Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-30 1.0.3
2023-12-21 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-22 0.5.1
2025-08-26 0.3.1
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.14.0 dated 2025-09-29 and 0.15.0 dated 2025-10-19
DESCRIPTION | 6 MD5 | 220 ++-- NEWS.md | 26 R/aaa_class.R | 8 R/build_tt.R | 59 - R/expand_style.R | 242 +--- R/grid_colspan.R | 9 R/grid_style.R | 54 R/group_tt_j.R | 16 R/html_finalize.R | 18 R/html_style.R | 403 ++++--- R/json.R | 23 R/plot_tt.R | 281 ++++- R/sanity.R | 2 R/style_tt.R | 126 +- R/tabularray_style.R | 308 +++-- R/tabulator_build.R | 15 R/tabulator_columns.R | 547 ++-------- R/tabulator_css.R | 1 R/tabulator_data.R | 34 R/tabulator_finalize.R | 152 ++ R/tabulator_plot.R |only R/tabulator_search.R | 151 +- R/tabulator_style.R | 348 ++++-- R/tabulator_stylesheet.R | 49 R/theme_html.R | 29 R/theme_html_tabulator.R | 11 R/theme_striped.R | 8 R/typst_style.R | 185 ++- R/typst_tt.R | 6 README.md | 2 build/partial.rdb |binary inst/tabulator.scss |only inst/tabulator_tinytable.css |only inst/tabulator_tinytable.css.map |only inst/tabulator_tinytable.min.css |only inst/tabulator_tinytable.min.css.map |only inst/tabulator_tinytable.scss |only inst/templates/html.html | 1 inst/templates/tabulator.html | 18 inst/tinytable.js | 174 +++ inst/tinytest/_tinysnapshot/ansi-style_groupj_01.md | 2 inst/tinytest/_tinysnapshot/ansi-styles_01.md | 2 inst/tinytest/_tinysnapshot/docx-issue98_01.txt | 2 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.html | 16 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.typ | 4 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.html | 16 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.typ | 4 inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 8 inst/tinytest/_tinysnapshot/group-3level.md | 4 inst/tinytest/_tinysnapshot/group-3level.typ | 25 inst/tinytest/_tinysnapshot/group-delim-all-delim.md | 2 inst/tinytest/_tinysnapshot/group-delim-some-delim.md | 2 inst/tinytest/_tinysnapshot/group-delim-x-delim.md | 2 inst/tinytest/_tinysnapshot/group-html_tutorial_01.html | 20 inst/tinytest/_tinysnapshot/group-issue165_extra_row.html | 32 inst/tinytest/_tinysnapshot/group-issue165_extra_row.md | 2 inst/tinytest/_tinysnapshot/group-issue165_extra_row.typ | 4 inst/tinytest/_tinysnapshot/group-issue165_html_centering_style.html | 40 inst/tinytest/_tinysnapshot/group-multilevel-basic.html | 20 inst/tinytest/_tinysnapshot/group-multilevel-basic.md | 2 inst/tinytest/_tinysnapshot/group-multilevel-basic.typ | 6 inst/tinytest/_tinysnapshot/group-multilevel-complex.html | 32 inst/tinytest/_tinysnapshot/group-multilevel-complex.md | 4 inst/tinytest/_tinysnapshot/group-multilevel-complex.typ | 14 inst/tinytest/_tinysnapshot/group-multilevel-empty.html | 42 inst/tinytest/_tinysnapshot/group-multilevel-empty.md | 4 inst/tinytest/_tinysnapshot/group-multilevel-empty.tex | 2 inst/tinytest/_tinysnapshot/group-multilevel-empty.typ | 13 inst/tinytest/_tinysnapshot/group-nse.html | 4 inst/tinytest/_tinysnapshot/group-shared-level-spanning.md | 2 inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.html | 8 inst/tinytest/_tinysnapshot/html-alignment.html | 32 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inst/tinytest/_tinysnapshot/markdown-long_column_group.txt | 2 inst/tinytest/_tinysnapshot/markdown-long_mixed_groups.txt | 2 inst/tinytest/_tinysnapshot/style-align_partial.html | 40 inst/tinytest/_tinysnapshot/style-groupj_colnames.md | 2 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.html | 44 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.md | 2 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.typ | 4 inst/tinytest/_tinysnapshot/style-issue514_white_blue.html | 12 inst/tinytest/_tinysnapshot/style-issue514_white_blue.typ | 20 inst/tinytest/_tinysnapshot/style-smallcap.html | 20 inst/tinytest/_tinysnapshot/theme-issue531_style_colors_override_stripes.html | 24 inst/tinytest/_tinysnapshot/typst-complicated.typ | 4 inst/tinytest/_tinysnapshot/typst-group_columns.typ | 5 inst/tinytest/_tinysnapshot/typst-issue-139_misaligned_rule_with_group_tt.typ | 4 inst/tinytest/_tinysnapshot/typst-issue323_group_tt_style_tt.typ | 5 inst/tinytest/_tinysnapshot/typst-issue592.typ |only inst/tinytest/_tinysnapshot/typst-no_headers.typ | 7 inst/tinytest/test-group.R | 23 inst/tinytest/test-latex.R | 11 inst/tinytest/test-markdown.R | 33 inst/tinytest/test-typst.R | 71 + man/plot_tt.Rd | 30 man/plot_vector.Rd | 7 man/style_tt.Rd | 24 man/theme_html.Rd | 17 man/tt.Rd | 2 116 files changed, 2753 insertions(+), 1794 deletions(-)
Title: Synthetic Control Group Method for Comparative Case Studies
Description: Implements the synthetic control group method for comparative case studies
as described in Abadie and Gardeazabal (2003) and Abadie, Diamond, and Hainmueller
(2010, 2011, 2014). The synthetic control method allows for effect estimation in
settings where a single unit (a state, country, firm, etc.) is exposed to an event
or intervention. It provides a data-driven procedure to construct synthetic control
units based on a weighted combination of comparison units that approximates the
characteristics of the unit that is exposed to the intervention. A combination of
comparison units often provides a better comparison for the unit exposed to the
intervention than any comparison unit alone.
Author: Jens Hainmueller [aut, cre],
Alexis Diamond [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between Synth versions 1.1-8 dated 2023-06-02 and 1.1-9 dated 2025-10-19
DESCRIPTION | 27 +++-- MD5 | 6 - man/fn.V.Rd | 12 +- man/synth.Rd | 310 +++++++++++------------------------------------------------ 4 files changed, 88 insertions(+), 267 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 1.0.1 dated 2025-03-13 and 1.1.0 dated 2025-10-19
HARplus-1.0.1/HARplus/vignettes/rsconnect |only HARplus-1.1.0/HARplus/DESCRIPTION | 8 HARplus-1.1.0/HARplus/MD5 | 28 HARplus-1.1.0/HARplus/NAMESPACE | 63 HARplus-1.1.0/HARplus/R/data_summary.R | 736 ++++----- HARplus-1.1.0/HARplus/R/get_data.R | 1638 +++++++++++----------- HARplus-1.1.0/HARplus/R/load_sl4x.R | 15 HARplus-1.1.0/HARplus/R/save_har.R |only HARplus-1.1.0/HARplus/README.md | 23 HARplus-1.1.0/HARplus/inst/doc/introduction.R | 20 HARplus-1.1.0/HARplus/inst/doc/introduction.Rmd | 44 HARplus-1.1.0/HARplus/inst/doc/introduction.html | 222 +- HARplus-1.1.0/HARplus/inst/docs |only HARplus-1.1.0/HARplus/man/export_data.Rd | 156 +- HARplus-1.1.0/HARplus/man/pivot_data_hierarchy.Rd | 152 +- HARplus-1.1.0/HARplus/man/save_har.Rd |only HARplus-1.1.0/HARplus/vignettes/introduction.Rmd | 44 17 files changed, 1669 insertions(+), 1480 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 3.1.13 dated 2025-07-22 and 3.1.18 dated 2025-10-19
DESCRIPTION | 8 MD5 | 49 ++-- NAMESPACE | 2 R/PVA.v3.r | 14 - R/byIndv4Times.r | 310 ++++++++++++++++++++++++++- R/calcs.r | 25 +- R/traitSmooth.r | 17 + build/partial.rdb |binary build/vignette.rds |binary inst/News.Rd | 26 ++ inst/doc/Rice.pdf |binary inst/doc/Tomato.pdf |binary inst/doc/growthPheno-manual.pdf |binary man/args4smoothing.Rd | 7 man/byIndv4Intvl_WaterUse.Rd | 2 man/byIndv4Times_GRsDiff.Rd | 6 man/byIndv4Times_SplinesGRs.Rd | 7 man/byIndv4Times_WaterUse.Rd |only man/byIndv4Times_periodicRates.Rd |only man/calcLagged.Rd | 3 man/growthPheno-pkg.Rd | 14 - man/plotCorrmatrix.Rd | 6 tests/testthat/data/water779DS.test.dat.rda |only tests/testthat/data/water797SH.check.dat.rda |only tests/testthat/data/water797SH.test.dat.rda |only tests/testthat/testTraitWrappers.r | 33 ++ tests/testthat/testbyIndv4Times.r | 105 +++++++++ tests/testthat/testexampleData.r | 2 28 files changed, 579 insertions(+), 57 deletions(-)
Title: Dataframe Difference Tool
Description: Functions for comparing two data.frames against
each other. The core functionality is to provide a detailed breakdown of any differences
between two data.frames as well as providing utility functions to help narrow down the
source of problems and differences.
Author: Craig Gower-Page [cre, aut],
Kieran Martin [aut]
Maintainer: Craig Gower-Page <craiggower@gmail.com>
Diff between diffdf versions 1.1.1 dated 2024-09-24 and 1.1.2 dated 2025-10-19
DESCRIPTION | 19 - LICENSE | 4 MD5 | 34 +- NEWS.md | 11 R/ascii_tables.R | 13 - R/diffdf.R | 32 -- R/identify.R | 2 R/print.R | 45 +++ build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/diffdf-basic.R | 6 inst/doc/diffdf-basic.html | 4 man/get_print_message.issue.Rd | 5 man/get_table.Rd | 3 man/print.diffdf.Rd | 21 + tests/testthat/_snaps/miscellaneous.md | 392 +++++++++++++++++++++++++++++++++ tests/testthat/test-miscellaneous.R | 154 ++++++++++++ tests/testthat/test-print_output.R | 40 +++ 18 files changed, 707 insertions(+), 79 deletions(-)
Title: Tidy Tools for Paleoenvironmental Archives
Description: Provides a set of functions with a common framework for age-depth model management,
stratigraphic visualization, and common statistical transformations. The focus of the
package is stratigraphic visualization, for which 'ggplot2' components are provided
to reproduce the scales, geometries, facets, and theme elements commonly used in
publication-quality stratigraphic diagrams. Helpers are also provided to reproduce
the exploratory statistical summaries that are frequently included on
stratigraphic diagrams. See Dunnington et al. (2021) <doi:10.18637/jss.v101.i07>.
Author: Dewey Dunnington [aut, cre, cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between tidypaleo versions 0.1.3 dated 2023-01-18 and 0.1.4 dated 2025-10-19
DESCRIPTION | 12 MD5 | 117 +++++- NEWS.md | 6 R/age_depth_model.R | 4 R/ggstrat-geoms.R | 12 R/ggstrat-plot_addons.R | 6 R/ggstrat-themes.R | 2 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/age_depth.R | 20 - inst/doc/age_depth.html | 89 ++-- inst/doc/nested_analysis.R | 6 inst/doc/nested_analysis.html | 424 +++++++++++------------ inst/doc/strat_diagrams.R | 68 +-- inst/doc/strat_diagrams.html | 620 +++++++++++++++++----------------- man/geom_point_exaggerate.Rd | 2 man/stat_nested_hclust.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps |only tests/testthat/test-age_depth_model.R | 4 tests/testthat/test-nested_chclust.R | 4 22 files changed, 741 insertions(+), 661 deletions(-)
Title: Cohort Data Analyses
Description: Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Diff between cohorttools versions 0.1.6 dated 2022-11-23 and 0.1.7 dated 2025-10-18
DESCRIPTION | 13 ++++++++----- MD5 | 12 ++++++------ NEWS.md | 2 +- R/cohorttools.R | 3 --- man/boxesLx.Rd | 3 --- man/mkratetable.Rd | 3 --- man/plotcuminc.Rd | 3 --- 7 files changed, 15 insertions(+), 24 deletions(-)
Title: Highlight Conserved Edits Across Versions of a Document
Description: Input multiple versions of a source document,
and receive HTML code for a highlighted version of the source document
indicating the frequency of occurrence of phrases in the different versions.
This method is described in Chapter 3 of
Rogers (2024) <https://digitalcommons.unl.edu/dissertations/AAI31240449/>.
Author: Center for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Rachel Rogers [aut, cre] ,
Susan VanderPlas [aut]
Maintainer: Rachel Rogers <rrogers.rpackages@gmail.com>
Diff between highlightr versions 1.1.2 dated 2025-06-26 and 1.2.0 dated 2025-10-18
DESCRIPTION | 8 MD5 | 56 +- NEWS.md | 14 R/collocate_comments.R | 163 +++--- R/collocate_comments_fuzzy.R | 28 - R/collocation_plot.R | 10 R/data.R | 88 +-- R/highlighted_text.R | 14 R/token_comments.R | 67 +- R/token_transcript.R | 67 +- R/transcript_frequency.R | 9 README.md | 31 + inst/doc/highlightr.R | 50 + inst/doc/highlightr.Rmd | 54 ++ inst/doc/highlightr.html | 291 ++++++---- inst/doc/wikipedia-highlighter.R | 69 +- inst/doc/wikipedia-highlighter.Rmd | 77 +- inst/doc/wikipedia-highlighter.html | 956 ++++++++++++++++++------------------ man/collocate_comments.Rd | 15 man/collocate_comments_fuzzy.Rd | 25 man/collocation_plot.Rd | 7 man/figures/highlight_example.PNG |binary man/highlighted_text.Rd | 11 man/token_comments.Rd | 2 man/token_transcript.Rd | 2 man/transcript_frequency.Rd | 6 man/wiki_pages.Rd | 2 vignettes/highlightr.Rmd | 54 ++ vignettes/wikipedia-highlighter.Rmd | 77 +- 29 files changed, 1362 insertions(+), 891 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-1 dated 2025-07-07 and 1.2-2 dated 2025-10-18
ChangeLog | 12 +++ DESCRIPTION | 8 +- MD5 | 14 +-- R/plotcpfa.R | 7 - inst/doc/cpfa.R | 83 ++++++++++++++++++++ inst/doc/cpfa.Rmd | 212 +++++++++++++++++++++++++++++++++++++++++++++++------ inst/doc/cpfa.pdf |binary vignettes/cpfa.Rmd | 212 +++++++++++++++++++++++++++++++++++++++++++++++------ 8 files changed, 488 insertions(+), 60 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre] ,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.14 dated 2025-07-11 and 1.2.15 dated 2025-10-18
DESCRIPTION | 10 ++-- MD5 | 42 +++++++++---------- NAMESPACE | 2 R/wiki_utils.R | 21 ++++++--- README.md | 4 - build/vignette.rds |binary inst/doc/wiki_utils.html | 39 +++++++++-------- man/filext.Rd | 58 +++++++++++++------------- man/getFiles.Rd | 102 +++++++++++++++++++++++------------------------ man/getWikiFiles.Rd | 88 ++++++++++++++++++++-------------------- man/httrGetJSON.Rd | 62 ++++++++++++++-------------- man/limitRequester.Rd | 3 - man/nametoWikiFrame.Rd | 74 +++++++++++++++++----------------- man/nametoWikiHtml.Rd | 70 ++++++++++++++++---------------- man/nametoWikiURL.Rd | 74 +++++++++++++++++----------------- man/preName.Rd | 60 +++++++++++++-------------- man/searchWiki.Rd | 96 ++++++++++++++++++++++---------------------- man/selectLang.Rd | 48 +++++++++++----------- man/urltoFrame.Rd | 70 ++++++++++++++++---------------- man/urltoHtml.Rd | 86 +++++++++++++++++++-------------------- man/validUrl.Rd | 56 ++++++++++++------------- man/w_query.Rd | 4 - 22 files changed, 537 insertions(+), 532 deletions(-)
Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting. The package is described in
Vollering et al. (2019; <doi:10.1002/ece3.5654>).
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph],
Michael Bedward [ctb]
Maintainer: Julien Vollering <julienvollering@gmail.com>
Diff between MIAmaxent versions 1.3.1 dated 2024-08-23 and 1.4.0 dated 2025-10-18
MIAmaxent-1.3.1/MIAmaxent/inst/doc/a-modeling-example.html.asis |only MIAmaxent-1.3.1/MIAmaxent/man/release_questions.Rd |only MIAmaxent-1.3.1/MIAmaxent/vignettes/a-modeling-example.html.asis |only MIAmaxent-1.4.0/MIAmaxent/DESCRIPTION | 12 MIAmaxent-1.4.0/MIAmaxent/MD5 | 32 MIAmaxent-1.4.0/MIAmaxent/NEWS.md | 158 ++-- MIAmaxent-1.4.0/MIAmaxent/R/deriveVars.R | 1 MIAmaxent-1.4.0/MIAmaxent/R/plotFOP.R | 2 MIAmaxent-1.4.0/MIAmaxent/R/testAUC.R | 9 MIAmaxent-1.4.0/MIAmaxent/R/utils.R | 30 MIAmaxent-1.4.0/MIAmaxent/README.md | 6 MIAmaxent-1.4.0/MIAmaxent/build/partial.rdb |binary MIAmaxent-1.4.0/MIAmaxent/build/vignette.rds |binary MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.R |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.Rmd |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.html |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.R |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.Rmd |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.html | 323 +++++----- MIAmaxent-1.4.0/MIAmaxent/vignettes/NCEAS.Rmd |only MIAmaxent-1.4.0/MIAmaxent/vignettes/a-modeling-example.Rmd | 73 -- MIAmaxent-1.4.0/MIAmaxent/vignettes/references.bib |only 22 files changed, 330 insertions(+), 316 deletions(-)
Title: Marginal Modeling for Exposure Data with Values Below the LOD
Description: Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates. For more details see Chen IC, Bertke SJ, Curwin BD (2021) <doi:10.1038/s41370-021-00345-1>, Chen IC, Bertke SJ, Estill CF (2024) <doi:10.1038/s41370-024-00640-7>, Chen IC, Bertke SJ, Dahm MM (2024) <doi:10.1093/annweh/wxae068>, and Chen IC (2025) <doi:10.1038/s41370-025-00752-8>.
Author: I-Chen Chen [cre, aut] ,
Philip Westgate [ctb],
Liya Fu [ctb]
Maintainer: I-Chen Chen <flecsh@gmail.com>
Diff between marlod versions 0.2.1 dated 2025-05-27 and 0.2.2 dated 2025-10-18
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS.md | 62 +++++++++++++++-------------- R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/marlod.html | 106 +++++++++++++++++++++++++-------------------------- man/Fillin.Rd | 6 +- man/Modified.QIF.Rd | 12 ++--- 9 files changed, 109 insertions(+), 103 deletions(-)
Title: Interpretation of Heterogeneous Single-Cell Gene Expression Data
Description: We develop a novel matrix factorization tool named 'scINSIGHT' to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. Given multiple gene expression samples from different biological conditions, 'scINSIGHT' simultaneously identifies common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space. With the factorized results, the inferred expression levels and memberships of common gene modules can be used to cluster cells and detect cell identities, and the condition-specific gene modules can help compare functional differences in transcriptomes from distinct conditions. Please also see Qian K, Fu SW, Li HW, Li WV (2022) <doi:10.1186/s13059-022-02649-3>.
Author: Kun Qian [aut, ctb, cre] ,
Wei Vivian Li [aut, ctb]
Maintainer: Kun Qian <Kun_Qian@foxmail.com>
Diff between scINSIGHT versions 0.1.4 dated 2022-05-29 and 0.1.5 dated 2025-10-18
DESCRIPTION | 14 ++++++++------ MD5 | 9 +++++---- R/RcppExports.R | 30 +++++++++++++++--------------- README.md |only src/Makevars | 2 +- src/Makevars.win | 2 +- 6 files changed, 30 insertions(+), 27 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 2.1 dated 2025-06-17 and 2.2 dated 2025-10-18
DESCRIPTION | 8 +-- MD5 | 110 +++++++++++++++++++++++++++------------------------- R/ABWilcox.R | 2 R/ABbinomial.R | 9 ++-- R/ABdescrip.R | 3 - R/ABma.R | 16 ++++--- R/ABregres.R | 21 +++++++-- R/ABrf2.R | 3 - R/ABrobust.R | 7 +-- R/ABttest.R | 6 ++ R/Aregres.R | 17 +++++--- R/Arimadiff.R | 6 +- R/Arimama.R | 5 +- R/Arobust.R | 2 R/CDCabove.R | 9 ++-- R/CDCbelow.R | 9 ++-- R/Cchart.R | 14 +++--- R/GABrf2.R | 2 R/GABttest.R | 2 R/Gindex.R | 15 ++++--- R/IRDabove.R | 6 +- R/IRDbelow.R | 6 +- R/NAPabove.R | 6 +- R/NAPbelow.R | 6 +- R/PANDabove.R | 6 +- R/PANDbelow.R | 3 - R/PEMabove.R | 6 +- R/PEMbelow.R | 8 +-- R/PNDabove.R | 6 +- R/PNDbelow.R | 6 +- R/Pchart.R | 17 ++++---- R/RMEffectsize.R |only R/RMttest.R |only R/RSIQRline.R | 3 - R/RSPCline.R |only R/Rchart.R | 16 +------ R/Rchartsd.R | 6 +- R/RobustCDCabove.R | 11 ++--- R/RobustCDCbelow.R | 10 ++-- R/SPClegend.R | 8 ++- R/SPCline.R | 4 - R/XRchart.R | 11 ----- R/Xmrchart.R | 9 ---- R/diffchart.R | 12 +++-- R/meanabove.R | 7 ++- R/meanbelow.R | 11 +++-- R/medabove.R | 10 ++-- R/medbelow.R | 7 +-- R/metareg.R | 2 R/metaregi.R | 3 - R/regabove.R | 13 +++--- R/regbelow.R | 10 +++- R/robregabove.R | 12 ++--- R/robregbelow.R | 11 +++-- R/trimabove.R | 8 ++- R/trimbelow.R | 8 ++- man/RMEffectsize.Rd |only man/RMttest.Rd |only man/RSPCline.Rd |only 59 files changed, 292 insertions(+), 242 deletions(-)
Title: Flexible Client for the 'Financial Modeling Prep' API
Description: Provides a flexible interface to the 'Financial Modeling Prep' API
<https://site.financialmodelingprep.com/developer/docs>. The package
supports all available endpoints and parameters, enabling R users
to interact with a wide range of financial data.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between fmpapi versions 0.2.1 dated 2025-05-07 and 1.0.0 dated 2025-10-18
DESCRIPTION | 6 +- MD5 | 12 ++--- NEWS.md | 6 ++ R/fmp_get.R | 44 +++++++++++++++---- README.md | 8 --- man/fmp_get.Rd | 2 tests/testthat/test-fmp_get.R | 96 ++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 147 insertions(+), 27 deletions(-)
Title: Transition Network Analysis (TNA)
Description: Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)
<doi:10.1145/3706468.3706513> for more details on TNA.
Author: Mohammed Saqr [aut],
Santtu Tikka [aut],
Sonsoles Lopez-Pernas [aut, cre]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between tna versions 1.0.0 dated 2025-07-15 and 1.1.0 dated 2025-10-18
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Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between huito versions 0.2.5 dated 2024-09-05 and 0.2.6 dated 2025-10-18
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Title: A 'ggplot2' Extension for Composable Visualization
Description: A 'ggplot2' extension providing an integrative framework for
composable visualization, enabling the creation of complex multi-plot
layouts such as insets, circular arrangements, and multi-panel compositions.
Built on the grammar of graphics, it offers tools to align, stack, and nest
plots, simplifying the construction of richly annotated figures for
high-dimensional data contexts—such as genomics, transcriptomics, and
microbiome studies—by making it easy to link related plots, overlay
clustering results, or highlight shared patterns.
Author: Yun Peng [aut, cre] ,
Shixiang Wang [aut] ,
Guangchuang Yu [ths]
Maintainer: Yun Peng <yunyunp96@163.com>
Diff between ggalign versions 1.1.0 dated 2025-09-11 and 1.2.0 dated 2025-10-18
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Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb] ,
Frederiek - Maarten Kerckhof [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.4 dated 2025-09-14 and 1.3.5 dated 2025-10-18
DESCRIPTION | 26 ++++-------- MD5 | 26 ++++++------ NEWS.md | 10 ++++ R/RcppExports.R | 4 + R/clustering_functions.R | 29 +++++++++++--- README.md | 20 ++------- build/vignette.rds |binary inst/doc/the_clusterR_package.html | 12 ++--- inst/include/ClusterRHeader.h | 76 ++++++++++++++++++++++++++++++++++++- man/predict_GMM.Rd | 3 - src/RcppExports.cpp | 15 +++++++ src/export_inst_folder_headers.cpp | 15 +++++++ src/init.c | 2 tests/testthat/test-gmm.R | 71 ++++++++++++++++++++++++++++++++++ 14 files changed, 251 insertions(+), 58 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.7.2 dated 2023-02-01 and 0.7.3 dated 2025-10-18
DESCRIPTION | 8 - MD5 | 44 ++++---- NEWS.md | 10 + R/box_m.R | 10 - R/sign_test.R | 2 R/wilcox_test.R | 2 README.md | 91 ++++++++---------- man/box_m.Rd | 10 - man/chisq_test.Rd | 2 man/cor_plot.Rd | 14 +- man/fisher_test.Rd | 8 - man/wilcox_test.Rd | 2 tests/testthat/test-remove_ns.R | 47 ++++++--- tests/testthat/test-wilcox_test.R | 32 +++++- tools/README-comaprison-against-reference-group-1.png |binary tools/README-comaprison-against-reference-group-2.png |binary tools/README-comparison-against-base-mean-1.png |binary tools/README-custoize-p-value-labels-1.png |binary tools/README-grouped-two-sample-t-test-1.png |binary tools/README-paired-t-test-1.png |binary tools/README-pairwise-comparisons-1.png |binary tools/README-unnamed-chunk-10-1.png |binary tools/README-unpaired-two-sample-t-test-1.png |binary 23 files changed, 161 insertions(+), 121 deletions(-)
Title: Non-Smooth Regularization for Structural Equation Models
Description: Provides regularized structural equation modeling
(regularized SEM) with non-smooth penalty functions (e.g., lasso) building
on 'lavaan'. The package is heavily inspired by the
['regsem'](<https://github.com/Rjacobucci/regsem>) and
['lslx'](<https://github.com/psyphh/lslx>) packages.
Author: Jannik H. Orzek [aut, cre, cph]
Maintainer: Jannik H. Orzek <jannik.orzek@mailbox.org>
Diff between lessSEM versions 1.5.6 dated 2025-08-25 and 1.5.7 dated 2025-10-18
DESCRIPTION | 6 +- MD5 | 30 +++++----- inst/doc/Definition-Variables-and-Multi-Group-SEM.html | 5 + inst/doc/Estimator-Settings.html | 5 + inst/doc/General-Purpose-Optimization.html | 5 + inst/doc/Mixed-Penalties.html | 5 + inst/doc/Parameter-transformations.html | 5 + inst/doc/The-Structural-Equation-Model.html | 5 + inst/doc/lessSEM.html | 5 + inst/include/lesstimate/include/lesstimate/bfgs.h | 2 inst/include/lesstimate/include/lesstimate/bfgsOptim.h | 4 - inst/include/lesstimate/include/lesstimate/glmnet_class.h | 4 - inst/include/lesstimate/include/lesstimate/glmnet_lsp.h | 2 inst/include/lesstimate/include/lesstimate/glmnet_mcp.h | 2 inst/include/lesstimate/include/lesstimate/ista_class.h | 6 +- inst/include/lesstimate/include/lesstimate/ista_mixedPenalty.h | 2 16 files changed, 51 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-11 0.3.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-06 0.6.3
2024-07-14 0.6.2
2024-04-09 0.6.1
2023-10-16 0.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-06 2.1.16
2022-01-20 2.1.9
2021-12-02 2.1.7
2021-03-15 2.0.7
2020-12-16 2.0.3
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani [aut, cre],
Maria Brigida Ferraro [aut],
Alessio Serafini [aut]
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 2.1.2 dated 2025-07-22 and 2.1.3 dated 2025-10-18
DESCRIPTION | 10 ++--- MD5 | 14 ++++---- NEWS.md | 4 ++ inst/CITATION | 2 - src/F.cpp | 4 +- src/FKM_rcpp.cpp | 92 +++++++++++++++++++++++++++---------------------------- src/func.cpp | 2 - src/memDeg.cpp | 2 - 8 files changed, 67 insertions(+), 63 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 3.1-8 dated 2025-08-18 and 3.1-9 dated 2025-10-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 16 ++++++++++++++++ data/austates.rda |binary data/shelling.rda |binary inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + 7 files changed, 28 insertions(+), 10 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Tommy Jones [aut, cre],
William Doane [ctb],
Mattias Attbom [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 3.0.5 dated 2021-06-28 and 3.0.6 dated 2025-10-18
DESCRIPTION | 11 MD5 | 68 - NEWS.md | 17 R/other_utilities.R | 5 R/textmineR.R | 3 R/topic_modeling_core.R | 22 README.md | 10 build/vignette.rds |binary inst/doc/a_start_here.R | 33 inst/doc/a_start_here.Rmd | 3 inst/doc/a_start_here.html | 604 ++++++++++------- inst/doc/b_document_clustering.R | 27 inst/doc/b_document_clustering.Rmd | 11 inst/doc/b_document_clustering.html | 353 +++++----- inst/doc/c_topic_modeling.R | 21 inst/doc/c_topic_modeling.Rmd | 11 inst/doc/c_topic_modeling.html | 1245 ++++++++++++++++++++---------------- inst/doc/d_text_embeddings.R | 14 inst/doc/d_text_embeddings.Rmd | 10 inst/doc/d_text_embeddings.html | 622 ++++++++++------- inst/doc/e_doc_summarization.R | 241 +++--- inst/doc/e_doc_summarization.Rmd | 27 inst/doc/e_doc_summarization.html | 536 ++++++++------- inst/doc/f_tidytext_example.R | 11 inst/doc/f_tidytext_example.Rmd | 11 inst/doc/f_tidytext_example.html | 317 +++++---- man/nih.Rd | 5 man/textmineR.Rd | 19 src/RcppExports.cpp | 5 vignettes/a_start_here.Rmd | 3 vignettes/b_document_clustering.Rmd | 11 vignettes/c_topic_modeling.Rmd | 11 vignettes/d_text_embeddings.Rmd | 10 vignettes/e_doc_summarization.Rmd | 27 vignettes/f_tidytext_example.Rmd | 11 35 files changed, 2485 insertions(+), 1850 deletions(-)
Title: Kalman Filter
Description: 'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations. There is also a function to handle time varying parameters.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kalmanfilter versions 2.1.1 dated 2024-03-07 and 2.2.0 dated 2025-10-18
kalmanfilter-2.1.1/kalmanfilter/man/Rginv.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/contains.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/gen_inv.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/kalman_filter_cpp.Rd |only kalmanfilter-2.2.0/kalmanfilter/DESCRIPTION | 10 kalmanfilter-2.2.0/kalmanfilter/MD5 | 32 kalmanfilter-2.2.0/kalmanfilter/NEWS.md | 6 kalmanfilter-2.2.0/kalmanfilter/R/RcppExports.R | 61 kalmanfilter-2.2.0/kalmanfilter/build/partial.rdb |binary kalmanfilter-2.2.0/kalmanfilter/build/vignette.rds |binary kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.R | 729 +++++----- kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.Rmd | 3 kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.html | 423 ++--- kalmanfilter-2.2.0/kalmanfilter/man/kalman_filter.Rd | 208 +- kalmanfilter-2.2.0/kalmanfilter/man/kalmanfilter-package.Rd | 30 kalmanfilter-2.2.0/kalmanfilter/man/sw_dcf.Rd | 48 kalmanfilter-2.2.0/kalmanfilter/man/treasuries.Rd | 42 kalmanfilter-2.2.0/kalmanfilter/src/kalmanfilter.cpp | 525 +++---- kalmanfilter-2.2.0/kalmanfilter/vignettes/kalmanfilter_vignette.Rmd | 3 19 files changed, 1033 insertions(+), 1087 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and (multivariate) longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>.
The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.5.1 dated 2025-07-23 and 1.5.2 dated 2025-10-18
DESCRIPTION | 11 MD5 | 45 - NAMESPACE | 4 NEWS.md | 4 R/CIF1mv.CR.R | 8 R/CIF2mv.CR.R | 8 R/FastJM.R | 2 R/Pkmv.us.R | 8 R/estepMV_worker.R |only R/estepMV_workerSF.R |only R/getbSig.R | 32 R/getbSig_grad.R | 13 R/getbSig_gradSF.R | 11 R/getbsigSF.R | 11 R/logLikCRmv.R |only R/mvdiff.R | 26 R/mvdiffSF.R | 20 R/mvjmcs.R | 585 +++++----------- R/survfitmvjmcs.R |only README.md | 631 +++++++++--------- man/mvjmcs.Rd | 9 man/survfitmvjmcs.Rd |only src/getmvCov.cpp | 16 src/getmvCovSF.cpp | 20 src/nonmix.cpp | 1691 +++++++++++++++++++++++++------------------------ src/normalApproxSF.cpp | 409 +++++------ 26 files changed, 1747 insertions(+), 1817 deletions(-)
Title: Probabilistic Regression Trees
Description: Implementation of Probabilistic Regression Trees (PRTree),
providing functions for model fitting and prediction, with specific adaptations
to handle missing values. The main computations are implemented in 'Fortran'
for high efficiency. The package is based on the PRTree methodology described in
Alkhoury et al. (2020), "Smooth and Consistent Probabilistic Regression Trees"
<https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Details on the treatment of missing data and implementation aspects are presented in
Prass, T.S.; Neimaier, A.S.; Pumi, G. (2025), "Handling Missing Data in Probabilistic Regression Trees:
Methods and Implementation in R" <doi:10.48550/arXiv.2510.03634>.
