Title: R Data Science Supporting Rattle
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
collection of utilities functions for the data scientist. This
package (v5.6.0) supports the companion graphical interface with
the aim to provide a simple and intuitive introduction to R
for data science, allowing a user to quickly load data from a CSV file
transform and explore the data, and to build and evaluate models.
A key aspect of the GUI is that all R commands are logged and
commented through the log tab.
This can be saved as a standalone R script file and as
an aid for the user to
learn R or to copy-and-paste directly into R itself. If you
want to use the older Rattle implementing the GUI in RGtk2
(which is no longer available from CRAN) then please install
the Rattle package v5.5.1.
See rattle.togaware.com for instructions on installing
the modern Rattle graphical user interface.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] ,
Brian Ripley [cph] ,
Jose Magana [ctb] ,
Surendra Tipparaju [ctb] ,
Durga Prasad Chappidi [ctb] ,
D [...truncated...]
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 5.5.1 dated 2022-03-21 and 5.6.2 dated 2026-02-08
rattle-5.5.1/rattle/inst/extdata |only rattle-5.6.2/rattle/DESCRIPTION | 68 rattle-5.6.2/rattle/MD5 | 128 rattle-5.6.2/rattle/R/associate.R | 118 rattle-5.6.2/rattle/R/data.R | 1455 ---------- rattle-5.6.2/rattle/R/evaluate.R | 604 ---- rattle-5.6.2/rattle/R/executeBoxPlot2.R | 6 rattle-5.6.2/rattle/R/explore.R | 634 ++-- rattle-5.6.2/rattle/R/export.R | 195 - rattle-5.6.2/rattle/R/hclust.R | 204 - rattle-5.6.2/rattle/R/kmeans.R | 75 rattle-5.6.2/rattle/R/log.R | 116 rattle-5.6.2/rattle/R/model.R | 178 - rattle-5.6.2/rattle/R/projects.R | 526 --- rattle-5.6.2/rattle/R/rattle.R | 1989 --------------- rattle-5.6.2/rattle/R/rattleng.R |only rattle-5.6.2/rattle/R/survival.R | 33 rattle-5.6.2/rattle/R/textview.R | 19 rattle-5.6.2/rattle/R/zzz.R | 63 rattle-5.6.2/rattle/build/vignette.rds |binary rattle-5.6.2/rattle/data/locationsAUS.RData |binary rattle-5.6.2/rattle/data/weather.RData |binary rattle-5.6.2/rattle/data/weatherAUS.RData |binary rattle-5.6.2/rattle/inst/CITATION | 28 rattle-5.6.2/rattle/inst/NEWS | 24 rattle-5.6.2/rattle/inst/doc/rattle.R | 11 rattle-5.6.2/rattle/inst/doc/rattle.Rnw | 76 rattle-5.6.2/rattle/inst/doc/rattle.pdf |binary rattle-5.6.2/rattle/inst/etc/rattle.ui | 2 rattle-5.6.2/rattle/man/acquireAuditData.Rd | 6 rattle-5.6.2/rattle/man/asRules.Rd | 2 rattle-5.6.2/rattle/man/asRules.rpart.Rd | 2 rattle-5.6.2/rattle/man/binning.Rd | 2 rattle-5.6.2/rattle/man/calcInitialDigitDistr.Rd | 2 rattle-5.6.2/rattle/man/calculateAUC.Rd | 2 rattle-5.6.2/rattle/man/centers.hclust.Rd | 2 rattle-5.6.2/rattle/man/comcat.Rd | 2 rattle-5.6.2/rattle/man/drawTreeNodes.Rd | 2 rattle-5.6.2/rattle/man/drawTreesAda.Rd | 2 rattle-5.6.2/rattle/man/errorMatrix.Rd | 2 rattle-5.6.2/rattle/man/evaluateRisk.Rd | 2 rattle-5.6.2/rattle/man/fancyRpartPlot.Rd | 2 rattle-5.6.2/rattle/man/find_fewest_levels.Rd |only rattle-5.6.2/rattle/man/genPlotTitleCmd.Rd | 2 rattle-5.6.2/rattle/man/ggVarImp.Rd | 2 rattle-5.6.2/rattle/man/grouper.Rd | 2 rattle-5.6.2/rattle/man/internal.Rd | 2 rattle-5.6.2/rattle/man/listAdaVarsUsed.Rd | 2 rattle-5.6.2/rattle/man/listTreesAda.Rd | 2 rattle-5.6.2/rattle/man/meta_data.Rd |only rattle-5.6.2/rattle/man/plotOptimalLine.Rd | 2 rattle-5.6.2/rattle/man/plotRisk.Rd | 2 rattle-5.6.2/rattle/man/printRandomForests.Rd | 2 rattle-5.6.2/rattle/man/randomForest2Rules.Rd | 2 rattle-5.6.2/rattle/man/rattle.Rd | 22 rattle-5.6.2/rattle/man/rattle.print.summary.multinom.Rd | 2 rattle-5.6.2/rattle/man/rattleInfo.Rd | 2 rattle-5.6.2/rattle/man/riskchart.Rd | 2 rattle-5.6.2/rattle/man/savePlotToFile.Rd | 2 rattle-5.6.2/rattle/man/setupDataset.Rd | 2 rattle-5.6.2/rattle/man/theme_rattle.Rd |only rattle-5.6.2/rattle/man/treeset.randomForest.Rd | 2 rattle-5.6.2/rattle/man/unique_columns.Rd |only rattle-5.6.2/rattle/man/weather.Rd | 25 rattle-5.6.2/rattle/man/weatherAUS.Rd | 32 rattle-5.6.2/rattle/man/whichNumerics.Rd | 2 rattle-5.6.2/rattle/man/wine.Rd | 42 rattle-5.6.2/rattle/vignettes/rattle.Rnw | 76 68 files changed, 968 insertions(+), 5845 deletions(-)
