Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.6.1 dated 2026-01-27 and 1.6.2 dated 2026-04-29
saros-1.6.1/saros/R/deprecated.R |only saros-1.6.1/saros/R/make_content.cat_freq_plot_docx.R |only saros-1.6.1/saros/R/make_content.cat_prop_plot_docx.R |only saros-1.6.1/saros/R/tabular_read.R |only saros-1.6.1/saros/R/tabular_write.R |only saros-1.6.1/saros/man/embed_cat_prop_plot.Rd |only saros-1.6.1/saros/man/embed_cat_table.Rd |only saros-1.6.1/saros/man/embed_chr_table_html.Rd |only saros-1.6.1/saros/man/filter_crowd_data.Rd |only saros-1.6.1/saros/man/generate_crowd_output.Rd |only saros-1.6.1/saros/man/handle_crowd_columns.Rd |only saros-1.6.1/saros/man/n_rng2.Rd |only saros-1.6.1/saros/man/summarize_data_by_type.Rd |only saros-1.6.1/saros/man/tabular_read.Rd |only saros-1.6.1/saros/man/tabular_write.Rd |only saros-1.6.1/saros/tests/testthat/test-tabular-read.R |only saros-1.6.1/saros/tests/testthat/test-tabular-write.R |only saros-1.6.2/saros/DESCRIPTION | 16 saros-1.6.2/saros/MD5 | 247 +++- saros-1.6.2/saros/NAMESPACE | 29 saros-1.6.2/saros/NEWS.md | 57 + saros-1.6.2/saros/R/check_quarto_website_index.R |only saros-1.6.2/saros/R/checks.R | 263 ++++- saros-1.6.2/saros/R/colour.R | 2 saros-1.6.2/saros/R/crowd_output.R |only saros-1.6.2/saros/R/crowd_plots_as_docx.R |only saros-1.6.2/saros/R/crowd_plots_as_officer.R |only saros-1.6.2/saros/R/crowd_plots_as_tabset.R | 45 saros-1.6.2/saros/R/crowd_tables_as_tabset.R |only saros-1.6.2/saros/R/fig_height_h_barchart.R | 498 +++++++++- saros-1.6.2/saros/R/get_fig_title_suffix_from_ggplot.R | 71 + saros-1.6.2/saros/R/get_main_question.R | 8 saros-1.6.2/saros/R/ggsaver.R | 127 ++ saros-1.6.2/saros/R/girafe-utils.R | 144 ++ saros-1.6.2/saros/R/girafe.R | 114 -- saros-1.6.2/saros/R/insert_text.R |only saros-1.6.2/saros/R/make_content.cat_plot_docx.R |only saros-1.6.2/saros/R/make_content.cat_plot_html.R | 10 saros-1.6.2/saros/R/make_content.cat_table_docx.R |only saros-1.6.2/saros/R/make_content.cat_table_html.R | 18 saros-1.6.2/saros/R/make_content.chr_table_docx.R |only saros-1.6.2/saros/R/make_content.chr_table_html.R | 2 saros-1.6.2/saros/R/make_content.int_plot_html.R | 39 saros-1.6.2/saros/R/make_content.int_table_html.R | 2 saros-1.6.2/saros/R/make_content.sigtest_table_html.R | 2 saros-1.6.2/saros/R/make_file_links.R |only saros-1.6.2/saros/R/make_link.R | 19 saros-1.6.2/saros/R/makeme.R | 20 saros-1.6.2/saros/R/makeme_helpers.R | 376 ++----- saros-1.6.2/saros/R/n_rng.R | 129 ++ saros-1.6.2/saros/R/output_format.R |only saros-1.6.2/saros/R/quarto_post_render.R |only saros-1.6.2/saros/R/simple_desciptives.R | 2 saros-1.6.2/saros/R/sorting_utils.R | 166 ++- saros-1.6.2/saros/R/summarize_cat_cat_data.R | 50 - saros-1.6.2/saros/R/txt_from_cat_mesos_plots.R | 164 ++- saros-1.6.2/saros/R/utils.R | 135 ++ saros-1.6.2/saros/R/validate_makeme_options.R | 111 -- saros-1.6.2/saros/R/zzz.R | 15 saros-1.6.2/saros/inst/WORDLIST | 41 saros-1.6.2/saros/inst/doc/for_chapter_author.html | 2 saros-1.6.2/saros/inst/doc/for_developers.html | 2 saros-1.6.2/saros/inst/doc/for_readers.html | 2 saros-1.6.2/saros/inst/doc/saros_name.html | 2 saros-1.6.2/saros/man/attach_dep_label_prefix.Rd |only saros-1.6.2/saros/man/auto_detect_makeme_type.Rd | 3 saros-1.6.2/saros/man/build_custom_palette.Rd |only saros-1.6.2/saros/man/check_quarto_website_index.Rd |only saros-1.6.2/saros/man/compute_full_category_levels.Rd |only saros-1.6.2/saros/man/count_max_wrapped_lines.Rd |only saros-1.6.2/saros/man/crowd_output.Rd |only saros-1.6.2/saros/man/crowd_plots_as_docx.Rd |only saros-1.6.2/saros/man/crowd_plots_as_officer.Rd |only saros-1.6.2/saros/man/crowd_plots_as_tabset.Rd | 10 saros-1.6.2/saros/man/crowd_tables_as_tabset.Rd |only saros-1.6.2/saros/man/detect_ghostscript.Rd |only saros-1.6.2/saros/man/dot-n_rng2_impl.Rd |only saros-1.6.2/saros/man/escape_for_regex.Rd |only saros-1.6.2/saros/man/escape_markdown.Rd |only saros-1.6.2/saros/man/escape_markdown_link.Rd |only saros-1.6.2/saros/man/extract_document_title.Rd |only saros-1.6.2/saros/man/extract_docx_title.Rd |only saros-1.6.2/saros/man/extract_ggplot_theme_info.Rd |only saros-1.6.2/saros/man/extract_pdf_title.Rd |only saros-1.6.2/saros/man/extract_pptx_title.Rd |only saros-1.6.2/saros/man/fig_height_h_barchart.Rd | 5 saros-1.6.2/saros/man/fig_height_h_barchart2.Rd | 58 + saros-1.6.2/saros/man/find_matching_docx.Rd |only saros-1.6.2/saros/man/generate_data_summary.Rd | 3 saros-1.6.2/saros/man/get_dep_label_prefix.Rd |only saros-1.6.2/saros/man/get_fig_title_suffix_from_ggplot.Rd | 16 saros-1.6.2/saros/man/get_fill_levels.Rd |only saros-1.6.2/saros/man/ggsaver.Rd | 81 + saros-1.6.2/saros/man/girafe.Rd | 5 saros-1.6.2/saros/man/hex_bw.Rd | 2 saros-1.6.2/saros/man/insert_text.Rd |only saros-1.6.2/saros/man/is_html_output_or_officer.Rd |only saros-1.6.2/saros/man/is_int_plot_html.Rd |only saros-1.6.2/saros/man/is_rendering.Rd |only saros-1.6.2/saros/man/make_file_links.Rd |only saros-1.6.2/saros/man/makeme.Rd | 16 saros-1.6.2/saros/man/n_range2.Rd | 37 saros-1.6.2/saros/man/output_format.Rd |only saros-1.6.2/saros/man/print.saros_officer_plots.Rd |only saros-1.6.2/saros/man/process_crowd_data.Rd | 3 saros-1.6.2/saros/man/process_single_pdf_post_render.Rd |only saros-1.6.2/saros/man/quarto_pdf_post_render.Rd |only saros-1.6.2/saros/man/read_quarto_post_render_input.Rd |only saros-1.6.2/saros/man/resolve_category_colors.Rd |only saros-1.6.2/saros/man/safe_file_write.Rd |only saros-1.6.2/saros/man/set_pdf_metadata_title.Rd |only saros-1.6.2/saros/man/summarize_cat_cat_data.Rd | 3 saros-1.6.2/saros/man/txt_from_cat_mesos_plots.Rd | 19 saros-1.6.2/saros/man/update_html_pdf_link_text.Rd |only saros-1.6.2/saros/man/validate_bool.Rd |only saros-1.6.2/saros/man/validate_bool_rule.Rd |only saros-1.6.2/saros/man/validate_character_vector_rule.Rd |only saros-1.6.2/saros/man/validate_double.Rd |only saros-1.6.2/saros/man/validate_double_rule.Rd |only saros-1.6.2/saros/man/validate_integerish.Rd |only saros-1.6.2/saros/man/validate_integerish_rule.Rd |only saros-1.6.2/saros/man/validate_palette_params.Rd |only saros-1.6.2/saros/man/validate_params.Rd |only saros-1.6.2/saros/man/validate_sort_category.Rd |only saros-1.6.2/saros/man/validate_sort_column.Rd |only saros-1.6.2/saros/man/validate_string.Rd |only saros-1.6.2/saros/man/validate_string_rule.Rd |only saros-1.6.2/saros/man/validate_type_variable_compatibility.Rd |only saros-1.6.2/saros/tests/testthat/_snaps/make_content.cat_plot_html/unused-categories-in-legend.svg | 48 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-diff-distributions.svg | 14 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-missing-data.svg | 36 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-multiple-dep-variables.svg | 16 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-multiple-dep-with-indep.svg | 36 saros-1.6.2/saros/tests/testthat/_snaps/makeme-int-plot-html-snapshots/int-plot-html-single-dep-variable.svg | 66 - 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saros-1.6.2/saros/tests/testthat/test-make_content.cat_table_html.R | 13 saros-1.6.2/saros/tests/testthat/test-make_content.int_plot_html.R |only saros-1.6.2/saros/tests/testthat/test-make_content.int_table_html.R | 40 saros-1.6.2/saros/tests/testthat/test-make_file_links.R |only saros-1.6.2/saros/tests/testthat/test-make_link.R | 61 + saros-1.6.2/saros/tests/testthat/test-makeme-int-plot-html-snapshots.R | 4 saros-1.6.2/saros/tests/testthat/test-makeme-mesos-color-consistency.R |only saros-1.6.2/saros/tests/testthat/test-n_rng.R | 59 + saros-1.6.2/saros/tests/testthat/test-output_format.R |only saros-1.6.2/saros/tests/testthat/test-quarto_post_render.R |only saros-1.6.2/saros/tests/testthat/test-safe_file_write.R |only saros-1.6.2/saros/tests/testthat/test-sort_dep_by_range.R |only saros-1.6.2/saros/tests/testthat/test-sort_indep_by_count.R |only saros-1.6.2/saros/tests/testthat/test-txt_from_cat_mesos_plots-validation.R | 17 saros-1.6.2/saros/tests/testthat/test-txt_from_cat_mesos_plots.R | 178 +++ saros-1.6.2/saros/tests/testthat/test-utils-ggsaver.R | 111 ++ saros-1.6.2/saros/tests/testthat/test-utils-makeme_helpers.R | 209 ++++ saros-1.6.2/saros/tests/testthat/test-validate_sort_helpers.R |only 173 files changed, 4185 insertions(+), 910 deletions(-)
Title: Interface to Open Collaboration Services (OCS) REST API
Description: Provides an Interface to Open Collaboration Services 'OCS' (<https://www.open-collaboration-services.org/>) REST API.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ocs4R versions 0.3 dated 2025-09-01 and 0.3.1 dated 2026-04-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ocsApiWebdavManager.R | 10 +++++----- README.md | 2 +- 5 files changed, 18 insertions(+), 14 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut, cre],
Mu Sigma, Inc. [cph]
Maintainer: Zubin Dowlaty <zubin.dowlaty@mu-sigma.com>
Diff between HVT versions 26.1.2 dated 2026-02-05 and 26.1.3 dated 2026-04-29
HVT-26.1.2/HVT/NEWS.md |only HVT-26.1.3/HVT/DESCRIPTION | 16 - HVT-26.1.3/HVT/MD5 | 67 +++--- HVT-26.1.3/HVT/R/Delete_Outpoints.R | 3 HVT-26.1.3/HVT/R/HVTMSM_support.R | 50 ----- HVT-26.1.3/HVT/R/HVTMSMoptimization.R | 2 HVT-26.1.3/HVT/R/OptimizationResults.R | 10 - HVT-26.1.3/HVT/R/clustHVT.R | 27 +- HVT-26.1.3/HVT/R/clusterPlot.R | 10 - HVT-26.1.3/HVT/R/constants.R |only HVT-26.1.3/HVT/R/diagPlot.R | 37 --- HVT-26.1.3/HVT/R/diagSuggestion.R | 5 HVT-26.1.3/HVT/R/edaPlots.R | 11 - HVT-26.1.3/HVT/R/getCellId.R | 10 - HVT-26.1.3/HVT/R/getCentroids.R | 44 +++- HVT-26.1.3/HVT/R/getOptimalCentroids.R | 3 HVT-26.1.3/HVT/R/getTransitionProbability.R | 4 HVT-26.1.3/HVT/R/hvq.R | 63 ------ HVT-26.1.3/HVT/R/madPlot.R | 1 HVT-26.1.3/HVT/R/mcmc_plots.R | 24 +- HVT-26.1.3/HVT/R/msm.R | 56 ----- HVT-26.1.3/HVT/R/plotAnimatedFlowmap.R | 12 - HVT-26.1.3/HVT/R/plotHVT.R | 115 ++--------- HVT-26.1.3/HVT/R/plotModelDiagnostics.R | 6 HVT-26.1.3/HVT/R/plotZscore.R | 1 HVT-26.1.3/HVT/R/scoreHVT.R | 226 ++++++---------------- HVT-26.1.3/HVT/R/scoreLayeredHVT.R | 16 - HVT-26.1.3/HVT/R/summary.R | 4 HVT-26.1.3/HVT/R/trainHVT.R | 113 ++--------- HVT-26.1.3/HVT/R/utilities.R |only HVT-26.1.3/HVT/README.md | 37 +++ HVT-26.1.3/HVT/inst/doc/HVT.Rmd | 22 ++ HVT-26.1.3/HVT/inst/doc/HVT.html | 49 ++++ HVT-26.1.3/HVT/man/getOptimalCentroids.Rd | 3 HVT-26.1.3/HVT/tests/testthat/testhvt.R | 278 +++++++++++++++++++++++----- HVT-26.1.3/HVT/vignettes/HVT.Rmd | 22 ++ 36 files changed, 603 insertions(+), 744 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface
for conducting a wide range of factor analysis procedures. 'FAfA'
(Factor Analysis for All) guides users through data uploading,
assumption checking (descriptives, collinearity, multivariate
normality, outliers), data wrangling (variable exclusion, data
splitting), factor retention analysis (e.g., Parallel Analysis, Hull
method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model
testing, Reliability Analysis (e.g., Cronbach's Alpha, McDonald's
Omega), Measurement Invariance testing across groups, and item
weighting techniques. The application leverages established R packages
such as 'lavaan' and 'psych' to perform these analyses, offering an
accessible platform for researchers and students. Results are
presented in user-friendly tables and plots, with options for
downloading outputs.
Author: Abdullah Faruk KILIC [aut, cre],
Ahmet Caliskan [aut]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 0.5 dated 2025-12-15 and 1.0 dated 2026-04-29
FAfA-0.5/FAfA/inst/app/www/favicon.ico |only FAfA-1.0/FAfA/DESCRIPTION | 17 - FAfA-1.0/FAfA/MD5 | 38 +- FAfA-1.0/FAfA/R/app_server.R | 23 - FAfA-1.0/FAfA/R/app_ui.R | 415 +++++++++++++++++++------------ FAfA-1.0/FAfA/R/mod_about_server.r | 56 +++- FAfA-1.0/FAfA/R/mod_assumptions_server.r | 41 ++- FAfA-1.0/FAfA/R/mod_assumptions_ui.R | 88 +++--- FAfA-1.0/FAfA/R/mod_cfa_server.r | 82 +++--- FAfA-1.0/FAfA/R/mod_cfa_ui.r | 6 FAfA-1.0/FAfA/R/mod_efa_server.r | 20 + FAfA-1.0/FAfA/R/mod_efa_ui.r | 232 ++++++++++------- FAfA-1.0/FAfA/R/mod_ega_server.r | 7 FAfA-1.0/FAfA/R/mod_ega_ui.r | 90 ++++-- FAfA-1.0/FAfA/R/mod_inv_ui.R | 6 FAfA-1.0/FAfA/R/mod_reliability_server.r | 17 - FAfA-1.0/FAfA/R/mod_reliability_ui.r | 54 ++-- FAfA-1.0/FAfA/R/mod_wrangling_server.r | 170 +++++++++--- FAfA-1.0/FAfA/R/mod_wrangling_ui.r | 113 +++++++- FAfA-1.0/FAfA/R/utils.r | 125 ++++++--- FAfA-1.0/FAfA/inst/app/www/logo.png |only 21 files changed, 1061 insertions(+), 539 deletions(-)
Title: Dataset Dependency Graphs for Leakage-Aware Evaluation
Description: Represent biomedical dataset structure as typed dependency
graphs so that sample provenance, repeated-measure structure, study
design, batch effects, and temporal relationships are explicit and
inspectable. Validates dataset structure, detects sample-level overlap,
derives deterministic split constraints, and produces a tool-agnostic
split specification for leakage-aware evaluation workflows.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between splitGraph versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-04-29
splitGraph-0.1.0/splitGraph/inst/extdata |only splitGraph-0.2.0/splitGraph/DESCRIPTION | 8 splitGraph-0.2.0/splitGraph/MD5 | 61 splitGraph-0.2.0/splitGraph/NAMESPACE | 4 splitGraph-0.2.0/splitGraph/NEWS.md | 73 splitGraph-0.2.0/splitGraph/R/constraints.R | 39 splitGraph-0.2.0/splitGraph/R/constructors.R | 15 splitGraph-0.2.0/splitGraph/R/graph-build-auto.R | 11 splitGraph-0.2.0/splitGraph/R/graph-build.R | 64 splitGraph-0.2.0/splitGraph/R/query.R | 29 splitGraph-0.2.0/splitGraph/R/serialization.R |only splitGraph-0.2.0/splitGraph/R/splitGraph-package.R | 26 splitGraph-0.2.0/splitGraph/R/validate.R | 35 splitGraph-0.2.0/splitGraph/README.md | 95 splitGraph-0.2.0/splitGraph/build/vignette.rds |binary splitGraph-0.2.0/splitGraph/inst/CITATION | 8 splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.R |only splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.Rmd |only splitGraph-0.2.0/splitGraph/inst/doc/adapter-cookbook.html |only splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.R | 62 splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.Rmd | 124 + splitGraph-0.2.0/splitGraph/inst/doc/leakage-aware-workflow.html | 969 +++++----- splitGraph-0.2.0/splitGraph/man/build_dependency_graph.Rd | 21 splitGraph-0.2.0/splitGraph/man/graph_from_metadata.Rd | 2 splitGraph-0.2.0/splitGraph/man/query_node_type.Rd | 7 splitGraph-0.2.0/splitGraph/man/write_dependency_graph.Rd |only splitGraph-0.2.0/splitGraph/man/write_split_spec.Rd |only splitGraph-0.2.0/splitGraph/tests/testthat/test-constructors.R | 18 splitGraph-0.2.0/splitGraph/tests/testthat/test-deprecations.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-graph-from-metadata.R | 4 splitGraph-0.2.0/splitGraph/tests/testthat/test-numeric-outcome.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-prefix-mismatch.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-query-paths-cap.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-schema-version.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-serialization.R |only splitGraph-0.2.0/splitGraph/tests/testthat/test-validate.R | 7 splitGraph-0.2.0/splitGraph/tests/testthat/test-validation-overrides.R |only splitGraph-0.2.0/splitGraph/vignettes/adapter-cookbook.Rmd |only splitGraph-0.2.0/splitGraph/vignettes/leakage-aware-workflow.Rmd | 124 + 39 files changed, 1280 insertions(+), 526 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 2.5.12 dated 2026-04-10 and 2.5.14 dated 2026-04-29
DESCRIPTION | 11 MD5 | 93 +- NEWS.md | 347 +++++++++++ R/compare_daa_results.R | 18 R/compare_gsea_daa.R | 29 R/compare_metagenome_results.R | 92 ++ R/data_utils.R | 266 ++++++++ R/ggpicrust2.R | 66 +- R/gsea_pathway_annotation.R | 21 R/import_MicrobiomeAnalyst_daa_results.R | 36 - R/ko2kegg_abundance.R | 107 ++- R/pathway_annotation.R | 234 ++++--- R/pathway_daa.R | 683 ++++++++++++++-------- R/pathway_errorbar.R | 285 ++++----- R/pathway_errorbar_table.R | 107 ++- R/pathway_gsea.R | 118 ++- R/pathway_heatmap.R | 17 R/pathway_pca.R | 46 - R/pathway_volcano.R | 13 R/taxa_contribution.R | 80 ++ R/taxa_contribution_viz.R | 44 + R/visualize_gsea.R | 116 ++- README.md | 21 man/compare_gsea_daa.Rd | 5 man/compare_metagenome_results.Rd | 2 man/ggpicrust2.Rd | 25 man/import_MicrobiomeAnalyst_daa_results.Rd | 8 man/ko2kegg_abundance.Rd | 16 man/pathway_daa.Rd | 83 +- man/pathway_errorbar.Rd | 3 man/pathway_errorbar_table.Rd | 7 man/pathway_gsea.Rd | 8 man/prepare_gene_sets.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-compare_metagenome_results.R |only tests/testthat/test-core-audit-followup.R |only tests/testthat/test-data_utils.R |only tests/testthat/test-find_sample_column.R |only tests/testthat/test-first-principles-fixes.R |only tests/testthat/test-ggpicrust2-return-structure.R | 236 +++++++ tests/testthat/test-ko2kegg_abundance.R | 133 ++++ tests/testthat/test-pathway_annotation.R | 138 ++++ tests/testthat/test-pathway_daa.R | 636 ++++++++++++++++++++ tests/testthat/test-pathway_errorbar.R | 149 ++++ tests/testthat/test-pathway_errorbar_table.R |only tests/testthat/test-pathway_gsea.R | 103 +++ tests/testthat/test-pathway_pca.R | 14 tests/testthat/test-pathway_volcano.R | 29 tests/testthat/test-reference_data_structure.R | 39 - tests/testthat/test-taxa_contribution.R | 33 + tests/testthat/test-visualize_gsea.R | 8 51 files changed, 3690 insertions(+), 839 deletions(-)
Title: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data
Description: Prevents and detects information leakage in biomedical machine learning.
