Title: 'RDF' and 'SPARQL' for R using 'Oxigraph'
Description: Provides 'RDF' storage and 'SPARQL' 1.1 query capabilities by wrapping
the 'Oxigraph' graph database library <https://github.com/oxigraph/oxigraph>.
Supports in-memory and persistent ('RocksDB') storage, multiple 'RDF'
serialization formats ('Turtle', 'N-Triples', 'RDF-XML', 'N-Quads', 'TriG'),
and full 'SPARQL' 1.1 Query and Update support. Built using the 'extendr'
framework for 'Rust'-R bindings.
Author: Carl Boettiger [aut, cre] ,
Oxigraph Contributors [cph] ,
Authors of the dependency Rust crates [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between roxigraph versions 0.1.1 dated 2026-02-12 and 0.1.2 dated 2026-05-04
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS.md | 13 +++ build/vignette.rds |binary inst/AUTHORS | 65 ++++++++++--------- src/rust/Cargo.lock | 161 ++++++++++++++++++++++++++++--------------------- src/rust/Cargo.toml | 4 - src/rust/src/lib.rs | 22 +++--- src/rust/vendor.tar.xz |binary 9 files changed, 164 insertions(+), 125 deletions(-)
Title: Computes Diversity Indices with Archaeological Data
Description: Companion package of Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2025), "Quantifying Diversity through Entropy Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave".
Author: Andreu Sanso [aut, cre],
Arnaud Barat [aut],
Jordi Rosell [aut]
Maintainer: Andreu Sanso <andreu.sanso@uib.eu>
Diff between diversityArch versions 0.2.0 dated 2026-04-27 and 0.3.0 dated 2026-05-04
DESCRIPTION | 13 ++---- MD5 | 22 ++++++----- NAMESPACE | 1 NEWS.md | 9 ++++ R/all_indices.R | 26 ++++++------- R/bs.R | 20 +++++----- R/bs_dec.R | 103 +++++++++++++++++++++++++++++------------------------ R/bs_frag.R |only R/shannon_frag.R | 2 - man/all_indices.Rd | 2 - man/bs.Rd | 6 ++- man/bs_dec.Rd | 17 ++++---- man/bs_frag.Rd |only 13 files changed, 121 insertions(+), 100 deletions(-)
Title: Creation of in-Text Summary Table
Description: Creation of tables of summary statistics or counts for clinical data (for 'TLFs').
These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report
(Word format) or a 'topline' presentation (PowerPoint format),
or as interactive table (with the 'DT' package) to an html document for clinical data review.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between inTextSummaryTable versions 3.3.5 dated 2025-09-25 and 3.4.0 dated 2026-05-04
inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-advanced.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-advanced.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-advanced.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-aesthetics.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-aesthetics.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-aesthetics.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-createTables.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-createTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-createTables.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-exportTables.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-exportTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-exportTables.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-introduction.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-introduction.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-introduction.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-standardTables.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-standardTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-standardTables.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-visualization.R |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-visualization.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/inst/doc/inTextSummaryTable-visualization.html |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-advanced.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-aesthetics.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-createTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-exportTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-introduction.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-standardTables.Rmd |only inTextSummaryTable-3.3.5/inTextSummaryTable/vignettes/inTextSummaryTable-visualization.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/DESCRIPTION | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/MD5 | 128 +++++----- inTextSummaryTable-3.4.0/inTextSummaryTable/R/computeSummaryStatisticsTable.R | 14 + inTextSummaryTable-3.4.0/inTextSummaryTable/R/flextable-convertSummaryStatisticsTableToFlextable.R | 33 +- inTextSummaryTable-3.4.0/inTextSummaryTable/R/flextable-formatSummaryStatisticsTableFlextable.R | 44 ++- inTextSummaryTable-3.4.0/inTextSummaryTable/R/inTextSummaryTable-common-args-doc.R | 14 - 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inTextSummaryTable-3.4.0/inTextSummaryTable/man/cv.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/exportSummaryStatisticsTable.Rd | 14 - inTextSummaryTable-3.4.0/inTextSummaryTable/man/exportSummaryStatisticsTableToFlextable.Rd | 14 - inTextSummaryTable-3.4.0/inTextSummaryTable/man/formatPercentage.Rd | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/man/geomCV.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/geomMean.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/geomSD.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/geomSE.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getMaxNDecimals.Rd | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getMaxNDecimalsData.Rd | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getNDecimals.Rd | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getNDecimalsData.Rd | 10 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getStats.Rd | 5 inTextSummaryTable-3.4.0/inTextSummaryTable/man/getSummaryStatisticsTable.Rd | 14 - inTextSummaryTable-3.4.0/inTextSummaryTable/man/inTextSummaryTable-common-args.Rd | 14 - inTextSummaryTable-3.4.0/inTextSummaryTable/man/inTextSummaryTable-stats.Rd | 11 inTextSummaryTable-3.4.0/inTextSummaryTable/man/inTextSummaryTable.Rd | 5 inTextSummaryTable-3.4.0/inTextSummaryTable/man/mergeHeaderCols.Rd | 3 inTextSummaryTable-3.4.0/inTextSummaryTable/man/pageDimPresentation.Rd | 5 inTextSummaryTable-3.4.0/inTextSummaryTable/man/se.Rd | 12 inTextSummaryTable-3.4.0/inTextSummaryTable/man/tableColorsPresentation.Rd | 5 inTextSummaryTable-3.4.0/inTextSummaryTable/man/tableColorsReport.Rd | 5 inTextSummaryTable-3.4.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-stats.R | 81 ++++++ inTextSummaryTable-3.4.0/inTextSummaryTable/tests/testthat/test_exportSummaryStatisticsTable-flextable.R | 74 +++++ inTextSummaryTable-3.4.0/inTextSummaryTable/tests/testthat/test_getStats.R | 39 +++ inTextSummaryTable-3.4.0/inTextSummaryTable/tests/testthat/test_getSummaryStatisticsTable.R | 37 ++ inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-01-introduction.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-02-createTables.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-03-standardTables.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-04-exportTables.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-05-advanced.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-06-aesthetics.Rmd |only inTextSummaryTable-3.4.0/inTextSummaryTable/vignettes/inTextSummaryTable-07-visualization.Rmd |only 93 files changed, 549 insertions(+), 219 deletions(-)
More information about inTextSummaryTable at CRAN
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Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574>,
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565> and
Laudanno et al. 2021. Syst. Biol. 70: 389–407,
<DOI:10.1093/sysbio/syaa048>.
Also contains functions to simulate the diversity-dependent
process.
Author: Rampal S. Etienne [aut, cre] ,
Bart Haegeman [aut] ,
Hanno Hildenbrandt [ctb] ,
Giovanni Laudanno [ctb]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 5.2.4 dated 2025-11-28 and 5.2.5 dated 2026-05-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/dd_utils.R | 38 +++++++++++++++++++++++++++++++------- man/optimizer.Rd | 16 ++++++++++------ 4 files changed, 48 insertions(+), 20 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.3.0 dated 2026-03-13 and 1.4.0 dated 2026-05-04
DESCRIPTION | 13 MD5 | 185 +- NEWS.md | 323 +-- R/as_bibentry.R | 16 R/as_cff.R | 38 R/as_cff_person.R | 9 R/as_cff_reference.R | 238 +- R/cff.R | 1 R/cff_create.R | 3 R/cff_gha_update.R | 1 R/cff_git_hook.R | 8 R/cff_modify.R | 3 R/cff_read.R | 21 R/cff_read_bib_text.R | 195 +- R/cff_validate.R | 39 R/cff_write.R | 6 R/cff_write_misc.R | 2 R/cffr-package.R | 24 R/data.R | 66 R/deprecated.R | 8 R/docs.R | 1 R/encoded_utf_to_latex.R | 1 R/methods.R | 26 R/utils-alerts.R | 4 R/utils-cff_read.R | 774 ++++---- R/utils-cff_ref.R | 73 R/utils-create.R | 450 ++-- R/utils-persons.R | 6 R/utils-schema.R | 13 R/utils.R | 13 R/zzz.R | 2 README.md | 168 - build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/REFERENCES.bib | 474 ++--- inst/WORDLIST | 29 inst/doc/bibtex-cff.R | 171 - inst/doc/bibtex-cff.html | 2749 ++++++++++++++++-------------- inst/doc/bibtex-cff.qmd | 1204 ++++--------- inst/doc/cffr.R | 4 inst/doc/cffr.html | 233 +- inst/doc/cffr.qmd | 47 inst/doc/joss-paper.html | 32 inst/doc/joss-paper.qmd | 42 inst/doc/r-cff.R | 3 inst/doc/r-cff.html | 925 ++++------ inst/doc/r-cff.qmd | 93 - inst/examples/CITATION_complete.cff | 1846 ++++++++++---------- inst/examples/CITATION_dx_doi |only inst/examples/CITATION_lang.cff |only inst/examples/DESCRIPTION_quint |only inst/extdata/crosswalk_tables.csv | 498 ++--- inst/schemaorg.json | 4 man/as_bibentry.Rd | 23 man/as_cff.Rd | 15 man/as_cff_person.Rd | 7 man/cff.Rd | 7 man/cff_class.Rd | 28 man/cff_create.Rd | 9 man/cff_gha_update.Rd | 1 man/cff_git_hook.Rd | 9 man/cff_modify.Rd | 7 man/cff_read.Rd | 19 man/cff_read_bib_text.Rd | 11 man/cff_schema.Rd | 7 man/cff_validate.Rd | 17 man/cff_write.Rd | 8 man/cff_write_misc.Rd | 13 man/cffr-package.Rd | 5 man/cran_to_spdx.Rd | 67 man/deprecated_cff_bibentry.Rd | 9 man/deprecated_cff_from_bib.Rd | 9 man/deprecated_cff_person.Rd | 9 man/deprecated_cff_to_bib.Rd | 9 man/deprecated_write.Rd | 9 man/encoded_utf_to_latex.Rd | 13 tests/testthat/_snaps/as_cff_reference.md | 43 tests/testthat/_snaps/cff_gha_update.md | 46 tests/testthat/_snaps/cff_validate.md | 109 + tests/testthat/_snaps/utils-create.md | 2465 +++++++++++++------------- tests/testthat/test-as_cff.R | 414 ++-- tests/testthat/test-as_cff_person.R | 380 ++-- tests/testthat/test-as_cff_reference.R | 1542 ++++++++-------- tests/testthat/test-cff_create.R | 1134 ++++++------ tests/testthat/test-cff_validate.R | 104 - tests/testthat/test-methods.R | 672 +++---- tests/testthat/test-mock-package.R | 266 +- tests/testthat/test-utils-cff_ref.R | 16 tests/testthat/test-utils-create.R | 98 - vignettes/REFERENCES.bib | 2 vignettes/bibtex-cff.qmd | 1204 ++++--------- vignettes/cffr.qmd | 47 vignettes/joss-paper.qmd | 42 vignettes/r-cff.qmd | 93 - 95 files changed, 10110 insertions(+), 9962 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.2.12 dated 2026-01-07 and 0.2.13 dated 2026-05-04
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/condeff.R | 4 ++-- R/condeff_boot.R | 4 ++-- R/plotmod.R | 4 ++-- README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/plotmod.html | 4 ++-- 10 files changed, 29 insertions(+), 21 deletions(-)
Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features
(i.e. lines and polygons) to make them more aesthetically pleasing.
Smooth curves, fill holes, and remove small fragments from lines and
polygons.
Author: Matthew Strimas-Mackey [aut, cre]
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>
Diff between smoothr versions 1.2.1 dated 2025-10-21 and 1.3.0 dated 2026-05-04
smoothr-1.2.1/smoothr/R/data.r |only smoothr-1.2.1/smoothr/tests/testthat/test_smooth.r |only smoothr-1.3.0/smoothr/DESCRIPTION | 12 - smoothr-1.3.0/smoothr/MD5 | 74 ++++----- smoothr-1.3.0/smoothr/NEWS.md | 7 smoothr-1.3.0/smoothr/R/data.R |only smoothr-1.3.0/smoothr/R/densify.R | 2 smoothr-1.3.0/smoothr/R/drop-crumbs.R | 46 +++-- smoothr-1.3.0/smoothr/R/fill-holes.R | 24 +- smoothr-1.3.0/smoothr/R/smooth-chaikin.R | 11 - smoothr-1.3.0/smoothr/R/smooth-densify.R | 15 - smoothr-1.3.0/smoothr/R/smooth-ksmooth.R | 58 +++++-- smoothr-1.3.0/smoothr/R/smooth-spline.R | 15 + smoothr-1.3.0/smoothr/R/smooth.R | 81 ++++++---- smoothr-1.3.0/smoothr/R/utils.R | 4 smoothr-1.3.0/smoothr/build/vignette.rds |binary smoothr-1.3.0/smoothr/inst/doc/smoothr.R | 51 +++--- smoothr-1.3.0/smoothr/inst/doc/smoothr.Rmd | 51 +++--- smoothr-1.3.0/smoothr/inst/doc/smoothr.html | 68 ++++---- smoothr-1.3.0/smoothr/man/densify.Rd | 2 smoothr-1.3.0/smoothr/man/drop_crumbs.Rd | 2 smoothr-1.3.0/smoothr/man/figures/README-smooth-lines-1.png |binary smoothr-1.3.0/smoothr/man/figures/README-smooth-polygons-1.png |binary smoothr-1.3.0/smoothr/man/fill_holes.Rd | 2 smoothr-1.3.0/smoothr/man/jagged_lines.Rd | 4 smoothr-1.3.0/smoothr/man/jagged_lines_3d.Rd | 4 smoothr-1.3.0/smoothr/man/jagged_polygons.Rd | 4 smoothr-1.3.0/smoothr/man/smooth.Rd | 25 +-- smoothr-1.3.0/smoothr/man/smooth_chaikin.Rd | 5 smoothr-1.3.0/smoothr/man/smooth_densify.Rd | 2 smoothr-1.3.0/smoothr/man/smooth_ksmooth.Rd | 4 smoothr-1.3.0/smoothr/man/smooth_spline.Rd | 6 smoothr-1.3.0/smoothr/man/smoothr-package.Rd | 5 smoothr-1.3.0/smoothr/tests/testthat/test_drop-crumbs.R | 16 + smoothr-1.3.0/smoothr/tests/testthat/test_fill-holes.R | 5 smoothr-1.3.0/smoothr/tests/testthat/test_smooth-chaikin.R | 5 smoothr-1.3.0/smoothr/tests/testthat/test_smooth-densify.R | 6 smoothr-1.3.0/smoothr/tests/testthat/test_smooth-spline.R | 10 + smoothr-1.3.0/smoothr/tests/testthat/test_smooth.R |only smoothr-1.3.0/smoothr/vignettes/smoothr.Rmd | 51 +++--- 40 files changed, 399 insertions(+), 278 deletions(-)
Title: Advanced Inference with Random Graphical Models
Description: Implements Random Graphical Models for multivariate data analysis across multiple environments, providing tools for exploring network interactions and structural relationships. Capabilities include joint inference across environments, integration of external covariates, and a Bayesian framework for uncertainty quantification. Applicable in various fields, including microbiome analysis. Methods based on Vinciotti, V., Wit, E. C., and Richter, F. (2026) "Random Graphical Model of Microbiome Interactions in Related Environments" <doi:10.1007/s13253-024-00638-6>.
Author: Francisco Richter [aut, cre],
Veronica Vinciotti [ctb],
Ernst Wit [ctb]
Maintainer: Francisco Richter <richtf@usi.ch>
This is a re-admission after prior archival of version 1.0.4 dated 2024-03-21
Diff between rgm versions 1.0.4 dated 2024-03-21 and 1.2.1 dated 2026-05-04
rgm-1.0.4/rgm/src/test.cpp |only rgm-1.2.1/rgm/DESCRIPTION | 13 ++--- rgm-1.2.1/rgm/MD5 | 25 +++++----- rgm-1.2.1/rgm/NAMESPACE | 7 ++ rgm-1.2.1/rgm/NEWS.md |only rgm-1.2.1/rgm/R/RcppExports.R | 4 - rgm-1.2.1/rgm/R/imports.R | 1 rgm-1.2.1/rgm/R/rgm.R | 6 -- rgm-1.2.1/rgm/R/sim.rgm.R | 24 --------- rgm-1.2.1/rgm/README.md | 95 ++++++++++++++++++++++++++++++-------- rgm-1.2.1/rgm/build/vignette.rds |binary rgm-1.2.1/rgm/inst/doc/rgm.R | 70 ++++++++++++++-------------- rgm-1.2.1/rgm/inst/doc/rgm.html | 13 ++--- rgm-1.2.1/rgm/man/rgm-package.Rd |only rgm-1.2.1/rgm/src/RcppExports.cpp | 12 ---- 15 files changed, 147 insertions(+), 123 deletions(-)
Title: Data Only: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Description: Contains example data for the 'rehh' package.
Author: Mathieu Gautier [aut, cre],
Alexander Klassmann [aut],
Renaud Vitalis [aut]
Maintainer: Mathieu Gautier <mathieu.gautier@inrae.fr>
Diff between rehh.data versions 1.0.0 dated 2016-11-08 and 1.0.1 dated 2026-05-04
DESCRIPTION | 29 ++++++++++++++++++++++------- MD5 | 6 +++--- inst/CITATION | 48 +++++++++++++++++++++++++++--------------------- man/rehh-package.Rd | 4 ++-- 4 files changed, 54 insertions(+), 33 deletions(-)
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2026a) <doi:10.1080/01621459.2025.2520467>, Kang and Oh (2026b) <doi:10.1080/00031305.2025.2563730>, and Kang (2025) <doi:10.23170/snu.000000188358.11032.0001856>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw@skku.edu>
Diff between L1centrality versions 0.5.0 dated 2026-04-29 and 0.5.1 dated 2026-05-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 10 ++++++++-- R/validate.R | 4 ++-- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short cgeneric, to
define a Gaussian Markov random (GMRF) model. The cgeneric contain
code to specify GMRF elements such as the graph and the precision
matrix, and also the initial and prior for its parameters, useful for
model inference. It can be accessed from a C program and is the
recommended way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>). The 'INLAtools' implement functions to
evaluate each one of the model specifications from R. The implemented
functionalities leverage the use of 'cgeneric' models and provide a
way to debug the code as well to work with the prior for the model
parameters and to sample from it. The `generic0` can be used to
implement intrinsic models with the scaling as proposed in Sørbye &
Rue (2014) <doi:10.1016/j.spasta.2013.06.004>, and the required
constraints. A very useful functionality is the Kronecker product
method that creates a new model from multiple cgen [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <elias.krainski@kaust.edu.sa>
This is a re-admission after prior archival of version 0.1.3 dated 2026-04-22
Diff between INLAtools versions 0.1.3 dated 2026-04-22 and 0.1.4 dated 2026-05-04
INLAtools-0.1.3/INLAtools/R/cgeneric_utils.R |only INLAtools-0.1.3/INLAtools/R/rgeneric_utils.R |only INLAtools-0.1.3/INLAtools/man/INLAtools-methods.Rd |only INLAtools-0.1.3/INLAtools/man/prec.inla.Rd |only INLAtools-0.1.3/INLAtools/src/Makevars.win |only INLAtools-0.1.4/INLAtools/DESCRIPTION | 83 ++++++--------- INLAtools-0.1.4/INLAtools/MD5 | 56 +++++----- INLAtools-0.1.4/INLAtools/NAMESPACE | 30 ++--- INLAtools-0.1.4/INLAtools/R/aaa_classes.R | 2 INLAtools-0.1.4/INLAtools/R/aaa_methods.R | 68 ------------- INLAtools-0.1.4/INLAtools/R/aaaaa.R | 1 INLAtools-0.1.4/INLAtools/R/cgeneric.R | 99 +++++++++---------- INLAtools-0.1.4/INLAtools/R/cgeneric_generic0.R | 14 +- INLAtools-0.1.4/INLAtools/R/cgeneric_get.R |only INLAtools-0.1.4/INLAtools/R/inla_methods.R | 4 INLAtools-0.1.4/INLAtools/R/kronecker.R | 52 ++++----- INLAtools-0.1.4/INLAtools/R/rgeneric.R | 29 +++-- INLAtools-0.1.4/INLAtools/R/rgeneric_get.R |only INLAtools-0.1.4/INLAtools/demo/cgeneric.R | 8 - INLAtools-0.1.4/INLAtools/demo/kronecker.R | 2 INLAtools-0.1.4/INLAtools/demo/kronecker3.R | 16 +-- INLAtools-0.1.4/INLAtools/demo/prior.R | 8 - INLAtools-0.1.4/INLAtools/man/cgeneric-class.Rd | 60 +++++------ INLAtools-0.1.4/INLAtools/man/cgeneric_generic0.Rd | 10 - INLAtools-0.1.4/INLAtools/man/cgeneric_get.Rd | 48 ++++----- INLAtools-0.1.4/INLAtools/man/inlaQ.Rd |only INLAtools-0.1.4/INLAtools/man/kronecker.Rd | 36 ++++-- INLAtools-0.1.4/INLAtools/man/multi_generic_model.Rd | 24 ---- INLAtools-0.1.4/INLAtools/man/rgeneric-class.Rd | 34 +++++- INLAtools-0.1.4/INLAtools/man/rgeneric_get.Rd | 47 ++++----- INLAtools-0.1.4/INLAtools/src/INLAtools.h | 14 +- INLAtools-0.1.4/INLAtools/src/INLAtools_init.c | 1 INLAtools-0.1.4/INLAtools/src/Makevars | 9 - 33 files changed, 334 insertions(+), 421 deletions(-)
Title: GLM-Based Estimation for Rasch Model Parameters
Description: Provides functions for estimating Rasch model parameters
using the Generalized Linear Model (GLM) framework. The methods
implemented are based on Brown (2018, ISBN:978-3-319-93547-8)
<doi:10.1007/978-3-319-93549-2> and Debelak et al. (2022,
ISBN:978-1-138-71046-7) <doi:10.1201/9781315200620>.
Author: Ahmed Samir Megahed [aut, cre],
Mustafa Ali Khalaf [aut],
Ibraheem Mohamed Mougy [aut]
Maintainer: Ahmed Samir Megahed <Asamir@foe.zu.edu.eg>
Diff between GLMBasedRaschEstimation versions 0.1.2 dated 2026-04-22 and 0.2.0 dated 2026-05-04
DESCRIPTION | 8 ++++---- MD5 | 7 +++++-- NAMESPACE | 6 ++++++ R/runGLMRaschSuite.R |only inst/shiny-examples |only man/runGLMRaschSuite.Rd |only 6 files changed, 15 insertions(+), 6 deletions(-)
More information about GLMBasedRaschEstimation at CRAN
Permanent link
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
Staysail Systems, Inc. [cph] ,
Capitar IT Group BV [cph] ,
The Mbed TLS Contributors [cph] ,
Pierre L'Ecuyer [cph] ,
sakura authors [cph] ,
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.8.2 dated 2026-04-04 and 1.9.0 dated 2026-05-04
nanonext-1.8.2/nanonext/R/messenger.R |only nanonext-1.8.2/nanonext/man/messenger.Rd |only nanonext-1.9.0/nanonext/DESCRIPTION | 29 nanonext-1.9.0/nanonext/LICENSE.note | 37 nanonext-1.9.0/nanonext/MD5 | 85 nanonext-1.9.0/nanonext/NAMESPACE | 8 nanonext-1.9.0/nanonext/NEWS.md | 16 nanonext-1.9.0/nanonext/R/aio.R | 5 nanonext-1.9.0/nanonext/R/context.R | 4 nanonext-1.9.0/nanonext/R/dispatcher.R | 110 + nanonext-1.9.0/nanonext/R/sendrecv.R | 7 nanonext-1.9.0/nanonext/README.md | 7 nanonext-1.9.0/nanonext/build/vignette.rds |binary nanonext-1.9.0/nanonext/configure | 4 nanonext-1.9.0/nanonext/man/close.Rd | 4 nanonext-1.9.0/nanonext/man/dot-dispatcher_capacity.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_gate.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_info.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_start.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_stop.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_try_gate.Rd |only nanonext-1.9.0/nanonext/man/dot-dispatcher_wait.Rd |only nanonext-1.9.0/nanonext/man/nanonext-package.Rd | 10 nanonext-1.9.0/nanonext/man/recv.Rd | 5 nanonext-1.9.0/nanonext/man/recv_aio.Rd | 5 nanonext-1.9.0/nanonext/man/request.Rd | 4 nanonext-1.9.0/nanonext/src/aio.c | 78 nanonext-1.9.0/nanonext/src/comms.c | 14 nanonext-1.9.0/nanonext/src/core.c | 42 nanonext-1.9.0/nanonext/src/dispatcher.c | 905 +++++++--- nanonext-1.9.0/nanonext/src/init.c | 19 nanonext-1.9.0/nanonext/src/nanonext.h | 50 nanonext-1.9.0/nanonext/src/ncurl.c | 23 nanonext-1.9.0/nanonext/src/nng/include/nng/nng.h | 4 nanonext-1.9.0/nanonext/src/nng/src/core/aio.c | 9 nanonext-1.9.0/nanonext/src/nng/src/core/aio.h | 2 nanonext-1.9.0/nanonext/src/nng/src/platform/posix/posix_ipcconn.c | 15 nanonext-1.9.0/nanonext/src/nng/src/platform/posix/posix_tcpconn.c | 15 nanonext-1.9.0/nanonext/src/nng/src/platform/windows/win_tcpconn.c | 12 nanonext-1.9.0/nanonext/src/nng/src/supplemental/http/http_server.c | 9 nanonext-1.9.0/nanonext/src/nng_structs.h | 37 nanonext-1.9.0/nanonext/src/proto.c | 6 nanonext-1.9.0/nanonext/src/server.c | 16 nanonext-1.9.0/nanonext/src/sync.c | 33 nanonext-1.9.0/nanonext/src/thread.c | 170 - nanonext-1.9.0/nanonext/src/tls.c | 13 nanonext-1.9.0/nanonext/src/utils.c | 10 nanonext-1.9.0/nanonext/tests/tests.R | 156 + 48 files changed, 1391 insertions(+), 587 deletions(-)
Title: Core Mathematical Functions for Multi-Objective Optimization
Description: Fast implementations of mathematical operations and performance metrics for multi-objective optimization, including filtering and ranking of dominated vectors according to Pareto optimality, hypervolume metric, C.M. Fonseca, L. Paquete, M. López-Ibáñez (2006) <doi:10.1109/CEC.2006.1688440>, epsilon indicator, inverted generational distance, computation of the empirical attainment function, V.G. da Fonseca, C.M. Fonseca, A.O. Hall (2001) <doi:10.1007/3-540-44719-9_15>, and Vorob'ev threshold, expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) <doi:10.1016/j.ejor.2014.07.032>, among others.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Carlos Fonseca [ctb],
Luis Paquete [ctb],
Andreia P. Guerreiro [ctb],
Mickael Binois [ctb],
Michael H. Buselli [cph] ,
Wessel Dankers [cph] ,
NumPy Developers [cph] ,
Jean-Sebastien Roy [cph] ,
Makoto Matsumoto [cph] [...truncated...]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between moocore versions 0.3.0 dated 2026-05-03 and 0.3.1 dated 2026-05-04
DESCRIPTION | 6 - MD5 | 20 +++-- NEWS.md | 6 + R/nondominated.R | 88 +++++++++++++++----------- build/partial.rdb |binary man/nondominated.Rd | 59 +---------------- man/pareto_rank.Rd |only src/libmoocore/Makefile | 2 src/libmoocore/NEWS.md | 4 + src/libmoocore/nondominated_kung.h | 16 ++-- tests/testthat/test-doctest-is_nondominated.R | 4 - tests/testthat/test-doctest-pareto_rank.R |only 12 files changed, 90 insertions(+), 115 deletions(-)
Title: Publication-Quality 'ggplot2' Themes
Description: Complete themes for publication-quality 'ggplot2' visualisation.
Also provides functions to modify these based on the positional axis scales
and focus of a particular plot.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggrefine versions 0.3.0 dated 2026-04-29 and 0.4.0 dated 2026-05-04
DESCRIPTION | 6 +- MD5 | 26 ++++----- NEWS.md | 8 ++ R/theme-dark.R | 15 ----- R/theme-grey.R | 12 ---- R/theme-light.R | 84 ++++++++++++++++++++----------- R/theme-oat.R | 12 ---- README.md | 43 +++++++++++++++ man/figures/README-unnamed-chunk-2-1.png |binary man/figures/logo.png |binary man/theme_dark.Rd | 21 ------- man/theme_grey.Rd | 18 ------ man/theme_light.Rd | 18 ------ man/theme_oat.Rd | 18 ------ 14 files changed, 125 insertions(+), 156 deletions(-)
Title: Mathematically Aggregating Expert Judgments
Description: The use of structured elicitation to inform decision making has grown dramatically in recent decades, however, judgements from multiple experts must be aggregated into a single estimate. Empirical evidence suggests that mathematical aggregation provides more reliable estimates than enforcing behavioural consensus on group estimates. 'aggreCAT' provides state-of-the-art mathematical aggregation methods for elicitation data including those defined in Hanea, A. et al. (2021) <doi:10.1371/journal.pone.0256919>. The package also provides functions to visualise and evaluate the performance of your aggregated estimates on validation data.
Author: David Wilkinson [aut, cre] ,
Elliot Gould [aut] ,
Aaron Willcox [aut] ,
Charles T. Gray [aut],
Rose E. O'Dea [aut] ,
Rebecca Groenewegen [aut]
Maintainer: David Wilkinson <david.wilkinson.research@gmail.com>
Diff between aggreCAT versions 1.0.0 dated 2025-05-28 and 1.1.0 dated 2026-05-04
DESCRIPTION | 58 +- MD5 | 128 +++-- NAMESPACE | 3 NEWS.md | 76 +++ R/AverageWAgg.R | 234 +++++----- R/BayesianWAgg.R | 269 +++++------ R/DistributionWAgg.R | 299 ++++++------- R/ExtremisationWAgg.R | 119 ++--- R/IntervalWAgg.R | 525 +++++++++++------------ R/LinearWAgg.R | 640 +++++++++++++--------------- R/ReasoningWAgg.R | 156 +++--- R/ShiftingWAgg.R | 749 ++++++++++++++++----------------- R/aggreCAT_package.R | 1 R/confidence_score_evaluation.R | 36 - R/confidence_score_heatmap.R | 75 +-- R/confidence_score_plots.R | 540 +++++++++++------------ R/confidence_score_ridgeplot.R | 53 +- R/data.R | 2 R/globals.R | 89 +++ R/method_placeholder.R | 7 R/postprocess_judgements.R | 7 R/preprocess_judgements.R | 86 +-- R/sysdata.rda |binary R/weight_asym.R | 61 +- R/weight_interval.R | 22 R/weight_nIndivInterval.R | 59 +- R/weight_outlier.R | 57 +- R/weight_reason.R | 25 - R/weight_reason2.R | 56 +- R/weight_varIndivInterval.R | 41 - R/zzz.R | 13 build/stage23.rdb |binary build/vignette.rds |binary inst/ISC_blog |only inst/doc/aggreCAT.pdf |binary inst/doc/aggregation_workflow.R |only inst/doc/aggregation_workflow.Rmd |only inst/doc/aggregation_workflow.html |only inst/doc/data.R |only inst/doc/data.Rmd |only inst/doc/data.html |only inst/html_check.R |only man/BayesianWAgg.Rd | 2 man/DistributionWAgg.Rd | 43 + man/ExtremisationWAgg.Rd | 12 man/IntervalWAgg.Rd | 2 man/LinearWAgg.Rd | 2 man/ReasoningWAgg.Rd | 2 man/ShiftingWAgg.Rd | 22 man/aggreCAT.Rd | 7 man/confidence_score_evaluation.Rd | 7 man/confidence_score_heatmap.Rd | 29 - man/confidence_score_ridgeplot.Rd | 15 man/data_supp_quiz.Rd | 2 man/weight_asym.Rd | 12 man/weight_interval.Rd | 10 man/weight_nIndivInterval.Rd | 10 man/weight_outlier.Rd | 12 man/weight_reason.Rd | 12 man/weight_reason2.Rd | 12 man/weight_varIndivInterval.Rd | 10 tests/testthat/test-agg_methods.R | 309 +++++-------- tests/testthat/test-expert_judgments.R | 14 tests/testthat/test-placeholders.R | 17 tests/testthat/test-test_errors.R | 140 ++++-- tests/testthat/test-weights.R | 3 vignettes/aggregation_workflow.Rmd |only vignettes/data.Rmd |only vignettes/vignette_references.bib |only 69 files changed, 2646 insertions(+), 2546 deletions(-)
Title: Spatial Concentration and Radius-Based Risk Calculations
Description: Provides methods for spatial concentration and radius-based risk
calculations. The package focuses on efficient determination of the sum of
observations within a given radius, identifying local concentration
hotspots, and aggregating point data to polygon geometries. These methods
are useful for applications such as insurance, urban analytics,
environmental exposure analysis, and other spatial point pattern workflows.
The underlying maximum covering problem is described by Church (1974)
<doi:10.1007/BF01942293>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.7.3 dated 2025-09-14 and 0.8.0 dated 2026-05-04
spatialrisk-0.7.3/spatialrisk/R/concentration.R |only spatialrisk-0.7.3/spatialrisk/R/data_Groningen.R |only spatialrisk-0.7.3/spatialrisk/R/data_insurance.R |only spatialrisk-0.7.3/spatialrisk/R/data_knmi_historic.R |only spatialrisk-0.7.3/spatialrisk/R/data_nl_gemeente.R |only spatialrisk-0.7.3/spatialrisk/R/map_choropleth.R |only spatialrisk-0.7.3/spatialrisk/R/map_ggplot2.R |only spatialrisk-0.7.3/spatialrisk/R/map_plot_points.R |only spatialrisk-0.7.3/spatialrisk/R/points_in_circle.R |only spatialrisk-0.7.3/spatialrisk/R/points_to_polygon.R |only spatialrisk-0.7.3/spatialrisk/R/smooth_sphere.R |only spatialrisk-0.7.3/spatialrisk/man/conc_per_cell_new.Rd |only spatialrisk-0.7.3/spatialrisk/man/concentration.Rd |only spatialrisk-0.7.3/spatialrisk/man/find_highest_concentration.Rd |only spatialrisk-0.7.3/spatialrisk/man/highest_conc.Rd |only spatialrisk-0.7.3/spatialrisk/man/plot.concentration.Rd |only spatialrisk-0.7.3/spatialrisk/man/plot_points.Rd |only spatialrisk-0.7.3/spatialrisk/man/points_in_circle.Rd |only spatialrisk-0.7.3/spatialrisk/man/points_in_circle_vec.Rd |only spatialrisk-0.7.3/spatialrisk/man/points_to_polygon.Rd |only spatialrisk-0.7.3/spatialrisk/man/update_db.Rd |only spatialrisk-0.8.0/spatialrisk/DESCRIPTION | 35 spatialrisk-0.8.0/spatialrisk/MD5 | 128 - spatialrisk-0.8.0/spatialrisk/NAMESPACE | 34 spatialrisk-0.8.0/spatialrisk/NEWS.md | 75 spatialrisk-0.8.0/spatialrisk/R/RcppExports.R | 64 spatialrisk-0.8.0/spatialrisk/R/choropleth.R |only spatialrisk-0.8.0/spatialrisk/R/concentration_hotspot_indexed.R |only spatialrisk-0.8.0/spatialrisk/R/concentration_hotspot_pair_refine.R |only spatialrisk-0.8.0/spatialrisk/R/data-groningen.R |only spatialrisk-0.8.0/spatialrisk/R/data-insurance.R |only spatialrisk-0.8.0/spatialrisk/R/data-knmi-stations.R |only spatialrisk-0.8.0/spatialrisk/R/data-spatial-nl.R |only spatialrisk-0.8.0/spatialrisk/R/deprecated-aliases.R |only spatialrisk-0.8.0/spatialrisk/R/deprecated.R | 2 spatialrisk-0.8.0/spatialrisk/R/deprecated_highest_concentration.R | 4 spatialrisk-0.8.0/spatialrisk/R/haversine.R | 54 spatialrisk-0.8.0/spatialrisk/R/highest_concentration_terra.R | 873 +++++-- spatialrisk-0.8.0/spatialrisk/R/knmi_historic_data.R |only spatialrisk-0.8.0/spatialrisk/R/map_points.R |only spatialrisk-0.8.0/spatialrisk/R/points_within_radius.R |only spatialrisk-0.8.0/spatialrisk/R/radius_sum.R |only spatialrisk-0.8.0/spatialrisk/R/summarise_points_by_polygon.R |only spatialrisk-0.8.0/spatialrisk/R/utils.R | 137 - spatialrisk-0.8.0/spatialrisk/build |only spatialrisk-0.8.0/spatialrisk/inst |only spatialrisk-0.8.0/spatialrisk/man/Groningen.Rd | 36 spatialrisk-0.8.0/spatialrisk/man/choropleth.Rd | 39 spatialrisk-0.8.0/spatialrisk/man/choropleth_ggplot2.Rd | 50 spatialrisk-0.8.0/spatialrisk/man/concentration_hotspot.Rd |only spatialrisk-0.8.0/spatialrisk/man/concentration_per_candidate_cell.Rd |only spatialrisk-0.8.0/spatialrisk/man/haversine.Rd | 20 spatialrisk-0.8.0/spatialrisk/man/highest_concentration_candidate.Rd |only spatialrisk-0.8.0/spatialrisk/man/insurance.Rd | 24 spatialrisk-0.8.0/spatialrisk/man/interpolate_spline.Rd | 50 spatialrisk-0.8.0/spatialrisk/man/knmi_historic_data.Rd | 45 spatialrisk-0.8.0/spatialrisk/man/knmi_stations.Rd | 26 spatialrisk-0.8.0/spatialrisk/man/map_points.Rd |only spatialrisk-0.8.0/spatialrisk/man/nl_corop.Rd | 28 spatialrisk-0.8.0/spatialrisk/man/nl_gemeente.Rd | 23 spatialrisk-0.8.0/spatialrisk/man/nl_postcode2.Rd | 27 spatialrisk-0.8.0/spatialrisk/man/nl_postcode3.Rd | 29 spatialrisk-0.8.0/spatialrisk/man/nl_postcode4.Rd | 38 spatialrisk-0.8.0/spatialrisk/man/nl_provincie.Rd | 19 spatialrisk-0.8.0/spatialrisk/man/plot.hotspot.Rd |only spatialrisk-0.8.0/spatialrisk/man/points_within_radius.Rd |only spatialrisk-0.8.0/spatialrisk/man/radius_sum.Rd |only spatialrisk-0.8.0/spatialrisk/man/spatialrisk-deprecated.Rd |only spatialrisk-0.8.0/spatialrisk/man/summarise_points_by_polygon.Rd |only spatialrisk-0.8.0/spatialrisk/man/update_hotspot_cache.Rd |only spatialrisk-0.8.0/spatialrisk/src/RcppExports.cpp | 275 +- spatialrisk-0.8.0/spatialrisk/src/concentration.cpp |only spatialrisk-0.8.0/spatialrisk/src/concentration.h |only spatialrisk-0.8.0/spatialrisk/src/concentration_hotspot_indexed.cpp |only spatialrisk-0.8.0/spatialrisk/src/distance.cpp |only spatialrisk-0.8.0/spatialrisk/src/geometry.h |only spatialrisk-0.8.0/spatialrisk/src/grid.cpp |only spatialrisk-0.8.0/spatialrisk/src/haversine_cpp.cpp | 1134 +++++----- spatialrisk-0.8.0/spatialrisk/src/radius.cpp |only spatialrisk-0.8.0/spatialrisk/src/utilities.cpp |only spatialrisk-0.8.0/spatialrisk/src/utilities.h |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test-concentration-hotspot-indexed.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test-concentration-hotspot-pair-refine.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_choropleth.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_concentration.R | 166 + spatialrisk-0.8.0/spatialrisk/tests/testthat/test_concentration_hotspot.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_data.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_haversine.R | 18 spatialrisk-0.8.0/spatialrisk/tests/testthat/test_interpolate_spline.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_map_points.R |only spatialrisk-0.8.0/spatialrisk/tests/testthat/test_pointsincircle.R | 43 spatialrisk-0.8.0/spatialrisk/tests/testthat/test_summarise_points_by_polygon.R |only spatialrisk-0.8.0/spatialrisk/vignettes |only 93 files changed, 2178 insertions(+), 1318 deletions(-)
Title: Periodic Autoregressive Time Series Models
Description: Basic functions to fit and predict periodic autoregressive time series models. These models are discussed in the book P.H. Franses (1996) "Periodicity and Stochastic Trends in Economic Time Series", Oxford University Press. Data set analyzed in that book is also provided. NOTE: the package was orphaned during several years. It is now only maintained, but no major enhancements are expected, and the maintainer cannot provide any support.
Author: Javier Lopez-de-Lacalle [aut, cph],
Matthieu Stigler [cre]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between partsm versions 1.1-4 dated 2025-04-21 and 1.1-5 dated 2026-05-04
partsm-1.1-4/partsm/vignettes/partsm.cls |only partsm-1.1-5/partsm/DESCRIPTION | 10 +-- partsm-1.1-5/partsm/MD5 | 19 ++---- partsm-1.1-5/partsm/build/vignette.rds |binary partsm-1.1-5/partsm/inst/ChangeLog | 4 + partsm-1.1-5/partsm/inst/doc/partsm.R | 22 +++---- partsm-1.1-5/partsm/inst/doc/partsm.Rnw | 64 ++++++++------------- partsm-1.1-5/partsm/inst/doc/partsm.pdf |binary partsm-1.1-5/partsm/inst/internal_tests_devtools.R | 30 +++++++-- partsm-1.1-5/partsm/vignettes/partsm.Rnw | 64 ++++++++------------- partsm-1.1-5/partsm/vignettes/partsm.bib | 2 11 files changed, 105 insertions(+), 110 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The 'netgwas' package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The 'netgwas'
implements the methodological developments in Behrouzi and Wit (2017)
<doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
Author: Pariya Behrouzi [aut, cre] ,
Ernst C. Wit [ctb]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
This is a re-admission after prior archival of version 1.14.4 dated 2025-11-10
Diff between netgwas versions 1.14.4 dated 2025-11-10 and 1.14.5 dated 2026-05-04
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Joint Latent Process Models
Description: Estimation of extended joint models with shared random effects. Longitudinal data are handled in latent process models for continuous (Gaussian or curvilinear) and ordinal outcomes while proportional hazard models are used for the survival part. We propose a frequentist approach using maximum likelihood estimation. See Saulnier et al, 2022 <doi:10.1016/j.ymeth.2022.03.003>.
Author: Viviane Philipps [aut, cre],
Tiphaine Saulnier [aut],
Cecile Proust-Lima [aut]
Maintainer: Viviane Philipps <Viviane.Philipps@u-bordeaux.fr>
Diff between JLPM versions 1.0.3 dated 2026-04-27 and 1.0.4 dated 2026-05-04
JLPM-1.0.3/JLPM/R/plotAsso.R |only JLPM-1.0.3/JLPM/build |only JLPM-1.0.3/JLPM/inst |only JLPM-1.0.3/JLPM/vignettes |only JLPM-1.0.4/JLPM/DESCRIPTION | 11 +++++------ JLPM-1.0.4/JLPM/MD5 | 10 +++------- JLPM-1.0.4/JLPM/README.md |only JLPM-1.0.4/JLPM/src/Makevars | 2 +- 8 files changed, 9 insertions(+), 14 deletions(-)
Title: Gene Registration from Expression and Time-Courses in R
Description: A tool for registering (aligning) gene expression profiles
between reference and query data.
Author: Ruth Kristianingsih [aut, cre]
Maintainer: Ruth Kristianingsih <ruth.kristianingsih30@gmail.com>
This is a re-admission after prior archival of version 2.0.0 dated 2024-04-09
Diff between greatR versions 2.0.0 dated 2024-04-09 and 2.1.0 dated 2026-05-04
DESCRIPTION | 14 +- MD5 | 30 ++-- NEWS.md | 19 ++ R/compare_dynamics.R | 2 R/distance.R | 164 +++++++++++++++--------- R/plots.R | 10 + build/vignette.rds |binary inst/doc/data-requirement.html | 9 - inst/doc/process-results.html | 21 +-- inst/doc/register-data-manually.R | 34 ++-- inst/doc/register-data-manually.html | 5 inst/doc/register-data.R | 54 +++---- inst/doc/register-data.html | 29 ++-- inst/extdata/brapa_arabidopsis_registration.rds |binary tests/testthat/test-registration.R | 4 tests/testthat/test-results.R | 2 16 files changed, 240 insertions(+), 157 deletions(-)
Title: Publication-Quality 'ggplot2' Annotation
Description: Annotation helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to annotate plots in
a way that stays consistent with the set theme.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggscribe versions 0.1.0 dated 2026-05-02 and 0.1.1 dated 2026-05-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 45 ++++++++++++++++++++++++++++++++++++++++++++- man/figures/logo.png |binary 5 files changed, 55 insertions(+), 8 deletions(-)
Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, <doi:10.1016/j.csda.2003.11.001>). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, <doi:10.1006/jmva.2000.1920>). There is a package vignette "subselect", which includes additional references.
Author: Jorge Orestes Cerdeira [aut],
Pedro Duarte Silva [aut, cre],
Jorge Cadima [aut],
Manuel Minhoto [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Diff between subselect versions 0.16.0 dated 2025-03-31 and 0.16.1 dated 2026-05-04
DESCRIPTION | 8 MD5 | 44 R/anneal.R | 17 R/eleaps.R | 349 +-- R/genetic.R | 79 R/improve.R | 76 R/prepRetOtp.R | 35 build/vignette.rds |binary inst/CHANGELOG | 2 inst/doc/subselect.Rnw | 4104 +++++++++++++++++++++++----------------------- inst/doc/subselect.pdf |binary man/subselect-internal.Rd | 2 src/ErrMReals.h | 1 src/Gstatma.cpp | 4 src/SRI_sscma.cpp | 86 src/SRI_sscma.h | 1 src/SR_datatrnsf.cpp | 4 src/SR_intf.cpp | 2 src/Sscma.cpp | 5 src/Sscma.h | 4 src/Subsets.cpp | 1 src/Wrkf1.cpp | 7 vignettes/subselect.Rnw | 4104 +++++++++++++++++++++++----------------------- 23 files changed, 4473 insertions(+), 4462 deletions(-)
Title: Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver", symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Jeroen van Raak [aut] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.28 dated 2026-04-07 and 1.29 dated 2026-05-04
liver-1.28/liver/data/NMES1988.RData |only liver-1.28/liver/data/corona.RData |only liver-1.28/liver/data/fertilizer.RData |only liver-1.28/liver/man/NMES1988.Rd |only liver-1.28/liver/man/corona.Rd |only liver-1.28/liver/man/fertilizer.Rd |only liver-1.29/liver/DESCRIPTION | 6 +- liver-1.29/liver/MD5 | 64 ++++++++++++------------ liver-1.29/liver/NEWS.md | 10 +++ liver-1.29/liver/data/creditcard_fraud.RData |only liver-1.29/liver/data/datalist | 6 +- liver-1.29/liver/data/purchase_intention.RData |only liver-1.29/liver/data/wholesale_customers.RData |only liver-1.29/liver/man/adult.Rd | 20 +++---- liver-1.29/liver/man/advertising.Rd | 3 - liver-1.29/liver/man/bank.Rd | 3 - liver-1.29/liver/man/bike_demand.Rd | 3 - liver-1.29/liver/man/caravan.Rd | 3 - liver-1.29/liver/man/cereal.Rd | 3 - liver-1.29/liver/man/churn.Rd | 3 - liver-1.29/liver/man/churn_mlc.Rd | 3 - liver-1.29/liver/man/churn_tel.Rd | 3 - liver-1.29/liver/man/cpu_price.Rd | 3 - liver-1.29/liver/man/credit.Rd | 4 - liver-1.29/liver/man/creditcard_fraud.Rd |only liver-1.29/liver/man/doctor_visits.Rd | 3 - liver-1.29/liver/man/drug.Rd | 3 - liver-1.29/liver/man/gapminder.Rd | 3 - liver-1.29/liver/man/house.Rd | 3 - liver-1.29/liver/man/house_price.Rd | 3 - liver-1.29/liver/man/insurance.Rd | 3 - liver-1.29/liver/man/loan.Rd | 3 - liver-1.29/liver/man/marketing.Rd | 3 - liver-1.29/liver/man/mortgage.Rd | 3 - liver-1.29/liver/man/purchase_intention.Rd |only liver-1.29/liver/man/red_wines.Rd | 3 - liver-1.29/liver/man/risk.Rd | 3 - liver-1.29/liver/man/white_wines.Rd | 3 - liver-1.29/liver/man/wholesale_customers.Rd |only 39 files changed, 80 insertions(+), 93 deletions(-)
Title: A Unified Framework for Machine Learning Ensembles in Survival
Analysis
Description: Implements a Super Learner framework for right-censored survival data.
The package fits convex combinations of parametric, semiparametric, and machine
learning survival learners by minimizing cross-validated risk using inverse
probability of censoring weighting (IPCW). It provides tools for automated
hyperparameter grid search, high-dimensional variable screening, and evaluation
of prediction performance using metrics such as the Brier score, Uno's C-index,
and time-dependent area under the curve (AUC). Additional utilities support
model interpretation for survival ensembles, including Shapley additive
explanations (SHAP), and estimation of covariate-adjusted restricted mean
survival time (RMST) contrasts. The methodology is related to treatment-specific
survival curve estimation using machine learning described by Westling et al.
(2024) <doi:10.1080/01621459.2023.2205060>, and the unified
ensemble framework described in Lyu et al. (2026) <doi:10.64898/2026.03.11.711010>.
Author: Yue Lyu [aut, cre]
Maintainer: Yue Lyu <yuelyu0521@gmail.com>
Diff between SuperSurv versions 0.1.1 dated 2026-03-26 and 0.1.2 dated 2026-05-04
SuperSurv-0.1.1/SuperSurv/man/predict.surv.aorsf.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.bart.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.coxboost.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.coxph.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.gam.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.gbm.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.glmnet.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.km.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.parametric.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.ranger.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.rfsrc.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.ridge.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.rpart.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.svm.Rd |only SuperSurv-0.1.1/SuperSurv/man/predict.surv.xgboost.Rd |only SuperSurv-0.1.2/SuperSurv/DESCRIPTION | 14 SuperSurv-0.1.2/SuperSurv/MD5 | 190 ++--- SuperSurv-0.1.2/SuperSurv/NAMESPACE | 16 SuperSurv-0.1.2/SuperSurv/R/SuperSurv-methods.R |only SuperSurv-0.1.2/SuperSurv/R/SuperSurv.R | 26 SuperSurv-0.1.2/SuperSurv/R/evaluation.R | 6 SuperSurv-0.1.2/SuperSurv/R/explainability.R | 7 SuperSurv-0.1.2/SuperSurv/R/global.R | 4 SuperSurv-0.1.2/SuperSurv/R/helper.R | 5 SuperSurv-0.1.2/SuperSurv/R/predict.SuperSurv.R | 42 - SuperSurv-0.1.2/SuperSurv/R/rmst.R | 396 ++++++++++-- SuperSurv-0.1.2/SuperSurv/R/utils_internal.R | 63 + SuperSurv-0.1.2/SuperSurv/R/visualization.R | 3 SuperSurv-0.1.2/SuperSurv/R/wrapper.R | 105 ++- SuperSurv-0.1.2/SuperSurv/README.md | 127 ++- SuperSurv-0.1.2/SuperSurv/build/vignette.rds |binary SuperSurv-0.1.2/SuperSurv/inst/doc/base-learner-rfsrc.R | 4 SuperSurv-0.1.2/SuperSurv/inst/doc/base-learner-rfsrc.Rmd | 9 SuperSurv-0.1.2/SuperSurv/inst/doc/base-learner-rfsrc.html | 14 SuperSurv-0.1.2/SuperSurv/inst/doc/causal-rmst.R | 111 ++- SuperSurv-0.1.2/SuperSurv/inst/doc/causal-rmst.Rmd | 58 + SuperSurv-0.1.2/SuperSurv/inst/doc/causal-rmst.html | 121 ++- SuperSurv-0.1.2/SuperSurv/inst/doc/extending-supersurv.R |only SuperSurv-0.1.2/SuperSurv/inst/doc/extending-supersurv.Rmd |only SuperSurv-0.1.2/SuperSurv/inst/doc/extending-supersurv.html |only SuperSurv-0.1.2/SuperSurv/inst/doc/grid-search.R | 2 SuperSurv-0.1.2/SuperSurv/inst/doc/grid-search.Rmd | 6 SuperSurv-0.1.2/SuperSurv/inst/doc/grid-search.html | 10 SuperSurv-0.1.2/SuperSurv/inst/doc/installation.Rmd | 4 SuperSurv-0.1.2/SuperSurv/inst/doc/installation.html | 4 SuperSurv-0.1.2/SuperSurv/inst/doc/model-performance.R | 2 SuperSurv-0.1.2/SuperSurv/inst/doc/model-performance.Rmd | 7 SuperSurv-0.1.2/SuperSurv/inst/doc/model-performance.html | 8 SuperSurv-0.1.2/SuperSurv/inst/doc/parametric-models.R | 6 SuperSurv-0.1.2/SuperSurv/inst/doc/parametric-models.Rmd | 10 SuperSurv-0.1.2/SuperSurv/inst/doc/parametric-models.html | 44 - SuperSurv-0.1.2/SuperSurv/inst/doc/screening-methods.R | 10 SuperSurv-0.1.2/SuperSurv/inst/doc/screening-methods.Rmd | 17 SuperSurv-0.1.2/SuperSurv/inst/doc/screening-methods.html | 42 - SuperSurv-0.1.2/SuperSurv/inst/doc/shap-explanations.Rmd | 5 SuperSurv-0.1.2/SuperSurv/inst/doc/shap-explanations.html | 22 SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-best.R | 4 SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-best.Rmd | 10 SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-best.html | 12 SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-ensemble.R | 26 SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-ensemble.Rmd | 59 + SuperSurv-0.1.2/SuperSurv/inst/doc/supersurv-ensemble.html | 249 +++++-- SuperSurv-0.1.2/SuperSurv/man/SuperSurv.Rd | 23 SuperSurv-0.1.2/SuperSurv/man/coef.SuperSurv.Rd |only SuperSurv-0.1.2/SuperSurv/man/create_grid.Rd | 3 SuperSurv-0.1.2/SuperSurv/man/estimate_marginal_rmst.Rd | 137 +++- SuperSurv-0.1.2/SuperSurv/man/eval_brier.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/eval_cindex.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/eval_timeROC.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/eval_times.Rd |only SuperSurv-0.1.2/SuperSurv/man/event_weights.Rd |only SuperSurv-0.1.2/SuperSurv/man/learner_names.Rd |only SuperSurv-0.1.2/SuperSurv/man/plot_marginal_rmst_curve.Rd | 49 + SuperSurv-0.1.2/SuperSurv/man/plot_predict.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/predict.SuperSurv.Rd | 35 - SuperSurv-0.1.2/SuperSurv/man/print.SuperSurv.Rd |only SuperSurv-0.1.2/SuperSurv/man/selected_variables.Rd |only SuperSurv-0.1.2/SuperSurv/man/summary.SuperSurv.Rd |only SuperSurv-0.1.2/SuperSurv/man/surv.aorsf.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.bart.Rd | 4 SuperSurv-0.1.2/SuperSurv/man/surv.coxboost.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.coxph.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.exponential.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.gam.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.gbm.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.glmnet.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.km.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.loglogistic.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.lognormal.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.parametric.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.ranger.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.rfsrc.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.ridge.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.rpart.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.svm.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.weibull.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/surv.xgboost.Rd | 2 SuperSurv-0.1.2/SuperSurv/man/training_variables.Rd |only SuperSurv-0.1.2/SuperSurv/tests |only SuperSurv-0.1.2/SuperSurv/vignettes/base-learner-rfsrc.Rmd | 9 SuperSurv-0.1.2/SuperSurv/vignettes/causal-rmst.Rmd | 58 + SuperSurv-0.1.2/SuperSurv/vignettes/extending-supersurv.Rmd |only SuperSurv-0.1.2/SuperSurv/vignettes/grid-search.Rmd | 6 SuperSurv-0.1.2/SuperSurv/vignettes/installation.Rmd | 4 SuperSurv-0.1.2/SuperSurv/vignettes/model-performance.Rmd | 7 SuperSurv-0.1.2/SuperSurv/vignettes/parametric-models.Rmd | 10 SuperSurv-0.1.2/SuperSurv/vignettes/screening-methods.Rmd | 17 SuperSurv-0.1.2/SuperSurv/vignettes/shap-explanations.Rmd | 5 SuperSurv-0.1.2/SuperSurv/vignettes/supersurv-best.Rmd | 10 SuperSurv-0.1.2/SuperSurv/vignettes/supersurv-ensemble.Rmd | 59 + 110 files changed, 1598 insertions(+), 762 deletions(-)
Title: Temporal Disaggregation and Benchmarking in 'JDemetra+' 3.x
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It provides a variety of methods for
temporal disaggregation & interpolation, benchmarking, reconciliation
and calendarization. It incorporates statistical methods described in
the latest European Statistical System (ESS) guidelines on temporal
disaggregation, benchmarking, and reconciliation (2018 edition). The package
implements highly efficient algorithms for fast and reliable computation.