Title: Waffle Style Chart with a Brick Layout in 'ggplot2'
Description: A new take on the bar chart. Similar to a waffle style chart but
instead of squares the layout resembles a brick wall.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between ggbrick versions 0.3.1 dated 2025-09-14 and 0.3.2 dated 2026-02-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++---- R/geom-brick.R | 2 +- 4 files changed, 9 insertions(+), 11 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Nuria Mercade-Besora [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.3.1 dated 2026-01-28 and 0.3.2 dated 2026-02-08
PhenotypeR-0.3.1/PhenotypeR/R/utils-pipe.R |only PhenotypeR-0.3.1/PhenotypeR/inst/shiny/data/appData.RData |only PhenotypeR-0.3.1/PhenotypeR/inst/shiny/data/raw/results.csv |only PhenotypeR-0.3.1/PhenotypeR/man/pipe.Rd |only PhenotypeR-0.3.2/PhenotypeR/DESCRIPTION | 36 PhenotypeR-0.3.2/PhenotypeR/MD5 | 51 PhenotypeR-0.3.2/PhenotypeR/NAMESPACE | 2 PhenotypeR-0.3.2/PhenotypeR/R/codelistDiagnostics.R | 36 PhenotypeR-0.3.2/PhenotypeR/R/cohortDiagnostics.R | 4 PhenotypeR-0.3.2/PhenotypeR/R/drugDiagnostics.R |only PhenotypeR-0.3.2/PhenotypeR/R/getCohortExpectations.R | 6 PhenotypeR-0.3.2/PhenotypeR/R/utilities.R |only PhenotypeR-0.3.2/PhenotypeR/inst/doc/CodelistDiagnostics.html | 726 ++-- PhenotypeR-0.3.2/PhenotypeR/inst/doc/DatabaseDiagnostics.html | 1752 ++-------- PhenotypeR-0.3.2/PhenotypeR/inst/doc/PhenotypeExpectations.html | 24 PhenotypeR-0.3.2/PhenotypeR/inst/doc/PopulationDiagnostics.html | 220 - PhenotypeR-0.3.2/PhenotypeR/inst/doc/ShinyDiagnostics.R | 37 PhenotypeR-0.3.2/PhenotypeR/inst/doc/ShinyDiagnostics.Rmd | 104 PhenotypeR-0.3.2/PhenotypeR/inst/doc/ShinyDiagnostics.html | 85 PhenotypeR-0.3.2/PhenotypeR/inst/shiny/global.R | 5 PhenotypeR-0.3.2/PhenotypeR/inst/shiny/server.R | 60 PhenotypeR-0.3.2/PhenotypeR/man/PhenotypeR-package.Rd | 2 PhenotypeR-0.3.2/PhenotypeR/tests/testthat/test-drugDiagnostics.R |only PhenotypeR-0.3.2/PhenotypeR/vignettes/ShinyDiagnostics.Rmd | 104 PhenotypeR-0.3.2/PhenotypeR/vignettes/ShinyDiagnosticsFigures |only 25 files changed, 1231 insertions(+), 2023 deletions(-)
More information about QuantileOnQuantile at CRAN
Permanent link
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.12.0-2 dated 2026-02-03 and 1.12.0-3 dated 2026-02-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/build_highs.sh | 10 +++++++--- 3 files changed, 12 insertions(+), 8 deletions(-)
Title: Functions to Simplify the Use of 'glmnet' for Machine Learning
Description: Provides several functions to simplify using the 'glmnet' package: converting data frames into matrices ready for 'glmnet'; b) imputing missing variables multiple times; c) fitting and applying prediction models straightforwardly; d) assigning observations to folds in a balanced way; e) cross-validate the models; f) selecting the most representative model across imputations and folds; and g) getting the relevance of the model regressors; as described in several publications: Solanes et al. (2022) <doi:10.1038/s41537-022-00309-w>, Palau et al. (2023) <doi:10.1016/j.rpsm.2023.01.001>, Salazar de Pablo et al. (2025) <doi:10.1038/s41380-025-03244-1>.
