Title: Standardized Economic Reporting and Automated Dynamic Writing /
Synthèse d'Écrits Avec des Règles Automatisées et Dynamiques
Description: Provides tools for generating dynamic and standardized
economic narratives in R Markdown documents. The package is primarily
designed for French-language statistical and economic publications.
It includes functions to describe changes in levels, percentages,
trends, accelerations and short-term economic developments using
consistent linguistic rules. The package supports automated reporting
workflows and reproducible economic writing.
Fournit des outils permettant de générer des textes économiques
dynamiques et standardisés dans des documents R Markdown. Le package
est principalement conçu pour les publications statistiques et
économiques en français. Il propose des fonctions permettant de
décrire les évolutions de niveaux, de pourcentages, de tendances,
d'accélérations et les évolutions conjoncturelles à l'aide de règles
linguistiques homogènes. Le package facilite l'automatisation de la
rédaction et la reproductibilité des publications économiques.
Author: Alexandre Cazenave-Lacroutz [aut] ,
Jules Lejas [cre],
Direction de l'animation de la recherche, des etudes et des
statistiques [cph]
Maintainer: Jules Lejas <jules.lejas@gmail.com>
Diff between serad versions 0.2.1 dated 2026-06-17 and 0.2.2 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/init_serad_en.R | 18 +++++++++--------- R/init_serad_fr.R | 18 +++++++++--------- 4 files changed, 24 insertions(+), 24 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on
metabolite quantifications and information on pathway metabolite
composition. The method, described in Guilmineau et al (2025)
<doi:10.1186/s12859-025-06118-z> is based on a Principal Component
Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut],
Remi Servien [aut, cre] ,
Nathalie Vialaneix [aut]
Maintainer: Remi Servien <remi.servien@inrae.fr>
Diff between phoenics versions 0.6 dated 2025-08-19 and 0.6.1 dated 2026-07-01
DESCRIPTION | 10 ++-- MD5 | 16 +++---- R/pathway_search.R | 2 R/test_pathway.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.html | 100 ++++++++++++++++++++++----------------------- man/pathway_search.Rd | 2 man/test_pathway.Rd | 2 9 files changed, 68 insertions(+), 66 deletions(-)
Title: Centering and Scaling of Numeric Data
Description: Provides simple methods for centering and scaling of numeric data.
Columns or rows can be ignored when normalizing or be normalized jointly.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between normalize versions 0.1.2 dated 2025-06-10 and 0.1.3 dated 2026-07-01
DESCRIPTION | 8 MD5 | 20 NAMESPACE | 18 NEWS.md | 34 - R/normalize-package.R | 16 R/normalize.R | 821 +++++++++++++++++++++++++++------------- README.md | 242 +++++------ man/normalize-package.Rd | 53 +- man/normalize.Rd | 191 ++++----- tests/testthat.R | 24 - tests/testthat/test-normalize.R | 780 +++++++++++++++++++++++--------------- 11 files changed, 1347 insertions(+), 860 deletions(-)
Title: Visualizing and Quantifying Space Use Data for Groups of Animals
Description: Offers an easy and automated way to scale up individual-level space use analysis to
that of groups. Contains functions from the 'move' package to calculate either a dynamic Brownian
bridge movement model or dynamic Bivariate Gaussian bridges from movement data for individual animals, as well as functions to
visualize and quantify space use for individuals aggregated in groups. Originally written with
passive acoustic telemetry in mind, this package also provides functionality to account for
unbalanced acoustic receiver array designs, and satellite tag data.
Author: Simon Dedman [aut, cre] ,
Maurits van Zinnicq Bergmann [aut] ,
Vital Heim [aut]
Maintainer: Simon Dedman <simondedman@gmail.com>
Diff between movegroup versions 2024.03.05 dated 2024-03-07 and 2026.07.01 dated 2026-07-01
DESCRIPTION | 23 LICENSE | 4 MD5 | 78 - NAMESPACE | 163 +-- NEWS.md | 32 R/alignraster.R | 288 ++--- R/data.R | 102 - R/globals.R |only R/moveLocErrorCalc.R | 204 +-- R/movegroup-package.R | 14 R/movegroup.R | 1571 ++++++++++++++++++------------ R/plotraster.R | 1491 +++++++++++++++------------- R/scaleraster.R | 693 ++++++------- R/stitchraster.R |only R/utils.R | 8 R/zzz.R |only README.md | 960 +++++++++--------- build/vignette.rds |binary inst/CITATION | 24 inst/Misc/RunScriptExample.R | 274 ++--- inst/doc/Using-the-movegroup-package.R | 18 inst/doc/Using-the-movegroup-package.Rmd | 4 inst/doc/Using-the-movegroup-package.html | 1456 +++++++++++++-------------- man/TracksCleaned.Rd | 64 - man/alignraster.Rd | 184 +-- man/argosFiltered.Rd | 76 - man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/moveLocErrorCalc.Rd | 124 +- man/movegroup-package.Rd | 43 man/movegroup.Rd | 522 +++++---- man/plotraster.Rd | 608 ++++++----- man/scaleraster.Rd | 272 ++--- man/stitchraster.Rd |only vignettes/Using-the-movegroup-package.Rmd | 4 42 files changed, 5160 insertions(+), 4538 deletions(-)
Title: Access Mexican Data via APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'World Bank API', and 'Nager.Date API', covering Mexico's economic
indicators, population statistics, literacy rates, and official public
holidays. The package also includes curated datasets related to Mexico
such as air quality monitoring stations, pollution zones, income surveys,
postal abbreviations, election studies, forest productivity and
demographic data by state. It supports research and analysis focused on
Mexico by integrating reliable global APIs with structured national
datasets drawn from open and academic sources.
For more information on the APIs, see:
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
and 'Nager.Date API' <https://date.nager.at/Api>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between MexicoDataAPI versions 0.2.0 dated 2025-09-13 and 0.3.0 dated 2026-07-01
MexicoDataAPI-0.2.0/MexicoDataAPI/R/get_country_info_mx.R |only MexicoDataAPI-0.2.0/MexicoDataAPI/man/get_country_info_mx.Rd |only MexicoDataAPI-0.2.0/MexicoDataAPI/tests/testthat/test-get_country_info_mx.R |only MexicoDataAPI-0.3.0/MexicoDataAPI/DESCRIPTION | 23 +- MexicoDataAPI-0.3.0/MexicoDataAPI/MD5 | 83 ++++------ MexicoDataAPI-0.3.0/MexicoDataAPI/NAMESPACE | 2 MexicoDataAPI-0.3.0/MexicoDataAPI/NEWS.md | 12 + MexicoDataAPI-0.3.0/MexicoDataAPI/R/data-documentation.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_cpi.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_gdp.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_holidays.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_life_expectancy.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_literacy_rate.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_population.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_unemployment.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/mexicodataapi-package.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/utils.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/view_datasets_MexicoDataAPI.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/README.md | 8 MexicoDataAPI-0.3.0/MexicoDataAPI/build/vignette.rds |binary MexicoDataAPI-0.3.0/MexicoDataAPI/inst/CITATION | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/inst/doc/MexicoDataAPI_vignette.Rmd | 10 - MexicoDataAPI-0.3.0/MexicoDataAPI/inst/doc/MexicoDataAPI_vignette.html | 54 +++--- MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSE | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSE.md | 14 - MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSES_DETAILS.md | 2 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-chiapas_dry_forests_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_cpi.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_gdp.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_holidays.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_life_expectancy.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_literacy_rate.R | 21 +- MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_population.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_unemployment.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mex_income_2008_tbl_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mex_income_2016_tbl_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_abb_chr.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_elections_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_states_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-pollution_stations_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-pollution_zones_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-stations_sinaica_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-view_datasets_MexicoDataAPI.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/vignettes/MexicoDataAPI_vignette.Rmd | 10 - 44 files changed, 171 insertions(+), 184 deletions(-)
Title: Diagnostic Tools for Asymptotic Theory
Description: Leveraging Monte Carlo simulations, this package provides
tools for diagnosing regression models. It implements a parametric
bootstrap framework to compute statistics, generates diagnostic
envelopes to assess goodness-of-fit, and evaluates type I error
control for Wald tests. By simulating data under the assumption that
the model is true, it helps to identify model mis-specifications and
enhances the reliability of the model inferences.
Author: Alvaro Kothe [aut, cre, cph] ,
Alexandre Patriota [aut]
Maintainer: Alvaro Kothe <kothe65@gmail.com>
Diff between asympDiag versions 0.3.2 dated 2026-02-15 and 0.3.3 dated 2026-07-01
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test-concat.R | 7 ++++-- tests/testthat/test-envelope.R | 14 +++++++++++-- tests/testthat/test-get_refit.R | 2 + tests/testthat/test-simulate_wald_pvalues.R | 29 +++++++++++++++++++--------- 7 files changed, 48 insertions(+), 22 deletions(-)
Title: Lossless CDISC-Native Input and Output for Clinical Datasets
Description: Reads and writes clinical-trial datasets losslessly across
'SAS' XPORT (XPT), Clinical Data Interchange Standards Consortium
(CDISC) Dataset-JSON, and 'Apache Parquet', applying a specification to
produce submission-ready Study Data Tabulation Model (SDTM) and
Analysis Data Model (ADaM) datasets. A single canonical metadata model
carries labels, CDISC data types, lengths, 'SAS' display formats,
controlled-terminology references, and sort keys identically across
every format, so conversion between any two formats is lossless by
construction. Pure 'R' and lightweight, with no external 'SAS' or
'Java' runtime. Implements the published format specifications for
CDISC Dataset-JSON
(<https://cdisc-org.github.io/DataExchange-DatasetJson/doc/dataset-json1-1.html>)
and 'SAS' XPORT
(<https://www.loc.gov/preservation/digital/formats/fdd/fdd000466.shtml>).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between artoo versions 0.1.1 dated 2026-06-24 and 0.1.2 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ man/artoo-package.Rd | 2 +- tests/testthat/test-codec_json.R | 15 +++++++++++++-- 5 files changed, 27 insertions(+), 10 deletions(-)
Title: AI Screening Tools in R for Systematic Reviewing
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://developers.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2025) <DOI:10.1037/met0000769>.
Author: Mikkel H. Vembye [aut, cre] ,
Thomas Olsen [aut]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Diff between AIscreenR versions 0.3.2 dated 2026-04-20 and 0.4.0 dated 2026-07-01
DESCRIPTION | 8 MD5 | 102 +- NAMESPACE | 7 NEWS.md | 144 ++- R/api_key_functions.R | 149 +++ R/claude_engine.r |only R/data.R | 41 + R/function-calling.R | 170 ++++ R/gemini_engine.r |only R/groq_engine.r | 40 - R/misc.func.hidden.price.R | 36 R/misc.func.hidden.tabscreen.R | 384 +++++++++- R/misc.helpers.R | 53 + R/ollama_engine.r | 59 - R/rate_limits.R | 73 + R/save_functions.r | 35 R/screen_analyzer.R | 2 R/screen_errors.R | 2 R/screen_errors.gpt.R | 2 R/tabscreen_claude.R |only R/tabscreen_gemini.R |only R/tabscreen_gpt.R | 41 - R/tabscreen_gpt.original.R | 8 R/tabscreen_gpt.tools.R |only R/tabscreen_mistral.R |only R/tabscreen_ollama.r | 33 build/partial.rdb |binary build/vignette.rds |binary data/claude_model_prizes.rda |only data/gemini_model_prizes.rda |only data/groq_model_prizes.rda |binary data/mistral_model_prizes.rda |only data/model_prizes.rda |binary inst/doc/Using-GPT-API-Models-For-Screening.html | 8 inst/doc/Using-GPT-API-Models-For-Screening.qmd | 2 inst/extdata/comparison-results/results_4omini_5mini_51_ministral_comparison.csv |only man/AIscreenR-package.Rd | 1 man/claude_model_prizes.Rd |only man/figures/AIscreenR_hex_light.png |only man/gemini_model_prizes.Rd |only man/get_api_key.Rd | 2 man/get_api_key_anthropic.Rd |only man/get_api_key_gemini.Rd |only man/get_api_key_groq.Rd | 2 man/get_api_key_mistral.Rd |only man/mistral_model_prizes.Rd |only man/rate_limits_per_minute.Rd | 16 man/screen_errors.gpt.Rd | 6 man/set_api_key.Rd | 2 man/tabscreen_claude.Rd |only man/tabscreen_gemini.Rd |only man/tabscreen_gpt.original.Rd | 4 man/tabscreen_gpt.tools.Rd | 26 man/tabscreen_gpt.tools_responses.Rd |only man/tabscreen_mistral.Rd |only man/tabscreen_ollama.Rd | 21 tests/testthat/test-save_functions.r | 4 tests/testthat/test-tabscreen_claude.R |only tests/testthat/test-tabscreen_gemini.R |only tests/testthat/test-tabscreen_gpt.R | 130 +-- tests/testthat/test-tabscreen_groq.R | 8 tests/testthat/test-tabscreen_mistral.R |only tests/testthat/test-tabscreen_ollama.r | 8 vignettes/Using-GPT-API-Models-For-Screening.qmd | 2 64 files changed, 1259 insertions(+), 372 deletions(-)
Title: 'A5' Discrete Global Grid System
Description: Bindings for the "A5 geospatial index"
<https://a5geo.org/>. 'A5' partitions the Earth's surface into
pentagonal cells across 31 resolution levels using an equal-area
projection onto a dodecahedron. Provides functions for indexing
coordinates to cells, traversing the cell hierarchy, computing cell
boundaries, and compacting/uncompacting cell sets. Powered by the
'A5' 'Rust' crate via 'extendr'.
