Title: Force-Directed Euclidean Embedding of Dissimilarity Data
Description: A robust implementation of Topolow algorithm. It embeds objects into a low-dimensional Euclidean space from a matrix of pairwise dissimilarities, even when the data do not satisfy metric or Euclidean axioms. The package is particularly well-suited for sparse, incomplete, and censored (thresholded) datasets such as antigenic relationships. The core is a physics-inspired, gradient-free optimization framework that models objects as particles in a physical system, where observed dissimilarities define spring rest lengths and unobserved pairs exert repulsive forces. The package also provides functions specific to antigenic mapping to transform cross-reactivity and binding affinity measurements into accurate spatial representations in a phenotype space.
Key features include:
* Robust Embedding from Sparse Data: Effectively creates complete and consistent maps (in optimal dimensions) even with high proportions of missing data (e.g., >95%).
* Physics-Inspired Optimization: Models objects (e [...truncated...]
Author: Omid Arhami [aut, cre, cph]
Maintainer: Omid Arhami <omid.arhami@uga.edu>
Diff between topolow versions 2.0.0 dated 2025-08-19 and 2.0.1 dated 2025-08-30
DESCRIPTION | 6 MD5 | 24 NEWS.md | 227 +++--- README.md | 4 build/vignette.rds |binary inst/WORDLIST | 8 inst/doc/Comprehensive_Evaluation.R |only inst/doc/Comprehensive_Evaluation.Rmd | 621 +++++++++++++++++ inst/doc/Comprehensive_Evaluation.html | 1124 +++++++++++++++++--------------- man/figures/combined_analysis-1.png |only man/figures/distance_preservation-1.png |only man/figures/distance_preservation-2.png |only man/figures/distorted_eigenvalues-1.png |only man/figures/distorted_performance-1.png |only man/figures/swiss_eigenvalues-1.png |only man/figures/swiss_performance-1.png |only vignettes/Comprehensive_Evaluation.Rmd | 621 +++++++++++++++++ 17 files changed, 1954 insertions(+), 681 deletions(-)
Title: Database Interface Class
Description: 'R6' class interface for handling relational database connections using 'DBI' package as backend.
The class allows handling of connections to e.g. PostgreSQL, MariaDB and SQLite.
The purpose is having an intuitive object allowing straightforward handling of SQL databases.
Author: Nikolaus Pawlowski [aut, cre, cph]
Maintainer: Nikolaus Pawlowski <niko@fr33.net>
Diff between rocker versions 0.3.1 dated 2022-08-20 and 0.3.2 dated 2025-08-30
DESCRIPTION | 8 MD5 | 52 NEWS.md | 5 R/functions-public.R | 2 R/rocker-R6-class.R | 2 R/rocker-S3-functions.R | 2 README.md | 2201 +++++++++++++++----------------- build/vignette.rds |binary inst/doc/DBI_objects_and_functions.R | 2 inst/doc/DBI_objects_and_functions.html | 457 +++--- inst/doc/Database_connections.R | 2 inst/doc/Database_connections.html | 219 +-- inst/doc/Installation_and_Object.R | 22 inst/doc/Installation_and_Object.html | 457 +++--- inst/doc/Packages_and_databases.R | 110 - inst/doc/Packages_and_databases.html | 233 +-- inst/doc/Password_storage.R | 154 +- inst/doc/Password_storage.html | 237 +-- inst/doc/S3_and_R6_functions.R | 2 inst/doc/S3_and_R6_functions.html | 189 +- inst/doc/Transactions.R | 2 inst/doc/Transactions.html | 239 +-- man/newDB.Rd | 2 man/rocker-R6-class.Rd | 2 man/rocker-README.Rd | 22 man/rocker-S3-functions.Rd | 2 man/rocker-package.Rd | 1 27 files changed, 2311 insertions(+), 2315 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.7 dated 2025-02-26 and 0.6.8 dated 2025-08-30
inti-0.6.7/inti/inst/doc/apps.Rmd |only inti-0.6.7/inti/inst/doc/heritability.Rmd |only inti-0.6.7/inti/inst/doc/policy.Rmd |only inti-0.6.7/inti/inst/doc/rticles.Rmd |only inti-0.6.7/inti/inst/doc/tarpuy.Rmd |only inti-0.6.7/inti/inst/doc/yupana.Rmd |only inti-0.6.7/inti/inst/rmarkdown |only inti-0.6.7/inti/inst/style.docx |only inti-0.6.7/inti/vignettes/apps.Rmd |only inti-0.6.7/inti/vignettes/heritability.Rmd |only inti-0.6.7/inti/vignettes/policy.Rmd |only inti-0.6.7/inti/vignettes/rticles.Rmd |only inti-0.6.7/inti/vignettes/tarpuy.Rmd |only inti-0.6.7/inti/vignettes/yupana.Rmd |only inti-0.6.8/inti/DESCRIPTION | 23 inti-0.6.8/inti/MD5 | 163 - inti-0.6.8/inti/NEWS.md | 11 inti-0.6.8/inti/R/design_noreps.R | 2 inti-0.6.8/inti/R/design_repblock.R | 2 inti-0.6.8/inti/R/gdoc2qmd.R | 65 inti-0.6.8/inti/R/plot_smr.R | 16 inti-0.6.8/inti/R/tarpuy_design.R | 2 inti-0.6.8/inti/R/tarpuy_plex.R | 3 inti-0.6.8/inti/R/utils.R | 90 inti-0.6.8/inti/build/partial.rdb |binary inti-0.6.8/inti/build/vignette.rds |binary inti-0.6.8/inti/inst/doc/apps.html | 168 - inti-0.6.8/inti/inst/doc/apps.qmd |only inti-0.6.8/inti/inst/doc/heritability.R | 12 inti-0.6.8/inti/inst/doc/heritability.html | 1057 ++++------ inti-0.6.8/inti/inst/doc/heritability.qmd |only inti-0.6.8/inti/inst/doc/policy.html | 217 -- inti-0.6.8/inti/inst/doc/policy.qmd |only inti-0.6.8/inti/inst/doc/rticles.R | 1 inti-0.6.8/inti/inst/doc/rticles.html | 355 --- inti-0.6.8/inti/inst/doc/rticles.qmd |only inti-0.6.8/inti/inst/doc/tarpuy.R | 1 inti-0.6.8/inti/inst/doc/tarpuy.html | 165 - inti-0.6.8/inti/inst/doc/tarpuy.qmd |only inti-0.6.8/inti/inst/doc/yupana.R | 6 inti-0.6.8/inti/inst/doc/yupana.html | 354 +-- inti-0.6.8/inti/inst/doc/yupana.qmd |only inti-0.6.8/inti/inst/extdata |only inti-0.6.8/inti/inst/rstudio/addins.dcf | 7 inti-0.6.8/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy-test.dcf | 2 inti-0.6.8/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 2 inti-0.6.8/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana-test.dcf | 2 inti-0.6.8/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 2 inti-0.6.8/inti/man/H2cal.Rd | 298 +- inti-0.6.8/inti/man/colortext.Rd | 68 inti-0.6.8/inti/man/design_noreps.Rd | 126 - inti-0.6.8/inti/man/design_repblock.Rd | 152 - inti-0.6.8/inti/man/figure2qmd.Rd | 48 inti-0.6.8/inti/man/figure2rmd.Rd | 42 inti-0.6.8/inti/man/footnotes.Rd | 58 inti-0.6.8/inti/man/gdoc2qmd.Rd | 4 inti-0.6.8/inti/man/include_table.Rd | 90 inti-0.6.8/inti/man/jc_tombola.Rd | 104 inti-0.6.8/inti/man/mean_comparison.Rd | 120 - inti-0.6.8/inti/man/met.Rd | 68 inti-0.6.8/inti/man/metamorphosis.Rd | 74 inti-0.6.8/inti/man/outliers_remove.Rd | 94 inti-0.6.8/inti/man/plot_diag.Rd | 88 inti-0.6.8/inti/man/plot_diagnostic.Rd | 66 inti-0.6.8/inti/man/plot_raw.Rd | 202 - inti-0.6.8/inti/man/plot_smr.Rd | 216 +- inti-0.6.8/inti/man/potato.Rd | 76 inti-0.6.8/inti/man/reexports.Rd | 32 inti-0.6.8/inti/man/remove_outliers.Rd | 94 inti-0.6.8/inti/man/split_folder.Rd | 88 inti-0.6.8/inti/man/table2qmd.Rd | 38 inti-0.6.8/inti/man/table2rmd.Rd | 38 inti-0.6.8/inti/man/tarpuy.Rd | 58 inti-0.6.8/inti/man/tarpuy_design.Rd | 154 - inti-0.6.8/inti/man/tarpuy_plex.Rd | 224 +- inti-0.6.8/inti/man/tarpuy_plotdesign.Rd | 126 - inti-0.6.8/inti/man/tarpuy_traits.Rd | 198 - inti-0.6.8/inti/man/web_table.Rd | 110 - inti-0.6.8/inti/man/yupana.Rd | 58 inti-0.6.8/inti/man/yupana_analysis.Rd | 128 - inti-0.6.8/inti/man/yupana_export.Rd | 206 - inti-0.6.8/inti/man/yupana_import.Rd | 70 inti-0.6.8/inti/man/yupana_mvr.Rd | 118 - inti-0.6.8/inti/man/yupana_reshape.Rd | 88 inti-0.6.8/inti/vignettes/apps.qmd |only inti-0.6.8/inti/vignettes/heritability.qmd |only inti-0.6.8/inti/vignettes/policy.qmd |only inti-0.6.8/inti/vignettes/rticles.qmd |only inti-0.6.8/inti/vignettes/tarpuy.qmd |only inti-0.6.8/inti/vignettes/yupana.qmd |only 90 files changed, 2924 insertions(+), 3626 deletions(-)
Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price
Sensitivity Meter in R, which is a survey-based approach
to analyze consumer price preferences and sensitivity
(van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>
Diff between pricesensitivitymeter versions 1.3.1 dated 2025-08-23 and 1.3.3 dated 2025-08-30
pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_af5c2bb5516e2f47a69fe0599650db16.RData |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_af5c2bb5516e2f47a69fe0599650db16.rdb |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_af5c2bb5516e2f47a69fe0599650db16.rdx |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_c4ae27400b97262232cb52c7b797de0d.RData |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_c4ae27400b97262232cb52c7b797de0d.rdb |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_c4ae27400b97262232cb52c7b797de0d.rdx |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_422b21abe62c955b66cb5d8959b0edc1.RData |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_422b21abe62c955b66cb5d8959b0edc1.rdb |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_422b21abe62c955b66cb5d8959b0edc1.rdx |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_2077bff8e98b4be3e816baed2dac836b.RData |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_2077bff8e98b4be3e816baed2dac836b.rdb |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_2077bff8e98b4be3e816baed2dac836b.rdx |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_58d19d83865f0f05972be5bca3bc5df7.RData |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_58d19d83865f0f05972be5bca3bc5df7.rdb |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_58d19d83865f0f05972be5bca3bc5df7.rdx |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/DESCRIPTION | 6 - pricesensitivitymeter-1.3.3/pricesensitivitymeter/MD5 | 42 +++++----- pricesensitivitymeter-1.3.3/pricesensitivitymeter/NEWS.md | 5 - pricesensitivitymeter-1.3.3/pricesensitivitymeter/R/psm_data_processing.R | 3 pricesensitivitymeter-1.3.3/pricesensitivitymeter/inst/doc/interpolation-in-small-samples.html | 4 pricesensitivitymeter-1.3.3/pricesensitivitymeter/inst/doc/visualizing-psm-results.html | 4 pricesensitivitymeter-1.3.3/pricesensitivitymeter/inst/doc/weighted-data.html | 4 pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_692ca07b323cd8afff4937db86d15c2c.RData |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_692ca07b323cd8afff4937db86d15c2c.rdb |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c1_692ca07b323cd8afff4937db86d15c2c.rdx |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_111957cd6e0204d68bca17a231a4697c.RData |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_111957cd6e0204d68bca17a231a4697c.rdb |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c2_111957cd6e0204d68bca17a231a4697c.rdx |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_7172a72026229358ef90685f84b5447d.RData |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_7172a72026229358ef90685f84b5447d.rdb |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c3_7172a72026229358ef90685f84b5447d.rdx |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_6e809420dc369e74ee47ee556e3bfbe3.RData |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_6e809420dc369e74ee47ee556e3bfbe3.rdb |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c4_6e809420dc369e74ee47ee556e3bfbe3.rdx |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_8c19c9f0d2fd1acb59c096b8cc621667.RData |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_8c19c9f0d2fd1acb59c096b8cc621667.rdb |only pricesensitivitymeter-1.3.3/pricesensitivitymeter/vignettes/weighted-data_cache/html/c5_8c19c9f0d2fd1acb59c096b8cc621667.rdx |only 37 files changed, 37 insertions(+), 31 deletions(-)
