More information about KWCChangepoint at CRAN
Permanent link
Title: Biterm Topic Models for Short Text
Description: Biterm Topic Models find topics in collections of short texts.
It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms.
This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis
which are word-document co-occurrence topic models.
A biterm consists of two words co-occurring in the same short text window.
This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier.
The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) <https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/BTM-WWW13.pdf>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Xiaohui Yan [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between BTM versions 0.3.7 dated 2023-02-11 and 0.3.8 dated 2025-11-26
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/btm.R | 15 +++++++-------- man/terms.BTM.Rd | 8 ++++---- man/terms.data.frame.Rd | 7 +++---- src/RcppExports.cpp | 5 +++++ 7 files changed, 33 insertions(+), 26 deletions(-)
Title: Client for 'GoFigr.io'
Description: Integrates with your 'RMarkdown' documents to automatically publish
figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive
execution within 'RStudio'.
Author: Maciej Pacula [cre, aut],
Flagstaff Solutions, LLC [cph]
Maintainer: Maciej Pacula <maciej@gofigr.io>
Diff between gofigR versions 1.1.2 dated 2025-07-31 and 1.1.3 dated 2025-11-26
gofigR-1.1.2/gofigR/man/print.gofigrdata.Rd |only gofigR-1.1.2/gofigR/tests/testthat/test_data.txt |only gofigR-1.1.2/gofigR/tests/testthat/testdata/test_data.txt |only gofigR-1.1.3/gofigR/DESCRIPTION | 8 - gofigR-1.1.3/gofigR/MD5 | 62 ++++----- gofigR-1.1.3/gofigR/R/analysis.R | 73 +++++++---- gofigR-1.1.3/gofigR/R/api.R | 45 ++++++- gofigR-1.1.3/gofigR/R/figure.R | 71 ++++++++--- gofigR-1.1.3/gofigR/R/gfconfig.R | 60 ++++++--- gofigR-1.1.3/gofigR/R/integrations.R | 87 ++++++++++++-- gofigR-1.1.3/gofigR/R/shiny_components.R | 4 gofigR-1.1.3/gofigR/R/workspace.R | 63 ++++++---- gofigR-1.1.3/gofigR/README.md | 23 +++ gofigR-1.1.3/gofigR/man/create_analysis.Rd | 17 +- gofigR-1.1.3/gofigR/man/create_figure.Rd | 19 +-- gofigR-1.1.3/gofigR/man/create_ggsave_args.Rd |only gofigR-1.1.3/gofigR/man/create_workspace.Rd | 13 +- gofigR-1.1.3/gofigR/man/delete_analysis.Rd | 11 - gofigR-1.1.3/gofigR/man/enable.Rd | 12 + gofigR-1.1.3/gofigR/man/find_analysis.Rd | 22 ++- gofigR-1.1.3/gofigR/man/find_figure.Rd | 23 ++- gofigR-1.1.3/gofigR/man/find_workspace.Rd | 19 +-- gofigR-1.1.3/gofigR/man/get_analysis.Rd | 10 - gofigR-1.1.3/gofigR/man/get_figure.Rd | 13 +- gofigR-1.1.3/gofigR/man/get_workspace.Rd | 11 - gofigR-1.1.3/gofigR/man/gfconfig.Rd | 15 +- gofigR-1.1.3/gofigR/man/infer_workspace.Rd | 16 +- gofigR-1.1.3/gofigR/man/list_analyses.Rd | 13 +- gofigR-1.1.3/gofigR/man/list_workspaces.Rd | 8 - gofigR-1.1.3/gofigR/man/login_with_api_key.Rd | 14 +- gofigR-1.1.3/gofigR/man/login_with_username.Rd | 11 + gofigR-1.1.3/gofigR/man/publish.Rd | 14 ++ gofigR-1.1.3/gofigR/man/read_prompt.Rd | 21 ++- gofigR-1.1.3/gofigR/man/response_to_JSON.Rd | 12 + 34 files changed, 539 insertions(+), 251 deletions(-)
Title: Wrapper Functions Around 'Charles Schwab Individual Trader API'
Description: For those wishing to interact with the 'Charles Schwab Individual Trader API' (<https://developer.schwab.com/products/trader-api--individual>) with R in a simplified manner, this package offers wrapper functions around authentication and the available API calls to streamline the process.
Author: Nick Bultman [aut, cre, cph],
Todd Sykes [ctb]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Diff between charlesschwabapi versions 1.0.4 dated 2024-12-10 and 1.0.5 dated 2025-11-26
DESCRIPTION | 17 ++- MD5 | 120 +++++++++++----------- NAMESPACE | 1 R/cancel_order.R | 42 +++++-- R/get_account.R | 43 +++++-- R/get_account_numbers.R | 36 ++++-- R/get_accounts.R | 35 ++++-- R/get_authentication_tokens.R | 12 +- R/get_instruments.R | 34 ++++-- R/get_instruments_cusip.R | 31 ++++- R/get_market_hours.R | 44 +++++--- R/get_market_hours_single.R | 41 +++++-- R/get_movers.R | 41 +++++-- R/get_option_chains.R | 107 +++++++++++-------- R/get_option_expiration_chain.R | 36 +++++- R/get_order_id.R | 45 +++++--- R/get_orders.R | 55 +++++++--- R/get_orders_account.R | 60 +++++++---- R/get_price_history.R | 114 ++++++++++++-------- R/get_quotes.R | 38 ++++-- R/get_quotes_single_symbol.R | 35 ++++-- R/get_transaction.R | 43 +++++-- R/get_transactions.R | 63 ++++++++--- R/get_user_preferences.R | 31 ++++- R/place_order.R | 64 ++++++++--- R/replace_order.R | 69 ++++++++---- README.md | 6 - man/cancel_order.Rd | 4 man/get_account.Rd | 6 - man/get_market_hours.Rd | 2 man/get_order_id.Rd | 4 man/get_orders.Rd | 15 ++ man/get_orders_account.Rd | 16 ++ man/get_quotes.Rd | 2 man/get_transaction.Rd | 4 man/get_transactions.Rd | 17 ++- man/place_order.Rd | 9 - man/replace_order.Rd | 15 +- tests/testthat/test-cancel_order.R | 30 ++--- tests/testthat/test-get_account.R | 28 ++--- tests/testthat/test-get_account_numbers.R | 8 - tests/testthat/test-get_accounts.R | 18 +-- tests/testthat/test-get_authentication_tokens.R | 16 +- tests/testthat/test-get_instruments.R | 18 +-- tests/testthat/test-get_instruments_cusip.R | 14 +- tests/testthat/test-get_market_hours.R | 20 +-- tests/testthat/test-get_market_hours_single.R | 20 +-- tests/testthat/test-get_movers.R | 34 ++---- tests/testthat/test-get_option_chains.R | 64 +++++------ tests/testthat/test-get_option_expiration_chain.R | 17 +-- tests/testthat/test-get_order_id.R | 34 +++--- tests/testthat/test-get_orders.R | 33 ++---- tests/testthat/test-get_orders_account.R | 47 ++++---- tests/testthat/test-get_price_history.R | 50 ++++----- tests/testthat/test-get_quotes.R | 24 ++-- tests/testthat/test-get_quotes_single_symbol.R | 22 ++-- tests/testthat/test-get_transaction.R | 34 +++--- tests/testthat/test-get_transactions.R | 54 ++++----- tests/testthat/test-get_user_preferences.R | 12 +- tests/testthat/test-place_order.R | 34 +++--- tests/testthat/test-replace_order.R | 42 +++---- 61 files changed, 1256 insertions(+), 774 deletions(-)
More information about charlesschwabapi at CRAN
Permanent link
Title: Automated Functional Annotation of Genetic Variants and Linked
Proxies
Description: To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 1.4.0 dated 2025-11-16 and 1.4.3 dated 2025-11-26
DESCRIPTION | 14 ++-- MD5 | 20 ++--- R/aaa.R | 2 R/data_funcs.R | 4 - R/misc_files.R | 135 ++++++++++++++++++++++----------------- R/parse_funcs.R | 15 ++-- R/runPipelineOnlist.R | 2 inst/doc/SNPannotator-intro.R | 6 - inst/doc/SNPannotator-intro.Rmd | 10 +- inst/doc/SNPannotator-intro.html | 12 +-- vignettes/SNPannotator-intro.Rmd | 10 +- 11 files changed, 128 insertions(+), 102 deletions(-)
Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision
trees and forests to Structural Equation Models (SEM). SEM trees hierarchically
split empirical data into homogeneous groups each sharing similar data patterns
with respect to a SEM by recursively selecting optimal predictors of these
differences. SEM forests are an extension of SEM trees. They are ensembles of
SEM trees each built on a random sample of the original data. By aggregating
over a forest, we obtain measures of variable importance that are more robust
than measures from single trees. A description of the method was published by
Brandmaier, von Oertzen, McArdle, & Lindenberger (2013) <doi:10.1037/a0030001>
and Arnold, Voelkle, & Brandmaier (2020) <doi:10.3389/fpsyg.2020.564403>.
Author: Andreas M. Brandmaier [aut, cre],
John J. Prindle [aut],
Manuel Arnold [aut],
Caspar J. Van Lissa [aut],
Moritz John [ctb]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
Diff between semtree versions 0.9.22 dated 2025-07-28 and 0.9.23 dated 2025-11-26
DESCRIPTION | 17 - MD5 | 107 ++++---- NEWS.md | 8 R/createBinaries.R | 1 R/fairSplit.R | 2 R/getModelType.R | 11 R/getPredictorsLavaan.R | 12 - R/getPredictorsOpenMx.R | 22 + R/growTree.R | 30 ++ R/naiveSplit.R | 19 - R/scoreSplit.R | 3 R/semtree.R | 17 + R/semtree.control.R | 14 - R/stoppingRuleDefault.R | 16 - R/surrogate.R |only build/vignette.rds |binary inst/doc/constraints.html | 53 ++-- inst/doc/forests.R | 10 inst/doc/forests.Rmd | 17 + inst/doc/forests.html | 322 +++++++++++++------------- inst/doc/future-parallel-semforest.R |only inst/doc/future-parallel-semforest.Rmd |only inst/doc/future-parallel-semforest.html |only inst/doc/getting-started.html | 6 inst/doc/score-based-tests.html | 30 +- inst/doc/semforest-focus.html | 32 +- inst/doc/spi-semtree.R |only inst/doc/spi-semtree.Rmd |only inst/doc/spi-semtree.html |only man/boruta.Rd | 130 +++++----- man/computePval_maxLR.Rd | 80 +++--- man/evaluateDataLikelihood.Rd | 84 +++---- man/evaluateTree.Rd | 106 ++++---- man/getParDiffForest.Rd | 70 ++--- man/getParDiffTree.Rd | 68 ++--- man/partialDependence.Rd | 106 ++++---- man/partialDependence_data.Rd | 94 +++---- man/partialDependence_growth.Rd | 126 +++++----- man/plotParDiffForest.Rd | 84 +++---- man/plotParDiffTree.Rd | 84 +++---- man/plotTreeStructure.Rd | 52 ++-- man/predict.semforest.Rd | 54 ++-- man/proximity.Rd | 96 ++++---- man/semforest.control.Rd | 80 +++--- man/semtree-package.Rd | 34 +- man/semtree.Rd | 232 +++++++++---------- man/semtree.control.Rd | 347 ++++++++++++++--------------- man/strip.Rd | 80 +++--- man/toTable.Rd | 56 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-basic-splitting-ext2.R | 4 tests/testthat/test-ncomp.R | 35 -- tests/testthat/test-openmx-lavaan.R | 2 tests/testthat/test-partial-dependence.R | 55 ++-- tests/testthat/test-semtree_control.R | 36 +-- tests/testthat/test.focus.R | 6 vignettes/forests.Rmd | 17 + vignettes/future-parallel-semforest.Rmd |only vignettes/spi-semtree.Rmd |only 59 files changed, 1505 insertions(+), 1462 deletions(-)
Title: Scalable and Efficient Derivation of Bioclimatic Variables
Description: Provides a high-performance framework for deriving bioclimatic and custom summary variables from
large-scale climate raster data. The package features a dual-backend architecture that intelligently switches
between fast in-memory processing for smaller datasets (via the 'terra' package) and a memory-safe tiled approach
for massive datasets that do not fit in RAM (via 'exactextractr' and 'Rfast'). The main functions,
derive_bioclim() and derive_statistics(), offer a unified interface with advanced options for
custom time periods and static indices, making it suitable for a wide range of ecological and
environmental modeling applications. A software note is in preparation. In the meantime, you can visit
the package website <https://gepinillab.github.io/fastbioclim/> to find tutorials in English and Spanish.
Author: Gonzalo E. Pinilla-Buitrago [aut, cre] ,
Luis Osorio-Olvera [aut]
Maintainer: Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>
Diff between fastbioclim versions 0.2.1 dated 2025-09-08 and 0.3.0 dated 2025-11-26
DESCRIPTION | 14 ++-- MD5 | 70 ++++++++++++----------- NAMESPACE | 2 NEWS.md | 15 +++++ R/average_fast.R | 30 +++++----- R/average_terra.R | 6 +- R/bioclim_fast.R | 90 ++++++++++++++++++------------ R/bioclim_terra.R | 8 +- R/calculate_average.R | 41 +++++++------ R/calculate_roll.R | 48 ++++++++-------- R/check_rasters.R | 13 ++-- R/derive_bioclim.R | 58 ++++++++++++------- R/derive_statistics.R | 37 ++++++------ R/helper_functions.R | 61 ++++---------------- R/roll_fast.R | 43 ++++++-------- R/roll_terra.R | 6 +- R/stats_fast.R | 139 ++++++++++++++++++++--------------------------- R/stats_terra.R | 5 + R/write_layers.R | 50 ++++++++-------- man/average_fast.Rd | 10 +++ man/average_terra.Rd | 2 man/bioclim_fast.Rd | 5 + man/bioclim_terra.Rd | 3 + man/calculate_average.Rd | 5 + man/calculate_roll.Rd | 5 + man/check_rasters.Rd | 4 + man/derive_bioclim.Rd | 3 + man/derive_statistics.Rd | 3 + man/roll_fast.Rd | 7 +- man/roll_terra.Rd | 3 - man/stats_fast.Rd | 3 - man/stats_terra.Rd | 1 man/write_layers.Rd | 15 +++-- tests |only 34 files changed, 423 insertions(+), 382 deletions(-)
Title: Image Processing Tools for Barnes Maze Experiments
Description: Tools to process the information obtained from experiments conducted in the Barnes Maze. These tools enable the detection of trajectories generated by subjects during trials, as well as the acquisition of precise coordinates and relevant statistical data regarding the results. Through this approach, it aims to facilitate the analysis and interpretation of observed behaviors, thereby contributing to a deeper understanding of learning and memory processes in such experiments.