Author: Hugh Graham [aut, cre],
belian.earth [cph]
Maintainer: Hugh Graham <hugh@belian.earth>
Diff between a5R versions 0.4.0 dated 2026-05-14 and 0.5.0 dated 2026-07-01
a5R-0.4.0/a5R/R/grid.R |only a5R-0.4.0/a5R/man/a5_grid.Rd |only a5R-0.4.0/a5R/src/rust/src/grid.rs |only a5R-0.4.0/a5R/tests/testthat/test-grid.R |only a5R-0.5.0/a5R/DESCRIPTION | 9 a5R-0.5.0/a5R/MD5 | 30 +- a5R-0.5.0/a5R/NAMESPACE | 1 a5R-0.5.0/a5R/NEWS.md | 23 + a5R-0.5.0/a5R/R/extendr-wrappers.R | 28 -- a5R-0.5.0/a5R/R/regions.R | 42 --- a5R-0.5.0/a5R/man/a5_polygon_to_cells.Rd | 12 a5R-0.5.0/a5R/src/rust/Cargo.lock | 336 --------------------------- a5R-0.5.0/a5R/src/rust/Cargo.toml | 5 a5R-0.5.0/a5R/src/rust/src/distance.rs | 61 ++++ a5R-0.5.0/a5R/src/rust/src/lib.rs | 2 a5R-0.5.0/a5R/src/rust/src/regions.rs | 84 ++++-- a5R-0.5.0/a5R/src/rust/vendor.tar.xz |binary a5R-0.5.0/a5R/tests/testthat/test-distance.R | 81 ++++++ 18 files changed, 249 insertions(+), 465 deletions(-)
Title: Fast and Scalable Cellwise-Robust Ensemble
Description: Functions to perform robust variable selection and regression using the Fast and Scalable
Cellwise-Robust Ensemble (FSCRE) algorithm. The approach establishes a robust foundation
using the Detect Deviating Cells (DDC) algorithm and robust correlation estimates. It then
employs a competitive ensemble architecture where a robust Least Angle Regression (LARS)
engine proposes candidate variables and cross-validation arbitrates their assignment. A final
robust MM-estimator is applied to the selected predictors.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between srlars versions 3.0.0 dated 2026-06-12 and 3.0.1 dated 2026-07-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 ++++- R/srlars.R | 6 +++--- man/srlars.Rd | 6 +++--- 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.4.6 dated 2026-02-21 and 3.5.0 dated 2026-07-01
DESCRIPTION | 10 +++--- MD5 | 70 +++++++++++++++++++++---------------------- NEWS | 5 +++ R/ifcookie.R | 2 - R/labkey.defaults.R | 2 - R/labkey.deleteRows.R | 2 - R/labkey.domain.R | 2 - R/labkey.executeSql.R | 2 - R/labkey.experiment.R | 2 - R/labkey.getFolders.R | 2 - R/labkey.getQueryInfo.R | 2 - R/labkey.getQueryLists.R | 2 - R/labkey.getSchemas.R | 2 - R/labkey.importRows.R | 2 - R/labkey.insertRows.R | 2 - R/labkey.moduleProperty.R | 2 - R/labkey.moveRows.R | 2 - R/labkey.pipeline.R | 2 - R/labkey.provenance.R | 2 - R/labkey.query.import.R | 2 - R/labkey.rstudio.R | 2 - R/labkey.saveBatch.R | 2 - R/labkey.security.R | 2 - R/labkey.selectRows.R | 2 - R/labkey.setCurlOptions.R | 2 - R/labkey.storage.R | 9 +++-- R/labkey.transform.R | 2 - R/labkey.updateRows.R | 2 - R/labkey.webdav.R | 2 - R/makeDF.R | 17 ++++++++-- R/makeFilter.R | 2 - R/parseHeader.R | 2 - R/schemaObjects.R | 2 - man/Rlabkey-package.Rd | 4 +- man/labkey.storage.delete.Rd | 13 +++++++ man/labkey.storage.update.Rd | 15 ++++++++- 36 files changed, 121 insertions(+), 78 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
Staysail Systems, Inc. [cph] ,
Capitar IT Group BV [cph] ,
The Mbed TLS Contributors [cph] ,
Pierre L'Ecuyer [cph] ,
sakura authors [cph] ,
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.9.1 dated 2026-06-01 and 1.10.0 dated 2026-07-01
nanonext-1.10.0/nanonext/DESCRIPTION | 11 nanonext-1.10.0/nanonext/MD5 | 343 ++--- nanonext-1.10.0/nanonext/NAMESPACE | 1 nanonext-1.10.0/nanonext/NEWS.md | 17 nanonext-1.10.0/nanonext/R/aio.R | 47 nanonext-1.10.0/nanonext/R/nano.R | 64 - nanonext-1.10.0/nanonext/R/ncurl.R | 17 nanonext-1.10.0/nanonext/README.md | 10 nanonext-1.10.0/nanonext/build/vignette.rds |binary nanonext-1.10.0/nanonext/cleanup | 6 nanonext-1.10.0/nanonext/cleanup.win | 7 nanonext-1.10.0/nanonext/configure | 396 +++++- nanonext-1.10.0/nanonext/inst/doc/nanonext.html | 2 nanonext-1.10.0/nanonext/inst/doc/v01-messaging.html | 2 nanonext-1.10.0/nanonext/inst/doc/v02-protocols.Rmd | 47 nanonext-1.10.0/nanonext/inst/doc/v02-protocols.html | 39 nanonext-1.10.0/nanonext/inst/doc/v03-configuration.html | 2 nanonext-1.10.0/nanonext/inst/doc/v04-web.html | 2 nanonext-1.10.0/nanonext/man/device_aio.Rd |only nanonext-1.10.0/nanonext/man/ncurl.Rd | 17 nanonext-1.10.0/nanonext/man/ncurl_aio.Rd | 17 nanonext-1.10.0/nanonext/man/ncurl_session.Rd | 17 nanonext-1.10.0/nanonext/src/Makevars.in | 337 +++++ nanonext-1.10.0/nanonext/src/Makevars.ucrt | 310 ++++ nanonext-1.10.0/nanonext/src/Makevars.win | 310 ++++ nanonext-1.10.0/nanonext/src/aio.c | 54 nanonext-1.10.0/nanonext/src/comms.c | 22 nanonext-1.10.0/nanonext/src/core.c | 68 - nanonext-1.10.0/nanonext/src/dispatcher.c | 4 nanonext-1.10.0/nanonext/src/init.c | 1 nanonext-1.10.0/nanonext/src/mbedtls/include/mbedtls/mbedtls_config.h | 16 nanonext-1.10.0/nanonext/src/mbedtls/library/aes.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/asn1parse.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/asn1write.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/bignum.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/ccm.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/constant_time.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/ctr_drbg.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/ecp.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/gcm.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_msg.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_tls.c | 20 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_tls12_server.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/x509.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/x509_create.c | 6 nanonext-1.10.0/nanonext/src/mbedtls/library/x509write.c | 2 nanonext-1.10.0/nanonext/src/nanonext.h | 11 nanonext-1.10.0/nanonext/src/ncurl.c | 96 - nanonext-1.10.0/nanonext/src/nng/include/nng/nng.h | 286 ++++ nanonext-1.10.0/nanonext/src/nng/include/nng/protocol/pubsub0/sub.h | 7 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/tls/engine.h | 8 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/tls/tls.h | 7 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/util/platform.h | 54 nanonext-1.10.0/nanonext/src/nng/src/core/aio.c | 23 nanonext-1.10.0/nanonext/src/nng/src/core/aio.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/dialer.c | 18 nanonext-1.10.0/nanonext/src/nng/src/core/dialer.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/idhash.c | 23 nanonext-1.10.0/nanonext/src/nng/src/core/idhash.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/init.c | 16 nanonext-1.10.0/nanonext/src/nng/src/core/listener.c | 42 nanonext-1.10.0/nanonext/src/nng/src/core/listener.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/lmq.c | 1 nanonext-1.10.0/nanonext/src/nng/src/core/message.c | 40 nanonext-1.10.0/nanonext/src/nng/src/core/message.h | 1 nanonext-1.10.0/nanonext/src/nng/src/core/msgqueue.c | 1 nanonext-1.10.0/nanonext/src/nng/src/core/options.h | 2 nanonext-1.10.0/nanonext/src/nng/src/core/pipe.c | 14 nanonext-1.10.0/nanonext/src/nng/src/core/pipe.h | 5 nanonext-1.10.0/nanonext/src/nng/src/core/platform.h | 11 nanonext-1.10.0/nanonext/src/nng/src/core/protocol.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/sockaddr.c |only nanonext-1.10.0/nanonext/src/nng/src/core/socket.c | 34 nanonext-1.10.0/nanonext/src/nng/src/core/sockfd.c | 4 nanonext-1.10.0/nanonext/src/nng/src/core/stream.c | 14 nanonext-1.10.0/nanonext/src/nng/src/core/url.c | 2 nanonext-1.10.0/nanonext/src/nng/src/nng.c | 358 ++++- nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_clock.c | 31 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_debug.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_ipcconn.c | 14 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_epoll.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_kqueue.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_port.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_resolv_gai.c | 49 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_sockaddr.c | 30 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcpconn.c | 13 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcpdial.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcplisten.c | 13 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_udp.c | 121 + nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_clock.c | 31 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_debug.c | 17 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_io.c | 6 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_ipcconn.c | 159 +- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_ipclisten.c | 38 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_resolv.c | 43 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_sockaddr.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcp.h | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcpconn.c | 187 +- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcpdial.c | 16 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcplisten.c | 281 ++-- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_udp.c | 88 + nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/bus0/bus.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair0/pair.c | 9 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair1/pair.c | 15 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair1/pair1_poly.c | 631 +++++----- nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pipeline0/pull.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pipeline0/push.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/pub.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/sub.c | 129 +- nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/xsub.c | 13 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/rep.c | 53 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/req.c | 17 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/xrep.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/xreq.c | 17 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/respond.c | 53 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/survey.c | 45 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/xrespond.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/xsurvey.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/transport.c | 10 nanonext-1.10.0/nanonext/src/nng/src/sp/transport.h | 4 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/ipc/ipc.c | 71 - nanonext-1.10.0/nanonext/src/nng/src/sp/transport/tcp/tcp.c | 22 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/tls/tls.c | 24 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/ws/websocket.c | 4 nanonext-1.10.0/nanonext/src/nng/src/supplemental/base64/base64.c | 18 nanonext-1.10.0/nanonext/src/nng/src/supplemental/base64/base64.h | 18 nanonext-1.10.0/nanonext/src/nng/src/supplemental/http/http_api.h | 1 nanonext-1.10.0/nanonext/src/nng/src/supplemental/http/http_server.c | 5 nanonext-1.10.0/nanonext/src/nng/src/supplemental/tls/mbedtls/tls.c | 232 ++- nanonext-1.10.0/nanonext/src/nng/src/supplemental/tls/tls_common.c | 93 - nanonext-1.10.0/nanonext/src/nng_structs.h | 2 nanonext-1.10.0/nanonext/src/proto.c | 12 nanonext-1.10.0/nanonext/src/server.c | 6 nanonext-1.10.0/nanonext/src/sync.c | 8 nanonext-1.10.0/nanonext/src/thread.c | 6 nanonext-1.10.0/nanonext/src/tls.c | 4 nanonext-1.10.0/nanonext/tests/tests.R | 41 nanonext-1.10.0/nanonext/tools |only nanonext-1.10.0/nanonext/vignettes/v02-protocols.Rmd | 47 nanonext-1.9.1/nanonext/configure.ucrt |only nanonext-1.9.1/nanonext/configure.win |only nanonext-1.9.1/nanonext/src/mbedtls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/cmake |only nanonext-1.9.1/nanonext/src/mbedtls/include/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/cmac.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_cache.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_cookie.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_ticket.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/timing.h |only nanonext-1.9.1/nanonext/src/mbedtls/library/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/library/block_cipher.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/cmac.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/hkdf.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/net_sockets.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_cache.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_cookie.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_debug_helpers_generated.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_ticket.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/timing.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/x509write_csr.c |only nanonext-1.9.1/nanonext/src/nng/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/cmake |only nanonext-1.9.1/nanonext/src/nng/include/nng/supplemental/util/options.h |only nanonext-1.9.1/nanonext/src/nng/src/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/core/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/posix/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/windows/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/bus0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pair0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pair1/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pipeline0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pubsub0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/reqrep0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/survey0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/inproc/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/ipc/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/socket/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/tcp/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/tls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/ws/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/base64/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/http/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/sha1/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/tls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/tls/mbedtls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/util |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/websocket/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/websocket/stub.c |only 193 files changed, 4463 insertions(+), 1788 deletions(-)
Title: Autodiff for Influence Function Based Estimates
Description: Implements an S7 class for estimates based on influence functions,
with forward mode automatic differentiation defined for standard arithmetic
operations.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between ife versions 0.2.3 dated 2026-02-07 and 0.2.5 dated 2026-07-01
DESCRIPTION | 6 ++-- MD5 | 13 +++++----- NAMESPACE | 2 + NEWS.md | 8 ++++++ R/influence_func_estimand.R | 49 ++++++++++++++++++++++++---------------- R/std_error.R | 24 ++++++++----------- man/ife_constructor.Rd | 21 ++++++++++++----- tests/testthat/test-std_error.R |only 8 files changed, 75 insertions(+), 48 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Estimates rates for continuous character evolution under Brownian motion and Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al. (2012).
Author: Jeremy M. Beaulieu [aut, cre],
Brian O'Meara [aut]
Maintainer: Jeremy M. Beaulieu <jmbeauli@uark.edu>
Diff between OUwie versions 2.10 dated 2022-06-15 and 3.0.2 dated 2026-07-01
OUwie-2.10/OUwie/README.md |only OUwie-3.0.2/OUwie/DESCRIPTION | 29 + OUwie-3.0.2/OUwie/MD5 | 61 +- OUwie-3.0.2/OUwie/NAMESPACE | 12 OUwie-3.0.2/OUwie/R/OUwie.R | 243 ++++++++--- OUwie-3.0.2/OUwie/R/OUwie.anc.R | 87 +++- OUwie-3.0.2/OUwie/R/OUwie.boot.R | 32 - OUwie-3.0.2/OUwie/R/OUwie.contour.r | 4 OUwie-3.0.2/OUwie/R/OUwie.dredge.R | 204 ++++++++- OUwie-3.0.2/OUwie/R/OUwie.fixed.R | 71 ++- OUwie-3.0.2/OUwie/R/OUwie.format.R |only OUwie-3.0.2/OUwie/R/OUwie.sim.R | 104 +++-- OUwie-3.0.2/OUwie/R/adjust_bounds.R | 4 OUwie-3.0.2/OUwie/R/check.identify.R | 11 OUwie-3.0.2/OUwie/R/varcov.ou.R | 434 +++++++++++++-------- OUwie-3.0.2/OUwie/R/vcvbypass.functions.R | 124 ++++-- OUwie-3.0.2/OUwie/R/weight.mat.R | 407 ++++++++++++------- OUwie-3.0.2/OUwie/build/vignette.rds |binary OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.R | 47 +- OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.Rmd | 14 OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.pdf |binary OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.R |only OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.Rmd |only OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.pdf |only OUwie-3.0.2/OUwie/man/OUwie.Rd | 12 OUwie-3.0.2/OUwie/man/OUwie.anc.Rd | 5 OUwie-3.0.2/OUwie/man/OUwie.boot.Rd | 4 OUwie-3.0.2/OUwie/man/OUwie.dredge.Rd | 11 OUwie-3.0.2/OUwie/man/OUwie.fixed.Rd | 7 OUwie-3.0.2/OUwie/man/OUwie.format.Rd |only OUwie-3.0.2/OUwie/man/OUwie.sim.Rd | 6 OUwie-3.0.2/OUwie/tests/testthat/test-likelihood.R | 31 - OUwie-3.0.2/OUwie/tests/testthat/test-restart.R | 4 OUwie-3.0.2/OUwie/vignettes/OUwie_2.1_adds.Rmd | 14 OUwie-3.0.2/OUwie/vignettes/calculationUpdate.Rmd |only 35 files changed, 1384 insertions(+), 598 deletions(-)
Title: Monte Carlo Simulations of Time Changes in Sequences
Description: Generates replicated sets of sequences with Monte Carlo simulated timing changes and computes various indicators for evaluating effects of timing uncertainty on sequence analysis results. See Ritschard, G. and Liao, T.F. (2026): "Assessing the Impact of Timing Errors in Sequence Analysis". International Journal of Social Research Methodology <doi:10.1080/13645579.2026.2666297>.
