pdf |binary camtrapR-3.0.2/camtrapR/inst/doc/camtrapr5.html | 395 +++++---- camtrapR-3.0.2/camtrapR/inst/pictures/sample_images_species_dir/StationA/PBE/20251112_100312.mp4 |only camtrapR-3.0.2/camtrapR/man/aggregateStations.Rd | 148 +-- camtrapR-3.0.2/camtrapR/man/cameraOperation.Rd | 7 camtrapR-3.0.2/camtrapR/man/surveyReport.Rd | 12 camtrapR-3.0.2/camtrapR/tests/testthat/fixtures |only camtrapR-3.0.2/camtrapR/tests/testthat/test-activity_plots.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-checkSpeciesIdentification.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-checkSpeciesNames.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-communityModels.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-detectionMaps.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-filterRecordTable.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-image_management_functions.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-readWildlifeInsights.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-readcamtrapDP.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-recordTableIndividual.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-spatialDetectionHistory.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-speciesAccum.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-surveyDashboard.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test-surveyReport.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test_createCovariates.R |only camtrapR-3.0.2/camtrapR/tests/testthat/test_recordTable.R | 9 42 files changed, 541 insertions(+), 761 deletions(-)
Title: Analysis of High-Dimensional Categorical Data Such as SNP Data
Description: Tools for the analysis of high-dimensional data developed/implemented
at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME).
Main focus is on SNP data. But most of the functions can also be applied to other
types of categorical data.
Author: Holger Schwender [aut, cre],
Arno Fritsch [ctb]
Maintainer: Holger Schwender <holger.schw@gmx.de>
Diff between scrime versions 1.3.5 dated 2018-12-01 and 1.3.7 dated 2026-01-25
DESCRIPTION | 14 +++++++++----- MD5 | 4 ++-- man/simulateSNPs.Rd | 4 ++-- 3 files changed, 13 insertions(+), 9 deletions(-)
Title: Apply Unsupervised Segmentation Algorithms from 'OTB'
Description: Apply unsupervised segmentation algorithms included in 'Orfeo ToolBox' software (<https://www.orfeo-toolbox.org/>), such as mean shift or watershed segmentation.
Author: Adrian Cidre Gonzalez [aut, cre]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between OTBsegm versions 0.1.0 dated 2025-05-06 and 0.1.2 dated 2026-01-25
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 22 ++++++- R/LSMS.R | 3 - R/algorithms.R | 18 +++++- README.md | 9 +-- man/segm_lsms.Rd | 4 - tests/testthat/test-algorithms.R | 110 ++++++++++++++++++++------------------- 8 files changed, 106 insertions(+), 80 deletions(-)
Title: Calibrated Model Fusion Approach to Combine Surrogate Markers
Description: Uses a calibrated model fusion approach to optimally combine multiple surrogate markers. Specifically, two initial estimates of optimal composite scores of the markers are obtained; the optimal calibrated combination of the two estimated scores is then constructed which ensures both validity of the final combined score and optimality with respect to the proportion of treatment effect explained (PTE) by the final combined score. The primary function, pte.estimate.multiple(), estimates the PTE of the identified combination of multiple surrogate markers. Details are described in Wang et al (2022) <doi:10.1111/biom.13677>. A tutorial for the package is available at <https://www.laylaparast.com/cmfsurrogate> and a Shiny App is available at <https://parastlab.shinyapps.io/CMFsurrogateApp/>.
Author: Xuan Wang [aut],
Layla Parast [cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between CMFsurrogate versions 1.0 dated 2022-09-23 and 1.1 dated 2026-01-25
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 1 + R/funs.R | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++--------- 4 files changed, 60 insertions(+), 18 deletions(-)
Title: Multivariate Statistical Methods
Description: Algorithms to build set partitions and commutator matrices and their use in the
construction of multivariate d-Hermite polynomials; estimation and derivation of theoretical vector moments and vector
cumulants of multivariate distributions; conversion formulae for multivariate moments and cumulants. Applications to
estimation and derivation of multivariate measures of skewness and kurtosis; estimation and derivation of asymptotic
covariances for d-variate Hermite polynomials, multivariate moments and cumulants and measures of skewness and kurtosis.
The formulae implemented are discussed in Terdik (2021, ISBN:9783030813925), "Multivariate Statistical Methods".
Author: Gyorgy Terdik [aut],
Emanuele Taufer [aut, cre]
Maintainer: Emanuele Taufer <emanuele.taufer@unitn.it>
Diff between MultiStatM versions 2.0.0 dated 2024-07-26 and 2.1.0 dated 2026-01-25
DESCRIPTION | 17 +- MD5 | 92 +++++++---- NAMESPACE | 58 +++++++ NEWS.md | 18 ++ R/Approximations.r |only R/CallFcts.R | 44 +++-- R/Commutators.R | 12 - R/Deprecated.r |only R/Distributions.R | 384 ++++++++++++++++++++++++++++++++++++++++++++++++- R/Estimation.r | 106 +------------ R/Hermite.r | 52 ++++++ R/RcppExports.R |only R/RecursionF.r |only R/SupportFun.r | 147 ++++++++++-------- R/zzz.r |only build/vignette.rds |binary inst/doc/Overview.R | 4 inst/doc/Overview.Rmd | 12 - inst/doc/Overview.html | 323 ++++++++++++++++++++--------------------- man/CommutatorIndx.Rd | 9 - man/CommutatorMatr.Rd | 2 man/Cum2Mom.Rd | 4 man/EVSKGenHyp.Rd |only man/EVSKSkewNorm.Rd | 6 man/EVSKSkewt.Rd |only man/EVSKUniS.Rd | 11 - man/Edgeworth.Rd |only man/EliminIndx.Rd | 4 man/EliminMatr.Rd | 4 man/GramCharlier.Rd |only man/IntEdgeworth.Rd |only man/IntGramCharlier.Rd |only man/IntHermiteN.Rd |only man/MTCE.Rd |only man/MargMomCum.Rd |only man/Mom2Cum.Rd | 4 man/MomCumCFUSN.Rd | 4 man/MomCumGenHyp.Rd |only man/MomCumMVt.Rd |only man/MomCumSkewNorm.Rd | 4 man/MomCumUniS.Rd | 4 man/MomCumZabs.Rd | 4 man/QplicIndx.Rd | 4 man/QplicMatr.Rd | 4 man/SampleEVSK.Rd | 4 man/SampleEdg.Rd |only man/SampleGC.Rd | 38 ---- man/SampleHermiteN.Rd | 23 -- man/SampleSkew.Rd | 7 man/SymIndx.Rd | 4 man/SymMatr.Rd | 4 man/UnivMomCum.Rd | 40 ----- man/rUniS.Rd | 4 src |only vignettes/Overview.Rmd | 12 - 55 files changed, 951 insertions(+), 522 deletions(-)
Title: Process Stream Temperature, Intermittency, and Conductivity
(STIC) Sensor Data
Description: A collection of functions for processing raw data from Stream Temperature, Intermittency, and Conductivity (STIC) loggers. 'STICr' (pronounced "sticker") includes functions for tidying, calibrating, classifying, and doing quality checks on data from STIC sensors. Some package functionality is described in Wheeler/Zipper et al. (2023) <doi:10.31223/X5636K>.
Author: Sam Zipper [aut, cre, cph] ,
Christopher T. Wheeler [aut] ,
Stephen Cook [ctb] ,
Delaney Peterson [ctb] ,
Sarah Godsey [ctb]
Maintainer: Sam Zipper <samzipper@ku.edu>
Diff between STICr versions 1.1.1 dated 2025-05-02 and 1.1.2 dated 2026-01-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/classify_wetdry.R | 2 +- README.md | 1 + build/vignette.rds |binary inst/doc/intro-to-STICr.html | 10 +++++----- 7 files changed, 20 insertions(+), 15 deletions(-)
Title: Ordination Methods for the Analysis of Beta-Diversity Indices
Description: The analysis of different aspects of biodiversity requires specific algorithms. For example, in regionalisation analyses, the high frequency of ties and zero values in dissimilarity matrices produced by Beta-diversity turnover produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, visualisation of biogeographical regionalisation can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to visualise and analyse pattern of biodiversity and to improve occurrence data for cryptic taxa.
Author: Leonardo Dapporto [aut, cre],
Matteo Ramazzotti [aut],
Simone Fattorini [aut],
Roger Vila [aut],
Gerard Talavera [aut],
Roger H.L. Dennis [aut]
Maintainer: Leonardo Dapporto <leondap@gmail.com>
Diff between recluster versions 2.9 dated 2020-07-26 and 3.4 dated 2026-01-25
DESCRIPTION | 49 ++++++++++------ MD5 | 47 ++++++++++----- NAMESPACE | 34 +++++++---- R/ah2sf.R |only R/ape_internal.R |only R/biodecrypt.R |only R/biodecrypt.cross.R |only R/biodecrypt.optimise.R |only R/biodecrypt.plot.R |only R/biodecrypt.view.R |only R/biodecrypt.wrap.R |only R/recluster.boot.R | 4 - R/recluster.cons.R | 11 +-- R/recluster.expl.R | 19 ++---- R/recluster.expl.diss.R | 79 ++++++++++++-------------- R/recluster.fst.R | 2 R/recluster.node.strength.R | 4 - R/recluster.plot.pie.R | 8 +- R/recluster.region.R | 132 ++++++++++++++++++++++---------------------- README.md |only man/biodecrypt.Rd |only man/biodecrypt.cross.Rd |only man/biodecrypt.optimise.Rd |only man/biodecrypt.plot.Rd |only man/biodecrypt.view.Rd |only man/biodecrypt.wrap.Rd |only man/recluster.Rd | 20 +++++- man/recluster.boot.Rd | 5 - man/recluster.cons.Rd | 6 -- man/recluster.expl.Rd | 4 - man/recluster.expl.diss.Rd | 15 +++-- man/recluster.region.Rd | 18 ++++-- 32 files changed, 252 insertions(+), 205 deletions(-)
Title: Interface for the 'QuickJS-NG' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript'
engine. The engine and all 'R' to 'JavaScript' interoperability is bundled
within the package, requiring no dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
QuickJS Authors [cph] ,
QuickJS-NG Authors [cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.8.1 dated 2025-09-20 and 1.9.0 dated 2026-01-25
QuickJSR-1.8.1/QuickJSR/R/utils.R |only QuickJSR-1.8.1/QuickJSR/inst/include |only QuickJSR-1.8.1/QuickJSR/src/quickjs/CMakeLists.txt |only QuickJSR-1.8.1/QuickJSR/src/quickjs/LICENSE |only QuickJSR-1.8.1/QuickJSR/src/quickjs/README.md |only QuickJSR-1.8.1/QuickJSR/src/quickjs/amalgam.js |only QuickJSR-1.8.1/QuickJSR/src/quickjs/api-test.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/builtin-array-fromasync.js |only QuickJSR-1.8.1/QuickJSR/src/quickjs/ctest.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/cxxtest.cc |only QuickJSR-1.8.1/QuickJSR/src/quickjs/dirent_compat.h |only QuickJSR-1.8.1/QuickJSR/src/quickjs/fuzz.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/meson.build |only QuickJSR-1.8.1/QuickJSR/src/quickjs/meson_options.txt |only QuickJSR-1.8.1/QuickJSR/src/quickjs/qjs.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/qjsc.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/repl.js |only QuickJSR-1.8.1/QuickJSR/src/quickjs/run-test262.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/standalone.js |only QuickJSR-1.8.1/QuickJSR/src/quickjs/test262-fast.conf |only QuickJSR-1.8.1/QuickJSR/src/quickjs/test262.conf |only QuickJSR-1.8.1/QuickJSR/src/quickjs/test262_errors.txt |only QuickJSR-1.8.1/QuickJSR/src/quickjs/tests.conf |only QuickJSR-1.8.1/QuickJSR/src/quickjs/unicode_download.sh |only QuickJSR-1.8.1/QuickJSR/src/quickjs/unicode_gen.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/unicode_gen_def.h |only QuickJSR-1.8.1/QuickJSR/src/quickjs/xsum.c |only QuickJSR-1.8.1/QuickJSR/src/quickjs/xsum.h |only QuickJSR-1.9.0/QuickJSR/DESCRIPTION | 7 QuickJSR-1.9.0/QuickJSR/LICENSE | 4 QuickJSR-1.9.0/QuickJSR/MD5 | 187 QuickJSR-1.9.0/QuickJSR/NAMESPACE | 16 QuickJSR-1.9.0/QuickJSR/NEWS.md | 182 QuickJSR-1.9.0/QuickJSR/R/JSContext.R | 338 - QuickJSR-1.9.0/QuickJSR/R/qjs.R | 158 QuickJSR-1.9.0/QuickJSR/R/quickjsr-package.R | 20 QuickJSR-1.9.0/QuickJSR/R/zzz.R | 8 QuickJSR-1.9.0/QuickJSR/README.md | 260 QuickJSR-1.9.0/QuickJSR/build/vignette.rds |binary QuickJSR-1.9.0/QuickJSR/inst/doc/working_with_js_types.R | 80 QuickJSR-1.9.0/QuickJSR/inst/doc/working_with_js_types.Rmd | 224 QuickJSR-1.9.0/QuickJSR/inst/doc/working_with_js_types.html | 1044 +-- QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_JSContext.R | 91 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_data_conversion.R | 144 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_qjs_eval.R | 16 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_to_json_asis.R | 20 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_to_json_dataframe.R | 32 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_to_json_date.R | 28 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_to_json_factor.R | 12 QuickJSR-1.9.0/QuickJSR/inst/tinytest/test_to_json_matrix.R | 22 QuickJSR-1.9.0/QuickJSR/man/JSContext-method-assign.Rd | 64 QuickJSR-1.9.0/QuickJSR/man/JSContext-method-call.Rd | 66 QuickJSR-1.9.0/QuickJSR/man/JSContext-method-get.Rd | 60 QuickJSR-1.9.0/QuickJSR/man/JSContext-method-source.Rd | 70 QuickJSR-1.9.0/QuickJSR/man/JSContext-method-validate.Rd | 58 QuickJSR-1.9.0/QuickJSR/man/JSContext.Rd | 42 QuickJSR-1.9.0/QuickJSR/man/QuickJSR-package.Rd | 58 QuickJSR-1.9.0/QuickJSR/man/from_json.Rd | 34 QuickJSR-1.9.0/QuickJSR/man/qjs_eval.Rd | 56 QuickJSR-1.9.0/QuickJSR/man/quickjs_version.Rd | 28 QuickJSR-1.9.0/QuickJSR/man/to_json.Rd | 38 QuickJSR-1.9.0/QuickJSR/src/Makevars | 10 QuickJSR-1.9.0/QuickJSR/src/include |only QuickJSR-1.9.0/QuickJSR/src/libquickjs.c | 2 QuickJSR-1.9.0/QuickJSR/src/quickjs/builtin-array-fromasync.h | 38 QuickJSR-1.9.0/QuickJSR/src/quickjs/cutils.c | 258 QuickJSR-1.9.0/QuickJSR/src/quickjs/cutils.h | 14 QuickJSR-1.9.0/QuickJSR/src/quickjs/dtoa.c |only QuickJSR-1.9.0/QuickJSR/src/quickjs/dtoa.h |only QuickJSR-1.9.0/QuickJSR/src/quickjs/quickjs-atom.h | 2 QuickJSR-1.9.0/QuickJSR/src/quickjs/quickjs-libc.c | 298 QuickJSR-1.9.0/QuickJSR/src/quickjs/quickjs-libc.h | 54 QuickJSR-1.9.0/QuickJSR/src/quickjs/quickjs.c | 3261 +++++----- QuickJSR-1.9.0/QuickJSR/src/quickjs/quickjs.h | 46 QuickJSR-1.9.0/QuickJSR/src/quickjsr.cpp | 131 QuickJSR-1.9.0/QuickJSR/tests/tinytest.R | 10 QuickJSR-1.9.0/QuickJSR/vignettes/working_with_js_types.Rmd | 224 77 files changed, 4151 insertions(+), 3664 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-30 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-22 1.0.1
2025-05-30 1.0.0
Title: Zero-Inflated and Hurdle INAR(1) Models
Description: Provides tools for estimating Zero-Inflated INAR(1)
(ZI-INAR(1)) and Hurdle INAR(1) (H-INAR(1)) models using 'Stan'.
It allows users to simulate time series data for these models,
estimate parameters, and evaluate model fit using various criteria.
Functions include model estimation, simulation, and likelihood-based metrics.
Author: Fusheng Yang [aut, cre],
Victor Hugo Lachos Davila [aut]
Maintainer: Fusheng Yang <fusheng.yang@uconn.edu>
Diff between ZIHINAR1 versions 0.1.0 dated 2025-10-16 and 0.2.0 dated 2026-01-25
DESCRIPTION | 8 MD5 | 37 +- NAMESPACE | 1 R/data_simu.R | 112 +++++--- R/get_est.R | 9 R/get_mol_sel.R | 28 +- R/get_pred.R | 138 +++++----- R/get_stanfit.R | 40 +-- R/mod_sel_criteria.R | 486 +++++++++++++++++++++----------------- README.md | 117 +++++---- build/partial.rdb |binary inst/stan/ZIIGP-INAR1.stan |only man/data_simu.Rd | 29 +- man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |only man/figures/README-example1-3.png |only man/figures/README-example1-4.png |only man/figures/README-example1-5.png |only man/get_est.Rd | 4 man/get_mod_sel.Rd | 4 man/get_pred.Rd | 2 man/get_stanfit.Rd | 8 22 files changed, 581 insertions(+), 442 deletions(-)
Title: The Skew-Normal and Related Distributions Such as the Skew-t and
the SUN
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t and the SUN families.
For the skew-normal and the skew-t distributions, statistical methods are
provided for data fitting and model diagnostics, in the univariate and the
multivariate case.
Author: Adelchi Azzalini [aut, cre]
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 2.1.1 dated 2023-04-04 and 2.1.2 dated 2026-01-25
DESCRIPTION | 11 ++++---- MD5 | 40 +++++++++++++++---------------- NAMESPACE | 2 + R/sn-funct.R | 55 +++++++++++++++++++++++++------------------ R/sn_S4.R | 4 +-- build/partial.rdb |binary build/vignette.rds |binary data/ais.rda |binary data/barolo.rda |binary data/frontier.rda |binary data/wines.rda |binary inst/CITATION | 2 - inst/NEWS.Rd | 8 ++++++ man/SUNdistr-base.Rd | 26 ++++++++++++++++---- man/dmst.Rd | 16 ++++++++++-- man/dp2cp.Rd | 26 ++++++++++---------- man/dst.Rd | 18 +++++++++----- man/plot.fitdistr.grouped.Rd | 2 + man/plot.selm.Rd | 6 ++-- man/summary.SECdistr.Rd | 5 +++ man/zeta.Rd | 2 - 21 files changed, 140 insertions(+), 83 deletions(-)
Title: XML-RPC Interface to NEOS
Description: Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
Author: Bernhard Pfaff [aut, cre],
Duncan Temple Lang [ctb]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between rneos versions 0.4-0 dated 2020-04-23 and 0.4-1 dated 2026-01-25
DESCRIPTION | 12 ++--- MD5 | 46 ++++++++++----------- R/CreateNeosComm.R | 19 ++++++-- R/CreateXmlString.R | 10 ++-- R/NemailHelp.R | 20 +++++---- R/NgetFinalResults.R | 44 +++++++++++--------- R/NgetFinalResultsNonBlocking.R | 44 +++++++++++--------- R/NgetIntermediateResults.R | 69 +++++++++++++++++--------------- R/NgetIntermediateResultsNonBlocking.R | 70 +++++++++++++++++---------------- R/NgetJobInfo.R | 28 +++++++------ R/NgetJobStatus.R | 28 +++++++------ R/NgetSolverTemplate.R | 32 ++++++++------- R/Nhelp.R | 20 +++++---- R/NkillJob.R | 42 ++++++++++--------- R/NlistAllSolvers.R | 24 ++++++----- R/NlistCategories.R | 26 ++++++------ R/NlistSolversInCategory.R | 42 +++++++++++-------- R/Nping.R | 20 +++++---- R/NprintQueue.R | 20 +++++---- R/NsubmitJob.R | 30 ++++++++------ R/Nversion.R | 20 +++++---- R/Nwelcome.R | 20 +++++---- man/NeosComm-class.Rd | 6 +- man/NlistServersInCategory.Rd | 2 24 files changed, 383 insertions(+), 311 deletions(-)
Title: Record Linkage Functions for Linking and Deduplicating Data Sets
Description: Provides functions for linking and deduplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain. For details,
see our paper "The RecordLinkage Package: Detecting Errors in Data"
Sariyar M / Borg A (2010) <doi:10.32614/RJ-2010-017>.
Author: Murat Sariyar [aut, cre],
Andreas Borg [aut]
Maintainer: Murat Sariyar <murat.sariyar@bfh.ch>
Diff between RecordLinkage versions 0.4-12.5 dated 2025-07-28 and 0.4-12.6 dated 2026-01-25
RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/BigData.pdf |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/BigData.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/EVT.pdf |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/EVT.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/Supervised.pdf |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/Supervised.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/WeightBased.pdf |only RecordLinkage-0.4-12.5/RecordLinkage/inst/doc/WeightBased.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/man/RLBigData-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/RLBigDataDedup-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/RLBigDataLinkage-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/RLResult-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/RecLinkClassif-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/RecLinkResult-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/append-methods.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/classifySupv.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/classifyUnsup.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/clone.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/deleteNULLs.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/editMatch.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/emClassify.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/emWeights.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/epiClassify.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/epiWeights.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/ff_vector-class.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/genSamples.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getExpectedSize.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getFrequencies-methods.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getMinimalTrain.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getPairsBackend.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getParetoThreshold.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/getTable-methods.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/gpdEst.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/internals.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/isFALSE.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/makeBlockingPairs.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/mrl.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/mygllm.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/optimalThreshold.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/phonetics.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/resample.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/show.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/splitData.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/subset.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/texSummary.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/trainSupv.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/man/unorderedPairs.Rd |only RecordLinkage-0.4-12.5/RecordLinkage/vignettes/BigData.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/vignettes/EVT.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/vignettes/Supervised.rnw |only RecordLinkage-0.4-12.5/RecordLinkage/vignettes/WeightBased.rnw |only RecordLinkage-0.4-12.6/RecordLinkage/DESCRIPTION | 10 RecordLinkage-0.4-12.6/RecordLinkage/MD5 | 126 +++++----- RecordLinkage-0.4-12.6/RecordLinkage/NAMESPACE | 2 RecordLinkage-0.4-12.6/RecordLinkage/R/classify.r | 2 RecordLinkage-0.4-12.6/RecordLinkage/R/classifySupv-methods.r | 4 RecordLinkage-0.4-12.6/RecordLinkage/R/getPairs-methods.r | 6 RecordLinkage-0.4-12.6/RecordLinkage/R/summary.r | 4 RecordLinkage-0.4-12.6/RecordLinkage/build/vignette.rds |binary RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/BigData.R | 47 +-- RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/BigData.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/BigData.html |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/EVT.R | 44 +-- RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/EVT.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/EVT.html |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/Supervised.R | 59 ++-- RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/Supervised.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/Supervised.html |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/WeightBased.R | 42 +-- RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/WeightBased.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/inst/doc/WeightBased.html |only RecordLinkage-0.4-12.6/RecordLinkage/man/RLBigData-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/RLBigDataDedup-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/RLBigDataLinkage-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/RLResult-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/RLdata.rd | 2 RecordLinkage-0.4-12.6/RecordLinkage/man/RecLinkClassif-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/RecLinkResult-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/append-methods.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/classifySupv.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/classifyUnsup.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/clone.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/deleteNULLs.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/editMatch.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/emClassify.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/emWeights.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/epiClassify.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/epiWeights.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/ff_vector-class.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/genSamples.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getExpectedSize.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getFrequencies-methods.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getMinimalTrain.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getPairsBackend.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getParetoThreshold.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/getTable-methods.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/gpdEst.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/internals.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/isFALSE.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/makeBlockingPairs.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/mrl.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/mygllm.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/optimalThreshold.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/phonetics.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/resample.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/show.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/splitData.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/subset.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/texSummary.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/trainSupv.rd |only RecordLinkage-0.4-12.6/RecordLinkage/man/unorderedPairs.rd |only RecordLinkage-0.4-12.6/RecordLinkage/vignettes/BigData.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/vignettes/EVT.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/vignettes/Supervised.Rmd |only RecordLinkage-0.4-12.6/RecordLinkage/vignettes/WeightBased.Rmd |only 115 files changed, 171 insertions(+), 177 deletions(-)
Title: Financial Risk Modelling and Portfolio Optimisation with R
Description: Accompanying package of the book 'Financial Risk Modelling
and Portfolio Optimisation with R', second edition. The data sets used in the book are contained in this package.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between FRAPO versions 0.4-1 dated 2016-12-11 and 0.4-2 dated 2026-01-25
DESCRIPTION | 13 +++----- MD5 | 74 ++++++++++++++++++++++++------------------------ R/methods-PortDD.R | 6 +-- data/ESCBFX.rda |binary data/EuroStoxx50.rda |binary data/FTSE100.rda |binary data/INDTRACK1.rda |binary data/INDTRACK2.rda |binary data/INDTRACK3.rda |binary data/INDTRACK4.rda |binary data/INDTRACK5.rda |binary data/INDTRACK6.rda |binary data/MIBTEL.rda |binary data/MultiAsset.rda |binary data/NASDAQ.rda |binary data/SP500.rda |binary data/StockIndex.rda |binary data/StockIndexAdj.rda |binary data/StockIndexAdjD.rda |binary inst/CITATION | 6 +-- man/DivRatios.Rd | 2 - man/ESCBFX.Rd | 2 - man/EuroStoxx50.Rd | 3 - man/FTSE100.Rd | 3 - man/INDTRACK1.Rd | 4 +- man/INDTRACK2.Rd | 4 +- man/INDTRACK3.Rd | 4 +- man/INDTRACK4.Rd | 4 +- man/INDTRACK5.Rd | 4 +- man/INDTRACK6.Rd | 4 +- man/MIBTEL.Rd | 3 - man/MultiAsset.Rd | 4 +- man/NASDAQ.Rd | 3 - man/PMD.Rd | 2 - man/SP500.Rd | 3 - man/StockIndex.Rd | 2 - man/StockIndexAdj.Rd | 2 - man/StockIndexAdjD.Rd | 2 - 38 files changed, 73 insertions(+), 81 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak [aut, cre],
Chen Ling [aut]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.7.1 dated 2026-01-21 and 1.7.2 dated 2026-01-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ inst/doc/fmtr-convenience.html | 4 ++-- inst/doc/fmtr-fapply.html | 4 ++-- inst/doc/fmtr-fapply2.html | 4 ++-- inst/doc/fmtr-fcat.html | 4 ++-- inst/doc/fmtr-fdata.html | 4 ++-- inst/doc/fmtr-helpers.html | 4 ++-- tests/testthat/test-timewd.R | 12 +++++++++++- 10 files changed, 39 insertions(+), 25 deletions(-)
Title: Additional Predictor with Maximum Effect Size
Description: Methods of selecting one from many numeric predictors
for a regression model, to ensure that the additional
predictor has the maximum effect size.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between maxEff versions 0.2.0 dated 2025-10-14 and 0.2.1 dated 2026-01-24
DESCRIPTION | 17 ++++++++--------- MD5 | 24 ++++++++++++------------ R/0PACKAGE.R | 12 ------------ R/add_dummy.R | 2 +- R/add_dummy_partition.R | 2 +- R/add_numeric.R | 2 +- R/node1.R | 13 +++++++------ build/vignette.rds |binary inst/doc/intro.html | 28 ++++++++++++++-------------- man/add_dummy.Rd | 2 +- man/add_dummy_partition.Rd | 2 +- man/add_numeric.Rd | 2 +- man/maxEff-package.Rd | 6 +++--- 13 files changed, 50 insertions(+), 62 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: Generalized additive models with a numeric hyper column. Sign-adjustment based on the
correlation of model prediction and a selected slice of the
hyper column. Visualization of the integrand surface over the
hyper column.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb] ,
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.2.0 dated 2025-10-12 and 0.2.1 dated 2026-01-24
hyper.gam-0.2.0/hyper.gam/inst/doc/applications.R |only hyper.gam-0.2.0/hyper.gam/inst/doc/applications.html |only hyper.gam-0.2.0/hyper.gam/inst/doc/applications.qmd |only hyper.gam-0.2.0/hyper.gam/vignettes/applications.qmd |only hyper.gam-0.2.1/hyper.gam/DESCRIPTION | 22 ++--- hyper.gam-0.2.1/hyper.gam/MD5 | 45 ++++++------ hyper.gam-0.2.1/hyper.gam/NAMESPACE | 10 +- hyper.gam-0.2.1/hyper.gam/R/0PACKAGE.R | 2 hyper.gam-0.2.1/hyper.gam/R/cor_xy.R | 12 +-- hyper.gam-0.2.1/hyper.gam/R/gam_ext.R | 8 +- hyper.gam-0.2.1/hyper.gam/R/hyper_gam.R | 4 - hyper.gam-0.2.1/hyper.gam/R/integrandSurface.R | 24 +++--- hyper.gam-0.2.1/hyper.gam/R/kfoldPredict.R | 4 - hyper.gam-0.2.1/hyper.gam/R/sign_adjust.R | 4 - hyper.gam-0.2.1/hyper.gam/R/update.R | 2 hyper.gam-0.2.1/hyper.gam/build/partial.rdb |binary hyper.gam-0.2.1/hyper.gam/build/vignette.rds |binary hyper.gam-0.2.1/hyper.gam/inst/CITATION | 2 hyper.gam-0.2.1/hyper.gam/inst/doc/intro.R |only hyper.gam-0.2.1/hyper.gam/inst/doc/intro.html |only hyper.gam-0.2.1/hyper.gam/inst/doc/intro.qmd |only hyper.gam-0.2.1/hyper.gam/man/cor_xy.Rd | 6 - hyper.gam-0.2.1/hyper.gam/man/getData.gam.Rd |only hyper.gam-0.2.1/hyper.gam/man/hyper.gam-package.Rd | 10 -- hyper.gam-0.2.1/hyper.gam/man/integrandSurface.Rd | 4 - hyper.gam-0.2.1/hyper.gam/man/sign_adjust.Rd | 2 hyper.gam-0.2.1/hyper.gam/vignettes/hypergam.bib | 71 +------------------ hyper.gam-0.2.1/hyper.gam/vignettes/intro.qmd |only 28 files changed, 85 insertions(+), 147 deletions(-)
Title: Simulated Grouped Hyper Data Frame
Description: An intuitive interface to simulate (1) superimposed (marked) point patterns with vectorized parameterization of random point pattern and distribution of marks; and (2) grouped hyper data frame based on population parameters and subject-specific random effects.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe.random versions 0.2.0 dated 2025-10-14 and 0.2.1 dated 2026-01-24
groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.html |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.qmd |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/vignettes/groupedHyperframe.random.qmd |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/DESCRIPTION | 14 +- groupedHyperframe.random-0.2.1/groupedHyperframe.random/MD5 | 26 ++-- groupedHyperframe.random-0.2.1/groupedHyperframe.random/NAMESPACE | 8 - groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/0PACKAGE.R | 10 - groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/mvrnorm2.R | 17 ++ groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/rppp.R | 20 +-- groupedHyperframe.random-0.2.1/groupedHyperframe.random/build/vignette.rds |binary groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.R |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.html |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.qmd |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/man/groupedHyperframe.random-package.Rd | 13 -- groupedHyperframe.random-0.2.1/groupedHyperframe.random/man/mvrnorm2.Rd | 12 +- groupedHyperframe.random-0.2.1/groupedHyperframe.random/vignettes/groupedHyperframe.random.bib | 57 +--------- groupedHyperframe.random-0.2.1/groupedHyperframe.random/vignettes/intro.qmd |only 18 files changed, 78 insertions(+), 99 deletions(-)
More information about groupedHyperframe.random at CRAN
Permanent link
Title: Utility Functions to Support and Extend the 'rbmi' Package
Description: Provides utility functions that extend the capabilities of the
reference-based multiple imputation package 'rbmi'. It supports clinical
trial analysis workflows with functions for managing imputed datasets,
applying analysis methods across imputations, and tidying results for
reporting.
Author: Mark Baillie [aut, cre, cph] ,
Tobias Muetze [aut] ,
Jack Talboys [aut],
Lukas A. Widmer [ctb]
Maintainer: Mark Baillie <bailliem@gmail.com>
This is a re-admission after prior archival of version 0.1.6 dated 2025-09-13
Diff between rbmiUtils versions 0.1.6 dated 2025-09-13 and 0.1.8 dated 2026-01-24
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/analysis_utils.R | 35 +++++++++++++++++++++++++++++++++++ R/utils.R | 3 +-- README.md | 8 ++++---- inst/doc/analyse2.html | 17 +++++++++-------- man/gcomp_binary.Rd | 2 +- man/gcomp_responder.Rd | 36 ++++++++++++++++++++++++++++++++++++ 9 files changed, 108 insertions(+), 29 deletions(-)
Title: Assessing Proximal, Distal, and Mediated Causal Excursion
Effects for Micro-Randomized Trials
Description: Provides methods to analyze micro-randomized trials (MRTs) with binary treatment options. Supports four types of analyses: (1) proximal causal excursion effects, including weighted and centered least squares (WCLS) for continuous proximal outcomes by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274> and the estimator for marginal excursion effect (EMEE) for binary proximal outcomes by Qian et al. (2021) <doi:10.1093/biomet/asaa070>; (2) distal causal excursion effects (DCEE) for continuous distal outcomes using a two-stage estimator by Qian (2025) <doi:10.1093/biomtc/ujaf134>; (3) mediated causal excursion effects (MCEE) for continuous distal outcomes, estimating natural direct and indirect excursion effects in the presence of time-varying mediators by Qian (2025) <doi:10.48550/arXiv.2506.20027>; and (4) standardized proximal effect size estimation for continuous proximal outcomes, generalizing the approach in Luers et al. (2019) <doi:10.1007/s11121- [...truncated...]