Author: Joaquim Radua [aut, cre]
Maintainer: Joaquim Radua <quimradua@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2024-09-11
Diff between easy.glmnet versions 1.0 dated 2024-09-11 and 1.1 dated 2026-02-08
DESCRIPTION | 13 - MD5 | 19 +- NAMESPACE | 5 NEWS |only R/source.R | 294 ++++++++++++++++++++++++-------------- man/assign.folds.Rd | 2 man/cv.Rd | 6 man/glmnet_fit.Rd | 6 man/glmnet_get.items.relevance.Rd | 4 man/impute.glmnet.matrix.Rd | 6 man/surv2binary.Rd | 8 - 11 files changed, 237 insertions(+), 126 deletions(-)
Title: 'R' Bindings to the 'C' Grammar for Tree-Sitter
Description: Provides bindings to a 'C' grammar for Tree-sitter, to be used
alongside the 'treesitter' package. Tree-sitter builds concrete syntax trees
for source files and can efficiently update them or generate code like producing
R C API wrappers from C functions, structs and global definitions from header files.
Author: Sounkou Mahamane Toure [aut, cre],
Tree-sitter authors [cph] ,
Eli Bendersky and Co-authors [cph]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between treesitter.c versions 0.0.1 dated 2025-12-10 and 0.0.4.2 dated 2026-02-08
treesitter.c-0.0.1/treesitter.c/tests/testthat |only treesitter.c-0.0.1/treesitter.c/tests/testthat.R |only treesitter.c-0.0.4.2/treesitter.c/DESCRIPTION | 17 treesitter.c-0.0.4.2/treesitter.c/MD5 | 171 +++++++++- treesitter.c-0.0.4.2/treesitter.c/NAMESPACE | 19 + treesitter.c-0.0.4.2/treesitter.c/NEWS.md |only treesitter.c-0.0.4.2/treesitter.c/R/abi.R | 3 treesitter.c-0.0.4.2/treesitter.c/R/fake_libc_utils.R |only treesitter.c-0.0.4.2/treesitter.c/R/language.R | 4 treesitter.c-0.0.4.2/treesitter.c/R/parse-headers.R |only treesitter.c-0.0.4.2/treesitter.c/R/treesitter_imports.R |only treesitter.c-0.0.4.2/treesitter.c/README.md | 171 +++++++++- treesitter.c-0.0.4.2/treesitter.c/inst |only treesitter.c-0.0.4.2/treesitter.c/man/fake_libc_path.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_defines_from_file.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_enum_members_from_root.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_enum_nodes.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_function_nodes.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_globals_from_root.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_globals_with_types_from_root.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_struct_members.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_struct_nodes.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_union_members_from_root.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/get_union_nodes.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/parse_header_text.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/parse_headers_collect.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/parse_r_include_headers.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/preprocess_header.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/preprocess_headers.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/r_cc.Rd |only treesitter.c-0.0.4.2/treesitter.c/man/treesitter.c-package.Rd | 3 treesitter.c-0.0.4.2/treesitter.c/src/init.c | 7 treesitter.c-0.0.4.2/treesitter.c/src/language.c | 11 treesitter.c-0.0.4.2/treesitter.c/tests/tinytest.R |only 34 files changed, 372 insertions(+), 34 deletions(-)
Title: Cell Type Annotation Using Large Language Models
Description: Automated cell type annotation for single-cell RNA sequencing data
using consensus predictions from multiple large language models. Integrates
with Seurat objects and provides uncertainty quantification for annotations.