Author: Alisson Silva Neimaier [aut] ,
Taiane Schaedler Prass [aut, ths, cre]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between PRTree versions 1.0.0 dated 2025-10-09 and 1.0.1 dated 2025-10-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/prtree_main.R | 2 +- inst/news.md | 7 ++++++- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.80 dated 2025-09-22 and 1.0.90 dated 2025-10-18
lme4breeding-1.0.80/lme4breeding/man/fillData.Rd |only lme4breeding-1.0.90/lme4breeding/ChangeLog | 15 lme4breeding-1.0.90/lme4breeding/DESCRIPTION | 8 lme4breeding-1.0.90/lme4breeding/MD5 | 82 lme4breeding-1.0.90/lme4breeding/NAMESPACE | 11 lme4breeding-1.0.90/lme4breeding/R/lmebreed.R | 420 +++- lme4breeding-1.0.90/lme4breeding/R/utils.R | 185 +- lme4breeding-1.0.90/lme4breeding/build/vignette.rds |binary lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.R | 178 +- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.Rmd | 215 +- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.html | 624 +++---- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.R | 59 lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.Rmd | 79 lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.html | 854 ++++------ lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.R |only lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.Rmd |only lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.html |only lme4breeding-1.0.90/lme4breeding/man/DT_augment.Rd | 13 lme4breeding-1.0.90/lme4breeding/man/DT_big.Rd | 16 lme4breeding-1.0.90/lme4breeding/man/DT_btdata.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_cornhybrids.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_cpdata.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_example.Rd | 29 lme4breeding-1.0.90/lme4breeding/man/DT_expdesigns.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_fulldiallel.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_gryphon.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_h2.Rd | 21 lme4breeding-1.0.90/lme4breeding/man/DT_halfdiallel.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_ige.Rd | 5 lme4breeding-1.0.90/lme4breeding/man/DT_legendre.Rd | 17 lme4breeding-1.0.90/lme4breeding/man/DT_mohring.Rd | 3 lme4breeding-1.0.90/lme4breeding/man/DT_polyploid.Rd | 7 lme4breeding-1.0.90/lme4breeding/man/DT_rice.Rd | 11 lme4breeding-1.0.90/lme4breeding/man/DT_sleepstudy.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_technow.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_wheat.Rd | 24 lme4breeding-1.0.90/lme4breeding/man/DT_yatesoats.Rd | 14 lme4breeding-1.0.90/lme4breeding/man/Dtable.Rd |only lme4breeding-1.0.90/lme4breeding/man/getCi.Rd |only lme4breeding-1.0.90/lme4breeding/man/lme4breeding-package.Rd | 90 - lme4breeding-1.0.90/lme4breeding/man/lmebreed-class.Rd | 52 lme4breeding-1.0.90/lme4breeding/man/lmebreed.Rd | 104 - lme4breeding-1.0.90/lme4breeding/man/mkMmeIndex.Rd |only lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.gxe.Rmd | 215 +- lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.qg.Rmd | 79 lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.summaries.Rmd |only 46 files changed, 1923 insertions(+), 1567 deletions(-)
Title: Create Color-Coded Choropleth Maps in R
Description: Easily create color-coded (choropleth) maps in R. No knowledge of
cartography or shapefiles needed; go directly from your geographically
identified data to a highly customizable map with a single line of code!
Supported geographies: U.S. states, counties, census tracts, and zip codes,
world countries and sub-country regions (e.g., provinces, prefectures, etc.).
Author: Ari Lamstein [aut],
Zhaochen He [ctb, cre],
Brian Johnson [ctb],
Trulia, Inc. [cph]
Maintainer: Zhaochen He <zhaochen.he@cnu.edu>
Diff between choroplethr versions 5.0.0 dated 2025-06-26 and 5.0.1 dated 2025-10-18
choroplethr-5.0.0/choroplethr/R/get_usa_demographics.R |only choroplethr-5.0.0/choroplethr/data/congress116.regions.rdata |only choroplethr-5.0.0/choroplethr/data/continental_us_states.rdata |only choroplethr-5.0.0/choroplethr/data/df_congress116_demographics.rdata |only choroplethr-5.0.0/choroplethr/data/df_congress116_party.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_country.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_county.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_ny_tract.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_state.rdata |only choroplethr-5.0.0/choroplethr/data/df_president_ts.rdata |only choroplethr-5.0.0/choroplethr/data/df_state_age_2010.rdata |only choroplethr-5.0.0/choroplethr/data/df_state_age_2015.rdata |only choroplethr-5.0.0/choroplethr/man/congress116.regions.Rd |only choroplethr-5.0.0/choroplethr/man/continental_us_states.Rd |only choroplethr-5.0.0/choroplethr/man/df_congress116_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/df_congress116_party.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_country.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_county.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_ny_tract.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_state.Rd |only choroplethr-5.0.0/choroplethr/man/df_president_ts.Rd |only choroplethr-5.0.0/choroplethr/man/df_state_age_2010.Rd |only choroplethr-5.0.0/choroplethr/man/df_state_age_2015.Rd |only choroplethr-5.0.0/choroplethr/man/get_admin1_map.Rd |only choroplethr-5.0.0/choroplethr/man/get_county_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/get_state_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/get_tract_demographics.Rd |only choroplethr-5.0.1/choroplethr/DESCRIPTION | 28 choroplethr-5.0.1/choroplethr/LICENSE | 4 choroplethr-5.0.1/choroplethr/MD5 | 164 - choroplethr-5.0.1/choroplethr/NAMESPACE | 76 choroplethr-5.0.1/choroplethr/NEWS.md | 22 choroplethr-5.0.1/choroplethr/R/acs.R | 355 +-- choroplethr-5.0.1/choroplethr/R/admin1.R | 251 +- choroplethr-5.0.1/choroplethr/R/choropleth.R | 973 ++++------ choroplethr-5.0.1/choroplethr/R/country.R | 249 +- choroplethr-5.0.1/choroplethr/R/county.R | 237 +- choroplethr-5.0.1/choroplethr/R/data.R | 474 +--- choroplethr-5.0.1/choroplethr/R/init.R | 4 choroplethr-5.0.1/choroplethr/R/internal-docs.R | 133 - choroplethr-5.0.1/choroplethr/R/state.R | 221 +- choroplethr-5.0.1/choroplethr/R/tract.R | 212 +- choroplethr-5.0.1/choroplethr/R/zip.R |only choroplethr-5.0.1/choroplethr/README.md | 283 +- choroplethr-5.0.1/choroplethr/data/admin1.map.rda |only choroplethr-5.0.1/choroplethr/data/admin1.regions.rda |only choroplethr-5.0.1/choroplethr/data/country.map.rda |binary choroplethr-5.0.1/choroplethr/data/country.regions.rda |binary choroplethr-5.0.1/choroplethr/data/county.map.2015.rda |binary choroplethr-5.0.1/choroplethr/data/county.map.2024.rda |binary choroplethr-5.0.1/choroplethr/data/county.regions.2015.rda |binary choroplethr-5.0.1/choroplethr/data/county.regions.2024.rda |binary choroplethr-5.0.1/choroplethr/data/df_country_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_county_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_ny_tract_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_ri_zip_demographics.rda |only choroplethr-5.0.1/choroplethr/data/df_state_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.bigdc.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.hex.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.hires.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.lores.rda |binary choroplethr-5.0.1/choroplethr/data/state.regions.rda |binary choroplethr-5.0.1/choroplethr/data/zip_lookup.rda |only choroplethr-5.0.1/choroplethr/man/Choropleth.Rd | 264 +- choroplethr-5.0.1/choroplethr/man/admin1.map.Rd |only choroplethr-5.0.1/choroplethr/man/admin1.regions.Rd |only choroplethr-5.0.1/choroplethr/man/admin1_choropleth.Rd | 358 +-- choroplethr-5.0.1/choroplethr/man/common_args.Rd | 251 +- choroplethr-5.0.1/choroplethr/man/country.map.Rd | 32 choroplethr-5.0.1/choroplethr/man/country.regions.Rd | 24 choroplethr-5.0.1/choroplethr/man/country_choropleth.Rd | 352 +-- choroplethr-5.0.1/choroplethr/man/county.map.2015.Rd | 30 choroplethr-5.0.1/choroplethr/man/county.map.2024.Rd | 30 choroplethr-5.0.1/choroplethr/man/county.regions.2015.Rd | 24 choroplethr-5.0.1/choroplethr/man/county.regions.2024.Rd | 24 choroplethr-5.0.1/choroplethr/man/county_choropleth.Rd | 310 +-- choroplethr-5.0.1/choroplethr/man/county_choropleth_acs.Rd | 105 - choroplethr-5.0.1/choroplethr/man/df_country_demographics.Rd | 34 choroplethr-5.0.1/choroplethr/man/df_county_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/df_japan_census.Rd | 35 choroplethr-5.0.1/choroplethr/man/df_ny_tract_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/df_president.Rd | 40 choroplethr-5.0.1/choroplethr/man/df_ri_zip_demographics.Rd |only choroplethr-5.0.1/choroplethr/man/df_state_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/get_acs_data.Rd | 82 choroplethr-5.0.1/choroplethr/man/get_tract_map.Rd | 39 choroplethr-5.0.1/choroplethr/man/get_zip_map.Rd |only choroplethr-5.0.1/choroplethr/man/state.map.bigdc.Rd | 24 choroplethr-5.0.1/choroplethr/man/state.map.hex.Rd | 30 choroplethr-5.0.1/choroplethr/man/state.map.hires.Rd | 2 choroplethr-5.0.1/choroplethr/man/state.map.lores.Rd | 30 choroplethr-5.0.1/choroplethr/man/state.regions.Rd | 24 choroplethr-5.0.1/choroplethr/man/state_choropleth.Rd | 354 +-- choroplethr-5.0.1/choroplethr/man/state_choropleth_acs.Rd | 108 - choroplethr-5.0.1/choroplethr/man/tract_choropleth.Rd | 305 +-- choroplethr-5.0.1/choroplethr/man/zip_choropleth.Rd |only choroplethr-5.0.1/choroplethr/man/zip_lookup.Rd |only choroplethr-5.0.1/choroplethr/tests/testthat.R | 24 choroplethr-5.0.1/choroplethr/tests/testthat/superceeded/test_legacy.R | 492 ++--- choroplethr-5.0.1/choroplethr/tests/testthat/test-core.R | 98 - choroplethr-5.0.1/choroplethr/tests/testthat/test-country.R | 48 choroplethr-5.0.1/choroplethr/tests/testthat/test-county.R | 44 102 files changed, 3678 insertions(+), 3733 deletions(-)
Title: Robust Markov Chain Monte Carlo Methods
Description: Functions for simulating Markov chains using the Barker proposal
to compute Markov chain Monte Carlo (MCMC) estimates of expectations with
respect to a target distribution on a real-valued vector space. The Barker
proposal, described in Livingstone and Zanella (2022)
<doi:10.1111/rssb.12482>, is a gradient-based MCMC algorithm inspired by the
Barker accept-reject rule. It combines the robustness of simpler MCMC
schemes, such as random-walk Metropolis, with the efficiency of
gradient-based methods, such as the Metropolis adjusted Langevin algorithm.
The key function provided by the package is sample_chain(), which allows
sampling a Markov chain with a specified target distribution as its
stationary distribution. The chain is sampled by generating proposals and
accepting or rejecting them using a Metropolis-Hasting acceptance rule.
During an initial warm-up stage, the parameters of the proposal distribution
can be adapted, with adapters available to both: tune the scale of the
prop [...truncated...]
Author: Matthew M. Graham [aut, cre] ,
Samuel Livingstone [aut] ,
University College London [cph],
Engineering and Physical Sciences Research Council [fnd]
Maintainer: Matthew M. Graham <m.graham@ucl.ac.uk>
Diff between rmcmc versions 0.1.1 dated 2025-02-04 and 0.1.2 dated 2025-10-17
DESCRIPTION | 22 +++- MD5 | 38 ++++---- NEWS.md | 9 ++ R/adaptation.R | 4 R/barker.R | 2 R/bridges.R | 24 ++++- R/chains.R | 130 +++++++++++++++++------------ R/proposal.R | 6 - R/utils.R | 8 - README.md | 15 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/adjusting-noise-distribution.R | 2 inst/doc/adjusting-noise-distribution.Rmd | 2 inst/doc/adjusting-noise-distribution.html | 10 +- inst/doc/barker-proposal.html | 14 +-- man/target_distribution_from_stan_model.Rd | 6 + tests/testthat/test-adaptation.R | 8 + tests/testthat/test-bridges-stan.R | 100 +++++++++++++--------- vignettes/adjusting-noise-distribution.Rmd | 2 20 files changed, 251 insertions(+), 151 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
This is a re-admission after prior archival of version 0.9-2.2 dated 2025-08-27
Diff between rlibkriging versions 0.9-2.2 dated 2025-08-27 and 0.9-2.3 dated 2025-10-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/libK/cmake/update_version.sh | 2 +- src/libK/lbfgsb_cpp/include/lbfgsb_cpp/lbfgsb.hpp | 9 ++++++++- src/libK/travis-ci/common/before_script.sh | 2 +- src/libK/travis-ci/linux-macos/install.sh | 2 +- src/libK/travis-ci/linux-macos/loadenv.sh | 2 +- src/libK/travis-ci/linux-macos/test.sh | 2 +- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Kim Filter
Description: 'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference.
The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kimfilter versions 1.0.3 dated 2024-03-08 and 1.1.0 dated 2025-10-17
DESCRIPTION | 10 MD5 | 36 +- NEWS.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/kimfilter_vignette.R | 543 +++++++++++++++++++------------------- inst/doc/kimfilter_vignette.Rmd | 1 inst/doc/kimfilter_vignette.html | 549 +++++++++++++++++++-------------------- man/Rginv.Rd | 34 +- man/contains.Rd | 38 +- man/gen_inv.Rd | 34 +- man/kim_filter.Rd | 214 +++++++-------- man/kim_filter_cpp.Rd | 76 ++--- man/kimfilter-package.Rd | 30 +- man/self_rbind.Rd | 38 +- man/ss_prob.Rd | 62 ++-- man/sw_dcf.Rd | 48 +-- src/kimfilter.cpp | 2 vignettes/kimfilter_vignette.Rmd | 1 19 files changed, 867 insertions(+), 857 deletions(-)
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Impect GmbH [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@impect.com>
Diff between impectR versions 2.5.1 dated 2025-10-15 and 2.5.2 dated 2025-10-17
DESCRIPTION | 6 +- MD5 | 18 ++++---- NEWS.md | 10 ++++ R/getEvents.R | 105 +++++++++++++++++++++++++++++------------------ R/getPlayerMatchScores.R | 92 +++++++++++++++++++++++------------------ R/getPlayerMatchsums.R | 75 ++++++++++++++++++++++----------- R/getSquadMatchScores.R | 75 ++++++++++++++++++++++----------- R/getSquadMatchsums.R | 75 ++++++++++++++++++++++----------- R/utils.R | 32 ++++++++++---- README.md | 6 +- 10 files changed, 318 insertions(+), 176 deletions(-)
Title: 'RSpace' API Wrapper
Description: Wrapper for the 'RSpace' Electronic Lab Notebook (<https://www.researchspace.com/>)
API. This packages provides convenience functions to browse, search, create,
and edit your 'RSpace' documents. In addition, it enables filling 'RSpace' templates
from R Markdown/Quarto templates or tabular data (e.g., 'Excel' files).
This R package is not developed or endorsed by 'Research Space'.
Author: Gerhard Burger [aut, cre] ,
Hanneke Leegwater [aut]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between rspacer versions 0.2.0 dated 2025-07-05 and 0.3.0 dated 2025-10-17
DESCRIPTION | 14 MD5 | 46 +- NAMESPACE | 3 NEWS.md | 13 R/documents.R | 75 ++-- R/fields.R | 55 ++- R/folders.R | 29 + R/mdtodoc.R | 104 ++++- R/utils.R | 77 ++++ README.md | 40 +- inst/CITATION |only inst/WORDLIST | 3 inst/doc/rspacer.Rmd | 653 +++++++++++++++++++++++++++++++++--- inst/doc/rspacer.html | 652 +++++++++++++++++++++++++++++++++-- man/document_create_from_tabular.Rd |only man/document_get_fields.Rd |only man/document_list_attachments.Rd | 16 man/document_search.Rd | 18 man/fields_to_data_frame.Rd |only man/folder_tree.Rd | 16 man/put_all_fields_in_one_field.Rd | 6 tests/testthat/test-documents.R | 24 - tests/testthat/test-fields.R | 18 tests/testthat/test-mdtodoc.R | 46 +- vignettes/rspacer.Rmd | 653 +++++++++++++++++++++++++++++++++--- vignettes/rspacer.Rmd.in | 18 26 files changed, 2239 insertions(+), 340 deletions(-)
More information about partialling.out at CRAN
Permanent link
Title: Parametric and Nonparametric Copula-Based Imputation Methods
Description: Copula-based imputation methods: parametric and nonparametric algorithms for missing multivariate data through conditional copulas.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Aurora Gatto [aut],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoImp versions 2.1.0 dated 2025-04-30 and 2.1.1 dated 2025-10-17
ChangeLog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/InternalFunction.R | 6 +++--- R/NPCoImp.R | 12 ++++++------ inst/CITATION | 4 ++-- man/NPCoImp-class.Rd | 6 +++--- man/NPCoImp.Rd | 21 +++++++++++---------- 8 files changed, 40 insertions(+), 36 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.1.0 dated 2025-04-28 and 2.1.1 dated 2025-10-17
DESCRIPTION | 9 - MD5 | 52 ++--- NEWS.md | 2 R/ClustCpObj.R | 12 - R/DetectCpObj.R | 26 +- R/RcppExports.R | 42 ++-- R/clust_cp.R | 18 +- R/detect_cp.R | 61 +++--- README.md | 394 ++++++++++++++++++++++++--------------------- inst/doc/tutorial.R | 10 - inst/doc/tutorial.Rmd | 10 - inst/doc/tutorial.html | 228 ++++++++++++-------------- man/ClustCpObj.Rd | 4 man/DetectCpObj.Rd | 6 man/clust_cp.Rd | 16 - man/clust_cp_epi.Rd | 8 man/detect_cp.Rd | 37 +--- man/detect_cp_epi.Rd | 18 +- man/detect_cp_multi.Rd | 10 - man/detect_cp_uni.Rd | 8 man/plot.ClustCpObj.Rd | 4 man/plot.DetectCpObj.Rd | 2 man/print.DetectCpObj.Rd | 2 man/summary.DetectCpObj.Rd | 2 src/RcppExports.cpp | 20 +- src/code.cpp | 182 ++++++++++---------- vignettes/tutorial.Rmd | 10 - 27 files changed, 607 insertions(+), 586 deletions(-)
Title: Memory-Based Learning in Spectral Chemometrics
Description: Functions for dissimilarity analysis and memory-based learning
(MBL, a.k.a local modeling) in complex spectral data sets.
Most of these functions are based on the methods presented in
Ramirez-Lopez et al. (2013) <doi:10.1016/j.geoderma.2012.12.014>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Antoine Stevens [aut, ctb] ,
Claudio Orellano [ctb],
Raphael Viscarra Rossel [ctb] ,
Alex Wadoux [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between resemble versions 2.2.4 dated 2025-05-19 and 2.2.5 dated 2025-10-17
DESCRIPTION | 10 +- MD5 | 18 +-- NEWS.md | 8 + README.md | 216 ++++++++++++++++++++++++++++++++++++++++++++- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/resemble.html | 10 +- man/resemble-package.Rd | 2 src/diss_helpers.cpp | 8 - src/regression_methods.cpp | 5 - 10 files changed, 248 insertions(+), 29 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut],
Roeland Voorrips [ctb],
Yanlin Liao [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.1.6 dated 2024-05-31 and 1.1.7 dated 2025-10-17
DESCRIPTION | 8 MD5 | 16 R/exported_functions.R | 71 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Vignette_genotype_probabilities.html | 72 +- inst/doc/Vignette_polymapR.Rmd | 2 inst/doc/Vignette_polymapR.html | 664 ++++++++++++-------------- vignettes/Vignette_polymapR.Rmd | 2 9 files changed, 409 insertions(+), 426 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.4 dated 2025-03-20 and 1.0.5 dated 2025-10-17
DESCRIPTION | 12 MD5 | 31 - NEWS.md | 5 R/clintrials_gov_convert.R | 2 R/eudract_convert.R | 2 R/relative_risk.R | 10 build/vignette.rds |binary inst/doc/eudract.html | 10 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/dotplot/dotplot-1group.svg | 94 ++-- tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 422 ++++++++++------------ tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 210 +++++----- tests/testthat/_snaps/dotplot/dotplot-ref.svg | 194 ++++------ tests/testthat/_snaps/dotplot/dotplot.svg | 194 ++++------ tests/testthat/data/four_groups |only tests/testthat/test_relative_risk.R | 8 16 files changed, 587 insertions(+), 607 deletions(-)
Title: Simplified Access to Brazilian Financial and Macroeconomic Data
Description: It offers simplified access to Brazilian macroeconomic and financial indicators selected from official sources, such as the 'IBGE' (Brazilian Institute of Geography and Statistics) via the 'SIDRA' API and the 'Central Bank of Brazil' via the 'SGS' API. It allows users to quickly retrieve and visualize data series such as the unemployment rate and the Selic interest rate. This package was developed for data access and visualization purposes, without generating forecasts or statistical results. For more information, see the official APIs: <https://sidra.ibge.gov.br/> and <https://dadosabertos.bcb.gov.br/dataset/>.
Author: Joao Paulo dos Santos Pereira Barbosa [aut, cre]
Maintainer: Joao Paulo dos Santos Pereira Barbosa <joao.31582129@gmail.com>
Diff between brfinance versions 0.2.0 dated 2025-10-16 and 0.2.1 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/globals.R | 6 +++++- R/plot_unemployment.R | 33 ++++++++++++++++++++++++--------- 4 files changed, 35 insertions(+), 16 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Goncalves Dosantos [aut, cre],
Ignacio Garcia Jurado [aut],
Julian Costa Bouzas [aut]
Maintainer: Juan Carlos Goncalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 2.0.2 dated 2024-10-24 and 2.1.4 dated 2025-10-17
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/ProjectManagement.R | 8 +------- R/function_pert_demora_unions.R | 12 ++++++++---- R/function_pert_estocastico_demora.R | 3 +++ R/function_pert_estocastico_demora_uniones.R | 24 ++++++++++++++++-------- man/ProjectManagement-package.Rd | 12 +++++++++++- 7 files changed, 51 insertions(+), 32 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains
functions and classes to be used in conjunction with other
'tidymodels' packages for finding reasonable values of
hyper-parameters in models, pre-processing methods, and
post-processing steps.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tune versions 2.0.0 dated 2025-09-01 and 2.0.1 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/parallel.R | 6 ++++-- tests/testthat/Rplots.pdf |binary 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of maximally distinct qualitative color palettes,
optionally tailored to color deficiency. A list of colors or a subspace
of a color space is used as input and then projected to the DIN99d color space,
where colors that are maximally distinct are chosen algorithmically.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <jolars@posteo.com>
Diff between qualpalr versions 1.0.0 dated 2025-08-18 and 1.0.1 dated 2025-10-17
DESCRIPTION | 6 - MD5 | 38 ++++++------ NEWS.md | 13 ++++ R/qualpal.R | 2 README.md | 5 + inst/CITATION | 58 +++++------------- inst/WORDLIST | 32 ++++++++-- inst/doc/comparisons.html | 46 +++++++------- inst/doc/introduction.html | 48 +++++++-------- inst/include/qualpal/analyze.h | 78 +++++++++++++++++------- inst/include/qualpal/color_difference.h | 59 +++++++++++++----- inst/include/qualpal/colors.h | 100 +++++++++++++++++++++++++------- inst/include/qualpal/matrix.h | 91 +++++++++++++++++++---------- inst/include/qualpal/metrics.h | 92 ++++++++++++++++++++--------- inst/include/qualpal/qualpal.h | 53 ++++++++++++---- inst/include/qualpal/threads.h | 36 +++++++---- man/analyze_palette.Rd | 2 man/qualpal.Rd | 2 man/qualpalr-package.Rd | 2 src/qualpal/colors.cpp | 6 - 20 files changed, 501 insertions(+), 268 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev] ,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.3.1 dated 2025-02-28 and 0.3.2 dated 2025-10-17
DESCRIPTION | 24 - MD5 | 48 +- NEWS.md | 347 ++++++++++---------- R/0_linters.R | 2 R/DiseasystoreBase.R | 2 R/test_diseasystore.R | 25 - README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/benchmarks.html | 2 inst/doc/diseasystore-ecdc-respiratory-viruses.html | 18 - inst/doc/diseasystore-google-covid-19.html | 14 inst/doc/diseasystore.html | 38 +- inst/doc/extending-diseasystore-example.html | 48 +- inst/extdata/benchmarks.rds |binary man/DiseasystoreBase.Rd | 2 man/DiseasystoreEcdcRespiratoryViruses.Rd | 2 man/DiseasystoreGoogleCovid19.Rd | 2 man/DiseasystoreSimulist.Rd | 2 man/FeatureHandler.Rd | 2 man/add_years.Rd | 2 man/age_on_date.Rd | 2 man/drop_diseasystore.Rd | 2 man/test_diseasystore.Rd | 25 - tests/testthat/test-age_helpers.R | 5 25 files changed, 312 insertions(+), 308 deletions(-)
Title: Statistical Tests for Covariance and Correlation Matrices and
their Structures
Description: A compilation of tests for hypotheses regarding covariance
and correlation matrices for one or more groups. The hypothesis can
be specified through a corresponding hypothesis matrix and a vector or
by choosing one of the basic hypotheses, while for the structure test,
only the latter works. Thereby Monte-Carlo and Bootstrap-techniques
are used, and the respective method must be chosen, and the functions
provide p-values and mostly also estimators of calculated covariance
matrices of test statistics. For more details on the methodology, see
Sattler et al. (2022) <doi:10.1016/j.jspi.2021.12.001>,
Sattler and Pauly (2024) <doi:10.1007/s11749-023-00906-6>, and
Sattler and Dobler (2025) <doi:10.48550/arXiv.2310.11799>.
Author: Paavo Sattler [aut] ,
Svenja Jedhoff [cre, aut] ,
Markus Pauly [ctb] ,
Arne C Bathke [ctb] ,
Dennis Dobler [ctb]
Maintainer: Svenja Jedhoff <jedhoff@statistik.tu-dortmund.de>
Diff between CovCorTest versions 1.0.0 dated 2025-06-06 and 1.1.0 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 11 ++++++++--- NAMESPACE | 1 + NEWS.md |only R/get_hypothesis.R |only README.md | 1 + man/get_extended_matrix.Rd |only man/get_hypothesis.Rd |only tests/testthat/test-gethypothesis.R |only 9 files changed, 13 insertions(+), 6 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 4041.110 dated 2024-09-22 and 4051.111 dated 2025-10-17
timeDate-4041.110/timeDate/R/options-currentYear.R |only timeDate-4041.110/timeDate/R/options-myFinCenter.R |only timeDate-4041.110/timeDate/R/options-myUnits.R |only timeDate-4051.111/timeDate/DESCRIPTION | 17 timeDate-4051.111/timeDate/MD5 | 106 ++-- timeDate-4051.111/timeDate/NAMESPACE | 30 - timeDate-4051.111/timeDate/NEWS.md | 78 ++- timeDate-4051.111/timeDate/R/AllClass.R | 75 ++ timeDate-4051.111/timeDate/R/base-format.R | 17 timeDate-4051.111/timeDate/R/base-round.R | 109 ++-- timeDate-4051.111/timeDate/R/calendar-align.R | 63 -- timeDate-4051.111/timeDate/R/calendar-firstDay.R | 98 ++- timeDate-4051.111/timeDate/R/calendar-nDay.R | 44 + timeDate-4051.111/timeDate/R/calendar-onOrAfter.R | 94 +-- timeDate-4051.111/timeDate/R/holiday-Dates.R | 16 timeDate-4051.111/timeDate/R/holiday-Listing.R | 259 +++++----- timeDate-4051.111/timeDate/R/methods-show.R | 46 + timeDate-4051.111/timeDate/R/options-RmetricsOptions.R | 34 - timeDate-4051.111/timeDate/R/pasteMat.R |only timeDate-4051.111/timeDate/R/stats-window.R | 11 timeDate-4051.111/timeDate/R/timeDate-listFinCenter.R | 8 timeDate-4051.111/timeDate/R/timeDate.R | 76 +- timeDate-4051.111/timeDate/R/timeInterval.R |only timeDate-4051.111/timeDate/README.md | 4 timeDate-4051.111/timeDate/inst/_pkgdown.yml | 34 - timeDate-4051.111/timeDate/inst/pkgdown.yml | 17 timeDate-4051.111/timeDate/inst/unitTests/runit.HolidayCalendars.R | 20 timeDate-4051.111/timeDate/man/00timeDate-package.Rd | 6 timeDate-4051.111/timeDate/man/base-diff.Rd | 28 - timeDate-4051.111/timeDate/man/base-difftimeDate.Rd | 32 - timeDate-4051.111/timeDate/man/base-round.Rd | 46 + timeDate-4051.111/timeDate/man/calendar-Easter.Rd | 19 timeDate-4051.111/timeDate/man/calendar-firstDay.Rd | 69 +- timeDate-4051.111/timeDate/man/calendar-isRegular.Rd | 9 timeDate-4051.111/timeDate/man/calendar-julian.Rd | 5 timeDate-4051.111/timeDate/man/calendar-nDay.Rd | 48 + timeDate-4051.111/timeDate/man/calendar-onOrAfter.Rd | 15 timeDate-4051.111/timeDate/man/class-timeDate.Rd | 64 +- timeDate-4051.111/timeDate/man/holiday-Dates.Rd | 61 +- timeDate-4051.111/timeDate/man/holiday-LONDON.Rd | 19 timeDate-4051.111/timeDate/man/holiday-Listing.Rd | 21 timeDate-4051.111/timeDate/man/holiday-NERC.Rd | 19 timeDate-4051.111/timeDate/man/holiday-NYSE.Rd | 22 timeDate-4051.111/timeDate/man/holiday-TSX.Rd | 19 timeDate-4051.111/timeDate/man/holiday-ZURICH.Rd | 20 timeDate-4051.111/timeDate/man/holiday.Rd | 22 timeDate-4051.111/timeDate/man/in_int.Rd |only timeDate-4051.111/timeDate/man/methods-mathOps.Rd | 20 timeDate-4051.111/timeDate/man/methods-show.Rd | 66 +- timeDate-4051.111/timeDate/man/options-RmetricsOptions.Rd | 4 timeDate-4051.111/timeDate/man/pasteMat.Rd |only timeDate-4051.111/timeDate/man/stats-kurtosis.Rd | 11 timeDate-4051.111/timeDate/man/stats-skewness.Rd | 6 timeDate-4051.111/timeDate/man/timeCeiling.Rd |only timeDate-4051.111/timeDate/man/timeDate-midnightStandard.Rd | 26 - timeDate-4051.111/timeDate/man/timeDate-whichFormat.Rd | 10 timeDate-4051.111/timeDate/man/timeDate.Rd | 71 ++ timeDate-4051.111/timeDate/man/timeInterval-class.Rd |only timeDate-4051.111/timeDate/man/timeInterval-methods.Rd |only 59 files changed, 1236 insertions(+), 778 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Author: Dayne L Filer [aut],
Jason Brown [ctb] ,
Madison Feshuk [cre] ,
Carter Thunes [ctb],
Sarah E Davidson-Fritz [ctb] ,
Kelly Carstens [ctb] ,
Elizabeth Gilson [ctb],
Lindsay Knupp [ctb],
Lori Kolaczkowski [ctb],
Ashley Ko [ctb],
Zhihui Zhao [ctb],
Kurt [...truncated...]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between tcpl versions 3.3.0 dated 2025-05-05 and 3.3.1 dated 2025-10-17
tcpl-3.3.0/tcpl/tests/testthat/ctx/api-ccte.epa.gov |only tcpl-3.3.0/tcpl/vignettes/api/0/api-ccte.epa.gov |only tcpl-3.3.1/tcpl/DESCRIPTION | 26 tcpl-3.3.1/tcpl/MD5 | 61 tcpl-3.3.1/tcpl/NAMESPACE | 2 tcpl-3.3.1/tcpl/NEWS.md | 6 tcpl-3.3.1/tcpl/R/tcplConf.R | 3 tcpl-3.3.1/tcpl/R/tcplLoadData.R | 4 tcpl-3.3.1/tcpl/R/tcplPlot.R | 4 tcpl-3.3.1/tcpl/R/tcplQueryAPI.R | 21 tcpl-3.3.1/tcpl/README.md | 2 tcpl-3.3.1/tcpl/data/test_api.rda |binary tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.R | 1433 +++++++++--------- tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.Rmd | 49 tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.html | 301 +-- tcpl-3.3.1/tcpl/tests/testthat/ctx/comptox.epa.gov |only tcpl-3.3.1/tcpl/tests/testthat/test-tcplConf.R | 2 tcpl-3.3.1/tcpl/tests/testthat/test-tcplLoadAeid.R | 2 tcpl-3.3.1/tcpl/tests/testthat/test-tcplLoadData.R | 8 tcpl-3.3.1/tcpl/tests/testthat/test-tcplPlot.R | 8 tcpl-3.3.1/tcpl/tests/testthat/test-tcplggplot2.R | 76 tcpl-3.3.1/tcpl/vignettes/Introduction_Appendices.Rmd | 49 tcpl-3.3.1/tcpl/vignettes/api/0/comptox.epa.gov |only 23 files changed, 1032 insertions(+), 1025 deletions(-)
Title: Stable Balancing Weights for Causal Inference and Missing Data
Description: Implements the Stable Balancing Weights by Zubizarreta (2015) <DOI:10.1080/01621459.2015.1023805>. These are the weights of minimum variance that approximately balance the empirical distribution of the observed covariates. For an overview, see Chattopadhyay, Hase and Zubizarreta (2020) <DOI:10.1002/sim.8659>. To solve the optimization problem in 'sbw', the default solver is 'quadprog', which is readily available through CRAN. The solver 'osqp' is also posted on CRAN. To enhance the performance of 'sbw', users are encouraged to install other solvers such as 'gurobi' and 'Rmosek', which require special installation. For the installation of gurobi and pogs, please follow the instructions at <https://docs.gurobi.com/projects/optimizer/en/current/reference/r.html> and <http://foges.github.io/pogs/stp/r>.