Author: Jean Palate [aut],
Corentin Lemasson [aut, cre],
Tanguy Barthelemy [ctb, art],
Nikolina Rizanovska [ctb]
Maintainer: Corentin Lemasson <corentin.lemasson@nbb.be>
Diff between rjd3bench versions 3.1.1 dated 2026-03-29 and 3.1.2 dated 2026-05-04
DESCRIPTION | 12 ++- MD5 | 50 +++++++------- NEWS.md | 15 +++- R/adl.R | 8 +- R/benchmark.R | 76 ++++++++++------------ R/mbdenton.R | 6 + R/tempdisagg.R | 48 ++++++++++---- inst/doc/rjd3bench.R | 11 +-- inst/doc/rjd3bench.Rmd | 28 ++++---- inst/doc/rjd3bench.html | 124 +++++++++++++++++++------------------ man/adl_disaggregation.Rd | 10 ++ man/cholette.Rd | 6 - man/cubicspline.Rd | 4 - man/denton.Rd | 4 - man/denton_modelbased.Rd | 8 +- man/denton_raw.Rd | 4 - man/deprecated-rjd3bench.Rd | 66 +++++++++---------- man/grp.Rd | 9 +- man/multivariatecholette.Rd | 57 +++++++---------- man/qna_data.Rd | 98 ++++++++++++++--------------- man/temporal_disaggregation.Rd | 12 ++- man/temporal_disaggregation_raw.Rd | 12 ++- man/temporal_interpolation.Rd | 12 ++- man/temporal_interpolation_raw.Rd | 12 ++- man/temporaldisaggregationI.Rd | 10 ++ vignettes/rjd3bench.Rmd | 28 ++++---- 26 files changed, 402 insertions(+), 328 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <diego.pedregal@uclm.es>
Diff between UComp versions 5.2 dated 2026-04-24 and 5.3.1 dated 2026-05-04
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 21 +++-- NAMESPACE | 2 R/UCmodel.R | 4 - R/rapidFunctions.R |only man/DAYforecast.Rd |only man/WEEKforecast.Rd |only src/ARIMAmodel.h | 35 +++++++- src/BSMmodel.h | 204 ++++++++++++++++++++++++++++++++-------------------- src/ETSmodel.h | 9 ++ src/UCompC.cpp | 6 + src/stats.h | 2 13 files changed, 192 insertions(+), 104 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous, ordinal, and continuous response data using latent space item response model ('LSIRM'). Provides 1PL and 2PL 'LSIRM' for binary response data as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>, graded response models ('GRM') for ordinal data (De Carolis et al., 2025, <doi:10.1080/00273171.2025.2605678>), and extensions for continuous response data. Supports Bayesian model selection with spike-and-slab priors, adaptive MCMC algorithms, and methods for handling missing data under missing at random ('MAR') and missing completely at random ('MCAR') assumptions. Provides various diagnostic plots to inspect the latent space and summaries of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 2.0.0 dated 2026-02-04 and 2.0.1 dated 2026-05-04
lsirm12pl-2.0.0/lsirm12pl/R/lsirmgrm2pl_mar.R |only lsirm12pl-2.0.0/lsirm12pl/R/lsirmgrm_mar.R |only lsirm12pl-2.0.0/lsirm12pl/man/lsirmgrm2pl_mar.Rd |only lsirm12pl-2.0.0/lsirm12pl/man/lsirmgrm_mar.Rd |only lsirm12pl-2.0.1/lsirm12pl/DESCRIPTION | 10 lsirm12pl-2.0.1/lsirm12pl/MD5 | 204 lsirm12pl-2.0.1/lsirm12pl/NAMESPACE | 2 lsirm12pl-2.0.1/lsirm12pl/R/lsirm.R | 3077 +++++----- lsirm12pl-2.0.1/lsirm12pl/R/lsirm12pl-package.R | 2 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_fixed_gamma.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_fixed_gamma_mar.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_fixed_gamma_mcar.R | 21 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_mar.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_mar_ss.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_mcar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_mcar_ss.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_fixed_gamma.R | 13 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mcar.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_mar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_mar_ss.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_mcar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_mcar_ss.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_o.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_normal_ss.R | 191 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_o.R | 36 lsirm12pl-2.0.1/lsirm12pl/R/lsirm1pl_ss.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_fixed_gamma.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_fixed_gamma_mar.R | 31 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_fixed_gamma_mcar.R | 20 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_mar.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_mar_ss.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_mcar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_mcar_ss.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_fixed_gamma.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mar.R | 30 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mcar.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_mar.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_mar_ss.R | 21 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_mcar.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_mcar_ss.R | 19 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_o.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_normal_ss.R | 17 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_o.R | 24 lsirm12pl-2.0.1/lsirm12pl/R/lsirm2pl_ss.R | 15 lsirm12pl-2.0.1/lsirm12pl/R/lsirmgrm.R | 188 lsirm12pl-2.0.1/lsirm12pl/R/lsirmgrm2pl.R | 201 lsirm12pl-2.0.1/lsirm12pl/R/lsirmgrm2pl_mcar.R | 1 lsirm12pl-2.0.1/lsirm12pl/R/lsirmgrm2pl_ss.R | 1 lsirm12pl-2.0.1/lsirm12pl/R/plot.lsirm.R | 7 lsirm12pl-2.0.1/lsirm12pl/R/utilities.R | 43 lsirm12pl-2.0.1/lsirm12pl/man/lsirm.Rd | 9 lsirm12pl-2.0.1/lsirm12pl/man/lsirm12pl.Rd | 3 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl.Rd | 30 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_fixed_gamma.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_fixed_gamma_mar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_fixed_gamma_mcar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_mar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_mar_ss.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_mcar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_mcar_ss.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_fixed_gamma.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_fixed_gamma_mar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_fixed_gamma_mcar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_mar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_mar_ss.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_mcar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_mcar_ss.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_o.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_normal_ss.Rd | 22 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_o.Rd | 14 lsirm12pl-2.0.1/lsirm12pl/man/lsirm1pl_ss.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl.Rd | 34 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_fixed_gamma.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_fixed_gamma_mar.Rd | 5 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_fixed_gamma_mcar.Rd | 3 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_mar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_mar_ss.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_mcar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_mcar_ss.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_fixed_gamma.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_fixed_gamma_mar.Rd | 22 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_fixed_gamma_mcar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_mar.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_mar_ss.Rd | 22 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_mcar.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_mcar_ss.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_o.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_normal_ss.Rd | 20 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_o.Rd | 14 lsirm12pl-2.0.1/lsirm12pl/man/lsirm2pl_ss.Rd | 18 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm.Rd | 48 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm2pl.Rd | 48 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm2pl_fixed_gamma.Rd | 19 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm2pl_mcar.Rd | 14 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm2pl_o.Rd | 28 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm2pl_ss.Rd | 19 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm_fixed_gamma.Rd | 19 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm_mcar.Rd | 14 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm_o.Rd | 28 lsirm12pl-2.0.1/lsirm12pl/man/lsirmgrm_ss.Rd | 19 lsirm12pl-2.0.1/lsirm12pl/man/plot.Rd | 7 lsirm12pl-2.0.1/lsirm12pl/src/lsirm1pl.cpp | 17 lsirm12pl-2.0.1/lsirm12pl/src/lsirm2pl.cpp | 19 lsirm12pl-2.0.1/lsirm12pl/src/lsirm_grm.cpp | 15 105 files changed, 3392 insertions(+), 2234 deletions(-)
Title: Easy Access for South Korea Census Data and Boundaries
Description: Census and administrative data in South Korea are a basic source of
quantitative and mixed-methods research for social and urban scientists.
This package provides a 'sf' (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>)
based standardized workflow based on direct open API access to the major census and
administrative data sources and pre-generated files in South Korea.
Author: Insang Song [aut, cre] ,
Sohyun Park [aut, ctb] ,
Hyesop Shin [aut, ctb]
Maintainer: Insang Song <geoissong@snu.ac.kr>
Diff between tidycensuskr versions 0.2.7 dated 2026-01-08 and 0.2.8 dated 2026-05-04
tidycensuskr-0.2.7/tidycensuskr/man/figures/barchart.png |only tidycensuskr-0.2.7/tidycensuskr/man/figures/population.png |only tidycensuskr-0.2.7/tidycensuskr/man/figures/seoul_ai.jpeg |only tidycensuskr-0.2.7/tidycensuskr/tests |only tidycensuskr-0.2.8/tidycensuskr/DESCRIPTION | 6 tidycensuskr-0.2.8/tidycensuskr/MD5 | 45 +- tidycensuskr-0.2.8/tidycensuskr/NAMESPACE | 1 tidycensuskr-0.2.8/tidycensuskr/NEWS.md | 1 tidycensuskr-0.2.8/tidycensuskr/R/utility.R |only tidycensuskr-0.2.8/tidycensuskr/README.md | 153 ++++++++- tidycensuskr-0.2.8/tidycensuskr/build/vignette.rds |binary tidycensuskr-0.2.8/tidycensuskr/inst/doc/v01_intro.R | 5 tidycensuskr-0.2.8/tidycensuskr/inst/doc/v01_intro.Rmd | 5 tidycensuskr-0.2.8/tidycensuskr/inst/doc/v01_intro.html | 9 tidycensuskr-0.2.8/tidycensuskr/inst/doc/v02_regional_analysis.R | 36 +- tidycensuskr-0.2.8/tidycensuskr/inst/doc/v02_regional_analysis.Rmd | 42 +- tidycensuskr-0.2.8/tidycensuskr/inst/doc/v02_regional_analysis.html | 167 +++++----- tidycensuskr-0.2.8/tidycensuskr/inst/doc/v03_gallery.html | 5 tidycensuskr-0.2.8/tidycensuskr/inst/doc/v04_data_cleaning_kosis.html | 3 tidycensuskr-0.2.8/tidycensuskr/inst/doc/v05_contributors_guide.html | 3 tidycensuskr-0.2.8/tidycensuskr/man/detect_adm2_type.Rd |only tidycensuskr-0.2.8/tidycensuskr/man/figures/README-final_map-1.png |binary tidycensuskr-0.2.8/tidycensuskr/man/figures/README-mapmaking-1.png |binary tidycensuskr-0.2.8/tidycensuskr/man/figures/README-seoul_map-1.png |binary tidycensuskr-0.2.8/tidycensuskr/vignettes/v01_intro.Rmd | 5 tidycensuskr-0.2.8/tidycensuskr/vignettes/v02_regional_analysis.Rmd | 42 +- 26 files changed, 335 insertions(+), 193 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.2.0 dated 2026-04-22 and 0.2.1 dated 2026-05-04
ChangeLog | 4 ++ DESCRIPTION | 8 ++--- MD5 | 18 ++++++----- R/RcppExports.R | 4 ++ R/zzz.R | 22 ++++++++++++++ src/Makevars.win | 2 - src/RcppExports.cpp | 10 ++++++ src/qdata_cpp_external_api.h | 9 +++-- src/qx_functions.cpp | 67 ++++++++++--------------------------------- src/qx_nthreads_guard.h |only tests/fork_tbb_testing.R |only 11 files changed, 77 insertions(+), 67 deletions(-)
Title: Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs
Sampling or EM-Algorithms
Description: Create forecasts from multiple predictions using ensemble Bayesian model averaging (EBMA). EBMA models can be estimated using an expectation maximization (EM) algorithm or as fully Bayesian models via Gibbs sampling. The methods in this package are Montgomery, Hollenbach, and Ward (2015) <doi:10.1016/j.ijforecast.2014.08.001> and Montgomery, Hollenbach, and Ward (2012) <doi:10.1093/pan/mps002>.
Author: Florian M. Hollenbach [aut, cre] ,
Jacob M. Montgomery [aut],
Michael D. Ward [aut]
Maintainer: Florian M. Hollenbach <fho.egb@cbs.dk>
This is a re-admission after prior archival of version 1.0.32 dated 2024-03-20
Diff between EBMAforecast versions 1.0.32 dated 2024-03-20 and 1.0.33 dated 2026-05-04
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- build/partial.rdb |binary man/EBMAforecast-package.Rd | 1 + src/Samplers.cpp | 7 +++---- tests/testthat/Rplots.pdf |binary 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Descriptive Statistics, Summary Tables, and Data Management
Tools
Description: Provides tools for descriptive data analysis,
variable inspection, data management, and tabulation workflows in 'R'.
Summarizes variable metadata, labels, classes, missing values, and
representative values, with support for readable frequency tables,
cross-tabulations, association measures for contingency tables
(Cramer's V, Phi, Goodman-Kruskal Gamma, Kendall's Tau-b, Somers' D,
and others), categorical and continuous summary tables, and
model-based bivariate tables for continuous outcomes, including
APA-style reporting outputs. Includes helpers for interactive
codebooks, variable label extraction, clipboard export, and row-wise
descriptive summaries. Designed to make descriptive analysis and
reporting faster, clearer, and easier to work with in practice.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.10.0 dated 2026-04-27 and 0.11.0 dated 2026-05-04
DESCRIPTION | 17 MD5 | 191 - NAMESPACE | 54 NEWS.md | 136 R/abort.R |only R/assoc.R | 209 - R/code_book-filename.R | 32 R/code_book-validation.R | 28 R/code_book.R | 16 R/copy_clipboard.R | 85 R/count_n.R | 32 R/cross_tab.R | 255 + R/freq.R | 134 R/freq_print.R | 34 R/label_from_names.R | 182 R/mean_n.R | 136 R/row_n_helpers.R |only R/selection_helpers.R | 32 R/spicy-package.R | 81 R/sum_n.R | 138 R/table_categorical.R | 889 ++++ R/table_categorical_print.R | 465 ++ R/table_continuous.R | 1248 ++++-- R/table_continuous_lm.R | 2346 ++++++++++-- R/table_continuous_lm_print.R | 416 +- R/table_continuous_print.R | 271 + R/table_helpers.R |only R/tables_ascii.R | 123 R/varlist-title.R | 95 R/varlist-validation.R | 47 R/varlist-values.R | 53 R/varlist.R | 34 README.md | 157 build/partial.rdb |only inst/doc/association-measures.html | 215 - inst/doc/frequency-tables.html | 668 +-- inst/doc/spicy.html | 226 - inst/doc/summary-tables-reporting.html | 114 inst/doc/table-categorical.R | 48 inst/doc/table-categorical.Rmd | 109 inst/doc/table-categorical.html | 422 +- inst/doc/table-continuous-lm.R | 113 inst/doc/table-continuous-lm.Rmd | 227 + inst/doc/table-continuous-lm.html | 401 +- inst/doc/table-continuous.R | 39 inst/doc/table-continuous.Rmd | 80 inst/doc/table-continuous.html | 765 ++-- man/as.data.frame.spicy_categorical_table.Rd |only man/as.data.frame.spicy_continuous_lm_table.Rd |only man/as.data.frame.spicy_continuous_table.Rd |only man/assoc_measures.Rd | 14 man/build_ascii_table.Rd | 35 man/code_book.Rd | 5 man/contingency_coef.Rd | 14 man/count_n.Rd | 8 man/cramer_v.Rd | 24 man/cross_tab.Rd | 21 man/freq.Rd | 30 man/gamma_gk.Rd | 14 man/goodman_kruskal_tau.Rd | 14 man/kendall_tau_b.Rd | 14 man/kendall_tau_c.Rd | 14 man/label_from_names.Rd | 82 man/lambda_gk.Rd | 14 man/mean_n.Rd | 27 man/phi.Rd | 23 man/print.spicy_assoc_detail.Rd | 5 man/print.spicy_assoc_table.Rd | 8 man/print.spicy_cross_table.Rd | 9 man/somers_d.Rd | 14 man/spicy-package.Rd | 61 man/spicy_print_table.Rd | 18 man/spicy_tables.Rd | 5 man/sum_n.Rd | 29 man/table_categorical.Rd | 296 + man/table_continuous.Rd | 340 + man/table_continuous_lm.Rd | 779 +++- man/tidy.spicy_categorical_table.Rd |only man/tidy.spicy_continuous_lm_table.Rd |only man/tidy.spicy_continuous_table.Rd |only man/uncertainty_coef.Rd | 27 man/varlist.Rd | 11 man/yule_q.Rd | 14 tests/testthat/_snaps |only tests/testthat/test-assoc.R | 150 tests/testthat/test-code_book.R | 16 tests/testthat/test-copy_clipboard.R | 89 tests/testthat/test-cross_tab.R | 126 tests/testthat/test-freq.R | 60 tests/testthat/test-label_from_names.R | 146 tests/testthat/test-mean_n.R | 41 tests/testthat/test-selection_helpers.R |only tests/testthat/test-snapshots.R |only tests/testthat/test-sum_n.R | 21 tests/testthat/test-table_categorical.R | 534 ++ tests/testthat/test-table_continuous.R | 683 +++ tests/testthat/test-table_continuous_lm.R | 4653 +++++++++++++++++++------ tests/testthat/test-tables_ascii.R | 115 tests/testthat/test-varlist.R | 117 tools/coverage_table_continuous_lm_probes.R | 8 vignettes/table-categorical.Rmd | 109 vignettes/table-continuous-lm.Rmd | 227 + vignettes/table-continuous.Rmd | 80 103 files changed, 15971 insertions(+), 4536 deletions(-)
Title: Simulate Data for Discrete Choice Experiments
Description: Supports simulating choice experiment data for given designs. It helps to quickly test different designs against each other and compare the performance of new models. The goal of 'simulateDCE' is to make it easy to simulate choice experiment datasets using designs from 'NGENE', 'idefix' or 'spdesign'. You have to store the design file(s) in a sub-directory and need to specify certain parameters and the utility functions for the data generating process. For more details on choice experiments see Mariel et al. (2021) <doi:10.1007/978-3-030-62669-3>.
Author: Julian Sagebiel [aut, cre]
Maintainer: Julian Sagebiel <julian.sagebiel@idiv.de>
This is a re-admission after prior archival of version 0.3.1 dated 2025-07-26
Diff between simulateDCE versions 0.3.1 dated 2025-07-26 and 0.3.2 dated 2026-05-04
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/aggregateResults.R | 2 +- R/sim_all.R | 2 +- R/sim_choice.R | 8 ++++---- R/simulate_choices.R | 12 +++++++++++- inst/doc/SE_Agri-vignette.html | 31 ++++++++++++++++--------------- inst/doc/SE_drive-vignette.html | 29 +++++++++++++++-------------- inst/doc/csa-vignette.html | 31 ++++++++++++++++--------------- man/simulate_choices.Rd | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-simulate_choices.R | 28 +++++++++++++++++++--------- 13 files changed, 107 insertions(+), 77 deletions(-)
Title: Fast Calculation of Feature Contributions in Boosting Trees
Description: Computes feature-specific R-squared (R2) contributions for
boosting tree models using a Shapley-value-based decomposition of the
total R-squared in polynomial time. Supports models fitted with
'XGBoost', 'LightGBM', and 'CatBoost', with optimized backend-specific
implementations and cached tree summaries suitable for large-scale
problems. Multiple
visualization tools are included for interpreting and communicating
feature contributions. The methodology is described in Jiang, Zhang,
and Zhang (2025) <doi:10.48550/arXiv.2407.03515>. Optional 'CatBoost'
support uses the R package 'catboost', which is not distributed on CRAN;
installation instructions and released binaries are provided by the
CatBoost project at <https://catboost.ai/docs/en/concepts/r-installation>.
Author: Steven He [aut],
Zhongli Jiang [aut, cre],
Dabao Zhang [aut]
Maintainer: Zhongli Jiang <zhongli.jiang.stats@gmail.com>
Diff between qshap versions 1.0 dated 2026-03-16 and 1.0.1 dated 2026-05-04
DESCRIPTION | 18 ++-- MD5 | 21 ++--- NAMESPACE | 1 R/RcppExports.R | 4 R/catboost_utils.R |only R/classes.R | 12 +- R/lightgbm_utils.R | 50 ++++-------- R/tree_explainer.R | 77 +++++++++++++++--- R/xgboost_utils.R | 52 ++++-------- man/gazer.Rd | 3 src/RcppExports.cpp | 18 ++++ src/qshap.cpp | 216 +++++++++++++++++++++++++++++++++++++++++++++++++--- 12 files changed, 360 insertions(+), 112 deletions(-)
Title: Extended Dynamic Quantile Linear Models
Description: Bayesian quantile-regression routines for dynamic state-space
models and static regression under the extended asymmetric Laplace
(exAL) error distribution. The dynamic state-space models are extended
dynamic quantile linear models (exDQLMs). The package combines dynamic
exDQLM inference via LDVB, MCMC, and legacy ISVB with static exAL
regression via LDVB and MCMC, reduced AL/DQLM paths through fixed
skewness, component builders for trend/seasonality/regression blocks,
static shrinkage priors including ridge, regularized horseshoe, and
'rhs_ns', evidence lower bound diagnostics, optional C++ accelerators,
and posterior predictive synthesis across separately fitted quantiles
through 'quantileSynthesis()'. Dynamic exDQLM methods are described in
Barata et al. (2020) <doi:10.1214/21-AOAS1497>.
Author: Raquel Barata [aut, cre],
Raquel Prado [ths],
Bruno Sanso [ths],
Antonio Aguirre [aut]
Maintainer: Raquel Barata <raquel.a.barata@gmail.com>
Diff between exdqlm versions 0.3.0 dated 2026-02-07 and 0.4.0 dated 2026-05-04
exdqlm-0.3.0/exdqlm/R/nino34.R |only exdqlm-0.3.0/exdqlm/R/transfn_exdqlmISVB.R |only exdqlm-0.3.0/exdqlm/data/nino34.rda |only exdqlm-0.3.0/exdqlm/man/nino34.Rd |only exdqlm-0.3.0/exdqlm/man/transfn_exdqlmISVB.Rd |only exdqlm-0.4.0/exdqlm/DESCRIPTION | 30 exdqlm-0.4.0/exdqlm/MD5 | 191 - exdqlm-0.4.0/exdqlm/NAMESPACE | 40 exdqlm-0.4.0/exdqlm/NEWS.md | 90 exdqlm-0.4.0/exdqlm/R/BTflow.R | 18 exdqlm-0.4.0/exdqlm/R/RcppExports.R | 20 exdqlm-0.4.0/exdqlm/R/climateIndices.R |only exdqlm-0.4.0/exdqlm/R/compPlot.R | 39 exdqlm-0.4.0/exdqlm/R/exal.R | 2 exdqlm-0.4.0/exdqlm/R/exalStaticDiagnostics.R |only exdqlm-0.4.0/exdqlm/R/exalStaticLDVB.R |only exdqlm-0.4.0/exdqlm/R/exalStaticMCMC.R |only exdqlm-0.4.0/exdqlm/R/exal_inference_config.R |only exdqlm-0.4.0/exdqlm/R/exdqlm-package.R | 58 exdqlm-0.4.0/exdqlm/R/exdqlmDiagnostics.R | 60 exdqlm-0.4.0/exdqlm/R/exdqlmForecast.R | 136 exdqlm-0.4.0/exdqlm/R/exdqlmISVB.R | 307 + exdqlm-0.4.0/exdqlm/R/exdqlmLDVB.R |only exdqlm-0.4.0/exdqlm/R/exdqlmMCMC.R | 1899 +++++++++- exdqlm-0.4.0/exdqlm/R/exdqlmPlot.R | 28 exdqlm-0.4.0/exdqlm/R/exdqlmTransferISVB.R |only exdqlm-0.4.0/exdqlm/R/exdqlmTransferLDVB.R |only exdqlm-0.4.0/exdqlm/R/exdqlmTransferMCMC.R |only exdqlm-0.4.0/exdqlm/R/generics_etc.R | 754 +++ exdqlm-0.4.0/exdqlm/R/polytrendMod.R | 78 exdqlm-0.4.0/exdqlm/R/quantileSynthesis.R |only exdqlm-0.4.0/exdqlm/R/regMod.R |only exdqlm-0.4.0/exdqlm/R/seasMod.R | 125 exdqlm-0.4.0/exdqlm/R/static_beta_prior.R |only exdqlm-0.4.0/exdqlm/R/transfer_function_helpers.R |only exdqlm-0.4.0/exdqlm/R/update_theta_bridge.R | 6 exdqlm-0.4.0/exdqlm/R/utils.R | 1474 +++++++ exdqlm-0.4.0/exdqlm/R/zzz.R | 6 exdqlm-0.4.0/exdqlm/README.md | 318 + exdqlm-0.4.0/exdqlm/data/BTflow.rda |binary exdqlm-0.4.0/exdqlm/data/climateIndices.rda |only exdqlm-0.4.0/exdqlm/man/BTflow.Rd | 17 exdqlm-0.4.0/exdqlm/man/as.exdqlm.Rd | 2 exdqlm-0.4.0/exdqlm/man/climateIndices.Rd |only exdqlm-0.4.0/exdqlm/man/compPlot.Rd | 30 exdqlm-0.4.0/exdqlm/man/exalStaticDiagnostics.Rd |only 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Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.3.2 dated 2026-04-22 and 0.3.3 dated 2026-05-04
DESCRIPTION | 8 +++--- MD5 | 17 +++++++------- NAMESPACE | 9 ------- NEWS.md | 4 +++ R/constants.R | 20 +++++++++-------- R/plotting.R | 2 + README.md | 10 ++++---- inst/doc/detzrcr-vignette.html | 4 +-- inst/shiny-apps/detzrcr_app/app.R | 35 ++++++++++++++++++++++++------ inst/shiny-apps/detzrcr_app/constants.yml |only 10 files changed, 65 insertions(+), 44 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON and GeoPackage, but from version 2.3.4, no longer ESRI Shapefile - use GeoPackage instead.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] ,
Jakub Nowosad [aut, cre] ,
Robin Lovelace [aut] ,
Angelos Mimis [ctb],
Mark Monmonier [ctb] ,
Greg Snow [ctb]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 2.3.4 dated 2025-01-08 and 2.3.5 dated 2026-05-04
DESCRIPTION | 17 +++++++++-------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ R/baltimore.R | 2 +- R/coffee_data.R | 8 ++++---- R/cycle_hire_osm.R | 2 +- R/nz.R | 24 ++++++++++++------------ R/nz_height.R | 2 +- R/seine.R | 6 +++--- R/urban_agglomerations.R | 4 ++-- man/baltimore.Rd | 2 +- man/coffee_data.Rd | 8 ++++---- man/cycle_hire_osm.Rd | 2 +- man/nz.Rd | 24 ++++++++++++------------ man/nz_height.Rd | 2 +- man/seine.Rd | 6 +++--- man/urban_agglomerations.Rd | 4 ++-- 17 files changed, 77 insertions(+), 72 deletions(-)
Title: A Discrete Colour Palette
Description: A discrete colour palette. These colours make it easier to create
relatively accessible and colour-blind safe visualisation.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between jumble versions 0.1.0 dated 2026-03-16 and 0.1.1 dated 2026-05-04
DESCRIPTION | 15 +++++---- MD5 | 41 +++++++++++++++---------- NEWS.md | 4 ++ R/grey.R |only R/jumble.R | 62 +++------------------------------------ R/navy.R |only R/orange.R |only R/pink.R |only R/red.R |only R/slate.R |only R/teal.R |only README.md | 62 +++++++++++++++++++++++++++++---------- inst |only man/figures/README-example-1.png |binary man/figures/logo.png |binary man/figures/logo.svg | 4 +- man/grey.Rd | 4 +- man/jumble.Rd | 16 ++-------- man/navy.Rd | 4 +- man/orange.Rd | 4 +- man/pink.Rd | 4 +- man/red.Rd | 4 +- man/slate.Rd | 4 +- man/teal.Rd | 4 +- tests/spelling.R |only tests/testthat/test-jumble.R | 4 +- 26 files changed, 112 insertions(+), 124 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd] ,
David Schoch [aut] ,
Maelle Salmon [a [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.3.0 dated 2026-04-21 and 2.3.1 dated 2026-05-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/aaa-auto.R | 5 +---- inst/doc/igraph.html | 40 ++++++++++++++++++++-------------------- inst/doc/igraph_ES.html | 40 ++++++++++++++++++++-------------------- src/cpp11.cpp | 12 ++++++------ 7 files changed, 63 insertions(+), 59 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see <doi:10.18637/jss.v033.i01> and <doi:10.18637/jss.v039.i05>. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (<doi:10.18637/jss.v106.i01>). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers cited.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Kenneth Tay [aut],
Noah Simon [aut],
Junyang Qian [ctb],
James Yang [aut],
Jonathan Taylor [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 4.1-10 dated 2025-07-17 and 5.0 dated 2026-05-04
glmnet-4.1-10/glmnet/R/coxpath.R |only glmnet-4.1-10/glmnet/inst/testscripts |only glmnet-4.1-10/glmnet/man/cox.fit.Rd |only glmnet-4.1-10/glmnet/man/cox.path.Rd |only glmnet-4.1-10/glmnet/man/cox_obj_function.Rd |only glmnet-4.1-10/glmnet/man/figures |only glmnet-4.1-10/glmnet/man/get_cox_lambda_max.Rd |only glmnet-4.1-10/glmnet/man/use.cox.path.Rd |only glmnet-4.1-10/glmnet/src/coxnet5dpclean.f |only glmnet-4.1-10/glmnet/src/glmnetpp/BUILD.bazel |only glmnet-4.1-10/glmnet/src/glmnetpp/CMakeLists.txt |only glmnet-4.1-10/glmnet/src/glmnetpp/README.md |only glmnet-4.1-10/glmnet/src/glmnetpp/WORKSPACE |only glmnet-4.1-10/glmnet/src/glmnetpp/benchmark |only glmnet-4.1-10/glmnet/src/glmnetpp/bug_reports |only glmnet-4.1-10/glmnet/src/glmnetpp/docs |only glmnet-4.1-10/glmnet/src/glmnetpp/environment.yml |only glmnet-4.1-10/glmnet/src/glmnetpp/generate_bazelrc |only glmnet-4.1-10/glmnet/src/glmnetpp/src |only glmnet-4.1-10/glmnet/src/glmnetpp/test |only glmnet-4.1-10/glmnet/src/pb.c |only glmnet-4.1-10/glmnet/vignettes/assets/coxnet.RDS |only glmnet-5.0/glmnet/DESCRIPTION | 18 glmnet-5.0/glmnet/MD5 | 257 +---- glmnet-5.0/glmnet/NAMESPACE | 1 glmnet-5.0/glmnet/NEWS.md | 170 ++- glmnet-5.0/glmnet/R/RcppExports.R | 24 glmnet-5.0/glmnet/R/coxgrad.R | 304 ------ glmnet-5.0/glmnet/R/coxnet.R | 247 ++++- glmnet-5.0/glmnet/R/coxnet.deviance.R | 472 +--------- glmnet-5.0/glmnet/R/cv.glmnet.R | 15 glmnet-5.0/glmnet/R/cv.glmnet.raw.R | 11 glmnet-5.0/glmnet/R/cv.relaxed.raw.R | 11 glmnet-5.0/glmnet/R/glmnet-package.R | 4 glmnet-5.0/glmnet/R/glmnet.R | 137 ++ glmnet-5.0/glmnet/R/glmnet.control.R | 357 +++++-- glmnet-5.0/glmnet/R/glmnetFlex.R | 100 +- glmnet-5.0/glmnet/R/nonzeroCoef.R | 16 glmnet-5.0/glmnet/R/pb.R | 6 glmnet-5.0/glmnet/R/relax.glmnet.R | 2 glmnet-5.0/glmnet/R/response.coxnet.R | 2 glmnet-5.0/glmnet/build/partial.rdb |binary glmnet-5.0/glmnet/build/vignette.rds |binary glmnet-5.0/glmnet/cleanup |only glmnet-5.0/glmnet/inst/doc/Coxnet.R | 11 glmnet-5.0/glmnet/inst/doc/Coxnet.Rmd | 21 glmnet-5.0/glmnet/inst/doc/Coxnet.pdf |binary glmnet-5.0/glmnet/inst/doc/coxdev.R |only glmnet-5.0/glmnet/inst/doc/coxdev.Rmd |only glmnet-5.0/glmnet/inst/doc/coxdev.html |only glmnet-5.0/glmnet/inst/doc/glmnet-history.R |only glmnet-5.0/glmnet/inst/doc/glmnet-history.Rmd |only glmnet-5.0/glmnet/inst/doc/glmnet-history.pdf |only glmnet-5.0/glmnet/inst/doc/glmnet.pdf |binary glmnet-5.0/glmnet/inst/doc/glmnetFamily.pdf |binary glmnet-5.0/glmnet/inst/doc/relax.pdf |binary glmnet-5.0/glmnet/man/coxgrad.Rd | 21 glmnet-5.0/glmnet/man/coxnet.Rd |only glmnet-5.0/glmnet/man/coxnet.deviance.Rd | 15 glmnet-5.0/glmnet/man/cv.glmnet.Rd | 5 glmnet-5.0/glmnet/man/elnet.fit.Rd | 20 glmnet-5.0/glmnet/man/glmnet-internal.Rd | 1 glmnet-5.0/glmnet/man/glmnet.Rd | 68 + glmnet-5.0/glmnet/man/glmnet.control.Rd | 207 +++- glmnet-5.0/glmnet/man/glmnet.fit.Rd | 24 glmnet-5.0/glmnet/man/glmnet.path.Rd | 25 glmnet-5.0/glmnet/src/Makevars | 6 glmnet-5.0/glmnet/src/RcppExports.cpp | 142 +++ glmnet-5.0/glmnet/src/cox_test_utils.cpp |only glmnet-5.0/glmnet/src/elnet_exp.cpp | 128 ++ glmnet-5.0/glmnet/src/glmnet_control.cpp |only glmnet-5.0/glmnet/src/glmnet_init.cpp | 102 -- glmnet-5.0/glmnet/src/glmnetpp/coxdev |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_driver/cox.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_path/cox_base.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_path/cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_path/sp_cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/cox_base.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_base.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/sp_cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/elnet_point/sp_cox_naive.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/util/cox_adapter.hpp |only glmnet-5.0/glmnet/src/glmnetpp/include/glmnetpp_bits/util/types.hpp | 12 glmnet-5.0/glmnet/src/internal.cpp | 65 - glmnet-5.0/glmnet/src/internal.h | 9 glmnet-5.0/glmnet/tests |only glmnet-5.0/glmnet/vignettes/Coxnet.Rmd | 21 glmnet-5.0/glmnet/vignettes/assets/figures |only glmnet-5.0/glmnet/vignettes/assets/glmnet_refs.bib | 89 + glmnet-5.0/glmnet/vignettes/coxdev.Rmd |only glmnet-5.0/glmnet/vignettes/glmnet-history.Rmd |only 93 files changed, 1739 insertions(+), 1407 deletions(-)
Title: Bindings to 'GDAL'
Description: API bindings to the Geospatial Data Abstraction Library ('GDAL',
<https://gdal.org>). Implements the 'GDAL' Raster and Vector Data Models.
Bindings are implemented with 'Rcpp' modules. Exposed C++ classes and
stand-alone functions wrap much of the 'GDAL' API and provide additional
functionality. Calling signatures resemble the native C, C++ and Python APIs
provided by the 'GDAL' project. Class 'GDALRaster' encapsulates a
'GDALDataset' and its raster band objects. Class 'GDALVector' encapsulates
an 'OGRLayer' and the 'GDALDataset' that contains it. Initial bindings are
provided to the unified 'gdal' command line interface added in 'GDAL' 3.11.
C++ stand-alone functions provide bindings to most 'GDAL' "traditional"
raster and vector utilities, including 'OGR' facilities for vector
geoprocessing, several algorithms, as well as the Geometry API ('GEOS' via
'GDAL' headers), the Spatial Reference Systems API, and methods for
coordinate transformation. Bindings to the Virtual Systems In [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [aut] ,
Pepijn de Vries [ctb] ,
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <jctoney@gmail.com>
Diff between gdalraster versions 2.5.0 dated 2026-03-25 and 2.6.0 dated 2026-05-04
gdalraster-2.5.0/gdalraster/man/vector_to_MEM.Rd |only gdalraster-2.6.0/gdalraster/DESCRIPTION | 12 gdalraster-2.6.0/gdalraster/MD5 | 177 ++- gdalraster-2.6.0/gdalraster/NEWS.md | 59 + gdalraster-2.6.0/gdalraster/R/RcppExports.R | 34 gdalraster-2.6.0/gdalraster/R/dem_derivatives.R |only gdalraster-2.6.0/gdalraster/R/display.R | 44 gdalraster-2.6.0/gdalraster/R/gdal_cli.R | 301 ++++++ gdalraster-2.6.0/gdalraster/R/gdal_create.R | 3 gdalraster-2.6.0/gdalraster/R/gdal_helpers.R | 116 ++ gdalraster-2.6.0/gdalraster/R/gdal_rat.R | 16 gdalraster-2.6.0/gdalraster/R/gdal_util.R | 7 gdalraster-2.6.0/gdalraster/R/gdalalg.R | 5 gdalraster-2.6.0/gdalraster/R/gdalraster.R | 60 + gdalraster-2.6.0/gdalraster/R/gdalraster_proc.R | 145 ++- gdalraster-2.6.0/gdalraster/R/geom.R | 136 ++ gdalraster-2.6.0/gdalraster/R/ogr_define.R | 17 gdalraster-2.6.0/gdalraster/R/ogr_manage.R | 4 gdalraster-2.6.0/gdalraster/R/ogr_proc.R | 9 gdalraster-2.6.0/gdalraster/R/ogr_reproject.R | 9 gdalraster-2.6.0/gdalraster/R/running_stats.R | 3 gdalraster-2.6.0/gdalraster/R/s3_methods.R | 6 gdalraster-2.6.0/gdalraster/README.md | 12 gdalraster-2.6.0/gdalraster/build/vignette.rds |binary gdalraster-2.6.0/gdalraster/configure | 18 gdalraster-2.6.0/gdalraster/configure.ac | 2 gdalraster-2.6.0/gdalraster/inst/doc/raster-api-tutorial.html | 77 - gdalraster-2.6.0/gdalraster/inst/doc/raster-attribute-tables.html | 112 +- gdalraster-2.6.0/gdalraster/inst/doc/vector-api-overview.R |only gdalraster-2.6.0/gdalraster/inst/doc/vector-api-overview.Rmd |only gdalraster-2.6.0/gdalraster/inst/doc/vector-api-overview.html |only gdalraster-2.6.0/gdalraster/inst/extdata/rgbsmall.tif |only gdalraster-2.6.0/gdalraster/inst/extdata/storml_elev_pal.txt |only gdalraster-2.6.0/gdalraster/man/DEFAULT_DEM_PROC.Rd | 5 gdalraster-2.6.0/gdalraster/man/DEFAULT_NODATA.Rd | 5 gdalraster-2.6.0/gdalraster/man/GDALAlg-class.Rd | 5 gdalraster-2.6.0/gdalraster/man/GDALRaster-class.Rd | 62 + gdalraster-2.6.0/gdalraster/man/RunningStats-class.Rd | 3 gdalraster-2.6.0/gdalraster/man/calc.Rd | 4 gdalraster-2.6.0/gdalraster/man/create.Rd | 3 gdalraster-2.6.0/gdalraster/man/data_type_helpers.Rd | 6 gdalraster-2.6.0/gdalraster/man/dem_derivatives.Rd |only gdalraster-2.6.0/gdalraster/man/g_query.Rd | 14 gdalraster-2.6.0/gdalraster/man/g_unary_op.Rd | 20 gdalraster-2.6.0/gdalraster/man/g_util.Rd | 30 gdalraster-2.6.0/gdalraster/man/gdal_cli.Rd | 104 ++ gdalraster-2.6.0/gdalraster/man/gdalraster-package.Rd | 6 gdalraster-2.6.0/gdalraster/man/is_los_visible.Rd | 17 gdalraster-2.6.0/gdalraster/man/lib_versions.Rd |only gdalraster-2.6.0/gdalraster/man/mdim_info.Rd | 4 gdalraster-2.6.0/gdalraster/man/plot_raster.Rd | 39 gdalraster-2.6.0/gdalraster/man/polygonize.Rd | 3 gdalraster-2.6.0/gdalraster/man/progress_bar_clear.Rd |only gdalraster-2.6.0/gdalraster/man/rasterFromRaster.Rd | 8 gdalraster-2.6.0/gdalraster/man/rasterize.Rd | 17 gdalraster-2.6.0/gdalraster/man/read_ds.Rd | 13 gdalraster-2.6.0/gdalraster/man/read_to_nativeRaster.Rd | 4 gdalraster-2.6.0/gdalraster/man/rvector_to_MEM.Rd |only gdalraster-2.6.0/gdalraster/man/vsi_constants.Rd | 9 gdalraster-2.6.0/gdalraster/man/warp.Rd | 7 gdalraster-2.6.0/gdalraster/src/RcppExports.cpp | 58 + gdalraster-2.6.0/gdalraster/src/cmb_table.cpp | 8 gdalraster-2.6.0/gdalraster/src/gdal_dt.cpp | 6 gdalraster-2.6.0/gdalraster/src/gdal_exp.cpp | 32 gdalraster-2.6.0/gdalraster/src/gdal_mdim.cpp | 12 gdalraster-2.6.0/gdalraster/src/gdal_vsi.cpp | 6 gdalraster-2.6.0/gdalraster/src/gdalalg.cpp | 458 ++++++---- gdalraster-2.6.0/gdalraster/src/gdalalg.h | 2 gdalraster-2.6.0/gdalraster/src/gdalraster.cpp | 433 +++++++-- gdalraster-2.6.0/gdalraster/src/gdalraster.h | 13 gdalraster-2.6.0/gdalraster/src/gdalvector.cpp | 308 ++++-- gdalraster-2.6.0/gdalraster/src/gdalvector.h | 6 gdalraster-2.6.0/gdalraster/src/geom_api.cpp | 131 ++ gdalraster-2.6.0/gdalraster/src/geom_api.h | 4 gdalraster-2.6.0/gdalraster/src/ogr_util.cpp | 102 +- gdalraster-2.6.0/gdalraster/src/progress_r.cpp | 27 gdalraster-2.6.0/gdalraster/src/r_rasterize.cpp |only gdalraster-2.6.0/gdalraster/src/rcpp_util.cpp | 78 + gdalraster-2.6.0/gdalraster/src/rcpp_util.h | 12 gdalraster-2.6.0/gdalraster/src/running_stats.cpp | 11 gdalraster-2.6.0/gdalraster/src/srs_api.cpp | 9 gdalraster-2.6.0/gdalraster/src/transform.cpp | 4 gdalraster-2.6.0/gdalraster/src/vsifile.cpp | 16 gdalraster-2.6.0/gdalraster/tests/testthat/test-CmbTable-class.R | 2 gdalraster-2.6.0/gdalraster/tests/testthat/test-GDALAlg-class.R | 42 gdalraster-2.6.0/gdalraster/tests/testthat/test-GDALRaster-class.R | 207 ++++ gdalraster-2.6.0/gdalraster/tests/testthat/test-GDALVector-class.R | 29 gdalraster-2.6.0/gdalraster/tests/testthat/test-RunningStats-class.R | 2 gdalraster-2.6.0/gdalraster/tests/testthat/test-VSIFile-class.R | 2 gdalraster-2.6.0/gdalraster/tests/testthat/test-dem_derivatives.R |only gdalraster-2.6.0/gdalraster/tests/testthat/test-gdal_cli.R | 116 ++ gdalraster-2.6.0/gdalraster/tests/testthat/test-gdal_dt.R | 16 gdalraster-2.6.0/gdalraster/tests/testthat/test-gdal_helpers.R | 77 + gdalraster-2.6.0/gdalraster/tests/testthat/test-gdalraster_proc.R | 4 gdalraster-2.6.0/gdalraster/tests/testthat/test-geom.R | 65 + gdalraster-2.6.0/gdalraster/tests/testthat/test-r_rasterize.R |only gdalraster-2.6.0/gdalraster/vignettes/vector-api-overview.Rmd |only 97 files changed, 3039 insertions(+), 1031 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), instrumental variables (IV), generalized linear models (GLM), maximum likelihood estimation (ML), and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Bergé, Butts, McDermott (2026) <doi:10.48550/arXiv.2601.21749>.
Further provides tools to export and view the results of several estimations with intuitive design to change the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb],
Grant McDermott [ctb] ,
Russell Lenth [ctb],
Kyle Butts [ctb]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.14.0 dated 2026-03-18 and 0.14.1 dated 2026-05-04
DESCRIPTION | 6 MD5 | 86 ++--- NEWS.md | 22 + R/coefplot.R | 2 R/data_documentation.R | 2 R/estimation.R | 25 - R/etable.R | 8 R/fitstats.R | 229 +++++++++++++-- R/fixest_env.R | 2 R/fixest_multi.R | 2 R/methods.R | 37 +- R/miscfuns.R | 10 R/panel.R | 2 inst/doc/collinearity.html | 4 inst/doc/exporting_tables.html | 4 inst/doc/fixest_walkthrough.html | 130 ++++---- inst/doc/multiple_estimations.html | 4 inst/doc/standard_errors.html | 4 man/AIC.fixest.Rd | 8 man/BIC.fixest.Rd | 2 man/as.dict.Rd | 2 man/as.list.fixest_multi.Rd | 2 man/base_stagg.Rd | 2 man/coefplot.Rd | 2 man/coeftable.fixest.Rd | 2 man/coeftable.fixest_multi.Rd | 2 man/demeaning_algo.Rd | 6 man/did_means.Rd | 2 man/etable.Rd | 6 man/feNmlm.Rd | 8 man/feglm.Rd | 8 man/femlm.Rd | 8 man/feols.Rd | 8 man/fitstat.Rd | 101 +++++- man/lag.formula.Rd | 2 man/panel.Rd | 2 man/plot.fixest.Rd | 554 ++++++++++++++++++------------------- man/print.fixest_fitstat.Rd | 9 man/print.fixest_multi.Rd | 2 man/setFixest_estimation.Rd | 2 man/sub-.fixest_multi.Rd | 2 man/sub-sub-.fixest_multi.Rd | 2 man/summary.fixest_multi.Rd | 2 tests/fixest_tests.R | 10 44 files changed, 807 insertions(+), 528 deletions(-)
Title: Exact Distributions for Rank and Permutation Tests
Description: Computes exact conditional p-values and quantiles using an
implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between exactRankTests versions 0.8-36 dated 2026-03-09 and 0.8-37 dated 2026-05-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS | 4 ++++ tests/reg-tests.Rout.save | 8 ++++---- 4 files changed, 15 insertions(+), 11 deletions(-)
More information about exactRankTests at CRAN
Permanent link
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects; glm(); geeglm() (from package 'geepack'); lm_robust(), lm_lin(), and
iv_robust() (from package 'estimatr'); ivreg() (from package 'AER'); ivreg() [...truncated...]
Author: James E. Pustejovsky [aut, cre] ,
Hazim Izani [ctb],
Samuel Pekofsky [ctb],
Jingru Zhang [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.6.2 dated 2026-02-02 and 0.7.0 dated 2026-05-04
DESCRIPTION | 24 ++++++++------ MD5 | 33 ++++++++++++-------- NAMESPACE | 12 +++++++ NEWS.md | 6 +++ R/gls.R | 4 +- R/iv_robust.R |only R/lm_robust.R | 4 +- R/mmrm.R |only R/utilities.R | 50 +++++++++++++++++++++++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Wald-tests-in-clubSandwich.html | 4 +- inst/doc/meta-analysis-with-CRVE.html | 4 +- inst/doc/panel-data-CRVE.html | 4 +- man/vcovCR.iv_robust.Rd |only man/vcovCR.mmrm.Rd |only tests/testthat/test_gls.R | 1 tests/testthat/test_iv_robust.R |only tests/testthat/test_mmrm.R |only tests/testthat/test_mmrm_weighted.R |only tests/testthat/test_rma-mv.R | 23 ++++++++------ 21 files changed, 124 insertions(+), 45 deletions(-)
Title: Blend Colours and Palettes
Description: Colour blend functions. These functions make it easier to blend
colours and palettes using digital blend modes such as multiply, screen,
and overlay.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between blends versions 0.1.0 dated 2026-03-25 and 0.1.1 dated 2026-05-04
blends-0.1.0/blends/R/blends.R |only blends-0.1.1/blends/DESCRIPTION | 18 ++++++----- blends-0.1.1/blends/MD5 | 49 ++++++++++++++++++------------ blends-0.1.1/blends/NEWS.md | 4 ++ blends-0.1.1/blends/R/colour-burn.R |only blends-0.1.1/blends/R/colour-dodge.R |only blends-0.1.1/blends/R/darken.R |only blends-0.1.1/blends/R/difference.R |only blends-0.1.1/blends/R/exclusion.R |only blends-0.1.1/blends/R/hard-light.R |only blends-0.1.1/blends/R/lighten.R |only blends-0.1.1/blends/R/multiply.R |only blends-0.1.1/blends/R/overlay.R |only blends-0.1.1/blends/R/screen.R |only blends-0.1.1/blends/R/soft-light.R |only blends-0.1.1/blends/R/utils.R |only blends-0.1.1/blends/README.md | 48 ++++++++++++++++++++++++++++- blends-0.1.1/blends/inst |only blends-0.1.1/blends/man/blends-package.Rd | 4 +- blends-0.1.1/blends/man/colour_burn.Rd | 2 - blends-0.1.1/blends/man/colour_dodge.Rd | 2 - blends-0.1.1/blends/man/darken.Rd | 2 - blends-0.1.1/blends/man/difference.Rd | 2 - blends-0.1.1/blends/man/exclusion.Rd | 2 - blends-0.1.1/blends/man/figures/logo.png |binary blends-0.1.1/blends/man/figures/logo.svg | 4 +- blends-0.1.1/blends/man/hard_light.Rd | 2 - blends-0.1.1/blends/man/lighten.Rd | 2 - blends-0.1.1/blends/man/multiply.Rd | 2 - blends-0.1.1/blends/man/overlay.Rd | 2 - blends-0.1.1/blends/man/screen.Rd | 2 - blends-0.1.1/blends/man/soft_light.Rd | 2 - blends-0.1.1/blends/tests/spelling.R |only 33 files changed, 107 insertions(+), 42 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner [aut, cre] ,
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.4.1.1 dated 2026-01-20 and 1.4.2 dated 2026-05-04
bartMachine-1.4.1.1/bartMachine/inst/benchmarks/bart_packages_comparisons_results |only bartMachine-1.4.1.1/bartMachine/inst/scripts/bartmachine_ggplot_tests.pdf |only bartMachine-1.4.2/bartMachine/CHANGELOG | 21 bartMachine-1.4.2/bartMachine/DESCRIPTION | 11 bartMachine-1.4.2/bartMachine/MD5 | 69 bartMachine-1.4.2/bartMachine/R/bart_package_builders.R | 1 bartMachine-1.4.2/bartMachine/R/bart_package_cross_validation.R | 60 bartMachine-1.4.2/bartMachine/R/bart_package_f_tests.R | 38 bartMachine-1.4.2/bartMachine/R/bart_package_variable_selection.R | 39 bartMachine-1.4.2/bartMachine/build/partial.rdb |binary bartMachine-1.4.2/bartMachine/build/vignette.rds |binary bartMachine-1.4.2/bartMachine/inst/doc/bartMachine.pdf |binary bartMachine-1.4.2/bartMachine/inst/java/bart_java.jar |binary bartMachine-1.4.2/bartMachine/java/OpenSourceExtensions/TDoubleHashSetAndArray.java | 654 +------- bartMachine-1.4.2/bartMachine/java/OpenSourceExtensions/UnorderedPair.java | 52 bartMachine-1.4.2/bartMachine/java/bartMachine/BartJarAgent.java |only bartMachine-1.4.2/bartMachine/java/bartMachine/Classifier.java | 31 bartMachine-1.4.2/bartMachine/java/bartMachine/GpuForestPredictor.java |only bartMachine-1.4.2/bartMachine/java/bartMachine/GpuPredictorBridge.java |only bartMachine-1.4.2/bartMachine/java/bartMachine/StatToolbox.java | 243 ++- bartMachine-1.4.2/bartMachine/java/bartMachine/Tools.java | 160 +- bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachineClassification.java | 13 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachineClassificationMultThread.java | 179 ++ bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachineRegressionMultThread.java | 764 +++++++++- bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachineTreeNode.java | 182 +- bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_a_base.java | 15 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_b_hyperparams.java | 81 - bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_d_init.java | 1 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_e_gibbs_base.java | 57 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_f_gibbs_internal.java | 25 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_g_mh.java | 75 bartMachine-1.4.2/bartMachine/java/bartMachine/bartMachine_i_prior_cov_spec.java | 28 bartMachine-1.4.2/bartMachine/java/bartMachine/package-info.java | 4 bartMachine-1.4.2/bartMachine/tests/testthat/BART_unnamed_iter_00001.png |binary bartMachine-1.4.2/bartMachine/tests/testthat/BART_unnamed_iter_00002.png |binary bartMachine-1.4.2/bartMachine/tests/testthat/BART_unnamed_iter_00003.png |binary bartMachine-1.4.2/bartMachine/tests/testthat/BART_unnamed_iter_00004.png |binary 37 files changed, 1806 insertions(+), 997 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] ,
Joris Mulder [aut],
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remify versions 3.2.9 dated 2025-09-26 and 4.0.0 dated 2026-05-04
remify-3.2.9/remify/R/rehshape.R |only remify-3.2.9/remify/R/remify.R |only remify-3.2.9/remify/inst/doc/rehshape.R |only remify-3.2.9/remify/inst/doc/rehshape.Rmd |only remify-3.2.9/remify/inst/doc/rehshape.html |only remify-3.2.9/remify/inst/tinytest/test-rehshape.R |only remify-3.2.9/remify/inst/tinytest/test-remify-error-messages.R |only remify-3.2.9/remify/inst/tinytest/test-remify-methods.R |only remify-3.2.9/remify/inst/tinytest/test-remify-warning-messages.R |only remify-3.2.9/remify/inst/tinytest/test-remify.R |only remify-3.2.9/remify/man/getActorID.Rd |only remify-3.2.9/remify/man/getActorName.Rd |only remify-3.2.9/remify/man/getDyad.Rd |only remify-3.2.9/remify/man/getDyadID.Rd |only remify-3.2.9/remify/man/getRiskset.Rd |only remify-3.2.9/remify/man/getTypeID.Rd |only remify-3.2.9/remify/man/getTypeName.Rd |only remify-3.2.9/remify/man/rehshape.Rd |only remify-3.2.9/remify/vignettes/rehshape.Rmd |only remify-4.0.0/remify/DESCRIPTION | 27 remify-4.0.0/remify/MD5 | 91 remify-4.0.0/remify/NAMESPACE | 15 remify-4.0.0/remify/NEWS.md | 15 remify-4.0.0/remify/R/RcppExports.R | 12 remify-4.0.0/remify/R/data.R | 39 remify-4.0.0/remify/R/remify2.R |only remify-4.0.0/remify/R/remify_util.R |only remify-4.0.0/remify/R/summary_remify.R |only remify-4.0.0/remify/build/partial.rdb |binary remify-4.0.0/remify/build/vignette.rds |binary remify-4.0.0/remify/data/history.rda |only remify-4.0.0/remify/data/randomREH.rda |binary remify-4.0.0/remify/data/randomREHsmall.rda |binary remify-4.0.0/remify/inst/doc/remify.R | 186 - remify-4.0.0/remify/inst/doc/remify.Rmd | 506 +--- remify-4.0.0/remify/inst/doc/remify.html | 1024 +++------ remify-4.0.0/remify/inst/doc/riskset.R | 518 +--- remify-4.0.0/remify/inst/doc/riskset.Rmd | 685 ++---- remify-4.0.0/remify/inst/doc/riskset.html | 1128 ++++++---- remify-4.0.0/remify/inst/include/remify/remify.h | 10 remify-4.0.0/remify/inst/include/remify_helpers.h |only remify-4.0.0/remify/inst/tinytest/simple-tests.R |only remify-4.0.0/remify/inst/tinytest/test-remify-methods2.R |only remify-4.0.0/remify/inst/tinytest/test-remify2-actor.R |only remify-4.0.0/remify/inst/tinytest/test-remify2-thin.R |only remify-4.0.0/remify/inst/tinytest/test-remify2-typed-events.R |only remify-4.0.0/remify/inst/tinytest/test-summary-remify.R |only remify-4.0.0/remify/inst/tinytest/tests_remify2.R |only remify-4.0.0/remify/man/dim.remify.Rd | 2 remify-4.0.0/remify/man/history.Rd |only remify-4.0.0/remify/man/plot.remify.Rd | 6 remify-4.0.0/remify/man/print.remify.Rd | 4 remify-4.0.0/remify/man/randomREH.Rd | 12 remify-4.0.0/remify/man/randomREHsmall.Rd | 1 remify-4.0.0/remify/man/remify-package.Rd | 6 remify-4.0.0/remify/man/remify.Rd | 157 + remify-4.0.0/remify/man/summary.remify.Rd | 2 remify-4.0.0/remify/src/RcppExports.cpp | 69 remify-4.0.0/remify/src/messages.h | 10 remify-4.0.0/remify/src/remify.cpp | 442 +-- remify-4.0.0/remify/src/remify2.cpp |only remify-4.0.0/remify/vignettes/remify.Rmd | 506 +--- remify-4.0.0/remify/vignettes/riskset.Rmd | 685 ++---- 63 files changed, 2713 insertions(+), 3445 deletions(-)
Title: Hierarchical Methods for Differential Equations
Description: Wrapper for 'Stan' that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.