Supports various LLM providers including OpenAI, Anthropic, and Google.
For details see Yang et al. (2025) <doi:10.1101/2025.04.10.647852>.
Author: Chen Yang [aut, cre, cph]
Maintainer: Chen Yang <cafferychen777@tamu.edu>
Diff between mLLMCelltype versions 1.3.2 dated 2025-09-02 and 2.0.0 dated 2026-02-08
mLLMCelltype-1.3.2/mLLMCelltype/R/summarize_discussion.R |only mLLMCelltype-1.3.2/mLLMCelltype/inst/doc/visualization-guide.R |only mLLMCelltype-1.3.2/mLLMCelltype/inst/doc/visualization-guide.Rmd |only mLLMCelltype-1.3.2/mLLMCelltype/inst/doc/visualization-guide.html |only mLLMCelltype-1.3.2/mLLMCelltype/man/QwenProcessor.Rd |only mLLMCelltype-1.3.2/mLLMCelltype/man/sanitize_base_url.Rd |only mLLMCelltype-1.3.2/mLLMCelltype/man/summarize_discussion.Rd |only mLLMCelltype-1.3.2/mLLMCelltype/man/validate_base_url.Rd |only mLLMCelltype-1.3.2/mLLMCelltype/vignettes/visualization-guide.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/.Rinstignore |only mLLMCelltype-2.0.0/mLLMCelltype/DESCRIPTION | 27 mLLMCelltype-2.0.0/mLLMCelltype/MD5 | 285 - mLLMCelltype-2.0.0/mLLMCelltype/NAMESPACE | 13 mLLMCelltype-2.0.0/mLLMCelltype/NEWS.md | 132 mLLMCelltype-2.0.0/mLLMCelltype/R/anthropic_processor.R | 63 mLLMCelltype-2.0.0/mLLMCelltype/R/api_utils.R | 24 mLLMCelltype-2.0.0/mLLMCelltype/R/base_api_processor.R | 284 - mLLMCelltype-2.0.0/mLLMCelltype/R/cache_manager.R | 145 mLLMCelltype-2.0.0/mLLMCelltype/R/cache_utils.R |only mLLMCelltype-2.0.0/mLLMCelltype/R/cell_type_annotation.R | 175 mLLMCelltype-2.0.0/mLLMCelltype/R/check_consensus.R | 132 mLLMCelltype-2.0.0/mLLMCelltype/R/compare_model_predictions.R | 180 mLLMCelltype-2.0.0/mLLMCelltype/R/consensus_annotation.R | 781 +-- mLLMCelltype-2.0.0/mLLMCelltype/R/custom_model_manager.R | 35 mLLMCelltype-2.0.0/mLLMCelltype/R/deepseek_processor.R | 29 mLLMCelltype-2.0.0/mLLMCelltype/R/facilitate_cluster_discussion.R | 218 mLLMCelltype-2.0.0/mLLMCelltype/R/gemini_processor.R | 32 mLLMCelltype-2.0.0/mLLMCelltype/R/get_model_response.R | 74 mLLMCelltype-2.0.0/mLLMCelltype/R/get_provider.R | 615 -- mLLMCelltype-2.0.0/mLLMCelltype/R/grok_processor.R | 25 mLLMCelltype-2.0.0/mLLMCelltype/R/minimax_processor.R | 25 mLLMCelltype-2.0.0/mLLMCelltype/R/openai_processor.R | 45 mLLMCelltype-2.0.0/mLLMCelltype/R/openrouter_processor.R | 25 mLLMCelltype-2.0.0/mLLMCelltype/R/print_consensus_summary.R | 117 mLLMCelltype-2.0.0/mLLMCelltype/R/process_anthropic.R | 21 mLLMCelltype-2.0.0/mLLMCelltype/R/process_deepseek.R | 28 mLLMCelltype-2.0.0/mLLMCelltype/R/process_gemini.R | 21 mLLMCelltype-2.0.0/mLLMCelltype/R/process_grok.R | 30 mLLMCelltype-2.0.0/mLLMCelltype/R/process_minimax.R | 23 mLLMCelltype-2.0.0/mLLMCelltype/R/process_openai.R | 21 mLLMCelltype-2.0.0/mLLMCelltype/R/process_openrouter.R | 28 mLLMCelltype-2.0.0/mLLMCelltype/R/process_qwen.R | 28 mLLMCelltype-2.0.0/mLLMCelltype/R/process_stepfun.R | 21 mLLMCelltype-2.0.0/mLLMCelltype/R/process_zhipu.R | 21 mLLMCelltype-2.0.0/mLLMCelltype/R/prompt_templates.R | 238 mLLMCelltype-2.0.0/mLLMCelltype/R/qwen_processor.R | 77 mLLMCelltype-2.0.0/mLLMCelltype/R/stepfun_processor.R | 25 mLLMCelltype-2.0.0/mLLMCelltype/R/unified_logger.R | 262 - mLLMCelltype-2.0.0/mLLMCelltype/R/url_utils.R | 137 mLLMCelltype-2.0.0/mLLMCelltype/R/zhipu_processor.R | 25 mLLMCelltype-2.0.0/mLLMCelltype/R/zzz.R | 16 mLLMCelltype-2.0.0/mLLMCelltype/build/vignette.rds |binary mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/advanced-features.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/advanced-features.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/advanced-features.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/consensus-principles.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/consensus-principles.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/consensus-principles.