Author: Jose R. Zubizarreta [aut, cre],
Yige Li [aut],
Kwangho Kim [aut],
Amine Allouah [ctb],
Noah Greifer [ctb]
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>
Diff between sbw versions 1.1.9 dated 2024-07-27 and 1.2 dated 2025-10-17
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/sbw.R | 2 +- R/summarize.R | 8 ++++---- man/sbw.Rd | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: 'shiny' App for TRAPD/ISPOR Survey Translation with LLMs
Description: A 'shiny' application to automate forward and back survey translation
with optional reconciliation using large language models (LLMs). Supports
OpenAI (GPT), Google Gemini, and Anthropic Claude models. It follows
the TRAPD (Translation, Review, Adjudication, Pretesting, Documentation)
framework and ISPOR (International Society for Pharmacoeconomics and
Outcomes Research) recommendations. See Harkness et al. (2010)
<doi:10.1002/9780470609927.ch7> and Wild et al. (2005)
<doi:10.1111/j.1524-4733.2005.04054.x>.
Author: Jonas R. Kunst [aut, cre]
Maintainer: Jonas R. Kunst <jonas.r.kunst@bi.no>
Diff between LLMTranslate versions 0.1.3 dated 2025-09-05 and 0.2.0 dated 2025-10-17
DESCRIPTION | 19 LICENSE | 4 MD5 | 29 NAMESPACE | 8 NEWS.md | 25 R/LLMTranslate-package.R | 112 +-- R/globals.R | 2 R/internal-helpers.R | 731 +++++++++++----------- R/run_app.R | 34 - README.md | 56 - inst/CITATION | 20 inst/WORDLIST |only inst/app/app.R | 1310 ++++++++++++++++++++++++---------------- man/LLMTranslate.Rd | 142 ++-- man/run_app.Rd | 44 - tests/testthat/test-internals.R | 164 ++--- 16 files changed, 1536 insertions(+), 1164 deletions(-)
Title: Utilities for Data Analysis in Agriculture
Description: Utilities designed to make the analysis of field trials easier and
more accessible for everyone working in plant breeding. It provides a simple
and intuitive interface for conducting single and multi-environmental trial
analysis, with minimal coding required. Whether you're a beginner or an
experienced user, 'agriutilities' will help you quickly and easily carry out
complex analyses with confidence. With built-in functions for fitting Linear
Mixed Models, 'agriutilities' is the ideal choice for anyone who wants to save
time and focus on interpreting their results.
Some of the functions require the R package 'asreml' for the 'ASReml' software,
this can be obtained upon purchase from 'VSN' international <https://vsni.co.uk/software/asreml-r/>.
Author: Johan Aparicio [aut, cre],
Alexia Bornhorst [aut],
The Alliance of Bioversity International and CIAT [cph]
Maintainer: Johan Aparicio <johanstevenapa@gmail.com>
This is a re-admission after prior archival of version 1.2.1 dated 2025-01-17
Diff between agriutilities versions 1.2.1 dated 2025-01-17 and 1.2.2 dated 2025-10-17
DESCRIPTION | 8 - MD5 | 24 ++--- R/utils_S3_methods.R | 4 README.md | 16 +-- build/vignette.rds |binary inst/doc/how-to-start.html | 27 +++--- inst/doc/repeated_measurements.html | 122 +++++++++++++++--------------- man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-11-2.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary 13 files changed, 100 insertions(+), 101 deletions(-)
Title: Linear Quantile Mixture Models
Description: Estimate linear quantile mixtures based on Time-Constant (TC) and/or Time-Varying (TV), discrete, random coefficients.
Author: Maria Francesca Marino [aut, cre],
Marco Alfo' [aut],
Nicola Salvati [aut],
Maria Giovanna Ranalli [aut]
Maintainer: Maria Francesca Marino <mariafrancesca.marino@unifi.it>
Diff between lqmix versions 1.1 dated 2025-03-21 and 1.2 dated 2025-10-17
DESCRIPTION | 14 - MD5 | 147 ++++++++------ NAMESPACE | 96 +++++---- NEWS | 8 R/cd4.R | 8 R/coef.lqmix.R | 12 - R/coef.lqr.R | 6 R/coef.seach_lqmix.R | 42 ++-- R/dal.R | 13 - R/logLik.lqmix.R | 8 R/logLik.lqr.R | 4 R/logLik.search_lqmix.R | 4 R/lqmix.R | 120 +++++------ R/lqmixTC.R | 177 ++++++----------- R/lqmixTCTV.fit_intermittent.R | 12 - R/lqmixTCTV_intermittent.R | 220 +++++++-------------- R/lqmixTV.fit_intermittent.R | 4 R/lqmixTV_intermittent.R | 196 ++++++------------- R/lqr.R | 104 +++++----- R/lqr.fit.R | 124 ++++++------ R/pain.R | 63 +++--- R/plot.lqmix.R | 133 ++++++------- R/plot.search_lqmix.R | 290 +++++++++++++++------------- R/postComputeTC.R | 18 - R/postComputeTV_intermittent.R | 6 R/predict.lqmix.R |only R/predict.lqr.R |only R/predict.search_lqmix.R |only R/print.lqmix.R | 4 R/print.lqr.R | 4 R/print.search_lqmix.R | 8 R/print.summary.lqmix.R | 4 R/print.summary.lqr.R | 56 ++--- R/print.summary.search_lqmix.R | 4 R/residuals.lqmix.R |only R/residuals.lqr.R |only R/residuals.search_lqmix.R |only R/search_lqmix.R | 171 +++++++--------- R/summary.lqmix.R | 388 +++++++++++++++++++------------------- R/summary.lqr.R | 4 R/summary.search_lqmix.R | 26 +- R/varAL.R | 14 + R/vcov.lqmix.R |only R/vcov.lqr.R |only R/vcov.search_lqmix.R |only R/xyBuildHOM.R |only R/xyBuildTC.R |only R/xyBuildTCTV.R |only R/xyBuildTV.R |only build/partial.rdb |binary inst/REFERENCES.bib | 51 +++- man/cd4.Rd | 7 man/coef.lqmix.Rd | 6 man/coef.lqr.Rd | 6 man/coef.search_lqmix.Rd | 6 man/dal.Rd | 12 - man/logLik.lqmix.Rd | 8 man/logLik.lqr.Rd | 4 man/logLik.search_lqmix.Rd | 4 man/lqmix-package.Rd | 6 man/lqmix.Rd | 68 +++--- man/lqr.Rd | 25 +- man/pain.Rd | 6 man/plot.lqmix.Rd | 6 man/plot.search_lqmix.Rd | 6 man/predict.lqmix.Rd |only man/predict.lqr.Rd |only man/predict.search_lqmix.Rd |only man/print.lqmix.Rd | 4 man/print.lqr.Rd | 4 man/print.search_lqmix.Rd | 4 man/print.summary.lqmix.Rd | 4 man/print.summary.lqr.Rd | 4 man/print.summary.search_lqmix.Rd | 4 man/residuals.lqmix.Rd |only man/residuals.lqr.Rd |only man/residuals.search_lqmix.Rd |only man/search_lqmix.Rd | 42 ++-- man/summary.lqmix.Rd | 10 man/summary.lqr.Rd | 4 man/summary.search_lqmix.Rd | 26 +- man/varAL.Rd | 17 + man/vcov.lqmix.Rd |only man/vcov.lqr.Rd |only man/vcov.search_lqmix.Rd |only tests |only 86 files changed, 1400 insertions(+), 1456 deletions(-)
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8.3 dated 2023-08-19 and 2.8.4 dated 2025-10-17
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/package.R | 3 +-- R/readMzXmlDir-functions.R | 2 -- R/readMzXmlFile-functions.R | 2 -- man/readMzXmlData-package.Rd | 1 + man/readMzXmlDir.Rd | 2 -- man/readMzXmlFile.Rd | 2 -- 9 files changed, 22 insertions(+), 25 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 1.0.4 dated 2025-09-17 and 1.0.5 dated 2025-10-17
DESCRIPTION | 7 ++- MD5 | 16 ++++---- NEWS.md | 5 ++ R/index_mean.R | 5 -- R/index_scale.R | 3 + R/sample_size_effect.R | 2 - inst/doc/more_descriptives.html | 39 ++------------------- inst/doc/ppi_diagnostics.html | 73 ++++++++++++---------------------------- inst/doc/spinebil.html | 41 +++------------------- 9 files changed, 54 insertions(+), 137 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.33.0 dated 2025-07-23 and 1.34.0 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/flip_img.R | 2 +- R/ortho2.R | 42 ++++++++++++++++++++++++++++++++++-------- R/overlay2.R | 12 ++++++++---- inst/doc/neurobase.html | 4 ++-- inst/doc/nifti_basics.html | 6 +++--- inst/doc/simple_io.html | 2 +- man/flip_img.Rd | 2 +- man/multi_overlay.Rd | 5 +++-- man/ortho2.Rd | 8 ++++++++ 12 files changed, 80 insertions(+), 36 deletions(-)
Title: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices.
The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use,
3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevicius [aut, cre]
Maintainer: Karolis Koncevicius <karolis.koncevicius@gmail.com>
Diff between matrixTests versions 0.2.3 dated 2023-10-05 and 0.2.3.1 dated 2025-10-17
matrixTests-0.2.3.1/matrixTests/DESCRIPTION | 6 +++--- matrixTests-0.2.3.1/matrixTests/MD5 | 7 ++----- matrixTests-0.2.3.1/matrixTests/inst/benchmarks/R/plot.R |only matrixTests-0.2.3/matrixTests/inst/benchmarks/R/plot.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_onesample_correctness.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_paired_correctness.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_twosample_correctness.r |only 7 files changed, 5 insertions(+), 8 deletions(-)
Title: 'Imath' Computer Graphics Linear Algebra Static Library
Description: Provides a static library for 'Imath'
(see <https://github.com/AcademySoftwareFoundation/Imath>),
a library for functions and data types common in computer graphics
applications, including a 16-bit floating-point type.
Author: Tyler Morgan-Wall [aut, cre] ,
Andrew Kunz [ctb, cph],
Antonio Rojas [ctb, cph],
Brecht Van Lommel [ctb, cph],
Cary Phillips [ctb, cph],
Christina Tempelaar-Lietz [ctb, cph],
Christopher Kulla [ctb, cph],
Daniel Kaneider [ctb, cph],
Dirk Lemstra [ctb [...truncated...]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between libimath versions 3.1.9-4 dated 2025-07-02 and 3.1.9-5 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.win.in | 10 +++++----- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Mueller [aut, cre] ,
R Consortium [fnd],
Posit Software, PBC [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between hms versions 1.1.3 dated 2023-03-21 and 1.1.4 dated 2025-10-17
DESCRIPTION | 35 ++++--- MD5 | 53 ++++++----- NAMESPACE | 7 + NEWS.md | 21 ++++ R/args.R | 26 +++-- R/cast.R | 9 +- R/coerce.R | 4 R/compat-purrr.R | 15 ++- R/hms-package.R |only R/hms.R | 101 +++++++++++++++++----- R/parse.R | 20 +++- R/pillar.R | 32 +++++-- R/round.R | 24 ++++- README.md | 135 +++++++++++++++++------------- man/hms-package.Rd | 5 - man/hms.Rd | 13 ++ man/round_hms.Rd | 12 ++ tests/testthat/_snaps/sequence.md |only tests/testthat/test-arith.R | 10 +- tests/testthat/test-coercion-deprecated.R | 25 +++-- tests/testthat/test-coercion.R | 59 +++++++++---- tests/testthat/test-combine.R | 4 tests/testthat/test-construct.R | 21 +++- tests/testthat/test-lubridate.R | 18 ++-- tests/testthat/test-output.R | 109 ++++++++++++------------ tests/testthat/test-parse.R | 15 ++- tests/testthat/test-round.R | 73 +++++++++++++++- tests/testthat/test-sequence.R |only tests/testthat/test-unique.R | 5 - 29 files changed, 586 insertions(+), 265 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.6.1 dated 2025-06-27 and 0.6.2 dated 2025-10-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/compare_means.R | 4 +++- tests/testthat/test-compare_means.R | 4 ++-- 5 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.8 dated 2025-08-30 and 0.6.9 dated 2025-10-17
inti-0.6.8/inti/inst/doc/apps.R |only inti-0.6.8/inti/inst/doc/heritability.qmd |only inti-0.6.8/inti/inst/doc/yupana.qmd |only inti-0.6.8/inti/vignettes/heritability.qmd |only inti-0.6.8/inti/vignettes/yupana.qmd |only inti-0.6.9/inti/DESCRIPTION | 13 inti-0.6.9/inti/MD5 | 114 - inti-0.6.9/inti/NEWS.md | 7 inti-0.6.9/inti/R/H2cal.R | 56 inti-0.6.9/inti/R/design_noreps.R | 16 inti-0.6.9/inti/R/design_repblock.R | 20 inti-0.6.9/inti/R/figure2qmd.R | 8 inti-0.6.9/inti/R/gdoc2qmd.R | 15 inti-0.6.9/inti/R/plot_smr.R | 22 inti-0.6.9/inti/R/table2qmd.R | 2 inti-0.6.9/inti/R/tarpuy_design.R | 12 inti-0.6.9/inti/R/tarpuy_plex.R | 6 inti-0.6.9/inti/R/tarpuy_traits.R | 6 inti-0.6.9/inti/R/yupana_mvr.R | 4 inti-0.6.9/inti/build/vignette.rds |binary inti-0.6.9/inti/inst/doc/apps.html | 6 inti-0.6.9/inti/inst/doc/apps.qmd | 7 inti-0.6.9/inti/inst/doc/heritability.R | 42 inti-0.6.9/inti/inst/doc/heritability.Rmd |only inti-0.6.9/inti/inst/doc/heritability.html | 1103 +++++----- inti-0.6.9/inti/inst/doc/policy.html | 2 inti-0.6.9/inti/inst/doc/rticles.html | 4 inti-0.6.9/inti/inst/doc/tarpuy.html | 2 inti-0.6.9/inti/inst/doc/yupana.R | 24 inti-0.6.9/inti/inst/doc/yupana.Rmd |only inti-0.6.9/inti/inst/doc/yupana.html | 408 ++- inti-0.6.9/inti/inst/extdata/_extensions/scihub/ReadMe.qmd | 69 inti-0.6.9/inti/inst/extdata/_extensions/scihub/article.qmd | 39 inti-0.6.9/inti/inst/extdata/_extensions/scihub/design/labels.qmd | 13 inti-0.6.9/inti/inst/extdata/_extensions/scihub/files/images |only inti-0.6.9/inti/inst/extdata/_extensions/scihub/files/zotero |only inti-0.6.9/inti/inst/extdata/_extensions/scihub/manuscript |only inti-0.6.9/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy-test.dcf | 2 inti-0.6.9/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 2 inti-0.6.9/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana-test.dcf | 2 inti-0.6.9/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 2 inti-0.6.9/inti/inst/yupana/server.R | 10 inti-0.6.9/inti/inst/yupana/www/auth.R | 6 inti-0.6.9/inti/man/H2cal.Rd | 33 inti-0.6.9/inti/man/design_noreps.Rd | 16 inti-0.6.9/inti/man/design_repblock.Rd | 20 inti-0.6.9/inti/man/figure2qmd.Rd | 8 inti-0.6.9/inti/man/gdoc2qmd.Rd | 10 inti-0.6.9/inti/man/jc_tombola.Rd | 4 inti-0.6.9/inti/man/met.Rd | 22 inti-0.6.9/inti/man/metamorphosis.Rd | 11 inti-0.6.9/inti/man/outliers_remove.Rd | 2 inti-0.6.9/inti/man/plot_smr.Rd | 6 inti-0.6.9/inti/man/potato.Rd | 38 inti-0.6.9/inti/man/remove_outliers.Rd | 2 inti-0.6.9/inti/man/table2qmd.Rd | 2 inti-0.6.9/inti/man/tarpuy_design.Rd | 22 inti-0.6.9/inti/man/tarpuy_plex.Rd | 10 inti-0.6.9/inti/man/tarpuy_plotdesign.Rd | 2 inti-0.6.9/inti/man/tarpuy_traits.Rd | 6 inti-0.6.9/inti/man/yupana_mvr.Rd | 4 inti-0.6.9/inti/vignettes/apps.qmd | 7 inti-0.6.9/inti/vignettes/heritability.Rmd |only inti-0.6.9/inti/vignettes/yupana.Rmd |only 64 files changed, 1332 insertions(+), 937 deletions(-)
Title: Static Library and Headers for 'OpenEXR' Image I/O
Description: Provides the 'OpenEXR' static library and 'C++' headers
for high-dynamic-range image I/O (see <https://openexr.com/>)
needed to link R packages against the 'OpenEXR' library, along
with a basic R interface to load 'EXR' images.
Author: Tyler Morgan-Wall [aut, cre] ,
Aaron Demolder [ctb, cph],
Abe Fettig [ctb, cph],
Aloys Baillet [ctb, cph],
Andre Mazzone [ctb, cph],
Andrew Kunz [ctb, cph],
Anton Dukhovnikov [ctb, cph],
Antonio Rojas [ctb, cph],
Aras Pranckevicius [ctb, cph],
Arkady [...truncated...]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between libopenexr versions 3.4.0-4 dated 2025-07-23 and 3.4.0-5 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.win.in | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Hierarchical Dirichlet Process Generalized Linear Models
Description: Implementation of MCMC algorithms to estimate the Hierarchical Dirichlet Process Generalized Linear Model (hdpGLM) presented in the paper Ferrari (2020) Modeling Context-Dependent Latent Heterogeneity, Political Analysis <DOI:10.1017/pan.2019.13> and <doi:10.18637/jss.v107.i10>.
Author: Diogo Ferrari [aut, cre]
Maintainer: Diogo Ferrari <diogoferrari@gmail.com>
Diff between hdpGLM versions 1.0.4 dated 2025-04-19 and 1.0.5 dated 2025-10-16
hdpGLM-1.0.4/hdpGLM/man/hdpGLM_package.Rd |only hdpGLM-1.0.5/hdpGLM/DESCRIPTION | 13 - hdpGLM-1.0.5/hdpGLM/MD5 | 17 - hdpGLM-1.0.5/hdpGLM/NEWS.md | 3 hdpGLM-1.0.5/hdpGLM/R/hdpGLM_package.R | 5 hdpGLM-1.0.5/hdpGLM/inst/doc/hdpGLM.html | 320 ++++++++++++++-------------- hdpGLM-1.0.5/hdpGLM/man/hdpGLM.Rd | 49 ++++ hdpGLM-1.0.5/hdpGLM/src/Makevars | 8 hdpGLM-1.0.5/hdpGLM/src/src_hdpGLM.cpp | 4 hdpGLM-1.0.5/hdpGLM/src/src_pi_z_update.cpp | 13 - 10 files changed, 252 insertions(+), 180 deletions(-)
Title: Space-Time Anomaly Detection using Scan Statistics
Description: Detection of anomalous space-time clusters using the scan
statistics methodology. Focuses on prospective surveillance of data streams,
scanning for clusters with ongoing anomalies. Hypothesis testing is made
possible by Monte Carlo simulation. Allévius (2018) <doi:10.21105/joss.00515>.
Author: Benjamin Allevius [aut],
Paul Romer Present [ctb, cre]
Maintainer: Paul Romer Present <paul.romerpresent@fastmail.fm>
Diff between scanstatistics versions 1.1.1 dated 2023-01-26 and 1.1.2 dated 2025-10-16
scanstatistics-1.1.1/scanstatistics/man/scanstatistics.Rd |only scanstatistics-1.1.2/scanstatistics/DESCRIPTION | 11 scanstatistics-1.1.2/scanstatistics/MD5 | 18 scanstatistics-1.1.2/scanstatistics/NEWS.md | 76 scanstatistics-1.1.2/scanstatistics/R/RcppExports.R | 454 +- scanstatistics-1.1.2/scanstatistics/R/scanstatistics.R | 60 scanstatistics-1.1.2/scanstatistics/build/vignette.rds |binary scanstatistics-1.1.2/scanstatistics/inst/doc/introduction.R | 212 - scanstatistics-1.1.2/scanstatistics/inst/doc/introduction.html | 1604 +++++----- scanstatistics-1.1.2/scanstatistics/man/scanstatistics-package.Rd |only scanstatistics-1.1.2/scanstatistics/src/Makevars.win | 1 11 files changed, 1219 insertions(+), 1217 deletions(-)
More information about scanstatistics at CRAN
Permanent link
Title: Creates a Harmonized Dataset Based on a Set of Instructions
Description: Functions which facilitate harmonization of data from multiple
different datasets. Data harmonization involves taking data sources with
differing values, creating coding instructions to create a harmonized
set of values, then making those data modifications. 'psHarmonize' will
assist with data modification once the harmonization instructions are
written. Coding instructions are written by the user to create a
"harmonization sheet". This sheet catalogs variable names, domains
(e.g. clinical, behavioral, outcomes), provides R code instructions for
mapping or conversion of data, specifies the variable name in the
harmonized data set, and tracks notes. The package will then harmonize
the source datasets according to the harmonization sheet to create a
harmonized dataset. Once harmonization is finished, the package also has
functions that will create descriptive statistics using 'RMarkdown'. Data
Harmonization guidelines have been described by Fortier I, Raina P,
Van den Heuvel ER, et al. ( [...truncated...]
Author: John Stephen [aut, cre] ,
Maxwell Mansolf [ctb]
Maintainer: John Stephen <John.Stephen@northwestern.edu>
Diff between psHarmonize versions 0.3.5 dated 2025-01-15 and 0.3.6 dated 2025-10-16
DESCRIPTION | 22 ++++++++++++++-------- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/Harmonization_function.R | 23 ++++++++++++++++++++--- inst/doc/Harmonization_sheet.html | 4 ++-- inst/doc/psHarmonize.html | 4 ++-- 6 files changed, 48 insertions(+), 20 deletions(-)
Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of
a sample set to detect congruence in taxon-specific changes of abundance
and occurrence frequency along an environmental gradient as evidence of
an ecological community threshold. Relevant references include Baker and King
(2010) <doi:10.1111/j.2041-210X.2009.00007.x>, King and Baker (2010)
<doi:10.1899/09-144.1>, and Baker and King (2013) <doi:10.1899/12-142.1>.
Author: Matthew E. Baker [aut, cph] ,
Ryan S. King [aut, cph] ,
David Kahle [aut, cph, cre]
Maintainer: David Kahle <david@kahle.io>
Diff between TITAN2 versions 2.4.3 dated 2023-11-14 and 2.4.4 dated 2025-10-16
DESCRIPTION | 19 +++++++++++-------- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + R/TITAN2.R | 5 ++--- R/plot_cps.R | 2 +- R/plot_taxa_ridges.R | 33 ++++++++++++++++++--------------- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/titan2-intro.R | 10 +++++----- inst/doc/titan2-intro.pdf |binary man/TITAN2.Rd | 3 +-- man/plot_taxa_ridges.Rd | 18 +++++++++--------- 12 files changed, 63 insertions(+), 58 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.0 dated 2025-09-23 and 0.8.1 dated 2025-10-16
DESCRIPTION | 6 MD5 | 44 ++-- NAMESPACE | 1 R/barplot.R | 15 - R/boxviolinplot.R | 434 +++++++++++++++++++++++++++++++++++------- R/dotplot.R | 5 R/heatmap.R | 305 +++++++++++++++++++++-------- R/jitterplot.R | 21 -- R/radarplot.R | 72 ++++++ R/volcanoplot.R | 10 man/BoxViolinPlot-internal.Rd | 8 man/BoxViolinPlotAtomic.Rd | 8 man/Heatmap.Rd | 35 ++- man/HeatmapAtomic.Rd | 9 man/JitterPlotAtomic.Rd | 4 man/RadarPlotAtomic.Rd | 6 man/VolcanoPlot.Rd | 4 man/VolcanoPlotAtomic.Rd | 3 man/boxviolinplot.Rd | 35 +++ man/heatmap-anno.Rd | 4 man/heatmap-layer.Rd | 23 ++ man/jitterplot.Rd | 6 man/radarplot.Rd | 9 23 files changed, 834 insertions(+), 233 deletions(-)
Title: Estimating Bivariate Dependency from Marginal Data
Description: Provides statistical methods for estimating bivariate dependency (correlation) from marginal summary statistics across multiple studies.
The package supports three modules: (1) bivariate correlation estimation for binary outcomes, (2) bivariate correlation estimation for continuous outcomes, and
(3) estimation of component-wise means and variances under a conditional two-component Gaussian mixture model for a continuous variable stratified by a binary class label.
These methods enable privacy-preserving joint estimation when individual-level data are unavailable.
The approaches are detailed in Shang, Tsao, and Zhang (2025a) <doi:10.48550/arXiv.2505.03995> and Shang, Tsao, and Zhang (2025b) <doi:10.48550/arXiv.2508.02057>.
Author: Longwen Shang [aut, cre],
Min Tsao [aut],
Xuekui Zhang [aut]
Maintainer: Longwen Shang <shanglongwen0918@gmail.com>
Diff between ebdm versions 1.1.0 dated 2025-07-17 and 3.0.0 dated 2025-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++++------ NAMESPACE | 4 ++++ R/bin_example.R | 2 +- R/cor_bin.R | 10 ++++++++++ R/cor_cont.R | 8 ++++++++ R/est_mixture.R |only R/mixture_example.R |only data/mixture_example.rda |only man/bin_example.Rd | 2 +- man/est_mixture.Rd |only man/mixture_example.Rd |only 12 files changed, 43 insertions(+), 16 deletions(-)
Title: A Tidy Framework for Changepoint Detection Analysis
Description: Changepoint detection algorithms for R are widespread but have
different interfaces and reporting conventions.
This makes the comparative analysis of results difficult.
We solve this problem by providing a tidy, unified interface for several
different changepoint detection algorithms.
We also provide consistent numerical and graphical reporting leveraging
the 'broom' and 'ggplot2' packages.
Author: Benjamin S. Baumer [aut, cre, cph] ,
Biviana Marcela Suarez Sierra [aut] ,
Arrigo Coen [aut] ,
Carlos A. Taimal [aut] ,
Xueheng Shi [ctb]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between tidychangepoint versions 1.0.1 dated 2025-07-09 and 1.0.2 dated 2025-10-16
tidychangepoint-1.0.1/tidychangepoint/R/segment_cga.R |only tidychangepoint-1.0.1/tidychangepoint/man/segment_cga.Rd |only tidychangepoint-1.0.2/tidychangepoint/DESCRIPTION | 8 - tidychangepoint-1.0.2/tidychangepoint/MD5 | 38 ++++----- tidychangepoint-1.0.2/tidychangepoint/NAMESPACE | 18 ++-- tidychangepoint-1.0.2/tidychangepoint/NEWS.md | 4 tidychangepoint-1.0.2/tidychangepoint/R/pkg-changepointGA.R | 42 ++++++---- tidychangepoint-1.0.2/tidychangepoint/R/segment.R | 8 - tidychangepoint-1.0.2/tidychangepoint/R/segment_cptga.R |only tidychangepoint-1.0.2/tidychangepoint/R/tidychangepoint-package.R | 4 tidychangepoint-1.0.2/tidychangepoint/README.md | 8 - tidychangepoint-1.0.2/tidychangepoint/inst/doc/tidychangepoint.html | 11 +- tidychangepoint-1.0.2/tidychangepoint/man/as.segmenter.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/changepoints.Rd | 6 - tidychangepoint-1.0.2/tidychangepoint/man/fitness.Rd | 6 - tidychangepoint-1.0.2/tidychangepoint/man/model_args.Rd | 5 - tidychangepoint-1.0.2/tidychangepoint/man/model_name.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/reexports.Rd | 8 - tidychangepoint-1.0.2/tidychangepoint/man/seg_params.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/segment.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/segment_cptga.Rd |only tidychangepoint-1.0.2/tidychangepoint/tests/testthat/test-changepointGA.R | 4 22 files changed, 106 insertions(+), 80 deletions(-)
More information about tidychangepoint at CRAN
Permanent link
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.4.0 dated 2025-09-05 and 0.5.0 dated 2025-10-16
DESCRIPTION | 11 MD5 | 126 +++---- R/Spower.R | 28 + R/SpowerBatch.R | 21 + R/SpowerCurve.R | 6 R/p_2r.R | 9 R/p_anova.test.R | 14 R/p_chisq.test.R | 16 R/p_glm.R | 10 R/p_kruskal.test.R | 8 R/p_ks.test.R | 11 R/p_lm.R2.R | 8 R/p_mauchly.test.R | 18 - R/p_mcnemar.test.R | 11 R/p_mediation.R | 8 R/p_prop.test.R | 19 - R/p_r.R | 20 - R/p_r.cat.R | 8 R/p_scale.R | 6 R/p_shapiro.test.R | 11 R/p_t.test.R | 67 ++-- R/p_var.test.R | 23 - R/p_wilcox.test.R | 9 R/util.R | 24 + README.md | 32 + build/vignette.rds |binary inst/doc/SpowerIntro.R | 3 inst/doc/SpowerIntro.Rmd | 90 ++--- inst/doc/SpowerIntro.html | 100 +++--- inst/doc/SpowerIntro_logicals.R | 100 +++--- inst/doc/SpowerIntro_logicals.Rmd | 377 ++++++++++++++++------ inst/doc/SpowerIntro_logicals.html | 514 +++++++++++++++++++++---------- inst/doc/Spower_TypeSM.R |only inst/doc/Spower_TypeSM.Rmd |only inst/doc/Spower_TypeSM.html |only inst/doc/gpower_examples.Rmd | 115 ++++-- inst/doc/gpower_examples.html | 121 ++++--- inst/intro.rds |binary inst/intro2.rds |binary inst/intro3.rds |only man/Spower.Rd | 37 +- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/p_2r.Rd | 7 man/p_anova.test.Rd | 7 man/p_chisq.test.Rd | 7 man/p_glm.Rd | 9 man/p_kruskal.test.Rd | 7 man/p_ks.test.Rd | 17 - man/p_lm.R2.Rd | 18 + man/p_mauchly.test.Rd | 15 man/p_mcnemar.test.Rd | 7 man/p_mediation.Rd | 7 man/p_prop.test.Rd | 7 man/p_r.Rd | 19 + man/p_r.cat.Rd | 7 man/p_scale.Rd | 6 man/p_shapiro.test.Rd | 8 man/p_t.test.Rd | 39 +- man/p_var.test.Rd | 7 man/p_wilcox.test.Rd | 9 vignettes/SpowerIntro.Rmd | 90 ++--- vignettes/SpowerIntro_logicals.Rmd | 377 ++++++++++++++++------ vignettes/Spower_TypeSM.Rmd |only vignettes/gpower_examples.Rmd | 115 ++++-- vignettes/precompile.R | 7 vignettes/precompileGpower.R |only 67 files changed, 1901 insertions(+), 872 deletions(-)
Title: Greedy Expected Posterior Loss
Description: Summarises a collection of partitions into a single optimal partition. The objective function is the expected posterior loss, and the minimisation is performed through a greedy algorithm described in Rastelli, R. and Friel, N. (2017) "Optimal Bayesian estimators for latent variable cluster models" <DOI:10.1007/s11222-017-9786-y>.
Author: Riccardo Rastelli [aut, cre]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between GreedyEPL versions 1.2 dated 2021-09-02 and 1.3 dated 2025-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/MinimiseEPL.Rd | 8 ++++---- src/core_minimise_epl.cpp | 3 ++- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Generating Multi-Omics Datasets for Testing and Benchmarking
Description: Provides tools to simulate multi-omics datasets with predefined signal structures. The generated data can be used for testing, validating, and benchmarking integrative analysis methods such as factor models and clustering approaches. This version includes enhanced signal customization, visualization tools (scatter, histogram, 3D), MOFA-based analysis pipelines, PowerPoint export, and statistical profiling of datasets. Designed for both method development and teaching, SUMO supports real and synthetic data pipelines with interpretable outputs. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.
Author: Bernard Isekah Osang'ir [aut, cre] ,
Ziv Shkedy [ctb],
Surya Gupta [ctb],
Juergen Claesen [ctb]
Maintainer: Bernard Isekah Osang'ir <Bernard.Osangir@sckcen.be>
Diff between SUMO versions 1.2.2 dated 2025-10-14 and 1.2.3 dated 2025-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Imbalanced Resampling using SMOTE with Boosting (SMOTEWB)
Description: Provides the SMOTE with Boosting (SMOTEWB) algorithm. See
F. Sağlam, M. A. Cengiz (2022) <doi:10.1016/j.eswa.2022.117023>. It is a
SMOTE-based resampling technique which creates synthetic data on the links
between nearest neighbors. SMOTEWB uses boosting weights to determine where
to generate new samples and automatically decides the number of neighbors
for each sample. It is robust to noise and outperforms most of the
alternatives according to Matthew Correlation Coefficient metric.
Alternative resampling methods are also available in the package.