Author: Antonio Guerrero [cre],
Vanessa Ramirez [aut],
Jorge Macias [ctb]
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>
Diff between BioTrajectory versions 1.0.1 dated 2025-06-06 and 1.1.0 dated 2025-11-26
BioTrajectory-1.0.1/BioTrajectory/R/heatmapFromPoints.R |only BioTrajectory-1.0.1/BioTrajectory/R/showTrajectory.R |only BioTrajectory-1.0.1/BioTrajectory/man/heatmapFromPoints.Rd |only BioTrajectory-1.0.1/BioTrajectory/man/showTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/DESCRIPTION | 8 - BioTrajectory-1.1.0/BioTrajectory/MD5 | 69 ++++++---- BioTrajectory-1.1.0/BioTrajectory/NAMESPACE | 31 +++- BioTrajectory-1.1.0/BioTrajectory/NEWS | 21 ++- BioTrajectory-1.1.0/BioTrajectory/R/centroid.R |only BioTrajectory-1.1.0/BioTrajectory/R/distanceToTarget.R | 14 -- BioTrajectory-1.1.0/BioTrajectory/R/distanceTraveled.R | 24 +-- BioTrajectory-1.1.0/BioTrajectory/R/getRadius.R | 1 BioTrajectory-1.1.0/BioTrajectory/R/getTrajectory.R | 48 ++++-- BioTrajectory-1.1.0/BioTrajectory/R/heatmapFromTrajectory.R |only BioTrajectory-1.1.0/BioTrajectory/R/interpolateTrajectory.R | 35 ++--- BioTrajectory-1.1.0/BioTrajectory/R/isClosed.R |only BioTrajectory-1.1.0/BioTrajectory/R/nearestTarget.R | 28 +--- BioTrajectory-1.1.0/BioTrajectory/R/normalVectors.R |only BioTrajectory-1.1.0/BioTrajectory/R/readtrackData.R | 8 - BioTrajectory-1.1.0/BioTrajectory/R/reverseTrajectory.R |only BioTrajectory-1.1.0/BioTrajectory/R/selFrame.R | 1 BioTrajectory-1.1.0/BioTrajectory/R/smoothTrajectory.R |only BioTrajectory-1.1.0/BioTrajectory/R/subsampleTrajectory.R |only BioTrajectory-1.1.0/BioTrajectory/R/tangentVectors.R |only BioTrajectory-1.1.0/BioTrajectory/R/trajectory.R |only BioTrajectory-1.1.0/BioTrajectory/R/trimTrajectory.R |only BioTrajectory-1.1.0/BioTrajectory/man/as.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/centroid.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/distanceToTarget.Rd | 9 - BioTrajectory-1.1.0/BioTrajectory/man/distanceTraveled.Rd | 17 -- BioTrajectory-1.1.0/BioTrajectory/man/getRadius.Rd | 2 BioTrajectory-1.1.0/BioTrajectory/man/getTrajectory.Rd | 41 +++-- BioTrajectory-1.1.0/BioTrajectory/man/heatmapFromTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/interpolateTrajectory.Rd | 19 -- BioTrajectory-1.1.0/BioTrajectory/man/is.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/isClosed.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/length.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/nearestTarget.Rd | 20 -- BioTrajectory-1.1.0/BioTrajectory/man/normalVectors.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/or.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/plot.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/print.summary.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/readtrackData.Rd | 5 BioTrajectory-1.1.0/BioTrajectory/man/reverseTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/smoothTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/subsampleTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/summary.trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/tangentVectors.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/trajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/trimTrajectory.Rd |only BioTrajectory-1.1.0/BioTrajectory/man/videoToFrames.Rd | 2 51 files changed, 209 insertions(+), 194 deletions(-)
Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS'
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [ctb]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.9 dated 2023-08-07 and 1.0.10 dated 2025-11-26
DESCRIPTION | 18 - MD5 | 34 +- NEWS.md | 4 R/dimensionality_reduction.R | 2 R/package.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/anndata.R | 2 inst/doc/anndata.html | 449 +++++++++++++++++++++++++++---------- inst/doc/ginhoux.R | 2 inst/doc/ginhoux.html | 417 ++++++++++++++++++++++++++-------- inst/doc/simulated-data.R | 6 inst/doc/simulated-data.html | 420 ++++++++++++++++++++++++++-------- inst/doc/singlecellexperiment.R | 2 inst/doc/singlecellexperiment.html | 424 +++++++++++++++++++++++++--------- man/SCORPIUS-package.Rd | 18 + man/reduce_dimensionality.Rd | 2 man/ti_scorpius.Rd | 4 18 files changed, 1342 insertions(+), 465 deletions(-)
Title: Gene Scoring from Count Tables
Description: Provides methods for automatic calculation of gene scores from gene count tables, including a Z-score method that requires a table of samples being scored and a count table with control samples; a geometric mean method that does not rely on control samples; and a principal component-based method that summarizes gene expression using user-selected principal components. The Z-score and geometric mean approaches are described in Kim et al. (2018) <doi:10.1089/jir.2017.0127>.
Author: Aris Syntakas [aut, cre]
Maintainer: Aris Syntakas <sejjsyn@ucl.ac.uk>
Diff between GeneScoreR versions 0.1.1 dated 2024-10-25 and 0.2.0 dated 2025-11-26
DESCRIPTION | 11 ++++++----- MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS.md |only R/geomean_calculator.R | 22 ++++++++++++++++------ R/pcscore_calculator.R |only R/z_score_calculator.R | 37 +++++++++++++++++++++++++------------ man/geomean.Rd | 15 +++++++++++---- man/pcscore.Rd |only man/zscore.Rd | 19 ++++++++++++------- 10 files changed, 81 insertions(+), 40 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.82 dated 2025-10-30 and 2.4.83 dated 2025-11-26
BCEA-2.4.82/BCEA/man/mce.plot.Rd |only BCEA-2.4.83/BCEA/DESCRIPTION | 6 - BCEA-2.4.83/BCEA/MD5 | 90 +++++++++---------- BCEA-2.4.83/BCEA/NEWS.md | 15 +++ BCEA-2.4.83/BCEA/R/BCEA-deprecated.R | 2 BCEA-2.4.83/BCEA/R/CEriskav.default.R | 3 BCEA-2.4.83/BCEA/R/CEriskav_plot_graph.R | 8 - BCEA-2.4.83/BCEA/R/ceac.plot.R | 4 BCEA-2.4.83/BCEA/R/ceaf.plot.R | 8 - BCEA-2.4.83/BCEA/R/ceef.plot.R | 8 - BCEA-2.4.83/BCEA/R/ceplane.plot.R | 9 - BCEA-2.4.83/BCEA/R/ceplane_plot_graph.R | 80 +++++++++-------- BCEA-2.4.83/BCEA/R/contour.R | 4 BCEA-2.4.83/BCEA/R/contour2.R | 4 BCEA-2.4.83/BCEA/R/contour_ggplot_params.R | 8 + BCEA-2.4.83/BCEA/R/eib.plot.R | 4 BCEA-2.4.83/BCEA/R/evi.plot.mixedAn.R | 3 BCEA-2.4.83/BCEA/R/ib.plot.R | 8 - BCEA-2.4.83/BCEA/R/ib_plot_ggplot.R | 2 BCEA-2.4.83/BCEA/R/info.rank.R | 7 - BCEA-2.4.83/BCEA/R/mce.plot.R | 128 +++------------------------- BCEA-2.4.83/BCEA/R/plot.CEriskav.R | 8 - BCEA-2.4.83/BCEA/R/plot.bcea.R | 8 - BCEA-2.4.83/BCEA/R/plot.evppi.R | 13 ++ BCEA-2.4.83/BCEA/R/plot.mixedAn.R | 6 - BCEA-2.4.83/BCEA/R/select_plot_type.R | 3 BCEA-2.4.83/BCEA/R/zzz.R | 11 +- BCEA-2.4.83/BCEA/build/partial.rdb |binary BCEA-2.4.83/BCEA/build/vignette.rds |binary BCEA-2.4.83/BCEA/inst/doc/BCEA_package.R |only BCEA-2.4.83/BCEA/inst/doc/BCEA_package.Rmd | 5 + BCEA-2.4.83/BCEA/man/BCEA-deprecated.Rd | 73 ++++++++++++++- BCEA-2.4.83/BCEA/man/GrassmannOptim.Rd | 4 BCEA-2.4.83/BCEA/man/ceac.plot.Rd | 11 +- BCEA-2.4.83/BCEA/man/ceaf.plot.Rd | 10 +- BCEA-2.4.83/BCEA/man/ceef.plot.Rd | 10 +- BCEA-2.4.83/BCEA/man/ceplane.plot.Rd | 8 + BCEA-2.4.83/BCEA/man/contour.Rd | 11 +- BCEA-2.4.83/BCEA/man/contour2.Rd | 11 +- BCEA-2.4.83/BCEA/man/eib.plot.Rd | 11 +- BCEA-2.4.83/BCEA/man/evi.plot.mixedAn.Rd | 3 BCEA-2.4.83/BCEA/man/ib.plot.Rd | 10 +- BCEA-2.4.83/BCEA/man/info.rank.Rd | 11 +- BCEA-2.4.83/BCEA/man/plot.CEriskav.Rd | 10 +- BCEA-2.4.83/BCEA/man/plot.bcea.Rd | 10 +- BCEA-2.4.83/BCEA/man/plot.evppi.Rd | 3 BCEA-2.4.83/BCEA/vignettes/BCEA_package.Rmd | 5 + 47 files changed, 350 insertions(+), 306 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to
Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>,
Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>,
Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>,
Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>,
Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and
Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Author: Romain Leroux [aut, cre] ,
France Mentre [aut] ,
Jeremy Seurat [ctb]
Maintainer: Romain Leroux <romainlerouxPFIM@gmail.com>
Diff between PFIM versions 7.0 dated 2025-07-02 and 7.0.1 dated 2025-11-26
DESCRIPTION | 13 MD5 | 56 R/PSOAlgorithm.R | 25 R/PopulationFim.R | 4 inst/CITATION | 5 inst/doc/Example01.R | 19 inst/doc/Example01.Rmd | 23 inst/doc/Example01.html | 617 ++++------ inst/doc/Example02.R | 82 - inst/doc/Example02.Rmd | 97 - inst/doc/Example02.html | 459 +++---- inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmBayesianFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmIndividualFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmPopulationFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmBayesianFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmIndividualFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmPopulationFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmBayesianFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmIndividualFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmPopulationFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmBayesianFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmIndividualFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmPopulationFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmBayesianFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmIndividualFIM.Rmd | 2 inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmPopulationFIM.Rmd | 2 man/PFIM-package.Rd | 206 +-- vignettes/Example01.Rmd | 23 vignettes/Example02.Rmd | 97 - 29 files changed, 848 insertions(+), 908 deletions(-)
Title: Fast Computation of Latent Correlations for Mixed Data
Description: The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated),
comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation.
The estimation is based on latent copula Gaussian models.
For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017).
For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <doi:10.48550/arXiv.1809.06255>.
For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>.
For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.
Author: Mingze Huang [aut] ,
Grace Yoon [aut] ,
Christian Müller [aut] ,
Irina Gaynanova [aut, cre]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between latentcor versions 2.0.1 dated 2022-09-05 and 2.0.2 dated 2025-11-26
DESCRIPTION | 28 MD5 | 82 - NAMESPACE | 68 - NEWS.md | 48 R/evaluation.R | 194 +-- R/gen_data.R | 211 +-- R/get_types.R | 104 - R/internal.R | 758 ++++++------ R/interpolant.R | 34 R/interpolation.R | 98 - R/ipol.R | 164 +- R/latentcor.R | 258 ++-- R/multilinear.R | 80 - R/tools.R | 102 - README.md | 260 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/latentcor.R | 198 +-- inst/doc/latentcor.Rmd | 430 +++--- inst/doc/latentcor.html | 1598 ++++++++++++------------- inst/doc/latentcor_math.R | 166 +- inst/doc/latentcor_math.Rmd | 1102 ++++++++--------- inst/doc/latentcor_math.html | 2522 ++++++++++++++++++++-------------------- man/evaluation.Rd | 128 +- man/examples/latentcor_ex.R | 39 man/gen_data.Rd | 145 +- man/get_types.Rd | 54 man/interpolant.Rd | 54 man/interpolation.Rd | 110 - man/ipol.Rd | 116 - man/latentcor.Rd | 173 +- man/mlappx.real.Rd | 74 - tests/testthat.R | 8 tests/testthat/test_encodeX.R | 14 tests/testthat/test_gen_data.R | 56 tests/testthat/test_get_types.R | 12 tests/testthat/test_latentcor.R | 384 +++--- tests/testthat/test_original.R | 118 - tests/testthat/test_zratio.R | 44 vignettes/latentcor.Rmd | 430 +++--- vignettes/latentcor.bib | 234 +-- vignettes/latentcor_math.Rmd | 1102 ++++++++--------- 42 files changed, 5905 insertions(+), 5895 deletions(-)
Title: Penalized Likelihood in Gaussian Processes
Description: Implements maximum likelihood estimation for Gaussian processes, supporting both isotropic and separable models with predictive capabilities. Includes penalized likelihood estimation following Li and Sudjianto (2005, <doi:10.1198/004017004000000671>), with cross-validation guided by decorrelated prediction error (DPE) metric. DPE metric, motivated by Mahalanobis distance, serves as evaluation criteria that accounts for predictive uncertainty in tuning parameter selection (Mutoh, Booth, and Stallrich, 2025, <doi:10.48550/arXiv.2511.18111>). Designed specifically for small datasets.
Author: Ayumi Mutoh [aut, cre]
Maintainer: Ayumi Mutoh <amutoh@ncsu.edu>
Diff between GPpenalty versions 1.0.0 dated 2025-11-15 and 1.0.1 dated 2025-11-26
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 7 ++++++- R/GPpenalty-package.R | 4 ++-- R/gp_cv.R | 7 ++++--- R/miscellaneous.R | 46 +--------------------------------------------- R/mle_gp.R | 3 +-- R/mle_penalty.R | 4 ++-- man/GPpenalty-package.Rd | 4 ++-- man/gp_cv.Rd | 2 +- man/kernel.Rd | 2 +- man/mle_gp.Rd | 2 +- man/mle_penalty.Rd | 4 ++-- 13 files changed, 39 insertions(+), 78 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [aut]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.9.0 dated 2025-08-22 and 1.0.0 dated 2025-11-26
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++++------------- NAMESPACE | 3 +++ NEWS.md | 6 ++++++ R/fc_filter.R | 5 ++++- R/fc_merge.R | 2 ++ R/fc_stack.R | 2 ++ R/plot.R |only R/print.R |only R/summary.R |only README.md | 2 +- man/plot.fc.Rd |only man/print.fc.Rd |only man/summary.fc.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/utils.md | 30 +----------------------------- tests/testthat/test-fc_draw.R | 7 +++++++ tests/testthat/test-fc_stack.R | 12 +++++++++++- tests/testthat/test-utils.R | 2 +- tests/testthat/test.pdf |binary 20 files changed, 60 insertions(+), 49 deletions(-)
Title: Canadian Hydrological Analyses
Description: A collection of user-submitted functions to aid in the analysis of hydrological data, particularly for users in Canada. The functions focus on the use of Canadian data sets, and are suited to Canadian hydrology, such as the important cold region hydrological processes and will work with Canadian hydrological models. The functions are grouped into several themes, currently including Statistical hydrology, Basic data manipulations, Visualization, and Spatial hydrology. Functions developed by the Floodnet project are also included. CSHShydRology has been developed with the assistance of the Canadian Society for Hydrological Sciences (CSHS) which is an affiliated society of the Canadian Water Resources Association (CWRA). As of version 1.2.6, functions now fail gracefully when attempting to download data from a url which is unavailable.