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/contributing-guide.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/contributing-guide.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/contributing-guide.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/faq.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/faq.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/faq.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/getting-started.R | 15 mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/getting-started.Rmd | 74 mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/getting-started.html | 2152 +------- mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/installation.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/installation.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/installation.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/introduction.Rmd | 44 mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/introduction.html | 1717 ------ mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/mLLMCelltype.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/mLLMCelltype.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/mLLMCelltype.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/usage-tutorial.R | 50 mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/usage-tutorial.Rmd | 105 mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/usage-tutorial.html | 2581 ++-------- mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/version-history.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/version-history.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/version-history.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/vs-single-agent.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/vs-single-agent.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/vs-single-agent.html |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/why-consensus.R |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/why-consensus.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/inst/doc/why-consensus.html |only mLLMCelltype-2.0.0/mLLMCelltype/man/AnthropicProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/BaseAPIProcessor.Rd | 57 mLLMCelltype-2.0.0/mLLMCelltype/man/CacheManager.Rd | 105 mLLMCelltype-2.0.0/mLLMCelltype/man/DeepSeekProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/GeminiProcessor.Rd | 48 mLLMCelltype-2.0.0/mLLMCelltype/man/GrokProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/MinimaxProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/OpenAIProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/OpenRouterProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/StepFunProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/UnifiedLogger.Rd | 150 mLLMCelltype-2.0.0/mLLMCelltype/man/ZhipuProcessor.Rd | 38 mLLMCelltype-2.0.0/mLLMCelltype/man/annotate_cell_types.Rd | 138 mLLMCelltype-2.0.0/mLLMCelltype/man/calculate_simple_consensus.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/check_consensus.Rd | 14 mLLMCelltype-2.0.0/mLLMCelltype/man/clean_annotation.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/combine_results.Rd | 10 mLLMCelltype-2.0.0/mLLMCelltype/man/compare_model_predictions.Rd | 99 mLLMCelltype-2.0.0/mLLMCelltype/man/configure_logger.Rd | 9 mLLMCelltype-2.0.0/mLLMCelltype/man/create_annotation_prompt.Rd | 14 mLLMCelltype-2.0.0/mLLMCelltype/man/create_consensus_check_prompt.Rd | 10 mLLMCelltype-2.0.0/mLLMCelltype/man/create_discussion_prompt.Rd | 14 mLLMCelltype-2.0.0/mLLMCelltype/man/create_initial_discussion_prompt.Rd | 12 mLLMCelltype-2.0.0/mLLMCelltype/man/create_standardization_prompt.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/dot-qwen_endpoint_cache.