Author: Fatih Saglam [aut, cre]
Maintainer: Fatih Saglam <saglamf89@gmail.com>
Diff between SMOTEWB versions 1.2.2 dated 2025-05-22 and 1.2.5 dated 2025-10-16
DESCRIPTION | 8 +- MD5 | 54 ++++++++--------- R/ADASYN.R | 15 +--- R/BLSMOTE.R | 14 +--- R/GSMOTE.R | 14 +--- R/ROS.R | 16 +---- R/ROSE.R | 23 +++---- R/RSLSMOTE.R | 15 +--- R/RUS.R | 3 R/RWO.R | 15 +--- R/SLSMOTE.R | 14 +--- R/SMOTE.R | 16 ++--- R/SMOTEWB.R | 14 +--- R/generateGSMOTE.R | 2 R/generateRSLSMOTE.R | 2 R/generateSLSMOTE.R | 2 R/generateSMOTEWB.R | 2 man/ADASYN.Rd | 124 +++++++++++++++++++-------------------- man/BLSMOTE.Rd | 134 +++++++++++++++++++++--------------------- man/GSMOTE.Rd | 148 +++++++++++++++++++++++----------------------- man/ROS.Rd | 98 +++++++++++++++--------------- man/ROSE.Rd | 120 ++++++++++++++++++------------------- man/RSLSMOTE.Rd | 162 +++++++++++++++++++++++++-------------------------- man/RUS.Rd | 102 ++++++++++++++++---------------- man/RWO.Rd | 6 - man/SLSMOTE.Rd | 148 +++++++++++++++++++++++----------------------- man/SMOTE.Rd | 128 ++++++++++++++++++++-------------------- man/SMOTEWB.Rd | 7 -- 28 files changed, 687 insertions(+), 719 deletions(-)
Title: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over
Time
Description: Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.
Author: Matheus Lima Araujo [aut, cre, cph] ,
Luiz Gabriel Souza e Souza Ferreira [aut] ,
Gabriel Nakamura [aut] ,
Marco Tulio Pacheco Coelho [aut] ,
Thiago Fernando Rangel [aut]
Maintainer: Matheus Lima Araujo <matheusaraujolima@live.com>
Diff between treesliceR versions 1.0.3 dated 2025-06-09 and 1.1.0 dated 2025-10-16
treesliceR-1.0.3/treesliceR/R/DR.R |only treesliceR-1.0.3/treesliceR/tests/testthat/test-DR.R |only treesliceR-1.1.0/treesliceR/DESCRIPTION |only treesliceR-1.1.0/treesliceR/LICENSE |only treesliceR-1.1.0/treesliceR/MD5 | 23 treesliceR-1.1.0/treesliceR/NAMESPACE |only treesliceR-1.1.0/treesliceR/NEWS.md |only treesliceR-1.1.0/treesliceR/R/CpB.R | 160 +--- treesliceR-1.1.0/treesliceR/R/CpB_RW.R | 124 --- treesliceR-1.1.0/treesliceR/R/CpD.R | 29 treesliceR-1.1.0/treesliceR/R/CpE.R | 44 - treesliceR-1.1.0/treesliceR/R/nodes_config.R | 10 treesliceR-1.1.0/treesliceR/R/r_phylo.R | 359 ++-------- treesliceR-1.1.0/treesliceR/README.md |only treesliceR-1.1.0/treesliceR/build |only treesliceR-1.1.0/treesliceR/data |only treesliceR-1.1.0/treesliceR/inst |only treesliceR-1.1.0/treesliceR/man |only treesliceR-1.1.0/treesliceR/vignettes/AllTrees_DR.png |only treesliceR-1.1.0/treesliceR/vignettes/AllTrees_turn.png |only treesliceR-1.1.0/treesliceR/vignettes/Intro-treesliceR.Rmd |only treesliceR-1.1.0/treesliceR/vignettes/OneTree_nest.png |binary treesliceR-1.1.0/treesliceR/vignettes/OneTree_sensitivity.png |only treesliceR-1.1.0/treesliceR/vignettes/OneTree_turn.png |only treesliceR-1.1.0/treesliceR/vignettes/Passeriformes-distribution.Rmd |only treesliceR-1.1.0/treesliceR/vignettes/Sliced_pas_tree.png |only 26 files changed, 194 insertions(+), 555 deletions(-)
Title: Analytical Methods for Stream DAGs
Description: Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.
Author: Ken Aho [aut, cre],
Arya Legg [dtc, ctb],
Rob Ramos [dtc],
Maggi Kraft [dtc],
Charles T. Bond [dtc],
Rebecca L. Hale [dtc]
Maintainer: Ken Aho <ahoken@isu.edu>
Diff between streamDAG versions 1.5-9 dated 2025-01-14 and 1.6 dated 2025-10-16
DESCRIPTION | 8 - MD5 | 80 +++++++----- R/get.AIMS.data.R | 150 ++++++++++++----------- R/global.summary.R | 4 R/local_summary.R | 60 ++++----- R/spatial_plot.R | 235 ++++++++++++++++++++++--------------- build/vignette.rds |binary data/AIMS.node.coords.rda |binary data/dc_arc_pres_abs.rda |binary data/dc_lengths.rda |binary data/dc_node_pres_abs.rda |binary data/gj_coords16.rda |binary data/gj_lengths.rda |binary data/gj_lengths_piezo_full.rda |binary data/gj_node_pres_abs.rda |binary data/gj_node_pres_abs16.rda |binary data/jd_lengths.rda |binary data/jd_lengths_2023.rda |binary data/jd_lengths_full.rda |binary data/jd_node_pres_abs.rda |binary data/kon_coords.rda |binary data/kon_lengths.rda |binary data/mur_arc_pres_abs.rda |binary data/mur_coords.rda |binary data/mur_lengths.rda |binary data/mur_node_pres_abs.rda |binary data/mur_seasons_arc_pa.rda |binary inst/CITATION | 2 inst/doc/alpha-centrality.R |only inst/doc/alpha-centrality.Rnw |only inst/doc/alpha-centrality.pdf |only inst/doc/streamDAG.R | 16 +- inst/doc/streamDAG.html | 62 ++++----- man/get.AIMS.data.rd | 4 man/global.summary.Rd | 6 man/local.summary.Rd | 18 +- man/spatial.plot.Rd | 53 ++++---- vignettes/DAGs.pdf |only vignettes/Fig_1_alpha.png |only vignettes/GT1_01.png |only vignettes/GT3_2_1.png |only vignettes/MMEbst.bst |only vignettes/acyclic_cyclic1.png |only vignettes/alpha-centrality.Rnw |only vignettes/book.bib |only vignettes/connect_disc_stream1.png |only vignettes/simo1_DAG.pdf |only vignettes/simo_DAG.pdf |only 48 files changed, 385 insertions(+), 313 deletions(-)
Title: A Dynamic Bipartite Latent Space Model to Analyse Irish
Companies' Boards from 2003 to 2013
Description: Provides the dataset and an implementation of the method illustrated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) <DOI:10.1073/pnas.1606295113>.
Author: Riccardo Rastelli [aut, cre]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between IrishDirectorates versions 1.4 dated 2019-08-29 and 1.5 dated 2025-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary src/Makevars | 3 ++- src/Makevars.win | 3 ++- src/RcppExports.cpp | 5 +++++ 6 files changed, 18 insertions(+), 11 deletions(-)
More information about IrishDirectorates at CRAN
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Title: An Exponential Stochastic Block Model for Interaction Lengths
Description: Given a continuous-time dynamic network, this package allows one to fit a stochastic blockmodel where nodes belonging to the same group create interactions and non-interactions of similar lengths. This package implements the methodology described by R. Rastelli and M. Fop (2020) <doi:10.1007/s11634-020-00403-w>.
Author: Riccardo Rastelli [aut, cre] ,
Michael Fop [aut]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between expSBM versions 1.3.5 dated 2019-10-15 and 1.3.6 dated 2025-10-16
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ build/partial.rdb |binary man/expSBM-package.Rd | 2 +- src/Makevars | 2 +- src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ 7 files changed, 22 insertions(+), 16 deletions(-)
Title: User-Friendly PostgreSQL Connection Management
Description: Provides a user-friendly interface for managing PostgreSQL
database connection settings. The package supplies helper functions to
create, edit and load connection and option configuration files stored in a
user-specific directory using the 'odbc' and 'RPostgres' back ends. These
helpers make it easy to construct a reproducible connection string from a
configuration file, either by reading user-defined YAML files or by parsing
an environment variable.
Author: Bobby Fatemi [aut, cre]
Maintainer: Bobby Fatemi <bfatemi07@gmail.com>
Diff between rpgconn versions 0.3.1 dated 2025-08-21 and 0.3.2 dated 2025-10-16
DESCRIPTION | 8 MD5 | 13 - NEWS.md |only R/pgdbconn.R | 408 ++++++++++++++++++++--------------------- R/use-config.R | 107 +++++----- inst/WORDLIST | 2 man/pgdbconn.Rd | 8 tests/testthat/test-pgdbconn.R | 154 +++++++++------ 8 files changed, 379 insertions(+), 321 deletions(-)
Title: Retrieve Archived Web Pages from the 'Internet Archive'
Description: Scraping content from archived web pages stored in
the 'Internet Archive' (<https://archive.org>) using a systematic
workflow. Get an overview of the mementos available from the
respective homepage, retrieve the Urls and links of the page and
finally scrape the content. The final output is stored in tibbles,
which can be then easily used for further analysis.
Author: Lukas Isermann [aut, cre] ,
Konstantin Gavras [aut]
Maintainer: Lukas Isermann <lukas.isermann@uni-mannheim.de>
Diff between archiveRetriever versions 0.4.0 dated 2024-06-11 and 0.4.1 dated 2025-10-16
archiveRetriever-0.4.0/archiveRetriever/tests/testthat/Rplots.pdf |only archiveRetriever-0.4.1/archiveRetriever/DESCRIPTION | 16 archiveRetriever-0.4.1/archiveRetriever/MD5 | 67 archiveRetriever-0.4.1/archiveRetriever/NEWS.md | 7 archiveRetriever-0.4.1/archiveRetriever/R/archive_overview.R | 4 archiveRetriever-0.4.1/archiveRetriever/R/retrieve_links.R | 2 archiveRetriever-0.4.1/archiveRetriever/R/retrieve_urls.R | 4 archiveRetriever-0.4.1/archiveRetriever/R/scrape_urls.R | 2 archiveRetriever-0.4.1/archiveRetriever/README.md | 19 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links1.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links2.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links3.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links4.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links5.yml | 7340 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links6.yml |only archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url1.yml | 2872 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url2.yml | 2872 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url3.yml | 2884 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url4.yml | 2884 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url5.yml | 3587 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url6.yml | 4254 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url7.yml |75307 +--------- archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url8.yml | 9095 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url9.yml | 5626 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/_vcr |only archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_archive_overview.R | 3 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_retrieve_links.R | 24 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_retrieve_urls.R | 2 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_scrape_urls.R | 9 29 files changed, 37748 insertions(+), 120596 deletions(-)
More information about archiveRetriever at CRAN
Permanent link
Title: Graphical User Interface with Integrated 'Diagrammer' for
'Lavaan'
Description: Provides a graphical user interface with an
integrated diagrammer for latent variable models from the 'lavaan' package.
It offers two core functions: first, lavaangui() launches a web application
that allows users to specify models by drawing path diagrams, fitting them,
assessing model fit, and more; second, plot_lavaan() creates
interactive path diagrams from models specified in 'lavaan'.
Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between lavaangui versions 0.2.6 dated 2025-08-19 and 0.3.0 dated 2025-10-16
lavaangui-0.2.6/lavaangui/inst/www/assets/index-f9f1a2f2.js |only lavaangui-0.3.0/lavaangui/DESCRIPTION | 12 ++-- lavaangui-0.3.0/lavaangui/MD5 | 17 +++--- lavaangui-0.3.0/lavaangui/NEWS.md | 31 ++++++------ lavaangui-0.3.0/lavaangui/R/miniSemPlot.R | 21 ++++---- lavaangui-0.3.0/lavaangui/R/serverLayout.R | 2 lavaangui-0.3.0/lavaangui/inst/www/assets/index-64e29f62.js |only lavaangui-0.3.0/lavaangui/inst/www/index.html | 26 +++++----- lavaangui-0.3.0/lavaangui/man/lavaangui.Rd | 2 lavaangui-0.3.0/lavaangui/man/plot_lavaan.Rd | 2 lavaangui-0.3.0/lavaangui/tests/manual/dofitFALSE.R |only 11 files changed, 63 insertions(+), 50 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.0 dated 2025-09-18 and 1.4.1 dated 2025-10-16
DESCRIPTION | 9 +- MD5 | 20 ++--- NEWS.md | 19 +++++ R/backend-dbplyr__duckdb_connection.R | 34 ++++----- R/release.R | 1 R/version.R | 2 src/duckdb.tar.xz |binary tests/testthat/_snaps/array.md | 2 tests/testthat/helper-skip.R |only tests/testthat/test-backend-dbplyr__duckdb_connection.R | 59 ++++++++++------ tests/testthat/test-duckdb-extensions.R |only tests/testthat/test-tbl__duckdb_connection.R | 9 ++ 12 files changed, 104 insertions(+), 51 deletions(-)
More information about sensitivityIxJ at CRAN
Permanent link
More information about QualityMeasure at CRAN
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More information about dispersionIndicators at CRAN
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More information about descsuppRplots at CRAN
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Title: Bayesian Spatial Blind Source Separation
Description: Gibbs sampling for Bayesian spatial blind source separation (BSP-BSS). BSP-BSS is designed for spatially dependent signals in high dimensional and large-scale data, such as neuroimaging. The method assumes the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, and constructs a Bayesian nonparametric prior by thresholding Gaussian processes. Details can be found in our paper: Wu, B., Guo, Y., & Kang, J. (2024). Bayesian spatial blind source separation via the thresholded gaussian process. Journal of the American Statistical Association, 119(545), 422-433.
Author: Ben Wu [aut, cre],
Ying Guo [aut],
Jian Kang [aut]
Maintainer: Ben Wu <wuben@ruc.edu.cn>
Diff between BSPBSS versions 1.0.5 dated 2022-11-25 and 1.0.6 dated 2025-10-16
DESCRIPTION | 8 ++--- MD5 | 8 ++--- inst/doc/BSPBSS-vignette.html | 64 +++++++++++++++++++++++------------------- src/Makevars | 1 src/Makevars.win | 2 - 5 files changed, 44 insertions(+), 39 deletions(-)
More information about BayesianDisaggregation at CRAN
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Title: Stochastic Data Envelopment Analysis
Description: Set of functions for Stochastic Data Envelopment Analysis. Chance constrained versions of radial, directional and additive DEA models are implemented, as long as super-efficiency models. See: Cooper, W.W.; Deng, H.; Huang, Z.; Li, S.X. (2002). <doi:10.1057/palgrave.jors.2601433>, Bolós, V.J.; Benítez, R.; Coll-Serrano, V. (2024) <doi:10.1016/j.orp.2024.100307>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between SdeaR versions 1.0.0 dated 2025-09-14 and 1.0.1 dated 2025-10-16
DESCRIPTION | 6 - MD5 | 28 ++++---- R/modelstoch_additive.R | 33 +++++++--- R/modelstoch_additive_p.R | 33 +++++++--- R/modelstoch_addsupereff.R | 17 ++++- R/modelstoch_dir.R | 138 +++++++++++++++++++++++++++--------------- R/modelstoch_dir_dd.R | 137 +++++++++++++++++++++++++++-------------- R/modelstoch_radial.R | 138 +++++++++++++++++++++++++++--------------- build/partial.rdb |binary man/modelstoch_additive.Rd | 4 + man/modelstoch_additive_p.Rd | 4 + man/modelstoch_addsupereff.Rd | 4 + man/modelstoch_dir.Rd | 6 + man/modelstoch_dir_dd.Rd | 6 + man/modelstoch_radial.Rd | 6 + 15 files changed, 380 insertions(+), 180 deletions(-)
Title: Gene Set Enrichment Meta-Analysis
Description: Performing the different steps of gene set enrichment meta-analysis. It provides different functions that allow the application of meta-analysis based on the combination of effect sizes from different pathways in different studies to obtain significant pathways that are common to all of them.
Author: Juan Antonio Villatoro-Garcia [aut, cre],
Pablo Jurado-Bascon [aut],
Pedro Carmona-Saez [aut]
Maintainer: Juan Antonio Villatoro-Garcia <juanantoniovillatorogarcia@gmail.com>
This is a re-admission after prior archival of version 0.99.3 dated 2024-10-14
Diff between GSEMA versions 0.99.3 dated 2024-10-14 and 0.99.4 dated 2025-10-16
DESCRIPTION | 14 ++--- MD5 | 12 ++-- NAMESPACE | 1 R/createObjectMApath.R | 56 +++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GSEMA.html | 129 ++++++++++++++++++++++--------------------------- 7 files changed, 103 insertions(+), 109 deletions(-)
Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson [aut, cre]
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.4.1 dated 2023-07-16 and 2.4.2 dated 2025-10-16
DESCRIPTION | 16 +++++++++------ MD5 | 46 ++++++++++++++++++++++---------------------- NEWS | 12 ++++++++++- R/calculateAllele.R | 3 +- R/calculateSpike.R | 3 +- R/calculateStatistics.r | 3 +- R/combine_gui.r | 6 +---- R/editData_gui.r | 5 ++-- R/ggsave_gui.r | 8 ++----- R/plotDistribution_gui.r | 4 +-- R/plotGroups_gui.r | 3 +- R/strvalidator-package.r | 35 +++++++++++++++++---------------- build/partial.rdb |binary man/calculateAllele.Rd | 2 - man/calculateSpike.Rd | 2 - man/calculateStatistics.Rd | 2 - man/combine_gui.Rd | 2 - man/editData_gui.Rd | 4 +-- man/ggsave_gui.Rd | 4 +-- man/plotDistribution_gui.Rd | 2 - man/plotGroups_gui.Rd | 2 - man/ref51.Rd | 2 - man/ref52.Rd | 2 - man/strvalidator-package.Rd | 33 +++++++++++++++++++++---------- 24 files changed, 114 insertions(+), 87 deletions(-)
Title: Robust Regression and Estimation Through Maximum Mean
Discrepancy Minimization
Description: The functions in this package compute robust estimators by minimizing a kernel-based distance known as MMD (Maximum Mean Discrepancy) between the sample and a statistical model. Recent works proved that these estimators enjoy a universal consistency property, and are extremely robust to outliers. Various optimization algorithms are implemented: stochastic gradient is available for most models, but the package also allows gradient descent in a few models for which an exact formula is available for the gradient. In terms of distribution fit, a large number of continuous and discrete distributions are available: Gaussian, exponential, uniform, gamma, Poisson, geometric, etc. In terms of regression, the models available are: linear, logistic, gamma, beta and Poisson.
Alquier, P. and Gerber, M. (2024) <doi:10.1093/biomet/asad031>
Cherief-Abdellatif, B.-E. and Alquier, P. (2022) <doi:10.3150/21-BEJ1338>.
Author: Pierre Alquier [aut, cre] ,
Mathieu Gerber [aut]
Maintainer: Pierre Alquier <pierre.alquier.stat@gmail.com>
Diff between regMMD versions 0.0.2 dated 2025-10-15 and 0.0.3 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/estimation_function.R | 5 +++-- R/models_Gaussian.R | 8 ++++++-- R/models_beta.R | 4 ++-- R/models_continuous_uniform.R | 8 ++++---- R/models_gamma.R | 4 ++-- R/models_multidim_Dirac.R | 4 ++-- R/models_multidim_Gaussian.R | 16 ++++++++-------- build/partial.rdb |binary 10 files changed, 39 insertions(+), 34 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics with the 'ggplot2', 'grid', 'rayrender', 'rayvertex', and 'rgl' packages. Specializes in game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can make graphics for other board game systems. Includes configurations for several public domain game systems such as checkers, (double-18) dominoes, go, 'piecepack', playing cards, etc.
Author: Trevor L. Davis [aut, cre] ,
Linux Foundation [dtc] ,
Delapouite <https://delapouite.com/> [ill] ,
Creative Commons [ill] ` uses "license badges"
from Creative Commons to describe the generated print-and-play
file's license)
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
This is a re-admission after prior archival of version 1.15.1 dated 2025-05-08
Diff between piecepackr versions 1.15.1 dated 2025-05-08 and 1.15.3 dated 2025-10-16
DESCRIPTION | 8 MD5 | 156 - NAMESPACE | 1 NEWS.md | 9 R/aabb_piece.R | 63 R/animate_piece.R | 459 +++-- R/basicPieceGrob.R | 749 +++++---- R/cropmarkGrob.R | 473 +++-- R/crosshairGrob.R | 509 +++--- R/game_systems.R | 1935 +++++++++++++----------- R/geom_piece.R | 323 ++-- R/hooks.R | 8 R/install_ppverse.R | 27 R/op_transform.R | 390 ++-- R/piece-rayrender.R | 196 +- R/piece3d-rgl.R | 249 ++- R/pieceGrob-grid.R | 508 ++++-- R/piece_mesh-rayvertex.R | 211 +- R/piecepackr-defunct.R | 20 R/pmap_piece.R | 162 +- R/pp_cfg.R | 1402 ++++++++++------- R/pp_shape.R | 716 ++++---- R/render_piece.R | 550 ++++-- R/save_piece_images.R | 275 +-- R/save_piece_obj.R | 1895 +++++++++++++---------- R/save_print_and_play.R | 281 +-- R/sysdata.rda |binary R/utils-bleed-grobs.R | 159 + R/utils-boards.R | 869 ++++++---- R/utils-cache.R | 31 R/utils-composite.R | 458 +++-- R/utils-d10.R | 644 ++++--- R/utils-d12.R | 370 ++-- R/utils-d20.R | 410 ++--- R/utils-d4.R | 658 ++++---- R/utils-d6.R | 155 - R/utils-d8.R | 465 +++-- R/utils-font.R | 139 - R/utils-fudge.R | 94 - R/utils-geometry.R | 298 +-- R/utils-grid.R | 26 R/utils-grobCoords.R | 64 R/utils-mat-grobs.R | 198 +- R/utils-misc.R | 389 ++-- R/utils-op-grobs.R | 1466 ++++++++++-------- R/utils-opt.R | 1193 ++++++++------ R/utils-pips.R | 1322 +++++++++------- R/utils-pnp-4x6.R | 226 +- R/utils-pnp-letter-bleed.R | 720 +++++--- R/utils-pnp-letter-both.R | 315 ++- R/utils-pnp-letter-compact.R | 888 ++++++----- R/utils-token.R | 678 ++++---- R/utils-transformation.R | 160 + R/utils-xyz.R | 74 R/zzz.R | 22 README.md | 93 - data/spdx_license_list.rda |binary man/geom_piece.Rd | 4 man/piece.Rd | 32 man/piece3d.Rd | 2 man/piece_mesh.Rd | 41 man/render_piece.Rd | 2 man/save_piece_obj.Rd | 2 man/scale_piece.Rd | 10 tests/testthat/_snaps/geom_piece/geom-piece.svg | 1 tests/testthat/test-animate_piece.R | 63 tests/testthat/test-cache.R | 28 tests/testthat/test-crop_marks.R | 56 tests/testthat/test-crosshairs.R | 41 tests/testthat/test-defunct.R | 32 tests/testthat/test-game_systems.R | 868 +++++++--- tests/testthat/test-geom_piece.R | 51 tests/testthat/test-obj.R | 247 +-- tests/testthat/test-op_transform.R | 299 ++- tests/testthat/test-options.R | 344 ++-- tests/testthat/test-pieceGrob.R | 812 +++++----- tests/testthat/test-pp_shape.R | 184 +- tests/testthat/test-ppverse.R | 5 tests/testthat/test-render_piece.R | 140 + 79 files changed, 15965 insertions(+), 11458 deletions(-)
Title: Robust Image Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables robust image grobs in
panels and theme elements.
Author: Sebastian Carl [aut, cre, cph]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between ggpath versions 1.1.0 dated 2025-09-17 and 1.1.1 dated 2025-10-16
DESCRIPTION | 6 +-- MD5 | 15 +++++---- NEWS.md | 6 +++ R/theme_element.R | 41 +++++++++++++++++++++++--- tests/testthat/_snaps/theme-elements/p1.svg | 6 +-- tests/testthat/_snaps/theme-elements/p2.svg | 6 +-- tests/testthat/_snaps/theme-elements/p5.svg |only tests/testthat/_snaps/theme-elements/p6.svg |only tests/testthat/_snaps/theme-elements/p7.svg |only tests/testthat/test-theme-elements.R | 43 ++++++++++++++++++++++++++++ 10 files changed, 102 insertions(+), 21 deletions(-)
Title: Smoother Change Tracking and Versioning for R Packages
Description: Streamlines the process of updating changelogs (NEWS.md)
and versioning R packages developed in git repositories.
Author: Kirill Mueller [aut, cre, cph] ,
Patrick Schratz [aut] ,
Maelle Salmon [ctb]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between fledge versions 0.1.2 dated 2024-02-18 and 0.1.3 dated 2025-10-16
DESCRIPTION | 17 +++++++------ MD5 | 18 +++++++------- NEWS.md | 5 +++ R/enc.R | 2 - build/vignette.rds |binary inst/doc/demo.R | 4 +-- inst/doc/demo.html | 54 +++++++++++++++++++++---------------------- inst/doc/fledge.html | 3 +- inst/doc/internals.html | 3 +- man/get_top_level_commits.Rd | 2 - 10 files changed, 58 insertions(+), 50 deletions(-)
Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.9.7 dated 2025-10-07 and 0.9.8 dated 2025-10-16
DESCRIPTION | 6 MD5 | 52 +-- NEWS.md | 28 ++ R/bage_mod-functions.R | 1 R/util.R | 2 inst/TMB-version | 2 inst/doc/vig01_intro.R | 4 inst/doc/vig01_intro.Rmd | 8 inst/doc/vig01_intro.html | 160 ++++++------ inst/doc/vig05_bdef.html | 64 ++-- inst/doc/vig06_mortality.R | 14 - inst/doc/vig06_mortality.Rmd | 16 - inst/doc/vig06_mortality.html | 91 +++--- inst/doc/vig07_simulation.R | 7 inst/doc/vig07_simulation.Rmd | 8 inst/doc/vig07_simulation.html | 37 -- inst/doc/vig09_covariates.R | 10 inst/doc/vig09_covariates.Rmd | 15 - inst/doc/vig09_covariates.html | 406 +++++++++++++++---------------- inst/doc/vig10_datamod.html | 38 +- tests/testthat/test-bage_mod-functions.R | 17 + tests/testthat/test-bage_mod-methods.R | 15 - tests/testthat/test-make-outputs.R | 44 +-- vignettes/vig01_intro.Rmd | 8 vignettes/vig06_mortality.Rmd | 16 - vignettes/vig07_simulation.Rmd | 8 vignettes/vig09_covariates.Rmd | 15 - 27 files changed, 543 insertions(+), 549 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.16.0 dated 2025-08-21 and 0.16.1 dated 2025-10-16
torch-0.16.0/torch/inst/doc/distributions.R |only torch-0.16.0/torch/inst/doc/distributions.Rmd |only torch-0.16.0/torch/inst/doc/distributions.html |only torch-0.16.0/torch/inst/doc/extending-autograd.R |only torch-0.16.0/torch/inst/doc/extending-autograd.Rmd |only torch-0.16.0/torch/inst/doc/extending-autograd.html |only torch-0.16.0/torch/inst/doc/indexing.R |only torch-0.16.0/torch/inst/doc/indexing.Rmd |only torch-0.16.0/torch/inst/doc/indexing.html |only torch-0.16.0/torch/inst/doc/loading-data.R |only torch-0.16.0/torch/inst/doc/loading-data.Rmd |only torch-0.16.0/torch/inst/doc/loading-data.html |only torch-0.16.0/torch/inst/doc/python-to-r.R |only torch-0.16.0/torch/inst/doc/python-to-r.Rmd |only torch-0.16.0/torch/inst/doc/python-to-r.html |only torch-0.16.0/torch/inst/doc/serialization.R |only torch-0.16.0/torch/inst/doc/serialization.Rmd |only torch-0.16.0/torch/inst/doc/serialization.html |only torch-0.16.0/torch/inst/doc/tensor-creation.R |only torch-0.16.0/torch/inst/doc/tensor-creation.Rmd |only torch-0.16.0/torch/inst/doc/tensor-creation.html |only torch-0.16.0/torch/inst/doc/torchscript.R |only torch-0.16.0/torch/inst/doc/torchscript.Rmd |only torch-0.16.0/torch/inst/doc/torchscript.html |only torch-0.16.0/torch/inst/doc/using-autograd.R |only torch-0.16.0/torch/inst/doc/using-autograd.Rmd |only torch-0.16.0/torch/inst/doc/using-autograd.html |only torch-0.16.0/torch/vignettes/distributions.Rmd |only torch-0.16.0/torch/vignettes/extending-autograd.Rmd |only torch-0.16.0/torch/vignettes/indexing.Rmd |only torch-0.16.0/torch/vignettes/loading-data.Rmd |only torch-0.16.0/torch/vignettes/python-to-r.Rmd |only torch-0.16.0/torch/vignettes/serialization.Rmd |only torch-0.16.0/torch/vignettes/tensor-creation.Rmd |only torch-0.16.0/torch/vignettes/torchscript.Rmd |only torch-0.16.0/torch/vignettes/using-autograd.Rmd |only torch-0.16.1/torch/DESCRIPTION | 6 +- torch-0.16.1/torch/MD5 | 54 +++----------------- torch-0.16.1/torch/NEWS.md | 4 + torch-0.16.1/torch/R/ignite.R | 2 torch-0.16.1/torch/R/install.R | 35 +++++++++++- torch-0.16.1/torch/R/utils-data-sampler.R | 5 - torch-0.16.1/torch/build/partial.rdb |binary torch-0.16.1/torch/build/vignette.rds |binary torch-0.16.1/torch/man/sampler.Rd | 5 - torch-0.16.1/torch/tools/renamelib.R | 2 46 files changed, 54 insertions(+), 59 deletions(-)
Title: Select Sparse Geoadditive Models for Spatial Prediction
Description: A model building procedure to build parsimonious geoadditive model from a large number of covariates. Continuous, binary and ordered categorical responses are supported. The model building is based on component wise gradient boosting with linear effects, smoothing splines and a smooth spatial surface to model spatial autocorrelation. The resulting covariate set after gradient boosting is further reduced through backward elimination and aggregation of factor levels. The package provides a model based bootstrap method to simulate prediction intervals for point predictions. A test data set of a soil mapping case study in Berne (Switzerland) is provided. Nussbaum, M., Walthert, L., Fraefel, M., Greiner, L., and Papritz, A. (2017) <doi:10.5194/soil-3-191-2017>.
Author: Madlene Nussbaum [cre, aut],
Andreas Papritz [ths]
Maintainer: Madlene Nussbaum <m.nussbaum@uu.nl>
Diff between geoGAM versions 0.1-3 dated 2023-11-14 and 0.1-4 dated 2025-10-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/geoGAM.Rd | 14 +++++++------- man/methods.geoGAM.Rd | 6 +++--- man/predict.geoGAM.Rd | 8 ++++---- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore the model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <https://jmlr.org/papers/v19/18 [...truncated...]
Author: Przemyslaw Biecek [aut, cre] ,
Szymon Maksymiuk [aut] ,
Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.5.2 dated 2025-07-27 and 2.5.3 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/misc_theme_drwhy.R | 12 ++++++------ R/plot_model_diagnostics.R | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Predict and Visualize Population-Level Changes in Allele
Frequencies in Response to Climate Change
Description: Methods (<doi:10.7717/peerj.11534>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon.ggplot()', 'shift.waffle.ggplot()' and 'shift.surf.ggplot()' that are made with input data sets that are prepared by helper functions for each visualization method. Examples in the documentation show how to prepare animated climate change graphics through a time series with the 'gganimate' package. Function 'amova.rda()' shows how Analysis of Molecular Variance can be directly conducted with the results from redundancy analysis.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between AlleleShift versions 1.1-2 dated 2023-10-28 and 1.1-3 dated 2025-10-16
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- inst/ChangeLog | 7 +++++++ man/count.model.Rd | 15 ++++++++------- 4 files changed, 24 insertions(+), 15 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb],
PoYen Chuang [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.10 dated 2025-07-02 and 1.0.11 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 2 ++ R/FD_Fun.R | 3 +++ R/PD_Fun.R | 1 + R/TD_Fun.R | 3 ++- inst/doc/Introduction.pdf |binary 7 files changed, 17 insertions(+), 10 deletions(-)
Title: Optimal Assignment of Students to Groups
Description: Integer programming models to assign students to groups by maximising
diversity within groups, or by maximising preference scores for topics.