Author: Kevin Shook [cre, aut],
Paul Whitfield [aut],
Robert Chlumsky [aut],
Daniel Moore [aut],
Martin Durocher [aut],
Matthew Lemieux [ctb],
Jason Chiang [ctb],
Joel Trubilowicz [ctb],
SJ Kim [ctb]
Maintainer: Kevin Shook <kevin.shook@usask.ca>
Diff between CSHShydRology versions 1.4.3 dated 2025-08-26 and 1.4.4 dated 2025-11-26
CSHShydRology-1.4.3/CSHShydRology/R/ch_flow_raster_trend.R |only CSHShydRology-1.4.3/CSHShydRology/R/ch_hydrograph_plot.R |only CSHShydRology-1.4.3/CSHShydRology/inst/doc/hydrograph_plot.R |only CSHShydRology-1.4.3/CSHShydRology/inst/doc/hydrograph_plot.Rmd |only CSHShydRology-1.4.3/CSHShydRology/inst/doc/hydrograph_plot.html |only CSHShydRology-1.4.3/CSHShydRology/man/ch_flow_raster_trend.Rd |only CSHShydRology-1.4.3/CSHShydRology/man/ch_hydrograph_plot.Rd |only CSHShydRology-1.4.3/CSHShydRology/vignettes/hydrograph_plot.Rmd |only CSHShydRology-1.4.4/CSHShydRology/DESCRIPTION | 15 CSHShydRology-1.4.4/CSHShydRology/MD5 | 46 +- CSHShydRology-1.4.4/CSHShydRology/NAMESPACE | 8 CSHShydRology-1.4.4/CSHShydRology/NEWS.md | 4 CSHShydRology-1.4.4/CSHShydRology/R/Visualization_functions.R | 6 CSHShydRology-1.4.4/CSHShydRology/R/ch_flow_raster.R | 2 CSHShydRology-1.4.4/CSHShydRology/R/ch_flow_raster_qa.R | 2 CSHShydRology-1.4.4/CSHShydRology/R/ch_gg_hydrographs.R |only CSHShydRology-1.4.4/CSHShydRology/R/ch_model_hydrograph.R |only CSHShydRology-1.4.4/CSHShydRology/R/ch_qa_hydrograph.R | 224 +++++----- CSHShydRology-1.4.4/CSHShydRology/R/ch_slice.R | 2 CSHShydRology-1.4.4/CSHShydRology/R/utils.R | 2 CSHShydRology-1.4.4/CSHShydRology/build/vignette.rds |binary CSHShydRology-1.4.4/CSHShydRology/inst/doc/ch_model_hydrograph.R |only CSHShydRology-1.4.4/CSHShydRology/inst/doc/ch_model_hydrograph.Rmd |only CSHShydRology-1.4.4/CSHShydRology/inst/doc/ch_model_hydrograph.html |only CSHShydRology-1.4.4/CSHShydRology/man/Visualization-functions.Rd | 6 CSHShydRology-1.4.4/CSHShydRology/man/ch_flow_raster.Rd | 2 CSHShydRology-1.4.4/CSHShydRology/man/ch_flow_raster_qa.Rd | 2 CSHShydRology-1.4.4/CSHShydRology/man/ch_gg_hydrographs.Rd |only CSHShydRology-1.4.4/CSHShydRology/man/ch_model_hydrograph.Rd |only CSHShydRology-1.4.4/CSHShydRology/man/ch_qa_hydrograph.Rd | 3 CSHShydRology-1.4.4/CSHShydRology/man/ch_slice.Rd | 2 CSHShydRology-1.4.4/CSHShydRology/vignettes/ch_model_hydrograph.Rmd |only 32 files changed, 169 insertions(+), 157 deletions(-)
Title: Small Area Estimation using Hierarchical Bayesian Method
Description: Provides several functions for area level of small area estimation using hierarchical Bayesian (HB) methods with several univariate distributions for variables of interest. The dataset that is used in every function is generated accordingly in the Example. The 'rjags' package is employed to obtain parameter estimates. Model-based estimators involve the HB estimators which include the mean and the variation of mean. For the reference, see Rao and Molina (2015) <doi:10.1002/9781118735855>.
Author: Zaza Yuda Perwira [aut, cre, cph],
Azka Ubaidillah [aut],
Ridson Al Farizal P [aut],
Ika Yuni Wulansari [aut]
Maintainer: Zaza Yuda Perwira <zazayudaperwira93@gmail.com>
Diff between saeHB versions 0.2.2 dated 2023-11-08 and 0.2.3 dated 2025-11-26
saeHB-0.2.2/saeHB/man/saeHB.Rd |only saeHB-0.2.3/saeHB/DESCRIPTION | 53 +- saeHB-0.2.3/saeHB/MD5 | 74 +-- saeHB-0.2.3/saeHB/NAMESPACE | 45 +- saeHB-0.2.3/saeHB/R/Beta.R | 523 ++++++++++++++----------- saeHB-0.2.3/saeHB/R/BetaDeff.R |only saeHB-0.2.3/saeHB/R/Binomial.R | 306 +++++++------- saeHB-0.2.3/saeHB/R/Exponential.R | 300 +++++++------- saeHB-0.2.3/saeHB/R/ExponentialDouble.R | 329 +++++++-------- saeHB-0.2.3/saeHB/R/Gamma.R | 333 +++++++-------- saeHB-0.2.3/saeHB/R/Logistic.R | 324 +++++++-------- saeHB-0.2.3/saeHB/R/Lognormal.R | 333 +++++++-------- saeHB-0.2.3/saeHB/R/NegativeBinomial.R | 317 +++++++-------- saeHB-0.2.3/saeHB/R/Normal.R | 313 +++++++------- saeHB-0.2.3/saeHB/R/Poisson.R | 286 ++++++------- saeHB-0.2.3/saeHB/R/PoissonGamma.R | 292 ++++++------- saeHB-0.2.3/saeHB/R/Student_t.R | 360 ++++++++--------- saeHB-0.2.3/saeHB/R/Student_tnc.R | 362 ++++++++--------- saeHB-0.2.3/saeHB/R/Weibull.R | 369 ++++++++--------- saeHB-0.2.3/saeHB/R/saeHB.R | 7 saeHB-0.2.3/saeHB/README.md | 1 saeHB-0.2.3/saeHB/build/vignette.rds |binary saeHB-0.2.3/saeHB/inst/doc/saeHB_vignette.R | 2 saeHB-0.2.3/saeHB/inst/doc/saeHB_vignette.html | 4 saeHB-0.2.3/saeHB/man/Beta.Rd | 92 ++-- saeHB-0.2.3/saeHB/man/BetaDeff.Rd |only saeHB-0.2.3/saeHB/man/Binomial.Rd | 68 +-- saeHB-0.2.3/saeHB/man/Exponential.Rd | 55 +- saeHB-0.2.3/saeHB/man/ExponentialDouble.Rd | 60 +- saeHB-0.2.3/saeHB/man/Gamma.Rd | 57 +- saeHB-0.2.3/saeHB/man/Logistic.Rd | 57 +- saeHB-0.2.3/saeHB/man/Lognormal.Rd | 59 +- saeHB-0.2.3/saeHB/man/NegativeBinomial.Rd | 51 +- saeHB-0.2.3/saeHB/man/Normal.Rd | 59 +- saeHB-0.2.3/saeHB/man/Poisson.Rd | 31 - saeHB-0.2.3/saeHB/man/PoissonGamma.Rd | 34 - saeHB-0.2.3/saeHB/man/Student_t.Rd | 57 +- saeHB-0.2.3/saeHB/man/Student_tnc.Rd | 59 +- saeHB-0.2.3/saeHB/man/Weibull.Rd | 62 +- saeHB-0.2.3/saeHB/man/saeHB-package.Rd |only 40 files changed, 2894 insertions(+), 2840 deletions(-)
Title: A Modular Two-Step Convex Optimization Estimator for Ill-Posed
Problems
Description: Convex Least Squares Programming (CLSP) is a two-step estimator
for solving underdetermined, ill-posed, or structurally constrained
least-squares problems. It combines pseudoinverse-based estimation with
convex-programming correction methods inspired by Lasso, Ridge, and
Elastic Net to ensure numerical stability, constraint enforcement, and
interpretability. The package also provides numerical stability analysis
and CLSP-specific diagnostics, including partial R^2, normalized RMSE
(NRMSE), Monte Carlo t-tests for mean NRMSE, and condition-number-based
confidence bands.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rclsp versions 0.1.0 dated 2025-11-17 and 0.2.0 dated 2025-11-26
DESCRIPTION | 6 +-- MD5 | 6 +-- R/clsp.R | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++++++------ man/clsp.Rd | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 172 insertions(+), 15 deletions(-)
Title: Inference on the Generalization Error
Description: Confidence interval and resampling methods for inference on
the generalization error.
Author: Sebastian Fischer [cre, aut] ,
Hannah Schulz-Kuempel [aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3inferr versions 0.2.0 dated 2025-08-28 and 0.2.1 dated 2025-11-26
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/MeasureAbstractCi.R | 2 +- R/ResamplingNestedCV.R | 4 ---- README.md | 8 ++++---- tests/testthat/test_MeasureCiCorT.R | 8 ++++++++ 7 files changed, 27 insertions(+), 18 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nicholasehamilton@gmail.com>
Diff between ggtern versions 3.5.0 dated 2024-03-24 and 4.0.0 dated 2025-11-26
DESCRIPTION | 74 ++++++++---------- MD5 | 152 ++++++++++++++++++------------------- NAMESPACE | 8 - NEWS | 7 + R/aes.R | 50 +++++++++++- R/annotation-raster-tern.R | 3 R/calc-kde2d-weighted.R | 2 R/coord-tern.R | 86 +++++++++++++++----- R/doc-data.R | 18 ++-- R/doc-theme-convenience.R | 4 R/geom-Xisoprop.R | 29 ++++--- R/geom-Xline.R | 50 +++++++----- R/geom-confidence-tern.R | 4 R/geom-crosshair-tern.R | 10 +- R/geom-density-tern.R | 4 R/geom-errorbarX.R | 2 R/geom-hex-tern.R | 6 - R/geom-interpolate-tern.R | 2 R/geom-mean-ellipse.R | 4 R/geom-polygon-closed.R | 2 R/geom-smooth-tern.R | 6 - R/geom-tri-tern.R | 4 R/gg-internal.R | 27 +++++- R/ggtern-package.R | 15 +-- R/labels-new.R | 10 +- R/onLoad.R | 2 R/plot-build.R | 106 +++++++++++++++---------- R/plot.R | 91 +++++++++++++++------- R/scales-tern.R | 8 - R/stat-confidence-tern.R | 2 R/stat-density-tern.R | 8 - R/stat-mean-ellipse.R | 2 R/strip-unapproved.R | 66 +++++++++++++--- R/theme-defaults.R | 43 +++++----- R/theme-elements.R | 14 ++- R/theme-latex.R | 4 R/theme-showgrid.R | 2 R/theme-ticks.R | 10 +- R/utilities.R | 82 +++++++++++-------- README.md | 4 build/partial.rdb |binary man/annotate.Rd | 31 ++++++- man/annotation_raster_tern.Rd | 3 man/approved_layers.Rd | 6 - man/coord_tern.Rd | 8 + man/data_Feldspar.Rd | 1 man/data_Fragments.Rd | 7 - man/data_WhiteCells.Rd | 10 +- man/dot-getFunctions.Rd | 6 + man/geom_Xisoprop.Rd | 50 +++++++++--- man/geom_Xline.Rd | 41 ++++++++- man/geom_confidence_tern.Rd | 69 ++++++++++++---- man/geom_crosshair_tern.Rd | 73 +++++++++++++---- man/geom_density_tern.Rd | 81 ++++++++++++++----- man/geom_errorbarX.Rd | 73 +++++++++++++---- man/geom_hex_tern.Rd | 79 ++++++++++++++----- man/geom_interpolate_tern.Rd | 59 +++++++++++--- man/geom_label_viewport.Rd | 76 ++++++++++++++---- man/geom_mean_ellipse.Rd | 63 +++++++++++---- man/geom_point_swap.Rd | 73 +++++++++++++---- man/geom_polygon_closed.Rd | 73 +++++++++++++---- man/geom_smooth_tern.Rd | 59 +++++++++++--- man/geom_text_viewport.Rd | 73 +++++++++++++---- man/geom_tri_tern.Rd | 58 ++++++++++---- man/ggplot_build.Rd | 2 man/ggplot_gtable.Rd | 8 - man/ggtern_labels.Rd | 10 +- man/ggtern_package.Rd | 10 +- man/kde2d.weighted.Rd | 2 man/scale_X_continuous.Rd | 11 +- man/strip_unapproved.Rd | 2 man/theme_convenience_functions.Rd | 4 man/theme_elements.Rd | 2 man/theme_latex.Rd | 4 man/theme_showgrid.Rd | 2 man/theme_ticklength.Rd | 6 - man/undocumented.Rd | 25 ------ 77 files changed, 1496 insertions(+), 687 deletions(-)
Title: R Functions for Generalized Simulated Annealing
Description: Performs search for global minimum of a very complex non-linear
objective function with a very large number of optima.