Provides leakage-resistant split policies (subject-grouped, batch-blocked, study leave-out, time-ordered),
guarded preprocessing (train-only imputation, normalization, filtering, feature selection),
cross-validated fitting with common learners, permutation-gap auditing, batch and fold association tests,
and duplicate detection.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between bioLeak versions 0.3.6 dated 2026-04-11 and 0.3.7 dated 2026-04-29
bioLeak-0.3.6/bioLeak/man/dot-guard_ensure_levels.Rd |only bioLeak-0.3.6/bioLeak/man/dot-guard_fit.Rd |only bioLeak-0.3.6/bioLeak/man/predict_guard.Rd |only bioLeak-0.3.7/bioLeak/DESCRIPTION | 16 bioLeak-0.3.7/bioLeak/MD5 | 68 ++- bioLeak-0.3.7/bioLeak/NAMESPACE | 20 - bioLeak-0.3.7/bioLeak/NEWS.md | 71 +++ bioLeak-0.3.7/bioLeak/R/accessors.R |only bioLeak-0.3.7/bioLeak/R/audit.R | 1 bioLeak-0.3.7/bioLeak/R/classes.R | 78 +++ bioLeak-0.3.7/bioLeak/R/fit_resample.R | 80 +++- bioLeak-0.3.7/bioLeak/R/guards.R | 69 ++- bioLeak-0.3.7/bioLeak/R/impute_guarded.R | 2 bioLeak-0.3.7/bioLeak/R/splitgraph_adapter.R |only bioLeak-0.3.7/bioLeak/R/tune_resample.R | 51 ++ bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.R | 18 bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.Rmd | 32 + bioLeak-0.3.7/bioLeak/inst/doc/bioLeak-intro.html | 196 +++++----- bioLeak-0.3.7/bioLeak/man/as_leaksplits.Rd |only bioLeak-0.3.7/bioLeak/man/audit_batch_assoc.Rd |only bioLeak-0.3.7/bioLeak/man/audit_duplicates.Rd |only bioLeak-0.3.7/bioLeak/man/audit_info.Rd |only bioLeak-0.3.7/bioLeak/man/audit_perm_gap.Rd |only bioLeak-0.3.7/bioLeak/man/audit_target_assoc.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_R_eff.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_ci.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_metric.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_p_value.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_repeats.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_robust.Rd |only bioLeak-0.3.7/bioLeak/man/dlsi_tier.Rd |only bioLeak-0.3.7/bioLeak/man/fit_metrics.Rd |only bioLeak-0.3.7/bioLeak/man/fit_resample.Rd | 2 bioLeak-0.3.7/bioLeak/man/guard_ensure_levels.Rd |only bioLeak-0.3.7/bioLeak/man/guard_fit.Rd |only bioLeak-0.3.7/bioLeak/man/predict.GuardFit.Rd |only bioLeak-0.3.7/bioLeak/man/print.LeakTune.Rd |only bioLeak-0.3.7/bioLeak/man/show-LeakAudit-method.Rd |only bioLeak-0.3.7/bioLeak/man/show-LeakFit-method.Rd |only bioLeak-0.3.7/bioLeak/tests/testthat/test-accessors.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-classes-summary.R | 2 bioLeak-0.3.7/bioLeak/tests/testthat/test-guard-fit-rename.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-guard-fit.R | 30 - bioLeak-0.3.7/bioLeak/tests/testthat/test-guards-utils.R | 4 bioLeak-0.3.7/bioLeak/tests/testthat/test-impute-guarded.R | 2 bioLeak-0.3.7/bioLeak/tests/testthat/test-invariants.R | 4 bioLeak-0.3.7/bioLeak/tests/testthat/test-predict-guardfit.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-show-methods.R |only bioLeak-0.3.7/bioLeak/tests/testthat/test-vignette-suggests.R |only bioLeak-0.3.7/bioLeak/vignettes/bioLeak-intro.Rmd | 32 + 50 files changed, 577 insertions(+), 201 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Kara Woo [aut, cre],
Toph Allen [aut],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Kara Woo <kara.woo@posit.co>
Diff between connectapi versions 0.12.0 dated 2026-04-13 and 0.12.1 dated 2026-04-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/git.R | 28 +++++++++++++++++++++------- inst/doc/customize-http.html | 4 ++-- inst/doc/getting-started.html | 4 ++-- tests/testthat/test-git.R | 15 +++++++++++++++ 7 files changed, 54 insertions(+), 20 deletions(-)
Title: Colour Palette for Reading and Code, Inspired by Moby-Dick
Description: The Pequod colour palette, named after the whaler in
Herman Melville's Moby-Dick. Provides the full Log base scale
from warm paper (Log 50) to deep ink (Log 950), eight crew
accent hues with light and dark variants, and 'ggplot2' scales
for discrete and continuous mapping. Designed for long-form
reading and code, with low saturation and a consistent earth-
pigment register. Full design rationale and accessibility notes
at <https://tiagojct.eu/projects/pequod/>.
Author: Tiago Jacinto [aut, cre]
Maintainer: Tiago Jacinto <tiagojacinto@med.up.pt>
This is a re-admission after prior archival of version 0.0-5 dated 2016-02-28
Diff between pequod versions 0.0-5 dated 2016-02-28 and 0.1.1 dated 2026-04-29
pequod-0.0-5/pequod/R/lmres.R |only pequod-0.0-5/pequod/R/plotSlope.R |only pequod-0.0-5/pequod/R/simpleSlope.R |only pequod-0.0-5/pequod/man/PlotSlope.Rd |only pequod-0.0-5/pequod/man/lmres.Rd |only pequod-0.0-5/pequod/man/simpleSlope.Rd |only pequod-0.0-5/pequod/man/summary.lmres.Rd |only pequod-0.0-5/pequod/man/summary.simpleSlope.Rd |only pequod-0.1.1/pequod/DESCRIPTION | 41 ++++++++++++++++-------- pequod-0.1.1/pequod/LICENSE |only pequod-0.1.1/pequod/MD5 | 30 +++++++++++------ pequod-0.1.1/pequod/NAMESPACE | 41 +++++++----------------- pequod-0.1.1/pequod/R/palettes-data.R |only pequod-0.1.1/pequod/R/palettes.R |only pequod-0.1.1/pequod/R/pequod-package.R |only pequod-0.1.1/pequod/R/preview.R |only pequod-0.1.1/pequod/R/scales.R |only pequod-0.1.1/pequod/README.md |only pequod-0.1.1/pequod/man/palette_pequod.Rd |only pequod-0.1.1/pequod/man/pequod-package.Rd |only pequod-0.1.1/pequod/man/pequod_crew.Rd |only pequod-0.1.1/pequod/man/pequod_crew_dark.Rd |only pequod-0.1.1/pequod/man/pequod_crew_light.Rd |only pequod-0.1.1/pequod/man/pequod_log.Rd |only pequod-0.1.1/pequod/man/pequod_preview.Rd |only pequod-0.1.1/pequod/man/scale_color_pequod_c.Rd |only pequod-0.1.1/pequod/man/scale_color_pequod_d.Rd |only pequod-0.1.1/pequod/tests |only 28 files changed, 62 insertions(+), 50 deletions(-)
Title: 'Geocoordinate Validation Service'
Description: The 'Geocoordinate Validation Service' (GVS) runs checks of coordinates in latitude/longitude format. It returns annotated coordinates with additional flags and metadata that can be used in data cleaning. Additionally, the package has functions related to attribution and metadata information. More information can be found at <https://github.com/ojalaquellueva/gvs/tree/master/api>.
Author: Brian Maitner [aut, cre] ,
Brad Boyle [aut],
Rethvick Sriram Yugendra Babu [aut]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between GVS versions 0.0.1 dated 2024-12-05 and 0.0.2 dated 2026-04-29
DESCRIPTION | 11 - LICENSE | 4 MD5 | 74 +++++----- NAMESPACE | 26 +-- NEWS | 26 ++- R/GVS.R | 124 ++++++++--------- R/GVS_citations.R | 32 ++-- R/GVS_collaborators.R | 30 ++-- R/GVS_data_dictionary.R | 30 ++-- R/GVS_metadata.R | 68 +++++---- R/GVS_sources.R | 42 +++--- R/GVS_version.R | 42 +++--- R/data.R | 24 +-- R/gvs_core.R | 210 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/GVS.R | 10 - inst/doc/GVS.Rmd | 174 ++++++++++++------------ inst/doc/GVS.html | 45 +----- man/GVS.Rd | 52 +++---- man/GVS_citations.Rd | 52 +++---- man/GVS_collaborators.Rd | 46 +++--- man/GVS_data_dictionary.Rd | 46 +++--- man/GVS_metadata.Rd | 60 ++++---- man/GVS_sources.Rd | 46 +++--- man/GVS_version.Rd | 46 +++--- man/check_internet.Rd | 30 ++-- man/gvs_core.Rd | 54 +++---- man/gvs_testfile.Rd | 48 +++--- tests/testthat.R | 10 - tests/testthat/setup-gvs.R | 36 ++--- tests/testthat/test-GVS.R | 40 ++--- tests/testthat/test-GVS_citations.R | 40 ++--- tests/testthat/test-GVS_collaborators.R | 40 ++--- tests/testthat/test-GVS_data_dictionary.R | 40 ++--- tests/testthat/test-GVS_metadata.R | 40 ++--- tests/testthat/test-GVS_sources.R | 38 ++--- tests/testthat/test-GVS_version.R | 36 ++--- vignettes/GVS.Rmd | 174 ++++++++++++------------ 38 files changed, 973 insertions(+), 973 deletions(-)
Title: Creates, Merges, and Reads Binary Dosage Files
Description: Tools to create binary dosage files from either VCF
or GEN files, merge binary dosage files, and read
binary dosage files. Binary dosage files tend to have quicker
read times than VCF and GEN formats. There is a small increase
in size compared to compressed VCF and GEN files.
Author: John Morrison [aut, cre],
NCI [fnd] ,
NCI [fnd] ,
NIEHS [fnd] ,
NHLBI [fnd]
Maintainer: John Morrison <jmorr@usc.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2020-01-13
Diff between BinaryDosage versions 1.0.0 dated 2020-01-13 and 2.0.0 dated 2026-04-29
DESCRIPTION | 39 MD5 | 246 ++- NAMESPACE | 50 NEWS.md | 37 R/Merge.R | 760 +++++----- R/RcppExports.R | 182 +- R/ReadBinaryDosage.R | 776 +++++------ R/WriteBinaryDosage.R | 822 +++++------ R/apply.R | 565 ++++---- R/convert.R | 1108 ++++++++++------ R/format5.R |only R/getinfo.R | 1275 +++++++++--------- R/getsnp.R | 146 +- R/mergebd.R |only R/subset.R |only README.md | 798 +++++------ build/vignette.rds |binary inst/WORDLIST | 200 +- inst/doc/bd5snpreaders.R |only inst/doc/bd5snpreaders.Rmd |only inst/doc/bd5snpreaders.html |only inst/doc/bdformats.R | 12 inst/doc/bdformats.Rmd | 215 +-- inst/doc/bdformats.html | 711 +++++----- inst/doc/geneticfileinfo.R | 18 inst/doc/geneticfileinfo.Rmd | 208 +-- inst/doc/geneticfileinfo.html | 917 +++++++------ inst/doc/legacy.R |only inst/doc/legacy.Rmd |only inst/doc/legacy.html |only inst/doc/mergingbd5files.R |only inst/doc/mergingbd5files.Rmd |only inst/doc/mergingbd5files.html |only inst/doc/mergingfiles.R | 48 inst/doc/mergingfiles.Rmd | 113 - inst/doc/mergingfiles.html | 772 +++++------ inst/doc/r2estimates.R | 12 inst/doc/r2estimates.Rmd | 110 - inst/doc/r2estimates.html | 561 ++++---- inst/doc/usingbdfiles.R | 48 inst/doc/usingbdfiles.Rmd | 164 +- inst/doc/usingbdfiles.html | 1194 +++++++++-------- inst/doc/usingformat5files.R |only inst/doc/usingformat5files.Rmd |only inst/doc/usingformat5files.html |only inst/doc/usinggenfiles.R | 228 +-- inst/doc/usinggenfiles.Rmd | 690 +++++---- inst/doc/usinggenfiles.html | 1525 ++++++++++++---------- inst/doc/usingvcffiles.R | 246 +-- inst/doc/usingvcffiles.Rmd | 602 ++++---- inst/doc/usingvcffiles.html | 2285 ++++++++++++++++++--------------- inst/extdata/bad1.imp | 22 inst/extdata/bad1.info | 22 inst/extdata/bad1.vcf | 36 inst/extdata/bad2.info | 22 inst/extdata/bad2.vcf | 36 inst/extdata/bad3.vcf | 36 inst/extdata/set1a.imp | 22 inst/extdata/set1a.info | 22 inst/extdata/set1a.vcf | 36 inst/extdata/set1a_nd.info | 22 inst/extdata/set1ars.vcf | 36 inst/extdata/set1b.imp | 22 inst/extdata/set1b.info | 22 inst/extdata/set1b.vcf | 36 inst/extdata/set1b_asnp.imp | 24 inst/extdata/set1b_asnp.info | 24 inst/extdata/set1b_asnp.vcf | 38 inst/extdata/set1b_rssnp.imp | 24 inst/extdata/set1b_rssnp.vcf | 38 inst/extdata/set1b_rsub.imp | 22 inst/extdata/set1b_rsub.info | 22 inst/extdata/set1b_rsub.vcf | 36 inst/extdata/set2a.imp | 20 inst/extdata/set2a.sample | 122 - inst/extdata/set2a.vcf | 36 inst/extdata/set2b.imp | 20 inst/extdata/set2b.sample | 82 - inst/extdata/set2b.vcf | 36 inst/extdata/set3a.imp | 20 inst/extdata/set3a.sample | 124 - inst/extdata/set3a.sample1 | 124 - inst/extdata/set3b.chr.imp | 20 inst/extdata/set3b.imp | 20 inst/extdata/set3b.sample | 84 - inst/extdata/set3bnh.sample | 80 - inst/extdata/set4a.sample | 124 - inst/extdata/set4b.imp | 20 inst/extdata/set4b.sample | 84 - man/bd1tobd5.Rd |only man/bd2tobd5.Rd |only man/bd3tobd5.Rd |only man/bd4tobd5.Rd |only man/bdapply.Rd | 108 - man/bdmerge.Rd | 178 +- man/closebd5con.Rd |only man/genapply.Rd | 108 - man/gentobd.Rd | 238 +-- man/getaaf.Rd | 64 man/getbd5snp.Rd |only man/getbd5snp_buf.Rd |only man/getbd5snp_con.Rd |only man/getbdinfo.Rd | 65 man/getgeninfo.Rd | 188 +- man/getmaf.Rd | 68 man/getrsq.Rd | 74 - man/getsnp.Rd | 72 - man/getvcfinfo.Rd | 4 man/mergebd.Rd |only man/openbd5con.Rd |only man/subsetbd.Rd |only man/updatebd.Rd |only man/vcfapply.Rd | 106 - man/vcftobd.Rd | 165 +- man/vcftobdlegacy.Rd |only src/Makevars | 2 src/RcppExports.cpp | 64 src/ReadBinaryDosage.cpp | 98 + tests/testthat.R | 8 tests/testthat/test-apply.R | 244 +-- tests/testthat/test-convert.R | 965 +++++++++---- tests/testthat/test-fileinfo_cpp.R | 6 tests/testthat/test-filemismatch.R | 138 - tests/testthat/test-format-subformat.R | 350 ++--- tests/testthat/test-getinfo.R | 548 +++---- tests/testthat/test-getsnp.R | 111 - tests/testthat/test-merge.R | 432 +++--- tests/testthat/test-mergebd.R |only tests/testthat/test-reading.R | 22 tests/testthat/test-subset.R |only vignettes/bd5snpreaders.Rmd |only vignettes/bdformats.Rmd | 215 +-- vignettes/geneticfileinfo.Rmd | 208 +-- vignettes/legacy.Rmd |only vignettes/mergingbd5files.Rmd |only vignettes/mergingfiles.Rmd | 113 - vignettes/r2estimates.Rmd | 110 - vignettes/usingbdfiles.Rmd | 164 +- vignettes/usingformat5files.Rmd |only vignettes/usinggenfiles.Rmd | 690 +++++---- vignettes/usingvcffiles.Rmd | 602 ++++---- 141 files changed, 13921 insertions(+), 11926 deletions(-)
Title: Dump 'R' Package Source, Documentation, and Vignettes into One
File
Description: Dump source code, documentation and vignettes of an 'R'
package into a single file. Supports installed packages, tar.gz
archives, and package source directories. If the package is not
installed, only its source is automatically downloaded from CRAN for
processing. The output is a single plain text file or a character
vector, which is useful to ingest complete package documentation and
source into a large language model (LLM) or pass it further to other
tools, such as 'ragnar' <https://github.com/tidyverse/ragnar> to
create a Retrieval-Augmented Generation (RAG) workflow.