Author: Daniel Falster [aut, ctb] ,
Tess O'Brien [aut, cre, cph] ,
Fonti Kar [ctb] ,
David Warton [aut, ctb]
Maintainer: Tess O'Brien <tess_obrien@fastmail.com>
Diff between hmde versions 1.3.1 dated 2025-12-22 and 1.4.0 dated 2026-05-04
hmde-1.3.1/hmde/R/hmde_S3_methods.R |only hmde-1.3.1/hmde/R/hmde_assign_data.R |only hmde-1.3.1/hmde/R/hmde_extract_estimates.R |only hmde-1.3.1/hmde/man/hmde_assign_data.Rd |only hmde-1.3.1/hmde/man/hmde_extract_estimates.Rd |only hmde-1.3.1/hmde/man/plot.hmde_model_template.Rd |only hmde-1.3.1/hmde/man/print.hmde_model_template.Rd |only hmde-1.3.1/hmde/man/summary.hmde_model_template.Rd |only hmde-1.3.1/hmde/tests/testthat/fixtures |only hmde-1.3.1/hmde/tests/testthat/helper-data_generation.R |only hmde-1.3.1/hmde/tests/testthat/helper-testing.R |only hmde-1.3.1/hmde/tests/testthat/test-S3_methods_hmde_model_template.r |only hmde-1.3.1/hmde/tests/testthat/test-hmde_assign_data.R |only hmde-1.3.1/hmde/tests/testthat/test-hmde_extract_estimates.R |only hmde-1.4.0/hmde/DESCRIPTION | 18 hmde-1.4.0/hmde/MD5 | 148 +- hmde-1.4.0/hmde/NAMESPACE | 74 + hmde-1.4.0/hmde/NEWS.md | 5 hmde-1.4.0/hmde/R/data.R | 21 hmde-1.4.0/hmde/R/hmde-package.R | 18 hmde-1.4.0/hmde/R/hmde_data_template.R |only hmde-1.4.0/hmde/R/hmde_depreciation.R |only hmde-1.4.0/hmde/R/hmde_estimates.R |only hmde-1.4.0/hmde/R/hmde_extract_Rhat.R | 4 hmde-1.4.0/hmde/R/hmde_global_and_generic.R |only hmde-1.4.0/hmde/R/hmde_model.R | 207 ++- hmde-1.4.0/hmde/R/hmde_plot_Rhat_hist.R | 7 hmde-1.4.0/hmde/R/hmde_plot_de_pieces.R | 32 hmde-1.4.0/hmde/R/hmde_plot_obs_est_inds.R | 30 hmde-1.4.0/hmde/R/hmde_run.R | 105 + hmde-1.4.0/hmde/build/partial.rdb |binary hmde-1.4.0/hmde/build/vignette.rds |binary hmde-1.4.0/hmde/data/Tree_Size_Ests.rda |binary hmde-1.4.0/hmde/inst/article/article.R | 160 +- hmde-1.4.0/hmde/inst/article/article.md | 2 hmde-1.4.0/hmde/inst/article/hmde_paper.pdf |binary hmde-1.4.0/hmde/inst/doc/canham.R | 66 - hmde-1.4.0/hmde/inst/doc/canham.Rmd | 70 - hmde-1.4.0/hmde/inst/doc/canham.html | 209 +-- hmde-1.4.0/hmde/inst/doc/constant-growth.R | 56 hmde-1.4.0/hmde/inst/doc/constant-growth.Rmd | 70 - hmde-1.4.0/hmde/inst/doc/constant-growth.html | 568 ++++------ hmde-1.4.0/hmde/inst/doc/here_be_dragons.R | 26 hmde-1.4.0/hmde/inst/doc/here_be_dragons.Rmd | 26 hmde-1.4.0/hmde/inst/doc/here_be_dragons.html | 140 +- hmde-1.4.0/hmde/inst/doc/hmde_for_mathematicians.R | 53 hmde-1.4.0/hmde/inst/doc/hmde_for_mathematicians.Rmd | 59 - hmde-1.4.0/hmde/inst/doc/hmde_for_mathematicians.html | 169 +- hmde-1.4.0/hmde/inst/doc/von-bertalanffy.R | 48 hmde-1.4.0/hmde/inst/doc/von-bertalanffy.Rmd | 48 hmde-1.4.0/hmde/inst/doc/von-bertalanffy.html | 329 ++--- hmde-1.4.0/hmde/man/Tree_Size_Ests.Rd | 21 hmde-1.4.0/hmde/man/error_ests-generic.Rd |only hmde-1.4.0/hmde/man/fit_summary-generic.Rd |only hmde-1.4.0/hmde/man/hmde_data_template-class.Rd |only hmde-1.4.0/hmde/man/hmde_estimates-class.Rd |only hmde-1.4.0/hmde/man/hmde_extract_Rhat.Rd | 4 hmde-1.4.0/hmde/man/hmde_model.Rd | 8 hmde-1.4.0/hmde/man/hmde_plot_Rhat_hist.Rd | 4 hmde-1.4.0/hmde/man/hmde_plot_de_pieces.Rd | 10 hmde-1.4.0/hmde/man/hmde_plot_obs_est_inds.Rd | 9 hmde-1.4.0/hmde/man/hmde_run.Rd | 10 hmde-1.4.0/hmde/man/individual_ests-generic.Rd |only hmde-1.4.0/hmde/man/measurement_ests-generic.Rd |only hmde-1.4.0/hmde/man/method-generic.Rd |only hmde-1.4.0/hmde/man/model_level-generic.Rd |only hmde-1.4.0/hmde/man/model_name-generic.Rd |only hmde-1.4.0/hmde/man/par_names-generic.Rd |only hmde-1.4.0/hmde/man/population_ests-generic.Rd |only hmde-1.4.0/hmde/man/prior_pars-generic.Rd |only hmde-1.4.0/hmde/man/runtime-generic.Rd |only hmde-1.4.0/hmde/tests/testthat/test-hmde_data_template.R |only hmde-1.4.0/hmde/tests/testthat/test-hmde_estimates.R |only hmde-1.4.0/hmde/tests/testthat/test-hmde_extract_Rhat.R | 6 hmde-1.4.0/hmde/tests/testthat/test-hmde_inbuilt_data.R | 3 hmde-1.4.0/hmde/tests/testthat/test-hmde_models_affine.R | 29 hmde-1.4.0/hmde/tests/testthat/test-hmde_models_canham.R | 78 - hmde-1.4.0/hmde/tests/testthat/test-hmde_models_constant.R | 66 - hmde-1.4.0/hmde/tests/testthat/test-hmde_models_vb.R | 74 - hmde-1.4.0/hmde/tests/testthat/test-hmde_plot_Rhat_hist.R | 12 hmde-1.4.0/hmde/tests/testthat/test-hmde_plot_de_pieces.R | 29 hmde-1.4.0/hmde/tests/testthat/test-hmde_plot_obs_est_inds.R | 10 hmde-1.4.0/hmde/tests/testthat/test-hmde_run.R |only hmde-1.4.0/hmde/vignettes/canham.Rmd | 70 - hmde-1.4.0/hmde/vignettes/constant-growth.Rmd | 70 - hmde-1.4.0/hmde/vignettes/here_be_dragons.Rmd | 26 hmde-1.4.0/hmde/vignettes/hmde_for_mathematicians.Rmd | 59 - hmde-1.4.0/hmde/vignettes/von-bertalanffy.Rmd | 48 88 files changed, 1769 insertions(+), 1645 deletions(-)
Title: Functional Utilities for Data Processing
Description: Covers several areas of data processing: batch-splitting, reading and writing of large
data files, data tiling, one-hot encoding and decoding of data tiles, stratified proportional
(random or probabilistic) data sampling, data normalization and thresholding, substring location
and commonalities inside strings, and location and tabulation of amino acids, modifications or
associated monoisotopic masses inside modified peptides. The extractor utility implements code from
'Matrix.utils', Varrichio C (2020), <https://cran.r-project.org/package=Matrix.utils>.
Author: Dragos Bandur [aut, cre]
Maintainer: Dragos Bandur <dbandur@sympatico.ca>
Diff between akin versions 0.3.1 dated 2026-04-26 and 0.3.2 dated 2026-05-04
akin-0.3.1/akin/man/common.Rd |only akin-0.3.1/akin/tests/testthat/test-common.R |only akin-0.3.2/akin/DESCRIPTION | 8 - akin-0.3.2/akin/MD5 | 39 +++--- akin-0.3.2/akin/NAMESPACE | 2 akin-0.3.2/akin/NEWS.md | 17 ++ akin-0.3.2/akin/R/akin-deprecated.R |only akin-0.3.2/akin/R/akin-package.R | 2 akin-0.3.2/akin/R/common.R | 143 ++----------------------- akin-0.3.2/akin/R/core.R | 2 akin-0.3.2/akin/R/corePar.R | 14 +- akin-0.3.2/akin/R/cover.R |only akin-0.3.2/akin/R/fcommon.R | 100 +++++++++-------- akin-0.3.2/akin/R/plot.R |only akin-0.3.2/akin/R/seqRead.R | 2 akin-0.3.2/akin/R/utils.R | 30 ++--- akin-0.3.2/akin/R/zzz.R | 13 +- akin-0.3.2/akin/man/akin-deprecated.Rd |only akin-0.3.2/akin/man/akin-package.Rd | 5 akin-0.3.2/akin/man/cover.Rd |only akin-0.3.2/akin/man/fcommon.Rd | 154 ++++++++++++++------------- akin-0.3.2/akin/man/findLoc.Rd | 4 akin-0.3.2/akin/man/splitH.Rd | 2 akin-0.3.2/akin/man/stratify.Rd | 2 24 files changed, 240 insertions(+), 299 deletions(-)
Title: Publication-Quality 'ggplot2' Geom Width
Description: Width helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to create geoms such
as bars that have a consistent width appearance across plots.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggwidth versions 0.1.0 dated 2026-03-06 and 0.1.1 dated 2026-05-03
DESCRIPTION | 21 ++++++---- MD5 | 24 ++++++----- NAMESPACE | 1 NEWS.md | 4 + R/get-width.R | 100 ++++++++++++++++++++++++++++--------------------- R/ggwidth-package.R |only R/set-equiwidth.R | 6 ++ R/utils.R | 39 ++++++++++++------- README.md | 45 ++++++++++++++++++++++ man/figures/logo.png |binary man/figures/logo.svg | 4 - man/get_width.Rd | 5 -- man/ggwidth-package.Rd |only tests |only 14 files changed, 171 insertions(+), 78 deletions(-)
Title: Multi-Objective Optimization in R
Description: The 'rmoo' package is a framework for multi- and many-objective
optimization, which allows researchers and users versatility
in parameter configuration, as well as tools for analysis, replication
and visualization of results. The 'rmoo' package was built as a fork of
the 'GA' package by Luca Scrucca(2017) <DOI:10.32614/RJ-2017-008> and
implementing the Non-Dominated Sorting Genetic Algorithms proposed
by K. Deb's.
Author: Francisco Benitez [aut, cre],
Diego P. Pinto-Roa [aut]
Maintainer: Francisco Benitez <benitezfj94@gmail.com>
Diff between rmoo versions 0.2.0 dated 2022-09-23 and 0.3.2 dated 2026-05-03
rmoo-0.2.0/rmoo/R/nsgaControl.R |only rmoo-0.2.0/rmoo/R/rmoo_func.R |only rmoo-0.2.0/rmoo/man/nsgaControl.Rd |only rmoo-0.2.0/rmoo/man/nsgaMonitor.Rd |only rmoo-0.2.0/rmoo/man/nsga_Crossover.Rd |only rmoo-0.2.0/rmoo/man/nsga_Mutation.Rd |only rmoo-0.2.0/rmoo/man/nsga_Population.Rd |only rmoo-0.2.0/rmoo/man/nsga_Selection.Rd |only rmoo-0.2.0/rmoo/man/rmoo_func.Rd |only rmoo-0.3.2/rmoo/DESCRIPTION | 34 rmoo-0.3.2/rmoo/MD5 | 98 - rmoo-0.3.2/rmoo/NAMESPACE | 63 rmoo-0.3.2/rmoo/R/AllClasses.R | 44 rmoo-0.3.2/rmoo/R/AllGenerics.R | 8 rmoo-0.3.2/rmoo/R/associate.R | 157 + rmoo-0.3.2/rmoo/R/crowding_distance.R | 230 ++ rmoo-0.3.2/rmoo/R/geneticoperator.R | 964 ++++++++--- rmoo-0.3.2/rmoo/R/miscfun.R | 5 rmoo-0.3.2/rmoo/R/modified_crowding_distance.R |only rmoo-0.3.2/rmoo/R/niching.R | 37 rmoo-0.3.2/rmoo/R/non_dominated_fronts.R | 237 ++ rmoo-0.3.2/rmoo/R/nsga.R | 50 rmoo-0.3.2/rmoo/R/nsga2.R | 179 +- rmoo-0.3.2/rmoo/R/nsga3.R | 206 +- rmoo-0.3.2/rmoo/R/parallel.R |only rmoo-0.3.2/rmoo/R/performance_metrics.R | 134 + rmoo-0.3.2/rmoo/R/rmoo.R | 3 rmoo-0.3.2/rmoo/R/rmooControl.R |only rmoo-0.3.2/rmoo/R/rmoo_main.R |only rmoo-0.3.2/rmoo/R/rnsga2.R |only rmoo-0.3.2/rmoo/R/update_points.R | 245 +- rmoo-0.3.2/rmoo/R/utils.R |only rmoo-0.3.2/rmoo/R/zzz.R | 18 rmoo-0.3.2/rmoo/README.md | 69 rmoo-0.3.2/rmoo/build/partial.rdb |binary rmoo-0.3.2/rmoo/man/calc_norm_pref_distance.Rd |only rmoo-0.3.2/rmoo/man/modifiedCrowdingDistance.Rd |only rmoo-0.3.2/rmoo/man/nsga-class.Rd | 4 rmoo-0.3.2/rmoo/man/nsga.Rd | 24 rmoo-0.3.2/rmoo/man/nsga2-class.Rd | 2 rmoo-0.3.2/rmoo/man/nsga2.Rd | 32 rmoo-0.3.2/rmoo/man/nsga3.Rd | 33 rmoo-0.3.2/rmoo/man/performance_metrics.Rd | 17 rmoo-0.3.2/rmoo/man/plot-methods.Rd | 15 rmoo-0.3.2/rmoo/man/rmoo-package.Rd | 3 rmoo-0.3.2/rmoo/man/rmoo.Rd |only rmoo-0.3.2/rmoo/man/rmooControl.Rd |only rmoo-0.3.2/rmoo/man/rmooMonitor.Rd |only rmoo-0.3.2/rmoo/man/rmoo_Crossover.Rd |only rmoo-0.3.2/rmoo/man/rmoo_Mutation.Rd |only rmoo-0.3.2/rmoo/man/rmoo_Population.Rd |only rmoo-0.3.2/rmoo/man/rmoo_huxCrossover.Rd |only rmoo-0.3.2/rmoo/man/rmoo_lrSelection.Rd |only rmoo-0.3.2/rmoo/man/rmoo_tourSelection.Rd |only rmoo-0.3.2/rmoo/man/rmoo_uxCrossover.Rd |only rmoo-0.3.2/rmoo/man/rmoo_uxMutation.Rd |only rmoo-0.3.2/rmoo/man/rnsga2-class.Rd |only rmoo-0.3.2/rmoo/man/rnsga2.Rd |only rmoo-0.3.2/rmoo/man/startParallel.Rd |only rmoo-0.3.2/rmoo/man/stopParallel.Rd |only rmoo-0.3.2/rmoo/tests/testthat/test-check_validators.r |only rmoo-0.3.2/rmoo/tests/testthat/test-crossover-fitness-dims.R |only rmoo-0.3.2/rmoo/tests/testthat/test-nsga.r | 2 rmoo-0.3.2/rmoo/tests/testthat/test-nsga2.r | 4 rmoo-0.3.2/rmoo/tests/testthat/test-nsga3.r | 9 rmoo-0.3.2/rmoo/tests/testthat/test-pcp.r | 17 rmoo-0.3.2/rmoo/tests/testthat/test-scatter.r | 38 67 files changed, 2316 insertions(+), 665 deletions(-)
Title: Argos Locations Filter
Description: Filters animal satellite tracking data obtained from the Argos system(<https://www.argos-system.org/>), following the algorithm described in Freitas et al (2008) <doi:10.1111/j.1748-7692.2007.00180.x>. It is especially indicated for telemetry studies of marine animals, where Argos locations are predominantly of low-quality.
Author: Carla Freitas [aut, cre]
Maintainer: Carla Freitas <carla.freitas.brandt@hi.no>
Diff between argosfilter versions 0.70 dated 2022-09-13 and 0.71 dated 2026-05-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/bearing.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extensions to Rcmdr (R Commander), randomness test,
variance test for one normal sample and predictions using active model,
made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez [aut, cre]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 5.1-3 dated 2026-04-13 and 5.1-4 dated 2026-05-03
ChangeLog | 3 + DESCRIPTION | 8 ++-- MD5 | 12 +++--- R/qualitycontrol.R | 83 +++++++++++++++++++++++++++-------------------- inst/doc/additions.html | 4 +- inst/doc/adiciones.html | 4 +- po/R-RcmdrPlugin.UCA.pot | 4 +- 7 files changed, 67 insertions(+), 51 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Collection of Methods Constructed using Kernel-Based Quadratic
Distances
Description: It includes test for multivariate normality, test for uniformity on the d-dimensional
Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson
kernel-based density and clustering algorithm for spherical data. For more information see
Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024)
<doi:10.48550/arXiv.2402.02290>
Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>,
Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>,
and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Author: Giovanni Saraceno [aut, cre] ,
Marianthi Markatou [aut],
Raktim Mukhopadhyay [aut],
Mojgan Golzy [aut],
Hingee Kassel [rev],
Emi Tanaka [rev]
Maintainer: Giovanni Saraceno <giovanni.saraceno@unipd.it>
Diff between QuadratiK versions 1.1.3 dated 2025-02-04 and 1.2.0 dated 2026-05-03
QuadratiK-1.1.3/QuadratiK/man/kb.test-class.Rd |only QuadratiK-1.1.3/QuadratiK/man/pk.test-class.Rd |only QuadratiK-1.1.3/QuadratiK/man/pkbc-class.Rd |only QuadratiK-1.2.0/QuadratiK/DESCRIPTION | 8 QuadratiK-1.2.0/QuadratiK/MD5 | 79 - QuadratiK-1.2.0/QuadratiK/NAMESPACE | 5 QuadratiK-1.2.0/QuadratiK/NEWS.md | 34 QuadratiK-1.2.0/QuadratiK/R/classes.R | 64 - QuadratiK-1.2.0/QuadratiK/R/clustering_functions.R | 532 +++++------- QuadratiK-1.2.0/QuadratiK/R/h_selection.R | 477 ++++++---- QuadratiK-1.2.0/QuadratiK/R/kb.test.R | 394 ++++---- QuadratiK-1.2.0/QuadratiK/R/pk.test.R | 63 - QuadratiK-1.2.0/QuadratiK/R/utility.R | 30 QuadratiK-1.2.0/QuadratiK/README.md | 2 QuadratiK-1.2.0/QuadratiK/build/vignette.rds |binary QuadratiK-1.2.0/QuadratiK/inst/doc/Introduction.R | 4 QuadratiK-1.2.0/QuadratiK/inst/doc/Introduction.Rmd | 8 QuadratiK-1.2.0/QuadratiK/inst/doc/Introduction.html | 123 +- QuadratiK-1.2.0/QuadratiK/inst/doc/TwoSample_test.html | 24 QuadratiK-1.2.0/QuadratiK/inst/doc/generate_rpkb.html | 69 - QuadratiK-1.2.0/QuadratiK/inst/doc/kSample_test.html | 14 QuadratiK-1.2.0/QuadratiK/inst/doc/uniformity.Rmd | 2 QuadratiK-1.2.0/QuadratiK/inst/doc/uniformity.html | 30 QuadratiK-1.2.0/QuadratiK/inst/doc/wireless_clustering.html | 4 QuadratiK-1.2.0/QuadratiK/man/kb.test.Rd | 75 - QuadratiK-1.2.0/QuadratiK/man/pk.test.Rd | 21 QuadratiK-1.2.0/QuadratiK/man/pkbc.Rd | 3 QuadratiK-1.2.0/QuadratiK/man/pkbc_validation.Rd | 3 QuadratiK-1.2.0/QuadratiK/man/plot.pkbc.Rd | 3 QuadratiK-1.2.0/QuadratiK/man/predict.pkbc.Rd | 3 QuadratiK-1.2.0/QuadratiK/man/row_log_sum_exp.Rd |only QuadratiK-1.2.0/QuadratiK/man/select_h.Rd | 58 - QuadratiK-1.2.0/QuadratiK/man/stats_clusters.Rd | 3 QuadratiK-1.2.0/QuadratiK/man/summary.kb.test.Rd | 4 QuadratiK-1.2.0/QuadratiK/man/summary.pk.test.Rd | 2 QuadratiK-1.2.0/QuadratiK/man/summary.pkbc.Rd | 3 QuadratiK-1.2.0/QuadratiK/tests/testthat/Rplots.pdf |only QuadratiK-1.2.0/QuadratiK/tests/testthat/test-kb.test.R | 68 + QuadratiK-1.2.0/QuadratiK/tests/testthat/test-pk.test.R | 12 QuadratiK-1.2.0/QuadratiK/tests/testthat/test-rpkb.R | 2 QuadratiK-1.2.0/QuadratiK/tests/testthat/test-select_h.R | 29 QuadratiK-1.2.0/QuadratiK/vignettes/Introduction.Rmd | 8 QuadratiK-1.2.0/QuadratiK/vignettes/uniformity.Rmd | 2 43 files changed, 1232 insertions(+), 1033 deletions(-)
Title: Statistical Modelling in Action with R
Description: Datasets and functions for the book "Modélisation statistique par la pratique avec R", F. Bertrand, E. Claeys and M. Maumy-Bertrand (2019, ISBN:9782100793525, Dunod, Paris). The first chapter of the book is dedicated to an introduction to the R statistical software. The second chapter deals with correlation analysis: Pearson, Spearman and Kendall simple, multiple and partial correlation coefficients. New wrapper functions for permutation tests or bootstrap of matrices of correlation are provided with the package. The third chapter is dedicated to data exploration with factorial analyses (PCA, CA, MCA, MDA) and clustering. The fourth chapter is dedicated to regression analysis: fitting and model diagnostics are detailed. The exercises focus on covariance analysis, logistic regression, Poisson regression, two-way analysis of variance for fixed or random factors. Various example datasets are shipped with the package: for instance on pokemon, world of warcraft, house tasks or food nutritio [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Emmanuelle Claeys [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between ModStatR versions 1.4.1 dated 2025-09-12 and 1.4.2 dated 2026-05-03
DESCRIPTION | 15 ++++++++------- MD5 | 6 +++--- NEWS.md | 4 ++++ man/ModStatR-package.Rd | 4 ++-- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Effect Sizes for Meta-Analysis of Interactions from Factorial
Experiments
Description: Compute effect sizes and their sampling variances from factorial experimental designs. The package supports calculation of simple effects, overall effects, and interaction effects for use in factorial meta-analyses. See Gurevitch et al. (2000) <doi:10.1086/303337>, Morris et al. (2007) <doi:10.1890/06-0442>, Lajeunesse (2011) <doi:10.1890/11-0423.1> and Macartney et al. (2022) <doi:10.1016/j.neubiorev.2022.104554>.
Author: Facundo Decunta [aut, cre] ,
Shinichi Nakagawa [ctb],
Daniel Noble [ctb]
Maintainer: Facundo Decunta <fdecunta@agro.uba.ar>
Diff between minter versions 0.1.0 dated 2025-10-06 and 0.1.1 dated 2026-05-03
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 4 +++ R/SMD.R | 7 ++++++ R/lnCVR.R | 6 ++--- README.md | 50 ++++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/minter-docs.html | 14 ++++++------ 8 files changed, 58 insertions(+), 43 deletions(-)
Title: Generalized Linear Models with Slab and Shrinkage Estimators
Description: Provides a flexible framework for fitting generalized linear models (GLMs)
with slab and shrinkage estimators. Methods include the Stein estimator (St),
Diagonal Shrinkage (DSh), Simple Slab Regression (SR), Generalized Slab Regression (GSR),
Ledoit-Wolf Linear Shrinkage (LW), Quadratic-Inverse Shrinkage (QIS),
and Shrinkage (Sh), all integrated into the iteratively reweighted least squares (IRLS)
algorithm. This approach enhances estimation accuracy, convergence, and robustness
in the presence of multicollinearity. The best-fitting model is selected based on
the Akaike Information Criterion (AIC). Methods are related to methods described in
Marschner (2011) <doi:10.32614/RJ-2011-012>,
Asimit et al. (2025) <https://openaccess.city.ac.uk/id/eprint/35005/>,
Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>, and
Ledoit and Wolf (2022) <doi:10.3150/20-BEJ1315>.
Author: Ziwei Chen [aut, cre] ,
Vali Asimit [aut] ,
Claudio Senatore [aut]
Maintainer: Ziwei Chen <Ziwei.Chen.3@citystgeorges.ac.uk>
Diff between savvyGLM versions 0.1.2 dated 2026-05-03 and 0.1.3 dated 2026-05-03
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface
for conducting a wide range of factor analysis procedures. 'FAfA'
(Factor Analysis for All) guides users through data uploading,
assumption checking (descriptives, collinearity, multivariate
normality, outliers), data wrangling (variable exclusion, data
splitting), factor retention analysis (e.g., Parallel Analysis, Hull
method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model
testing, Reliability Analysis (e.g., Cronbach's Alpha, McDonald's
Omega), Measurement Invariance testing across groups, and item
weighting techniques. The application leverages established R packages
such as 'lavaan' and 'psych' to perform these analyses, offering an
accessible platform for researchers and students. Results are
presented in user-friendly tables and plots, with options for
downloading outputs.
Author: Abdullah Faruk KILIC [aut, cre],
Ahmet Caliskan [aut]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 1.0 dated 2026-04-29 and 1.1 dated 2026-05-03
FAfA-1.0/FAfA/man/about_server.Rd |only FAfA-1.0/FAfA/man/assumptions_server.Rd |only FAfA-1.0/FAfA/man/cfa_server.Rd |only FAfA-1.0/FAfA/man/cfa_ui.Rd |only FAfA-1.0/FAfA/man/data_selection_server.Rd |only FAfA-1.0/FAfA/man/efa_server_analysis.Rd |only FAfA-1.0/FAfA/man/efa_server_fac_ret.Rd |only FAfA-1.0/FAfA/man/efa_server_report.Rd |only FAfA-1.0/FAfA/man/inv_server.Rd |only FAfA-1.0/FAfA/man/item_weighting_server.Rd |only FAfA-1.0/FAfA/man/mod_itemrest_server.Rd |only FAfA-1.0/FAfA/man/mod_itemrest_ui.Rd |only FAfA-1.0/FAfA/man/mod_missing_server.Rd |only FAfA-1.0/FAfA/man/mod_missing_ui.Rd |only FAfA-1.0/FAfA/man/op_null_or.Rd |only FAfA-1.0/FAfA/man/reliability_server.Rd |only FAfA-1.0/FAfA/man/wrangling_server_ex_var.Rd |only FAfA-1.1/FAfA/DESCRIPTION | 16 - FAfA-1.1/FAfA/MD5 | 69 ++--- FAfA-1.1/FAfA/NAMESPACE | 142 +++++------- FAfA-1.1/FAfA/R/app_server.R | 73 ++---- FAfA-1.1/FAfA/R/app_ui.R | 24 +- FAfA-1.1/FAfA/R/itemrest_internal.R |only FAfA-1.1/FAfA/R/mod_about_server.r | 61 +++-- FAfA-1.1/FAfA/R/mod_assumptions_server.r | 37 ++- FAfA-1.1/FAfA/R/mod_assumptions_ui.R | 2 FAfA-1.1/FAfA/R/mod_cfa_server.r | 280 ++++++++++++++++++++--- FAfA-1.1/FAfA/R/mod_cfa_ui.r | 317 ++++++++++++++++----------- FAfA-1.1/FAfA/R/mod_data_selection_server.r | 152 +++++++++--- FAfA-1.1/FAfA/R/mod_data_selection_ui.r | 103 ++++---- FAfA-1.1/FAfA/R/mod_efa_server.r | 280 +++++++++++++++++------ FAfA-1.1/FAfA/R/mod_efa_ui.r | 153 ++++++++----- FAfA-1.1/FAfA/R/mod_inv_server.r | 152 +++++++++++- FAfA-1.1/FAfA/R/mod_inv_ui.R | 32 ++ FAfA-1.1/FAfA/R/mod_item_weighting_server.r | 4 FAfA-1.1/FAfA/R/mod_itemrest_server.r | 309 +++++++++++++++++++++----- FAfA-1.1/FAfA/R/mod_itemrest_ui.r | 146 +++++++++++- FAfA-1.1/FAfA/R/mod_missing_server.r | 36 +-- FAfA-1.1/FAfA/R/mod_missing_ui.r | 27 ++ FAfA-1.1/FAfA/R/mod_reliability_server.r | 196 ++++++++++++++-- FAfA-1.1/FAfA/R/mod_reliability_ui.r | 16 + FAfA-1.1/FAfA/R/mod_replicability_server.r |only FAfA-1.1/FAfA/R/mod_replicability_ui.r |only FAfA-1.1/FAfA/R/mod_wrangling_server.r | 46 ++- FAfA-1.1/FAfA/R/utils.r | 186 +++++++++------ FAfA-1.1/FAfA/man/print.itemrest_result.Rd |only 46 files changed, 2041 insertions(+), 818 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.0.3 dated 2026-04-25 and 0.0.4 dated 2026-05-03
DESCRIPTION | 13 MD5 | 23 NEWS.md | 18 R/plotting.R | 1562 ++++++++++++++++++++-------------------- R/setup.R | 2 README.md | 7 build |only inst/doc |only man/colleyRstats_setup.Rd | 2 man/generateMoboPlot2.Rd | 17 tests/testthat/test-plotting.R | 46 + tests/testthat/test-reporting.R | 36 vignettes |only 13 files changed, 924 insertions(+), 802 deletions(-)
Title: Peak Detection and Fire History from Sediment-Charcoal Records
Description: A program for reconstructing local fire histories from
high-resolution, continuously sampled lake-sediment charcoal records.
'CharAnalysis' decomposes a charcoal record into low- and high-frequency
components and uses locally defined thresholds to separate fire signal
from noise, following the approach of Higuera et al. (2009)
<doi:10.1890/07-2019.1>, with underlying assumptions and rationale
described in Higuera et al. (2010) <doi:10.1071/WF09134>. The package is
designed for macroscopic charcoal records with contiguous sampling fine
enough to resolve individual fire events, and is not appropriate for
low-resolution or discontinuously sampled records. See the package URL
for the User's Guide and application examples.
Author: Philip Higuera [aut, cre]
Maintainer: Philip Higuera <philip.higuera@umontana.edu>
Diff between CharAnalysis versions 2.0.2 dated 2026-04-28 and 2.0.3 dated 2026-05-03
DESCRIPTION | 8 MD5 | 14 NEWS.md | 39 ++ inst/doc/CharAnalysis_intro.R | 139 ++++----- inst/doc/CharAnalysis_intro.Rmd | 149 +++++---- inst/doc/CharAnalysis_intro.html | 396 +++++++++++++++++--------- inst/validation/CO_compensated_charData.csv |only inst/validation/CO_compensated_charParams.csv |only vignettes/CharAnalysis_intro.Rmd | 149 +++++---- 9 files changed, 547 insertions(+), 347 deletions(-)
Title: Multivariate Conditional Volatility Modelling and Forecasting
Description: Methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndt–Hall–Hall–Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>. For an overview, we refer the reader to Fülle et al. (2024) <doi:10.18637/jss.v111.i04>.
Author: Markus J. Fuelle [aut, cre],
Alexander Lange [aut],
Christian M. Hafner [aut],
Helmut Herwartz [aut]
Maintainer: Markus J. Fuelle <markus.fuelle@gmail.com>
Diff between BEKKs versions 1.4.6 dated 2025-12-07 and 1.4.7 dated 2026-05-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/BEKKs.R | 2 +- build/stage23.rdb |binary man/BEKKs.Rd | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Adaptive Optimal Two-Stage Designs
Description: Optimize one or two-arm, two-stage designs for clinical trials with
respect to several implemented objective criteria or custom objectives.
Optimization under uncertainty and conditional (given stage-one outcome)
constraints are supported.
See Pilz et al. (2019) <doi:10.1002/sim.8291> and
Kunzmann et al. (2021) <doi:10.18637/jss.v098.i09> for details.
Author: Kevin Kunzmann [aut, cph] ,
Maximilian Pilz [aut, cre] ,
Jan Meis [aut] ,
Nico Bruder [aut]
Maintainer: Maximilian Pilz <maximilian.pilz@th-nuernberg.de>
Diff between adoptr versions 1.1.1 dated 2024-10-02 and 1.1.2 dated 2026-05-03
DESCRIPTION | 22 LICENSE | 2 MD5 | 258 +- NAMESPACE | 214 - NEWS.md | 197 - R/BinomialDistribution.R | 328 +- R/ChiSquaredDistribution.R | 378 +-- R/CompositeScore.R | 240 +- R/ConditionalPower.R | 256 +- R/ConditionalSampleSize.R | 140 - R/ContinuousPrior.R | 400 +-- R/DataDistribution.R | 124 - R/FDistribution.R | 344 +-- R/GroupSequentialDesign.R | 328 +- R/MaximumSampleSize.R | 80 R/NormalDistribution.R | 220 - R/OneStageDesign.R | 424 +-- R/PointMassPrior.R | 282 +- R/Prior.R | 272 +- R/Scores.R | 326 +- R/StudentDistribution.R | 170 - R/Survival.R | 174 - R/TwoStageDesign.R | 1630 +++++++------- R/adoptr.R | 122 - R/constraints.R | 436 +-- R/minimize.R | 1678 +++++++------- R/regularization.R | 226 +- R/util.R | 100 README.md | 94 build/vignette.rds |binary inst/CITATION | 50 inst/doc/adoptr.R | 166 - inst/doc/adoptr.Rmd | 488 ++-- inst/doc/adoptr.html | 1059 ++++----- inst/doc/adoptr_jss.R | 738 +++--- inst/doc/adoptr_jss.Rmd | 2422 ++++++++++----------- inst/doc/adoptr_jss.html | 2817 ++++++++++++------------- inst/doc/composite-scores.R | 120 - inst/doc/composite-scores.Rmd | 210 - inst/doc/composite-scores.html | 847 +++---- inst/doc/conditional-scores.R | 128 - inst/doc/conditional-scores.Rmd | 268 +- inst/doc/conditional-scores.html | 919 ++++---- inst/doc/defining-new-scores.R | 92 inst/doc/defining-new-scores.Rmd | 170 - inst/doc/defining-new-scores.html | 817 +++---- inst/doc/other-endpoints.R | 120 - inst/doc/other-endpoints.Rmd | 720 +++--- inst/doc/other-endpoints.html | 1443 ++++++------ inst/doc/working-with-priors.R | 56 inst/doc/working-with-priors.Rmd | 174 - inst/doc/working-with-priors.html | 835 +++---- man/ANOVA-class.Rd | 78 man/AverageN2-class.Rd | 100 man/BinomialDataDistribution-class.Rd | 152 - man/ChiSquaredDataDistribution-class.Rd | 108 man/ConditionalPower-class.Rd | 110 man/ConditionalSampleSize-class.Rd | 120 - man/Constraints.Rd | 176 - man/ContinuousPrior-class.Rd | 124 - man/DataDistribution-class.Rd | 86 man/GroupSequentialDesign-class.Rd | 142 - man/GroupSequentialDesignSurvival-class.Rd | 28 man/MaximumSampleSize-class.Rd | 76 man/N1-class.Rd | 90 man/NestedModels-class.Rd | 128 - man/NormalDataDistribution-class.Rd | 110 man/OneStageDesign-class.Rd | 138 - man/OneStageDesignSurvival-class.Rd | 28 man/Pearson2xK-class.Rd | 70 man/PointMassPrior-class.Rd | 84 man/Prior-class.Rd | 70 man/Scores.Rd | 164 - man/StudentDataDistribution-class.Rd | 94 man/SurvivalDataDistribution-class.Rd | 110 man/SurvivalDesign.Rd | 108 man/TwoStageDesign-class.Rd | 250 +- man/TwoStageDesignSurvival-class.Rd | 56 man/ZSquared-class.Rd | 72 man/adoptr.Rd | 165 - man/boundary-designs.Rd | 212 - man/bounds.Rd | 68 man/composite.Rd | 116 - man/condition.Rd | 82 man/critical-values.Rd | 124 - man/cumulative_distribution_function.Rd | 146 - man/expectation.Rd | 82 man/get_initial_design.Rd | 180 - man/make_tunable.Rd | 106 man/minimize.Rd | 160 - man/n.Rd | 152 - man/plot-TwoStageDesign-method.Rd | 80 man/posterior.Rd | 78 man/predictive_cdf.Rd | 100 man/predictive_pdf.Rd | 100 man/print.adoptrOptimizationResult.Rd | 30 man/probability_density_function.Rd | 146 - man/simulate-TwoStageDesign-numeric-method.Rd | 98 man/subject_to.Rd | 92 man/tunable_parameters.Rd | 106 tests/figs/deps.txt | 6 tests/figs/twostagedesign/design-print.svg | 2 tests/testthat.R | 8 tests/testthat/test_ANOVA.R | 232 +- tests/testthat/test_BinomialDistribution.R | 354 +-- tests/testthat/test_ChiSquaredDistribution.R | 280 +- tests/testthat/test_ConditionalScores.R | 252 +- tests/testthat/test_ContinuousPrior.R | 598 ++--- tests/testthat/test_GaussLegendreIntegration.R | 120 - tests/testthat/test_GroupSequentialDesign.R | 352 +-- tests/testthat/test_IntegralScores.R | 240 +- tests/testthat/test_NormalDistribution.R | 204 - tests/testthat/test_OneStageDesign.R | 432 +-- tests/testthat/test_PointMassPrior.R | 376 +-- tests/testthat/test_StudentDistribution.R | 316 +- tests/testthat/test_Survival.R | 200 - tests/testthat/test_TwoStageDesign.R | 482 ++-- tests/testthat/test_composite.R | 252 +- tests/testthat/test_constraints.R | 282 +- tests/testthat/test_minimize.R | 1176 +++++----- tests/testthat/test_regularizer.R | 154 - tests/testthat/test_tunable.R | 420 +-- vignettes/adoptr.Rmd | 488 ++-- vignettes/adoptr_jss.Rmd | 2422 ++++++++++----------- vignettes/composite-scores.Rmd | 210 - vignettes/conditional-scores.Rmd | 268 +- vignettes/defining-new-scores.Rmd | 170 - vignettes/other-endpoints.Rmd | 720 +++--- vignettes/ref.bib | 992 ++++---- vignettes/working-with-priors.Rmd | 174 - 130 files changed, 20807 insertions(+), 20794 deletions(-)
Title: Generalized Linear Models with Slab and Shrinkage Estimators
Description: Provides a flexible framework for fitting generalized linear models (GLMs)
with slab and shrinkage estimators. Methods include the Stein estimator (St),
Diagonal Shrinkage (DSh), Simple Slab Regression (SR), Generalized Slab Regression (GSR),
Ledoit-Wolf Linear Shrinkage (LW), Quadratic-Inverse Shrinkage (QIS),
and Shrinkage (Sh), all integrated into the iteratively reweighted least squares (IRLS)
algorithm. This approach enhances estimation accuracy, convergence, and robustness
in the presence of multicollinearity. The best-fitting model is selected based on
the Akaike Information Criterion (AIC). Methods are related to methods described in
Marschner (2011) <doi:10.32614/RJ-2011-012>,
Asimit et al. (2025) <https://openaccess.city.ac.uk/id/eprint/35005/>,
Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>, and
Ledoit and Wolf (2022) <doi:10.3150/20-BEJ1315>.
Author: Ziwei Chen [aut, cre] ,
Vali Asimit [aut] ,
Claudio Senatore [aut]
Maintainer: Ziwei Chen <Ziwei.Chen.3@citystgeorges.ac.uk>
Diff between savvyGLM versions 0.1.1 dated 2026-05-02 and 0.1.2 dated 2026-05-03
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] ,
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.2-15 dated 2026-01-12 and 0.2-16 dated 2026-05-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/snap_to_grid.R | 4 ++-- man/st_snap_to_grid.Rd | 4 ++-- src/lwgeom.cpp | 3 ++- 6 files changed, 22 insertions(+), 15 deletions(-)
Title: Client for the 'World Bank' APIs
Description: Download and search data from the 'World Bank' APIs,
including the 'Indicators' API, the 'Poverty and Inequality Platform
(PIP)' API, the 'Finances One' API, and the 'Projects' API. See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889386-developer-information-overview>
for further details.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between worldbank versions 0.8.0 dated 2026-03-15 and 0.9.0 dated 2026-05-03
DESCRIPTION | 9 +- MD5 | 70 ++++++++------- NAMESPACE | 3 NEWS.md | 26 +++-- R/fone.R | 17 +-- R/httr2.R | 7 + R/indicators.R | 172 +++++++++++++++++++++++++++++++++------ R/pip.R | 13 +- R/projects.R | 7 - R/utils.R | 6 + R/worldbank-package.R | 1 README.md | 23 ++--- man/figures/README-demo-1.png |binary man/fone.Rd | 12 +- man/pip_aux.Rd | 20 ++-- man/pip_citation.Rd | 18 ++-- man/pip_cp.Rd | 18 ++-- man/pip_data.Rd | 22 ++-- man/pip_group.Rd | 22 ++-- man/pip_health_check.Rd | 18 ++-- man/pip_info.Rd | 20 ++-- man/pip_valid_params.Rd | 18 ++-- man/pip_versions.Rd | 18 ++-- man/wb_bulk.Rd |only man/wb_country.Rd | 19 ++-- man/wb_data.Rd | 14 +++ man/wb_income_level.Rd | 19 ++-- man/wb_indicator.Rd | 19 ++-- man/wb_language.Rd | 19 ++-- man/wb_lending_type.Rd | 21 ++-- man/wb_region.Rd | 19 ++-- man/wb_search.Rd |only man/wb_source.Rd | 19 ++-- man/wb_topic.Rd | 19 ++-- man/worldbank-package.Rd | 5 + tests/testthat/test-indicators.R | 84 ++++++++++++++++++- tests/testthat/test-utils.R | 17 +++ 37 files changed, 543 insertions(+), 271 deletions(-)
Title: Result Stability Checks for Empirical R Projects
Description: Lightweight helpers for checking whether empirical results remain
substantively unchanged across code revisions, platform differences,
and package updates. The package supports regression-style testing of
derived datasets, statistical model outputs, tables, and plots, helping
researchers detect unintended result drift early and distinguish material
from non-material changes in empirical workflows.
Author: Dianyi Yang [aut, cre, ctb]
Maintainer: Dianyi Yang <dianyi.yang@politics.ox.ac.uk>
Diff between resultcheck versions 0.1.4 dated 2026-04-21 and 0.2.0 dated 2026-05-03
DESCRIPTION | 9 MD5 | 32 + NEWS.md | 87 ++-- R/sandbox.R | 51 +- R/snapshot.R | 637 ++++++++++++++++++++++++++---- README.md | 45 +- build/vignette.rds |binary inst/doc/faq.R |only inst/doc/faq.Rmd |only inst/doc/faq.html |only inst/doc/resultcheck.R |only inst/doc/resultcheck.Rmd |only inst/doc/resultcheck.html |only inst/extdata/snapshot-method-defaults.R |only inst/extdata/snapshot-method-defaults.yml |only man/detect_script_name.Rd |only man/get_snapshot_path.Rd | 4 man/serialize_value.Rd | 8 man/snapshot.Rd | 43 +- tests/testthat/test-snapshot.R | 321 +++++++++++++-- vignettes/faq.Rmd |only vignettes/img |only vignettes/resultcheck.Rmd |only 23 files changed, 1033 insertions(+), 204 deletions(-)
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Maximilian Muecke [aut, cre] ,
Sebastian Fischer [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3fda versions 0.4.0 dated 2026-03-30 and 0.5.0 dated 2026-05-03
DESCRIPTION | 19 +++-- MD5 | 87 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 4 + R/PipeOpFDABsignal.R | 16 ++-- R/PipeOpFDACor.R | 6 + R/PipeOpFDAExtract.R | 104 +++++++++++++++----------------- R/PipeOpFDAFlatten.R | 19 ++--- R/PipeOpFDAFourier.R | 10 +-- R/PipeOpFDAInterpol.R | 39 +++++++----- R/PipeOpFDARandomEffect.R | 16 ++-- R/PipeOpFDARegister.R |only R/PipeOpFDAScaleRange.R | 14 ++-- R/PipeOpFDASmooth.R | 20 ++++-- R/PipeOpFDATsfeatures.R | 28 ++++---- R/PipeOpFDAWavelets.R | 19 +++-- R/PipeOpFDAZoom.R | 8 +- R/PipeOpFPCA.R | 6 + R/TaskClassif_phoneme.R | 2 R/bibentries.R | 14 ++-- R/zzz.R | 16 +++- README.md | 3 build/partial.rdb |binary man/mlr3fda-package.Rd | 4 - man/mlr_pipeops_fda.bsignal.Rd | 87 +++++++++++++------------- man/mlr_pipeops_fda.cor.Rd | 85 +++++++++++++------------- man/mlr_pipeops_fda.extract.Rd | 97 +++++++++++++++-------------- man/mlr_pipeops_fda.flatten.Rd | 89 +++++++++++++-------------- man/mlr_pipeops_fda.fourier.Rd | 87 +++++++++++++------------- man/mlr_pipeops_fda.fpca.Rd | 85 +++++++++++++------------- man/mlr_pipeops_fda.interpol.Rd | 101 ++++++++++++++++--------------- man/mlr_pipeops_fda.random_effect.Rd | 89 ++++++++++++++------------- man/mlr_pipeops_fda.register.Rd |only man/mlr_pipeops_fda.scalerange.Rd | 83 ++++++++++++------------- man/mlr_pipeops_fda.smooth.Rd | 87 +++++++++++++------------- man/mlr_pipeops_fda.tsfeats.Rd | 87 +++++++++++++------------- man/mlr_pipeops_fda.wavelets.Rd | 91 ++++++++++++++-------------- man/mlr_pipeops_fda.zoom.Rd | 83 ++++++++++++------------- man/mlr_tasks_dti.Rd | 4 - man/mlr_tasks_fuel.Rd | 4 - man/mlr_tasks_phoneme.Rd | 8 +- tests/testthat/test_PipeOpFDACor.R | 6 - tests/testthat/test_PipeOpFDAExtract.R | 9 +- tests/testthat/test_PipeOpFDAFlatten.R | 15 ++++ tests/testthat/test_PipeOpFDARegister.R |only tests/testthat/test_PipeOpFPCA.R | 25 +++++-- 46 files changed, 887 insertions(+), 790 deletions(-)
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon [aut, cre],
Nicolas Hengartner [aut],
Eric Matzner-Lober [aut]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 2.0-5 dated 2025-09-12 and 2.4-0 dated 2026-05-03
ibr-2.0-5/ibr/R/kernel.R |only ibr-2.0-5/ibr/man/kernel.Rd |only ibr-2.0-5/ibr/man/poids.Rd |only ibr-2.0-5/ibr/man/tracekernel.Rd |only ibr-2.0-5/ibr/src/ibr_init.c |only ibr-2.4-0/ibr/DESCRIPTION | 8 ibr-2.4-0/ibr/MD5 | 64 ++-- ibr-2.4-0/ibr/NAMESPACE | 9 ibr-2.4-0/ibr/R/bwchoice.R | 30 - ibr-2.4-0/ibr/R/calcA.R | 32 -- ibr-2.4-0/ibr/R/departnoyau.r | 28 - ibr-2.4-0/ibr/R/dssmoother.R | 4 ibr-2.4-0/ibr/R/dssplines.R | 19 - ibr-2.4-0/ibr/R/ibr.R | 4 ibr-2.4-0/ibr/R/ibr.fit.R | 564 ++++++++++++++++++++---------------- ibr-2.4-0/ibr/R/kernelKx.R |only ibr-2.4-0/ibr/R/kernelSx.R | 30 - ibr-2.4-0/ibr/R/npregress.R | 80 ----- ibr-2.4-0/ibr/R/predict.ibr.R | 2 ibr-2.4-0/ibr/R/predict.npregress.R | 32 -- ibr-2.4-0/ibr/R/print.ibr.R | 2 ibr-2.4-0/ibr/man/dssmoother.Rd | 8 ibr-2.4-0/ibr/man/ibr.Rd | 11 ibr-2.4-0/ibr/man/ibr.fit.Rd | 9 ibr-2.4-0/ibr/man/kernelKx.Rd |only ibr-2.4-0/ibr/man/kernelSx.Rd | 24 - ibr-2.4-0/ibr/man/npregress.Rd | 6 ibr-2.4-0/ibr/src/dssplines.c | 272 ++++++++++------- ibr-2.4-0/ibr/src/dssplines.h |only ibr-2.4-0/ibr/src/ibr.c | 171 +++++----- ibr-2.4-0/ibr/src/ibr.h |only ibr-2.4-0/ibr/src/init.c |only ibr-2.4-0/ibr/src/kernel.c |only ibr-2.4-0/ibr/src/kernel.h |only ibr-2.4-0/ibr/src/polynomlocaux.c | 393 +++---------------------- ibr-2.4-0/ibr/src/polynomlocaux.h |only ibr-2.4-0/ibr/src/product.c |only ibr-2.4-0/ibr/src/product.h |only ibr-2.4-0/ibr/src/regression.c | 362 ++++------------------- ibr-2.4-0/ibr/src/regression.h |only ibr-2.4-0/ibr/src/smoother.c |only ibr-2.4-0/ibr/src/smoother.h |only 42 files changed, 830 insertions(+), 1334 deletions(-)
Title: Secretary Bird Optimization for Continuous Optimization and
Neural Network Training
Description: Provides an implementation of Secretary Bird Optimization for
general-purpose continuous optimization, benchmark optimization, and
training single-hidden-layer feed-forward neural network models. The
implemented optimizer is based on the Secretary Bird Optimization Algorithm
proposed by Fu et al. (2024) <doi:10.1007/s10462-024-10729-y>. The neural
network training functionality is based on Dilber and Özdemir (2026)
<doi:10.1007/s00521-026-11874-x>.
Author: Burak Dilber [aut, cre, cph],
A. Firat Oezdemir [aut, cph]
Maintainer: Burak Dilber <burakdilber91@gmail.com>
Diff between SBOAtools versions 0.1.0 dated 2026-04-10 and 0.1.1 dated 2026-05-03
DESCRIPTION | 20 ++++++----- MD5 | 24 +++++++------ NAMESPACE | 2 + NEWS.md |only R/benchmarks.R |only R/sboa.R | 43 +++++++++++++++++++++++ R/sboa_methods.R | 8 ++-- R/sboa_mlp.R | 6 ++- README.md | 88 +++++++++++++++++++++++++++++++++++++++++++------ man/get_benchmark.Rd |only man/list_benchmarks.Rd |only man/plot.sboa.Rd | 2 - man/plot.sboa_mlp.Rd | 2 - man/print.sboa.Rd | 2 - man/sboa.Rd | 16 ++++++++ 15 files changed, 175 insertions(+), 38 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut],
Milan Bouchet-Valat [aut],
Manuel Munoz-Marquez [aut, cre],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ct [...truncated...]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between Rcmdr versions 2.12.2 dated 2026-04-11 and 2.12.3 dated 2026-05-03
DESCRIPTION | 8 +- MD5 | 36 ++++++---- NEWS | 6 + R/Rcmdr-package.R | 4 - R/data-menu.R | 85 +++++++++++++++++++++++-- R/statistics-models-menu.R | 30 +++++++- R/stepwiseRegression.R |only R/utilities.R | 2 inst/doc/Commander-ru.pdf |binary inst/doc/Empezando-con-Rcmdr-es.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ko.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 4 - man/RemoveRows.Rd |only man/SelectRows.Rd |only man/linearRegressionModel.Rd |only man/readDataFromPackage.Rd |only man/stepwiseRegression.Rd |only po/R-Rcmdr.pot | 4 - po/R-es.po | 10 +- 22 files changed, 150 insertions(+), 39 deletions(-)
Title: A Tidy Physics Engine for Building and Visualizing Orbital
Simulations
Description: A lightweight, fully vectorized N-body physics engine built for
the R ecosystem. Simulate and visualize complex orbital mechanics,
celestial trajectories, and gravitational interactions using tidy data
principles. Features multiple numerical integration methods, including
the energy-conserving velocity Verlet algorithm
(Verlet (1967) <doi:10.1103/PhysRev.159.98>), to ensure highly stable
orbital propagation. Gravitational N-body methods follow
Aarseth (2003, ISBN:0-521-43272-3).
Author: Dave Rosenman [aut, cre]
Maintainer: Dave Rosenman <dave.rosenman.data@gmail.com>
Diff between orbitr versions 0.2.0 dated 2026-04-21 and 0.3.0 dated 2026-05-03
DESCRIPTION | 6 +- MD5 | 36 ++++++++++---- NAMESPACE | 6 ++ NEWS.md | 23 +++++++++ R/get_bodies.R |only R/print.R |only R/remove_body.R |only R/save_load.R |only README.md | 7 ++ inst/doc/custom-visualization.html | 4 - inst/doc/examples.html | 8 +-- inst/doc/plotting-3d.html | 8 +-- inst/doc/quick-start.R | 13 +++++ inst/doc/quick-start.Rmd | 46 ++++++++++++++++-- inst/doc/quick-start.html | 92 ++++++++++++++++++++++++------------- man/export_bodies.Rd |only man/get_bodies.Rd |only man/load_system.Rd |only man/print.orbit_system.Rd |only man/remove_body.Rd |only man/save_system.Rd |only tests/testthat/test-get_bodies.R |only tests/testthat/test-print.R |only tests/testthat/test-remove_body.R |only tests/testthat/test-save_load.R |only vignettes/quick-start.Rmd | 46 ++++++++++++++++-- 26 files changed, 229 insertions(+), 66 deletions(-)
Title: Core Mathematical Functions for Multi-Objective Optimization
Description: Fast implementations of mathematical operations and performance metrics for multi-objective optimization, including filtering and ranking of dominated vectors according to Pareto optimality, hypervolume metric, C.M. Fonseca, L. Paquete, M. López-Ibáñez (2006) <doi:10.1109/CEC.2006.1688440>, epsilon indicator, inverted generational distance, computation of the empirical attainment function, V.G. da Fonseca, C.M. Fonseca, A.O. Hall (2001) <doi:10.1007/3-540-44719-9_15>, and Vorob'ev threshold, expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) <doi:10.1016/j.ejor.2014.07.032>, among others.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Carlos Fonseca [ctb],
Luis Paquete [ctb],
Andreia P. Guerreiro [ctb],
Mickael Binois [ctb],
Michael H. Buselli [cph] ,
Wessel Dankers [cph] ,
NumPy Developers [cph] ,
Jean-Sebastien Roy [cph] ,
Makoto Matsumoto [cph] [...truncated...]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between moocore versions 0.2.0 dated 2026-01-11 and 0.3.0 dated 2026-05-03
moocore-0.2.0/moocore/tests/testthat/test-eafdiff.R |only moocore-0.3.0/moocore/DESCRIPTION | 12 moocore-0.3.0/moocore/MD5 | 157 +- moocore-0.3.0/moocore/NAMESPACE | 1 moocore-0.3.0/moocore/NEWS.md | 11 moocore-0.3.0/moocore/R/eaf.R | 10 moocore-0.3.0/moocore/R/generate.R | 133 +- moocore-0.3.0/moocore/R/hv.R | 38 moocore-0.3.0/moocore/R/hv_approx.R | 83 - moocore-0.3.0/moocore/R/nondominated.R | 35 moocore-0.3.0/moocore/R/r2.R |only moocore-0.3.0/moocore/R/utils.R | 4 moocore-0.3.0/moocore/R/whv.R | 6 moocore-0.3.0/moocore/build/partial.rdb |binary moocore-0.3.0/moocore/inst/REFERENCES.bib | 122 + moocore-0.3.0/moocore/inst/WORDLIST | 12 moocore-0.3.0/moocore/man/eaf.Rd | 10 moocore-0.3.0/moocore/man/generate_ndset.Rd | 118 + moocore-0.3.0/moocore/man/hv_approx.Rd | 70 - moocore-0.3.0/moocore/man/hv_contributions.Rd | 2 moocore-0.3.0/moocore/man/hypervolume.Rd | 43 moocore-0.3.0/moocore/man/macros/macros.Rd | 7 moocore-0.3.0/moocore/man/nondominated.Rd | 29 moocore-0.3.0/moocore/man/r2_exact.Rd |only moocore-0.3.0/moocore/man/whv_hype.Rd | 4 moocore-0.3.0/moocore/src/Makevars | 2 moocore-0.3.0/moocore/src/Rcommon.h | 13 moocore-0.3.0/moocore/src/Rmoocore.c | 103 + moocore-0.3.0/moocore/src/init.h | 4 moocore-0.3.0/moocore/src/libmoocore/Makefile | 27 moocore-0.3.0/moocore/src/libmoocore/NEWS.md | 15 moocore-0.3.0/moocore/src/libmoocore/avl.c | 1 moocore-0.3.0/moocore/src/libmoocore/common.h | 28 moocore-0.3.0/moocore/src/libmoocore/config.h | 10 moocore-0.3.0/moocore/src/libmoocore/eaf.c | 307 ++-- moocore-0.3.0/moocore/src/libmoocore/eaf.h | 77 - moocore-0.3.0/moocore/src/libmoocore/eaf3d.c | 155 +- moocore-0.3.0/moocore/src/libmoocore/eaf_main.c | 33 moocore-0.3.0/moocore/src/libmoocore/epsilon.c | 36 moocore-0.3.0/moocore/src/libmoocore/epsilon.h | 10 moocore-0.3.0/moocore/src/libmoocore/gcc.mk | 5 moocore-0.3.0/moocore/src/libmoocore/hv.c | 244 ++- moocore-0.3.0/moocore/src/libmoocore/hv3d_priv.h | 6 moocore-0.3.0/moocore/src/libmoocore/hv4d_priv.h | 15 moocore-0.3.0/moocore/src/libmoocore/hv_contrib.c | 90 - moocore-0.3.0/moocore/src/libmoocore/hv_priv.h | 25 moocore-0.3.0/moocore/src/libmoocore/hvapprox.c | 282 +++- moocore-0.3.0/moocore/src/libmoocore/hvapprox.h | 23 moocore-0.3.0/moocore/src/libmoocore/hvc4d_priv.h |only moocore-0.3.0/moocore/src/libmoocore/igd.c | 22 moocore-0.3.0/moocore/src/libmoocore/igd.h | 12 moocore-0.3.0/moocore/src/libmoocore/io.c | 5 moocore-0.3.0/moocore/src/libmoocore/io.h | 6 moocore-0.3.0/moocore/src/libmoocore/libhv.mk | 2 moocore-0.3.0/moocore/src/libmoocore/libmoocore-config.h | 1 moocore-0.3.0/moocore/src/libmoocore/main-hvapprox.c | 37 moocore-0.3.0/moocore/src/libmoocore/maxminclamp.h | 21 moocore-0.3.0/moocore/src/libmoocore/ndsort.c | 32 moocore-0.3.0/moocore/src/libmoocore/nondominated.c | 18 moocore-0.3.0/moocore/src/libmoocore/nondominated.h | 653 ++++++---- moocore-0.3.0/moocore/src/libmoocore/nondominated_kung.h |only moocore-0.3.0/moocore/src/libmoocore/pareto.c | 324 +++- moocore-0.3.0/moocore/src/libmoocore/pow_int.h | 4 moocore-0.3.0/moocore/src/libmoocore/r2_exact.c |only moocore-0.3.0/moocore/src/libmoocore/r2_exact.h |only moocore-0.3.0/moocore/src/libmoocore/sort.h | 183 +- moocore-0.3.0/moocore/src/libmoocore/whv.c | 30 moocore-0.3.0/moocore/src/libmoocore/whv_hype.c | 2 moocore-0.3.0/moocore/tests/testthat/test-doctest-eafdiff.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-epsilon_additive.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-hv_approx.R | 6 moocore-0.3.0/moocore/tests/testthat/test-doctest-hv_contributions.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-hypervolume.R |only moocore-0.3.0/moocore/tests/testthat/test-doctest-igd.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-is_nondominated.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-r2_exact.R |only moocore-0.3.0/moocore/tests/testthat/test-doctest-vorob_t.R | 1 moocore-0.3.0/moocore/tests/testthat/test-doctest-whv_hype.R | 1 moocore-0.3.0/moocore/tests/testthat/test-eafdiff2d.R |only moocore-0.3.0/moocore/tests/testthat/test-eafdiff3d.R |only moocore-0.3.0/moocore/tests/testthat/test-generate.R |only moocore-0.3.0/moocore/tests/testthat/test-hv.R | 51 moocore-0.3.0/moocore/tests/testthat/test-hv_approx.R |only moocore-0.3.0/moocore/tests/testthat/test-nondominated.R | 28 moocore-0.3.0/moocore/tests/testthat/test-r2_exact.R |only moocore-0.3.0/moocore/tests/testthat/test-whv_hype.R | 17 moocore-0.3.0/moocore/tests/testthat/test_r2.R |only 87 files changed, 2526 insertions(+), 1353 deletions(-)
Title: Distributions and Gradients
Description: Provides density, distribution function, quantile function and random
generation for the split normal and split-t distributions, and computes their
mean, variance, skewness and kurtosis for the two distributions (Li, F,
Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
Author: Feng Li [aut, cre] ,
Jiayue Zeng [aut]
Maintainer: Feng Li <feng.li@gsm.pku.edu.cn>
Diff between dng versions 0.2.1 dated 2018-06-27 and 1.0.0 dated 2026-05-03
DESCRIPTION | 20 MD5 | 37 + NEWS.md |only R/RcppExports.R | 619 ++++++++++++++++-------------- README.md |only inst/CITATION | 79 +-- man/figures |only man/ghypergeo.Rd |only man/splitn.Rd | 27 + man/splitn_moments.Rd | 8 man/splitt.Rd | 27 + man/splitt_moments.Rd | 8 src/RcppExports.cpp | 50 ++ src/rcpp_dsplitn.cpp | 6 src/rcpp_dsplitt.cpp | 4 src/rcpp_gsplitn.cpp |only src/rcpp_gsplitt.cpp |only src/rcpp_psplitn.cpp | 3 src/rcpp_rsplitn.cpp | 6 src/rcpp_splitt_kurtosis.cpp | 2 tests/testthat/test-gsplitn-gradients.R |only tests/testthat/test-gsplitt-gradients.R |only tests/testthat/test-moments.R |only tests/testthat/test-splitn-distribution.R |only tests/testthat/test-splitt-distribution.R |only 25 files changed, 522 insertions(+), 374 deletions(-)
Title: Automatic Short Form Creation
Description: Performs automatic creation of short forms of scales with an
ant colony optimization algorithm and a Tabu search. As implemented in the
package, the ant colony algorithm randomly selects items to build a model of
a specified length, then updates the probability of item selection according
to the fit of the best model within each set of searches. The algorithm
continues until the same items are selected by multiple ants a given number
of times in a row. On the other hand, the Tabu search changes one parameter at
a time to be either free, constrained, or fixed while keeping track of the
changes made and putting changes that result in worse fit in a "tabu" list
so that the algorithm does not revisit them for some number of searches.