More information about pricesensitivitymeter at CRAN
Permanent link
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb [...truncated...]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.11.0 dated 2024-07-01 and 0.11.1 dated 2025-08-30
ProjectTemplate-0.11.0/ProjectTemplate/tests/testthat/helper-functions.R |only ProjectTemplate-0.11.0/ProjectTemplate/tests/testthat/test-qs.R |only ProjectTemplate-0.11.1/ProjectTemplate/DESCRIPTION | 8 ProjectTemplate-0.11.1/ProjectTemplate/MD5 | 29 - ProjectTemplate-0.11.1/ProjectTemplate/NEWS.md | 6 ProjectTemplate-0.11.1/ProjectTemplate/R/cache.R | 34 - ProjectTemplate-0.11.1/ProjectTemplate/build/partial.rdb |binary ProjectTemplate-0.11.1/ProjectTemplate/inst/defaults/templates/full/config/global.dcf | 2 ProjectTemplate-0.11.1/ProjectTemplate/inst/defaults/templates/minimal/config/global.dcf | 2 ProjectTemplate-0.11.1/ProjectTemplate/man/cache.Rd | 11 ProjectTemplate-0.11.1/ProjectTemplate/man/internal.cache.format.Rd | 2 ProjectTemplate-0.11.1/ProjectTemplate/man/internal.check.version.Rd | 2 ProjectTemplate-0.11.1/ProjectTemplate/tests/testthat/helper-functions_and_data.R |only ProjectTemplate-0.11.1/ProjectTemplate/tests/testthat/test-cache.R | 232 +++++----- ProjectTemplate-0.11.1/ProjectTemplate/tests/testthat/test-load.R | 216 +++++---- ProjectTemplate-0.11.1/ProjectTemplate/tests/testthat/test-migration.R | 99 ++-- ProjectTemplate-0.11.1/ProjectTemplate/tests/testthat/test-readers.R | 4 17 files changed, 360 insertions(+), 287 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Fast Data Aggregation, Modification, and Filtering with Pipes
and 'data.table'
Description: Provides pipe-style interface for 'data.table'. Package preserves all 'data.table' features without
significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data
manipulation tasks. For example, you can write 'take(mtcars, mean(mpg), by = am)' for aggregation or
'let(mtcars, hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional
aggregation/modification. Additionally there are some conveniences such as automatic 'data.frame'
conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between maditr versions 0.8.5 dated 2024-11-10 and 0.8.6 dated 2025-08-30
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NAMESPACE | 1 NEWS | 5 +++ R/let.R | 31 ------------------- build/vignette.rds |binary inst/doc/Introduction.R | 72 ++++++++++++++++++++++----------------------- inst/tinytest/test_utils.R | 16 +++++----- man/let_if.Rd | 16 ---------- 9 files changed, 63 insertions(+), 104 deletions(-)
Title: Bayesian Change-Point Detection for Process Monitoring with
Fault Detection
Description: Bayes Watch fits an array of Gaussian Graphical Mixture Models to groupings of homogeneous data in time, called regimes, which are modeled as the observed states of a Markov process with unknown transition probabilities. In doing so, Bayes Watch defines a posterior distribution on a vector of regime assignments, which gives meaningful expressions on the probability of every possible change-point. Bayes Watch also allows for an effective and efficient fault detection system that assesses what features in the data where the most responsible for a given change-point. For further details, see: Alexander C. Murph et al. (2023) <doi:10.48550/arXiv.2310.02940>.
Author: Alexander C. Murph [aut, cre],
Reza Mohammadi [ctb, cph],
Alex Lenkoski [ctb, cph],
Andrew Johnson [ctb]
Maintainer: Alexander C. Murph <murph290@gmail.com>
Diff between bayesWatch versions 0.1.3 dated 2024-01-27 and 0.1.4 dated 2025-08-30
bayesWatch-0.1.3/bayesWatch/data/example_data.RData |only bayesWatch-0.1.4/bayesWatch/DESCRIPTION | 40 +++++++++----------- bayesWatch-0.1.4/bayesWatch/MD5 | 14 +++---- bayesWatch-0.1.4/bayesWatch/NEWS.md | 4 +- bayesWatch-0.1.4/bayesWatch/data/full_data.RData |only bayesWatch-0.1.4/bayesWatch/man/bayeswatch.Rd | 7 +++ bayesWatch-0.1.4/bayesWatch/man/full_data.Rd | 16 +++----- bayesWatch-0.1.4/bayesWatch/src/MHratios.cpp | 2 - bayesWatch-0.1.4/bayesWatch/src/RcppExports.cpp | 4 -- 9 files changed, 42 insertions(+), 45 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.15.0 dated 2025-07-10 and 0.15.1 dated 2025-08-30
DESCRIPTION | 24 +++--- MD5 | 31 ++++--- NEWS.md | 8 ++ R/check_group_variation.R | 8 +- R/check_itemscale.R | 2 R/display.R | 44 +++++++---- R/item_difficulty.R | 7 + R/item_discrimination.R | 2 R/item_omega.R | 7 + R/item_reliability.R | 2 R/model_performance.lavaan.R | 98 +++++++++++++++---------- R/print-methods.R | 11 ++ R/print_md.R | 9 ++ R/test_likelihoodratio.R | 17 +++- R/test_performance.R | 17 +++- man/display.performance_model.Rd | 30 +++++-- tests/testthat/test-model_performance.lavaan.R |only 17 files changed, 214 insertions(+), 103 deletions(-)
Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0)
"Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences".