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Xinyi Song [aut],
John Dziak [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.4.0 dated 2026-01-24 and 0.4.1 dated 2026-01-24
DESCRIPTION | 6 ++-- MD5 | 17 ++++++------- NEWS.md | 14 +++++++--- inst/doc/mrt-distal-causal-effect.html | 8 +++--- inst/doc/mrt-mediated-causal-effect-on-distal-outcome.html | 4 +-- inst/doc/mrt-proximal-causal-effect.html | 4 +-- inst/doc/mrt-standardized-effect-size.Rmd | 4 +-- inst/doc/mrt-standardized-effect-size.html | 11 ++++---- tests/manual |only vignettes/mrt-standardized-effect-size.Rmd | 4 +-- 10 files changed, 40 insertions(+), 32 deletions(-)
Title: Biodiversity Data Cleaning
Description: It brings together several aspects of biodiversity
data-cleaning in one place. 'bdc' is organized in thematic modules
related to different biodiversity dimensions, including 1) Merge
datasets: standardization and integration of different datasets; 2)
pre-filter: flagging and removal of invalid or non-interpretable
information, followed by data amendments; 3) taxonomy: cleaning,
parsing, and harmonization of scientific names from several taxonomic
groups against taxonomic databases locally stored through the
application of exact and partial matching algorithms; 4) space:
flagging of erroneous, suspect, and low-precision geographic
coordinates; and 5) time: flagging and, whenever possible, correction
of inconsistent collection date. In addition, it contains
features to visualize, document, and report data quality – which is
essential for making data quality assessment transparent and
reproducible. The reference for the methodology is Ribeiro and colleagues (2022)
<doi:10.1111/2041-210 [...truncated...]
Author: Bruno Ribeiro [aut, cre] ,
Santiago Velazco [aut] ,
Karlo Guidoni-Martins [aut] ,
Geiziane Tessarolo [aut] ,
Lucas Jardim [aut] ,
Steven Bachman [ctb] ,
Rafael Loyola [ctb]
Maintainer: Bruno Ribeiro <ribeiro.brr@gmail.com>
This is a re-admission after prior archival of version 1.1.5 dated 2024-12-17
Diff between bdc versions 1.1.5 dated 2024-12-17 and 1.1.6 dated 2026-01-24
bdc-1.1.5/bdc/inst/extdata/countries_names/reword-countries.csv |only bdc-1.1.6/bdc/DESCRIPTION | 39 +++++----- bdc-1.1.6/bdc/MD5 | 30 +++---- bdc-1.1.6/bdc/NAMESPACE | 4 - bdc-1.1.6/bdc/NEWS.md | 5 + bdc-1.1.6/bdc/R/bdc_clean_names.R | 37 +++++---- bdc-1.1.6/bdc/R/bdc_create_figures.R | 35 +++++--- bdc-1.1.6/bdc/R/bdc_query_names_taxadb.R | 1 bdc-1.1.6/bdc/R/bdc_standardize_country.R | 4 - bdc-1.1.6/bdc/R/bdc_standardize_datasets.R | 30 ++++--- bdc-1.1.6/bdc/R/bdc_stdz_cntr.R | 7 - bdc-1.1.6/bdc/inst/extdata/countries_names/country_names.txt | 30 +++++++ bdc-1.1.6/bdc/inst/extdata/countries_names/reword-countries.txt |only bdc-1.1.6/bdc/man/bdc_clean_names.Rd | 7 + bdc-1.1.6/bdc/man/bdc_query_names_taxadb.Rd | 3 bdc-1.1.6/bdc/man/bdc_standardize_datasets.Rd | 5 - bdc-1.1.6/bdc/tests/testthat/test-bdc_standardize_datasets.R | 30 ++++--- 17 files changed, 165 insertions(+), 102 deletions(-)
Title: Simple Multivariate Statistical Estimation and Tests
Description: A collection of simple parameter estimation and tests for the comparison of multivariate means and variation, to accompany Chapters 4 and 5 of the book Multivariate Statistical Methods. A Primer (5th edition), by Manly BFJ, Navarro Alberto JA & Gerow K (2024) <doi:10.1201/9781003453482>.
Author: Jorge Navarro Alberto [aut, cre, cph]
Maintainer: Jorge Navarro Alberto <ganava4@gmail.com>
Diff between smsets versions 1.2.3 dated 2025-07-08 and 2.0.0 dated 2026-01-24
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++++--------------- NAMESPACE | 9 +++++++++ NEWS.md | 6 ++++++ R/LeveneT2.R | 3 +-- R/Levenetestsms.mv.R |only R/OnewayMANOVA.R | 3 ++- R/print.Levenetestsms.mv.R |only R/smsets-package.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/smsets-vignette.R | 8 ++++++++ inst/doc/smsets-vignette.Rmd | 27 ++++++++++++++++++++++++--- inst/doc/smsets-vignette.pdf |binary man/LeveneT2.Rd | 3 +-- man/Levenetestsms.mv.Rd |only man/print.Levenetestsms.mv.Rd |only man/smsets-package.Rd | 6 +++--- vignettes/REFVIGNETTE.bib | 27 ++++++++++++++++++++++++++- vignettes/smsets-vignette.Rmd | 27 ++++++++++++++++++++++++--- 20 files changed, 132 insertions(+), 39 deletions(-)
Title: Dynamic and Interactive EEG Graphics
Description: Allows to visualize high-density electroencephalography (HD-EEG) data through interactive plots and animations, enabling exploratory and communicative analysis of temporal-spatial brain signals. Funder: Masaryk University (Grant No. MUNI/A/1457/2023).
Author: Zdeňka Gerslova [aut, cre] ,
Stanislav Katina [rev] ,
Martin Lamos [ctb]
Maintainer: Zdeňka Gerslova <gerslovaz@math.muni.cz>
Diff between diegr versions 0.1.0 dated 2025-09-23 and 0.2.0 dated 2026-01-24
diegr-0.1.0/diegr/R/interactive_waveforms.R |only diegr-0.1.0/diegr/R/pick_region.R |only diegr-0.1.0/diegr/R/topo_plot.R |only diegr-0.2.0/diegr/DESCRIPTION | 10 diegr-0.2.0/diegr/MD5 | 92 +- diegr-0.2.0/diegr/NAMESPACE | 3 diegr-0.2.0/diegr/NEWS.md |only diegr-0.2.0/diegr/R/animations.R | 187 +--- diegr-0.2.0/diegr/R/baseline_correction.R | 81 + diegr-0.2.0/diegr/R/boxplots.R | 212 ++--- diegr-0.2.0/diegr/R/compute_mean.R | 700 +++++------------ diegr-0.2.0/diegr/R/create_scale.R | 85 +- diegr-0.2.0/diegr/R/helper_functions.R | 276 +++--- diegr-0.2.0/diegr/R/outliers_epoch.R | 111 +- diegr-0.2.0/diegr/R/pick_functions.R |only diegr-0.2.0/diegr/R/point_mesh.R | 11 diegr-0.2.0/diegr/R/scalp_plot.R | 62 - diegr-0.2.0/diegr/R/summary_stats.R |only diegr-0.2.0/diegr/R/timeplots.R |only diegr-0.2.0/diegr/R/topoplots.R |only diegr-0.2.0/diegr/README.md | 59 - diegr-0.2.0/diegr/build/vignette.rds |binary diegr-0.2.0/diegr/inst/doc/diegr.R | 171 ++-- diegr-0.2.0/diegr/inst/doc/diegr.Rmd | 210 +++-- diegr-0.2.0/diegr/inst/doc/diegr.html | 375 +++++---- diegr-0.2.0/diegr/man/animate_scalp.Rd | 6 diegr-0.2.0/diegr/man/animate_topo.Rd | 6 diegr-0.2.0/diegr/man/animate_topo_mean.Rd | 11 diegr-0.2.0/diegr/man/baseline_correction.Rd | 29 diegr-0.2.0/diegr/man/boxplot_epoch.Rd | 34 diegr-0.2.0/diegr/man/boxplot_rt.Rd | 12 diegr-0.2.0/diegr/man/boxplot_subject.Rd | 31 diegr-0.2.0/diegr/man/compute_mean.Rd | 96 +- diegr-0.2.0/diegr/man/create_scale.Rd | 22 diegr-0.2.0/diegr/man/figures/README-timemean-1.png |binary diegr-0.2.0/diegr/man/figures/README-topoplot-1.png |binary diegr-0.2.0/diegr/man/interactive_waveforms.Rd | 44 - diegr-0.2.0/diegr/man/outliers_epoch.Rd | 42 - diegr-0.2.0/diegr/man/pick_data.Rd | 27 diegr-0.2.0/diegr/man/pick_region.Rd | 2 diegr-0.2.0/diegr/man/plot_time_mean.Rd | 57 - diegr-0.2.0/diegr/man/plot_topo_mean.Rd | 16 diegr-0.2.0/diegr/man/scalp_plot.Rd | 14 diegr-0.2.0/diegr/man/summary_stats_rt.Rd |only diegr-0.2.0/diegr/man/topo_plot.Rd | 21 diegr-0.2.0/diegr/tests/testthat/test-animations.R | 2 diegr-0.2.0/diegr/tests/testthat/test-boxplots.R | 14 diegr-0.2.0/diegr/tests/testthat/test-compute_mean.R | 39 diegr-0.2.0/diegr/tests/testthat/test-outliers_epoch.R | 22 diegr-0.2.0/diegr/tests/testthat/test-topo_plot.R | 6 diegr-0.2.0/diegr/vignettes/diegr.Rmd | 210 +++-- diegr-0.2.0/diegr/vignettes/example_animation.gif |only 52 files changed, 1792 insertions(+), 1616 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping
functions to apply a function to each combination of elements in a
list of inputs. Also includes functions for automatically detecting
output type in mapping functions, finding every combination of
elements of lists or rows of data frames, and applying multiple models
to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.4.3 dated 2025-12-22 and 0.5.0 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/future_xmap.R | 7 ++----- R/xmap.R | 4 ++-- man/future_xmap.Rd | 8 -------- man/xmap.Rd | 2 -- tests/testthat/test-future_xmap.R | 6 ------ tests/testthat/test-xmap.R | 10 ---------- 9 files changed, 19 insertions(+), 44 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information see Sparapani, Spanbauer and McCulloch <doi:10.18637/jss.v097.i01>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [ctb],
Matthew Pratola [ctb],
Charles Spanbauer [ctb],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.9.9 dated 2024-06-21 and 2.9.10 dated 2026-01-24
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- build/vignette.rds |binary data/ACTG175.rda |binary data/alligator.rda |binary data/arq.rda |binary data/bladder.rda |binary data/leukemia.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/leuk.R | 9 ++++++--- inst/doc/the-BART-R-package.pdf |binary 16 files changed, 26 insertions(+), 23 deletions(-)
Title: 'REDCap' Data Management
Description: REDCap Data Management - 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data. REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on previously identified queries.
Author: Joao Carmezim [aut, cre],
Pau Satorra [aut],
Judith Penafiel [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 1.0.0 dated 2025-11-26 and 1.0.1 dated 2026-01-24
DESCRIPTION | 8 MD5 | 60 ++--- NAMESPACE | 1 NEWS.md | 39 +++ R/rd_checkbox.R | 29 ++ R/rd_query.R | 3 R/redcap_data.R | 5 R/utils-transform.R | 34 +++ README.md | 1 inst/doc/REDCapDM.html | 374 ++++++++++++++++----------------- man/check_proj.Rd | 44 +-- man/checkbox_names.Rd | 40 +-- man/covican.Rd | 96 ++++---- man/figures/lifecycle-deprecated.svg | 42 +-- man/figures/lifecycle-experimental.svg | 42 +-- man/figures/lifecycle-stable.svg | 58 ++--- man/figures/lifecycle-superseded.svg | 42 +-- man/rd_checkbox.Rd | 144 ++++++------ man/rd_dates.Rd | 88 +++---- man/rd_delete_vars.Rd | 130 +++++------ man/rd_dictionary.Rd | 94 ++++---- man/rd_factor.Rd | 100 ++++---- man/rd_recalculate.Rd | 134 +++++------ man/rd_split.Rd | 136 ++++++------ man/recalculate.Rd | 44 +-- man/redcap_data.Rd | 3 man/round.Rd | 50 ++-- man/split_form.Rd | 44 +-- man/to_factor.Rd | 36 +-- man/transform_checkboxes.Rd | 44 +-- tests/testthat.R | 24 +- 31 files changed, 1045 insertions(+), 944 deletions(-)
Title: Generalized Orthogonal GARCH (GO-GARCH) Models
Description: Provision of classes and methods for estimating generalized
orthogonal GARCH models. This is an alternative approach to CC-GARCH models
in the context of multivariate volatility modeling.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between gogarch versions 0.7-5 dated 2022-04-29 and 0.7-6 dated 2026-01-24
DESCRIPTION | 13 +++++-------- MD5 | 14 +++++++------- data/BVDW.rda |binary data/BVDWAIR.rda |binary data/BVDWSTOXX.rda |binary data/VDW.rda |binary man/BVDWAIR.Rd | 2 +- man/BVDWSTOXX.Rd | 16 ++++++++-------- 8 files changed, 21 insertions(+), 24 deletions(-)
Title: Gene Set Analysis Using the Gene Set Ordinal Association Test
Description: Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.
Author: Frank Koopmans [aut, cre]
Maintainer: Frank Koopmans <ftwkoopmans@gmail.com>
Diff between goat versions 1.1.3 dated 2025-08-27 and 1.1.4 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 11 ++++++++++- R/simplify_similarity.R | 6 +++++- 4 files changed, 21 insertions(+), 8 deletions(-)
Title: Easy Visualization of Conditional Effects from Regression Models
Description: Offers a flexible and user-friendly interface for visualizing conditional
effects from a broad range of regression models, including mixed-effects and generalized
additive (mixed) models. Compatible model types include lm(), rlm(), glm(), glm.nb(),
betareg(), and gam() (from 'mgcv'); nonlinear models via nls(); generalized least
squares via gls(); and survival models via coxph() (from 'survival').
Mixed-effects models with random intercepts and/or slopes can be fitted using lmer(),
glmer(), glmer.nb(), glmmTMB(), or gam() (from 'mgcv', via smooth terms).
Plots are rendered using base R graphics with extensive customization options.
Approximate confidence intervals for nls() and betareg() models are computed using
the delta method. Robust standard errors for rlm() are computed using the sandwich
estimator (Zeileis 2004) <doi:10.18637/jss.v011.i10>. For beta regression using
'betareg', see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. For
mixed-effects models w [...truncated...]
Author: Luca Corlatti [aut, cre]
Maintainer: Luca Corlatti <lucac1980@yahoo.it>
Diff between easyViz versions 2.0.0 dated 2026-01-08 and 2.0.1 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/easyViz.R | 18 +++++++++--------- R/ez-utils.R | 23 ++++++++++------------- man/easyViz.Rd | 18 +++++++++--------- 6 files changed, 44 insertions(+), 39 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2025) <doi:10.18637/jss.v115.i02>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.8.1 dated 2026-01-08 and 1.0.0 dated 2026-01-24
sdmTMB-0.8.1/sdmTMB/man/sdmTMB_simulate.Rd |only sdmTMB-1.0.0/sdmTMB/DESCRIPTION | 8 sdmTMB-1.0.0/sdmTMB/MD5 | 22 +- sdmTMB-1.0.0/sdmTMB/NAMESPACE | 1 sdmTMB-1.0.0/sdmTMB/NEWS.md | 13 + sdmTMB-1.0.0/sdmTMB/R/fit.R | 25 ++ sdmTMB-1.0.0/sdmTMB/R/tmb-sim.R | 136 +++++++-------- sdmTMB-1.0.0/sdmTMB/inst/CITATION | 23 +- sdmTMB-1.0.0/sdmTMB/man/sdmTMB.Rd | 6 sdmTMB-1.0.0/sdmTMB/man/simulate.sdmTMB.Rd | 4 sdmTMB-1.0.0/sdmTMB/man/simulate_new.Rd |only sdmTMB-1.0.0/sdmTMB/tests/testthat/test-betabinomial.R | 151 +++++++++++++++++ sdmTMB-1.0.0/sdmTMB/tests/testthat/test-time-varying.R | 2 13 files changed, 289 insertions(+), 102 deletions(-)
Title: A Collection of Tools for Network Analysis
Description: Provides a collection of network analytic (convenience) functions which are missing in other standard packages. This includes triad census with attributes <doi:10.1016/j.socnet.2019.04.003>, core-periphery models <doi:10.1016/S0378-8733(99)00019-2>, and several graph generators. Most functions are build upon 'igraph'.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between netUtils versions 0.8.3 dated 2024-10-10 and 0.8.4 dated 2026-01-24
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 4 ++-- src/lfr.cpp | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Assessing Proximal, Distal, and Mediated Causal Excursion
Effects for Micro-Randomized Trials
Description: Provides methods to analyze micro-randomized trials (MRTs) with binary treatment options. Supports four types of analyses: (1) proximal causal excursion effects, including weighted and centered least squares (WCLS) for continuous proximal outcomes by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274> and the estimator for marginal excursion effect (EMEE) for binary proximal outcomes by Qian et al. (2021) <doi:10.1093/biomet/asaa070>; (2) distal causal excursion effects (DCEE) for continuous distal outcomes using a two-stage estimator by Qian (2025) <doi:10.1093/biomtc/ujaf134>; (3) mediated causal excursion effects (MCEE) for continuous distal outcomes, estimating natural direct and indirect excursion effects in the presence of time-varying mediators by Qian (2025) <doi:10.48550/arXiv.2506.20027>; and (4) standardized proximal effect size estimation for continuous proximal outcomes, generalizing the approach in Luers et al. (2019) <doi:10.1007/s11121- [...truncated...]
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Xinyi Song [aut],
John Dziak [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.3.1 dated 2025-11-05 and 0.4.0 dated 2026-01-24
DESCRIPTION | 16 +++-- MD5 | 36 +++++++++---- NAMESPACE | 14 +++++ NEWS.md | 7 ++ R/calculate_mrt_effect_size.R |only R/calculate_mrt_effect_size_helper.R |only R/data_example_for_standardized_effect.R |only R/dcee.R | 5 + R/summary.mrt_effect_size.R |only README.md | 31 +++++++++-- build/vignette.rds |binary data/data_example_for_standardized_effect.rda |only inst/doc/mrt-distal-causal-effect.html | 12 ++-- inst/doc/mrt-mediated-causal-effect-on-distal-outcome.html | 4 - inst/doc/mrt-proximal-causal-effect.html | 17 +++--- inst/doc/mrt-standardized-effect-size.R |only inst/doc/mrt-standardized-effect-size.Rmd |only inst/doc/mrt-standardized-effect-size.html |only man/calculate_mrt_effect_size.Rd |only man/data_example_for_standardized_effect.Rd |only man/dcee.Rd | 5 + man/plot.mrt_effect_size.Rd |only man/summary.mrt_effect_size.Rd |only tests/testthat/test-calculate_mrt_effect_size.R |only vignettes/mhealth-ref.bib | 23 ++++++-- vignettes/mrt-standardized-effect-size.Rmd |only 26 files changed, 129 insertions(+), 41 deletions(-)
Title: Integrative Subtype Generation
Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations. See Fox et al. (2024) <doi:10.1016/j.crmeth.2024.100884> for details.
Author: Mao Tian [cre],
Paul Boutros [aut],
Natalie Fox [aut],
Dan Knight [ctb]
Maintainer: Mao Tian <mtian@sbpdiscovery.org>
Diff between iSubGen versions 1.0.1 dated 2021-04-22 and 1.0.4 dated 2026-01-24
DESCRIPTION | 24 ++++-- MD5 | 47 ++++++------ NEWS.md |only R/apply.scaling.R | 67 ++++++++--------- R/calculate.cis.matrix.R | 28 ++++--- R/calculate.integrative.similarity.matrix.R | 76 ++++++++++++-------- R/calculate.scaling.R | 16 ++-- R/cluster.patients.R | 24 ++---- R/combine.integrative.features.R | 24 +++--- R/create.autoencoder.R | 26 +++--- R/create.autoencoder.irf.matrix.R | 10 +- R/load.molecular.aberration.data.R | 10 +- R/read.scaling.factors.R | 12 +-- R/write.scaling.factors.R | 12 +-- README.md | 73 +++++++++++-------- build/vignette.rds |binary inst/doc/iSubGenGuide.Rnw | 94 ++++++++++++------------- inst/doc/iSubGenGuide.pdf |binary man/apply.scaling.Rd | 4 - man/calculate.cis.matrix.Rd | 20 ++--- man/calculate.integrative.similarity.matrix.Rd | 10 +- man/calculate.scaling.Rd | 4 - man/create.autoencoder.irf.matrix.Rd | 4 - man/write.scaling.factors.Rd | 10 +- vignettes/iSubGenGuide.Rnw | 94 ++++++++++++------------- 25 files changed, 366 insertions(+), 323 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.9.0 dated 2025-11-23 and 0.10.0 dated 2026-01-24
DESCRIPTION | 6 MD5 | 92 +- NAMESPACE | 31 NEWS.md | 23 R/composition.R | 721 ++++++++++++++-------- R/count-mono.R | 11 R/glyrepr-package.R | 1 R/mono-type.R | 159 ++-- R/reorder-graph.R | 29 R/smap.R | 690 ++++++++++++++------- R/structure-level.R | 33 - R/structure-to-iupac.R | 7 R/structure.R | 625 ++++++++++++------- R/substituent.R | 2 README.md | 17 inst/doc/glycan-graph.html | 17 inst/doc/glyrepr.R | 21 inst/doc/glyrepr.Rmd | 21 inst/doc/glyrepr.html | 82 +- inst/doc/smap.html | 43 - man/as_glycan_composition.Rd | 40 - man/convert_to_generic.Rd | 5 man/count_mono.Rd | 2 man/get_mono_type.Rd | 14 man/get_structure_graphs.Rd | 2 man/get_structure_level.Rd | 10 man/glycan_composition.Rd | 5 man/glycan_structure.Rd | 20 man/remove_substituents.Rd | 2 man/simap.Rd | 4 man/smap.Rd | 2 man/smap2.Rd | 8 man/smap_predicates.Rd | 2 man/smap_unique.Rd | 2 man/spmap.Rd | 10 man/structure_to_iupac.Rd | 2 tests/testthat/_snaps/composition.md | 4 tests/testthat/_snaps/structure-level.md | 2 tests/testthat/_snaps/structure.md | 16 tests/testthat/test-composition.R | 348 +++++++++- tests/testthat/test-count-mono.R | 34 + tests/testthat/test-iupac-to-structure.R | 4 tests/testthat/test-mono-type.R | 88 ++ tests/testthat/test-smap.R | 486 ++++++++++++--- tests/testthat/test-structure-level.R | 90 +- tests/testthat/test-structure.R | 992 ++++++++++++++++++++++++++----- vignettes/glyrepr.Rmd | 21 47 files changed, 3469 insertions(+), 1377 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.8 dated 2025-04-09 and 1.1.9 dated 2026-01-24
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 5 R/define_simulation.R | 3 README.md | 7 - build/vignette.rds |binary inst/doc/simTool.R | 298 +++++++++++++++++++++++++------------------------- inst/doc/simTool.html | 196 ++++++++------------------------ 8 files changed, 223 insertions(+), 308 deletions(-)
Title: MareFrame DB Querying Library
Description: Creates and manages a PostgreSQL database suitable for storing fisheries data
and aggregating ready for use within a Gadget <https://gadget-framework.github.io/gadget2/> model.
See <https://mareframe.github.io/mfdb/> for more information.
Author: Jamie Lentin [aut, cre, cph],
Bjarki Thor Elvarsson [aut]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between mfdb versions 7.3-1 dated 2022-06-21 and 7.4-0 dated 2026-01-24
mfdb-7.3-1/mfdb/demo/inttest-tibble.R |only mfdb-7.4-0/mfdb/DESCRIPTION | 15 - mfdb-7.4-0/mfdb/MD5 | 52 +-- mfdb-7.4-0/mfdb/NEWS.md |only mfdb-7.4-0/mfdb/R/mfdb.R | 12 mfdb-7.4-0/mfdb/README.md | 49 ++- mfdb-7.4-0/mfdb/build/vignette.rds |binary mfdb-7.4-0/mfdb/demo/00Index | 1 mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.R | 173 +++++------ mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.Rmd | 7 mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.html | 183 ++++++------ mfdb-7.4-0/mfdb/inst/doc/population.R | 7 mfdb-7.4-0/mfdb/inst/doc/population.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/population.html | 171 ++++++----- mfdb-7.4-0/mfdb/inst/doc/tow_data.R | 17 - mfdb-7.4-0/mfdb/inst/doc/tow_data.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/tow_data.html | 251 +++++++++-------- mfdb-7.4-0/mfdb/inst/doc/trip.R | 11 mfdb-7.4-0/mfdb/inst/doc/trip.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/trip.html | 198 +++++++------ mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.R | 13 mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.html | 174 ++++++----- mfdb-7.4-0/mfdb/vignettes/import_hydrography_cmems.Rmd | 7 mfdb-7.4-0/mfdb/vignettes/population.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/tow_data.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/trip.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/weightmeasurements.Rmd | 3 28 files changed, 738 insertions(+), 627 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] ,
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] ,
Pedro Despouy [aut],
Salim Brueggemann [ctb] ,
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.11.0 dated 2025-06-19 and 4.12.0 dated 2026-01-24
plotly-4.11.0/plotly/tests/testthat/Rplots.pdf |only plotly-4.12.0/plotly/DESCRIPTION | 10 plotly-4.12.0/plotly/MD5 | 704 +++++----- plotly-4.12.0/plotly/NAMESPACE | 1 plotly-4.12.0/plotly/NEWS.md | 40 plotly-4.12.0/plotly/R/api_exports.R | 22 plotly-4.12.0/plotly/R/ggplotly.R | 56 plotly-4.12.0/plotly/R/kaleido.R | 65 plotly-4.12.0/plotly/R/layers2traces.R | 21 plotly-4.12.0/plotly/R/layout.R | 2 plotly-4.12.0/plotly/R/plotly.R | 2 plotly-4.12.0/plotly/R/plotly_build.R | 5 plotly-4.12.0/plotly/R/sysdata.rda |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/001.json | 32 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/001_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/002.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/002_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/003.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/003_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/004.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/004_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/test-shinytest2.R | 19 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/es-pe.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/fr.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/hr.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/nl.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/no.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/si.js |only plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/sk.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/zh-tw.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 69 plotly-4.12.0/plotly/man/TeX.Rd | 2 plotly-4.12.0/plotly/man/add_data.Rd | 2 plotly-4.12.0/plotly/man/add_trace.Rd | 2 plotly-4.12.0/plotly/man/animation.Rd | 2 plotly-4.12.0/plotly/man/api.Rd | 20 plotly-4.12.0/plotly/man/as_widget.Rd | 2 plotly-4.12.0/plotly/man/colorbar.Rd | 2 plotly-4.12.0/plotly/man/config.Rd | 2 plotly-4.12.0/plotly/man/group2NA.Rd | 2 plotly-4.12.0/plotly/man/hide_colorbar.Rd | 2 plotly-4.12.0/plotly/man/hide_legend.Rd | 2 plotly-4.12.0/plotly/man/highlight.Rd | 2 plotly-4.12.0/plotly/man/last_plot.Rd | 2 plotly-4.12.0/plotly/man/layout.Rd | 2 plotly-4.12.0/plotly/man/orca.Rd | 2 plotly-4.12.0/plotly/man/partial_bundle.Rd | 2 plotly-4.12.0/plotly/man/plot_dendro.Rd | 2 plotly-4.12.0/plotly/man/plot_geo.Rd | 2 plotly-4.12.0/plotly/man/plot_ly.Rd | 2 plotly-4.12.0/plotly/man/plotlyProxy.Rd | 2 plotly-4.12.0/plotly/man/plotly_build.Rd | 2 plotly-4.12.0/plotly/man/plotly_data.Rd | 2 plotly-4.12.0/plotly/man/plotly_json.Rd | 2 plotly-4.12.0/plotly/man/rangeslider.Rd | 2 plotly-4.12.0/plotly/man/raster2uri.Rd | 2 plotly-4.12.0/plotly/man/remove_typedarray_polyfill.Rd | 2 plotly-4.12.0/plotly/man/save_image.Rd | 2 plotly-4.12.0/plotly/man/schema.Rd | 2 plotly-4.12.0/plotly/man/showRGB.Rd | 2 plotly-4.12.0/plotly/man/style.Rd | 2 plotly-4.12.0/plotly/man/subplot.Rd | 2 plotly-4.12.0/plotly/man/toRGB.Rd | 2 plotly-4.12.0/plotly/man/toWebGL.Rd | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-minor-major.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-minor.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-x.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-y.svg | 2 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plotly-4.12.0/plotly/tests/testthat/test-ggplot-blank.R | 26 plotly-4.12.0/plotly/tests/testthat/test-ggplot-boxplot.R | 26 plotly-4.12.0/plotly/tests/testthat/test-ggplot-color.R | 33 plotly-4.12.0/plotly/tests/testthat/test-ggplot-theme.R | 62 plotly-4.12.0/plotly/tests/testthat/test-ggplot-tooltip.R | 16 plotly-4.12.0/plotly/tools/update_plotlyjs.R | 19 354 files changed, 1095 insertions(+), 905 deletions(-)
Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to
Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to
define table format and styling without the data, and later apply the
format to the data.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
Ellis Hughes [aut] ,
Karima Ahmad [aut] ,
Shannon Haughton [aut],
Dragoș Moldovan-Gruenfeld [aut],
Alanah Jonas [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd],
Atorus Research LLC [ [...truncated...]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmt versions 0.2.1 dated 2025-10-04 and 0.3.0 dated 2026-01-24
DESCRIPTION | 14 MD5 | 98 +++--- NAMESPACE | 9 NEWS.md | 43 +- R/JSON.R | 61 ++- R/apply_col_plan.R | 79 +++-- R/apply_col_style_plan.R | 13 R/apply_footnote_meta.R | 24 + R/apply_footnote_plan.R | 16 - R/apply_frmt_methods.R | 8 R/apply_page_plan.R | 89 ++++- R/apply_row_grp_plan.R | 89 +++-- R/apply_table_frmt_plan.R | 7 R/apply_tfrmt.R | 55 ++- R/body_plan.R | 5 R/col_plan.R | 148 +++++---- R/display_insights.R | 49 ++- R/eval_tidyselect.R | 17 - R/mock_tbl.R | 32 +- R/page_plan.R | 67 +++- R/prep_card.R | 2 R/print_to_ggplot.R | 9 R/print_to_gt.R | 116 +++++-- R/shuffle_card.R | 23 + R/struct_utils.R | 9 R/tfrmt_checks.R | 13 R/tfrmt_sigdig.R | 21 + README.md | 27 - inst/create_json_example_tfrmts.R | 6 man/col_plan.Rd | 12 man/display_row_frmts.Rd | 6 man/page_plan.Rd | 40 ++ man/print_mock_gt.Rd | 2 man/print_to_ggplot.Rd | 2 man/print_to_gt.Rd | 6 man/tfrmt_sigdig.Rd | 4 man/tfrmt_to_json.Rd | 2 tests/testthat/_snaps/JSON.md | 64 +++- tests/testthat/_snaps/prep_card.md | 320 ++++++++++---------- tests/testthat/test-JSON.R | 94 +++++- tests/testthat/test-apply_col_plan.R |only tests/testthat/test-apply_page_plan.R | 485 ++++++++++++++++++++++++++++++- tests/testthat/test-apply_row_grp_plan.R | 139 ++++++-- tests/testthat/test-big_n.R | 8 tests/testthat/test-col_plan.R | 73 ++++ tests/testthat/test-make_mock_data.R | 3 tests/testthat/test-mrkdown_labels.R | 14 tests/testthat/test-print_to_gt.R |only tests/testthat/test-shuffle_card.R | 11 tests/testthat/test-tfrmt_checks.R | 6 tests/testthat/test-utils_tfrmt.R | 34 +- 51 files changed, 1842 insertions(+), 632 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.11.1 dated 2025-11-14 and 0.12.0 dated 2026-01-24
DESCRIPTION | 6 MD5 | 64 - NAMESPACE | 2 NEWS.md | 17 R/covmatrix.R | 460 +++---- R/data.R | 466 +++---- R/dispersion_optim2orig.R | 40 R/dispersion_orig2optim.R | 34 R/eacf.R |only R/esv.R | 2 R/get_data_object.R | 1179 +++++++++---------- R/get_data_object_glm.R | 1289 ++++++++++----------- R/get_eacf.R |only R/get_eacf_dotlist.R |only R/get_esv.R | 146 +- R/get_local_list.R | 407 +++--- R/glances.R | 308 ++--- R/glances_glm.R | 82 - R/laploglik_products.R | 1026 ++++++++--------- R/predict.R | 2550 +++++++++++++++++++++---------------------- R/predict_block.R | 496 ++++---- R/sf_to_df.R | 54 R/spcov_matrix.R | 426 +++---- R/spcov_vector.R | 306 ++--- R/use_gloglik_iid.R | 116 - inst/doc/introduction.Rmd | 810 ++++++------- inst/doc/introduction.html | 8 inst/references.bib | 1612 +++++++++++++-------------- man/eacf.Rd |only man/fc_borders.Rd | 56 man/predict.spmodel.Rd | 2 tests/testthat/test-extras.R | 92 + tests/testthat/test-spglm.R | 9 tests/testthat/test-splm.R | 959 ++++++++-------- vignettes/introduction.Rmd | 810 ++++++------- 35 files changed, 7008 insertions(+), 6826 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier [aut, cre],
William Muir [aut],
Katy Rainey [aut],
Shizhong Xu [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.7.3 dated 2019-09-23 and 1.8.0 dated 2026-01-24
NAM-1.7.3/NAM/inst/doc/background_stat_gen.pdf |only NAM-1.7.3/NAM/inst/doc/gwa_description.pdf |only NAM-1.7.3/NAM/inst/doc/gwa_ge_interactions.pdf |only NAM-1.8.0/NAM/DESCRIPTION | 15 NAM-1.8.0/NAM/MD5 | 40 NAM-1.8.0/NAM/NAMESPACE | 3 NAM-1.8.0/NAM/R/RcppExports.R | 318 ++-- NAM-1.8.0/NAM/R/gibbs.R | 24 NAM-1.8.0/NAM/R/pegs.R |only NAM-1.8.0/NAM/R/reml.R | 14 NAM-1.8.0/NAM/build/vignette.rds |binary NAM-1.8.0/NAM/data/test.RData |only NAM-1.8.0/NAM/demo/fieldvar.R | 51 NAM-1.8.0/NAM/inst/CITATION | 20 NAM-1.8.0/NAM/inst/doc/vignette1.html | 1774 +++++++++++++------------ NAM-1.8.0/NAM/inst/doc/vignette2.R | 38 NAM-1.8.0/NAM/inst/doc/vignette2.html | 756 ++++++---- NAM-1.8.0/NAM/man/Internals.Rd | 52 NAM-1.8.0/NAM/man/NAM-package.Rd | 6 NAM-1.8.0/NAM/man/pegs.Rd |only NAM-1.8.0/NAM/src/Functions.cpp | 13 NAM-1.8.0/NAM/src/Makevars |only NAM-1.8.0/NAM/src/Makevars.win |only NAM-1.8.0/NAM/src/RcppExports.cpp | 8 NAM-1.8.0/NAM/src/init.cpp |only NAM-1.8.0/NAM/src/pegs.cpp |only 26 files changed, 1744 insertions(+), 1388 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-5 dated 2026-01-22 and 1.2-6 dated 2026-01-24
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS.md | 14 +++++ inst/doc/FAQ.html | 8 +-- inst/doc/Optimalgo.html | 96 ++++++++++++++++++------------------ inst/doc/fitdistrplus_vignette.html | 4 - inst/doc/starting-values.html | 4 - tests/t-ppcomp.R | 68 +++++++++++++------------ tests/t-qqcomp.R | 68 +++++++++++++------------ 9 files changed, 151 insertions(+), 133 deletions(-)
Title: Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'
Description: Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
Author: Syed Haider [aut],
Daryl Waggott [aut],
Emilie Lalonde [ctb],
Clement Fung [ctb],
Helena Winata [ctb],
Dan Knight [ctb],
Michael Chirico [ctb],
Melinda Luo [ctb],
Paul C. Boutros [aut, cre, cph]
Maintainer: Paul C. Boutros <pboutros@sbpdiscovery.org>
Diff between bedr versions 1.1.3 dated 2025-04-06 and 1.1.5 dated 2026-01-24
DESCRIPTION | 15 MD5 | 8 NEWS.md | 15 build/vignette.rds |binary inst/doc/Using-bedr.html | 821 +---------------------------------------------- 5 files changed, 45 insertions(+), 814 deletions(-)
Title: Tidy Population Genetics
Description: We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.