See Leite, Huang, & Marcoulides (2008) <doi:10.1080/00273170802285743> for
an applied example of the ant colony algorithm, and Marcoulides & Falk (2018)
<doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
Author: Anthony Raborn [aut, cre] ,
Walter Leite [aut]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between ShortForm versions 0.5.6 dated 2024-11-27 and 0.5.7 dated 2026-05-03
DESCRIPTION | 17 MD5 | 108 - NAMESPACE | 55 NEWS | 326 +-- NEWS.md | 370 ++-- R/ACO.R | 495 ++--- R/ACO_MPlus.R | 1384 +++++++-------- R/ACO_internals.R | 204 +- R/ACO_lavaan.R | 1244 +++++++------ R/SA.R | 328 +-- R/ShortForm.R | 118 - R/TS.R | 398 ++-- R/Tabu_addparam.R | 178 - R/Tabu_internal.R | 260 +- R/Tabu_refit.R | 144 - R/Tabu_searchprep.R | 240 +- R/Tabu_sem.R | 246 +- R/data.R | 50 R/lavaan_copied_internal_functions.R | 1044 +++++------ R/simulated_annealing.R | 782 ++++---- R/simulated_annealing_internals.R | 1316 +++++++------- R/simulated_annealing_temperatures.R | 26 R/tabu_sem_shortform.R | 782 ++++---- build/partial.rdb |binary man/ACO-class.Rd | 60 man/SA-class.Rd | 66 man/ShortForm.Rd | 24 man/ShortFormStartup.Rd | 34 man/TS-class.Rd | 62 man/add.param.Rd | 160 - man/antcolony.lavaan.Rd | 593 +++--- man/antcolony.mplus.Rd | 582 +++--- man/dot-onAttach.Rd | 46 man/exampleAntModel.Rd | 32 man/modelCheck-class.Rd | 48 man/par.matches.Rd | 28 man/plot-ACO-ANY-method.Rd | 38 man/plot-SA-ANY-method.Rd | 32 man/plot-TS-ANY-method.Rd | 32 man/refit.model.Rd | 66 man/search.prep.Rd | 136 - man/shortExampleAntModel.Rd | 32 man/show-ACO-method.Rd | 28 man/show-SA-method.Rd | 28 man/show-TS-method.Rd | 28 man/simulatedAnnealing.Rd | 230 +- man/simulated_test_data.Rd | 48 man/summary-ACO-method.Rd | 28 man/summary-SA-method.Rd | 28 man/summary-TS-method.Rd | 28 man/tabu.sem.Rd | 126 - man/tabuShortForm.Rd | 290 +-- tests/testthat.R | 8 tests/testthat/test-simulated_annealing_internals.R | 1794 ++++++++++---------- tests/testthat/test-temperatures.R | 66 55 files changed, 7509 insertions(+), 7407 deletions(-)
Title: Download and Tidy Data from the Australian Prudential Regulation
Authority
Description: Download the latest data from the Australian Prudential Regulation
Authority <https://www.apra.gov.au/> and import it into R as a tidy data
frame.
Author: Jarrod van der Wal [aut, cre, cph]
Maintainer: Jarrod van der Wal <jarvanderwal@gmail.com>
Diff between readapra versions 0.2.2 dated 2026-03-22 and 0.2.3 dated 2026-05-03
readapra-0.2.2/readapra/man/figures/README-ggplot_roa-1.png |only readapra-0.2.2/readapra/man/figures/README-plot_madis-1.png |only readapra-0.2.3/readapra/DESCRIPTION | 9 +- readapra-0.2.3/readapra/MD5 | 21 ++-- readapra-0.2.3/readapra/NEWS.md | 3 readapra-0.2.3/readapra/R/read_adipops.R | 1 readapra-0.2.3/readapra/R/read_madis.R | 1 readapra-0.2.3/readapra/R/read_qadicp.R | 1 readapra-0.2.3/readapra/R/readapra_package.R | 2 readapra-0.2.3/readapra/R/universal_helpers.R | 12 ++ readapra-0.2.3/readapra/README.md | 52 +++++++++--- readapra-0.2.3/readapra/man/figures/README-plot_madis-1.svg |only readapra-0.2.3/readapra/man/readapra-package.Rd | 47 +++++----- 13 files changed, 97 insertions(+), 52 deletions(-)
Title: Enhanced R Package for 'GEMPACK' .har and .sl4 Files
Description: Provides tools for processing and analyzing .har and .sl4 files, making it easier
for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets.
It simplifies the management of multiple experiment results, enabling faster
and more efficient comparisons without complexity. Users can extract, restructure,
and merge data seamlessly, ensuring compatibility across different tools.
The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or
any software that supports Text, CSV, or 'Excel' formats.
Author: Pattawee Puangchit [aut, cre]
Maintainer: Pattawee Puangchit <ppuangch@purdue.edu>
Diff between HARplus versions 1.1.2 dated 2025-10-20 and 1.2.0 dated 2026-05-03
DESCRIPTION | 8 MD5 | 26 R/load_HARplus.R | 47 + R/load_sl4x.R | 77 ++ R/save_har.R | 1097 +++++++++++++++++++++-------------------- R/shock_cal.R | 135 ++++- README.md | 43 + build/vignette.rds |binary inst/doc/introduction.html | 4 inst/docs/HARplus_1.1.2.pdf |binary inst/docs/HARplus_1.1.3.pdf |only inst/docs/HARplus_1.2.0.pdf |only man/save_har.Rd | 256 +++++---- man/shock_calculate.Rd | 15 man/shock_calculate_uniform.Rd | 15 15 files changed, 1050 insertions(+), 673 deletions(-)
Title: A Bridge Between 'keras' and 'tidymodels'
Description: Provides a seamless bridge between 'keras' and the 'tidymodels'
frameworks. It allows for the dynamic creation of 'parsnip' model
specifications for 'keras' models.
Author: David Diaz [aut, cph, cre]
Maintainer: David Diaz <daviddrsch@gmail.com>
Diff between kerasnip versions 0.1.0 dated 2025-12-06 and 0.1.2 dated 2026-05-02
kerasnip-0.1.0/kerasnip/inst/doc/applications.R |only kerasnip-0.1.0/kerasnip/inst/doc/autoplot_uniqueness.R |only kerasnip-0.1.0/kerasnip/inst/doc/functional_api.R |only kerasnip-0.1.0/kerasnip/inst/doc/getting_started.R |only kerasnip-0.1.0/kerasnip/inst/doc/sequential_model.R |only kerasnip-0.1.0/kerasnip/inst/doc/tuning_fit_compile_args.R |only kerasnip-0.1.0/kerasnip/inst/doc/workflows_functional.R |only kerasnip-0.1.0/kerasnip/inst/doc/workflows_sequential.R |only kerasnip-0.1.2/kerasnip/DESCRIPTION | 37 kerasnip-0.1.2/kerasnip/MD5 | 172 - kerasnip-0.1.2/kerasnip/NAMESPACE | 28 kerasnip-0.1.2/kerasnip/R/axe_methods.R |only kerasnip-0.1.2/kerasnip/R/build_and_compile_model.R | 49 kerasnip-0.1.2/kerasnip/R/build_spec_function.R | 177 - kerasnip-0.1.2/kerasnip/R/compile_keras_grid.R | 27 kerasnip-0.1.2/kerasnip/R/create_keras_functional_spec.R | 48 kerasnip-0.1.2/kerasnip/R/create_keras_sequential_spec.R | 30 kerasnip-0.1.2/kerasnip/R/create_keras_spec_helpers.R | 9 kerasnip-0.1.2/kerasnip/R/generate_roxygen_docs.R | 103 kerasnip-0.1.2/kerasnip/R/generic_fit_helpers.R | 43 kerasnip-0.1.2/kerasnip/R/generic_functional_fit.R | 19 kerasnip-0.1.2/kerasnip/R/generic_sequential_fit.R | 31 kerasnip-0.1.2/kerasnip/R/keras_tools.R | 92 kerasnip-0.1.2/kerasnip/R/kerasnip_spec_methods.R |only kerasnip-0.1.2/kerasnip/R/register_core_model.R | 3 kerasnip-0.1.2/kerasnip/R/register_fit_predict.R | 17 kerasnip-0.1.2/kerasnip/R/register_model_args.R | 14 kerasnip-0.1.2/kerasnip/R/register_update_method.R | 172 - kerasnip-0.1.2/kerasnip/R/remove_keras_spec.R | 15 kerasnip-0.1.2/kerasnip/R/step_collapse.R | 327 +- kerasnip-0.1.2/kerasnip/R/utils.R | 96 kerasnip-0.1.2/kerasnip/R/zzz.R | 24 kerasnip-0.1.2/kerasnip/README.md | 4 kerasnip-0.1.2/kerasnip/build/vignette.rds |binary kerasnip-0.1.2/kerasnip/inst/doc/applications.Rmd | 57 kerasnip-0.1.2/kerasnip/inst/doc/applications.html | 61 kerasnip-0.1.2/kerasnip/inst/doc/autoplot_uniqueness.Rmd | 123 - kerasnip-0.1.2/kerasnip/inst/doc/autoplot_uniqueness.html | 217 + kerasnip-0.1.2/kerasnip/inst/doc/conformal_intervals.Rmd |only kerasnip-0.1.2/kerasnip/inst/doc/conformal_intervals.html |only kerasnip-0.1.2/kerasnip/inst/doc/functional_api.Rmd | 120 - kerasnip-0.1.2/kerasnip/inst/doc/functional_api.html | 106 kerasnip-0.1.2/kerasnip/inst/doc/getting_started.Rmd | 275 ++ kerasnip-0.1.2/kerasnip/inst/doc/getting_started.html | 335 +-- kerasnip-0.1.2/kerasnip/inst/doc/saving_and_reloading.Rmd |only kerasnip-0.1.2/kerasnip/inst/doc/saving_and_reloading.html |only kerasnip-0.1.2/kerasnip/inst/doc/sequential_model.Rmd | 66 kerasnip-0.1.2/kerasnip/inst/doc/sequential_model.html | 81 kerasnip-0.1.2/kerasnip/inst/doc/tuning_fit_compile_args.Rmd | 385 +++ kerasnip-0.1.2/kerasnip/inst/doc/tuning_fit_compile_args.html | 555 ++--- kerasnip-0.1.2/kerasnip/inst/doc/workflows_functional.Rmd | 393 +++ kerasnip-0.1.2/kerasnip/inst/doc/workflows_functional.html | 609 +---- kerasnip-0.1.2/kerasnip/inst/doc/workflows_sequential.Rmd | 358 +++ kerasnip-0.1.2/kerasnip/inst/doc/workflows_sequential.html | 1108 +--------- kerasnip-0.1.2/kerasnip/man/axe-kerasnip_model_fit.Rd |only kerasnip-0.1.2/kerasnip/man/compile_keras_grid.Rd | 5 kerasnip-0.1.2/kerasnip/man/create_keras_functional_spec.Rd | 49 kerasnip-0.1.2/kerasnip/man/create_keras_sequential_spec.Rd | 31 kerasnip-0.1.2/kerasnip/man/extract_valid_grid.Rd | 3 kerasnip-0.1.2/kerasnip/man/fit.kerasnip_spec.Rd |only kerasnip-0.1.2/kerasnip/man/fit_xy.kerasnip_spec.Rd |only kerasnip-0.1.2/kerasnip/man/generic_functional_fit.Rd | 10 kerasnip-0.1.2/kerasnip/man/generic_sequential_fit.Rd | 22 kerasnip-0.1.2/kerasnip/man/get_model_env.Rd | 6 kerasnip-0.1.2/kerasnip/man/glance.kerasnip_model_fit.Rd |only kerasnip-0.1.2/kerasnip/man/inform_errors.Rd | 3 kerasnip-0.1.2/kerasnip/man/keras_evaluate.Rd | 4 kerasnip-0.1.2/kerasnip/man/keras_objects.Rd | 12 kerasnip-0.1.2/kerasnip/man/model_exists.Rd | 4 kerasnip-0.1.2/kerasnip/man/predict.kerasnip_model_fit.Rd |only kerasnip-0.1.2/kerasnip/man/process_x_functional.Rd | 3 kerasnip-0.1.2/kerasnip/man/process_y_functional.Rd | 13 kerasnip-0.1.2/kerasnip/man/process_y_sequential.Rd | 9 kerasnip-0.1.2/kerasnip/man/register_keras_loss.Rd | 56 kerasnip-0.1.2/kerasnip/man/register_keras_optimizer.Rd | 86 kerasnip-0.1.2/kerasnip/man/remove_keras_spec.Rd | 15 kerasnip-0.1.2/kerasnip/man/set_args.kerasnip_spec.Rd |only kerasnip-0.1.2/kerasnip/man/set_engine.kerasnip_spec.Rd |only kerasnip-0.1.2/kerasnip/man/step_collapse.Rd | 8 kerasnip-0.1.2/kerasnip/man/tidy.kerasnip_model_fit.Rd |only kerasnip-0.1.2/kerasnip/tests/testthat/test_butcher.R |only kerasnip-0.1.2/kerasnip/tests/testthat/test_compile_keras_grid.R | 70 kerasnip-0.1.2/kerasnip/tests/testthat/test_conformal.R |only kerasnip-0.1.2/kerasnip/tests/testthat/test_e2e_seq_classification.R | 2 kerasnip-0.1.2/kerasnip/tests/testthat/test_e2e_spec_removal.R | 4 kerasnip-0.1.2/kerasnip/tests/testthat/test_generic_fit_helpers.R | 195 - kerasnip-0.1.2/kerasnip/tests/testthat/test_keras_tools.R | 114 - kerasnip-0.1.2/kerasnip/tests/testthat/test_postprocessing_helpers.R | 46 kerasnip-0.1.2/kerasnip/tests/testthat/test_save_load.R |only kerasnip-0.1.2/kerasnip/tests/testthat/test_step_collapse.R | 229 +- kerasnip-0.1.2/kerasnip/tests/testthat/test_tidy_glance.R |only kerasnip-0.1.2/kerasnip/vignettes/applications.Rmd | 57 kerasnip-0.1.2/kerasnip/vignettes/autoplot_uniqueness.Rmd | 123 - kerasnip-0.1.2/kerasnip/vignettes/conformal_intervals.Rmd |only kerasnip-0.1.2/kerasnip/vignettes/functional_api.Rmd | 120 - kerasnip-0.1.2/kerasnip/vignettes/getting_started.Rmd | 275 ++ kerasnip-0.1.2/kerasnip/vignettes/saving_and_reloading.Rmd |only kerasnip-0.1.2/kerasnip/vignettes/sequential_model.Rmd | 66 kerasnip-0.1.2/kerasnip/vignettes/tuning_fit_compile_args.Rmd | 385 +++ kerasnip-0.1.2/kerasnip/vignettes/workflows_functional.Rmd | 393 +++ kerasnip-0.1.2/kerasnip/vignettes/workflows_sequential.Rmd | 358 +++ 101 files changed, 5933 insertions(+), 3229 deletions(-)
Title: Download and Process Public Domain Works from Project Gutenberg
Description: Download and process public domain works in the Project
Gutenberg collection <https://www.gutenberg.org/>. Includes metadata
for all Project Gutenberg works, so that they can be searched and
retrieved.
Author: Jordan Bradford [aut, cre] ,
Jon Harmon [aut] ,
Myfanwy Johnston [aut],
David Robinson [aut, cph]
Maintainer: Jordan Bradford <jrdnbradford@gmail.com>
Diff between gutenbergr versions 0.5.0 dated 2026-03-15 and 0.5.1 dated 2026-05-02
DESCRIPTION | 6 +- MD5 | 29 +++++++------- NEWS.md | 4 + R/gutenberg_cache.R | 18 +++----- R/gutenberg_download.R | 49 +++++++++++++++++++++++- README.md | 4 - data/gutenberg_authors.rda |binary data/gutenberg_languages.rda |binary data/gutenberg_metadata.rda |binary data/gutenberg_subjects.rda |binary inst/doc/intro.html | 32 +++++++-------- inst/doc/text-mining.html | 4 - man/figures/tf-idf-1.png |binary man/figures/top-words-1.png |binary man/gutenberg_tidy_metadata.Rd |only tests/testthat/test-gutenberg_download.R | 63 +++++++++++++++++++++++++++++++ 16 files changed, 159 insertions(+), 50 deletions(-)
Title: Independence Testing via Hilbert Schmidt Independence Criterion
Description: Contains an implementation of the
d-variable Hilbert Schmidt independence criterion
and several hypothesis tests based on it, as described
in Pfister et al. (2018) <doi:10.1111/rssb.12235>.
Author: Niklas Pfister [aut, cre],
Jonas Peters [aut]
Maintainer: Niklas Pfister <niklas.pfister@gmail.com>
Diff between dHSIC versions 2.1 dated 2019-01-04 and 2.2 dated 2026-05-02
DESCRIPTION | 26 ++--- LICENSE |only MD5 | 24 ++-- NAMESPACE | 8 - R/RcppExports.R | 10 - R/dhsic.R | 100 ++++++++++++++++++- R/dhsic.test.R | 161 ++++++++++++++++++++++++++++--- README.md |only build/partial.rdb |binary man/dHSIC-package.Rd | 7 - man/dhsic.Rd | 161 +++++++++++++------------------ man/dhsic.test.Rd | 253 +++++++++++++++++++++++-------------------------- src/RcppExports.cpp | 26 +---- src/rcpp_functions.cpp | 26 ----- 14 files changed, 486 insertions(+), 316 deletions(-)
Title: Formatting Numbers in 'rmarkdown' Documents
Description: Provides a small set of tools for formatting numbers in R-markdown
documents. Convert a numerical vector to character strings in power-of-ten
form, decimal form, or measurement-units form; convert symbols for chemical
isotopes from hyphenated form to nuclear form; all are math-delimited for
rendering as inline equations. Can also convert text into math-delimited
text to match the font face and size of math-delimited numbers. Useful for
rendering single numbers in inline R code chunks and for rendering columns
in tables.
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>
Diff between formatdown versions 0.1.4 dated 2024-05-07 and 0.2.0 dated 2026-05-02
formatdown-0.1.4/formatdown/R/format_decimal.R |only formatdown-0.1.4/formatdown/R/format_power.R |only formatdown-0.1.4/formatdown/R/format_units.R |only formatdown-0.1.4/formatdown/R/formatdown-deprecated.R |only formatdown-0.1.4/formatdown/inst/doc/format_numbers.R |only formatdown-0.1.4/formatdown/inst/doc/format_numbers.Rmd |only formatdown-0.1.4/formatdown/inst/doc/format_numbers.html |only formatdown-0.1.4/formatdown/inst/doc/format_text.R |only formatdown-0.1.4/formatdown/inst/doc/format_text.Rmd |only formatdown-0.1.4/formatdown/inst/doc/format_text.html |only formatdown-0.1.4/formatdown/inst/doc/global_settings.R |only formatdown-0.1.4/formatdown/inst/doc/global_settings.Rmd |only formatdown-0.1.4/formatdown/inst/doc/global_settings.html |only formatdown-0.1.4/formatdown/man/figures/latex_math_formatting_text_table.png |only formatdown-0.1.4/formatdown/man/figures/latex_math_formatting_text_table_2.png |only formatdown-0.1.4/formatdown/man/figures/options-img.jpg |only formatdown-0.1.4/formatdown/man/figures/options-img.png |only formatdown-0.1.4/formatdown/man/figures/powers-of-ten-chart-2.png |only formatdown-0.1.4/formatdown/man/figures/real-number-line.png |only formatdown-0.1.4/formatdown/man/figures/si-base-units-v2.png |only formatdown-0.1.4/formatdown/man/figures/si-base-units.png |only formatdown-0.1.4/formatdown/man/format_decimal-deprecated.Rd |only formatdown-0.1.4/formatdown/man/format_power-deprecated.Rd |only formatdown-0.1.4/formatdown/man/format_units-deprecated.Rd |only formatdown-0.1.4/formatdown/man/formatdown-deprecated.Rd |only formatdown-0.1.4/formatdown/vignettes/format_numbers.Rmd |only formatdown-0.1.4/formatdown/vignettes/format_text.Rmd |only formatdown-0.1.4/formatdown/vignettes/global_settings.Rmd |only formatdown-0.2.0/formatdown/DESCRIPTION | 18 formatdown-0.2.0/formatdown/MD5 | 113 - formatdown-0.2.0/formatdown/NAMESPACE | 5 formatdown-0.2.0/formatdown/NEWS.md | 47 formatdown-0.2.0/formatdown/R/data.R | 39 formatdown-0.2.0/formatdown/R/format_nucl.R |only formatdown-0.2.0/formatdown/R/format_numbers.R | 1020 +++++----- formatdown-0.2.0/formatdown/R/format_text.R | 231 +- formatdown-0.2.0/formatdown/R/formatdown-package.R | 32 formatdown-0.2.0/formatdown/R/formatdown_options.R | 123 - formatdown-0.2.0/formatdown/R/roxygen.R | 171 - formatdown-0.2.0/formatdown/R/utils.R | 19 formatdown-0.2.0/formatdown/README.md | 84 formatdown-0.2.0/formatdown/build/vignette.rds |binary formatdown-0.2.0/formatdown/data/element_set.rda |only formatdown-0.2.0/formatdown/inst/REFERENCES.bib | 11 formatdown-0.2.0/formatdown/inst/WORDLIST | 17 formatdown-0.2.0/formatdown/inst/doc/formatdown.Rmd |only formatdown-0.2.0/formatdown/inst/doc/formatdown.html |only formatdown-0.2.0/formatdown/inst/information-science-and-technology.csl | 38 formatdown-0.2.0/formatdown/inst/tinytest/test_big_mark.R | 130 - formatdown-0.2.0/formatdown/inst/tinytest/test_delim.R | 214 +- formatdown-0.2.0/formatdown/inst/tinytest/test_format_nucl.R |only formatdown-0.2.0/formatdown/inst/tinytest/test_format_numbers.R | 4 formatdown-0.2.0/formatdown/inst/tinytest/test_formatdown_options.R | 302 +- formatdown-0.2.0/formatdown/inst/tinytest/test_multiply_mark.R |only formatdown-0.2.0/formatdown/inst/tinytest/test_size.R | 10 formatdown-0.2.0/formatdown/inst/tinytest/test_whitespace.R | 112 - formatdown-0.2.0/formatdown/man/air_meas.Rd | 4 formatdown-0.2.0/formatdown/man/atmos.Rd | 4 formatdown-0.2.0/formatdown/man/element_set.Rd |only formatdown-0.2.0/formatdown/man/examples/examples_format_dcml.R |only formatdown-0.2.0/formatdown/man/examples/examples_format_engr.R |only formatdown-0.2.0/formatdown/man/examples/examples_format_nucl.R |only formatdown-0.2.0/formatdown/man/examples/examples_format_numbers.R | 52 formatdown-0.2.0/formatdown/man/examples/examples_format_sci.R |only formatdown-0.2.0/formatdown/man/examples/examples_format_text.R | 52 formatdown-0.2.0/formatdown/man/examples/examples_formatdown_options.R | 164 - formatdown-0.2.0/formatdown/man/figures/imgfile.png |only formatdown-0.2.0/formatdown/man/format_dcml.Rd | 74 formatdown-0.2.0/formatdown/man/format_engr.Rd | 90 formatdown-0.2.0/formatdown/man/format_nucl.Rd |only formatdown-0.2.0/formatdown/man/format_numbers.Rd | 65 formatdown-0.2.0/formatdown/man/format_sci.Rd | 76 formatdown-0.2.0/formatdown/man/format_text.Rd | 15 formatdown-0.2.0/formatdown/man/formatdown-package.Rd | 2 formatdown-0.2.0/formatdown/man/formatdown_options.Rd | 45 formatdown-0.2.0/formatdown/man/metals.Rd | 4 formatdown-0.2.0/formatdown/man/water.Rd | 60 formatdown-0.2.0/formatdown/vignettes/formatdown.Rmd |only formatdown-0.2.0/formatdown/vignettes/style_guide_isotopic_conversion.qmd |only 79 files changed, 1772 insertions(+), 1675 deletions(-)
Title: Extract Trends from Time Series
Description: Extract trends from monthly and quarterly economic time series.
Provides two main functions: augment_trends() for pipe-friendly 'tibble'
workflows and extract_trends() for direct time series analysis. Includes
established econometric filters such as Hodrick-Prescott (HP),
Baxter-King, Christiano-Fitzgerald, and Hamilton, alongside moving
averages and smoothing methods. Smart defaults are tuned for common
economic frequencies following Ravn and Uhlig (2002)
<doi:10.1162/003465302317411604>.
Author: Vinicius Oike [aut, cre, cph]
Maintainer: Vinicius Oike <viniciusoike@gmail.com>
Diff between trendseries versions 1.1.0 dated 2025-11-12 and 1.2.0 dated 2026-05-02
trendseries-1.1.0/trendseries/data/retail_households.rda |only trendseries-1.1.0/trendseries/inst/doc/economic-filters.R |only trendseries-1.1.0/trendseries/inst/doc/economic-filters.Rmd |only trendseries-1.1.0/trendseries/inst/doc/economic-filters.html |only trendseries-1.1.0/trendseries/man/retail_households.Rd |only trendseries-1.1.0/trendseries/vignettes/economic-filters.Rmd |only trendseries-1.2.0/trendseries/DESCRIPTION | 25 trendseries-1.2.0/trendseries/LICENSE | 2 trendseries-1.2.0/trendseries/MD5 | 88 trendseries-1.2.0/trendseries/NEWS.md | 32 trendseries-1.2.0/trendseries/R/augment_trends.R | 146 + trendseries-1.2.0/trendseries/R/converters.R | 70 trendseries-1.2.0/trendseries/R/data.R | 129 - trendseries-1.2.0/trendseries/R/extract_trends.R | 76 trendseries-1.2.0/trendseries/R/filters_econometric.R | 54 trendseries-1.2.0/trendseries/R/filters_ma.R | 5 trendseries-1.2.0/trendseries/R/filters_smoothing.R | 12 trendseries-1.2.0/trendseries/R/utils.R | 108 trendseries-1.2.0/trendseries/README.md | 41 trendseries-1.2.0/trendseries/build/vignette.rds |binary trendseries-1.2.0/trendseries/data/retail_autofuel.rda |binary trendseries-1.2.0/trendseries/data/retail_volume.rda |only trendseries-1.2.0/trendseries/data/transit_london_avgs.rda |only trendseries-1.2.0/trendseries/data/transit_london_monthly.rda |only trendseries-1.2.0/trendseries/inst/WORDLIST |only trendseries-1.2.0/trendseries/inst/doc/moving-averages.R | 647 +---- trendseries-1.2.0/trendseries/inst/doc/moving-averages.Rmd | 955 +------- trendseries-1.2.0/trendseries/inst/doc/moving-averages.html | 1171 ++-------- trendseries-1.2.0/trendseries/inst/doc/trendseries.R | 330 -- trendseries-1.2.0/trendseries/inst/doc/trendseries.Rmd | 589 +---- trendseries-1.2.0/trendseries/inst/doc/trendseries.html | 842 ++----- trendseries-1.2.0/trendseries/man/augment_trends.Rd | 25 trendseries-1.2.0/trendseries/man/coffee_arabica.Rd | 18 trendseries-1.2.0/trendseries/man/coffee_robusta.Rd | 17 trendseries-1.2.0/trendseries/man/df_to_ts.Rd | 8 trendseries-1.2.0/trendseries/man/extract_trends.Rd | 22 trendseries-1.2.0/trendseries/man/figures/README-unnamed-chunk-4-1.svg | 515 +++- trendseries-1.2.0/trendseries/man/figures/README-unnamed-chunk-5-1.svg |only trendseries-1.2.0/trendseries/man/figures/index_example.png |only trendseries-1.2.0/trendseries/man/gdp_construction.Rd | 4 trendseries-1.2.0/trendseries/man/ibcbr.Rd | 7 trendseries-1.2.0/trendseries/man/oil_derivatives.Rd | 4 trendseries-1.2.0/trendseries/man/retail_autofuel.Rd | 16 trendseries-1.2.0/trendseries/man/retail_volume.Rd |only trendseries-1.2.0/trendseries/man/transit_london_avgs.Rd |only trendseries-1.2.0/trendseries/man/transit_london_monthly.Rd |only trendseries-1.2.0/trendseries/man/ts_to_df.Rd | 8 trendseries-1.2.0/trendseries/man/vehicles.Rd | 6 trendseries-1.2.0/trendseries/tests/testthat/test-augment_trends.R | 51 trendseries-1.2.0/trendseries/tests/testthat/test-extract_trends.R | 22 trendseries-1.2.0/trendseries/tests/testthat/test-params-stl.R |only trendseries-1.2.0/trendseries/vignettes/moving-averages.Rmd | 955 +------- trendseries-1.2.0/trendseries/vignettes/trendseries.Rmd | 589 +---- 53 files changed, 2898 insertions(+), 4691 deletions(-)
Title: Scale Mixture of Normal Distribution in Linear Mixed-Effects
Model
Description: Bayesian analysis of censored linear mixed-effects models that replace Gaussian assumptions with a flexible class of distributions, such as the scale mixture of normal family distributions, considering a damped exponential correlation structure which was employed to account for within-subject autocorrelation among irregularly observed measures. For more details, see Kelin Zhong, Fernanda L. Schumacher, Luis M. Castro, Victor H. Lachos (2025) <doi:10.1002/sim.10295>.
Author: Kelin Zhong [aut, cre],
Fernanda L. Schumacher [aut],
Luis M. Castro [aut],
Victor H. Lachos [aut],
Jalmar M.F. Carrasco [aut]
Maintainer: Kelin Zhong <kelinzhonguconn@gmail.com>
Diff between SMNlmec versions 1.0.1 dated 2026-04-04 and 1.0.2 dated 2026-05-02
SMNlmec-1.0.1/SMNlmec/man/SMNlmecfit.creator.Rd |only SMNlmec-1.0.2/SMNlmec/DESCRIPTION | 6 SMNlmec-1.0.2/SMNlmec/MD5 | 12 - SMNlmec-1.0.2/SMNlmec/NAMESPACE | 2 SMNlmec-1.0.2/SMNlmec/R/SMNlmec.S4class.R | 102 +++++----- SMNlmec-1.0.2/SMNlmec/man/SMNlmec.summary-SMNlmecfit-method.Rd |only SMNlmec-1.0.2/SMNlmec/man/SMNlmec.summary.Rd | 8 SMNlmec-1.0.2/SMNlmec/man/SMNlmecfit-class.Rd | 5 8 files changed, 70 insertions(+), 65 deletions(-)
Title: Groupwise Regularized Adaptive Sparse Precision Solution
Description: Provides a unified framework for sparse-group regularization and
precision matrix estimation in Gaussian graphical models. It implements
multiple sparse-group penalties, including sparse-group lasso, sparse-group
adaptive lasso, sparse-group SCAD, and sparse-group MCP, and solves them
efficiently using ADMM-based optimization. The package is designed for
high-dimensional network inference where both sparsity and group structure
are present.
Author: Shiying Xiao [aut, cre] ,
Jun Yan [aut] ,
Panpan Zhang [aut]
Maintainer: Shiying Xiao <shiying.xiao@outlook.com>
Diff between grasps versions 0.1.0 dated 2025-11-27 and 0.1.1 dated 2026-05-02
grasps-0.1.0/grasps/inst/example/ex-performance.R |only grasps-0.1.1/grasps/DESCRIPTION | 23 +- grasps-0.1.1/grasps/MD5 | 67 +++--- grasps-0.1.1/grasps/NAMESPACE | 2 grasps-0.1.1/grasps/NEWS.md |only grasps-0.1.1/grasps/R/gen_prec_sbm.R | 41 +--- grasps-0.1.1/grasps/R/grasps.R | 30 +-- grasps-0.1.1/grasps/R/line_search_lambda_max.R | 2 grasps-0.1.1/grasps/R/performance.R | 31 --- grasps-0.1.1/grasps/R/plot.adjmat.R |only grasps-0.1.1/grasps/R/plot.blkmat.R | 17 - grasps-0.1.1/grasps/R/prec_to_adj.R |only grasps-0.1.1/grasps/R/sparsify_block_banded.R | 12 - grasps-0.1.1/grasps/README.md | 109 +++++++---- grasps-0.1.1/grasps/build/partial.rdb |binary grasps-0.1.1/grasps/build/vignette.rds |binary grasps-0.1.1/grasps/inst/doc/crit.html | 20 +- grasps-0.1.1/grasps/inst/doc/crit.qmd | 8 grasps-0.1.1/grasps/inst/doc/pen_est.html | 64 +++--- grasps-0.1.1/grasps/inst/doc/pen_est.qmd | 81 +++----- grasps-0.1.1/grasps/inst/example/ex-gen_prec_sbm.R | 4 grasps-0.1.1/grasps/inst/example/ex-grasps.R | 25 +- grasps-0.1.1/grasps/inst/example/ex-plot.blkmat.R | 2 grasps-0.1.1/grasps/man/figures/README-unnamed-chunk-2-1.png |binary grasps-0.1.1/grasps/man/figures/README-unnamed-chunk-2-2.png |only grasps-0.1.1/grasps/man/figures/README-unnamed-chunk-2-3.png |only grasps-0.1.1/grasps/man/figures/cv-diagram.png |binary grasps-0.1.1/grasps/man/figures/workflow.png |only grasps-0.1.1/grasps/man/gen_prec_sbm.Rd | 16 - grasps-0.1.1/grasps/man/grasps.Rd | 49 ++-- grasps-0.1.1/grasps/man/performance.Rd | 35 ++- grasps-0.1.1/grasps/man/plot.adjmat.Rd |only grasps-0.1.1/grasps/man/plot.blkmat.Rd | 2 grasps-0.1.1/grasps/man/prec_to_adj.Rd |only grasps-0.1.1/grasps/man/sparsify_block_banded.Rd | 4 grasps-0.1.1/grasps/src/ADMM.cpp | 27 +- grasps-0.1.1/grasps/src/utils.cpp | 6 grasps-0.1.1/grasps/vignettes/crit.qmd | 8 grasps-0.1.1/grasps/vignettes/pen_est.qmd | 81 +++----- 39 files changed, 401 insertions(+), 365 deletions(-)
Title: Automated Mendelian Randomization Workflows and Visualizations
Description: Provides tools to summarize, analyze, and visualize results
from Mendelian randomization studies using summarized genetic
association data. The package includes functions for generating forest
plots and scatter plots at the single-nucleotide polymorphism
and Mendelian randomization method levels, and for fitting multiple
estimators in a unified workflow, including inverse-variance weighted
estimation, Mendelian randomization Egger regression,
the weighted median estimator, the robust adjusted
profile score, Mendelian randomization pleiotropy residual sum
and outlier, Mendelian randomization with the genotype
recoding invariance property, and a Bayesian horseshoe
method. Related methods are described by Burgess (2013)
<doi:10.1002/gepi.21758>, Bowden (2015) <doi:10.1093/ije/dyv080>,
Bowden (2016) <doi:10.1002/gepi.21965>, Zhao (2020)
<doi:10.1214/19-AOS1866>, Verbanck (2018)
<doi:10.1038/s41588-018-0099-7>, Dudbridge (2025)
<doi:10.1371/journal.pgen.1011 [...truncated...]
Author: Kelin Zhong [aut, cre],
Chia-Ling Kuo [aut]
Maintainer: Kelin Zhong <kelinzhonguconn@gmail.com>
Diff between autoMR versions 1.1.1 dated 2026-04-22 and 1.1.2 dated 2026-05-02
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++++---------- NAMESPACE | 3 -- R/mr_forest_class.R | 20 +++++++++++++---- R/mr_scatter_class.R | 41 +++++++++++++++++++++++++++--------- R/mr_workflows.R | 19 ++++++++++------ man/GWASForestPlots-class.Rd | 1 man/MRForestPlots-class.Rd | 1 man/MRScatterPlots-class.Rd | 1 man/dot-draw_scatter_plot.Rd |only man/export_forest_plots-methods.Rd |only man/export_forest_plots.Rd | 31 --------------------------- man/export_scatter_plots-methods.Rd |only man/export_scatter_plots.Rd | 16 -------------- man/plot_mr_scatter.Rd | 11 ++++++--- man/showplot-methods.Rd |only man/showplot.Rd | 18 --------------- 17 files changed, 87 insertions(+), 109 deletions(-)
Title: Kernel Partial Correlation Coefficient
Description: Implementations of two empirical versions the kernel partial correlation (KPC) coefficient
and the associated variable selection algorithms. KPC is a measure of the strength of conditional
association between Y and Z given X, with X, Y, Z being random variables taking values in
general topological spaces. As the name suggests, KPC is defined in terms of kernels on
reproducing kernel Hilbert spaces (RKHSs). The population KPC is a deterministic number
between 0 and 1; it is 0 if and only if Y is conditionally independent of Z given X, and it is 1 if
and only if Y is a measurable function of Z and X. One empirical KPC estimator is based on
geometric graphs, such as K-nearest neighbor graphs and minimum spanning trees, and is
consistent under very weak conditions. The other empirical estimator, defined using conditional
mean embeddings (CMEs) as used in the RKHS literature, is also consistent under suitable
conditions. Using KPC, a stepwise forward variable selection algorithm KFOCI (usin [...truncated...]
Author: Zhen Huang [aut, cre],
Nabarun Deb [ctb],
Bodhisattva Sen [ctb],
Benjamin Lang [ctb]
Maintainer: Zhen Huang <zh2395@columbia.edu>
Diff between KPC versions 0.1.2 dated 2022-10-05 and 0.1.3 dated 2026-05-02
DESCRIPTION | 17 +++--- MD5 | 10 +-- NEWS.md | 20 +++++-- R/KPC.R | 154 +++++++++++++++++++++++++++++++++++++---------------------- README.md | 19 +++---- man/KFOCI.Rd | 17 +++--- 6 files changed, 149 insertions(+), 88 deletions(-)
Title: Guidelines and Checklists for Building CRAN-Worthy Packages
Description: Provides essential checklists for R package developers, whether
you're creating your first package or beginning a new project. This tool
guides you through each step of the development process, including specific
considerations for submitting your package to the Comprehensive R Archive
Network (CRAN). Simplify your workflow and ensure adherence to best
practices with 'packagepal'.
Author: Lee Durbin [aut, cre, cph]
Maintainer: Lee Durbin <l.d.durbin@gmail.com>
Diff between packagepal versions 0.1.0 dated 2023-08-14 and 0.1.1 dated 2026-05-02
DESCRIPTION | 11 ++--- MD5 | 14 +++--- NAMESPACE | 9 ---- NEWS.md | 10 +++- R/checklists.R | 12 +++-- R/packagepal-package.R | 9 ---- README.md | 79 ++++++++++++++++++------------------ tests/testthat/_snaps/checklists.md | 22 +++++----- 8 files changed, 79 insertions(+), 87 deletions(-)
Title: Classify Open Street Map Features
Description: Classify Open Street Map (OSM) features into meaningful functional
or analytical categories. Designed for OSM PBF files, e.g. from <https://download.geofabrik.de/>
imported as spatial data frames. A classification consists of a list of categories that are related to
certain OSM tags and values. Given a layer from an OSM PBF file and a classification, the main
osm_classify() function returns a classification data table giving, for each feature, the primary and
alternative categories (if there is overlap) assigned, and the tag(s) and value(s) matched on.
The package also contains a classification of OSM features by economic function/significance,
following Krantz (2023) <https://www.ssrn.com/abstract=4537867>.
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between osmclass versions 0.1.3 dated 2023-08-17 and 0.1.4 dated 2026-05-02
DESCRIPTION | 9 - MD5 | 16 - NAMESPACE | 1 NEWS.md | 4 R/classifications.R | 395 ++++++++++++++++++++++++++++++++++++++++++++++-- R/functions.R | 1 README.md | 9 - man/classifications.Rd | 17 +- man/osmclass-package.Rd | 1 9 files changed, 422 insertions(+), 31 deletions(-)
Title: A Tidy Format Datasets of Dengue by Country
Description: Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Author: Thiyanga S. Talagala [aut, cre]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between denguedatahub versions 3.2.0 dated 2025-06-25 and 4.1.0 dated 2026-05-02
denguedatahub-3.2.0/denguedatahub/man/figures/README-unnamed-chunk-2-1.png |only denguedatahub-3.2.0/denguedatahub/man/figures/README-unnamed-chunk-2-2.png |only denguedatahub-3.2.0/denguedatahub/man/figures/README-unnamed-chunk-2-3.png |only denguedatahub-3.2.0/denguedatahub/man/figures/README-unnamed-chunk-2-4.png |only denguedatahub-4.1.0/denguedatahub/DESCRIPTION | 8 - denguedatahub-4.1.0/denguedatahub/MD5 | 74 ++++------ denguedatahub-4.1.0/denguedatahub/NAMESPACE | 44 ++--- denguedatahub-4.1.0/denguedatahub/README.md | 20 ++ denguedatahub-4.1.0/denguedatahub/data/srilanka_weekly_data.rda |binary denguedatahub-4.1.0/denguedatahub/man/americas_annual_data.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/cdc_casesby_week.Rd | 56 +++---- denguedatahub-4.1.0/denguedatahub/man/cdc_dengue_agesex.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/cdc_dengue_casesbyjurisdiction.Rd | 60 ++++---- denguedatahub-4.1.0/denguedatahub/man/cdc_dengue_countyyear.Rd | 60 ++++---- denguedatahub-4.1.0/denguedatahub/man/cdc_local_dengue_cases.Rd | 54 +++---- denguedatahub-4.1.0/denguedatahub/man/cdc_travel_associated_dengue_cases.Rd | 54 +++---- denguedatahub-4.1.0/denguedatahub/man/cdc_usa_dengue_infection.Rd | 60 ++++---- denguedatahub-4.1.0/denguedatahub/man/china_annual_data.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/convert_slwer_to_tidy.Rd | 68 ++++----- denguedatahub-4.1.0/denguedatahub/man/convert_srilanka_wer_to_tidy.Rd | 74 +++++----- denguedatahub-4.1.0/denguedatahub/man/download_pdfwer_srilanka.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/figures/README-unnamed-chunk-3-1.png |binary denguedatahub-4.1.0/denguedatahub/man/figures/README-unnamed-chunk-4-1.png |binary denguedatahub-4.1.0/denguedatahub/man/figures/README-unnamed-chunk-4-2.png |binary denguedatahub-4.1.0/denguedatahub/man/filter_year_wer.Rd | 38 ++--- denguedatahub-4.1.0/denguedatahub/man/get_addresses.Rd | 40 ++--- denguedatahub-4.1.0/denguedatahub/man/get_pdflinks_srilanka.Rd | 52 +++---- denguedatahub-4.1.0/denguedatahub/man/india_annual_data.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/korea_dengue.Rd | 62 ++++---- denguedatahub-4.1.0/denguedatahub/man/level_of_risk.Rd | 56 +++---- denguedatahub-4.1.0/denguedatahub/man/min_max.Rd | 46 +++--- denguedatahub-4.1.0/denguedatahub/man/philippines_daily_data.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/singapore_weekly_data.Rd | 54 +++---- denguedatahub-4.1.0/denguedatahub/man/sl_annual.Rd | 54 +++---- denguedatahub-4.1.0/denguedatahub/man/sl_dengue_serotype.Rd | 52 +++---- denguedatahub-4.1.0/denguedatahub/man/sl_province_districts.Rd | 52 +++---- denguedatahub-4.1.0/denguedatahub/man/sl_sites.Rd | 58 +++---- denguedatahub-4.1.0/denguedatahub/man/srilanka_weekly_data.Rd | 60 ++++---- denguedatahub-4.1.0/denguedatahub/man/taiwan_dengue.Rd | 54 +++---- denguedatahub-4.1.0/denguedatahub/man/world_annual.Rd | 68 ++++----- 40 files changed, 866 insertions(+), 860 deletions(-)
Title: Area Correction Methods
Description: Post-construction fatality monitoring studies at wind
facilities are based on data from searches for bird and bat carcasses
in plots beneath turbines. Bird and bat carcasses can fall outside of
the search plot. Bird and bat carcasses from wind turbines often fall
outside of the searched area. To compensate, area correction (AC)
estimations are calculated to estimate the percentage of fatalities
that fall within the searched area versus those that fall outside of
it. This package provides two likelihood based methods and one physics
based method (Hull and Muir (2010)
<doi:10.1080/14486563.2010.9725253>, Huso and Dalthorp (2014)
<doi:10.1002/jwmg.663>) to estimate the carcass fall distribution.
There are also functions for calculating the proportion of area
searched within one unit annuli, log logistic distribution functions,
and truncated distribution functions.
Author: Paul Rabie [aut],
Daniel Riser-Espinoza [aut, cre],
Trent McDonald [ctb],
Western EcoSystems Technology, Inc. [cph, fnd]
Maintainer: Daniel Riser-Espinoza <despinoza@west-inc.com>
Diff between windAC versions 1.2.10 dated 2023-03-22 and 1.3.0 dated 2026-05-02
windAC-1.2.10/windAC/data/turbineSpatial.RData |only windAC-1.3.0/windAC/DESCRIPTION | 48 + windAC-1.3.0/windAC/MD5 | 27 windAC-1.3.0/windAC/NAMESPACE | 4 windAC-1.3.0/windAC/NEWS.md |only windAC-1.3.0/windAC/R/calcAC.R | 4 windAC-1.3.0/windAC/R/geometricRoadPadPropSearchTable.R | 6 windAC-1.3.0/windAC/R/getProportionAreaSearched.R | 437 +++++-------- windAC-1.3.0/windAC/R/secondDerivative.R | 27 windAC-1.3.0/windAC/R/windAC.R | 95 +- windAC-1.3.0/windAC/build |only windAC-1.3.0/windAC/data/turbineSpatial.rda |only windAC-1.3.0/windAC/man/geometricRoadPadPropSearchTable.Rd | 3 windAC-1.3.0/windAC/man/getProportionAreaSearched.Rd | 52 + windAC-1.3.0/windAC/man/secondDerivative.Rd | 16 windAC-1.3.0/windAC/man/windAC-package.Rd |only windAC-1.3.0/windAC/man/windAC.Rd | 79 +- 17 files changed, 411 insertions(+), 387 deletions(-)
Title: Spatial Transfer of Statistics among Spanish Census Sections
Description: Transfers/imputes statistics among Spanish spatial polygons (census sections or postal code areas) from different moments in time (2001-2026) without need of spatial files, just linking statistics to the ID codes of the spatial units.
The data available in the census sections of a partition/division (cartography) into force in a moment of time is transferred to the census sections of another partition/division employing the geometric approach (also known as areal weighting or polygon overlay).
References:
Goerlich (2022) <doi:10.12842/WPIVIE_0322>.
Pavía and Cantarino (2017a, b) <doi:10.1111/gean.12112>, <doi:10.1016/j.apgeog.2017.06.021>.
Pérez and Pavía (2024a, b) <doi:10.4995/CARMA2024.2024.17796>, <doi:10.38191/iirr-jorr.24.057>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Cultura, Universidades y Empleo, Generalitat Valenciana (grant CIACIO/2023/031), Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (g [...truncated...]
Author: Virgilio Perez [aut] ,
Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between sc2sc versions 0.0.1-18 dated 2025-11-01 and 0.0.1-19 dated 2026-05-02
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/auxiliary_functions.R | 42 ++++++++++++++++++++---------------------- R/cp2sc.R | 2 +- R/sc2cp.R | 2 +- R/sc2sc.R | 4 ++-- R/sysdata.rda |binary build/partial.rdb |binary man/cp2sc.Rd | 2 +- man/sc2cp.Rd | 2 +- man/sc2sc.Rd | 4 ++-- 12 files changed, 50 insertions(+), 47 deletions(-)
Title: Nonparametric Multiple Change Point Detection Using Wild Binary
Segmentation
Description: Implements a procedure for detecting multiple location-scale change points in a sequence of univariate observations, as described in Ross (2026) "Nonparametric Detection of Multiple Location-Scale Change Points via Wild Binary Segmentation" <doi:10.48550/arXiv.2107.01742>. The method combines Wild Binary Segmentation with a rank-based statistic and provides calibrated thresholds for controlling the probability of incorrectly detecting a change point in a homogeneous sequence.
Author: Gordon J. Ross [aut, cre]
Maintainer: Gordon J. Ross <gordon.ross@ed.ac.uk>
Diff between npwbs versions 0.2.0 dated 2021-07-06 and 0.3.0 dated 2026-05-02
DESCRIPTION | 19 ++++++---- MD5 | 12 +++--- NEWS.md |only R/package-functions.R | 91 ++++++++++++++++++++++++++++++++++++-------------- R/sysdata.rda |binary inst/CITATION | 27 ++++++++------ man/detectChanges.Rd | 14 ++++--- tests |only 8 files changed, 109 insertions(+), 54 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-20 dated 2026-02-12 and 0.70-1 dated 2026-05-02
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Title: Language Server Protocol
Description: An implementation of the Language Server Protocol
for R. The Language Server protocol is used by an editor client to
integrate features like auto completion. See
<https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre],
Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.17 dated 2026-03-07 and 0.3.18 dated 2026-05-02
DESCRIPTION | 11 +- MD5 | 40 ++++----- NEWS.md | 15 +++ R/capabilities.R | 9 +- R/diagnostics.R | 23 +++-- R/document.R | 25 +++--- R/handlers-general.R | 22 +++-- R/handlers-langfeatures.R | 157 +++++++++++++++++++++++++++------------ R/handlers-textsync.R | 39 ++++++--- R/handlers-workspace.R | 77 +++++++++++-------- R/languageclient.R | 21 ++++- R/languageserver.R | 105 ++++++++++++++++++++++++-- R/symbol.R | 7 + R/task.R | 22 ++++- R/utils.R | 3 R/workspace.R | 24 +---- src/reader.c | 15 ++- src/token.c | 46 +++++------ tests/testthat/helper-utils.R | 4 tests/testthat/test-completion.R | 6 - tests/testthat/test-workspace.R | 108 ++++++++++++++++++++++++++ 21 files changed, 566 insertions(+), 213 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: Tools for Creating and Visualizing Fixed-Effects Event Study
Models
Description: Provides functions for creating, analyzing, and visualizing event study models using fixed-effects regression. Supports staggered adoption, multiple confidence intervals, flexible clustering, and panel/time transformations in a simple workflow.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between fixes versions 0.5.0 dated 2025-07-07 and 0.7.2 dated 2026-05-02
fixes-0.5.0/fixes/R/event_study.R |only fixes-0.5.0/fixes/R/globals.R |only fixes-0.5.0/fixes/man/figures/logo.png |only fixes-0.7.2/fixes/DESCRIPTION | 11 fixes-0.7.2/fixes/MD5 | 38 fixes-0.7.2/fixes/NAMESPACE | 32 fixes-0.7.2/fixes/NEWS.md | 90 ++ fixes-0.7.2/fixes/R/autoplot-es_result.R |only fixes-0.7.2/fixes/R/plot_es.R |only fixes-0.7.2/fixes/R/plot_es_interactive.R |only fixes-0.7.2/fixes/R/run_es.R |only fixes-0.7.2/fixes/R/s3_methods.R |only fixes-0.7.2/fixes/README.md | 161 ++- fixes-0.7.2/fixes/build/vignette.rds |binary fixes-0.7.2/fixes/inst/doc/fixes-intro.R | 76 + fixes-0.7.2/fixes/inst/doc/fixes-intro.Rmd | 152 +-- fixes-0.7.2/fixes/inst/doc/fixes-intro.html | 209 ++--- fixes-0.7.2/fixes/man/autoplot.es_result.Rd |only fixes-0.7.2/fixes/man/figures/README-plot-basic-1.png |only fixes-0.7.2/fixes/man/figures/README-plot-custom-1.png |only fixes-0.7.2/fixes/man/figures/README-plot-errorbar-1.png |only fixes-0.7.2/fixes/man/figures/README-plot-sunab-1.png |only fixes-0.7.2/fixes/man/plot_es.Rd | 125 +-- fixes-0.7.2/fixes/man/plot_es_interactive.Rd |only fixes-0.7.2/fixes/man/run_es.Rd | 212 ++--- fixes-0.7.2/fixes/tests/testthat/test-event_study.R | 613 +++++++++++---- fixes-0.7.2/fixes/vignettes/fixes-intro.Rmd | 152 +-- 27 files changed, 1148 insertions(+), 723 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
This is a re-admission after prior archival of version 2.2.1 dated 2022-09-01
Diff between ggRandomForests versions 2.2.1 dated 2022-09-01 and 2.7.2 dated 2026-05-02
ggRandomForests-2.2.1/ggRandomForests/R/combine.gg_partial.R |only ggRandomForests-2.2.1/ggRandomForests/R/gg_interaction.R |only ggRandomForests-2.2.1/ggRandomForests/R/gg_minimal_depth.R |only ggRandomForests-2.2.1/ggRandomForests/R/gg_minimal_vimp.R |only ggRandomForests-2.2.1/ggRandomForests/R/gg_partial_coplot.R |only ggRandomForests-2.2.1/ggRandomForests/R/plot.gg_interaction.R |only ggRandomForests-2.2.1/ggRandomForests/R/plot.gg_minimal_depth.R |only ggRandomForests-2.2.1/ggRandomForests/R/plot.gg_minimal_vimp.R |only ggRandomForests-2.2.1/ggRandomForests/R/plot.gg_partial_list.R |only ggRandomForests-2.2.1/ggRandomForests/R/print.gg_minimal_depth.R |only ggRandomForests-2.2.1/ggRandomForests/R/surface_matrix.gg_partial_coplot.R |only ggRandomForests-2.2.1/ggRandomForests/inst/doc/ggrfRegression.R |only ggRandomForests-2.2.1/ggRandomForests/inst/doc/ggrfRegression.Rmd |only ggRandomForests-2.2.1/ggRandomForests/inst/doc/ggrfRegression.html |only ggRandomForests-2.2.1/ggRandomForests/man/combine.gg_partial.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/gg_interaction.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/gg_minimal_depth.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/gg_minimal_vimp.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/gg_partial_coplot.rfsrc.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/plot.gg_interaction.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/plot.gg_minimal_depth.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/plot.gg_minimal_vimp.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/plot.gg_partial_list.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/print.gg_minimal_depth.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/shift.Rd |only ggRandomForests-2.2.1/ggRandomForests/man/surface_matrix.Rd |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/Rplots.pdf |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_gg_interaction.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_gg_minimal_depth.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_gg_minimal_vimp.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_gg_partial_coplot.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_partial.rfsrc.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_surface_matrix.R |only ggRandomForests-2.2.1/ggRandomForests/tests/testthat/test_survival_datasets.R |only ggRandomForests-2.2.1/ggRandomForests/vignettes/ggrfRegression.Rmd |only ggRandomForests-2.7.2/ggRandomForests/DESCRIPTION | 41 ggRandomForests-2.7.2/ggRandomForests/LICENSE |only ggRandomForests-2.7.2/ggRandomForests/MD5 | 179 +- ggRandomForests-2.7.2/ggRandomForests/NAMESPACE | 75 - ggRandomForests-2.7.2/ggRandomForests/NEWS.md | 177 ++ ggRandomForests-2.7.2/ggRandomForests/R/calc_roc.R | 250 +--- ggRandomForests-2.7.2/ggRandomForests/R/gg_error.R | 334 +++-- ggRandomForests-2.7.2/ggRandomForests/R/gg_partial.R | 422 +----- ggRandomForests-2.7.2/ggRandomForests/R/gg_partial_rfsrc.R |only ggRandomForests-2.7.2/ggRandomForests/R/gg_partialpro.R |only ggRandomForests-2.7.2/ggRandomForests/R/gg_rfsrc.R | 519 ++++---- ggRandomForests-2.7.2/ggRandomForests/R/gg_roc.R | 137 +- ggRandomForests-2.7.2/ggRandomForests/R/gg_survival.R | 162 +- ggRandomForests-2.7.2/ggRandomForests/R/gg_variable.R | 355 ++--- ggRandomForests-2.7.2/ggRandomForests/R/gg_vimp.R | 314 +++-- ggRandomForests-2.7.2/ggRandomForests/R/ggrandomforests.news.R |only ggRandomForests-2.7.2/ggRandomForests/R/help.R | 120 - ggRandomForests-2.7.2/ggRandomForests/R/kaplan.R | 110 - ggRandomForests-2.7.2/ggRandomForests/R/nelson.R | 132 -- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_error.R | 154 +- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_partial.R | 525 ++++---- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_rfsrc.R | 361 +++-- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_roc.R | 200 +-- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_survival.R | 158 +- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_variable.R | 622 +++++----- ggRandomForests-2.7.2/ggRandomForests/R/plot.gg_vimp.R | 137 +- ggRandomForests-2.7.2/ggRandomForests/R/quantile_pts.R | 98 - ggRandomForests-2.7.2/ggRandomForests/R/surv_partial.rfsrc.R |only ggRandomForests-2.7.2/ggRandomForests/R/utils.R |only ggRandomForests-2.7.2/ggRandomForests/R/varpro_feature_names.R |only ggRandomForests-2.7.2/ggRandomForests/R/zzz.R |only ggRandomForests-2.7.2/ggRandomForests/README.md | 127 +- ggRandomForests-2.7.2/ggRandomForests/build/vignette.rds |binary ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-regression.R |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-regression.html |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-regression.qmd |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-survival.R |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-survival.html |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests-survival.qmd |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests.R |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests.html |only ggRandomForests-2.7.2/ggRandomForests/inst/doc/ggRandomForests.qmd |only ggRandomForests-2.7.2/ggRandomForests/man/bootstrap_survival.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/calc_auc.Rd | 8 ggRandomForests-2.7.2/ggRandomForests/man/calc_roc.rfsrc.Rd | 42 ggRandomForests-2.7.2/ggRandomForests/man/ggRandomForests-package.Rd | 92 - ggRandomForests-2.7.2/ggRandomForests/man/gg_error.Rd | 89 - ggRandomForests-2.7.2/ggRandomForests/man/gg_partial.Rd | 270 ---- ggRandomForests-2.7.2/ggRandomForests/man/gg_partial_rfsrc.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/gg_partialpro.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/gg_rfsrc.rfsrc.Rd | 219 +-- ggRandomForests-2.7.2/ggRandomForests/man/gg_roc.rfsrc.Rd | 57 ggRandomForests-2.7.2/ggRandomForests/man/gg_survival.Rd | 103 + ggRandomForests-2.7.2/ggRandomForests/man/gg_variable.Rd | 200 +-- ggRandomForests-2.7.2/ggRandomForests/man/gg_vimp.Rd | 120 + ggRandomForests-2.7.2/ggRandomForests/man/ggrandomforests.news.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/kaplan.Rd | 24 ggRandomForests-2.7.2/ggRandomForests/man/nelson.Rd | 34 ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_error.Rd | 75 - ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_partial.Rd | 152 -- ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_partial_rfsrc.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_partialpro.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_rfsrc.Rd | 164 +- ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_roc.Rd | 71 - ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_survival.Rd | 53 ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_variable.Rd | 111 - ggRandomForests-2.7.2/ggRandomForests/man/plot.gg_vimp.Rd | 36 ggRandomForests-2.7.2/ggRandomForests/man/quantile_pts.Rd | 32 ggRandomForests-2.7.2/ggRandomForests/man/surv_partial.rfsrc.Rd |only ggRandomForests-2.7.2/ggRandomForests/man/varpro_feature_names.Rd |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_error.R | 262 ++-- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_partial.R | 538 ++++++-- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_partialpro.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_rfsrc.R | 441 ++++++- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_roc.R | 158 +- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_survival.R | 140 +- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_variable.R | 344 ++++- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_gg_vimp.R | 237 ++- ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_ggrandomforests_news.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_kaplan_nelson.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_plot_layer_data.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_quantile_pts.R | 31 ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_randomForest_helpers.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_shift.R | 14 ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_snapshots.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_surv_partial.R |only ggRandomForests-2.7.2/ggRandomForests/tests/testthat/test_varpro_feature_names.R |only ggRandomForests-2.7.2/ggRandomForests/vignettes/ggRandomForests-regression.qmd |only ggRandomForests-2.7.2/ggRandomForests/vignettes/ggRandomForests-survival.qmd |only ggRandomForests-2.7.2/ggRandomForests/vignettes/ggRandomForests.bib | 607 +++------ ggRandomForests-2.7.2/ggRandomForests/vignettes/ggRandomForests.qmd |only 126 files changed, 5815 insertions(+), 4618 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Sparse Multiple Canonical Correlation Network Analysis Tool
('SmCCNet')
Description: A canonical correlation based framework ('SmCCNet') designed for the construction of phenotype-specific multi-omics networks. This framework adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. It offers a streamlined setup process that can be tailored manually or configured automatically, ensuring a flexible and user-friendly experience. Methods are described in Shi et al. (2019) "Unsupervised discovery of phenotype-specific multi-omics networks" <doi:10.1093/bioinformatics/btz226>.