Author: Vik Gopal [aut, cre],
Kevin Lam [aut],
Ju Xue [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between grouper versions 0.3.1 dated 2025-07-09 and 0.5.0 dated 2025-10-16
DESCRIPTION | 6 LICENSE | 4 MD5 | 98 +- NAMESPACE | 18 NEWS.md | 36 - R/data.R | 115 ++- R/extract_fns.R | 435 ++++++------ R/model_prep.R | 262 +++---- R/post_process.R | 134 +-- R/utils-pipe.R | 28 R/zzz.R | 2 README.md | 60 - build/vignette.rds |binary data/dba_gc_ex003.rda |only data/dba_gc_ex004.rda |only inst/doc/a-related-work.R | 12 inst/doc/a-related-work.Rmd | 356 +++++----- inst/doc/a-related-work.html | 1010 +++++++++++++++--------------- inst/doc/b-diversity-skill.R | 12 inst/doc/b-diversity-skill.Rmd | 260 +++---- inst/doc/b-diversity-skill.html | 788 +++++++++++------------ inst/doc/c-subgroups-preference.R | 12 inst/doc/c-subgroups-preference.Rmd | 238 +++---- inst/doc/c-subgroups-preference.html | 766 +++++++++++----------- inst/doc/d-sanity-checks.R | 195 +++-- inst/doc/d-sanity-checks.Rmd | 387 ++++++----- inst/doc/d-sanity-checks.html | 1176 +++++++++++++++++++---------------- inst/extdata/dba_params_ex001.yml | 12 inst/extdata/dba_params_ex003.yml |only inst/extdata/dba_params_ex004.yml |only inst/extdata/pba_params_ex002.yml | 14 inst/shiny |only man/assign_groups.Rd | 78 +- man/dba_gc_ex001.Rd | 58 - man/dba_gc_ex003.Rd |only man/dba_gc_ex004.Rd |only man/extract_params_yaml.Rd | 82 +- man/extract_student_info.Rd | 177 ++--- man/pba_gc_ex002.Rd | 54 - man/pba_prefmat_ex002.Rd | 50 - man/pipe.Rd | 40 - man/prepare_model.Rd | 66 - vignettes/a-related-work.Rmd | 356 +++++----- vignettes/b-diversity-skill.Rmd | 260 +++---- vignettes/c-subgroups-preference.Rmd | 238 +++---- vignettes/d-sanity-checks.Rmd | 387 ++++++----- vignettes/diversity_skill.R |only vignettes/diversity_skill.html |only vignettes/references.bib | 98 +- vignettes/related_work.R |only vignettes/related_work.html |only vignettes/sanity_checks.R |only vignettes/sanity_checks.html |only vignettes/subgroups_preference.R |only vignettes/subgroups_preference.html |only 55 files changed, 4392 insertions(+), 3988 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.6 dated 2025-09-17 and 2.3.7 dated 2025-10-16
DESCRIPTION | 6 LICENSE | 4 MD5 | 284 - NAMESPACE | 102 NEWS.md | 568 +-- R/Engine.R | 44 R/EngineGraphQL.R | 401 +- R/EngineGraphQLGitHub.R | 1516 +++----- R/EngineGraphQLGitLab.R | 1564 ++++---- R/EngineRest.R | 225 - R/EngineRestGitHub.R | 626 +-- R/EngineRestGitLab.R | 1357 +++---- R/GQLQueryGitHub.R | 632 +-- R/GQLQueryGitLab.R | 636 +-- R/GitHost.R | 3188 ++++++++--------- R/GitHostGitHub.R | 705 ++- R/GitHostGitLab.R | 965 ++--- R/GitStats-package.R | 22 R/GitStats.R | 2142 +++++------ R/get_commits.R | 242 - R/get_files.R | 208 - R/get_issues.R | 250 - R/get_orgs.R | 78 R/get_release_logs.R | 78 R/get_repos.R | 390 +- R/get_users.R | 82 R/gitstats_functions.R | 166 R/global.R | 26 R/message_handler.R | 76 R/set_host.R | 168 R/test_helpers.R | 516 +- R/utils-pipe.R | 28 R/utils.R | 146 README.md | 372 - build/vignette.rds |binary inst/WORDLIST | 80 inst/doc/get_repos_with_code.R | 74 inst/doc/get_repos_with_code.Rmd | 110 inst/doc/get_repos_with_code.html | 779 ++-- inst/doc/set_hosts.R | 118 inst/doc/set_hosts.Rmd | 298 - 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Title: Tools for Post-Processing Predicted Values
Description: Models can be improved by post-processing class
probabilities, by: recalibration, conversion to hard probabilities,
assessment of equivocal zones, and other activities. 'probably'
contains tools for conducting these operations as well as calibration
tools and conformal inference techniques for regression models.
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
Edgar Ruiz [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between probably versions 1.1.1 dated 2025-07-30 and 1.2.0 dated 2025-10-16
probably-1.1.1/probably/R/cal-estimate-multinom.R |only probably-1.1.1/probably/R/conformal_infer.R |only probably-1.1.1/probably/tests/testthat/_snaps/bound-prediction.md |only probably-1.1.1/probably/tests/testthat/_snaps/cal-estimate.md |only probably-1.1.1/probably/tests/testthat/_snaps/cal-plot.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals-quantile.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals-split.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals.md |only probably-1.1.1/probably/tests/testthat/_snaps/make-class-pred.md |only probably-1.1.1/probably/tests/testthat/_snaps/threshold-perf.md |only probably-1.1.1/probably/tests/testthat/test-bound-prediction.R |only probably-1.1.1/probably/tests/testthat/test-cal-estimate.R |only probably-1.1.1/probably/tests/testthat/test-cal-plot.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals-quantile.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals-split.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals.R |only probably-1.1.1/probably/tests/testthat/test-make-class-pred.R |only probably-1.1.1/probably/tests/testthat/test-threshold-perf.R |only probably-1.2.0/probably/DESCRIPTION | 20 probably-1.2.0/probably/MD5 | 161 +-- probably-1.2.0/probably/NAMESPACE | 4 probably-1.2.0/probably/NEWS.md | 6 probably-1.2.0/probably/R/bound_prediction.R | 15 probably-1.2.0/probably/R/butcher.R |only probably-1.2.0/probably/R/cal-apply-binary.R | 20 probably-1.2.0/probably/R/cal-apply-impl.R | 5 probably-1.2.0/probably/R/cal-apply.R | 70 - probably-1.2.0/probably/R/cal-estimate-beta.R | 86 - probably-1.2.0/probably/R/cal-estimate-isotonic.R | 29 probably-1.2.0/probably/R/cal-estimate-linear.R | 65 - probably-1.2.0/probably/R/cal-estimate-logistic.R | 8 probably-1.2.0/probably/R/cal-estimate-multinomial.R |only probably-1.2.0/probably/R/cal-estimate-none.R | 63 - probably-1.2.0/probably/R/cal-estimate-utils.R | 99 +- probably-1.2.0/probably/R/cal-plot-breaks.R | 212 ++-- probably-1.2.0/probably/R/cal-plot-logistic.R | 184 ++-- probably-1.2.0/probably/R/cal-plot-regression.R | 60 - probably-1.2.0/probably/R/cal-plot-utils.R | 104 +- probably-1.2.0/probably/R/cal-plot-windowed.R | 230 ++--- probably-1.2.0/probably/R/cal-utils.R | 5 probably-1.2.0/probably/R/cal-validate.R | 448 +++++----- probably-1.2.0/probably/R/class-pred.R | 15 probably-1.2.0/probably/R/conformal_infer_cv.R | 35 probably-1.2.0/probably/R/conformal_infer_full.R |only probably-1.2.0/probably/R/conformal_infer_quantile.R | 14 probably-1.2.0/probably/R/conformal_infer_split.R | 28 probably-1.2.0/probably/R/make_class_pred.R | 36 probably-1.2.0/probably/R/printing.R | 8 probably-1.2.0/probably/R/probably-package.R | 23 probably-1.2.0/probably/R/threshold_perf.R | 21 probably-1.2.0/probably/R/utils.R | 4 probably-1.2.0/probably/R/vctrs-compat.R | 8 probably-1.2.0/probably/R/zzz.R | 24 probably-1.2.0/probably/build/vignette.rds |binary probably-1.2.0/probably/inst/doc/equivocal-zones.html | 9 probably-1.2.0/probably/inst/doc/where-to-use.html | 9 probably-1.2.0/probably/man/cal_estimate_multinomial.Rd | 4 probably-1.2.0/probably/man/control_conformal_full.Rd | 2 probably-1.2.0/probably/man/inf_conformal-butcher.Rd |only probably-1.2.0/probably/man/int_conformal_cv.Rd | 2 probably-1.2.0/probably/man/int_conformal_full.Rd | 73 + probably-1.2.0/probably/man/int_conformal_quantile.Rd | 2 probably-1.2.0/probably/man/int_conformal_split.Rd | 2 probably-1.2.0/probably/man/predict.int_conformal_full.Rd | 10 probably-1.2.0/probably/man/probably-package.Rd | 2 probably-1.2.0/probably/man/required_pkgs.cal_object.Rd | 4 probably-1.2.0/probably/man/required_pkgs.int_conformal_cv.Rd |only probably-1.2.0/probably/tests/testthat/_snaps/bound_prediction.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-estimate-isotonic.md | 17 probably-1.2.0/probably/tests/testthat/_snaps/cal-estimate-linear.md | 35 probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-breaks.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-logistic.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-regression.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-windowed.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_cv.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_full.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_quantile.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_split.md |only probably-1.2.0/probably/tests/testthat/_snaps/make_class_pred.md |only probably-1.2.0/probably/tests/testthat/_snaps/threshold_perf.md |only probably-1.2.0/probably/tests/testthat/helper-cal.R | 29 probably-1.2.0/probably/tests/testthat/test-bound_prediction.R |only probably-1.2.0/probably/tests/testthat/test-butcher.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-binary.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-multi.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-regression.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply.R | 84 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-beta.R | 5 probably-1.2.0/probably/tests/testthat/test-cal-estimate-isotonic.R | 55 + probably-1.2.0/probably/tests/testthat/test-cal-estimate-linear.R | 72 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-logistic.R | 48 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-multinomial.R | 50 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-none.R | 5 probably-1.2.0/probably/tests/testthat/test-cal-plot-breaks.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-logistic.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-regression.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-windowed.R |only probably-1.2.0/probably/tests/testthat/test-cal-validate-multiclass.R | 20 probably-1.2.0/probably/tests/testthat/test-cal-validate.R | 210 ++++ probably-1.2.0/probably/tests/testthat/test-class-pred.R | 20 probably-1.2.0/probably/tests/testthat/test-conformal_infer_cv.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_full.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_quantile.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_split.R |only probably-1.2.0/probably/tests/testthat/test-make_class_pred.R |only probably-1.2.0/probably/tests/testthat/test-threshold_perf.R |only 106 files changed, 1780 insertions(+), 1099 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 3.1.0 dated 2024-04-04 and 3.1.1 dated 2025-10-16
DESCRIPTION | 14 ++-- MD5 | 136 +++++++++++++++++++++---------------------- NEWS.md | 7 ++ R/plot_global.R | 2 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/Bootstrapping.Rd | 38 +++++++----- man/NBS.Rd | 43 +++++++++---- man/attributes.Rd | 19 ++++-- man/brainGraph.Rd | 14 ++++ man/brainGraphList.Rd | 81 ++++++++++++++++++------- man/brainGraph_permute.Rd | 67 ++++++++++++++------- man/brain_atlases.Rd | 42 ++++++++++++- man/centr_betw_comm.Rd | 3 man/centr_lev.Rd | 3 man/correlation_matrices.Rd | 38 ++++++++---- man/count_edges.Rd | 7 +- man/create_mats.Rd | 16 +++-- man/efficiency.Rd | 13 +++- man/glm.Rd | 60 +++++++++++++----- man/glm_brainGraphList.Rd | 62 ++++++++++++++----- man/glm_design.Rd | 20 ++++-- man/glm_fit.Rd | 88 ++++++++++++++++++++------- man/glm_graph_plots.Rd | 64 ++++++++++++++------ man/glm_helpers.Rd | 14 +++- man/import_scn.Rd | 21 ++++-- man/individ_contrib.Rd | 24 ++++--- man/inverse.Rd | 10 ++- man/make_auc_brainGraph.Rd | 3 man/make_brainGraph.Rd | 99 ++++++++++++++++++++++--------- man/make_ego_brainGraph.Rd | 7 +- man/matrix_utils.Rd | 3 man/mean_distance_wt.Rd | 10 ++- man/mediation.Rd | 42 ++++++++++--- man/mtpc.Rd | 69 +++++++++++++++------ man/plot.brainGraph.Rd | 32 +++++++--- man/plot.brainGraphList.Rd | 10 +-- man/plot_brainGraph_multi.Rd | 33 +++++++--- man/plot_global.Rd | 14 +++- man/plot_rich_norm.Rd | 16 +++-- man/plot_vertex_measures.Rd | 13 +++- man/plot_volumetric.Rd | 21 ++++-- man/random_graphs.Rd | 49 +++++++++++---- man/randomise.Rd | 38 ++++++++++-- man/residuals.Rd | 29 +++++---- man/rich_club.Rd | 8 +- man/rich_club_attrs.Rd | 5 - man/robustness.Rd | 8 +- man/vertex_roles.Rd | 9 ++ man/write_brainnet.Rd | 9 ++ 69 files changed, 1007 insertions(+), 426 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA-seq data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.1.7 dated 2025-03-30 and 1.2.0 dated 2025-10-15
inferCSN-1.1.7/inferCSN/R/import.R |only inferCSN-1.1.7/inferCSN/man/as_matrix.Rd |only inferCSN-1.1.7/inferCSN/man/check_sparsity.Rd |only inferCSN-1.1.7/inferCSN/man/coef.srm.Rd |only inferCSN-1.1.7/inferCSN/man/grapes-ss-grapes.Rd |only inferCSN-1.1.7/inferCSN/man/log_message.Rd |only inferCSN-1.1.7/inferCSN/man/matrix_to_table.Rd |only inferCSN-1.1.7/inferCSN/man/normalization.Rd |only inferCSN-1.1.7/inferCSN/man/parallelize_fun.Rd |only inferCSN-1.1.7/inferCSN/man/pearson_correlation.Rd |only inferCSN-1.1.7/inferCSN/man/plot_all_metrics.Rd |only inferCSN-1.1.7/inferCSN/man/predict.srm.Rd |only inferCSN-1.1.7/inferCSN/man/print.srm.Rd |only inferCSN-1.1.7/inferCSN/man/r_square.Rd |only inferCSN-1.1.7/inferCSN/man/simulate_sparse_matrix.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_cor.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_cov_cor.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_regression.Rd |only inferCSN-1.1.7/inferCSN/man/split_indices.Rd |only inferCSN-1.1.7/inferCSN/man/table_to_matrix.Rd |only inferCSN-1.1.7/inferCSN/src/BetaVector.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012LogisticSwaps.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012SquaredHingeSwaps.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012Swaps.cpp |only inferCSN-1.1.7/inferCSN/src/Grid.cpp |only inferCSN-1.1.7/inferCSN/src/Grid1D.cpp |only inferCSN-1.1.7/inferCSN/src/Grid2D.cpp |only inferCSN-1.1.7/inferCSN/src/Interface.cpp |only inferCSN-1.1.7/inferCSN/src/Makevars |only inferCSN-1.1.7/inferCSN/src/Makevars.win |only inferCSN-1.1.7/inferCSN/src/Normalize.cpp |only inferCSN-1.1.7/inferCSN/src/Test_Interface.cpp |only inferCSN-1.1.7/inferCSN/src/asMatrix.cpp |only inferCSN-1.1.7/inferCSN/src/include |only inferCSN-1.1.7/inferCSN/src/matrix_to_table.cpp |only inferCSN-1.1.7/inferCSN/src/split_indices.cpp |only inferCSN-1.1.7/inferCSN/src/table_to_matrix.cpp |only inferCSN-1.1.7/inferCSN/src/utils.cpp |only inferCSN-1.2.0/inferCSN/DESCRIPTION | 21 inferCSN-1.2.0/inferCSN/MD5 | 168 +-- inferCSN-1.2.0/inferCSN/NAMESPACE | 24 inferCSN-1.2.0/inferCSN/R/RcppExports.R | 188 --- inferCSN-1.2.0/inferCSN/R/calculate_gene_rank.R | 2 inferCSN-1.2.0/inferCSN/R/inferCSN-package.R | 109 +- inferCSN-1.2.0/inferCSN/R/inferCSN.R | 69 - inferCSN-1.2.0/inferCSN/R/meta_cells.R | 54 - inferCSN-1.2.0/inferCSN/R/network_evaluation.R | 92 - inferCSN-1.2.0/inferCSN/R/network_sift.R | 41 inferCSN-1.2.0/inferCSN/R/network_visualization.R | 80 - inferCSN-1.2.0/inferCSN/R/plotting_functions.R | 31 inferCSN-1.2.0/inferCSN/R/reexports.R |only inferCSN-1.2.0/inferCSN/R/single_network.R | 12 inferCSN-1.2.0/inferCSN/R/sparse_regression_model.R | 361 ------ inferCSN-1.2.0/inferCSN/R/subsampling.R | 14 inferCSN-1.2.0/inferCSN/R/utils.R | 857 ---------------- inferCSN-1.2.0/inferCSN/README.md | 29 inferCSN-1.2.0/inferCSN/man/calculate_accuracy.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auprc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auroc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_f1.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_gene_rank.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_ji.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_metrics.Rd | 47 inferCSN-1.2.0/inferCSN/man/calculate_precision.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_recall.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_si.Rd | 2 inferCSN-1.2.0/inferCSN/man/figures/logo.svg | 538 ++-------- inferCSN-1.2.0/inferCSN/man/filter_sort_matrix.Rd | 5 inferCSN-1.2.0/inferCSN/man/fit_srm.Rd | 28 inferCSN-1.2.0/inferCSN/man/inferCSN-package.Rd | 8 inferCSN-1.2.0/inferCSN/man/inferCSN.Rd | 46 inferCSN-1.2.0/inferCSN/man/infercsn_logo.Rd |only inferCSN-1.2.0/inferCSN/man/meta_cells.Rd | 48 inferCSN-1.2.0/inferCSN/man/network_format.Rd | 2 inferCSN-1.2.0/inferCSN/man/network_sift.Rd | 26 inferCSN-1.2.0/inferCSN/man/plot_coefficient.Rd | 22 inferCSN-1.2.0/inferCSN/man/plot_coefficients.Rd | 10 inferCSN-1.2.0/inferCSN/man/plot_contrast_networks.Rd | 13 inferCSN-1.2.0/inferCSN/man/plot_dynamic_networks.Rd | 44 inferCSN-1.2.0/inferCSN/man/plot_edges_comparison.Rd | 10 inferCSN-1.2.0/inferCSN/man/plot_embedding.Rd | 4 inferCSN-1.2.0/inferCSN/man/plot_histogram.Rd | 2 inferCSN-1.2.0/inferCSN/man/plot_network_heatmap.Rd | 29 inferCSN-1.2.0/inferCSN/man/plot_scatter.Rd | 2 inferCSN-1.2.0/inferCSN/man/plot_static_networks.Rd | 2 inferCSN-1.2.0/inferCSN/man/print.infercsn_logo.Rd |only inferCSN-1.2.0/inferCSN/man/single_network.Rd | 28 inferCSN-1.2.0/inferCSN/man/subsampling.Rd | 14 inferCSN-1.2.0/inferCSN/man/weight_sift.Rd | 2 inferCSN-1.2.0/inferCSN/src/RcppExports.cpp | 463 -------- inferCSN-1.2.0/inferCSN/src/filter_sort_matrix.cpp | 41 inferCSN-1.2.0/inferCSN/src/network_format.cpp | 4 inferCSN-1.2.0/inferCSN/src/network_format.h |only inferCSN-1.2.0/inferCSN/src/weight_sift.cpp | 2 95 files changed, 845 insertions(+), 2767 deletions(-)
Title: The Directed Prediction Index for Causal Inference from
Observational Data
Description: The Directed Prediction Index ('DPI') is
a quasi-causal inference (causal discovery) method for observational data
designed to quantify the relative endogeneity (relative dependence)
of outcome (Y) versus predictor (X) variables in regression models.
By comparing the proportion of variance explained (R-squared)
between the Y-as-outcome model and the X-as-outcome model
while controlling for a sufficient number of possible confounders,
it can suggest a plausible (admissible) direction of influence
from a more exogenous variable (X) to a more endogenous variable (Y).
Methodological details are provided at
<https://psychbruce.github.io/DPI/>.
This package also provides functions for data simulation and network
analysis (correlation, partial correlation, and Bayesian networks).
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between DPI versions 2025.9 dated 2025-09-20 and 2025.10 dated 2025-10-15
DPI-2025.10/DPI/DESCRIPTION | 20 DPI-2025.10/DPI/MD5 | 28 DPI-2025.10/DPI/NAMESPACE | 18 DPI-2025.10/DPI/NEWS.md | 17 DPI-2025.10/DPI/R/DPI.R | 987 +++++++++++++++++++++++--------- DPI-2025.10/DPI/README.md | 128 +++- DPI-2025.10/DPI/man/BNs_dag.Rd |only DPI-2025.10/DPI/man/DPI-package.Rd | 4 DPI-2025.10/DPI/man/DPI.Rd | 87 ++ DPI-2025.10/DPI/man/DPI_curve.Rd | 46 + DPI-2025.10/DPI/man/DPI_dag.Rd |only DPI-2025.10/DPI/man/S3method.network.Rd | 83 ++ DPI-2025.10/DPI/man/cor_matrix.Rd |only DPI-2025.10/DPI/man/cor_net.Rd |only DPI-2025.10/DPI/man/p_to_bf.Rd |only DPI-2025.10/DPI/man/sim_data.Rd | 10 DPI-2025.9/DPI/man/cor_network.Rd |only DPI-2025.9/DPI/man/dag_network.Rd |only DPI-2025.9/DPI/man/matrix_cor.Rd |only 19 files changed, 1040 insertions(+), 388 deletions(-)
Title: 'StreamCatTools'
Description: Tools for using the 'StreamCat' and 'LakeCat' API and
interacting with the 'StreamCat' and 'LakeCat' database.
Convenience functions in the package wrap the API for 'StreamCat'
on <https://api.epa.gov/StreamCat/streams/metrics>.
Author: Marc Weber [aut, cre],
Ryan Hill [ctb],
Travis Hudson [ctb],
Allen Brookes [ctb],
David Rebhuhn [ctb],
Michael Dumelle [ctb],
Zachary Smith [ctb]
Maintainer: Marc Weber <weber.marc@epa.gov>
Diff between StreamCatTools versions 0.8.0 dated 2025-10-09 and 0.9.0 dated 2025-10-15
DESCRIPTION | 6 - MD5 | 36 +++++----- NEWS.md | 6 + R/lc_get_data.R | 27 +++++-- R/lc_get_params.R | 129 +++++++++++++++++++----------------- R/sc_get_data.R | 15 +++- R/sc_get_params.R | 129 +++++++++++++++++++----------------- inst/doc/Applications.html | 4 - inst/doc/Introduction.R | 4 + inst/doc/Introduction.Rmd | 8 ++ inst/doc/Introduction.html | 76 +++++++++++++-------- inst/doc/LakeCat.R | 4 + inst/doc/LakeCat.Rmd | 7 + inst/doc/LakeCat.html | 38 +++++++--- man/lc_get_metric_names.Rd | 2 man/sc_get_metric_names.Rd | 2 tests/testthat/test-lc_get_params.R | 2 vignettes/Introduction.Rmd | 8 ++ vignettes/LakeCat.Rmd | 7 + 19 files changed, 321 insertions(+), 189 deletions(-)
More information about StreamCatTools at CRAN
Permanent link
Title: Interactive Plotting for Functional Data Analyses
Description: Produces Shiny applications for different types of popular functional data analyses. The functional data analyses are implemented in the refund package, then refund.shiny reads in the refund object and implements an object-specific set of plots based on the object class using S3.
Author: Julia Wrobel [aut, cre],
Jeff Goldsmith [aut]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund.shiny versions 1.0 dated 2022-10-10 and 1.1 dated 2025-10-15
DESCRIPTION | 16 +++++++++------- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/plot_shiny.R | 8 ++++---- R/plot_shiny.lfpca.R | 4 ++++ README.md | 4 +--- man/plot_shiny.Rd | 8 ++++---- 8 files changed, 36 insertions(+), 25 deletions(-)
Title: Community Estimation in G-Models via CORD
Description: Partitions data points (variables) into communities/clusters,
similar to clustering algorithms such as k-means and hierarchical
clustering. This package implements a clustering algorithm based on a new
metric CORD, defined for high-dimensional parametric or semiparametric
distributions. For more details see Bunea et al. (2020), Annals of Statistics
<doi:10.1214/18-AOS1794>.
Author: Xi LUO [aut, cre],
Florentina Bunea [aut],
Christophe Giraud [aut]
Maintainer: Xi (Rossi) LUO <xi.rossi.luo@gmail.com>
Diff between cord versions 0.1.1 dated 2015-09-20 and 0.2.0 dated 2025-10-15
ChangeLog | 4 ++ DESCRIPTION | 32 +++++++++++++++----- MD5 | 17 +++++----- R/RcppExports.R | 6 +-- R/cord.R | 41 ++++++++++++-------------- build |only man/cord.Rd | 14 +++++--- src/RcppExports.cpp | 38 +++++++++++++++++------- src/cordDist.cpp | 35 ++++++++++++++++++++-- src/greedyCord.cpp | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++-- 10 files changed, 209 insertions(+), 60 deletions(-)
Title: Fully Parameterized Generalized Wendland Covariance Function
Description: A fully parameterized Generalized Wendland covariance function for use in Gaussian process models, as well as multiple methods for approximating it via covariance interpolation. The available methods are linear interpolation, polynomial interpolation, and cubic spline interpolation.
Moreno Bevilacqua and Reinhard Furrer and Tarik Faouzi and Emilio Porcu (2019) <url:<https://projecteuclid.org/journalArticle/Download?urlId=10.1214%2F17-AOS1652 >>.
Moreno Bevilacqua and Christian Caamaño-Carrillo and Emilio Porcu (2022) <doi:10.48550/arXiv.2008.02904>.
Reinhard Furrer and Roman Flury and Florian Gerber (2022) <url:<https://CRAN.R-project.org/package=spam >>.
Author: Thomas C. Fischer [aut, cre],
Reinhard Furrer [aut, ths],
Josef Stocker [aut]
Maintainer: Thomas C. Fischer <thomascasparfischer@gmail.com>
Diff between GeneralizedWendland versions 0.6.0 dated 2024-02-18 and 0.6.1 dated 2025-10-15
DESCRIPTION | 10 - MD5 | 34 ++--- R/helper_functions.R | 70 +++++------ build/vignette.rds |binary man/GeneralizedWendland-package.Rd | 60 +++++----- man/Rcpp_Wendland.Rd | 138 +++++++++++------------ man/cov.askey.Rd | 98 ++++++++-------- man/cov.wendland.Rd | 178 ++++++++++++++--------------- man/factory-choleskyFactory.Rd | 114 +++++++++---------- man/factory-covDiag.Rd | 220 ++++++++++++++++++------------------- man/factory-covarianceFactory.Rd | 124 ++++++++++---------- man/factory-mleFactory.Rd | 85 ++++++++++---- man/factory-neg2loglikDiag.Rd | 134 +++++++++++----------- man/factory-neg2loglikFactory.Rd | 172 ++++++++++++++-------------- man/factory-optimFactory.Rd | 204 ++++++++++++++++++++-------------- man/factory_predict.Rd | 152 ++++++++++++------------- man/generalizedwendland-error.Rd | 56 ++++----- man/generalizedwendland-warning.Rd | 58 ++++----- 18 files changed, 990 insertions(+), 917 deletions(-)
More information about GeneralizedWendland at CRAN
Permanent link
Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process
Emulations
Description: Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process,
and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI).
The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and
Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and
Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package,
see <https://mingdeyu.github.io/dgpsi-R/>.
Author: Deyu Ming [aut, cre, cph],
Daniel Williamson [aut]
Maintainer: Deyu Ming <deyu.ming.16@ucl.ac.uk>
Diff between dgpsi versions 2.5.0 dated 2024-12-14 and 2.6.0 dated 2025-10-15
dgpsi-2.5.0/dgpsi/man/combine.Rd |only dgpsi-2.5.0/dgpsi/man/set_linked_idx.Rd |only dgpsi-2.6.0/dgpsi/DESCRIPTION | 8 dgpsi-2.6.0/dgpsi/MD5 | 88 ++---- dgpsi-2.6.0/dgpsi/NAMESPACE | 2 dgpsi-2.6.0/dgpsi/NEWS.md | 21 + dgpsi-2.6.0/dgpsi/R/alm.R | 15 - dgpsi-2.6.0/dgpsi/R/design.R | 215 ++++++++++---- dgpsi-2.6.0/dgpsi/R/dgp.R | 303 +++++++++++--------- dgpsi-2.6.0/dgpsi/R/draw.R | 76 +++-- dgpsi-2.6.0/dgpsi/R/gp.R | 101 +----- dgpsi-2.6.0/dgpsi/R/initi_py.R | 36 +- dgpsi-2.6.0/dgpsi/R/lgp.R | 106 +------ dgpsi-2.6.0/dgpsi/R/mice.R | 15 - dgpsi-2.6.0/dgpsi/R/plot.R | 465 ++++++++++++++++---------------- dgpsi-2.6.0/dgpsi/R/prediction.R | 339 ++++------------------- dgpsi-2.6.0/dgpsi/R/serialization.R | 231 +++++++++------ dgpsi-2.6.0/dgpsi/R/update.R | 22 - dgpsi-2.6.0/dgpsi/R/utils.R | 369 +++++++++++-------------- dgpsi-2.6.0/dgpsi/R/validation.R | 427 +++++++++-------------------- dgpsi-2.6.0/dgpsi/R/vigf.R | 39 +- dgpsi-2.6.0/dgpsi/README.md | 8 dgpsi-2.6.0/dgpsi/inst/WORDLIST | 7 dgpsi-2.6.0/dgpsi/inst/doc/dgpsi.Rmd | 6 dgpsi-2.6.0/dgpsi/inst/doc/dgpsi.html | 2 dgpsi-2.6.0/dgpsi/man/alm.Rd | 8 dgpsi-2.6.0/dgpsi/man/deserialize.Rd | 39 -- dgpsi-2.6.0/dgpsi/man/design.Rd | 16 - dgpsi-2.6.0/dgpsi/man/dgp.Rd | 134 ++++----- dgpsi-2.6.0/dgpsi/man/draw.Rd | 4 dgpsi-2.6.0/dgpsi/man/get_thread_num.Rd | 2 dgpsi-2.6.0/dgpsi/man/gp.Rd | 52 --- dgpsi-2.6.0/dgpsi/man/init_py.Rd | 4 dgpsi-2.6.0/dgpsi/man/lgp.Rd | 31 -- dgpsi-2.6.0/dgpsi/man/mice.Rd | 8 dgpsi-2.6.0/dgpsi/man/plot.Rd | 23 - dgpsi-2.6.0/dgpsi/man/predict.Rd | 95 +----- dgpsi-2.6.0/dgpsi/man/serialize.Rd | 32 +- dgpsi-2.6.0/dgpsi/man/set_id.Rd | 2 dgpsi-2.6.0/dgpsi/man/set_thread_num.Rd | 2 dgpsi-2.6.0/dgpsi/man/set_vecchia.Rd | 18 - dgpsi-2.6.0/dgpsi/man/summary.Rd | 5 dgpsi-2.6.0/dgpsi/man/update.Rd | 2 dgpsi-2.6.0/dgpsi/man/validate.Rd | 51 +-- dgpsi-2.6.0/dgpsi/man/vigf.Rd | 10 dgpsi-2.6.0/dgpsi/vignettes/dgpsi.Rmd | 6 46 files changed, 1487 insertions(+), 1958 deletions(-)
Title: Multivariate Histograms
Description: Tabulate and plot directional and other multivariate histograms.
Author: John P. Nolan [aut, cre, cph]
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvhist versions 1.1 dated 2023-10-03 and 1.2 dated 2025-10-15
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- man/mvhist.Rd | 28 +++++++++++----------------- man/mvhistDirectional.Rd | 17 ++++++++++++++--- man/mvhistMisc.Rd | 6 +++--- 6 files changed, 39 insertions(+), 34 deletions(-)
Title: A 'shiny' App to Evaluate Diagnostic Tests Performance
Description: Evaluate diagnostic test performance using data from laboratory or diagnostic research. It supports both binary and continuous test variables. It allows users to compute key performance indicators and visualize Receiver Operating Characteristic (ROC) curves, determine optimal cut-off thresholds, display confusion matrix, and export publication-ready plot. It aims to facilitate the application of statistical methods in diagnostic test evaluation by healthcare professionals. The methodology used to compute the performance indicators follows the overview described by Habibzadeh (2025) <doi:10.11613/BM.2025.010101>. Thanks to 'shiny' package.
Author: Nassim AYAD [aut, cre]
Maintainer: Nassim AYAD <nassim.ayad.ph@gmail.com>
Diff between EvalTest versions 1.0.2 dated 2025-09-14 and 1.0.3 dated 2025-10-15
DESCRIPTION | 8 MD5 | 19 - NEWS.md |only README.md | 31 + inst/app/app.R | 714 +++++++++++++++++++++--------------------- inst/doc/introduction.R | 5 inst/doc/introduction.Rmd | 40 +- inst/doc/introduction.html | 60 ++- vignettes/img/screenshot2.png |binary vignettes/img/screenshot3.png |binary vignettes/introduction.Rmd | 40 +- 11 files changed, 503 insertions(+), 414 deletions(-)
Title: Simultaneous Confidence Intervals for Multinomial Proportions
Description: Several authors have proposed methods for constructing simultaneous confidence intervals for multinomial proportions. The package implements seven classical approaches—Wilson, Quesenberry and Hurst, Goodman, Wald (with and without continuity correction), Fitzpatrick and Scott, and Sison and Glaz—along with Bayesian methods based on Dirichlet models. Both equal and unequal Dirichlet priors are supported, providing a broad framework for inference, data analysis, and sensitivity evaluation.