Author: Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica [aut, cre, cph] ,
Chang Christopher [ctb] ),
Shaun Purcell [ctb] ),
Bengtsson Henrik [ctb] )
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidypopgen versions 0.4.2 dated 2026-01-22 and 0.4.3 dated 2026-01-23
DESCRIPTION | 6 - MD5 | 20 +++--- NEWS.md | 4 + R/gt_admixture.R | 4 - R/gt_as_plink.R | 2 inst/doc/a01_overview.html | 86 ++++++++++++++-------------- inst/doc/a02_qc.html | 20 +++--- inst/doc/tidypopgen.html | 6 - tests/testthat/Rplots.pdf |binary tests/testthat/test_gen_tibble_versioning.R | 4 - tests/testthat/test_gt_as_plink.R | 4 - 11 files changed, 81 insertions(+), 75 deletions(-)
Title: Detection of Kataegis
Description: Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 <doi:10.1101/287839>.
Author: Fouad Yousif [aut],
Xihui Lin [aut],
Fan Fan [aut],
Christopher Lalansingh [aut],
John Macdonald [aut],
Paul C. Boutros [cre]
Maintainer: Paul C. Boutros <pboutros@sbpdiscovery.org>
Diff between SeqKat versions 0.0.8 dated 2020-03-10 and 0.0.9 dated 2026-01-23
DESCRIPTION | 31 ++++++++++++++++++++++--------- MD5 | 9 +++++---- NEWS | 5 +++++ README.md |only build/vignette.rds |binary inst/doc/vignette.pdf |binary 6 files changed, 32 insertions(+), 13 deletions(-)
Title: Optimization-Based Stable Balancing Weights
Description: Use optimization to estimate weights that balance covariates for binary, multi-category, continuous, and multivariate treatments in the spirit of Zubizarreta (2015) <doi:10.1080/01621459.2015.1023805>. The degree of balance can be specified for each covariate. In addition, sampling weights can be estimated that allow a sample to generalize to a population specified with given target moments of covariates, as in matching-adjusted indirect comparison (MAIC).
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between optweight versions 1.0.0 dated 2025-09-09 and 2.0.0 dated 2026-01-23
optweight-1.0.0/optweight/R/optweight.fit.R |only optweight-1.0.0/optweight/R/optweight.svy.fit.R |only optweight-1.0.0/optweight/R/summary.R |only optweight-1.0.0/optweight/man/optweight.fit.Rd |only optweight-1.0.0/optweight/man/optweight.svy.fit.Rd |only optweight-2.0.0/optweight/DESCRIPTION | 15 optweight-2.0.0/optweight/MD5 | 68 optweight-2.0.0/optweight/NAMESPACE | 3 optweight-2.0.0/optweight/NEWS.md | 40 optweight-2.0.0/optweight/R/chk-utilities.R | 67 optweight-2.0.0/optweight/R/functions_for_processing.R | 119 optweight-2.0.0/optweight/R/opt_prep.R | 327 +- optweight-2.0.0/optweight/R/optweight-package.R | 3 optweight-2.0.0/optweight/R/optweight.R | 612 ++- optweight-2.0.0/optweight/R/optweight.svy.R | 243 + optweight-2.0.0/optweight/R/optweightMV.R |only optweight-2.0.0/optweight/R/plot.optweight.R | 178 - optweight-2.0.0/optweight/R/process_targets.R | 56 optweight-2.0.0/optweight/R/process_tols.R | 49 optweight-2.0.0/optweight/R/summary.optweight.R |only optweight-2.0.0/optweight/R/utils.R | 771 ---- optweight-2.0.0/optweight/README.md | 57 optweight-2.0.0/optweight/build/stage23.rdb |binary optweight-2.0.0/optweight/build/vignette.rds |binary optweight-2.0.0/optweight/inst/doc/optweight.Rmd | 499 ++- optweight-2.0.0/optweight/inst/doc/optweight.html | 1607 ++++++---- optweight-2.0.0/optweight/man/figures/README-unnamed-chunk-4-1.png |binary optweight-2.0.0/optweight/man/macros/macros.Rd | 5 optweight-2.0.0/optweight/man/optweight-package.Rd | 2 optweight-2.0.0/optweight/man/optweight.Rd | 236 + optweight-2.0.0/optweight/man/optweight.svy.Rd | 118 optweight-2.0.0/optweight/man/optweightMV.Rd |only optweight-2.0.0/optweight/man/plot.optweight.Rd | 72 optweight-2.0.0/optweight/man/process_targets.Rd | 14 optweight-2.0.0/optweight/man/process_tols.Rd | 10 optweight-2.0.0/optweight/man/summary.optweight.Rd | 60 optweight-2.0.0/optweight/tests/testthat/test-optweight.R | 4 optweight-2.0.0/optweight/vignettes/optweight.Rmd | 499 ++- optweight-2.0.0/optweight/vignettes/references.bib | 159 39 files changed, 3407 insertions(+), 2486 deletions(-)
Title: Nominating Quality Control Outliers in Genomic Profiling Studies
Description: A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.
Author: Anders Hugo Frelin [aut],
Helen Zhu [aut],
Paul C. Boutros [aut, cre]
Maintainer: Paul C. Boutros <PBoutros@sbpdiscovery.org>
Diff between OmicsQC versions 1.1.0 dated 2024-03-01 and 1.1.1 dated 2026-01-23
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/accumulate.zscores.R | 2 +- R/fit.and.evaluate.R | 4 ++-- build/vignette.rds |binary inst/doc/Intro_to_omicsQC.R | 8 ++++---- inst/doc/Intro_to_omicsQC.html | 17 +++++++++-------- 8 files changed, 36 insertions(+), 28 deletions(-)
Title: Utilities for the Application of a Polygenic Score to a VCF
Description: Simple and transparent parsing of genotype/dosage data
from an input Variant Call Format (VCF) file, matching of genotype
coordinates to the component Single Nucleotide Polymorphisms (SNPs)
of an existing polygenic score (PGS), and application of SNP weights
to dosages for the calculation of a polygenic score for each individual
in accordance with the additive weighted sum of dosages model. Methods
are designed in reference to best practices described by
Collister, Liu, and Clifton (2022) <doi:10.3389/fgene.2022.818574>.
Author: Paul Boutros [cre],
Nicole Zeltser [aut] ,
Rachel Dang [ctb],
Raag Agrawal [ctb]
Maintainer: Paul Boutros <PBoutros@sbpdiscovery.org>
Diff between ApplyPolygenicScore versions 4.0.0 dated 2025-08-20 and 4.0.1 dated 2026-01-23
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 5 ++++- build/vignette.rds |binary inst/doc/UserGuide.html | 39 ++++++++++++++++++++------------------- 5 files changed, 33 insertions(+), 29 deletions(-)
More information about ApplyPolygenicScore at CRAN
Permanent link
Title: Memory Management in R by Delayed Assignments
Description: Allows objects to be stored on disc and automatically
recalled into memory, as required, by delayed assignment.
Author: Bill Venables [aut, cre],
based on original code by David Brahm [aut]
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between SOAR versions 0.99-11 dated 2013-12-11 and 1.0-1 dated 2026-01-23
SOAR-0.99-11/SOAR/inst/NEWS |only SOAR-0.99-11/SOAR/man/NAME.Rd |only SOAR-0.99-11/SOAR/vignettes/Makefile |only SOAR-1.0-1/SOAR/DESCRIPTION | 20 SOAR-1.0-1/SOAR/MD5 | 31 SOAR-1.0-1/SOAR/NAMESPACE | 18 SOAR-1.0-1/SOAR/R/SOAR.R | 640 ++++++------ SOAR-1.0-1/SOAR/build/vignette.rds |binary SOAR-1.0-1/SOAR/inst/doc/SOAR.R | 46 SOAR-1.0-1/SOAR/inst/doc/SOAR.Rnw | 1796 +++++++++++++++++------------------ SOAR-1.0-1/SOAR/inst/doc/SOAR.pdf |binary SOAR-1.0-1/SOAR/man/Attach.Rd | 3 SOAR-1.0-1/SOAR/man/Objects.Rd | 3 SOAR-1.0-1/SOAR/man/Remove.Rd | 3 SOAR-1.0-1/SOAR/man/SOAR-package.Rd | 3 SOAR-1.0-1/SOAR/man/Search.Rd | 108 +- SOAR-1.0-1/SOAR/man/Store.Rd | 3 SOAR-1.0-1/SOAR/vignettes/SOAR.Rnw | 1796 +++++++++++++++++------------------ 18 files changed, 2257 insertions(+), 2213 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Distributed reproducible computing framework, adopting
ideas from git, docker and other software. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple times
over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Martin Eden [aut],
Alex Hill [aut],
Wes Hinsley [aut],
Mantra Kusumgar [aut],
Paul Lietar [aut],
James Thompson [aut],
Katy Gaythorpe [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 2.0.0 dated 2025-10-09 and 2.0.3 dated 2026-01-23
DESCRIPTION | 11 MD5 | 30 - R/location_packit.R | 2 build/vignette.rds |binary inst/doc/collaboration.html | 29 - inst/doc/dependencies.html | 61 +-- inst/doc/details.html | 5 inst/doc/introduction.html | 167 +++++----- inst/doc/migrating.html | 7 inst/doc/plugins.R | 212 ------------- inst/doc/plugins.html | 529 ---------------------------------- inst/doc/query.html | 11 inst/doc/troubleshooting.html | 33 +- tests/testthat/test-location-packit.R | 6 tests/testthat/test-location.R | 2 tests/testthat/test-util.R | 2 16 files changed, 187 insertions(+), 920 deletions(-)
Title: R Markdown Templates for Journal of Data Science
Description: Customized R Markdown templates for authoring articles
for Journal of Data Science.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between jds.rmd versions 0.3.3 dated 2023-06-20 and 0.3.4 dated 2026-01-23
jds.rmd-0.3.3/jds.rmd/man/jds.rmd-package.Rd |only jds.rmd-0.3.4/jds.rmd/DESCRIPTION | 12 +- jds.rmd-0.3.4/jds.rmd/MD5 | 10 - jds.rmd-0.3.4/jds.rmd/NEWS.md | 7 + jds.rmd-0.3.4/jds.rmd/R/pkg-doc.R | 7 - jds.rmd-0.3.4/jds.rmd/inst/rmarkdown/templates/pdf_article/resources/jdsart.cls | 60 +++++++--- jds.rmd-0.3.4/jds.rmd/man/jds.rmd.Rd |only 7 files changed, 67 insertions(+), 29 deletions(-)
Title: Within Outlying Mean Indexes: Refining the 'OMI' Analysis
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays. For details see Karasiewicz 'et al.' (2017) <doi:10.7717/peerj.3364>.
Author: Stephane Karasiewicz [aut, cre]
Maintainer: Stephane Karasiewicz <skaraz.science@gmail.com>
This is a re-admission after prior archival of version 1.5 dated 2022-07-15
Diff between subniche versions 1.5 dated 2022-07-15 and 1.6 dated 2026-01-23
DESCRIPTION | 30 +++++++++++++++------------- MD5 | 54 ++++++++++++++++++++++++++------------------------- NAMESPACE | 2 - R/convexhull.R |only R/eigenbar.R | 1 R/plot.subniche.R | 48 ++++----------------------------------------- R/plot_NR.R | 6 ++--- R/plot_NR_sp.R | 6 ++--- R/plot_dym.R | 6 ++--- R/plot_dym_sp.R | 6 ++--- R/subarea.R | 13 ++++++------ R/subniche.R | 5 ++-- R/subplot.R | 11 +++++----- R/subplot_K.R | 11 +++++----- R/subplot_sp.R | 6 ++--- build/partial.rdb |binary inst/CITATION | 33 +++++++++++++++++-------------- man/convexhull.Rd |only man/eigenbar.Rd | 1 man/plot.subniche.Rd | 3 +- man/plot_NR.Rd | 5 ++-- man/plot_NR_sp.Rd | 5 ++-- man/plot_dym.Rd | 5 ++-- man/plot_dym_sp.Rd | 5 ++-- man/subarea.Rd | 1 man/subniche.Rd | 5 ++-- man/subplot.Rd | 5 ++-- man/subplot_K.Rd | 5 ++-- man/subplot_sp.Rd | 5 ++-- 29 files changed, 134 insertions(+), 149 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Title: Probabilistic Record Linkage Using Pretrained Text Embeddings
Description: Links datasets through fuzzy string matching using pretrained text embeddings. Produces more accurate record linkage when lexical string distance metrics are a poor guide to match quality (e.g., "Patricia" is more lexically similar to "Patrick" than it is to "Trish"). Capable of performing multilingual record linkage. Methods are described in Ornstein (2025) <doi:10.1017/pan.2025.10016>.
Author: Joe Ornstein [aut, cre, cph]
Maintainer: Joe Ornstein <jornstein@uga.edu>
Diff between fuzzylink versions 0.2.5 dated 2025-08-29 and 0.3.0 dated 2026-01-23
DESCRIPTION | 10 - LICENSE | 4 MD5 | 36 ++-- NEWS.md | 4 R/check_match.R | 120 ++------------- R/dot.R | 26 +-- R/fuzzylink.R | 4 R/get_embeddings.R | 362 +++++++++++++++++++++++----------------------- R/get_similarity_matrix.R | 88 +++++------ R/get_training_set.R | 160 ++++++++++---------- R/hand_label.R | 66 ++++---- R/mistral_api_key.R | 144 +++++++++--------- R/openai_api_key.R | 144 +++++++++--------- R/utils.R | 28 +-- README.md | 27 +-- man/check_match.Rd | 2 man/dot.Rd | 44 ++--- man/fuzzylink.Rd | 4 man/hand_label.Rd | 34 ++-- 19 files changed, 611 insertions(+), 696 deletions(-)
Title: Docorate (Decorate + Output) Displays
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
Author: Becca Krouse [aut, cre],
Shannon Haughton [aut],
Seongbin Hong [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between docorator versions 0.5.1 dated 2026-01-08 and 0.5.2 dated 2026-01-23
DESCRIPTION | 6 MD5 | 19 - NAMESPACE | 1 NEWS.md | 6 R/render.R | 4 R/scale_gt.R | 4 R/utils_fancyhdr.R | 2 R/utils_gt.R | 41 ++- inst/doc/display_sizing.html | 440 ++++++++++++++++++++--------------------- man/apply_to_gt_group.Rd |only tests/testthat/test-utils_gt.R | 17 - 11 files changed, 278 insertions(+), 262 deletions(-)
More information about BinaryReplicates at CRAN
Permanent link
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.4.1 dated 2025-09-30 and 1.4.2 dated 2026-01-23
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS | 4 ++ R/plot_group_boxplots.R | 5 +- R/plot_tox_endpoints.R | 6 +-- README.md | 36 +++++++++++------- inst/doc/Chemical_names.html | 2 - inst/doc/Introduction.html | 8 ++-- inst/doc/PrepareData.html | 62 +++++++++++++++---------------- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-3.png |binary man/figures/logo.png |binary man/plot_tox_boxplots.Rd | 5 +- man/plot_tox_endpoints.Rd | 6 +-- 14 files changed, 86 insertions(+), 80 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Lukas A. Widmer [aut, cre],
Craig Gower-Page [aut],
Isaac Gravestock [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Lukas A. Widmer <lukas_andreas.widmer@novartis.com>
This is a re-admission after prior archival of version 1.5.2 dated 2025-10-28
Diff between rbmi versions 1.5.2 dated 2025-10-28 and 1.6.0 dated 2026-01-23
rbmi-1.5.2/rbmi/man/clear_model_cache.Rd |only rbmi-1.5.2/rbmi/man/get_session_hash.Rd |only rbmi-1.5.2/rbmi/tests/scripts/rcmdcheck.sh |only rbmi-1.5.2/rbmi/tests/scripts/testthat-full.sh |only rbmi-1.5.2/rbmi/tests/scripts/testthat.sh |only rbmi-1.6.0/rbmi/DESCRIPTION | 20 - rbmi-1.6.0/rbmi/MD5 | 66 ++--- rbmi-1.6.0/rbmi/NAMESPACE | 3 rbmi-1.6.0/rbmi/NEWS.md | 8 rbmi-1.6.0/rbmi/R/utilities.R | 178 ++++++------- rbmi-1.6.0/rbmi/README.md | 6 rbmi-1.6.0/rbmi/build/partial.rdb |binary rbmi-1.6.0/rbmi/build/vignette.rds |binary rbmi-1.6.0/rbmi/inst/doc/advanced.html | 2 rbmi-1.6.0/rbmi/inst/doc/quickstart.html | 236 +++++++++--------- rbmi-1.6.0/rbmi/man/get_unique_hash.Rd |only rbmi-1.6.0/rbmi/man/rbmi-package.Rd | 9 rbmi-1.6.0/rbmi/man/rbmi-settings.Rd | 9 rbmi-1.6.0/rbmi/tests/scripts/core.sh |only rbmi-1.6.0/rbmi/tests/scripts/cran.sh |only rbmi-1.6.0/rbmi/tests/scripts/documentation.sh |only rbmi-1.6.0/rbmi/tests/scripts/extended.sh |only rbmi-1.6.0/rbmi/tests/scripts/vignettes.sh | 12 rbmi-1.6.0/rbmi/tests/testthat.R | 8 rbmi-1.6.0/rbmi/tests/testthat/_snaps/mmrm.md | 8 rbmi-1.6.0/rbmi/tests/testthat/helper-misc.R | 12 rbmi-1.6.0/rbmi/tests/testthat/setup.R | 18 - rbmi-1.6.0/rbmi/tests/testthat/test-draws.R | 3 rbmi-1.6.0/rbmi/tests/testthat/test-fullusage.R | 32 +- rbmi-1.6.0/rbmi/tests/testthat/test-longData.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-mcmc.R | 44 +-- rbmi-1.6.0/rbmi/tests/testthat/test-mmrm.R | 20 + rbmi-1.6.0/rbmi/tests/testthat/test-parallel.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-pool.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-print.R | 28 +- rbmi-1.6.0/rbmi/tests/testthat/test-reproducibility.R | 6 rbmi-1.6.0/rbmi/tests/testthat/test-utilities.R | 21 - rbmi-1.6.0/rbmi/vignettes/build.R | 2 rbmi-1.6.0/rbmi/vignettes/quickstart.Rmd | 6 39 files changed, 386 insertions(+), 377 deletions(-)
Title: Easy Access to NetCDF Files with CF Metadata Conventions
Description: Network Common Data Form ('netCDF') files are widely used for
scientific data. Library-level access in R is provided through packages
'RNetCDF' and 'ncdf4'. Package 'ncdfCF' is built on top of 'RNetCDF' and
makes the data and its attributes available as a set of R6 classes that are
informed by the Climate and Forecasting Metadata Conventions. Access to the
data uses standard R subsetting operators and common function forms.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between ncdfCF versions 0.7.0 dated 2025-09-13 and 0.8.0 dated 2026-01-23
ncdfCF-0.7.0/ncdfCF/R/CFResource.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.Rmd |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.html |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.Rmd |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.html |only ncdfCF-0.7.0/ncdfCF/man/CFResource.Rd |only ncdfCF-0.7.0/ncdfCF/vignettes/R-CF.Rmd |only ncdfCF-0.7.0/ncdfCF/vignettes/Using_ncdfCF.Rmd |only ncdfCF-0.8.0/ncdfCF/DESCRIPTION | 23 ncdfCF-0.8.0/ncdfCF/LICENSE | 2 ncdfCF-0.8.0/ncdfCF/MD5 | 179 +-- ncdfCF-0.8.0/ncdfCF/NAMESPACE | 5 ncdfCF-0.8.0/ncdfCF/NEWS.md | 31 ncdfCF-0.8.0/ncdfCF/R/AOI.R | 38 ncdfCF-0.8.0/ncdfCF/R/AOImethod.R | 2 ncdfCF-0.8.0/ncdfCF/R/CFAuxiliaryLongLat.R | 56 - ncdfCF-0.8.0/ncdfCF/R/CFAxis.R | 166 ++ ncdfCF-0.8.0/ncdfCF/R/CFAxisCharacter.R | 41 ncdfCF-0.8.0/ncdfCF/R/CFAxisDiscrete.R | 22 ncdfCF-0.8.0/ncdfCF/R/CFAxisLatitude.R | 38 ncdfCF-0.8.0/ncdfCF/R/CFAxisLongitude.R | 36 ncdfCF-0.8.0/ncdfCF/R/CFAxisNumeric.R | 46 ncdfCF-0.8.0/ncdfCF/R/CFAxisTime.R | 136 +- ncdfCF-0.8.0/ncdfCF/R/CFAxisVertical.R | 127 +- ncdfCF-0.8.0/ncdfCF/R/CFBounds.R | 77 - ncdfCF-0.8.0/ncdfCF/R/CFData.R |only ncdfCF-0.8.0/ncdfCF/R/CFDataset.R | 209 ++- ncdfCF-0.8.0/ncdfCF/R/CFGridMapping.R | 18 ncdfCF-0.8.0/ncdfCF/R/CFGroup.R |only ncdfCF-0.8.0/ncdfCF/R/CFLabel.R | 141 +- ncdfCF-0.8.0/ncdfCF/R/CFObject.R | 407 ++----- ncdfCF-0.8.0/ncdfCF/R/CFStandardNames.R | 2 ncdfCF-0.8.0/ncdfCF/R/CFVariable.R | 559 +++++----- ncdfCF-0.8.0/ncdfCF/R/CFVariableL3b.R | 43 ncdfCF-0.8.0/ncdfCF/R/CFVerticalParametricTerm.R | 5 ncdfCF-0.8.0/ncdfCF/R/NCDimension.R | 21 ncdfCF-0.8.0/ncdfCF/R/NCGroup.R | 405 ++----- ncdfCF-0.8.0/ncdfCF/R/NCObject.R | 65 - ncdfCF-0.8.0/ncdfCF/R/NCResource.R |only ncdfCF-0.8.0/ncdfCF/R/NCVariable.R | 107 + ncdfCF-0.8.0/ncdfCF/R/makeCFObjects.R | 256 +++- ncdfCF-0.8.0/ncdfCF/R/ncdfCF-package.R | 12 ncdfCF-0.8.0/ncdfCF/R/ops.R | 8 ncdfCF-0.8.0/ncdfCF/R/readCF.R | 431 ++++--- ncdfCF-0.8.0/ncdfCF/R/utils.R | 29 ncdfCF-0.8.0/ncdfCF/README.md | 190 +-- ncdfCF-0.8.0/ncdfCF/TODO | 68 - ncdfCF-0.8.0/ncdfCF/build/vignette.rds |binary ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.R |only ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.Rmd |only ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.html |only ncdfCF-0.8.0/ncdfCF/inst/extdata/ERA5land_Rwanda_20160101.nc |binary ncdfCF-0.8.0/ncdfCF/inst/extdata/pr_day_EC-Earth3-CC_ssp245_r1i1p1f1_gr_20230101-20231231_vncdfCF.nc |binary ncdfCF-0.8.0/ncdfCF/man/CFAuxiliaryLongLat.Rd | 33 ncdfCF-0.8.0/ncdfCF/man/CFAxis.Rd | 77 + ncdfCF-0.8.0/ncdfCF/man/CFAxisCharacter.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisDiscrete.Rd | 21 ncdfCF-0.8.0/ncdfCF/man/CFAxisLatitude.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisLongitude.Rd | 24 ncdfCF-0.8.0/ncdfCF/man/CFAxisNumeric.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisTime.Rd | 57 - ncdfCF-0.8.0/ncdfCF/man/CFAxisVertical.Rd | 62 - ncdfCF-0.8.0/ncdfCF/man/CFBounds.Rd | 50 ncdfCF-0.8.0/ncdfCF/man/CFData.Rd |only ncdfCF-0.8.0/ncdfCF/man/CFDataset.Rd | 197 +++ ncdfCF-0.8.0/ncdfCF/man/CFGridMapping.Rd | 35 ncdfCF-0.8.0/ncdfCF/man/CFGroup.Rd |only ncdfCF-0.8.0/ncdfCF/man/CFLabel.Rd | 117 +- ncdfCF-0.8.0/ncdfCF/man/CFObject.Rd | 171 +-- ncdfCF-0.8.0/ncdfCF/man/CFVariable.Rd | 199 ++- ncdfCF-0.8.0/ncdfCF/man/CFVariableL3b.Rd | 27 ncdfCF-0.8.0/ncdfCF/man/CFVerticalParametricTerm.Rd | 27 ncdfCF-0.8.0/ncdfCF/man/NCDimension.Rd | 10 ncdfCF-0.8.0/ncdfCF/man/NCGroup.Rd | 263 +--- ncdfCF-0.8.0/ncdfCF/man/NCObject.Rd | 16 ncdfCF-0.8.0/ncdfCF/man/NCResource.Rd |only ncdfCF-0.8.0/ncdfCF/man/NCVariable.Rd | 66 + ncdfCF-0.8.0/ncdfCF/man/arrayOps.Rd | 3 ncdfCF-0.8.0/ncdfCF/man/as_CF.Rd | 38 ncdfCF-0.8.0/ncdfCF/man/create_ncdf.Rd |only ncdfCF-0.8.0/ncdfCF/man/dim.CFAxis.Rd | 7 ncdfCF-0.8.0/ncdfCF/man/dimnames.Rd | 6 ncdfCF-0.8.0/ncdfCF/man/figures/README-export-1.png |binary ncdfCF-0.8.0/ncdfCF/man/groups.Rd |only ncdfCF-0.8.0/ncdfCF/man/makeAxis.Rd | 12 ncdfCF-0.8.0/ncdfCF/man/makeCharacterAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeDiscreteAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeLatitudeAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/makeLongitudeAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/makeTimeAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeVerticalAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/ncdfCF-package.Rd | 13 ncdfCF-0.8.0/ncdfCF/man/open_ncdf.Rd | 10 ncdfCF-0.8.0/ncdfCF/man/str.CFAxis.Rd | 1 ncdfCF-0.8.0/ncdfCF/man/str.CFDataset.Rd | 1 ncdfCF-0.8.0/ncdfCF/man/sub-sub-.CFDataset.Rd | 2 ncdfCF-0.8.0/ncdfCF/tests/testthat/test-CFVariableL3b.R |only ncdfCF-0.8.0/ncdfCF/tests/testthat/test-CFobjects.R | 60 - ncdfCF-0.8.0/ncdfCF/tests/testthat/test-all.R | 73 - ncdfCF-0.8.0/ncdfCF/vignettes/ncdfCF.Rmd |only 102 files changed, 3410 insertions(+), 2395 deletions(-)
Title: Preprocessing and Analyzing Web Tracking Data
Description: Data structures and methods to work with web tracking data. The functions cover data preprocessing steps, enriching web tracking data with external information and methods for the analysis of digital behavior as used in several academic papers (e.g., Clemm von Hohenberg et al., 2023 <doi:10.17605/OSF.IO/M3U9P>; Stier et al., 2022 <doi:10.1017/S0003055421001222>).
Author: David Schoch [aut, cre] ,
Bernhard Clemm von Hohenberg [aut] ,
Frank Mangold [aut] ,
Sebastian Stier [aut]
Maintainer: David Schoch <david@schochastics.net>
Diff between webtrackR versions 0.3.1 dated 2024-04-30 and 0.3.2 dated 2026-01-23
DESCRIPTION | 26 +++---- MD5 | 20 ++--- NEWS.md | 5 + R/wt_dt.R | 3 README.md | 102 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/webtrackR.Rmd | 4 - inst/doc/webtrackR.html | 172 +++++++++++++++++++++++------------------------ man/webtrackR-package.Rd | 5 - vignettes/webtrackR.Rmd | 4 - 11 files changed, 172 insertions(+), 169 deletions(-)
Title: Text Plots
Description: Visualise complex relations in texts. This is done by providing functionalities for displaying
text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering and semantic text 'embeddings'.
Feel free to join the effort of providing interesting text visualisations. Do note that to avoid the risk of CRAN archival that you should put packages as much as possible in Suggests.
Package 'ggalt' is available in the CRAN archive: <https://cran.r-project.org/package=ggalt>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Sacha Epskamp [ctb, cph] ,
Ingo Feinerer and Kurt Hornik [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textplot versions 0.2.2 dated 2022-07-17 and 0.2.3 dated 2026-01-23
DESCRIPTION | 11 - MD5 | 40 ++-- NEWS.md | 5 R/textplot_embedding_2d.R | 4 build/vignette.rds |binary inst/doc/textplot-examples.R | 298 ++++++++++++++++---------------- inst/doc/textplot-examples.Rnw | 4 inst/doc/textplot-examples.pdf |binary man/example_btm.Rd | 50 ++--- man/example_embedding.Rd | 26 +- man/example_embedding_clusters.Rd | 30 +-- man/example_udpipe.Rd | 28 +-- man/textplot_bar.Rd | 180 +++++++++---------- man/textplot_bitermclusters.Rd | 174 +++++++++--------- man/textplot_cooccurrence.Rd | 138 +++++++------- man/textplot_correlation_glasso.Rd | 132 +++++++------- man/textplot_correlation_lines.Rd | 230 ++++++++++++------------ man/textplot_correlation_lines_attrs.Rd | 56 +++--- man/textplot_dependencyparser.Rd | 160 ++++++++--------- man/textplot_embedding_2d.Rd | 164 ++++++++--------- vignettes/textplot-examples.Rnw | 4 21 files changed, 870 insertions(+), 864 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.3 dated 2026-01-08 and 1.3.4 dated 2026-01-23
SEQTaRget-1.3.3/SEQTaRget/man/prepare.data.Rd |only SEQTaRget-1.3.4/SEQTaRget/DESCRIPTION | 10 - SEQTaRget-1.3.4/SEQTaRget/MD5 | 36 ++-- SEQTaRget-1.3.4/SEQTaRget/NEWS.md | 8 SEQTaRget-1.3.4/SEQTaRget/R/SEQexpand.R | 3 SEQTaRget-1.3.4/SEQTaRget/R/SEQuential.R | 5 SEQTaRget-1.3.4/SEQTaRget/R/globals.R |only SEQTaRget-1.3.4/SEQTaRget/R/internal_analysis.R | 122 +++++++++++--- SEQTaRget-1.3.4/SEQTaRget/R/internal_fatglmHelpers.R | 163 +++++++++++++++---- SEQTaRget-1.3.4/SEQTaRget/R/internal_hazard.R | 43 +++-- SEQTaRget-1.3.4/SEQTaRget/R/internal_survival.R | 61 ++++--- SEQTaRget-1.3.4/SEQTaRget/R/internal_weights.R | 21 +- SEQTaRget-1.3.4/SEQTaRget/inst/doc/SEQuential.html | 94 +++++----- SEQTaRget-1.3.4/SEQTaRget/inst/doc/seqopts.Rmd | 2 SEQTaRget-1.3.4/SEQTaRget/inst/doc/seqopts.html | 2 SEQTaRget-1.3.4/SEQTaRget/man/init_formula_cache.Rd |only SEQTaRget-1.3.4/SEQTaRget/man/inline.pred.Rd | 11 + SEQTaRget-1.3.4/SEQTaRget/man/internal.hazard.Rd | 2 SEQTaRget-1.3.4/SEQTaRget/man/internal.weights.Rd | 4 SEQTaRget-1.3.4/SEQTaRget/man/prepare.data_cached.Rd |only SEQTaRget-1.3.4/SEQTaRget/vignettes/seqopts.Rmd | 2 21 files changed, 401 insertions(+), 188 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.2.1 dated 2025-08-19 and 0.3.0 dated 2026-01-23
DESCRIPTION | 19 MD5 | 113 ++- NAMESPACE | 6 NEWS.md | 192 ++++-- R/aaa-utils.R | 41 - R/ellmer.R | 147 ++++ R/embed-azure.R |only R/embed-bedrock.R | 30 R/embed-databricks.R | 1 R/embed-gemini.R | 7 R/embed-snowflake.R |only R/embed-vertex.R | 5 R/embed.R | 76 ++ R/ingest.R | 303 ++++++++-- R/markdown-chunk.R | 6 R/ragnar-package.R | 75 ++ R/read-html.R | 15 R/read-markdown.R | 108 +++ R/retrieve.R | 19 R/store-v1.R | 7 R/store-v2.R | 26 R/store.R | 96 ++- README.md | 142 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ragnar.Rmd | 12 inst/doc/ragnar.html | 24 inst/python/_ragnartools/__pycache__/__init__.cpython-312.pyc |only inst/python/_ragnartools/__pycache__/__init__.cpython-313.pyc |only inst/python/_ragnartools/__pycache__/atlas.cpython-311.pyc |only inst/python/_ragnartools/__pycache__/markitdown.cpython-311.pyc |binary inst/python/_ragnartools/__pycache__/markitdown.cpython-312.pyc |only inst/python/_ragnartools/__pycache__/markitdown.cpython-313.pyc |only inst/python/_ragnartools/atlas.py |only inst/python/_ragnartools/markitdown.py | 43 + inst/python/unpin-youtube-transcript-api.txt |only inst/store-inspector/modules.R | 269 ++++++-- inst/store-inspector/www/inspector.js |only man/embed_azure_openai.Rd |only man/embed_bedrock.Rd | 4 man/embed_google_vertex.Rd | 9 man/embed_ollama.Rd | 2 man/embed_snowflake.Rd |only man/mcp_serve_store.Rd |only man/ragnar-package.Rd | 2 man/ragnar_find_links.Rd | 6 man/ragnar_read.Rd | 2 man/ragnar_register_tool_retrieve.Rd | 2 man/ragnar_retrieve.Rd | 2 man/ragnar_retrieve_bm25.Rd | 4 man/ragnar_retrieve_vss.Rd | 2 man/ragnar_retrieve_vss_and_bm25.Rd | 2 man/ragnar_store_atlas.Rd |only man/ragnar_store_create.Rd | 2 man/ragnar_store_ingest.Rd |only man/ragnar_store_inspect.Rd | 31 - man/read_as_markdown.Rd | 63 ++ tests/testthat/_snaps/store.md | 2 tests/testthat/test-embed-azure.R |only tests/testthat/test-embed-snowflake.R |only tests/testthat/test-extra-cols.R | 2 tests/testthat/test-ingest.R |only tests/testthat/test-read-markdown-youtube.R |only tests/testthat/test-read-markdown.R | 20 tests/testthat/test-store-v2.R | 65 ++ tools/configure_deps.R | 1 vignettes/ragnar.Rmd | 12 67 files changed, 1580 insertions(+), 437 deletions(-)
Title: Inference on the Overlap Coefficient
Description: Provides functions to construct confidence intervals for the Overlap Coefficient (OVL). OVL measures the similarity between two distributions through the overlapping area of their distribution functions. Given its intuitive description and ease of visual representation by the straightforward depiction of the amount of overlap between the two corresponding histograms based on samples of measurements from each one of the two distributions, the development of accurate methods for confidence interval construction can be useful for applied researchers. Implements methods based on the work of Franco-Pereira, A.M., Nakas, C.T., Reiser, B., and Pardo, M.C. (2021) <doi:10.1177/09622802211046386> as well as extensions for multimodal distributions proposed by Alcaraz-Peñalba, A., Franco-Pereira, A., and Pardo, M.C. (2025) <doi:10.1007/s10182-025-00545-2>.