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/execute_consensus_check.Rd | 17 mLLMCelltype-2.0.0/mLLMCelltype/man/extract_labeled_value.Rd | 10 mLLMCelltype-2.0.0/mLLMCelltype/man/facilitate_cluster_discussion.Rd | 3 mLLMCelltype-2.0.0/mLLMCelltype/man/filter_valid_responses.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/find_majority_prediction.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/get_api_key.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/get_initial_predictions.Rd | 16 mLLMCelltype-2.0.0/mLLMCelltype/man/get_logger.Rd | 3 mLLMCelltype-2.0.0/mLLMCelltype/man/get_model_response.Rd | 2 mLLMCelltype-2.0.0/mLLMCelltype/man/get_provider.Rd | 49 mLLMCelltype-2.0.0/mLLMCelltype/man/identify_controversial_clusters.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/initialize_logger.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/interactive_consensus_annotation.Rd | 154 mLLMCelltype-2.0.0/mLLMCelltype/man/list_custom_models.Rd | 3 mLLMCelltype-2.0.0/mLLMCelltype/man/list_custom_providers.Rd | 3 mLLMCelltype-2.0.0/mLLMCelltype/man/logging_functions.Rd | 7 mLLMCelltype-2.0.0/mLLMCelltype/man/mLLMCelltype-package.Rd | 2 mLLMCelltype-2.0.0/mLLMCelltype/man/mllmcelltype_cache_dir.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/mllmcelltype_clear_cache.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/normalize_annotation.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/normalize_cluster_gene_list.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/parse_consensus_response.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/parse_flexible_format.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/parse_standard_format.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/parse_text_predictions.Rd |only mLLMCelltype-2.0.0/mLLMCelltype/man/prepare_models_list.Rd | 6 mLLMCelltype-2.0.0/mLLMCelltype/man/print_consensus_summary.Rd | 16 mLLMCelltype-2.0.0/mLLMCelltype/man/process_anthropic.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_controversial_clusters.Rd | 33 mLLMCelltype-2.0.0/mLLMCelltype/man/process_deepseek.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_gemini.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_grok.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_minimax.Rd | 17 mLLMCelltype-2.0.0/mLLMCelltype/man/process_openai.Rd | 24 mLLMCelltype-2.0.0/mLLMCelltype/man/process_openrouter.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_qwen.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_stepfun.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/process_zhipu.Rd | 15 mLLMCelltype-2.0.0/mLLMCelltype/man/register_custom_model.Rd | 8 mLLMCelltype-2.0.0/mLLMCelltype/man/register_custom_provider.Rd | 7 mLLMCelltype-2.0.0/mLLMCelltype/man/resolve_provider_base_url.Rd | 12 mLLMCelltype-2.0.0/mLLMCelltype/man/select_best_prediction.Rd | 8 mLLMCelltype-2.0.0/mLLMCelltype/man/standardize_cell_type_names.Rd | 25 mLLMCelltype-2.0.0/mLLMCelltype/tests |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/advanced-features.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/consensus-principles.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/contributing-guide.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/faq.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/getting-started.Rmd | 74 mLLMCelltype-2.0.0/mLLMCelltype/vignettes/installation.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/introduction.Rmd | 44 mLLMCelltype-2.0.0/mLLMCelltype/vignettes/mLLMCelltype.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/usage-tutorial.Rmd | 105 mLLMCelltype-2.0.0/mLLMCelltype/vignettes/version-history.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/vs-single-agent.Rmd |only mLLMCelltype-2.0.0/mLLMCelltype/vignettes/why-consensus.Rmd |only 168 files changed, 3711 insertions(+), 9351 deletions(-)