Author: Sylvain Gubian [aut, cre],
Yang Xiang [aut],
Brian Suomela [aut],
Julia Hoeng [aut],
PMP SA. [aut]
Maintainer: Sylvain Gubian <DL.RSupport@pmi.com>
Diff between GenSA versions 1.1.14.1 dated 2024-09-21 and 1.1.15 dated 2025-11-26
DESCRIPTION | 33 +++++++++++++++++++++++++++------ MD5 | 6 +++--- NEWS | 19 ++++++++++++++----- src/Engine.cpp | 10 ++++------ 4 files changed, 48 insertions(+), 20 deletions(-)
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth [aut, cre],
Peter Reichert [aut]
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.2.9 dated 2021-12-10 and 1.2.10 dated 2025-11-26
DESCRIPTION | 20 MD5 | 36 R/msk.macrophytes.2017.prepare.data.R | 3292 ++++++++++++------------- R/msk.macrophytes.2017.read.compile.evaluate.R | 1056 ++++---- build/partial.rdb |binary data/ecoval_data.RData |binary inst/NEWS | 6 man/ecoval-package.Rd | 4 man/figures/lakemorphol2016.pdf |binary man/figures/lakemorphol2016.png |binary man/figures/lakemorphol2016French.pdf |binary man/figures/lakemorphol2016German.pdf |binary man/figures/lakemorphol2016German.png |binary man/lake.morphol.2016.create.Rd | 6 man/msk.fish.2004.create.Rd | 2 man/msk.invertebrates.2010.create.Rd | 2 man/msk.morphol.1998.aggregate.Rd | 2 man/msk.morphol.1998.create.Rd | 2 man/val.invertebrates.create.Rd | 2 19 files changed, 2222 insertions(+), 2208 deletions(-)
Title: Representing and Inferring Single-Cell Trajectories
Description: Provides functionality to infer trajectories from single-cell data,
represent them into a common format, and adapt them. Other biological information
can also be added, such as cellular grouping, RNA velocity and annotation.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynwrap versions 1.2.4 dated 2023-07-19 and 1.2.5 dated 2025-11-26
DESCRIPTION | 20 MD5 | 38 - NEWS.md | 4 R/method_create_ti_method_r.R | 7 R/method_process_definition.R | 12 R/wrap_add_dimred.R | 4 README.md | 64 - build/vignette.rds |binary inst/doc/create_ti_method_container.R | 32 inst/doc/create_ti_method_container.html | 527 +++++++++++----- inst/doc/create_ti_method_definition.R | 40 - inst/doc/create_ti_method_definition.Rmd | 2 inst/doc/create_ti_method_definition.html | 518 +++++++++++---- inst/doc/create_ti_method_r.R | 12 inst/doc/create_ti_method_r.html | 483 ++++++++++---- inst/doc/create_ti_method_wrappers.R | 8 inst/doc/create_ti_method_wrappers.html | 397 +++++++++--- tests/testthat/test-method_create_ti_method_container.R | 1 tests/testthat/test-wrap_add_timings.R | 2 vignettes/create_ti_method_definition.Rmd | 2 20 files changed, 1520 insertions(+), 653 deletions(-)
Title: Benchmark for Publication Bias Correction Methods
Description: Implements a unified interface for benchmarking meta-analytic
publication bias correction methods through simulation studies (see
Bartoš et al., 2025, <doi:10.48550/arXiv.2510.19489>). It provides
1) predefined data-generating mechanisms from the literature, 2) functions
for running meta-analytic methods on simulated data, 3) pre-simulated
datasets and pre-computed results for reproducible benchmarks, 4) tools for
visualizing and comparing method performance.
Author: Frantisek Bartos [aut, cre] ,
Samuel Pawel [aut] ,
Bjoern S. Siepe [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between PublicationBiasBenchmark versions 0.1.1 dated 2025-11-17 and 0.1.2 dated 2025-11-26
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/download.R | 14 +++++++++----- build/partial.rdb |binary inst/doc/Using_Precomputed_Results.R | 4 ++-- inst/doc/Using_Precomputed_Results.Rmd | 4 ++-- inst/doc/Using_Precomputed_Results.html | 4 ++-- vignettes/Using_Precomputed_Results.Rmd | 4 ++-- 9 files changed, 33 insertions(+), 24 deletions(-)
More information about PublicationBiasBenchmark at CRAN
Permanent link
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.6.0 dated 2025-11-08 and 0.7.0 dated 2025-11-26
DESCRIPTION | 13 +++++++------ MD5 | 27 ++++++++++++++++----------- NAMESPACE | 5 +++++ NEWS.md | 22 ++++++++++++++++++---- R/grouped_tbl_pivot_wider.R | 2 +- R/gtsummary_tests.R |only R/gtsummary_themes.R |only R/gtsummary_utilities.R | 19 +++++++++++-------- R/plot_multiple_answers.R | 15 +++++++++------ R/view_dictionary.R | 12 ++++++++++++ man/grouped_tbl_pivot_wider.Rd | 2 +- man/gtsummary_test.Rd |only man/gtsummary_themes.Rd |only man/gtsummary_utilities.Rd | 19 +++++++++++-------- man/plot_multiple_answers.Rd | 7 +++++-- man/view_dictionary.Rd | 13 +++++++++++++ tests/testthat/test-gtsummary-themes.R |only 17 files changed, 109 insertions(+), 47 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph]
,
Milan Straka [aut, cph] ,
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.13 dated 2025-11-26 and 0.8.14 dated 2025-11-26
DESCRIPTION | 27 +++++++++--------- MD5 | 18 ++++++------ NEWS.md | 4 ++ inst/doc/udpipe-annotation.html | 6 ++-- inst/doc/udpipe-parallel.html | 6 ++-- inst/doc/udpipe-train.html | 6 ++-- inst/doc/udpipe-tryitout.html | 4 +- inst/doc/udpipe-universe.html | 4 +- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 4 +- inst/doc/udpipe-usecase-topicmodelling.html | 4 +- 10 files changed, 44 insertions(+), 39 deletions(-)
Title: Multi-Horizon Probabilistic Ensemble with Copulas for Time
Series Forecasting
Description: Trains per-horizon probabilistic ensembles from a univariate time series. It supports 'rpart', 'glmnet', and 'kNN' engines with flexible residual distributions and heteroscedastic scale models, weighting variants by calibration-aware scores. A Gaussian/t copula couples the marginals to simulate joint forecast paths, returning quantiles, means, and step increments across horizons.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between organik versions 1.0.0 dated 2025-11-25 and 1.0.1 dated 2025-11-26
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 4 R/main.R | 245 +++++++++++++++++++++++---------------------------------- man/organik.Rd | 4 5 files changed, 115 insertions(+), 152 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak [aut, cre],
Chen Ling [aut]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.6.9 dated 2025-09-09 and 1.7.0 dated 2025-11-26
fmtr-1.6.9/fmtr/R/best_backup.R |only fmtr-1.6.9/fmtr/man/images/archive/fmtr2.png |only fmtr-1.6.9/fmtr/man/images/archive/mat_antique.svg |only fmtr-1.6.9/fmtr/man/images/archive/mat_star.svg |only fmtr-1.6.9/fmtr/man/images/archive/tree_large.png |only fmtr-1.6.9/fmtr/man/images/archive/tree_small.png |only fmtr-1.7.0/fmtr/DESCRIPTION | 20 fmtr-1.7.0/fmtr/MD5 | 81 +-- fmtr-1.7.0/fmtr/NAMESPACE | 1 fmtr-1.7.0/fmtr/NEWS.md | 6 fmtr-1.7.0/fmtr/R/datew.R |only fmtr-1.7.0/fmtr/R/fapply.R | 153 +++++- fmtr-1.7.0/fmtr/R/fmtr.R | 29 + fmtr-1.7.0/fmtr/R/helpers.R | 43 + fmtr-1.7.0/fmtr/README.md | 3 fmtr-1.7.0/fmtr/build/vignette.rds |binary fmtr-1.7.0/fmtr/inst/doc/fmtr-convenience.html | 4 fmtr-1.7.0/fmtr/inst/doc/fmtr-example1.Rmd | 2 fmtr-1.7.0/fmtr/inst/doc/fmtr-example1.html | 7 fmtr-1.7.0/fmtr/inst/doc/fmtr-example2.Rmd | 2 fmtr-1.7.0/fmtr/inst/doc/fmtr-example2.html | 7 fmtr-1.7.0/fmtr/inst/doc/fmtr-fapply.html | 9 fmtr-1.7.0/fmtr/inst/doc/fmtr-fapply2.html | 9 fmtr-1.7.0/fmtr/inst/doc/fmtr-faq.html | 5 fmtr-1.7.0/fmtr/inst/doc/fmtr-fcat.html | 9 fmtr-1.7.0/fmtr/inst/doc/fmtr-fdata.html | 9 fmtr-1.7.0/fmtr/inst/doc/fmtr-helpers.Rmd | 1 fmtr-1.7.0/fmtr/inst/doc/fmtr-helpers.html | 5 fmtr-1.7.0/fmtr/inst/doc/fmtr.html | 5 fmtr-1.7.0/fmtr/man/FormattingStrings.Rd | 253 ++++++----- fmtr-1.7.0/fmtr/man/fapply.Rd | 483 +++++++++++---------- fmtr-1.7.0/fmtr/man/fmt_cnt_pct.Rd | 1 fmtr-1.7.0/fmtr/man/fmt_mean_sd.Rd | 1 fmtr-1.7.0/fmtr/man/fmt_mean_stderr.Rd |only fmtr-1.7.0/fmtr/man/fmt_median.Rd | 1 fmtr-1.7.0/fmtr/man/fmt_n.Rd | 1 fmtr-1.7.0/fmtr/man/fmt_quantile_range.Rd | 1 fmtr-1.7.0/fmtr/man/fmt_range.Rd | 1 fmtr-1.7.0/fmtr/man/fmtr.Rd | 5 fmtr-1.7.0/fmtr/tests/testthat/test-best.R | 24 + fmtr-1.7.0/fmtr/tests/testthat/test-datew.R |only fmtr-1.7.0/fmtr/tests/testthat/test-fapply.R | 27 + fmtr-1.7.0/fmtr/tests/testthat/test-helpers.R | 15 fmtr-1.7.0/fmtr/vignettes/fmtr-example1.Rmd | 2 fmtr-1.7.0/fmtr/vignettes/fmtr-example2.Rmd | 2 fmtr-1.7.0/fmtr/vignettes/fmtr-helpers.Rmd | 1 46 files changed, 779 insertions(+), 449 deletions(-)
Title: Interface to 'AppEEARS' NASA Web Services
Description: Programmatic interface to the NASA Application for Extracting and Exploring Analysis Ready Samples services (AppEEARS; <https://appeears.earthdatacloud.nasa.gov/>).
The package provides easy access to analysis ready earth observation data in R.
Author: Koen Hufkens [aut, cre] ,
Elio Campitelli [ctb] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between appeears versions 1.1 dated 2023-09-15 and 1.2 dated 2025-11-26
DESCRIPTION | 17 - MD5 | 15 - R/rs_request.R | 2 R/service-appeears.R | 30 +- build/vignette.rds |binary inst/doc/appeears_vignette.R | 218 +++++++------- inst/doc/appeears_vignette.html | 586 ++++++++++++++++++++-------------------- man/figures |only man/rs_request.Rd | 2 9 files changed, 447 insertions(+), 423 deletions(-)
Title: 'REDCap' Data Management
Description: REDCap Data Management - 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data. REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on previously identified queries.
Author: Joao Carmezim [aut, cre],
Pau Satorra [aut],
Judith Penafiel [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 0.9.9 dated 2024-05-06 and 1.0.0 dated 2025-11-26
REDCapDM-0.9.9/REDCapDM/R/REDCapDM_PACKAGE.R |only REDCapDM-0.9.9/REDCapDM/R/utils-pipe.R |only REDCapDM-0.9.9/REDCapDM/inst/doc/Data-reading-and-processing.R |only REDCapDM-0.9.9/REDCapDM/inst/doc/Data-reading-and-processing.Rmd |only REDCapDM-0.9.9/REDCapDM/inst/doc/Data-reading-and-processing.html |only REDCapDM-0.9.9/REDCapDM/inst/doc/Queries.R |only REDCapDM-0.9.9/REDCapDM/inst/doc/Queries.Rmd |only REDCapDM-0.9.9/REDCapDM/inst/doc/Queries.html |only REDCapDM-0.9.9/REDCapDM/man/pipe.Rd |only REDCapDM-0.9.9/REDCapDM/vignettes/Data-reading-and-processing.Rmd |only REDCapDM-0.9.9/REDCapDM/vignettes/Queries.Rmd |only REDCapDM-0.9.9/REDCapDM/vignettes/markdown.css |only REDCapDM-1.0.0/REDCapDM/DESCRIPTION | 22 REDCapDM-1.0.0/REDCapDM/MD5 | 129 REDCapDM-1.0.0/REDCapDM/NAMESPACE | 14 REDCapDM-1.0.0/REDCapDM/R/REDCapDM-package.R |only REDCapDM-1.0.0/REDCapDM/R/check_queries.R | 220 - REDCapDM-1.0.0/REDCapDM/R/covican.R | 6 REDCapDM-1.0.0/REDCapDM/R/rd_checkbox.R |only REDCapDM-1.0.0/REDCapDM/R/rd_dates.R |only REDCapDM-1.0.0/REDCapDM/R/rd_delete_vars.R |only REDCapDM-1.0.0/REDCapDM/R/rd_dictionary.R |only REDCapDM-1.0.0/REDCapDM/R/rd_event.R | 557 ++- REDCapDM-1.0.0/REDCapDM/R/rd_export.R | 121 REDCapDM-1.0.0/REDCapDM/R/rd_factor.R |only REDCapDM-1.0.0/REDCapDM/R/rd_insert_na.R | 297 + REDCapDM-1.0.0/REDCapDM/R/rd_query.R | 1495 +++++----- REDCapDM-1.0.0/REDCapDM/R/rd_recalculate.R |only REDCapDM-1.0.0/REDCapDM/R/rd_rlogic.R | 484 +-- REDCapDM-1.0.0/REDCapDM/R/rd_split.R |only REDCapDM-1.0.0/REDCapDM/R/rd_transform.R | 452 +-- REDCapDM-1.0.0/REDCapDM/R/redcap_data.R | 449 +-- REDCapDM-1.0.0/REDCapDM/R/suplementary_package.R | 126 REDCapDM-1.0.0/REDCapDM/R/utils-suplement.R |only REDCapDM-1.0.0/REDCapDM/R/utils-transform.R | 324 +- REDCapDM-1.0.0/REDCapDM/R/zzz.R | 7 REDCapDM-1.0.0/REDCapDM/README.md | 57 REDCapDM-1.0.0/REDCapDM/build/vignette.rds |binary REDCapDM-1.0.0/REDCapDM/inst/doc/REDCapDM.R | 249 + REDCapDM-1.0.0/REDCapDM/inst/doc/REDCapDM.Rmd | 449 +-- REDCapDM-1.0.0/REDCapDM/inst/doc/REDCapDM.html | 1445 +++++---- REDCapDM-1.0.0/REDCapDM/man/REDCapDM-package.Rd | 89 REDCapDM-1.0.0/REDCapDM/man/check_proj.Rd |only REDCapDM-1.0.0/REDCapDM/man/check_queries.Rd | 136 REDCapDM-1.0.0/REDCapDM/man/checkbox_names.Rd | 40 REDCapDM-1.0.0/REDCapDM/man/covican.Rd | 56 REDCapDM-1.0.0/REDCapDM/man/figures/Thumbs.db |binary REDCapDM-1.0.0/REDCapDM/man/figures/lifecycle-deprecated.svg |only REDCapDM-1.0.0/REDCapDM/man/figures/lifecycle-experimental.svg |only REDCapDM-1.0.0/REDCapDM/man/figures/lifecycle-stable.svg |only REDCapDM-1.0.0/REDCapDM/man/figures/lifecycle-superseded.svg |only REDCapDM-1.0.0/REDCapDM/man/figures/logo.png |binary REDCapDM-1.0.0/REDCapDM/man/fill_data.Rd | 10 REDCapDM-1.0.0/REDCapDM/man/rd_checkbox.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_dates.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_delete_vars.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_dictionary.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_event.Rd | 136 REDCapDM-1.0.0/REDCapDM/man/rd_export.Rd | 81 REDCapDM-1.0.0/REDCapDM/man/rd_factor.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_insert_na.Rd | 97 REDCapDM-1.0.0/REDCapDM/man/rd_query.Rd | 211 - REDCapDM-1.0.0/REDCapDM/man/rd_recalculate.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_rlogic.Rd | 94 REDCapDM-1.0.0/REDCapDM/man/rd_split.Rd |only REDCapDM-1.0.0/REDCapDM/man/rd_transform.Rd | 147 REDCapDM-1.0.0/REDCapDM/man/recalculate.Rd | 8 REDCapDM-1.0.0/REDCapDM/man/redcap_data.Rd | 146 REDCapDM-1.0.0/REDCapDM/man/round.Rd |only REDCapDM-1.0.0/REDCapDM/man/split_event.Rd | 8 REDCapDM-1.0.0/REDCapDM/man/split_form.Rd | 8 REDCapDM-1.0.0/REDCapDM/man/to_factor.Rd | 10 REDCapDM-1.0.0/REDCapDM/man/transform_checkboxes.Rd | 8 REDCapDM-1.0.0/REDCapDM/tests |only REDCapDM-1.0.0/REDCapDM/vignettes/REDCapDM.Rmd | 449 +-- 75 files changed, 4918 insertions(+), 3719 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.8.0 dated 2025-11-06 and 1.8.1 dated 2025-11-26
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 4 +++ src/local_search.c | 32 ++++++++++-------------- tests/testthat/test_OptimizerBatchLocalSearch.R | 22 ++++++++++++++++ tests/testthat/test_c_functions.R | 20 +++++++++++++++ 6 files changed, 68 insertions(+), 26 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.5 dated 2025-05-09 and 1.0.7 dated 2025-11-26
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 14 + R/findStartData.R | 24 ++ R/readActicalCount.R | 4 R/readAxivity.R | 2 R/readParmayMatrix.R | 312 +++++++++++++++++++++++++-------- README.md | 2 man/GGIRread-package.Rd | 4 man/findStartData.Rd | 6 man/readParmayMatrix.Rd | 8 tests/testthat/test_readParmayMatrix.R | 4 12 files changed, 309 insertions(+), 101 deletions(-)
Title: GeoJSON to Simple Feature Converter
Description: Converts Between GeoJSON and simple feature objects.