Author: Alba M. Franco-Pereira [aut, cre, cph],
Christos T. Nakas [aut],
Benjamin Reiser [aut],
M.Carmen Pardo [aut],
Alba Alcaraz-Penalba [aut, cph]
Maintainer: Alba M. Franco-Pereira <albfranc@ucm.es>
Diff between OVL.CI versions 0.1.0 dated 2023-11-13 and 0.1.1 dated 2026-01-23
DESCRIPTION | 23 +- MD5 | 145 ++++++++++-------- NAMESPACE | 20 +- NEWS.md | 8 R/EM.R |only R/FIM_mixture_normals.R |only R/OVL.BCAN.R | 14 - R/OVL.BCPB.R | 14 - R/OVL.BCbias.R | 14 - R/OVL.D.R | 10 - R/OVL.DBC.R | 12 - R/OVL.DBCL.R | 12 - R/OVL.Delta.mix.R |only R/OVL.GPQ.R |only R/OVL.GPQ.mix.R |only R/OVL.K.R | 12 - R/OVL.KPB.R | 12 - R/OVL.LogitBCAN.R | 14 - R/OVL.LogitD.R | 10 - R/OVL.LogitDBC.R | 12 - R/OVL.LogitDBCL.R | 11 - R/OVL.LogitK.R | 12 - R/OVL_derivates_1.R |only R/OVL_derivates_2.R |only R/OVL_mix.R |only R/U.R | 17 -- R/data.R | 10 - R/data_mix.R |only R/dnorm_mixture.R |only R/encontrar_raices.R |only R/kernel.e.R | 12 - R/kernel.e.density.R | 18 -- R/kernel.g.R | 13 - R/kernel.g.density.R | 18 -- R/likbox.R | 18 -- R/ssdd.R | 12 - data/mixnorm_data.rda |only man/EM.Rd |only man/FIM_mixture_normals.Rd |only man/OVL.BCAN.Rd | 14 - man/OVL.BCPB.Rd | 14 - man/OVL.BCbias.Rd | 14 - man/OVL.D.Rd | 10 - man/OVL.DBC.Rd | 12 - man/OVL.DBCL.Rd | 12 - man/OVL.Delta.mix.Rd |only man/OVL.GPQ.Rd |only man/OVL.GPQ.mix.Rd |only man/OVL.K.Rd | 12 - man/OVL.KPB.Rd | 12 - man/OVL.LogitBCAN.Rd | 14 - man/OVL.LogitD.Rd | 10 - man/OVL.LogitDBC.Rd | 12 - man/OVL.LogitDBCL.Rd | 12 - man/OVL.LogitK.Rd | 12 - man/OVL_derivates_1.Rd |only man/OVL_derivates_2.Rd |only man/OVL_mix.Rd |only man/U.Rd | 18 -- man/dnorm_mixture.Rd |only man/encontrar_raices.Rd |only man/kernel.e.Rd | 13 - man/kernel.e.density.Rd | 19 -- man/kernel.g.Rd | 13 - man/kernel.g.density.Rd | 19 -- man/likbox.Rd | 19 -- man/mixnorm_data.Rd |only man/ssdd.Rd | 13 - man/test_data.Rd | 10 - tests/testthat/test_EM.R |only tests/testthat/test_FIM_mixture_normals.R |only tests/testthat/test_LogitBCAN.R | 4 tests/testthat/test_LogitD.R | 4 tests/testthat/test_LogitDBC.R | 4 tests/testthat/test_LogitDBCL.R | 4 tests/testthat/test_LogitK.R | 4 tests/testthat/test_OVL.BCAN.R | 4 tests/testthat/test_OVL.BCPB.R | 4 tests/testthat/test_OVL.BCbias.R | 4 tests/testthat/test_OVL.D.R | 4 tests/testthat/test_OVL.DBCL.R | 4 tests/testthat/test_OVL.Delta.mix.R |only tests/testthat/test_OVL.GPQ.R |only tests/testthat/test_OVL.GPQ.mix.R |only tests/testthat/test_OVL.K.R | 4 tests/testthat/test_OVL.KPB.R | 4 tests/testthat/test_OVL_derivates_1&OVL_derivates_2.R |only tests/testthat/test_dnorm_mixture.R |only tests/testthat/test_encontrar_raices.R |only 89 files changed, 393 insertions(+), 412 deletions(-)
Title: Model-Based Clustering of Network Data
Description: Clustering unilayer and multilayer network data by means of finite mixtures is the main utility of netClust.
Author: Shuchismita Sarkar [aut, cre],
Volodymyr Melnykov [aut]
Maintainer: Shuchismita Sarkar <ssarkar@bgsu.edu>
This is a re-admission after prior archival of version 1.0.1 dated 2020-07-07
Diff between netClust versions 1.0.1 dated 2020-07-07 and 1.0.2 dated 2026-01-23
netClust-1.0.1/netClust/data/netData.RData |only netClust-1.0.1/netClust/data/netDataID.RData |only netClust-1.0.2/netClust/DESCRIPTION | 18 +++--- netClust-1.0.2/netClust/MD5 | 26 ++++----- netClust-1.0.2/netClust/R/RcppExports.R | 16 +++++ netClust-1.0.2/netClust/build/partial.rdb |binary netClust-1.0.2/netClust/data/netData.rda |only netClust-1.0.2/netClust/data/netDataID.rda |only netClust-1.0.2/netClust/man/netClust-package.Rd | 45 +++++++++------ netClust-1.0.2/netClust/man/netData.Rd | 4 - netClust-1.0.2/netClust/man/netDataID.Rd | 2 netClust-1.0.2/netClust/man/rcpparma_hello_world.Rd |only netClust-1.0.2/netClust/src/Makevars | 2 netClust-1.0.2/netClust/src/Makevars.win | 2 netClust-1.0.2/netClust/src/RcppExports.cpp | 52 ++++++++++++++++++ netClust-1.0.2/netClust/src/netClust.cpp | 54 +++++++++---------- netClust-1.0.2/netClust/src/rcpparma_hello_world.cpp |only 17 files changed, 148 insertions(+), 73 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2024-10-11
Diff between healthyR.ts versions 0.3.1 dated 2024-10-11 and 0.3.2 dated 2026-01-23
DESCRIPTION | 16 MD5 | 242 ++--- NAMESPACE | 1 NEWS.md | 775 +++++++++--------- R/00_global_variables.R | 36 R/augment-ts-acceleration.R | 170 +-- R/augment-ts-growth.R | 142 +-- R/augment-ts-velocity.R | 164 +-- R/boilerplate-autoarima-xgboost.R | 546 ++++++------ R/boilerplate-autoarima.R | 550 ++++++------ R/boilerplate-croston.R | 546 ++++++------ R/boilerplate-exp-smoothing.R | 554 ++++++------ R/boilerplate-glmnet.R | 546 ++++++------ R/boilerplate-lm.R | 362 ++++---- R/boilerplate-mars.R | 536 ++++++------ R/boilerplate-misc-functions.R | 76 - R/boilerplate-nnetar.R | 546 ++++++------ R/boilerplate-prophet-reg.R | 548 ++++++------ R/boilerplate-prophet-xgboost.R | 560 ++++++------- R/boilerplate-smooth-es.R | 564 ++++++------- R/boilerplate-svm-poly.R | 552 ++++++------ R/boilerplate-svm-rbf.R | 548 ++++++------ R/boilerplate-theta.R | 352 ++++---- R/boilerplate-xgboost.R | 536 ++++++------ R/brownian-motion-plot.R | 200 ++-- R/calibrate-plot-list.R | 264 +++--- R/diagnostic_plots.R | 630 +++++++------- R/helper-model-extraction.R | 176 ++-- R/internal-event-backward.R | 126 +- R/internal-event-both.R | 128 +- R/internal-event-forward.R | 126 +- R/simulate-ts-arima.R | 2 R/stat-adf-test.R | 226 ++--- R/stats-confidence-intervals.R | 130 +-- R/step-ts-acceleration.R | 368 ++++---- R/step-ts-velocity.R | 366 ++++---- R/tidy-fft.R | 572 ++++++------- R/ts-auto-recipe.R | 370 ++++---- R/ts-brownian-motion-augment.R | 368 ++++---- R/ts-brownian-motion.R | 202 ++-- R/ts-calendar-heatmap-plt.R | 266 +++--- R/ts-compare-data.R | 234 ++--- R/ts-event-analysis-plot.R | 512 +++++------ R/ts-event-analysis-tbl.R | 374 ++++---- R/ts-fcst-sim.R | 554 ++++++------ R/ts-feature-cluster-plt.R | 354 ++++---- R/ts-feature-cluster-tbl.R | 380 ++++---- R/ts-geometric-brownian-motion-augment.R | 432 +++++----- R/ts-geometric-brownian-motion.R | 238 ++--- R/ts-info-tbl.R | 294 +++--- R/ts-lag-correlation.R | 400 ++++----- R/ts-ma-plt.R | 507 ++++------- R/ts-model-compare.R | 500 +++++------ R/ts-model-rank.R | 220 ++--- R/ts-model-tuner.R | 612 +++++++------- R/ts-qq-plot.R | 266 +++--- R/ts-random-walk-plot.R |only R/ts-random-walk.R | 224 ++--- R/ts-skedactiy-plot.R | 268 +++--- R/ts-sma-plot.R | 312 +++---- R/ts-splits-plot.R | 148 +-- R/ts-to-tbl.R | 128 +- R/ts-tune-spec-template.R | 476 +++++------ R/ts-vva-plot.R | 214 ++-- R/utils-auto-stationarize.R | 148 +-- R/utils-difflog-stationary.R | 184 ++-- R/utils-doublediff-stationary.R | 168 +-- R/utils-doubledifflog-stationary.R | 176 ++-- R/utils-get-boilerplate-fit-wflw.R | 150 +-- R/utils-log-trans-stationary.R | 164 +-- R/utils-singlediff-stationary.R | 166 +-- R/utils-tidy-eval.R | 98 +- R/utils-time-helpers.R | 156 +-- R/vec-ts-acceleration.R | 120 +- R/vec-ts-growth-rate.R | 232 ++--- R/vec-ts-velocity.R | 120 +- R/wfs-arima-boost.R | 368 ++++---- R/wfs-arima-reg.R | 220 ++--- R/wfs-ets-reg.R | 390 ++++----- R/wfs-linear-reg.R | 250 ++--- R/wfs-mars-reg.R | 274 +++--- R/wfs-nnetar-reg.R | 270 +++--- R/wfs-prophet-reg.R | 440 +++++----- R/wfs-svm-poly-reg.R | 274 +++--- R/wfs-svm-rbf.R | 260 +++--- R/wfs-xgboost-reg.R | 284 +++--- README.md | 322 +++++-- build/vignette.rds |binary inst/doc/getting-started.html | 31 inst/doc/using-tidy-fft.html | 35 man/auto_stationarize.Rd | 140 +-- man/ci_hi.Rd | 72 - man/ci_lo.Rd | 72 - man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/ts_adf_test.Rd | 98 +- man/ts_arima_simulator.Rd | 2 man/ts_brownian_motion.Rd | 136 +-- man/ts_brownian_motion_augment.Rd | 166 +-- man/ts_brownian_motion_plot.Rd | 111 +- man/ts_event_analysis_plot.Rd | 145 +-- man/ts_extract_auto_fitted_workflow.Rd | 106 +- man/ts_geometric_brownian_motion.Rd | 166 +-- man/ts_geometric_brownian_motion_augment.Rd | 194 ++-- man/ts_get_date_columns.Rd | 108 +- man/ts_growth_rate_augment.Rd | 94 +- man/ts_growth_rate_vec.Rd | 136 +-- man/ts_is_date_class.Rd | 100 +- man/ts_lag_correlation.Rd | 206 ++-- man/ts_ma_plot.Rd | 18 man/ts_qq_plot.Rd | 1 man/ts_random_walk_plot.Rd |only man/ts_scedacity_scatter_plot.Rd | 3 man/ts_wfs_xgboost.Rd | 226 ++--- man/util_difflog_ts.Rd | 150 +-- man/util_doublediff_ts.Rd | 150 +-- man/util_doubledifflog_ts.Rd | 152 +-- man/util_log_ts.Rd | 148 +-- man/util_singlediff_ts.Rd | 148 +-- 123 files changed, 15052 insertions(+), 14931 deletions(-)
Title: Plotting Football Matches Expected Goals (xG) Stats with
'Understat' Data
Description: Scrapes football match shots data from 'Understat' <https://understat.com/> and visualizes it using interactive plots:
- A detailed shot map displaying the location, type, and xG value of shots taken by both teams.
- An xG timeline chart showing the cumulative xG for each team over time, annotated with the details of scored goals.
Author: Aymen Nasri [aut, cre, cph]
Maintainer: Aymen Nasri <aymennasrii@proton.me>
Diff between ggfootball versions 0.2.2 dated 2026-01-23 and 0.3.0 dated 2026-01-23
DESCRIPTION | 11 +--- MD5 | 10 +-- NEWS.md | 14 +++++ R/understat_scraper.R | 137 ++++++++++++++++++++++---------------------------- R/xg_chart.R | 27 +++++++-- R/xg_map.R | 72 +++++++++++++++++++------- 6 files changed, 161 insertions(+), 110 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Gabriel Garcia de Almeida [aut] ,
Arthur Bazolli [ctb],
Pedro Milreu Cunha [ctb],
ITpS - Instituto Todos pela Saude [fnd],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.5.0 dated 2025-12-09 and 0.6.0 dated 2026-01-23
geocodebr-0.5.0/geocodebr/tests/tests_rafa/benchmark_callr.R |only geocodebr-0.5.0/geocodebr/tests/tests_rafa/utils2_noserialize.R |only geocodebr-0.6.0/geocodebr/DESCRIPTION | 12 geocodebr-0.6.0/geocodebr/MD5 | 78 +- geocodebr-0.6.0/geocodebr/NEWS.md | 22 geocodebr-0.6.0/geocodebr/R/busca_por_cep.R | 53 + geocodebr-0.6.0/geocodebr/R/cache.R | 36 - geocodebr-0.6.0/geocodebr/R/create_geocodebr_db.R | 25 geocodebr-0.6.0/geocodebr/R/definir_campos.R | 19 geocodebr-0.6.0/geocodebr/R/download_cnefe.R | 35 - geocodebr-0.6.0/geocodebr/R/geocode.R | 308 +++++----- geocodebr-0.6.0/geocodebr/R/geocode_orig.R | 169 ++--- geocodebr-0.6.0/geocodebr/R/geocode_reverso.R | 95 +-- geocodebr-0.6.0/geocodebr/R/geocodebr-package.R | 43 + geocodebr-0.6.0/geocodebr/R/match_cases.R | 39 - geocodebr-0.6.0/geocodebr/R/match_cases_probabilistic.R | 76 +- geocodebr-0.6.0/geocodebr/R/match_weighted_cases.R | 53 + geocodebr-0.6.0/geocodebr/R/match_weighted_cases_probabilistic.R | 65 +- geocodebr-0.6.0/geocodebr/R/progress_bar.R | 14 geocodebr-0.6.0/geocodebr/R/register_cnefe_tables.R | 68 -- geocodebr-0.6.0/geocodebr/R/string_dist.R | 18 geocodebr-0.6.0/geocodebr/R/trata_empates_geocode_duckdb.R | 46 - geocodebr-0.6.0/geocodebr/R/utils.R | 299 ++++++--- geocodebr-0.6.0/geocodebr/README.md | 2 geocodebr-0.6.0/geocodebr/inst/doc/geocode.R | 52 - geocodebr-0.6.0/geocodebr/inst/doc/geocode.Rmd | 11 geocodebr-0.6.0/geocodebr/inst/doc/geocode.html | 55 + geocodebr-0.6.0/geocodebr/inst/doc/geocode_reverso.R | 38 - geocodebr-0.6.0/geocodebr/inst/doc/geocode_reverso.html | 55 + geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.R | 116 +-- geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.Rmd | 12 geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.html | 26 geocodebr-0.6.0/geocodebr/man/geocode.Rd | 10 geocodebr-0.6.0/geocodebr/man/geocodebr.Rd | 1 geocodebr-0.6.0/geocodebr/man/roxygen/templates/precision_section.R | 10 geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_20k.R |only geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 12 geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 274 ++------ geocodebr-0.6.0/geocodebr/tests/tests_rafa/group_for_parallel.R |only geocodebr-0.6.0/geocodebr/tests/testthat/test-geocode.R | 2 geocodebr-0.6.0/geocodebr/vignettes/geocode.Rmd | 11 geocodebr-0.6.0/geocodebr/vignettes/geocodebr.Rmd | 12 42 files changed, 1231 insertions(+), 1041 deletions(-)
Title: High-Performance 'GeoJSON' and 'JSON' Serialization
Description: Converts R data frames and 'sf' spatial objects into 'JSON' and
'GeoJSON' strings. The core encoders are implemented in 'Rust' using the
'extendr' framework and are designed to efficiently serialize large
tabular and spatial datasets. Returns serialized 'JSON' text, allowing
applications such as 'shiny' or web APIs to transfer data to
client-side 'JavaScript' libraries without additional encoding overhead.
Author: Alex Jorion [aut, cre],
The authors of the dependency Rust crates [ctb]
Maintainer: Alex Jorion <alex.jorion@firstzeroenergy.com>
Diff between fastgeojson versions 0.1.2 dated 2026-01-19 and 0.1.3 dated 2026-01-23
DESCRIPTION | 6 ++--- MD5 | 16 ++++++------- NEWS.md | 4 +++ README.md | 5 ---- configure | 38 ++++++++++++++++++++++++++++++-- src/Makevars.in | 59 +++++++++++++++++++++++++++----------------------- src/Makevars.win | 61 ++++++++++++++++++++++++++-------------------------- src/rust/Cargo.lock | 2 - src/rust/Cargo.toml | 2 - 9 files changed, 116 insertions(+), 77 deletions(-)
Title: Create, Stow, and Read Data Packages
Description: Data frame, tibble, or tbl objects are converted to data package objects using specific metadata labels (name, version, title, homepage, description). A data package object ('dpkg') can be written to disk as a 'parquet' file or released to a 'GitHub' repository. Data package objects can be read into R from online repositories and downloaded files are cached locally across R sessions.
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Diff between dpkg versions 0.6.1 dated 2025-01-08 and 0.6.2 dated 2026-01-23
DESCRIPTION | 14 ++-- MD5 | 26 ++++---- NEWS.md | 7 ++ R/dpkg_release_gh.R | 95 ++++++++++++++++++++++++++------ R/dpkg_tibble.R | 31 +++++++--- R/read_write_dpkg.R | 34 +++++++++-- R/stow.R | 70 +++++++++++++++-------- man/stow.Rd | 20 +++--- tests/testthat/test-check_name.R | 4 - tests/testthat/test-dpkg.R | 19 ++++-- tests/testthat/test-dpkg_tidy_methods.R | 13 +++- tests/testthat/test-read_dpkg.R | 23 ++++++- tests/testthat/test-stow.R | 17 ++++- tests/testthat/test-write_dpkg.R | 5 + 14 files changed, 269 insertions(+), 109 deletions(-)
Title: Predict Carbon Emissions for UK SMEs
Description: Predict Scope 1, 2 and 3 carbon emissions for UK Small and Medium-sized Enterprises (SMEs), using Standard Industrial Classification (SIC) codes and annual turnover data, as well as Scope 1 carbon emissions for UK farms. The 'carbonpredict' package provides single and batch prediction, plotting, and workflow tools for carbon accounting and reporting. The package utilises pre-trained models, leveraging rich classified transaction data to accurately predict Scope 1, 2 and 3 carbon emissions for UK SMEs as well as identifying emissions hotspots. It also provides Scope 1 carbon emissions predictions for UK farms of types: Cereals ex. rice, Dairy, Mixed farming, Sheep and goats, Cattle & buffaloes, Poultry, Animal production and Support for crop production. The methodology used to produce the estimates in this package is fully detailed in the following peer-reviewed publications: Phillpotts, A., Owen. A., Norman, J., Trendl, A., Gathergood, J., Jobst, Norbert., Leake, D. (2025) <doi [...truncated...]
Author: Hamza Suleman [aut, cre, cph],
Alec Phillpotts [ctb, aut],
Jasmine Wells [ctb, aut],
David Leake [ctb, aut]
Maintainer: Hamza Suleman <Hamza.Suleman@lloydsbanking.com>
Diff between carbonpredict versions 2.0.0 dated 2025-10-29 and 2.0.1 dated 2026-01-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 6 ++++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are used to
provide tools for consistent and well-founded type-coercion and
size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Davis Vaughan [aut, cre],
data.table team [cph] and
their contribution to R's order),
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between vctrs versions 0.7.0 dated 2026-01-16 and 0.7.1 dated 2026-01-23
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 4 +++ inst/doc/stability.html | 4 +-- src/rlang/env.h | 5 +++- src/type-data-frame.c | 14 +++++++----- src/type-factor.c | 54 +++++++++++++++++++++++++++--------------------- src/version.c | 2 - 8 files changed, 60 insertions(+), 43 deletions(-)
Title: Standardization-Based Effect Estimation with Optional Prior
Covariance Adjustment
Description: The Prognostic Regression Offsets with Propagation of
ERrors (for Treatment Effect Estimation) package facilitates
direct adjustment for experiments and observational studies that
is compatible with a range of study designs and covariance
adjustment strategies. It uses explicit specification of clusters,
blocks and treatment allocations to furnish probability of
assignment-based weights targeting any of several average
treatment effect parameters, and for standard error calculations
reflecting these design parameters. For covariance adjustment of
its Hajek and (one-way) fixed effects estimates, it enables
offsetting the outcome against predictions from a dedicated
covariance model, with standard error calculations propagating
error as appropriate from the covariance model.
Author: Josh Errickson [cre, aut],
Josh Wasserman [aut],
Mark Fredrickson [ctb],
Adam Sales [ctb],
Xinhe Wang [ctb],
Ben Hansen [aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between propertee versions 1.0.3 dated 2025-10-28 and 1.0.4 dated 2026-01-23
DESCRIPTION | 6 MD5 | 42 +- NAMESPACE | 1 NEWS.md | 6 R/SandwichLayerVariance.R | 413 ++++++++++++++++++++-------- R/as.lmitt.R | 58 ++- R/summary.teeMod.R | 38 ++ R/teeMod.R | 170 +++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/RDD.html | 9 inst/doc/intro-to-propertee.html | 15 - inst/doc/non-binary-treatment.html | 9 man/as_lmitt.Rd | 10 man/cluster_iss.Rd | 58 ++- man/dot-compute_IK_dof.Rd | 48 ++- man/dot-get_dof.Rd | 70 ++++ man/dot-rcorrect.Rd | 28 + tests/testthat/test.SandwichLayerVariance.R | 229 +++++++++++---- tests/testthat/test.summary.teeMod.R | 15 - tests/testthat/test.teeMod.R | 388 +++++++++++++++++--------- tests/testthat/test.variations_of_lm.R | 24 + 22 files changed, 1167 insertions(+), 470 deletions(-)
Title: Model and Learner Summaries for 'mlr3'
Description: Concise and interpretable summaries for machine learning
models and learners of the 'mlr3' ecosystem. The package takes
inspiration from the summary function for (generalized) linear models
but extends it to non-parametric machine learning models, based on
generalization performance, model complexity, feature importances and
effects, and fairness metrics.
Author: Susanne Dandl [aut, cre] ,
Marc Becker [aut] ,
Bernd Bischl [aut] ,
Giuseppe Casalicchio [aut] ,
Ludwig Bothmann [aut]
Maintainer: Susanne Dandl <dandls.datascience@gmail.com>
Diff between mlr3summary versions 0.1.0 dated 2024-04-24 and 0.1.1 dated 2026-01-23
mlr3summary-0.1.0/mlr3summary/README.md |only mlr3summary-0.1.0/mlr3summary/demo |only mlr3summary-0.1.0/mlr3summary/inst/mlr3summary_playground.Rmd |only mlr3summary-0.1.0/mlr3summary/inst/results.rda |only mlr3summary-0.1.0/mlr3summary/inst/results_runtime.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtime.png |only mlr3summary-0.1.0/mlr3summary/inst/runtime_experiments.R |only mlr3summary-0.1.0/mlr3summary/inst/runtimes.txt |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_lm.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_lm_parallel.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_rf.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_rf_parallel.rda |only mlr3summary-0.1.1/mlr3summary/DESCRIPTION | 46 +++-- mlr3summary-0.1.1/mlr3summary/MD5 | 40 +---- mlr3summary-0.1.1/mlr3summary/NAMESPACE | 1 mlr3summary-0.1.1/mlr3summary/NEWS.md |only mlr3summary-0.1.1/mlr3summary/R/bibentries.R | 34 ++-- mlr3summary-0.1.1/mlr3summary/R/credit_data.R | 5 mlr3summary-0.1.1/mlr3summary/R/get_complexity.R | 53 +++--- mlr3summary-0.1.1/mlr3summary/R/get_effects.R | 73 ++++----- mlr3summary-0.1.1/mlr3summary/R/get_importances.R | 74 ++++----- mlr3summary-0.1.1/mlr3summary/R/summary.R | 77 ++++------ mlr3summary-0.1.1/mlr3summary/R/utils.R | 13 - mlr3summary-0.1.1/mlr3summary/R/zzz.R | 3 mlr3summary-0.1.1/mlr3summary/inst/CITATION |only mlr3summary-0.1.1/mlr3summary/man/summary.Learner.Rd | 5 mlr3summary-0.1.1/mlr3summary/man/summary_control.Rd | 2 27 files changed, 202 insertions(+), 224 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joeseph Zemm [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.21 dated 2025-08-20 and 2.7.22 dated 2026-01-23
dataRetrieval-2.7.21/dataRetrieval/man/constructUseURL.Rd |only dataRetrieval-2.7.22/dataRetrieval/DESCRIPTION | 15 dataRetrieval-2.7.22/dataRetrieval/MD5 | 166 +-- dataRetrieval-2.7.22/dataRetrieval/NAMESPACE | 4 dataRetrieval-2.7.22/dataRetrieval/NEWS | 17 dataRetrieval-2.7.22/dataRetrieval/R/AAA.R | 12 dataRetrieval-2.7.22/dataRetrieval/R/constructNWISURL.R | 63 - dataRetrieval-2.7.22/dataRetrieval/R/construct_api_requests.R | 324 +----- dataRetrieval-2.7.22/dataRetrieval/R/dataRetrievals-package.R | 46 dataRetrieval-2.7.22/dataRetrieval/R/deal_with_empty.R |only dataRetrieval-2.7.22/dataRetrieval/R/findNLDI.R | 24 dataRetrieval-2.7.22/dataRetrieval/R/get_ogc_data.R |only dataRetrieval-2.7.22/dataRetrieval/R/get_ogc_documentation.R |only dataRetrieval-2.7.22/dataRetrieval/R/readNWISpCode.R | 1 dataRetrieval-2.7.22/dataRetrieval/R/readNWISunit.R | 126 -- dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata.R | 35 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_continuous.R |only dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_daily.R | 85 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_field_measurements.R | 49 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_latest_continuous.R | 46 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_latest_daily.R |only dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_metadata.R | 64 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_monitoring_location.R | 95 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_parameter_codes.R | 59 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_samples.R | 4 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_ts_meta.R | 67 - dataRetrieval-2.7.22/dataRetrieval/R/rejigger_cols.R |only dataRetrieval-2.7.22/dataRetrieval/R/setAccess.R | 2 dataRetrieval-2.7.22/dataRetrieval/R/sysdata.rda |binary dataRetrieval-2.7.22/dataRetrieval/R/walk_pages.R | 318 +---- dataRetrieval-2.7.22/dataRetrieval/inst/CITATION | 5 dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.R | 79 - dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.Rmd | 164 --- dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.html | 533 +++------- dataRetrieval-2.7.22/dataRetrieval/inst/extdata/temperatureAndFlow.RData |binary dataRetrieval-2.7.22/dataRetrieval/man/check_OGC_requests.Rd | 4 dataRetrieval-2.7.22/dataRetrieval/man/check_waterdata_sample_params.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/constructNWISURL.Rd | 4 dataRetrieval-2.7.22/dataRetrieval/man/construct_api_requests.Rd | 8 dataRetrieval-2.7.22/dataRetrieval/man/construct_waterdata_sample_request.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/countyCd.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/countyCdLookup.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/findNLDI.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/getWebServiceData.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/get_nldi_sources.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/get_ogc_params.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/importNGWMN.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importRDB1.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWQP.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWaterML1.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWaterML2.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/parameterCdFile.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/parse_WQP.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNlevels.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNsites.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNWISdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNWISgwl.Rd | 16 dataRetrieval-2.7.22/dataRetrieval/man/readNWISmeas.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/readNWISpCode.Rd | 1 dataRetrieval-2.7.22/dataRetrieval/man/readNWISpeak.Rd | 7 dataRetrieval-2.7.22/dataRetrieval/man/readNWISrating.Rd | 3 dataRetrieval-2.7.22/dataRetrieval/man/readNWISstat.Rd | 7 dataRetrieval-2.7.22/dataRetrieval/man/readNWISuse.Rd | 30 dataRetrieval-2.7.22/dataRetrieval/man/readNWISuv.Rd | 20 dataRetrieval-2.7.22/dataRetrieval/man/readWQPdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readWQPqw.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readWQPsummary.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata.Rd | 5 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_continuous.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_daily.Rd | 55 - dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_field_measurements.Rd | 36 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_latest_continuous.Rd | 40 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_latest_daily.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_metadata.Rd | 18 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_monitoring_location.Rd | 61 - dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_parameter_codes.Rd | 13 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_samples.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_ts_meta.Rd | 59 - dataRetrieval-2.7.22/dataRetrieval/man/stateCd.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/stateCdLookup.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/summarize_waterdata_samples.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/whatWQPdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/wqpSpecials.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/wqp_check_status.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_general.R | 70 - dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_imports.R | 60 - dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 178 +-- dataRetrieval-2.7.22/dataRetrieval/vignettes/dataRetrieval.Rmd | 164 --- 89 files changed, 1257 insertions(+), 2091 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.4.6 dated 2025-12-16 and 1.4.9 dated 2026-01-23
DESCRIPTION | 10 MD5 | 235 ++++----- NAMESPACE | 20 NEWS.md | 16 R/BasicRun.R | 486 ++++++++++++++++-- R/CaseControl_Regression.R | 30 - R/Cox_Regression.R | 72 +- R/LogitRegression.R | 10 R/ObjValidate.R | 107 +--- R/PlotTypes.R | 50 + R/Poisson_Regression.R | 238 ++++----- R/RcppExports.R | 253 ++++----- R/SurvTypes.R | 172 ++++-- R/Utility.R | 385 ++++++++------ R/utils-roxygen.R | 17 configure | 2 inst/WORDLIST | 1 inst/doc/Alt_Run_Opt.R | 9 inst/doc/Alt_Run_Opt.Rmd | 29 - inst/doc/Alt_Run_Opt.html | 127 ++-- inst/doc/Control_Options.Rmd | 6 inst/doc/Control_Options.html | 32 + inst/doc/Dose_Formula_Inputs.R | 1 inst/doc/Dose_Formula_Inputs.Rmd | 20 inst/doc/Dose_Formula_Inputs.html | 51 + inst/doc/Equation_Expression.R | 11 inst/doc/Equation_Expression.Rmd | 52 + inst/doc/Equation_Expression.html | 141 +---- inst/doc/Excess_and_Predicted_Cases.R | 1 inst/doc/Excess_and_Predicted_Cases.Rmd | 5 inst/doc/Excess_and_Predicted_Cases.html | 9 inst/doc/Grad_Hess.R | 38 - inst/doc/Grad_Hess.Rmd | 45 - inst/doc/Grad_Hess.html | 146 ++--- inst/doc/Logistic.R | 3 inst/doc/Logistic.Rmd | 3 inst/doc/Logistic.html | 165 +++--- inst/doc/Matched_Case_Control.R | 3 inst/doc/Matched_Case_Control.Rmd | 3 inst/doc/Matched_Case_Control.html | 113 ++-- inst/doc/Multi_Realization.R | 17 inst/doc/Multi_Realization.Rmd | 17 inst/doc/Multi_Realization.html | 21 inst/doc/Plotting_And_Analysis.R | 123 ++-- inst/doc/Plotting_And_Analysis.Rmd | 125 ++-- inst/doc/Plotting_And_Analysis.html | 139 ++--- inst/doc/SMR_Analysis.R | 10 inst/doc/SMR_Analysis.Rmd | 12 inst/doc/SMR_Analysis.html | 90 ++- inst/doc/Script_Comparison_Epicure.R | 9 inst/doc/Script_Comparison_Epicure.Rmd | 9 inst/doc/Script_Comparison_Epicure.html | 15 inst/doc/Starting-Description.R | 32 - inst/doc/Starting-Description.Rmd | 73 -- inst/doc/Starting-Description.html | 231 +++----- inst/doc/Time_Dep_Cov.R | 1 inst/doc/Time_Dep_Cov.Rmd | 5 inst/doc/Time_Dep_Cov.html | 13 inst/doc/Wald_and_Log_Bound.R | 14 inst/doc/Wald_and_Log_Bound.Rmd | 36 - inst/doc/Wald_and_Log_Bound.html | 287 +++++----- inst/doc/count_time_tables.R | 1 inst/doc/count_time_tables.Rmd | 3 inst/doc/count_time_tables.html | 11 man/Event_Time_Gen.Rd | 21 man/Likelihood_Ratio_Test.Rd | 17 man/get_form_joint.Rd | 4 man/plot.coxres.Rd | 7 man/plotMartingale.Rd |only man/plotMartingale.coxres.Rd |only man/plotMartingale.default.Rd |only man/plotRisk.Rd |only man/plotRisk.coxres.Rd |only man/plotRisk.default.Rd |only man/plotSchoenfeld.Rd |only man/plotSchoenfeld.coxres.Rd |only man/plotSchoenfeld.default.Rd |only man/plotSurvival.Rd |only man/plotSurvival.coxres.Rd |only man/plotSurvival.default.Rd |only src/Calc_Repeated.cpp | 809 +++++-------------------------- src/Calc_Repeated.h | 18 src/Grouping.cpp |only src/Grouping.h |only src/Main_Bound.cpp | 176 +++--- src/Main_Bound.h | 6 src/Main_Functions.cpp | 190 +++++-- src/Main_Functions.h | 2 src/Main_Multi.cpp | 156 +++-- src/Main_Multi.h | 4 src/Omnibus_Pieces.cpp | 334 +++++++----- src/Omnibus_Pieces.h | 13 src/Plot_Extensions.cpp | 73 ++ src/Plot_Extensions.h | 4 src/R_Interface.cpp | 138 ----- src/R_Interface.h | 12 src/RcppExports.cpp | 54 +- src/Step_Calc.cpp | 2 src/Subterms_Risk.cpp | 72 -- src/Subterms_Risk.h | 6 tests/testthat/temp.R |only tests/testthat/test-Assigned.R | 26 tests/testthat/test-Cox_Plot.R | 128 +++- tests/testthat/test-Cox_Regression.R | 4 tests/testthat/test-Formula.R | 72 ++ tests/testthat/test-Logit.R | 4 tests/testthat/test-Multidose.R | 6 tests/testthat/test-Omnibus.R | 68 +- tests/testthat/test-Poisson_Regression.R | 29 - tests/testthat/test-Utility.R | 59 +- vignettes/Alt_Run_Opt.Rmd | 29 - vignettes/Control_Options.Rmd | 6 vignettes/Dose_Formula_Inputs.Rmd | 20 vignettes/Equation_Expression.Rmd | 52 + vignettes/Excess_and_Predicted_Cases.Rmd | 5 vignettes/Grad_Hess.Rmd | 45 - vignettes/Logistic.Rmd | 3 vignettes/Matched_Case_Control.Rmd | 3 vignettes/Multi_Realization.Rmd | 17 vignettes/Plotting_And_Analysis.Rmd | 125 ++-- vignettes/SMR_Analysis.Rmd | 12 vignettes/Script_Comparison_Epicure.Rmd | 9 vignettes/Starting-Description.Rmd | 73 -- vignettes/Time_Dep_Cov.Rmd | 5 vignettes/Wald_and_Log_Bound.Rmd | 36 - vignettes/count_time_tables.Rmd | 3 126 files changed, 3886 insertions(+), 3482 deletions(-)
Title: Vaccine Extension Package for ADaM in 'R' Asset Library
Description: Programming vaccine specific Clinical Data Interchange
Standards Consortium (CDISC) compliant Analysis Data Model (ADaM)
datasets in 'R'. Flat model is followed as per Center for Biologics
Evaluation and Research (CBER) guidelines for creating vaccine
specific domains. ADaM datasets are a mandatory part of any New Drug
or Biologics License Application submitted to the United States Food
and Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team (2021),
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
The package is an extension package of the 'admiral' package.