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between rdocdump versions 0.1.1 dated 2025-08-21 and 0.2.0 dated 2026-04-29
rdocdump-0.1.1/rdocdump/tools |only rdocdump-0.2.0/rdocdump/DESCRIPTION | 10 rdocdump-0.2.0/rdocdump/MD5 | 38 +- rdocdump-0.2.0/rdocdump/NEWS.md | 4 rdocdump-0.2.0/rdocdump/R/extract_code.R | 16 - rdocdump-0.2.0/rdocdump/R/to_txt.R | 29 +- rdocdump-0.2.0/rdocdump/R/util_resolve_pkg_path.R | 6 rdocdump-0.2.0/rdocdump/R/util_resolve_remote.R |only rdocdump-0.2.0/rdocdump/build/vignette.rds |binary rdocdump-0.2.0/rdocdump/inst/doc/rdocdump.html | 144 ++++++++++- rdocdump-0.2.0/rdocdump/inst/schemaorg.json | 4 rdocdump-0.2.0/rdocdump/man/create_remote.Rd |only rdocdump-0.2.0/rdocdump/man/figures |only rdocdump-0.2.0/rdocdump/man/find_pkg_dir.Rd |only rdocdump-0.2.0/rdocdump/man/get_remote_cache_dir.Rd |only rdocdump-0.2.0/rdocdump/man/is_remote_reference.Rd |only rdocdump-0.2.0/rdocdump/man/parse_remote_ref.Rd |only rdocdump-0.2.0/rdocdump/man/parse_remote_url.Rd |only rdocdump-0.2.0/rdocdump/man/rdd_extract_code.Rd | 16 - rdocdump-0.2.0/rdocdump/man/rdd_to_txt.Rd | 29 +- rdocdump-0.2.0/rdocdump/man/resolve_pkg_path.Rd | 16 - rdocdump-0.2.0/rdocdump/man/resolve_remote_pkg.Rd |only rdocdump-0.2.0/rdocdump/tests/testthat/test-remote.R |only rdocdump-0.2.0/rdocdump/tests/testthat/test-set_cache_path.R | 8 rdocdump-0.2.0/rdocdump/tests/testthat/test-to_txt.R | 7 25 files changed, 285 insertions(+), 42 deletions(-)
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, least-cost corridors, least-cost networks using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 2.1 dated 2024-02-12 and 2.2 dated 2026-04-29
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++--------------- NEWS.md | 11 ++++++--- R/movealloc.r | 7 +++--- R/movebound.r | 5 ++-- R/movecomp.r | 7 +++--- R/movecorr.r | 11 +++++---- R/movecost.r | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- R/movenetw.r | 5 ++-- R/moverank.r | 29 ++++++++++++------------ README.md | 9 ++++++- man/movealloc.Rd | 3 ++ man/movebound.Rd | 3 ++ man/movecomp.Rd | 3 ++ man/movecorr.Rd | 3 ++ man/movecost.Rd | 36 ++++++++++++++++++++++++++++++ man/movenetw.Rd | 3 ++ man/moverank.Rd | 3 ++ 18 files changed, 187 insertions(+), 55 deletions(-)
Title: Data for Exploring Curricular Complexity
Description: Provides 'igraph' objects representing engineering plans of study
across multiple disciplines and institutions. The data are intended for use
with the 'CurricularComplexity' package (Reeping, 2026)
<doi:10.32614/CRAN.package.CurricularComplexity> to support analyses of
curricular structure.
Author: David Reeping [aut, cre],
Olivia Ryan [aut],
Nahal Rashedi [ctb],
Elliot Setser [ctb],
Sushant Padhye [ctb],
Autri Banerjee [ctb],
Emily Hodge [ctb],
Levi Smith [ctb]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexityData versions 0.1.0 dated 2026-02-04 and 0.2.0 dated 2026-04-29
DESCRIPTION | 15 ++++++++------- MD5 | 9 ++++++--- R/NSF_SUCCESS.R | 25 +++++++++++++++++-------- R/ThreeEngineeringDisciplines_Ryan.R |only data/ThreeEngineeringDisciplines_Ryan.rda |only man/NSF_SUCCESS.Rd | 25 +++++++++++++++++-------- man/ThreeEngineeringDisciplines_Ryan.Rd |only 7 files changed, 48 insertions(+), 26 deletions(-)
More information about CurricularComplexityData at CRAN
Permanent link
Title: R Interface for the RAPIDS cuML Suite of Libraries
Description: R interface for RAPIDS cuML (<https://github.com/rapidsai/cuml>),
a suite of GPU-accelerated machine learning libraries powered by CUDA
(<https://en.wikipedia.org/wiki/CUDA>).
Author: Yitao Li [aut, cph] ,
Tomasz Kalinowski [aut, cre, cph],
Daniel Falbel [aut, cph],
RStudio [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between cuda.ml versions 0.3.2 dated 2022-01-07 and 0.3.3 dated 2026-04-29
cuda.ml-0.3.2/cuda.ml/man/cuda.ml.Rd |only cuda.ml-0.3.3/cuda.ml/DESCRIPTION | 26 +- cuda.ml-0.3.3/cuda.ml/MD5 | 90 +++++----- cuda.ml-0.3.3/cuda.ml/NAMESPACE | 21 ++ cuda.ml-0.3.3/cuda.ml/R/agglomerative.R | 4 cuda.ml-0.3.3/cuda.ml/R/cuml_utils.R | 16 - cuda.ml-0.3.3/cuda.ml/R/fil.R | 8 cuda.ml-0.3.3/cuda.ml/R/knn.R | 6 cuda.ml-0.3.3/cuda.ml/R/logistic_reg.R | 2 cuda.ml-0.3.3/cuda.ml/R/model.R | 19 +- cuda.ml-0.3.3/cuda.ml/R/ols.R | 2 cuda.ml-0.3.3/cuda.ml/R/package.R | 4 cuda.ml-0.3.3/cuda.ml/R/pca.R | 2 cuda.ml-0.3.3/cuda.ml/R/rand_forest.R | 2 cuda.ml-0.3.3/cuda.ml/R/rand_proj.R | 2 cuda.ml-0.3.3/cuda.ml/R/sgd.R | 6 cuda.ml-0.3.3/cuda.ml/R/svm.R | 6 cuda.ml-0.3.3/cuda.ml/R/tsne.R | 4 cuda.ml-0.3.3/cuda.ml/R/umap.R | 6 cuda.ml-0.3.3/cuda.ml/man/cuML_major_version.Rd | 8 cuda.ml-0.3.3/cuda.ml/man/cuML_minor_version.Rd | 8 cuda.ml-0.3.3/cuda.ml/man/cuda.ml-package.Rd |only cuda.ml-0.3.3/cuda.ml/man/cuda_ml_agglomerative_clustering.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_dbscan.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_fil_enabled.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_fil_load_model.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_kmeans.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_knn.Rd | 26 +- cuda.ml-0.3.3/cuda.ml/man/cuda_ml_knn_algo_ivfsq.Rd | 4 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_logistic_reg.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_ols.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_pca.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_rand_forest.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_sgd.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_svm.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_tsne.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_tsvd.Rd | 2 cuda.ml-0.3.3/cuda.ml/man/cuda_ml_umap.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/has_cuML.Rd | 6 cuda.ml-0.3.3/cuda.ml/man/predict.cuda_ml_rand_forest.Rd | 2 cuda.ml-0.3.3/cuda.ml/src/CMakeLists.txt.in | 1 cuda.ml-0.3.3/cuda.ml/tests/testthat.R | 3 cuda.ml-0.3.3/cuda.ml/tests/testthat/helper-initialize.R | 8 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-elastic-net.R | 2 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-lasso.R | 2 cuda.ml-0.3.3/cuda.ml/tests/testthat/test-tsvd.R | 49 +++-- cuda.ml-0.3.3/cuda.ml/tools/config/configure.R | 4 47 files changed, 226 insertions(+), 169 deletions(-)
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplementary tools for evaluating and validating partial least
squares structural equation models estimated with 'seminr'. Provides methods
for predictive model assessment, importance-performance analysis with
necessary condition testing, overfitting diagnostics, measurement model
verification, mediator contribution analysis, unobserved heterogeneity
detection via latent class and prediction-oriented segmentation, and
congruence coefficient testing. All functions accept estimated 'seminr'
model objects and return results with print, summary, and plot methods.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminrExtras versions 0.9.0 dated 2026-01-29 and 1.0.0 dated 2026-04-29
DESCRIPTION | 32 - MD5 | 82 +++ NAMESPACE | 82 +++ NEWS.md |only R/feature_cipma.R |only R/feature_coa.R |only R/feature_congruence.R | 221 +++++++--- R/feature_cta.R |only R/feature_cvpat.R | 632 +++++++++++++---------------- R/feature_fimix.R |only R/feature_nca.R |only R/feature_pcm.R |only R/feature_pos.R |only R/helpers.R | 243 +++++++++++ README.md | 275 +++++++++++- demo/00Index | 10 demo/seminr-pls-cipma.R |only demo/seminr-pls-coa.R |only demo/seminr-pls-congruence.R |only demo/seminr-pls-cta.R |only demo/seminr-pls-fimix.R |only demo/seminr-pls-nca.R |only demo/seminr-pls-pcm.R |only demo/seminr-pls-pos.R |only demo/seminr-primer-v2-chap6.R | 14 inst/doc/SEMinRExtras.R | 263 +++++++++++- inst/doc/SEMinRExtras.Rmd | 407 ++++++++++++++++++ inst/doc/SEMinRExtras.html | 649 +++++++++++++++++++++++++++--- man/assess_cipma.Rd |only man/assess_coa.Rd |only man/assess_cta.Rd |only man/assess_cvpat.Rd | 21 man/assess_cvpat_compare.Rd | 10 man/assess_fimix.Rd |only man/assess_fimix_compare.Rd |only man/assess_ipma.Rd |only man/assess_nca.Rd |only man/assess_nca_esse.Rd |only man/assess_pcm.Rd |only man/assess_pos.Rd |only man/assess_pos_compare.Rd |only man/competes.Rd |only man/congruence_test.Rd | 25 - man/deviance_tree.Rd |only man/group_rules.Rd |only man/plot.cipma_analysis.Rd |only man/plot.coa_analysis.Rd |only man/plot.fimix_analysis.Rd |only man/plot.fimix_comparison.Rd |only man/plot.nca_analysis.Rd |only man/plot.nca_esse.Rd |only man/plot.pcm_analysis.Rd |only man/pos_segments.Rd |only man/predictive_deviance.Rd |only man/unstable_params.Rd |only tests/testthat/test-cipma-comprehensive.R |only tests/testthat/test-coa.R |only tests/testthat/test-congruence.R |only tests/testthat/test-cta.R |only tests/testthat/test-cvpat-comprehensive.R |only tests/testthat/test-cvpat.R | 221 +++++----- tests/testthat/test-extended-edge-cases.R |only tests/testthat/test-fimix.R |only tests/testthat/test-nca.R |only tests/testthat/test-pcm.R |only tests/testthat/test-pos.R |only vignettes/SEMinRExtras.Rmd | 407 ++++++++++++++++++ 67 files changed, 2922 insertions(+), 672 deletions(-)
Title: Automatically Runs 18 Individual and 14 Ensembles of Models
Description: Automatically runs 18 individual models and 14 ensembles on numeric data, for a total of 32 models. The package automatically returns complete results on all 32 models,
25 charts and six tables. The user simply provides the tidy data, and answers a few questions (for example, how many times would you like to resample the data).
From there the package randomly splits the data into train, test and validation sets as the user requests (for example, train = 0.60, test = 0.20, validation = 0.20),
fits each of models on the training data, makes predictions on the test and validation sets, measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling
all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions
using the 32 pre trained models on totally new (untrained) data if the user selects that feature [...truncated...]
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between NumericEnsembles versions 1.0.5 dated 2026-03-01 and 1.2 dated 2026-04-29
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++---------- NAMESPACE | 1 NEWS.md | 5 +++ R/NumericEnsembles.R | 54 ++++++++++++++++++++++------------------- R/data.R | 4 +-- inst/doc/NumericEnsembles.Rmd | 4 +-- inst/doc/NumericEnsembles.html | 4 +-- inst/doc/Template.Rmd | 5 ++- inst/doc/Template.html | 5 ++- man/Boston_housing.Rd | 2 - man/New_Boston.Rd | 2 - vignettes/NumericEnsembles.Rmd | 4 +-- vignettes/Template.Rmd | 5 ++- 14 files changed, 71 insertions(+), 58 deletions(-)
More information about NumericEnsembles at CRAN
Permanent link
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Description: Contains functions to query and visualize the Neuroimaging features
associated with genetically regulated gene expression (GReX). The primary utility,
neuroimaGene(), relies on a list of user-defined genes and returns a table of
neuroimaging features (NIDPs) associated with each gene. This resource
is designed to assist in the interpretation of genome-wide and transcriptome-wide
association studies that evaluate brain related traits. Bledsoe (2024)
<doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization
functions that generate summary plots and 2-dimensional visualizations of regional
brain measures. Mowinckel (2020).
Author: Xavier Bledsoe [aut, cre] ,
Eric Gamazon [aut]
Maintainer: Xavier Bledsoe <xbledsoe22@gmail.com>
Diff between neuroimaGene versions 0.1.3 dated 2026-04-25 and 0.1.4 dated 2026-04-29
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NAMESPACE | 1 R/check_db.R | 70 +++++++++++++++++++++++++++++++++++++++++---- inst/doc/neuroimaGene.R | 2 - inst/doc/neuroimaGene.Rmd | 42 +++++++++++++++++++++++++-- inst/doc/neuroimaGene.html | 61 +++++++++++++++++++++++++++++++++++++-- man/check_db.Rd | 4 +- vignettes/neuroimaGene.Rmd | 42 +++++++++++++++++++++++++-- 9 files changed, 220 insertions(+), 28 deletions(-)
Title: Meta-Analysis Datasets
Description: A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Author: Wolfgang Viechtbauer [aut, cre] ,
Thomas White [aut] ,
Daniel Noble [aut] ,
Alistair Senior [aut] ,
W. Kyle Hamilton [aut] ,
Guido Schwarzer [dtc] ,
Christian Roever [dtc]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metadat versions 1.4-0 dated 2025-02-04 and 1.6-0 dated 2026-04-29
DESCRIPTION | 30 +++--- MD5 | 148 +++++++++++++++++++++--------- NEWS.md | 6 + R/datsearch.r | 27 ++--- README.md | 2 build/metadat.pdf |binary build/stage23.rdb |binary data/dat.anker2025.rda |only data/dat.baskerville2012.rda |binary data/dat.bauer2002.rda |only data/dat.berkey1998r.rda |only data/dat.chiarito2020.rda |only data/dat.demir2022.rda |only data/dat.feng2019.rda |only data/dat.furukawa2003.rda |binary data/dat.greb2008.rda |only data/dat.greenland1992.rda |only data/dat.higgins2008.rda |only data/dat.huber2000.rda |only data/dat.karner2014.rda |only data/dat.linde2016.rda |binary data/dat.lloyd2010.rda |only data/dat.meeker2017.rda |only data/dat.metap.rda |only data/dat.moore1998.rda |only data/dat.nissen2007.rda |only data/dat.poole2003.rda |only data/dat.quan2000.rda |only data/dat.rivera2025.rda |only data/dat.spooner2002.rda |binary data/dat.steurer2006.rda |only data/dat.thompson1999.rda |only data/dat.tian2009.rda |only inst/help.rdata |binary man/dat.anker2025.Rd |only man/dat.baker2009.Rd | 7 - man/dat.baskerville2012.Rd | 4 man/dat.bassler2004.Rd | 2 man/dat.bauer2002.Rd |only man/dat.berkey1998.Rd | 4 man/dat.chiarito2020.Rd |only man/dat.crisafulli2020.Rd | 5 - man/dat.curtin2002.Rd | 2 man/dat.damico2009.Rd | 3 man/dat.demir2022.Rd |only man/dat.dogliotti2014.Rd | 2 man/dat.dong2013.Rd | 2 man/dat.dumouchel1994.Rd | 5 - man/dat.feng2019.Rd |only man/dat.franchini2012.Rd | 2 man/dat.furukawa2003.Rd | 23 ++-- man/dat.greb2008.Rd |only man/dat.greenland1992.Rd |only man/dat.gurusamy2011.Rd | 2 man/dat.higgins2008.Rd |only man/dat.huber2000.Rd |only man/dat.ishak2007.Rd | 2 man/dat.karner2014.Rd |only man/dat.laopaiboon2015.Rd | 3 man/dat.linde2015.Rd | 10 +- man/dat.linde2016.Rd | 68 +++++++------ man/dat.lloyd2010.Rd |only man/dat.lopez2019.Rd | 42 +++++++- man/dat.meeker2017.Rd |only man/dat.metap.Rd |only man/dat.moore1998.Rd |only man/dat.nissen2007.Rd |only man/dat.poole2003.Rd |only man/dat.pritz1997.Rd | 3 man/dat.quan2000.Rd |only man/dat.rivera2025.Rd |only man/dat.roever2022.Rd | 6 - man/dat.spooner2002.Rd | 7 + man/dat.steurer2006.Rd |only man/dat.stowe2010.Rd | 4 man/dat.thompson1999.Rd |only man/dat.tian2009.Rd |only man/dat.ursino2021.Rd | 6 - man/dat.woods2010.Rd | 2 man/datsearch.Rd | 6 - tests/testthat/test_dat.anker2025.r |only tests/testthat/test_dat.baskerville2012.r | 2 tests/testthat/test_dat.bauer2002.r |only tests/testthat/test_dat.berkey1998.r | 1 tests/testthat/test_dat.chiarito2020.r |only tests/testthat/test_dat.demir2022.r |only tests/testthat/test_dat.feng2019.r |only tests/testthat/test_dat.furukawa2003.r | 2 tests/testthat/test_dat.greb2008.r |only tests/testthat/test_dat.greenland1992.r |only tests/testthat/test_dat.higgins2008.r |only tests/testthat/test_dat.huber2000.r |only tests/testthat/test_dat.karner2014.r |only tests/testthat/test_dat.linde2016.r | 2 tests/testthat/test_dat.lloyd2010.r |only tests/testthat/test_dat.meeker2017.r |only tests/testthat/test_dat.metap.r |only tests/testthat/test_dat.moore1998.r |only tests/testthat/test_dat.nissen2007.r |only tests/testthat/test_dat.poole2003.r |only tests/testthat/test_dat.quan2000.r |only tests/testthat/test_dat.riley2003.r | 6 + tests/testthat/test_dat.rivera2025.r |only tests/testthat/test_dat.spooner2002.r | 2 tests/testthat/test_dat.steurer2006.r |only tests/testthat/test_dat.thompson1999.r |only tests/testthat/test_dat.tian2009.r |only 107 files changed, 293 insertions(+), 157 deletions(-)
Title: Methods to Enrich R Objects with Extra Components
Description: Provides the "enrich()" method for augmenting list-like R objects with additional, model-specific components. Methods are currently available for objects of class "family", "link-glm", "lm", "glm", and "betareg". Enriched objects retain their original class and remain compatible with existing methods. For example, enriching a "glm" object produces an "enriched_glm" object that also inherits from "glm". In addition to the standard components, the "enriched_glm" object includes methods for simulation and functions to compute scores, observed and expected information matrices, first-order bias, and other model quantities such as densities, probabilities, and quantiles, which can be evaluated at use-supplied parameter values. The package also provides tools for generating customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between enrichwith versions 0.4.0 dated 2025-09-08 and 0.5.0 dated 2026-04-29
DESCRIPTION | 14 - MD5 | 18 - NEWS.md | 37 ++- R/enrich.glm.R | 459 +++++++++++++++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GLMs.html | 15 - inst/doc/bias.html | 18 - inst/doc/exponential_family.html | 16 - man/enrich.glm.Rd | 7 10 files changed, 376 insertions(+), 208 deletions(-)
Title: Wrangle and Modify Ts Object with Classic Frequencies and Exact
Dates
Description: The ts objects in R are managed using a very specific date format (in the form c(2022, 9) for September 2022 or c(2021, 2) for the second quarter of 2021, depending on the frequency, for example). We focus solely on monthly and quarterly series to manage the dates of ts objects. The general idea is to offer a set of functions to manage this date format without it being too restrictive or too imprecise depending on the rounding. This is a compromise between simplicity, precision and use of the basic 'stats' functions for creating and managing time series (ts(), window()).