Author: Abhinav Pundir [cre],
Weixuan Liu [aut],
Yonghua Zhuang [aut],
W. Jenny Shi [aut],
Thao Vu [aut],
Iain Konigsberg [aut],
Katherine Pratte [aut],
Laura Saba [aut],
Katerina Kechris [aut]
Maintainer: Abhinav Pundir <abhinav.pundir@ucdenver.edu>
Diff between SmCCNet versions 2.0.6 dated 2026-04-28 and 2.0.7 dated 2026-05-01
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- inst/doc/SmCCNet_Vignette_AutoSmCCNet.pdf |binary inst/doc/SmCCNet_Vignette_MultiOmics.R | 6 +++--- inst/doc/SmCCNet_Vignette_MultiOmics.Rmd | 12 ++++++------ inst/doc/SmCCNet_Vignette_MultiOmics.pdf |binary inst/doc/SmCCNet_Vignette_SingleOmics.R | 6 +++--- inst/doc/SmCCNet_Vignette_SingleOmics.Rmd | 10 +++++----- inst/doc/SmCCNet_Vignette_SingleOmics.pdf |binary vignettes/SmCCNet_Vignette_MultiOmics.Rmd | 12 ++++++------ vignettes/SmCCNet_Vignette_SingleOmics.Rmd | 10 +++++----- 11 files changed, 44 insertions(+), 44 deletions(-)
Title: Wrapper for Statistics Portugal API
Description: An R6-based client to facilitate interaction with the Statistics
Portugal (Instituto Nacional de Estatistica - INE) API
(<https://www.ine.pt/xportal/xmain?xpid=INE&xpgid=ine_api&INST=322751522&xlang=en>).
Author: Carlos Matos [aut, cre, cph]
Maintainer: Carlos Matos <carlosmdmatos@gmail.com>
Diff between ineptr2 versions 0.3.0 dated 2026-04-28 and 0.3.1 dated 2026-05-01
DESCRIPTION | 6 MD5 | 98 NAMESPACE | 8 NEWS.md | 10 R/INEClient-fields.R | 76 R/INEClient.R | 2400 +++++++++++------------ R/utils.R | 528 ++--- README.md | 10 inst/doc/ineptr2.R | 5 inst/doc/ineptr2.Rmd | 372 +-- inst/doc/ineptr2.html | 38 man/INEClient-fields.Rd | 94 man/INEClient.Rd | 1096 +++++----- man/calc_dims_length_from_raw.Rd | 36 man/extract_dim_values.Rd | 36 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/filter_cached_data.Rd | 44 man/finalize_chunk.Rd | 40 man/gracefully_fail.Rd | 42 man/ineptr2-package.Rd | 52 man/is_filter_subset.Rd | 40 man/normalize_dim_filters.Rd | 36 man/process_ine_catalog.Rd | 36 man/process_ine_data.Rd | 36 man/records_to_df.Rd | 38 tests/testthat/fixtures/mock_catalog.xml | 154 - tests/testthat/helper-catalog.R | 48 tests/testthat/test-INEClient-clear_cache.R | 80 tests/testthat/test-INEClient-constructor.R | 110 - tests/testthat/test-INEClient-download_catalog.R | 88 tests/testthat/test-INEClient-download_data.R | 286 +- tests/testthat/test-INEClient-get_catalog.R | 56 tests/testthat/test-INEClient-get_data.R | 70 tests/testthat/test-INEClient-get_dim_info.R | 58 tests/testthat/test-INEClient-get_dim_values.R | 54 tests/testthat/test-INEClient-get_metadata.R | 52 tests/testthat/test-INEClient-info.R | 116 - tests/testthat/test-INEClient-is_updated.R | 142 - tests/testthat/test-INEClient-is_valid.R | 56 tests/testthat/test-INEClient-list_cached.R | 192 - tests/testthat/test-INEClient-load_raw_data.R | 126 - tests/testthat/test-INEClient-preview_chunks.R | 110 - tests/testthat/test-INEClient-print.R | 60 tests/testthat/test-INEClient-use_cache.R | 134 - tests/testthat/test-process_ine_catalog.R | 106 - tests/testthat/test-utils-filters.R | 244 +- vignettes/ineptr2.Rmd | 372 +-- 50 files changed, 4040 insertions(+), 4035 deletions(-)
Title: Spacing Tests for Multi-Modality
Description: Tests for modality of data using its spacing. The main approach
evaluates features (peaks, flats) using a combination of parametric models
and non-parametric tests, either after smoothing the spacing by a low-pass
filter or by looking over larger intervals.
Author: Greg Kreider [aut, cre],
Melissa O'Neill [cph],
Primordial Machine Vision Systems, Inc. [cph]
Maintainer: Greg Kreider <support@primachvis.com>
Diff between Dimodal versions 1.0.3 dated 2026-02-18 and 1.0.4 dated 2026-05-01
ChangeLog | 9 +++++-- DESCRIPTION | 8 +++--- MD5 | 24 ++++++++++---------- R/Dimodal.R | 10 ++++---- R/methods.R | 4 +-- R/sigtests.R | 6 +++-- R/utility.R | 15 ++++++------ man/Diopt.Rd | 4 +-- man/utilities.Rd | 22 +++++++----------- src/sigtests.c | 7 +---- tests/test_Dimodal.Rtest | 54 +++++++++++++++++++++++----------------------- tests/test_sigtests.Rtest | 31 ++++++++++++++------------ tests/test_utility.Rtest | 16 ++++++------- 13 files changed, 107 insertions(+), 103 deletions(-)
Title: Categorical Regression Splines
Description: Regression splines that handle a mix of continuous and categorical (discrete) data often encountered in applied settings. I would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://www.sharcnet.ca>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Zhenghua Nie [aut],
Brian D. Ripley [ctb]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between crs versions 0.15-41 dated 2026-04-11 and 0.15-42 dated 2026-05-01
CHANGELOG | 30 + DESCRIPTION | 8 MD5 | 54 - R/zzz.R | 7 build/vignette.rds |binary demo/crsiv.R | 31 - demo/crsiv_exog.R | 31 - demo/crsiv_exog_persp.R | 35 + demo/nomad_factor.R | 5 demo/radial_persp.R | 31 - demo/radial_rgl.R | 31 - demo/sine_rgl.R | 31 - inst/doc/crs_getting_started.html | 66 +- man/clsd.Rd | 161 +++-- man/crs.Rd | 292 ++++++---- man/crsiv.Rd | 123 +++- man/crsivderiv.Rd | 87 ++ man/crssigtest.Rd | 31 - man/data-cps71.Rd | 11 man/frscv.Rd | 80 +- man/frscvNOMAD.Rd | 141 +++- man/gsl-bs.Rd | 50 + man/krscv.Rd | 85 ++ man/krscvNOMAD.Rd | 174 +++-- man/snomadr.Rd | 218 ++++--- src/nomad4_src/src/Algos/MainStep.cpp | 18 src/nomad4_src/src/Param/EvaluatorControlGlobalParameters.cpp | 22 src/nomad4_src/src/Param/RunParameters.cpp | 22 28 files changed, 1272 insertions(+), 603 deletions(-)
Title: Create ToxPi Prioritization Models
Description: Enables users to build 'ToxPi' prioritization models and provides
functionality within the grid framework for plotting ToxPi graphs.
'toxpiR' allows for more customization than the 'ToxPi GUI'
(<https://toxpi.github.io/>) and integration into existing workflows for greater
ease-of-use, reproducibility, and transparency.
toxpiR package behaves nearly identically to the GUI; the package
documentation includes notes about all differences.
The vignettes download example files from
<https://github.com/ToxPi/ToxPi-example-files>.
Author: Jonathon F Fleming [aut, cre] ,
Dayne L Filer [aut, fnd] ,
Dillon T Lloyd [aut],
Preethi Thunga [aut] ,
Skylar W Marvel [aut],
Alison A Motsinger-Reif [fnd] ,
David M Reif [aut, fnd]
Maintainer: Jonathon F Fleming <jffleming0129@gmail.com>
Diff between toxpiR versions 1.3.1 dated 2025-12-16 and 1.3.2 dated 2026-05-01
DESCRIPTION | 6 MD5 | 24 NEWS.md | 4 R/txpImportGui.R | 260 ++++---- build/vignette.rds |binary data/txp_example_model.rda |binary inst/doc/exportToGui.rmd | 220 +++---- inst/doc/importFromGui.Rmd | 192 +++--- inst/doc/introduction.Rmd | 1302 ++++++++++++++++++++++---------------------- inst/doc/introduction.html | 52 - vignettes/exportToGui.rmd | 220 +++---- vignettes/importFromGui.Rmd | 192 +++--- vignettes/introduction.Rmd | 1302 ++++++++++++++++++++++---------------------- 13 files changed, 1889 insertions(+), 1885 deletions(-)
Title: Coarse-to-Fine Spatial Modeling
Description: Provides functions for coarse-to-fine spatial modeling (CFSM), enabling fast spatial prediction, regression, and uncertainty quantification. This method is suitable for moderate to large samples. For further details, see Murakami et al. (2026) <doi:10.1111/gean.70034>.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.1.0 dated 2026-01-19 and 0.1.1 dated 2026-05-01
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Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph] ,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 7.3.3 dated 2025-09-03 and 8.0.0 dated 2026-05-01
roxygen2-7.3.3/roxygen2/R/rd-find-link-files.R |only roxygen2-7.3.3/roxygen2/inst/doc/rd-other.R |only roxygen2-7.3.3/roxygen2/inst/doc/rd-other.Rmd |only roxygen2-7.3.3/roxygen2/inst/doc/rd-other.html |only roxygen2-7.3.3/roxygen2/inst/doc/rd.R |only roxygen2-7.3.3/roxygen2/inst/doc/rd.Rmd |only roxygen2-7.3.3/roxygen2/inst/doc/rd.html |only roxygen2-7.3.3/roxygen2/man/tags-rd-other.Rd |only roxygen2-7.3.3/roxygen2/man/tags-rd.Rd |only roxygen2-7.3.3/roxygen2/tests/testthat/_snaps/rd-find-link-files.md |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-1.R |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-2.R |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-3-A.Rd |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-3-B.Rd |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-3-C.Rd |only roxygen2-7.3.3/roxygen2/tests/testthat/roxygen-block-3.R |only roxygen2-7.3.3/roxygen2/tests/testthat/test-rd-find-link-files.R |only roxygen2-7.3.3/roxygen2/tests/testthat/testMdLinks2 |only roxygen2-7.3.3/roxygen2/vignettes/rd-other.Rmd |only roxygen2-7.3.3/roxygen2/vignettes/rd.Rmd |only roxygen2-8.0.0/roxygen2/DESCRIPTION | 21 roxygen2-8.0.0/roxygen2/MD5 | 465 ++++--- roxygen2-8.0.0/roxygen2/NAMESPACE | 35 roxygen2-8.0.0/roxygen2/NEWS.md | 97 + roxygen2-8.0.0/roxygen2/R/block.R | 69 - 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roxygen2-8.0.0/roxygen2/tests/testthat/test-roxygenize-needs.R |only roxygen2-8.0.0/roxygen2/tests/testthat/test-roxygenize-setup.R | 11 roxygen2-8.0.0/roxygen2/tests/testthat/test-select-args.R | 23 roxygen2-8.0.0/roxygen2/tests/testthat/test-tag-parser.R | 47 roxygen2-8.0.0/roxygen2/tests/testthat/test-tag.R | 62 roxygen2-8.0.0/roxygen2/tests/testthat/test-tokenize.R | 51 roxygen2-8.0.0/roxygen2/tests/testthat/test-utils-warn.R |only roxygen2-8.0.0/roxygen2/tests/testthat/test-utils.R | 34 roxygen2-8.0.0/roxygen2/tests/testthat/testCollateOverwrite/R/b.R | 2 roxygen2-8.0.0/roxygen2/tests/testthat/testCollateParse/R/b.R | 3 roxygen2-8.0.0/roxygen2/tests/testthat/testCollateParse/R/c.R | 3 roxygen2-8.0.0/roxygen2/tests/testthat/testMdLinks/DESCRIPTION | 65 - roxygen2-8.0.0/roxygen2/tests/testthat/testNonASCII/R/a.R | 3 roxygen2-8.0.0/roxygen2/tests/testthat/testR6 |only roxygen2-8.0.0/roxygen2/tests/testthat/testRawNamespace/DESCRIPTION | 2 roxygen2-8.0.0/roxygen2/tests/testthat/up-to-date |only roxygen2-8.0.0/roxygen2/vignettes/extending.Rmd | 212 ++- roxygen2-8.0.0/roxygen2/vignettes/index-crossref.Rmd | 20 roxygen2-8.0.0/roxygen2/vignettes/namespace.Rmd | 155 -- roxygen2-8.0.0/roxygen2/vignettes/rd-R6.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-S3.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-S4.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-S7.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-datasets.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-formatting.Rmd | 163 +- roxygen2-8.0.0/roxygen2/vignettes/rd-functions.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/rd-packages.Rmd |only roxygen2-8.0.0/roxygen2/vignettes/reuse.Rmd | 127 + roxygen2-8.0.0/roxygen2/vignettes/roxygen2.Rmd | 92 + 283 files changed, 8670 insertions(+), 5221 deletions(-)
Title: Phased or Unphased Linkage Disequilibrium
Description: Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) <doi:10.1016/j.humimm.2019.01.010>, and Osoegawa et. al. (2019b) <doi:10.1016/j.humimm.2019.05.018>.
Author: Steven Mack [aut, cre]
Maintainer: Steven Mack <steven.mack@ucsf.edu>
This is a re-admission after prior archival of version 1.0.1 dated 2020-10-16
Diff between pould versions 1.0.1 dated 2020-10-16 and 1.0.2 dated 2026-05-01
DESCRIPTION | 11 - MD5 | 30 +-- NAMESPACE | 1 NEWS | 69 +++---- R/LD.heatmap.R | 136 +++++++++----- R/LD.sign.test.R | 54 ++--- R/LocusExtractor.R | 9 R/cALD_FamilyFunctions.R | 147 +++++++-------- build/vignette.rds |binary inst/doc/pould.Rmd | 10 - inst/doc/pould.html | 452 ++++++++++++++++++++++++++++++++++++++--------- man/LD.heat.map.Rd | 19 + man/LD.sign.test.Rd | 10 - man/LDWrap.Rd | 2 man/cALD.Rd | 10 - vignettes/pould.Rmd | 10 - 16 files changed, 667 insertions(+), 303 deletions(-)
Title: Colour Palette for Reading and Code, Inspired by Moby-Dick
Description: The Pequod colour palette, named after the whaler in
Herman Melville's Moby-Dick. Provides the full Log base scale
from warm paper (Log 50) to deep ink (Log 950), eight crew
accent hues with light and dark variants, and 'ggplot2' scales
for discrete and continuous mapping. Designed for long-form
reading and code, with low saturation and a consistent earth-
pigment register. Full design rationale and accessibility notes
at <https://tiagojct.eu/projects/pequod/>.
Author: Tiago Jacinto [aut, cre]
Maintainer: Tiago Jacinto <tiagojacinto@med.up.pt>
Diff between pequod versions 0.1.1 dated 2026-04-29 and 0.2.0 dated 2026-05-01
DESCRIPTION | 6 ++--- MD5 | 4 +-- R/palettes-data.R | 58 +++++++++++++++++++++++++++--------------------------- 3 files changed, 34 insertions(+), 34 deletions(-)
Title: Run GWAS/GWEIS Scans Using Binary Dosage Files
Description: Tools to run genome-wide association study (GWAS) and
genome-wide by environment interaction study (GWEIS) scans using the genetic
data stored in a binary dosage file. The user provides a data frame with
the subject's covariate data and the information about the binary dosage
file returned by the BinaryDosage::getbdinfo() routine.
Author: John Morrison [aut, cre],
W. James Gauderman [aut],
NCI [fnd] ,
NCI [fnd] ,
NIEHS [fnd] ,
NHLBI [fnd]
Maintainer: John Morrison <jmorr@usc.edu>
This is a re-admission after prior archival of version 2.0.2 dated 2020-10-02
Diff between GxEScanR versions 2.0.2 dated 2020-10-02 and 3.0.0 dated 2026-05-01
GxEScanR-2.0.2/GxEScanR/R/LinReg.R |only GxEScanR-2.0.2/GxEScanR/R/LogReg.R |only GxEScanR-2.0.2/GxEScanR/R/RcppExports.R |only GxEScanR-2.0.2/GxEScanR/inst/WORDLIST |only GxEScanR-2.0.2/GxEScanR/inst/extdata/covdata.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/defaultblk.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/largebdinfo.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/lingwas.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/lingweis.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/loggwas.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/loggweis.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/loggweisc.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/models.rds |only GxEScanR-2.0.2/GxEScanR/inst/extdata/pdata_4_1.bdinfo |only GxEScanR-2.0.2/GxEScanR/inst/extdata/pdata_4_1.bdose |only GxEScanR-2.0.2/GxEScanR/inst/extdata/pdata_4_2.bdinfo |only GxEScanR-2.0.2/GxEScanR/inst/extdata/pdata_4_2.bdose |only GxEScanR-2.0.2/GxEScanR/inst/extdata/skipreason.rds |only GxEScanR-2.0.2/GxEScanR/man/gwas.Rd |only GxEScanR-2.0.2/GxEScanR/man/gweis.Rd |only GxEScanR-2.0.2/GxEScanR/src |only GxEScanR-2.0.2/GxEScanR/tests/testthat/test-gwasinput.R |only GxEScanR-2.0.2/GxEScanR/tests/testthat/test-results.R |only GxEScanR-3.0.0/GxEScanR/DESCRIPTION | 24 GxEScanR-3.0.0/GxEScanR/MD5 | 56 GxEScanR-3.0.0/GxEScanR/NAMESPACE | 14 GxEScanR-3.0.0/GxEScanR/NEWS.md | 10 GxEScanR-3.0.0/GxEScanR/R/GxEScanR.R | 696 +++------ GxEScanR-3.0.0/GxEScanR/README.md |only GxEScanR-3.0.0/GxEScanR/build/vignette.rds |binary GxEScanR-3.0.0/GxEScanR/inst/doc/UsingGxEScanR.R | 202 +- GxEScanR-3.0.0/GxEScanR/inst/doc/UsingGxEScanR.Rmd | 416 ++--- GxEScanR-3.0.0/GxEScanR/inst/doc/UsingGxEScanR.html | 1217 ++++++---------- GxEScanR-3.0.0/GxEScanR/inst/extdata/gendata.bdose |only GxEScanR-3.0.0/GxEScanR/inst/extdata/gendata.bdose.bdi |only GxEScanR-3.0.0/GxEScanR/inst/extdata/gendata.vcf.gz |only GxEScanR-3.0.0/GxEScanR/inst/extdata/subdata.rds |only GxEScanR-3.0.0/GxEScanR/man/gweis.mem.Rd |only GxEScanR-3.0.0/GxEScanR/man/rungweis.Rd |only GxEScanR-3.0.0/GxEScanR/tests/testthat.R | 8 GxEScanR-3.0.0/GxEScanR/tests/testthat/test-gweis.R |only GxEScanR-3.0.0/GxEScanR/vignettes/UsingGxEScanR.Rmd | 416 ++--- 42 files changed, 1372 insertions(+), 1687 deletions(-)
Title: Graphical Output in Terminals
Description: Defines a graphics device and functions for graphical output in
terminal emulators that support graphical output. Currently terminals that
support the Terminal Graphics Protocol
(<https://sw.kovidgoyal.net/kitty/graphics-protocol/>) and terminal supporting Sixel
(<https://en.wikipedia.org/wiki/Sixel>) are supported.
Author: Jan van der Laan [aut, cre] ,
Doug Kelkhoff [ctb]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between terminalgraphics versions 0.2.1 dated 2025-11-26 and 0.3.0 dated 2026-05-01
terminalgraphics-0.2.1/terminalgraphics/man/tgp_diacritics.Rd |only terminalgraphics-0.3.0/terminalgraphics/DESCRIPTION | 10 - terminalgraphics-0.3.0/terminalgraphics/MD5 | 42 +++---- terminalgraphics-0.3.0/terminalgraphics/NAMESPACE | 3 terminalgraphics-0.3.0/terminalgraphics/NEWS.md | 24 ++++ terminalgraphics-0.3.0/terminalgraphics/R/RcppExports.R | 4 terminalgraphics-0.3.0/terminalgraphics/R/device_manager.R | 54 ++++++++- terminalgraphics-0.3.0/terminalgraphics/R/has_sixel_support.R | 7 + terminalgraphics-0.3.0/terminalgraphics/R/has_tgp_support.R | 13 +- terminalgraphics-0.3.0/terminalgraphics/R/is_terminal.R | 30 ++++- terminalgraphics-0.3.0/terminalgraphics/R/kitty_colors.R | 8 + terminalgraphics-0.3.0/terminalgraphics/R/sixel.R | 19 +-- terminalgraphics-0.3.0/terminalgraphics/R/term_colors.R | 17 +- terminalgraphics-0.3.0/terminalgraphics/R/term_dim.R | 7 + terminalgraphics-0.3.0/terminalgraphics/R/tgp.R | 59 ++++------ terminalgraphics-0.3.0/terminalgraphics/README.md | 16 ++ terminalgraphics-0.3.0/terminalgraphics/man/is_terminal.Rd | 9 + terminalgraphics-0.3.0/terminalgraphics/man/kitty_colors.Rd | 2 terminalgraphics-0.3.0/terminalgraphics/man/sixel.Rd | 6 - terminalgraphics-0.3.0/terminalgraphics/man/tgp.Rd | 6 - terminalgraphics-0.3.0/terminalgraphics/src/Makevars |only terminalgraphics-0.3.0/terminalgraphics/src/RcppExports.cpp | 9 - terminalgraphics-0.3.0/terminalgraphics/src/query_sixel_support.cpp | 53 +++----- 23 files changed, 267 insertions(+), 131 deletions(-)
More information about terminalgraphics at CRAN
Permanent link
Title: Simulate Experimental Crosses
Description: Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between simcross versions 0.6 dated 2023-11-29 and 0.8 dated 2026-05-01
DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 9 +++++++++ R/plot_cross.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary data/AILped.RData |binary data/mouseL_cox.RData |binary data/mouseL_mgi.RData |binary inst/doc/simcross.html | 7 ++++--- man/plot_crosslines.Rd | 2 +- 11 files changed, 32 insertions(+), 21 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 14. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood estimation" , Hammond (2021, <doi:10.2166/nh.2021.059>). "The FEH 2025 statistical method update", UK Centre for Ecology and Hydrology (2025). "Low flow es [...truncated...]
Author: Anthony Hammond [aut, cre]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 2.0.0 dated 2025-10-28 and 2.0.1 dated 2026-05-01
UKFE-2.0.0/UKFE/man/AggDayHour.Rd |only UKFE-2.0.0/UKFE/man/QMEDPOT.Rd |only UKFE-2.0.1/UKFE/DESCRIPTION | 6 UKFE-2.0.1/UKFE/MD5 | 33 ++-- UKFE-2.0.1/UKFE/R/All.R | 246 +++++++++++++++-------------------- UKFE-2.0.1/UKFE/R/FEH08.R |only UKFE-2.0.1/UKFE/R/FlowAnalysis.R | 112 +++++++++++++++ UKFE-2.0.1/UKFE/R/GetData.R | 60 ++++++-- UKFE-2.0.1/UKFE/R/RainfallAnalysis.R | 2 UKFE-2.0.1/UKFE/R/ReFH.R | 167 ++++++++++------------- UKFE-2.0.1/UKFE/man/AggMonDayHour.Rd |only UKFE-2.0.1/UKFE/man/Bootstrap.Rd | 2 UKFE-2.0.1/UKFE/man/DesHydro.Rd | 5 UKFE-2.0.1/UKFE/man/GetDataNRFA.Rd | 2 UKFE-2.0.1/UKFE/man/LowFlows.Rd | 19 +- UKFE-2.0.1/UKFE/man/PoolEst_FEH08.Rd |only UKFE-2.0.1/UKFE/man/Pool_FEH08.Rd |only UKFE-2.0.1/UKFE/man/QMED.Rd | 2 UKFE-2.0.1/UKFE/man/QMED_FEH08.Rd |only UKFE-2.0.1/UKFE/man/Rating.Rd | 4 UKFE-2.0.1/UKFE/man/ReFH.Rd | 8 - 21 files changed, 391 insertions(+), 277 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and routines for graphical display.
Author: Michael Dewey [aut, cre]
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.13 dated 2025-12-18 and 1.14 dated 2026-05-01
DESCRIPTION | 12 ++++++------ MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 2 +- NEWS | 7 +++++++ R/truncated.R | 7 +++++-- build/metap.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/doc/compare.R | 2 -- inst/doc/compare.Rnw | 15 +++++++++++---- inst/doc/compare.pdf |binary inst/doc/metap.R | 2 -- inst/doc/metap.pdf |binary inst/doc/plotmetap.R | 2 -- inst/doc/plotmetap.pdf |binary man/macros/macros.Rd | 6 +++--- man/truncated.Rd | 13 ++++++++++--- vignettes/compare.Rnw | 15 +++++++++++---- 19 files changed, 72 insertions(+), 47 deletions(-)
Title: Quality Control for Label-Free Proteomics Expression Data
Description: Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluati [...truncated...]
Author: Kabilan S [aut, cre],
Dr Shashi Bhushan Lal [aut, ths],
Dr Sudhir Srivastava [aut, ths],
Dr Krishna Kumar Chaturvedi [ths],
Dr Yasin Jeshima K [ths],
Dr Ramasubramanian V [ths],
Dr Girish Kumar Jha [ctb],
Dr Sharanbasappa [ctb]
Maintainer: Kabilan S <kabilan151414@gmail.com>
Diff between lfproQC versions 1.4.1 dated 2025-07-02 and 1.4.2 dated 2026-05-01
DESCRIPTION | 13 ++++--- MD5 | 10 ++--- NEWS | 7 ++++ inst/CITATION | 3 - inst/doc/user_guide.html | 81 +++++++++++++++++++++++++---------------------- man/lfproQC-package.Rd | 1 6 files changed, 65 insertions(+), 50 deletions(-)
Title: 'binb' is not 'Beamer'
Description: A collection of 'LaTeX' styles using 'Beamer' customization for
pdf-based presentation slides in 'RMarkdown'. At present it contains
'RMarkdown' adaptations of the LaTeX themes 'Metropolis' (formerly 'mtheme')
theme by Matthias Vogelgesang and others (now included in 'TeXLive'), the
'IQSS' them by Ista Zahn (which is included here), and the 'Monash' theme by
Rob J Hyndman. Additional (free) fonts may be needed: 'Metropolis' prefers
'Fira', and 'IQSS' requires 'Libertinus'.
Author: Dirk Eddelbuettel [aut, cre] ,
Ista Zahn [aut] ,
Rob Hyndman [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between binb versions 0.0.7 dated 2024-07-06 and 0.0.8 dated 2026-05-01
ChangeLog | 39 +++++++++++++ DESCRIPTION | 23 +++++-- MD5 | 25 ++++---- README.md | 10 +-- build/vignette.rds |binary inst/NEWS.Rd | 17 +++++ inst/doc/metropolisDemo.R | 14 ++-- inst/doc/metropolisDemo.pdf |binary inst/rmarkdown/templates/iqss/resources/auto |only inst/rmarkdown/templates/iqss/resources/template.tex | 2 inst/rmarkdown/templates/metropolis/resources/template.tex | 2 inst/rmarkdown/templates/monash/resources/auto |only inst/rmarkdown/templates/monash/resources/template.tex | 2 inst/rmarkdown/templates/presento/resources/auto |only inst/rmarkdown/templates/presento/resources/template.tex | 6 +- 15 files changed, 109 insertions(+), 31 deletions(-)
Title: Functions for Nonlinear Least Squares Solutions - Updated 2022
Description: Provides tools for working with nonlinear least squares problems.
For the estimation of models reliable and robust tools than nls(), where the
the Gauss-Newton method frequently stops with 'singular gradient' messages.
This is accomplished by using, where possible, analytic derivatives to compute
the matrix of derivatives and a stabilization of the solution of the estimation
equations. Tools for approximate or externally supplied derivative matrices
are included. Bounds and masks on parameters are handled properly.
Author: John C Nash [aut, cre],
Duncan Murdoch [aut],
Fernando Miguez [ctb],
Arkajyoti Bhattacharjee [ctb]
Maintainer: John C Nash <profjcnash@gmail.com>
Diff between nlsr versions 2023.8.31 dated 2023-09-05 and 2026.4.29 dated 2026-05-01
nlsr-2023.8.31/nlsr/inst/doc/development |only nlsr-2026.4.29/nlsr/DESCRIPTION | 12 nlsr-2026.4.29/nlsr/MD5 | 37 - nlsr-2026.4.29/nlsr/build/vignette.rds |binary nlsr-2026.4.29/nlsr/inst/doc/FixedParameters.pdf |binary nlsr-2026.4.29/nlsr/inst/doc/Intro-to-nlsr.R | 46 - nlsr-2026.4.29/nlsr/inst/doc/Intro-to-nlsr.pdf |binary nlsr-2026.4.29/nlsr/inst/doc/R-analytic-derivatives.R | 266 +++++----- nlsr-2026.4.29/nlsr/inst/doc/R-analytic-derivatives.pdf |binary nlsr-2026.4.29/nlsr/inst/doc/nlsr-derivs.pdf |binary nlsr-2026.4.29/nlsr/inst/doc/nlsr-devdoc.R | 402 ++++++++-------- nlsr-2026.4.29/nlsr/inst/doc/nlsr-devdoc.Rmd | 5 nlsr-2026.4.29/nlsr/inst/doc/nlsr-devdoc.pdf |binary nlsr-2026.4.29/nlsr/vignettes/ImproveNLS.bib | 181 +++---- nlsr-2026.4.29/nlsr/vignettes/nlsr-devdoc.Rmd | 5 15 files changed, 477 insertions(+), 477 deletions(-)
Title: Automatic Plotting and Theming of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 1.0.0 dated 2026-04-04 and 1.0.3 dated 2026-05-01
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Title: Numeric Matrices K-NN and PCA Imputation
Description: Fast k-nearest neighbors (K-NN) and principal component
analysis (PCA) imputation algorithms for missing values in
high-dimensional numeric matrices, i.e., epigenetic data. For
extremely high-dimensional data with ordered features, a sliding
window approach for K-NN or PCA imputation is provided. Additional
features include group-wise imputation (e.g., by chromosome),
hyperparameter tuning with repeated cross-validation, multi-core
parallelization, and optional subset imputation. The K-NN algorithm is
described in: Hastie, T., Tibshirani, R., Sherlock, G., Eisen, M.,
Brown, P. and Botstein, D. (1999) "Imputing Missing Data for Gene
Expression Arrays". The PCA imputation is an optimized version of the
imputePCA() function from the 'missMDA' package described in: Josse,
J. and Husson, F. (2016) <doi:10.18637/jss.v070.i01> "missMDA: A
Package for Handling Missing Values in Multivariate Data Analysis".
Author: Hung Pham [aut, cre, cph]
Maintainer: Hung Pham <amser.hoanghung@gmail.com>
Diff between slideimp versions 1.0.0 dated 2026-04-16 and 1.1.0 dated 2026-05-01
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Title: Visualizes Preferential Data in One and More Contests
Description: A visualization toolkit for preferential data, such as ranked-choice election results, tournament outcomes,
and survey responses. The package provides methods to visualise the preference distribution of one contest with
bar charts and pairwise comparisons of two contestants, as well as methods to visualise multiple contests through
2D and high-dimensional simplex plots both statically and interactively. HD simplex displays are implemented via projection
methods using the 'tourr' and 'detourr' packages, enabling dynamic exploration of high-dimensional preference structure.
For more details on HD simplex projection, see Wickham et al. (2011) <doi:10.21105/joss.03419>.
Author: Linh Ngo [aut, cre],
Dianne Cook [aut] ,
Damjan Vukcevic [aut]
Maintainer: Linh Ngo <linhngo66.work@gmail.com>
Diff between prefviz versions 0.1.1 dated 2026-04-13 and 0.1.2 dated 2026-05-01
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Title: Parallel Nonparametric Kernel Smoothing Methods for Mixed Data
Types Using 'MPI'
Description: Nonparametric (and semiparametric) kernel methods that seamlessly
handle a mix of continuous, unordered, and ordered factor data types. This
package is a parallel implementation of the 'np' package based on the 'MPI'
specification that incorporates the 'Rmpi' package (Hao Yu
<hyu@stats.uwo.ca>) with minor modifications and we are extremely grateful
to Hao Yu for his contributions to the 'R' community. We would like to
gratefully acknowledge support from the Natural Sciences and Engineering
Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the
Social Sciences and Humanities Research Council of Canada (SSHRC,
<https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would
also like to acknowledge the contributions of the 'GNU GSL' authors. In
particular, we adapt the 'GNU GSL' B-spline routine 'gsl_bspline.c' adding
automated support for quantile knots (in addition t [...truncated...]
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut],
Hao Yu [ctb, cph],
The GSL Team [cph],
Numerical Recipes Software [cph]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between npRmpi versions 0.60-20 dated 2026-02-16 and 0.70-1 dated 2026-05-01
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Title: Lagged Cross-Correlation Analysis of Environmental Time Series
Description: Tools for analysing lagged relationships between
environmental variables and ecological or epidemiological time series.
The package implements a workflow to aggregate meteorological data
over multiple lagged intervals, fit regression models, including
mixed-effect models using 'glmmTMB', for each lag window, and
visualise varied models outcomes (effect strength and direction, model
prediction error...) using cross-correlation maps ('CCM').
Author: Nicolas Moiroux [aut, cre] ,
Colombine Bartholomee [aut] ,
Paul Taconet [aut]
Maintainer: Nicolas Moiroux <nicolas.moiroux@ird.fr>
Diff between ecoXCorr versions 0.2.1 dated 2026-04-01 and 0.2.2 dated 2026-05-01
DESCRIPTION | 45 +++++++++++++++++--------------------- MD5 | 16 ++++++------- NEWS.md | 10 ++++++++ R/funs.R | 18 ++++++++++++--- build/partial.rdb |binary inst/CITATION | 2 - inst/shiny/app.R | 12 ++++++++-- man/aggregate_lagged_intervals.Rd | 2 - man/ecoXCorr.Rd | 19 +++++++++++++--- 9 files changed, 82 insertions(+), 42 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut, cre],
Julian Zhou [aut],
Nima Nouri [aut],
Noah Yann Lee [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between shazam versions 1.3.1 dated 2026-01-08 and 1.3.2 dated 2026-05-01
DESCRIPTION | 8 +++---- MD5 | 40 ++++++++++++++++++------------------ NEWS.md | 13 +++++++++++ R/Deprecated.R | 3 ++ R/DistToNearest.R | 32 +++++++++++++++++++++++++--- R/MutationProfiling.R | 5 ++++ R/Shmulate.R | 2 + README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.R | 6 +++++ inst/doc/Shmulate-Vignette.Rmd | 6 +++++ inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/plotSlideWindowTune.Rd | 5 ++++ man/shmulateTree.Rd | 2 + man/slideWindowTunePlot.Rd | 3 ++ vignettes/Shmulate-Vignette.Rmd | 6 +++++ 21 files changed, 104 insertions(+), 29 deletions(-)
Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers
both distribution-free modeling using Taylor polynomials and parametric
modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution.
Originally developed for achievement tests, it is applicable to a wide
range of mental, physical, or other test scores dependent on continuous or
discrete explanatory variables. The package provides several advantages:
It minimizes deviations from representativeness in subsamples, interpolates
between discrete levels of explanatory variables, and significantly reduces
the required sample size compared to conventional norming per age group.
cNORM enables graphical and analytical evaluation of model fit,
accommodates a wide range of scales including those with negative and
descending values, and even supports conventional norming. It generates
norm tables including confidence intervals. It also includes methods f [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS Publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.5.2 dated 2026-02-26 and 3.5.3 dated 2026-05-01
cNORM-3.5.2/cNORM/man/prettyPrint.Rd |only cNORM-3.5.3/cNORM/DESCRIPTION | 6 cNORM-3.5.3/cNORM/MD5 | 111 - cNORM-3.5.3/cNORM/NAMESPACE | 2 cNORM-3.5.3/cNORM/NEWS.md | 36 cNORM-3.5.3/cNORM/R/betaBinomial.R | 250 +- cNORM-3.5.3/cNORM/R/cNORM.R | 471 ++-- cNORM-3.5.3/cNORM/R/data.R | 13 cNORM-3.5.3/cNORM/R/modelling.R | 1530 ++++++++------- cNORM-3.5.3/cNORM/R/plot.R | 1264 ++++++++---- cNORM-3.5.3/cNORM/R/predict.R | 562 ++--- cNORM-3.5.3/cNORM/R/preparation.R | 626 ++++-- cNORM-3.5.3/cNORM/R/raking.R | 127 - cNORM-3.5.3/cNORM/R/roots.R | 136 - cNORM-3.5.3/cNORM/R/shash.R | 346 ++- cNORM-3.5.3/cNORM/R/utilities.R | 204 +- cNORM-3.5.3/cNORM/inst/doc/BetaBinomial.html | 4 cNORM-3.5.3/cNORM/inst/doc/WeightedRegression.html | 16 cNORM-3.5.3/cNORM/inst/doc/cNORM-Demo.Rmd | 2 cNORM-3.5.3/cNORM/inst/doc/cNORM-Demo.html | 155 - cNORM-3.5.3/cNORM/inst/doc/sinh.html | 12 cNORM-3.5.3/cNORM/man/CDC.Rd | 9 cNORM-3.5.3/cNORM/man/bestModel.Rd | 194 - cNORM-3.5.3/cNORM/man/betaCoefficients.Rd | 8 cNORM-3.5.3/cNORM/man/cNORM.Rd | 263 +- cNORM-3.5.3/cNORM/man/checkConsistency.Rd | 9 cNORM-3.5.3/cNORM/man/computePowers.Rd | 26 cNORM-3.5.3/cNORM/man/computeWeights.Rd | 168 - cNORM-3.5.3/cNORM/man/derivationTable.Rd | 2 cNORM-3.5.3/cNORM/man/derive.Rd | 6 cNORM-3.5.3/cNORM/man/elfe.Rd | 6 cNORM-3.5.3/cNORM/man/getGroups.Rd | 2 cNORM-3.5.3/cNORM/man/getNormCurve.Rd | 3 cNORM-3.5.3/cNORM/man/normTable.Rd | 8 cNORM-3.5.3/cNORM/man/plotDerivative.Rd | 3 cNORM-3.5.3/cNORM/man/plotPercentileSeries.Rd | 8 cNORM-3.5.3/cNORM/man/plotPercentiles.Rd | 8 cNORM-3.5.3/cNORM/man/plotRaw.Rd | 8 cNORM-3.5.3/cNORM/man/plotSubset.Rd | 2 cNORM-3.5.3/cNORM/man/predictNorm.Rd | 7 cNORM-3.5.3/cNORM/man/predictRaw.Rd | 3 cNORM-3.5.3/cNORM/man/prepareData.Rd | 190 - cNORM-3.5.3/cNORM/man/printSubset.Rd | 8 cNORM-3.5.3/cNORM/man/rangeCheck.Rd | 6 cNORM-3.5.3/cNORM/man/rankByGroup.Rd | 3 cNORM-3.5.3/cNORM/man/rankBySlidingWindow.Rd | 248 +- cNORM-3.5.3/cNORM/man/rawTable.Rd | 4 cNORM-3.5.3/cNORM/man/regressionFunction.Rd | 7 cNORM-3.5.3/cNORM/man/shash.Rd | 2 cNORM-3.5.3/cNORM/man/simMean.Rd | 44 cNORM-3.5.3/cNORM/man/simSD.Rd | 44 cNORM-3.5.3/cNORM/man/simulateRasch.Rd | 2 cNORM-3.5.3/cNORM/man/standardize.Rd | 2 cNORM-3.5.3/cNORM/man/weighted.quantile.Rd | 90 cNORM-3.5.3/cNORM/man/weighted.quantile.harrell.davis.Rd | 46 cNORM-3.5.3/cNORM/man/weighted.quantile.type7.Rd | 46 cNORM-3.5.3/cNORM/vignettes/cNORM-Demo.Rmd | 2 57 files changed, 4395 insertions(+), 2965 deletions(-)
Title: Rounded Bar Plots
Description: Creates bar plots with rounded corners using 'ggplot2'.
The code in this package was adapted from a solution provided by
Stack Overflow user 'sthoch' in the following post
<https://stackoverflow.com/questions/62176038/r-ggplot2-bar-chart-with-round-corners-on-top-of-bar>.
Author: Botan Agin [aut, cre, cph]
Maintainer: Botan Agin <aginbotan@gmail.com>
Diff between ggrounded versions 0.1.0 dated 2026-04-10 and 0.2.0 dated 2026-05-01
DESCRIPTION | 6 +- MD5 | 20 +++++---- NEWS.md | 10 ++++ R/geom-col-rounded.R | 22 ++++++++-- R/geom-histogram-rounded.R | 32 ++++++++------ R/utils.R | 72 ++++++++++++++++++++++++++++++++- README.md | 19 ++++++-- man/figures/README-example5-1.png |only tests/testthat/Rplots.pdf |only tests/testthat/test-geom-bar-rounded.R | 12 +++++ tests/testthat/test-geom-col-rounded.R | 28 ++++++++++++ tests/testthat/test-radius.R | 37 ++++++++++++++++ 12 files changed, 221 insertions(+), 37 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Lars van der Burg [aut],
Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between smcfcs versions 2.0.1 dated 2025-07-17 and 2.0.2 dated 2026-05-01
DESCRIPTION | 9 +++-- MD5 | 16 ++++----- R/smcfcs.r | 4 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/coarsening.html | 25 ++++++++------- inst/doc/coverror.html | 7 ++-- inst/doc/smcfcs-vignette.html | 7 ++-- tests/testthat/test_podds.r | 68 ++++++++++++++++++++++++++++++++++++++++++ 9 files changed, 104 insertions(+), 32 deletions(-)
Title: Cryptographic Hash Functions and Data Encoding
Description: Fast and memory-efficient streaming hash functions,
binary/text encoding and serialization. Hashes strings and raw vectors
directly. Stream hashes files which can be larger than memory, as
well as in-memory objects through R's serialization mechanism.
Implements the SHA-256, SHA-3 and 'Keccak' cryptographic hash
functions, SHAKE256 extendable-output function (XOF), 'SipHash'
pseudo-random function, base64 and base58 encoding, 'CBOR' and 'JSON'
serialization.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
The Mbed TLS Contributors [cph] ,
Red Hat, Inc. [cph] ,
Luke Dashjr [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between secretbase versions 1.2.1 dated 2026-03-30 and 1.2.2 dated 2026-05-01
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/partial.rdb |binary man/secretbase-package.Rd | 5 ++++- src/json.c | 3 +-- src/sha3.c | 15 +++++++++------ tests/tests.R | 6 +++++- 8 files changed, 47 insertions(+), 24 deletions(-)
Title: Learning from Black-Box Models by Maximum Interpretation
Decomposition
Description: The goal of 'midr' is to provide a model-agnostic method for interpreting and explaining black-box predictive models by creating a globally interpretable surrogate model. The package implements 'Maximum Interpretation Decomposition' (MID), a functional decomposition technique that finds an optimal additive approximation of the original model. This approximation is achieved by minimizing the squared error between the predictions of the black-box model and the surrogate model. The theoretical foundations of MID are described in Iwasawa & Matsumori (2025) [Forthcoming], and the package itself is detailed in Asashiba et al. (2025) <doi:10.48550/arXiv.2506.08338>.
Author: Ryoichi Asashiba [aut, cre] ,
Hirokazu Iwasawa [aut],
Reiji Kozuma [ctb]
Maintainer: Ryoichi Asashiba <ryoichi.asashiba@gmail.com>
Diff between midr versions 0.6.0 dated 2026-03-08 and 0.6.1 dated 2026-05-01
DESCRIPTION | 11 - MD5 | 40 ++-- NAMESPACE | 4 NEWS.md | 23 ++ R/get_yhat.R | 264 +++++++++++++++++++++++-------- R/ggmid.R | 42 ++-- R/ggmid_midbrk.R | 33 ++- R/ggmid_midbrks.R | 6 R/ggmid_midcons.R | 33 ++- R/ggmid_midimp.R | 28 +-- R/ggmid_midimps.R | 6 R/ggmid_mids.R | 10 - R/interpret.R | 13 + R/misc_functions.R | 20 +- R/theme_midr.R | 22 +- README.md | 2 man/figures/README-mid_breakdown-1.png |binary man/figures/README-mid_conditional-1.png |binary man/get.yhat.Rd | 20 +- man/midr-package.Rd | 2 man/theme_midr.Rd | 5 21 files changed, 384 insertions(+), 200 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.14.0 dated 2026-03-08 and 2.14.1 dated 2026-05-01
inlabru-2.14.0/inlabru/inst/examples |only inlabru-2.14.0/inlabru/man/gg.SpatialGridDataFrame.Rd |only inlabru-2.14.0/inlabru/man/gg.SpatialLines.Rd |only inlabru-2.14.0/inlabru/man/gg.SpatialPixels.Rd |only inlabru-2.14.0/inlabru/man/gg.SpatialPixelsDataFrame.Rd |only inlabru-2.14.0/inlabru/man/gg.SpatialPoints.Rd |only inlabru-2.14.0/inlabru/man/gg.SpatialPolygons.Rd |only inlabru-2.14.0/inlabru/man/globe.Rd |only inlabru-2.14.0/inlabru/man/summary.bru.Rd |only inlabru-2.14.1/inlabru/DESCRIPTION | 12 inlabru-2.14.1/inlabru/MD5 | 190 ++-- inlabru-2.14.1/inlabru/NAMESPACE | 6 inlabru-2.14.1/inlabru/NEWS.md | 26 inlabru-2.14.1/inlabru/R/bru.gof.R | 248 +++++- inlabru-2.14.1/inlabru/R/bru.inference.R | 375 ++++++++- inlabru-2.14.1/inlabru/R/bru_input.R | 4 inlabru-2.14.1/inlabru/R/data.mrsea.R | 2 inlabru-2.14.1/inlabru/R/data.shrimp.R | 4 inlabru-2.14.1/inlabru/R/data.toygroups.R | 32 inlabru-2.14.1/inlabru/R/deltaIC.R | 211 +++++ inlabru-2.14.1/inlabru/R/effect.R | 80 +- inlabru-2.14.1/inlabru/R/environment.R | 1 inlabru-2.14.1/inlabru/R/fmesher.R | 14 inlabru-2.14.1/inlabru/R/ggplot.R | 390 +++++++--- inlabru-2.14.1/inlabru/R/hierarchical_basis.R | 32 inlabru-2.14.1/inlabru/R/inla.R | 2 inlabru-2.14.1/inlabru/R/local_testthat.R | 10 inlabru-2.14.1/inlabru/R/mappers.R | 10 inlabru-2.14.1/inlabru/R/model.R | 2 inlabru-2.14.1/inlabru/R/object_upgrade.R | 304 ++++--- inlabru-2.14.1/inlabru/R/rgl.R | 140 +-- inlabru-2.14.1/inlabru/R/sampling.R | 2 inlabru-2.14.1/inlabru/R/spde.R | 64 + inlabru-2.14.1/inlabru/R/utils.R | 75 + inlabru-2.14.1/inlabru/README.md | 1 inlabru-2.14.1/inlabru/build/partial.rdb |binary inlabru-2.14.1/inlabru/build/vignette.rds |binary inlabru-2.14.1/inlabru/inst/doc/component.html | 2 inlabru-2.14.1/inlabru/inst/doc/linearapprox.R | 3 inlabru-2.14.1/inlabru/inst/doc/linearapprox.Rmd | 3 inlabru-2.14.1/inlabru/inst/doc/linearapprox.html | 91 +- inlabru-2.14.1/inlabru/inst/doc/prediction_scores.html | 62 - inlabru-2.14.1/inlabru/inst/misc/2d_lgcp_residuals_functions.R | 3 inlabru-2.14.1/inlabru/inst/misc/2d_lgcp_residuals_functions_sf.R | 3 inlabru-2.14.1/inlabru/man/bincount.Rd | 2 inlabru-2.14.1/inlabru/man/bm_fm_mesh_1d.Rd | 6 inlabru-2.14.1/inlabru/man/bru.Rd | 29 inlabru-2.14.1/inlabru/man/bru_comp.Rd | 2 inlabru-2.14.1/inlabru/man/bru_info.Rd | 7 inlabru-2.14.1/inlabru/man/bru_obs.Rd | 13 inlabru-2.14.1/inlabru/man/bru_safe_inla.Rd | 4 inlabru-2.14.1/inlabru/man/deltaIC.Rd | 12 inlabru-2.14.1/inlabru/man/devel.cvmeasure.Rd | 17 inlabru-2.14.1/inlabru/man/evaluate_model.Rd | 2 inlabru-2.14.1/inlabru/man/figures/README-plot-1.png |binary inlabru-2.14.1/inlabru/man/generate.Rd | 24 inlabru-2.14.1/inlabru/man/gg.RasterLayer.Rd | 13 inlabru-2.14.1/inlabru/man/gg.Rd | 30 inlabru-2.14.1/inlabru/man/gg.SpatRaster.Rd | 16 inlabru-2.14.1/inlabru/man/gg.Spatial.Rd |only inlabru-2.14.1/inlabru/man/gg.bru_prediction.Rd | 44 - inlabru-2.14.1/inlabru/man/gg.fm_mesh_1d.Rd | 14 inlabru-2.14.1/inlabru/man/gg.fm_mesh_2d.Rd | 16 inlabru-2.14.1/inlabru/man/gg.matrix.Rd | 12 inlabru-2.14.1/inlabru/man/gg.sf.Rd | 88 +- inlabru-2.14.1/inlabru/man/glplot.Rd | 55 - inlabru-2.14.1/inlabru/man/lgcp.Rd | 6 inlabru-2.14.1/inlabru/man/lgcp_IC.Rd |only inlabru-2.14.1/inlabru/man/local_testthat.Rd | 2 inlabru-2.14.1/inlabru/man/mrsea.Rd | 2 inlabru-2.14.1/inlabru/man/pcmatern_B.Rd | 32 inlabru-2.14.1/inlabru/man/plot.bru.Rd | 9 inlabru-2.14.1/inlabru/man/predict.bru.Rd | 36 inlabru-2.14.1/inlabru/man/reexports.Rd | 4 inlabru-2.14.1/inlabru/man/sample.lgcp.Rd | 2 inlabru-2.14.1/inlabru/man/shrimp.Rd | 4 inlabru-2.14.1/inlabru/man/spde.posterior.Rd | 4 inlabru-2.14.1/inlabru/man/toygroups.Rd | 6 inlabru-2.14.1/inlabru/tests/testthat/setup.R | 4 inlabru-2.14.1/inlabru/tests/testthat/test-02_predict.R | 14 inlabru-2.14.1/inlabru/tests/testthat/test-aggregate.R | 5 inlabru-2.14.1/inlabru/tests/testthat/test-bru_sf.R | 4 inlabru-2.14.1/inlabru/tests/testthat/test-bru_sp.R |only inlabru-2.14.1/inlabru/tests/testthat/test-component.R | 13 inlabru-2.14.1/inlabru/tests/testthat/test-copy.R | 9 inlabru-2.14.1/inlabru/tests/testthat/test-data.R | 1 inlabru-2.14.1/inlabru/tests/testthat/test-environment.R | 18 inlabru-2.14.1/inlabru/tests/testthat/test-fmesher_pixels.R | 15 inlabru-2.14.1/inlabru/tests/testthat/test-gcpo.R | 7 inlabru-2.14.1/inlabru/tests/testthat/test-latent_clinear.R | 5 inlabru-2.14.1/inlabru/tests/testthat/test-latent_factor.R | 25 inlabru-2.14.1/inlabru/tests/testthat/test-latent_linear.R | 10 inlabru-2.14.1/inlabru/tests/testthat/test-latent_spde_2d.R | 4 inlabru-2.14.1/inlabru/tests/testthat/test-mapper.R | 151 +++ inlabru-2.14.1/inlabru/tests/testthat/test-mdata.R | 2 inlabru-2.14.1/inlabru/vignettes/linearapprox.Rmd | 3 96 files changed, 2306 insertions(+), 901 deletions(-)
Title: Goodness-of-Fit Functions for Comparison of Simulated and
Observed Hydrological Time Series
Description: S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph]
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
Diff between hydroGOF versions 0.6-0.1 dated 2024-11-04 and 0.7-0 dated 2026-05-01
DESCRIPTION | 20 +- MD5 | 85 ++++++---- NAMESPACE | 23 ++ NEWS.md | 38 ++++ R/APFB.R | 222 ++++++++++++--------------- R/HFB.R | 148 ++++++++++-------- R/JDKGE.R |only R/KGE.R | 158 ++++++++++++------- R/KGEkm.R | 26 ++- R/LCE.R |only R/LME.R |only R/PMR.R |only R/ggof.R | 92 ++++++++--- R/gof.R | 326 +++++++++++++++++++++++++++++----------- R/nrmse.R | 72 ++++---- R/pfactor.R | 6 R/plot2.R | 77 ++++++--- R/rfactor.R | 6 R/sKGE.R | 40 ++-- build/vignette.rds |binary data/EgaEnEstellaQts.RData |binary inst/CITATION | 14 - inst/doc/hydroGOF_Vignette.R | 252 +++++++++++++++++++----------- inst/doc/hydroGOF_Vignette.Rmd | 325 ++++++++++++++++++++++++++------------- inst/doc/hydroGOF_Vignette.pdf |binary man/APFB.Rd | 51 ++++-- man/HFB.Rd | 56 +++++- man/JDKGE.Rd |only man/KGEkm.Rd | 94 ++++++++--- man/LCE.Rd |only man/LME.Rd |only man/PMR.Rd |only man/figures |only man/ggof.Rd | 14 + man/gof.Rd | 111 +++++++++++-- man/hydroGOF-package.Rd | 25 ++- man/nrmse.Rd | 14 + man/pfactor.Rd | 22 +- man/plot2.Rd | 4 man/rfactor.Rd | 28 ++- man/sKGE.Rd | 76 ++++++++- man/wNSE.Rd | 2 man/wsNSE.Rd | 42 ++++- tests |only vignettes/hydroGOF_Vignette.Rmd | 325 ++++++++++++++++++++++++++------------- 45 files changed, 1867 insertions(+), 927 deletions(-)
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.4 dated 2025-07-10 and 1.0.5 dated 2026-05-01
DESCRIPTION | 8 +-- MD5 | 15 +++-- R/BPLSR.R | 6 +- README.md | 98 ++++++++++---------------------------- build/partial.rdb |binary data/milk_MIR.rda |binary man/bplsr.Rd | 2 man/bplsr.predict.Rd | 2 man/figures/README-pressure-1.png |only 9 files changed, 43 insertions(+), 88 deletions(-)
Title: Rocket-Fast Clinical Research Reporting
Description: Description of the tables, both grouped and not grouped, with some associated data management actions,
such as sorting the terms of the variables and deleting terms with zero numbers.