Author: David Cooley [aut, cre],
Andy Teucher [ctb]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between geojsonsf versions 2.0.3 dated 2022-05-30 and 2.0.5 dated 2025-11-26
DESCRIPTION | 25 MD5 | 28 NEWS.md | 8 R/geojson_sf.R | 2 README.md | 35 - build/vignette.rds |binary inst/doc/geojson-sf-conversions.Rmd | 2 inst/doc/geojson-sf-conversions.html | 572 +++++++++--------- inst/include/geojsonsf/geojson/geojson_properties.hpp | 37 - inst/tinytest/test-geojson_sf.R | 54 + man/geojson_sf.Rd | 2 man/geojson_sfc.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 vignettes/geojson-sf-conversions.Rmd | 2 15 files changed, 420 insertions(+), 353 deletions(-)
Title: Genetic Population Level Functions
Description: This collection of gene representation-independent functions
implements the population layer of extended evolutionary and genetic
algorithms and its support. The population layer consists of functions
for initializing, logging, observing, evaluating a population of genes,
as well as of computing the next population. For parallel evaluation of a
population of genes 4 execution models - named Sequential, MultiCore,
FutureApply, and Cluster - are provided. They are implemented by
configuring the lapply() function. The execution model FutureApply can be
externally configured as recommended by Bengtsson (2021)
<doi:10.32614/RJ-2021-048>. Configurable acceptance rules and cooling
schedules (see Kirkpatrick, S., Gelatt, C. D. J, and Vecchi, M. P. (1983)
<doi:10.1126/science.220.4598.671>, and Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7) offer simulated annealing or greedy randomized
approximate search procedure elements. Adaptive crossover and mutation
rates depending on po [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPopulation versions 1.0.0.10 dated 2025-08-22 and 1.0.0.11 dated 2025-11-26
DESCRIPTION | 10 ++++++---- MD5 | 7 ++++--- NEWS | 4 ++++ R/xegaEvalPopulation.R | 2 +- inst |only 5 files changed, 15 insertions(+), 8 deletions(-)
More information about xegaPopulation at CRAN
Permanent link
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.12 dated 2025-09-04 and 0.8.13 dated 2025-11-26
DESCRIPTION | 8 MD5 | 248 - NAMESPACE | 242 - NEWS.md | 470 +- R/RcppExports.R | 70 R/datasets.R | 254 - R/nlp_collocation.R | 230 - R/nlp_cooccurrence.R | 472 +- R/nlp_dependency_parsing.R | 304 - R/nlp_dependency_utlities.R | 862 ++--- R/nlp_flow.R | 3004 +++++++++--------- R/nlp_morphological.R | 254 - R/nlp_phrase_sequences.R | 360 +- R/nlp_rake.R | 186 - R/pkg.R | 20 R/sentiment.R | 382 +- R/topicmodels.R | 288 - R/udpipe_models.R | 996 ++--- R/udpipe_parse.R | 1034 +++--- R/udpipe_reconstruct.R | 352 +- R/udpipe_train.R | 738 ++-- R/utils.R | 1808 +++++----- README.md | 200 - build/vignette.rds |binary inst/doc/udpipe-annotation.R | 158 inst/doc/udpipe-annotation.Rmd | 366 +- inst/doc/udpipe-annotation.html | 1152 +++--- inst/doc/udpipe-parallel.R | 84 inst/doc/udpipe-parallel.Rmd | 224 - inst/doc/udpipe-parallel.html | 870 ++--- inst/doc/udpipe-train.R | 318 - inst/doc/udpipe-train.Rmd | 1108 +++--- inst/doc/udpipe-train.html | 2418 +++++++------- inst/doc/udpipe-tryitout.R | 62 inst/doc/udpipe-tryitout.Rmd | 144 inst/doc/udpipe-tryitout.html | 917 ++--- inst/doc/udpipe-universe.R | 8 inst/doc/udpipe-universe.Rmd | 82 inst/doc/udpipe-universe.html | 588 +-- inst/doc/udpipe-usecase-postagging-lemmatisation.R | 236 - inst/doc/udpipe-usecase-postagging-lemmatisation.Rmd | 446 +- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 1190 +++---- inst/doc/udpipe-usecase-topicmodelling.R | 292 - inst/doc/udpipe-usecase-topicmodelling.Rmd | 530 +-- inst/doc/udpipe-usecase-topicmodelling.html | 1355 ++++---- inst/dummydata/traindata.conllu | 80 inst/models-ud-2.0/params_parser | 136 inst/models-ud-2.0/params_tagger | 136 inst/models-ud-2.0/params_tokenizer | 136 man/as.data.frame.udpipe_connlu.Rd | 92 man/as.matrix.cooccurrence.Rd | 64 man/as_conllu.Rd | 112 man/as_cooccurrence.Rd | 60 man/as_fasttext.Rd | 56 man/as_phrasemachine.Rd | 100 man/as_word2vec.Rd | 64 man/brussels_listings.Rd | 44 man/brussels_reviews.Rd | 52 man/brussels_reviews_anno.Rd | 120 man/brussels_reviews_w2v_embeddings_lemma_nl.Rd | 28 man/cbind_dependencies.Rd | 136 man/cbind_morphological.Rd | 118 man/cooccurrence.Rd | 248 - man/document_term_frequencies.Rd | 200 - man/document_term_frequencies_statistics.Rd | 76 man/document_term_matrix.Rd | 354 +- man/dtm_align.Rd | 172 - man/dtm_bind.Rd | 156 man/dtm_chisq.Rd | 118 man/dtm_colsums.Rd | 132 man/dtm_conform.Rd | 178 - man/dtm_cor.Rd | 60 man/dtm_remove_lowfreq.Rd | 80 man/dtm_remove_sparseterms.Rd | 74 man/dtm_remove_terms.Rd | 70 man/dtm_remove_tfidf.Rd | 104 man/dtm_reverse.Rd | 60 man/dtm_sample.Rd | 72 man/dtm_svd_similarity.Rd | 230 - man/dtm_tfidf.Rd | 62 man/keywords_collocation.Rd | 164 man/keywords_phrases.Rd | 220 - man/keywords_rake.Rd | 152 man/paste.data.frame.Rd | 90 man/predict.LDA.Rd | 218 - man/strsplit.data.frame.Rd | 102 man/syntaxpatterns.Rd | 22 man/syntaxrelation.Rd | 58 man/txt_collapse.Rd | 58 man/txt_contains.Rd | 88 man/txt_context.Rd | 132 man/txt_count.Rd | 58 man/txt_freq.Rd | 56 man/txt_grepl.Rd | 116 man/txt_highlight.Rd | 56 man/txt_next.Rd | 62 man/txt_nextgram.Rd | 90 man/txt_overlap.Rd | 50 man/txt_paste.Rd | 78 man/txt_previous.Rd | 62 man/txt_previousgram.Rd | 90 man/txt_recode.Rd | 88 man/txt_recode_ngram.Rd | 100 man/txt_sample.Rd | 54 man/txt_sentiment.Rd | 234 - man/txt_show.Rd | 46 man/txt_tagsequence.Rd | 132 man/udpipe.Rd | 212 - man/udpipe_accuracy.Rd | 132 man/udpipe_annotate.Rd | 228 - man/udpipe_annotation_params.Rd | 64 man/udpipe_download_model.Rd | 383 +- man/udpipe_load_model.Rd | 104 man/udpipe_read_conllu.Rd | 46 man/udpipe_train.Rd | 258 - man/unique_identifier.Rd | 70 man/unlist_tokens.Rd | 50 src/udpipe.cpp | 20 vignettes/udpipe-annotation.Rmd | 366 +- vignettes/udpipe-parallel.Rmd | 224 - vignettes/udpipe-train.Rmd | 1108 +++--- vignettes/udpipe-tryitout.Rmd | 144 vignettes/udpipe-universe.Rmd | 82 vignettes/udpipe-usecase-postagging-lemmatisation.Rmd | 446 +- vignettes/udpipe-usecase-topicmodelling.Rmd | 530 +-- 125 files changed, 18468 insertions(+), 17985 deletions(-)
Title: Graphical Output in Terminals
Description: Defines a graphics device and functions for graphical output in
terminal emulators that support graphical output. Currently terminals that
support the Terminal Graphics Protocol
(<https://sw.kovidgoyal.net/kitty/graphics-protocol/>) and terminal supporting Sixel
(<https://en.wikipedia.org/wiki/Sixel>) are supported.