Les objets ts en R sont gérés par un format de date très particulier (sous la forme c(2022, 9) pour septembre 2022 ou c(2021, 2) pour le deuxième trimestre 2021 selon la fréquence par exemple). On se concentre uniquement sur les séries mensuelles et trimestrielles pour gérer les dates des objets ts. Lidée générale est de proposer un ensemble de fonctions pour gérer ce format de date sans que ce soit trop contraignant o [...truncated...]
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tangbarth@hotmail.fr>
Diff between date4ts versions 0.1.1 dated 2026-02-01 and 0.1.2 dated 2026-04-29
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- NEWS.md | 7 ++++++- README.md | 20 ++++++++++++++------ 4 files changed, 27 insertions(+), 13 deletions(-)
Title: Process Text and Compute Linguistic Alignment in Conversation
Transcripts
Description: Imports conversation transcripts into R, concatenates them into a single dataframe appending event identifiers, cleans and formats the text, then yokes user-specified psycholinguistic database values to each word. 'ConversationAlign' then computes alignment indices between two interlocutors across each transcript for >40 possible semantic, lexical, and affective dimensions. In addition to alignment, 'ConversationAlign' also produces a table of analytics (e.g., token count, type-token-ratio) in a summary table describing your particular text corpus.
Author: Jamie Reilly [aut, cre] ,
Virginia Ulichney [aut],
Ben Sacks [aut],
Sarah Weinstein [ctb],
Chelsea Helion [ctb],
Gus Cooney [ctb]
Maintainer: Jamie Reilly <jamie_reilly@temple.edu>
This is a re-admission after prior archival of version 0.4.0 dated 2025-11-12
Diff between ConversationAlign versions 0.4.0 dated 2025-11-12 and 0.4.1 dated 2026-04-29
DESCRIPTION | 8 MD5 | 34 +- R/compute_lagcorr.R | 333 ++++++++++++------------ R/globals.R | 2 R/prep_dyads.R | 4 R/read_1file.R | 2 build/vignette.rds |binary inst/NEWS.md | 13 inst/doc/ConversationAlign_Introduction.Rmd | 7 inst/doc/ConversationAlign_Introduction.html | 17 - inst/doc/ConversationAlign_Step1_Read.R | 8 inst/doc/ConversationAlign_Step1_Read.Rmd | 2 inst/doc/ConversationAlign_Step1_Read.html | 83 ----- inst/doc/ConversationAlign_Step2_Prep.html | 4 inst/doc/ConversationAlign_Step3_Summarize.html | 4 inst/doc/ConversationAlign_Step4_Analytics.html | 4 vignettes/ConversationAlign_Introduction.Rmd | 7 vignettes/ConversationAlign_Step1_Read.Rmd | 2 18 files changed, 233 insertions(+), 301 deletions(-)
More information about ConversationAlign at CRAN
Permanent link
Title: A Directed Acyclic Graph Extension for 'blockr'
Description: Building on the docking layout manager provided by 'blockr.dock', this
provides an extension that allows for visualizing and manipulating a 'blockr'
board using a DAG-based user interface powered by the 'g6R'
graph visualisation HTML widget.
Author: David Granjon [aut, cre],
Nicolas Bennett [aut],
Christoph Sax [aut],
Bristol Myers Squibb [fnd]
Maintainer: David Granjon <david@cynkra.com>
Diff between blockr.dag versions 0.1.0 dated 2025-12-18 and 0.1.2 dated 2026-04-29
DESCRIPTION | 10 MD5 | 81 + NAMESPACE | 4 NEWS.md | 13 R/action.R | 238 ++++- R/ctx.R | 38 R/ext.R | 169 ++- R/g6r.R | 392 +++++++- R/meta.R | 27 R/srv.R | 155 ++- R/subboard.R |only R/tool.R | 34 R/ui.R | 7 R/utils.R | 10 inst/assets/css/empty-state.css | 14 inst/assets/js/copy-paste.js |only inst/doc/block-callback.html | 2 inst/doc/blockr.dag.html | 1103 ++++++++++++++++-------- inst/doc/context-menu.html | 2 inst/doc/toolbar.html | 2 inst/examples/empty/app.R | 1 inst/examples/variadic |only man/create_block_ports.Rd |only man/g6r.Rd | 6 man/get_children_from_links.Rd |only man/is_variadic_block.Rd |only man/resolve_target_ports.Rd |only tests/testthat/_snaps/e2e/empty-app-001.json | 109 +- tests/testthat/_snaps/e2e/empty-app-001_.png |binary tests/testthat/_snaps/e2e/empty-app-002.json | 142 ++- tests/testthat/_snaps/e2e/empty-app-002_.png |binary tests/testthat/_snaps/e2e/empty-app-003.json | 195 +++- tests/testthat/_snaps/e2e/empty-app-003_.png |binary tests/testthat/_snaps/e2e/empty-app-004.json | 206 +++- tests/testthat/_snaps/e2e/empty-app-004_.png |binary tests/testthat/_snaps/e2e/empty-app-005.json | 176 ++- tests/testthat/_snaps/e2e/empty-app-005_.png |binary tests/testthat/_snaps/e2e/variadic-app-001.json |only tests/testthat/_snaps/e2e/variadic-app-001_.png |only tests/testthat/test-action.R | 339 ++++++- tests/testthat/test-children.R |only tests/testthat/test-ctx.R | 6 tests/testthat/test-e2e.R | 98 +- tests/testthat/test-ext.R | 50 - tests/testthat/test-g6r.R | 60 + tests/testthat/test-meta.R | 50 - tests/testthat/test-subboard.R |only 47 files changed, 2822 insertions(+), 917 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit()' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reducing adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bi [...truncated...]
Author: Ioannis Kosmidis [aut, cre] ,
Euloge Clovis Kenne Pagui [aut] ,
Federico Boiocchi [ctb],
Philipp Sterzinger [ctb] ,
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 1.0.1 dated 2025-11-22 and 1.1.0 dated 2026-04-29
brglm2-1.0.1/brglm2/inst/tinytest/test-median-binomial.R |only brglm2-1.1.0/brglm2/DESCRIPTION | 8 brglm2-1.1.0/brglm2/MD5 | 27 +- brglm2-1.1.0/brglm2/NEWS.md | 12 + brglm2-1.1.0/brglm2/R/brglmFit.R | 13 - brglm2-1.1.0/brglm2/R/ordinal_superiority.R | 101 +++++++---- brglm2-1.1.0/brglm2/build/partial.rdb |binary brglm2-1.1.0/brglm2/build/vignette.rds |binary brglm2-1.1.0/brglm2/inst/doc/adjacent.html | 9 brglm2-1.1.0/brglm2/inst/doc/expo.html | 6 brglm2-1.1.0/brglm2/inst/doc/iteration.html | 33 +-- brglm2-1.1.0/brglm2/inst/doc/multinomial.html | 5 brglm2-1.1.0/brglm2/inst/doc/negativeBinomial.html | 41 ++-- brglm2-1.1.0/brglm2/inst/simulation |only brglm2-1.1.0/brglm2/inst/tinytest/test-ordinal_superiority.R |only brglm2-1.1.0/brglm2/man/brnb.Rd | 4 16 files changed, 150 insertions(+), 109 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.4.2 dated 2025-12-16 and 1.4.3 dated 2026-04-29
DESCRIPTION | 10 ++--- MD5 | 74 ++++++++++++++++++++++++++------------- NEWS.md | 15 +++++++ R/Core.R | 6 ++- R/Diversity.R | 1 R/Fastq.R | 18 +++++++-- R/Gene.R | 34 ++++++++++------- R/Topology.R | 2 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.R | 3 + inst/doc/Diversity-Vignette.Rmd | 3 + inst/doc/Diversity-Vignette.pdf |binary inst/doc/Fastq-Vignette.pdf |binary inst/doc/Files-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary man/alakazam-package.Rd | 1 man/alphaDiversity.Rd | 1 man/makeTempDir.Rd | 2 + man/permuteLabels.Rd | 1 man/plotMRCATest.Rd | 1 man/readChangeoDb.Rd | 2 - man/writeChangeoDb.Rd | 2 - tests |only vignettes/Diversity-Vignette.Rmd | 3 + 26 files changed, 129 insertions(+), 50 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>),
Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>),
ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>),
ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 2.0.0.2 dated 2026-03-11 and 2.0.2 dated 2026-04-29
DESCRIPTION | 24 MD5 | 46 - R/combineMultFilterNAimput.R | 132 +- R/extractTestingResults.R | 150 ++- R/matrixNAneighbourImpute.R | 11 R/readProteomeDiscovererFile.R | 2 R/readSampleMetaData.R | 2 R/readSdrf.R | 20 R/removeSampleInList.R | 43 R/testRobustToNAimputation.R | 352 +++---- build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 10 inst/doc/wrProteoVignette1.Rmd | 25 inst/doc/wrProteoVignette1.html | 598 +++---------- inst/doc/wrProteoVignetteUPS1.R | 4 inst/doc/wrProteoVignetteUPS1.Rmd | 8 inst/doc/wrProteoVignetteUPS1.html | 1679 ++++++++++++++++--------------------- man/combineMultFilterNAimput.Rd | 30 man/extractTestingResults.Rd | 35 man/matrixNAneighbourImpute.Rd | 11 man/readSdrf.Rd | 4 man/testRobustToNAimputation.Rd | 18 vignettes/wrProteoVignette1.Rmd | 25 vignettes/wrProteoVignetteUPS1.Rmd | 8 24 files changed, 1489 insertions(+), 1748 deletions(-)
Title: Density Ratio Estimation
Description: Density ratio estimation. The estimated density ratio
function can be used in many applications such as anomaly detection,
change-point detection, covariate shift adaptation. The implemented
methods are uLSIF (Hido et al. (2011)
<doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al. (2011)
<doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007)
<doi:10.1007/s10463-008-0197-x>).
Author: Koji Makiyama [aut, cre]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Diff between densratio versions 0.2.1 dated 2019-06-30 and 0.3.1 dated 2026-04-29
DESCRIPTION | 27 LICENSE | 4 MD5 | 70 NAMESPACE | 22 NEWS.md | 28 R/KLIEP.R | 114 - R/KLIEP_compute_score.R | 42 R/KLIEP_optimize_alpha.R | 86 R/KLIEP_search_sigma.R | 38 R/KLIEP_search_sigma_list.R | 28 R/RuLSIF.R | 134 - R/RuLSIF_search_sigma_and_lambda.R | 90 R/compute_kernel_Gaussian.R | 42 R/densratio.R | 118 - R/print.R | 88 R/uLSIF.R | 48 README.md | 592 ++--- build/vignette.rds |binary inst/doc/densratio.R | 152 - inst/doc/densratio.Rmd | 476 ++-- inst/doc/densratio.html | 1138 +++++----- man/KLIEP.Rd | 55 man/RuLSIF.Rd | 72 man/densratio.Rd | 102 man/figures/README-basics-compute-estimated-density-ratio-1.png |binary man/figures/README-compare-2d-1.png |binary man/figures/README-compare-true-estimate-1.png |binary man/figures/README-compute-estimated-density-ratio-1.png |binary man/squared_euclid_distance.Rd | 38 man/uLSIF.Rd | 63 tests/testthat.R | 8 tests/testthat/test-KLIEP.R | 55 tests/testthat/test-RuLSIF.R | 57 tests/testthat/test-compute_kernel_Gaussian.R | 28 tests/testthat/test-uLSIF.R | 55 vignettes/densratio.Rmd | 476 ++-- 36 files changed, 2273 insertions(+), 2073 deletions(-)
Title: A Docking Layout Manager for 'blockr'
Description: Building on the docking layout manager provided by 'dockViewR',
this provides a flexible front-end to 'blockr.core'. It provides an extension mechanism which allows for providing means to manipulate a board
object via panel-based user interface components.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.dock versions 0.1.0 dated 2025-12-11 and 0.1.1 dated 2026-04-29
blockr.dock-0.1.0/blockr.dock/inst/examples/dock |only blockr.dock-0.1.1/blockr.dock/DESCRIPTION | 13 blockr.dock-0.1.1/blockr.dock/MD5 | 95 blockr.dock-0.1.1/blockr.dock/NAMESPACE | 35 blockr.dock-0.1.1/blockr.dock/NEWS.md | 25 blockr.dock-0.1.1/blockr.dock/R/action-block.R | 495 ++-- blockr.dock-0.1.1/blockr.dock/R/action-class.R | 282 +- blockr.dock-0.1.1/blockr.dock/R/action-link.R | 172 - blockr.dock-0.1.1/blockr.dock/R/action-modal.R | 67 blockr.dock-0.1.1/blockr.dock/R/action-stack.R | 295 +- blockr.dock-0.1.1/blockr.dock/R/action-utils.R | 32 blockr.dock-0.1.1/blockr.dock/R/block-meta.R | 54 blockr.dock-0.1.1/blockr.dock/R/block-ui.R | 66 blockr.dock-0.1.1/blockr.dock/R/board-server.R | 1085 ++++++++-- blockr.dock-0.1.1/blockr.dock/R/board-ui.R | 109 - blockr.dock-0.1.1/blockr.dock/R/dock-board.R | 104 blockr.dock-0.1.1/blockr.dock/R/ext-ui.R | 29 blockr.dock-0.1.1/blockr.dock/R/layout-class.R | 39 blockr.dock-0.1.1/blockr.dock/R/layouts-class.R |only blockr.dock-0.1.1/blockr.dock/R/plugin-block.R | 143 - blockr.dock-0.1.1/blockr.dock/R/utils-dock.R | 36 blockr.dock-0.1.1/blockr.dock/R/utils-id.R | 28 blockr.dock-0.1.1/blockr.dock/R/utils-misc.R | 24 blockr.dock-0.1.1/blockr.dock/R/utils-serdes.R | 47 blockr.dock-0.1.1/blockr.dock/R/utils-ui.R | 18 blockr.dock-0.1.1/blockr.dock/R/view-ui.R |only blockr.dock-0.1.1/blockr.dock/README.md | 97 blockr.dock-0.1.1/blockr.dock/build |only blockr.dock-0.1.1/blockr.dock/inst/assets/css/blockr-dock.css | 660 ++++-- blockr.dock-0.1.1/blockr.dock/inst/assets/js/show-hide-block.js | 5 blockr.dock-0.1.1/blockr.dock/inst/assets/js/view-binding.js |only blockr.dock-0.1.1/blockr.dock/inst/doc |only blockr.dock-0.1.1/blockr.dock/inst/examples/empty |only blockr.dock-0.1.1/blockr.dock/inst/examples/locked-dock |only blockr.dock-0.1.1/blockr.dock/inst/examples/single-page |only blockr.dock-0.1.1/blockr.dock/inst/examples/views |only blockr.dock-0.1.1/blockr.dock/man/action.Rd | 87 blockr.dock-0.1.1/blockr.dock/man/dock.Rd | 26 blockr.dock-0.1.1/blockr.dock/man/figures |only blockr.dock-0.1.1/blockr.dock/man/view.Rd |only blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-block.R | 73 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-class.R | 51 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-link.R | 78 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-action-stack.R | 117 - blockr.dock-0.1.1/blockr.dock/tests/testthat/test-block-meta.R | 23 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-class.R | 46 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-server.R | 240 +- blockr.dock-0.1.1/blockr.dock/tests/testthat/test-board-ui.R | 2 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-layouts-class.R |only blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-misc.R | 16 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-serdes.R | 18 blockr.dock-0.1.1/blockr.dock/tests/testthat/test-utils-serve.R | 2 blockr.dock-0.1.1/blockr.dock/vignettes |only 53 files changed, 3251 insertions(+), 1583 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.3.0 dated 2026-03-31 and 1.4.0 dated 2026-04-29
glmmrBase-1.3.0/glmmrBase/R/stanmodels.R |only glmmrBase-1.3.0/glmmrBase/README.md |only glmmrBase-1.3.0/glmmrBase/configure |only glmmrBase-1.3.0/glmmrBase/configure.win |only glmmrBase-1.3.0/glmmrBase/inst/cmdstan |only glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/sparse.h |only glmmrBase-1.3.0/glmmrBase/inst/include/stan_meta_header.hpp |only glmmrBase-1.3.0/glmmrBase/inst/stan |only glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.cc |only glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.h |only glmmrBase-1.4.0/glmmrBase/DESCRIPTION | 15 glmmrBase-1.4.0/glmmrBase/MD5 | 107 - glmmrBase-1.4.0/glmmrBase/NAMESPACE | 4 glmmrBase-1.4.0/glmmrBase/R/R6Model.R | 985 +--------- glmmrBase-1.4.0/glmmrBase/R/R6covariance.R | 4 glmmrBase-1.4.0/glmmrBase/R/RcppExports.R | 36 glmmrBase-1.4.0/glmmrBase/R/extrafunctions.R | 32 glmmrBase-1.4.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.4.0/glmmrBase/inst/include/glmmr.h | 10 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/matrixw.hpp | 10 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/model.hpp | 25 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modelbits.hpp | 3 glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 686 ++++++ glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 293 +- glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/randomeffects.hpp | 122 + glmmrBase-1.4.0/glmmrBase/inst/include/glmmr/spdecovariance.hpp |only glmmrBase-1.4.0/glmmrBase/man/Beta.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/Model.Rd | 571 +---- glmmrBase-1.4.0/glmmrBase/man/Salamanders.Rd | 28 glmmrBase-1.4.0/glmmrBase/man/SimGeospat.Rd | 48 glmmrBase-1.4.0/glmmrBase/man/SimTrial.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/coef.Model.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/coef.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/confint.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/family.Model.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/family.mcml.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/fitted.Model.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/fitted.mcml.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/fixed.effects.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/formula.Model.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/formula.mcml.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/hessian_from_formula.Rd | 80 glmmrBase-1.4.0/glmmrBase/man/hsgp_rescale.Rd | 58 glmmrBase-1.4.0/glmmrBase/man/lme4_to_glmmr.Rd | 60 glmmrBase-1.4.0/glmmrBase/man/logLik.Model.Rd | 38 glmmrBase-1.4.0/glmmrBase/man/logLik.mcml.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/mcml_lmer.Rd | 132 - glmmrBase-1.4.0/glmmrBase/man/mesh_helper.Rd |only glmmrBase-1.4.0/glmmrBase/man/predict.Model.Rd | 62 glmmrBase-1.4.0/glmmrBase/man/predict.mcml.Rd | 40 glmmrBase-1.4.0/glmmrBase/man/random.effects.Rd | 34 glmmrBase-1.4.0/glmmrBase/man/residuals.Model.Rd | 56 glmmrBase-1.4.0/glmmrBase/man/residuals.mcml.Rd | 50 glmmrBase-1.4.0/glmmrBase/man/summary.Model.Rd | 42 glmmrBase-1.4.0/glmmrBase/man/vcov.Model.Rd | 44 glmmrBase-1.4.0/glmmrBase/man/vcov.mcml.Rd | 46 glmmrBase-1.4.0/glmmrBase/src/Makevars | 8 glmmrBase-1.4.0/glmmrBase/src/Makevars.win | 8 glmmrBase-1.4.0/glmmrBase/src/RcppExports.cpp | 126 + glmmrBase-1.4.0/glmmrBase/src/model_module.cpp | 269 ++ 60 files changed, 2368 insertions(+), 2292 deletions(-)
Title: Automatic Construction of Forced-Choice Tests
Description: Forced-choice (FC) response has gained increasing popularity
and interest for its resistance to faking when well-designed (Cao &
Drasgow, 2019 <doi:10.1037/apl0000414>). To established well-designed
FC scales, typically each item within a block should measure different
trait and have similar level of social desirability (Zhang et al.,
2020 <doi:10.1177/1094428119836486>). Recent study also suggests the
importance of high inter-item agreement of social desirability between
items within a block (Pavlov et al., 2021 <doi:10.31234/osf.io/hmnrc>).