Title: Three Dimensional High Throughput 'GoMiner'
Description: The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes
into hierarchical categories based on biological process (BP), molecular function (MF) and
cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R.,
Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform
ontological analysis of microarray and proteomics studies, typically generating a list of
significant functional categories. To capture the benefit of all three ontologies,
I developed 'HTGM3D', a three-dimensional version of 'GoMiner'.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2025-05-30
Diff between HTGM3D versions 1.0 dated 2025-05-30 and 1.0.1 dated 2026-02-08
DESCRIPTION | 12 +++--- MD5 | 27 +++++++------- NAMESPACE | 2 + R/HTGM3D.R | 78 ++++++++++++++++++++++++++++++------------ build/vignette.rds |binary data/Housekeeping_Genes.RData |binary data/cluster52.RData |binary data/x_cg.RData |binary data/x_l.RData |binary data/x_m11.RData |binary data/x_mat.RData |binary data/x_mat3d.RData |binary inst/doc/HTGM3D.html | 4 +- man/interactWithGraph3D.Rd | 2 - man/whichOS.Rd |only 15 files changed, 81 insertions(+), 44 deletions(-)
Title: A Super K-Nearest Neighbor (SKNN) Classification Algorithm
Description: It's a Super K-Nearest Neighbor(SKNN) classification method with using kernel density to describe weight of the distance between a training observation and the testing sample. Comparison of performance between SKNN and KNN shows that SKNN is significantly superior to KNN.
Author: Yarong Yang [aut, cre],
Nader Ebrahimi [ctb],
Yoram Rubin [ctb],
Jacob Zhang [ctb]
Maintainer: Yarong Yang <Yi.YA_yaya@hotmail.com>
Diff between SKNN versions 4.1.2 dated 2025-09-18 and 4.1.3 dated 2026-02-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SKNN.R | 38 +++++++++++++++++++++++++++++--------- man/SKNN-package.Rd | 6 +++--- man/SKNN.Rd | 7 ++++--- 5 files changed, 44 insertions(+), 23 deletions(-)
Title: Extract Matching Lines from Matching Files
Description: Provides a simple interface to recursively list files from a
directory, filter them using a regular expression, read their
contents, and extract lines that match a user-defined pattern. The
package returns a dataframe containing the matched lines, their
line numbers, file paths, and the corresponding matched substrings.
Designed for quick code base exploration, log inspection, or any use
case involving pattern-based file and line filtering.
Author: Sacha Martingay [aut, cre, cph]
Maintainer: Sacha Martingay <martingay.sacha@hotmail.com>
Diff between seekr versions 0.1.3 dated 2025-05-10 and 0.1.4 dated 2026-02-08
seekr-0.1.3/seekr/R/test_wclass.R |only seekr-0.1.4/seekr/DESCRIPTION | 6 seekr-0.1.4/seekr/LICENSE | 4 seekr-0.1.4/seekr/MD5 | 37 +- seekr-0.1.4/seekr/NEWS.md | 36 +- seekr-0.1.4/seekr/R/aaa.R | 20 - seekr-0.1.4/seekr/R/seekr-package.R | 14 seekr-0.1.4/seekr/R/zzz.R | 24 - seekr-0.1.4/seekr/man/assert_flag_or_scalar_integerish.Rd | 40 +- seekr-0.1.4/seekr/man/check_flag_or_scalar_integerish.Rd | 38 +- seekr-0.1.4/seekr/man/figures/lifecycle-deprecated.svg | 42 +- seekr-0.1.4/seekr/man/figures/lifecycle-experimental.svg | 42 +- seekr-0.1.4/seekr/man/figures/lifecycle-stable.svg | 58 +-- seekr-0.1.4/seekr/man/figures/lifecycle-superseded.svg | 42 +- seekr-0.1.4/seekr/man/has_null_bytes.Rd | 48 +- seekr-0.1.4/seekr/man/print_cli.Rd | 52 +-- seekr-0.1.4/seekr/tests/testthat.R | 24 - seekr-0.1.4/seekr/tests/testthat/test-checkmate-extension.R | 68 ++-- seekr-0.1.4/seekr/tests/testthat/test-list-files.R | 132 ++++---- seekr-0.1.4/seekr/tests/testthat/test-read-filter-lines.R | 194 +++++------- 20 files changed, 451 insertions(+), 470 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-07 0.10.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-21 0.6.0