Author: Jan van der Laan [aut, cre] ,
Doug Kelkhoff [ctb]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between terminalgraphics versions 0.2.0 dated 2025-11-25 and 0.2.1 dated 2025-11-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 10 +++++++++- R/device_manager.R | 5 +++-- 4 files changed, 18 insertions(+), 9 deletions(-)
More information about terminalgraphics at CRAN
Permanent link
Title: R Analyzer for Large-Scale Assessments
Description: Download, prepare and analyze data from large-scale assessments and
surveys with complex sampling and assessment design (see 'Rutkowski',
2010 <doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of
the package, see 'Mirazchiyski', 2021b (< [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.5.5 dated 2025-02-24 and 1.6.0 dated 2025-11-26
RALSA-1.5.5/RALSA/R/lsa.convert.data2.r |only RALSA-1.5.5/RALSA/man/lsa.convert.data2.Rd |only RALSA-1.6.0/RALSA/DESCRIPTION | 18 RALSA-1.6.0/RALSA/MD5 | 32 RALSA-1.6.0/RALSA/NAMESPACE | 8 RALSA-1.6.0/RALSA/NEWS.md | 44 RALSA-1.6.0/RALSA/R/RALSA.r | 12 RALSA-1.6.0/RALSA/R/common.r | 805 ++++++++++---- RALSA-1.6.0/RALSA/R/lsa.aggregate.vars.r |only RALSA-1.6.0/RALSA/R/lsa.convert.data.r | 4 RALSA-1.6.0/RALSA/R/lsa.cut.vars.r |only RALSA-1.6.0/RALSA/R/lsa.download.data.r | 39 RALSA-1.6.0/RALSA/R/zzz.r | 2 RALSA-1.6.0/RALSA/README.md | 4 RALSA-1.6.0/RALSA/inst/shiny/GUI/server.r | 1529 +++++++++++++++++++++++----- RALSA-1.6.0/RALSA/inst/shiny/GUI/ui.r | 284 +++++ RALSA-1.6.0/RALSA/man/RALSA.Rd | 4 RALSA-1.6.0/RALSA/man/lsa.aggregate.vars.Rd |only RALSA-1.6.0/RALSA/man/lsa.cut.vars.Rd |only RALSA-1.6.0/RALSA/man/lsa.download.data.Rd | 12 20 files changed, 2263 insertions(+), 534 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.1.2 dated 2025-09-22 and 0.3.1 dated 2025-11-26
OrgHeatmap-0.1.2/OrgHeatmap/man/organ_systems.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/DESCRIPTION | 17 OrgHeatmap-0.3.1/OrgHeatmap/MD5 | 45 OrgHeatmap-0.3.1/OrgHeatmap/NAMESPACE | 98 OrgHeatmap-0.3.1/OrgHeatmap/NEWS.md | 25 OrgHeatmap-0.3.1/OrgHeatmap/R/OrgHeatmap.R | 975 +++++--- OrgHeatmap-0.3.1/OrgHeatmap/R/data.R | 94 OrgHeatmap-0.3.1/OrgHeatmap/R/utils-global.R | 18 OrgHeatmap-0.3.1/OrgHeatmap/README.md | 306 +- OrgHeatmap-0.3.1/OrgHeatmap/build/vignette.rds |binary OrgHeatmap-0.3.1/OrgHeatmap/data/human_organ_systems.rda |only OrgHeatmap-0.3.1/OrgHeatmap/data/mouse_bodycontour.rda |only OrgHeatmap-0.3.1/OrgHeatmap/data/mouse_organ_coord.rda |only OrgHeatmap-0.3.1/OrgHeatmap/data/mouse_organ_systems.rda |only OrgHeatmap-0.3.1/OrgHeatmap/data/organelle_bodycontour.rda |only OrgHeatmap-0.3.1/OrgHeatmap/data/organelle_organ_coord.rda |only OrgHeatmap-0.3.1/OrgHeatmap/inst/WORDLIST |only OrgHeatmap-0.3.1/OrgHeatmap/inst/doc/introduction.R | 24 OrgHeatmap-0.3.1/OrgHeatmap/inst/doc/introduction.Rmd | 476 ++- OrgHeatmap-0.3.1/OrgHeatmap/inst/doc/introduction.html | 1202 ++++++---- OrgHeatmap-0.3.1/OrgHeatmap/inst/extdata/clean_data.rds |only OrgHeatmap-0.3.1/OrgHeatmap/inst/extdata/mouse_digestive_plot.png |only OrgHeatmap-0.3.1/OrgHeatmap/inst/extdata/organelle_expression_plot.png |only OrgHeatmap-0.3.1/OrgHeatmap/man/OrgHeatmap.Rd | 86 OrgHeatmap-0.3.1/OrgHeatmap/man/human_organ_systems.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/man/mouse_bodycontour.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/man/mouse_organ_coord.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/man/mouse_organ_systems.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/man/organelle_bodycontour.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/man/organelle_organ_coord.Rd |only OrgHeatmap-0.3.1/OrgHeatmap/tests/testthat/test-OrgHeatmap.R | 722 +++--- OrgHeatmap-0.3.1/OrgHeatmap/vignettes/introduction.Rmd | 476 ++- 32 files changed, 2914 insertions(+), 1650 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <tom.hartl96@gmail.com>
This is a re-admission after prior archival of version 2.2.0 dated 2025-03-11
Diff between opendataformat versions 2.2.0 dated 2025-03-11 and 2.2.2 dated 2025-11-26
opendataformat-2.2.0/opendataformat/tests/testthat/testdata/test_odf.odf.zip |only opendataformat-2.2.2/opendataformat/DESCRIPTION | 15 opendataformat-2.2.2/opendataformat/LICENSE | 4 opendataformat-2.2.2/opendataformat/MD5 | 101 opendataformat-2.2.2/opendataformat/NAMESPACE | 30 opendataformat-2.2.2/opendataformat/R/as_odf_tbl.R | 318 - opendataformat-2.2.2/opendataformat/R/data.R | 36 opendataformat-2.2.2/opendataformat/R/docu_odf.R | 956 +-- opendataformat-2.2.2/opendataformat/R/getmetadata_odf.R | 214 opendataformat-2.2.2/opendataformat/R/merge.R | 362 - opendataformat-2.2.2/opendataformat/R/opendataformat-package.R | 92 opendataformat-2.2.2/opendataformat/R/read_odf.R | 698 +- opendataformat-2.2.2/opendataformat/R/setlanguage_odf.R | 96 opendataformat-2.2.2/opendataformat/R/write_odf.R | 744 +- opendataformat-2.2.2/opendataformat/build/vignette.rds |binary opendataformat-2.2.2/opendataformat/inst/doc/opendataformat.R | 616 +- opendataformat-2.2.2/opendataformat/inst/doc/opendataformat.Rmd | 1276 ++--- opendataformat-2.2.2/opendataformat/inst/doc/opendataformat.html | 2504 ++++------ opendataformat-2.2.2/opendataformat/man/data_odf.Rd | 56 opendataformat-2.2.2/opendataformat/man/docu_odf.Rd | 176 opendataformat-2.2.2/opendataformat/man/getmetadata_odf.Rd | 90 opendataformat-2.2.2/opendataformat/man/opendataformat-package.Rd | 108 opendataformat-2.2.2/opendataformat/man/read_odf.Rd | 122 opendataformat-2.2.2/opendataformat/man/setlanguage_odf.Rd | 64 opendataformat-2.2.2/opendataformat/man/write_odf.Rd | 148 opendataformat-2.2.2/opendataformat/tests/testthat.R | 10 opendataformat-2.2.2/opendataformat/tests/testthat/test-as_odf_tbl.R | 1078 ++-- opendataformat-2.2.2/opendataformat/tests/testthat/test-docu_odf.R | 268 - opendataformat-2.2.2/opendataformat/tests/testthat/test-read-and-write-odf.R | 334 - opendataformat-2.2.2/opendataformat/tests/testthat/test-read_odf.R | 1563 +++--- opendataformat-2.2.2/opendataformat/tests/testthat/test-write_odf.R | 238 opendataformat-2.2.2/opendataformat/tests/testthat/test_getmetadata_odf.R | 430 - opendataformat-2.2.2/opendataformat/tests/testthat/test_merge.R | 476 - opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/categories.csv | 70 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/data/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/data/metadata.xml | 528 +- opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/dataset.csv | 4 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv/variables.csv | 16 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/categories.csv | 70 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/data_with_default/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/data_with_default/metadata.xml | 628 +- opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/dataset.csv | 4 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_default/variables.csv | 16 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/categories.csv | 70 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/data_with_missings/data.csv | 42 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/data_with_missings/metadata.xml | 468 - opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/dataset.csv | 4 opendataformat-2.2.2/opendataformat/tests/testthat/testdata/csv_with_missings/variables.csv | 16 opendataformat-2.2.2/opendataformat/vignettes/opendataformat.Rmd | 1276 ++--- 52 files changed, 8298 insertions(+), 8347 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Access 'Nomis' UK Labour Market Data and Statistics
Description: Interface to the 'Nomis' database (<https://www.nomisweb.co.uk>), a comprehensive resource of United Kingdom labour market statistics provided by the Office for National Statistics (ONS). Facilitates programmatic access to census data, labour force surveys, benefit statistics, and socioeconomic indicators through a modern HTTP client with intelligent caching, automatic query pagination, and tidy data principles. Includes spatial data integration, interactive helpers, and visualization utilities. Independent implementation unaffiliated with ONS or Durham University.
Author: Cheryl Isabella Lim [aut, cre]
Maintainer: Cheryl Isabella Lim <cheryl.academic@gmail.com>
Diff between nomisdata versions 0.1.0 dated 2025-11-24 and 0.1.1 dated 2025-11-26
DESCRIPTION | 6 - MD5 | 47 +++++++------- R/auth.R | 5 + R/cache-enhanced.R | 6 + R/cache_old.R | 44 +++++++------ R/cache_utils.R |only inst/doc/advanced-queries.R | 4 - inst/doc/advanced-queries.Rmd | 6 + inst/doc/advanced-queries.html | 2 inst/doc/quickstart.R | 2 inst/doc/quickstart.Rmd | 4 - inst/doc/spatial-analysis.R | 2 inst/doc/spatial-analysis.Rmd | 4 - inst/doc/visualisation.R | 2 inst/doc/visualisation.Rmd | 4 - man/clear_cache.Rd | 2 man/enable_cache.Rd | 12 +-- tests/testthat.R | 8 +- tests/testthat/test-cache.R | 118 ++++++++++++++++++++++-------------- tests/testthat/test-documentation.R | 67 ++++++++++++-------- tests/testthat/test-performance.R | 4 - vignettes/advanced-queries.Rmd | 6 + vignettes/quickstart.Rmd | 4 - vignettes/spatial-analysis.Rmd | 4 - vignettes/visualisation.Rmd | 4 - 25 files changed, 230 insertions(+), 137 deletions(-)
Title: An R Package of Minorization-Maximization Algorithm via the
Assembly--Decomposition Technology
Description: The minorization-maximization (MM) algorithm is a powerful tool for maximizing nonconcave target function. However, for most existing MM algorithms, the surrogate function in the minorization step is constructed in a case-specific manner and requires manual programming. To address this limitation, we develop the R package MMAD, which systematically integrates the assembly--decomposition technology in the MM framework. This new package provides a comprehensive computational toolkit for one-stop inference of complex target functions, including function construction, evaluation, minorization and optimization via MM algorithm. By representing the target function through a hierarchical composition of assembly functions, we design a hierarchical algorithmic structure that supports both bottom-up operations (construction, evaluation) and top-down operation (minorization).
Author: Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 1.0.0 dated 2023-07-08 and 2.0 dated 2025-11-26
MMAD-1.0.0/MMAD/R/CZIGPCR.R |only MMAD-1.0.0/MMAD/R/CZIGPMM.R |only MMAD-1.0.0/MMAD/R/CoxMM.R |only MMAD-1.0.0/MMAD/R/CoxProfile.R |only MMAD-1.0.0/MMAD/R/DataDesc.R |only MMAD-1.0.0/MMAD/R/FrailtyPro.R |only MMAD-1.0.0/MMAD/R/GaFrailtyMM.R |only MMAD-1.0.0/MMAD/R/HessianC.R |only MMAD-1.0.0/MMAD/R/HessianF.R |only MMAD-1.0.0/MMAD/R/IC2Control.R |only MMAD-1.0.0/MMAD/R/IC2MM.R |only MMAD-1.0.0/MMAD/R/IC2Pro.R |only MMAD-1.0.0/MMAD/R/LTNCR.R |only MMAD-1.0.0/MMAD/R/LTNMM.R |only MMAD-1.0.0/MMAD/R/LogLik.R |only MMAD-1.0.0/MMAD/R/ZIGPCR.R |only MMAD-1.0.0/MMAD/R/ZIGPMM.R |only MMAD-1.0.0/MMAD/R/plot.Cox.R |only MMAD-1.0.0/MMAD/R/plot.GaF.R |only MMAD-1.0.0/MMAD/R/plot.IC2.R |only MMAD-1.0.0/MMAD/R/summary.CZIGP.R |only MMAD-1.0.0/MMAD/R/summary.Cox.R |only MMAD-1.0.0/MMAD/R/summary.GaF.R |only MMAD-1.0.0/MMAD/R/summary.IC2.R |only MMAD-1.0.0/MMAD/R/summary.LTN.R |only MMAD-1.0.0/MMAD/R/summary.ZIGP.R |only MMAD-1.0.0/MMAD/data |only MMAD-1.0.0/MMAD/demo |only MMAD-1.0.0/MMAD/man/CZIGPMM.Rd |only MMAD-1.0.0/MMAD/man/CoxMM.Rd |only MMAD-1.0.0/MMAD/man/GaFrailtyMM.Rd |only MMAD-1.0.0/MMAD/man/IC2Control.Rd |only MMAD-1.0.0/MMAD/man/IC2MM.Rd |only MMAD-1.0.0/MMAD/man/IC2Pro.Rd |only MMAD-1.0.0/MMAD/man/LTNMM.Rd |only MMAD-1.0.0/MMAD/man/ZIGPMM.Rd |only MMAD-1.0.0/MMAD/man/bcos.Rd |only MMAD-1.0.0/MMAD/man/cadi.Rd |only MMAD-1.0.0/MMAD/man/kidney.Rd |only MMAD-1.0.0/MMAD/man/lung.Rd |only MMAD-1.0.0/MMAD/man/plot.Cox.Rd |only MMAD-1.0.0/MMAD/man/plot.GaF.Rd |only MMAD-1.0.0/MMAD/man/plot.IC2.Rd |only MMAD-1.0.0/MMAD/man/summary.CZIGP.Rd |only MMAD-1.0.0/MMAD/man/summary.Cox.Rd |only MMAD-1.0.0/MMAD/man/summary.GaF.Rd |only MMAD-1.0.0/MMAD/man/summary.IC2.Rd |only MMAD-1.0.0/MMAD/man/summary.LTN.Rd |only MMAD-1.0.0/MMAD/man/summary.ZIGP.Rd |only MMAD-1.0.0/MMAD/man/vijc.Rd |only MMAD-2.0/MMAD/DESCRIPTION | 45 ++++------- MMAD-2.0/MMAD/MD5 | 88 ++++++++--------------- MMAD-2.0/MMAD/NAMESPACE | 38 +-------- MMAD-2.0/MMAD/R/Exponential.R |only MMAD-2.0/MMAD/R/Function_construction.R |only MMAD-2.0/MMAD/R/Function_evaluation.R |only MMAD-2.0/MMAD/R/Function_minorization.R |only MMAD-2.0/MMAD/R/Gradient_Exponential.R |only MMAD-2.0/MMAD/R/Gradient_Linear_combination.R |only MMAD-2.0/MMAD/R/Gradient_Logarithmic.R |only MMAD-2.0/MMAD/R/Gradient_Logarithmic_one_minus.R |only MMAD-2.0/MMAD/R/Gradient_Power.R |only MMAD-2.0/MMAD/R/Hessian_Exponential.R |only MMAD-2.0/MMAD/R/Hessian_Linear_combination.R |only MMAD-2.0/MMAD/R/Hessian_Logarithmic.R |only MMAD-2.0/MMAD/R/Hessian_Logarithmic_one_minus.R |only MMAD-2.0/MMAD/R/Hessian_Power.R |only MMAD-2.0/MMAD/R/Linear_combination.R |only MMAD-2.0/MMAD/R/Logarithmic.R |only MMAD-2.0/MMAD/R/Logarithmic_one_minus.R |only MMAD-2.0/MMAD/R/MMAD.R |only MMAD-2.0/MMAD/R/Power.R |only MMAD-2.0/MMAD/R/convexity.R |only MMAD-2.0/MMAD/R/is_natural_number.R |only MMAD-2.0/MMAD/man/Function_construction.Rd |only MMAD-2.0/MMAD/man/Function_evaluation.Rd |only MMAD-2.0/MMAD/man/Function_minorization.Rd |only MMAD-2.0/MMAD/man/MMAD.Rd |only MMAD-2.0/MMAD/tests |only 79 files changed, 54 insertions(+), 117 deletions(-)
Title: Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liveR," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.25 dated 2025-11-14 and 1.26 dated 2025-11-26
DESCRIPTION | 8 +++--- MD5 | 44 ++++++++++++++++++---------------- NEWS.md | 4 +++ data/datalist | 1 data/gapminder.RData |only man/adult.Rd | 26 +++++++++++++++++++- man/advertising.Rd | 30 +++++++++++++++++++++-- man/bank.Rd | 27 ++++++++++++++++++++- man/caravan.Rd | 23 +++++++++++++++--- man/cereal.Rd | 23 +++++++++++++++++- man/churn.Rd | 23 ++++++++++++++++-- man/churnCredit.Rd | 65 +++++++++++++++++++++++++++++++++------------------ man/churnTel.Rd | 28 +++++++++++++++++++++ man/corona.Rd | 20 ++++++++++++++- man/drug.Rd | 19 ++++++++++++++ man/fertilizer.Rd | 19 ++++++++++++++ man/gapminder.Rd |only man/house.Rd | 29 +++++++++++++++++++++- man/housePrice.Rd | 30 +++++++++++++++++++++-- man/insurance.Rd | 28 ++++++++++++++++++++- man/marketing.Rd | 28 +++++++++++++++++++++ man/redWines.Rd | 26 +++++++++++++++++++- man/risk.Rd | 25 +++++++++++++++++-- man/whiteWines.Rd | 26 +++++++++++++++++++- 24 files changed, 479 insertions(+), 73 deletions(-)
Title: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
Description: Generates interactive Jellyfish plots to visualize spatiotemporal tumor
evolution by integrating sample and phylogenetic trees into a unified plot.