In addition to this, FC developers may
also need to maximize factor loading differences (Brown &
Maydeu-Olivares, 2011 <doi:10.1177/0013164410375112>) or minimize item
location differences (Cao & Drasgow, 2019 <doi:10.1037/apl0000414>)
depending on scoring models. Decision of which items should be
assigned to the same block, termed item pairing, is thus critical to
the quality of an FC test. This pairing p [...truncated...]
Author: Mengtong Li [cre, aut] ,
Tianjun Sun [aut] ,
Bo Zhang [aut]
Maintainer: Mengtong Li <mt_li@fudan.edu.cn>
This is a re-admission after prior archival of version 0.2.0.1002 dated 2025-03-13
Diff between autoFC versions 0.2.0.1002 dated 2025-03-13 and 0.2.0.1010 dated 2026-04-29
DESCRIPTION | 22 ++++----- MD5 | 27 ++++++----- NAMESPACE | 5 +- R/bp.coeff.raw.R |only R/cal_block_energy_with_iia.R | 1 R/convert_to_TIRT_response.R | 17 +++---- R/fit_TIRT_model.R | 8 +-- R/get_iia.R | 75 +++++++++++++++---------------- R/gwet.ac1.raw.R |only R/identity.weights.R |only R/linear.weights.R |only R/quadratic.weights.R |only R/sa_pairing_generalized.R | 1 inst/doc/autoFC.html | 93 +++++++++++++++++++++++++++++++++------ man/cal_block_energy_with_iia.Rd | 1 man/convert_to_TIRT_response.Rd | 14 ++--- man/fit_TIRT_model.Rd | 1 17 files changed, 167 insertions(+), 98 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 23.0.1.2 dated 2026-03-25 and 24.0.0 dated 2026-04-29
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arrow-24.0.0/arrow/tools/cpp/src/parquet/arrow/schema.cc | 216 ++- arrow-24.0.0/arrow/tools/cpp/src/parquet/bloom_filter.cc | 162 ++ arrow-24.0.0/arrow/tools/cpp/src/parquet/bloom_filter.h | 29 arrow-24.0.0/arrow/tools/cpp/src/parquet/bloom_filter_reader.cc | 60 - arrow-24.0.0/arrow/tools/cpp/src/parquet/bloom_filter_writer.cc |only arrow-24.0.0/arrow/tools/cpp/src/parquet/bloom_filter_writer.h |only arrow-24.0.0/arrow/tools/cpp/src/parquet/chunker_internal.cc | 11 arrow-24.0.0/arrow/tools/cpp/src/parquet/column_page.h | 2 arrow-24.0.0/arrow/tools/cpp/src/parquet/column_writer.cc | 98 + arrow-24.0.0/arrow/tools/cpp/src/parquet/column_writer.h | 12 arrow-24.0.0/arrow/tools/cpp/src/parquet/decoder.cc | 79 + arrow-24.0.0/arrow/tools/cpp/src/parquet/encoder.cc | 19 arrow-24.0.0/arrow/tools/cpp/src/parquet/encoding.h | 22 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/encryption.h | 3 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal.cc | 112 - arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal.h | 23 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal_nossl.cc | 26 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_decryptor.cc | 6 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_decryptor.h | 4 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.cc | 8 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.h | 4 arrow-24.0.0/arrow/tools/cpp/src/parquet/encryption/key_toolkit_internal.cc | 6 arrow-24.0.0/arrow/tools/cpp/src/parquet/file_writer.cc | 73 + arrow-24.0.0/arrow/tools/cpp/src/parquet/file_writer.h | 15 arrow-24.0.0/arrow/tools/cpp/src/parquet/geospatial/util_internal.cc | 16 arrow-24.0.0/arrow/tools/cpp/src/parquet/geospatial/util_internal.h | 15 arrow-24.0.0/arrow/tools/cpp/src/parquet/hasher.h | 5 arrow-24.0.0/arrow/tools/cpp/src/parquet/index_location.h |only arrow-24.0.0/arrow/tools/cpp/src/parquet/level_conversion_inc.h | 9 arrow-24.0.0/arrow/tools/cpp/src/parquet/meson.build | 7 arrow-24.0.0/arrow/tools/cpp/src/parquet/metadata.cc | 76 - arrow-24.0.0/arrow/tools/cpp/src/parquet/metadata.h | 30 arrow-24.0.0/arrow/tools/cpp/src/parquet/page_index.cc | 47 arrow-24.0.0/arrow/tools/cpp/src/parquet/page_index.h | 11 arrow-24.0.0/arrow/tools/cpp/src/parquet/properties.cc | 4 arrow-24.0.0/arrow/tools/cpp/src/parquet/properties.h | 100 + arrow-24.0.0/arrow/tools/cpp/src/parquet/size_statistics.cc | 7 arrow-24.0.0/arrow/tools/cpp/src/parquet/size_statistics.h | 5 arrow-24.0.0/arrow/tools/cpp/src/parquet/statistics.cc | 31 arrow-24.0.0/arrow/tools/cpp/src/parquet/stream_reader.cc | 3 arrow-24.0.0/arrow/tools/cpp/src/parquet/stream_reader.h | 1 arrow-24.0.0/arrow/tools/cpp/src/parquet/stream_writer.h | 5 arrow-24.0.0/arrow/tools/cpp/src/parquet/thrift_internal.h | 6 arrow-24.0.0/arrow/tools/cpp/src/parquet/type_fwd.h | 6 arrow-24.0.0/arrow/tools/cpp/src/parquet/types.h | 11 arrow-24.0.0/arrow/tools/cpp/src/parquet/visit_type_inline.h |only arrow-24.0.0/arrow/tools/cpp/src/parquet/xxhasher.cc | 11 arrow-24.0.0/arrow/tools/cpp/src/parquet/xxhasher.h | 1 arrow-24.0.0/arrow/tools/cpp/thirdparty/versions.txt | 65 - arrow-24.0.0/arrow/tools/cpp/tools/parquet/parquet_scan.cc | 2 arrow-24.0.0/arrow/tools/cpp/vcpkg.json | 11 arrow-24.0.0/arrow/tools/dotenv | 15 arrow-24.0.0/arrow/tools/nixlibs.R | 17 arrow-24.0.0/arrow/tools/test-nixlibs.R | 4 311 files changed, 5600 insertions(+), 2965 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.13 dated 2026-03-16 and 1.3.15 dated 2026-04-29
wrGraph-1.3.13/wrGraph/man/dot-colorByPvalue.Rd |only wrGraph-1.3.15/wrGraph/DESCRIPTION | 8 wrGraph-1.3.15/wrGraph/MD5 | 23 wrGraph-1.3.15/wrGraph/NAMESPACE | 1 wrGraph-1.3.15/wrGraph/R/MAplotW.R | 658 ++++++++++-------- wrGraph-1.3.15/wrGraph/R/VolcanoPlotW.R | 350 +++------ wrGraph-1.3.15/wrGraph/build/vignette.rds |binary wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.R | 14 wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.Rmd | 18 wrGraph-1.3.15/wrGraph/inst/doc/wrGraphVignette1.html | 89 +- wrGraph-1.3.15/wrGraph/man/MAplotW.Rd | 35 wrGraph-1.3.15/wrGraph/man/VolcanoPlotW.Rd | 24 wrGraph-1.3.15/wrGraph/vignettes/wrGraphVignette1.Rmd | 18 13 files changed, 669 insertions(+), 569 deletions(-)
Title: Space Filling Optimal Covariate Designs
Description: We have designed this package to address experimental scenarios involving multiple covariates. It focuses on construction of Optimal Covariate Designs (OCDs), checking space filling property of the developed design. The primary objective of the package is to generate OCDs using four methods viz., M array method, Juxtapose method, Orthogonal Integer Array and Hadamard method. The package also evaluates space filling properties of both the base design and OCDs using the MaxPro criterion, providing a meaningful basis for comparison. In addition, it includes tool to visualize the spread offered by the design points in the form of scatterplot, which help users to assess distribution and coverage of design points.
Author: Neethu RS [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Ashutosh Dalal [aut, ctb, cre]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between SFOCDs versions 1.1.0 dated 2026-04-15 and 1.2.0 dated 2026-04-29
DESCRIPTION | 7 ++-- MD5 | 18 ++++++----- NAMESPACE | 1 R/HadamardOCDs.R | 2 + R/JuxtaOCDs.R | 3 + R/MOCDs.R | 79 +++++++++++++++++++++++++++++++++++++-------------- R/MaxDot.R | 4 +- R/OIAOCDs.R | 4 +- R/reshuffle_des.R |only man/MaxDot.Rd | 2 - man/reshuffle_des.Rd |only 11 files changed, 85 insertions(+), 35 deletions(-)
Title: Constitution of Core Collections by Principal Component Scoring
Strategy
Description: Generate a Core Collection with Principal Component Scoring
Strategy (PCSS) using qualitative and/or quantitative trait data according
to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>,
Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003)
<https://www.documentation.ird.fr/hor/fdi:010031886>.
Author: J. Aravind [aut, cre] ,
Anju Mahendru Singh [aut] ,
ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.org.in>
This is a re-admission after prior archival of version 0.1.0 dated 2025-02-17
Diff between rpcss versions 0.1.0 dated 2025-02-17 and 0.1.1 dated 2026-04-29
DESCRIPTION | 36 MD5 | 50 - NEWS.md | 5 R/biplot.pcss.core.R | 938 +++++++++++------------ R/contrib.pcss.core.R | 684 ++++++++--------- R/coreplot.pcss.core.R | 804 +++++++++++++------- R/generics.R | 2 R/globals.R | 6 R/pcss.core.R | 1383 ++++++++++++++++++----------------- R/print.pcss.core.R | 101 +- R/screeplot.pcss.core.R | 379 ++++----- R/subset.pcss.core.R | 457 +++++++---- R/xtra.R | 88 +- README.md | 112 ++ build/partial.rdb |binary build/rpcss.pdf |binary build/stage23.rdb |binary inst/CITATION | 13 inst/pkgdown.yml | 4 man/biplot.pcss.core.Rd | 138 +-- man/contrib.Rd | 158 +-- man/coreplot.Rd | 88 +- man/figures/README-readme-plot-1.png |binary man/pcss.core.Rd | 66 - man/screeplot.pcss.core.Rd | 77 + man/subset.pcss.core.Rd | 100 +- 26 files changed, 3104 insertions(+), 2585 deletions(-)
Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.7 dated 2025-12-14 and 1.8 dated 2026-04-29
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/iSCMEB.R | 4 ++-- README.md | 2 ++ inst/doc/CosMx.html | 6 +++--- inst/doc/FASTdlpfc.html | 6 +++--- inst/doc/FASTdlpfc2.html | 6 +++--- inst/doc/FASTsimu.html | 6 +++--- inst/doc/pbmc3k.html | 6 +++--- 10 files changed, 33 insertions(+), 31 deletions(-)
Title: Group Elastic Net Regularized GLMs and GAMs
Description: Efficient algorithms for fitting generalized linear and additive models with group elastic net penalties as described in Helwig (2025) <doi:10.1080/10618600.2024.2362232>. Implements group LASSO, group MCP, and group SCAD with an optional group ridge penalty. Computes the regularization path for linear regression (gaussian), multivariate regression (multigaussian), smoothed support vector machines (svm1), squared support vector machines (svm2), logistic regression (binomial), proportional odds logistic regression (ordinal), multinomial logistic regression (multinomial), log-linear count regression (poisson and negative.binomial), and log-linear continuous regression (gamma and inverse gaussian). Supports default and formula methods for model specification, k-fold cross-validation for tuning the regularization parameters, and nonparametric regression via tensor product reproducing kernel (smoothing spline) basis function expansion.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between grpnet versions 1.1 dated 2026-01-07 and 1.2 dated 2026-04-29
ChangeLog | 28 +++++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 66 ++++++++++++++++++++++++----------------------- NAMESPACE | 9 +++++- R/R_grpnet_binomial.R | 10 +++---- R/R_grpnet_gamma.R | 10 +++---- R/R_grpnet_gaussian.R | 10 +++---- R/R_grpnet_invgaus.R | 10 +++---- R/R_grpnet_logit.R | 10 +++---- R/R_grpnet_multigaus.R | 10 +++---- R/R_grpnet_multinom.R | 10 +++---- R/R_grpnet_negbin.R | 10 +++---- R/R_grpnet_ordinal.R | 10 +++---- R/R_grpnet_poisson.R | 10 +++---- R/R_grpnet_svm1.R | 10 +++---- R/R_grpnet_svm2.R | 10 +++---- R/cv.compare.R | 4 +- R/cv.grpnet.R | 5 ++- R/cv.grpnet.default.R | 12 ++++---- R/cv.grpnet.formula.R | 5 ++- R/grpnet.R | 12 ++++---- R/grpnet.default.R | 13 +++++++-- R/grpnet.formula.R | 6 +++- R/predict.grpnet.R | 14 ++++----- R/row.kronecker.R | 15 +++++++--- R/summary.cv.grpnet.R |only R/summary.grpnet.R |only R/zzz.R | 4 -- build/partial.rdb |binary man/cv.grpnet.Rd | 38 +++++++++++++++++++++++++++ man/grpnet.Rd | 43 ++++++++++++++++++++++++++++++ man/plot.cv.grpnet.Rd | 5 ++- man/predict.cv.grpnet.Rd | 2 - man/predict.grpnet.Rd | 2 - man/summary.cv.grpnet.Rd |only man/summary.grpnet.Rd |only 36 files changed, 278 insertions(+), 133 deletions(-)
Title: Visualizing Classification Results
Description: Tools to visualize the results of a classification or a regression.
The graphical displays include stacked plots, silhouette plots, quasi residual plots, class maps, predictions plots, and predictions correlation plots.
Implements the techniques described and illustrated in Raymaekers J., Rousseeuw P.J., Hubert M. (2022). Class maps for visualizing classification results. \emph{Technometrics}, 64(2), 151–165. <doi:10.1080/00401706.2021.1927849>
(open access), Raymaekers J., Rousseeuw P.J.(2022). Silhouettes and quasi residual plots for neural nets and tree-based classifiers. \emph{Journal of Computational and Graphical Statistics}, 31(4), 1332–1343. <doi:10.1080/10618600.2022.2050249>, and Rousseeuw, P.J. (2026). Explainable Linear and Generalized Linear Models by the Predictions Plot. The American Statistician, 80, 157-163, <doi:10.1080/00031305.2025.2539235> (open access), and Montalcini, C., Rousseeuw, P.J. (2025). The bixplot: A variation on the boxplot suited for [...truncated...]
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between classmap versions 1.2.6 dated 2025-07-14 and 1.2.7 dated 2026-04-29
DESCRIPTION | 26 MD5 | 35 - NAMESPACE | 14 R/bixplot.R |only R/predsplot.R | 91 ++ build/partial.rdb |binary build/vignette.rds |binary data/data_latenc.rdata |only inst/doc/Discriminant_analysis_examples.html | 651 ++++++++++---------- inst/doc/K_nearest_neighbors_examples.html | 221 +++--- inst/doc/Neural_net_examples.html | 67 +- inst/doc/Random_forest_examples.html | 340 +++++----- inst/doc/Rpart_examples.html | 31 inst/doc/Support_vector_machine_examples.html | 835 ++++++++++++-------------- inst/doc/bixplot_examples.R |only inst/doc/bixplot_examples.Rmd |only inst/doc/bixplot_examples.html |only inst/doc/predsplot_examples.html | 53 - man/bixplot.Rd |only man/data_latenc.Rd |only man/pamc1d.Rd |only man/predsplot.Rd | 41 - vignettes/bixplot_examples.Rmd |only 23 files changed, 1234 insertions(+), 1171 deletions(-)
Title: Spatial Prediction Tools
Description: Methods for spatial predictive modeling, especially for spatial distribution models. This includes algorithms for model fitting and prediction, as well as methods for model evaluation.