Author: Arjun Rubalingam [aut, cre],
Sukalpo Saha [aut, ctb],
Ben Straub [aut],
Vikram S [aut],
Dhivya Kanagaraj [aut],
Federico Baratin [aut],
Yamini Purna Bollu [aut],
Ilse Augustyns [aut],
Kalyani Bodicherla [aut],
Hilde Delanghe [aut],
Lee Armishaw [aut] [...truncated...]
Maintainer: Arjun Rubalingam <arjun.rubalingam@pfizer.com>
Diff between admiralvaccine versions 0.5.0 dated 2025-09-18 and 0.6.0 dated 2026-01-23
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 2 NEWS.md | 13 R/admiralvaccine.R | 1 R/derive_diam_to_sev_records.R | 2 R/derive_var_aval_adis.R | 10 R/derive_vars_crit.R | 2 R/derive_vars_event_flag.R | 4 R/derive_vars_max_flag.R | 6 R/derive_vars_merged_vaccine.R | 2 R/derive_vars_vaxdt.R | 2 R/post_process_reacto.R | 2 README.md | 2 build/vignette.rds |binary inst/WORDLIST | 154 inst/doc/adce.R | 344 +- inst/doc/adce.html | 2811 ++++++++-------- inst/doc/adface.R | 710 ++-- inst/doc/adface.html | 4548 +++++++++++++-------------- inst/doc/adis.R | 882 ++--- inst/doc/adis.html | 4277 ++++++++++++------------- inst/doc/admiralvaccine.R | 78 inst/doc/admiralvaccine.Rmd | 8 inst/doc/admiralvaccine.html | 834 ++-- inst/doc/adsl.R | 294 - inst/doc/adsl.html | 1591 ++++----- tests/testthat/test-derive_fever_records.R | 5 tests/testthat/test-derive_var_aval_adis.R | 118 tests/testthat/test-derive_vars_event_flag.R | 2 tests/testthat/test-derive_vars_params.R | 2 tests/testthat/test-derive_vars_vaxdt.R | 13 vignettes/admiralvaccine.Rmd | 8 33 files changed, 8414 insertions(+), 8395 deletions(-)
More information about admiralvaccine at CRAN
Permanent link
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev] ,
Marcus Munch Gruenewald [aut] ,
Lasse Engbo Christiansen [rev, ctb] ,
Sofia Myrup Otero [rev],
Kim Daniel Jacobsen [ctb],
Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between SCDB versions 0.5.2 dated 2026-01-08 and 0.6.0 dated 2026-01-23
DESCRIPTION | 6 MD5 | 39 + NAMESPACE | 2 NEWS.md | 690 +++++++++++++++++----------------- R/0_miscellaneous.R | 5 R/Logger.R | 43 +- R/delta-loading.R |only R/digest_to_checksum.R | 31 - R/update_snapshot.R | 61 ++- build/vignette.rds |binary inst/WORDLIST | 179 ++++++++ inst/doc/benchmarks.html | 4 inst/doc/delta-loading.R |only inst/doc/delta-loading.Rmd |only inst/doc/delta-loading.html |only inst/extdata/benchmarks.rds |binary man/Logger.Rd | 19 man/LoggerNull.Rd | 1 man/delta_loading.Rd |only man/digest_to_checksum.Rd | 5 tests/testthat/setup.R | 2 tests/testthat/test-delta-loading.R |only tests/testthat/test-update_snapshot.R | 79 +++ vignettes/delta-loading.Rmd |only 24 files changed, 741 insertions(+), 425 deletions(-)
Title: Nonparametric Bootstrap and Permutation Tests
Description: Robust nonparametric bootstrap and permutation tests for goodness of fit, distribution equivalence, location, correlation, and regression problems, as described in Helwig (2019a) <doi:10.1002/wics.1457> and Helwig (2019b) <doi:10.1016/j.neuroimage.2019.116030>. Univariate and multivariate tests are supported. For each problem, exact tests and Monte Carlo approximations are available. Five different nonparametric bootstrap confidence intervals are implemented. Parallel computing is implemented via the 'parallel' package.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
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Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
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Title: Parametric Mixture Models for Uncertainty Estimation of
Fatalities in UCDP Conflict Data
Description: Provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).
Author: David Randahl [cre, aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Diff between uncertainUCDP versions 0.7.0 dated 2026-01-20 and 0.7.6 dated 2026-01-23
DESCRIPTION | 12 ++--- MD5 | 10 ++-- NAMESPACE | 2 R/sysdata.rda |binary R/uncertainUCDP.R | 107 ++++++++++++++++++++++++++++++++++++++-------- man/mean_uncertainUCDP.Rd | 8 +-- 6 files changed, 106 insertions(+), 33 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Author: Olivier Broennimann [cre, aut, ctb],
Valeria Di Cola [aut, ctb],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Daniel Scherrer [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Heidi Mod [ctb],
Julien Potti [...truncated...]
Maintainer: Olivier Broennimann <olivier.broennimann@unil.ch>
Diff between ecospat versions 4.1.2 dated 2025-01-31 and 4.1.3 dated 2026-01-23
DESCRIPTION | 16 +++++++------- MD5 | 38 +++++++++++++++++----------------- NEWS | 6 +++++ R/ecospat.CCV.R | 4 ++- R/ecospat.ESM.R | 13 +++++++---- R/ecospat.boyce.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette_ecospat_package.pdf |binary man/ecospat.CCV.modeling.Rd | 5 ++++ man/ecospat.binary.model.Rd | 4 +-- man/ecospat.grid.clim.dyn.Rd | 2 - man/ecospat.niche.dyn.index.Rd | 3 +- man/ecospat.niche.dynIndexProjGeo.Rd | 8 +++---- man/ecospat.niche.equivalency.test.Rd | 2 - man/ecospat.niche.overlap.Rd | 2 - man/ecospat.niche.similarity.test.Rd | 2 - man/ecospat.niche.zProjGeo.Rd | 6 ++--- man/ecospat.occupied.patch.Rd | 4 +-- man/ecospat.rangesize.Rd | 4 +-- 20 files changed, 69 insertions(+), 52 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 1.0.1 dated 2025-11-20 and 1.1.0 dated 2026-01-23
DESCRIPTION | 12 MD5 | 56 ++-- NEWS.md | 264 +++++++++--------- R/autoplot.R | 47 ++- R/combined_seasonal_output.R | 216 +++++++++------ R/epi_calendar.R | 6 R/estimate_disease_threshold.R | 10 R/fit_growth_rate.R | 4 R/fit_percentiles.R | 6 R/generate_seasonal_data.R | 3 R/predict.R | 22 - R/seasonal_burden_levels.R | 14 - R/seasonal_onset.R | 20 - R/summary.R | 40 ++ R/to_time_series.R | 4 inst/doc/aedseo.R | 15 - inst/doc/aedseo.Rmd | 49 ++- inst/doc/aedseo.html | 349 ++++++++++++++----------- inst/doc/burden_levels.html | 6 inst/doc/generate_seasonal_wave.html | 18 - inst/doc/multiple_waves.R | 1 inst/doc/multiple_waves.Rmd | 34 +- inst/doc/multiple_waves.html | 50 ++- inst/doc/seasonal_onset.html | 33 +- man/autoplot.Rd | 19 - man/combined_seasonal_output.Rd | 24 + tests/testthat/test-combined_seasonal_output.R | 142 +++++++++- vignettes/aedseo.Rmd | 49 ++- vignettes/multiple_waves.Rmd | 34 +- 29 files changed, 962 insertions(+), 585 deletions(-)
Title: Auxiliary Functions for Phenological Data Analysis
Description: Provides some easy-to-use functions for time series
analyses of (plant-) phenological data sets. These functions
mainly deal with the estimation of combined phenological time
series and are usually wrappers for functions that are already
implemented in other R packages adapted to the special
structure of phenological data and the needs of phenologists.
Some date conversion functions to handle Julian dates are also
provided.
Author: Joerg Schaber [aut],
Maximilian Lange [cre]
Maintainer: Maximilian Lange <maximilian.lange@ufz.de>
Diff between pheno versions 1.7-0 dated 2022-05-12 and 1.7-1 dated 2026-01-23
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- man/connectedSets.Rd | 10 +++++----- man/maxConnectedSet.Rd | 26 +++++++++++++------------- 4 files changed, 30 insertions(+), 26 deletions(-)
Title: Ordinal Regression for High-Dimensional Data
Description: Provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer [aut, cre] ,
Jiayi Hou [aut],
Qing Zhou [aut],
Kyle Ferber [aut],
John G. Layne [com, ctr],
Amanda Gentry [rev]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between ordinalgmifs versions 1.0.8 dated 2023-05-05 and 1.0.9 dated 2026-01-23
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- build/partial.rdb |binary data/eyedisease.rda |binary data/hccframe.rda |binary inst/CITATION | 12 ++++++------ inst/doc/ordinalgmifs.Rnw | 11 +---------- inst/doc/ordinalgmifs.pdf |binary vignettes/ordinalgmifs.bib | 2 +- 9 files changed, 22 insertions(+), 31 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.15 dated 2025-12-22 and 1.0.16 dated 2026-01-23
DESCRIPTION | 6 MD5 | 69 ++-- R/bootstrap.R | 2 R/calc_se_da.R | 122 ++++++- R/construct_matrices_da.R | 23 - R/equations_lms.R | 10 R/est_h0.R | 70 +++- R/formatted_objects.R | 75 ++++ R/generics_lavaan.R | 6 R/generics_modsem_da.R | 48 +- R/generics_modsem_mplus.R | 8 R/generics_modsem_pi.R | 22 + R/inspect_da.R | 84 ++-- R/labelled_params_da.R | 8 R/model_da.R | 68 ++- R/modsem.R | 2 R/modsem_da.R | 5 R/modsem_pi.R | 2 R/plot_interaction.R | 20 - R/quadrature.R | 204 +++++++---- R/scale_correction_ordered.R | 11 R/simple_slopes.R | 7 R/standardized_solution.R | 9 R/utils.R | 27 + R/utils_da.R | 67 +++ inst/doc/customize_plot_interactions.html | 2 inst/doc/observed_lms_qml.R | 4 inst/doc/observed_lms_qml.Rmd | 17 inst/doc/observed_lms_qml.html | 512 +++++++++++++++++------------- inst/doc/plot_interactions.html | 4 man/parameter_estimates.Rd | 52 ++- man/standardized_estimates.Rd | 3 tests/testthat/test_adaptive_quad.R | 3 tests/testthat/test_ov_int.R |only tests/testthat/test_ovchecks_da.R | 30 - vignettes/observed_lms_qml.Rmd | 17 36 files changed, 1092 insertions(+), 527 deletions(-)
Title: Working with 'MCSim' Models
Description: Tools that facilitate ordinary differential equation (ODE) modeling in 'R'. This package allows one to perform simulations for ODE models that are encoded in the GNU 'MCSim' model specification language (Bois, 2009) <doi:10.1093/bioinformatics/btp162> using ODE solvers from the 'R' package 'deSolve' (Soetaert et al., 2010) <doi:10.18637/jss.v033.i09>.
Author: Dustin F. Kapraun [aut, cre] ,
Todd J. Zurlinden [aut] ,
Andrew J. Shapiro [aut] ,
Ryan D. Friese [aut] ,
Frederic Y. Bois [ctb] ,
Free Software Foundation, Inc. [cph]
Maintainer: Dustin F. Kapraun <kapraun.dustin@epa.gov>
Diff between MCSimMod versions 1.0 dated 2025-08-19 and 1.2 dated 2026-01-23
DESCRIPTION | 10 +- MD5 | 38 +++++----- R/MCSim_model.R | 70 ++++++++++++++---- R/compileModel.R | 142 +++++++++++++++++++++++++++++++------- R/createModel.R | 5 - R/fileHasChanged.R | 6 - R/fixPath.R | 4 - inst/CITATION | 2 inst/doc/details.html | 4 - inst/doc/events_demo.html | 4 - inst/doc/inputs_demo.html | 4 - inst/doc/intro.html | 4 - inst/doc/model_specification.html | 4 - inst/doc/newt_cool_demo.html | 4 - inst/doc/pbpk_demo.html | 4 - inst/doc/pk1_demo.html | 4 - inst/doc/pred_prey_demo.html | 4 - man/Model-class.Rd | 10 +- man/compileModel.Rd | 16 +++- man/createModel.Rd | 9 ++ 20 files changed, 253 insertions(+), 95 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.2-0 dated 2025-12-18 and 2.2-1 dated 2026-01-23
Changelog | 4 + DESCRIPTION | 12 ++-- MD5 | 10 +-- R/plot.R | 124 ++++++++++++++++++++++++++++++++---------------- inst/doc/kstMatrix.html | 28 +++++----- man/plot.Rd | 11 +++- 6 files changed, 120 insertions(+), 69 deletions(-)
Title: Mass-Spectra Prediction Using the FIORA Model
Description: Provides a wrapper for the python module 'FIORA' as well as a
'shiny'-App to facilitate data processing and visualization. 'FIORA' allows
to predict Mass-Spectra based on the SMILES code of chemical compounds. It
is described in the Nature Communications article by Nowatzky (2025)
<doi:10.1038/s41467-025-57422-4>.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between fioRa versions 0.3.4 dated 2025-11-11 and 0.3.7 dated 2026-01-23
DESCRIPTION | 13 - MD5 | 43 ++-- NAMESPACE | 1 NEWS.md | 22 ++ R/app_ui.R | 10 R/app_utils.R | 222 +++++++++++++++++--- R/fct_install_fiora.R | 25 +- R/fct_read_fiora.R | 37 ++- R/mod_page_fioRa.R | 38 +++ R/mod_selectInputWithButtons.R | 244 ++++++++++------------- R/run_script.R | 42 +++ README.md | 12 - inst/WORDLIST | 4 man/install_fiora.Rd | 5 man/read_fiora.Rd |only man/run_script.Rd | 24 +- tests/spelling.R | 6 tests/testthat.R | 2 tests/testthat/_snaps |only tests/testthat/setup.R |only tests/testthat/test-app_utils.R |only tests/testthat/test-fct_read_fiora.R | 15 + tests/testthat/test-mod_selectInputWithButtons.R |only tests/testthat/test-run_script.R | 5 24 files changed, 534 insertions(+), 236 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.5 dated 2025-10-29 and 1.2.7 dated 2026-01-23
DESCRIPTION | 6 MD5 | 41 ++--- NAMESPACE | 1 NEWS.md | 8 + R/hydro_imgw_daily.R | 21 ++ R/match_imgw_wmoid_inds.R |only R/meteo_imgw_daily.R | 296 +++++++++++++++++++++++---------------- R/meteo_imgw_hourly.R | 224 +++++++++++++++++------------ R/meteo_imgw_monthly.R | 242 +++++++++++++++++-------------- R/meteo_noaa_hourly.R | 6 R/nearest_stations_noaa.R | 8 - R/nearest_stations_ogimet.R | 2 R/test_url.R | 51 ++---- README.md | 11 - inst/doc/getstarted.Rmd | 4 inst/doc/getstarted.html | 333 +++++++++++++++++++++++++++++++++++--------- man/meteo_imgw_daily.Rd | 8 - man/meteo_imgw_hourly.Rd | 4 man/meteo_imgw_monthly.Rd | 14 + man/meteo_noaa_hourly.Rd | 4 man/test_url.Rd | 8 - vignettes/getstarted.Rmd | 4 22 files changed, 834 insertions(+), 462 deletions(-)
Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre] ,
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
Cy [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.2.1 dated 2025-08-20 and 0.3.0 dated 2026-01-23
DESCRIPTION | 10 +- MD5 | 37 +++++------ NAMESPACE | 1 NEWS.md | 40 +++++++++-- R/bin_utils.R | 8 +- R/derive_interp_records.R | 8 ++ R/derive_params_growth_age.R | 52 +++++++++------ R/derive_params_growth_height.R | 35 ++++++---- README.md | 10 +- build/vignette.rds |binary inst/WORDLIST | 5 + inst/templates/ad_advs.R | 8 +- man/derive_interp_records.Rd | 21 +++++- man/derive_params_growth_age.Rd | 84 +++++++++++++++++++------ man/derive_params_growth_height.Rd | 68 ++++++++++++++++---- man/find_closest_bin.Rd | 18 ++++- man/get_bins.Rd | 12 ++- man/roxygen/rdx_meta.R |only tests/testthat/test-derive_interp_records.R | 2 tests/testthat/test-derive_params_growth_age.R | 7 +- 20 files changed, 304 insertions(+), 122 deletions(-)
Title: Official Gridded Data from the German Census 2022
Description: Provides fast and easy access to German census grid data
from the 2011 and 2022 censuses <https://www.zensus2022.de/>, including a
wide range of socio-economic indicators at multiple spatial resolutions
(100m, 1km, 10km). Enables efficient download, processing, and analysis
of large census datasets covering population, households, families,
dwellings, and buildings. Harmonized data structures allow direct
comparison with the 2011 census, supporting temporal and spatial analyses.
Facilitates conversion of data into common formats for spatial analysis and
mapping ('terra', 'sf', 'ggplot2').
Author: Jonas Lieth [cre, aut, cph]
Maintainer: Jonas Lieth <jslth@outlook.com>
Diff between z22 versions 1.1.0 dated 2025-10-29 and 1.1.4 dated 2026-01-23
DESCRIPTION | 10 - MD5 | 42 ++++---- NEWS.md | 7 + R/categories.R | 155 +++++++++++++++++++++++------- R/check.R | 4 R/data.R | 31 ------ R/utils.R | 2 inst/doc/z22.Rmd | 58 +++++------ inst/doc/z22.html | 73 ++++++-------- man/categories.Rd | 81 +++++++++++++-- man/figures/vignette/100m_plot-1.png |binary man/figures/vignette/allcells_plot-1.png |binary man/figures/vignette/multiplot-1.png |binary man/figures/vignette/normalize_plot-1.png |binary man/figures/vignette/patchwork_plot-1.png |binary man/z22-package.Rd | 2 man/z22_data.Rd | 5 man/z22_grid.Rd | 2 tests/testthat/test-pkg.R | 9 + vignettes/precompute.R |only vignettes/z22.Rmd | 58 +++++------ vignettes/z22.Rmd.orig | 14 ++ vignettes/z22.md |only 23 files changed, 343 insertions(+), 210 deletions(-)
Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate
time series forecasting models including automatically selected exponential
smoothing (ETS) and autoregressive integrated moving average (ARIMA) models.
These models work within the 'fable' framework provided by the 'fabletools'
package, which provides the tools to evaluate, visualise, and combine models
in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Gabriel Caceres [ctb] ,
Christoph Bergmeir [ctb] ,
Tim-Gunnar Hensel [ctb],
Timothy Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fable versions 0.4.1 dated 2024-11-04 and 0.5.0 dated 2026-01-23
DESCRIPTION | 17 - MD5 | 73 +++--- NAMESPACE | 10 NEWS.md | 23 ++ R/00_specials.R | 6 R/VARIMA.R | 115 ++++++---- R/ar.R | 4 R/arfima.R |only R/arima.R | 172 ++++++++++----- R/checks.R | 8 R/compat-purrr.R | 4 R/croston.R | 14 - R/ets.R | 80 ++++--- R/etsmodel.R | 34 +-- R/lagwalk.R | 24 +- R/lm.R | 2 R/mean.R | 8 R/nnetar.R | 25 +- R/theta.R | 8 R/utils.R | 10 R/var.R | 4 R/vecm.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 16 + inst/doc/fable.R | 8 inst/doc/fable.html | 81 +++---- inst/doc/transformations.html | 3 man/ARFIMA.Rd |only man/ARIMA.Rd | 12 + man/ETS.Rd | 2 man/RW.Rd | 1 man/VARIMA.Rd | 73 ++++-- man/interpolate.ETS.Rd |only src/etsTargetFunction.cpp | 4 src/etsTargetFunction.h | 6 src/etscalc.c | 465 +++++++++++++++++++++--------------------- tests/testthat/test-ets.R | 39 ++- 39 files changed, 804 insertions(+), 551 deletions(-)
Title: A Rainclouds Geom for 'ggplot2'
Description: The 'geom_rain()' function adds different geoms together using 'ggplot2' to create raincloud plots.
Author: Nicholas Judd [aut, cre] ,
Jordy van Langen [aut] ,
Micah Allen [ctb] ,
Rogier Kievit [aut]
Maintainer: Nicholas Judd <nickkjudd@gmail.com>
Diff between ggrain versions 0.1.1 dated 2026-01-21 and 0.1.2 dated 2026-01-23
ggrain-0.1.1/ggrain/inst/book.bib |only ggrain-0.1.1/ggrain/inst/paper.md |only ggrain-0.1.2/ggrain/DESCRIPTION | 6 +++--- ggrain-0.1.2/ggrain/MD5 | 8 +++----- ggrain-0.1.2/ggrain/NEWS.md | 4 ++++ ggrain-0.1.2/ggrain/README.md | 3 +-- 6 files changed, 11 insertions(+), 10 deletions(-)
Title: Visualisation of Sequential Probability Distributions Using Fan
Charts
Description: Visualise sequential distributions using a range of plotting
styles. Sequential distribution data can be input as either simulations or
values corresponding to percentiles over time. Plots are added to
existing graphic devices using the fan function. Users can choose from four
different styles, including fan chart type plots, where a set of coloured
polygon, with shadings corresponding to the percentile values are layered
to represent different uncertainty levels. Full details in R Journal article; Abel (2015) <doi:10.32614/RJ-2015-002>.
Author: Guy J. Abel [aut, cre]
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between fanplot versions 4.0.0 dated 2021-08-02 and 4.0.1 dated 2026-01-23
DESCRIPTION | 16 ++++++++------ MD5 | 22 ++++++++++---------- NAMESPACE | 8 ------- NEWS.md | 7 ++++++ R/fan.R | 62 ++++++++++++++++++++++++++++----------------------------- R/fan0.R | 2 - R/psplitnorm.R | 4 +-- R/qsplitnorm.R | 4 +-- R/rsplitnorm.R | 2 - demo/sv_fan.R | 2 - inst/CITATION | 15 ++++++------- man/fan.Rd | 4 +-- 12 files changed, 75 insertions(+), 73 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.1.4 dated 2025-11-28 and 3.2.0 dated 2026-01-23
SVEMnet-3.1.4/SVEMnet/tests/testthat/testthat-problems.rds |only SVEMnet-3.2.0/SVEMnet/DESCRIPTION | 11 SVEMnet-3.2.0/SVEMnet/MD5 | 49 - SVEMnet-3.2.0/SVEMnet/NAMESPACE | 4 SVEMnet-3.2.0/SVEMnet/NEWS | 5 SVEMnet-3.2.0/SVEMnet/R/SVEMnet.R | 169 +++- SVEMnet-3.2.0/SVEMnet/R/bigexp.R | 346 ++++++++- SVEMnet-3.2.0/SVEMnet/R/glmnet_with_cv.R | 191 ++++- SVEMnet-3.2.0/SVEMnet/R/lipid_screen.R | 3 SVEMnet-3.2.0/SVEMnet/R/plot.svemtest.R | 14 SVEMnet-3.2.0/SVEMnet/R/select_candidates.R | 61 + SVEMnet-3.2.0/SVEMnet/R/spec_limit_utility.R | 188 +--- SVEMnet-3.2.0/SVEMnet/R/svem_random_table_multi.R | 403 ++++++---- SVEMnet-3.2.0/SVEMnet/R/svem_score_random.R | 416 +++++------ SVEMnet-3.2.0/SVEMnet/R/svem_select_score_from_table.R | 188 ---- SVEMnet-3.2.0/SVEMnet/R/svem_significance_test_parallel.R | 277 +++++-- SVEMnet-3.2.0/SVEMnet/R/svem_wmt_multi.R | 105 +- SVEMnet-3.2.0/SVEMnet/man/SVEMnet-package.Rd | 7 SVEMnet-3.2.0/SVEMnet/man/bigexp_terms.Rd | 94 ++ SVEMnet-3.2.0/SVEMnet/man/lipid_screen.Rd | 3 SVEMnet-3.2.0/SVEMnet/man/svem_random_table_multi.Rd | 144 --- SVEMnet-3.2.0/SVEMnet/man/svem_score_random.Rd | 22 SVEMnet-3.2.0/SVEMnet/man/svem_select_from_score_table.Rd | 152 ---- SVEMnet-3.2.0/SVEMnet/man/svem_significance_test_parallel.Rd | 34 SVEMnet-3.2.0/SVEMnet/tests/testthat/test_extras.R | 5 SVEMnet-3.2.0/SVEMnet/tests/testthat/test_scoring.R | 179 ++++ 26 files changed, 1870 insertions(+), 1200 deletions(-)
Title: Schumaker Shape-Preserving Spline
Description: This is a shape preserving spline <doi:10.1137/0720057>
which is guaranteed to be monotonic and concave or convex if the
data is monotonic and concave or convex. It does not use any
optimisation and is therefore quick and smoothly converges to a
fixed point in economic dynamics problems including value function
iteration. It also automatically gives the first two derivatives
of the spline and options for determining behaviour when evaluated
outside the interpolation domain.