Author: Gilbert Ritschard [aut, cre, cph] ,
Tim F. Liao [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between MCseqReplic versions 1.0.0 dated 2026-04-29 and 1.1.0 dated 2026-07-01
MCseqReplic-1.0.0/MCseqReplic/R/seqdistMCSE.R |only MCseqReplic-1.0.0/MCseqReplic/man/seqdistMCSE.Rd |only MCseqReplic-1.1.0/MCseqReplic/DESCRIPTION | 32 ++- MCseqReplic-1.1.0/MCseqReplic/MD5 | 52 +++-- MCseqReplic-1.1.0/MCseqReplic/NAMESPACE | 15 + MCseqReplic-1.1.0/MCseqReplic/R/MCclustcomp.R | 23 +- MCseqReplic-1.1.0/MCseqReplic/R/MCclustqual.R | 179 +++++++++++++++++--- MCseqReplic-1.1.0/MCseqReplic/R/MCcomgrp.R |only MCseqReplic-1.1.0/MCseqReplic/R/MCdisscorr.R | 1 MCseqReplic-1.1.0/MCseqReplic/R/MCmdscorr.R | 18 +- MCseqReplic-1.1.0/MCseqReplic/R/MCmethods.R | 3 MCseqReplic-1.1.0/MCseqReplic/R/MCmisc.R | 15 + MCseqReplic-1.1.0/MCseqReplic/R/MCratios.R | 9 - MCseqReplic-1.1.0/MCseqReplic/R/MCseqReplicate.R | 8 MCseqReplic-1.1.0/MCseqReplic/R/MCseqdistSE.R | 2 MCseqReplic-1.1.0/MCseqReplic/R/seqMCsple.R |only MCseqReplic-1.1.0/MCseqReplic/build |only MCseqReplic-1.1.0/MCseqReplic/inst/CITATION | 8 MCseqReplic-1.1.0/MCseqReplic/inst/NEWS.Rd | 38 ++++ MCseqReplic-1.1.0/MCseqReplic/inst/REFERENCES.bib |only MCseqReplic-1.1.0/MCseqReplic/inst/doc |only MCseqReplic-1.1.0/MCseqReplic/man/MCclustcomp.Rd | 18 +- MCseqReplic-1.1.0/MCseqReplic/man/MCclustqual.Rd | 67 ++++++- MCseqReplic-1.1.0/MCseqReplic/man/MCcompgrp.Rd |only MCseqReplic-1.1.0/MCseqReplic/man/MCmdscorr.Rd | 7 MCseqReplic-1.1.0/MCseqReplic/man/MCratios.Rd | 8 MCseqReplic-1.1.0/MCseqReplic/man/MCseqReplicate.Rd | 3 MCseqReplic-1.1.0/MCseqReplic/man/MCseqdistSE.Rd | 2 MCseqReplic-1.1.0/MCseqReplic/man/print.MCratios.Rd | 2 MCseqReplic-1.1.0/MCseqReplic/vignettes |only 30 files changed, 408 insertions(+), 102 deletions(-)
Title: Help with Preparing a New Version of an R Package
Description: Helps to prepare a release. Before releasing an R package it is important to update the DESCRIPTION file and the changelog. This package prepares these files and also updates the versions according to the branches. It relies heavily on the 'desc' packages.
Author: Tanguy Barthelemy [aut, cre, art]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between releaser versions 1.1.1 dated 2026-06-08 and 1.2.0 dated 2026-07-01
DESCRIPTION | 6 +-- MD5 | 36 ++++++++++---------- NAMESPACE | 1 NEWS.md | 10 +++-- R/cran-check.R | 25 +++++++++++++- R/get_information.R | 14 +++---- R/update_description.R | 64 ++++++++++++++++++++++++++++++++---- README.md | 31 +++++++++-------- inst/WORDLIST | 1 man/change_remotes_field.Rd | 7 ++- man/check.Rd | 13 +++++++ man/check_docs.Rd | 8 ++++ man/get_changes.Rd | 7 ++- man/get_different_future_version.Rd | 4 +- man/get_github_branches.Rd | 4 +- man/get_latest_version.Rd | 4 +- man/print.releaser_doc_check.Rd |only man/set_latest_deps_version.Rd | 10 +++-- man/set_rjdverse_remotes.Rd |only man/update_news_md.Rd | 7 ++- 20 files changed, 180 insertions(+), 72 deletions(-)
Title: Data Sets for Keith McNulty's Handbook of Regression Modeling in
People Analytics
Description: Data sets for statistical inference modeling related to People Analytics.
Contains various data sets from the book 'Handbook of Regression Modeling in People Analytics'
by Keith McNulty (2026).
Author: Keith McNulty [aut, cre]
Maintainer: Keith McNulty <keith.mcnulty@gmail.com>
Diff between peopleanalyticsdata versions 0.2.1 dated 2021-04-13 and 0.2.2 dated 2026-07-01
DESCRIPTION | 17 +++++++++-------- LICENSE | 2 +- MD5 | 21 +++++++++++++++------ NEWS.md | 6 ++++++ R/data-absenteeism.R |only R/data-complaints.R |only R/data-selection.R |only R/data-speed_dating.R | 2 +- README.md | 3 +-- data/absenteeism.rda |only data/complaints.rda |only data/selection.rda |only man/absenteeism.Rd |only man/complaints.Rd |only man/selection.Rd |only man/speed_dating.Rd | 2 +- 16 files changed, 34 insertions(+), 19 deletions(-)
More information about peopleanalyticsdata at CRAN
Permanent link
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.8-0 dated 2026-04-14 and 1.8-1 dated 2026-07-01
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/mmlt.R | 2 +- build/partial.rdb |binary cleanup | 4 ++++ inst/NEWS.Rd | 8 ++++++++ 6 files changed, 23 insertions(+), 11 deletions(-)
Title: Post-Processing of Markov Chain Monte Carlo Simulations for
Chronological Modelling
Description: Statistical analysis of archaeological dates and groups of
dates. This package allows to post-process Markov Chain Monte Carlo
(MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>,
'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal'
<https://bcal.shef.ac.uk/>. It provides functions for the study of
rhythms of the long term from the posterior distribution of a series
of dates (tempo and activity plot). It also allows the estimation and
visualization of time ranges from the posterior distribution of groups
of dates (e.g. duration, transition and hiatus between successive
phases) as described in Philippe and Vibet (2020)
<doi:10.18637/jss.v093.c01>.
Author: Anne Philippe [aut, cre] ,
Marie-Anne Vibet [aut] ,
Nicolas Frerebeau [aut] ,
Thomas S. Dye [ctb] ,
Nantes Universite [fnd] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between ArchaeoPhases versions 2.1.0 dated 2025-09-26 and 2.1.1 dated 2026-07-01
DESCRIPTION | 10 +- MD5 | 159 +++++++++++++++++++------------------- NAMESPACE | 13 +-- NEWS.md | 5 + R/AllGenerics.R | 28 +++++- R/ArchaeoPhases-package.R | 5 - R/activity.R | 2 R/coerce.R | 23 +++++ README.md | 63 +++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/ArchaeoPhases.Rmd | 2 inst/doc/ArchaeoPhases.html | 37 ++++---- inst/doc/allen.Rmd | 2 inst/doc/allen.html | 12 +- inst/doc/import.Rmd | 2 inst/doc/import.html | 9 +- man/ActivityEvents-class.Rd | 4 man/AgeDepthModel-class.Rd | 2 man/ArchaeoPhases-package.Rd | 3 man/CumulativeEvents-class.Rd | 4 man/DurationsMCMC-class.Rd | 4 man/EventsMCMC-class.Rd | 4 man/MCMC-class.Rd | 2 man/OccurrenceEvents-class.Rd | 4 man/PhasesMCMC-class.Rd | 2 man/TimeRange-class.Rd | 2 man/activity.Rd | 16 +-- man/allen_analyze.Rd | 30 +++---- man/allen_analyze_relations.Rd | 30 +++---- man/allen_complement.Rd | 30 +++---- man/allen_composition.Rd | 30 +++---- man/allen_converse.Rd | 30 +++---- man/allen_illustrate.Rd | 30 +++---- man/allen_illustrate_relations.Rd | 30 +++---- man/allen_intersect.Rd | 30 +++---- man/allen_joint_concurrency.Rd | 34 ++++---- man/allen_observe.Rd | 32 +++---- man/allen_observe_frequency.Rd | 32 +++---- man/allen_plot.Rd | 30 +++---- man/allen_relate_intervals.Rd | 2 man/allen_relation.Rd | 30 +++---- man/allen_relation_code.Rd | 30 +++---- man/allen_union.Rd | 30 +++---- man/as.array.Rd |only man/as_coda.Rd | 12 +- man/as_events.Rd | 14 +-- man/as_phases.Rd | 14 +-- man/bind.Rd | 14 +-- man/boundaries.Rd | 10 +- man/bury.Rd | 14 +-- man/check.Rd | 14 +-- man/data.frame.Rd | 14 --- man/duration.Rd | 6 - man/elapse.Rd | 10 +- man/hiatus.Rd | 12 +- man/interpolate.Rd | 4 man/interval_credible.Rd | 12 +- man/interval_hdr.Rd | 12 +- man/mcmc_events.Rd | 2 man/mcmc_phases.Rd | 2 man/names.Rd | 9 -- man/occurrence.Rd | 14 +-- man/older.Rd | 2 man/phases.Rd | 8 - man/plot_events.Rd | 6 - man/plot_phases.Rd | 6 - man/read_bcal.Rd | 14 +-- man/read_chronomodel.Rd | 16 +-- man/read_oxcal.Rd | 14 +-- man/sensitivity.Rd | 10 +- man/sort.Rd | 11 -- man/sort.list.Rd | 11 -- man/subset.Rd | 10 -- man/summary.Rd | 12 +- man/tempo.Rd | 16 +-- man/transition.Rd | 10 +- vignettes/ArchaeoPhases.Rmd | 2 vignettes/allen.Rmd | 2 vignettes/import.Rmd | 2 81 files changed, 619 insertions(+), 603 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Lina Patil [aut, cre],
Stefan Bundfuss [aut] ,
Kristin Dahnert [aut],
Fanny Gautier [aut] ,
Edoardo Mancini [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Kiran Peddamudium [aut],
Gerardo Jose Rodriguez [aut] ,
Vladyslav Shuliar [aut] ,
Cytel Inc. [...truncated...]
Maintainer: Lina Patil <lina.patil@cytel.com>
Diff between pharmaversesdtm versions 1.4.1 dated 2026-03-30 and 1.5.0 dated 2026-07-01
DESCRIPTION | 13 ++++++++----- MD5 | 27 +++++++++++++++------------ NEWS.md | 15 +++++++++++++++ R/lb_neuro.R | 5 +++-- R/oe_ophtha.R | 4 +++- R/rs_onco_lymphoma.R |only README.md | 2 ++ data/lb_neuro.rda |binary data/oe_ophtha.rda |binary data/rs_onco_lymphoma.rda |only inst/WORDLIST | 7 +++++-- inst/extdata/sdtms-specs.json | 8 ++++++++ man/lb_neuro.Rd | 5 +++-- man/oe_ophtha.Rd | 4 +++- man/pharmaversesdtm-package.Rd | 2 ++ man/rs_onco_lymphoma.Rd |only 16 files changed, 67 insertions(+), 25 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Programmatic Interface to 'Orthanc' DICOM Servers
Description: An R Interface to 'Orthanc' DICOM servers for medical imaging workflows.
'Orthanc' is a lightweight, open-source DICOM server that exposes a comprehensive
REST API for managing, querying, retrieving, and modifying DICOM resources
(<https://www.orthanc-server.com>). The goal of this package is to provide
comprehensive and user-friendly access to the 'Orthanc' REST API, designed to
align with idiomatic R workflows while preserving the structure and semantics
of DICOM resources.
Author: Matthew T. Warkentin [aut, cre, cph]
Maintainer: Matthew T. Warkentin <matthew.warkentin@ucalgary.ca>
Diff between orthanc versions 0.2.0 dated 2026-03-11 and 0.3.0 dated 2026-07-01
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 14 +++ R/Orthanc.R | 142 +++++++++++++++++++++++++++++++++++++--- R/filtering.R | 2 man/Orthanc.Rd | 33 +++++++++ man/find_and_filter_patients.Rd | 2 7 files changed, 191 insertions(+), 20 deletions(-)
Title: Quantitative Analysis and Visualization of LUCC
Description: Tools for the analysis of land use and cover (LUC) time series. It
includes support for loading spatiotemporal raster data and synthesized
spatial plotting. Several LUC change (LUCC) metrics in regular or irregular
time intervals can be extracted and visualized through one- and multistep
sankey and chord diagrams. A complete intensity analysis according to
Aldwaik and Pontius (2012) <doi:10.1016/j.landurbplan.2012.02.010> is
implemented, including tools for the generation of standardized multilevel
output graphics.
Author: Reginal Exavier [aut, cre] ,
Peter Zeilhofer [aut]
Maintainer: Reginal Exavier <reginalexavier@rocketmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2024-05-03
Diff between OpenLand versions 1.0.3 dated 2024-05-03 and 1.0.4 dated 2026-07-01
DESCRIPTION | 14 MD5 | 89 +- NEWS.md | 11 R/contingencyTable.R | 380 ++++---- R/data.R | 2 R/demolandscape.R | 173 ++-- R/generalfunctions.R | 472 ++++++----- R/generic_method.R | 86 +- R/intensityAnalysis.R | 1001 ++++++++++++----------- R/intensityClass.R | 525 +++++------- R/otherplots.R | 1115 +++++++++++++------------- R/plotMethods.R | 1042 ++++++++++++------------ R/rasters_input.R | 169 ++- README.md | 69 - build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/openland_vignette.R | 235 ++--- inst/doc/openland_vignette.Rmd | 798 +++++++++--------- inst/doc/openland_vignette.html | 735 ++++++----------- man/SL_2002_2014.Rd | 2 man/acc_changes.Rd | 10 man/barplotLand.Rd | 31 man/chordDiagramLand.Rd | 28 man/contingencyTable.Rd | 17 man/dot-demo_landscape.Rd | 8 man/dot-openland_try_download_and_load_rda.Rd |only man/figures/README-cat_level-1.png |binary man/figures/README-chordDiagram-1.png |binary man/figures/README-ng_plot-1.png |binary man/intensityAnalysis.Rd | 25 man/netgrossplot.Rd | 29 man/plot.Rd | 9 man/sankeyLand.Rd | 37 man/summary_dir.Rd | 11 man/summary_map.Rd | 9 tests/spelling.R |only tests/testthat/Rplots.pdf |binary tests/testthat/test_contingencyTable.R | 128 +- tests/testthat/test_demolandscape.R | 27 tests/testthat/test_generalfunctions.R | 292 +++++- tests/testthat/test_inputrasters.R | 72 - tests/testthat/test_intensityAnalysis.R | 208 ++-- tests/testthat/test_intensityClasses.R | 216 ++--- tests/testthat/test_plots.R | 116 +- vignettes/openland_vignette.Rmd | 798 +++++++++--------- vignettes/papers_OpenLand.bib | 2 47 files changed, 4687 insertions(+), 4304 deletions(-)
Title: Machine Learning and Visualization
Description: Machine learning and visualization package with an 'S7' backend
featuring comprehensive type checking and validation, paired with an efficient functional
user-facing API. train(), cluster(), and decomp() provide one-call access to supervised and
unsupervised learning. All configuration steps are performed using setup functions and
validated. A single call to train() handles preprocessing, hyperparameter tuning, and testing
with nested resampling. Supports 'data.frame', 'data.table', and 'tibble' inputs, parallel
execution, and interactive visualizations. The package first appeared in E.D. Gennatas (2017)
<https://repository.upenn.edu/entities/publication/d81892ea-3087-4b71-a6f5-739c58626d64>.