This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting
functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between HDANOVA versions 0.8.3 dated 2025-04-03 and 0.8.4 dated 2025-08-30
HDANOVA-0.8.3/HDANOVA/man/HDANOVA.Rd |only HDANOVA-0.8.4/HDANOVA/DESCRIPTION | 15 HDANOVA-0.8.4/HDANOVA/MD5 | 60 ++- HDANOVA-0.8.4/HDANOVA/NAMESPACE | 9 HDANOVA-0.8.4/HDANOVA/NEWS | 12 HDANOVA-0.8.4/HDANOVA/R/HDANOVA-package.R | 6 HDANOVA-0.8.4/HDANOVA/R/ML_variance_partition.R |only HDANOVA-0.8.4/HDANOVA/R/apca.R | 2 HDANOVA-0.8.4/HDANOVA/R/apls.R |only HDANOVA-0.8.4/HDANOVA/R/asca.R | 164 --------- HDANOVA-0.8.4/HDANOVA/R/asca_plots.R | 24 + HDANOVA-0.8.4/HDANOVA/R/asca_results.R | 19 + HDANOVA-0.8.4/HDANOVA/R/extract_estimates.R | 2 HDANOVA-0.8.4/HDANOVA/R/hdanova.R | 230 +++++++------- HDANOVA-0.8.4/HDANOVA/R/limmpca.R | 15 HDANOVA-0.8.4/HDANOVA/R/permutation.R | 5 HDANOVA-0.8.4/HDANOVA/R/pls.R |only HDANOVA-0.8.4/HDANOVA/R/sca.R | 2 HDANOVA-0.8.4/HDANOVA/README.md | 2 HDANOVA-0.8.4/HDANOVA/build/vignette.rds |binary HDANOVA-0.8.4/HDANOVA/inst/doc/vignette_B_ANOVA.html | 75 +--- HDANOVA-0.8.4/HDANOVA/inst/doc/vignette_C_ASCA.R | 2 HDANOVA-0.8.4/HDANOVA/inst/doc/vignette_C_ASCA.Rmd | 2 HDANOVA-0.8.4/HDANOVA/inst/doc/vignette_C_ASCA.html | 86 ++--- HDANOVA-0.8.4/HDANOVA/inst/doc/vignette_D_additional.html | 4 HDANOVA-0.8.4/HDANOVA/man/HDANOVA-package.Rd |only HDANOVA-0.8.4/HDANOVA/man/apls.Rd |only HDANOVA-0.8.4/HDANOVA/man/asca.Rd | 2 HDANOVA-0.8.4/HDANOVA/man/extract_estimates.Rd | 2 HDANOVA-0.8.4/HDANOVA/man/hdanova.Rd |only HDANOVA-0.8.4/HDANOVA/man/limmpca.Rd | 10 HDANOVA-0.8.4/HDANOVA/man/pls.Rd |only HDANOVA-0.8.4/HDANOVA/man/sca.Rd | 2 HDANOVA-0.8.4/HDANOVA/man/timeplot.Rd | 2 HDANOVA-0.8.4/HDANOVA/vignettes/vignette_C_ASCA.Rmd | 2 35 files changed, 323 insertions(+), 433 deletions(-)
Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent
time series, possibly mixed with ARMA, regression, transfer-function
components.
Exact methods (MLE, forecasting, simulation) are used.
Bug reports should be done via GitHub (at
<https://github.com/JQVeenstra/arfima>), where the development version
of this package lives; it can be installed using devtools.
Author: JQ Veenstra [aut, cre] ,
A.I. McLeod [aut]
Maintainer: JQ Veenstra <jqveenstra@gmail.com>
Diff between arfima versions 1.8-1 dated 2022-08-19 and 1.8-2 dated 2025-08-30
arfima-1.8-1/arfima/R/arfima.R |only arfima-1.8-2/arfima/DESCRIPTION | 22 arfima-1.8-2/arfima/MD5 | 26 arfima-1.8-2/arfima/R/arfima_PACKAGE.R |only arfima-1.8-2/arfima/R/arfima_function.R | 3182 +++++++++++++++--------------- arfima-1.8-2/arfima/R/iARMA.R | 1342 ++++++------ arfima-1.8-2/arfima/R/predict.ARFIMA.R | 833 +++---- arfima-1.8-2/arfima/R/utilityfcns.R | 1823 ++++++++--------- arfima-1.8-2/arfima/inst/CITATION | 2 arfima-1.8-2/arfima/man/SeriesJ.Rd | 2 arfima-1.8-2/arfima/man/arfima-package.Rd | 5 arfima-1.8-2/arfima/man/arfima.Rd | 2 arfima-1.8-2/arfima/man/iARFIMA.Rd | 8 arfima-1.8-2/arfima/man/logLik.arfima.Rd | 4 arfima-1.8-2/arfima/man/tmpyr.Rd | 2 15 files changed, 3632 insertions(+), 3621 deletions(-)
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 1.3.6 dated 2025-04-23 and 1.3.7 dated 2025-08-30
mets-1.3.6/mets/data/base1cumhaz.txt |only mets-1.3.6/mets/data/base44cumhaz.txt |only mets-1.3.6/mets/data/base4cumhaz.txt |only mets-1.3.6/mets/data/drcumhaz.txt |only mets-1.3.6/mets/data/hHaplos.rda |only mets-1.3.6/mets/data/hapfreqs.rda |only mets-1.3.6/mets/data/haploX.rda |only mets-1.3.6/mets/man/base1cumhaz.Rd |only mets-1.3.6/mets/man/base44cumhaz.Rd |only mets-1.3.6/mets/man/base4cumhaz.Rd |only mets-1.3.6/mets/man/drcumhaz.Rd |only mets-1.3.6/mets/man/ghaplos.Rd |only mets-1.3.6/mets/man/hapfreqs.Rd |only mets-1.3.6/mets/man/haploX.Rd |only mets-1.3.7/mets/DESCRIPTION | 16 mets-1.3.7/mets/MD5 | 278 - mets-1.3.7/mets/NAMESPACE | 43 mets-1.3.7/mets/NEWS.md | 7 mets-1.3.7/mets/R/WA-estimands.R | 234 - mets-1.3.7/mets/R/binomial.regression.R | 695 +-- mets-1.3.7/mets/R/binregTSR.R | 40 mets-1.3.7/mets/R/cifreg.R | 761 ---- mets-1.3.7/mets/R/discrete-survival-haplo.R | 598 --- mets-1.3.7/mets/R/event.r | 4 mets-1.3.7/mets/R/interval-cumoddsreg.r |only mets-1.3.7/mets/R/lifetable.R | 2 mets-1.3.7/mets/R/mediator-survival.R | 8 mets-1.3.7/mets/R/mets-package.R | 60 mets-1.3.7/mets/R/mutinomialreg.R | 24 mets-1.3.7/mets/R/phreg.R | 564 +-- mets-1.3.7/mets/R/phreg_rct.R | 57 mets-1.3.7/mets/R/plot_twin.R |only mets-1.3.7/mets/R/ratio.regression.R |only mets-1.3.7/mets/R/recreg.R | 1855 +--------- mets-1.3.7/mets/R/recurrent.marginal.R | 490 +- mets-1.3.7/mets/R/restricted.mean.R | 329 - mets-1.3.7/mets/R/sim-pc-hazard.R | 17 mets-1.3.7/mets/README.md | 66 mets-1.3.7/mets/build/partial.rdb |binary mets-1.3.7/mets/build/vignette.rds |binary mets-1.3.7/mets/data/CPH_HPN_CRBSI.rda |only mets-1.3.7/mets/data/haplo.rda |only mets-1.3.7/mets/data/hfactioncpx12.rda |binary mets-1.3.7/mets/inst/doc/basic-dutils.html | 36 mets-1.3.7/mets/inst/doc/binomial-family.R | 3 mets-1.3.7/mets/inst/doc/binomial-family.Rmd | 19 mets-1.3.7/mets/inst/doc/binomial-family.html | 119 mets-1.3.7/mets/inst/doc/binomial-twin.html | 264 - mets-1.3.7/mets/inst/doc/binreg-TRS.R | 1 mets-1.3.7/mets/inst/doc/binreg-TRS.Rmd | 2 mets-1.3.7/mets/inst/doc/binreg-TRS.html | 733 +-- mets-1.3.7/mets/inst/doc/binreg-ate.R | 28 mets-1.3.7/mets/inst/doc/binreg-ate.Rmd | 114 mets-1.3.7/mets/inst/doc/binreg-ate.html | 513 +- mets-1.3.7/mets/inst/doc/binreg.R | 4 mets-1.3.7/mets/inst/doc/binreg.Rmd | 59 mets-1.3.7/mets/inst/doc/binreg.html | 277 - mets-1.3.7/mets/inst/doc/cifreg.R | 67 mets-1.3.7/mets/inst/doc/cifreg.Rmd | 95 mets-1.3.7/mets/inst/doc/cifreg.html | 221 - mets-1.3.7/mets/inst/doc/cooking-survival-data.R | 60 mets-1.3.7/mets/inst/doc/cooking-survival-data.Rmd | 67 mets-1.3.7/mets/inst/doc/cooking-survival-data.html | 485 +- mets-1.3.7/mets/inst/doc/glm-utility.R | 3 mets-1.3.7/mets/inst/doc/glm-utility.Rmd | 3 mets-1.3.7/mets/inst/doc/glm-utility.html | 77 mets-1.3.7/mets/inst/doc/haplo-discrete-ttp.R | 7 mets-1.3.7/mets/inst/doc/haplo-discrete-ttp.Rmd | 7 mets-1.3.7/mets/inst/doc/haplo-discrete-ttp.html | 85 mets-1.3.7/mets/inst/doc/interval-discrete-survival.R | 8 mets-1.3.7/mets/inst/doc/interval-discrete-survival.Rmd | 27 mets-1.3.7/mets/inst/doc/interval-discrete-survival.html | 262 - mets-1.3.7/mets/inst/doc/marginal-cox.html | 50 mets-1.3.7/mets/inst/doc/mediation-survival.R | 2 mets-1.3.7/mets/inst/doc/mediation-survival.Rmd | 2 mets-1.3.7/mets/inst/doc/mediation-survival.html | 603 +-- mets-1.3.7/mets/inst/doc/phreg_rct.R | 13 mets-1.3.7/mets/inst/doc/phreg_rct.Rmd | 15 mets-1.3.7/mets/inst/doc/phreg_rct.html | 121 mets-1.3.7/mets/inst/doc/quantitative-twin.R | 32 mets-1.3.7/mets/inst/doc/quantitative-twin.Rmd | 37 mets-1.3.7/mets/inst/doc/quantitative-twin.html | 28 mets-1.3.7/mets/inst/doc/recurrent-events.R | 68 mets-1.3.7/mets/inst/doc/recurrent-events.Rmd | 76 mets-1.3.7/mets/inst/doc/recurrent-events.html | 412 +- mets-1.3.7/mets/inst/doc/rmst-ate.Rmd | 17 mets-1.3.7/mets/inst/doc/rmst-ate.html | 389 +- mets-1.3.7/mets/inst/doc/survival-ate.R | 11 mets-1.3.7/mets/inst/doc/survival-ate.Rmd | 11 mets-1.3.7/mets/inst/doc/survival-ate.html | 323 - mets-1.3.7/mets/inst/doc/time-to-event-family-studies-arev.html | 67 mets-1.3.7/mets/inst/doc/twostage-survival.html | 51 mets-1.3.7/mets/inst/doc/while-alive.R | 15 mets-1.3.7/mets/inst/doc/while-alive.Rmd | 40 mets-1.3.7/mets/inst/doc/while-alive.html | 224 - mets-1.3.7/mets/inst/tinytest/test_recreg.R | 29 mets-1.3.7/mets/man/BinAugmentCifstrata.Rd | 1 mets-1.3.7/mets/man/CPH_HPN_CRBSI.Rd |only mets-1.3.7/mets/man/WA_recurrent.Rd | 3 mets-1.3.7/mets/man/binreg.Rd | 15 mets-1.3.7/mets/man/binregATE.Rd | 4 mets-1.3.7/mets/man/binregRatio.Rd |only mets-1.3.7/mets/man/binregTSR.Rd | 2 mets-1.3.7/mets/man/cifreg.Rd | 7 mets-1.3.7/mets/man/count.history.Rd | 33 mets-1.3.7/mets/man/evalTerminal.Rd | 15 mets-1.3.7/mets/man/haplo.Rd |only mets-1.3.7/mets/man/haplo.surv.discrete.Rd | 10 mets-1.3.7/mets/man/iidBaseline.Rd |only mets-1.3.7/mets/man/interval.logitsurv.discrete.Rd | 35 mets-1.3.7/mets/man/lifetable.matrix.Rd | 2 mets-1.3.7/mets/man/mediatorSurv.Rd | 2 mets-1.3.7/mets/man/mlogit.Rd | 9 mets-1.3.7/mets/man/phreg.Rd | 20 mets-1.3.7/mets/man/phreg_rct.Rd | 3 mets-1.3.7/mets/man/plot_twin.Rd |only mets-1.3.7/mets/man/recreg.Rd | 4 mets-1.3.7/mets/man/resmean.phreg.Rd | 14 mets-1.3.7/mets/man/resmeanATE.Rd | 8 mets-1.3.7/mets/man/resmeanIPCW.Rd | 24 mets-1.3.7/mets/man/sim.cox.Rd | 1 mets-1.3.7/mets/man/sim.recurrent.Rd |only mets-1.3.7/mets/man/simGLcox.Rd |only mets-1.3.7/mets/man/simMultistate.Rd | 15 mets-1.3.7/mets/man/simRecurrentII.Rd | 52 mets-1.3.7/mets/man/simRecurrentTS.Rd | 11 mets-1.3.7/mets/man/survivalG.Rd | 5 mets-1.3.7/mets/src/fastcox.cpp | 3 mets-1.3.7/mets/vignettes/binomial-family.Rmd | 19 mets-1.3.7/mets/vignettes/binreg-TRS.Rmd | 2 mets-1.3.7/mets/vignettes/binreg-ate.Rmd | 114 mets-1.3.7/mets/vignettes/binreg.Rmd | 59 mets-1.3.7/mets/vignettes/cifreg.Rmd | 95 mets-1.3.7/mets/vignettes/cooking-survival-data.Rmd | 67 mets-1.3.7/mets/vignettes/data/MultMed.rds |binary mets-1.3.7/mets/vignettes/data/cse.rds |binary mets-1.3.7/mets/vignettes/data/fitace.rds |binary mets-1.3.7/mets/vignettes/data/fitco1.rds |binary mets-1.3.7/mets/vignettes/data/fitco2.rds |binary mets-1.3.7/mets/vignettes/data/fitco3.rds |binary mets-1.3.7/mets/vignettes/data/fitco4.rds |binary mets-1.3.7/mets/vignettes/data/fitde.rds |binary mets-1.3.7/mets/vignettes/data/slr.rds |binary mets-1.3.7/mets/vignettes/glm-utility.Rmd | 3 mets-1.3.7/mets/vignettes/haplo-discrete-ttp.Rmd | 7 mets-1.3.7/mets/vignettes/interval-discrete-survival.Rmd | 27 mets-1.3.7/mets/vignettes/mediation-survival.Rmd | 2 mets-1.3.7/mets/vignettes/phreg_rct.Rmd | 15 mets-1.3.7/mets/vignettes/quantitative-twin.Rmd | 37 mets-1.3.7/mets/vignettes/recurrent-events.Rmd | 76 mets-1.3.7/mets/vignettes/rmst-ate.Rmd | 17 mets-1.3.7/mets/vignettes/survival-ate.Rmd | 11 mets-1.3.7/mets/vignettes/while-alive.Rmd | 40 153 files changed, 5473 insertions(+), 7846 deletions(-)