2025-10-19 0.2.2
2025-10-17 0.2.1
2025-10-16 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-16 1.0.0
2017-04-28 0.1.1
2017-01-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-27 0.0.148
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-27 0.2.6
2026-01-19 0.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-21 0.2.0
2021-09-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-29 0.4.0
2018-10-19 0.3.0
2017-12-21 0.2.0
2017-05-05 0.1.4
2017-04-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-13 0.1.3
2021-07-26 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-15 0.5.5
2023-01-18 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-14 2.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-16 2.3.3
2021-07-12 2.3.1
2021-07-05 2.2.0
2021-05-25 2.1.5
2017-09-22 1.4.0
2017-05-17 1.3.0
2017-02-05 1.2.0
2016-06-13 1.1.0
2016-01-14 1.0.1
2015-06-01 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-19 0.1.2
2022-09-22 0.1.1
2022-09-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-04 0.6.0
2024-07-29 0.5.9
2024-03-28 0.5.8
2023-03-10 0.5.7
2023-01-31 0.5.6
2022-10-31 0.5.5
2022-08-06 0.5.4
2022-06-07 0.5.3
2022-05-18 0.5.2
2022-03-11 0.5.1
2022-01-26 0.5.0
2021-09-14 0.4.2
2021-08-04 0.4.1
2021-07-31 0.4.0
2021-06-07 0.3.0
2021-04-19 0.2.0
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre] ,
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.6.5 dated 2026-01-23 and 2.6.6 dated 2026-02-08
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 6 + R/runexamples.R | 91 +++++++++++++----- build/partial.rdb |binary inst/doc/Inserting_bibtex_references.pdf |binary inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary 7 files changed, 83 insertions(+), 32 deletions(-)
Title: Extension Types for Spatial Data for Use with 'Arrow'
Description: Provides extension types and conversions to between R-native
object types and 'Arrow' columnar types. This includes integration among
the 'arrow', 'nanoarrow', 'sf', and 'wk' packages such that spatial
metadata is preserved wherever possible. Extension type implementations
ensure first-class geometry data type support in the 'arrow' and 'nanoarrow'
packages.
Author: Dewey Dunnington [aut, cre] ,
Anthony North [ctb],
Apache Software Foundation [cph],
Ulf Adams [cph],
Daniel Lemire [cph],
Joao Paulo Magalhaes [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between geoarrow versions 0.4.1 dated 2025-11-19 and 0.4.2 dated 2026-02-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/pkg-nanoarrow.R | 2 +- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Autoregressive Integrated Moving Average (ARIMA) Based
Disaggregation Methods
Description: We have the code for
disaggregation as found in Wei and Stram
(1990, <doi:10.1111/j.2517-6161.1990.tb01799.x>),
and Hodgess and Wei (1996, "Temporal Disaggregation of Time
Series" in Statistical Science I, Nova Publishing). The disaggregation models have different orders
of the moving average component. These are based on ARIMA
models rather than differencing or using similar time series.
Author: Erin Hodgess [aut, cre]
Maintainer: Erin Hodgess <erinm.hodgess@gmail.com>
Diff between disagmethod versions 0.1.0 dated 2026-01-30 and 0.1.1 dated 2026-02-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/lower3.R | 49 +++++++++++++++++++++++++++++++++++++++++++------ 3 files changed, 48 insertions(+), 11 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.30 dated 2026-01-16 and 1.31 dated 2026-02-08
ChangeLog | 7 + DESCRIPTION | 10 +- MD5 | 14 +-- NAMESPACE | 1 R/cgam.R | 33 ++++++++ R/cgamm.R | 209 +++++++++++++++++++++++++++++++++++++++++++++++++++++--- man/COforest.Rd | 4 - man/cgamm.Rd | 2 8 files changed, 254 insertions(+), 26 deletions(-)