Author: USMR CHU de Bordeaux [aut, cre],
Valentine Renaudeau [aut],
Marion Kret [aut],
Matisse Decilap [aut],
Sahardid Mohamed Houssein [aut],
Thomas Ferte [aut]
Maintainer: USMR CHU de Bordeaux <astreinte.usmr@chu-bordeaux.fr>
Diff between RastaRocket versions 1.1.3 dated 2026-03-23 and 1.1.4 dated 2026-05-01
RastaRocket-1.1.3/RastaRocket/R/write_datestamp_output_file.R |only RastaRocket-1.1.3/RastaRocket/man/write_datestamp_output_file.Rd |only RastaRocket-1.1.4/RastaRocket/DESCRIPTION | 11 RastaRocket-1.1.4/RastaRocket/MD5 | 72 RastaRocket-1.1.4/RastaRocket/NAMESPACE | 2 RastaRocket-1.1.4/RastaRocket/NEWS.md | 13 RastaRocket-1.1.4/RastaRocket/R/add_pvalues.R | 2 RastaRocket-1.1.4/RastaRocket/R/base_table.R | 18 RastaRocket-1.1.4/RastaRocket/R/custom_format.R | 40 RastaRocket-1.1.4/RastaRocket/R/customize_table.R | 22 RastaRocket-1.1.4/RastaRocket/R/desc_var_function.R | 7 RastaRocket-1.1.4/RastaRocket/R/globals.R | 9 RastaRocket-1.1.4/RastaRocket/R/indent_table.R |only RastaRocket-1.1.4/RastaRocket/R/prepare_table.R | 39 RastaRocket-1.1.4/RastaRocket/R/select_plus.R | 4 RastaRocket-1.1.4/RastaRocket/R/start_new_reporting.R | 16 RastaRocket-1.1.4/RastaRocket/R/write_html_file.R | 2 RastaRocket-1.1.4/RastaRocket/R/write_qmd.R | 118 RastaRocket-1.1.4/RastaRocket/R/write_rendercopy.R |only RastaRocket-1.1.4/RastaRocket/R/zzz.R | 3 RastaRocket-1.1.4/RastaRocket/inst/doc/DescribeAE.R | 16 RastaRocket-1.1.4/RastaRocket/inst/doc/DescribeAE.Rmd | 33 RastaRocket-1.1.4/RastaRocket/inst/doc/DescribeAE.html | 2457 +++++++++- RastaRocket-1.1.4/RastaRocket/inst/doc/RastaRocketVignette.R | 18 RastaRocket-1.1.4/RastaRocket/inst/doc/RastaRocketVignette.Rmd | 27 RastaRocket-1.1.4/RastaRocket/inst/doc/RastaRocketVignette.html | 1259 ++++- RastaRocket-1.1.4/RastaRocket/inst/doc/SetupProject.html | 5 RastaRocket-1.1.4/RastaRocket/man/base_table.Rd | 21 RastaRocket-1.1.4/RastaRocket/man/custom_format.Rd | 4 RastaRocket-1.1.4/RastaRocket/man/customize_table.Rd | 31 RastaRocket-1.1.4/RastaRocket/man/desc_var.Rd | 5 RastaRocket-1.1.4/RastaRocket/man/indent_table.Rd |only RastaRocket-1.1.4/RastaRocket/man/prepare_table.Rd | 19 RastaRocket-1.1.4/RastaRocket/man/select_plus.Rd | 2 RastaRocket-1.1.4/RastaRocket/man/write_qmd.Rd | 8 RastaRocket-1.1.4/RastaRocket/man/write_rendercopy.Rd |only RastaRocket-1.1.4/RastaRocket/tests |only RastaRocket-1.1.4/RastaRocket/vignettes/DescribeAE.Rmd | 33 RastaRocket-1.1.4/RastaRocket/vignettes/RastaRocketVignette.Rmd | 27 39 files changed, 3794 insertions(+), 549 deletions(-)
Title: Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson [...truncated...]
Author: Jeffrey Doser [aut, cre],
Hunter Stanke [aut],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between rFIA versions 1.1.2 dated 2025-09-29 and 1.1.3 dated 2026-04-30
DESCRIPTION | 10 MD5 | 24 - NAMESPACE | 1 NEWS.md | 5 R/biomassStarter.R | 7 R/fsi.R | 841 +++++++++++++++++++++++++------------------------- R/fsiHelper.R | 861 ++++++++++++++++++++++++++-------------------------- R/fsiStarter.R | 195 ++++++----- R/getDesignInfo.R | 6 R/invasiveStarter.R | 2 R/tpa.R | 3 R/tpaStarter.R | 3 R/util.R | 430 ++++--------------------- 13 files changed, 1051 insertions(+), 1337 deletions(-)
Title: Tools for Multilayer and Single Layer Network Modeling
Description: Estimation and bootstrap utilities for single layer and multilayer
Mixed Graphical Models, including functions for centrality, bridge metrics,
membership stability, and plotting (De Martino et al. (2026) <doi:10.48550/arXiv.2602.05716>).
Author: Maria De Martino [aut, cre],
Caterina Gregorio [aut],
Adrien Perigord [ctb],
Hudson Golino [ctb],
Jonas Haslbeck [ctb]
Maintainer: Maria De Martino <maria.demartino@uniud.it>
Diff between MixMashNet versions 0.6.0 dated 2026-03-03 and 1.0.0 dated 2026-04-30
MixMashNet-0.6.0/MixMashNet/R/mixmashnet-plot.R |only MixMashNet-0.6.0/MixMashNet/R/mixmashnet-print.R |only MixMashNet-0.6.0/MixMashNet/R/mixmashnet-summary.R |only MixMashNet-0.6.0/MixMashNet/R/nhgh_data.R |only MixMashNet-0.6.0/MixMashNet/data/nhgh_data.rda |only MixMashNet-0.6.0/MixMashNet/man/nhgh_data.Rd |only MixMashNet-0.6.0/MixMashNet/man/plot.mixmashnet.Rd |only MixMashNet-0.6.0/MixMashNet/man/print.mixmashnet.Rd |only MixMashNet-0.6.0/MixMashNet/man/summary.mixmashnet.Rd |only MixMashNet-1.0.0/MixMashNet/DESCRIPTION | 14 MixMashNet-1.0.0/MixMashNet/MD5 | 101 +- MixMashNet-1.0.0/MixMashNet/NAMESPACE | 40 - MixMashNet-1.0.0/MixMashNet/NEWS.md | 9 MixMashNet-1.0.0/MixMashNet/R/bacteremia.R | 5 MixMashNet-1.0.0/MixMashNet/R/bridge_metrics.R | 393 ++++++---- MixMashNet-1.0.0/MixMashNet/R/community_scores.R | 152 ++- MixMashNet-1.0.0/MixMashNet/R/find_bridge_communities.R | 247 ++++-- MixMashNet-1.0.0/MixMashNet/R/find_bridge_layers.R |only MixMashNet-1.0.0/MixMashNet/R/get_centrality.R |only MixMashNet-1.0.0/MixMashNet/R/get_edges.R |only MixMashNet-1.0.0/MixMashNet/R/globals.R | 3 MixMashNet-1.0.0/MixMashNet/R/layer_slice.R |only MixMashNet-1.0.0/MixMashNet/R/membershipStab.R | 181 ++++ MixMashNet-1.0.0/MixMashNet/R/membershipStab_plot.R | 2 MixMashNet-1.0.0/MixMashNet/R/mgm_masked.R | 2 MixMashNet-1.0.0/MixMashNet/R/mixMN.R | 109 +- MixMashNet-1.0.0/MixMashNet/R/mixMN_from_wadj.R | 48 - MixMashNet-1.0.0/MixMashNet/R/multimixMN.R | 84 +- MixMashNet-1.0.0/MixMashNet/R/nhanes.R | 5 MixMashNet-1.0.0/MixMashNet/R/plot-network.R | 48 + MixMashNet-1.0.0/MixMashNet/R/plot.R |only MixMashNet-1.0.0/MixMashNet/R/plotCentrality.R | 4 MixMashNet-1.0.0/MixMashNet/R/plotInterlayer.R | 23 MixMashNet-1.0.0/MixMashNet/R/print.R |only MixMashNet-1.0.0/MixMashNet/R/summary.R |only MixMashNet-1.0.0/MixMashNet/R/update_palette.R | 275 ++++-- MixMashNet-1.0.0/MixMashNet/R/utils-mgm.R | 3 MixMashNet-1.0.0/MixMashNet/R/utils_clustering.R |only MixMashNet-1.0.0/MixMashNet/README.md | 65 - MixMashNet-1.0.0/MixMashNet/man/bacteremia.Rd | 5 MixMashNet-1.0.0/MixMashNet/man/bridge_metrics.Rd | 4 MixMashNet-1.0.0/MixMashNet/man/community_scores.Rd | 18 MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-10-1.png |binary MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-11-1.png |binary MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-12-1.png |binary MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-13-1.png |binary MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-14-1.png |only MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-15-1.png |only MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-5-1.png |only MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-7-1.png |only MixMashNet-1.0.0/MixMashNet/man/figures/README-unnamed-chunk-9-1.png |binary MixMashNet-1.0.0/MixMashNet/man/find_bridge_communities.Rd | 43 - MixMashNet-1.0.0/MixMashNet/man/find_bridge_layers.Rd |only MixMashNet-1.0.0/MixMashNet/man/get_centrality.Rd |only MixMashNet-1.0.0/MixMashNet/man/get_edges.Rd |only MixMashNet-1.0.0/MixMashNet/man/layer_slice.Rd |only MixMashNet-1.0.0/MixMashNet/man/membershipStab.Rd | 10 MixMashNet-1.0.0/MixMashNet/man/mixMN.Rd | 33 MixMashNet-1.0.0/MixMashNet/man/multimixMN.Rd | 29 MixMashNet-1.0.0/MixMashNet/man/nhanes.Rd | 5 MixMashNet-1.0.0/MixMashNet/man/plot.mixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/plot.multimixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/print.mixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/print.multimixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/summary.mixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/summary.multimixMN_fit.Rd |only MixMashNet-1.0.0/MixMashNet/man/update_palette.Rd | 71 + 67 files changed, 1416 insertions(+), 615 deletions(-)
Title: Integration Unit Tests for Pharmacoepidemiological Studies
Description: An R interface to load testing data in the 'OMOP' Common Data Model ('CDM'). An input file, csv or xlsx, can be converted to a 'CDMConnector' object. This object can be used to execute and test studies that use the 'CDM' <https://www.ohdsi.org/data-standardization/>.
Author: Cesar Barboza [aut] ,
Ioanna Nika [aut],
Ger Inberg [aut, cre] ,
Adam Black [aut]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between TestGenerator versions 0.6.0 dated 2026-04-16 and 0.7.0 dated 2026-04-30
DESCRIPTION | 9 +++--- MD5 | 17 +++++++---- NEWS.md | 10 ++++++ R/patients.R | 60 ++++++++++++++++++++++++++++++++++++++--- README.md | 36 ++++++++++++++---------- build |only inst/doc |only man/patientsCDM.Rd | 2 - tests/testthat/test-patients.R | 1 vignettes |only 10 files changed, 105 insertions(+), 30 deletions(-)
Title: Assessing Package Test Reliability and Quality
Description: A reliable and validated tool that calculates unit test coverage for R packages with standard testing frameworks and non-standard testing frameworks.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between test.assessr versions 2.0.0 dated 2026-04-16 and 2.1.0 dated 2026-04-30
DESCRIPTION | 6 - MD5 | 22 ++-- NEWS.md | 17 ++- R/get_package_coverage.R | 50 +++++---- R/run_covr_modes.R | 151 ++++++++++++---------------- R/run_covr_skip_stf.R | 4 man/create_empty_covr_list.Rd | 5 man/get_package_coverage.Rd | 17 ++- tests/testthat/test-get_package_coverage.R | 122 ++++++++++++++++++++++ tests/testthat/test-install_package_local.R | 5 tests/testthat/test-run_covr_modes.R | 17 ++- tests/testthat/test-run_covr_skip_stf.R | 4 12 files changed, 287 insertions(+), 133 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.10.2 dated 2026-02-02 and 1.0.2 dated 2026-04-30
DESCRIPTION | 16 MD5 | 33 NAMESPACE | 6 R/RcppExports.R | 24 R/disaggregate.R | 2 R/griddata_class.R | 1189 ++++++++++++++++------- R/rts2-package.R | 3 build/partial.rdb |binary inst/include |only man/disaggregate_covariate.Rd | 70 - man/disaggregate_positive.Rd | 88 - man/flat_disaggregate.Rd | 38 man/grid.Rd | 181 ++- src/RcppExports.cpp | 85 + src/region_model.cpp | 1898 ++++++++++++++++++++++++++++++++++---- src/region_model.h | 91 + src/stanExports_rtsbayes.cc | 34 src/stanExports_rtslgcp_region.cc | 34 18 files changed, 3010 insertions(+), 782 deletions(-)
Title: Convert Data among QTL Mapping Packages
Description: Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2convert versions 0.30 dated 2024-04-04 and 0.32 dated 2026-04-30
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS.md | 8 ++++++++ src/RcppExports.cpp | 5 +++++ src/encode_geno.cpp | 2 +- 5 files changed, 25 insertions(+), 11 deletions(-)
Title: Estimation of Relative Risks, Risk Differences, and Marginal
Effects from Mixed Models Using Marginal Standardization
Description: Estimation of relative risks, risk differences, and
partial effects from mixed model. Marginalisation over random effect terms is accomplished using Markov Chain Monte Carlo.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between marginme versions 0.1.0 dated 2025-07-28 and 0.1.1 dated 2026-04-30
DESCRIPTION | 12 +-- MD5 | 18 ++-- NAMESPACE | 1 R/adjrr.R | 76 ++++++++----------- R/marginal.R |only man/confint.margin.Rd | 85 ++++++++++----------- man/glmm_marginal.Rd |only man/margin.Rd | 195 ++++++++++++++++++++++++-------------------------- man/print.margin.Rd | 61 +++++++-------- man/summary.margin.Rd | 63 +++++++--------- man/trial_data.Rd | 20 ++--- 11 files changed, 257 insertions(+), 274 deletions(-)
Title: Fast and Efficient Processing of PAM Data
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
Author: Julien Boehm [cre, aut] ,
Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Diff between pam versions 2.2.0 dated 2026-04-23 and 2.2.1 dated 2026-04-30
DESCRIPTION | 6 +- MD5 | 64 +++++++++++------------ R/compare_regression_models.R | 2 R/device_dual_pam.R | 2 R/device_dual_pam_single_channel_fluo.R | 2 R/device_dual_pam_single_channel_p700.R | 2 R/device_junior_pam.R | 2 R/device_pam_2500.R | 2 R/device_universal_data.R | 2 R/model_eilers_peeters.R | 4 - R/model_platt.R | 4 - R/model_vollenweider.R | 4 - R/model_walsby.R | 4 - R/plot.R | 4 - R/write_model_result_csv.R | 2 man/combo_plot_control.Rd | 2 man/compare_regression_models_ETR_I.Rd | 2 man/eilers_peeters_generate_regression_ETR_I.Rd | 2 man/eilers_peeters_generate_regression_ETR_II.Rd | 2 man/platt_generate_regression_ETR_I.Rd | 2 man/platt_generate_regression_ETR_II.Rd | 2 man/plot_control.Rd | 2 man/read_dual_pam_data.Rd | 2 man/read_dual_pam_single_channel_fluo_data.Rd | 2 man/read_dual_pam_single_channel_p700_data.Rd | 2 man/read_junior_pam_data.Rd | 2 man/read_pam_2500_data.Rd | 2 man/read_universal_data.Rd | 2 man/vollenweider_generate_regression_ETR_I.Rd | 2 man/vollenweider_generate_regression_ETR_II.Rd | 2 man/walsby_generate_regression_ETR_I.Rd | 2 man/walsby_generate_regression_ETR_II.Rd | 2 man/write_model_result_csv.Rd | 2 33 files changed, 71 insertions(+), 71 deletions(-)
Title: R Client for the 'OMOPHub' Medical Vocabulary API
Description: Provides an R interface to the 'OMOPHub' API for accessing
'OHDSI ATHENA' standardized medical vocabularies. Supports concept search,
semantic search using neural embeddings, concept similarity, vocabulary
exploration, hierarchy navigation, relationship queries, concept
mappings, and FHIR-to-OMOP concept resolution with automatic pagination.
Author: Alex Chen [aut, cre, cph],
Observational Health Data Science and Informatics [cph]
Maintainer: Alex Chen <alex@omophub.com>
Diff between omophub versions 1.6.0 dated 2026-04-14 and 1.7.0 dated 2026-04-30
DESCRIPTION | 6 MD5 | 43 ++-- NAMESPACE | 4 NEWS.md | 31 +++ R/fhir.R | 209 +++++++++++++++++++++++ R/fhir_interop.R |only README.md | 154 +++++++++++++++-- inst/doc/getting-started.R | 69 +++++++ inst/doc/getting-started.Rmd | 111 ++++++++++++ inst/doc/getting-started.html | 99 +++++++++++ inst/examples/basic_usage.R | 8 inst/examples/error_handling.R | 252 +++++++++++++--------------- inst/examples/fhir_interop.R |only inst/examples/fhir_resolver.R |only inst/examples/map_between_vocabularies.R | 6 inst/examples/navigate_hierarchy.R | 86 ++++++--- inst/examples/search_concepts.R | 6 man/FhirResource.Rd | 16 + man/fhir_batch_to_tibble.Rd |only man/fhir_resolve.Rd |only man/fhir_resolve_batch.Rd |only man/fhir_resolve_codeable_concept.Rd |only man/omophub_fhir_url.Rd |only tests/testthat/test-fhir-integration.R | 56 ++++++ tests/testthat/test-fhir-interop.R |only tests/testthat/test-fhir.R | 271 +++++++++++++++++++++++++++++++ vignettes/getting-started.Rmd | 111 ++++++++++++ 27 files changed, 1327 insertions(+), 211 deletions(-)
Title: Compute Decision Interval and Average Run Length for CUSUM
Charts
Description: Computation of decision intervals (H) and average run lengths (ARL) for CUSUM charts. Details of the method are seen in Hawkins and Olwell (2012): Cumulative sum charts and charting for quality improvement, Springer Science & Business Media.
Author: Douglas M. Hawkins [aut],
David H. Olwell [aut],
Boxiang Wang [aut, cre]
Maintainer: Boxiang Wang <boxiang-wang@uiowa.edu>
Diff between CUSUMdesign versions 1.1.6 dated 2026-04-20 and 1.1.7 dated 2026-04-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/ANYSUBS.f | 6 +++++- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Bivariate Laplace Transforms, Stochastic Orders, and Entropy
Measures in Reliability
Description: Implements methods for bivariate and univariate Laplace transforms
of residual lives and reversed residual lives, associated stochastic ordering
concepts, and entropy measures for reliability analysis. The package covers:
(1) Bivariate Laplace transform of residual lives and stochastic comparisons
based on the bivariate Laplace transform order of residual lives (BLt-rl),
including weak bivariate hazard rate, mean residual life, and relative mean
residual life orders, nonparametric estimation, and NBUHR/NWUHR aging class
characterisation; Jayalekshmi, Rajesh, and Nair (2022)
"Bivariate Laplace Transform of Residual Lives and Their Properties"
<doi:10.1080/03610926.2022.2085874>;
(2) Bivariate Laplace transform order of reversed residual lives (BLt-Rrl),
reversed hazard gradient, reversed mean residual life, and the associated
stochastic orders (weak bivariate reversed hazard rate, weak bivariate
reversed mean residual life); Jayalekshmi, Rajesh, and Nair (2022)
"Bivariate Laplace [...truncated...]
Author: Mahesh Divakaran [aut, cre] ,
S. Jayalekshmi [aut, ctb] ,
G. Rajesh [aut] ,
N. Unnikrishnan Nair [aut]
Maintainer: Mahesh Divakaran <imaheshdivakaran@gmail.com>
Diff between BivLaplaceRL versions 0.2.0 dated 2026-04-29 and 1.0.0 dated 2026-04-30
BivLaplaceRL-0.2.0/BivLaplaceRL/man/np_residual_info_gen.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/plot_regf.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/regf_characterise.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/regf_profile.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/residual_entropy.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/residual_info_gen.Rd |only BivLaplaceRL-0.2.0/BivLaplaceRL/man/sim_regf.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/DESCRIPTION | 62 - BivLaplaceRL-1.0.0/BivLaplaceRL/MD5 | 46 - BivLaplaceRL-1.0.0/BivLaplaceRL/NAMESPACE | 14 BivLaplaceRL-1.0.0/BivLaplaceRL/NEWS.md | 23 BivLaplaceRL-1.0.0/BivLaplaceRL/R/BivLaplaceRL-package.R | 38 - BivLaplaceRL-1.0.0/BivLaplaceRL/R/plotting.R | 61 - BivLaplaceRL-1.0.0/BivLaplaceRL/R/residual_entropy.R | 346 ---------- BivLaplaceRL-1.0.0/BivLaplaceRL/R/univariate.R |only BivLaplaceRL-1.0.0/BivLaplaceRL/README.md | 71 +- BivLaplaceRL-1.0.0/BivLaplaceRL/inst/doc/introduction.R | 96 +- BivLaplaceRL-1.0.0/BivLaplaceRL/inst/doc/introduction.Rmd | 147 ++-- BivLaplaceRL-1.0.0/BivLaplaceRL/inst/doc/introduction.html | 274 +++---- BivLaplaceRL-1.0.0/BivLaplaceRL/man/BivLaplaceRL-package.Rd | 41 - BivLaplaceRL-1.0.0/BivLaplaceRL/man/hazard_rate.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/hr_order.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/info_gen_function.Rd | 2 BivLaplaceRL-1.0.0/BivLaplaceRL/man/lt_residual.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/lt_rl_order.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/mean_residual.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/mrl_order.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/np_lt_residual.Rd |only BivLaplaceRL-1.0.0/BivLaplaceRL/man/shannon_entropy.Rd | 5 BivLaplaceRL-1.0.0/BivLaplaceRL/tests/testthat/test-residual_entropy.R | 80 -- BivLaplaceRL-1.0.0/BivLaplaceRL/tests/testthat/test-univariate.R |only BivLaplaceRL-1.0.0/BivLaplaceRL/vignettes/introduction.Rmd | 147 ++-- 32 files changed, 491 insertions(+), 962 deletions(-)
Title: Legends for Maps
Description: Create legends for maps and other graphics. Thematic maps need to
be accompanied by legible legends to be fully comprehensible. This package
offers a wide range of legends useful for cartography, some of which may
also be useful for other types of graphics.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maplegend versions 0.6.2 dated 2026-04-14 and 0.6.3 dated 2026-04-30
DESCRIPTION | 6 MD5 | 10 - NEWS.md | 6 R/leg.R | 4 R/lg_utils.R | 4 inst/tinytest/tests.R | 384 +++++++++++++++++++++++++------------------------- 6 files changed, 211 insertions(+), 203 deletions(-)
Title: Detecting Extremal Values in a Normal Linear Model
Description: Provides a method to detect values poorly explained by a Gaussian linear model. The procedure is based on the maximum of the absolute value of the studentized residuals, which is a parameter-free statistic. This approach generalizes several procedures used to detect abnormal values during longitudinal monitoring of biological markers. For methodological details, see: Berthelot G., Saulière G., Dedecker J. (2025). "DEViaN-LM An R Package for Detecting Abnormal Values in the Gaussian Linear Model". HAL Id: hal-05230549. <https://hal.science/hal-05230549>.
Author: Guillaume Sauliere [aut] ,
Geoffroy Berthelot [aut, cre] ,
Jerome Dedecker [aut]
Maintainer: Geoffroy Berthelot <geoffroy.berthelot@insep.fr>
Diff between devianLM versions 1.0.7 dated 2025-11-21 and 1.1.0 dated 2026-04-30
DESCRIPTION | 10 +- MD5 | 25 +++--- NAMESPACE | 1 NEWS.md | 8 ++ R/RcppExports.R | 14 +-- R/data.R | 78 ++++++++++---------- R/devianLM-package.R |only R/devianlm_stats.R | 86 ++++++++++++++++------ R/print.R |only build |only man/devianLM-package.Rd | 62 ++++++++-------- man/devianlm_stats.Rd | 139 +++++++++++++++++++----------------- man/get_devianlm_threshold.Rd | 72 +++++++++--------- man/salary.Rd | 94 ++++++++++++------------ src/devianlm_cpp.cpp | 161 ++++++++++++++++++++++++++++++------------ 15 files changed, 447 insertions(+), 303 deletions(-)
Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Cascade versions 2.3 dated 2025-09-19 and 2.4 dated 2026-04-30
Cascade-2.3/Cascade/inst/doc/E-MTAB-1475_re-analysis.pdf |only Cascade-2.3/Cascade/inst/doc/E-MTAB-1475_re-analysis.pdf.asis |only Cascade-2.3/Cascade/vignettes/E-MTAB-1475_re-analysis.pdf.asis |only Cascade-2.4/Cascade/DESCRIPTION | 16 +- Cascade-2.4/Cascade/MD5 | 33 +--- Cascade-2.4/Cascade/NAMESPACE | 23 +-- Cascade-2.4/Cascade/NEWS.md | 8 + Cascade-2.4/Cascade/R/Cascade-package.R | 13 - Cascade-2.4/Cascade/R/micro_array-network.R | 2 Cascade-2.4/Cascade/R/micro_array.R | 37 +--- Cascade-2.4/Cascade/R/network.R | 7 Cascade-2.4/Cascade/README.md | 76 +++++----- Cascade-2.4/Cascade/build/partial.rdb |binary Cascade-2.4/Cascade/build/vignette.rds |binary Cascade-2.4/Cascade/inst/_pkgdown.yml | 2 Cascade-2.4/Cascade/inst/doc/Cascade.pdf |binary Cascade-2.4/Cascade/man/Cascade-package.Rd | 4 Cascade-2.4/Cascade/man/evolution-network-method.Rd | 3 Cascade-2.4/Cascade/tests/testthat/Rplots.pdf |binary 19 files changed, 114 insertions(+), 110 deletions(-)
Title: An R Package for Evaluating Expertise Indices for Research
Strength Assessment
Description: Institutional performance assessment remains a key challenge to a multitude of stakeholders. Existing indicators such as h-type indicators, g-type indicators, and many others do not reflect expertise of institutions that defines their research portfolio. The package offers functionality to compute and visualise two novel indices: the x-index and the xd-index. The x-index evaluates an institution's scholarly expertise within a specific discipline or field, while the xd-index provides a broader assessment of overall scholarly expertise considering an institution's publication pattern and strengths across coarse thematic areas. These indices offer a nuanced understanding of institutional research capabilities, aiding stakeholders in research management and resource allocation decisions. Lathabai, H.H., Nandy, A., and Singh, V.K. (2021) <doi:10.1007/s11192-021-04188-3>. Nandy, A., Lathabai, H.H., and Singh, V.K. (2023) <doi:10.5281/zenodo.8305585>. This package provides the h-, [...truncated...]
Author: Nilabhra R Das [cre, aut] ,
Abhirup Nandy [aut]
Maintainer: Nilabhra R Das <nr.das@yahoo.com>
Diff between xxdi versions 1.3.1 dated 2026-01-12 and 1.26.4 dated 2026-04-30
DESCRIPTION | 20 ++++++++++---------- MD5 | 29 ++++++++++++++++------------- NAMESPACE | 6 +----- NEWS.md | 9 +++++++++ R/g_index.R | 21 +++++++-------------- R/h_index.R | 26 ++++++++++---------------- R/ivw_xd_index.R | 28 +++++++--------------------- R/x_index.R | 26 ++++++-------------------- R/xc_index.R | 35 +++++++++++++---------------------- R/xd_index.R | 12 +++++------- R/xo_index.R |only inst |only man/ivw_xd_index.Rd | 2 +- man/x_index.Rd | 2 +- man/xc_index.Rd | 5 ++--- man/xd_index.Rd | 2 +- man/xo_index.Rd |only 17 files changed, 89 insertions(+), 134 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'OpenAI', 'Gemini', 'Mistral', and local models via 'Ollama' into R workflows. The package supports text, image, audio, video, and document interactions; a unified media interface for attaching inline files or uploading to provider file stores; batch request APIs for cost-efficient large-scale processing; and a pipeline-oriented interface for seamless integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.4.0 dated 2026-03-17 and 0.5.0 dated 2026-04-30
tidyllm-0.4.0/tidyllm/tests/testthat/claude/api.anthropic.com/v1/messages-e050b5-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/deepseek/api.deepseek.com/chat/completions-051628-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/groq/api.groq.com/openai/v1/chat/completions-0b59b0-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/mistral/api.mistral.ai/v1/chat/completions-2551cb-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/ollama/localhost-11434/api/chat-1e1974-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/openai/api.openai.com/v1/chat/completions-8333f0-POST.R |only tidyllm-0.4.0/tidyllm/tests/testthat/perplexity/api.perplexity.ai/chat/completions-11588b-POST.R |only tidyllm-0.5.0/tidyllm/DESCRIPTION | 19 tidyllm-0.5.0/tidyllm/MD5 | 145 tidyllm-0.5.0/tidyllm/NAMESPACE | 14 tidyllm-0.5.0/tidyllm/NEWS.md | 193 + tidyllm-0.5.0/tidyllm/R/APIProvider.R | 29 tidyllm-0.5.0/tidyllm/R/LLMMessage.R | 73 tidyllm-0.5.0/tidyllm/R/api_azure_openai.R | 8 tidyllm-0.5.0/tidyllm/R/api_chat_completions.R |only tidyllm-0.5.0/tidyllm/R/api_claude.R | 156 tidyllm-0.5.0/tidyllm/R/api_deepseek.R | 13 tidyllm-0.5.0/tidyllm/R/api_ellmer.R | 6 tidyllm-0.5.0/tidyllm/R/api_gemini.R | 220 - tidyllm-0.5.0/tidyllm/R/api_groq.R | 10 tidyllm-0.5.0/tidyllm/R/api_llamacpp.R | 2 tidyllm-0.5.0/tidyllm/R/api_mistral.R | 54 tidyllm-0.5.0/tidyllm/R/api_ollama.R | 4 tidyllm-0.5.0/tidyllm/R/api_openai.R | 1887 +++------- tidyllm-0.5.0/tidyllm/R/api_openrouter.R | 80 tidyllm-0.5.0/tidyllm/R/api_perplexity.R | 2 tidyllm-0.5.0/tidyllm/R/api_voyage.R | 4 tidyllm-0.5.0/tidyllm/R/llm_message.R | 149 tidyllm-0.5.0/tidyllm/R/llm_verbs.R | 164 tidyllm-0.5.0/tidyllm/R/media.R | 255 + tidyllm-0.5.0/tidyllm/R/rate_limits.R | 3 tidyllm-0.5.0/tidyllm/README.md | 91 tidyllm-0.5.0/tidyllm/build/vignette.rds |binary tidyllm-0.5.0/tidyllm/inst/doc/tidyllm.R | 44 tidyllm-0.5.0/tidyllm/inst/doc/tidyllm.Rmd | 76 tidyllm-0.5.0/tidyllm/inst/doc/tidyllm.html | 143 tidyllm-0.5.0/tidyllm/man/audio_file.Rd |only tidyllm-0.5.0/tidyllm/man/cancel_openai_batch.Rd | 2 tidyllm-0.5.0/tidyllm/man/chat_completions_chat.Rd |only tidyllm-0.5.0/tidyllm/man/chatgpt.Rd | 11 tidyllm-0.5.0/tidyllm/man/check_job.Rd | 2 tidyllm-0.5.0/tidyllm/man/check_openai_batch.Rd | 2 tidyllm-0.5.0/tidyllm/man/deepseek_chat.Rd | 6 tidyllm-0.5.0/tidyllm/man/delete_file.Rd |only tidyllm-0.5.0/tidyllm/man/fetch_job.Rd | 2 tidyllm-0.5.0/tidyllm/man/fetch_openai_batch.Rd | 2 tidyllm-0.5.0/tidyllm/man/file_info.Rd |only tidyllm-0.5.0/tidyllm/man/groq_chat.Rd | 2 tidyllm-0.5.0/tidyllm/man/img.Rd | 11 tidyllm-0.5.0/tidyllm/man/list_files.Rd |only tidyllm-0.5.0/tidyllm/man/list_openai_batches.Rd | 2 tidyllm-0.5.0/tidyllm/man/llm_message.Rd | 10 tidyllm-0.5.0/tidyllm/man/mistral_chat.Rd | 3 tidyllm-0.5.0/tidyllm/man/openai.Rd | 13 tidyllm-0.5.0/tidyllm/man/openai_chat.Rd | 80 tidyllm-0.5.0/tidyllm/man/openai_check_research.Rd |only tidyllm-0.5.0/tidyllm/man/openai_code_interpreter.Rd |only tidyllm-0.5.0/tidyllm/man/openai_deep_research.Rd |only tidyllm-0.5.0/tidyllm/man/openai_embedding.Rd | 2 tidyllm-0.5.0/tidyllm/man/openai_fetch_research.Rd |only tidyllm-0.5.0/tidyllm/man/openai_list_models.Rd | 2 tidyllm-0.5.0/tidyllm/man/openai_websearch.Rd |only tidyllm-0.5.0/tidyllm/man/openrouter_chat.Rd | 12 tidyllm-0.5.0/tidyllm/man/pdf_file.Rd |only tidyllm-0.5.0/tidyllm/man/send_openai_batch.Rd | 2 tidyllm-0.5.0/tidyllm/man/tidyllm-package.Rd | 2 tidyllm-0.5.0/tidyllm/man/upload_file.Rd |only tidyllm-0.5.0/tidyllm/man/video_file.Rd |only tidyllm-0.5.0/tidyllm/man/voyage_embedding.Rd | 2 tidyllm-0.5.0/tidyllm/tests/testthat/claude/api.anthropic.com/v1/messages-f84379-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/deepseek/api.deepseek.com/chat/completions-019017-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/groq/api.groq.com/openai/v1/chat/completions-2a2aa4-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/groq/api.groq.com/openai/v1/chat/completions-bf210d-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/mistral/api.mistral.ai/v1/chat/completions-c2ce32-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/ollama/localhost-11434/api/chat-a2ac00-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/openai/api.openai.com/v1/chat/completions-f382f0-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/openai_schema_multiple/api.openai.com/v1/responses-94040c-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/openai_schema_single/api.openai.com/v1/responses-d98d41-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/perplexity/api.perplexity.ai/chat/completions-cca835-POST.R |only tidyllm-0.5.0/tidyllm/tests/testthat/test_api_claude.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_deepseek.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_gemini.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_groq.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_mistral.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_ollama.R | 10 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_openai.R | 24 tidyllm-0.5.0/tidyllm/tests/testthat/test_api_perplexity.R | 2 tidyllm-0.5.0/tidyllm/tests/testthat/test_llm_message.R | 63 tidyllm-0.5.0/tidyllm/vignettes/tidyllm.Rmd | 76 89 files changed, 2453 insertions(+), 1746 deletions(-)
Title: Recency, Frequency and Monetary Value Analysis
Description: Tools for RFM (recency, frequency and monetary value) analysis.
Generate RFM score from both transaction and customer level data. Visualize the
relationship between recency, frequency and monetary value using heatmap,
histograms, bar charts and scatter plots. Includes a 'shiny' app for
interactive segmentation. References:
i. Blattberg R.C., Kim BD., Neslin S.A (2008) <doi:10.1007/978-0-387-72579-6_12>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between rfm versions 0.3.0 dated 2024-02-26 and 0.4.0 dated 2026-04-30
DESCRIPTION | 19 MD5 | 34 NEWS.md | 14 R/rfm-plots.R | 89 R/rfm-segment.R | 307 - R/rfm-table-customer.R | 15 R/rfm-table-transaction.R | 3 README.md | 20 build/vignette.rds |binary inst/doc/rfm-introduction.R | 6 inst/doc/rfm-introduction.html | 43 man/rfm.Rd | 1 tests/testthat/_snaps/rfm-plots/rfm-barchart.svg | 1800 +++++----- tests/testthat/_snaps/rfm-plots/rfm-heatmap.svg | 64 tests/testthat/_snaps/rfm-plots/rfm-histograms.svg | 48 tests/testthat/_snaps/rfm-plots/rfm-plot-revenue-dist-flipped.svg | 14 tests/testthat/_snaps/rfm-plots/rfm-plot-revenue-dist.svg | 16 tests/testthat/_snaps/rfm-plots/rfm-plot-segment-scatter.svg | 50 18 files changed, 1125 insertions(+), 1418 deletions(-)
Title: Multi-Objective Spatial Planning
Description: Provides a modular framework for exact multi-objective spatial
planning using mixed-integer programming. The package supports the
definition of planning problems through planning units, features,
management actions, action effects, spatial relations, targets,
constraints, and objective functions. It enables the optimisation of
spatial planning portfolios under considerations such as boundary
structure, connectivity, and fragmentation. Supported multi-objective
methods include weighted-sum aggregation, epsilon-constraint, and the
augmented epsilon-constraint method. Problems can be solved with several
commercial and open-source optimisation solvers. Optional solver backends
include the 'gurobi' R package, which is distributed with the Gurobi Optimizer
installation <https://docs.gurobi.com/projects/optimizer/en/13.0/reference/r/setup.html>,
and the 'rcbc' R package, available from GitHub at
<https://github.com/dirkschumacher/rcbc>. For background on multi-objective
optimisati [...truncated...]
Author: Jose Salgado-Rojas [aut, cre] ,
Matias Moreno-Faguett [aut] ,
Nuria Aquilue [aut]
Maintainer: Jose Salgado-Rojas <jose.salgroj@gmail.com>
Diff between multiscape versions 1.0.6 dated 2026-04-28 and 1.0.7 dated 2026-04-30
DESCRIPTION | 6 MD5 | 16 +- NEWS.md | 4 R/build_model.R | 102 ++++++++++++++++ R/internal.R | 86 ++++++++++++++ R/internalMO.R | 182 +++++++++++++++++++++++++++--- README.md | 12 + man/figures/README-unnamed-chunk-10-1.png |binary src/init.c | 2 9 files changed, 381 insertions(+), 29 deletions(-)
Title: Make Symmetric and Asymmetric ARDL Estimations
Description: Implements estimation procedures for Autoregressive Distributed Lag (ARDL)
and Nonlinear ARDL (NARDL) models, which allow researchers to investigate both
short- and long-run relationships in time series data under mixed orders of integration.
The package supports simultaneous modeling of symmetric and asymmetric regressors,
flexible treatment of short-run and long-run asymmetries, and automated equation handling.
It includes several cointegration testing approaches such as the Pesaran-Shin-Smith F
and t bounds tests, and narayan test.
Methodological foundations are provided in Pesaran, Shin, and Smith (2001)
<doi:10.1016/S0304-4076(01)00049-5> and Shin, Yu, and Greenwood-Nimmo (2014, ISBN:9780123855079).
Author: Huseyin Karamelikli [aut, cre] ,
Huseyin Utku Demir [aut]
Maintainer: Huseyin Karamelikli <hakperest@gmail.com>
Diff between kardl versions 1.3.0 dated 2026-04-18 and 1.3.1 dated 2026-04-30
kardl-1.3.0/kardl/R/settings.R |only kardl-1.3.1/kardl/DESCRIPTION | 9 kardl-1.3.1/kardl/MD5 | 76 +- kardl-1.3.1/kardl/NEWS.md | 14 kardl-1.3.1/kardl/R/kardl.R | 531 ++++++++---------- kardl-1.3.1/kardl/R/longrun.R | 20 kardl-1.3.1/kardl/R/miscellaneous.R | 128 ++-- kardl-1.3.1/kardl/R/multipliers.R | 61 +- kardl-1.3.1/kardl/R/prepare.R | 273 ++++++++- kardl-1.3.1/kardl/R/print.R | 87 ++ kardl-1.3.1/kardl/R/srr-stats-standards.R |only kardl-1.3.1/kardl/R/tests.R | 257 +++++--- kardl-1.3.1/kardl/R/zzz.R |only kardl-1.3.1/kardl/README.md | 468 ++++++--------- kardl-1.3.1/kardl/inst/doc/intro.R | 29 kardl-1.3.1/kardl/inst/doc/intro.Rmd | 58 + kardl-1.3.1/kardl/inst/doc/intro.html | 113 ++- kardl-1.3.1/kardl/inst/examples/getData.R | 42 - kardl-1.3.1/kardl/man/bootstrap.Rd | 25 kardl-1.3.1/kardl/man/ecm.Rd | 357 +++++------- kardl-1.3.1/kardl/man/imf_example_data.Rd | 8 kardl-1.3.1/kardl/man/kardl.Rd | 275 ++++----- kardl-1.3.1/kardl/man/kardl_get.Rd | 8 kardl-1.3.1/kardl/man/kardl_longrun.Rd | 36 - kardl-1.3.1/kardl/man/kardl_reset.Rd | 43 - kardl-1.3.1/kardl/man/kardl_set.Rd | 39 - kardl-1.3.1/kardl/man/lmerge.Rd | 28 kardl-1.3.1/kardl/man/modelCriterion.Rd | 28 kardl-1.3.1/kardl/man/mplier.Rd | 29 kardl-1.3.1/kardl/man/narayan.Rd | 56 + kardl-1.3.1/kardl/man/parse_formula_vars.Rd | 2 kardl-1.3.1/kardl/man/pssf.Rd | 53 - kardl-1.3.1/kardl/man/psst.Rd | 50 - kardl-1.3.1/kardl/man/symmetrytest.Rd | 8 kardl-1.3.1/kardl/tests/testthat/Rplots.pdf |only kardl-1.3.1/kardl/tests/testthat/test-kardl.R | 159 +++++ kardl-1.3.1/kardl/tests/testthat/test-multipliers.R |only kardl-1.3.1/kardl/tests/testthat/test-print-summary.R |only kardl-1.3.1/kardl/tests/testthat/test-settings.R | 19 kardl-1.3.1/kardl/tests/testthat/test-tests.R | 292 +++++++++ kardl-1.3.1/kardl/tests/testthat/test-utils.R | 126 ++++ kardl-1.3.1/kardl/vignettes/intro.Rmd | 58 + 42 files changed, 2459 insertions(+), 1406 deletions(-)
Title: Fixed Effects Counterfactual Estimators
Description: Provides tools for estimating causal effects in panel data using counterfactual methods, as well as other modern DID estimators. It is designed for causal panel analysis with binary treatments under the parallel trends assumption. The package supports scenarios where treatments can switch on and off and allows for limited carryover effects. It includes several imputation estimators, such as Gsynth (Xu 2017), linear factor models, and the matrix completion method. Detailed methodology is described in Liu, Wang, and Xu (2024) <doi:10.48550/arXiv.2107.00856> and Chiu et al. (2025) <doi:10.48550/arXiv.2309.15983>. Optionally integrates with the "HonestDiDFEct" package for sensitivity analyses compatible with imputation estimators. "HonestDiDFEct" is not on CRAN but can be obtained from <https://github.com/lzy318/HonestDiDFEct>.
Author: Licheng Liu [aut],
Ziyi Liu [aut],
Ye Wang [aut],
Yiqing Xu [aut, cre],
Tianzhu Qin [aut],
Shiyun Hu [aut],
Rivka Lipkovitz [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between fect versions 2.2.0 dated 2026-03-27 and 2.4.1 dated 2026-04-30
DESCRIPTION | 10 MD5 | 116 +- NAMESPACE | 5 R/boot.R | 619 +++++-------- R/cfe.R | 7 R/cumu.R | 8 R/cv-helpers.R |only R/cv-rolling.R |only R/cv-rule-helpers.R |only R/cv.R | 748 +++++++++++++--- R/cv_binary.R | 78 + R/default.R | 276 +++++- R/diagtest.R | 14 R/did_wrapper.R | 2 R/effect.R | 6 R/esplot.R | 157 ++- R/fe.R | 7 R/fect_iden.R | 12 R/fect_mspe.R | 36 R/fect_nevertreated.R | 1231 ++++++++++++++++----------- R/fect_sens.R | 4 R/fittest.R | 2 R/impute_Y0.R |only R/loading_bound.R |only R/mc.R | 7 R/permutation.R | 2 R/plot.R | 453 +++++++-- R/po-estimands.R |only R/polynomial.R | 7 R/print.R | 10 R/support.R | 57 + R/theme-helpers.R |only R/valid_controls.R |only data/simdata.rda |binary man/esplot.Rd | 8 man/estimand.Rd |only man/fect.Rd | 74 + man/fect_iden.Rd | 41 man/fect_mspe.Rd | 12 man/imputed_outcomes.Rd |only man/plot.fect.Rd | 13 man/r.cv.rolling.Rd |only man/simdata.Rd | 71 + src/Makevars | 2 tests/testthat.R | 15 tests/testthat/fixtures |only tests/testthat/make-paraboot-baseline.R |only tests/testthat/test-carryover-rm-slot.R |only tests/testthat/test-cov-ar-parametric-boot.R |only tests/testthat/test-cv-parallel.R |only tests/testthat/test-estimand-aptt.R |only tests/testthat/test-estimand-att-cumu.R |only tests/testthat/test-estimand-att.R |only tests/testthat/test-estimand-deprecation.R |only tests/testthat/test-estimand-log-att.R |only tests/testthat/test-estimand-parametric.R |only tests/testthat/test-factors-from-refactor.R | 87 - tests/testthat/test-fect-basic.R | 6 tests/testthat/test-gsynth-r0-boot.R |only tests/testthat/test-imputed-outcomes.R |only tests/testthat/test-loading-bound-solver.R |only tests/testthat/test-loading-bound.R |only tests/testthat/test-modern-theme.R |only tests/testthat/test-paraboot-dispatcher.R |only tests/testthat/test-paraboot-parity.R |only tests/testthat/test-parallel-vector-form.R |only tests/testthat/test-parametric-notyet-gate.R |only tests/testthat/test-phase-a-future-state.R |only tests/testthat/test-rolling-cv-methods.R |only tests/testthat/test-rolling-via-dispatcher.R |only tests/testthat/test-rolling-window-cv.R |only tests/testthat/test-weights-consistency.R |only tests/testthat/test-yctfull-gsc.R |only 73 files changed, 2909 insertions(+), 1294 deletions(-)
Title: Evaluates Present Values and Health Economic Models with Dynamic
Pricing and Uptake
Description: The goal of 'dynamicpv' is to provide a simple way to calculate (net) present values and outputs from health economic models (especially cost-effectiveness and budget impact) in discrete time that reflect dynamic pricing and dynamic uptake. Dynamic pricing is also known as life cycle pricing; dynamic uptake is also known as multiple or stacked cohorts, or dynamic disease prevalence. Shafrin (2024) <doi:10.1515/fhep-2024-0014> provides an explanation of dynamic value elements, in the context of Generalized Cost Effectiveness Analysis, and Puls (2024) <doi:10.1016/j.jval.2024.03.006> reviews challenges of incorporating such dynamic value elements. This package aims to reduce those challenges.
Author: Dominic Muston [aut, cre] ,
John Blischak [ctb] ,
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph, fnd]
Maintainer: Dominic Muston <dom.muston@gmail.com>
Diff between dynamicpv versions 0.4.1 dated 2026-01-15 and 0.4.2 dated 2026-04-30
DESCRIPTION | 16 - MD5 | 18 - NEWS.md | 4 inst/doc/budget-impact-applications.R | 147 ++++++++-- inst/doc/budget-impact-applications.Rmd | 228 ++++++++++++---- inst/doc/budget-impact-applications.html | 429 +++++++++++++++++++++---------- inst/doc/math-framework.html | 8 man/dynamicpv-package.Rd | 2 vignettes/bibliography.bib | 3 vignettes/budget-impact-applications.Rmd | 228 ++++++++++++---- 10 files changed, 790 insertions(+), 293 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>
This is a re-admission after prior archival of version 3.0.3 dated 2026-02-08
Diff between camtrapR versions 3.0.3 dated 2026-02-08 and 3.0.4 dated 2026-04-30
camtrapR-3.0.3/camtrapR/man/dot-check_memory_usage.Rd |only camtrapR-3.0.4/camtrapR/DESCRIPTION | 8 camtrapR-3.0.4/camtrapR/MD5 | 278 camtrapR-3.0.4/camtrapR/NAMESPACE | 564 camtrapR-3.0.4/camtrapR/NEWS.md | 1085 camtrapR-3.0.4/camtrapR/R/OCRdataFields.R | 358 camtrapR-3.0.4/camtrapR/R/PPC.residuals.R | 1642 camtrapR-3.0.4/camtrapR/R/activityDensity.R | 416 camtrapR-3.0.4/camtrapR/R/activityHistogram.R | 428 camtrapR-3.0.4/camtrapR/R/activityOverlap.R | 544 camtrapR-3.0.4/camtrapR/R/activityRadial.R | 512 camtrapR-3.0.4/camtrapR/R/addCopyrightTag.R | 240 camtrapR-3.0.4/camtrapR/R/addToPath.R | 78 camtrapR-3.0.4/camtrapR/R/aggregateStations.R | 382 camtrapR-3.0.4/camtrapR/R/appendSpeciesNames.R | 588 camtrapR-3.0.4/camtrapR/R/cameraOperation.R | 1660 camtrapR-3.0.4/camtrapR/R/camtrapR-package.R | 728 camtrapR-3.0.4/camtrapR/R/checkSpeciesIdentification.R | 710 camtrapR-3.0.4/camtrapR/R/checkSpeciesNames.R | 418 camtrapR-3.0.4/camtrapR/R/communityModel.R | 5826 +- camtrapR-3.0.4/camtrapR/R/createCovariates.R | 1460 camtrapR-3.0.4/camtrapR/R/createSpeciesFolders.R | 284 camtrapR-3.0.4/camtrapR/R/createStationFolders.R | 220 camtrapR-3.0.4/camtrapR/R/detectionHistory.R | 1750 camtrapR-3.0.4/camtrapR/R/detectionMaps.R | 1098 camtrapR-3.0.4/camtrapR/R/exifTagNames.R | 324 camtrapR-3.0.4/camtrapR/R/filterRecordTable.R | 1036 camtrapR-3.0.4/camtrapR/R/fixDateTimeOriginal.R | 106 camtrapR-3.0.4/camtrapR/R/getSpeciesImages.R | 656 camtrapR-3.0.4/camtrapR/R/imageRename.R | 1080 camtrapR-3.0.4/camtrapR/R/onAttach.R | 84 camtrapR-3.0.4/camtrapR/R/plot.R | 1734 camtrapR-3.0.4/camtrapR/R/predict.R | 2068 camtrapR-3.0.4/camtrapR/R/readWildlifeInsights.R | 844 camtrapR-3.0.4/camtrapR/R/readcamtrapDP.R | 1460 camtrapR-3.0.4/camtrapR/R/recordTable.R | 1348 camtrapR-3.0.4/camtrapR/R/recordTableIndividual.R | 1272 camtrapR-3.0.4/camtrapR/R/spatialDetectionHistory.R | 1636 camtrapR-3.0.4/camtrapR/R/speciesAccum.R | 717 camtrapR-3.0.4/camtrapR/R/surveyDashboard.R |22939 +++++----- camtrapR-3.0.4/camtrapR/R/surveyReport.R | 1210 camtrapR-3.0.4/camtrapR/R/timeShiftImages.R | 466 camtrapR-3.0.4/camtrapR/R/variousOtherHelperFunctions.R | 4814 +- camtrapR-3.0.4/camtrapR/R/variousPlottingHelperFunctions.R | 542 camtrapR-3.0.4/camtrapR/R/writeDateTimeOriginal.R | 256 camtrapR-3.0.4/camtrapR/R/zzz.R | 36 camtrapR-3.0.4/camtrapR/README.md | 200 camtrapR-3.0.4/camtrapR/build/vignette.rds |binary camtrapR-3.0.4/camtrapR/inst/CITATION | 40 camtrapR-3.0.4/camtrapR/inst/dashboard_help/communityModels_help.html | 180 camtrapR-3.0.4/camtrapR/inst/dashboard_help/covariateCorrelation_help.html | 170 camtrapR-3.0.4/camtrapR/inst/dashboard_help/covariateExtraction_help.html | 148 camtrapR-3.0.4/camtrapR/inst/dashboard_help/detectionHistories_help.html | 184 camtrapR-3.0.4/camtrapR/inst/dashboard_help/goodnessOfFit_help.html | 160 camtrapR-3.0.4/camtrapR/inst/dashboard_help/singleSpeciesOccupancy_help.html | 262 camtrapR-3.0.4/camtrapR/inst/dashboard_help/speciesAccum_help.html | 232 camtrapR-3.0.4/camtrapR/inst/doc/camtrapr1.pdf.asis | 12 camtrapR-3.0.4/camtrapR/inst/doc/camtrapr2.pdf.asis | 12 camtrapR-3.0.4/camtrapR/inst/doc/camtrapr3.pdf.asis | 12 camtrapR-3.0.4/camtrapR/inst/doc/camtrapr4.pdf.asis | 12 camtrapR-3.0.4/camtrapR/inst/doc/camtrapr5.html |11426 ++-- camtrapR-3.0.4/camtrapR/inst/doc/camtrapr5.html.asis | 12 camtrapR-3.0.4/camtrapR/inst/pictures/full_size_for_ocr/StationA/mousedeer_detections.jpg |only camtrapR-3.0.4/camtrapR/man/OCRdataFields.Rd | 262 camtrapR-3.0.4/camtrapR/man/PPC.community.Rd | 408 camtrapR-3.0.4/camtrapR/man/PPC.residuals.Rd | 314 camtrapR-3.0.4/camtrapR/man/activityDensity.Rd | 242 camtrapR-3.0.4/camtrapR/man/activityHistogram.Rd | 212 camtrapR-3.0.4/camtrapR/man/activityOverlap.Rd | 318 camtrapR-3.0.4/camtrapR/man/activityRadial.Rd | 266 camtrapR-3.0.4/camtrapR/man/addCopyrightTag.Rd | 190 camtrapR-3.0.4/camtrapR/man/addToPath.Rd | 88 camtrapR-3.0.4/camtrapR/man/aggregateStations.Rd | 154 camtrapR-3.0.4/camtrapR/man/appendSpeciesNames.Rd | 178 camtrapR-3.0.4/camtrapR/man/cameraOperation.Rd | 450 camtrapR-3.0.4/camtrapR/man/camtrapR-package.Rd | 312 camtrapR-3.0.4/camtrapR/man/camtraps.Rd | 68 camtrapR-3.0.4/camtrapR/man/camtrapsMultiSeason.Rd | 144 camtrapR-3.0.4/camtrapR/man/checkSpeciesIdentification.Rd | 288 camtrapR-3.0.4/camtrapR/man/checkSpeciesNames.Rd | 172 camtrapR-3.0.4/camtrapR/man/commOccu-class.Rd | 98 camtrapR-3.0.4/camtrapR/man/communityModel.Rd | 584 camtrapR-3.0.4/camtrapR/man/createCovariates.Rd | 460 camtrapR-3.0.4/camtrapR/man/createSpeciesFolders.Rd | 184 camtrapR-3.0.4/camtrapR/man/createStationFolders.Rd | 128 camtrapR-3.0.4/camtrapR/man/detectionHistory.Rd | 674 camtrapR-3.0.4/camtrapR/man/detectionMaps.Rd | 348 camtrapR-3.0.4/camtrapR/man/exifTagNames.Rd | 192 camtrapR-3.0.4/camtrapR/man/filterRecordTable.Rd | 238 camtrapR-3.0.4/camtrapR/man/fit-commOccu-method.Rd | 112 camtrapR-3.0.4/camtrapR/man/fixDateTimeOriginal.Rd | 104 camtrapR-3.0.4/camtrapR/man/getSpeciesImages.Rd | 258 camtrapR-3.0.4/camtrapR/man/imageRename.Rd | 330 camtrapR-3.0.4/camtrapR/man/plot_coef-commOccu-method.Rd | 112 camtrapR-3.0.4/camtrapR/man/plot_effects-commOccu-method.Rd | 100 camtrapR-3.0.4/camtrapR/man/predict-commOccu-method.Rd | 106 camtrapR-3.0.4/camtrapR/man/readWildlifeInsights.Rd | 94 camtrapR-3.0.4/camtrapR/man/readcamtrapDP.Rd | 268 camtrapR-3.0.4/camtrapR/man/recordTable.Rd | 684 camtrapR-3.0.4/camtrapR/man/recordTableIndividual.Rd | 562 camtrapR-3.0.4/camtrapR/man/recordTableIndividualSample.Rd | 78 camtrapR-3.0.4/camtrapR/man/recordTableIndividualSampleMultiSeason.Rd | 98 camtrapR-3.0.4/camtrapR/man/recordTableSample.Rd | 66 camtrapR-3.0.4/camtrapR/man/recordTableSampleMultiSeason.Rd | 94 camtrapR-3.0.4/camtrapR/man/spatialDetectionHistory.Rd | 606 camtrapR-3.0.4/camtrapR/man/speciesAccum.Rd | 284 camtrapR-3.0.4/camtrapR/man/summary-commOccu-method.Rd | 44 camtrapR-3.0.4/camtrapR/man/surveyDashboard.Rd | 346 camtrapR-3.0.4/camtrapR/man/surveyReport.Rd | 432 camtrapR-3.0.4/camtrapR/man/timeShiftImages.Rd | 292 camtrapR-3.0.4/camtrapR/man/timeShiftTable.Rd | 48 camtrapR-3.0.4/camtrapR/man/writeDateTimeOriginal.Rd | 226 camtrapR-3.0.4/camtrapR/tests/test-all.R | 10 camtrapR-3.0.4/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/datapackage.json | 548 camtrapR-3.0.4/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/deployments.csv | 10 camtrapR-3.0.4/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/media.csv | 848 camtrapR-3.0.4/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/observations.csv | 1100 camtrapR-3.0.4/camtrapR/tests/testthat/test-activity_plots.R | 420 camtrapR-3.0.4/camtrapR/tests/testthat/test-checkSpeciesIdentification.R | 498 camtrapR-3.0.4/camtrapR/tests/testthat/test-checkSpeciesNames.R | 434 camtrapR-3.0.4/camtrapR/tests/testthat/test-communityModels.R | 1129 camtrapR-3.0.4/camtrapR/tests/testthat/test-detectionMaps.R | 396 camtrapR-3.0.4/camtrapR/tests/testthat/test-filterRecordTable.R | 280 camtrapR-3.0.4/camtrapR/tests/testthat/test-image_management_functions.R | 744 camtrapR-3.0.4/camtrapR/tests/testthat/test-readWildlifeInsights.R | 462 camtrapR-3.0.4/camtrapR/tests/testthat/test-readcamtrapDP.R | 462 camtrapR-3.0.4/camtrapR/tests/testthat/test-recordTableIndividual.R | 370 camtrapR-3.0.4/camtrapR/tests/testthat/test-spatialDetectionHistory.R | 466 camtrapR-3.0.4/camtrapR/tests/testthat/test-speciesAccum.R | 426 camtrapR-3.0.4/camtrapR/tests/testthat/test-surveyDashboard.R | 128 camtrapR-3.0.4/camtrapR/tests/testthat/test-surveyReport.R | 620 camtrapR-3.0.4/camtrapR/tests/testthat/test_cameraOperation.R | 602 camtrapR-3.0.4/camtrapR/tests/testthat/test_createCovariates.R | 442 camtrapR-3.0.4/camtrapR/tests/testthat/test_detectionHistory.R | 892 camtrapR-3.0.4/camtrapR/tests/testthat/test_imageRename.R | 32 camtrapR-3.0.4/camtrapR/tests/testthat/test_recordTable.R | 284 camtrapR-3.0.4/camtrapR/vignettes/camtrapr1.pdf.asis | 12 camtrapR-3.0.4/camtrapR/vignettes/camtrapr2.pdf.asis | 12 camtrapR-3.0.4/camtrapR/vignettes/camtrapr3.pdf.asis | 12 camtrapR-3.0.4/camtrapR/vignettes/camtrapr4.pdf.asis | 12 camtrapR-3.0.4/camtrapR/vignettes/camtrapr5.html.asis | 12 141 files changed, 51493 insertions(+), 51453 deletions(-)
Title: Case-Cotrol Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas [aut],
Livia Tran [aut],
Steve Mack [aut, cre],
Jill Hollenbach [aut]
Maintainer: Steve Mack <Steven.Mack@ucsf.edu>
This is a re-admission after prior archival of version 3.0.3 dated 2021-11-17
Diff between BIGDAWG versions 3.0.3 dated 2021-11-17 and 3.1.0 dated 2026-04-30
DESCRIPTION | 28 - MD5 | 78 +- NAMESPACE | 10 NEWS | 584 +++++++++++----------- R/A.R | 424 ++++++++-------- R/A_ExonPtnAlign_functions.R | 576 ++++++++++------------ R/A_support_functions.R | 518 +++++++++---------- R/A_wrapper.R | 223 ++++---- R/BIGDAWG.R | 1103 +++++++++++++++++++++--------------------- R/DRB_Parser.R | 362 ++++++------- R/ErrLog.R | 132 ++--- R/GL2TAB.R | 296 +++++------ R/GLSconvert.R | 124 ++-- R/HWE.R | 48 - R/HWE_support_functions.R | 418 ++++++++-------- R/HWE_wrapper.R | 62 +- R/H_MC.R | 286 +++++----- R/H_support_functions.R | 118 ++-- R/H_wrapper_MC.R | 320 ++++++------ R/L.R | 324 ++++++------ R/L_wrapper.R | 128 ++-- R/TAB2GL.R | 292 +++++------ R/check_functions.R | 948 ++++++++++++++++++------------------ R/data.R | 26 R/general_functions.R | 750 ++++++++++++++-------------- R/stat_functions.R | 1054 ++++++++++++++++++++-------------------- R/sysdata.rda |binary R/update_wrapper.R | 231 ++++---- build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 596 +++++++++++----------- inst/doc/BIGDAWG.html | 1120 ++++++++++++++++++++++++++++++------------- inst/doc/GLSconvert.Rmd | 275 +++++----- inst/doc/GLSconvert.html | 702 +++++++++++++++++++------- man/BIGDAWG.Rd | 8 man/L.Rd | 2 man/cci.Rd | 6 man/cci.pval.list.Rd | 4 man/prepData.Rd | 6 vignettes/BIGDAWG.Rmd | 596 +++++++++++----------- vignettes/GLSconvert.Rmd | 275 +++++----- 40 files changed, 6955 insertions(+), 6098 deletions(-)
Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including:
- bivariate generalized linear mixed models for synthesizing odds ratios, relative risks,
and risk differences
(Chu et al., 2012 <doi:10.1177/0962280210393712>)
- tests and measures for between-study heterogeneity
(Lin et al., 2017 <doi:10.1111/biom.12543>;
Wang et al., 2022 <doi:10.1002/sim.9261>;
Yu et al., 2025 <doi:10.1186/s12874-025-02719-7>);
- measures, tests, and visualization tools for publication bias or small-study effects
(Lin and Chu, 2018 <doi:10.1111/biom.12817>;
Lin, 2019 <doi:10.1002/jrsm.1340>;
Lin, 2020 <doi:10.1177/0962280220910172>;
Shi et al., 2020 <doi:10.1002/jrsm.1415>);
- meta-analysis of combining standardized mean differences and odds ratios
(Jing et al., 2023 <doi:10.1080/10543406.2022.2105345>);
- meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.