Author: Robert J. Hijmans [cre, aut] ,
Steven Phillips [ctb],
Marcia Barbosa [ctb],
Chris Brunsdon [ctb],
Barry Rowlingson [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between predicts versions 0.1-19 dated 2025-05-06 and 0.2-2 dated 2026-04-29
predicts-0.1-19/predicts/ChangeLog |only predicts-0.1-19/predicts/man/divpol.Rd |only predicts-0.2-2/predicts/DESCRIPTION | 8 predicts-0.2-2/predicts/MD5 | 35 predicts-0.2-2/predicts/NEWS.md |only predicts-0.2-2/predicts/R/divpol.R | 4 predicts-0.2-2/predicts/R/envelope.R | 446 +++---- predicts-0.2-2/predicts/R/maxent.R | 1119 ++++++++++---------- predicts-0.2-2/predicts/build/partial.rdb |binary predicts-0.2-2/predicts/inst/ex/biome.tif |binary predicts-0.2-2/predicts/inst/ex/biome.tif.aux.xml | 1 predicts-0.2-2/predicts/inst/java/maxent.jar |binary predicts-0.2-2/predicts/inst/java/maxent_readme.txt | 610 +++++----- predicts-0.2-2/predicts/man/envelope.Rd | 166 +- predicts-0.2-2/predicts/man/maxent.Rd | 13 predicts-0.2-2/predicts/man/mess.Rd | 146 +- predicts-0.2-2/predicts/man/plot.Rd | 74 - predicts-0.2-2/predicts/man/pycnophy.Rd | 110 - predicts-0.2-2/predicts/man/response.Rd | 100 - predicts-0.2-2/predicts/man/varImportance.Rd | 78 - 20 files changed, 1489 insertions(+), 1421 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 2.0.0 dated 2026-03-09 and 2.0.2 dated 2026-04-29
DESCRIPTION | 6 MD5 | 61 +++--- NAMESPACE | 4 R/convPairwiseSetup.R |only R/findHeadAndTail.R |only R/getPWseparator.R |only R/getPairwiseSetup.R |only R/gitDataUrl.R | 39 ++- R/indexGroupsFromPW.R | 200 +++----------------- R/matchMatrixLinesToRef.R | 41 +++- R/matchSampToPairw.R | 2 R/moderTest2grp.R | 12 - R/moderTestXgrp.R | 190 ++++++++----------- R/presenceFilt.R | 20 +- R/pwSeparatorList.R |only R/rmSharedWords.R | 2 R/sampNoDeMArrayLM.R | 117 +++++++++-- build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 64 ++++++ inst/doc/wrMiscVignette1.Rmd | 115 +++++++++++ inst/doc/wrMiscVignette1.html | 419 ++++++++++++++++++++++++++++++++++-------- man/convPairwiseSetup.Rd |only man/dot-getPWseparator.Rd | 7 man/findHeadAndTail.Rd |only man/getPWseparator.Rd | 19 + man/getPairwiseSetup.Rd |only man/gitDataUrl.Rd | 23 +- man/indexGroupsFromPW.Rd | 8 man/matchSampToPairw.Rd | 2 man/moderTest2grp.Rd | 4 man/moderTestXgrp.Rd | 38 ++- man/presenceFilt.Rd | 4 man/pwSeparatorList.Rd |only man/replacePWseparator.Rd | 2 man/sampNoDeMArrayLM.Rd | 32 ++- vignettes/wrMiscVignette1.Rmd | 115 +++++++++++ 36 files changed, 1046 insertions(+), 500 deletions(-)
Title: Compute Least Squares Estimates of One Bounded or Two Ordered
Isotonic Regression Curves
Description: We consider the problem of estimating two isotonic regression curves g1* and g2* under the constraint that they are ordered, i.e. g1* <= g2*. Given two sets of n data points y_1, ..., y_n and z_1, ..., z_n that are observed at (the same) deterministic design points x_1, ..., x_n, the estimates are obtained by minimizing the Least Squares criterion L(a, b) = sum_{i=1}^n (y_i - a_i)^2 w1(x_i) + sum_{i=1}^n (z_i - b_i)^2 w2(x_i) over the class of pairs of vectors (a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, ..., n. We offer two different approaches to compute the estimates: a projected subgradient algorithm where the projection is calculated using a PAVA as well as Dykstra's cyclical projection algorithm.
Author: Fadoua Balabdaoui [aut],
Kaspar Rufibach [aut, cre],
Filippo Santambrogio [aut]
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between OrdMonReg versions 1.0.3 dated 2011-12-01 and 1.0.4 dated 2026-04-29
DESCRIPTION | 28 ++++++++++++++++++---------- MD5 | 24 ++++++++++++------------ NEWS | 4 ++++ data/mechIng.rda |binary man/BoundedAntiMeanTwo.Rd | 15 ++++++++------- man/BoundedIsoMean.Rd | 8 ++++---- man/BoundedIsoMeanTwoDykstra.Rd | 8 ++++---- man/LSfunctional.Rd | 8 ++++---- man/MA.Rd | 8 ++++---- man/Subgradient.Rd | 8 ++++---- man/bstar_n.Rd | 8 ++++---- man/minK.Rd | 10 +++++----- man/ordMonReg-package.Rd | 14 +++++++------- 13 files changed, 78 insertions(+), 65 deletions(-)
Title: 'MADGRAD' Method for Stochastic Optimization
Description: A Momentumized, Adaptive, Dual Averaged Gradient Method for Stochastic
Optimization algorithm. MADGRAD is a 'best-of-both-worlds' optimizer with the
generalization performance of stochastic gradient descent and at least as fast
convergence as that of Adam, often faster. A drop-in optim_madgrad() implementation
is provided based on Defazio et al (2020) <doi:10.48550/arXiv.2101.11075>.
Author: Daniel Falbel [aut, cre, cph],
Posit Software, PBC [cph],
MADGRAD original implementation authors. [cph]
Maintainer: Daniel Falbel <dfalbel@gmail.com>
Diff between madgrad versions 0.1.0 dated 2021-05-10 and 0.2.0 dated 2026-04-29
DESCRIPTION | 18 +++++++++--------- MD5 | 9 +++++---- NAMESPACE | 4 ++++ NEWS.md |only R/madgrad.R | 2 ++ README.md | 11 +++++++++-- 6 files changed, 29 insertions(+), 15 deletions(-)
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2026a) <doi:10.1080/01621459.2025.2520467>, Kang and Oh (2026b) <doi:10.1080/00031305.2025.2563730>, and Kang (2025) <doi:10.23170/snu.000000188358.11032.0001856>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw@skku.edu>
Diff between L1centrality versions 0.4.0 dated 2025-10-27 and 0.5.0 dated 2026-04-29
DESCRIPTION | 17 ++- MD5 | 52 +++++------ NAMESPACE | 1 NEWS.md | 24 +++++ R/L1cent.R | 50 ++++++----- R/L1centEDGE.R | 32 ++++--- R/L1centGROUP.R | 191 +++++++++++++++++++++++++++----------------- R/L1centLOC.R | 97 ++++++++++++++++------ R/L1centMDS.R | 70 +++++++++++----- R/L1centNB.R | 31 ++++--- R/L1centrality-package.R | 7 - R/Lorenz_plot.R | 6 - R/MCUmovie.R | 2 R/rokassembly21.R | 2 R/validate.R | 7 - inst/CITATION | 12 +- man/Heterogeneity.Rd | 6 - man/L1cent.Rd | 47 +++++----- man/L1centEDGE.Rd | 27 +++--- man/L1centGROUP.Rd | 42 +++++---- man/L1centLOC.Rd | 45 ++++++---- man/L1centMDS.Rd | 46 ++++++---- man/L1centNB.Rd | 40 +++++---- man/L1centrality-package.Rd | 8 - man/MCUmovie.Rd | 2 man/group_reduce.Rd | 33 ++++--- man/rokassembly21.Rd | 2 27 files changed, 567 insertions(+), 332 deletions(-)
Title: A Performance-Focused Package for Clinical Trial Tables
Description: Create high-performance clinical reporting tables (TLGs) from
ADaM-like inputs. The package provides a consistent, programmatic API
to generate common tables such as demographics, adverse event incidence,
and laboratory summaries, using 'data.table' for fast aggregation over
large populations. Functions support flexible target-variable selection,
stratification by treatment, and customizable summary statistics, and
return tidy, machine-readable results ready to render with downstream
table/formatting packages in analysis pipelines.
Author: Max Ebenezer-Brown [aut],
Max Norman [aut],
Xinye Li [aut],
Anja Peebles-Brown [aut],
Ashley Baldry [aut],
Ramiro Magno [aut, cre]
Maintainer: Ramiro Magno <ramiro.morgado@acuityanalytics.com>
Diff between dtlg versions 0.0.3 dated 2026-01-12 and 0.1.0 dated 2026-04-29
dtlg-0.0.3/dtlg/tests/testthat/test-calc-stats.R |only dtlg-0.1.0/dtlg/DESCRIPTION | 58 +++---- dtlg-0.1.0/dtlg/LICENSE | 2 dtlg-0.1.0/dtlg/MD5 | 70 ++++----- dtlg-0.1.0/dtlg/NEWS.md | 40 +++++ dtlg-0.1.0/dtlg/R/AET01_table.R | 6 dtlg-0.1.0/dtlg/R/AET02_table.R | 1 dtlg-0.1.0/dtlg/R/calc-stats.R | 141 +++++++++++++++---- dtlg-0.1.0/dtlg/R/data-table-utils.R | 16 -- dtlg-0.1.0/dtlg/R/dt-copy-semantics.R | 2 dtlg-0.1.0/dtlg/R/dt-helpers.R | 3 dtlg-0.1.0/dtlg/R/events.R | 24 +-- dtlg-0.1.0/dtlg/R/level-set.R | 2 dtlg-0.1.0/dtlg/R/merge-table-lists.R | 1 dtlg-0.1.0/dtlg/R/near.R | 2 dtlg-0.1.0/dtlg/R/package-availability.R | 5 dtlg-0.1.0/dtlg/R/round.R | 2 dtlg-0.1.0/dtlg/R/summary-table.R | 129 +++++++++++------ dtlg-0.1.0/dtlg/R/tern.R | 6 dtlg-0.1.0/dtlg/README.md | 6 dtlg-0.1.0/dtlg/man/calc_desc.Rd | 14 + dtlg-0.1.0/dtlg/man/calc_stats.Rd | 11 - dtlg-0.1.0/dtlg/man/dtlg-package.Rd | 13 - dtlg-0.1.0/dtlg/man/print_dtlg.Rd | 2 dtlg-0.1.0/dtlg/man/summary_table.Rd | 11 + dtlg-0.1.0/dtlg/man/summary_table_by.Rd | 13 + dtlg-0.1.0/dtlg/man/summary_table_by_targets.Rd | 25 ++- dtlg-0.1.0/dtlg/man/total_events.Rd | 4 dtlg-0.1.0/dtlg/tests/testthat/test-AET01_table.R |only dtlg-0.1.0/dtlg/tests/testthat/test-calc-desc.R | 16 +- dtlg-0.1.0/dtlg/tests/testthat/test-dt-count.R | 14 - dtlg-0.1.0/dtlg/tests/testthat/test-dt-expand-grid.R | 10 - dtlg-0.1.0/dtlg/tests/testthat/test-dt-relevel_col.R | 128 ++++++++--------- dtlg-0.1.0/dtlg/tests/testthat/test-formatters.R | 1 dtlg-0.1.0/dtlg/tests/testthat/test-level-set.R | 6 dtlg-0.1.0/dtlg/tests/testthat/test-round.R |only dtlg-0.1.0/dtlg/tests/testthat/test-summary-table.R | 123 +++++++++++----- dtlg-0.1.0/dtlg/tests/testthat/test-tern.R |only 38 files changed, 586 insertions(+), 321 deletions(-)
Title: Download Spanish Election Results
Description: Download official election results for Spain at polling station,
municipality and province level, format them and import them to the R
environment. Data are provided by the Spanish Ministry of the Interior
(<https://infoelectoral.interior.gob.es/es/inicio/>).
Author: Hector Meleiro [aut, cre]
Maintainer: Hector Meleiro <hmeleiros@gmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2024-05-30
Diff between infoelectoral versions 1.0.2 dated 2024-05-30 and 1.0.3 dated 2026-04-29
DESCRIPTION | 18 +- MD5 | 74 ++++++------ NAMESPACE | 2 R/candidatos_nosenado.R | 4 R/data.R | 6 R/download_bin.R | 9 + R/election_type_code.R | 4 R/examples/candidatos.R | 8 - R/examples/mesas.R | 8 - R/examples/municipios.R | 6 R/examples/provincias.R | 6 R/globals.R |only R/mesas.R | 14 +- R/provincias.R | 9 - R/senado_mesas.R | 14 +- R/senado_municipios.R | 8 - README.md | 12 - build/vignette.rds |binary inst/doc/infoelectoral.R | 22 +-- inst/doc/infoelectoral.Rmd | 6 inst/doc/infoelectoral.html | 151 +----------------------- inst/doc/municipios.R | 152 ++++++++++++------------- inst/doc/municipios.Rmd | 8 - inst/doc/municipios.html | 25 ---- man/candidatos.Rd | 8 - man/codigos_ccaa.Rd | 2 man/codigos_municipios.Rd | 2 man/mesas.Rd | 8 - man/municipios.Rd | 6 man/provincias.Rd | 6 man/renta.Rd | 2 tests/testthat/helper-skip.R |only tests/testthat/test-all-elections-provincias.R | 1 tests/testthat/test-candidatos.R | 21 +-- tests/testthat/test-mesas.R | 23 +-- tests/testthat/test-municipios.R | 24 +-- tests/testthat/test-provincias.R | 27 ++-- vignettes/infoelectoral.Rmd | 6 vignettes/municipios.Rmd | 8 - 39 files changed, 293 insertions(+), 417 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski [aut, cre],
Moritz Berger [aut],
David Koehler [aut],
Matthias Schmid [aut]
Maintainer: Thomas Welchowski <t.welchowski@psychologie.uzh.ch>
Diff between discSurv versions 2.0.0 dated 2022-03-02 and 2.5.1 dated 2026-04-29
discSurv-2.0.0/discSurv/R/SurvTreeLaplaceHazards_ranger.R |only discSurv-2.0.0/discSurv/man/calibrationPlot.Rd |only discSurv-2.0.0/discSurv/man/compRisksGEE.Rd |only discSurv-2.0.0/discSurv/man/estCumInz.Rd |only discSurv-2.0.0/discSurv/man/intPredErrCompRisks.Rd |only discSurv-2.0.0/discSurv/man/plotCumInc.Rd |only discSurv-2.0.0/discSurv/man/plotSurv.Rd |only discSurv-2.0.0/discSurv/man/predErrCompRisks.Rd |only discSurv-2.0.0/discSurv/man/survTreeLaplaceHazardRanger.Rd |only discSurv-2.5.1/discSurv/DESCRIPTION | 27 discSurv-2.5.1/discSurv/MD5 | 131 - discSurv-2.5.1/discSurv/NAMESPACE | 53 discSurv-2.5.1/discSurv/R/DiscSurvAuxiliary.R | 57 discSurv-2.5.1/discSurv/R/DiscSurvDataTransform.R | 280 +- discSurv-2.5.1/discSurv/R/DiscSurvEstimation.R | 946 ++++--- discSurv-2.5.1/discSurv/R/DiscSurvEstimationCR.R | 1141 +++++++++ discSurv-2.5.1/discSurv/R/DiscSurvEvaluation.R | 1211 ++++------ discSurv-2.5.1/discSurv/R/DiscSurvEvaluationCR.R | 201 + discSurv-2.5.1/discSurv/R/DiscSurvLifeTable.R | 53 discSurv-2.5.1/discSurv/R/DiscSurvPlot.R | 578 ++++ discSurv-2.5.1/discSurv/R/dataSets.R | 20 discSurv-2.5.1/discSurv/R/discSurv-package.R | 66 discSurv-2.5.1/discSurv/R/minNodeSizePruning.R | 100 discSurv-2.5.1/discSurv/R/minNodeSizePruningCompRisks.R | 111 discSurv-2.5.1/discSurv/R/survTreeLaplaceHazards.R | 150 - discSurv-2.5.1/discSurv/build/partial.rdb |binary discSurv-2.5.1/discSurv/inst/REFERENCES.bib | 149 + discSurv-2.5.1/discSurv/man/adjDevResid.Rd | 29 discSurv-2.5.1/discSurv/man/cIndex.Rd | 140 - discSurv-2.5.1/discSurv/man/cIndexCompRisks.Rd | 12 discSurv-2.5.1/discSurv/man/calPlot.Rd |only discSurv-2.5.1/discSurv/man/contToDisc.Rd | 24 discSurv-2.5.1/discSurv/man/covarGEE.Rd | 20 discSurv-2.5.1/discSurv/man/crash2.Rd | 16 discSurv-2.5.1/discSurv/man/dataCensoring.Rd | 36 discSurv-2.5.1/discSurv/man/dataLong.Rd | 38 discSurv-2.5.1/discSurv/man/dataLongCompRisks.Rd | 43 discSurv-2.5.1/discSurv/man/dataLongCompRisksTimeDep.Rd | 29 discSurv-2.5.1/discSurv/man/dataLongMultiSpell.Rd | 30 discSurv-2.5.1/discSurv/man/dataLongSubDist.Rd | 29 discSurv-2.5.1/discSurv/man/dataLongTimeDep.Rd | 27 discSurv-2.5.1/discSurv/man/devResid.Rd | 12 discSurv-2.5.1/discSurv/man/discSurv-package.Rd | 49 discSurv-2.5.1/discSurv/man/estCompRisksGEE.Rd |only discSurv-2.5.1/discSurv/man/estCumHaz.Rd |only discSurv-2.5.1/discSurv/man/estCumHazCompRisks.Rd |only discSurv-2.5.1/discSurv/man/estCumInc.Rd |only discSurv-2.5.1/discSurv/man/estForest.Rd |only discSurv-2.5.1/discSurv/man/estForestCompRisks.Rd |only discSurv-2.5.1/discSurv/man/estMargProb.Rd | 24 discSurv-2.5.1/discSurv/man/estMargProbCompRisks.Rd | 19 discSurv-2.5.1/discSurv/man/estMeasures.Rd |only discSurv-2.5.1/discSurv/man/estMeasuresCompRisks.Rd |only discSurv-2.5.1/discSurv/man/estRecal.Rd | 49 discSurv-2.5.1/discSurv/man/estReg.Rd |only discSurv-2.5.1/discSurv/man/estRegCompRisks.Rd |only discSurv-2.5.1/discSurv/man/estRegFrailty.Rd |only discSurv-2.5.1/discSurv/man/estRegSmooth.Rd |only discSurv-2.5.1/discSurv/man/estRegSmoothCompRisks.Rd |only discSurv-2.5.1/discSurv/man/estRegSubDist.Rd |only discSurv-2.5.1/discSurv/man/estSurv.Rd | 53 discSurv-2.5.1/discSurv/man/estSurvCens.Rd | 22 discSurv-2.5.1/discSurv/man/estSurvCompRisks.Rd | 26 discSurv-2.5.1/discSurv/man/estTree.Rd |only discSurv-2.5.1/discSurv/man/estTreeCompRisks.Rd |only discSurv-2.5.1/discSurv/man/gumbel.Rd | 2 discSurv-2.5.1/discSurv/man/intPredErr.Rd | 36 discSurv-2.5.1/discSurv/man/intpredErrCurveCompRisks.Rd |only discSurv-2.5.1/discSurv/man/lifeTable.Rd | 42 discSurv-2.5.1/discSurv/man/martingaleResid.Rd | 27 discSurv-2.5.1/discSurv/man/minNodePruning.Rd | 199 - discSurv-2.5.1/discSurv/man/minNodePruningCompRisks.Rd | 75 discSurv-2.5.1/discSurv/man/predErrCurve.Rd | 80 discSurv-2.5.1/discSurv/man/predErrCurveCompRisks.Rd |only discSurv-2.5.1/discSurv/man/survTreeLaplaceHazard.Rd | 60 discSurv-2.5.1/discSurv/man/unempMultiSpell.Rd | 4 discSurv-2.5.1/discSurv/man/weightsLtoT.Rd | 32 discSurv-2.5.1/discSurv/tests/UnitTestsDiscSurvDataTransform.R | 676 ++--- discSurv-2.5.1/discSurv/tests/UnitTestsDiscSurvEstimation.R | 118 discSurv-2.5.1/discSurv/tests/UnitTestsDiscSurvLifeTable.R | 184 - discSurv-2.5.1/discSurv/tests/UnitTestsPlots.R |only 81 files changed, 5009 insertions(+), 2527 deletions(-)
Title: Gradient Projection Factor Rotation
Description: Gradient projection algorithms for orthogonal and oblique rotation
of factor loadings matrices in factor analysis. Implements a comprehensive
set of rotation criteria including quartimax, quartimin, oblimin, geomin,
simplimax, the Crawford-Ferguson family, and target rotation, among others.