Author: Subbiah M [aut, cre]
Maintainer: Subbiah M <sisufive@gmail.com>
This is a re-admission after prior archival of version 1.1 dated 2013-05-28
Diff between CoinMinD versions 1.1 dated 2013-05-28 and 1.2.1 dated 2025-10-15
CoinMinD-1.1/CoinMinD/man/CoinMinD-package.Rd |only CoinMinD-1.2.1/CoinMinD/DESCRIPTION | 34 +-- CoinMinD-1.2.1/CoinMinD/MD5 | 41 ++-- CoinMinD-1.2.1/CoinMinD/NAMESPACE | 22 +- CoinMinD-1.2.1/CoinMinD/R/BMDE.R | 95 ++++++---- CoinMinD-1.2.1/CoinMinD/R/BMDU.R | 112 +++++++----- CoinMinD-1.2.1/CoinMinD/R/FS.R | 89 ++++++--- CoinMinD-1.2.1/CoinMinD/R/GM.R | 106 ++++++++--- CoinMinD-1.2.1/CoinMinD/R/QH.R | 104 ++++++++--- CoinMinD-1.2.1/CoinMinD/R/SG.R | 240 +++++++++++++------------- CoinMinD-1.2.1/CoinMinD/R/WALD.R | 95 +++++++--- CoinMinD-1.2.1/CoinMinD/R/WALDCC.R | 96 +++++++--- CoinMinD-1.2.1/CoinMinD/R/WS.R | 97 +++++++--- CoinMinD-1.2.1/CoinMinD/man/BMDE.Rd | 63 +++--- CoinMinD-1.2.1/CoinMinD/man/BMDU.Rd | 62 +++--- CoinMinD-1.2.1/CoinMinD/man/FS.Rd | 65 +++---- CoinMinD-1.2.1/CoinMinD/man/GM.Rd | 79 +++++--- CoinMinD-1.2.1/CoinMinD/man/QH.Rd | 81 +++++--- CoinMinD-1.2.1/CoinMinD/man/SG.Rd | 84 +++++---- CoinMinD-1.2.1/CoinMinD/man/WALD.Rd | 77 ++++---- CoinMinD-1.2.1/CoinMinD/man/WALDCC.Rd | 76 ++++---- CoinMinD-1.2.1/CoinMinD/man/WS.Rd | 79 ++++---- 22 files changed, 1083 insertions(+), 714 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Candace Savonen [aut, cre]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between rsynthbio versions 2.2.1 dated 2025-09-12 and 3.0.0 dated 2025-10-15
DESCRIPTION | 8 MD5 | 40 +- NAMESPACE | 4 NEWS.md | 56 +++ R/call_model_api.R | 455 +++++++++++++++++++++++++++----- R/utils.R | 30 +- README.md | 54 +++ build/vignette.rds |binary inst/doc/getting-started.R | 28 + inst/doc/getting-started.Rmd | 72 ++++- inst/doc/getting-started.html | 173 +++++++----- man/DEFAULT_POLL_INTERVAL_SECONDS.Rd |only man/DEFAULT_POLL_TIMEOUT_SECONDS.Rd |only man/DEFAULT_TIMEOUT.Rd |only man/MODEL_MODALITIES.Rd | 3 man/get_json.Rd |only man/get_valid_query.Rd | 14 man/poll_model_query.Rd |only man/predict_query.Rd | 33 +- man/resolve_api_slug.Rd |only man/start_model_query.Rd |only man/transform_result_to_frames.Rd |only tests/testthat/helper-mocks.R |only tests/testthat/test-call_model_api.R | 496 ++++++++++++++++++++++++++--------- tests/testthat/test-live-api.R |only vignettes/getting-started.Rmd | 72 ++++- 26 files changed, 1178 insertions(+), 360 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression or any other function. Also includes a comprehensive framework for discrete-time
simulation, and networks-based simulation which can generate even more complex longitudinal and dependent data.
For more details, see Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.4.0 dated 2025-08-27 and 0.4.1 dated 2025-10-15
DESCRIPTION | 9 MD5 | 77 ++-- NAMESPACE | 3 NEWS.md | 16 R/dag.r | 32 + R/input_checks.r | 44 ++ R/node.r | 8 R/node_binomial.r | 19 - R/node_gaussian.r | 15 R/node_lmer.r | 3 R/node_negative_binomial.r | 13 R/node_poisson.r | 14 R/node_zeroinfl.r | 7 R/sim_n_datasets.r | 2 R/structural_equations.r | 86 ++++- inst/doc/simDAG.html | 2 inst/doc/v_cookbook.R | 46 ++ inst/doc/v_cookbook.Rmd | 71 ++++ inst/doc/v_cookbook.html | 363 ++++++++++++++-------- inst/doc/v_covid_example.html | 2 man/as.dagitty.DAG.Rd |only man/as.igraph.DAG.Rd | 6 man/node_binomial.Rd | 13 man/node_gaussian.Rd | 7 man/node_negative_binomial.Rd | 7 man/node_poisson.Rd | 9 man/node_zeroinfl.Rd | 7 man/sim_n_datasets.Rd | 7 tests/testthat/test_as.dagitty.DAG.r |only tests/testthat/test_node.r | 30 + tests/testthat/test_node_binomial.r | 72 ++++ tests/testthat/test_node_gaussian.r | 40 ++ tests/testthat/test_node_lmer.r | 31 + tests/testthat/test_node_negative_binomial.r | 27 + tests/testthat/test_node_poisson.r | 38 ++ tests/testthat/test_node_zeroinfl.r | 31 + tests/testthat/test_str_eq_binomial.r | 24 + tests/testthat/test_str_eq_gaussian.r | 4 tests/testthat/test_str_eq_poisson.r | 11 vignettes/images_v_joss/disc_time_sim.bib.sav.tmp |only vignettes/v_cookbook.Rmd | 71 ++++ 41 files changed, 1037 insertions(+), 230 deletions(-)
Title: Processing Agro-Environmental Data
Description: A set of tools for processing and analyzing data developed in the
context of the "Who Has Eaten the Planet" (WHEP) project, funded by the
European Research Council (ERC). For more details on multi-regional
input–output model "Food and Agriculture Biomass Input–Output" (FABIO) see
Bruckner et al. (2019) <doi:10.1021/acs.est.9b03554>.
Author: Catalin Covaci [aut, cre] ,
Eduardo Aguilera [aut, cph] ,
Joao Serra [ctb] ,
European Research Council [fnd]
Maintainer: Catalin Covaci <catalin.covaci@csic.es>
Diff between whep versions 0.1.0 dated 2025-07-25 and 0.2.0 dated 2025-10-15
whep-0.1.0/whep/inst/doc/workflow-intro.R |only whep-0.1.0/whep/inst/doc/workflow-intro.Rmd |only whep-0.1.0/whep/inst/doc/workflow-intro.html |only whep-0.1.0/whep/tests/testthat/test_scrape_faostat.R |only whep-0.1.0/whep/vignettes/workflow-intro.Rmd |only whep-0.2.0/whep/DESCRIPTION | 8 whep-0.2.0/whep/MD5 | 100 ++- whep-0.2.0/whep/NAMESPACE | 4 whep-0.2.0/whep/NEWS.md | 5 whep-0.2.0/whep/R/bilateral_trade.R | 10 whep-0.2.0/whep/R/code_names.R | 42 - whep-0.2.0/whep/R/commodity_balance_sheet.R | 4 whep-0.2.0/whep/R/gapfilling.R |only whep-0.2.0/whep/R/input_files.R | 54 + whep-0.2.0/whep/R/livestock.R | 2 whep-0.2.0/whep/R/pins_internal.R | 37 - whep-0.2.0/whep/R/production.R | 4 whep-0.2.0/whep/R/scrape_faostat.R | 4 whep-0.2.0/whep/R/sources.R | 4 whep-0.2.0/whep/R/supply_use.R | 52 - whep-0.2.0/whep/R/utils.R | 8 whep-0.2.0/whep/README.md | 31 - whep-0.2.0/whep/build/partial.rdb |binary whep-0.2.0/whep/build/vignette.rds |binary whep-0.2.0/whep/inst/doc/trade-sources-coverage.html | 2 whep-0.2.0/whep/inst/extdata/examples |only whep-0.2.0/whep/inst/scripts/check_lint.R | 5 whep-0.2.0/whep/man/build_supply_use.Rd | 10 whep-0.2.0/whep/man/get_bilateral_trade.Rd | 4 whep-0.2.0/whep/man/get_feed_intake.Rd | 2 whep-0.2.0/whep/man/get_primary_production.Rd | 2 whep-0.2.0/whep/man/get_primary_residues.Rd | 2 whep-0.2.0/whep/man/get_processing_coefs.Rd | 2 whep-0.2.0/whep/man/get_wide_cbs.Rd | 2 whep-0.2.0/whep/man/linear_fill.Rd |only whep-0.2.0/whep/man/proxy_fill.Rd |only whep-0.2.0/whep/man/sum_fill.Rd |only whep-0.2.0/whep/tests/testthat/test_bilateral_trade.R | 71 +- whep-0.2.0/whep/tests/testthat/test_commodity_balance_sheet.R | 101 +-- whep-0.2.0/whep/tests/testthat/test_gapfilling.R |only whep-0.2.0/whep/tests/testthat/test_input_files.R | 39 - whep-0.2.0/whep/tests/testthat/test_sources.R | 11 whep-0.2.0/whep/tests/testthat/test_supply_use.R | 295 ++++------ 43 files changed, 510 insertions(+), 407 deletions(-)
Title: Automatically Builds 12 Classification Models
Description: Automatically builds 12 classification models from data. The package returns 26 plots, 5 tables and a summary report.
The package automatically builds six individual classification models, including error (RMSE) and predictions. That data is used to create an ensemble, which is then modeled using six methods.
The process is repeated as many times as the user requests. The mean of the results are presented in a summary table.
The package returns the confusion matrices for all 12 models, tables of the correlation of the numeric data, the results of the variance inflation process, the head of the ensemble and the head of the data frame.
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between ClassificationEnsembles versions 0.7.0 dated 2025-10-12 and 0.7.1 dated 2025-10-15
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 3 ++ R/ClassificationEnsembles.R | 48 ++++++++++++++++++++++---------------------- 4 files changed, 33 insertions(+), 30 deletions(-)
More information about ClassificationEnsembles at CRAN
Permanent link
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Impect GmbH [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@impect.com>
Diff between impectR versions 2.4.3 dated 2025-09-08 and 2.5.1 dated 2025-10-15
impectR-2.4.3/impectR/R/getPlayerMatchSums.R |only impectR-2.4.3/impectR/R/getSquadMatchSums.R |only impectR-2.5.1/impectR/DESCRIPTION | 8 impectR-2.5.1/impectR/MD5 | 84 ++-- impectR-2.5.1/impectR/NAMESPACE | 1 impectR-2.5.1/impectR/NEWS.md | 20 + impectR-2.5.1/impectR/R/getAccessToken.R | 11 impectR-2.5.1/impectR/R/getEvents.R | 156 +++++++- impectR-2.5.1/impectR/R/getFormations.R | 18 - impectR-2.5.1/impectR/R/getIterations.R | 6 impectR-2.5.1/impectR/R/getMatches.R | 12 impectR-2.5.1/impectR/R/getPlayerIterationAverages.R | 21 - impectR-2.5.1/impectR/R/getPlayerIterationScores.R | 221 ++++++++---- impectR-2.5.1/impectR/R/getPlayerMatchScores.R | 285 ++++++++++++---- impectR-2.5.1/impectR/R/getPlayerMatchsums.R |only impectR-2.5.1/impectR/R/getPlayerProfileScores.R | 22 - impectR-2.5.1/impectR/R/getSetPieces.R | 20 - impectR-2.5.1/impectR/R/getSquadCoefficients.R |only impectR-2.5.1/impectR/R/getSquadIterationAverages.R | 18 - impectR-2.5.1/impectR/R/getSquadIterationScores.R | 18 - impectR-2.5.1/impectR/R/getSquadMatchScores.R | 127 ++++++- impectR-2.5.1/impectR/R/getSquadMatchsums.R |only impectR-2.5.1/impectR/R/getSquadRatings.R | 15 impectR-2.5.1/impectR/R/getStartingPositions.R | 21 - impectR-2.5.1/impectR/R/getSubstitutions.R | 21 - impectR-2.5.1/impectR/R/utils.R | 14 impectR-2.5.1/impectR/README.md | 65 +++ impectR-2.5.1/impectR/man/getAccessToken.Rd | 9 impectR-2.5.1/impectR/man/getEvents.Rd | 10 impectR-2.5.1/impectR/man/getFormations.Rd | 4 impectR-2.5.1/impectR/man/getIterations.Rd | 4 impectR-2.5.1/impectR/man/getMatches.Rd | 4 impectR-2.5.1/impectR/man/getPlayerIterationAverages.Rd | 4 impectR-2.5.1/impectR/man/getPlayerIterationScores.Rd | 16 impectR-2.5.1/impectR/man/getPlayerMatchScores.Rd | 16 impectR-2.5.1/impectR/man/getPlayerMatchsums.Rd | 6 impectR-2.5.1/impectR/man/getPlayerProfileScores.Rd | 9 impectR-2.5.1/impectR/man/getSetPieces.Rd | 4 impectR-2.5.1/impectR/man/getSquadCoefficients.Rd |only impectR-2.5.1/impectR/man/getSquadIterationAverages.Rd | 4 impectR-2.5.1/impectR/man/getSquadIterationScores.Rd | 4 impectR-2.5.1/impectR/man/getSquadMatchScores.Rd | 4 impectR-2.5.1/impectR/man/getSquadMatchsums.Rd | 6 impectR-2.5.1/impectR/man/getSquadRatings.Rd | 4 impectR-2.5.1/impectR/man/getStartingPositions.Rd | 4 impectR-2.5.1/impectR/man/getSubstitutions.Rd | 4 46 files changed, 961 insertions(+), 339 deletions(-)
Title: Fast Approximation of Time-Varying Infectious Disease
Transmission Rates
Description: A fast method for approximating time-varying infectious disease
transmission rates from disease incidence time series and other
data, based on a discrete time approximation of an SEIR model, as
analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.4.0 dated 2025-04-28 and 0.5.0 dated 2025-10-15
fastbeta-0.4.0/fastbeta/R/lambertW.R |only fastbeta-0.5.0/fastbeta/DESCRIPTION | 11 fastbeta-0.5.0/fastbeta/MD5 | 42 - fastbeta-0.5.0/fastbeta/NAMESPACE | 1 fastbeta-0.5.0/fastbeta/R/aoi.R | 296 ++++++---- fastbeta-0.5.0/fastbeta/R/cbind.ts.R |only fastbeta-0.5.0/fastbeta/R/deconvolve.R | 7 fastbeta-0.5.0/fastbeta/R/fastbeta.R | 3 fastbeta-0.5.0/fastbeta/data/datalist | 1 fastbeta-0.5.0/fastbeta/data/pneumonia.rda |only fastbeta-0.5.0/fastbeta/inst/NEWS.Rd | 152 +++-- fastbeta-0.5.0/fastbeta/inst/de.R |only fastbeta-0.5.0/fastbeta/inst/scripts/1918KeatCush-Chart2-SolidLine.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/1979MoseBend-Figure1-Bars.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/2009GoldDush-SupplementFigure1-Points.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/pneumonia.R |only fastbeta-0.5.0/fastbeta/inst/scripts/pneumonia.csv |only fastbeta-0.5.0/fastbeta/inst/test.R |only fastbeta-0.5.0/fastbeta/man/cbind.ts.Rd |only fastbeta-0.5.0/fastbeta/man/deconvolve.Rd | 99 ++- fastbeta-0.5.0/fastbeta/man/fastbeta.Rd | 3 fastbeta-0.5.0/fastbeta/man/fastbeta.bootstrap.Rd | 3 fastbeta-0.5.0/fastbeta/man/fastbeta.matrix.Rd | 3 fastbeta-0.5.0/fastbeta/man/pneumonia.Rd |only fastbeta-0.5.0/fastbeta/man/ptpi.Rd | 3 fastbeta-0.5.0/fastbeta/man/seir.Rd | 4 fastbeta-0.5.0/fastbeta/man/sir.aoi.Rd | 226 ++++--- fastbeta-0.5.0/fastbeta/man/smallpox.Rd | 8 28 files changed, 560 insertions(+), 302 deletions(-)
Title: NPMLE for Logistic-Cox Cure-Rate Model
Description: Expectation-Maximization (EM) algorithm for point estimation and variance estimation to
the nonparametric maximum likelihood estimator (NPMLE) for
logistic-Cox cure-rate model with left truncation and right-
censoring. See Hou, Chambers and Xu (2017) <doi:10.1007/s10985-017-9415-2>.
Author: Evan Ren [aut],
Jue Hou [cre]
Maintainer: Jue Hou <hou00123@umn.edu>
Diff between curephEM versions 0.3.0 dated 2024-02-02 and 0.3.2 dated 2025-10-15
DESCRIPTION | 25 +++++-- MD5 | 18 ++--- build/vignette.rds |binary data/sim.cureph.data.rda |binary inst/doc/curephEM-vignette.R | 33 +-------- inst/doc/curephEM-vignette.Rmd | 83 +++++------------------ inst/doc/curephEM-vignette.html | 141 ++-------------------------------------- man/Survcure.Rd | 2 tests |only vignettes/curephEM-vignette.Rmd | 83 +++++------------------ 10 files changed, 83 insertions(+), 302 deletions(-)
Title: Computerized Adaptive Testing for Survey Research
Description: Provides methods of computerized adaptive testing for survey researchers. See Montgomery and Rossiter (2020) <doi:10.1093/jssam/smz027>. Includes functionality for data fit with the classic item response methods including the latent trait model, the Birnbaum three parameter model, the graded response, and the generalized partial credit model. Additionally, includes several ability parameter estimation and item selection routines. During item selection, all calculations are done in compiled C++ code.
Author: Jacob Montgomery [aut],
Erin Rossiter [aut, cre]
Maintainer: Erin Rossiter <erossite@nd.edu>
Diff between catSurv versions 1.5.0 dated 2022-12-03 and 1.6.0 dated 2025-10-15
DESCRIPTION | 15 ++++++------ MD5 | 56 ++++++++++++++++++++++----------------------- NEWS.md | 8 ++++++ R/data.R | 44 +++++++++++++++++------------------ R/simulateFisherInfo.R | 3 ++ R/simulateThetas.R | 3 ++ man/agree_cat.Rd | 2 - man/consc_cat.Rd | 2 - man/empathy_cat.Rd | 2 - man/extra_cat.Rd | 2 - man/mach_cat.Rd | 2 - man/neuro_cat.Rd | 2 - man/nfa_cat.Rd | 4 +-- man/nfc_cat.Rd | 4 +-- man/npi_cat.Rd | 2 - man/nte_cat.Rd | 4 +-- man/open_cat.Rd | 2 - man/polknowMT.Rd | 2 - man/rwa_cat.Rd | 2 - man/sdo_cat.Rd | 2 - man/simulateFisherInfo.Rd | 3 ++ man/simulateThetas.Rd | 3 ++ man/sv_conservation_cat.Rd | 2 - man/sv_open_cat.Rd | 2 - man/sv_selfenhance_cat.Rd | 2 - man/sv_selftransc_cat.Rd | 2 - man/systemizing_cat.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 3 -- 29 files changed, 102 insertions(+), 82 deletions(-)
Title: Ridge Redundancy Analysis for High-Dimensional Omics Data
Description: Efficient framework for ridge redundancy analysis (rrda),
tailored for high-dimensional omics datasets where the number of
predictors exceeds the number of samples. The method leverages
Singular Value Decomposition (SVD) to avoid direct inversion of the
covariance matrix, enhancing scalability and performance. It also
introduces a memory-efficient storage strategy for coefficient
matrices, enabling practical use in large-scale applications. The
package supports cross-validation for selecting regularization
parameters and reduced-rank dimensions, making it a robust and
flexible tool for multivariate analysis in omics research. Please
refer to our article (Yoshioka et al., 2025) for more details.
Author: Hayato Yoshioka [aut] ,
Julie Aubert [aut, cre] ,
Tristan Mary-Huard [aut]
Maintainer: Julie Aubert <julie.aubert@inrae.fr>
Diff between rrda versions 0.1.1 dated 2025-04-29 and 0.2.3 dated 2025-10-15
DESCRIPTION | 17 +- MD5 | 22 +-- NAMESPACE | 3 R/cv.R | 18 +- R/graphs.R | 236 ++++++++++++++++++++++++++++++++++++++- man/figures |only man/get_lambda.Rd | 11 + man/rrda.cv.Rd | 11 + man/rrda.heatmap.Rd | 4 man/rrda.plot.Rd | 4 man/rrda.top.Rd |only tests/testing_RCMD_hayato.Rmd | 4 tests/testthat/test-rrda_graph.R | 98 ++++++++++++++++ 13 files changed, 397 insertions(+), 31 deletions(-)
Title: R Bindings for Calling the 'Earth Engine' API
Description: Earth Engine <https://earthengine.google.com/> client library for R. All
of the 'Earth Engine' API classes, modules, and functions are made available. Additional
functions implemented include importing (exporting) of Earth Engine spatial objects,
extraction of time series, interactive map display, assets management interface,
and metadata display. See <https://r-spatial.github.io/rgee/> for further details.
Author: Cesar Aybar [aut] ,
Wu Qiusheng [ctb] ,
Lesly Bautista [ctb] ,
Roy Yali [ctb] ,
Antony Barja [ctb] ,
Kevin Ushey [ctb],
Jeroen Ooms [ctb] ,
Tim Appelhans [ctb],
JJ Allaire [ctb],
Yuan Tang [ctb],
Samapriya Roy [ctb],
MariaElena Adauto [ctb] ,
Gabriel [...truncated...]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between rgee versions 1.1.7 dated 2023-09-27 and 1.1.8 dated 2025-10-15
rgee-1.1.7/rgee/inst/python/__pycache__ |only rgee-1.1.8/rgee/DESCRIPTION | 48 rgee-1.1.8/rgee/MD5 | 104 rgee-1.1.8/rgee/NEWS.md | 13 rgee-1.1.8/rgee/R/Deprecated.R | 18 rgee-1.1.8/rgee/R/ee_Initialize.R | 10 rgee-1.1.8/rgee/R/ee_as_sf.R | 18 rgee-1.1.8/rgee/R/ee_check.R | 2 rgee-1.1.8/rgee/R/ee_download.R | 4 rgee-1.1.8/rgee/R/ee_image.R | 64 rgee-1.1.8/rgee/R/ee_imagecollection.R | 42 rgee-1.1.8/rgee/R/ee_install.R | 8 rgee-1.1.8/rgee/R/ee_utils.R | 9 rgee-1.1.8/rgee/R/ee_version.R | 2 rgee-1.1.8/rgee/R/utils-auth.R | 2 rgee-1.1.8/rgee/R/utils-upload.R | 20 rgee-1.1.8/rgee/build/vignette.rds |binary rgee-1.1.8/rgee/inst/WORDLIST | 506 ++-- rgee-1.1.8/rgee/inst/dataset.json | 2 rgee-1.1.8/rgee/inst/devtools_internal_tests.R |only rgee-1.1.8/rgee/inst/doc/rgee01.R | 52 rgee-1.1.8/rgee/inst/doc/rgee01.html | 8 rgee-1.1.8/rgee/inst/doc/rgee02.R | 2 rgee-1.1.8/rgee/inst/doc/rgee02.html | 4 rgee-1.1.8/rgee/inst/doc/rgee03.R | 1412 ++++++------- rgee-1.1.8/rgee/inst/doc/rgee03.html | 28 rgee-1.1.8/rgee/inst/doc/rgee04.R | 74 rgee-1.1.8/rgee/inst/doc/rgee04.Rmd | 3 rgee-1.1.8/rgee/inst/doc/rgee04.html | 16 rgee-1.1.8/rgee/inst/doc/rgee05.R | 148 - rgee-1.1.8/rgee/inst/doc/rgee05.html | 50 rgee-1.1.8/rgee/inst/doc/rgee06.R | 140 - rgee-1.1.8/rgee/inst/doc/rgee06.Rmd | 10 rgee-1.1.8/rgee/inst/doc/rgee06.html | 21 rgee-1.1.8/rgee/man/ee_Authenticate.Rd | 2 rgee-1.1.8/rgee/man/ee_Initialize.Rd | 2 rgee-1.1.8/rgee/man/ee_as_rast.Rd | 18 rgee-1.1.8/rgee/man/ee_as_raster.Rd | 18 rgee-1.1.8/rgee/man/ee_as_sf.Rd | 18 rgee-1.1.8/rgee/man/ee_as_stars.Rd | 50 rgee-1.1.8/rgee/man/ee_as_thumbnail.Rd | 2 rgee-1.1.8/rgee/man/ee_drive_to_local.Rd | 2 rgee-1.1.8/rgee/man/ee_gcs_to_local.Rd | 2 rgee-1.1.8/rgee/man/ee_imagecollection_to_local.Rd | 46 rgee-1.1.8/rgee/man/ee_install.Rd | 6 rgee-1.1.8/rgee/man/ee_install_set_pyenv.Rd | 6 rgee-1.1.8/rgee/man/ee_install_upgrade.Rd | 4 rgee-1.1.8/rgee/man/ee_utils_cog_metadata.Rd | 6 rgee-1.1.8/rgee/man/rgee-package.Rd | 7 rgee-1.1.8/rgee/tests/testthat/test-ee_utils_get_crs_web.R |only rgee-1.1.8/rgee/vignettes/rgee04.Rmd | 3 rgee-1.1.8/rgee/vignettes/rgee06.Rmd | 10 52 files changed, 1527 insertions(+), 1515 deletions(-)
Title: Develop Clinical Prediction Models Using the Common Data Model
Description: A user friendly way to create patient level prediction models using
the Observational Medical Outcomes Partnership Common Data Model. Given a cohort
of interest and an outcome of interest, the package can use data in the Common
Data Model to build a large set of features. These features can then be used to
fit a predictive model with a number of machine learning algorithms. This is
further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Author: Egill Fridgeirsson [aut, cre],
Jenna Reps [aut],
Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Peter Rijnbeek [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Egill Fridgeirsson <e.fridgeirsson@erasmusmc.nl>
Diff between PatientLevelPrediction versions 6.5.0 dated 2025-07-25 and 6.5.1 dated 2025-10-15
PatientLevelPrediction-6.5.0/PatientLevelPrediction/inst/sql/postgresql/Migration_1-store_version.sql |only PatientLevelPrediction-6.5.1/PatientLevelPrediction/DESCRIPTION | 18 PatientLevelPrediction-6.5.1/PatientLevelPrediction/MD5 | 145 +++---- PatientLevelPrediction-6.5.1/PatientLevelPrediction/NEWS.md | 10 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/AdditionalCovariates.R | 15 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/DatabaseMigration.R | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/ExistingSklearn.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/ExtractData.R | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/GradientBoostingMachine.R | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/HelperFunctions.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/Plotting.R | 195 +++++++--- PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/SaveLoadPlp.R | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/SklearnClassifierHelpers.R | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/build/vignette.rds |binary PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomFeatureEngineering.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomSamples.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomSplitting.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BenchmarkTasks.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BestPractices.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BuildingMultiplePredictiveModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BuildingPredictiveModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/ClinicalModels.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/ConstrainedPredictors.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingLearningCurves.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.Rmd | 54 -- PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.html | 195 +--------- PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/GISExample.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/InstallationGuide.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/sql/postgresql/migrations |only PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createDatabaseDetails.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createLearningCurve.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createPlpResultTables.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createRareFeatureRemover.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createSampleSettings.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/diagnosePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/externalValidateDbPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getCohortCovariateData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getEunomiaPlpData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getPlpData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/insertResultsToSqlite.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/outcomeSurvivalPlot.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotDemographicSummary.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotF1Measure.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotGeneralizability.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotLearningCurve.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotNetBenefit.Rd | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPrecisionRecall.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPredictedPDF.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPredictionDistribution.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPreferencePDF.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSmoothCalibration.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseCalibration.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseCalibration2.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseRoc.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotVariableScatterplot.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/runMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setGradientBoostingMachine.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setIterativeHardThresholding.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setLightGBM.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/validateExternal.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/validateMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewDatabaseResultPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/setup.R | 124 +++++- PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-UploadToDatabase.R | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-evaluation.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-plotting.R | 38 + PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnClassifier.R | 3 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnClassifierSettings.R | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnJson.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/vignettes/CreatingNetworkStudies.Rmd | 54 -- PatientLevelPrediction-6.5.1/PatientLevelPrediction/vignettes/maintainers |only 75 files changed, 537 insertions(+), 520 deletions(-)
More information about PatientLevelPrediction at CRAN
Permanent link
Title: Machine Learning Experiments
Description: Provides 'R6' objects to perform parallelized hyperparameter
optimization and cross-validation. Hyperparameter optimization can be
performed with Bayesian optimization (via 'ParBayesianOptimization'
<https://cran.r-project.org/package=ParBayesianOptimization>) and grid
search. The optimized hyperparameters can be validated using k-fold
cross-validation. Alternatively, hyperparameter optimization and
validation can be performed with nested cross-validation. While
'mlexperiments' focuses on core wrappers for machine learning
experiments, additional learner algorithms can be supplemented by
inheriting from the provided learner base class.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlexperiments versions 0.0.7 dated 2025-09-09 and 0.0.8 dated 2025-10-15
DESCRIPTION | 7 MD5 | 32 - R/MLNestedCV.R | 13 R/MLTuneParameters.R | 21 R/cv_helper_base.R | 29 - R/cv_helper_nested.R | 20 R/ml_helper_base.R | 50 +- R/optimizer_helper_bayesian.R | 62 +- R/tune_helper_base.R | 55 +- R/utils_metrics.R | 668 +++++++++++++-------------- build/vignette.rds |binary inst/doc/mlexperiments_knn_binary.html | 180 +++++-- inst/doc/mlexperiments_knn_multiclass.html | 180 +++++-- inst/doc/mlexperiments_rpart_binary.html | 180 +++++-- inst/doc/mlexperiments_rpart_multiclass.html | 180 +++++-- inst/doc/mlexperiments_rpart_regression.html | 180 +++++-- inst/doc/mlexperiments_starter.html | 180 +++++-- 17 files changed, 1376 insertions(+), 661 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.6.1 dated 2025-09-25 and 0.6.2 dated 2025-10-15
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- R/alloc_dmd.R | 3 ++ README.md | 2 + inst/doc/get_started.html | 24 ++++++++++----------- inst/doc/user_cases.html | 52 +++++++++++++++++++++++----------------------- 6 files changed, 51 insertions(+), 46 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.5 dated 2025-10-10 and 1.5.1 dated 2025-10-15
gdverse-1.5.1/gdverse/DESCRIPTION | 6 gdverse-1.5.1/gdverse/MD5 | 45 - gdverse-1.5.1/gdverse/NEWS.md | 214 +++-- gdverse-1.5.1/gdverse/R/rgd.R | 13 gdverse-1.5.1/gdverse/R/rid.R | 13 gdverse-1.5.1/gdverse/R/robustdisc.R | 13 gdverse-1.5.1/gdverse/inst/doc/consistency.html | 5 gdverse-1.5.1/gdverse/inst/doc/gd.Rmd | 862 ++++++++++++------------ gdverse-1.5.1/gdverse/inst/doc/gd.html | 5 gdverse-1.5.1/gdverse/inst/doc/idsa.Rmd | 2 gdverse-1.5.1/gdverse/inst/doc/idsa.html | 7 gdverse-1.5.1/gdverse/inst/doc/opgd.html | 5 gdverse-1.5.1/gdverse/inst/doc/rgdrid.html | 5 gdverse-1.5.1/gdverse/inst/doc/sesu.html | 5 gdverse-1.5.1/gdverse/inst/doc/shegd.html | 5 gdverse-1.5.1/gdverse/inst/doc/spade.Rmd | 441 ++++++------ gdverse-1.5.1/gdverse/inst/doc/spade.html | 34 gdverse-1.5.1/gdverse/man/rgd.Rd | 13 gdverse-1.5.1/gdverse/man/rid.Rd | 13 gdverse-1.5.1/gdverse/man/robust_disc.Rd | 13 gdverse-1.5.1/gdverse/vignettes/gd.Rmd | 862 ++++++++++++------------ gdverse-1.5.1/gdverse/vignettes/idsa.Rmd | 2 gdverse-1.5.1/gdverse/vignettes/spade.Rmd | 441 ++++++------ gdverse-1.5/gdverse/inst/python/__pycache__ |only 24 files changed, 1519 insertions(+), 1505 deletions(-)
Title: Globally-Applicable Area Disaggregated General Ecosystem Toolbox
V3
Description: A framework to assist creation of marine ecosystem models,
generating either 'R' or 'C++' code which can then be optimised using
the 'TMB' package and standard 'R' tools. Principally designed to
reproduce gadget2 models in 'TMB', but can be extended beyond
gadget2's capabilities.
Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.".
Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Author: Jamie Lentin [aut, cre] ,
Bjarki Thor Elvarsson [aut] ,
William Butler [aut] ,
Marine and Freshwater Research Institute [cph]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between gadget3 versions 0.13-0 dated 2025-04-19 and 0.14-0 dated 2025-10-15
gadget3-0.13-0/gadget3/inst/doc/random-effects.R |only gadget3-0.13-0/gadget3/inst/doc/random-effects.Rmd |only gadget3-0.13-0/gadget3/inst/doc/random-effects.html |only gadget3-0.13-0/gadget3/vignettes/random-effects.Rmd |only gadget3-0.14-0/gadget3/DESCRIPTION | 16 gadget3-0.14-0/gadget3/MD5 | 228 ++++----- gadget3-0.14-0/gadget3/NAMESPACE | 9 gadget3-0.14-0/gadget3/NEWS.md | 21 gadget3-0.14-0/gadget3/R/aab_env.R | 25 gadget3-0.14-0/gadget3/R/action_age.R | 7 gadget3-0.14-0/gadget3/R/action_grow.R | 38 + gadget3-0.14-0/gadget3/R/action_mature.R | 123 +--- gadget3-0.14-0/gadget3/R/action_migrate.R | 9 gadget3-0.14-0/gadget3/R/action_predate.R | 24 gadget3-0.14-0/gadget3/R/action_renewal.R | 27 - gadget3-0.14-0/gadget3/R/action_spawn.R | 9 gadget3-0.14-0/gadget3/R/action_tagging.R | 2 gadget3-0.14-0/gadget3/R/action_time.R | 2 gadget3-0.14-0/gadget3/R/action_trace.R |only gadget3-0.14-0/gadget3/R/action_weightloss.R | 4 gadget3-0.14-0/gadget3/R/array_utils.R | 50 + gadget3-0.14-0/gadget3/R/debug_utils.R | 2 gadget3-0.14-0/gadget3/R/eval.R | 4 gadget3-0.14-0/gadget3/R/formula_utils.R | 3 gadget3-0.14-0/gadget3/R/headtail.R |only gadget3-0.14-0/gadget3/R/init_val.R | 25 gadget3-0.14-0/gadget3/R/param_project.R | 252 +++++----- gadget3-0.14-0/gadget3/R/params.R | 12 gadget3-0.14-0/gadget3/R/quota.R | 53 +- gadget3-0.14-0/gadget3/R/run.R | 25 gadget3-0.14-0/gadget3/R/run_r.R | 9 gadget3-0.14-0/gadget3/R/run_tmb.R | 100 +++ gadget3-0.14-0/gadget3/R/step.R | 149 ++++- gadget3-0.14-0/gadget3/R/test_utils.R | 110 ++-- gadget3-0.14-0/gadget3/R/timedata.R | 2 gadget3-0.14-0/gadget3/README.md | 5 gadget3-0.14-0/gadget3/build/vignette.rds |binary gadget3-0.14-0/gadget3/inst/doc/incorporating-observation-data.R | 30 - gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.R | 56 +- gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.Rmd | 13 gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.html | 45 + gadget3-0.14-0/gadget3/inst/doc/model-customisation.R | 10 gadget3-0.14-0/gadget3/inst/doc/model-debugging.R | 82 ++- gadget3-0.14-0/gadget3/inst/doc/model-debugging.Rmd | 120 +++- gadget3-0.14-0/gadget3/inst/doc/model-debugging.html | 158 ++++-- gadget3-0.14-0/gadget3/inst/doc/model-structure.html | 66 ++ gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.R | 137 +++-- gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.Rmd | 115 ++-- gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.html | 136 +++-- gadget3-0.14-0/gadget3/inst/doc/writing_actions.R | 24 gadget3-0.14-0/gadget3/inst/doc/writing_actions.html | 11 gadget3-0.14-0/gadget3/man/aaa_lang.Rd | 6 gadget3-0.14-0/gadget3/man/aab_env.Rd | 4 gadget3-0.14-0/gadget3/man/action_renewal.Rd | 22 gadget3-0.14-0/gadget3/man/action_trace.Rd |only gadget3-0.14-0/gadget3/man/action_weightloss.Rd | 2 gadget3-0.14-0/gadget3/man/array_utils.Rd | 14 gadget3-0.14-0/gadget3/man/init_val.Rd | 1 gadget3-0.14-0/gadget3/man/param_project.Rd | 58 +- gadget3-0.14-0/gadget3/man/quota.Rd | 130 +++-- gadget3-0.14-0/gadget3/man/run_tmb.Rd | 46 + gadget3-0.14-0/gadget3/man/step.Rd | 9 gadget3-0.14-0/gadget3/tests/test-aab_env.R | 70 +- gadget3-0.14-0/gadget3/tests/test-action_age.R | 47 - gadget3-0.14-0/gadget3/tests/test-action_grow-methods.R | 4 gadget3-0.14-0/gadget3/tests/test-action_grow-weightjones.R |only gadget3-0.14-0/gadget3/tests/test-action_grow.R | 53 -- gadget3-0.14-0/gadget3/tests/test-action_mature.R | 52 -- gadget3-0.14-0/gadget3/tests/test-action_migrate.R | 31 - gadget3-0.14-0/gadget3/tests/test-action_naturalmortality.R | 27 - gadget3-0.14-0/gadget3/tests/test-action_predate-catchability.R | 22 gadget3-0.14-0/gadget3/tests/test-action_predate-catchability_project.R |only gadget3-0.14-0/gadget3/tests/test-action_predate-numberfleet.R | 13 gadget3-0.14-0/gadget3/tests/test-action_predate-predator.R | 10 gadget3-0.14-0/gadget3/tests/test-action_predate-timebasedsuitability.R | 4 gadget3-0.14-0/gadget3/tests/test-action_predate.R | 70 -- gadget3-0.14-0/gadget3/tests/test-action_renewal-otherfood.R | 7 gadget3-0.14-0/gadget3/tests/test-action_renewal.R | 51 -- gadget3-0.14-0/gadget3/tests/test-action_report.R | 39 - gadget3-0.14-0/gadget3/tests/test-action_spawn-multipleoutputs.R | 8 gadget3-0.14-0/gadget3/tests/test-action_spawn.R | 16 gadget3-0.14-0/gadget3/tests/test-action_tagging.R | 36 - gadget3-0.14-0/gadget3/tests/test-action_time.R | 72 -- gadget3-0.14-0/gadget3/tests/test-action_trace-timing.R |only gadget3-0.14-0/gadget3/tests/test-action_weightloss.R | 6 gadget3-0.14-0/gadget3/tests/test-array_utils.R | 33 + gadget3-0.14-0/gadget3/tests/test-env_dif.R | 5 gadget3-0.14-0/gadget3/tests/test-formula_utils.R | 4 gadget3-0.14-0/gadget3/tests/test-init_val.R | 25 gadget3-0.14-0/gadget3/tests/test-likelihood_bounds.R | 44 + gadget3-0.14-0/gadget3/tests/test-likelihood_distribution-surveyindices.R | 13 gadget3-0.14-0/gadget3/tests/test-likelihood_distribution.R | 93 +-- gadget3-0.14-0/gadget3/tests/test-likelihood_random.R | 25 gadget3-0.14-0/gadget3/tests/test-likelihood_sparsesample.R | 4 gadget3-0.14-0/gadget3/tests/test-likelihood_tagging_ckmr.R | 27 - gadget3-0.14-0/gadget3/tests/test-param_project-ar1.R | 174 ++++-- gadget3-0.14-0/gadget3/tests/test-param_project-logar1.R | 190 ++++--- gadget3-0.14-0/gadget3/tests/test-param_project.R | 181 ++++--- gadget3-0.14-0/gadget3/tests/test-params.R | 15 gadget3-0.14-0/gadget3/tests/test-quota-assess.R | 10 gadget3-0.14-0/gadget3/tests/test-quota-hockeyfleet.R | 243 ++++++--- gadget3-0.14-0/gadget3/tests/test-regression.R | 4 gadget3-0.14-0/gadget3/tests/test-run_r.R | 16 gadget3-0.14-0/gadget3/tests/test-run_tmb-reporting_enabled.R | 4 gadget3-0.14-0/gadget3/tests/test-run_tmb.R | 130 +++-- gadget3-0.14-0/gadget3/tests/test-step.R | 100 +++ gadget3-0.14-0/gadget3/tests/test-stock.R | 23 gadget3-0.14-0/gadget3/tests/test-stock_age.R | 31 - gadget3-0.14-0/gadget3/tests/test-stock_areas.R | 15 gadget3-0.14-0/gadget3/tests/test-stock_tag.R | 7 gadget3-0.14-0/gadget3/tests/test-stock_time-fishingyear.R | 3 gadget3-0.14-0/gadget3/tests/test-stock_time.R | 26 - gadget3-0.14-0/gadget3/tests/test-suitability-report.R | 10 gadget3-0.14-0/gadget3/tests/test-suitability.R | 24 gadget3-0.14-0/gadget3/tests/test-timedata.R | 22 gadget3-0.14-0/gadget3/tests/test-timevariable.R | 18 gadget3-0.14-0/gadget3/vignettes/introduction-single-stock.Rmd | 13 gadget3-0.14-0/gadget3/vignettes/model-debugging.Rmd | 120 +++- gadget3-0.14-0/gadget3/vignettes/multiple-substocks.Rmd | 115 ++-- gadget3-0.14-0/gadget3/vignettes/random-effect-recruitment.R |only gadget3-0.14-0/gadget3/vignettes/random-effect-recruitment.html |only 121 files changed, 2932 insertions(+), 2113 deletions(-)
Title: Estimation of Cell Infiltration Based on Cell Crosstalk
Description: A systematic biology tool was developed to identify cell infiltration via Individualized Cell-Cell interaction network. 'CITMIC' first constructed a weighted cell interaction network through integrating Cell-target interaction information, molecular function data from Gene Ontology (GO) database and gene transcriptomic data in specific sample, and then, it used a network propagation algorithm on the network to identify cell infiltration for the sample. Ultimately, cell infiltration in the patient dataset was obtained by normalizing the centrality scores of the cells.
Author: Junwei Han [aut, cre, cph],
Xilong Zhao [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between CITMIC versions 0.1.2 dated 2024-11-08 and 0.1.3 dated 2025-10-15
CITMIC-0.1.2/CITMIC/man/figures |only CITMIC-0.1.3/CITMIC/DESCRIPTION | 8 +-- CITMIC-0.1.3/CITMIC/MD5 | 17 +++----- CITMIC-0.1.3/CITMIC/R/CITMIC.R | 32 +++++++-------- CITMIC-0.1.3/CITMIC/build/vignette.rds |binary CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.R | 7 --- CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.Rmd | 13 ++---- CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.html | 63 ++++++++++++------------------- CITMIC-0.1.3/CITMIC/man/CITMIC.Rd | 2 CITMIC-0.1.3/CITMIC/vignettes/CITMIC.Rmd | 13 ++---- 10 files changed, 65 insertions(+), 90 deletions(-)
Title: Testing for Partial Copulas and the Simplifying Assumption in
Vine Copulas
Description: Routines for two different test types, the Constant Conditional Correlation (CCC) test and the Vectorial Independence (VI) test are provided (Kurz and Spanhel (2022) <doi:10.1214/22-EJS2051>). The tests can be applied to check whether a conditional copula coincides with its partial copula. Functions to test whether a regular vine copula satisfies the so-called simplifying assumption or to test a single copula within a regular vine copula to be a (j-1)-th order partial copula are available. The CCC test comes with a decision tree approach to allow testing in high-dimensional settings.
Author: Malte S. Kurz [aut, cre]
Maintainer: Malte S. Kurz <mkurz-software@gmx.de>
Diff between pacotest versions 0.4.2 dated 2022-11-04 and 0.4.3 dated 2025-10-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 +++++- README.md | 2 +- inst/CITATION | 9 ++++----- src/Grouping.cpp | 21 ++++++++++++++++----- src/pacotestFunctions.cpp | 2 +- 7 files changed, 36 insertions(+), 22 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a
penalized likelihood estimation on the hazard function but also a
parametric estimation can be fit using this R package: 1) A shared
frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can
be studied. 2) Additive frailty models for proportional hazard models
with two correlated random effects (intercept random effect with
random slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma random
effects. 4) Joint frailty models in the context of the joint
modelling for recurrent events with terminal event for clustered data
or not. A joint frailty model for two semi-competing risks and
clustered data is also proposed. 5) Joint general frailty models in
the context of the joint modelling for recurrent events with terminal
event data with two independent frailty terms. 6) Joint Neste [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.7.0 dated 2025-03-06 and 3.7.1 dated 2025-10-15
DESCRIPTION | 13 MD5 | 18 NEWS | 3 R/longiPenal.R | 217 ++-- build/vignette.rds |binary inst/doc/Package_summary.html | 2276 +++++++++++++++++++++--------------------- man/frailtypack-package.Rd | 2 man/longiPenal.Rd | 113 +- src/funcpajlongisplines.f90 | 2 src/joint_longi.f90 | 4 10 files changed, 1405 insertions(+), 1243 deletions(-)
Title: Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Description: Package computes and displays tables with support for 'SPSS'-style
labels, multiple and nested banners, weights, multiple-response variables
and significance testing. There are facilities for nice output of tables
in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods
for labelled variables add value labels support to base R functions and to
some functions from other packages. Additionally, the package brings
popular data transformation functions from 'SPSS' Statistics and 'Excel':
'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc.
These functions are very useful for data processing in marketing research
surveys. Package intended to help people to move data
processing from 'Excel' and 'SPSS' to R.
Author: Gregory Demin [aut, cre],
Sebastian Jeworutzki [ctb] ,
Dan Chaltiel [ctb],
John Williams [ctb],
Tom Elliott [ctb]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.11.6 dated 2023-07-15 and 0.11.7 dated 2025-10-15
DESCRIPTION | 11 ++- MD5 | 112 +++++++++++++++++++-------------------- NAMESPACE | 7 ++ NEWS | 6 +- R/S3_methods.R | 4 - R/compute.R | 12 ++-- R/count_if.R | 8 +- R/criteria_functions.R | 72 ++++++++++++------------- R/cross.R | 32 +++++------ R/cross_fun.R | 29 +++++----- R/custom_tables.R | 72 ++++++++++++------------- R/dichotomy.R | 10 +-- R/expss.R | 50 ++++++++--------- R/expss_options.R | 20 +++--- R/if_na.R | 12 ++-- R/labels.R | 32 +++++------ R/mrset.R | 12 ++-- R/product_test.R | 38 ++++++------- R/qc.R | 6 +- R/recode.R | 24 ++++---- R/selectors.R | 32 +++++------ R/significance_cpct.R | 47 ++++++++-------- R/sum.R | 2 R/vec_ops.R | 32 +++++------ R/weighted_stats.R | 26 ++++----- R/window_fun.R | 3 - R/write_labelled.R | 41 ++++++-------- build/vignette.rds |binary inst/doc/examples.R | 50 ++++++++--------- inst/doc/examples.html | 4 - inst/doc/labels-support.R | 20 +++--- inst/doc/labels-support.html | 10 +-- inst/doc/tables-with-labels.R | 10 +-- inst/doc/tables-with-labels.html | 4 - inst/doc/xlsx-export.R | 8 +- inst/doc/xlsx-export.html | 8 +- man/as.dichotomy.Rd | 10 +-- man/compute.Rd | 12 ++-- man/count_if.Rd | 8 +- man/criteria.Rd | 70 ++++++++++++------------ man/cross_cases.Rd | 24 ++++---- man/cross_fun.Rd | 27 ++++----- man/expss.Rd | 52 +++++++++--------- man/expss.options.Rd | 20 +++--- man/if_na.Rd | 12 ++-- man/mrset.Rd | 12 ++-- man/product_test.Rd | 38 ++++++------- man/qc.Rd | 6 +- man/recode.Rd | 24 ++++---- man/significance.Rd | 48 ++++++++-------- man/tables.Rd | 72 ++++++++++++------------- man/val_lab.Rd | 18 +++--- man/var_lab.Rd | 14 ++-- man/vars.Rd | 32 +++++------ man/vectors.Rd | 32 +++++------ man/w_mean.Rd | 26 ++++----- man/write_labelled_csv.Rd | 41 ++++++-------- 57 files changed, 741 insertions(+), 723 deletions(-)
Title: Proximity Measure Based Diagnostics for Standard, Soft, and
Multi-Way Clustering
Description: Quantifies clustering quality by measuring both cohesion within clusters and separation between clusters. Implements advanced silhouette width computations for diverse clustering structures, including: simplified silhouette (Van der Laan et al., 2003) <doi:10.1080/0094965031000136012>, Probability of Alternative Cluster normalization methods (Raymaekers & Rousseeuw, 2022) <doi:10.1080/10618600.2022.2050249>, fuzzy clustering and silhouette diagnostics using membership probabilities (Campello & Hruschka, 2006; Menardi, 2011; Bhat & Kiruthika, 2024) <doi:10.1016/j.fss.2006.07.006>, <doi:10.1007/s11222-010-9169-0>, <doi:10.1080/23737484.2024.2408534>, and multi-way clustering extensions such as block and tensor clustering (Schepers et al., 2008; Bhat & Kiruthika, 2025) <doi:10.1007/s00357-008-9005-9>, <doi:10.21203/rs.3.rs-6973596/v1>. Provides tools for computation and visualization (Rousseeuw, 1987) <doi:10.1016/0377-0427(87)9 [...truncated...]
Author: Shrikrishna Bhat K [aut, cre, cph] ,
Kiruthika C [aut]
Maintainer: Shrikrishna Bhat K <skbhat.in@gmail.com>
Diff between Silhouette versions 0.9.4 dated 2025-07-30 and 0.9.6 dated 2025-10-15
Silhouette-0.9.4/Silhouette/R/summary.silhouette.R |only Silhouette-0.9.6/Silhouette/DESCRIPTION | 19 Silhouette-0.9.6/Silhouette/MD5 | 68 Silhouette-0.9.6/Silhouette/NAMESPACE | 27 Silhouette-0.9.6/Silhouette/NEWS.md | 47 Silhouette-0.9.6/Silhouette/R/Silhouette-package.R |only Silhouette-0.9.6/Silhouette/R/Silhouette.R | 216 -- Silhouette-0.9.6/Silhouette/R/calSilhouette.R |only Silhouette-0.9.6/Silhouette/R/cerSilhouette.R |only Silhouette-0.9.6/Silhouette/R/dbSilhouette.R |only Silhouette-0.9.6/Silhouette/R/extSilhouette.R | 9 Silhouette-0.9.6/Silhouette/R/getSilhouette.R |only Silhouette-0.9.6/Silhouette/R/is.Silhouette.R |only Silhouette-0.9.6/Silhouette/R/plotSilhouette.R | 497 ++-- Silhouette-0.9.6/Silhouette/R/softSilhouette.R | 106 Silhouette-0.9.6/Silhouette/R/summary.Silhouette.R |only Silhouette-0.9.6/Silhouette/README.md | 75 Silhouette-0.9.6/Silhouette/inst/CITATION |only Silhouette-0.9.6/Silhouette/inst/WORDLIST | 20 Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.R | 327 ++- Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.Rmd | 641 +++++ Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.html | 1071 +++++++--- Silhouette-0.9.6/Silhouette/man/Silhouette-package.Rd |only Silhouette-0.9.6/Silhouette/man/Silhouette.Rd | 68 Silhouette-0.9.6/Silhouette/man/calSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/cerSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/dbSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/extSilhouette.Rd | 5 Silhouette-0.9.6/Silhouette/man/figures |only Silhouette-0.9.6/Silhouette/man/getSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/is.Silhouette.Rd |only Silhouette-0.9.6/Silhouette/man/plotSilhouette.Rd | 251 +- Silhouette-0.9.6/Silhouette/man/softSilhouette.Rd | 37 Silhouette-0.9.6/Silhouette/tests/testthat.R | 24 Silhouette-0.9.6/Silhouette/tests/testthat/test-cerSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-dbSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-extSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-getSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-is.Silhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-plotSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-silhouette.R | 305 ++ Silhouette-0.9.6/Silhouette/tests/testthat/test-softSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-summary.silhouette.R |only Silhouette-0.9.6/Silhouette/vignettes/Silhouette.Rmd | 641 +++++ Silhouette-0.9.6/Silhouette/vignettes/references.bib | 11 45 files changed, 3327 insertions(+), 1138 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
This is a re-admission after prior archival of version 0.7.5 dated 2025-09-29
Diff between sentopics versions 0.7.5 dated 2025-09-29 and 0.7.6 dated 2025-10-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/conversions.R | 1 + man/as.LDA.Rd | 1 + tests/testthat.R | 4 +++- 6 files changed, 18 insertions(+), 10 deletions(-)
Title: Rho for Inter Rater Reliability
Description: Rho is used to test the generalization of inter rater reliability
(IRR) statistics. Calculating rho starts by generating a large number of
simulated, fully-coded data sets: a sizable collection of hypothetical
populations, all of which have a kappa value below a given threshold -- which
indicates unacceptable agreement. Then kappa is calculated on a sample from
each of those sets in the collection to see if it is equal to or higher than
the kappa in then real sample. If less than five percent of the distribution
of samples from the simulated data sets is greater than actual observed kappa,
the null hypothesis is rejected and one can conclude that if the two raters had
coded the rest of the data, we would have acceptable agreement (kappa above the
threshold).
Author: Brendan Eagan [aut],
Brad Rogers [aut],
Rebecca Pozen [aut],
Cody L Marquart [cre, aut] ,
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rhoR versions 1.3.0.3 dated 2020-09-13 and 1.3.1 dated 2025-10-15
rhoR-1.3.0.3/rhoR/data/codeSet.csv |only rhoR-1.3.0.3/rhoR/data/contingencyTable.csv |only rhoR-1.3.1/rhoR/DESCRIPTION | 11 +++--- rhoR-1.3.1/rhoR/MD5 | 34 ++++++++++----------- rhoR-1.3.1/rhoR/NEWS.md | 3 + rhoR-1.3.1/rhoR/R/rho.R | 3 + rhoR-1.3.1/rhoR/R/rho.file.R | 3 + rhoR-1.3.1/rhoR/R/rhoCT.R | 3 + rhoR-1.3.1/rhoR/R/rhoSet.R | 6 ++- rhoR-1.3.1/rhoR/README.md | 19 ++++++++--- rhoR-1.3.1/rhoR/data/codeSet.csv.gz |only rhoR-1.3.1/rhoR/data/contingencyTable.csv.gz |only rhoR-1.3.1/rhoR/inst/_pkgdown.yml | 8 ++-- rhoR-1.3.1/rhoR/man/rho.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rho.file.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rhoCT.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rhoK.Rd | 2 - rhoR-1.3.1/rhoR/man/rhoSet.Rd | 7 +++- rhoR-1.3.1/rhoR/src/RcppExports.cpp | 5 +++ rhoR-1.3.1/rhoR/tests/testthat/test-util-methods.R | 6 +-- 20 files changed, 82 insertions(+), 49 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: Sebastian Fischer [aut, cre] ,
Maximilian Muecke [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3fda versions 0.2.0 dated 2024-07-22 and 0.3.0 dated 2025-10-15
mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpCor.R |only mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpScaleRange.R |only mlr3fda-0.3.0/mlr3fda/DESCRIPTION | 30 ++- mlr3fda-0.3.0/mlr3fda/MD5 | 81 ++++++---- mlr3fda-0.3.0/mlr3fda/NAMESPACE | 6 mlr3fda-0.3.0/mlr3fda/NEWS.md | 10 + mlr3fda-0.3.0/mlr3fda/R/PipeOpFDABsignal.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDACor.R | 4 mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAExtract.R | 27 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAFlatten.R | 26 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAInterpol.R | 58 +++---- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDARandomEffect.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAScaleRange.R | 28 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDASmooth.R | 24 +- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDATsfeatures.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAWavelets.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAZoom.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFPCA.R | 13 - mlr3fda-0.3.0/mlr3fda/R/TaskRegr_dti.R | 2 mlr3fda-0.3.0/mlr3fda/R/TaskRegr_fuel.R | 2 mlr3fda-0.3.0/mlr3fda/R/bibentries.R | 3 mlr3fda-0.3.0/mlr3fda/R/zzz.R | 39 +--- mlr3fda-0.3.0/mlr3fda/README.md | 45 +++-- mlr3fda-0.3.0/mlr3fda/build/partial.rdb |binary mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.bsignal.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.cor.Rd | 4 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.extract.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.flatten.Rd | 2 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.fpca.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.interpol.Rd | 10 - mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.random_effect.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.scalerange.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.smooth.Rd | 4 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.tsfeats.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.wavelets.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.zoom.Rd |only mlr3fda-0.3.0/mlr3fda/tests/testthat/_snaps |only mlr3fda-0.3.0/mlr3fda/tests/testthat/helper.R | 6 mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDABsignal.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDACor.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAExtract.R | 33 +--- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAFlatten.R | 20 +- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAInterpolate.R | 57 +++---- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDARandomEffect.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAScaleRange.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDASmooth.R | 32 ++- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDATsfeatures.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAWavelets.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAZoom.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFPCA.R | 17 +- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_tf.R | 2 51 files changed, 327 insertions(+), 282 deletions(-)
Title: Synthesizing Causal Evidence in a Distributed Research Network
Description: Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data.
Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
Author: Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Fan Bu [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EvidenceSynthesis versions 1.0.0 dated 2025-08-26 and 1.1.0 dated 2025-10-15
DESCRIPTION | 16 MD5 | 61 +-- NAMESPACE | 1 NEWS.md | 12 R/BayesianMetaAnalysis.R | 34 + R/EvidenceSynthesis.R | 2 R/FixedEffectMetaAnalysis.R | 5 R/LikelihoodApproximation.R | 2 R/MetaAnalysis.R | 301 +++++++++------- R/Plots.R | 26 - README.md | 4 inst/doc/BayesianBiasCorrection.pdf |binary inst/doc/NonNormalEffectSynthesis.pdf |binary inst/doc/VideoVignette.pdf |binary man/computeBayesianMetaAnalysis.Rd | 5 man/computeFixedEffectMetaAnalysis.Rd | 5 man/plotLikelihoodFit.Rd | 4 man/plotMcmcTrace.Rd | 5 man/plotMetaAnalysisForest.Rd | 11 man/plotPerDbMcmcTrace.Rd | 5 man/plotPerDbPosterior.Rd | 5 man/plotPosterior.Rd | 5 tests/testthat/resources/gsPredictionInterval.rds |only tests/testthat/resources/pooledFixedFxEstimate.rds |binary tests/testthat/resources/pooledRandomFxEstimate.rds |binary tests/testthat/resources/populations.rds |binary tests/testthat/resources/sccsPooledFixedFxEstimate.rds |binary tests/testthat/resources/sccsPooledRandomFxEstimate.rds |binary tests/testthat/resources/sccsPopulations.rds |binary tests/testthat/resources/tracesForPi.rds |only tests/testthat/test-nonNormalMetaAnalysis.R | 28 - tests/testthat/test-plots.R | 10 tests/testthat/test_predictionInterval.R |only 33 files changed, 340 insertions(+), 207 deletions(-)
More information about EvidenceSynthesis at CRAN
Permanent link
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut] ,
Jasper Cooper [aut] ,
Alexander Coppock [aut, cre] ,
Macartan Humphreys [aut] ,
Neal Fultz [aut]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between DeclareDesign versions 1.0.10 dated 2024-04-21 and 1.1.0 dated 2025-10-15
DeclareDesign-1.0.10/DeclareDesign/man/edit.Rd |only DeclareDesign-1.0.10/DeclareDesign/man/expand_conditions.Rd |only DeclareDesign-1.1.0/DeclareDesign/DESCRIPTION | 36 DeclareDesign-1.1.0/DeclareDesign/MD5 | 152 +-- DeclareDesign-1.1.0/DeclareDesign/NAMESPACE | 12 DeclareDesign-1.1.0/DeclareDesign/NEWS.md | 7 DeclareDesign-1.1.0/DeclareDesign/R/DeclareDesign.R | 2 DeclareDesign-1.1.0/DeclareDesign/R/aaa.R | 434 ++++++++-- DeclareDesign-1.1.0/DeclareDesign/R/compare_diagnoses.R | 364 ++++---- DeclareDesign-1.1.0/DeclareDesign/R/declare_assignment.R | 4 DeclareDesign-1.1.0/DeclareDesign/R/declare_diagnosands.R | 2 DeclareDesign-1.1.0/DeclareDesign/R/declare_estimator.R | 215 ++-- DeclareDesign-1.1.0/DeclareDesign/R/declare_inquiry.R | 17 DeclareDesign-1.1.0/DeclareDesign/R/declare_measurement.R | 8 DeclareDesign-1.1.0/DeclareDesign/R/declare_model.R | 58 - DeclareDesign-1.1.0/DeclareDesign/R/declare_potential_outcomes.R | 322 ++----- DeclareDesign-1.1.0/DeclareDesign/R/declare_sampling.R | 3 DeclareDesign-1.1.0/DeclareDesign/R/declare_test.R | 5 DeclareDesign-1.1.0/DeclareDesign/R/design_helper_functions.R | 3 DeclareDesign-1.1.0/DeclareDesign/R/design_print_summary.R | 22 DeclareDesign-1.1.0/DeclareDesign/R/diagnose_design.R | 380 +++++--- DeclareDesign-1.1.0/DeclareDesign/R/diagnosis_helper_functions.R | 7 DeclareDesign-1.1.0/DeclareDesign/R/expand_design.R | 24 DeclareDesign-1.1.0/DeclareDesign/R/modify_design.R | 4 DeclareDesign-1.1.0/DeclareDesign/R/modify_edit.R | 152 ++- DeclareDesign-1.1.0/DeclareDesign/R/object_handlers.R |only DeclareDesign-1.1.0/DeclareDesign/R/redesign.R | 36 DeclareDesign-1.1.0/DeclareDesign/R/select_diagnosands.R |only DeclareDesign-1.1.0/DeclareDesign/R/simulate_design.R | 19 DeclareDesign-1.1.0/DeclareDesign/R/utilities.R | 24 DeclareDesign-1.1.0/DeclareDesign/build |only DeclareDesign-1.1.0/DeclareDesign/inst/doc |only DeclareDesign-1.1.0/DeclareDesign/man/DeclareDesign-deprecated.Rd | 6 DeclareDesign-1.1.0/DeclareDesign/man/DeclareDesign.Rd | 38 DeclareDesign-1.1.0/DeclareDesign/man/compare_diagnoses.Rd | 10 DeclareDesign-1.1.0/DeclareDesign/man/declare_assignment.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/declare_estimator.Rd | 42 DeclareDesign-1.1.0/DeclareDesign/man/declare_inquiry.Rd | 11 DeclareDesign-1.1.0/DeclareDesign/man/declare_internal_inherit_params.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/declare_measurement.Rd | 15 DeclareDesign-1.1.0/DeclareDesign/man/declare_model.Rd | 58 - DeclareDesign-1.1.0/DeclareDesign/man/declare_potential_outcomes.Rd | 28 DeclareDesign-1.1.0/DeclareDesign/man/declare_reveal.Rd | 12 DeclareDesign-1.1.0/DeclareDesign/man/declare_sampling.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/declare_test.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/diagnose_design.Rd | 71 - DeclareDesign-1.1.0/DeclareDesign/man/expand_design.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/find_all_objects.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/modify_design.Rd | 4 DeclareDesign-1.1.0/DeclareDesign/man/modify_edit.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/redesign.Rd | 8 DeclareDesign-1.1.0/DeclareDesign/man/select_diagnosands.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/simulate_design.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/tidy.diagnosis.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat.R | 10 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-allow-custom-functions.R | 4 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-alternative-df-compatibility.R | 24 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-assignment.R | 10 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-bootstrap-diagnosands.R | 9 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-citation.R | 3 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-compare-designs.R | 3 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-compare-diagnoses.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-demo.R | 13 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-describe_variable.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-design-library.R | 171 +++ DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-design-summary.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-diagnosands.R | 15 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-diagnose-design.R | 24 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-environment-issues.R | 15 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-environments.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-fanout.R | 6 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-find-objects.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-multiple-estimands-one-estimator.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-multiple-pos.R | 12 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-potential-outcomes.R | 282 ++++-- DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-redesign.R | 223 ++++- DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-reshape-diagnosis.R | 21 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-reveal-outcomes.R | 14 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-select-diagnosands.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-simulate-design.R | 33 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-test.R | 7 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-utilities.R | 14 DeclareDesign-1.1.0/DeclareDesign/vignettes |only 83 files changed, 2311 insertions(+), 1237 deletions(-)
Title: Tools to Use and Explore the 'BioTIME' Database
Description: The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.
Author: Alban Sagouis [aut, cre] ,
Faye Moyes [aut] ,
Ines S. Martins [aut, rev] ,
Shane A. Blowes [ctb] ,
Viviana Brambilla [ctb] ,
Cher F. Y. Chow [ctb] ,
Ada Fontrodona-Eslava [ctb] ,
Laura Antao [ctb, rev] ,
Jonathan M. Chase [fnd] ,
Maria Dornelas [fnd, [...truncated...]
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
Diff between BioTIMEr versions 0.2.5 dated 2025-09-19 and 0.2.6 dated 2025-10-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/vignette1.html | 10 +++++----- tests/testthat/test-metrics.R | 8 ++++---- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: Background-Parallel Jobs
Description: Easily launch, track, and control functions as
background-parallel jobs. Includes robust utilities for job status,
error handling, resource monitoring, and result collection. Designed
for scalable workflows in interactive and automated settings (local or
remote). Integrates with multiple backends; supports flexible
automation pipelines and live job tracking. For more information, see
<https://anirbanshaw24.github.io/bakerrr/>.
Author: Anirban Shaw [aut, cre]
Maintainer: Anirban Shaw <anirbanshaw24@gmail.com>
Diff between bakerrr versions 0.1.0 dated 2025-10-01 and 0.2.0 dated 2025-10-15
DESCRIPTION | 10 + MD5 | 35 +++--- NEWS.md | 6 - R/01_bakerrr.R | 78 +++++++++++++-- R/print.R | 36 +++--- R/summary.R | 28 ++--- README.md | 182 ++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/multi_function.R |only inst/doc/multi_function.Rmd |only inst/doc/multi_function.html |only inst/doc/simple_example.html | 80 +++++++++------ inst/doc/vs_mirai.R | 20 +-- inst/doc/vs_mirai.Rmd | 20 +-- inst/doc/vs_mirai.html | 117 ++++++++++------------ inst/pkgdown.yml | 3 tests/testthat/test-bakerrr_class.R | 2 tests/testthat/test-multi_function.R |only vignettes/multi_function.Rmd |only vignettes/vs_mirai.Rmd | 20 +-- 21 files changed, 433 insertions(+), 208 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-29 0.7.5
2024-09-20 0.7.4
2024-04-18 0.7.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-26 2.1.0
2024-11-15 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-29 0.1.1
2024-01-29 0.1.2
2024-01-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-05 1.2.1
2025-01-10 1.1.1
2024-12-19 1.1.0
2024-08-20 1.0.2
2024-04-08 1.0.1
2024-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-17 1.2.1
2024-01-20 1.2.0
2023-03-19 1.1.0
2023-02-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-16 1.2.0
2025-02-21 1.1.0
2025-01-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-01 2.0
2023-02-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-08 1.15.1
2025-01-12 1.14.1
2024-08-16 1.13.11
2023-12-18 1.13.10
2023-09-22 1.13.8
2023-08-25 1.13.6
2023-06-19 1.13.3
2023-03-23 1.13.1
2022-11-07 1.12.2
2022-08-31 1.12.0
2022-06-16 1.11.1
2022-03-22 1.10.3
2022-02-22 1.10.1
2021-11-21 1.9.2
2021-11-12 1.9.1
2021-08-11 1.8.1
2021-04-26 1.7.2
2021-03-25 1.7.1
2021-01-10 1.6.5
2020-12-17 1.6.2
2020-12-17 1.6.3
2020-08-10 1.5.1
2020-06-11 1.4.1
2020-05-13 1.3.1
2020-01-09 1.2.1
2019-10-29 1.1.1
2019-06-28 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 0.1.9
2020-03-13 0.1.8
2020-02-01 0.1.7
2019-12-16 0.1.6
2019-11-16 0.1.5
2019-08-01 0.1.4
2019-06-24 0.1.3
2019-06-09 0.1.2
2019-04-22 0.1.1
2019-04-07 0.1.0
Title: Robust Regression and Estimation Through Maximum Mean
Discrepancy Minimization
Description: The functions in this package compute robust estimators by minimizing a kernel-based distance known as MMD (Maximum Mean Discrepancy) between the sample and a statistical model. Recent works proved that these estimators enjoy a universal consistency property, and are extremely robust to outliers. Various optimization algorithms are implemented: stochastic gradient is available for most models, but the package also allows gradient descent in a few models for which an exact formula is available for the gradient. In terms of distribution fit, a large number of continuous and discrete distributions are available: Gaussian, exponential, uniform, gamma, Poisson, geometric, etc. In terms of regression, the models available are: linear, logistic, gamma, beta and Poisson.