Author: Stuart Baumann [aut, cre],
Margaryta Klymak [aut]
Maintainer: Stuart Baumann <stuart@stuartbaumann.com>
Diff between schumaker versions 1.2.1 dated 2021-09-09 and 1.2.2 dated 2026-01-23
DESCRIPTION | 19 MD5 | 18 NAMESPACE | 1 R/Schumaker.R | 140 ++-- build/vignette.rds |binary inst/doc/schumaker.R | 266 +++------ inst/doc/schumaker.Rmd | 501 +++++++---------- inst/doc/schumaker.html | 1066 +++++++++++++++++++++++--------------- man/impute_gradients.Rd |only tests/testthat/test_schumaker_2.R |only vignettes/schumaker.Rmd | 501 +++++++---------- 11 files changed, 1302 insertions(+), 1210 deletions(-)
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-tests, ANOVA, ANCOVA, repeated-measures models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <mirzaghaderi@gmail.com>
Diff between rtpcr versions 2.1.1 dated 2026-01-08 and 2.1.2 dated 2026-01-23
rtpcr-2.1.1/rtpcr/R/ANOVA_DCt.r |only rtpcr-2.1.1/rtpcr/R/ANOVA_DDCt.r |only rtpcr-2.1.1/rtpcr/R/Means_DDCt.r |only rtpcr-2.1.1/rtpcr/R/REPEATED_DDCt.r |only rtpcr-2.1.1/rtpcr/R/TTEST_DDCt.r |only rtpcr-2.1.1/rtpcr/R/efficiency.r |only rtpcr-2.1.1/rtpcr/R/globalVariables.r |only rtpcr-2.1.1/rtpcr/R/meanTech.r |only rtpcr-2.1.1/rtpcr/R/multiplot.r |only rtpcr-2.1.1/rtpcr/R/package_data.r |only rtpcr-2.1.1/rtpcr/R/plotFactor.r |only rtpcr-2.1.1/rtpcr/R/qpcrhlpr.r |only rtpcr-2.1.1/rtpcr/data/Lee_etal2020qPCR.rda |only rtpcr-2.1.1/rtpcr/data/data_efficiency.rda |only rtpcr-2.1.1/rtpcr/inst/extdata/Lee_etal2020qPCR.csv |only rtpcr-2.1.1/rtpcr/inst/extdata/data_efficiency.csv |only rtpcr-2.1.1/rtpcr/inst/extdata/farokh_et_al_2025.csv |only rtpcr-2.1.1/rtpcr/man/Lee_etal2020qPCR.Rd |only rtpcr-2.1.1/rtpcr/man/data_efficiency.Rd |only rtpcr-2.1.2/rtpcr/DESCRIPTION | 17 rtpcr-2.1.2/rtpcr/MD5 | 167 ++-- rtpcr-2.1.2/rtpcr/NAMESPACE | 4 rtpcr-2.1.2/rtpcr/NEWS.md | 30 rtpcr-2.1.2/rtpcr/R/ANCOVA_DDCt.R |only rtpcr-2.1.2/rtpcr/R/ANOVA_DCt.R |only rtpcr-2.1.2/rtpcr/R/ANOVA_DDCt.R |only rtpcr-2.1.2/rtpcr/R/Means_DDCt.R |only rtpcr-2.1.2/rtpcr/R/REPEATED_DDCt.R |only rtpcr-2.1.2/rtpcr/R/TTEST_DDCt.R |only rtpcr-2.1.2/rtpcr/R/WILCOX_DDCt.R |only rtpcr-2.1.2/rtpcr/R/compute_wDCt.R |only rtpcr-2.1.2/rtpcr/R/efficiency.R |only rtpcr-2.1.2/rtpcr/R/globalVariables.R |only rtpcr-2.1.2/rtpcr/R/long_to_wide.R |only rtpcr-2.1.2/rtpcr/R/meanTech.R |only rtpcr-2.1.2/rtpcr/R/multiplot.R |only rtpcr-2.1.2/rtpcr/R/package_data.R |only rtpcr-2.1.2/rtpcr/R/plotFactor.R |only rtpcr-2.1.2/rtpcr/R/qpcrhlpr.R |only rtpcr-2.1.2/rtpcr/data/data_1factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_Two_ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_one_ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_one_ref_Eff.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factor3ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factorBlock.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factorBlock3ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_3factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_Heffer2020PlosOne.rda |only rtpcr-2.1.2/rtpcr/data/data_Lee_etal2020qPCR.rda |only rtpcr-2.1.2/rtpcr/data/data_Yuan2006PMCBioinf.rda |only rtpcr-2.1.2/rtpcr/data/data_efficiency1.rda |only rtpcr-2.1.2/rtpcr/data/data_efficiency_Yuan2006PMCBioinf.rda |only rtpcr-2.1.2/rtpcr/data/data_repeated_measure_3bLock.rda |only rtpcr-2.1.2/rtpcr/data/data_ttest18genes.rda |only rtpcr-2.1.2/rtpcr/data/data_withTechRep.rda |binary rtpcr-2.1.2/rtpcr/inst/doc/Manual.R | 78 -- rtpcr-2.1.2/rtpcr/inst/doc/Manual.Rmd | 183 ++--- rtpcr-2.1.2/rtpcr/inst/doc/Manual.html | 366 +++++----- rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_Two_ref.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_one_ref.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_one_ref_Eff.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factorBlock.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factorBlock3ref.csv | 50 - rtpcr-2.1.2/rtpcr/inst/extdata/data_3factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_Heffer2020PlosOne.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_Lee_etal2020qPCR.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_Yuan2006PMCBioinf.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_efficiency1.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_efficiency_Yuan2006PMCBioinf.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_1.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_2.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_3bLock.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_ttest18genes.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_withTechRep.csv | 38 - rtpcr-2.1.2/rtpcr/man/ANCOVA_DDCt.Rd |only rtpcr-2.1.2/rtpcr/man/ANOVA_DCt.Rd | 37 - rtpcr-2.1.2/rtpcr/man/ANOVA_DDCt.Rd | 104 +- rtpcr-2.1.2/rtpcr/man/Means_DDCt.Rd | 33 rtpcr-2.1.2/rtpcr/man/REPEATED_DDCt.Rd | 118 +-- rtpcr-2.1.2/rtpcr/man/TTEST_DDCt.Rd | 47 - rtpcr-2.1.2/rtpcr/man/WILCOX_DDCt.Rd |only rtpcr-2.1.2/rtpcr/man/compute_wDCt.Rd |only rtpcr-2.1.2/rtpcr/man/data_1factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_1factor_Two_ref.Rd | 8 rtpcr-2.1.2/rtpcr/man/data_1factor_one_ref.Rd | 10 rtpcr-2.1.2/rtpcr/man/data_1factor_one_ref_Eff.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_2factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_2factor3ref.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_2factorBlock.Rd | 10 rtpcr-2.1.2/rtpcr/man/data_2factorBlock3ref.Rd | 24 rtpcr-2.1.2/rtpcr/man/data_3factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_Heffer2020PlosOne.Rd |only rtpcr-2.1.2/rtpcr/man/data_Lee_etal2020qPCR.Rd |only rtpcr-2.1.2/rtpcr/man/data_Yuan2006PMCBioinf.Rd |only rtpcr-2.1.2/rtpcr/man/data_efficiency1.Rd |only rtpcr-2.1.2/rtpcr/man/data_efficiency_Yuan2006PMCBioinf.Rd |only rtpcr-2.1.2/rtpcr/man/data_repeated_measure_1.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_repeated_measure_2.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_repeated_measure_3bLock.Rd |only rtpcr-2.1.2/rtpcr/man/data_ttest18genes.Rd |only rtpcr-2.1.2/rtpcr/man/data_withTechRep.Rd | 10 rtpcr-2.1.2/rtpcr/man/efficiency.Rd | 101 +- rtpcr-2.1.2/rtpcr/man/figures/dataStructure1.png |binary rtpcr-2.1.2/rtpcr/man/figures/logo.png |binary rtpcr-2.1.2/rtpcr/man/figures/techrep.png |binary rtpcr-2.1.2/rtpcr/man/globalVariables.Rd | 2 rtpcr-2.1.2/rtpcr/man/long_to_wide.Rd |only rtpcr-2.1.2/rtpcr/man/meanTech.Rd | 21 rtpcr-2.1.2/rtpcr/man/multiplot.Rd | 36 rtpcr-2.1.2/rtpcr/man/plotFactor.Rd | 52 - rtpcr-2.1.2/rtpcr/vignettes/Manual.Rmd | 183 ++--- 114 files changed, 987 insertions(+), 792 deletions(-)
Title: Mechanistic Simulation of Species Range Dynamics
Description: Integrates population dynamics and dispersal into a
mechanistic virtual species simulator. The package can be used to
study the effects of environmental change on population growth and
range shifts. It allows for simple and straightforward definition of
population dynamics (including positive density dependence), extensive
possibilities for defining dispersal kernels, and the ability to
generate virtual ecologist data. Learn more about the 'rangr' at
<https://docs.ropensci.org/rangr/>. This work was supported by
the National Science Centre, Poland, grant no. 2018/29/B/NZ8/00066 and
the Poznań Supercomputing and Networking Centre (grant no. pl0090-01).
Author: Katarzyna Markowska [aut, cre],
Lechoslaw Kuczynski [aut],
Tad Dallas [rev],
Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between rangr versions 1.0.8 dated 2025-12-17 and 1.0.9 dated 2026-01-23
DESCRIPTION | 10 ++++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/doc/rangr.html | 2 +- man/rangr-package.Rd | 2 +- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <doi:10.48550/arXiv.2102.00968> <doi:10.1016/j.jeconom.2021.11.008>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <doi:10.48550/arXiv.1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [aut, cre] ,
Florian Ziel [aut]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between profoc versions 1.3.3 dated 2024-09-21 and 1.3.4 dated 2026-01-23
profoc-1.3.3/profoc/vignettes/methods.html |only profoc-1.3.4/profoc/DESCRIPTION | 13 profoc-1.3.4/profoc/MD5 | 21 profoc-1.3.4/profoc/NEWS.md | 10 profoc-1.3.4/profoc/build/partial.rdb |binary profoc-1.3.4/profoc/inst/doc/class.html | 4 profoc-1.3.4/profoc/inst/doc/production.html | 4 profoc-1.3.4/profoc/inst/doc/profoc.html | 4 profoc-1.3.4/profoc/src/batch.cpp | 628 +++++++++----------- profoc-1.3.4/profoc/src/conline.cpp | 137 ++-- profoc-1.3.4/profoc/src/oracle.cpp | 846 +++++++++++++-------------- profoc-1.3.4/profoc/src/splines.cpp | 264 ++++---- 12 files changed, 968 insertions(+), 963 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction
package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>;
Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains
the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness
Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636.
<doi:10.1029/2020JG005636>;
Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing
global MODIS EVI ti [...truncated...]
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
This is a re-admission after prior archival of version 0.3.10 dated 2025-05-25
Diff between phenofit versions 0.3.10 dated 2025-05-25 and 0.3.11 dated 2026-01-23
DESCRIPTION | 8 MD5 | 12 R/findpeaks.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/phenofit-procedures.html | 493 +++++++++++++++++++------------------- inst/doc/phenofit_CA-NS6.html | 388 ++++++++++++++--------------- 7 files changed, 459 insertions(+), 444 deletions(-)
Title: Data Manipulation Functions Implemented in C
Description: Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.
Author: Morgan Jacob [aut, cph],
Sebastian Krantz [ctb, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between kit versions 0.0.20 dated 2025-04-17 and 0.0.21 dated 2026-01-23
kit-0.0.20/kit/inst/NEWS.Rd |only kit-0.0.20/kit/tests/test_kit.Rout.save |only kit-0.0.21/kit/DESCRIPTION | 23 - kit-0.0.21/kit/MD5 | 42 +- kit-0.0.21/kit/NAMESPACE | 6 kit-0.0.21/kit/NEWS.md |only kit-0.0.21/kit/R/call.R | 7 kit-0.0.21/kit/build |only kit-0.0.21/kit/inst/doc |only kit-0.0.21/kit/man/count.Rd | 6 kit-0.0.21/kit/man/fpos.Rd | 8 kit-0.0.21/kit/man/funique.Rd | 6 kit-0.0.21/kit/man/iif.Rd | 4 kit-0.0.21/kit/man/nif.Rd | 2 kit-0.0.21/kit/man/psort.Rd | 10 kit-0.0.21/kit/man/psum.Rd | 59 ++- kit-0.0.21/kit/man/shareData.Rd | 6 kit-0.0.21/kit/man/topn.Rd | 8 kit-0.0.21/kit/man/vswitch.Rd | 12 kit-0.0.21/kit/src/init.c | 6 kit-0.0.21/kit/src/kit.h | 3 kit-0.0.21/kit/src/psum.c | 504 ++++++++++++++++++++++++++++++++ kit-0.0.21/kit/tests/test_kit.R | 98 +++++- kit-0.0.21/kit/vignettes |only 24 files changed, 716 insertions(+), 94 deletions(-)
Title: Plotting Football Matches Expected Goals (xG) Stats with
'Understat' Data
Description: Scrapes football match shots data from 'Understat' <https://understat.com/> and visualizes it using interactive plots:
- A detailed shot map displaying the location, type, and xG value of shots taken by both teams.
- An xG timeline chart showing the cumulative xG for each team over time, annotated with the details of scored goals.
Author: Aymen Nasri [aut, cre, cph]
Maintainer: Aymen Nasri <aymennasrii@proton.me>
This is a re-admission after prior archival of version 0.2.1 dated 2025-03-22
Diff between ggfootball versions 0.2.1 dated 2025-03-22 and 0.2.2 dated 2026-01-23
ggfootball-0.2.1/ggfootball/R/team_formation.R |only ggfootball-0.2.2/ggfootball/DESCRIPTION | 8 +-- ggfootball-0.2.2/ggfootball/MD5 | 17 +++---- ggfootball-0.2.2/ggfootball/NEWS.md | 4 + ggfootball-0.2.2/ggfootball/R/understat_scraper.R | 49 ++++++++++++++++++++-- ggfootball-0.2.2/ggfootball/R/xg_chart.R | 4 + ggfootball-0.2.2/ggfootball/R/xg_map.R | 4 + ggfootball-0.2.2/ggfootball/README.md | 3 - ggfootball-0.2.2/ggfootball/man/xg_chart.Rd | 2 ggfootball-0.2.2/ggfootball/man/xg_map.Rd | 2 10 files changed, 74 insertions(+), 19 deletions(-)
Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: Francois Rousset [aut, cre, cph] ,
Jimmy Lopez [ctb],
Alexandre Genin [ctb],
Khalid Belkhir [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between genepop versions 1.2.11 dated 2025-08-27 and 1.2.14 dated 2026-01-23
DESCRIPTION | 8 MD5 | 34 inst/NEWS.Rd | 5 inst/doc/GenepopS.Rmd | 9 inst/doc/GenepopS.pdf |binary inst/doc/GenepopS.tex | 15 inst/doc/all-menu-options.html | 10 inst/doc/bibliography.html | 10 inst/doc/code-maintenance-credits-contact-etc..html | 10 inst/doc/copyright.html | 10 inst/doc/evaluating-the-performance-of-inferences-for-isolation-by-distance.html | 10 inst/doc/installing-genepop-and-session-examples.html | 16 inst/doc/introduction.html | 16 inst/doc/methods.html | 10 inst/doc/sec-settings.html | 10 inst/doc/the-input-file.html | 10 src/F_est.cpp | 525 +++++----- src/GenepopS.cpp | 2 18 files changed, 364 insertions(+), 346 deletions(-)
Title: Describe, Package, and Share Biodiversity Data
Description: The Darwin Core data standard is widely used to share
biodiversity information, most notably by the Global Biodiversity Information
Facility and its partner nodes; but converting data to this standard can be
tricky. 'galaxias' is functionally similar to 'devtools', but with a focus on
building Darwin Core Archives rather than R packages, enabling data to be
shared and re-used with relative ease. For details see
Wieczorek and colleagues (2012) <doi:10.1371/journal.pone.0029715>.
Author: Martin Westgate [aut, cre],
Shandiya Balasubramaniam [aut],
Dax Kellie [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
This is a re-admission after prior archival of version 0.1.1 dated 2025-10-22
Diff between galaxias versions 0.1.1 dated 2025-10-22 and 0.1.2 dated 2026-01-23
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 5 build/vignette.rds |binary inst/doc/events-example.R | 4 inst/doc/events-example.html | 54 +-- inst/doc/occurrences-example.R | 17 - inst/doc/occurrences-example.Rmd | 53 ++- inst/doc/occurrences-example.html | 620 +++++++++++++++++++------------------- inst/doc/quick_start_guide.R | 82 ++--- inst/doc/quick_start_guide.Rmd | 6 inst/doc/quick_start_guide.html | 65 ++- vignettes/occurrences-example.Rmd | 53 ++- vignettes/quick_start_guide.Rmd | 6 14 files changed, 534 insertions(+), 465 deletions(-)
Title: Comparison of Bioregionalization Methods
Description: The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Author: Maxime Lenormand [aut, cre] ,
Boris Leroy [aut] ,
Pierre Denelle [aut]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between bioregion versions 1.2.0 dated 2025-01-31 and 1.3.0 dated 2026-01-23
bioregion-1.2.0/bioregion/NEWS.md |only bioregion-1.2.0/bioregion/README.md |only bioregion-1.2.0/bioregion/man/figures/zscore_scheme.svg |only bioregion-1.3.0/bioregion/DESCRIPTION | 28 bioregion-1.3.0/bioregion/MD5 | 154 - bioregion-1.3.0/bioregion/NAMESPACE | 18 bioregion-1.3.0/bioregion/R/as_bioregion_pairwise.R |only bioregion-1.3.0/bioregion/R/betapart_to_bioregion.R | 12 bioregion-1.3.0/bioregion/R/bind_pairwise.R |only bioregion-1.3.0/bioregion/R/bioregion_colors.R |only bioregion-1.3.0/bioregion/R/bioregion_metrics.R | 2 bioregion-1.3.0/bioregion/R/bioregionalization_metrics.R | 27 bioregion-1.3.0/bioregion/R/compare_bioregionalizations.R | 50 bioregion-1.3.0/bioregion/R/cut_tree.R | 37 bioregion-1.3.0/bioregion/R/dissimilarity.R | 6 bioregion-1.3.0/bioregion/R/exportGDF.R | 340 ++ bioregion-1.3.0/bioregion/R/find_optimal_n.R | 108 bioregion-1.3.0/bioregion/R/generic_functions.R | 1344 +++++++--- bioregion-1.3.0/bioregion/R/hclu_diana.R | 55 bioregion-1.3.0/bioregion/R/hclu_hierarclust.R | 153 - bioregion-1.3.0/bioregion/R/hclu_optics.R | 28 bioregion-1.3.0/bioregion/R/install_binaries.R | 190 - bioregion-1.3.0/bioregion/R/iterative_hierarchical_consensus_tree.R | 5 bioregion-1.3.0/bioregion/R/map_bioregions.R | 219 + bioregion-1.3.0/bioregion/R/net_to_mat.R | 8 bioregion-1.3.0/bioregion/R/netclu_beckett.R | 12 bioregion-1.3.0/bioregion/R/netclu_greedy.R | 29 bioregion-1.3.0/bioregion/R/netclu_infomap.R | 30 bioregion-1.3.0/bioregion/R/netclu_labelprop.R | 29 bioregion-1.3.0/bioregion/R/netclu_leadingeigen.R | 28 bioregion-1.3.0/bioregion/R/netclu_leiden.R | 29 bioregion-1.3.0/bioregion/R/netclu_louvain.R | 28 bioregion-1.3.0/bioregion/R/netclu_oslom.R | 28 bioregion-1.3.0/bioregion/R/netclu_walktrap.R | 29 bioregion-1.3.0/bioregion/R/nhclu_affprop.R | 130 bioregion-1.3.0/bioregion/R/nhclu_clara.R | 27 bioregion-1.3.0/bioregion/R/nhclu_clarans.R | 28 bioregion-1.3.0/bioregion/R/nhclu_dbscan.R | 35 bioregion-1.3.0/bioregion/R/nhclu_kmeans.R | 27 bioregion-1.3.0/bioregion/R/nhclu_pam.R | 27 bioregion-1.3.0/bioregion/R/similarity.R | 12 bioregion-1.3.0/bioregion/R/similarity_dissimilarity_conversion.R | 12 bioregion-1.3.0/bioregion/R/site_species_metrics.R | 1150 +++++--- bioregion-1.3.0/bioregion/R/site_species_subset.R | 59 bioregion-1.3.0/bioregion/R/utils.R | 742 +++++ bioregion-1.3.0/bioregion/build/partial.rdb |binary bioregion-1.3.0/bioregion/build/vignette.rds |binary bioregion-1.3.0/bioregion/inst/CITATION |only bioregion-1.3.0/bioregion/inst/REFERENCES.bib | 58 bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.R |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.html |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.R |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.html |only bioregion-1.3.0/bioregion/inst/doc/bioregion.Rmd | 37 bioregion-1.3.0/bioregion/inst/doc/bioregion.html | 163 - bioregion-1.3.0/bioregion/inst/doc/citations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/citations.html |only bioregion-1.3.0/bioregion/man/as_bioregion_pairwise.Rd |only bioregion-1.3.0/bioregion/man/betapart_to_bioregion.Rd | 8 bioregion-1.3.0/bioregion/man/bind_pairwise.Rd |only bioregion-1.3.0/bioregion/man/bioregion_colors.Rd |only bioregion-1.3.0/bioregion/man/bioregion_metrics.Rd | 2 bioregion-1.3.0/bioregion/man/bioregionalization_metrics.Rd | 2 bioregion-1.3.0/bioregion/man/compare_bioregionalizations.Rd | 8 bioregion-1.3.0/bioregion/man/cut_tree.Rd | 8 bioregion-1.3.0/bioregion/man/dissimilarity.Rd | 6 bioregion-1.3.0/bioregion/man/dissimilarity_to_similarity.Rd | 6 bioregion-1.3.0/bioregion/man/exportGDF.Rd |only bioregion-1.3.0/bioregion/man/figures/05_map_fish_bipartite_infomap.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_basic.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_bipartite_colored.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_unipartite_weighted.png |only bioregion-1.3.0/bioregion/man/figures/comparison_Bray-Curtis.png |only bioregion-1.3.0/bioregion/man/figures/comparison_Jaccard.png |only bioregion-1.3.0/bioregion/man/figures/core_terms.svg |only bioregion-1.3.0/bioregion/man/find_optimal_n.Rd | 6 bioregion-1.3.0/bioregion/man/hclu_diana.Rd | 8 bioregion-1.3.0/bioregion/man/hclu_hierarclust.Rd | 25 bioregion-1.3.0/bioregion/man/install_binaries.Rd | 6 bioregion-1.3.0/bioregion/man/map_bioregions.Rd | 45 bioregion-1.3.0/bioregion/man/nhclu_affprop.Rd | 6 bioregion-1.3.0/bioregion/man/nhclu_dbscan.Rd | 4 bioregion-1.3.0/bioregion/man/similarity.Rd | 8 bioregion-1.3.0/bioregion/man/similarity_to_dissimilarity.Rd | 6 bioregion-1.3.0/bioregion/man/site_species_metrics.Rd | 379 ++ bioregion-1.3.0/bioregion/man/site_species_subset.Rd | 12 bioregion-1.3.0/bioregion/vignettes/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/vignettes/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/vignettes/bioregion.Rmd | 37 bioregion-1.3.0/bioregion/vignettes/citations.Rmd |only bioregion-1.3.0/bioregion/vignettes/style_citation.csl |only 93 files changed, 4708 insertions(+), 1407 deletions(-)
Title: Custom Legends with Statistical Comparison Brackets
Description: Add publication-quality custom legends with vertical brackets. Designed for displaying statistical comparisons between groups,
commonly used in scientific publications for showing significance levels.
Features include adaptive positioning, automatic bracket spacing for overlapping
comparisons, font family inheritance, and support for asterisks, p-values,
or custom labels. Compatible with 'ggplot2' graphics.
Author: Yoshiaki Sato [aut, cre]
Maintainer: Yoshiaki Sato <h20gg702@outlook.jp>
Diff between vbracket versions 1.0.2 dated 2026-01-07 and 1.1.0 dated 2026-01-23
DESCRIPTION | 6 +-- MD5 | 6 +-- R/annotation_grob.R | 57 ++++++++++++++++++++------------- R/custom_legend_with_brackets.R | 69 +++++++++++++++++++++++----------------- 4 files changed, 82 insertions(+), 56 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] ,
R Core Team [cph] ,
Michael Chirico [ctb]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.19 dated 2025-11-23 and 0.2.20 dated 2026-01-23
DESCRIPTION | 6 MD5 | 135 ++++++++++----------- NEWS.md | 16 ++ R/abstract.R | 26 ++-- R/alike.R | 2 R/benchmark.R | 2 R/cstringr.R | 2 R/helper.R | 2 R/misc.R | 2 R/settings.R | 2 R/system.R | 2 R/templates.R | 2 R/type.R | 2 R/validate.R | 2 R/validators.R | 2 R/vetr-package.R | 2 inst/doc/alike.html | 12 - inst/doc/vetr.html | 10 - man/abstract.Rd | 19 +-- src/alike.c | 115 ++++++++---------- src/alike.h | 5 src/assumptions.c | 2 src/attr.c | 189 ++++++++++++++---------------- src/backports.c |only src/backports.h | 10 + src/cstringr-ext.c | 2 src/cstringr.c | 2 src/cstringr.h | 2 src/cstringrtest.c | 2 src/envtrack.c | 2 src/eval.c | 2 src/fun.c | 4 src/init.c | 3 src/lang.c | 12 - src/merge.c | 2 src/misc-alike.c | 87 ++++--------- src/misc.c | 2 src/parse.c | 2 src/pfhash.c | 2 src/pfhash.h | 2 src/r-copied.c | 2 src/recurse.c | 2 src/settings.c | 2 src/settings.h | 2 src/strsub.c | 2 src/trackinghash.c | 2 src/trackinghash.h | 2 src/type.c | 18 +- src/validate.c | 2 src/validate.h | 2 src/valname.c | 2 tests/unitizer/abstract.R | 26 +++- tests/unitizer/abstract.unitizer/data.rds |binary tests/unitizer/alike.R | 16 ++ tests/unitizer/alike.unitizer/data.rds |binary tests/unitizer/all-bw.R | 2 tests/unitizer/classes.R | 2 tests/unitizer/cstringr.R | 2 tests/unitizer/eval.R | 2 tests/unitizer/internal.R | 2 tests/unitizer/internal.unitizer/data.rds |binary tests/unitizer/language.R | 2 tests/unitizer/misc.R | 13 +- tests/unitizer/misc.unitizer/data.rds |binary tests/unitizer/parse.R | 2 tests/unitizer/tev.R | 2 tests/unitizer/type.R | 2 tests/unitizer/validate.R | 2 tests/unitizer/validate.args.R | 2 69 files changed, 417 insertions(+), 395 deletions(-)
Title: Tools for Generating and Handling of UUIDs
Description: Tools for generating and handling of UUIDs (Universally Unique Identifiers).
Author: Simon Urbanek [aut, cre, cph] ,
Theodore Ts'o [aut, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between uuid versions 1.2-1 dated 2024-07-29 and 1.2-2 dated 2026-01-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 +++++++ man/UUIDgenerate.Rd | 13 ++++++++++++- src/R.c | 11 +++++++++-- src/Ruuid.c | 7 +++++++ src/randutils.c | 2 +- 7 files changed, 46 insertions(+), 14 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] ,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph] ,
Andrea Manica [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.7.2 dated 2025-04-14 and 1.0.0 dated 2026-01-23
tidyterra-0.7.2/tidyterra/R/as_coordinates.R |only tidyterra-0.7.2/tidyterra/R/as_sf.R |only tidyterra-0.7.2/tidyterra/R/as_spatraster.R |only tidyterra-0.7.2/tidyterra/R/as_spatvector.R |only tidyterra-0.7.2/tidyterra/R/as_tibble-Spat.R |only tidyterra-0.7.2/tidyterra/R/compare_spatrasters.R |only tidyterra-0.7.2/tidyterra/R/drop_na-Spat.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour_fill.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour_text.R |only tidyterra-0.7.2/tidyterra/R/geom_spatraster.R |only tidyterra-0.7.2/tidyterra/R/geom_spatraster_rgb.R |only tidyterra-0.7.2/tidyterra/R/geom_spatvector.R |only tidyterra-0.7.2/tidyterra/R/is_regular_grid.R |only tidyterra-0.7.2/tidyterra/R/pull_crs.R |only tidyterra-0.7.2/tidyterra/R/replace_na-Spat.R |only tidyterra-0.7.2/tidyterra/R/scales_coltab.R |only tidyterra-0.7.2/tidyterra/R/scales_cross_blended.R |only tidyterra-0.7.2/tidyterra/R/scales_grass.R |only 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Title: Visualizing the Performance of Scoring Classifiers
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR is a
flexible tool for creating cutoff-parameterized 2D performance curves
by freely combining two from over 25 performance measures (new
performance measures can be added using a standard interface).
Curves from different cross-validation or bootstrapping runs can be
averaged by different methods, and standard deviations, standard
errors or box plots can be used to visualize the variability across
the runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with only
three commands and reasonable default values for all optional
parameters.
Author: Tobias Sing [aut],
Oliver Sander [aut],
Niko Beerenwinkel [aut],
Thomas Lengauer [aut],
Thomas Unterthiner [ctb],
Felix G.M. Ernst [cre]
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>
Diff between ROCR versions 1.0-11 dated 2020-05-02 and 1.0-12 dated 2026-01-23
DESCRIPTION | 14 +++++----- MD5 | 32 +++++++++++------------ R/performance.R | 10 +++---- R/prediction.R | 2 - R/zzz.R | 6 ++-- README.md | 6 ++-- build/vignette.rds |binary inst/CITATION | 22 ++++++++-------- inst/doc/ROCR.R | 28 ++++++++++---------- inst/doc/ROCR.Rmd | 4 +- inst/doc/ROCR.html | 63 ++++++++++++++++++++++++++++++++++------------- man/performance-class.Rd | 2 - man/performance.Rd | 8 ++--- man/plot-methods.Rd | 6 ++-- man/prediction-class.Rd | 2 - man/prediction.Rd | 2 - vignettes/ROCR.Rmd | 4 +- 17 files changed, 121 insertions(+), 90 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre] ,
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.6.4 dated 2025-04-08 and 2.6.5 dated 2026-01-23
Rdpack-2.6.4/Rdpack/man/set_Rdpack_bibstyle.Rd |only Rdpack-2.6.5/Rdpack/DESCRIPTION | 23 Rdpack-2.6.5/Rdpack/MD5 | 56 Rdpack-2.6.5/Rdpack/NAMESPACE | 5 Rdpack-2.6.5/Rdpack/NEWS.md | 24 Rdpack-2.6.5/Rdpack/R/bib.R | 2670 ++++------ Rdpack-2.6.5/Rdpack/build/partial.rdb |binary Rdpack-2.6.5/Rdpack/build/vignette.rds |binary Rdpack-2.6.5/Rdpack/inst/REFERENCES.bib | 15 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.R | 36 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.Rnw | 2 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.R | 18 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.Rnw | 21 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-2.6.5/Rdpack/inst/pkgdown.yml |only Rdpack-2.6.5/Rdpack/man/Rdpack-package.Rd | 43 Rdpack-2.6.5/Rdpack/man/Rdpack_bibstyles.Rd | 18 Rdpack-2.6.5/Rdpack/man/insert_ref.Rd | 4 Rdpack-2.6.5/Rdpack/man/macros/refmacros.Rd | 50 Rdpack-2.6.5/Rdpack/man/predefined.Rd | 8 Rdpack-2.6.5/Rdpack/tests/testthat/StructureClasses.Rd | 362 - Rdpack-2.6.5/Rdpack/tests/testthat/as.character.f_usage.Rd | 124 Rdpack-2.6.5/Rdpack/tests/testthat/myshow-methods.Rd | 40 Rdpack-2.6.5/Rdpack/tests/testthat/show.Rd | 162 Rdpack-2.6.5/Rdpack/tests/testthat/test-bib.R | 9 Rdpack-2.6.5/Rdpack/vignettes/Inserting_bibtex_references.Rnw | 2 Rdpack-2.6.5/Rdpack/vignettes/Inserting_bibtex_references.org | 14 Rdpack-2.6.5/Rdpack/vignettes/Inserting_figures_and_evaluated_examples.Rnw | 21 Rdpack-2.6.5/Rdpack/vignettes/Inserting_figures_and_evaluated_examples.org | 2 30 files changed, 1821 insertions(+), 1908 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.8.2 dated 2024-10-28 and 0.8.3 dated 2026-01-23
pdp-0.8.2/pdp/inst/tinytest/test_xgboost_pima.R |only pdp-0.8.3/pdp/DESCRIPTION | 17 +++--- pdp-0.8.3/pdp/MD5 | 39 +++++++------- pdp-0.8.3/pdp/NEWS.md | 7 ++ pdp-0.8.3/pdp/R/autoplot.R | 4 - pdp-0.8.3/pdp/R/get_predictions.R | 9 +-- pdp-0.8.3/pdp/R/get_task.R | 14 ++--- pdp-0.8.3/pdp/README.md | 2 pdp-0.8.3/pdp/build/vignette.rds |binary pdp-0.8.3/pdp/inst/doc/pdp-approximate.pdf |binary pdp-0.8.3/pdp/inst/doc/pdp-intro.pdf |binary pdp-0.8.3/pdp/inst/doc/pdp-link-function.pdf |binary pdp-0.8.3/pdp/inst/tinytest/test_get_training_data.R | 5 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_C50.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_MASS.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_e1071.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_party.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_ranger.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_stats.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_xgboost.R | 50 ++++++++----------- pdp-0.8.3/pdp/tests/tinytest.R | 2 21 files changed, 99 insertions(+), 74 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 3.0.2 dated 2025-09-26 and 3.0.3 dated 2026-01-23
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++----------- NEWS.md | 10 +++++++++ R/getTimeIndex.R | 5 +++- R/getZipUrls.R | 5 ++-- R/schemaFromVar.R | 5 ++++ R/stackByTable.R | 4 +-- R/stackDataFilesArrow.R | 13 +++++++++-- R/stackFrameFiles.R | 42 ++++++++++++++++++++++++++++++++++---- R/sysdata.rda |binary R/zipsByProduct.R | 26 ++++++++++++++++------- README.md | 53 +++++++++++++++++++++++++++++++++++++++++++++--- data/table_types.rda |binary 13 files changed, 156 insertions(+), 39 deletions(-)
Title: Minimal Type Guesser
Description: Port the type guesser from 'readr' (so-called 'readr' first edition parsing engine, now superseded by 'vroom').
Author: Chung-hong Chan [aut, cre] ,
Hadley Wickham [aut] ,
Jim Hester [aut] ,
Romain Francois [ctb] ,
Jennifer Bryan [aut] ,
Shelby Bearrows [ctb] ,
Posit Software, PBC [cph] ,
David Olson [aut]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between minty versions 0.0.5 dated 2025-01-07 and 0.0.6 dated 2026-01-23
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- README.md | 10 ++++------ 3 files changed, 15 insertions(+), 16 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
This method draws from the simulation framework used in the Gelman and Hill (2007) textbook:
Data Analysis Using Regression and Multilevel/Hierarchical Models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut],
Alex Whitworth [ctb]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between merTools versions 0.6.3 dated 2025-09-05 and 0.6.4 dated 2026-01-23
DESCRIPTION | 8 MD5 | 20 NEWS.md | 94 - R/helpers.R | 27 R/merExtract.R | 1 build/vignette.rds |binary inst/doc/Using_predictInterval.html | 1841 +++++++++++++++--------------- inst/doc/imputation.html | 2147 ++++++++++++++++++------------------ inst/doc/marginal_effects.html | 859 +++++++------- inst/doc/merToolsIntro.html | 1557 +++++++++++++------------- tests/testthat/_snaps/predict2.md | 20 11 files changed, 3300 insertions(+), 3274 deletions(-)
Title: Fast K-Mer Counting and Clustering for Biological Sequence
Analysis
Description: Contains tools for rapidly computing distance matrices
and clustering large sequence datasets using fast alignment-free
k-mer counting and recursive k-means partitioning.
See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005>
for a review of k-mer counting methods and applications for
biological sequence analysis.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between kmer versions 1.1.2 dated 2019-05-20 and 1.1.3 dated 2026-01-23
DESCRIPTION | 13 MD5 | 30 - README.md | 13 build/vignette.rds |binary inst/CITATION | 13 inst/doc/kmer-vignette.R | 12 inst/doc/kmer-vignette.Rmd | 2 inst/doc/kmer-vignette.html | 720 +++++++++++++++++++++++++++++++++----------- man/kcount.Rd | 11 man/kdistance.Rd | 11 man/kmer.Rd | 14 man/mbed.Rd | 3 man/otu.Rd | 11 src/Makevars | 3 src/RcppExports.cpp | 5 vignettes/kmer-vignette.Rmd | 2 16 files changed, 646 insertions(+), 217 deletions(-)
Title: Datasets, Functions and Scripts for Semiparametric Regression
Supporting Harezlak, Ruppert & Wand (2018)
Description: The book "Semiparametric Regression with R" by J. Harezlak, D. Ruppert & M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets and scripts to explain semiparametric regression concepts. Each of the book's scripts are contained in this package as well as datasets that are not within other R packages. Functions that aid semiparametric regression analysis are also included.