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis versions 1.0.0 dated 2026-03-26 and 1.2.7 dated 2026-07-01
rtemis-1.0.0/rtemis/R/00_S7init.R |only rtemis-1.0.0/rtemis/R/07_Supervised.R |only rtemis-1.0.0/rtemis/R/08_MassUni.R |only rtemis-1.0.0/rtemis/R/09_ClusteringConfig.R |only rtemis-1.0.0/rtemis/R/10_Clustering.R |only rtemis-1.0.0/rtemis/R/11_DecompositionConfig.R |only rtemis-1.0.0/rtemis/R/12_Decomposition.R |only rtemis-1.0.0/rtemis/R/13_Themes.R |only rtemis-1.0.0/rtemis/R/14_SuperConfig.R |only rtemis-1.0.0/rtemis/R/15_CheckData.R |only rtemis-1.0.0/rtemis/R/16_S7utils.R |only rtemis-1.0.0/rtemis/R/ddSci.R |only rtemis-1.0.0/rtemis/R/msg.R |only rtemis-1.0.0/rtemis/R/utils_checks.R |only rtemis-1.0.0/rtemis/man/clean_colnames.Rd |only rtemis-1.0.0/rtemis/man/clean_names.Rd |only rtemis-1.0.0/rtemis/man/ddSci.Rd |only rtemis-1.0.0/rtemis/man/describe.factor.Rd |only rtemis-1.0.0/rtemis/man/labelify.Rd |only rtemis-1.0.0/rtemis/man/present.list.Rd |only rtemis-1.0.0/rtemis/man/rtemis_colors.Rd |only rtemis-1.0.0/rtemis/man/write_toml.Rd |only rtemis-1.2.7/rtemis/DESCRIPTION | 33 rtemis-1.2.7/rtemis/MD5 | 406 ++--- rtemis-1.2.7/rtemis/NAMESPACE | 30 rtemis-1.2.7/rtemis/R/00_init.R |only rtemis-1.2.7/rtemis/R/01_ExecutionConfig.R | 77 rtemis-1.2.7/rtemis/R/02_Hyperparameters.R | 161 +- rtemis-1.2.7/rtemis/R/03_Metrics.R | 140 + rtemis-1.2.7/rtemis/R/04_Preprocessor.R | 16 rtemis-1.2.7/rtemis/R/05_Resampler.R | 55 rtemis-1.2.7/rtemis/R/06_Tuner.R | 55 rtemis-1.2.7/rtemis/R/07_ClusteringConfig.R |only rtemis-1.2.7/rtemis/R/08_Clustering.R |only rtemis-1.2.7/rtemis/R/09_DecompositionConfig.R |only rtemis-1.2.7/rtemis/R/10_Decomposition.R |only rtemis-1.2.7/rtemis/R/11_Session.R |only rtemis-1.2.7/rtemis/R/12_Supervised.R |only rtemis-1.2.7/rtemis/R/13_MassUni.R |only rtemis-1.2.7/rtemis/R/14_Themes.R |only rtemis-1.2.7/rtemis/R/15_SuperConfig.R |only rtemis-1.2.7/rtemis/R/16_DecomposeConfig.R |only rtemis-1.2.7/rtemis/R/17_ClusterConfig.R |only rtemis-1.2.7/rtemis/R/18_CheckData.R |only rtemis-1.2.7/rtemis/R/19_S7utils.R |only rtemis-1.2.7/rtemis/R/algorithmDB.R | 91 - rtemis-1.2.7/rtemis/R/calibrate.R | 7 rtemis-1.2.7/rtemis/R/check_input_data.R | 99 - rtemis-1.2.7/rtemis/R/cluster.R | 59 rtemis-1.2.7/rtemis/R/cluster_CMeans.R | 4 rtemis-1.2.7/rtemis/R/cluster_DBSCAN.R | 6 rtemis-1.2.7/rtemis/R/cluster_flexclust.R | 4 rtemis-1.2.7/rtemis/R/conditions.R |only rtemis-1.2.7/rtemis/R/decomp.R | 62 rtemis-1.2.7/rtemis/R/decomp_ICA.R | 52 rtemis-1.2.7/rtemis/R/decomp_Isomap.R | 8 rtemis-1.2.7/rtemis/R/decomp_NMF.R | 39 rtemis-1.2.7/rtemis/R/decomp_PCA.R | 32 rtemis-1.2.7/rtemis/R/decomp_UMAP.R | 35 rtemis-1.2.7/rtemis/R/decomp_tSNE.R | 8 rtemis-1.2.7/rtemis/R/draw_3Dscatter.R | 26 rtemis-1.2.7/rtemis/R/draw_bar.R | 15 rtemis-1.2.7/rtemis/R/draw_box.R | 38 rtemis-1.2.7/rtemis/R/draw_confusion.R | 25 rtemis-1.2.7/rtemis/R/draw_dist.R | 21 rtemis-1.2.7/rtemis/R/draw_graphjs.R | 13 rtemis-1.2.7/rtemis/R/draw_heatmap.R | 28 rtemis-1.2.7/rtemis/R/draw_leaflet.R | 8 rtemis-1.2.7/rtemis/R/draw_pie.R | 6 rtemis-1.2.7/rtemis/R/draw_protein.R | 8 rtemis-1.2.7/rtemis/R/draw_pvals.R | 2 rtemis-1.2.7/rtemis/R/draw_roc.R | 232 ++ rtemis-1.2.7/rtemis/R/draw_scatter.R | 23 rtemis-1.2.7/rtemis/R/draw_spectrogram.R | 23 rtemis-1.2.7/rtemis/R/draw_survfit.R | 2 rtemis-1.2.7/rtemis/R/draw_ts.R | 7 rtemis-1.2.7/rtemis/R/draw_varimp.R | 10 rtemis-1.2.7/rtemis/R/draw_volcano.R | 39 rtemis-1.2.7/rtemis/R/draw_xt.R | 31 rtemis-1.2.7/rtemis/R/fmt.R | 530 ------ rtemis-1.2.7/rtemis/R/massGLM.R | 59 rtemis-1.2.7/rtemis/R/metrics.R | 226 -- rtemis-1.2.7/rtemis/R/preprocess.R | 156 - rtemis-1.2.7/rtemis/R/present.R | 24 rtemis-1.2.7/rtemis/R/read.R | 40 rtemis-1.2.7/rtemis/R/read_config.R |only rtemis-1.2.7/rtemis/R/reexports.R |only rtemis-1.2.7/rtemis/R/resample.R | 7 rtemis-1.2.7/rtemis/R/rtemis-package.R | 13 rtemis-1.2.7/rtemis/R/rtemis_color_system.R | 109 - rtemis-1.2.7/rtemis/R/train.R | 436 ++++- rtemis-1.2.7/rtemis/R/train_CART.R | 17 rtemis-1.2.7/rtemis/R/train_GAM.R | 50 rtemis-1.2.7/rtemis/R/train_GLM.R | 19 rtemis-1.2.7/rtemis/R/train_GLMNET.R | 57 rtemis-1.2.7/rtemis/R/train_Isotonic.R | 28 rtemis-1.2.7/rtemis/R/train_LightCART.R | 9 rtemis-1.2.7/rtemis/R/train_LightGBM.R | 24 rtemis-1.2.7/rtemis/R/train_LightRF.R | 11 rtemis-1.2.7/rtemis/R/train_LightRuleFit.R | 23 rtemis-1.2.7/rtemis/R/train_Ranger.R | 42 rtemis-1.2.7/rtemis/R/train_SVM.R | 39 rtemis-1.2.7/rtemis/R/train_TabNet.R | 24 rtemis-1.2.7/rtemis/R/tune.R | 18 rtemis-1.2.7/rtemis/R/tune_GridSearch.R | 195 +- rtemis-1.2.7/rtemis/R/utils.R | 23 rtemis-1.2.7/rtemis/R/utils_art.R | 8 rtemis-1.2.7/rtemis/R/utils_async.R | 20 rtemis-1.2.7/rtemis/R/utils_color.R | 63 rtemis-1.2.7/rtemis/R/utils_data.R | 33 rtemis-1.2.7/rtemis/R/utils_data.table.R | 10 rtemis-1.2.7/rtemis/R/utils_date.R | 3 rtemis-1.2.7/rtemis/R/utils_df.R | 30 rtemis-1.2.7/rtemis/R/utils_exec.R | 15 rtemis-1.2.7/rtemis/R/utils_files.R | 2 rtemis-1.2.7/rtemis/R/utils_io.R | 95 - rtemis-1.2.7/rtemis/R/utils_lightgbm.R | 1 rtemis-1.2.7/rtemis/R/utils_palettes.R | 18 rtemis-1.2.7/rtemis/R/utils_plotly.R | 14 rtemis-1.2.7/rtemis/R/utils_print.R | 1028 ------------- rtemis-1.2.7/rtemis/R/utils_rt.R | 1 rtemis-1.2.7/rtemis/R/utils_rules.R | 2 rtemis-1.2.7/rtemis/R/utils_strings.R | 558 ------- rtemis-1.2.7/rtemis/R/utils_supervised.R | 86 - rtemis-1.2.7/rtemis/R/utils_uniprot.R | 1 rtemis-1.2.7/rtemis/R/write_config.R |only rtemis-1.2.7/rtemis/R/zzz.R | 26 rtemis-1.2.7/rtemis/README.md | 49 rtemis-1.2.7/rtemis/inst/WORDLIST |only rtemis-1.2.7/rtemis/man/apply_decomp.Rd |only rtemis-1.2.7/rtemis/man/available_algorithms.Rd | 11 rtemis-1.2.7/rtemis/man/available_draw.Rd | 7 rtemis-1.2.7/rtemis/man/calibrate.Rd | 2 rtemis-1.2.7/rtemis/man/classification_metrics.Rd | 2 rtemis-1.2.7/rtemis/man/cluster.Rd | 10 rtemis-1.2.7/rtemis/man/decomp.Rd | 9 rtemis-1.2.7/rtemis/man/describe.Rd | 40 rtemis-1.2.7/rtemis/man/df_movecolumn.Rd | 3 rtemis-1.2.7/rtemis/man/dot-list_to_DecompositionConfig.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_Hyperparameters.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_ResamplerConfig.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_TunerConfig.Rd |only rtemis-1.2.7/rtemis/man/draw_3Dscatter.Rd | 14 rtemis-1.2.7/rtemis/man/draw_bar.Rd | 15 rtemis-1.2.7/rtemis/man/draw_box.Rd | 23 rtemis-1.2.7/rtemis/man/draw_confusion.Rd | 12 rtemis-1.2.7/rtemis/man/draw_dist.Rd | 14 rtemis-1.2.7/rtemis/man/draw_graphjs.Rd | 10 rtemis-1.2.7/rtemis/man/draw_heatmap.Rd | 28 rtemis-1.2.7/rtemis/man/draw_leaflet.Rd | 8 rtemis-1.2.7/rtemis/man/draw_pie.Rd | 6 rtemis-1.2.7/rtemis/man/draw_protein.Rd | 4 rtemis-1.2.7/rtemis/man/draw_pvals.Rd | 2 rtemis-1.2.7/rtemis/man/draw_roc.Rd | 4 rtemis-1.2.7/rtemis/man/draw_scatter.Rd | 10 rtemis-1.2.7/rtemis/man/draw_spectrogram.Rd | 18 rtemis-1.2.7/rtemis/man/draw_ts.Rd | 4 rtemis-1.2.7/rtemis/man/draw_varimp.Rd | 5 rtemis-1.2.7/rtemis/man/draw_volcano.Rd | 9 rtemis-1.2.7/rtemis/man/draw_xt.Rd | 2 rtemis-1.2.7/rtemis/man/exc.Rd | 2 rtemis-1.2.7/rtemis/man/feature_names.Rd | 2 rtemis-1.2.7/rtemis/man/features.Rd | 2 rtemis-1.2.7/rtemis/man/figures/logo.svg | 35 rtemis-1.2.7/rtemis/man/get_factor_names.Rd | 2 rtemis-1.2.7/rtemis/man/get_palette.Rd | 2 rtemis-1.2.7/rtemis/man/get_varimp.Rd |only rtemis-1.2.7/rtemis/man/inc.Rd | 2 rtemis-1.2.7/rtemis/man/inspect.Rd | 2 rtemis-1.2.7/rtemis/man/massGLM.Rd | 7 rtemis-1.2.7/rtemis/man/matchcases.Rd | 2 rtemis-1.2.7/rtemis/man/numeric_features.Rd |only rtemis-1.2.7/rtemis/man/outcome.Rd | 2 rtemis-1.2.7/rtemis/man/outcome_name.Rd | 2 rtemis-1.2.7/rtemis/man/plot.MassGLM.Rd | 4 rtemis-1.2.7/rtemis/man/plot_manhattan.Rd | 4 rtemis-1.2.7/rtemis/man/plot_roc.Rd | 2 rtemis-1.2.7/rtemis/man/plot_true_pred.Rd | 2 rtemis-1.2.7/rtemis/man/plot_varimp.Rd | 2 rtemis-1.2.7/rtemis/man/preprocess.Rd | 2 rtemis-1.2.7/rtemis/man/preprocessed.Rd | 2 rtemis-1.2.7/rtemis/man/present.Rd | 2 rtemis-1.2.7/rtemis/man/previewcolor.Rd | 14 rtemis-1.2.7/rtemis/man/read.Rd | 8 rtemis-1.2.7/rtemis/man/read_config.Rd | 38 rtemis-1.2.7/rtemis/man/reexports.Rd |only rtemis-1.2.7/rtemis/man/resample.Rd | 2 rtemis-1.2.7/rtemis/man/roc_curve.Rd |only rtemis-1.2.7/rtemis/man/rtemis-package.Rd | 17 rtemis-1.2.7/rtemis/man/rtemis_conditions.Rd |only rtemis-1.2.7/rtemis/man/set_outcome.Rd | 2 rtemis-1.2.7/rtemis/man/set_positive_class.Rd |only rtemis-1.2.7/rtemis/man/setup_CMeans.Rd | 2 rtemis-1.2.7/rtemis/man/setup_ClusterConfig.Rd |only rtemis-1.2.7/rtemis/man/setup_DBSCAN.Rd | 2 rtemis-1.2.7/rtemis/man/setup_DecomposeConfig.Rd |only rtemis-1.2.7/rtemis/man/setup_ExecutionConfig.Rd | 11 rtemis-1.2.7/rtemis/man/setup_HardCL.Rd | 2 rtemis-1.2.7/rtemis/man/setup_ICA.Rd | 8 rtemis-1.2.7/rtemis/man/setup_Isomap.Rd | 2 rtemis-1.2.7/rtemis/man/setup_KMeans.Rd | 2 rtemis-1.2.7/rtemis/man/setup_NMF.Rd | 12 rtemis-1.2.7/rtemis/man/setup_NeuralGas.Rd | 2 rtemis-1.2.7/rtemis/man/setup_PCA.Rd | 7 rtemis-1.2.7/rtemis/man/setup_Preprocessor.Rd | 10 rtemis-1.2.7/rtemis/man/setup_Ranger.Rd | 69 rtemis-1.2.7/rtemis/man/setup_SuperConfig.Rd | 19 rtemis-1.2.7/rtemis/man/setup_SuperConfigLive.Rd |only rtemis-1.2.7/rtemis/man/setup_TabNet.Rd | 2 rtemis-1.2.7/rtemis/man/setup_UMAP.Rd | 8 rtemis-1.2.7/rtemis/man/setup_tSNE.Rd | 2 rtemis-1.2.7/rtemis/man/show_color_key.Rd |only rtemis-1.2.7/rtemis/man/to_json.Rd |only rtemis-1.2.7/rtemis/man/train.Rd | 22 rtemis-1.2.7/rtemis/man/uniprot_get.Rd | 3 rtemis-1.2.7/rtemis/man/write_config.Rd |only rtemis-1.2.7/rtemis/tests/testthat/test_ClusterConfig.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Clustering.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_DecomposeConfig.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Decomposition.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Hyperparameters.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Metrics.R | 11 rtemis-1.2.7/rtemis/tests/testthat/test_Preprocessor.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_SuperConfig.R | 106 - rtemis-1.2.7/rtemis/tests/testthat/test_SuperConfigLive.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Supervised.R | 14 rtemis-1.2.7/rtemis/tests/testthat/test_Theme.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Tuner.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_checks.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_colorsystem.R | 11 rtemis-1.2.7/rtemis/tests/testthat/test_draw.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_idx.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_massGLM.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_strings.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_to_json.R |only 235 files changed, 3209 insertions(+), 3853 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 3.0.1 dated 2026-06-29 and 3.0.2 dated 2026-07-01
DESCRIPTION | 13 MD5 | 24 NEWS.md | 9 R/enrichment.R | 2 build/vignette.rds |binary inst/doc/comparing_results.html | 4 inst/doc/intro_vignette.html | 397 +++++----------- inst/doc/non_hs_analysis.html | 489 +++++++++----------- inst/doc/obtain_data.html | 4 inst/doc/visualization_vignette.html | 16 man/enrichment_analyses.Rd | 2 tests/testthat/test-enrichment.R | 9 tests/testthat/test-search-and-enrichment-wrapper.R | 146 +++-- 13 files changed, 497 insertions(+), 618 deletions(-)
Title: Methods for Optimizing Scales of Effect
Description: A tool for optimizing scales of effect when modeling ecological processes in space. Specifically, the scale parameter of a distance-weighted kernel distribution is identified for all environmental layers included in the model. Includes functions to assist in model selection, model evaluation, efficient transformation of raster surfaces using fast Fourier transformation, and projecting models. For more details see Peterman (2026) <doi:10.1007/s10980-025-02267-x>.