(Reitsma et al., 2005 <doi:10.1016/j.jclinepi.200 [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Yaqi Jing [ctb],
Kristine J. Rosenberger [ctb],
Linyu Shi [ctb],
Yipeng Wang [ctb],
Xing Xing [ctb] ,
Zhiyuan Yu [ctb],
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between altmeta versions 4.3 dated 2025-10-13 and 4.3.1 dated 2026-04-30
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 1 + build/partial.rdb |binary man/metahet.Rd | 4 +++- man/metahet.hybrid.Rd | 5 +++++ 6 files changed, 20 insertions(+), 11 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing two major classes of shrinkage priors
(the spike-and-slab priors and the horseshoe family of priors) leads to efficient Bayesian
shrinkage estimation, variable selection and valid statistical inference. In this package,
we have implemented robust Bayesian variable selection with spike-and-slab priors under
high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models with spike-and-slab priors include
robust Bayesian group LASSO and robust binary Bayesian LASSO (Fan and Wu (2025)
<doi:10.1002/sta4.70078>). Besides, robust sparse Bayesian regression with the horseshoe
family of (hor [...truncated...]
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.2.1 dated 2026-03-14 and 1.2.2 dated 2026-04-30
DESCRIPTION | 8 MD5 | 100 +++++------ NAMESPACE | 24 +- NEWS.md | 4 R/NonRobust.R | 150 ++++++++--------- R/NonRobust_vc.R | 157 ++++++++---------- R/RcppExports.R | 16 - R/Robust_vc.R | 171 +++++++++---------- R/coverage.R | 95 ++++++----- R/coverage_lin.R | 22 +- R/coverage_vc.R | 88 +++++----- R/data.R | 148 ++++++++--------- R/estimation.R | 101 ++++++----- R/estimation_lin.R | 24 +- R/estimation_vc.R | 126 +++++++------- R/nonrobust_bin.R | 81 ++++----- R/nonrobust_g.R | 87 ++++------ R/nonrobust_lin.R | 122 +++++++------- R/pqrBayes-package.R | 136 +++++++-------- R/pqrBayes.R | 388 +++++++++++++++++++++++---------------------- R/pqrBayes_bin.R | 75 +++----- R/pqrBayes_g.R | 49 ++--- R/pqrBayes_lin.R | 74 +++----- R/pqrBayes_vc.R | 56 ++---- R/predict.pqrBayes.R | 129 ++++++++------ R/predict_bin.R | 106 ++++++------ R/predict_lin.R | 68 +++---- R/predict_lin_nonrobust.R | 112 ++++++------ R/predict_lin_robust.R | 114 ++++++------- R/predict_vc.R | 68 +++---- R/predict_vc_nonrobust.R | 148 ++++++++--------- R/predict_vc_robust.R | 148 ++++++++--------- R/print.pqrBayes.R | 106 ++++++------ R/robust_bin.R | 89 ++++------ R/robust_g.R | 98 +++++------ R/robust_lin.R | 130 +++++++-------- R/select.pqrBayes.R | 162 +++++++++--------- R/select_lin.R | 76 ++++---- R/select_vc.R | 88 +++++----- README.md | 24 +- man/coverage.Rd | 6 man/estimation.pqrBayes.Rd | 6 man/pqrBayes.Rd | 62 ++----- man/predict_pqrBayes.Rd | 8 man/select.pqrBayes.Rd | 20 -- src/BBL.cpp | 22 -- src/BBLSS.cpp | 25 +- src/BRBL.cpp | 26 +-- src/BRBLSS.cpp | 25 +- src/BVCUtilities.cpp | 34 +-- src/RcppExports.cpp | 36 +--- 51 files changed, 2088 insertions(+), 2150 deletions(-)
Title: Spatial Null Models and Transforms for Brain Map Comparison
Description: Implements spatial null models and coordinate-space
transformations for statistical comparison of brain maps, following the
framework described in Markello et al. (2022)
<doi:10.1038/s41592-022-01625-w>. Provides variogram-matching
surrogates (Burt et al. 2020), Moran spectral randomization (Wagner &
Dray 2015), and spin-based permutation tests (Alexander-Bloch et al.
2018). Includes an R interface to the 'neuromaps' annotation registry
for browsing, downloading, and comparing brain map annotations from the
Open Science Framework ('OSF').
Integrates with 'ciftiTools' for coordinate-space transforms.
Author: Athanasia Mo Mowinckel [aut, cre, cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between neuromapr versions 0.2.1 dated 2026-02-27 and 0.2.2 dated 2026-04-30
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 12 ++++++++++++ README.md | 11 +++++------ inst/doc/neuromapr.html | 13 ++++++------- inst/doc/null-models.html | 4 ++-- inst/doc/rotation-methods.html | 2 +- inst/doc/surface-geometry.html | 6 +++--- tests/testthat/test-nulls-moran.R | 2 +- tests/testthat/test-nulls-spin.R | 6 +++--- tests/testthat/test-nulls-variogram.R | 2 +- 11 files changed, 47 insertions(+), 37 deletions(-)
Title: Methods and Reproducible Workflows for Partial Least Squares
with Missing Data
Description: Methods-first tooling for reproducing and extending the
partial least squares regression studies on incomplete data described in
Nengsih et al. (2019) <doi:10.1515/sagmb-2018-0059>. The package
provides simulation helpers, missingness generators, imputation wrappers,
component-selection utilities, real-data diagnostics, and reproducible
study orchestration for Nonlinear Iterative Partial Least Squares (NIPALS)-Partial
Least Squares (PLS) workflows.
Author: Titin Agustin Nengsih [aut],
Frederic Bertrand [aut, cre],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between missPLS versions 0.2.0 dated 2026-04-13 and 0.2.1 dated 2026-04-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 15 +++++++++++++++ inst/doc/missPLS.html | 12 ++++++------ tests/testthat/test-selection.R | 10 ++++++++-- 5 files changed, 36 insertions(+), 15 deletions(-)
Title: Greedy Experimental Design Construction
Description: Computes experimental designs for two-arm experiments with
covariates using multiple methods, including: (0) complete randomization
and randomization with forced-balance; (1) greedy optimization of a balance
objective function via pairwise switching; (2) numerical optimization via
'gurobi'; (3) rerandomization; (4) Karp's method for one covariate; (5)
exhaustive enumeration for small sample sizes; (6) binary pair matching
using 'nbpMatching'; (7) binary pair matching plus method (1) to further
optimize balance; (8) binary pair matching plus method (3) to further
optimize balance; (9) Hadamard designs; and (10) simultaneous multiple
kernels. For the greedy, rerandomization, and related methods, three
objective functions are supported: Mahalanobis distance, standardized sums
of absolute differences, and kernel distances via the 'kernlab' library.
This package is the result of a stream of research that can be found in
Krieger, A. M., Azriel, D. A., and Kapelner, A. (2019). "Nearly Random
[...truncated...]
Author: Adam Kapelner [aut, cre] ,
David Azriel [aut],
Abba Krieger [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between GreedyExperimentalDesign versions 1.6 dated 2026-01-09 and 1.6.1 dated 2026-04-30
CHANGELOG | 12 DESCRIPTION | 12 MD5 | 76 +- NAMESPACE | 9 R/GreedyExperimentalDesign.R | 1 R/RcppExports.R | 36 + R/binary_match_search.R | 7 R/gpu_backend.R |only R/greedy_multiple_kernel_search.R | 482 ++++++-------- R/greedy_search.R | 4 R/karp_search.R | 4 R/optimal_search.R | 4 R/rerandomization_search.R | 4 R/shared.R | 31 R/zzz.R | 46 + cleanup |only configure |only configure.win |only inst/java/GreedyExperimentalDesign.jar |binary man/compute_distance_matrix_gpu.Rd |only man/compute_kernel_matrix_gpu.Rd |only man/compute_multiple_kernel_objective_vals_gpu.Rd |only man/compute_objective_vals_gpu.Rd |only man/compute_randomization_metrics_gpu.Rd |only man/full_greedy_search_gpu.Rd |only man/ged_gpu_available.Rd |only man/ged_gpu_devices.Rd |only man/initGreedyMultipleKernelExperimentalDesignObject.Rd | 98 +- man/plot.greedy_multiple_kernel_experimental_design.Rd | 7 man/print.greedy_multiple_kernel_experimental_design.Rd | 4 man/resultsMultipleKernelGreedySearch.Rd | 40 - man/summary.greedy_multiple_kernel_experimental_design.Rd | 2 src/Makevars.in |only src/Makevars.win.in |only src/RcppExports.cpp | 124 +++ src/fast_shuffle.cpp | 4 src/ged_gpu_config.h |only src/ged_native_backend.cpp |only src/ged_native_backend.h |only src/ged_wgpu_backend.cpp |only src/gpu_backend_exports.cpp |only src/kernel_matrix.cpp | 8 src/objective_and_standardize.cpp | 1 src/objective_batch.cpp | 1 tests/testthat.R | 2 tests/testthat/ged-failures.log | 2 tests/testthat/helper-package.R | 2 tests/testthat/test-multiple-kernel-results.R |only tests/testthat/test-suite.R | 3 49 files changed, 641 insertions(+), 385 deletions(-)
More information about GreedyExperimentalDesign at CRAN
Permanent link
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Winston Chang [aut],
Jennifer Bryan [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between devtools versions 2.5.1 dated 2026-04-16 and 2.5.2 dated 2026-04-30
DESCRIPTION | 12 ++++++------ MD5 | 17 ++++++++++------- NEWS.md | 4 ++++ R/install.R | 2 ++ R/session-info.R | 4 +++- build/vignette.rds |binary man/install.Rd | 2 +- tests/testthat/test-install.R | 16 ++++++++++++++++ tests/testthat/testInstallWithDeps |only 9 files changed, 42 insertions(+), 15 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It works with data from a Freesurfer analysis (cortical thickness,
volumes, local gyrification index, surface area), diffusion tensor
tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from
DPABI). It contains a graphical user interface for graph visualization and
data exploration, along with several functions for generating useful
figures.
Author: Christopher G. Watson [aut, cre]
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 3.1.1 dated 2025-10-16 and 3.1.2 dated 2026-04-30
DESCRIPTION | 8 +++---- MD5 | 52 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 - NEWS.md | 7 ++++++ R/glm_stats.R | 6 ++--- R/sysdata.rda |binary build/partial.rdb |binary data/aal116.rda |binary data/aal2.120.rda |binary data/aal2.94.rda |binary data/aal90.rda |binary data/brainnetome.rda |binary data/brainsuite.rda |binary data/craddock200.rda |binary data/destrieux.rda |binary data/destrieux.scgm.rda |binary data/dk.rda |binary data/dk.scgm.rda |binary data/dkt.rda |binary data/dkt.scgm.rda |binary data/dosenbach160.rda |binary data/gordon333.rda |binary data/hcp_mmp1.0.rda |binary data/hoa112.rda |binary data/lpba40.rda |binary data/power264.rda |binary man/glm_influence.Rd | 6 ++--- 27 files changed, 44 insertions(+), 37 deletions(-)
Title: Tools for Accessing the Botanical Information and Ecology
Network Database
Description: Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
Author: Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between BIEN versions 1.2.7 dated 2025-01-31 and 1.2.8 dated 2026-04-30
DESCRIPTION | 10 MD5 | 221 +++++------ NEWS | 22 + R/BIEN.R | 132 +++++- R/BIEN_sql.R | 27 - R/internals.R | 6 README.md | 2 build/vignette.rds |binary inst/doc/BIEN.html | 4 inst/doc/BIEN_tutorial.R | 15 inst/doc/BIEN_tutorial.Rmd | 15 inst/doc/BIEN_tutorial.html | 24 - man/BIEN.Rd | 44 +- man/BIEN_list_all.Rd | 58 +- man/BIEN_list_country.Rd | 96 ++-- man/BIEN_list_county.Rd | 130 +++--- man/BIEN_list_sf.Rd | 86 ++-- man/BIEN_list_state.Rd | 108 ++--- man/BIEN_metadata_citation.Rd | 100 ++--- man/BIEN_metadata_data_dictionaries.Rd | 72 +-- man/BIEN_metadata_database_version.Rd | 62 +-- man/BIEN_metadata_list_political_names.Rd | 68 +-- man/BIEN_metadata_match_data.Rd | 82 ++-- man/BIEN_occurrence_box.Rd | 168 ++++---- man/BIEN_occurrence_country.Rd | 150 +++---- man/BIEN_occurrence_county.Rd | 176 ++++---- man/BIEN_occurrence_family.Rd | 140 +++---- man/BIEN_occurrence_genus.Rd | 136 +++--- man/BIEN_occurrence_records_per_species.Rd | 70 +-- man/BIEN_occurrence_sf.Rd | 159 ++++---- man/BIEN_occurrence_species.Rd | 142 +++---- man/BIEN_occurrence_state.Rd | 160 ++++---- man/BIEN_phylogeny_complete.Rd | 74 +-- man/BIEN_phylogeny_conservative.Rd | 60 +-- man/BIEN_phylogeny_label_nodes.Rd | 124 +++--- man/BIEN_plot_country.Rd | 144 +++---- man/BIEN_plot_dataset.Rd | 136 +++--- man/BIEN_plot_datasource.Rd | 132 +++--- man/BIEN_plot_list_datasource.Rd | 68 +-- man/BIEN_plot_list_sampling_protocols.Rd | 68 +-- man/BIEN_plot_metadata.Rd | 86 ++-- man/BIEN_plot_name.Rd | 136 +++--- man/BIEN_plot_sampling_protocol.Rd | 132 +++--- man/BIEN_plot_sf.Rd | 148 +++---- man/BIEN_plot_state.Rd | 160 ++++---- man/BIEN_ranges_box.Rd | 136 +++--- man/BIEN_ranges_genus.Rd | 182 ++++----- man/BIEN_ranges_intersect_species.Rd | 124 +++--- man/BIEN_ranges_list.Rd | 86 ++-- man/BIEN_ranges_load_species.Rd | 92 ++-- man/BIEN_ranges_sf.Rd | 144 +++---- man/BIEN_ranges_shapefile_to_skinny.Rd | 90 ++-- man/BIEN_ranges_skinny_ranges_to_richness_raster.Rd | 108 ++--- man/BIEN_ranges_species.Rd | 160 ++++---- man/BIEN_ranges_species_bulk.Rd | 106 ++--- man/BIEN_stem_datasource.Rd | 130 +++--- man/BIEN_stem_family.Rd | 132 +++--- man/BIEN_stem_genus.Rd | 132 +++--- man/BIEN_stem_sampling_protocol.Rd | 122 +++--- man/BIEN_stem_species.Rd | 132 +++--- man/BIEN_taxonomy_family.Rd | 62 +-- man/BIEN_taxonomy_genus.Rd | 62 +-- man/BIEN_taxonomy_species.Rd | 62 +-- man/BIEN_trait_country.Rd | 106 ++--- man/BIEN_trait_family.Rd | 102 ++--- man/BIEN_trait_genus.Rd | 102 ++--- man/BIEN_trait_list.Rd | 70 +-- man/BIEN_trait_mean.Rd | 84 ++-- man/BIEN_trait_species.Rd | 102 ++--- man/BIEN_trait_trait.Rd | 108 ++--- man/BIEN_trait_traitbyfamily.Rd | 116 ++--- man/BIEN_trait_traitbygenus.Rd | 116 ++--- man/BIEN_trait_traitbyspecies.Rd | 116 ++--- man/BIEN_trait_traits_per_species.Rd | 74 +-- man/dot-collection_check.Rd | 24 - man/dot-collection_check_plot.Rd | 24 - man/dot-collection_check_stem.Rd | 24 - man/dot-cultivated_check.Rd | 24 - man/dot-cultivated_check_plot.Rd | 24 - man/dot-cultivated_check_stem.Rd | 24 - man/dot-genus_check.Rd | 30 - man/dot-geovalid_check.Rd | 24 - man/dot-is_char.Rd | 32 - man/dot-is_log.Rd | 32 - man/dot-is_log_or_null.Rd | 32 - man/dot-is_num.Rd | 32 - man/dot-md_check_plot.Rd | 24 - man/dot-md_check_stem.Rd | 24 - man/dot-native_check.Rd | 24 - man/dot-native_check_plot.Rd | 24 - man/dot-native_check_stem.Rd | 24 - man/dot-natives_check.Rd | 24 - man/dot-natives_check_plot.Rd | 24 - man/dot-natives_check_stem.Rd | 24 - man/dot-newworld_check.Rd | 24 - man/dot-newworld_check_plot.Rd | 24 - man/dot-newworld_check_stem.Rd | 24 - man/dot-observation_check.Rd | 24 - man/dot-political_check.Rd | 24 - man/dot-political_check_plot.Rd | 24 - man/dot-political_check_stem.Rd | 24 - man/dot-political_check_traits.Rd | 24 - man/dot-source_check_traits.Rd | 24 - man/dot-species_check.Rd | 30 - man/dot-taxonomy_check.Rd | 24 - man/dot-taxonomy_check_plot.Rd | 24 - man/dot-taxonomy_check_stem.Rd | 24 - man/dot-taxonomy_check_traits.Rd | 24 - man/dot-vfoi_check_stem.Rd | 24 - tests/testthat/helper-bien.R |only tests/testthat/test-BIEN.r | 395 +++++++++----------- vignettes/BIEN_tutorial.Rmd | 15 112 files changed, 4365 insertions(+), 4240 deletions(-)
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to fourth-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of the package can be found in Puy et al. (2022) <doi:10.18637/jss.v102.i05>.
Author: Arnald Puy [aut, cre] ,
Bertrand Ioos [ctb] ,
Gilles Pujol [ctb] ,
RStudio [cph]
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 1.1.8 dated 2026-04-05 and 1.1.9 dated 2026-04-30
DESCRIPTION | 8 - MD5 | 30 +++---- NAMESPACE | 1 NEWS.md | 18 ++++ R/sobol_convergence.R | 5 - R/sobol_indices.R | 71 ++++++++++++----- R/sobol_matrices.R | 141 ++++++++++++++++++++++++++++------- build/partial.rdb |binary inst/doc/sensobol.pdf |binary man/load_packages.Rd | 6 - man/sensobol-package.Rd | 2 man/sobol_convergence.Rd | 20 ++++ man/sobol_indices.Rd | 26 +++++- man/sobol_matrices.Rd | 36 ++++++++ tests/testthat/test-sobol_boot.R | 56 +++++++++++++ tests/testthat/test-sobol_matrices.R | 126 +++++++++++++++++++++++++++++++ 16 files changed, 468 insertions(+), 78 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 1.0.18 dated 2026-03-28 and 1.0.19 dated 2026-04-30
DESCRIPTION | 8 ++-- MD5 | 12 +++--- R/print_partable.R | 29 +++++++++++---- R/utils.R | 6 +-- inst/doc/customize_plot_interactions.html | 2 - inst/doc/observed_lms_qml.html | 55 ++++++++++++++---------------- inst/doc/plot_interactions.html | 2 - 7 files changed, 63 insertions(+), 51 deletions(-)
Title: Kernel-Based Regularized Least Squares
Description: Implements Kernel-based Regularized Least Squares (KRLS), a
machine learning method to fit multidimensional functions y = f(x) for
regression and classification problems without relying on linearity or
additivity assumptions. KRLS finds the best fitting function by
minimizing the squared loss of a Tikhonov regularization problem,
using Gaussian kernels as radial basis functions. For further details
see Hainmueller and Hazlett (2014, <doi:10.1093/pan/mpt019>).
Author: Jens Hainmueller [aut, cre],
Chad Hazlett [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between KRLS versions 1.0-0 dated 2017-07-10 and 1.1-0 dated 2026-04-30
DESCRIPTION | 32 +++++++++++++----- MD5 | 25 +++++++++----- NAMESPACE | 19 +++++++---- NEWS.md |only R/krls.R | 95 +++++++++++++++++-------------------------------------- R/lambdasearch.r | 20 +++++------ R/plot.krls.R | 6 +-- R/predict.krls.R | 18 ++++------ R/solveforc.R | 46 +++++++++++++------------- R/summary.krls.R | 6 +-- man/krls.Rd | 5 ++ tests |only 12 files changed, 130 insertions(+), 142 deletions(-)
Title: Core Tools for Packages in the 'fable' Framework
Description: Provides tools, helpers and data structures for
developing models and time series functions for 'fable' and extension
packages. These tools support a consistent and tidy interface for time
series modelling and analysis.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Rob Hyndman [aut],
Earo Wang [aut] ,
Di Cook [ctb],
George Athanasopoulos [ctb],
David Holt [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fabletools versions 0.6.1 dated 2026-02-16 and 0.7.0 dated 2026-04-30
DESCRIPTION | 11 +++-- MD5 | 68 ++++++++++++++++++---------------- NAMESPACE | 24 +++++++++++- NEWS.md | 16 ++++++++ R/00_factory.R |only R/broom.R | 48 +++++++++++++++++++----- R/coherent.R |only R/dplyr-mable.R | 11 ++++- R/fitted.R | 16 ++++++-- R/forecast.R | 5 ++ R/generate.R | 4 +- R/lst_mdl.R | 16 +++++--- R/mable.R | 12 ++++-- R/model_combination.R | 6 ++- R/model_null.R | 2 - R/reconciliation.R | 45 +++++++++++++--------- R/refit.R | 4 +- R/stream.R | 4 +- R/zzz.R | 2 - build/stage23.rdb |binary man/augment.Rd | 3 + man/autoplot.dcmp_ts.Rd | 2 - man/autoplot.tbl_ts.Rd | 2 - man/coherent_cmat.Rd |only man/coherent_smat.Rd |only man/common_xregs.Rd | 2 - man/directional_accuracy_measures.Rd | 5 -- man/distribution_accuracy_measures.Rd | 5 -- man/fabletools-package.Rd | 1 man/features.Rd | 2 - man/glance.Rd | 3 + man/interval_accuracy_measures.Rd | 5 -- man/mable.Rd | 2 - man/point_accuracy_measures.Rd | 5 -- man/reexports.Rd | 10 ++--- man/tidy.Rd | 10 ++++- man/unpack_hilo.Rd | 2 - 37 files changed, 227 insertions(+), 126 deletions(-)
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre],
Silvia Grieder [aut],
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb],
Johan Braeken [ctb],
Andreas Soteriad [...truncated...]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.6.1 dated 2025-07-30 and 0.7.0 dated 2026-04-30
DESCRIPTION | 16 MD5 | 114 - NAMESPACE | 10 NEWS.md | 27 R/EFA.R | 317 +++ R/EFA_AVERAGE.R | 2 R/EFA_POOLED.R |only R/EKC.R | 2 R/MAP.R |only R/ML.R | 1 R/N_FACTORS.R | 29 R/OMEGA_helper.R | 4 R/PAF.R | 1 R/PARALLEL.R | 12 R/PROCRUSTES.R |only R/PROMAX.R | 2 R/ROTATE_OBLQ.R | 2 R/RcppExports.R | 69 R/ULS.R | 3 R/helper.R | 1079 ++++++++++++ R/print.EFA.R | 2261 +++++++++++++++++++++++--- R/print.LOADINGS.R | 651 ++++++- R/print.MAP.R |only R/print.N_FACTORS.R | 34 R/residuals.EFA.R |only README.md | 35 build/vignette.rds |binary inst/doc/EFAtools.html | 1486 ++++++++++------- inst/doc/Replicate_SPSS_psych.html | 139 - man/CONSENSUS_PROCRUSTES.Rd |only man/EFA.Rd | 18 man/EFA_AVERAGE.Rd | 2 man/EFA_POOLED.Rd |only man/EFAtools-package.Rd | 1 man/MAP.Rd |only man/N_FACTORS.Rd | 4 man/PROCRUSTES.Rd |only man/dot-average_matrices.Rd |only man/dot-calc_cis.Rd |only man/dot-change_class.Rd |only man/dot-consensus_loss.Rd |only man/dot-consensus_target_procrustes_single.Rd |only man/dot-extract_list_object.Rd |only man/dot-hyperplane_count.Rd |only man/dot-numformat.Rd | 5 man/dot-oblique_procrustes.Rd |only man/dot-orthogonal_procrustes.Rd |only man/dot-stat_over_list.Rd |only man/dot-tucker_congruence.Rd |only man/figures/README-unnamed-chunk-5-1.png |binary man/print.EFA.Rd | 184 ++ man/print.LOADINGS.Rd | 75 man/print.MAP.Rd |only man/residuals.EFA.Rd |only src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 24 src/factor_corres.cpp | 177 +- src/oblique_procrustes.cpp |only tests/testthat/test-EFA.R | 45 tests/testthat/test-EFA_AVERAGE.R | 43 tests/testthat/test-ML.R | 6 tests/testthat/test-N_FACTORS.R | 3 tests/testthat/test-PAF.R | 32 tests/testthat/test-PROCRUSTES.R |only tests/testthat/test-PROMAX.R | 2 tests/testthat/test-ROTATE_OBLQ.R | 12 tests/testthat/test-SL.R | 8 tests/testthat/test-ULS.R | 8 tests/testthat/test-helper.R | 8 70 files changed, 5773 insertions(+), 1182 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.4 dated 2026-03-11 and 7.5 dated 2026-04-30
DESCRIPTION | 8 +-- MD5 | 33 ++++++++------- R/gcpc.mle.R | 6 +- R/gcpc.mle2.R |only R/spher.esag.contour.R | 95 +++++++++++++++++++++++++-------------------- R/spher.kent.contour.R | 65 ++++++++++++++++++------------ R/spher.mixvmf.contour.R | 64 +++++++++++++++++------------- R/spher.pkbd.contour.R | 57 ++++++++++++++++++--------- R/spher.purka.contour.R | 65 ++++++++++++++++++------------ R/spher.sespc.contour.R | 69 +++++++++++++++++++------------- R/spher.spcauchy.contour.R | 59 +++++++++++++++------------ R/spher.vmf.contour.R | 59 +++++++++++++++------------ man/Directional-package.Rd | 4 - man/dsespc.Rd | 3 - man/sespc.mle.Rd | 2 man/spml.mle.Rd | 11 ++++- man/spml.reg.Rd | 13 ++++-- man/vmf.mle.Rd | 3 - 18 files changed, 366 insertions(+), 250 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre] ,
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb],
Stephen Roecker [aut, ctb],
David Rossiter [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.3.1 dated 2026-03-20 and 2.3.2 dated 2026-04-30
DESCRIPTION | 6 MD5 | 73 ++++++------ NAMESPACE | 1 NEWS.md | 12 + R/AAAA.R | 5 R/colorChart.R | 2 R/colorContrast.R | 27 ++++ R/colorVariation.R | 9 - R/contrastChart.R | 2 R/equivalentMunsellChips.R | 8 - R/estimateSoilColor.R | 50 +++++--- R/formatMunsell.R |only R/launderMunsell.R | 57 +++++++-- R/mixMunsell.R | 2 R/simulateColor.R | 2 R/soilColorIndices.R | 2 R/soilColorSignature.R | 2 R/validateMunsell.R | 2 data/munsell.rda |binary data/munsell.spectra.rda |binary data/munsell.spectra.wide.rda |binary inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 68 +++++------ inst/doc/Munsell-color-conversion.R | 4 inst/doc/Munsell-color-conversion.Rmd | 13 +- inst/doc/Munsell-color-conversion.html | 16 +- inst/doc/label-placement.html | 12 - man/colorChart.Rd | 2 man/equivalentMunsellChips.Rd | 2 man/formatMunsell.Rd |only man/horizonColorIndices.Rd | 2 man/launderMunsell.Rd | 38 +++++- man/soilColorSignature.Rd | 2 man/validateMunsell.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-color-conversion.R | 28 ++-- tests/testthat/test-color-signature.R | 6 tests/testthat/test-formatMunsell.R |only tests/testthat/test-spec2Munsell.R | 2 vignettes/Munsell-color-conversion.Rmd | 13 +- 39 files changed, 309 insertions(+), 163 deletions(-)
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.6.1 dated 2026-01-27 and 1.6.2 dated 2026-04-29
saros-1.6.1/saros/R/deprecated.R |only saros-1.6.1/saros/R/make_content.cat_freq_plot_docx.R |only saros-1.6.1/saros/R/make_content.cat_prop_plot_docx.R |only saros-1.6.1/saros/R/tabular_read.R |only saros-1.6.1/saros/R/tabular_write.R |only saros-1.6.1/saros/man/embed_cat_prop_plot.Rd |only saros-1.6.1/saros/man/embed_cat_table.Rd |only saros-1.6.1/saros/man/embed_chr_table_html.Rd |only saros-1.6.1/saros/man/filter_crowd_data.Rd |only saros-1.6.1/saros/man/generate_crowd_output.Rd |only saros-1.6.1/saros/man/handle_crowd_columns.Rd |only saros-1.6.1/saros/man/n_rng2.Rd |only saros-1.6.1/saros/man/summarize_data_by_type.Rd |only saros-1.6.1/saros/man/tabular_read.Rd |only saros-1.6.1/saros/man/tabular_write.Rd |only saros-1.6.1/saros/tests/testthat/test-tabular-read.R |only saros-1.6.1/saros/tests/testthat/test-tabular-write.R |only saros-1.6.2/saros/DESCRIPTION | 16 saros-1.6.2/saros/MD5 | 247 +++- saros-1.6.2/saros/NAMESPACE | 29 saros-1.6.2/saros/NEWS.md | 57 + saros-1.6.2/saros/R/check_quarto_website_index.R |only saros-1.6.2/saros/R/checks.R | 263 ++++- saros-1.6.2/saros/R/colour.R | 2 saros-1.6.2/saros/R/crowd_output.R |only saros-1.6.2/saros/R/crowd_plots_as_docx.R |only saros-1.6.2/saros/R/crowd_plots_as_officer.R |only saros-1.6.2/saros/R/crowd_plots_as_tabset.R | 45 saros-1.6.2/saros/R/crowd_tables_as_tabset.R |only saros-1.6.2/saros/R/fig_height_h_barchart.R | 498 +++++++++- saros-1.6.2/saros/R/get_fig_title_suffix_from_ggplot.R | 71 + saros-1.6.2/saros/R/get_main_question.R | 8 saros-1.6.2/saros/R/ggsaver.R | 127 ++ saros-1.6.2/saros/R/girafe-utils.R | 144 ++ saros-1.6.2/saros/R/girafe.R | 114 -- saros-1.6.2/saros/R/insert_text.R |only saros-1.6.2/saros/R/make_content.cat_plot_docx.R |only saros-1.6.2/saros/R/make_content.cat_plot_html.R | 10 saros-1.6.2/saros/R/make_content.cat_table_docx.R |only saros-1.6.2/saros/R/make_content.cat_table_html.R | 18 saros-1.6.2/saros/R/make_content.chr_table_docx.R |only saros-1.6.2/saros/R/make_content.chr_table_html.R | 2 saros-1.6.2/saros/R/make_content.int_plot_html.R | 39 saros-1.6.2/saros/R/make_content.int_table_html.R | 2 saros-1.6.2/saros/R/make_content.sigtest_table_html.R | 2 saros-1.6.2/saros/R/make_file_links.R |only saros-1.6.2/saros/R/make_link.R | 19 saros-1.6.2/saros/R/makeme.R | 20 saros-1.6.2/saros/R/makeme_helpers.R | 376 ++----- saros-1.6.2/saros/R/n_rng.R | 129 ++ saros-1.6.2/saros/R/output_format.R |only saros-1.6.2/saros/R/quarto_post_render.R |only saros-1.6.2/saros/R/simple_desciptives.R | 2 saros-1.6.2/saros/R/sorting_utils.R | 166 ++- saros-1.6.2/saros/R/summarize_cat_cat_data.R | 50 - saros-1.6.2/saros/R/txt_from_cat_mesos_plots.R | 164 ++- saros-1.6.2/saros/R/utils.R | 135 ++ saros-1.6.2/saros/R/validate_makeme_options.R | 111 -- saros-1.6.2/saros/R/zzz.R | 15 saros-1.6.2/saros/inst/WORDLIST | 41 saros-1.6.2/saros/inst/doc/for_chapter_author.html | 2 saros-1.6.2/saros/inst/doc/for_developers.html | 2 saros-1.6.2/saros/inst/doc/for_readers.html | 2 saros-1.6.2/saros/inst/doc/saros_name.html | 2 saros-1.6.2/saros/man/attach_dep_label_prefix.Rd |only saros-1.6.2/saros/man/auto_detect_makeme_type.Rd | 3 saros-1.6.2/saros/man/build_custom_palette.Rd |only saros-1.6.2/saros/man/check_quarto_website_index.Rd |only saros-1.6.2/saros/man/compute_full_category_levels.Rd |only saros-1.6.2/saros/man/count_max_wrapped_lines.Rd |only saros-1.6.2/saros/man/crowd_output.Rd |only saros-1.6.2/saros/man/crowd_plots_as_docx.Rd |only saros-1.6.2/saros/man/crowd_plots_as_officer.Rd |only saros-1.6.2/saros/man/crowd_plots_as_tabset.Rd | 10 saros-1.6.2/saros/man/crowd_tables_as_tabset.Rd |only saros-1.6.2/saros/man/detect_ghostscript.Rd |only saros-1.6.2/saros/man/dot-n_rng2_impl.Rd |only saros-1.6.2/saros/man/escape_for_regex.Rd |only saros-1.6.2/saros/man/escape_markdown.Rd |only saros-1.6.2/saros/man/escape_markdown_link.Rd |only saros-1.6.2/saros/man/extract_document_title.Rd |only saros-1.6.2/saros/man/extract_docx_title.Rd |only saros-1.6.2/saros/man/extract_ggplot_theme_info.Rd |only saros-1.6.2/saros/man/extract_pdf_title.Rd |only saros-1.6.2/saros/man/extract_pptx_title.Rd |only saros-1.6.2/saros/man/fig_height_h_barchart.Rd | 5 saros-1.6.2/saros/man/fig_height_h_barchart2.Rd | 58 + saros-1.6.2/saros/man/find_matching_docx.Rd |only saros-1.6.2/saros/man/generate_data_summary.Rd | 3 saros-1.6.2/saros/man/get_dep_label_prefix.Rd |only saros-1.6.2/saros/man/get_fig_title_suffix_from_ggplot.Rd | 16 saros-1.6.2/saros/man/get_fill_levels.Rd |only saros-1.6.2/saros/man/ggsaver.Rd | 81 + saros-1.6.2/saros/man/girafe.Rd | 5 saros-1.6.2/saros/man/hex_bw.Rd | 2 saros-1.6.2/saros/man/insert_text.Rd |only saros-1.6.2/saros/man/is_html_output_or_officer.Rd |only saros-1.6.2/saros/man/is_int_plot_html.Rd |only saros-1.6.2/saros/man/is_rendering.Rd |only saros-1.6.2/saros/man/make_file_links.Rd |only saros-1.6.2/saros/man/makeme.Rd | 16 saros-1.6.2/saros/man/n_range2.Rd | 37 saros-1.6.2/saros/man/output_format.Rd |only saros-1.6.2/saros/man/print.saros_officer_plots.Rd |only saros-1.6.2/saros/man/process_crowd_data.Rd | 3 saros-1.6.2/saros/man/process_single_pdf_post_render.Rd |only saros-1.6.2/saros/man/quarto_pdf_post_render.Rd |only saros-1.6.2/saros/man/read_quarto_post_render_input.Rd |only saros-1.6.2/saros/man/resolve_category_colors.Rd |only saros-1.6.2/saros/man/safe_file_write.Rd |only saros-1.6.2/saros/man/set_pdf_metadata_title.Rd |only saros-1.6.2/saros/man/summarize_cat_cat_data.Rd | 3 saros-1.6.2/saros/man/txt_from_cat_mesos_plots.Rd | 19 saros-1.6.2/saros/man/update_html_pdf_link_text.Rd |only saros-1.6.2/saros/man/validate_bool.Rd |only saros-1.6.2/saros/man/validate_bool_rule.Rd |only saros-1.6.2/saros/man/validate_character_vector_rule.Rd |only saros-1.6.2/saros/man/validate_double.Rd |only saros-1.6.2/saros/man/validate_double_rule.Rd |only saros-1.6.2/saros/man/validate_integerish.Rd |only saros-1.6.2/saros/man/validate_integerish_rule.Rd |only saros-1.6.2/saros/man/validate_palette_params.Rd |only saros-1.6.2/saros/man/validate_params.Rd |only saros-1.6.2/saros/man/validate_sort_category.Rd |only saros-1.6.2/saros/man/validate_sort_column.Rd |only saros-1.6.2/saros/man/validate_string.Rd |only saros-1.6.2/saros/man/validate_string_rule.Rd |only saros-1.6.2/saros/man/validate_type_variable_compatibility.Rd |only saros-1.6.2/saros/tests/testthat/_snaps/make_content.cat_plot_html/unused-categories-in-legend.svg | 48 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-diff-distributions.svg | 14 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-missing-data.svg | 36 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-multiple-dep-variables.svg | 16 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-multiple-dep-with-indep.svg | 36 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-single-dep-variable.svg | 66 - 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saros-1.6.2/saros/tests/testthat/test-make_content.cat_table_html.R | 13 saros-1.6.2/saros/tests/testthat/test-make_content.int_plot_html.R |only saros-1.6.2/saros/tests/testthat/test-make_content.int_table_html.R | 40 saros-1.6.2/saros/tests/testthat/test-make_file_links.R |only saros-1.6.2/saros/tests/testthat/test-make_link.R | 61 + saros-1.6.2/saros/tests/testthat/test-makeme-int-plot-html-snapshots.R | 4 saros-1.6.2/saros/tests/testthat/test-makeme-mesos-color-consistency.R |only saros-1.6.2/saros/tests/testthat/test-n_rng.R | 59 + saros-1.6.2/saros/tests/testthat/test-output_format.R |only saros-1.6.2/saros/tests/testthat/test-quarto_post_render.R |only saros-1.6.2/saros/tests/testthat/test-safe_file_write.R |only saros-1.6.2/saros/tests/testthat/test-sort_dep_by_range.R |only saros-1.6.2/saros/tests/testthat/test-sort_indep_by_count.R |only saros-1.6.2/saros/tests/testthat/test-txt_from_cat_mesos_plots-validation.R | 17 saros-1.6.2/saros/tests/testthat/test-txt_from_cat_mesos_plots.R | 178 +++ saros-1.6.2/saros/tests/testthat/test-utils-ggsaver.R | 111 ++ saros-1.6.2/saros/tests/testthat/test-utils-makeme_helpers.R | 209 ++++ saros-1.6.2/saros/tests/testthat/test-validate_sort_helpers.R |only 173 files changed, 4185 insertions(+), 910 deletions(-)
Title: Interface to Open Collaboration Services (OCS) REST API
Description: Provides an Interface to Open Collaboration Services 'OCS' (<https://www.open-collaboration-services.org/>) REST API.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ocs4R versions 0.3 dated 2025-09-01 and 0.3.1 dated 2026-04-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ocsApiWebdavManager.R | 10 +++++----- README.md | 2 +- 5 files changed, 18 insertions(+), 14 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 26.1.2 dated 2026-02-05 and 26.1.3 dated 2026-04-29
HVT-26.1.2/HVT/NEWS.md |only HVT-26.1.3/HVT/DESCRIPTION | 16 - HVT-26.1.3/HVT/MD5 | 67 +++--- HVT-26.1.3/HVT/R/Delete_Outpoints.R | 3 HVT-26.1.3/HVT/R/HVTMSM_support.R | 50 ----- HVT-26.1.3/HVT/R/HVTMSMoptimization.R | 2 HVT-26.1.3/HVT/R/OptimizationResults.R | 10 - HVT-26.1.3/HVT/R/clustHVT.R | 27 +- HVT-26.1.3/HVT/R/clusterPlot.R | 10 - HVT-26.1.3/HVT/R/constants.R |only HVT-26.1.3/HVT/R/diagPlot.R | 37 --- HVT-26.1.3/HVT/R/diagSuggestion.R | 5 HVT-26.1.3/HVT/R/edaPlots.R | 11 - HVT-26.1.3/HVT/R/getCellId.R | 10 - HVT-26.1.3/HVT/R/getCentroids.R | 44 +++- HVT-26.1.3/HVT/R/getOptimalCentroids.R | 3 HVT-26.1.3/HVT/R/getTransitionProbability.R | 4 HVT-26.1.3/HVT/R/hvq.R | 63 ------ HVT-26.1.3/HVT/R/madPlot.R | 1 HVT-26.1.3/HVT/R/mcmc_plots.R | 24 +- HVT-26.1.3/HVT/R/msm.R | 56 ----- HVT-26.1.3/HVT/R/plotAnimatedFlowmap.R | 12 - HVT-26.1.3/HVT/R/plotHVT.R | 115 ++--------- HVT-26.1.3/HVT/R/plotModelDiagnostics.R | 6 HVT-26.1.3/HVT/R/plotZscore.R | 1 HVT-26.1.3/HVT/R/scoreHVT.R | 226 ++++++---------------- HVT-26.1.3/HVT/R/scoreLayeredHVT.R | 16 - HVT-26.1.3/HVT/R/summary.R | 4 HVT-26.1.3/HVT/R/trainHVT.R | 113 ++--------- HVT-26.1.3/HVT/R/utilities.R |only HVT-26.1.3/HVT/README.md | 37 +++ HVT-26.1.3/HVT/inst/doc/HVT.Rmd | 22 ++ HVT-26.1.3/HVT/inst/doc/HVT.html | 49 ++++ HVT-26.1.3/HVT/man/getOptimalCentroids.Rd | 3 HVT-26.1.3/HVT/tests/testthat/testhvt.R | 278 +++++++++++++++++++++++----- HVT-26.1.3/HVT/vignettes/HVT.Rmd | 22 ++ 36 files changed, 603 insertions(+), 744 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface
for conducting a wide range of factor analysis procedures. 'FAfA'
(Factor Analysis for All) guides users through data uploading,
assumption checking (descriptives, collinearity, multivariate
normality, outliers), data wrangling (variable exclusion, data
splitting), factor retention analysis (e.g., Parallel Analysis, Hull
method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model
testing, Reliability Analysis (e.g., Cronbach's Alpha, McDonald's
Omega), Measurement Invariance testing across groups, and item
weighting techniques. The application leverages established R packages
such as 'lavaan' and 'psych' to perform these analyses, offering an
accessible platform for researchers and students. Results are
presented in user-friendly tables and plots, with options for
downloading outputs.
Author: Abdullah Faruk KILIC [aut, cre],
Ahmet Caliskan [aut]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 0.5 dated 2025-12-15 and 1.0 dated 2026-04-29
FAfA-0.5/FAfA/inst/app/www/favicon.ico |only FAfA-1.0/FAfA/DESCRIPTION | 17 - FAfA-1.0/FAfA/MD5 | 38 +- FAfA-1.0/FAfA/R/app_server.R | 23 - FAfA-1.0/FAfA/R/app_ui.R | 415 +++++++++++++++++++------------ FAfA-1.0/FAfA/R/mod_about_server.r | 56 +++- FAfA-1.0/FAfA/R/mod_assumptions_server.r | 41 ++- FAfA-1.0/FAfA/R/mod_assumptions_ui.R | 88 +++--- FAfA-1.0/FAfA/R/mod_cfa_server.r | 82 +++--- FAfA-1.0/FAfA/R/mod_cfa_ui.r | 6 FAfA-1.0/FAfA/R/mod_efa_server.r | 20 + FAfA-1.0/FAfA/R/mod_efa_ui.r | 232 ++++++++++------- FAfA-1.0/FAfA/R/mod_ega_server.r | 7 FAfA-1.0/FAfA/R/mod_ega_ui.r | 90 ++++-- FAfA-1.0/FAfA/R/mod_inv_ui.R | 6 FAfA-1.0/FAfA/R/mod_reliability_server.r | 17 - FAfA-1.0/FAfA/R/mod_reliability_ui.r | 54 ++-- FAfA-1.0/FAfA/R/mod_wrangling_server.r | 170 +++++++++--- FAfA-1.0/FAfA/R/mod_wrangling_ui.r | 113 +++++++- FAfA-1.0/FAfA/R/utils.r | 125 ++++++--- FAfA-1.0/FAfA/inst/app/www/logo.png |only 21 files changed, 1061 insertions(+), 539 deletions(-)
Title: Dataset Dependency Graphs for Leakage-Aware Evaluation
Description: Represent biomedical dataset structure as typed dependency
graphs so that sample provenance, repeated-measure structure, study
design, batch effects, and temporal relationships are explicit and
inspectable. Validates dataset structure, detects sample-level overlap,
derives deterministic split constraints, and produces a tool-agnostic
split specification for leakage-aware evaluation workflows.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between splitGraph versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-04-29
splitGraph-0.1.0/splitGraph/inst/extdata |only splitGraph-0.2.0/splitGraph/DESCRIPTION | 8 splitGraph-0.2.0/splitGraph/MD5 | 61 splitGraph-0.2.0/splitGraph/NAMESPACE | 4 splitGraph-0.2.0/splitGraph/NEWS.md | 73 splitGraph-0.2.0/splitGraph/R/constraints.R | 39 splitGraph-0.2.0/splitGraph/R/constructors.R | 15 splitGraph-0.2.0/splitGraph/R/graph-build-auto.R | 11 splitGraph-0.2.0/splitGraph/R/graph-build.R | 64 splitGraph-0.2.0/splitGraph/R/query.R | 29 splitGraph-0.2.0/splitGraph/R/serialization.R |only splitGraph-0.2.0/splitGraph/R/splitGraph-package.R | 26 splitGraph-0.2.0/splitGraph/R/validate.R | 35 splitGraph-0.2.0/splitGraph/README.md | 95 splitGraph-0.2.0/splitGraph/build/vignette.rds |binary splitGraph-0.2.0/splitGraph/inst/CITATION | 8 splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.R |only splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.Rmd |only splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.html |only splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.R | 62 splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.Rmd | 124 + splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.html | 969 +++++----- splitGraph-0.2.0/splitGraph/man/build_dependency_graph.Rd | 21 splitGraph-0.2.0/splitGraph/man/graph_from_metadata.Rd | 2 splitGraph-0.2.0/splitGraph/man/query_node_type.Rd | 7 splitGraph-0.2.0/splitGraph/man/write_dependency_graph.Rd |only splitGraph-0.2.0/splitGraph/man/write_split_spec.Rd |only splitGraph-0.2.0/splitGraph/tests/testthat/test-constructors.R | 18 splitGraph-0.2.0/splitGraph/tests/testthat/test-deprecations.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-graph-from-metadata.R | 4 splitGraph-0.2.0/splitGraph/tests/testthat/test-numeric-outcome.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-prefix-mismatch.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-query-paths-cap.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-schema-version.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-serialization.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-validate.R | 7 splitGraph-0.2.0/splitGraph/tests/testthat/test-validation-overrides.R |only splitGraph-0.2.0/splitGraph/vignettes/adapter-cookbook.Rmd |only splitGraph-0.2.0/splitGraph/vignettes/leakage-aware-workflow.Rmd | 124 + 39 files changed, 1280 insertions(+), 526 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 2.5.12 dated 2026-04-10 and 2.5.14 dated 2026-04-29
DESCRIPTION | 11 MD5 | 93 +- NEWS.md | 347 +++++++++++ R/compare_daa_results.R | 18 R/compare_gsea_daa.R | 29 R/compare_metagenome_results.R | 92 ++ R/data_utils.R | 266 ++++++++ R/ggpicrust2.R | 66 +- R/gsea_pathway_annotation.R | 21 R/import_MicrobiomeAnalyst_daa_results.R | 36 - R/ko2kegg_abundance.R | 107 ++- R/pathway_annotation.R | 234 ++++--- R/pathway_daa.R | 683 ++++++++++++++-------- R/pathway_errorbar.R | 285 ++++----- R/pathway_errorbar_table.R | 107 ++- R/pathway_gsea.R | 118 ++- R/pathway_heatmap.R | 17 R/pathway_pca.R | 46 - R/pathway_volcano.R | 13 R/taxa_contribution.R | 80 ++ R/taxa_contribution_viz.R | 44 + R/visualize_gsea.R | 116 ++- README.md | 21 man/compare_gsea_daa.Rd | 5 man/compare_metagenome_results.Rd | 2 man/ggpicrust2.Rd | 25 man/import_MicrobiomeAnalyst_daa_results.Rd | 8 man/ko2kegg_abundance.Rd | 16 man/pathway_daa.Rd | 83 +- man/pathway_errorbar.Rd | 3 man/pathway_errorbar_table.Rd | 7 man/pathway_gsea.Rd | 8 man/prepare_gene_sets.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-compare_metagenome_results.R |only tests/testthat/test-core-audit-followup.R |only tests/testthat/test-data_utils.R |only tests/testthat/test-find_sample_column.R |only tests/testthat/test-first-principles-fixes.R |only tests/testthat/test-ggpicrust2-return-structure.R | 236 +++++++ tests/testthat/test-ko2kegg_abundance.R | 133 ++++ tests/testthat/test-pathway_annotation.R | 138 ++++ tests/testthat/test-pathway_daa.R | 636 ++++++++++++++++++++ tests/testthat/test-pathway_errorbar.R | 149 ++++ tests/testthat/test-pathway_errorbar_table.R |only tests/testthat/test-pathway_gsea.R | 103 +++ tests/testthat/test-pathway_pca.R | 14 tests/testthat/test-pathway_volcano.R | 29 tests/testthat/test-reference_data_structure.R | 39 - tests/testthat/test-taxa_contribution.R | 33 + tests/testthat/test-visualize_gsea.R | 8 51 files changed, 3690 insertions(+), 839 deletions(-)
Title: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data
Description: Prevents and detects information leakage in biomedical machine learning.
Provides leakage-resistant split policies (subject-grouped, batch-blocked, study leave-out, time-ordered),
guarded preprocessing (train-only imputation, normalization, filtering, feature selection),
cross-validated fitting with common learners, permutation-gap auditing, batch and fold association tests,
and duplicate detection.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between bioLeak versions 0.3.6 dated 2026-04-11 and 0.3.7 dated 2026-04-29
bioLeak-0.3.6/bioLeak/man/dot-guard_ensure_levels.Rd |only bioLeak-0.3.6/bioLeak/man/dot-guard_fit.Rd |only bioLeak-0.3.6/bioLeak/man/predict_guard.Rd |only bioLeak-0.3.7/bioLeak/DESCRIPTION | 16 bioLeak-0.3.7/bioLeak/MD5 | 68 ++- bioLeak-0.3.7/bioLeak/NAMESPACE | 20 - bioLeak-0.3.7/bioLeak/NEWS.md | 71 +++ bioLeak-0.3.7/bioLeak/R/accessors.R |only bioLeak-0.3.7/bioLeak/R/audit.R | 1 bioLeak-0.3.7/bioLeak/R/classes.R | 78 +++ bioLeak-0.3.7/bioLeak/R/fit_resample.R | 80 +++- bioLeak-0.3.7/bioLeak/R/guards.R | 69 ++- bioLeak-0.3.7/bioLeak/R/impute_guarded.R | 2 bioLeak-0.3.7/bioLeak/R/splitgraph_adapter.R |only bioLeak-0.3.7/bioLeak/R/tune_resample.R | 51 ++ bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.R | 18 bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.Rmd | 32 + bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.html | 196 +++++----- bioLeak-0.3.7/bioLeak/man/as_leaksplits.Rd |only bioLeak-0.3.7/bioLeak/man/audit_batch_assoc.Rd |only bioLeak-0.3.7/bioLeak/man/audit_duplicates.Rd |only bioLeak-0.3.7/bioLeak/man/audit_info.Rd |only bioLeak-0.3.7/bioLeak/man/audit_perm_gap.Rd |only bioLeak-0.3.7/bioLeak/man/audit_target_assoc.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_R_eff.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_ci.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_metric.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_p_value.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_repeats.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_robust.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_tier.Rd |only bioLeak-0.3.7/bioLeak/man/fit_metrics.Rd |only bioLeak-0.3.7/bioLeak/man/fit_resample.Rd | 2 bioLeak-0.3.7/bioLeak/man/guard_ensure_levels.Rd |only bioLeak-0.3.7/bioLeak/man/guard_fit.Rd |only bioLeak-0.3.7/bioLeak/man/predict.GuardFit.Rd |only bioLeak-0.3.7/bioLeak/man/print.LeakTune.Rd |only bioLeak-0.3.7/bioLeak/man/show-LeakAudit-method.Rd |only bioLeak-0.3.7/bioLeak/man/show-LeakFit-method.Rd |only bioLeak-0.3.7/bioLeak/tests/testthat/test-accessors.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-classes-summary.R | 2 bioLeak-0.3.7/bioLeak/tests/testthat/test-guard-fit-rename.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-guard-fit.R | 30 - bioLeak-0.3.7/bioLeak/tests/testthat/test-guards-utils.R | 4 bioLeak-0.3.7/bioLeak/tests/testthat/test-impute-guarded.R | 2 bioLeak-0.3.7/bioLeak/tests/testthat/test-invariants.R | 4 bioLeak-0.3.7/bioLeak/tests/testthat/test-predict-guardfit.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-show-methods.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-vignette-suggests.R |only bioLeak-0.3.7/bioLeak/vignettes/bioLeak-intro.Rmd | 32 + 50 files changed, 577 insertions(+), 201 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Kara Woo [aut, cre],
Toph Allen [aut],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Kara Woo <kara.woo@posit.co>
Diff between connectapi versions 0.12.0 dated 2026-04-13 and 0.12.1 dated 2026-04-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/git.R | 28 +++++++++++++++++++++------- inst/doc/customize-http.html | 4 ++-- inst/doc/getting-started.html | 4 ++-- tests/testthat/test-git.R | 15 +++++++++++++++ 7 files changed, 54 insertions(+), 20 deletions(-)
Title: Colour Palette for Reading and Code, Inspired by Moby-Dick
Description: The Pequod colour palette, named after the whaler in
Herman Melville's Moby-Dick. Provides the full Log base scale
from warm paper (Log 50) to deep ink (Log 950), eight crew
accent hues with light and dark variants, and 'ggplot2' scales
for discrete and continuous mapping. Designed for long-form
reading and code, with low saturation and a consistent earth-
pigment register. Full design rationale and accessibility notes
at <https://tiagojct.eu/projects/pequod/>.