Author: Jaroslaw Harezlak [aut],
David Ruppert [aut],
Matt P. Wand [aut, cre]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between HRW versions 1.0-5 dated 2021-11-23 and 1.0-6 dated 2026-01-23
DESCRIPTION | 13 ++++---- MD5 | 62 +++++++++++++++++++++--------------------- R/createBoundary.r | 6 ++-- data/BCR.rda |binary data/BanglaContrac.rda |binary data/BostonMortgages.rda |binary data/CHD.rda |binary data/SydneyRealEstate.rda |binary data/SydneyRealEstateBdry.rda |binary data/TreasuryRate.rda |binary data/UtahPEF.rda |binary data/WarsawApts.rda |binary data/brainImage.rda |binary data/capm.rda |binary data/carAuction.rda |binary data/coral.rda |binary data/femSBMD.rda |binary data/growthIndiana.rda |binary data/indonRespir.rda |binary data/lidar.rda |binary data/ozoneSub.rda |binary data/plankton.rda |binary data/protein.rda |binary data/ragweed.rda |binary data/scallop.rda |binary data/schoolResults.rda |binary data/yields.rda |binary demo/BCRana.R | 2 - demo/npReg.R | 8 +---- demo/ozoneAna.R | 2 - man/BostonMortgages.Rd | 2 - man/SydneyRealEstate.Rd | 2 - 32 files changed, 47 insertions(+), 50 deletions(-)
Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information
System of the Commission) Eurostat database
<https://ec.europa.eu/eurostat/web/gisco>. Global and European map
data available. This package is in no way officially related to or
endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 1.0.0 dated 2025-12-10 and 1.0.1 dated 2026-01-23
giscoR-1.0.0/giscoR/R/zzz.R |only giscoR-1.0.1/giscoR/DESCRIPTION | 6 giscoR-1.0.1/giscoR/MD5 | 143 - giscoR-1.0.1/giscoR/NEWS.md | 14 giscoR-1.0.1/giscoR/R/data.R | 2 giscoR-1.0.1/giscoR/R/gisco-address-api.R | 712 ++++----- giscoR-1.0.1/giscoR/R/gisco-attributions.R | 8 giscoR-1.0.1/giscoR/R/gisco-bulk-download.R | 4 giscoR-1.0.1/giscoR/R/gisco-cache.R | 734 +++++----- giscoR-1.0.1/giscoR/R/gisco-get-cached-db.R | 13 giscoR-1.0.1/giscoR/R/gisco-get-communes.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-countries.R | 2 giscoR-1.0.1/giscoR/R/gisco-get-education.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-grid.R | 6 giscoR-1.0.1/giscoR/R/gisco-get-healthcare.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-lau.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-metadata.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-unit-urban-audit.R | 6 giscoR-1.0.1/giscoR/R/gisco-get-urban-audit.R | 4 giscoR-1.0.1/giscoR/R/gisco-id-api.R | 2 giscoR-1.0.1/giscoR/R/utils-country.R | 11 giscoR-1.0.1/giscoR/R/utils-sf.R | 2 giscoR-1.0.1/giscoR/R/utils-url.R | 10 giscoR-1.0.1/giscoR/R/utils.R | 295 ++-- giscoR-1.0.1/giscoR/README.md | 6 giscoR-1.0.1/giscoR/build/stage23.rdb |binary giscoR-1.0.1/giscoR/data/gisco_db.rda |binary giscoR-1.0.1/giscoR/inst/COPYRIGHTS | 2 giscoR-1.0.1/giscoR/inst/WORDLIST | 4 giscoR-1.0.1/giscoR/inst/doc/giscoR.Rmd | 4 giscoR-1.0.1/giscoR/inst/doc/giscoR.html | 4 giscoR-1.0.1/giscoR/inst/schemaorg.json | 2 giscoR-1.0.1/giscoR/man/chunks/education_meta.Rmd | 2 giscoR-1.0.1/giscoR/man/chunks/healthcare_meta.Rmd | 2 giscoR-1.0.1/giscoR/man/gisco_address_api.Rd | 4 giscoR-1.0.1/giscoR/man/gisco_attributions.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_bulk_download.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_clear_cache.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_db.Rd | 4 giscoR-1.0.1/giscoR/man/gisco_get_airports.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_cached_db.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_census.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_coastal_lines.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_communes.Rd | 6 giscoR-1.0.1/giscoR/man/gisco_get_countries.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_education.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_grid.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_healthcare.Rd | 10 giscoR-1.0.1/giscoR/man/gisco_get_lau.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_metadata.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_nuts.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_ports.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_postal_codes.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_unit.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_units.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_urban_audit.Rd | 6 giscoR-1.0.1/giscoR/man/gisco_nuts_2024.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_set_cache_dir.Rd | 12 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-bulk-download.md | 60 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-get-metadata.md | 4 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-get-unit-urban-audit.md | 2 giscoR-1.0.1/giscoR/tests/testthat/_snaps/utils-country.md | 4 giscoR-1.0.1/giscoR/tests/testthat/_snaps/utils-url.md | 24 giscoR-1.0.1/giscoR/tests/testthat/test-gisco-cache.R | 315 ++-- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-metadata.R | 162 +- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-unit-urban-audit.R | 412 ++--- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-urban-audit.R | 500 +++--- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-id-api.R | 12 giscoR-1.0.1/giscoR/tests/testthat/test-utils-url.R | 627 ++++---- giscoR-1.0.1/giscoR/tests/testthat/test-utils.R | 313 ++-- giscoR-1.0.1/giscoR/vignettes/africa-1.png |binary giscoR-1.0.1/giscoR/vignettes/country-1.png |binary giscoR-1.0.1/giscoR/vignettes/giscoR.Rmd | 4 73 files changed, 2306 insertions(+), 2261 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.3.5 dated 2022-12-05 and 1.3.6 dated 2026-01-23
DESCRIPTION | 13 +- MD5 | 32 ++--- R/aphid.R | 4 R/derivePHMM.R | 10 - R/utils.R | 2 README.md | 9 + build/vignette.rds |binary inst/CITATION | 10 - inst/doc/aphid-vignette.R | 14 +- inst/doc/aphid-vignette.Rmd | 5 inst/doc/aphid-vignette.html | 270 +++++++++++++++++++++---------------------- man/aphid.Rd | 13 +- man/derivePHMM.Rd | 4 src/Makevars | 3 src/RcppExports.cpp | 5 vignettes/aphid-vignette.Rmd | 5 vignettes/aphid.bib | 10 - 17 files changed, 220 insertions(+), 189 deletions(-)
Title: Render 'LaTeX' in Plots
Description: High-level functions to render 'LaTeX' fragments in plots,
including as labels and data symbols in 'ggplot2' plots, plus
low-level functions to
author 'LaTeX' fragments (to produce 'LaTeX' documents),
typeset 'LaTeX' documents (to produce 'DVI' files),
read 'DVI' files (to produce "DVI" objects),
and render "DVI" objects.
Author: Paul Murrell [aut, cre]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between xdvir versions 0.1-3 dated 2025-07-15 and 0.2-0 dated 2026-01-22
DESCRIPTION | 7 ++--- MD5 | 49 +++++++++++++++++++------------------ NAMESPACE | 2 + R/engine.R | 1 R/fontLib.R | 15 +++++++++-- R/fontspec.R | 32 +++++++++++++++++++++--- R/freetype.R | 7 ++++- R/grob.R | 14 +++++++++- R/harfbuzz.R |only R/luatex.R | 12 ++++++--- R/ops.R | 5 ++- R/xetex.R | 4 +-- R/zzz.R | 21 ++++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 9 ++++++ inst/doc/xdvir-intro.R | 49 ++++++++++++++++++++++++++++++------- inst/doc/xdvir-intro.Rmd | 53 +++++++++++++++++++++++++++++++++------- inst/doc/xdvir-intro.html | 7 ++--- man/fontspecPackage.Rd | 9 ++++++ man/grid.latex.Rd | 4 ++- src/freetype.c | 60 ++++++++++++++++++++++++++++++++++++++++++---- src/freetype.h | 2 + src/register.c | 1 tests/dpi.R | 7 ++++- vignettes/xdvir-intro.Rmd | 53 +++++++++++++++++++++++++++++++++------- vignettes/xdvir-intro.bib | 2 - 26 files changed, 337 insertions(+), 88 deletions(-)
Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC)
classification system using R and C++.
Author: Peter DeWitt [aut] ,
Tell Bennett [ctb] ,
James Feinstein [aut] ,
Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@cuanschutz.edu>
Diff between pccc versions 1.0.6 dated 2025-05-16 and 1.0.7 dated 2026-01-22
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++--------- NAMESPACE | 4 -- NEWS.md | 4 ++ R/get_codes.R | 12 -------- R/pccc-package.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/pccc-example.R | 64 +++++++++++++++++++++---------------------- inst/doc/pccc-example.html | 9 +++--- inst/doc/pccc-icd-codes.html | 9 +++--- inst/doc/pccc-overview.R | 20 ++++++------- inst/doc/pccc-overview.html | 9 +++--- tests/test_get_codes.R | 9 ------ 14 files changed, 79 insertions(+), 99 deletions(-)
Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD
intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512).
By placing this library in this package, we offer an efficient distribution system for
Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre],
Andrew J. Holbrook [aut],
Observational Health Data Sciences and Informatics [cph],
Johan Mabille [cph, ctb] ,
Sylvain Corlay [cph, ctb] ,
Alexander J. Lee [cph, ctb]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between RcppXsimd versions 7.1.6-1 dated 2025-11-29 and 7.1.6-2 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/include/xsimd/memory/xsimd_aligned_allocator.hpp | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.1.8 dated 2025-12-19 and 0.2.1 dated 2026-01-22
DESCRIPTION | 6 MD5 | 16 NAMESPACE | 24 NEWS.md | 236 +- R/Ganttify.R | 4144 ++++++++++++++++++++++++++++------------------------ R/data.R | 106 - README.md | 762 +++++---- man/Ganttify.Rd | 574 +++---- man/test_project.Rd | 130 - 9 files changed, 3260 insertions(+), 2738 deletions(-)
Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tile map display from spatial polygons. Each
polygon is represented by a hexagon tile, placed as close to it's original
centroid as possible, with a focus on maintaining spatial relationship to
a focal point. Developed to aid visualisation and analysis of spatial
distributions across Australia, which can be challenging due to the
concentration of the population on the coast and wide open interior.
Author: Dianne Cook [aut, cre, ths] ,
Stephanie Kobakian [aut] ,
Matt Cowgill [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between sugarbag versions 0.1.9 dated 2025-12-06 and 0.1.10 dated 2026-01-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/global.R | 3 ++- inst/doc/Tasmania.html | 4 ++-- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Tidy Population Genetics
Description: We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.
Author: Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica [aut, cre, cph] ,
Chang Christopher [ctb] ),
Shaun Purcell [ctb] ),
Bengtsson Henrik [ctb] )
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidypopgen versions 0.4.1 dated 2025-12-20 and 0.4.2 dated 2026-01-22
DESCRIPTION | 6 - MD5 | 23 +++--- NEWS.md | 4 + R/annotate_group_info.R | 4 - R/gt_pca_tidiers.R | 2 R/predict_gt_pca.R | 71 +++++++++++--------- inst/doc/a01_overview.html | 92 +++++++++++++------------- inst/doc/a02_qc.html | 26 +++---- inst/doc/a03_example_clustering_and_dapc.html | 3 inst/doc/tidypopgen.html | 6 - man/predict_gt_pca.Rd | 7 + tests/testthat/Rplots.pdf |only tests/testthat/test_gt_pca.R | 67 ++++++++++++++++++ 13 files changed, 200 insertions(+), 111 deletions(-)
More information about alphavantagepf at CRAN
Permanent link
Title: Bounded Time Series Regression
Description: Simulate, estimate and forecast a wide range of regression
based dynamic models for bounded time series, covering the most
commonly applied models in the literature. The main calculations are
done in FORTRAN, which translates into very fast algorithms.
Author: Taiane Schaedler Prass [aut, cre, com] ,
Guilherme Pumi [ctb, aut] ,
Fabio Mariano Bayer [ctb] ,
Jack Joseph Dongarra [ctb] ),
Cleve Moler [ctb] ),
Gilbert Wright Stewart [ctb] ),
Ciyou Zhu [ctb] ,
Richard H. Byrd [ctb] ,
Jorge Nocedal [ctb] ,
Jose L [...truncated...]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between BTSR versions 1.0.0 dated 2025-06-18 and 1.0.1 dated 2026-01-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/btsr.R | 1 - R/functions_misc.R | 4 ++-- build/partial.rdb |binary inst/NEWS.md | 6 ++++++ man/fit.control.Rd | 2 +- man/print.btsr.Rd | 52 ++++++++++++++++++++++++++-------------------------- man/summary.Rd | 2 +- src/01_distrib.f90 | 24 +++++++++++++++--------- 10 files changed, 65 insertions(+), 54 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut, cre],
Mu Sigma, Inc. [cph]
Maintainer: Zubin Dowlaty <zubin.dowlaty@mu-sigma.com>
Diff between HVT versions 25.2.8 dated 2025-12-18 and 26.1.1 dated 2026-01-22
HVT-25.2.8/HVT/NEWS.md |only HVT-26.1.1/HVT/DESCRIPTION | 8 HVT-26.1.1/HVT/MD5 | 31 +- HVT-26.1.1/HVT/R/clusterPlot.R | 187 ++++++++++++++-- HVT-26.1.1/HVT/R/global.R | 2 HVT-26.1.1/HVT/R/mcmc_plots.R | 37 ++- HVT-26.1.1/HVT/R/msm.R | 15 + HVT-26.1.1/HVT/R/plotAnimatedFlowmap.R | 5 HVT-26.1.1/HVT/R/plotHVT.R | 374 +++++++++++++++++++++++++-------- HVT-26.1.1/HVT/R/scoreHVT.R | 257 +++++++++++++++++++++- HVT-26.1.1/HVT/README.md | 52 +++- HVT-26.1.1/HVT/inst/doc/HVT.Rmd | 21 + HVT-26.1.1/HVT/inst/doc/HVT.html | 46 +++- HVT-26.1.1/HVT/man/msm.Rd | 4 HVT-26.1.1/HVT/man/plotHVT.Rd | 11 HVT-26.1.1/HVT/man/scoreHVT.Rd | 18 + HVT-26.1.1/HVT/vignettes/HVT.Rmd | 21 + 17 files changed, 889 insertions(+), 200 deletions(-)
Title: Tree Guided Machine Learning for Personalized Predictions and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.3.0 dated 2025-12-11 and 0.4.0 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/05b.combML_mse.R | 36 ++++++++++++++++++------------------ R/05c.combML_bs.R | 36 ++++++++++++++++++------------------ R/tgml.R | 2 ++ man/tgml.Rd | 34 ++++++++++++++++++---------------- 6 files changed, 65 insertions(+), 61 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.6.1 dated 2025-08-22 and 1.7.2 dated 2026-01-22
DESCRIPTION | 8 +- MD5 | 40 +++++++------- NAMESPACE | 1 NEWS.md | 38 ++++++++++++++ R/Aaaa.R | 2 R/class_build.R | 4 - R/handle_spec_block.R | 9 +++ R/modspec.R | 1 R/mread.R | 5 + inst/WORDLIST | 2 inst/base/modelheader.h | 2 inst/base/mrgsolv.h | 8 +- inst/include/dataobject.h | 6 +- inst/include/odeproblem.h | 31 +++++++---- inst/project/housemodel.cpp | 2 src/dataobject.cpp | 18 +++++- src/devtran.cpp | 52 +++++++++++++++---- src/housemodel-mread-header.h | 2 src/housemodel-mread-source.cpp | 3 - src/odeproblem.cpp | 108 ++++++++++++++++++++++++++++------------ tests/testthat/test-mread.R | 15 +++++ 21 files changed, 268 insertions(+), 89 deletions(-)
Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost
algorithm and Friedman's gradient boosting machine. Includes regression
methods for least squares, absolute loss, t-distribution loss, quantile
regression, logistic, multinomial logistic, Poisson, Cox proportional hazards
partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and
Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Newer version available at github.com/gbm-developers/gbm3.
Author: Greg Ridgeway [aut, cre] ,
Daniel Edwards [ctb],
Brian Kriegler [ctb],
Stefan Schroedl [ctb],
Harry Southworth [ctb],
Brandon Greenwell [ctb] ,
Bradley Boehmke [ctb] ,
Jay Cunningham [ctb],
GBM Developers [aut]
Maintainer: Greg Ridgeway <gridge@upenn.edu>
Diff between gbm versions 2.2.2 dated 2024-06-28 and 2.2.3 dated 2026-01-22
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 +++++++------ R/plot.gbm.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/gbm.pdf |binary inst/tinytest/desktop.ini |only man/plot.gbm.Rd | 2 +- 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Topological Connectivity Analysis for Numeric Data
Description: Description: Implementation of topological data analysis methods based on
graph-theoretic approaches for discovering topological structures in data.
The core algorithm constructs topological spaces from graphs following
Nada et al. (2018) <doi:10.1002/mma.4726> "New types of topological
structures via graphs".
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between topologyR versions 0.1.1 dated 2025-10-03 and 0.1.2 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Create and Manage Todolist using 'Todoist.com' API
Description: Allows you to interact with the API of the "Todoist"
platform. 'Todoist' <https://www.todoist.com/> provides an online task
manager service for teams.
Author: Cervan Girard [cre, aut] ,
Vincent Guyader [aut] ,
ThinkR [cph, fnd]
Maintainer: Cervan Girard <cervan@thinkr.fr>
Diff between rtodoist versions 0.1.0 dated 2020-05-14 and 0.2.0 dated 2026-01-22
rtodoist-0.1.0/rtodoist/R/form_presta.R |only rtodoist-0.1.0/rtodoist/man/add_task_in_project.Rd |only rtodoist-0.1.0/rtodoist/man/get_all.Rd |only rtodoist-0.1.0/rtodoist/man/get_id_project.Rd |only rtodoist-0.1.0/rtodoist/man/get_projects.Rd |only rtodoist-0.1.0/rtodoist/man/get_user_id.Rd |only rtodoist-0.1.0/rtodoist/man/get_users.Rd |only rtodoist-0.1.0/rtodoist/man/init_project.Rd |only rtodoist-0.2.0/rtodoist/DESCRIPTION | 49 rtodoist-0.2.0/rtodoist/MD5 | 75 - rtodoist-0.2.0/rtodoist/NAMESPACE | 46 rtodoist-0.2.0/rtodoist/R/all_objects.R | 70 - rtodoist-0.2.0/rtodoist/R/clean_tools.R |only rtodoist-0.2.0/rtodoist/R/open_todoist_website.R | 34 rtodoist-0.2.0/rtodoist/R/projects.R | 67 rtodoist-0.2.0/rtodoist/R/section.R |only rtodoist-0.2.0/rtodoist/R/tasks.R | 449 ++++-- rtodoist-0.2.0/rtodoist/R/todoist-package.R | 1 rtodoist-0.2.0/rtodoist/R/users.R | 200 ++ rtodoist-0.2.0/rtodoist/R/utils-pipe.R | 6 rtodoist-0.2.0/rtodoist/R/utils.R | 32 rtodoist-0.2.0/rtodoist/R/zzz.R | 2 rtodoist-0.2.0/rtodoist/README.md | 87 - rtodoist-0.2.0/rtodoist/build/vignette.rds |binary rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.R | 105 - rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.Rmd | 72 - rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.html | 823 ++++++------ rtodoist-0.2.0/rtodoist/man/add_project.Rd | 4 rtodoist-0.2.0/rtodoist/man/add_responsible_to_task.Rd | 18 rtodoist-0.2.0/rtodoist/man/add_section.Rd |only rtodoist-0.2.0/rtodoist/man/add_tasks_in_project.Rd | 50 rtodoist-0.2.0/rtodoist/man/add_tasks_in_project_from_df.Rd |only rtodoist-0.2.0/rtodoist/man/add_user_in_project.Rd | 11 rtodoist-0.2.0/rtodoist/man/add_users_in_project.Rd | 16 rtodoist-0.2.0/rtodoist/man/call_api.Rd | 10 rtodoist-0.2.0/rtodoist/man/call_api_project_data.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_data.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_projects.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_users.Rd |only rtodoist-0.2.0/rtodoist/man/get_project_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_section_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_tasks.Rd | 2 rtodoist-0.2.0/rtodoist/man/get_tasks_of_project.Rd |only rtodoist-0.2.0/rtodoist/man/get_users_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_users_in_project.Rd |only rtodoist-0.2.0/rtodoist/man/open_todoist_website_profile.Rd | 2 rtodoist-0.2.0/rtodoist/man/pipe.Rd | 9 rtodoist-0.2.0/rtodoist/man/rtodoist-package.Rd | 3 rtodoist-0.2.0/rtodoist/vignettes/how_it_works.Rmd | 72 - 49 files changed, 1463 insertions(+), 852 deletions(-)
Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification
(IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are
available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>)
simplified and advanced endpoints to easily download the data in a clean and
tidy format.
Author: Giulia Martini [aut, cre, cph]
Maintainer: Giulia Martini <giulia.martini@un.org>
Diff between ripc versions 0.3.2 dated 2026-01-10 and 1.0.0 dated 2026-01-22
DESCRIPTION | 9 +- MD5 | 17 ++-- NEWS.md | 4 + R/create_areas_df.R | 172 +++++++++++++++++++++---------------------- R/create_base_df.R | 200 +++++++++++++++++++++++++-------------------------- R/create_groups_df.R | 76 +++++++++---------- R/extract_dates.R | 78 +++++++++---------- R/null_converter.R | 50 ++++++------ R/population_utils.R | 3 tests |only 10 files changed, 309 insertions(+), 300 deletions(-)
Title: AI Coding Agent for 'RStudio'
Description: Provides an 'RStudio' extension with a chat interface for an AI coding agent to help
users with R programming tasks.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Diff between myownrobs versions 0.1.0 dated 2025-09-30 and 1.0.0 dated 2026-01-22
myownrobs-0.1.0/myownrobs/R/execute_llm_tools.R |only myownrobs-0.1.0/myownrobs/R/llm_commands.R |only myownrobs-0.1.0/myownrobs/R/myownrobs-package.R |only myownrobs-0.1.0/myownrobs/R/parse_agent_response.R |only myownrobs-0.1.0/myownrobs/R/send_prompt.R |only myownrobs-0.1.0/myownrobs/man/execute_llm_tools.Rd |only myownrobs-0.1.0/myownrobs/man/parse_agent_response.Rd |only myownrobs-0.1.0/myownrobs/man/save_api_key.Rd |only myownrobs-0.1.0/myownrobs/man/send_prompt.Rd |only myownrobs-0.1.0/myownrobs/man/send_prompt_async.Rd |only myownrobs-0.1.0/myownrobs/man/validate_command_args.Rd |only myownrobs-0.1.0/myownrobs/tests/testthat/test-execute_llm_tools.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-llm_commands.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-parse_agent_response.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-send_prompt.R |only myownrobs-1.0.0/myownrobs/DESCRIPTION | 10 myownrobs-1.0.0/myownrobs/MD5 | 118 +++-- myownrobs-1.0.0/myownrobs/NAMESPACE | 29 - myownrobs-1.0.0/myownrobs/R/ai_tool_create_new_file.R | 32 - myownrobs-1.0.0/myownrobs/R/ai_tool_edit_existing_file.R | 36 - myownrobs-1.0.0/myownrobs/R/ai_tool_fetch_url_content.R | 26 - myownrobs-1.0.0/myownrobs/R/ai_tool_file_glob_search.R | 25 - myownrobs-1.0.0/myownrobs/R/ai_tool_grep_search.R | 29 - myownrobs-1.0.0/myownrobs/R/ai_tool_ls_tool.R | 24 - myownrobs-1.0.0/myownrobs/R/ai_tool_read_currently_open_file.R | 21 - myownrobs-1.0.0/myownrobs/R/ai_tool_read_file.R | 27 - myownrobs-1.0.0/myownrobs/R/ai_tool_run_r_command.R | 28 - myownrobs-1.0.0/myownrobs/R/ai_tool_search_and_replace_in_file.R | 61 +- myownrobs-1.0.0/myownrobs/R/ai_tool_search_web.R | 26 - myownrobs-1.0.0/myownrobs/R/config.R | 2 myownrobs-1.0.0/myownrobs/R/configure_provider.R |only myownrobs-1.0.0/myownrobs/R/get_api_key.R | 11 myownrobs-1.0.0/myownrobs/R/get_available_models.R |only myownrobs-1.0.0/myownrobs/R/get_chat_instance.R |only myownrobs-1.0.0/myownrobs/R/get_llm_tools.R |only myownrobs-1.0.0/myownrobs/R/myownrobs.R | 206 +++------- myownrobs-1.0.0/myownrobs/R/settings_module.R | 18 myownrobs-1.0.0/myownrobs/R/turns.R |only myownrobs-1.0.0/myownrobs/R/validate_credentials.R | 72 --- myownrobs-1.0.0/myownrobs/R/validate_policy_acceptance.R | 4 myownrobs-1.0.0/myownrobs/README.md | 63 ++- myownrobs-1.0.0/myownrobs/inst/app/style.css | 2 myownrobs-1.0.0/myownrobs/inst/policy.yaml | 8 myownrobs-1.0.0/myownrobs/man/configure_provider.Rd |only myownrobs-1.0.0/myownrobs/man/content_to_ui.Rd |only myownrobs-1.0.0/myownrobs/man/get_api_key.Rd | 2 myownrobs-1.0.0/myownrobs/man/get_available_models.Rd |only myownrobs-1.0.0/myownrobs/man/get_chat_instance.Rd |only myownrobs-1.0.0/myownrobs/man/get_ellmer_models.Rd |only myownrobs-1.0.0/myownrobs/man/get_llm_tools.Rd |only myownrobs-1.0.0/myownrobs/man/load_turns.Rd |only myownrobs-1.0.0/myownrobs/man/models_deepseek.Rd |only myownrobs-1.0.0/myownrobs/man/myownrobs.Rd | 13 myownrobs-1.0.0/myownrobs/man/myownrobs_server.Rd | 7 myownrobs-1.0.0/myownrobs/man/myownrobs_ui.Rd | 5 myownrobs-1.0.0/myownrobs/man/nice_names.Rd |only myownrobs-1.0.0/myownrobs/man/save_turns.Rd |only myownrobs-1.0.0/myownrobs/man/set_config.Rd | 2 myownrobs-1.0.0/myownrobs/man/turns_to_ui.Rd |only myownrobs-1.0.0/myownrobs/man/validate_credentials.Rd | 7 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_create_new_file.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_edit_existing_file.R | 8 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_fetch_url_content.R | 16 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_file_glob_search.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_grep_search.R | 8 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_ls_tool.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_read_currently_open_file.R | 4 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_read_file.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_run_r_command.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_search_and_replace_in_file.R | 55 +- myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_search_web.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-configure_provider.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_api_key.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_available_models.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_chat_instance.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_llm_tools.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-myownrobs.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-turns.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-validate_credentials.R | 109 ----- 79 files changed, 478 insertions(+), 672 deletions(-)
Title: Adverse Event Enrichment Tests
Description: We extend existing gene enrichment tests to perform adverse
event enrichment analysis. Unlike the continuous gene expression data,
adverse event data are counts. Therefore, adverse event data has many zeros
and ties. We propose two enrichment tests. One is a modified Fisher's exact
test based on pre-selected significant adverse events, while the other is
based on a modified Kolmogorov-Smirnov statistic. We add Covariate
adjustment to improve the analysis."Adverse event enrichment tests using
VAERS" Shuoran Li, Lili Zhao (2020) <doi:10.48550/arXiv.2007.02266>.
Author: Shuoran Li [aut],
Hongfan Chen [aut],
Lili Zhao [aut],
Michael Kleinsasser [aut, cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between AEenrich versions 1.1.0 dated 2021-11-01 and 1.1.1 dated 2026-01-22
DESCRIPTION | 10 - MD5 | 23 +-- R/count_cases.R | 351 +++++++++++++++++++++++------------------------- R/data.R | 81 +++++------ R/enrich.R | 275 ++++++++++++++++++------------------- R/odds_ratio.R | 8 - build |only man/AEenrich-package.Rd | 43 +---- man/count_cases.Rd | 2 man/covid1.Rd | 17 +- man/covid2.Rd | 19 +- man/enrich.Rd | 6 man/group.Rd | 13 - 13 files changed, 410 insertions(+), 438 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-20 dated 2025-10-14 and 1.2-21 dated 2026-01-22
ChangeLog | 34 -- DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 30 +- R/emmeans-support.r |only R/plot.r | 17 - R/predict.scam.R | 10 R/scam.r | 45 +-- R/summary.scam.R | 571 ++++++++++++++++++++--------------------- R/uni.smooth.const-with-po.r | 93 +++++- R/vis.scam.r | 2 R/zzz.R |only build/partial.rdb |binary man/linear.functional.terms.Rd | 6 man/scam.Rd | 2 man/scam.emmeans.support.Rd |only man/vcov.scam.Rd |only 17 files changed, 445 insertions(+), 403 deletions(-)
Title: Parametric Time Warping
Description: Parametric Time Warping aligns patterns, i.e., it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation). Both
warping of peak profiles and of peak lists are supported. A
vignette for the latter is contained in the inst/doc directory
of the source package - the vignette source can be found on
the package github site. See `citation("ptw")` for more details.
Author: Jan Gerretzen [ctb],
Paul Eilers [aut],
Hans Wouters [ctb],
Tom Bloemberg [aut],
Ron Wehrens [aut, cre]
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ptw versions 1.9-16 dated 2022-01-19 and 1.9-17 dated 2026-01-22
ptw-1.9-16/ptw/build |only ptw-1.9-17/ptw/DESCRIPTION | 11 ++--- ptw-1.9-17/ptw/MD5 | 14 +++--- ptw-1.9-17/ptw/R/ptw-package.R |only ptw-1.9-17/ptw/R/summary.ptw.R | 6 +- ptw-1.9-17/ptw/inst/CITATION | 74 ++++++++++++++++------------------ ptw-1.9-17/ptw/man/mzchannel2pktab.Rd | 4 - ptw-1.9-17/ptw/man/ptw-package.Rd | 50 +++++++++------------- ptw-1.9-17/ptw/man/ptw.Rd | 3 - 9 files changed, 76 insertions(+), 86 deletions(-)
Title: Less Code with More Comprehensive Results
Description: Each function replaces multiple standard R functions. For example,
two function calls, Read() and CountAll(), generate summary statistics for
all variables in the data frame, plus histograms and bar charts. Other
functions provide data aggregation via pivot tables; comprehensive
regression, ANOVA, and t-test; visualizations including integrated
Violin/Box/Scatter plot for a numerical variable, bar chart, histogram,
box plot, density curves, calibrated power curve; reading multiple data
formats with the same call; variable labels; time series with aggregation
and forecasting; color themes; and Trellis (facet) graphics. Also includes
a confirmatory factor analysis of multiple-indicator measurement models,
pedagogical routines for data simulation (e.g., Central Limit Theorem),
generation and rendering of regression instructions for interpretative output,
and both interactive construction of visualizations and interactive
visualizations with plotly.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.5 dated 2025-12-11 and 4.5.1 dated 2026-01-22
DESCRIPTION | 6 MD5 | 53 - NEWS.md | 57 + R/Chart.R | 135 +++ R/X.R | 117 -- R/XY.R | 271 ++++-- R/dn.main.R | 6 R/dn.plotly.R | 40 R/hier.plotly.R | 397 +++++---- R/param.VBS.R | 2 R/plt.main.R | 105 +- R/plt.plotly.R | 167 +++- R/plt.time.R | 145 +++ R/plt.time_truncate_groups.R |only R/plt.txt.R | 2 R/radar.plotly.R | 18 R/style.R | 2 R/zzz.R | 58 - R/zzz_plotly.R | 101 +- R/zzz_ts.R | 15 data/dataStockPrice.rda |binary inst/doc/intro.Rmd | 2 inst/doc/intro.html | 1775 ++++++++++++++++++++----------------------- man/Chart.Rd | 7 man/Flows.Rd | 20 man/X.Rd | 10 man/XY.Rd | 30 vignettes/intro.Rmd | 2 28 files changed, 1998 insertions(+), 1545 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-4 dated 2025-07-03 and 1.2-5 dated 2026-01-22
fitdistrplus-1.2-4/fitdistrplus/tests/t-cvg-algo.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-fitbench.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-getparam.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-init-actuar.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-manageparam.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-mledist-cvg-NelderMead.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-prefit.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-qmedist-cvg-NelderMead.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startfixarg-overall.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-starting-value-scale-rate.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-fellerpareto-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-inv-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-invBurr-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-invtrgamma-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-othercont-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-trgamma-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-zeromod-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-zerotrunc-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-mmedist-vcov.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-npmle.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-npsurv-mainfunction.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-testdensity.R |only fitdistrplus-1.2-5/fitdistrplus/DESCRIPTION | 6 fitdistrplus-1.2-5/fitdistrplus/MD5 | 149 +- fitdistrplus-1.2-5/fitdistrplus/R/fitdist.R | 16 fitdistrplus-1.2-5/fitdistrplus/build/partial.rdb |binary fitdistrplus-1.2-5/fitdistrplus/build/vignette.rds |binary fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.R | 11 fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.Rmd | 11 fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.html | 389 +++--- fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.R | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.html | 580 +++++----- fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.R | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.html | 51 fitdistrplus-1.2-5/fitdistrplus/inst/doc/starting-values.html | 4 fitdistrplus-1.2-5/fitdistrplus/man/CIcdfplot.Rd | 3 fitdistrplus-1.2-5/fitdistrplus/man/bootdist.Rd | 1 fitdistrplus-1.2-5/fitdistrplus/man/bootdistcens.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/descdist.Rd | 3 fitdistrplus-1.2-5/fitdistrplus/man/fitdist.Rd | 27 fitdistrplus-1.2-5/fitdistrplus/man/gofstat.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/logLik-plot.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/logLik-surface.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/mgedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/mledist.Rd | 5 fitdistrplus-1.2-5/fitdistrplus/man/mmedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/msedist.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/plotdist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/prefit.Rd | 1 fitdistrplus-1.2-5/fitdistrplus/man/qmedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-CIcdfplot.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-bootdist.R | 6 fitdistrplus-1.2-5/fitdistrplus/tests/t-bootdistcens.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-cdfcomp.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-denscomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-descdist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-customoptim.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-hessianpb.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-test-arguments.R | 10 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist.R | 9 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdistcens.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-gen-max-spacing-estim.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-gofstat.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-llplot.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-lnL-surf.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mgedist.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-asymptotic-vcov.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-nocens.R | 15 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-paramsupport.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mmedist-asymptotic-vcov.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mmedist.R | 6 fitdistrplus-1.2-5/fitdistrplus/tests/t-msedist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-parallel.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-plotdist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-ppcomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-qme-discrete.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-qmedist.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-qqcomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-quantiledist.R | 1 fitdistrplus-1.2-5/fitdistrplus/tests/t-weird-ppcomp-cens.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-weird-qqcomp-cens.R | 2 fitdistrplus-1.2-5/fitdistrplus/vignettes/FAQ.Rmd | 11 fitdistrplus-1.2-5/fitdistrplus/vignettes/Optimalgo.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/vignettes/fitdistrplus_vignette.Rmd | 2 87 files changed, 688 insertions(+), 737 deletions(-)
Title: Dose-Response Network Meta-Analysis in a Frequentist Way
Description: A set of functions providing the implementation of the network meta-analysis model with dose-response relationships, predicted values of the fitted model and dose-response plots in a frequentist way.