Author: Bill Peterman [aut, cre]
Maintainer: Bill Peterman <Peterman.73@osu.edu>
Diff between multiScaleR versions 0.6.13 dated 2026-04-18 and 0.7.0 dated 2026-07-01
DESCRIPTION | 12 MD5 | 151 +- NAMESPACE | 8 NEWS | 371 +++++ R/RcppExports.R | 16 R/aic_tab.R | 330 +++-- R/diagnostics.R | 64 R/estimate_multiscale_ram.R |only R/kernel_bins.R |only R/kernel_dist.R | 134 +- R/kernel_prep.R | 327 ++++- R/kernel_scale.raster.R | 251 +++ R/kernel_scale_fn.R | 721 ++++++++--- R/landscape_metrics.R |only R/marginal_effects.R | 198 ++- R/multiScale_optim.R | 688 +++++++++- R/parallel_helpers.R | 309 ++-- R/plot_kernel.R | 58 R/plot_method.R | 31 R/print_methods.R | 76 + R/profile_sigma.R | 164 ++ R/scale_type.R | 69 - R/scale_vars.R |only R/sim_dat.R | 101 + R/sim_dat_unmarked.R | 179 +- R/sim_rast.R | 76 - R/surface_metrics.R |only R/validation_helpers.R | 87 + README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/landscape_metric_covariates.R |only inst/doc/landscape_metric_covariates.Rmd |only inst/doc/landscape_metric_covariates.html |only inst/doc/multiScaleR_Guide.R | 474 +++---- inst/doc/multiScaleR_Guide.Rmd | 370 +++-- inst/doc/multiScaleR_Guide.html | 1620 +++++++++++-------------- inst/doc/quickstart.R | 50 inst/doc/quickstart.Rmd | 163 +- inst/doc/quickstart.html | 265 ++-- inst/doc/spatial_projection_clamping.R | 8 inst/doc/spatial_projection_clamping.Rmd | 20 inst/doc/spatial_projection_clamping.html | 162 +- inst/doc/surface_metric_covariates.R |only inst/doc/surface_metric_covariates.Rmd |only inst/doc/surface_metric_covariates.html |only inst/extdata/opt_umf_p.rds |only inst/extdata/vignette_cache.rds |only man/aic_tab.Rd | 215 +-- man/bic_tab.Rd | 36 man/diagnostics.Rd | 65 - man/estimate_multiscale_ram.Rd |only man/kernel_dist.Rd | 55 man/kernel_prep.Rd | 250 ++- man/kernel_scale.raster.Rd | 164 +- man/kernel_scale_fn.Rd | 8 man/msr_vars.Rd |only man/multiScaleR-package.Rd | 5 man/multiScale_optim.Rd | 238 +++ man/plot.multiScaleR.Rd | 33 man/plot_kernel.Rd | 64 man/plot_marginal_effects.Rd | 150 +- man/profile_sigma.Rd | 56 man/sim_dat.Rd | 112 + man/sim_dat_unmarked.Rd | 156 +- man/sim_rast.Rd | 84 - src/RcppExports.cpp | 66 + src/init.c | 8 src/landscape_metrics_cpp.cpp |only src/surface_metrics_cpp.cpp |only tests/testthat/test-coverage-expansion.R | 4 tests/testthat/test-estimate-multiscale-ram.R |only tests/testthat/test-internals-and-helpers.R | 4 tests/testthat/test-kernel-bins.R |only tests/testthat/test-landscape-metrics.R |only tests/testthat/test-optimization-workflow.R | 883 ++++++++++--- tests/testthat/test-raster-and-plotting.R | 391 ++++-- tests/testthat/test-simulation-and-selection.R | 67 + tests/testthat/test-surface-metrics.R |only tools |only vignettes/landscape_metric_covariates.Rmd |only vignettes/multiScaleR_Guide.Rmd | 370 +++-- vignettes/quickstart.Rmd | 163 +- vignettes/spatial_projection_clamping.Rmd | 20 vignettes/surface_metric_covariates.Rmd |only 85 files changed, 7699 insertions(+), 3523 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene set collections. It stores gene set membership, names, gene identifiers, species, versions, and source metadata, with utilities for reading, writing, validating, and converting gene set data for enrichment analysis and related workflows.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.1.0 dated 2023-03-06 and 0.2.0 dated 2026-07-01
DESCRIPTION | 23 MD5 | 46 NAMESPACE | 52 NEWS.md | 13 R/00-AllClasses.R | 101 - R/GMT.R | 139 - R/IO.R | 153 - R/gson-package.R |only R/gson.R | 77 R/gsonList.R | 20 R/methods.R |only R/print.R | 80 R/utilities.r |only R/validate.R |only README.md |only inst/extdata/wikipathways-20220310-gmt-Homo_sapiens.gmt | 1448 ++++++++-------- man/GSON-class.Rd | 80 man/IO.Rd | 58 man/as.data.frame.GSON.Rd |only man/extract.GSON.Rd |only man/gson-package.Rd |only man/gson.Rd | 110 - man/gsonList.Rd | 34 man/read-gmt.Rd | 59 man/show-methods.Rd | 42 man/validate_gson.Rd |only tests |only 27 files changed, 1334 insertions(+), 1201 deletions(-)
Title: A Fast Algorithm for Kernel Quantile Regression
Description: Implements fast algorithms for kernel quantile regression and
related models, including non-crossing kernel quantile regression and
regularized linear quantile regression. The methods are described in
Tang, Gu and Wang (2026) <doi:10.1080/10618600.2025.2541004>.
Author: Qian Tang [aut, cre],
Yuwen Gu [aut],
Boxiang Wang [aut]
Maintainer: Qian Tang <qian-tang@uiowa.edu>
Diff between fastkqr versions 1.0.0 dated 2024-05-13 and 1.0.1 dated 2026-07-01
fastkqr-1.0.0/fastkqr/R/utilities.R |only fastkqr-1.0.1/fastkqr/DESCRIPTION | 27 +-- fastkqr-1.0.1/fastkqr/MD5 | 63 ++++--- fastkqr-1.0.1/fastkqr/NAMESPACE | 11 - fastkqr-1.0.1/fastkqr/NEWS.md |only fastkqr-1.0.1/fastkqr/R/cv.kqr.R | 103 ++++++++++-- fastkqr-1.0.1/fastkqr/R/cv.nckqr.R | 96 ++++++++--- fastkqr-1.0.1/fastkqr/R/cv.qr.R |only fastkqr-1.0.1/fastkqr/R/helpers.R |only fastkqr-1.0.1/fastkqr/R/kqr-methods.R | 79 +++++---- fastkqr-1.0.1/fastkqr/R/kqr.R | 75 ++++++--- fastkqr-1.0.1/fastkqr/R/nckqr-methods.R | 96 ++++++----- fastkqr-1.0.1/fastkqr/R/nckqr.R | 98 ++++++++--- fastkqr-1.0.1/fastkqr/R/qr-methods.R |only fastkqr-1.0.1/fastkqr/R/qr.R |only fastkqr-1.0.1/fastkqr/build/vignette.rds |binary fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.R | 61 +++++-- fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.Rmd | 141 ++++++++--------- fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.html | 193 +++++++++-------------- fastkqr-1.0.1/fastkqr/man/coef.cv.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/coef.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/coef.kqr.Rd | 31 +-- fastkqr-1.0.1/fastkqr/man/coef.nckqr.Rd | 35 ++-- fastkqr-1.0.1/fastkqr/man/cv.kqr.Rd | 47 ++++- fastkqr-1.0.1/fastkqr/man/cv.nckqr.Rd | 38 +++- fastkqr-1.0.1/fastkqr/man/cv.qr.Rd |only fastkqr-1.0.1/fastkqr/man/kqr.Rd | 22 +- fastkqr-1.0.1/fastkqr/man/nckqr.Rd | 27 +-- fastkqr-1.0.1/fastkqr/man/predict.cv.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/predict.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/predict.kqr.Rd | 15 - fastkqr-1.0.1/fastkqr/man/predict.nckqr.Rd | 21 +- fastkqr-1.0.1/fastkqr/man/qr.Rd |only fastkqr-1.0.1/fastkqr/src/fast_kqr.f90 | 34 ++-- fastkqr-1.0.1/fastkqr/src/fast_nckqr.f90 | 22 ++ fastkqr-1.0.1/fastkqr/src/fast_qr.f90 |only fastkqr-1.0.1/fastkqr/src/init.c | 40 +++- fastkqr-1.0.1/fastkqr/src/utilities.f90 | 198 +++++++++++++++++++++++- fastkqr-1.0.1/fastkqr/vignettes/fastkqr.Rmd | 141 ++++++++--------- 39 files changed, 1094 insertions(+), 620 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.1.5 dated 2026-06-16 and 0.2.0 dated 2026-07-01
enrichit-0.1.5/enrichit/build/vignette.rds |only enrichit-0.1.5/enrichit/inst |only enrichit-0.1.5/enrichit/vignettes |only enrichit-0.2.0/enrichit/DESCRIPTION | 31 ++- enrichit-0.2.0/enrichit/MD5 | 78 +++++--- enrichit-0.2.0/enrichit/NAMESPACE | 27 ++ enrichit-0.2.0/enrichit/NEWS.md | 57 ++++- enrichit-0.2.0/enrichit/R/00-AllClasses.R | 100 +++++++++- enrichit-0.2.0/enrichit/R/AllGenerics.R | 4 enrichit-0.2.0/enrichit/R/RcppExports.R | 13 + enrichit-0.2.0/enrichit/R/gsea.R | 51 +++++ enrichit-0.2.0/enrichit/R/mnsea.R |only enrichit-0.2.0/enrichit/R/mnsea_contribution.R |only enrichit-0.2.0/enrichit/R/mnsea_subnetwork.R |only enrichit-0.2.0/enrichit/R/multi_omics.R |only enrichit-0.2.0/enrichit/R/nsea.R |only enrichit-0.2.0/enrichit/R/omics_contribution.R |only enrichit-0.2.0/enrichit/R/ora.R | 49 ++++- enrichit-0.2.0/enrichit/R/ora_gson.R | 16 + enrichit-0.2.0/enrichit/R/print.R | 86 ++++++++ enrichit-0.2.0/enrichit/README.md | 126 +++++++----- enrichit-0.2.0/enrichit/man/aggregate_enrichment.Rd |only enrichit-0.2.0/enrichit/man/aggregate_omics.Rd |only enrichit-0.2.0/enrichit/man/classify_omics_pattern.Rd |only enrichit-0.2.0/enrichit/man/collapse_multilayer_scores.Rd |only enrichit-0.2.0/enrichit/man/enrichit-package.Rd | 9 enrichit-0.2.0/enrichit/man/extract_mnsea_subnetwork.Rd |only enrichit-0.2.0/enrichit/man/geneID.Rd | 2 enrichit-0.2.0/enrichit/man/geneInCategory.Rd | 2 enrichit-0.2.0/enrichit/man/get_mnsea_contribution.Rd |only enrichit-0.2.0/enrichit/man/get_omics_contribution.Rd |only enrichit-0.2.0/enrichit/man/gsea.Rd | 3 enrichit-0.2.0/enrichit/man/gsea_gson.Rd | 3 enrichit-0.2.0/enrichit/man/harmonize_ids.Rd |only enrichit-0.2.0/enrichit/man/mnsea.Rd |only enrichit-0.2.0/enrichit/man/mnseaResult-class.Rd |only enrichit-0.2.0/enrichit/man/mnsea_gson.Rd |only enrichit-0.2.0/enrichit/man/nsea.Rd |only enrichit-0.2.0/enrichit/man/nseaResult-class.Rd |only enrichit-0.2.0/enrichit/man/nsea_gson.Rd |only enrichit-0.2.0/enrichit/man/ora.Rd | 4 enrichit-0.2.0/enrichit/man/ora_gson.Rd | 3 enrichit-0.2.0/enrichit/man/prepare_multilayer_network.Rd |only enrichit-0.2.0/enrichit/man/prepare_network.Rd |only enrichit-0.2.0/enrichit/man/propagate_multilayer.Rd |only enrichit-0.2.0/enrichit/man/select_features_for_ora.Rd |only enrichit-0.2.0/enrichit/man/show-methods.Rd | 14 + enrichit-0.2.0/enrichit/src/RcppExports.cpp | 17 + enrichit-0.2.0/enrichit/src/nsea.cpp |only enrichit-0.2.0/enrichit/tests/testthat/test-accessors.R |only enrichit-0.2.0/enrichit/tests/testthat/test-gsea.R | 136 ++++++++++++++ enrichit-0.2.0/enrichit/tests/testthat/test-mnsea.R |only enrichit-0.2.0/enrichit/tests/testthat/test-multi-omics.R |only enrichit-0.2.0/enrichit/tests/testthat/test-nsea.R |only enrichit-0.2.0/enrichit/tests/testthat/test-ora.R | 64 ++++++ 55 files changed, 780 insertions(+), 115 deletions(-)
Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList()
and caretStack(). caretList() is a convenience function for fitting multiple
caret::train() models to the same dataset. caretStack() will make linear or
non-linear combinations of these models, using a caret::train() model as a
meta-model.