Author: Tiago Jacinto [aut, cre]
Maintainer: Tiago Jacinto <tiagojacinto@med.up.pt>
This is a re-admission after prior archival of version 0.0-5 dated 2016-02-28
Diff between pequod versions 0.0-5 dated 2016-02-28 and 0.1.1 dated 2026-04-29
pequod-0.0-5/pequod/R/lmres.R |only pequod-0.0-5/pequod/R/plotSlope.R |only pequod-0.0-5/pequod/R/simpleSlope.R |only pequod-0.0-5/pequod/man/PlotSlope.Rd |only pequod-0.0-5/pequod/man/lmres.Rd |only pequod-0.0-5/pequod/man/simpleSlope.Rd |only pequod-0.0-5/pequod/man/summary.lmres.Rd |only pequod-0.0-5/pequod/man/summary.simpleSlope.Rd |only pequod-0.1.1/pequod/DESCRIPTION | 41 ++++++++++++++++-------- pequod-0.1.1/pequod/LICENSE |only pequod-0.1.1/pequod/MD5 | 30 +++++++++++------ pequod-0.1.1/pequod/NAMESPACE | 41 +++++++----------------- pequod-0.1.1/pequod/R/palettes-data.R |only pequod-0.1.1/pequod/R/palettes.R |only pequod-0.1.1/pequod/R/pequod-package.R |only pequod-0.1.1/pequod/R/preview.R |only pequod-0.1.1/pequod/R/scales.R |only pequod-0.1.1/pequod/README.md |only pequod-0.1.1/pequod/man/palette_pequod.Rd |only pequod-0.1.1/pequod/man/pequod-package.Rd |only pequod-0.1.1/pequod/man/pequod_crew.Rd |only pequod-0.1.1/pequod/man/pequod_crew_dark.Rd |only pequod-0.1.1/pequod/man/pequod_crew_light.Rd |only pequod-0.1.1/pequod/man/pequod_log.Rd |only pequod-0.1.1/pequod/man/pequod_preview.Rd |only pequod-0.1.1/pequod/man/scale_color_pequod_c.Rd |only pequod-0.1.1/pequod/man/scale_color_pequod_d.Rd |only pequod-0.1.1/pequod/tests |only 28 files changed, 62 insertions(+), 50 deletions(-)
Title: 'Geocoordinate Validation Service'
Description: The 'Geocoordinate Validation Service' (GVS) runs checks of coordinates in latitude/longitude format. It returns annotated coordinates with additional flags and metadata that can be used in data cleaning. Additionally, the package has functions related to attribution and metadata information. More information can be found at <https://github.com/ojalaquellueva/gvs/tree/master/api>.
Author: Brian Maitner [aut, cre] ,
Brad Boyle [aut],
Rethvick Sriram Yugendra Babu [aut]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between GVS versions 0.0.1 dated 2024-12-05 and 0.0.2 dated 2026-04-29
DESCRIPTION | 11 - LICENSE | 4 MD5 | 74 +++++----- NAMESPACE | 26 +-- NEWS | 26 ++- R/GVS.R | 124 ++++++++--------- R/GVS_citations.R | 32 ++-- R/GVS_collaborators.R | 30 ++-- R/GVS_data_dictionary.R | 30 ++-- R/GVS_metadata.R | 68 +++++---- R/GVS_sources.R | 42 +++--- R/GVS_version.R | 42 +++--- R/data.R | 24 +-- R/gvs_core.R | 210 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/GVS.R | 10 - inst/doc/GVS.Rmd | 174 ++++++++++++------------ inst/doc/GVS.html | 45 +----- man/GVS.Rd | 52 +++---- man/GVS_citations.Rd | 52 +++---- man/GVS_collaborators.Rd | 46 +++--- man/GVS_data_dictionary.Rd | 46 +++--- man/GVS_metadata.Rd | 60 ++++---- man/GVS_sources.Rd | 46 +++--- man/GVS_version.Rd | 46 +++--- man/check_internet.Rd | 30 ++-- man/gvs_core.Rd | 54 +++---- man/gvs_testfile.Rd | 48 +++--- tests/testthat.R | 10 - tests/testthat/setup-gvs.R | 36 ++--- tests/testthat/test-GVS.R | 40 ++--- tests/testthat/test-GVS_citations.R | 40 ++--- tests/testthat/test-GVS_collaborators.R | 40 ++--- tests/testthat/test-GVS_data_dictionary.R | 40 ++--- tests/testthat/test-GVS_metadata.R | 40 ++--- tests/testthat/test-GVS_sources.R | 38 ++--- tests/testthat/test-GVS_version.R | 36 ++--- vignettes/GVS.Rmd | 174 ++++++++++++------------ 38 files changed, 973 insertions(+), 973 deletions(-)
Title: Creates, Merges, and Reads Binary Dosage Files
Description: Tools to create binary dosage files from either VCF
or GEN files, merge binary dosage files, and read
binary dosage files. Binary dosage files tend to have quicker
read times than VCF and GEN formats. There is a small increase
in size compared to compressed VCF and GEN files.
Author: John Morrison [aut, cre],
NCI [fnd] ,
NCI [fnd] ,
NIEHS [fnd] ,
NHLBI [fnd]
Maintainer: John Morrison <jmorr@usc.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2020-01-13
Diff between BinaryDosage versions 1.0.0 dated 2020-01-13 and 2.0.0 dated 2026-04-29
DESCRIPTION | 39 MD5 | 246 ++- NAMESPACE | 50 NEWS.md | 37 R/Merge.R | 760 +++++----- R/RcppExports.R | 182 +- R/ReadBinaryDosage.R | 776 +++++------ R/WriteBinaryDosage.R | 822 +++++------ R/apply.R | 565 ++++---- R/convert.R | 1108 ++++++++++------ R/format5.R |only R/getinfo.R | 1275 +++++++++--------- R/getsnp.R | 146 +- R/mergebd.R |only R/subset.R |only README.md | 798 +++++------ build/vignette.rds |binary inst/WORDLIST | 200 +- inst/doc/bd5snpreaders.R |only inst/doc/bd5snpreaders.Rmd |only inst/doc/bd5snpreaders.html |only inst/doc/bdformats.R | 12 inst/doc/bdformats.Rmd | 215 +-- inst/doc/bdformats.html | 711 +++++----- inst/doc/geneticfileinfo.R | 18 inst/doc/geneticfileinfo.Rmd | 208 +-- inst/doc/geneticfileinfo.html | 917 +++++++------ inst/doc/legacy.R |only inst/doc/legacy.Rmd |only inst/doc/legacy.html |only inst/doc/mergingbd5files.R |only inst/doc/mergingbd5files.Rmd |only inst/doc/mergingbd5files.html |only inst/doc/mergingfiles.R | 48 inst/doc/mergingfiles.Rmd | 113 - inst/doc/mergingfiles.html | 772 +++++------ inst/doc/r2estimates.R | 12 inst/doc/r2estimates.Rmd | 110 - inst/doc/r2estimates.html | 561 ++++---- inst/doc/usingbdfiles.R | 48 inst/doc/usingbdfiles.Rmd | 164 +- inst/doc/usingbdfiles.html | 1194 +++++++++-------- inst/doc/usingformat5files.R |only inst/doc/usingformat5files.Rmd |only inst/doc/usingformat5files.html |only inst/doc/usinggenfiles.R | 228 +-- inst/doc/usinggenfiles.Rmd | 690 +++++---- inst/doc/usinggenfiles.html | 1525 ++++++++++++---------- inst/doc/usingvcffiles.R | 246 +-- inst/doc/usingvcffiles.Rmd | 602 ++++---- inst/doc/usingvcffiles.html | 2285 ++++++++++++++++++--------------- inst/extdata/bad1.imp | 22 inst/extdata/bad1.info | 22 inst/extdata/bad1.vcf | 36 inst/extdata/bad2.info | 22 inst/extdata/bad2.vcf | 36 inst/extdata/bad3.vcf | 36 inst/extdata/set1a.imp | 22 inst/extdata/set1a.info | 22 inst/extdata/set1a.vcf | 36 inst/extdata/set1a_nd.info | 22 inst/extdata/set1ars.vcf | 36 inst/extdata/set1b.imp | 22 inst/extdata/set1b.info | 22 inst/extdata/set1b.vcf | 36 inst/extdata/set1b_asnp.imp | 24 inst/extdata/set1b_asnp.info | 24 inst/extdata/set1b_asnp.vcf | 38 inst/extdata/set1b_rssnp.imp | 24 inst/extdata/set1b_rssnp.vcf | 38 inst/extdata/set1b_rsub.imp | 22 inst/extdata/set1b_rsub.info | 22 inst/extdata/set1b_rsub.vcf | 36 inst/extdata/set2a.imp | 20 inst/extdata/set2a.sample | 122 - inst/extdata/set2a.vcf | 36 inst/extdata/set2b.imp | 20 inst/extdata/set2b.sample | 82 - inst/extdata/set2b.vcf | 36 inst/extdata/set3a.imp | 20 inst/extdata/set3a.sample | 124 - inst/extdata/set3a.sample1 | 124 - inst/extdata/set3b.chr.imp | 20 inst/extdata/set3b.imp | 20 inst/extdata/set3b.sample | 84 - inst/extdata/set3bnh.sample | 80 - inst/extdata/set4a.sample | 124 - inst/extdata/set4b.imp | 20 inst/extdata/set4b.sample | 84 - man/bd1tobd5.Rd |only man/bd2tobd5.Rd |only man/bd3tobd5.Rd |only man/bd4tobd5.Rd |only man/bdapply.Rd | 108 - man/bdmerge.Rd | 178 +- man/closebd5con.Rd |only man/genapply.Rd | 108 - man/gentobd.Rd | 238 +-- man/getaaf.Rd | 64 man/getbd5snp.Rd |only man/getbd5snp_buf.Rd |only man/getbd5snp_con.Rd |only man/getbdinfo.Rd | 65 man/getgeninfo.Rd | 188 +- man/getmaf.Rd | 68 man/getrsq.Rd | 74 - man/getsnp.Rd | 72 - man/getvcfinfo.Rd | 4 man/mergebd.Rd |only man/openbd5con.Rd |only man/subsetbd.Rd |only man/updatebd.Rd |only man/vcfapply.Rd | 106 - man/vcftobd.Rd | 165 +- man/vcftobdlegacy.Rd |only src/Makevars | 2 src/RcppExports.cpp | 64 src/ReadBinaryDosage.cpp | 98 + tests/testthat.R | 8 tests/testthat/test-apply.R | 244 +-- tests/testthat/test-convert.R | 965 +++++++++---- tests/testthat/test-fileinfo_cpp.R | 6 tests/testthat/test-filemismatch.R | 138 - tests/testthat/test-format-subformat.R | 350 ++--- tests/testthat/test-getinfo.R | 548 +++---- tests/testthat/test-getsnp.R | 111 - tests/testthat/test-merge.R | 432 +++--- tests/testthat/test-mergebd.R |only tests/testthat/test-reading.R | 22 tests/testthat/test-subset.R |only vignettes/bd5snpreaders.Rmd |only vignettes/bdformats.Rmd | 215 +-- vignettes/geneticfileinfo.Rmd | 208 +-- vignettes/legacy.Rmd |only vignettes/mergingbd5files.Rmd |only vignettes/mergingfiles.Rmd | 113 - vignettes/r2estimates.Rmd | 110 - vignettes/usingbdfiles.Rmd | 164 +- vignettes/usingformat5files.Rmd |only vignettes/usinggenfiles.Rmd | 690 +++++---- vignettes/usingvcffiles.Rmd | 602 ++++---- 141 files changed, 13921 insertions(+), 11926 deletions(-)
Title: Dump 'R' Package Source, Documentation, and Vignettes into One
File
Description: Dump source code, documentation and vignettes of an 'R'
package into a single file. Supports installed packages, tar.gz
archives, and package source directories. If the package is not
installed, only its source is automatically downloaded from CRAN for
processing. The output is a single plain text file or a character
vector, which is useful to ingest complete package documentation and
source into a large language model (LLM) or pass it further to other
tools, such as 'ragnar' <https://github.com/tidyverse/ragnar> to
create a Retrieval-Augmented Generation (RAG) workflow.
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between rdocdump versions 0.1.1 dated 2025-08-21 and 0.2.0 dated 2026-04-29
rdocdump-0.1.1/rdocdump/tools |only rdocdump-0.2.0/rdocdump/DESCRIPTION | 10 rdocdump-0.2.0/rdocdump/MD5 | 38 +- rdocdump-0.2.0/rdocdump/NEWS.md | 4 rdocdump-0.2.0/rdocdump/R/extract_code.R | 16 - rdocdump-0.2.0/rdocdump/R/to_txt.R | 29 +- rdocdump-0.2.0/rdocdump/R/util_resolve_pkg_path.R | 6 rdocdump-0.2.0/rdocdump/R/util_resolve_remote.R |only rdocdump-0.2.0/rdocdump/build/vignette.rds |binary rdocdump-0.2.0/rdocdump/inst/doc/rdocdump.html | 144 ++++++++++- rdocdump-0.2.0/rdocdump/inst/schemaorg.json | 4 rdocdump-0.2.0/rdocdump/man/create_remote.Rd |only rdocdump-0.2.0/rdocdump/man/figures |only rdocdump-0.2.0/rdocdump/man/find_pkg_dir.Rd |only rdocdump-0.2.0/rdocdump/man/get_remote_cache_dir.Rd |only rdocdump-0.2.0/rdocdump/man/is_remote_reference.Rd |only rdocdump-0.2.0/rdocdump/man/parse_remote_ref.Rd |only rdocdump-0.2.0/rdocdump/man/parse_remote_url.Rd |only rdocdump-0.2.0/rdocdump/man/rdd_extract_code.Rd | 16 - rdocdump-0.2.0/rdocdump/man/rdd_to_txt.Rd | 29 +- rdocdump-0.2.0/rdocdump/man/resolve_pkg_path.Rd | 16 - rdocdump-0.2.0/rdocdump/man/resolve_remote_pkg.Rd |only rdocdump-0.2.0/rdocdump/tests/testthat/test-remote.R |only rdocdump-0.2.0/rdocdump/tests/testthat/test-set_cache_path.R | 8 rdocdump-0.2.0/rdocdump/tests/testthat/test-to_txt.R | 7 25 files changed, 285 insertions(+), 42 deletions(-)
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, least-cost corridors, least-cost networks using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 2.1 dated 2024-02-12 and 2.2 dated 2026-04-29
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++--------------- NEWS.md | 11 ++++++--- R/movealloc.r | 7 +++--- R/movebound.r | 5 ++-- R/movecomp.r | 7 +++--- R/movecorr.r | 11 +++++---- R/movecost.r | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- R/movenetw.r | 5 ++-- R/moverank.r | 29 ++++++++++++------------ README.md | 9 ++++++- man/movealloc.Rd | 3 ++ man/movebound.Rd | 3 ++ man/movecomp.Rd | 3 ++ man/movecorr.Rd | 3 ++ man/movecost.Rd | 36 ++++++++++++++++++++++++++++++ man/movenetw.Rd | 3 ++ man/moverank.Rd | 3 ++ 18 files changed, 187 insertions(+), 55 deletions(-)
Title: Data for Exploring Curricular Complexity
Description: Provides 'igraph' objects representing engineering plans of study
across multiple disciplines and institutions. The data are intended for use
with the 'CurricularComplexity' package (Reeping, 2026)
<doi:10.32614/CRAN.package.CurricularComplexity> to support analyses of
curricular structure.
Author: David Reeping [aut, cre],
Olivia Ryan [aut],
Nahal Rashedi [ctb],
Elliot Setser [ctb],
Sushant Padhye [ctb],
Autri Banerjee [ctb],
Emily Hodge [ctb],
Levi Smith [ctb]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexityData versions 0.1.0 dated 2026-02-04 and 0.2.0 dated 2026-04-29
DESCRIPTION | 15 ++++++++------- MD5 | 9 ++++++--- R/NSF_SUCCESS.R | 25 +++++++++++++++++-------- R/ThreeEngineeringDisciplines_Ryan.R |only data/ThreeEngineeringDisciplines_Ryan.rda |only man/NSF_SUCCESS.Rd | 25 +++++++++++++++++-------- man/ThreeEngineeringDisciplines_Ryan.Rd |only 7 files changed, 48 insertions(+), 26 deletions(-)
More information about CurricularComplexityData at CRAN
Permanent link
Title: R Interface for the RAPIDS cuML Suite of Libraries
Description: R interface for RAPIDS cuML (<https://github.com/rapidsai/cuml>),
a suite of GPU-accelerated machine learning libraries powered by CUDA
(<https://en.wikipedia.org/wiki/CUDA>).
Author: Yitao Li [aut, cph] ,
Tomasz Kalinowski [aut, cre, cph],
Daniel Falbel [aut, cph],
RStudio [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between cuda.ml versions 0.3.2 dated 2022-01-07 and 0.3.3 dated 2026-04-29
cuda.ml-0.3.2/cuda.ml/man/cuda.ml.Rd |only cuda.ml-0.3.3/cuda.ml/DESCRIPTION | 26 +- cuda.ml-0.3.3/cuda.ml/MD5 | 90 +++++----- cuda.ml-0.3.3/cuda.ml/NAMESPACE | 21 ++ cuda.ml-0.3.3/cuda.ml/R/agglomerative.R | 4 cuda.ml-0.3.3/cuda.ml/R/cuml_utils.R | 16 - cuda.ml-0.3.3/cuda.ml/R/fil.R | 8 cuda.ml-0.3.3/cuda.ml/R/knn.R | 6 cuda.ml-0.3.3/cuda.ml/R/logistic_reg.R | 2 cuda.ml-0.3.3/cuda.ml/R/model.R | 19 +- cuda.ml-0.3.3/cuda.ml/R/ols.R | 2 cuda.ml-0.3.3/cuda.ml/R/package.R | 4 cuda.ml-0.3.3/cuda.ml/R/pca.R | 2 cuda.ml-0.3.3/cuda.ml/R/rand_forest.R | 2 cuda.ml-0.3.3/cuda.ml/R/rand_proj.R | 2 cuda.ml-0.3.3/cuda.ml/R/sgd.R | 6 cuda.ml-0.3.3/cuda.ml/R/svm.R | 6 cuda.ml-0.3.3/cuda.ml/R/tsne.R | 4 cuda.ml-0.3.3/cuda.ml/R/umap.R | 6 cuda.ml-0.3.3/cuda.ml/man/cuML_major_version.Rd | 8 cuda.ml-0.3.3/cuda.ml/man/cuML_minor_version.Rd | 8 cuda.ml-0.3.3/cuda.ml/man/cuda.ml-package.Rd |only cuda.ml-0.3.3/cuda.ml/man/cuda_ml_agglomerative_clustering.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_dbscan.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_fil_enabled.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_fil_load_model.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_kmeans.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_knn.Rd | 26 +- cuda.ml-0.3.3/cuda.ml/man/cuda_ml_knn_algo_ivfsq.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_logistic_reg.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_ols.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_pca.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_rand_forest.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_sgd.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_svm.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_tsne.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_tsvd.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_umap.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/has_cuML.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/predict.cuda_ml_rand_forest.Rd | 2 cuda.ml-0.3.3/cuda.ml/src/CMakeLists.txt.in | 1 cuda.ml-0.3.3/cuda.ml/tests/testthat.R | 3 cuda.ml-0.3.3/cuda.ml/tests/testthat/helper-initialize.R | 8 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-elastic-net.R | 2 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-lasso.R | 2 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-tsvd.R | 49 +++-- cuda.ml-0.3.3/cuda.ml/tools/config/configure.R | 4 47 files changed, 226 insertions(+), 169 deletions(-)
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplementary tools for evaluating and validating partial least
squares structural equation models estimated with 'seminr'. Provides methods
for predictive model assessment, importance-performance analysis with
necessary condition testing, overfitting diagnostics, measurement model
verification, mediator contribution analysis, unobserved heterogeneity
detection via latent class and prediction-oriented segmentation, and
congruence coefficient testing. All functions accept estimated 'seminr'
model objects and return results with print, summary, and plot methods.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminrExtras versions 0.9.0 dated 2026-01-29 and 1.0.0 dated 2026-04-29
DESCRIPTION | 32 - MD5 | 82 +++ NAMESPACE | 82 +++ NEWS.md |only R/feature_cipma.R |only R/feature_coa.R |only R/feature_congruence.R | 221 +++++++--- R/feature_cta.R |only R/feature_cvpat.R | 632 +++++++++++++---------------- R/feature_fimix.R |only R/feature_nca.R |only R/feature_pcm.R |only R/feature_pos.R |only R/helpers.R | 243 +++++++++++ README.md | 275 +++++++++++- demo/00Index | 10 demo/seminr-pls-cipma.R |only demo/seminr-pls-coa.R |only demo/seminr-pls-congruence.R |only demo/seminr-pls-cta.R |only demo/seminr-pls-fimix.R |only demo/seminr-pls-nca.R |only demo/seminr-pls-pcm.R |only demo/seminr-pls-pos.R |only demo/seminr-primer-v2-chap6.R | 14 inst/doc/SEMinRExtras.R | 263 +++++++++++- inst/doc/SEMinRExtras.Rmd | 407 ++++++++++++++++++ inst/doc/SEMinRExtras.html | 649 +++++++++++++++++++++++++++--- man/assess_cipma.Rd |only man/assess_coa.Rd |only man/assess_cta.Rd |only man/assess_cvpat.Rd | 21 man/assess_cvpat_compare.Rd | 10 man/assess_fimix.Rd |only man/assess_fimix_compare.Rd |only man/assess_ipma.Rd |only man/assess_nca.Rd |only man/assess_nca_esse.Rd |only man/assess_pcm.Rd |only man/assess_pos.Rd |only man/assess_pos_compare.Rd |only man/competes.Rd |only man/congruence_test.Rd | 25 - man/deviance_tree.Rd |only man/group_rules.Rd |only man/plot.cipma_analysis.Rd |only man/plot.coa_analysis.Rd |only man/plot.fimix_analysis.Rd |only man/plot.fimix_comparison.Rd |only man/plot.nca_analysis.Rd |only man/plot.nca_esse.Rd |only man/plot.pcm_analysis.Rd |only man/pos_segments.Rd |only man/predictive_deviance.Rd |only man/unstable_params.Rd |only tests/testthat/test-cipma-comprehensive.R |only tests/testthat/test-coa.R |only tests/testthat/test-congruence.R |only tests/testthat/test-cta.R |only tests/testthat/test-cvpat-comprehensive.R |only tests/testthat/test-cvpat.R | 221 +++++----- tests/testthat/test-extended-edge-cases.R |only tests/testthat/test-fimix.R |only tests/testthat/test-nca.R |only tests/testthat/test-pcm.R |only tests/testthat/test-pos.R |only vignettes/SEMinRExtras.Rmd | 407 ++++++++++++++++++ 67 files changed, 2922 insertions(+), 672 deletions(-)
Title: Automatically Runs 18 Individual and 14 Ensembles of Models
Description: Automatically runs 18 individual models and 14 ensembles on numeric data, for a total of 32 models. The package automatically returns complete results on all 32 models,
25 charts and six tables. The user simply provides the tidy data, and answers a few questions (for example, how many times would you like to resample the data).
From there the package randomly splits the data into train, test and validation sets as the user requests (for example, train = 0.60, test = 0.20, validation = 0.20),
fits each of models on the training data, makes predictions on the test and validation sets, measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling
all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions
using the 32 pre trained models on totally new (untrained) data if the user selects that feature [...truncated...]
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between NumericEnsembles versions 1.0.5 dated 2026-03-01 and 1.2 dated 2026-04-29
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++---------- NAMESPACE | 1 NEWS.md | 5 +++ R/NumericEnsembles.R | 54 ++++++++++++++++++++++------------------- R/data.R | 4 +-- inst/doc/NumericEnsembles.Rmd | 4 +-- inst/doc/NumericEnsembles.html | 4 +-- inst/doc/Template.Rmd | 5 ++- inst/doc/Template.html | 5 ++- man/Boston_housing.Rd | 2 - man/New_Boston.Rd | 2 - vignettes/NumericEnsembles.Rmd | 4 +-- vignettes/Template.Rmd | 5 ++- 14 files changed, 71 insertions(+), 58 deletions(-)
More information about NumericEnsembles at CRAN
Permanent link
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Description: Contains functions to query and visualize the Neuroimaging features
associated with genetically regulated gene expression (GReX). The primary utility,
neuroimaGene(), relies on a list of user-defined genes and returns a table of
neuroimaging features (NIDPs) associated with each gene. This resource
is designed to assist in the interpretation of genome-wide and transcriptome-wide
association studies that evaluate brain related traits. Bledsoe (2024)
<doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization
functions that generate summary plots and 2-dimensional visualizations of regional
brain measures. Mowinckel (2020).
Author: Xavier Bledsoe [aut, cre] ,
Eric Gamazon [aut]
Maintainer: Xavier Bledsoe <xbledsoe22@gmail.com>
Diff between neuroimaGene versions 0.1.3 dated 2026-04-25 and 0.1.4 dated 2026-04-29
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NAMESPACE | 1 R/check_db.R | 70 +++++++++++++++++++++++++++++++++++++++++---- inst/doc/neuroimaGene.R | 2 - inst/doc/neuroimaGene.Rmd | 42 +++++++++++++++++++++++++-- inst/doc/neuroimaGene.html | 61 +++++++++++++++++++++++++++++++++++++-- man/check_db.Rd | 4 +- vignettes/neuroimaGene.Rmd | 42 +++++++++++++++++++++++++-- 9 files changed, 220 insertions(+), 28 deletions(-)
Title: Meta-Analysis Datasets
Description: A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Author: Wolfgang Viechtbauer [aut, cre] ,
Thomas White [aut] ,
Daniel Noble [aut] ,
Alistair Senior [aut] ,
W. Kyle Hamilton [aut] ,
Guido Schwarzer [dtc] ,
Christian Roever [dtc]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metadat versions 1.4-0 dated 2025-02-04 and 1.6-0 dated 2026-04-29
DESCRIPTION | 30 +++--- MD5 | 148 +++++++++++++++++++++--------- NEWS.md | 6 + R/datsearch.r | 27 ++--- README.md | 2 build/metadat.pdf |binary build/stage23.rdb |binary data/dat.anker2025.rda |only data/dat.baskerville2012.rda |binary data/dat.bauer2002.rda |only data/dat.berkey1998r.rda |only data/dat.chiarito2020.rda |only data/dat.demir2022.rda |only data/dat.feng2019.rda |only data/dat.furukawa2003.rda |binary data/dat.greb2008.rda |only data/dat.greenland1992.rda |only data/dat.higgins2008.rda |only data/dat.huber2000.rda |only data/dat.karner2014.rda |only data/dat.linde2016.rda |binary data/dat.lloyd2010.rda |only data/dat.meeker2017.rda |only data/dat.metap.rda |only data/dat.moore1998.rda |only data/dat.nissen2007.rda |only data/dat.poole2003.rda |only data/dat.quan2000.rda |only data/dat.rivera2025.rda |only data/dat.spooner2002.rda |binary data/dat.steurer2006.rda |only data/dat.thompson1999.rda |only data/dat.tian2009.rda |only inst/help.rdata |binary man/dat.anker2025.Rd |only man/dat.baker2009.Rd | 7 - man/dat.baskerville2012.Rd | 4 man/dat.bassler2004.Rd | 2 man/dat.bauer2002.Rd |only man/dat.berkey1998.Rd | 4 man/dat.chiarito2020.Rd |only man/dat.crisafulli2020.Rd | 5 - man/dat.curtin2002.Rd | 2 man/dat.damico2009.Rd | 3 man/dat.demir2022.Rd |only man/dat.dogliotti2014.Rd | 2 man/dat.dong2013.Rd | 2 man/dat.dumouchel1994.Rd | 5 - man/dat.feng2019.Rd |only man/dat.franchini2012.Rd | 2 man/dat.furukawa2003.Rd | 23 ++-- man/dat.greb2008.Rd |only man/dat.greenland1992.Rd |only man/dat.gurusamy2011.Rd | 2 man/dat.higgins2008.Rd |only man/dat.huber2000.Rd |only man/dat.ishak2007.Rd | 2 man/dat.karner2014.Rd |only man/dat.laopaiboon2015.Rd | 3 man/dat.linde2015.Rd | 10 +- man/dat.linde2016.Rd | 68 +++++++------ man/dat.lloyd2010.Rd |only man/dat.lopez2019.Rd | 42 +++++++- man/dat.meeker2017.Rd |only man/dat.metap.Rd |only man/dat.moore1998.Rd |only man/dat.nissen2007.Rd |only man/dat.poole2003.Rd |only man/dat.pritz1997.Rd | 3 man/dat.quan2000.Rd |only man/dat.rivera2025.Rd |only man/dat.roever2022.Rd | 6 - man/dat.spooner2002.Rd | 7 + man/dat.steurer2006.Rd |only man/dat.stowe2010.Rd | 4 man/dat.thompson1999.Rd |only man/dat.tian2009.Rd |only man/dat.ursino2021.Rd | 6 - man/dat.woods2010.Rd | 2 man/datsearch.Rd | 6 - tests/testthat/test_dat.anker2025.r |only tests/testthat/test_dat.baskerville2012.r | 2 tests/testthat/test_dat.bauer2002.r |only tests/testthat/test_dat.berkey1998.r | 1 tests/testthat/test_dat.chiarito2020.r |only tests/testthat/test_dat.demir2022.r |only tests/testthat/test_dat.feng2019.r |only tests/testthat/test_dat.furukawa2003.r | 2 tests/testthat/test_dat.greb2008.r |only tests/testthat/test_dat.greenland1992.r |only tests/testthat/test_dat.higgins2008.r |only tests/testthat/test_dat.huber2000.r |only tests/testthat/test_dat.karner2014.r |only tests/testthat/test_dat.linde2016.r | 2 tests/testthat/test_dat.lloyd2010.r |only tests/testthat/test_dat.meeker2017.r |only tests/testthat/test_dat.metap.r |only tests/testthat/test_dat.moore1998.r |only tests/testthat/test_dat.nissen2007.r |only tests/testthat/test_dat.poole2003.r |only tests/testthat/test_dat.quan2000.r |only tests/testthat/test_dat.riley2003.r | 6 + tests/testthat/test_dat.rivera2025.r |only tests/testthat/test_dat.spooner2002.r | 2 tests/testthat/test_dat.steurer2006.r |only tests/testthat/test_dat.thompson1999.r |only tests/testthat/test_dat.tian2009.r |only 107 files changed, 293 insertions(+), 157 deletions(-)
Title: Methods to Enrich R Objects with Extra Components
Description: Provides the "enrich()" method for augmenting list-like R objects with additional, model-specific components. Methods are currently available for objects of class "family", "link-glm", "lm", "glm", and "betareg". Enriched objects retain their original class and remain compatible with existing methods. For example, enriching a "glm" object produces an "enriched_glm" object that also inherits from "glm". In addition to the standard components, the "enriched_glm" object includes methods for simulation and functions to compute scores, observed and expected information matrices, first-order bias, and other model quantities such as densities, probabilities, and quantiles, which can be evaluated at use-supplied parameter values. The package also provides tools for generating customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between enrichwith versions 0.4.0 dated 2025-09-08 and 0.5.0 dated 2026-04-29
DESCRIPTION | 14 - MD5 | 18 - NEWS.md | 37 ++- R/enrich.glm.R | 459 +++++++++++++++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GLMs.html | 15 - inst/doc/bias.html | 18 - inst/doc/exponential_family.html | 16 - man/enrich.glm.Rd | 7 10 files changed, 376 insertions(+), 208 deletions(-)
Title: Wrangle and Modify Ts Object with Classic Frequencies and Exact
Dates
Description: The ts objects in R are managed using a very specific date format (in the form c(2022, 9) for September 2022 or c(2021, 2) for the second quarter of 2021, depending on the frequency, for example). We focus solely on monthly and quarterly series to manage the dates of ts objects. The general idea is to offer a set of functions to manage this date format without it being too restrictive or too imprecise depending on the rounding. This is a compromise between simplicity, precision and use of the basic 'stats' functions for creating and managing time series (ts(), window()).
Les objets ts en R sont gérés par un format de date très particulier (sous la forme c(2022, 9) pour septembre 2022 ou c(2021, 2) pour le deuxième trimestre 2021 selon la fréquence par exemple). On se concentre uniquement sur les séries mensuelles et trimestrielles pour gérer les dates des objets ts. Lidée générale est de proposer un ensemble de fonctions pour gérer ce format de date sans que ce soit trop contraignant o [...truncated...]
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tangbarth@hotmail.fr>
Diff between date4ts versions 0.1.1 dated 2026-02-01 and 0.1.2 dated 2026-04-29
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- NEWS.md | 7 ++++++- README.md | 20 ++++++++++++++------ 4 files changed, 27 insertions(+), 13 deletions(-)
Title: Process Text and Compute Linguistic Alignment in Conversation
Transcripts
Description: Imports conversation transcripts into R, concatenates them into a single dataframe appending event identifiers, cleans and formats the text, then yokes user-specified psycholinguistic database values to each word. 'ConversationAlign' then computes alignment indices between two interlocutors across each transcript for >40 possible semantic, lexical, and affective dimensions. In addition to alignment, 'ConversationAlign' also produces a table of analytics (e.g., token count, type-token-ratio) in a summary table describing your particular text corpus.
Author: Jamie Reilly [aut, cre] ,
Virginia Ulichney [aut],
Ben Sacks [aut],
Sarah Weinstein [ctb],
Chelsea Helion [ctb],
Gus Cooney [ctb]
Maintainer: Jamie Reilly <jamie_reilly@temple.edu>
This is a re-admission after prior archival of version 0.4.0 dated 2025-11-12
Diff between ConversationAlign versions 0.4.0 dated 2025-11-12 and 0.4.1 dated 2026-04-29
DESCRIPTION | 8 MD5 | 34 +- R/compute_lagcorr.R | 333 ++++++++++++------------ R/globals.R | 2 R/prep_dyads.R | 4 R/read_1file.R | 2 build/vignette.rds |binary inst/NEWS.md | 13 inst/doc/ConversationAlign_Introduction.Rmd | 7 inst/doc/ConversationAlign_Introduction.html | 17 - inst/doc/ConversationAlign_Step1_Read.R | 8 inst/doc/ConversationAlign_Step1_Read.Rmd | 2 inst/doc/ConversationAlign_Step1_Read.html | 83 ----- inst/doc/ConversationAlign_Step2_Prep.html | 4 inst/doc/ConversationAlign_Step3_Summarize.html | 4 inst/doc/ConversationAlign_Step4_Analytics.html | 4 vignettes/ConversationAlign_Introduction.Rmd | 7 vignettes/ConversationAlign_Step1_Read.Rmd | 2 18 files changed, 233 insertions(+), 301 deletions(-)
More information about ConversationAlign at CRAN
Permanent link
Title: A Directed Acyclic Graph Extension for 'blockr'
Description: Building on the docking layout manager provided by 'blockr.dock', this
provides an extension that allows for visualizing and manipulating a 'blockr'
board using a DAG-based user interface powered by the 'g6R'
graph visualisation HTML widget.
Author: David Granjon [aut, cre],
Nicolas Bennett [aut],
Christoph Sax [aut],
Bristol Myers Squibb [fnd]
Maintainer: David Granjon <david@cynkra.com>
Diff between blockr.dag versions 0.1.0 dated 2025-12-18 and 0.1.2 dated 2026-04-29
DESCRIPTION | 10 MD5 | 81 + NAMESPACE | 4 NEWS.md | 13 R/action.R | 238 ++++- R/ctx.R | 38 R/ext.R | 169 ++- R/g6r.R | 392 +++++++- R/meta.R | 27 R/srv.R | 155 ++- R/subboard.R |only R/tool.R | 34 R/ui.R | 7 R/utils.R | 10 inst/assets/css/empty-state.css | 14 inst/assets/js/copy-paste.js |only inst/doc/block-callback.html | 2 inst/doc/blockr.dag.html | 1103 ++++++++++++++++-------- inst/doc/context-menu.html | 2 inst/doc/toolbar.html | 2 inst/examples/empty/app.R | 1 inst/examples/variadic |only man/create_block_ports.Rd |only man/g6r.Rd | 6 man/get_children_from_links.Rd |only man/is_variadic_block.Rd |only man/resolve_target_ports.Rd |only tests/testthat/_snaps/e2e/empty-app-001.json | 109 +- tests/testthat/_snaps/e2e/empty-app-001_.png |binary tests/testthat/_snaps/e2e/empty-app-002.json | 142 ++- tests/testthat/_snaps/e2e/empty-app-002_.png |binary tests/testthat/_snaps/e2e/empty-app-003.json | 195 +++- tests/testthat/_snaps/e2e/empty-app-003_.png |binary tests/testthat/_snaps/e2e/empty-app-004.json | 206 +++- tests/testthat/_snaps/e2e/empty-app-004_.png |binary tests/testthat/_snaps/e2e/empty-app-005.json | 176 ++- tests/testthat/_snaps/e2e/empty-app-005_.png |binary tests/testthat/_snaps/e2e/variadic-app-001.json |only tests/testthat/_snaps/e2e/variadic-app-001_.png |only tests/testthat/test-action.R | 339 ++++++- tests/testthat/test-children.R |only tests/testthat/test-ctx.R | 6 tests/testthat/test-e2e.R | 98 +- tests/testthat/test-ext.R | 50 - tests/testthat/test-g6r.R | 60 + tests/testthat/test-meta.R | 50 - tests/testthat/test-subboard.R |only 47 files changed, 2822 insertions(+), 917 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit()' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reducing adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bi [...truncated...]
Author: Ioannis Kosmidis [aut, cre] ,
Euloge Clovis Kenne Pagui [aut] ,
Federico Boiocchi [ctb],
Philipp Sterzinger [ctb] ,
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 1.0.1 dated 2025-11-22 and 1.1.0 dated 2026-04-29
brglm2-1.0.1/brglm2/inst/tinytest/test-median-binomial.R |only brglm2-1.1.0/brglm2/DESCRIPTION | 8 brglm2-1.1.0/brglm2/MD5 | 27 +- brglm2-1.1.0/brglm2/NEWS.md | 12 + brglm2-1.1.0/brglm2/R/brglmFit.R | 13 - brglm2-1.1.0/brglm2/R/ordinal_superiority.R | 101 +++++++---- brglm2-1.1.0/brglm2/build/partial.rdb |binary brglm2-1.1.0/brglm2/build/vignette.rds |binary brglm2-1.1.0/brglm2/inst/doc/adjacent.html | 9 brglm2-1.1.0/brglm2/inst/doc/expo.html | 6 brglm2-1.1.0/brglm2/inst/doc/iteration.html | 33 +-- brglm2-1.1.0/brglm2/inst/doc/multinomial.html | 5 brglm2-1.1.0/brglm2/inst/doc/negativeBinomial.html | 41 ++-- brglm2-1.1.0/brglm2/inst/simulation |only brglm2-1.1.0/brglm2/inst/tinytest/test-ordinal_superiority.R |only brglm2-1.1.0/brglm2/man/brnb.Rd | 4 16 files changed, 150 insertions(+), 109 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.4.2 dated 2025-12-16 and 1.4.3 dated 2026-04-29
DESCRIPTION | 10 ++--- MD5 | 74 ++++++++++++++++++++++++++------------- NEWS.md | 15 +++++++ R/Core.R | 6 ++- R/Diversity.R | 1 R/Fastq.R | 18 +++++++-- R/Gene.R | 34 ++++++++++------- R/Topology.R | 2 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.R | 3 + inst/doc/Diversity-Vignette.Rmd | 3 + inst/doc/Diversity-Vignette.pdf |binary inst/doc/Fastq-Vignette.pdf |binary inst/doc/Files-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary man/alakazam-package.Rd | 1 man/alphaDiversity.Rd | 1 man/makeTempDir.Rd | 2 + man/permuteLabels.Rd | 1 man/plotMRCATest.Rd | 1 man/readChangeoDb.Rd | 2 - man/writeChangeoDb.Rd | 2 - tests |only vignettes/Diversity-Vignette.Rmd | 3 + 26 files changed, 129 insertions(+), 50 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>),
Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>),
ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>),
ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 2.0.0.2 dated 2026-03-11 and 2.0.2 dated 2026-04-29
DESCRIPTION | 24 MD5 | 46 - R/combineMultFilterNAimput.R | 132 +- R/extractTestingResults.R | 150 ++- R/matrixNAneighbourImpute.R | 11 R/readProteomeDiscovererFile.R | 2 R/readSampleMetaData.R | 2 R/readSdrf.R | 20 R/removeSampleInList.R | 43 R/testRobustToNAimputation.R | 352 +++---- build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 10 inst/doc/wrProteoVignette1.Rmd | 25 inst/doc/wrProteoVignette1.html | 598 +++---------- inst/doc/wrProteoVignetteUPS1.R | 4 inst/doc/wrProteoVignetteUPS1.Rmd | 8 inst/doc/wrProteoVignetteUPS1.html | 1679 ++++++++++++++++--------------------- man/combineMultFilterNAimput.Rd | 30 man/extractTestingResults.Rd | 35 man/matrixNAneighbourImpute.Rd | 11 man/readSdrf.Rd | 4 man/testRobustToNAimputation.Rd | 18 vignettes/wrProteoVignette1.Rmd | 25 vignettes/wrProteoVignetteUPS1.Rmd | 8 24 files changed, 1489 insertions(+), 1748 deletions(-)
Title: Density Ratio Estimation
Description: Density ratio estimation. The estimated density ratio
function can be used in many applications such as anomaly detection,
change-point detection, covariate shift adaptation. The implemented
methods are uLSIF (Hido et al. (2011)
<doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al. (2011)
<doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007)
<doi:10.1007/s10463-008-0197-x>).
Author: Koji Makiyama [aut, cre]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Diff between densratio versions 0.2.1 dated 2019-06-30 and 0.3.1 dated 2026-04-29
DESCRIPTION | 27 LICENSE | 4 MD5 | 70 NAMESPACE | 22 NEWS.md | 28 R/KLIEP.R | 114 - R/KLIEP_compute_score.R | 42 R/KLIEP_optimize_alpha.R | 86 R/KLIEP_search_sigma.R | 38 R/KLIEP_search_sigma_list.R | 28 R/RuLSIF.R | 134 - R/RuLSIF_search_sigma_and_lambda.R | 90 R/compute_kernel_Gaussian.R | 42 R/densratio.R | 118 - R/print.R | 88 R/uLSIF.R | 48 README.md | 592 ++--- build/vignette.rds |binary inst/doc/densratio.R | 152 - inst/doc/densratio.Rmd | 476 ++-- inst/doc/densratio.html | 1138 +++++----- man/KLIEP.Rd | 55 man/RuLSIF.Rd | 72 man/densratio.Rd | 102 man/figures/README-basics-compute-estimated-density-ratio-1.png |binary man/figures/README-compare-2d-1.png |binary man/figures/README-compare-true-estimate-1.png |binary man/figures/README-compute-estimated-density-ratio-1.png |binary man/squared_euclid_distance.Rd | 38 man/uLSIF.Rd | 63 tests/testthat.R | 8 tests/testthat/test-KLIEP.R | 55 tests/testthat/test-RuLSIF.R | 57 tests/testthat/test-compute_kernel_Gaussian.R | 28 tests/testthat/test-uLSIF.R | 55 vignettes/densratio.Rmd | 476 ++-- 36 files changed, 2273 insertions(+), 2073 deletions(-)
Title: A Docking Layout Manager for 'blockr'
Description: Building on the docking layout manager provided by 'dockViewR',
this provides a flexible front-end to 'blockr.core'. It provides an extension mechanism which allows for providing means to manipulate a board
object via panel-based user interface components.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.dock versions 0.1.0 dated 2025-12-11 and 0.1.1 dated 2026-04-29
blockr.dock-0.1.0/blockr.dock/inst/examples/dock |only blockr.dock-0.1.1/blockr.dock/DESCRIPTION | 13 blockr.dock-0.1.1/blockr.dock/MD5 | 95 blockr.dock-0.1.1/blockr.dock/NAMESPACE | 35 blockr.dock-0.1.1/blockr.dock/NEWS.md | 25 blockr.dock-0.1.1/blockr.dock/R/action-block.R | 495 ++-- blockr.dock-0.1.1/blockr.dock/R/action-class.R | 282 +- blockr.dock-0.1.1/blockr.dock/R/action-link.R | 172 - blockr.dock-0.1.1/blockr.dock/R/action-modal.R | 67 blockr.dock-0.1.1/blockr.dock/R/action-stack.R | 295 +- blockr.dock-0.1.1/blockr.dock/R/action-utils.R | 32 blockr.dock-0.1.1/blockr.dock/R/block-meta.R | 54 blockr.dock-0.1.1/blockr.dock/R/block-ui.R | 66 blockr.dock-0.1.1/blockr.dock/R/board-server.R | 1085 ++++++++-- blockr.dock-0.1.1/blockr.dock/R/board-ui.R | 109 - blockr.dock-0.1.1/blockr.dock/R/dock-board.R | 104 blockr.dock-0.1.1/blockr.dock/R/ext-ui.R | 29 blockr.dock-0.1.1/blockr.dock/R/layout-class.R | 39 blockr.dock-0.1.1/blockr.dock/R/layouts-class.R |only blockr.dock-0.1.1/blockr.dock/R/plugin-block.R | 143 - blockr.dock-0.1.1/blockr.dock/R/utils-dock.R | 36 blockr.dock-0.1.1/blockr.dock/R/utils-id.R | 28 blockr.dock-0.1.1/blockr.dock/R/utils-misc.R | 24 blockr.dock-0.1.1/blockr.dock/R/utils-serdes.R | 47 blockr.dock-0.1.1/blockr.dock/R/utils-ui.R | 18 blockr.dock-0.1.1/blockr.dock/R/view-ui.R |only blockr.dock-0.1.1/blockr.dock/README.md | 97 blockr.dock-0.1.1/blockr.dock/build |only blockr.dock-0.1.1/blockr.dock/inst/assets/css/blockr-dock.css | 660 ++++-- blockr.dock-0.1.1/blockr.dock/inst/assets/js/show-hide-block.js | 5 blockr.dock-0.1.1/blockr.dock/inst/assets/js/view-binding.js |only blockr.dock-0.1.1/blockr.dock/inst/doc |only blockr.dock-0.1.1/blockr.dock/inst/examples/empty |only blockr.dock-0.1.1/blockr.dock/inst/examples/locked-dock |only blockr.dock-0.1.1/blockr.dock/inst/examples/single-page |only blockr.dock-0.1.1/blockr.dock/inst/examples/views |only blockr.dock-0.1.1/blockr.dock/man/action.Rd | 87 blockr.dock-0.1.1/blockr.dock/man/dock.Rd | 26 blockr.dock-0.1.1/blockr.dock/man/figures |only blockr.dock-0.1.1/blockr.dock/man/view.Rd |only blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-block.R | 73 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-class.R | 51 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-link.R | 78 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-stack.R | 117 - blockr.dock-0.1.1/blockr.dock/tests/testthat/test-block-meta.R | 23 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-class.R | 46 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-server.R | 240 +- blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-ui.R | 2 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-layouts-class.R |only blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-misc.R | 16 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-serdes.R | 18 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-serve.R | 2 blockr.dock-0.1.1/blockr.dock/vignettes |only 53 files changed, 3251 insertions(+), 1583 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.3.0 dated 2026-03-31 and 1.4.0 dated 2026-04-29
glmmrBase-1.3.0/glmmrBase/R/stanmodels.R |only glmmrBase-1.3.0/glmmrBase/README.md |only glmmrBase-1.3.0/glmmrBase/configure |only glmmrBase-1.3.0/glmmrBase/configure.win |only glmmrBase-1.3.0/glmmrBase/inst/cmdstan |only glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/sparse.h |only glmmrBase-1.3.0/glmmrBase/inst/include/stan_meta_header.hpp |only glmmrBase-1.3.0/glmmrBase/inst/stan |only glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.cc |only glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.h |only glmmrBase-1.4.0/glmmrBase/DESCRIPTION | 15 glmmrBase-1.4.0/glmmrBase/MD5 | 107 - glmmrBase-1.4.0/glmmrBase/NAMESPACE | 4 glmmrBase-1.4.0/glmmrBase/R/R6Model.R | 985 +--------- glmmrBase-1.4.0/glmmrBase/R/R6covariance.R | 4 glmmrBase-1.4.0/glmmrBase/R/RcppExports.R | 36 glmmrBase-1.4.0/glmmrBase/R/extrafunctions.R | 32 glmmrBase-1.4.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.4.0/glmmrBase/inst/include/glmmr.h | 10 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/matrixw.hpp | 10 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/model.hpp | 25 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modelbits.hpp | 3 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 686 ++++++ glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 293 +- glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/randomeffects.hpp | 122 + glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/spdecovariance.hpp |only glmmrBase-1.4.0/glmmrBase/man/Beta.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/Model.Rd | 571 +---- glmmrBase-1.4.0/glmmrBase/man/Salamanders.Rd | 28 glmmrBase-1.4.0/glmmrBase/man/SimGeospat.Rd | 48 glmmrBase-1.4.0/glmmrBase/man/SimTrial.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/coef.Model.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/coef.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/confint.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/family.Model.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/family.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/fitted.Model.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/fitted.mcml.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/fixed.effects.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/formula.Model.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/formula.mcml.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/hessian_from_formula.Rd | 80 glmmrBase-1.4.0/glmmrBase/man/hsgp_rescale.Rd | 58 glmmrBase-1.4.0/glmmrBase/man/lme4_to_glmmr.Rd | 60 glmmrBase-1.4.0/glmmrBase/man/logLik.Model.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/logLik.mcml.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/mcml_lmer.Rd | 132 - glmmrBase-1.4.0/glmmrBase/man/mesh_helper.Rd |only glmmrBase-1.4.0/glmmrBase/man/predict.Model.Rd | 62 glmmrBase-1.4.0/glmmrBase/man/predict.mcml.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/random.effects.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/residuals.Model.Rd | 56 glmmrBase-1.4.0/glmmrBase/man/residuals.mcml.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/summary.Model.Rd | 42 glmmrBase-1.4.0/glmmrBase/man/vcov.Model.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/vcov.mcml.Rd | 46 glmmrBase-1.4.0/glmmrBase/src/Makevars | 8 glmmrBase-1.4.0/glmmrBase/src/Makevars.win | 8 glmmrBase-1.4.0/glmmrBase/src/RcppExports.cpp | 126 + glmmrBase-1.4.0/glmmrBase/src/model_module.cpp | 269 ++ 60 files changed, 2368 insertions(+), 2292 deletions(-)
Title: Automatic Construction of Forced-Choice Tests
Description: Forced-choice (FC) response has gained increasing popularity
and interest for its resistance to faking when well-designed (Cao &
Drasgow, 2019 <doi:10.1037/apl0000414>). To established well-designed
FC scales, typically each item within a block should measure different
trait and have similar level of social desirability (Zhang et al.,
2020 <doi:10.1177/1094428119836486>). Recent study also suggests the
importance of high inter-item agreement of social desirability between
items within a block (Pavlov et al., 2021 <doi:10.31234/osf.io/hmnrc>).
In addition to this, FC developers may
also need to maximize factor loading differences (Brown &
Maydeu-Olivares, 2011 <doi:10.1177/0013164410375112>) or minimize item
location differences (Cao & Drasgow, 2019 <doi:10.1037/apl0000414>)
depending on scoring models. Decision of which items should be
assigned to the same block, termed item pairing, is thus critical to
the quality of an FC test. This pairing p [...truncated...]
Author: Mengtong Li [cre, aut] ,
Tianjun Sun [aut] ,
Bo Zhang [aut]
Maintainer: Mengtong Li <mt_li@fudan.edu.cn>
This is a re-admission after prior archival of version 0.2.0.1002 dated 2025-03-13
Diff between autoFC versions 0.2.0.1002 dated 2025-03-13 and 0.2.0.1010 dated 2026-04-29
DESCRIPTION | 22 ++++----- MD5 | 27 ++++++----- NAMESPACE | 5 +- R/bp.coeff.raw.R |only R/cal_block_energy_with_iia.R | 1 R/convert_to_TIRT_response.R | 17 +++---- R/fit_TIRT_model.R | 8 +-- R/get_iia.R | 75 +++++++++++++++---------------- R/gwet.ac1.raw.R |only R/identity.weights.R |only R/linear.weights.R |only R/quadratic.weights.R |only R/sa_pairing_generalized.R | 1 inst/doc/autoFC.html | 93 +++++++++++++++++++++++++++++++++------ man/cal_block_energy_with_iia.Rd | 1 man/convert_to_TIRT_response.Rd | 14 ++--- man/fit_TIRT_model.Rd | 1 17 files changed, 167 insertions(+), 98 deletions(-)
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>
Diff between arrow versions 23.0.1.2 dated 2026-03-25 and 24.0.0 dated 2026-04-29
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arrow-24.0.0/arrow/src/arrow_types.h | 2 arrow-24.0.0/arrow/src/compute-exec.cpp | 23 arrow-24.0.0/arrow/src/config.cpp | 2 arrow-24.0.0/arrow/src/parquet.cpp | 54 arrow-24.0.0/arrow/src/r_to_arrow.cpp | 2 arrow-24.0.0/arrow/tests/testthat/helper-expectation.R | 5 arrow-24.0.0/arrow/tests/testthat/test-Array.R | 13 arrow-24.0.0/arrow/tests/testthat/test-RecordBatch.R | 5 arrow-24.0.0/arrow/tests/testthat/test-Table.R | 2 arrow-24.0.0/arrow/tests/testthat/test-chunked-array.R | 4 arrow-24.0.0/arrow/tests/testthat/test-compute-aggregate.R | 2 arrow-24.0.0/arrow/tests/testthat/test-compute-no-bindings.R | 4 arrow-24.0.0/arrow/tests/testthat/test-dataset-csv.R | 18 arrow-24.0.0/arrow/tests/testthat/test-dataset-write.R | 23 arrow-24.0.0/arrow/tests/testthat/test-dataset.R | 6 arrow-24.0.0/arrow/tests/testthat/test-dplyr-filter.R | 48 arrow-24.0.0/arrow/tests/testthat/test-dplyr-funcs-conditional.R | 363 ++++++ arrow-24.0.0/arrow/tests/testthat/test-dplyr-funcs-string.R | 10 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Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.13 dated 2026-03-16 and 1.3.15 dated 2026-04-29
wrGraph-1.3.13/wrGraph/man/dot-colorByPvalue.Rd |only wrGraph-1.3.15/wrGraph/DESCRIPTION | 8 wrGraph-1.3.15/wrGraph/MD5 | 23 wrGraph-1.3.15/wrGraph/NAMESPACE | 1 wrGraph-1.3.15/wrGraph/R/MAplotW.R | 658 ++++++++++-------- wrGraph-1.3.15/wrGraph/R/VolcanoPlotW.R | 350 +++------ wrGraph-1.3.15/wrGraph/build/vignette.rds |binary wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.R | 14 wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.Rmd | 18 wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.html | 89 +- wrGraph-1.3.15/wrGraph/man/MAplotW.Rd | 35 wrGraph-1.3.15/wrGraph/man/VolcanoPlotW.Rd | 24 wrGraph-1.3.15/wrGraph/vignettes/wrGraphVignette1.Rmd | 18 13 files changed, 669 insertions(+), 569 deletions(-)
Title: Space Filling Optimal Covariate Designs
Description: We have designed this package to address experimental scenarios involving multiple covariates. It focuses on construction of Optimal Covariate Designs (OCDs), checking space filling property of the developed design. The primary objective of the package is to generate OCDs using four methods viz., M array method, Juxtapose method, Orthogonal Integer Array and Hadamard method. The package also evaluates space filling properties of both the base design and OCDs using the MaxPro criterion, providing a meaningful basis for comparison. In addition, it includes tool to visualize the spread offered by the design points in the form of scatterplot, which help users to assess distribution and coverage of design points.
Author: Neethu RS [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Ashutosh Dalal [aut, ctb, cre]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between SFOCDs versions 1.1.0 dated 2026-04-15 and 1.2.0 dated 2026-04-29
DESCRIPTION | 7 ++-- MD5 | 18 ++++++----- NAMESPACE | 1 R/HadamardOCDs.R | 2 + R/JuxtaOCDs.R | 3 + R/MOCDs.R | 79 +++++++++++++++++++++++++++++++++++++-------------- R/MaxDot.R | 4 +- R/OIAOCDs.R | 4 +- R/reshuffle_des.R |only man/MaxDot.Rd | 2 - man/reshuffle_des.Rd |only 11 files changed, 85 insertions(+), 35 deletions(-)
Title: Constitution of Core Collections by Principal Component Scoring
Strategy
Description: Generate a Core Collection with Principal Component Scoring
Strategy (PCSS) using qualitative and/or quantitative trait data according
to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>,
Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003)
<https://www.documentation.ird.fr/hor/fdi:010031886>.
Author: J. Aravind [aut, cre] ,
Anju Mahendru Singh [aut] ,
ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.org.in>
This is a re-admission after prior archival of version 0.1.0 dated 2025-02-17
Diff between rpcss versions 0.1.0 dated 2025-02-17 and 0.1.1 dated 2026-04-29
DESCRIPTION | 36 MD5 | 50 - NEWS.md | 5 R/biplot.pcss.core.R | 938 +++++++++++------------ R/contrib.pcss.core.R | 684 ++++++++--------- R/coreplot.pcss.core.R | 804 +++++++++++++------- R/generics.R | 2 R/globals.R | 6 R/pcss.core.R | 1383 ++++++++++++++++++----------------- R/print.pcss.core.R | 101 +- R/screeplot.pcss.core.R | 379 ++++----- R/subset.pcss.core.R | 457 +++++++---- R/xtra.R | 88 +- README.md | 112 ++ build/partial.rdb |binary build/rpcss.pdf |binary build/stage23.rdb |binary inst/CITATION | 13 inst/pkgdown.yml | 4 man/biplot.pcss.core.Rd | 138 +-- man/contrib.Rd | 158 +-- man/coreplot.Rd | 88 +- man/figures/README-readme-plot-1.png |binary man/pcss.core.Rd | 66 - man/screeplot.pcss.core.Rd | 77 + man/subset.pcss.core.Rd | 100 +- 26 files changed, 3104 insertions(+), 2585 deletions(-)
Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.7 dated 2025-12-14 and 1.8 dated 2026-04-29
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/iSCMEB.R | 4 ++-- README.md | 2 ++ inst/doc/CosMx.html | 6 +++--- inst/doc/FASTdlpfc.html | 6 +++--- inst/doc/FASTdlpfc2.html | 6 +++--- inst/doc/FASTsimu.html | 6 +++--- inst/doc/pbmc3k.html | 6 +++--- 10 files changed, 33 insertions(+), 31 deletions(-)