Title: Bayesian Recurrent Events Analysis
Description: Functions to produce MCMC samples for posterior inference in semiparametric Bayesian discrete time competing risks recurrent events models and multistate models.
Author: Adam J King [aut, cre]
Maintainer: Adam J King <king@cpp.edu>
Diff between brea versions 0.4.1 dated 2025-07-26 and 0.4.2 dated 2025-08-30
DESCRIPTION | 8 ++-- MD5 | 16 +++++--- build/vignette.rds |binary inst/doc/brea.Rmd | 24 ++++++------ inst/doc/brea.html | 41 +++++++++++----------- inst/doc/brea_gmrf.R |only inst/doc/brea_gmrf.Rmd |only inst/doc/brea_gmrf.html |only vignettes/brea.Rmd | 24 ++++++------ vignettes/brea.bib | 89 +++++++++++++++++++++++++----------------------- vignettes/brea_gmrf.Rmd |only 11 files changed, 107 insertions(+), 95 deletions(-)
Title: Targeted Maximum Likelihood Estimation
Description: Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings c [...truncated...]
Author: Susan Gruber [aut, cre],
Mark van der Laan [aut],
Chris Kennedy [ctr]
Maintainer: Susan Gruber <sgruber@cal.berkeley.edu>
Diff between tmle versions 2.0.1.1 dated 2024-05-28 and 2.1.1 dated 2025-08-30
DESCRIPTION | 8 - MD5 | 16 +- NEWS | 10 + R/tmle.R | 262 ++++++++++++++++++++++++++++++------------------- R/zzz.R | 2 man/tmle-package.Rd | 2 man/tmle.Rd | 9 - man/tmle.Sl.dbarts2.Rd | 2 man/tmleNews.Rd | 2 9 files changed, 192 insertions(+), 121 deletions(-)
Title: Access 'iNaturalist' Data Through APIs
Description: A programmatic interface to the API provided by the 'iNaturalist' website <https://www.inaturalist.org/> to download species occurrence data submitted by citizen scientists.
Author: Vijay Barve [aut] ,
Edmund Hart [aut],
Stephane Guillou [cre]
Maintainer: Stephane Guillou <stephane.guillou@member.fsf.org>
Diff between rinat versions 0.1.9 dated 2022-06-14 and 0.1.10 dated 2025-08-30
DESCRIPTION | 14 MD5 | 22 - NEWS.md | 15 R/get_inat_obs.R | 197 +++++---- R/get_inat_obs_project.R | 19 R/inat_map.R | 19 README.md | 18 build/vignette.rds |binary inst/doc/rinat-intro.html | 752 ++++++++++++++++++------------------- inst/doc/species-distribution.html | 342 ++++++++-------- man/get_inat_obs.Rd | 43 +- man/inat_map.Rd | 12 12 files changed, 750 insertions(+), 703 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.12.0 dated 2025-07-10 and 0.13.0 dated 2025-08-30
modelbased-0.12.0/modelbased/R/joint_test.R |only modelbased-0.13.0/modelbased/DESCRIPTION | 28 - modelbased-0.13.0/modelbased/MD5 | 186 ++++----- modelbased-0.13.0/modelbased/NAMESPACE | 9 modelbased-0.13.0/modelbased/NEWS.md | 65 +++ modelbased-0.13.0/modelbased/R/clean_names.R | 2 modelbased-0.13.0/modelbased/R/display.R | 44 +- modelbased-0.13.0/modelbased/R/estimate_contrasts.R | 107 ++++- modelbased-0.13.0/modelbased/R/estimate_means.R | 116 +++-- modelbased-0.13.0/modelbased/R/estimate_predicted.R | 5 modelbased-0.13.0/modelbased/R/estimate_slopes.R | 38 + modelbased-0.13.0/modelbased/R/format.R | 101 ++++ modelbased-0.13.0/modelbased/R/get_emcontrasts.R | 2 modelbased-0.13.0/modelbased/R/get_emmeans.R | 28 - modelbased-0.13.0/modelbased/R/get_inequalitycontrasts.R |only modelbased-0.13.0/modelbased/R/get_jointtest.R |only modelbased-0.13.0/modelbased/R/get_marginalcontrasts.R | 164 ++++---- modelbased-0.13.0/modelbased/R/get_marginaleffects_type.R | 113 +++-- modelbased-0.13.0/modelbased/R/get_marginalmeans.R | 205 ++++++---- modelbased-0.13.0/modelbased/R/get_marginaltrends.R | 57 +- modelbased-0.13.0/modelbased/R/options.R | 14 modelbased-0.13.0/modelbased/R/p_adjust.R | 7 modelbased-0.13.0/modelbased/R/print.R | 16 modelbased-0.13.0/modelbased/R/print_html.R | 6 modelbased-0.13.0/modelbased/R/residualize_over_grid.R |only modelbased-0.13.0/modelbased/R/table_footer.R | 22 - modelbased-0.13.0/modelbased/R/tinyplot.R |only modelbased-0.13.0/modelbased/R/utils.R | 61 ++ modelbased-0.13.0/modelbased/R/visualisation_recipe.R | 20 modelbased-0.13.0/modelbased/R/visualisation_recipe_internal.R | 126 +++++- modelbased-0.13.0/modelbased/inst/WORDLIST | 10 modelbased-0.13.0/modelbased/inst/doc/overview_of_vignettes.Rmd | 1 modelbased-0.13.0/modelbased/inst/doc/overview_of_vignettes.html | 2 modelbased-0.13.0/modelbased/man/estimate_contrasts.Rd | 199 ++++++--- modelbased-0.13.0/modelbased/man/estimate_means.Rd | 102 +++- modelbased-0.13.0/modelbased/man/estimate_slopes.Rd | 174 ++++++-- modelbased-0.13.0/modelbased/man/figures/unnamed-chunk-12-1.png |binary modelbased-0.13.0/modelbased/man/figures/unnamed-chunk-14-1.png |binary modelbased-0.13.0/modelbased/man/figures/unnamed-chunk-3-1.png |binary modelbased-0.13.0/modelbased/man/get_emmeans.Rd | 69 ++- modelbased-0.13.0/modelbased/man/modelbased-options.Rd | 11 modelbased-0.13.0/modelbased/man/print.estimate_contrasts.Rd | 27 + modelbased-0.13.0/modelbased/man/puppy_love.Rd | 64 +-- modelbased-0.13.0/modelbased/man/residualize_over_grid.Rd |only modelbased-0.13.0/modelbased/man/visualisation_recipe.estimate_predicted.Rd | 70 ++- modelbased-0.13.0/modelbased/tests/testthat/test-attributes_estimatefun.R | 6 modelbased-0.13.0/modelbased/tests/testthat/test-backtransform_invlink.