Author: Zachary A. Deane-Mayer [aut, cre, cph],
Jared E. Knowles [ctb],
Anton Lopez [ctb]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>
Diff between caretEnsemble versions 4.0.1 dated 2024-09-12 and 4.0.2 dated 2026-07-01
DESCRIPTION | 14 - MD5 | 55 ++++--- NAMESPACE | 4 NEWS.md | 99 ++++++++----- R/caretList.R | 58 +++++-- R/caretPredict.R | 37 ++-- R/caretStack.R | 87 ++++++++++- R/plot_variable_importance.R |only build/vignette.rds |binary inst/data-raw/test-all_models.R | 5 inst/doc/Version-4.0-New-Features.html | 97 ++++++------- inst/doc/caretEnsemble-intro.html | 11 - man/add_cross_group_stats.Rd |only man/caretEnsemble.Rd | 7 man/caretList.Rd | 7 man/caretModelSpec.Rd | 2 man/caretPredict.Rd | 10 + man/caretStack.Rd | 8 + man/caretTrain.Rd | 10 + man/check_original_features.Rd |only man/extractBestPreds.Rd | 4 man/figures/README-greedy-stack-6-plot-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/plot_group.Rd |only man/plot_variable_importance.Rd |only man/predict.caretList.Rd | 11 + man/predict.caretStack.Rd | 3 man/prepare_importance.Rd |only man/varImp.caretStack.Rd | 2 tests/testthat/test-caretList.R | 4 tests/testthat/test-caretStack.R | 186 +++++++++++++++++++++++++ tests/testthat/test-plot_variable_importance.R |only 32 files changed, 551 insertions(+), 170 deletions(-)
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.2.1 dated 2025-12-22 and 1.3.0 dated 2026-07-01
DESCRIPTION | 6 MD5 | 50 +-- R/RcppExports.R | 27 + README.md | 176 ++++++++---- inst/include/jmotif.h | 89 +++++- man/find_discords_brute_force.Rd | 9 man/find_discords_hotsax.Rd | 7 man/find_discords_rra.Rd | 10 src/RcppExports.cpp | 28 + src/discord.cpp | 52 ++- src/distance.cpp | 21 + src/hot-sax.cpp | 60 ++-- src/paa.cpp | 8 src/repair.cpp | 20 - src/repair_priority_queue.cpp | 433 ++++++------------------------ src/rra.cpp | 237 ++++++++++++---- src/sax.cpp | 6 src/visit_registry.cpp | 18 + src/znorm.cpp | 6 tests/testthat/test_SAX_simple.R | 10 tests/testthat/test_SAX_strategies.R | 13 tests/testthat/test_SAX_via_window.R | 5 tests/testthat/test_discord_brute_force.R | 26 - tests/testthat/test_discord_hot_sax.R | 13 tests/testthat/test_discord_rra.R | 9 tests/testthat/test_znorm.R | 18 - 26 files changed, 762 insertions(+), 595 deletions(-)
Title: High-Dimensional Factor-Analytic Representation Modeling and
Metrics
Description: The goal of 'HAMMER' is to provide factor analytic representation
learning and associated determinacy metrics for very-high-dimensional data.
It projects high-dimensional data onto low-dimensional generative latent
sources and assesses the uncertainty in the projection. The projection is
distribution-free, scale-equivariant, and efficient. For details, see
Peeters (2026) <doi:10.48550/arXiv.2606.28854>.
Author: Carel F.W. Peeters [aut, cre, cph]
Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
Diff between HAMMER versions 1.0 dated 2026-06-08 and 1.1 dated 2026-07-01
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- NEWS.md | 10 ++++++++++ R/HAMMER-package.R | 8 ++++++++ R/HAMMER.R | 46 ++++++++++++++++++++++++++++++++++++---------- build |only man/HAMMER-package.Rd | 10 ++++++++++ man/HAMMER.determinacy.Rd | 6 ++++-- man/HAMMER.dimension.Rd | 15 ++++++++++++--- man/HAMMER.estimate.Rd | 6 ++++-- man/HAMMER.score.Rd | 6 ++++-- 11 files changed, 104 insertions(+), 33 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including
those where counts or mortality rates of the reference population are
used. Currently supported: excess hazard models (Dickman, Sloggett,
Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean
survival times, relative/net survival (in particular the Ederer II
(Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and
Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and
standardized incidence and mortality ratios, all of which can be
easily adjusted for by covariates such as age. Fast splitting and
aggregation of 'Lexis' objects (from package 'Epi') and other
computations achieved using 'data.table'.
Author: Joonas Miettinen [cre, aut] ,
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.4.14 dated 2026-02-12 and 0.5.0 dated 2026-07-01
popEpi-0.4.14/popEpi/man/Lexis_fpa.Rd |only popEpi-0.4.14/popEpi/tests/testthat/test_prevtab.R |only popEpi-0.4.14/popEpi/tests/testthat/test_splitting_randomly_on_fixed_data.R |only popEpi-0.4.14/popEpi/tests/testthat/test_splitting_randomly_on_random_data.R |only popEpi-0.5.0/popEpi/DESCRIPTION | 28 popEpi-0.5.0/popEpi/LICENSE | 2 popEpi-0.5.0/popEpi/MD5 | 261 +- popEpi-0.5.0/popEpi/NAMESPACE | 7 popEpi-0.5.0/popEpi/NEWS.md | 34 popEpi-0.5.0/popEpi/R/Lexis_funs.R |only popEpi-0.5.0/popEpi/R/S3_definitions.R | 815 ++++-- popEpi-0.5.0/popEpi/R/Surv.R | 66 popEpi-0.5.0/popEpi/R/aggregating.R | 321 +- popEpi-0.5.0/popEpi/R/data_document.R | 16 popEpi-0.5.0/popEpi/R/direct_adjusting.R | 12 popEpi-0.5.0/popEpi/R/evaluation.R | 436 ++- popEpi-0.5.0/popEpi/R/flexyargs.R | 17 popEpi-0.5.0/popEpi/R/fractional_years.R | 30 popEpi-0.5.0/popEpi/R/incidence_rates.R | 244 + popEpi-0.5.0/popEpi/R/incidence_rates_utils.R | 86 popEpi-0.5.0/popEpi/R/lexpand.R | 620 +++- popEpi-0.5.0/popEpi/R/long_df_and_array.R | 76 popEpi-0.5.0/popEpi/R/ltable.R | 84 popEpi-0.5.0/popEpi/R/mean_survival.R | 417 ++- popEpi-0.5.0/popEpi/R/popEpi-package.R | 9 popEpi-0.5.0/popEpi/R/pophaz.R | 12 popEpi-0.5.0/popEpi/R/prevalence.R | 142 - popEpi-0.5.0/popEpi/R/relative_poisson.R | 365 +- popEpi-0.5.0/popEpi/R/relative_poisson_net_survival.R | 67 popEpi-0.5.0/popEpi/R/sir.R | 1273 ++++++---- popEpi-0.5.0/popEpi/R/sir_utils.R | 75 popEpi-0.5.0/popEpi/R/splitLexisDT.R | 134 - popEpi-0.5.0/popEpi/R/splitMulti.R | 125 popEpi-0.5.0/popEpi/R/splitting_utility_functions.R | 1019 ++++---- popEpi-0.5.0/popEpi/R/startup_message.R | 49 popEpi-0.5.0/popEpi/R/survival_aggregated.R | 732 +++-- popEpi-0.5.0/popEpi/R/survival_lexis.R | 346 +- popEpi-0.5.0/popEpi/R/survival_utility_functions.R | 606 +++- popEpi-0.5.0/popEpi/R/sysdata.rda |only popEpi-0.5.0/popEpi/R/utility_functions.R | 814 +++--- popEpi-0.5.0/popEpi/R/weighted_table.R | 414 ++- popEpi-0.5.0/popEpi/R/wip_lexis_merge.R |only popEpi-0.5.0/popEpi/R/wip_lexis_split_merge_aggregate.R |only popEpi-0.5.0/popEpi/R/wip_lexis_utils.R |only popEpi-0.5.0/popEpi/R/wip_prev_lexis.R |only popEpi-0.5.0/popEpi/R/wip_surv_args.R |only popEpi-0.5.0/popEpi/R/wip_surv_estimate.R |only popEpi-0.5.0/popEpi/R/wip_surv_individual_weights.R |only popEpi-0.5.0/popEpi/R/wip_surv_lexis.R |only popEpi-0.5.0/popEpi/R/wip_surv_utils.R |only popEpi-0.5.0/popEpi/R/wip_utils.R |only popEpi-0.5.0/popEpi/R/wip_utils_cut.R |only popEpi-0.5.0/popEpi/R/wip_utils_dataset.R |only popEpi-0.5.0/popEpi/R/wip_utils_dt.R |only popEpi-0.5.0/popEpi/R/wip_utils_regex.R |only popEpi-0.5.0/popEpi/R/wip_utils_unit_test.R |only popEpi-0.5.0/popEpi/README.md | 69 popEpi-0.5.0/popEpi/build/partial.rdb |binary popEpi-0.5.0/popEpi/build/vignette.rds |binary popEpi-0.5.0/popEpi/inst/WORDLIST | 6 popEpi-0.5.0/popEpi/inst/doc/sir.R | 7 popEpi-0.5.0/popEpi/inst/doc/sir.Rmd | 8 popEpi-0.5.0/popEpi/inst/doc/sir.html | 6 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.R | 7 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.Rmd | 8 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.html | 6 popEpi-0.5.0/popEpi/man/ICSS.Rd | 9 popEpi-0.5.0/popEpi/man/RPL.Rd | 10 popEpi-0.5.0/popEpi/man/Surv.Rd | 74 popEpi-0.5.0/popEpi/man/adjust.Rd | 5 popEpi-0.5.0/popEpi/man/aggre.Rd | 15 popEpi-0.5.0/popEpi/man/array_df_ratetable_utils.Rd | 5 popEpi-0.5.0/popEpi/man/as.Date.yrs.Rd | 5 popEpi-0.5.0/popEpi/man/as.aggre.Rd | 15 popEpi-0.5.0/popEpi/man/cast_simple.Rd | 5 popEpi-0.5.0/popEpi/man/cut_bound.Rd | 5 popEpi-0.5.0/popEpi/man/direct_standardization.Rd | 4 popEpi-0.5.0/popEpi/man/fac2num.Rd | 5 popEpi-0.5.0/popEpi/man/flexible_argument.Rd | 7 popEpi-0.5.0/popEpi/man/get.yrs.Rd | 5 popEpi-0.5.0/popEpi/man/is_leap_year.Rd | 5 popEpi-0.5.0/popEpi/man/lexis_funs.Rd |only popEpi-0.5.0/popEpi/man/lexpand.Rd | 23 popEpi-0.5.0/popEpi/man/lines.sirspline.Rd | 12 popEpi-0.5.0/popEpi/man/lines.survmean.Rd | 8 popEpi-0.5.0/popEpi/man/lines.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/ltable.Rd | 5 popEpi-0.5.0/popEpi/man/meanpop_fi.Rd | 2 popEpi-0.5.0/popEpi/man/plot.sir.Rd | 5 popEpi-0.5.0/popEpi/man/plot.sirspline.Rd | 12 popEpi-0.5.0/popEpi/man/plot.survmean.Rd | 8 popEpi-0.5.0/popEpi/man/plot.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/poisson.ci.Rd | 5 popEpi-0.5.0/popEpi/man/popEpi-package.Rd | 3 popEpi-0.5.0/popEpi/man/popmort.Rd | 2 popEpi-0.5.0/popEpi/man/print.survtab.Rd | 14 popEpi-0.5.0/popEpi/man/rate.Rd | 27 popEpi-0.5.0/popEpi/man/rate_ratio.Rd | 9 popEpi-0.5.0/popEpi/man/relpois.Rd | 29 popEpi-0.5.0/popEpi/man/relpois_ag.Rd | 29 popEpi-0.5.0/popEpi/man/robust_values.Rd | 5 popEpi-0.5.0/popEpi/man/rpcurve.Rd | 11 popEpi-0.5.0/popEpi/man/setaggre.Rd | 15 popEpi-0.5.0/popEpi/man/sibr.Rd | 4 popEpi-0.5.0/popEpi/man/sir.Rd | 35 popEpi-0.5.0/popEpi/man/sir_exp.Rd | 24 popEpi-0.5.0/popEpi/man/sir_ratio.Rd | 17 popEpi-0.5.0/popEpi/man/sire.Rd | 4 popEpi-0.5.0/popEpi/man/sirspline.Rd | 36 popEpi-0.5.0/popEpi/man/splitLexisDT.Rd | 21 popEpi-0.5.0/popEpi/man/splitMulti.Rd | 28 popEpi-0.5.0/popEpi/man/stdpop101.Rd | 4 popEpi-0.5.0/popEpi/man/stdpop18.Rd | 4 popEpi-0.5.0/popEpi/man/summary.aggre.Rd | 10 popEpi-0.5.0/popEpi/man/summary.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/survmean.Rd | 33 popEpi-0.5.0/popEpi/man/survtab.Rd | 39 popEpi-0.5.0/popEpi/man/survtab_ag.Rd | 39 popEpi-0.5.0/popEpi/tests/testthat.R | 12 popEpi-0.5.0/popEpi/tests/testthat/test_aggre.R | 239 + popEpi-0.5.0/popEpi/tests/testthat/test_call_with_arg_list__.R |only popEpi-0.5.0/popEpi/tests/testthat/test_epi.R | 47 popEpi-0.5.0/popEpi/tests/testthat/test_expo.R | 79 popEpi-0.5.0/popEpi/tests/testthat/test_infer_cut_args.R |only popEpi-0.5.0/popEpi/tests/testthat/test_lexis_crop.R |only popEpi-0.5.0/popEpi/tests/testthat/test_lexpand.R | 648 +++-- popEpi-0.5.0/popEpi/tests/testthat/test_rate.R | 902 +++++-- popEpi-0.5.0/popEpi/tests/testthat/test_relpois_mean_curve.R | 63 popEpi-0.5.0/popEpi/tests/testthat/test_sir.R | 820 ++++-- popEpi-0.5.0/popEpi/tests/testthat/test_splitLexisDT.R | 155 - 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Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.10 dated 2026-05-23 and 1.3.11 dated 2026-07-01