Author: Maria Petropoulou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Maria Petropoulou <m.petropoulou.a@gmail.com>
Diff between netdose versions 0.7-3 dated 2026-01-13 and 0.7-4 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 10 +++++++++- R/netdose.R | 6 +++--- man/netdose.Rd | 6 +++--- 5 files changed, 23 insertions(+), 15 deletions(-)
Title: Analysis of Korean National Forest Inventory Database
Description: Understanding the current status of forest resources is essential for monitoring changes
in forest ecosystems and generating related statistics. In South Korea, the National Forest
Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items,
including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI
as the primary data for research, such as biomass estimation or analyzing the importance value of
each species over time and space, depending on the research purpose. However, the large volume
of accumulated forest survey data from across the country can make it challenging to manage and
utilize such a vast dataset. To address this issue, we developed an R package that efficiently
handles large-scale NFI data across time and space. The package offers a comprehensive
workflow for NFI data analysis. It starts with data processing, where read_nfi() function
reconstructs NFI data according to the researcher's needs while [...truncated...]
Author: Sinyoung Park [aut, cre] ,
Wonhee Cho [aut, ctb] ,
Inyoo Kim [aut, ctb] ,
Wontaek Lim [aut, ctb] ,
Dongwook W. Ko [aut, ths]
Maintainer: Sinyoung Park <youngsin0306@kookmin.ac.kr>
Diff between knfi versions 1.0.1.9 dated 2024-12-03 and 1.0.2 dated 2026-01-22
DESCRIPTION | 18 ++++++++++-------- MD5 | 44 ++++++++++++++++++++++++-------------------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/biomass_nfi.R | 4 +++- R/cwd_biomass_nfi.R | 3 ++- R/diversity_nfi.R | 6 +++++- R/info_nfi.R | 1 - R/iv_nfi.R | 3 ++- R/read_nfi.R | 4 ++-- R/summary_nfi.R | 3 ++- R/sysdata.rda |binary R/tsvis_nfi.R | 9 +++++---- build/vignette.rds |binary inst/doc/Published.R |only inst/doc/Published.Rmd |only inst/doc/Published.html |only man/biomass_nfi.Rd | 2 +- man/cwd_biomass_nfi.Rd | 2 +- man/diversity_nfi.Rd | 2 +- man/iv_nfi.Rd | 2 +- man/read_nfi.Rd | 4 ++-- man/summary_nfi.Rd | 2 +- man/tsvis_nfi.Rd | 4 ++-- vignettes/Published.Rmd |only 25 files changed, 68 insertions(+), 50 deletions(-)
Title: R Client Package for Circle CI
Description: Tools for interacting with the 'Circle CI' API
(<https://circleci.com/docs/api/v2/>). Besides executing common tasks
such as querying build logs and restarting builds, this package also
helps setting up permissions to deploy from builds.
Author: David Munoz Tord [cre, ctb],
Patrick Schratz [aut] ,
Max Joseph [rev] ,
Sharla Gelfand [rev]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between circle versions 0.7.3 dated 2024-07-31 and 0.7.4 dated 2026-01-22
DESCRIPTION | 14 MD5 | 130 - NAMESPACE | 66 NEWS.md | 21 R/auth.R | 212 +- R/builds.R | 352 +-- R/checkout-key.R | 396 +-- R/circle-package.R | 62 R/circle.R | 152 - R/env-var.R | 268 +- R/format-builds-helpers.R | 316 +-- R/general.R | 380 +-- R/helpers-github.R | 108 - R/use-circle-deploy.R | 138 - README.md | 134 - build/vignette.rds |binary inst/doc/advanced.R |only inst/doc/advanced.Rmd |only inst/doc/advanced.html |only inst/doc/circle.R | 28 inst/doc/circle.Rmd | 308 +-- inst/doc/circle.html | 1011 ++++----- inst/doc/tic.R | 13 inst/doc/tic.Rmd | 275 +- inst/doc/tic.html | 975 ++++----- man/browse_circle_token.Rd | 102 man/builds.Rd | 182 - man/checkout_key.Rd | 220 +- man/circle-package.Rd | 114 - man/circle.Rd | 122 - man/edit_circle_config.Rd | 28 man/enable_repo.Rd | 94 man/env_var.Rd | 166 - man/get_build_artifacts.Rd | 96 man/get_circle_user.Rd | 52 man/github_info.Rd | 62 man/list_projects.Rd | 84 man/new_build.Rd | 102 man/use_circle_deploy.Rd | 98 tests/fixtures/create_checkout_key().yml | 80 tests/fixtures/delete_checkout_key().yml | 166 - tests/fixtures/delete_env_var().yml | 78 tests/fixtures/enable_repo().yml | 78 tests/fixtures/get_build_artifacts().yml | 2662 +++++++++++++------------- tests/fixtures/get_circle_user().yml | 82 tests/fixtures/get_env_vars().yml | 82 tests/fixtures/get_jobs().yml | 2582 ++++++++++++------------- tests/fixtures/has_checkout_key().yml | 86 tests/fixtures/list_projects().yml | 82 tests/fixtures/new_build().yml | 150 - tests/fixtures/retry_workflow().yml | 1856 +++++++++--------- tests/fixtures/s3-print-circle_collection.yml | 1782 ++++++++--------- tests/fixtures/s3-print-circle_job.yml | 2662 +++++++++++++------------- tests/fixtures/s3-print-circle_pipeline.yml | 100 tests/fixtures/s3-print-circle_workflow.yml | 1782 ++++++++--------- tests/fixtures/set_env_var().yml | 76 tests/testthat.R | 8 tests/testthat/helper-circle.R | 30 tests/testthat/test-1-builds.R | 106 - tests/testthat/test-2-print.R | 142 - tests/testthat/test-auth.R | 28 tests/testthat/test-checkout-keys.R | 84 tests/testthat/test-env-vars.R | 98 tests/testthat/test-general.R | 134 - tests/testthat/test-helpers-github.R | 46 vignettes/advanced.Rmd |only vignettes/circle.Rmd | 308 +-- vignettes/tic.Rmd | 275 +- 68 files changed, 11293 insertions(+), 11233 deletions(-)
Title: Download Infectious Disease Data from 'SurvStat' (Robert Koch
Institute)
Description: Provides an interface to the 'SurvStat' web service from the
Robert Koch Institute (<https://tools.rki.de/SurvStat/SurvStatWebService.svc>)
allowing downloads of disease time series stratified
by pathogen type and subtype, age, and geography from notifiable disease
reports in Germany.
Author: Robert Challen [aut, cre] ,
Bristol Vaccine Centre [fnd, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between rsurvstat versions 0.1.2 dated 2026-01-17 and 0.1.3 dated 2026-01-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/sysdata.rda |binary data/CountyKey71Map.rda |binary 5 files changed, 12 insertions(+), 7 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 7.2.1-3 dated 2025-04-10 and 7.2.1-4 dated 2026-01-22
r2sundials-7.2.1-3/r2sundials/NEWS |only r2sundials-7.2.1-3/r2sundials/R/translate.R |only r2sundials-7.2.1-4/r2sundials/DESCRIPTION | 10 +++++----- r2sundials-7.2.1-4/r2sundials/MD5 | 17 ++++++++--------- r2sundials-7.2.1-4/r2sundials/NEWS.md |only r2sundials-7.2.1-4/r2sundials/R/RcppExports.R | 3 --- r2sundials-7.2.1-4/r2sundials/build/partial.rdb |binary r2sundials-7.2.1-4/r2sundials/inst/COPYRIGHTS | 2 +- r2sundials-7.2.1-4/r2sundials/man/r2cvodes.Rd | 5 ----- r2sundials-7.2.1-4/r2sundials/src/lib/readme.txt | 2 +- r2sundials-7.2.1-4/r2sundials/src/r2sundials.cpp | 3 --- 11 files changed, 15 insertions(+), 27 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens [aut, cre],
Johannes Kruisselbrink [aut]
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 3.0.12 dated 2023-06-09 and 3.0.13 dated 2026-01-22
kohonen-3.0.12/kohonen/inst/doc/kohonen-manual_2007.pdf |only kohonen-3.0.13/kohonen/DESCRIPTION | 17 ++++++++-- kohonen-3.0.13/kohonen/MD5 | 13 +++----- kohonen-3.0.13/kohonen/NEWS | 13 +++++++- kohonen-3.0.13/kohonen/R/classvec2classmat.R | 5 ++- kohonen-3.0.13/kohonen/R/plot.kohonen.R | 9 ++++- kohonen-3.0.13/kohonen/R/predict.kohonen.R | 25 ++++++++++------ kohonen-3.0.13/kohonen/build/partial.rdb |binary 8 files changed, 58 insertions(+), 24 deletions(-)
Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <doi:10.48550/arXiv.2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <doi:10.48550/arXiv.2209.03218>.
Author: Robert Adamek [cre, aut],
Stephan Smeekes [aut],
Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>
Diff between desla versions 0.3.0 dated 2023-06-29 and 0.3.1 dated 2026-01-22
DESCRIPTION | 9 - MD5 | 52 ++++++++- NEWS.md | 6 + README.md | 1 build/partial.rdb |binary inst/unit_test_reference_files |only inst/unit_tests.R |only src/rcpp_functions.cpp | 216 ++++++++++++++++++++--------------------- 8 files changed, 167 insertions(+), 117 deletions(-)
Title: Causal Graph Interface
Description: Create, query, and modify causal graphs. 'caugi' (Causal Graph
Interface) is a causality-first, high performance graph package that
provides a simple interface to build, structure, and examine causal
relationships.
Author: Frederik Fabricius-Bjerre [aut, cre, cph],
Johan Larsson [aut] ,
Michael Sachs [aut]
Maintainer: Frederik Fabricius-Bjerre <frederik@fabriciusbjerre.dk>
Diff between caugi versions 0.3.1 dated 2025-12-04 and 1.0.0 dated 2026-01-22
caugi-0.3.1/caugi/inst/examples |only caugi-0.3.1/caugi/src/rust/src/graph/dag.rs |only caugi-0.3.1/caugi/src/rust/src/graph/pdag.rs |only caugi-0.3.1/caugi/tools/coding-helpers.R |only caugi-1.0.0/caugi/DESCRIPTION | 25 caugi-1.0.0/caugi/MD5 | 280 caugi-1.0.0/caugi/NAMESPACE | 42 caugi-1.0.0/caugi/NEWS.md | 133 caugi-1.0.0/caugi/R/DSL-parser.R | 44 caugi-1.0.0/caugi/R/aaa-env.R | 22 caugi-1.0.0/caugi/R/adjustment.R | 272 caugi-1.0.0/caugi/R/all-classes.R |only caugi-1.0.0/caugi/R/as_caugi.R | 229 caugi-1.0.0/caugi/R/caugi-package.R | 1 caugi-1.0.0/caugi/R/caugi.R | 171 caugi-1.0.0/caugi/R/caugi_to.R | 56 caugi-1.0.0/caugi/R/edge_operators.R | 4 caugi-1.0.0/caugi/R/extendr-wrappers.R | 44 caugi-1.0.0/caugi/R/format-caugi.R |only caugi-1.0.0/caugi/R/format-dot.R |only caugi-1.0.0/caugi/R/format-graphml.R |only caugi-1.0.0/caugi/R/format-mermaid.R |only caugi-1.0.0/caugi/R/methods.R | 28 caugi-1.0.0/caugi/R/metrics.R | 11 caugi-1.0.0/caugi/R/operations.R | 431 caugi-1.0.0/caugi/R/options.R |only caugi-1.0.0/caugi/R/plot.R |only caugi-1.0.0/caugi/R/queries.R | 573 caugi-1.0.0/caugi/R/registry.R | 37 caugi-1.0.0/caugi/R/simulation.R | 176 caugi-1.0.0/caugi/R/verbs.R | 140 caugi-1.0.0/caugi/R/zzz.R | 1 caugi-1.0.0/caugi/README.md | 42 caugi-1.0.0/caugi/build/partial.rdb |only caugi-1.0.0/caugi/build/vignette.rds |binary caugi-1.0.0/caugi/inst/WORDLIST |only caugi-1.0.0/caugi/inst/doc/get_started.html | 8 caugi-1.0.0/caugi/inst/doc/package_use.html | 4 caugi-1.0.0/caugi/inst/doc/serialization.R |only caugi-1.0.0/caugi/inst/doc/serialization.Rmd |only caugi-1.0.0/caugi/inst/doc/serialization.html |only caugi-1.0.0/caugi/inst/doc/visualization.R |only caugi-1.0.0/caugi/inst/doc/visualization.Rmd |only caugi-1.0.0/caugi/inst/doc/visualization.html |only caugi-1.0.0/caugi/man/add-caugi_plot-caugi_plot.Rd |only caugi-1.0.0/caugi/man/adjustment_set.Rd | 2 caugi-1.0.0/caugi/man/all_adjustment_sets_admg.Rd |only 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More information about vald.extractor at CRAN
Permanent link
Title: Extra Functions for 'gtsummary' Table Styling
Description: Provides additional convenience functions for 'gtsummary'
(Sjoberg et al. (2021) <doi:10.32614/RJ-2021-053>) & 'gt' tables,
including automatic variable labeling from dictionaries, standardized
missing value display, and consistent formatting helpers for streamlined
table styling workflows.
Author: Kyle Grealis [aut, cre] ,
Raymond Balise [ctb] ,
Daniel Maya [ctb]
Maintainer: Kyle Grealis <kyleGrealis@proton.me>
Diff between sumExtras versions 0.2.0 dated 2026-01-19 and 0.3.0 dated 2026-01-22
DESCRIPTION | 16 MD5 | 18 NEWS.md | 14 R/clean_table.R | 13 R/extras.R | 54 inst/doc/labeling.html | 1652 +++++++++++++-------------- inst/doc/styling.html | 2530 +++++++++++++++++++++--------------------- inst/doc/sumExtras-intro.html | 1210 ++++++++++---------- man/extras.Rd | 22 man/sumExtras-package.Rd | 1 10 files changed, 2808 insertions(+), 2722 deletions(-)
Title: Causal Inference in Spatiotemporal Event Data
Description: Implementation of Matched Wake Analysis (mwa) for studying causal relationships in spatiotemporal event data, introduced by Schutte and Donnay (2014) <doi:10.1016/j.polgeo.2014.03.001>.
Author: Sebastian Schutte [aut],
Karsten Donnay [aut, cre]
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between mwa versions 0.5.0 dated 2025-09-29 and 0.5.1 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/mwa.R | 19 +------------------ 4 files changed, 12 insertions(+), 25 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-07 1.5.0
2025-09-30 1.4.0
2023-03-21 1.3
2022-09-04 1.2
2021-04-27 1.1
Title: Simulate Survival Data
Description: Simulate survival times from standard parametric survival
distributions (exponential, Weibull, Gompertz), 2-component mixture
distributions, or a user-defined hazard, log hazard, cumulative hazard,
or log cumulative hazard function. Baseline covariates can be included
under a proportional hazards assumption.
Time dependent effects (i.e. non-proportional hazards) can be included by
interacting covariates with linear time or a user-defined function of time.
Clustered event times are also accommodated.
The 2-component mixture distributions can allow for a variety of flexible
baseline hazard functions reflecting those seen in practice.
If the user wishes to provide a user-defined
hazard or log hazard function then this is possible, and the resulting
cumulative hazard function does not need to have a closed-form solution.
For details see the supporting paper <doi:10.18637/jss.v097.i03>.
Note that this package is modelled on the 'survsim' package available in
the 'Stata' software (see [...truncated...]
Author: Sam Brilleman [cre, aut, cph],
Alessandro Gasparini [ctb]
Maintainer: Sam Brilleman <sam.brilleman@gmail.com>
Diff between simsurv versions 1.0.0 dated 2021-01-13 and 1.0.1 dated 2026-01-22
DESCRIPTION | 12 LICENSE | 1348 ++++++++--------- MD5 | 58 NAMESPACE | 8 NEWS.md | 145 - R/brcancer.R | 52 R/simsurv.R | 2422 +++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 42 inst/doc/simsurv_technical.R | 6 inst/doc/simsurv_technical.Rmd | 574 +++---- inst/doc/simsurv_technical.html | 981 ++++++------ inst/doc/simsurv_usage.R | 474 +++--- inst/doc/simsurv_usage.Rmd | 798 +++++----- inst/doc/simsurv_usage.html | 1369 ++++++++--------- man/simsurv.Rd | 2 tests/testthat.R | 8 tests/testthat/helpers/check_bias.R | 24 tests/testthat/helpers/is_exponential.R | 6 tests/testthat/helpers/is_gompertz.R | 6 tests/testthat/helpers/is_weibull.R | 6 tests/testthat/helpers/recover_betas.R | 12 tests/testthat/helpers/recover_gammas.R | 18 tests/testthat/helpers/recover_lambdas.R | 26 tests/testthat/helpers/recover_params.R | 32 tests/testthat/helpers/sim_run.R | 66 tests/testthat/test_simsurv.R | 156 - vignettes/simsurv_technical.Rmd | 574 +++---- vignettes/simsurv_usage.Rmd | 798 +++++----- 30 files changed, 5012 insertions(+), 5011 deletions(-)
Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on
an additive model where non-linear trends are fit with yearly, weekly, and
daily seasonality, plus holiday effects. It works best with time series
that have strong seasonal effects and several seasons of historical data.
Prophet is robust to missing data and shifts in the trend, and typically
handles outliers well.
Author: Cuong Duong [cre, aut],
Sean Taylor [aut],
Ben Letham [aut]
Maintainer: Cuong Duong <cuong.duong242@gmail.com>
Diff between prophet versions 1.0 dated 2021-03-30 and 1.1.7 dated 2026-01-22
prophet-1.0/prophet/data |only prophet-1.1.7/prophet/DESCRIPTION | 24 prophet-1.1.7/prophet/MD5 | 59 prophet-1.1.7/prophet/NAMESPACE | 1 prophet-1.1.7/prophet/R/data.R | 8 prophet-1.1.7/prophet/R/diagnostics.R | 59 prophet-1.1.7/prophet/R/plot.R | 4 prophet-1.1.7/prophet/R/prophet.R | 143 prophet-1.1.7/prophet/R/stan_backends.R |only prophet-1.1.7/prophet/R/stanmodels.R | 2 prophet-1.1.7/prophet/R/sysdata.rda |only prophet-1.1.7/prophet/R/utilities.R | 2 prophet-1.1.7/prophet/build/vignette.rds |binary prophet-1.1.7/prophet/inst/doc/quick_start.R | 4 prophet-1.1.7/prophet/inst/doc/quick_start.html | 630 ++- prophet-1.1.7/prophet/inst/stan/prophet.stan | 17 prophet-1.1.7/prophet/man/check_cmdstanr.Rd |only prophet-1.1.7/prophet/man/dot-fit.Rd |only prophet-1.1.7/prophet/man/dot-load_model.Rd |only prophet-1.1.7/prophet/man/dot-sampling.Rd |only prophet-1.1.7/prophet/man/dot-stan_args.Rd |only prophet-1.1.7/prophet/man/dyplot.prophet.Rd | 2 prophet-1.1.7/prophet/man/flat_growth_init.Rd | 2 prophet-1.1.7/prophet/man/generated_holidays.Rd | 9 prophet-1.1.7/prophet/man/get_stan_backend.Rd |only prophet-1.1.7/prophet/man/make_all_seasonality_features.Rd | 2 prophet-1.1.7/prophet/man/prophet.Rd | 28 prophet-1.1.7/prophet/man/setup_dataframe.Rd | 2 prophet-1.1.7/prophet/src/Makevars | 5 prophet-1.1.7/prophet/src/Makevars.win | 5 prophet-1.1.7/prophet/src/RcppExports.cpp | 5 prophet-1.1.7/prophet/src/stanExports_prophet.cc | 34 prophet-1.1.7/prophet/src/stanExports_prophet.h | 2161 +++++++------ prophet-1.1.7/prophet/tests/testthat/test_diagnostics.R | 2 prophet-1.1.7/prophet/tests/testthat/test_prophet.R | 5 35 files changed, 1929 insertions(+), 1286 deletions(-)
Title: Spatial Lag Model Trees
Description: Model-based linear model trees adjusting for spatial correlation using a
simultaneous autoregressive spatial lag, Wagner and Zeileis (2019)
<doi:10.1111/geer.12146>.
Author: Martin Wagner [aut] ,
Achim Zeileis [aut, cre] ,
Roger Bivand [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between lagsarlmtree versions 1.0-1 dated 2019-04-08 and 1.0-2 dated 2026-01-22
lagsarlmtree-1.0-1/lagsarlmtree/NEWS |only lagsarlmtree-1.0-2/lagsarlmtree/DESCRIPTION | 18 ++++++++++-------- lagsarlmtree-1.0-2/lagsarlmtree/MD5 | 14 +++++++------- lagsarlmtree-1.0-2/lagsarlmtree/NEWS.md |only lagsarlmtree-1.0-2/lagsarlmtree/build/partial.rdb |binary lagsarlmtree-1.0-2/lagsarlmtree/data/GrowthNUTS2.rda |binary lagsarlmtree-1.0-2/lagsarlmtree/data/WeightsNUTS2.rda |binary lagsarlmtree-1.0-2/lagsarlmtree/man/WeightsNUTS2.Rd | 7 ++++--- lagsarlmtree-1.0-2/lagsarlmtree/man/lagsarlmtree.Rd | 2 +- 9 files changed, 22 insertions(+), 19 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, and streaming responses in real-time. Supports local
inference without requiring cloud APIs or internet connectivity, ensuring complete
data privacy and control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb]
Maintainer: Pawan Rama Mali <prm@outlook.in>
This is a re-admission after prior archival of version 0.1.0 dated 2025-09-22
Diff between edgemodelr versions 0.1.0 dated 2025-09-22 and 0.1.4 dated 2026-01-22
edgemodelr-0.1.0/edgemodelr/src/r_output_redirect.h |only edgemodelr-0.1.4/edgemodelr/DESCRIPTION | 37 edgemodelr-0.1.4/edgemodelr/LICENSE | 2 edgemodelr-0.1.4/edgemodelr/MD5 | 80 edgemodelr-0.1.4/edgemodelr/NAMESPACE | 8 edgemodelr-0.1.4/edgemodelr/R/api.R | 1008 +++++++++- edgemodelr-0.1.4/edgemodelr/R/edgemodelr-package.R | 2 edgemodelr-0.1.4/edgemodelr/R/ollama.R |only edgemodelr-0.1.4/edgemodelr/R/zzz.R | 8 edgemodelr-0.1.4/edgemodelr/cleanup |only edgemodelr-0.1.4/edgemodelr/inst/CITATION |only edgemodelr-0.1.4/edgemodelr/inst/COPYRIGHTS |only edgemodelr-0.1.4/edgemodelr/inst/examples/07_modern_bslib_streaming_chat.R |only edgemodelr-0.1.4/edgemodelr/inst/examples/ollama_integration_example.R |only edgemodelr-0.1.4/edgemodelr/inst/examples/small_model_optimization_example.R |only edgemodelr-0.1.4/edgemodelr/inst/include |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_curl.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_r.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_wget.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-is_valid_gguf_file.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-robust_download.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_benchmark.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_clean_cache.Rd | 4 edgemodelr-0.1.4/edgemodelr/man/edge_download_model.Rd | 80 edgemodelr-0.1.4/edgemodelr/man/edge_download_url.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_find_gguf_models.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_find_ollama_models.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_load_ollama_model.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_small_model_config.Rd |only edgemodelr-0.1.4/edgemodelr/man/edgemodelr-package.Rd | 6 edgemodelr-0.1.4/edgemodelr/man/test_ollama_model_compatibility.Rd |only edgemodelr-0.1.4/edgemodelr/src/Makevars | 31 edgemodelr-0.1.4/edgemodelr/src/Makevars.win | 86 edgemodelr-0.1.4/edgemodelr/src/RcppExports.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/bindings.cpp | 316 ++- edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-backend-reg.cpp | 149 + edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/ggml-cpu.c | 20 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/ops.h | 10 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/unary-ops.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-opt.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-quants.c | 25 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml.c | 20 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml.h | 7 edgemodelr-0.1.4/edgemodelr/src/llama/llama-grammar.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-impl.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-impl.h | 5 edgemodelr-0.1.4/edgemodelr/src/llama/llama-model.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-quant.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/unicode.cpp | 2 edgemodelr-0.1.4/edgemodelr/tests/testthat/test-e2e-integration.R |only edgemodelr-0.1.4/edgemodelr/tests/testthat/test-model-loading.R | 24 edgemodelr-0.1.4/edgemodelr/tests/testthat/test-small-model-config.R |only edgemodelr-0.1.4/edgemodelr/tests/testthat/test-utility-functions.R |only 53 files changed, 1590 insertions(+), 354 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-09 0.15.1
2016-09-06 0.15.0
2016-02-12 0.13.10
2016-02-11 0.13.9
2015-07-29 0.13.7
2015-06-19 0.13.6
2015-03-06 0.13.4
2014-12-17 0.13.2
2014-11-21 0.13.1
2014-07-19 0.12.1
2014-06-25 0.11.0
2014-06-09 0.10.0
2014-05-28 0.9.1
2014-05-19 0.9.0
2014-03-13 0.8.1
2014-02-28 0.8
2014-02-12 0.7
2013-12-06 0.6
2013-11-11 0.5
2013-10-28 0.4
2013-08-13 0.3
2013-08-06 0.2
2013-05-09 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-04 0.1.1
2017-07-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-05 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-18 1.3.0
2017-04-08 1.2.0
2016-09-02 1.1.1
2015-10-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-20 1.2.1
2016-11-16 1.2.0
2016-11-08 1.1.0
2016-07-21 1.0.0
Title: Fitting Multivariate Bidirectional Mendelian Randomization
Networks Using Bayesian Directed Cyclic Graphical Models
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. The [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.5 dated 2025-09-29 and 0.1.0 dated 2026-01-22
MR.RGM-0.0.5/MR.RGM/src/Generate.cpp |only MR.RGM-0.0.5/MR.RGM/src/code.cpp |only MR.RGM-0.1.0/MR.RGM/DESCRIPTION | 19 MR.RGM-0.1.0/MR.RGM/MD5 | 55 MR.RGM-0.1.0/MR.RGM/NAMESPACE | 1 MR.RGM-0.1.0/MR.RGM/R/Imports.R |only MR.RGM-0.1.0/MR.RGM/R/NetworkMotif.R | 2 MR.RGM-0.1.0/MR.RGM/R/RGM.R | 1371 ++++++++-- MR.RGM-0.1.0/MR.RGM/R/RcppExports.R | 100 MR.RGM-0.1.0/MR.RGM/README.md | 382 +- MR.RGM-0.1.0/MR.RGM/inst |only MR.RGM-0.1.0/MR.RGM/man/NetworkMotif.Rd | 2 MR.RGM-0.1.0/MR.RGM/man/RGM.Rd | 221 - MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-11-1.png |binary MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-11-2.png |binary MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-12-2.png |only MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-14-1.png |only MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-8-1.png |binary MR.RGM-0.1.0/MR.RGM/src/NetworkMotif.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RcppExports.cpp | 641 ++-- 44 files changed, 2051 insertions(+), 743 deletions(-)
Title: Wavelet System Prediction
Description: The wavelet-based variance transformation method is used for system modelling and prediction. It refines predictor spectral representation using Wavelet Theory, which leads to improved model specifications and prediction accuracy. Details of methodologies used in the package can be found in Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962>, Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>, and Jiang, Z., Sharma, A., & Johnson, F. (2021) <doi:10.1016/J.JHYDROL.2021.126816>.
Author: Ze Jiang [aut, cre] ,
Md. Mamunur Rashid [aut] ,
Ashish Sharma [aut] ,
Fiona Johnson [aut]
Maintainer: Ze Jiang <ze.jiang@unsw.edu.au>
Diff between WASP versions 1.4.4 dated 2024-07-20 and 1.4.5 dated 2026-01-22
DESCRIPTION | 21 MD5 | 14 build/vignette.rds |binary data/datalist | 22 inst/doc/WASP.R | 1587 ++++++++--------- inst/doc/WASP.Rmd | 9 inst/doc/WASP.html | 4680 ++++++++++++++++++++++++++--------------------------- vignettes/WASP.Rmd | 9 8 files changed, 3172 insertions(+), 3170 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Ya-Mei Chang [ctb],
Jean-Francois Coeurjolly [ctb],
Lucia Cobo Sanchez [ctb, cph],
Ottma [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.6-0 dated 2025-11-22 and 3.7-0 dated 2026-01-22
DESCRIPTION | 18 +-- MD5 | 178 +++++++++++++++++------------------ NAMESPACE | 2 NEWS | 48 +++++++++ R/FGmultiInhom.R | 20 ++-- R/Fest.R | 6 - R/Gest.R | 7 - R/Gmulti.R | 24 ++-- R/Jest.R | 8 + R/Jinhom.R | 15 +-- R/Jmulti.R | 21 ++-- R/Kinhom.R | 6 - R/Kmulti.R | 27 ++--- R/Kmulti.inhom.R | 16 +-- R/Ksector.R | 6 - R/bw.CvL.R | 2 R/bw.CvL.adaptive.R | 2 R/bw.diggle.R | 2 R/cdftest.R | 2 R/clarkevans.R | 2 R/clusterset.R | 4 R/compileCDF.R | 2 R/exactppm.R | 6 + R/fasp.R | 16 ++- R/hasenvelope.R | 2 R/laslett.R | 2 R/localpcf.R | 2 R/markcorr.R | 194 +++++++++++++++++++++++++-------------- R/metriccontact.R | 6 - R/nncount.R | 2 R/pairs.im.R | 2 R/pcf.R | 6 - R/pcfinhom.R | 6 - R/pcfmulti.R | 14 +- R/pcfmulti.inhom.R | 14 +- R/plot.fasp.R | 145 ++++++++++++++++------------- R/plot.fv.R | 12 +- R/rho2hat.R | 2 R/rhohat.R | 2 R/smoothfun.R | 2 R/spatialcdf.R | 2 R/ssf.R | 2 R/tolcon.R | 2 R/transect.R | 2 inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Emark.Rd | 8 + man/Fest.Rd | 6 + man/Finhom.Rd | 6 + man/FmultiInhom.Rd | 8 + man/Gcross.Rd | 7 + man/Gcross.inhom.Rd | 6 + man/Gdot.Rd | 7 + man/Gdot.inhom.Rd | 7 + man/Gest.Rd | 6 + man/Ginhom.Rd | 6 + man/Gmulti.Rd | 6 + man/GmultiInhom.Rd | 8 + man/Jcross.Rd | 6 + man/Jdot.Rd | 6 + man/Jest.Rd | 6 + man/Jinhom.Rd | 6 + man/Jmulti.Rd | 8 + man/Kcross.Rd | 9 + man/Kcross.inhom.Rd | 7 + man/Kdot.Rd | 8 + man/Kdot.inhom.Rd | 7 + man/Kinhom.Rd | 5 - man/Kmark.Rd | 6 + man/Kmulti.inhom.Rd | 6 + man/Ksector.Rd | 6 + man/markconnect.Rd | 6 + man/markcorr.Rd | 56 ++++++++--- man/markcrosscorr.Rd | 15 ++- man/markequal.Rd | 6 + man/markvario.Rd | 6 + man/pcf.ppp.Rd | 6 + man/pcfcross.Rd | 6 + man/pcfcross.inhom.Rd | 6 + man/pcfdot.Rd | 6 + man/pcfdot.inhom.Rd | 6 + man/pcfinhom.Rd | 7 + man/pcfmulti.Rd | 6 + man/plot.fasp.Rd | 7 + man/rectcontact.Rd | 7 + man/spatstat.explore-internal.Rd | 4 man/spatstat.explore-package.Rd | 2 tests/testsEtoF.R | 16 +++ tests/testsGtoJ.R | 2 tests/testsS.R | 45 +++++++++ 90 files changed, 828 insertions(+), 417 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre] ,
Paula Reimer [ctb] ,
Vegard Martinsen [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.6.0 dated 2026-01-08 and 1.6.2 dated 2026-01-22
DESCRIPTION | 6 +- MD5 | 26 ++++----- NEWS.md | 8 ++ R/calibrate.R | 6 +- R/marine.R | 140 ++++++++++++++------------------------------------- R/rice.R | 1 README.md | 7 -- build/partial.rdb |binary build/vignette.rds |binary data/shells.rda |binary inst/doc/rice.R | 16 ++++- inst/doc/rice.Rmd | 20 +++++-- inst/doc/rice.html | 144 ++++++++++++++++++++++++++--------------------------- vignettes/rice.Rmd | 20 +++++-- 14 files changed, 186 insertions(+), 208 deletions(-)