Supports multiple random starts. For details see Bernaards and Jennrich (2005)
<doi:10.1177/0013164404272507>.
Author: Coen Bernaards [aut, cre],
Paul Gilbert [aut],
Robert Jennrich [aut]
Maintainer: Coen Bernaards <cab.gparotation@gmail.com>
Diff between GPArotation versions 2025.3-1 dated 2025-04-12 and 2026.4-1 dated 2026-04-29
GPArotation-2025.3-1/GPArotation/inst/doc/GPAguide.R |only GPArotation-2025.3-1/GPArotation/inst/doc/GPAguide.Stex |only GPArotation-2025.3-1/GPArotation/inst/doc/GPAguide.pdf |only GPArotation-2025.3-1/GPArotation/inst/doc/GPArotateDF.R |only GPArotation-2025.3-1/GPArotation/inst/doc/GPArotateDF.Stex |only GPArotation-2025.3-1/GPArotation/inst/doc/GPArotateDF.pdf |only GPArotation-2025.3-1/GPArotation/vignettes/GPAguide.Stex |only GPArotation-2025.3-1/GPArotation/vignettes/GPArotateDF.Stex |only GPArotation-2026.4-1/GPArotation/DESCRIPTION | 35 GPArotation-2026.4-1/GPArotation/MD5 | 82 GPArotation-2026.4-1/GPArotation/NAMESPACE | 89 GPArotation-2026.4-1/GPArotation/NEWS | 247 + GPArotation-2026.4-1/GPArotation/R/GPF.R | 256 + GPArotation-2026.4-1/GPArotation/R/GPFRS.R | 175 - GPArotation-2026.4-1/GPArotation/R/NormalizingWeight.R | 35 GPArotation-2026.4-1/GPArotation/R/RandomStart.R | 47 GPArotation-2026.4-1/GPArotation/R/lp.R | 403 +-- GPArotation-2026.4-1/GPArotation/R/printsummary.R | 258 + GPArotation-2026.4-1/GPArotation/R/rotations.R | 1449 ++++++----- GPArotation-2026.4-1/GPArotation/build/vignette.rds |binary GPArotation-2026.4-1/GPArotation/data/CCAI.rda |only GPArotation-2026.4-1/GPArotation/data/Harman.rda |binary GPArotation-2026.4-1/GPArotation/data/WansbeekMeijer.rda |binary GPArotation-2026.4-1/GPArotation/inst/doc/GPA1guide.R |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA1guide.Stex |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA1guide.pdf |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA2local.R |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA2local.Stex |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA2local.pdf |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA3bifactor.R |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA3bifactor.Stex |only GPArotation-2026.4-1/GPArotation/inst/doc/GPA3bifactor.pdf |only GPArotation-2026.4-1/GPArotation/man/00.GPArotation.Rd | 253 + GPArotation-2026.4-1/GPArotation/man/CCAI.Rd |only GPArotation-2026.4-1/GPArotation/man/GPA.Rd | 461 ++- GPArotation-2026.4-1/GPArotation/man/Harman.Rd | 55 GPArotation-2026.4-1/GPArotation/man/NormalizingWeight.Rd | 76 GPArotation-2026.4-1/GPArotation/man/Random.Start.Rd | 125 GPArotation-2026.4-1/GPArotation/man/Thurstone.Rd | 54 GPArotation-2026.4-1/GPArotation/man/WansbeekMeijer.Rd | 55 GPArotation-2026.4-1/GPArotation/man/echelon.Rd | 160 - GPArotation-2026.4-1/GPArotation/man/eiv.Rd | 159 - GPArotation-2026.4-1/GPArotation/man/lp.Rd | 156 - GPArotation-2026.4-1/GPArotation/man/print.GPArotation.Rd | 108 GPArotation-2026.4-1/GPArotation/man/rotations.Rd | 402 +-- GPArotation-2026.4-1/GPArotation/man/vgQ.Rd | 153 - GPArotation-2026.4-1/GPArotation/tests/errormessages.R | 103 GPArotation-2026.4-1/GPArotation/tests/legacyVsNew.R |only GPArotation-2026.4-1/GPArotation/tests/print-GPArotation.R | 156 - GPArotation-2026.4-1/GPArotation/tests/tableTests.r |only GPArotation-2026.4-1/GPArotation/tests/vgQOLD.R |only GPArotation-2026.4-1/GPArotation/tests/vgQtestOldVsNew.R |only GPArotation-2026.4-1/GPArotation/vignettes/GPA1guide.Stex |only GPArotation-2026.4-1/GPArotation/vignettes/GPA2local.Stex |only GPArotation-2026.4-1/GPArotation/vignettes/GPA3bifactor.Stex |only 55 files changed, 3335 insertions(+), 2217 deletions(-)
Title: Publication-Quality 'ggplot2' Themes
Description: Complete themes for publication-quality 'ggplot2' visualisation.
Also provides functions to modify these based on the positional axis scales
and focus of a particular plot.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggrefine versions 0.2.0 dated 2026-04-14 and 0.3.0 dated 2026-04-29
ggrefine-0.2.0/ggrefine/R/refine.R |only ggrefine-0.2.0/ggrefine/R/theme.R |only ggrefine-0.2.0/ggrefine/R/utils.R |only ggrefine-0.2.0/ggrefine/man/refine_classic.Rd |only ggrefine-0.2.0/ggrefine/man/refine_fusion.Rd |only ggrefine-0.2.0/ggrefine/man/refine_modern.Rd |only ggrefine-0.2.0/ggrefine/man/refine_none.Rd |only ggrefine-0.2.0/ggrefine/man/refine_void.Rd |only ggrefine-0.3.0/ggrefine/DESCRIPTION | 17 +- ggrefine-0.3.0/ggrefine/MD5 | 49 +++++--- ggrefine-0.3.0/ggrefine/NAMESPACE | 12 +- ggrefine-0.3.0/ggrefine/NEWS.md | 8 + ggrefine-0.3.0/ggrefine/R/classic.R |only ggrefine-0.3.0/ggrefine/R/hybrid.R |only ggrefine-0.3.0/ggrefine/R/minimal.R |only ggrefine-0.3.0/ggrefine/R/modern.R |only ggrefine-0.3.0/ggrefine/R/none.R |only ggrefine-0.3.0/ggrefine/R/theme-dark.R |only ggrefine-0.3.0/ggrefine/R/theme-grey.R |only ggrefine-0.3.0/ggrefine/R/theme-light.R |only ggrefine-0.3.0/ggrefine/R/theme-oat.R |only ggrefine-0.3.0/ggrefine/R/void.R |only ggrefine-0.3.0/ggrefine/README.md | 60 +++++----- ggrefine-0.3.0/ggrefine/inst |only ggrefine-0.3.0/ggrefine/man/classic.Rd |only ggrefine-0.3.0/ggrefine/man/figures/README-example-1.png |binary ggrefine-0.3.0/ggrefine/man/figures/README-unnamed-chunk-2-1.png |binary ggrefine-0.3.0/ggrefine/man/figures/logo.png |binary ggrefine-0.3.0/ggrefine/man/figures/logo.svg | 4 ggrefine-0.3.0/ggrefine/man/hybrid.Rd |only ggrefine-0.3.0/ggrefine/man/minimal.Rd |only ggrefine-0.3.0/ggrefine/man/modern.Rd |only ggrefine-0.3.0/ggrefine/man/none.Rd |only ggrefine-0.3.0/ggrefine/man/theme_dark.Rd | 12 +- ggrefine-0.3.0/ggrefine/man/theme_grey.Rd | 21 ++- ggrefine-0.3.0/ggrefine/man/theme_light.Rd | 12 +- ggrefine-0.3.0/ggrefine/man/theme_oat.Rd |only ggrefine-0.3.0/ggrefine/man/void.Rd |only ggrefine-0.3.0/ggrefine/tests |only 39 files changed, 111 insertions(+), 84 deletions(-)
Title: Entropy Reweighting to Create Balanced Samples
Description: Implements entropy balancing, a data preprocessing procedure
described in Hainmueller (2012, <doi:10.1093/pan/mpr025>) that allows
users to reweight a dataset such that the covariate distributions in
the reweighted data satisfy a set of user-specified moment conditions.
Useful for creating balanced samples in observational studies with a
binary treatment where the control group is reweighted to match the
covariate moments of the treatment group, and for reweighting a
survey sample to known characteristics from a target population.
Author: Jens Hainmueller [aut, cre]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between ebal versions 0.1-8 dated 2022-06-09 and 0.2.1 dated 2026-04-29
DESCRIPTION | 31 ++++-- MD5 | 32 ++++-- NAMESPACE | 35 +++++- NEWS.md |only R/eb.R | 4 R/ebalance.R | 247 +++++++++++++++++++++++++++--------------------- R/ebalance.trim.r | 128 ++++++++++++++++-------- R/getsquares.R | 24 ++-- R/line.searcher.r | 25 ++-- R/matrixmaker.R | 29 ++--- R/methods.R |only R/utils.R |only R/zzz.r | 14 -- man/ebalance-methods.Rd |only man/ebalance.Rd | 167 +++++++++++++++++++++----------- man/ebalance.trim.Rd | 88 ++++++++++------- tests |only 17 files changed, 505 insertions(+), 319 deletions(-)
Title: 'DataSHIELD' 'Tidyverse' Clientside Package
Description: Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, 'DataSHIELD' contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the client-side package which should be installed locally, and is used in conjunction with the server-side package 'dsTidyverse' which is installed on the remote server holding the data. For more information, see <https://tidyverse.org/> and <https://datashield.org/>.
Author: Tim Cadman [aut, cre] ,
Mariska Slofstra [aut] ,
Stuart Wheater [aut],
Demetris Avraam [aut]
Maintainer: Tim Cadman <t.j.cadman@umcg.nl>
Diff between dsTidyverseClient versions 1.0.3 dated 2025-12-15 and 1.1.0 dated 2026-04-29
DESCRIPTION | 11 MD5 | 60 ++--- NEWS.md | 3 R/ds.arrange.R | 4 R/ds.distinct.R | 4 R/ds.filter.R | 4 R/ds.group_by.R | 6 R/ds.group_keys.R | 4 R/ds.mutate.R | 2 R/ds.rename.R | 4 R/ds.select.R | 4 R/ds.slice.R | 4 R/utils.R | 6 inst/doc/dstidyverse.Rmd | 105 ++++---- inst/doc/dstidyverse.html | 276 +++++++++++------------ man/ds.arrange.Rd | 4 man/ds.distinct.Rd | 4 man/ds.filter.Rd | 4 man/ds.group_by.Rd | 4 man/ds.group_keys.Rd | 4 man/ds.mutate.Rd | 2 man/ds.rename.Rd | 4 man/ds.select.Rd | 4 man/ds.slice.Rd | 4 man/ds.ungroup.Rd | 2 tests/testthat/helpers.R | 15 + tests/testthat/test-mutate-permitted-functions.R |only tests/testthat/test-select-permitted-functions.R |only tests/testthat/test-select.R | 135 ----------- tests/testthat/test-utils.R | 6 vignettes/dstidyverse.Rmd | 105 ++++---- vignettes/dstidyverse.Rmd.orig | 2 32 files changed, 338 insertions(+), 458 deletions(-)
More information about dsTidyverseClient at CRAN
Permanent link
Title: Ready to Use Extra Datasets for Torch
Description: Provides datasets in a format that can be easily consumed by torch 'dataloaders'.
Handles data downloading from multiple sources, caching and pre-processing so
users can focus only on their model implementations.
Author: Tomasz Kalinowski [ctb, cre],
Daniel Falbel [aut, cph],
RStudio [cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between torchdatasets versions 0.3.1 dated 2024-06-20 and 0.3.2 dated 2026-04-29
DESCRIPTION | 20 +++++++++----------- MD5 | 17 ++++++++++------- NAMESPACE | 1 + NEWS.md | 2 ++ R/bird-species.R | 1 - R/spam-dataset.R |only README.md | 1 + man/bird_species_dataset.Rd | 1 - man/spam_dataset.Rd |only tests/testthat/test-oxford-flowers-dataset.R | 1 + tests/testthat/test-spam-dataset.R |only 11 files changed, 24 insertions(+), 20 deletions(-)
Title: Tools for Handling Extraction of Features from Time Series
Description: Consolidates and calculates different sets of time-series features from multiple
'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>,
'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>,
'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020)
<https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J.,
and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020)
<doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021)
<https://facebookresearch.github.io/Kats/>.
Author: Trent Henderson [cre, aut],
Annie Bryant [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theft versions 0.8.2 dated 2025-07-29 and 0.8.4 dated 2026-04-29
DESCRIPTION | 10 +- MD5 | 39 +++++----- NAMESPACE | 5 + R/calculate_features.R | 89 +++++++++++++++++++++-- R/init_theft.R | 87 ++++++++++++++++++++++ R/installs.R | 31 +++++++- R/quantiles.R | 4 - README.md | 74 +++++++++++-------- build/vignette.rds |binary inst/doc/theft.Rmd | 10 +- inst/doc/theft.html | 59 ++++++++------- inst/python/pyhctsa_calculator.py |only inst/yaml |only man/calculate_features.Rd | 2 man/figures/workflow-graphic_ecosystem-final.png |binary man/init_theft.Rd | 4 - man/init_theft_hctsa.Rd |only man/init_theft_kats.Rd |only man/init_theft_tsfel.Rd |only man/init_theft_tsfresh.Rd |only man/install_pyhctsa.Rd |only man/install_python_pkgs.Rd | 4 - man/quantiles.Rd | 4 - vignettes/theft.Rmd | 10 +- 24 files changed, 332 insertions(+), 100 deletions(-)
Title: Synthetic Control Group Method for Comparative Case Studies
Description: Implements the synthetic control group method for comparative case studies
as described in Abadie and Gardeazabal (2003) and Abadie, Diamond, and Hainmueller
(2010, 2011, 2014). The synthetic control method allows for effect estimation in
settings where a single unit (a state, country, firm, etc.) is exposed to an event
or intervention. It provides a data-driven procedure to construct synthetic control
units based on a weighted combination of comparison units that approximates the
characteristics of the unit that is exposed to the intervention. A combination of
comparison units often provides a better comparison for the unit exposed to the
intervention than any comparison unit alone.
Author: Jens Hainmueller [aut, cre],
Alexis Diamond [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between Synth versions 1.1-9 dated 2025-10-19 and 1.1-10 dated 2026-04-29
DESCRIPTION | 10 ++-- MD5 | 18 +++++--- NEWS.md |only R/dataprep.R | 21 +++++---- R/fn.V.R | 24 ++++------- R/path.plot.R | 48 ++++++++++------------ R/synth.R | 126 +++++++++++++++++++++++++--------------------------------- tests |only 8 files changed, 117 insertions(+), 130 deletions(-)
Title: Deep Neural Networks for Survival Analysis with R 'torch'
Description: Provides deep learning models for right-censored survival data using the 'torch' backend.
Supports multiple loss functions, including Cox partial likelihood, L2-penalized Cox, time-dependent Cox,
and accelerated failure time (AFT) loss. Offers a formula-based interface, built-in support for cross-validation,
hyperparameter tuning, survival curve plotting, and evaluation metrics such as the C-index, Brier score,
and integrated Brier score. For methodological details, see Kvamme et al. (2019) <https://www.jmlr.org/papers/v20/18-424.html>.
Author: Imad EL BADISY [aut, cre]
Maintainer: Imad EL BADISY <elbadisyimad@gmail.com>
Diff between survdnn versions 0.7.5 dated 2026-01-07 and 0.7.6 dated 2026-04-29
DESCRIPTION | 6 - MD5 | 52 ++++++------- NEWS.md | 11 ++ R/evaluation.R | 95 ++++++++++++++++++------- R/gridsearch_survdnn.R | 79 ++++++++++----------- R/metrics.R | 51 +++++++------ R/plot.survdnn.R | 13 +-- R/print.survdnn.R | 11 +- R/summary.survdnn.R | 29 +++++-- R/survdnn.R | 39 +++++++++- R/tune_survdnn.R | 67 ++++++++++++++++- R/zzz.R | 16 ++++ README.md | 139 +++++++++++++++++++++++-------------- man/brier.Rd | 15 ++- man/cindex_survmat.Rd | 15 ++- man/cv_survdnn.Rd | 33 +++++--- man/gridsearch_survdnn.Rd | 68 +++++++++--------- man/ibs_survmat.Rd | 21 ++--- man/plot.survdnn.Rd | 13 +-- man/print.survdnn.Rd | 11 +- man/summarize_cv_survdnn.Rd | 27 +++---- man/summary.survdnn.Rd | 27 ++++--- man/survdnn.Rd | 7 + man/tune_survdnn.Rd | 8 ++ tests/testthat/test-cv_survdnn.R | 45 +++++++++++ tests/testthat/test-survdnn.R | 24 ++++++ tests/testthat/test-tune_survdnn.R | 63 ++++++++++++++++ 27 files changed, 676 insertions(+), 309 deletions(-)
Title: Social Mixing Matrices for Infectious Disease Modelling
Description: Methods for sampling contact matrices from diary data for
use in infectious disease modelling, as discussed in Mossong et al.
(2008) <doi:10.1371/journal.pmed.0050074>.