mets-1.3.10/mets/inst/doc/basic-dutils.R |only mets-1.3.10/mets/inst/doc/binomial-family.R |only mets-1.3.10/mets/inst/doc/binomial-twin.R |only mets-1.3.10/mets/inst/doc/binreg-TRS.R |only mets-1.3.10/mets/inst/doc/binreg-ate.R |only mets-1.3.10/mets/inst/doc/binreg.R |only mets-1.3.10/mets/inst/doc/cifreg.R |only mets-1.3.10/mets/inst/doc/cooking-survival-data.R |only mets-1.3.10/mets/inst/doc/cumulative-cost.R |only mets-1.3.10/mets/inst/doc/glm-utility.R |only mets-1.3.10/mets/inst/doc/haplo-discrete-ttp.R |only mets-1.3.10/mets/inst/doc/interval-discrete-survival.R |only mets-1.3.10/mets/inst/doc/marginal-cox.R |only mets-1.3.10/mets/inst/doc/mediation-survival.R |only mets-1.3.10/mets/inst/doc/phreg_rct.R |only mets-1.3.10/mets/inst/doc/quantitative-twin.R |only mets-1.3.10/mets/inst/doc/recurrent-events.R |only mets-1.3.10/mets/inst/doc/rmst-ate.R |only mets-1.3.10/mets/inst/doc/survival-ate.R |only mets-1.3.10/mets/inst/doc/time-to-event-family-studies-arev.R |only mets-1.3.10/mets/inst/doc/twostage-survival.R |only mets-1.3.10/mets/inst/doc/while-alive.R |only mets-1.3.10/mets/man/glm_IPTW.Rd |only mets-1.3.10/mets/vignettes/competing.org |only mets-1.3.10/mets/vignettes/data |only mets-1.3.10/mets/vignettes/quantitative-twin.org |only mets-1.3.11/mets/DESCRIPTION | 8 mets-1.3.11/mets/MD5 | 230 +- mets-1.3.11/mets/NAMESPACE | 16 mets-1.3.11/mets/NEWS.md | 11 mets-1.3.11/mets/R/binomial.regression.R | 495 +++++ mets-1.3.11/mets/R/brier_binreg.R |only mets-1.3.11/mets/R/clusterindex-reshape.R | 64 mets-1.3.11/mets/R/glm-utils.R | 148 + mets-1.3.11/mets/R/phreg.R | 42 mets-1.3.11/mets/R/procformula.R | 2 mets-1.3.11/mets/R/recreg.R | 14 mets-1.3.11/mets/R/recurrent.marginal.R | 5 mets-1.3.11/mets/R/score-mean-tests.R | 21 mets-1.3.11/mets/R/utils.R | 8 mets-1.3.11/mets/build/vignette.rds |binary mets-1.3.11/mets/inst/doc/basic-dutils.Rmd | 551 +++++- mets-1.3.11/mets/inst/doc/basic-dutils.html | 27 mets-1.3.11/mets/inst/doc/binomial-family.Rmd | 436 ++++- mets-1.3.11/mets/inst/doc/binomial-family.html | 26 mets-1.3.11/mets/inst/doc/binomial-twin.Rmd | 405 ++++ mets-1.3.11/mets/inst/doc/binomial-twin.html | 25 mets-1.3.11/mets/inst/doc/binreg-TRS.Rmd | 434 ++++- mets-1.3.11/mets/inst/doc/binreg-TRS.html | 36 mets-1.3.11/mets/inst/doc/binreg-ate.Rmd | 271 +++ mets-1.3.11/mets/inst/doc/binreg-ate.html | 25 mets-1.3.11/mets/inst/doc/binreg.Rmd | 134 + mets-1.3.11/mets/inst/doc/binreg.html | 26 mets-1.3.11/mets/inst/doc/cifreg.Rmd | 202 ++ mets-1.3.11/mets/inst/doc/cifreg.html | 32 mets-1.3.11/mets/inst/doc/cooking-survival-data.Rmd | 392 ++++ mets-1.3.11/mets/inst/doc/cooking-survival-data.html | 70 mets-1.3.11/mets/inst/doc/cumulative-cost.Rmd | 245 ++ mets-1.3.11/mets/inst/doc/cumulative-cost.html | 175 +- mets-1.3.11/mets/inst/doc/glm-utility.Rmd | 100 + mets-1.3.11/mets/inst/doc/glm-utility.html | 28 mets-1.3.11/mets/inst/doc/haplo-discrete-ttp.Rmd | 171 +- mets-1.3.11/mets/inst/doc/haplo-discrete-ttp.html | 26 mets-1.3.11/mets/inst/doc/interval-discrete-survival.Rmd | 180 +- mets-1.3.11/mets/inst/doc/interval-discrete-survival.html | 28 mets-1.3.11/mets/inst/doc/marginal-cox.Rmd | 135 + mets-1.3.11/mets/inst/doc/marginal-cox.html | 32 mets-1.3.11/mets/inst/doc/mediation-survival.Rmd | 325 +++ mets-1.3.11/mets/inst/doc/mediation-survival.html | 161 - 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Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data. Streams vector operations (spatial transforms,
point-in-polygon and nearest-feature joins including a two-sided
grid-partitioned join, select-by-location, clip, erase, dissolve,
'rasterization', 'polygonization', and contouring) through 'sf', and runs
raster operations (zonal statistics, focal windows, terrain derivatives,
resample or 'reproject' warp, polygon masking, map algebra, and 'mosaicking')
in native C or over the tiled '.vec' format, one batch or tile at [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.9.1 dated 2026-06-29 and 0.9.8 dated 2026-07-01
DESCRIPTION | 18 MD5 | 183 +++-- NAMESPACE | 32 + NEWS.md | 246 +++++++ R/embedding.R |only R/expr.R | 115 +++ R/geom_expr.R |only R/joins.R | 85 ++ R/network.R |only R/resample.R |only R/spatial.R | 954 ++++++++++++++++++++++++++++-- R/spatial_topology.R |only R/windows.R | 32 - README.md | 53 + build/vignette.rds |binary inst/doc/coverage-topology.R |only inst/doc/coverage-topology.Rmd |only inst/doc/coverage-topology.html |only inst/doc/engine.html | 4 inst/doc/formats.html | 54 - inst/doc/geometry-expressions.R |only inst/doc/geometry-expressions.Rmd |only inst/doc/geometry-expressions.html |only inst/doc/indexing.Rmd | 13 inst/doc/indexing.html | 30 inst/doc/joins.Rmd | 4 inst/doc/joins.html | 10 inst/doc/large-data.Rmd | 10 inst/doc/large-data.html | 23 inst/doc/networks.R |only inst/doc/networks.Rmd |only inst/doc/networks.html |only inst/doc/offload.Rmd | 12 inst/doc/offload.html | 40 - inst/doc/quickstart.R | 13 inst/doc/quickstart.Rmd | 14 inst/doc/quickstart.html | 33 - inst/doc/schema.Rmd | 8 inst/doc/schema.html | 14 inst/doc/sdm.html | 4 inst/doc/spatial.R | 14 inst/doc/spatial.Rmd | 26 inst/doc/spatial.html | 52 - inst/doc/streaming-spatial.R | 41 + inst/doc/streaming-spatial.Rmd | 90 ++ inst/doc/streaming-spatial.html | 423 ++++++++----- inst/doc/string-ops.Rmd | 2 inst/doc/string-ops.html | 17 man/as_embedding.Rd |only man/embedding_distance.Rd |only man/floor_time.Rd |only man/geom_expressions.Rd |only man/interval_join.Rd |only man/resample.Rd |only man/rolling.Rd |only man/spatial_centerline.Rd |only man/spatial_construct.Rd |only man/spatial_eliminate.Rd |only man/spatial_explode.Rd |only man/spatial_knn.Rd |only man/spatial_line_merge.Rd |only man/spatial_locate.Rd |only man/spatial_network.Rd |only man/spatial_overlay.Rd | 46 + man/spatial_polygonize.Rd |only man/spatial_route.Rd |only man/spatial_service_area.Rd |only man/spatial_simplify.Rd |only man/spatial_smooth.Rd |only man/spatial_snap.Rd |only man/spatial_snap_grid.Rd |only man/spatial_split.Rd |only man/spatial_topology.Rd |only src/edt.c | 4 src/expr.c | 7 src/expr.h | 30 src/expr_datetime.c | 78 ++ src/expr_geom.c |only src/expr_vec.c |only src/focal.c | 4 src/fuzzy_join.c | 274 -------- src/fuzzy_join.h | 14 src/init.c | 11 src/interval_join.c |only src/interval_join.h |only src/join_partition.c |only src/join_partition.h |only src/network.c |only src/r_bridge.h | 6 src/r_bridge_core.c | 61 + src/r_bridge_nodes.c | 84 ++ src/vec_distance.h |only src/vec_omp.h | 28 src/vtr_overlay.c | 4 src/vtr_spatial.c | 4 src/warp.c | 4 src/window.c | 151 ++++ src/window.h | 9 tests/testthat/test-embedding.R |only tests/testthat/test-geom-expr.R |only tests/testthat/test-interval-join.R |only tests/testthat/test-network.R |only tests/testthat/test-resample.R |only tests/testthat/test-rolling.R |only tests/testthat/test-spatial-construct.R |only tests/testthat/test-spatial-explode.R |only tests/testthat/test-spatial-knn.R |only tests/testthat/test-spatial-overlay-two.R |only tests/testthat/test-spatial-smooth.R |only tests/testthat/test-spatial-snap.R |only tests/testthat/test-spatial-split.R |only tests/testthat/test-spatial-topology.R |only vignettes/coverage-topology.Rmd |only vignettes/geometry-expressions.Rmd |only vignettes/indexing.Rmd | 13 vignettes/joins.Rmd | 4 vignettes/large-data.Rmd | 10 vignettes/networks.Rmd |only vignettes/offload.Rmd | 12 vignettes/quickstart.Rmd | 14 vignettes/schema.Rmd | 8 vignettes/spatial.Rmd | 26 vignettes/streaming-spatial.Rmd | 90 ++ vignettes/string-ops.Rmd | 2 124 files changed, 2829 insertions(+), 838 deletions(-)
Title: Struct-Like Data Type Checking and Enforcement
Description: Enforcement of field types in lists. A drop-in tool to allow for
dynamic input data that might be questionably parsed or cast to be coerced
into the specific desired format in a reasonably performant manner.
Author: Samuel Sapire [aut, cre, cph],
Sean Barrett [ctb]
Maintainer: Samuel Sapire <sapires@protonmail.com>
Diff between structenforcement versions 0.3.0 dated 2026-06-30 and 0.3.1 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/functions.c | 19 ++++++++++--------- tests/testthat/test-type_check.R | 1 + tests/testthat/test-type_check_each.R | 24 ++++++++++++++++++++++++ 6 files changed, 47 insertions(+), 17 deletions(-)
More information about structenforcement at CRAN
Permanent link
More information about saeHB.Spatial.Beta at CRAN
Permanent link
Title: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Description: Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. Miscellaneous other tools.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.7.1 dated 2025-12-02 and 4.7.2 dated 2026-07-01
doBy-4.7.1/doBy/man/beets.Rd |only doBy-4.7.1/doBy/man/carcass.Rd |only doBy-4.7.1/doBy/man/child_growth.Rd |only doBy-4.7.1/doBy/man/codstom.Rd |only doBy-4.7.1/doBy/man/crickets.Rd |only doBy-4.7.1/doBy/man/crimeRate.Rd |only doBy-4.7.1/doBy/man/crime_rate.Rd |only doBy-4.7.1/doBy/man/cropyield.Rd |only doBy-4.7.1/doBy/man/data-wine.Rd |only doBy-4.7.1/doBy/man/dietox.Rd |only doBy-4.7.1/doBy/man/fatacid.Rd |only doBy-4.7.1/doBy/man/fev.Rd |only doBy-4.7.1/doBy/man/haldCement.Rd |only doBy-4.7.1/doBy/man/income.Rd |only doBy-4.7.1/doBy/man/math_teachers.Rd |only doBy-4.7.1/doBy/man/milkman.Rd |only doBy-4.7.1/doBy/man/nir_milk.Rd |only doBy-4.7.1/doBy/man/potatoes.Rd |only doBy-4.7.1/doBy/man/shoes.Rd |only doBy-4.7.2/doBy/DESCRIPTION | 15 doBy-4.7.2/doBy/MD5 | 104 ++-- doBy-4.7.2/doBy/NAMESPACE | 10 doBy-4.7.2/doBy/NEWS.md | 9 doBy-4.7.2/doBy/R/DATA_doby.R | 46 +- doBy-4.7.2/doBy/R/NAMESPACE_doby.R | 14 doBy-4.7.2/doBy/R/by_lmBy.R | 11 doBy-4.7.2/doBy/R/by_scaleBy.R | 2 doBy-4.7.2/doBy/R/compute_on_forecast.R | 582 ++++++++++++++++++++++---- doBy-4.7.2/doBy/R/data_firstobs_lastobs.R | 3 doBy-4.7.2/doBy/R/doby_utilities.R | 3 doBy-4.7.2/doBy/R/lag_data.R |only doBy-4.7.2/doBy/R/linest_LSmeans.R | 3 doBy-4.7.2/doBy/R/linest_compute.R | 3 doBy-4.7.2/doBy/R/linest_utilities.R | 7 doBy-4.7.2/doBy/R/model_stability.r | 322 +++++--------- doBy-4.7.2/doBy/R/modelling.R | 160 +++---- doBy-4.7.2/doBy/build/vignette.rds |binary doBy-4.7.2/doBy/inst/doc/doby.html | 22 doBy-4.7.2/doBy/inst/doc/pipe_arithmetic.html | 6 doBy-4.7.2/doBy/inst/doc/sectioning_fun.html | 59 +- doBy-4.7.2/doBy/inst/doc/vtools.html | 6 doBy-4.7.2/doBy/man/add_pred.Rd | 18 doBy-4.7.2/doBy/man/add_resid.Rd | 10 doBy-4.7.2/doBy/man/align_coefs.Rd | 33 - doBy-4.7.2/doBy/man/by-lmby.Rd | 7 doBy-4.7.2/doBy/man/cv_glm_fitlist.Rd | 6 doBy-4.7.2/doBy/man/data_beets.Rd |only doBy-4.7.2/doBy/man/data_berkeley_growth.Rd |only doBy-4.7.2/doBy/man/data_carcass.Rd |only doBy-4.7.2/doBy/man/data_codstom.Rd |only doBy-4.7.2/doBy/man/data_crickets.Rd |only doBy-4.7.2/doBy/man/data_crimeRate.Rd |only doBy-4.7.2/doBy/man/data_crime_rate.Rd |only doBy-4.7.2/doBy/man/data_cropyield.Rd |only doBy-4.7.2/doBy/man/data_dietox.Rd |only doBy-4.7.2/doBy/man/data_fatacid.Rd |only doBy-4.7.2/doBy/man/data_fev.Rd |only doBy-4.7.2/doBy/man/data_haldCement.Rd |only doBy-4.7.2/doBy/man/data_income.Rd |only doBy-4.7.2/doBy/man/data_math_teachers.Rd |only doBy-4.7.2/doBy/man/data_milkman.Rd |only doBy-4.7.2/doBy/man/data_nir_milk.Rd |only doBy-4.7.2/doBy/man/data_potatoes.Rd |only doBy-4.7.2/doBy/man/data_shoes.Rd |only doBy-4.7.2/doBy/man/data_wine.Rd |only doBy-4.7.2/doBy/man/generate_data_list.Rd | 26 + doBy-4.7.2/doBy/man/get_formulas.Rd | 4 doBy-4.7.2/doBy/man/is_estimable.Rd | 2 doBy-4.7.2/doBy/man/lag_data.Rd |only doBy-4.7.2/doBy/man/model_stability_glm.Rd | 75 +++ doBy-4.7.2/doBy/man/response.Rd | 6 doBy-4.7.2/doBy/man/set_list_set_matrix.Rd | 4 doBy-4.7.2/doBy/man/transform_forecast.Rd | 74 ++- 73 files changed, 1082 insertions(+), 570 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.general versions 0.6.0 dated 2025-12-03 and 0.7.0 dated 2026-07-01
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teal.modules.general-0.7.0/teal.modules.general/R/tm_a_regression.R | 15 teal.modules.general-0.7.0/teal.modules.general/R/tm_data_table.R | 14 teal.modules.general-0.7.0/teal.modules.general/R/tm_front_page.R | 2 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_association.R | 8 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_bivariate.R | 8 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_distribution.R | 77 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_response.R | 8 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_scatterplot.R | 8 teal.modules.general-0.7.0/teal.modules.general/R/tm_g_scatterplotmatrix.R | 366 +- teal.modules.general-0.7.0/teal.modules.general/R/tm_missing_data.R | 32 teal.modules.general-0.7.0/teal.modules.general/R/tm_outliers.R | 18 teal.modules.general-0.7.0/teal.modules.general/R/tm_rmarkdown.R | 12 teal.modules.general-0.7.0/teal.modules.general/R/tm_t_crosstable.R | 8 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More information about teal.modules.general at CRAN
Permanent link
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available mon [...truncated...]