Alquier, P. and Gerber, M. (2024) <doi:10.1093/biomet/asad031>
Cherief-Abdellatif, B.-E. and Alquier, P. (2022) <doi:10.3150/21-BEJ1338>.
Author: Pierre Alquier [aut, cre] ,
Mathieu Gerber [aut]
Maintainer: Pierre Alquier <pierre.alquier.stat@gmail.com>
Diff between regMMD versions 0.0.1 dated 2024-10-25 and 0.0.2 dated 2025-10-15
DESCRIPTION | 11 ++++---- MD5 | 56 +++++++++++++++++++++--------------------- R/Beta_hat.R | 4 +-- R/Beta_tilde.R | 4 +-- R/Gamma_hat.R | 4 +-- R/Gamma_tilde.R | 4 +-- R/LG_hat.R | 8 +++--- R/LG_tilde.R | 8 +++--- R/Logistic_hat.R | 2 - R/Logistic_tilde.R | 2 - R/Poisson_hat.R | 2 - R/Poisson_tilde.R | 2 - R/estimation_function.R | 3 +- R/models_Cauchy.R | 6 +++- R/models_Dirac.R | 6 +++- R/models_Gaussian.R | 20 ++++++++++++--- R/models_Pareto.R | 6 +++- R/models_Poisson.R | 8 +++++- R/models_beta.R | 6 +++- R/models_binomial.R | 33 +++++++++++++++++++----- R/models_continuous_uniform.R | 24 +++++++++++++++--- R/models_discrete_uniform.R | 4 ++- R/models_gamma.R | 18 +++++++++++-- R/models_geometric.R | 8 +++++- R/models_multidim_Dirac.R | 6 +++- R/models_multidim_Gaussian.R | 26 ++++++++++++++++--- R/reg_function.R | 28 ++++++++++----------- build/partial.rdb |binary man/mmd_est.Rd | 1 29 files changed, 212 insertions(+), 98 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.16.0 dated 2025-09-19 and 0.17.0 dated 2025-10-15
progressr-0.16.0/progressr/tests/debug.R |only progressr-0.16.0/progressr/tests/demo.R |only progressr-0.16.0/progressr/tests/exceptions.R |only progressr-0.16.0/progressr/tests/globals,relay.R |only progressr-0.16.0/progressr/tests/handler_cli.R |only progressr-0.16.0/progressr/tests/handler_filesize.R |only progressr-0.16.0/progressr/tests/handler_make_progression.R |only progressr-0.16.0/progressr/tests/handler_pbmcapply.R |only progressr-0.16.0/progressr/tests/handler_progress.R |only progressr-0.16.0/progressr/tests/handler_rstudio.R |only progressr-0.16.0/progressr/tests/handler_shiny.R |only progressr-0.16.0/progressr/tests/handler_tkprogressbar.R |only progressr-0.16.0/progressr/tests/handler_txtprogressbar.R |only progressr-0.16.0/progressr/tests/handlers.R |only progressr-0.16.0/progressr/tests/incl |only progressr-0.16.0/progressr/tests/progress_aggregator.R |only progressr-0.16.0/progressr/tests/progression.R |only progressr-0.16.0/progressr/tests/progressor.R |only progressr-0.16.0/progressr/tests/utils.R |only progressr-0.16.0/progressr/tests/with_progress,delay.R |only progressr-0.16.0/progressr/tests/with_progress,relay.R |only progressr-0.16.0/progressr/tests/with_progress.R |only progressr-0.16.0/progressr/tests/without_progress.R |only progressr-0.16.0/progressr/tests/zzz,doFuture.R |only progressr-0.16.0/progressr/tests/zzz,foreach_do.R |only progressr-0.16.0/progressr/tests/zzz,furrr.R |only progressr-0.16.0/progressr/tests/zzz,future.apply.R |only progressr-0.16.0/progressr/tests/zzz,plyr.R |only progressr-0.16.0/progressr/tests/zzz,purrr.R |only progressr-0.16.0/progressr/tests/zzz,shiny.R |only progressr-0.17.0/progressr/DESCRIPTION | 6 progressr-0.17.0/progressr/MD5 | 136 ++++++---- progressr-0.17.0/progressr/NEWS.md | 19 + progressr-0.17.0/progressr/R/global_progression_handler.R | 15 - progressr-0.17.0/progressr/R/handler_cli.R | 2 progressr-0.17.0/progressr/R/handler_rpushbullet.R | 4 progressr-0.17.0/progressr/R/make_calling_handler.R | 2 progressr-0.17.0/progressr/R/options.R | 4 progressr-0.17.0/progressr/R/progress_aggregator.R | 7 progressr-0.17.0/progressr/R/rstudio-console.R | 15 - progressr-0.17.0/progressr/R/testme.R |only progressr-0.17.0/progressr/R/warn_about_too_many_progressions.R |only progressr-0.17.0/progressr/R/with_progress.R | 29 +- progressr-0.17.0/progressr/R/without_progress.R | 5 progressr-0.17.0/progressr/inst/doc/progressr-91-appendix.html | 12 progressr-0.17.0/progressr/inst/doc/progressr-91-appendix.md | 10 progressr-0.17.0/progressr/inst/testme |only progressr-0.17.0/progressr/man/with_progress.Rd | 5 progressr-0.17.0/progressr/tests/test-debug.R |only progressr-0.17.0/progressr/tests/test-demo.R |only progressr-0.17.0/progressr/tests/test-exceptions.R |only progressr-0.17.0/progressr/tests/test-globals,relay.R |only progressr-0.17.0/progressr/tests/test-handler_cli.R |only progressr-0.17.0/progressr/tests/test-handler_filesize.R |only progressr-0.17.0/progressr/tests/test-handler_make_progression.R |only progressr-0.17.0/progressr/tests/test-handler_pbmcapply.R |only progressr-0.17.0/progressr/tests/test-handler_progress.R |only progressr-0.17.0/progressr/tests/test-handler_rstudio.R |only progressr-0.17.0/progressr/tests/test-handler_shiny.R |only progressr-0.17.0/progressr/tests/test-handler_tkprogressbar.R |only progressr-0.17.0/progressr/tests/test-handler_txtprogressbar.R |only progressr-0.17.0/progressr/tests/test-handlers.R |only progressr-0.17.0/progressr/tests/test-progress_aggregator.R |only progressr-0.17.0/progressr/tests/test-progression.R |only progressr-0.17.0/progressr/tests/test-progressor.R |only progressr-0.17.0/progressr/tests/test-utils.R |only progressr-0.17.0/progressr/tests/test-with_progress,delay.R |only progressr-0.17.0/progressr/tests/test-with_progress,relay.R |only progressr-0.17.0/progressr/tests/test-with_progress.R |only progressr-0.17.0/progressr/tests/test-without_progress.R |only progressr-0.17.0/progressr/tests/test-zzz,doFuture.R |only progressr-0.17.0/progressr/tests/test-zzz,foreach_do.R |only progressr-0.17.0/progressr/tests/test-zzz,furrr.R |only progressr-0.17.0/progressr/tests/test-zzz,future.apply.R |only progressr-0.17.0/progressr/tests/test-zzz,plyr.R |only progressr-0.17.0/progressr/tests/test-zzz,purrr.R |only progressr-0.17.0/progressr/tests/test-zzz,shiny.R |only progressr-0.17.0/progressr/vignettes/progressr-91-appendix.md | 10 78 files changed, 188 insertions(+), 93 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering several procedures), omnibus tests for
univariate normality, functions to compute the multivariate skewness, kurtosis, the
Mahalanobis distance (checking the positive defineteness), and t [...truncated...]
Author: Felipe Osorio [aut, cre] ,
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <faosorios.stat@gmail.com>
Diff between fastmatrix versions 0.6 dated 2025-07-07 and 0.6-2 dated 2025-10-15
ChangeLog | 8 +++++ DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++++++----------------- NAMESPACE | 6 ++-- R/RNG.R | 6 ++-- R/bezier.R | 4 +- R/ccc.R | 20 +++++++------- R/condition.R | 2 - R/floyd.R |only R/fnc_matrix.R |only R/harris.R | 12 +++++--- R/jarque.bera.R | 4 ++ R/krylov.R | 2 - R/polymat.R | 2 - R/root_matrix.R | 38 +++++++++++++++++----------- R/schur.R |only R/symmetrizer.R | 2 - R/whitening.R | 2 - R/wilson_hilferty.R | 4 +- inst/CITATION | 4 +- inst/include/fastmatrix.h | 3 +- inst/include/fastmatrix_API.h | 11 +++++++- man/floyd.Rd |only man/matrix.fun.Rd |only man/matrix.sqrt.Rd | 18 +++++++++---- man/schur.Rd |only src/R_init_fastmatrix.c | 12 +++++++- src/fastmatrix.h | 16 ++++++++++- src/floyd_warshall.f |only src/fnc_matrix.f |only src/matrix_API.c | 21 ++++++++++++++- src/schur.c |only src/schur_decomp.f |only src/sqrt_matrix.c | 57 +++++++++++++++++++++++++++++++++++++----- 34 files changed, 226 insertions(+), 92 deletions(-)
Title: Finding Recurrent DNA Copy Number Alterations and Differences
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
can be found at <doi: 10.1093/bioinformatics/ [...truncated...]
Author: Vonn Walter [aut, cre] ,
Hyo Young Choi [aut] ,
Xiaobei Zhao [aut] ,
Yan Gao [aut] ,
David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between DiNAMIC.Duo versions 1.0.3 dated 2025-04-03 and 1.0.4 dated 2025-10-15
DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS.md | 9 +++++++++ R/dataPrep.R | 19 ++++++++++++------- R/findNull.R | 2 +- man/dataPrep.Rd | 8 ++++---- man/findNull.Rd | 2 +- 8 files changed, 45 insertions(+), 31 deletions(-)
Title: Crop Growing Degree Days and Agrometeorological Calculations
Description: Calculate agrometeorological variables for crops
including growing degree days (McMaster, GS & Wilhelm, WW
(1997) <doi:10.1016/S0168-1923(97)00027-0>), cumulative
rainfall, number of stress days and cumulative or mean
radiation and evaporation. Convert dates to day of year
and vice versa. Also, download curated and interpolated
Australian weather data from the Queensland Government
DES longpaddock website
<https://www.longpaddock.qld.gov.au/>. This data is
freely available under the Creative Commons 4.0 licence.
Author: Peter Baker [aut, cre] ,
Miranda Mortlock [aut]
Maintainer: Peter Baker <drpetebaker@gmail.com>
Diff between cropgrowdays versions 0.2.1 dated 2024-03-12 and 0.2.2 dated 2025-10-15
DESCRIPTION | 12 +++++----- MD5 | 34 ++++++++++++++--------------- NEWS.md | 9 +++++++ R/cumulative.R | 2 - R/get_multi_silodata.R | 2 - R/growing_degree_days.R | 4 +-- README.md | 8 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/crop-grow-days.R | 42 ++++++++++++++++++------------------- inst/doc/crop-grow-days.html | 7 ++---- inst/doc/getting-weather-data.R | 30 +++++++++++++------------- man/cumulative.Rd | 2 - man/fragments/agro_met_calcs.Rmd | 2 - man/fragments/auto/cropgrowdays.el | 6 ++++- man/fragments/cropgrowdays.bib | 17 +++++++------- man/get_multi_silodata.Rd | 2 - man/growing_degree_days.Rd | 4 +-- 18 files changed, 97 insertions(+), 86 deletions(-)
Title: Computation and Visualization of Package Download Counts and
Percentile Ranks
Description: Compute and visualize package download counts and percentile ranks
from Posit/RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.9.6 dated 2025-05-01 and 0.9.7 dated 2025-10-14
packageRank-0.9.6/packageRank/R/annualDownloads.R |only packageRank-0.9.7/packageRank/DESCRIPTION | 16 packageRank-0.9.7/packageRank/MD5 | 85 - packageRank-0.9.7/packageRank/NAMESPACE | 16 packageRank-0.9.7/packageRank/NEWS.md | 42 packageRank-0.9.7/packageRank/R/annualPlot.R |only packageRank-0.9.7/packageRank/R/bioconductorDownloads.R | 12 packageRank-0.9.7/packageRank/R/countryDistribution.R | 25 packageRank-0.9.7/packageRank/R/countryPackage.R | 42 packageRank-0.9.7/packageRank/R/cranDownloads.R | 40 packageRank-0.9.7/packageRank/R/cranDownloadsA.R | 16 packageRank-0.9.7/packageRank/R/cranDownloadsB.R | 16 packageRank-0.9.7/packageRank/R/cranDownloadsPlotFunctions.R | 774 ++++++---- packageRank-0.9.7/packageRank/R/cranDownloadsPlotSmoother.R | 146 - packageRank-0.9.7/packageRank/R/data.R | 7 packageRank-0.9.7/packageRank/R/fetchLog.R | 10 packageRank-0.9.7/packageRank/R/filteredDownloads.R | 24 packageRank-0.9.7/packageRank/R/gg_axis.annotation_polygon.R |only packageRank-0.9.7/packageRank/R/importFrom.R | 7 packageRank-0.9.7/packageRank/R/ipPackage.R | 42 packageRank-0.9.7/packageRank/R/logInfo.R | 33 packageRank-0.9.7/packageRank/R/missingDatesPolygons.R |only packageRank-0.9.7/packageRank/R/packageCountry.R | 15 packageRank-0.9.7/packageRank/R/packageDistribution.R | 4 packageRank-0.9.7/packageRank/R/packageHistory.R | 8 packageRank-0.9.7/packageRank/R/packageLog.R | 42 packageRank-0.9.7/packageRank/R/packageRank-package.R | 1 packageRank-0.9.7/packageRank/R/packageRank.R | 4 packageRank-0.9.7/packageRank/R/packageVersionPercent.R | 8 packageRank-0.9.7/packageRank/R/populationPlot.R | 2 packageRank-0.9.7/packageRank/R/topCountry.R | 11 packageRank-0.9.7/packageRank/R/versionFilter.R |only packageRank-0.9.7/packageRank/R/versionPlot.R | 12 packageRank-0.9.7/packageRank/R/weeklyDownloads.R | 18 packageRank-0.9.7/packageRank/README.md | 57 packageRank-0.9.7/packageRank/data/missing.dates.rda |only packageRank-0.9.7/packageRank/man/annualPlot.Rd |only packageRank-0.9.7/packageRank/man/countryDistribution.Rd | 13 packageRank-0.9.7/packageRank/man/countryPackage.Rd | 17 packageRank-0.9.7/packageRank/man/figures/README-missing-1.png |only packageRank-0.9.7/packageRank/man/filteredDownloads.Rd | 14 packageRank-0.9.7/packageRank/man/ipPackage.Rd | 13 packageRank-0.9.7/packageRank/man/logInfo.Rd | 5 packageRank-0.9.7/packageRank/man/missing.dates.Rd |only packageRank-0.9.7/packageRank/man/packageCountry.Rd | 13 packageRank-0.9.7/packageRank/man/packageLog.Rd | 6 packageRank-0.9.7/packageRank/man/packageRank-package.Rd | 1 packageRank-0.9.7/packageRank/man/plot.cranDownloads.Rd | 2 48 files changed, 922 insertions(+), 697 deletions(-)
Title: Exponential-Family Random Network Models
Description: Estimation of fully and partially observed Exponential-Family Random Network Models (ERNM). Exponential-family Random Graph Models (ERGM) and Gibbs Fields are special cases of ERNMs and can also be estimated with the package. Please cite Fellows and Handcock (2012), "Exponential-family Random Network Models" available at <doi:10.48550/arXiv.1208.0121>.
Author: Ian Fellows [aut],
Duncan Clark [aut, cre]
Maintainer: Duncan Clark <dac6@williams.edu>
Diff between ernm versions 1.0.3 dated 2025-10-06 and 1.0.4 dated 2025-10-14
ernm-1.0.3/ernm/R/00-classes.R |only ernm-1.0.4/ernm/DESCRIPTION | 8 +-- ernm-1.0.4/ernm/MD5 | 23 ++++---- ernm-1.0.4/ernm/R/ernm-gof.R | 9 ++- ernm-1.0.4/ernm/R/ernm.R | 2 ernm-1.0.4/ernm/R/zzz.R | 2 ernm-1.0.4/ernm/inst/include/Model.h | 60 ++++++++++++++++++++--- ernm-1.0.4/ernm/man/createCppSampler.Rd | 1 ernm-1.0.4/ernm/man/ernm.Rd | 3 - ernm-1.0.4/ernm/man/ernm_gof.Rd | 5 + ernm-1.0.4/ernm/src/RcppModule.cpp | 2 ernm-1.0.4/ernm/tests/testthat/test-model.R | 69 ++++++++++++++++++++++++++ ernm-1.0.4/ernm/tests/testthat/test-stats.R | 73 ++++++++++++++++++++++++++-- 13 files changed, 221 insertions(+), 36 deletions(-)
Title: Multi-Modal Immune Repertoire Analytics for Immunotherapy and
Vaccine Design in R
Description: A comprehensive analytics framework for building reproducible pipelines on T-cell and B-cell immune receptor repertoire data.
Delivers multi-modal immune profiling (bulk, single-cell, CITE-seq/AbSeq, spatial, immunogenicity data),
feature engineering (ML-ready feature tables and matrices), and biomarker discovery workflows
(cohort comparisons, longitudinal tracking, repertoire similarity, enrichment).
Provides a user-friendly interface to widely used AIRR methods —
clonality/diversity, V(D)J usage, similarity, annotation, tracking, and many more.
Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or
VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).
Author: Vadim I. Nazarov [aut, cre] ,
Vasily O. Tsvetkov [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Diff between immunarch versions 0.9.1 dated 2024-03-18 and 0.10.3 dated 2025-10-14
immunarch-0.10.3/immunarch/DESCRIPTION | 91 +- immunarch-0.10.3/immunarch/MD5 | 323 +++++----- immunarch-0.10.3/immunarch/NAMESPACE | 132 ++-- immunarch-0.10.3/immunarch/R/aaa-registry.R |only immunarch-0.10.3/immunarch/R/globals.R |only immunarch-0.10.3/immunarch/R/immunarch-package.R | 64 + immunarch-0.10.3/immunarch/R/import-standalone-purrr.R |only immunarch-0.10.3/immunarch/R/v0_align_lineage.R |only immunarch-0.10.3/immunarch/R/v0_annotation.R |only immunarch-0.10.3/immunarch/R/v0_clonality.R |only immunarch-0.10.3/immunarch/R/v0_clustering.R |only immunarch-0.10.3/immunarch/R/v0_data_docs.R |only immunarch-0.10.3/immunarch/R/v0_dimensions.R |only immunarch-0.10.3/immunarch/R/v0_distance.R |only immunarch-0.10.3/immunarch/R/v0_diversity.R |only immunarch-0.10.3/immunarch/R/v0_dynamics.R |only immunarch-0.10.3/immunarch/R/v0_explore.R |only immunarch-0.10.3/immunarch/R/v0_filters.R |only immunarch-0.10.3/immunarch/R/v0_gene_usage.R |only immunarch-0.10.3/immunarch/R/v0_gene_usage_analysis.R |only immunarch-0.10.3/immunarch/R/v0_germline.R |only immunarch-0.10.3/immunarch/R/v0_immunr_data_format.R |only immunarch-0.10.3/immunarch/R/v0_info_theory.R |only immunarch-0.10.3/immunarch/R/v0_io.R |only immunarch-0.10.3/immunarch/R/v0_io_parsers.R |only immunarch-0.10.3/immunarch/R/v0_io_savers.R |only immunarch-0.10.3/immunarch/R/v0_io_utility.R |only immunarch-0.10.3/immunarch/R/v0_kmers.R |only immunarch-0.10.3/immunarch/R/v0_overlap.R |only immunarch-0.10.3/immunarch/R/v0_overlap_analysis.R |only immunarch-0.10.3/immunarch/R/v0_phylip.R |only immunarch-0.10.3/immunarch/R/v0_preprocessing.R |only immunarch-0.10.3/immunarch/R/v0_public.R |only immunarch-0.10.3/immunarch/R/v0_sampling.R |only immunarch-0.10.3/immunarch/R/v0_seqCluster.R |only immunarch-0.10.3/immunarch/R/v0_shiny.R |only immunarch-0.10.3/immunarch/R/v0_singlecell.R |only immunarch-0.10.3/immunarch/R/v0_somatic_hypermutation.R |only immunarch-0.10.3/immunarch/R/v0_spectratyping.R |only immunarch-0.10.3/immunarch/R/v0_tools.R |only immunarch-0.10.3/immunarch/R/v0_vis.R |only immunarch-0.10.3/immunarch/R/v1_aaa_commons_vis.R |only immunarch-0.10.3/immunarch/R/v1_aaa_registry_utils.R |only immunarch-0.10.3/immunarch/R/v1_clonality_airr.R |only immunarch-0.10.3/immunarch/R/v1_clonality_annotate.R |only immunarch-0.10.3/immunarch/R/v1_clonality_base.R |only immunarch-0.10.3/immunarch/R/v1_diversity_airr.R |only immunarch-0.10.3/immunarch/R/v1_diversity_vis.R |only immunarch-0.10.3/immunarch/R/v1_migration_updates.R |only immunarch-0.10.3/immunarch/R/v1_migration_utils.R |only immunarch-0.10.3/immunarch/R/v1_package.R |only immunarch-0.10.3/immunarch/R/v1_public_airr.R |only immunarch-0.10.3/immunarch/R/v1_public_vis.R |only immunarch-0.10.3/immunarch/R/v1_stats_airr.R |only immunarch-0.10.3/immunarch/R/v1_stats_vis.R |only immunarch-0.10.3/immunarch/R/wip-v1-planning.R |only immunarch-0.10.3/immunarch/R/zzz.R |only immunarch-0.10.3/immunarch/README.md | 307 +++++---- immunarch-0.10.3/immunarch/build/vignette.rds |binary immunarch-0.10.3/immunarch/inst/doc/immunarch.Rmd |only immunarch-0.10.3/immunarch/inst/doc/immunarch.html |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.R |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.Rmd |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.html |only immunarch-0.10.3/immunarch/man/aa_properties.Rd | 2 immunarch-0.10.3/immunarch/man/aa_table.Rd | 2 immunarch-0.10.3/immunarch/man/add_class.Rd | 2 immunarch-0.10.3/immunarch/man/airr_clonality.Rd |only immunarch-0.10.3/immunarch/man/airr_diversity.Rd |only immunarch-0.10.3/immunarch/man/airr_public.Rd |only immunarch-0.10.3/immunarch/man/airr_stats.Rd |only immunarch-0.10.3/immunarch/man/annotate_clonality.Rd |only immunarch-0.10.3/immunarch/man/apply_symm.Rd | 4 immunarch-0.10.3/immunarch/man/bcrdata.Rd | 8 immunarch-0.10.3/immunarch/man/bunch_translate.Rd | 2 immunarch-0.10.3/immunarch/man/check_distribution.Rd | 2 immunarch-0.10.3/immunarch/man/coding.Rd | 14 immunarch-0.10.3/immunarch/man/dbAnnotate.Rd | 20 immunarch-0.10.3/immunarch/man/dbLoad.Rd | 6 immunarch-0.10.3/immunarch/man/dot-quant_column_choice.Rd | 2 immunarch-0.10.3/immunarch/man/entropy.Rd | 4 immunarch-0.10.3/immunarch/man/figures |only immunarch-0.10.3/immunarch/man/fixVis.Rd | 4 immunarch-0.10.3/immunarch/man/geneUsage.Rd | 18 immunarch-0.10.3/immunarch/man/geneUsageAnalysis.Rd | 18 immunarch-0.10.3/immunarch/man/gene_segments.Rd | 2 immunarch-0.10.3/immunarch/man/gene_stats.Rd | 4 immunarch-0.10.3/immunarch/man/getKmers.Rd | 8 immunarch-0.10.3/immunarch/man/get_immunarch_news.Rd |only immunarch-0.10.3/immunarch/man/group_from_metadata.Rd | 2 immunarch-0.10.3/immunarch/man/has_class.Rd | 2 immunarch-0.10.3/immunarch/man/im_common_args.Rd |only immunarch-0.10.3/immunarch/man/immdata.Rd | 8 immunarch-0.10.3/immunarch/man/immunarch_v1_updates.Rd |only immunarch-0.10.3/immunarch/man/immunr_data_format.Rd | 48 - 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Title: Information Analysis for Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.3.5 dated 2024-09-18 and 3.3.6 dated 2025-10-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 - R/Ffuns_plot.R | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Execute R in a 'Docker' Context
Description: The goal of 'jetty' is to execute R functions and code
snippets in an isolated R subprocess within a 'Docker' container
and return the evaluated results to the local R session. 'jetty'
can install necessary packages at runtime and seamlessly propagates
errors and outputs from the 'Docker' subprocess back to the main
session. 'jetty' is primarily designed for sandboxed testing and
quick execution of example code.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between jetty versions 0.2.1 dated 2025-04-14 and 0.2.2 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/run.R | 13 ++++++++++--- R/script.R | 4 ++-- README.md | 12 ++++++------ man/run.Rd | 4 ++-- man/run_script.Rd | 4 ++-- tests/testthat/test-docker.R | 28 ++++++++++++---------------- 9 files changed, 51 insertions(+), 43 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Cole Jensen [aut],
Jessie Fielding [aut],
Hunter Melton [aut],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>
Diff between dowser versions 2.3 dated 2024-10-22 and 2.4.0 dated 2025-10-14
DESCRIPTION | 42 +- MD5 | 154 +++++--- NAMESPACE | 10 NEWS.md | 10 R/Classes.R | 2 R/Clones.R | 376 ++++++++++++++++----- R/Data.R | 28 + R/Dowser.R | 1 R/Germlines.R | 15 R/Plotting.R | 122 +++++-- R/Statistics.R | 13 R/TimeTreesFunctions.R |only R/TreeFunctions.R | 394 +++++++++++++++++++--- README.md | 25 + build/partial.rdb |binary build/vignette.rds |binary data/ExampleAirrTyCHE.rda |only inst/doc/Building-Time-Trees-Vignette.R |only inst/doc/Building-Time-Trees-Vignette.Rmd |only inst/doc/Building-Time-Trees-Vignette.pdf |only inst/doc/Building-Trees-Vignette.R | 172 +++++----- inst/doc/Building-Trees-Vignette.Rmd | 2 inst/doc/Building-Trees-Vignette.pdf |binary inst/doc/Discrete-Trait-Vignette.R | 446 +++++++++++++------------- inst/doc/Discrete-Trait-Vignette.Rmd | 6 inst/doc/Discrete-Trait-Vignette.pdf |binary inst/doc/Germlines-Vignette.R | 38 +- inst/doc/Germlines-Vignette.Rmd | 2 inst/doc/Germlines-Vignette.pdf |binary inst/doc/Measurable-Evolution.R | 126 +++---- inst/doc/Measurable-Evolution.pdf |binary inst/doc/NonB-Cell-Data.R |only inst/doc/NonB-Cell-Data.Rmd |only inst/doc/NonB-Cell-Data.html |only inst/doc/Plotting-Trees-Vignette.R | 10 inst/doc/Plotting-Trees-Vignette.pdf |binary inst/doc/Quickstart-Vignette.pdf |binary inst/doc/Resolve-Light-Chains-Vignette.R | 52 +-- inst/doc/Resolve-Light-Chains-Vignette.Rmd | 6 inst/doc/Resolve-Light-Chains-Vignette.pdf |binary inst/doc/Sequences-Vignette.R | 8 inst/doc/Sequences-Vignette.pdf |binary man/ExampleAirrTyCHE.Rd |only man/airrClone-class.Rd | 2 man/bootstrapTrees.Rd | 8 man/buildBeast.Rd |only man/buildIgphyml.Rd | 6 man/buildPML.Rd | 16 man/buildPhylo.Rd | 2 man/buildPratchet.Rd | 2 man/buildRAxML.Rd | 10 man/checkDivergence.Rd |only man/createGermlines.Rd | 2 man/create_MRCA_prior_germline.Rd |only man/create_MRCA_prior_observed.Rd |only man/create_alignment.Rd |only man/create_height_prior.Rd |only man/create_max_height_prior.Rd |only man/create_root_freqs.Rd |only man/create_starting_tree.Rd |only man/create_traitset.Rd |only man/dowser-package.Rd | 6 man/exportTrees.Rd | 2 man/findSwitches.Rd | 8 man/formatClones.Rd | 6 man/getBootstraps.Rd | 2 man/getSkylines.Rd |only man/getTimeTrees.Rd |only man/getTimeTreesIterate.Rd |only man/getTrees.Rd | 9 man/makeAirrClone.Rd | 2 man/makeSkyline.Rd |only man/plotSkylines.Rd |only man/plotTrees.Rd | 11 man/readBEAST.Rd |only man/readIMGT.Rd | 4 man/readModelFile.Rd | 2 man/sampleCloneMultiGroup.Rd |only man/sampleClones.Rd |only man/stitchRegions.Rd | 4 man/stopCodonCheck.Rd |only man/testPS.Rd | 2 man/testSC.Rd | 2 man/testSP.Rd | 2 man/writeLineageFile.Rd | 5 man/write_clone_to_xml.Rd |only man/write_clones_to_xmls.Rd |only vignettes/Building-Time-Trees-Vignette.Rmd |only vignettes/Building-Time-Trees-gc-trees.png |only vignettes/Building-Time-Trees-mixed-trees.png |only vignettes/Building-Trees-Vignette.Rmd | 2 vignettes/Discrete-Trait-Vignette.Rmd | 6 vignettes/Germlines-Vignette.Rmd | 2 vignettes/NonB-Cell-Data.Rmd |only vignettes/Resolve-Light-Chains-Vignette.Rmd | 6 95 files changed, 1429 insertions(+), 762 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre] ,
Nicolas Campos [ctb] ,
Joaquin Riquelme [ctb] ,
Nicolas Pino [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.1.4 dated 2025-09-23 and 1.1.5 dated 2025-10-14
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- R/descstat.r | 36 ++++++++++++++++++++++++------- R/valesta.r | 65 +++++++++++++++++++++++++++++++++++++------------------- inst/CITATION | 4 +-- man/descstat.Rd | 12 +++++++++- man/valesta.Rd | 15 ++++++++++++ 7 files changed, 108 insertions(+), 42 deletions(-)
Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
Diff between biodosetools versions 3.6.2 dated 2025-10-10 and 3.7 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/app_ui.R | 9 ++++++--- inst/doc/interlab.html | 12 ++++++------ 4 files changed, 18 insertions(+), 15 deletions(-)
Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description: Fast functions implemented in C++ via 'Rcpp' to support the
'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large
speed-ups for basic manipulation of neuronal skeletons over pure R
functions found in the 'nat' package. The expectation is that end
users will not use this package directly, but instead the 'nat'
package will automatically use routines from this package when it is
available to enable large performance gains.
Author: Gregory Jefferis [aut, cre]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natcpp versions 0.1.0 dated 2021-07-13 and 0.2 dated 2025-10-14
DESCRIPTION | 13 ++++---- MD5 | 24 +++++++++----- NAMESPACE | 4 ++ NEWS.md | 14 ++++++++ R/RcppExports.R | 61 ++++++++++++++++++++++++++++++++++++++ README.md | 20 +++++++----- inst/WORDLIST | 1 man/c_ListofMatrixRows.Rd |only man/c_coords21dindex.Rd |only man/c_ijkpos.Rd |only man/c_sub2ind.Rd |only man/natcpp-package.Rd | 9 +---- src/RcppExports.cpp | 57 +++++++++++++++++++++++++++++++++++ src/coordinates.cpp |only src/matrix.cpp |only tests/testthat/test-coordinates.R |only tests/testthat/test-matrix.R |only 17 files changed, 174 insertions(+), 29 deletions(-)
Title: Simulation Tools for Small Area Estimation
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between saeSim versions 0.11.0 dated 2022-02-07 and 0.12.0 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 30 +++---- NEWS | 163 +++++++++++++++++++++++----------------- R/01-sim.R | 56 +++++++------ R/01-sim_setup.R | 9 -- R/03-sim_base.R | 45 ++++++----- build/vignette.rds |binary inst/doc/Introduction.R | 42 +++++----- inst/doc/Introduction.html | 117 +++++++++++++++++----------- man/sim.Rd | 22 ++--- man/sim_base.Rd | 4 man/sim_resp.Rd | 2 man/sim_setup_preconfigured.Rd | 18 +++- tests/testthat/test-sim.R | 2 tests/testthat/test-sim_comp.R | 2 tests/testthat/test-sim_setup.R | 4 16 files changed, 299 insertions(+), 225 deletions(-)
Title: Randomization Inference for Randomized Experiments
Description: Randomization inference procedures for simple and complex randomized designs, including multi-armed trials, as described in Gerber and Green (2012, ISBN: 978-0393979954). Users formally describe their randomization procedure and test statistic. The randomization distribution of the test statistic under some null hypothesis is efficiently simulated.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between ri2 versions 0.4.0 dated 2022-05-26 and 0.4.1 dated 2025-10-14
ri2-0.4.0/ri2/man/ri2.Rd |only ri2-0.4.1/ri2/DESCRIPTION | 8 ri2-0.4.1/ri2/MD5 | 16 ri2-0.4.1/ri2/NEWS.md | 5 ri2-0.4.1/ri2/R/conduct_ri.R | 4 ri2-0.4.1/ri2/R/ri2.R | 10 ri2-0.4.1/ri2/build/vignette.rds |binary ri2-0.4.1/ri2/inst/doc/ri2_vignette.html | 834 ++++++++++++++++++++----------- ri2-0.4.1/ri2/man/conduct_ri.Rd | 4 ri2-0.4.1/ri2/man/ri2-package.Rd |only 10 files changed, 589 insertions(+), 292 deletions(-)