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-betareg.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-bias_correction.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-brms-marginaleffects.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-brms.R | 9 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts-average.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts.R | 47 +- modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts_bookexamples.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts_effectsize.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts_inequality.R |only modelbased-0.13.0/modelbased/tests/testthat/test-estimate_contrasts_methods.R | 7 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_expectation.R | 4 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_filter.R | 43 ++ modelbased-0.13.0/modelbased/tests/testthat/test-estimate_grouplevel.R | 35 + modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means-average.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means.R | 24 - modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means_ci.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means_counterfactuals.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means_dotargs.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means_marginalization.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_means_mixed.R | 7 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_predicted.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-estimate_slopes.R | 24 + modelbased-0.13.0/modelbased/tests/testthat/test-g_computation.R | 3 modelbased-0.13.0/modelbased/tests/testthat/test-get_marginaltrends.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-glmmTMB.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-joint_test.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-keep_iterations.R | 10 modelbased-0.13.0/modelbased/tests/testthat/test-mgcv.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-mice.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-multivariate_response.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-offset.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-ordinal.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-plot-facet.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-plot-flexible_numeric.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-plot-ordinal.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-plot-slopes.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-plot.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-predict-dpar.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-print.R | 13 modelbased-0.13.0/modelbased/tests/testthat/test-residualize_over_grid.R |only modelbased-0.13.0/modelbased/tests/testthat/test-scoping_issues.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-standardize.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-summary_estimate_slopes.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-table_footer.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-transform_response.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-vcov.R | 21 - modelbased-0.13.0/modelbased/tests/testthat/test-verbose.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-visualisation_recipe.R | 2 modelbased-0.13.0/modelbased/tests/testthat/test-zeroinfl.R | 2 modelbased-0.13.0/modelbased/vignettes/bibliography.bib | 17 modelbased-0.13.0/modelbased/vignettes/overview_of_vignettes.Rmd | 1 98 files changed, 1814 insertions(+), 798 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between parameters versions 0.28.0 dated 2025-08-20 and 0.28.1 dated 2025-08-30
DESCRIPTION | 18 +-- MD5 | 52 ++++----- NAMESPACE | 1 NEWS.md | 21 +++ R/display.R | 7 + R/equivalence_test.R | 10 + R/methods_glmmTMB.R | 58 +++++----- R/methods_marginaleffects.R | 126 ++++++++++++++--------- R/options.R |only R/standardize_info.R | 4 R/standardize_parameters.R | 2 R/utils_model_parameters.R | 5 inst/WORDLIST | 1 man/model_parameters.glmmTMB.Rd | 31 +++++ man/parameters-options.Rd |only man/standardize_info.Rd | 2 tests/testthat/test-equivalence_test.R | 30 +++++ tests/testthat/test-glmmTMB.R | 21 ++- tests/testthat/test-marginaleffects.R | 119 ++++++++++++++++++++- tests/testthat/test-model_parameters.anova.R | 2 tests/testthat/test-model_parameters.aov.R | 4 tests/testthat/test-model_parameters.aov_es_ci.R | 73 ++++++++----- tests/testthat/test-model_parameters_ordinal.R | 4 tests/testthat/test-p_significance.R | 2 tests/testthat/test-random_effects_ci-glmmTMB.R | 2 tests/testthat/test-standardize_info.R | 2 tests/testthat/test-standardize_parameters.R | 2 tests/testthat/test-weightit.R | 2 28 files changed, 436 insertions(+), 165 deletions(-)
Title: Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit
Description: Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.