Author: Sebastian Funk [aut, cre],
Lander Willem [aut],
Hugo Gruson [aut],
Nicholas Tierney [aut] ,
Maria Bekker-Nielsen Dunbar [ctb],
Carl A. B. Pearson [ctb],
Sam Clifford [ctb],
Christopher Jarvis [ctb],
Alexis Robert [ctb],
Niel Hens [ctb],
Pietro Colett [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between socialmixr versions 0.5.1 dated 2026-02-04 and 0.6.0 dated 2026-04-29
socialmixr-0.5.1/socialmixr/R/cite.R |only socialmixr-0.5.1/socialmixr/R/download_survey.R |only socialmixr-0.5.1/socialmixr/R/get_survey.R |only socialmixr-0.5.1/socialmixr/tests/testthat/_snaps/countries.md |only socialmixr-0.5.1/socialmixr/tests/testthat/_snaps/download-survey.md |only socialmixr-0.5.1/socialmixr/tests/testthat/_snaps/surveys.md |only socialmixr-0.5.1/socialmixr/tests/testthat/test-download-survey.R |only socialmixr-0.6.0/socialmixr/DESCRIPTION | 14 socialmixr-0.6.0/socialmixr/LICENSE | 2 socialmixr-0.6.0/socialmixr/MD5 | 164 - socialmixr-0.6.0/socialmixr/NAMESPACE | 13 socialmixr-0.6.0/socialmixr/NEWS.md | 121 + socialmixr-0.6.0/socialmixr/R/as_contact_survey.R | 19 socialmixr-0.6.0/socialmixr/R/assign-age-groups.R | 22 socialmixr-0.6.0/socialmixr/R/check.R | 121 - socialmixr-0.6.0/socialmixr/R/checkers.R | 5 socialmixr-0.6.0/socialmixr/R/clean.R | 5 socialmixr-0.6.0/socialmixr/R/compute-matrix.R |only socialmixr-0.6.0/socialmixr/R/contact-age-distribution.R |only socialmixr-0.6.0/socialmixr/R/contact-matrix-result.R |only socialmixr-0.6.0/socialmixr/R/contact-matrix-utils.R | 199 +- socialmixr-0.6.0/socialmixr/R/contact_matrix.R | 307 +-- socialmixr-0.6.0/socialmixr/R/deprecate-args.R | 2 socialmixr-0.6.0/socialmixr/R/deprecated.R |only socialmixr-0.6.0/socialmixr/R/globals.R | 23 socialmixr-0.6.0/socialmixr/R/limits_to_agegroups.R | 24 socialmixr-0.6.0/socialmixr/R/lists.R | 156 - socialmixr-0.6.0/socialmixr/R/load-survey-utils.R | 446 ++-- socialmixr-0.6.0/socialmixr/R/matrix_plot.R | 61 socialmixr-0.6.0/socialmixr/R/new_contact_survey.R | 28 socialmixr-0.6.0/socialmixr/R/pop_age.R | 20 socialmixr-0.6.0/socialmixr/R/postprocess-matrix.R |only socialmixr-0.6.0/socialmixr/R/subset-contact-survey.R |only socialmixr-0.6.0/socialmixr/R/survey.R | 23 socialmixr-0.6.0/socialmixr/R/utils.R | 5 socialmixr-0.6.0/socialmixr/R/weigh.R |only socialmixr-0.6.0/socialmixr/R/wpp_age.R | 41 socialmixr-0.6.0/socialmixr/README.md | 30 socialmixr-0.6.0/socialmixr/build/partial.rdb |binary socialmixr-0.6.0/socialmixr/build/vignette.rds |binary socialmixr-0.6.0/socialmixr/inst/doc/socialmixr.R | 198 +- socialmixr-0.6.0/socialmixr/inst/doc/socialmixr.Rmd | 285 ++- socialmixr-0.6.0/socialmixr/inst/doc/socialmixr.html | 948 +++++----- socialmixr-0.6.0/socialmixr/man/add_age.Rd | 3 socialmixr-0.6.0/socialmixr/man/agegroups_to_limits.Rd |only socialmixr-0.6.0/socialmixr/man/as_contact_survey.Rd | 18 socialmixr-0.6.0/socialmixr/man/assemble_survey.Rd |only socialmixr-0.6.0/socialmixr/man/check.Rd | 31 socialmixr-0.6.0/socialmixr/man/clean.Rd | 5 socialmixr-0.6.0/socialmixr/man/compute_matrix.Rd |only socialmixr-0.6.0/socialmixr/man/contact_age_distribution.Rd |only socialmixr-0.6.0/socialmixr/man/contact_matrix.Rd | 161 + socialmixr-0.6.0/socialmixr/man/copy_survey.Rd |only socialmixr-0.6.0/socialmixr/man/deprecate_arg.Rd | 2 socialmixr-0.6.0/socialmixr/man/dot-get_survey.Rd | 6 socialmixr-0.6.0/socialmixr/man/download_survey.Rd | 5 socialmixr-0.6.0/socialmixr/man/get_citation.Rd | 2 socialmixr-0.6.0/socialmixr/man/get_survey.Rd | 9 socialmixr-0.6.0/socialmixr/man/is_contact_matrix.Rd |only socialmixr-0.6.0/socialmixr/man/is_doi.Rd | 2 socialmixr-0.6.0/socialmixr/man/list_surveys.Rd | 2 socialmixr-0.6.0/socialmixr/man/matrix_plot.Rd | 54 socialmixr-0.6.0/socialmixr/man/new_contact_matrix.Rd |only socialmixr-0.6.0/socialmixr/man/new_contact_survey.Rd | 9 socialmixr-0.6.0/socialmixr/man/normalise_weights.Rd |only socialmixr-0.6.0/socialmixr/man/per_capita.Rd |only socialmixr-0.6.0/socialmixr/man/pop_age.Rd | 19 socialmixr-0.6.0/socialmixr/man/resolve_survey_pop.Rd |only socialmixr-0.6.0/socialmixr/man/sample_from_age_distribution.Rd |only socialmixr-0.6.0/socialmixr/man/split_matrix.Rd |only socialmixr-0.6.0/socialmixr/man/sub-.contact_survey.Rd |only socialmixr-0.6.0/socialmixr/man/survey.Rd | 4 socialmixr-0.6.0/socialmixr/man/survey_countries.Rd | 4 socialmixr-0.6.0/socialmixr/man/symmetrise.Rd |only socialmixr-0.6.0/socialmixr/man/validate_age_distribution.Rd |only socialmixr-0.6.0/socialmixr/man/warn_multiple_observations.Rd |only socialmixr-0.6.0/socialmixr/man/weigh.Rd |only socialmixr-0.6.0/socialmixr/man/wpp_age.Rd | 24 socialmixr-0.6.0/socialmixr/man/wpp_countries.Rd | 15 socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/agegroups.md | 5 socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/as_contact_survey.md | 4 socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/assign-age-groups.md | 38 socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/checks.md | 2 socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/matrix.md | 243 +- socialmixr-0.6.0/socialmixr/tests/testthat/_snaps/survey-country-population.md | 20 socialmixr-0.6.0/socialmixr/tests/testthat/test-agegroups.r | 28 socialmixr-0.6.0/socialmixr/tests/testthat/test-assign-age-groups.R | 117 + socialmixr-0.6.0/socialmixr/tests/testthat/test-compute-matrix.R |only socialmixr-0.6.0/socialmixr/tests/testthat/test-contact-matrix-result.R |only socialmixr-0.6.0/socialmixr/tests/testthat/test-convert-factor-to-integer.R | 2 socialmixr-0.6.0/socialmixr/tests/testthat/test-countries.r | 2 socialmixr-0.6.0/socialmixr/tests/testthat/test-load-survey.R | 27 socialmixr-0.6.0/socialmixr/tests/testthat/test-matrix.r | 89 socialmixr-0.6.0/socialmixr/tests/testthat/test-plot.r | 4 socialmixr-0.6.0/socialmixr/tests/testthat/test-postprocess-matrix.R |only socialmixr-0.6.0/socialmixr/tests/testthat/test-subset-contact-survey.R |only socialmixr-0.6.0/socialmixr/tests/testthat/test-survey-country-population.R | 5 socialmixr-0.6.0/socialmixr/tests/testthat/test-surveys.r | 56 socialmixr-0.6.0/socialmixr/tests/testthat/test-weigh.R |only socialmixr-0.6.0/socialmixr/vignettes/intro.qmd | 303 ++- socialmixr-0.6.0/socialmixr/vignettes/socialmixr.Rmd | 285 ++- 101 files changed, 3158 insertions(+), 1729 deletions(-)
Title: High-Dimensional Location Testing with Normal-Reference
Approaches
Description: Provides inverse-free high-dimensional location tests for two-sample
and general linear hypothesis testing (GLHT) problems under equal or unequal
covariance structures. The package implements classical normal-approximation
procedures, scale-invariant procedures, normal-reference procedures based on
covariance-matched Gaussian companions, and F-type normal-reference
calibrations for heteroscedastic Behrens-Fisher and GLHT settings. Implemented
two-sample normal-approximation and scale-invariant procedures include Bai and
Saranadasa (1996) <https://www.jstor.org/stable/24306018>, Chen and Qin
(2010) <doi:10.1214/09-aos716>, Srivastava and Du (2008)
<doi:10.1016/j.jmva.2006.11.002>, and Srivastava et al. (2013)
<doi:10.1016/j.jmva.2012.08.014>. Implemented two-sample normal-reference
procedures include Zhang, Guo, Zhou and Cheng (2020)
<doi:10.1080/01621459.2019.1604366>, Zhang, Zhou, Guo and Zhu (2021)
<doi:10.1016/j.jspi.2020.11.008>, Zhang, Zhu and Z [...truncated...]
Author: Pengfei Wang [aut, cre],
Shuqi Luo [aut],
Tianming Zhu [aut],
Bu Zhou [aut]
Maintainer: Pengfei Wang <nie23.wp8738@e.ntu.edu.sg>
Diff between HDNRA versions 2.0.1 dated 2024-10-22 and 2.1.0 dated 2026-04-29
DESCRIPTION | 51 + MD5 | 26 NAMESPACE | 4 NEWS.md | 34 + R/CCXH2024.GLHTBF.2cNRT.R |only R/LHNB2025.GLHTBF.NABT.R |only R/RcppExports.R | 12 R/WZ2026.GLHTBF.2cNRT.R |only README.md | 217 +++---- build/partial.rdb |binary inst/REFERENCES.bib | 26 man/CCXH2024.GLHTBF.2cNRT.Rd |only man/HDNRA-package.Rd | 3 man/LHNB2025.GLHTBF.NABT.Rd |only man/WZ2026.GLHTBF.2cNRT.Rd |only src/HDNRA.cpp | 1267 ++++++++++++++++++++++++++++++++++--------- src/RcppExports.cpp | 47 + 17 files changed, 1309 insertions(+), 378 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan [aut, cre],
Luke Bornn [aut]
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.2 dated 2016-02-02 and 1.3 dated 2026-04-29
DESCRIPTION | 23 +++++++--- MD5 | 10 ++-- NAMESPACE | 4 - R/RcppExports.R | 20 ++++----- demo/FastGPdemo.R | 35 +++++---------- src/RcppExports.cpp | 115 +++++++++++++++++++++++++++++++--------------------- 6 files changed, 115 insertions(+), 92 deletions(-)
Title: Canonical Correlation Analysis via Reduced Rank Regression
Description: Canonical correlation analysis (CCA) via reduced-rank regression with support for regularization and cross-validation. Several methods for estimating CCA in high-dimensional settings are implemented. The first set of methods, cca_rrr() (and variants: cca_group_rrr() and cca_graph_rrr()), assumes that one dataset is high-dimensional and the other is low-dimensional, while the second, ecca() (for Efficient CCA) assumes that both datasets are high-dimensional. For both methods, standard l1 regularization as well as group-lasso regularization are available. cca_graph_rrr further supports total variation regularization when there is a known graph structure among the variables of the high-dimensional dataset. In this case, the loadings of the canonical directions of the high-dimensional dataset are assumed to be smooth on the graph. For more details see Donnat and Tuzhilina (2024) <doi:10.48550/arXiv.2405.19539> and Wu, Tuzhilina and Donnat (2025) <doi:10.48550/arXiv.2507.11160> [...truncated...]
Author: Claire Donnat [aut, cre] ,
Elena Tuzhilina [aut] ,
Zixuan Wu [aut]
Maintainer: Claire Donnat <cdonnat@uchicago.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2025-09-16
Diff between ccar3 versions 0.1.0 dated 2025-09-16 and 0.1.1 dated 2026-04-29
ccar3-0.1.0/ccar3/man/setup_parallel_backend.Rd |only ccar3-0.1.1/ccar3/DESCRIPTION | 18 ccar3-0.1.1/ccar3/LICENSE | 2 ccar3-0.1.1/ccar3/MD5 | 54 ccar3-0.1.1/ccar3/R/alt_SAR.R | 4 ccar3-0.1.1/ccar3/R/alt_Witten_CrossValidation.R | 14 ccar3-0.1.1/ccar3/R/benchmarks.r | 12 ccar3-0.1.1/ccar3/R/ecca.r | 1809 ++++++---- ccar3-0.1.1/ccar3/R/graph_reduced_rank_regression.R | 760 +++- ccar3-0.1.1/ccar3/R/group_reduced_rank_regression.R | 394 +- ccar3-0.1.1/ccar3/R/package.R |only ccar3-0.1.1/ccar3/R/reduced_rank_regression.R | 966 ++++- ccar3-0.1.1/ccar3/R/utils.R | 342 + ccar3-0.1.1/ccar3/build |only ccar3-0.1.1/ccar3/man/cca_graph_rrr.Rd | 9 ccar3-0.1.1/ccar3/man/cca_graph_rrr_cv.Rd | 19 ccar3-0.1.1/ccar3/man/cca_group_rrr.Rd | 19 ccar3-0.1.1/ccar3/man/cca_group_rrr_cv.Rd | 29 ccar3-0.1.1/ccar3/man/cca_rrr.Rd | 32 ccar3-0.1.1/ccar3/man/cca_rrr_cv.Rd | 69 ccar3-0.1.1/ccar3/man/ccar3-package.Rd |only ccar3-0.1.1/ccar3/man/ecca.Rd | 50 ccar3-0.1.1/ccar3/man/ecca.cv.Rd | 73 ccar3-0.1.1/ccar3/tests/testthat/helper-generate_example_rrr.R | 4 ccar3-0.1.1/ccar3/tests/testthat/test-cca_graph_rrr.R | 26 ccar3-0.1.1/ccar3/tests/testthat/test-cca_graph_rrr_cv.R | 58 ccar3-0.1.1/ccar3/tests/testthat/test-cca_group_rrr.R | 47 ccar3-0.1.1/ccar3/tests/testthat/test-cca_group_rrr_cv.R | 88 ccar3-0.1.1/ccar3/tests/testthat/test-cca_rrr.R | 89 ccar3-0.1.1/ccar3/tests/testthat/test-cca_rrr_cv.R | 35 30 files changed, 3847 insertions(+), 1175 deletions(-)
Title: Backfill Bayesian Optimal Interval Design Using Efficacy and
Toxicity
Description: Implements the Backfill Bayesian Optimal Interval Design (BF-BOIN-ET),
a novel clinical trial methodology for dose optimization that simultaneously consider both efficacy
and toxicity outcome as described in (Takeda et al (2025) <doi:10.1002/pst.2470>).
The package has been extended to include a seamless two-stage phase I/II trial design with backfill
and joint efficacy and toxicity monitoring as described in (Takeda et al (2026) <doi:10.1002/pst.70092>).
Author: Jing Zhu [cre, aut],
Kentaro Takeda [aut],
Belay Birlie Yimer [aut]
Maintainer: Jing Zhu <zhujing716@gmail.com>
Diff between bfboinet versions 1.0.0 dated 2026-04-14 and 1.1.0 dated 2026-04-29
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 22 +++++++++++++--------- 3 files changed, 20 insertions(+), 16 deletions(-)
Title: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq
Data as Reference
Description: Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.
Author: Yuanhang Liu [aut, cre]
Maintainer: Yuanhang Liu <liu.yuanhang@mayo.edu>
Diff between SCdeconR versions 1.0.0 dated 2024-03-22 and 1.0.2 dated 2026-04-29
SCdeconR-1.0.0/SCdeconR/inst/extdata/image |only SCdeconR-1.0.2/SCdeconR/DESCRIPTION | 10 ++--- SCdeconR-1.0.2/SCdeconR/MD5 | 35 +++++++++----------- SCdeconR-1.0.2/SCdeconR/R/deconvolution.R | 27 ++++++--------- SCdeconR-1.0.2/SCdeconR/R/differential_expression.R | 23 +++++-------- SCdeconR-1.0.2/SCdeconR/R/helpers.R | 2 - SCdeconR-1.0.2/SCdeconR/R/pathway_analysis.R | 13 ++----- SCdeconR-1.0.2/SCdeconR/R/reference_construction.R | 5 +- SCdeconR-1.0.2/SCdeconR/R/simulate_bulk.R | 8 ++-- SCdeconR-1.0.2/SCdeconR/README.md | 2 - SCdeconR-1.0.2/SCdeconR/man/bulk_generator.Rd | 2 - SCdeconR-1.0.2/SCdeconR/man/comparedeg_scatter.Rd | 3 - SCdeconR-1.0.2/SCdeconR/man/compute_metrics.Rd | 6 +-- SCdeconR-1.0.2/SCdeconR/man/construct_ref.Rd | 4 +- SCdeconR-1.0.2/SCdeconR/man/gsea_sumplot.Rd | 3 - SCdeconR-1.0.2/SCdeconR/man/prop_barplot.Rd | 3 - SCdeconR-1.0.2/SCdeconR/man/run_de.Rd | 14 ++++---- SCdeconR-1.0.2/SCdeconR/man/scaling.Rd | 2 - SCdeconR-1.0.2/SCdeconR/man/scdecon.Rd | 12 ++---- 19 files changed, 74 insertions(+), 100 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, WURCS,
Linear Code, and GlycoCT format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.5.7 dated 2026-03-14 and 0.6.0 dated 2026-04-29
DESCRIPTION | 8 - MD5 | 50 ++++---- NEWS.md | 6 R/auto-parse.R | 6 R/parse-glycoct.R | 6 R/parse-iupac-condensed.R | 6 R/parse-iupac-extended.R | 6 R/parse-iupac-short.R | 6 R/parse-linear-code.R | 6 R/parse-pglyco.R | 6 R/parse-strucgp.R | 6 R/parse-wurcs.R | 6 R/struc-parser-wrapper.R | 232 ++++++++++++++++++++++++++++++-------- README.md | 2 inst/doc/glyparse.html | 9 - man/auto_parse.Rd | 5 man/parse_glycoct.Rd | 5 man/parse_iupac_condensed.Rd | 5 man/parse_iupac_extended.Rd | 5 man/parse_iupac_short.Rd | 5 man/parse_linear_code.Rd | 5 man/parse_pglyco_struc.Rd | 5 man/parse_strucgp_struc.Rd | 5 man/parse_wurcs.Rd | 5 tests/testthat/test-na-support.R | 80 +++++++++++-- tests/testthat/test-performance.R | 23 +++ 26 files changed, 395 insertions(+), 114 deletions(-)