Author: Michael Hoehle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths] ,
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Sophie Reichert [ctb],
Andrea Riebler [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.25.0 dated 2025-06-25 and 1.26.0 dated 2026-07-01
DESCRIPTION | 20 +-- MD5 | 188 ++++++++++++++++----------------- NAMESPACE | 13 -- NEWS.md | 20 +++ R/AllClass.R | 2 R/addSeason2formula.R | 8 - R/algo_call.R | 2 R/algo_farrington.R | 32 ++--- R/disProg.R | 2 R/epidataCS_methods.R | 2 R/epidataCS_plot.R | 28 ++-- R/farringtonFlexible.R | 91 ++++----------- R/functionTable.R | 15 +- R/hhh4.R | 10 - R/hhh4_W_powerlaw.R | 53 ++++++++- R/hhh4_amplitudeShift.R | 23 ++-- R/hhh4_methods.R | 4 R/hhh4_simulate.R | 11 + R/knox.R | 10 - R/makeControl.R | 4 R/options.R | 2 R/spatial_tools.R | 4 R/sts.R | 28 ++-- R/sts_toLatex.R | 16 -- R/sysdata.rda |binary R/twinstim.R | 16 +- R/twinstim_intensity.R | 9 + R/twinstim_methods.R | 27 +--- R/twinstim_simulation.R | 6 - R/zzz.R | 12 -- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/datalist |only demo/v77i11.R | 1 inst/CITATION | 3 inst/REFERENCES.bib |only inst/doc/glrnb.R | 2 inst/doc/glrnb.Rnw | 6 - inst/doc/glrnb.pdf |binary inst/doc/hhh4.R | 2 inst/doc/hhh4.Rnw | 18 +-- inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.Rnw | 23 ++-- inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.R | 2 inst/doc/monitoringCounts.Rnw | 12 +- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.R | 2 inst/doc/surveillance.Rnw | 6 - inst/doc/surveillance.pdf |binary inst/doc/twinSIR.Rnw | 11 + inst/doc/twinSIR.pdf |binary inst/doc/twinstim.R | 1 inst/doc/twinstim.Rnw | 56 +++++---- inst/doc/twinstim.pdf |binary man/LRCUSUM.runlength.Rd | 2 man/addSeason2formula.Rd | 11 + man/algo.quality.Rd | 4 man/epidata.Rd | 2 man/epidataCS.Rd | 4 man/epidataCS_plot.Rd | 1 man/hagelloch.Rd | 4 man/hhh4.Rd | 8 - man/hhh4_formula.Rd | 4 man/hhh4_methods.Rd | 2 man/hhh4_plot.Rd | 2 man/hhh4_validation.Rd | 2 man/knox.Rd | 3 man/macros/linkSPclass.Rd | 2 man/macros/vignette.Rd |only man/measles.weser.Rd | 2 man/stsplot_time.Rd | 11 + man/surveillance-defunct.Rd | 4 man/surveillance-package.Rd | 100 ++++++++++------- man/surveillance.options.Rd | 2 man/toLatex.sts.Rd | 3 man/twinSIR.Rd | 2 man/twinSIR_intensityplot.Rd | 2 man/twinstim.Rd | 4 man/twinstim_iaf.Rd | 2 man/twinstim_iafplot.Rd | 2 man/twinstim_methods.Rd | 8 - man/twinstim_plot.Rd | 2 tests/testthat/test-hhh4+derivatives.R | 14 ++ tests/testthat/test-toLatex.sts.R | 2 tests/testthat/test-twinstim_misc.R | 12 ++ vignettes/fixjss.sty |only vignettes/glrnb.Rnw | 6 - vignettes/hhh4.Rnw | 18 +-- vignettes/hhh4_spacetime.Rnw | 23 ++-- vignettes/monitoringCounts.Rnw | 12 +- vignettes/monitoringCounts.bib | 9 - vignettes/references.bib | 153 +------------------------- vignettes/surveillance.Rnw | 6 - vignettes/twinSIR.Rnw | 11 + vignettes/twinstim.Rnw | 56 +++++---- 97 files changed, 651 insertions(+), 671 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9.2 dated 2026-05-21 and 1.0.9.3 dated 2026-07-01
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.html | 4 ++-- inst/tinytest/serieOut |binary inst/tinytest/splineEst |binary inst/tinytest/test_detectSerieOut.R | 9 ++++----- inst/tinytest/test_fitSpline.R | 2 +- tests/tinytest.R | 5 ++--- 11 files changed, 29 insertions(+), 27 deletions(-)
Title: Make Interactive 'PRISMA' Flow Diagrams
Description: Systematic reviews should be described in a high degree of
methodological detail. The 'PRISMA' Statement calls for a high level of
reporting detail in systematic reviews and meta-analyses. An integral part
of the methodological description of a review is a flow diagram.
This package produces an interactive flow diagram that conforms to the
'PRISMA2020' preprint. When made interactive, the reader/user can click
on each box and be directed to another website or file online (e.g. a
detailed description of the screening methods, or a list of excluded full
texts), with a mouse-over tool tip that describes the information linked
to in more detail. Interactive versions can be saved as HTML files,
whilst static versions for inclusion in manuscripts can be saved as
HTML, PDF, PNG, SVG, PS or WEBP files.
Author: Neal Haddaway [aut] ,
Luke McGuinness [aut] ,
Chris Pritchard [aut, cre] ,
Brennan Chapman [ctb],
Hossam Hammady [ctb],
Anders Kolstad [ctb] ,
Shreya Dimri [ctb] ,
Matt Lloyd Jones [ctb] ,
John-o Kulas [ctb]
Maintainer: Chris Pritchard <chris@christopherpritchard.co.uk>
Diff between PRISMA2020 versions 1.1.1 dated 2023-02-09 and 1.1.4 dated 2026-07-01
PRISMA2020-1.1.1/PRISMA2020/R/utils.R |only PRISMA2020-1.1.4/PRISMA2020/DESCRIPTION | 39 PRISMA2020-1.1.4/PRISMA2020/LICENSE | 2 PRISMA2020-1.1.4/PRISMA2020/MD5 | 56 PRISMA2020-1.1.4/PRISMA2020/NAMESPACE | 4 PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_add_hyperlink.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_calc_filetype.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_data.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_default_or_csv.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_flowdiagram.R | 1355 +++----------- PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_format.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_gen_tmp_svg.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_get.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_insert_js.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_interactive.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_save.R |only PRISMA2020-1.1.4/PRISMA2020/R/defunct.R |only PRISMA2020-1.1.4/PRISMA2020/R/globals.R | 6 PRISMA2020-1.1.4/PRISMA2020/R/imports.R |only PRISMA2020-1.1.4/PRISMA2020/README.md | 1 PRISMA2020-1.1.4/PRISMA2020/inst/extdata/PRISMA.csv | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_add_hyperlink_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_calc_filetype_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_data.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_default_or_csv_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_flowdiagram.Rd | 16 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_format_number_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_format_reasons_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_gen_tmp_svg_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_get_height_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_get_pos_.Rd | 12 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_insert_js_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_interactive_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_parse_reasons_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_save.Rd | 16 PRISMA2020-1.1.4/PRISMA2020/man/read_PRISMAdata.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/sr_flow_interactive.Rd | 2 37 files changed, 482 insertions(+), 1047 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Brant Deppa [aut] ,
James Curran [aut, cre] ,
Hannah Yun [ctb],
Rachel Fewster [ctb],
Russell Millar [ctb],
Ben Stevenson [ctb],
Andrew Balemi [ctb],
Chris Wild [ctb],
Sophie Jones [ctb],
Dineika Chandra [ctb],
Brendan McArdle [ctb]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.2.2 dated 2026-01-14 and 3.3.0 dated 2026-07-01
DESCRIPTION | 25 MD5 | 320 +++++++---- NAMESPACE | 227 +++++--- NEWS.md |only R/autocor.plot.R | 83 +-- R/boxqq.r | 103 --- R/casestudy.R | 137 +++-- R/ciReg.R | 58 +- R/cooks20x.R | 77 +- R/crosstabs.R | 168 +++--- R/displayPairs.R | 280 +++++----- R/eovcheck.R | 465 +++++++++++------ R/estimateContrasts.R | 95 +-- R/estimateContrasts1.R | 101 ++- R/estimateContrasts2.R | 107 ++- R/freq1way.r | 307 ++++++----- R/getVersion.R | 33 - R/graphics-parameter-helpers.R |only R/interactionPlots.R | 11 R/internal-predict-helper.R |only R/layout20x.R | 49 - R/levene.test.R | 140 ++--- R/listCaseStudies.R | 107 ++- R/modcheck.R | 135 ---- R/model-diagnostic-helpers.R |only R/modelcheck.R | 328 ++++++++++-- R/multipleComp.R | 113 ++-- R/normcheck.R | 613 ++++++++++++++++++---- R/openCaseStudy.R | 127 +++- R/pairs20x.R | 232 +++++++- R/plotting-engine-helpers.R |only R/predict20x.R | 199 ++++--- R/predictCount.R | 132 ++-- R/predictGLM.R | 173 +++--- R/propslsd.new.R | 121 ++-- R/residPlot.R | 132 ++-- R/rowdistr.r | 675 +++++++++++++++--------- R/rr.r | 21 R/s20x-data.R | 576 ++++++++++++--------- R/s20x-package.R | 21 R/skewness.r | 49 - R/stripqq.r | 100 --- R/summary1way.R | 238 +++++--- R/summary2way.R | 920 +++++++++++++++++----------------- R/summaryStats.R | 393 +++++++------- R/trendscatter.R | 243 ++++---- R/tslm.R |only README.md | 137 +++-- data/airpass.df.rda |binary data/nzalc.df.rda |only data/nzarrivals.df.rda |only inst/case_studies/CS10_3.Rmd | 4 inst/case_studies/CS11_3.Rmd | 6 inst/case_studies/CS12_4.Rmd | 4 inst/case_studies/CS14_3.Rmd | 2 inst/case_studies/CS14_4.Rmd | 2 inst/case_studies/CS15_3.Rmd | 2 inst/case_studies/CS15_4.Rmd | 4 inst/case_studies/CS5_2.Rmd | 6 inst/case_studies/CS6_3.Rmd | 2 inst/case_studies/CS6_4.Rmd | 2 inst/case_studies/CS8_3.Rmd | 2 inst/case_studies/CS9_6.Rmd | 2 inst/extdata/Galton3.csv | 396 +++++++------- man/anova.tslm.Rd |only man/apples.df.Rd | 26 man/arousal.df.Rd | 6 man/autocor.plot.Rd |only man/autocorPlot.Rd | 4 man/beer.df.Rd | 4 man/body.df.Rd | 37 - man/books.df.Rd | 10 man/boxqq.Rd | 28 - man/bursary.df.Rd | 4 man/butterfat.df.Rd | 6 man/camplake.df.Rd | 6 man/captureOptionalName.Rd |only man/casestudy.Rd | 16 man/chalk.df.Rd | 6 man/ciReg.Rd | 2 man/computer.df.Rd | 4 man/cooks20x.Rd | 4 man/course.df.Rd | 30 - man/course2way.df.Rd | 6 man/crosstabs.Rd | 17 man/diamonds.df.Rd | 4 man/displayPairs.Rd | 20 man/drawPlot.Rd |only man/eovcheck.Rd | 52 + man/estimateContrasts.Rd | 38 - man/estimateContrasts1.Rd |only man/estimateContrasts2.Rd |only man/extractTslmErrorSpec.Rd |only man/extractTslmFit.Rd |only man/fire.df.Rd | 6 man/formatTslmAnovaTable.Rd |only man/formatTslmResidualTypeLabel.Rd |only man/freq1way.Rd | 14 man/fruitfly.df.Rd | 4 man/getModelResidualFittedData.Rd |only man/getTslmArParameters.Rd |only man/getTslmCoefficientTable.Rd |only man/getTslmDiagnosticData.Rd |only man/getTslmErrorTerms.Rd |only man/getTslmResidualDf.Rd |only man/getTslmTimeValues.Rd |only man/getVersion.Rd | 6 man/house.df.Rd | 4 man/incomes.df.Rd | 5 man/interactionPlots.Rd | 11 man/isTslmErrorTerm.Rd |only man/lakemary.df.Rd | 4 man/layout20x.Rd | 19 man/listCaseStudies.Rd | 6 man/makeTslmModelData.Rd |only man/matchPlottingEngine.Rd |only man/matchTslmResidualType.Rd |only man/mazda.df.Rd | 4 man/mening.df.Rd | 7 man/mergers.df.Rd | 5 man/modcheck.Rd | 68 -- man/modelcheck.Rd | 82 ++- man/mozart.df.Rd | 6 man/multipleComp.Rd | 15 man/nail.df.Rd | 4 man/normcheck.Rd | 122 +++- man/nzalc.df.Rd |only man/nzarrivals.df.Rd |only man/openCaseStudy.Rd | 18 man/oysters.df.Rd | 8 man/pairs20x.Rd | 30 - man/parseTslmFormula.Rd |only man/peru.df.Rd | 10 man/plotTslmResiduals.Rd |only man/plotTslmTimeResiduals.Rd |only man/predict20x.Rd | 47 + man/predictCount.Rd | 36 - man/predictGLM.Rd | 35 - man/prepCrosstabList.Rd |only man/print.s20xModelcheck_ggplot2.Rd |only man/print.s20xNormcheck_ggplot2.Rd |only man/printOutput.Rd |only man/propslsd.new.Rd | 3 man/rain.df.Rd | 6 man/removeTslmErrorTerms.Rd |only man/requirePlottingPackage.Rd |only man/requireSuggestedPackage.Rd |only man/residPlot.Rd | 6 man/resolveCaseStudyDestinationDir.Rd |only man/resolveCaseStudyOutputArgs.Rd |only man/rowdistr.Rd | 16 man/rr.Rd | 2 man/s20x-package.Rd | 18 man/s20x_ggplot2_base_theme.Rd |only man/saveGraphicsParameters.Rd |only man/seeds.df.Rd | 6 man/sentenceCase.Rd |only man/sheep.df.Rd | 9 man/skewness.Rd | 4 man/skulls.df.Rd | 4 man/snapper.df.Rd | 9 man/soyabean.df.Rd | 6 man/stripqq.Rd | 35 - man/summary1way.Rd | 31 - man/summary2way.Rd | 41 - man/summaryStats.Rd | 60 +- man/teach.df.Rd | 6 man/technitron.df.Rd | 16 man/thyroid.df.Rd | 8 man/toothpaste.df.Rd | 4 man/trendscatter.Rd | 7 man/tslm.Rd |only man/zoo.df.Rd | 12 tests |only 174 files changed, 6011 insertions(+), 4209 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-16 1.1.3
2022-08-06 1.1.2
2021-03-31 1.1.1
2021-01-28 1.1
2020-12-07 1.0