This approach provides an intuitive way to analyze tumor heterogeneity and
evolution over time and across anatomical locations. The Jellyfish plot
visualization design was first introduced by Lahtinen, Lavikka, et al.
(2023, <doi:10.1016/j.ccell.2023.04.017>).
This package also supports visualizing ClonEvol results, a tool developed
by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal
evolution from multi-sample sequencing data. The 'clonevol' package is not
available on CRAN but can be installed from its GitHub
repository (<https://github.com/hdng/clonevol>).
Author: Kari Lavikka [cph, aut, cre]
Maintainer: Kari Lavikka <kari.lavikka@helsinki.fi>
Diff between jellyfisher versions 1.0.4 dated 2025-02-06 and 1.1.1 dated 2025-11-26
DESCRIPTION | 14 MD5 | 33 - NAMESPACE | 1 NEWS.md | 9 R/jellyfisher.R | 32 + R/utils.R | 191 +++++++ README.md | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/jellyfisher.R | 16 inst/doc/jellyfisher.Rmd | 50 + inst/doc/jellyfisher.html | 640 +++++++++--------------- inst/htmlwidgets/lib/jellyfish/jellyfish.umd.js | 316 ++--------- inst/htmlwidgets/lib/jellyfish/lib.css | 2 man/add_inferred_sample.Rd |only man/jellyfisher.Rd | 6 tests |only vignettes/jellyfisher.Rmd | 50 + 18 files changed, 707 insertions(+), 663 deletions(-)
Title: Generalized Additive Latent and Mixed Models
Description: Estimates generalized additive latent and
mixed models using maximum marginal likelihood,
as defined in Sorensen et al. (2023)
<doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
Skrondal (2004)'s unifying framework for multilevel latent variable
modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse
matrix methods, Laplace approximation, and automatic differentiation. The
framework includes generalized multilevel models with heteroscedastic
residuals, mixed response types, factor loadings, smoothing splines,
crossed random effects, and combinations thereof. Syntax for model
formulation is close to 'lme4' (Bates et al. (2015)
<doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019)
<doi:10.1080/00273171.2018.1516541>).
Author: Oeystein Soerensen [aut, cre] ,
Douglas Bates [ctb],
Ben Bolker [ctb],
Martin Maechler [ctb],
Allan Leal [ctb],
Fabian Scheipl [ctb],
Steven Walker [ctb],
Simon Wood [ctb]
Maintainer: Oeystein Soerensen <oystein.sorensen@psykologi.uio.no>
Diff between galamm versions 0.2.3 dated 2025-07-03 and 0.3.0 dated 2025-11-26
galamm-0.2.3/galamm/tests/testthat/Rplots.pdf |only galamm-0.3.0/galamm/DESCRIPTION | 10 galamm-0.3.0/galamm/MD5 | 224 +-- galamm-0.3.0/galamm/NAMESPACE | 1 galamm-0.3.0/galamm/R/VarCorr.R | 4 galamm-0.3.0/galamm/R/data.R | 20 galamm-0.3.0/galamm/R/define_factor_mappings.R | 10 galamm-0.3.0/galamm/R/extract_optim_parameters.R | 4 galamm-0.3.0/galamm/R/factor_loadings.R | 2 galamm-0.3.0/galamm/R/family.R | 6 galamm-0.3.0/galamm/R/fitted.galamm.R | 2 galamm-0.3.0/galamm/R/formula.R | 6 galamm-0.3.0/galamm/R/galamm-object.R |only galamm-0.3.0/galamm/R/galamm.R | 217 +-- galamm-0.3.0/galamm/R/gamm4-functions.R | 2 galamm-0.3.0/galamm/R/gfam.R |only galamm-0.3.0/galamm/R/logLik.galamm.R | 4 galamm-0.3.0/galamm/R/mgcv-functions.R | 1 galamm-0.3.0/galamm/R/misc.R | 61 galamm-0.3.0/galamm/R/plot.galamm.R | 15 galamm-0.3.0/galamm/R/plot_smooth.R | 2 galamm-0.3.0/galamm/R/residuals.galamm.R | 15 galamm-0.3.0/galamm/R/response.R | 2 galamm-0.3.0/galamm/R/sigma.R | 2 galamm-0.3.0/galamm/R/smooths.R | 8 galamm-0.3.0/galamm/R/summary.galamm.R | 6 galamm-0.3.0/galamm/R/vcov.R | 4 galamm-0.3.0/galamm/README.md | 40 galamm-0.3.0/galamm/build/partial.rdb |binary galamm-0.3.0/galamm/build/vignette.rds |binary galamm-0.3.0/galamm/data/cognition.rda |binary galamm-0.3.0/galamm/data/diet.rda |binary galamm-0.3.0/galamm/data/mresp.rda |binary galamm-0.3.0/galamm/data/mresp_hsced.rda |binary galamm-0.3.0/galamm/inst/REFERENCES.bib | 13 galamm-0.3.0/galamm/inst/doc/galamm.html | 5 galamm-0.3.0/galamm/inst/doc/glmm_factor.Rmd | 15 galamm-0.3.0/galamm/inst/doc/glmm_factor.html | 30 galamm-0.3.0/galamm/inst/doc/latent_observed_interaction.Rmd | 10 galamm-0.3.0/galamm/inst/doc/latent_observed_interaction.html | 17 galamm-0.3.0/galamm/inst/doc/lmm_factor.Rmd | 22 galamm-0.3.0/galamm/inst/doc/lmm_factor.html | 29 galamm-0.3.0/galamm/inst/doc/lmm_heteroscedastic.Rmd | 3 galamm-0.3.0/galamm/inst/doc/lmm_heteroscedastic.html | 52 galamm-0.3.0/galamm/inst/doc/mixed_response.Rmd | 120 + galamm-0.3.0/galamm/inst/doc/mixed_response.html | 574 ++++---- galamm-0.3.0/galamm/inst/doc/optimization.Rmd | 46 galamm-0.3.0/galamm/inst/doc/optimization.html | 345 ++--- galamm-0.3.0/galamm/inst/doc/scaling.Rmd | 14 galamm-0.3.0/galamm/inst/doc/scaling.html | 29 galamm-0.3.0/galamm/inst/doc/semiparametric.Rmd | 117 - galamm-0.3.0/galamm/inst/doc/semiparametric.html | 344 ++--- galamm-0.3.0/galamm/man/VarCorr.Rd | 2 galamm-0.3.0/galamm/man/cognition.Rd | 6 galamm-0.3.0/galamm/man/deviance.galamm.Rd | 2 galamm-0.3.0/galamm/man/diet.Rd | 4 galamm-0.3.0/galamm/man/extract_optim_parameters.galamm.Rd | 4 galamm-0.3.0/galamm/man/factor_loadings.galamm.Rd | 2 galamm-0.3.0/galamm/man/family.galamm.Rd | 6 galamm-0.3.0/galamm/man/fitted.galamm.Rd | 2 galamm-0.3.0/galamm/man/formula.galamm.Rd | 6 galamm-0.3.0/galamm/man/galamm.Rd | 122 - galamm-0.3.0/galamm/man/galammObject.Rd |only galamm-0.3.0/galamm/man/gfam.Rd |only galamm-0.3.0/galamm/man/logLik.galamm.Rd | 2 galamm-0.3.0/galamm/man/mresp.Rd | 4 galamm-0.3.0/galamm/man/mresp_hsced.Rd | 6 galamm-0.3.0/galamm/man/plot.galamm.Rd | 11 galamm-0.3.0/galamm/man/plot_smooth.galamm.Rd | 2 galamm-0.3.0/galamm/man/print.VarCorr.galamm.Rd | 2 galamm-0.3.0/galamm/man/print.galamm.Rd | 2 galamm-0.3.0/galamm/man/print.summary.galamm.Rd | 2 galamm-0.3.0/galamm/man/residuals.galamm.Rd | 15 galamm-0.3.0/galamm/man/response.Rd | 2 galamm-0.3.0/galamm/man/sigma.galamm.Rd | 2 galamm-0.3.0/galamm/man/sl.Rd | 6 galamm-0.3.0/galamm/man/summary.galamm.Rd | 2 galamm-0.3.0/galamm/man/t2l.Rd | 6 galamm-0.3.0/galamm/man/vcov.galamm.Rd | 2 galamm-0.3.0/galamm/tests/testthat/_snaps/galamm-heteroscedastic.md | 2 galamm-0.3.0/galamm/tests/testthat/_snaps/galamm-mixed-resp.md | 1 galamm-0.3.0/galamm/tests/testthat/test-galamm-glmm.R | 6 galamm-0.3.0/galamm/tests/testthat/test-galamm-heteroscedastic.R | 23 galamm-0.3.0/galamm/tests/testthat/test-galamm-latent-covariates-interaction.R | 20 galamm-0.3.0/galamm/tests/testthat/test-galamm-lmm.R | 57 galamm-0.3.0/galamm/tests/testthat/test-galamm-mixed-resp.R | 140 +- galamm-0.3.0/galamm/tests/testthat/test-galamm-semiparametric.R | 640 +--------- galamm-0.3.0/galamm/tests/testthat/test-galamm-setup.R | 109 + galamm-0.3.0/galamm/tests/testthat/test-model_diagnostics.R |only galamm-0.3.0/galamm/tests/testthat/test-parameter-recovery.R | 2 galamm-0.3.0/galamm/vignettes/glmm_factor.Rmd | 15 galamm-0.3.0/galamm/vignettes/latent-observed-smooth-1.png |binary galamm-0.3.0/galamm/vignettes/latent_observed_interaction.Rmd | 10 galamm-0.3.0/galamm/vignettes/lmm_factor.Rmd | 22 galamm-0.3.0/galamm/vignettes/lmm_factor_diagnostic_plot-1.png |binary galamm-0.3.0/galamm/vignettes/lmm_heteroscedastic.Rmd | 3 galamm-0.3.0/galamm/vignettes/mixed_response.Rmd | 120 + galamm-0.3.0/galamm/vignettes/optimization.Rmd | 46 galamm-0.3.0/galamm/vignettes/scaling-glmm-plot-1.png |binary galamm-0.3.0/galamm/vignettes/scaling-hsced-plot-1.png |binary galamm-0.3.0/galamm/vignettes/scaling-lmm-plot-1.png |binary galamm-0.3.0/galamm/vignettes/scaling-semiparametric-binomial-plot-1.png |binary galamm-0.3.0/galamm/vignettes/scaling-semiparametric-gaussian-plot-1.png |binary galamm-0.3.0/galamm/vignettes/scaling.Rmd | 14 galamm-0.3.0/galamm/vignettes/semiparametric-gamm-binomial-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gamm4-binomial-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-by-factor1-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-by-factor2-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-factor-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-gamm-smooth1-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-gamm-smooth2-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-gamm4-diagnostic-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-gaussian-gamm4-smooth-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-mixed-by-factor1-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric-mixed-by-factor2-1.png |binary galamm-0.3.0/galamm/vignettes/semiparametric.Rmd | 117 - 116 files changed, 1829 insertions(+), 2193 deletions(-)
Title: 'Domino Data R SDK'
Description: A wrapper on top of the 'Domino Data Python SDK' library. It lets
you query and access 'Domino Data Sources' directly from your R environment.
Under the hood, 'Domino Data R SDK' leverages the API provided by the
'Domino Data Python SDK', which must be installed as a prerequisite.
'Domino' is a platform that makes it easy to run your code on scalable
hardware, with integrated version control and collaboration features
designed for analytical workflows. See
<https://docs.dominodatalab.com/en/latest/api_guide/140b48/domino-data-api>
for more information.