Author: Wei Cui [aut, cre, cph]
Maintainer: Wei Cui <m2c.w@outlook.com>
Diff between easybio versions 1.1.1 dated 2025-02-11 and 1.2.1 dated 2025-08-30
easybio-1.1.1/easybio/R/misc.R |only easybio-1.1.1/easybio/inst/doc/example-bulk-rna-seq-workflow.R |only easybio-1.1.1/easybio/inst/doc/example-bulk-rna-seq-workflow.Rmd |only easybio-1.1.1/easybio/inst/doc/example-bulk-rna-seq-workflow.html |only easybio-1.1.1/easybio/inst/doc/example-single-cell-annotation.R |only easybio-1.1.1/easybio/inst/doc/example-single-cell-annotation.Rmd |only easybio-1.1.1/easybio/inst/doc/example-single-cell-annotation.html |only easybio-1.1.1/easybio/vignettes/example-bulk-rna-seq-workflow.Rmd |only easybio-1.1.1/easybio/vignettes/example-single-cell-annotation.Rmd |only easybio-1.2.1/easybio/DESCRIPTION | 17 easybio-1.2.1/easybio/LICENSE | 4 easybio-1.2.1/easybio/MD5 | 86 - easybio-1.2.1/easybio/NAMESPACE | 6 easybio-1.2.1/easybio/NEWS.md | 19 easybio-1.2.1/easybio/R/easybio-package.R | 22 easybio-1.2.1/easybio/R/limma.R | 3 easybio-1.2.1/easybio/R/ora.R | 3 easybio-1.2.1/easybio/R/prepare.R | 2 easybio-1.2.1/easybio/R/sc.R | 593 ++++++---- easybio-1.2.1/easybio/R/uniprot.R | 1 easybio-1.2.1/easybio/R/utils.R |only easybio-1.2.1/easybio/README.md | 2 easybio-1.2.1/easybio/build/partial.rdb |only easybio-1.2.1/easybio/build/vignette.rds |binary easybio-1.2.1/easybio/inst/doc/example-sc-seq-workflow.R |only easybio-1.2.1/easybio/inst/doc/example-sc-seq-workflow.Rmd |only easybio-1.2.1/easybio/inst/doc/example-sc-seq-workflow.html |only easybio-1.2.1/easybio/inst/doc/example_limma.R |only easybio-1.2.1/easybio/inst/doc/example_limma.Rmd |only easybio-1.2.1/easybio/inst/doc/example_limma.html |only easybio-1.2.1/easybio/inst/example-single-cell.R | 151 ++ easybio-1.2.1/easybio/man/CHOL_DEGs.Rd | 18 easybio-1.2.1/easybio/man/available_ele.Rd |only easybio-1.2.1/easybio/man/available_tissue_class.Rd | 51 easybio-1.2.1/easybio/man/available_tissue_type.Rd | 51 easybio-1.2.1/easybio/man/check_marker.Rd | 92 - easybio-1.2.1/easybio/man/easybio-package.Rd |only easybio-1.2.1/easybio/man/finsert.Rd | 65 - easybio-1.2.1/easybio/man/get_attr.Rd | 2 easybio-1.2.1/easybio/man/get_marker.Rd | 2 easybio-1.2.1/easybio/man/groupStat.Rd | 2 easybio-1.2.1/easybio/man/groupStatI.Rd | 2 easybio-1.2.1/easybio/man/list2dt.Rd | 6 easybio-1.2.1/easybio/man/list2graph.Rd | 2 easybio-1.2.1/easybio/man/matchCellMarker2.Rd | 113 + easybio-1.2.1/easybio/man/plotSeuratDot.Rd | 62 - easybio-1.2.1/easybio/man/setSavedir.Rd | 2 easybio-1.2.1/easybio/man/setcolnames.Rd | 2 easybio-1.2.1/easybio/man/setrownames.Rd | 2 easybio-1.2.1/easybio/man/split_matrix.Rd | 2 easybio-1.2.1/easybio/man/suggest_best_match.Rd |only easybio-1.2.1/easybio/man/workIn.Rd | 2 easybio-1.2.1/easybio/vignettes/example-bulk-rna-seq-workflow.html |only easybio-1.2.1/easybio/vignettes/example-sc-seq-workflow.Rmd |only easybio-1.2.1/easybio/vignettes/example-single-cell-annotation.html |only easybio-1.2.1/easybio/vignettes/example_limma.Rmd |only 56 files changed, 946 insertions(+), 441 deletions(-)
Title: Quantile Treatment Effects under the Regression Discontinuity
Design
Description: Provides comprehensive methods for testing, estimating, and conducting uniform inference on quantile treatment effects (QTEs) in sharp regression discontinuity (RD) designs, incorporating covariates and implementing robust bias correction methods of Qu, Yoon, Perron (2024) <doi:10.1162/rest_a_01168>.
Author: Zhongjun Qu [aut, cph],
Jungmo Yoon [aut, cre, cph]
Maintainer: Jungmo Yoon <jmyoon@hanyang.ac.kr>
Diff between QTE.RD versions 1.1.0 dated 2024-08-29 and 1.2.0 dated 2025-08-30
DESCRIPTION | 14 +++-- MD5 | 121 ++++++++++++++++++++++++++++------------------- NAMESPACE | 4 - NEWS.md | 10 +++ R/QTE.RD-package.R | 4 - R/compute.bands.R |only R/cv.bandwidth.R | 7 +- R/ddk_2011.R |only R/depa.R | 2 R/make.band.R | 42 +++++----------- R/make.band.cq.R | 69 ++++++++++++-------------- R/plot.qte.R | 8 +-- R/print.band.qte.R | 1 R/print.bw.qte.R | 1 R/print.qte.R | 2 R/print.summary.qte.R | 2 R/print.test.qte.R | 1 R/rd.qte.R | 38 ++++++-------- R/rdq.R | 21 +++----- R/rdq.band.R | 48 ++++++++++-------- R/rdq.bandwidth.R | 24 ++++----- R/rdq.bias.R | 17 +++--- R/rdq.condf.R | 4 - R/rdq.sim.R | 32 ++++++------ R/rdq.test.R | 82 +++++++++++++++++-------------- R/run.test.R | 29 +++++------ R/summary.qte.R | 18 +++--- README.md | 54 ++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |only data |only inst/doc |only man/QTE.RD-package.Rd | 4 - man/compute.bands.Rd |only man/cv.bandwidth.Rd | 1 man/ddk_2011.Rd |only man/depa.Rd | 1 man/figures |only man/make.band.Rd | 5 + man/make.band.cq.Rd | 5 + man/plot.qte.Rd | 8 +-- man/print.band.qte.Rd | 1 man/print.bw.qte.Rd | 1 man/print.qte.Rd | 1 man/print.summary.qte.Rd | 1 man/print.test.qte.Rd | 1 man/rd.qte.Rd | 25 ++++----- man/rdq.Rd | 4 - man/rdq.band.Rd | 34 +++++++------ man/rdq.bandwidth.Rd | 18 ++---- man/rdq.bias.Rd | 6 +- man/rdq.condf.Rd | 4 - man/rdq.sim.Rd | 3 - man/rdq.test.Rd | 36 +++++++------ man/run.test.Rd | 6 +- man/summary.qte.Rd | 16 +++--- tests/testthat |only tests/testthat.R |only vignettes |only 59 files changed, 464 insertions(+), 372 deletions(-)