Author: Murat Cetin [cre],
Gabriel Haim [aut]
Maintainer: Murat Cetin <murat.cetin@dominodatalab.com>
Diff between DominoDataR versions 0.3.0 dated 2025-10-21 and 0.3.1 dated 2025-11-26
DESCRIPTION | 16 +++++++++------- MD5 | 2 +- 2 files changed, 10 insertions(+), 8 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages (notably 'ggplot2')
to help facilitate the plotting of data over long time intervals, including,
but not limited to, geological, evolutionary, and ecological data. The
primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to
assist with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 2.3.0 dated 2025-11-20 and 2.3.1 dated 2025-11-26
DESCRIPTION | 6 MD5 | 23 - NEWS.md | 12 R/coord_geo_radial.R | 123 +++++++--- inst/doc/geo.html | 12 inst/doc/phylogenies.R | 6 inst/doc/phylogenies.Rmd | 8 inst/doc/phylogenies.html | 58 ++-- man/coord_geo_radial.Rd | 31 ++ tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/ggplot4/coord_geo_radial/stacked-scales-reverse-new.svg |only tests/testthat/test-coord_geo_radial.R | 23 + vignettes/phylogenies.Rmd | 8 13 files changed, 222 insertions(+), 88 deletions(-)
Title: Synthetic Microdata Generator
Description: This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
Author: Juhee Lee [aut, cre],
Hang J. Kim [aut],
Young-Min Kim [aut],
Jared Murray [aut]
Maintainer: Juhee Lee <ljh988488@gmail.com>
Diff between synMicrodata versions 2.1.2 dated 2025-11-18 and 2.1.3 dated 2025-11-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/R_functions.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Tidy C++ Header-Only Definitions for Parts of the C API of R
Description: Core parts of the C API of R are wrapped in a C++ namespace via a set
of inline functions giving a tidier representation of the underlying data structures
and functionality using a header-only implementation without additional dependencies.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tidyCpp versions 0.0.7 dated 2023-12-02 and 0.0.8 dated 2025-11-26
ChangeLog | 43 ++++++++++ DESCRIPTION | 15 ++- MD5 | 24 ++--- README.md | 8 + build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 10 ++ inst/doc/motivation.html | 154 ++++++++++++++++++------------------ inst/include/tidy/defines.h | 4 inst/include/tidy/internals.h | 12 +- inst/snippets/createMatrix.cpp | 11 +- inst/snippets/rollminmaxExample.cpp | 5 - inst/snippets/shieldExamples.cpp | 4 13 files changed, 181 insertions(+), 109 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.4.3 dated 2025-07-30 and 4.4.4 dated 2025-11-26
sommer-4.4.3/sommer/R/DEPRECATED_FUN_special.R |only sommer-4.4.3/sommer/R/FUN_markers.R |only sommer-4.4.3/sommer/data |only sommer-4.4.3/sommer/man/DEPRECATED_MMER.Rd |only sommer-4.4.3/sommer/man/DT_augment.Rd |only sommer-4.4.3/sommer/man/DT_btdata.Rd |only sommer-4.4.3/sommer/man/DT_cornhybrids.Rd |only sommer-4.4.3/sommer/man/DT_cpdata.Rd |only sommer-4.4.3/sommer/man/DT_example.Rd |only sommer-4.4.3/sommer/man/DT_expdesigns.Rd |only sommer-4.4.3/sommer/man/DT_fulldiallel.Rd |only sommer-4.4.3/sommer/man/DT_gryphon.Rd |only sommer-4.4.3/sommer/man/DT_h2.Rd |only sommer-4.4.3/sommer/man/DT_halfdiallel.Rd |only sommer-4.4.3/sommer/man/DT_ige.Rd |only sommer-4.4.3/sommer/man/DT_legendre.Rd |only sommer-4.4.3/sommer/man/DT_mohring.Rd |only sommer-4.4.3/sommer/man/DT_polyploid.Rd |only sommer-4.4.3/sommer/man/DT_rice.Rd |only sommer-4.4.3/sommer/man/DT_sleepstudy.Rd |only sommer-4.4.3/sommer/man/DT_technow.Rd |only sommer-4.4.3/sommer/man/DT_wheat.Rd |only sommer-4.4.3/sommer/man/DT_yatesoats.Rd |only sommer-4.4.3/sommer/man/LD.decay.Rd |only sommer-4.4.3/sommer/man/add.diallel.vars.Rd |only sommer-4.4.3/sommer/man/adiag1.Rd |only sommer-4.4.3/sommer/man/atcg1234.Rd |only sommer-4.4.3/sommer/man/atcg1234BackTransform.Rd |only sommer-4.4.3/sommer/man/bathy.colors.Rd |only sommer-4.4.3/sommer/man/bbasis.Rd |only sommer-4.4.3/sommer/man/build.HMM.Rd |only sommer-4.4.3/sommer/man/impute.Rd |only sommer-4.4.3/sommer/man/jet.colors.Rd |only sommer-4.4.3/sommer/man/leg.Rd |only sommer-4.4.3/sommer/man/logspace.Rd |only sommer-4.4.3/sommer/man/manhattan.Rd |only sommer-4.4.3/sommer/man/map.plot.Rd |only sommer-4.4.3/sommer/man/neMarker.Rd |only sommer-4.4.3/sommer/man/overlay.Rd |only sommer-4.4.3/sommer/man/propMissing.Rd |only sommer-4.4.3/sommer/man/redmm.Rd |only sommer-4.4.3/sommer/man/rrm.Rd |only sommer-4.4.3/sommer/man/simGECorMat.Rd |only sommer-4.4.3/sommer/man/stan.Rd |only sommer-4.4.3/sommer/man/tps.Rd |only sommer-4.4.3/sommer/man/transp.Rd |only sommer-4.4.3/sommer/man/wald.Rd |only sommer-4.4.4/sommer/CHANGELOG | 5 sommer-4.4.4/sommer/DESCRIPTION | 12 sommer-4.4.4/sommer/MD5 | 175 +---- sommer-4.4.4/sommer/NAMESPACE | 37 - sommer-4.4.4/sommer/R/DEPRECATED_FUN_special_mmer.R |only sommer-4.4.4/sommer/R/DEPRECATED_mmer.R | 4 sommer-4.4.4/sommer/R/FUN_methods_mmes.R | 15 sommer-4.4.4/sommer/R/FUN_plotting.R | 621 -------------------- sommer-4.4.4/sommer/R/FUN_spatial.R | 450 -------------- sommer-4.4.4/sommer/R/FUN_special.R | 232 ------- sommer-4.4.4/sommer/R/FUN_stats.R | 344 ----------- sommer-4.4.4/sommer/R/FUN_vsm.R | 16 sommer-4.4.4/sommer/R/mmes.R | 2 sommer-4.4.4/sommer/inst/doc/sommer.gxe.R | 8 sommer-4.4.4/sommer/inst/doc/sommer.gxe.Rmd | 8 sommer-4.4.4/sommer/inst/doc/sommer.gxe.html | 12 sommer-4.4.4/sommer/inst/doc/sommer.qg.R | 51 - sommer-4.4.4/sommer/inst/doc/sommer.qg.Rmd | 51 - sommer-4.4.4/sommer/inst/doc/sommer.qg.html | 57 + sommer-4.4.4/sommer/inst/doc/sommer.spatial.R | 2 sommer-4.4.4/sommer/inst/doc/sommer.spatial.Rmd | 2 sommer-4.4.4/sommer/inst/doc/sommer.spatial.html | 4 sommer-4.4.4/sommer/inst/doc/sommer.vs.lme4.R | 2 sommer-4.4.4/sommer/inst/doc/sommer.vs.lme4.Rmd | 2 sommer-4.4.4/sommer/inst/doc/sommer.vs.lme4.html | 4 sommer-4.4.4/sommer/man/AR1mat.Rd | 2 sommer-4.4.4/sommer/man/DEPRECATED_GWAS.Rd | 2 sommer-4.4.4/sommer/man/DEPRECATED_VS.Rd | 4 sommer-4.4.4/sommer/man/DEPRECATED_VSR.Rd | 4 sommer-4.4.4/sommer/man/MNR.Rd |only sommer-4.4.4/sommer/man/anova_mmes.Rd | 1 sommer-4.4.4/sommer/man/atm.Rd | 3 sommer-4.4.4/sommer/man/coef_mmes.Rd | 1 sommer-4.4.4/sommer/man/corImputation.Rd | 4 sommer-4.4.4/sommer/man/covm.Rd | 2 sommer-4.4.4/sommer/man/csm.Rd | 1 sommer-4.4.4/sommer/man/dsm.Rd | 3 sommer-4.4.4/sommer/man/fitted_mmes.Rd | 3 sommer-4.4.4/sommer/man/ism.Rd | 2 sommer-4.4.4/sommer/man/mmer.Rd |only sommer-4.4.4/sommer/man/mmes.Rd | 94 +-- sommer-4.4.4/sommer/man/plot.monitor.Rd | 2 sommer-4.4.4/sommer/man/plot_mmes.Rd | 3 sommer-4.4.4/sommer/man/predict_mmes.Rd | 3 sommer-4.4.4/sommer/man/r2.Rd | 2 sommer-4.4.4/sommer/man/residuals_mmes.Rd | 1 sommer-4.4.4/sommer/man/sommer-package.Rd | 94 +-- sommer-4.4.4/sommer/man/spl2Dc.Rd | 4 sommer-4.4.4/sommer/man/spl2Dmats.Rd | 2 sommer-4.4.4/sommer/man/unsm.Rd | 1 sommer-4.4.4/sommer/man/usm.Rd | 3 sommer-4.4.4/sommer/man/vpredict.Rd | 2 sommer-4.4.4/sommer/man/vsm.Rd | 2 sommer-4.4.4/sommer/vignettes/sommer.gxe.Rmd | 8 sommer-4.4.4/sommer/vignettes/sommer.qg.Rmd | 51 - sommer-4.4.4/sommer/vignettes/sommer.spatial.Rmd | 2 sommer-4.4.4/sommer/vignettes/sommer.vs.lme4.Rmd | 2 104 files changed, 406 insertions(+), 2018 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.7.4 dated 2025-07-29 and 0.8.0 dated 2025-11-26
DESCRIPTION | 32 MD5 | 136 +-- NAMESPACE | 8 NEWS.md | 136 +++ R/cross-val.R | 313 ++++++- R/deprecated.R | 14 R/dharma.R | 2 R/emmeans.R | 64 + R/enum.R | 3 R/extra-optimization.R | 2 R/families.R | 157 +++ R/fit.R | 337 ++++++-- R/gather-spread.R | 17 R/get-range-edge.R |only R/index.R | 120 ++ R/methods.R | 174 +++- R/plot.R | 75 + R/predict.R | 82 - R/print.R | 111 ++ R/residuals.R | 91 +- R/tidy.R | 181 ++++ R/tmb-sim.R | 111 ++ R/utils.R | 184 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/model-description.R | 21 inst/doc/model-description.Rmd | 611 ++++++++------ inst/doc/model-description.html | 1327 ++++++++++++++++++-------------- man/add_barrier_mesh.Rd | 4 man/cv_to_waywiser.Rd |only man/dharma_residuals.Rd | 2 man/emmeans.sdmTMB.Rd | 16 man/extract_mcmc.Rd | 6 man/families.Rd | 46 - man/gather_sims.Rd | 6 man/get_index.Rd | 76 + man/get_range_edge.Rd |only man/make_category_svc.Rd |only man/predict.sdmTMB.Rd | 68 - man/residuals.sdmTMB.Rd | 6 man/sdmTMB.Rd | 104 +- man/sdmTMB_cv.Rd | 76 + man/sdmTMB_simulate.Rd | 18 man/sdmTMBcontrol.Rd | 26 man/set_delta_model.Rd | 6 man/sigma.sdmTMB.Rd |only man/simulate.sdmTMB.Rd | 2 man/update.sdmTMB.Rd |only src/sdmTMB.cpp | 168 +++- src/utils.h | 77 + tests/testthat/test-1-fit-basic.R | 2 tests/testthat/test-2-tidy.R | 117 ++ tests/testthat/test-3-families.R | 77 + tests/testthat/test-3-spatial-varying.R | 2 tests/testthat/test-5-residuals.R | 80 + tests/testthat/test-9-mvn-simulation.R | 4 tests/testthat/test-betabinomial.R |only tests/testthat/test-collapse.R |only tests/testthat/test-cross-validation.R | 379 ++++++++- tests/testthat/test-emmeans.R |only tests/testthat/test-extra-time.R | 2 tests/testthat/test-ggeffect.R | 80 + tests/testthat/test-index.R | 95 ++ tests/testthat/test-link-prediction.R | 4 tests/testthat/test-make-category-svc.R |only tests/testthat/test-methods.R | 28 tests/testthat/test-mix.R | 67 + tests/testthat/test-offset.R | 2 tests/testthat/test-range-edge.R |only tests/testthat/test-smooths.R | 34 tests/testthat/test-time-varying.R | 10 tests/testthat/test-tmb-simulation.R | 124 ++ tests/testthat/test-waywiser.R |only vignettes/model-description.Rmd | 611 ++++++++------ vignettes/refs.bib | 61 + 75 files changed, 5031 insertions(+), 1764 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.4.4 dated 2025-11-05 and 3.4.5 dated 2025-11-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 4 ++-- R/utilities.R | 24 +++++++++++++++++++----- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS | 11 ++++++++--- man/print.rfsrc.Rd | 1 - 9 files changed, 52 insertions(+), 34 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with Stan, NIMBLE, JAGS, and other software.
Author: Casey Youngflesh [aut, cre] ,
Christian Che-Castaldo [aut] ,
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.16.3 dated 2023-10-17 and 0.16.5 dated 2025-11-26
DESCRIPTION | 16 +-- MD5 | 20 +-- NEWS.md | 14 ++ R/MCMCdiag.R | 48 +++++++-- R/MCMCplot.R | 30 ++++- R/MCMCtrace.R | 44 +++++++- build/vignette.rds |binary inst/doc/MCMCvis.R | 254 +++++++++++++++++++++++++------------------------- inst/doc/MCMCvis.html | 37 +++---- man/MCMCdiag.Rd | 12 ++ man/MCMCplot.Rd | 5 11 files changed, 294 insertions(+), 186 deletions(-)
Title: Retail Shopping Data
Description: Retail shopping transactions for 2,469 households over one year.
Originates from the 84.51° Complete Journey 2.0 source files
<https://www.8451.com/area51> which also includes useful metadata on
products, coupons, campaigns, and promotions.
Author: Brad Boehmke [aut, cre] ,
Steven M. Mortimer [aut]
Maintainer: Brad Boehmke <bradleyboehmke@gmail.com>
Diff between completejourney versions 1.1.0 dated 2019-09-28 and 1.1.1 dated 2025-11-26
completejourney-1.1.0/completejourney/data/datalist |only completejourney-1.1.1/completejourney/DESCRIPTION | 13 completejourney-1.1.1/completejourney/MD5 | 73 completejourney-1.1.1/completejourney/NEWS.md | 14 completejourney-1.1.1/completejourney/R/campaign_descriptions.R | 8 completejourney-1.1.1/completejourney/R/campaigns.R | 10 completejourney-1.1.1/completejourney/R/completejourney.R | 2 completejourney-1.1.1/completejourney/R/coupon_redemptions.R | 6 completejourney-1.1.1/completejourney/R/coupons.R | 8 completejourney-1.1.1/completejourney/R/demographics.R | 12 completejourney-1.1.1/completejourney/R/get_data.R | 40 completejourney-1.1.1/completejourney/R/get_promotions.R | 24 completejourney-1.1.1/completejourney/R/get_transactions.R | 24 completejourney-1.1.1/completejourney/R/products.R | 10 completejourney-1.1.1/completejourney/R/promotions.R | 24 completejourney-1.1.1/completejourney/R/transactions.R | 6 completejourney-1.1.1/completejourney/R/utils.R | 75 completejourney-1.1.1/completejourney/R/zzz.R | 6 completejourney-1.1.1/completejourney/README.md | 35 completejourney-1.1.1/completejourney/build/vignette.rds |binary completejourney-1.1.1/completejourney/inst/doc/completejourney.R | 452 ++--- completejourney-1.1.1/completejourney/inst/doc/completejourney.Rmd | 2 completejourney-1.1.1/completejourney/inst/doc/completejourney.html | 792 ++++++---- completejourney-1.1.1/completejourney/man/campaign_descriptions.Rd | 6 completejourney-1.1.1/completejourney/man/campaigns.Rd | 8 completejourney-1.1.1/completejourney/man/completejourney.Rd | 4 completejourney-1.1.1/completejourney/man/coupon_redemptions.Rd | 6 completejourney-1.1.1/completejourney/man/coupons.Rd | 6 completejourney-1.1.1/completejourney/man/demographics.Rd | 8 completejourney-1.1.1/completejourney/man/get_data.Rd | 16 completejourney-1.1.1/completejourney/man/get_promotions.Rd | 6 completejourney-1.1.1/completejourney/man/get_transactions.Rd | 6 completejourney-1.1.1/completejourney/man/products.Rd | 8 completejourney-1.1.1/completejourney/man/promotions_sample.Rd | 16 completejourney-1.1.1/completejourney/man/transactions_sample.Rd | 6 completejourney-1.1.1/completejourney/tests/testthat/test_dimensions.R | 4 completejourney-1.1.1/completejourney/tests/testthat/test_downloads.R | 49 completejourney-1.1.1/completejourney/vignettes/completejourney.Rmd | 2 38 files changed, 1040 insertions(+), 747 deletions(-)
More information about completejourney at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-28 0.4.15
2023-08-21 0.4.14
2022-10-14 0.4.10
2022-09-29 0.4.8
2022-03-13 0.4.6
2022-02-16 0.4.4
2022-02-14 0.4.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-11 1.6.1
2025-07-29 1.6.0
2025-06-12 1.5.3
2025-05-04 1.5.2
2025-05-01 1.5.1
2025-03-17 1.5.0
2024-01-21 1.4.0
2023-09-11 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-21 1.2-18
2022-04-06 1.2-17
2018-07-20 1.2-16
2013-09-22 1.2-15