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 2.3.2 dated 2025-07-15 and 2.5.2 dated 2025-08-25
ggpicrust2-2.3.2/ggpicrust2/NEWS.md |only ggpicrust2-2.3.2/ggpicrust2/README.md |only ggpicrust2-2.3.2/ggpicrust2/build |only ggpicrust2-2.3.2/ggpicrust2/inst/doc |only ggpicrust2-2.3.2/ggpicrust2/inst/extdata/EC_reference.RData |only ggpicrust2-2.3.2/ggpicrust2/inst/extdata/KO_reference.RData |only ggpicrust2-2.3.2/ggpicrust2/inst/extdata/MetaCyc_reference.RData |only ggpicrust2-2.3.2/ggpicrust2/inst/extdata/kegg_reference.RData |only ggpicrust2-2.3.2/ggpicrust2/tests/testthat/Rplots.pdf |only ggpicrust2-2.3.2/ggpicrust2/vignettes |only ggpicrust2-2.5.2/ggpicrust2/DESCRIPTION | 23 ggpicrust2-2.5.2/ggpicrust2/MD5 | 117 +- ggpicrust2-2.5.2/ggpicrust2/NAMESPACE | 20 ggpicrust2-2.5.2/ggpicrust2/R/color_themes.R |only ggpicrust2-2.5.2/ggpicrust2/R/compare_daa_results.R | 4 ggpicrust2-2.5.2/ggpicrust2/R/daa_annotated_results_df.R | 2 ggpicrust2-2.5.2/ggpicrust2/R/daa_results_df.R | 2 ggpicrust2-2.5.2/ggpicrust2/R/ggpicrust2.R | 45 ggpicrust2-2.5.2/ggpicrust2/R/gsea_pathway_annotation.R | 109 + ggpicrust2-2.5.2/ggpicrust2/R/kegg_abundance.R | 2 ggpicrust2-2.5.2/ggpicrust2/R/ko2kegg_abundance.R | 59 - ggpicrust2-2.5.2/ggpicrust2/R/ko_abundance.R | 2 ggpicrust2-2.5.2/ggpicrust2/R/legend_annotation_utils.R |only ggpicrust2-2.5.2/ggpicrust2/R/metadata.R | 2 ggpicrust2-2.5.2/ggpicrust2/R/pathway_annotation.R | 97 + ggpicrust2-2.5.2/ggpicrust2/R/pathway_daa.R | 560 ++++++++-- ggpicrust2-2.5.2/ggpicrust2/R/pathway_errorbar.R | 300 ++++- ggpicrust2-2.5.2/ggpicrust2/R/pathway_errorbar_table.R |only ggpicrust2-2.5.2/ggpicrust2/R/pathway_gsea.R | 441 +++++++ ggpicrust2-2.5.2/ggpicrust2/R/pathway_heatmap.R | 447 +++++++ ggpicrust2-2.5.2/ggpicrust2/R/visualize_gsea.R | 208 +++ ggpicrust2-2.5.2/ggpicrust2/R/zzz.R | 6 ggpicrust2-2.5.2/ggpicrust2/inst/PICRUST_COMPATIBILITY.md |only ggpicrust2-2.5.2/ggpicrust2/inst/extdata/create_metacyc_to_ec_mapping.R |only ggpicrust2-2.5.2/ggpicrust2/man/calculate_smart_text_size.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/color_themes.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/compare_daa_results.Rd | 1 ggpicrust2-2.5.2/ggpicrust2/man/create_basic_go_mapping.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/create_dendrogram.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/create_empty_plot.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/create_gradient_colors.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/create_legend_theme.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/create_pathway_class_theme.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/format_pvalue_smart.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/generate_nested_colors.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/get_available_themes.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/get_color_theme.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/get_significance_colors.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/get_significance_stars.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/legend_annotation_utils.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/pathway_daa.Rd | 58 - ggpicrust2-2.5.2/ggpicrust2/man/pathway_errorbar.Rd | 54 ggpicrust2-2.5.2/ggpicrust2/man/pathway_errorbar_table.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/pathway_gsea.Rd | 5 ggpicrust2-2.5.2/ggpicrust2/man/pathway_heatmap.Rd | 157 ++ ggpicrust2-2.5.2/ggpicrust2/man/prepare_gene_sets.Rd | 5 ggpicrust2-2.5.2/ggpicrust2/man/preview_color_theme.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/resolve_annotation_overlaps.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/smart_color_selection.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/validate_abundance_data.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/validate_group_sizes.Rd |only ggpicrust2-2.5.2/ggpicrust2/man/visualize_gsea.Rd | 35 ggpicrust2-2.5.2/ggpicrust2/tests/testthat/TEST_SUITE_DOCUMENTATION.md |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-compare_gsea_daa-comprehensive.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-compare_gsea_daa_advanced.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-cross_pathway_consistency.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-error_handling_edge_cases.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-go_pathway_support.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_core_functions.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_mathematical_correctness.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_pathway_annotation-comprehensive-fixed.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_pathway_annotation-comprehensive.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_utilities_final.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-gsea_utility_functions_working.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-heatmap_plot_detailed.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-issue-166.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-metacyc_annotation_system.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-metacyc_error_handling_edge_cases.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-metacyc_gsea_implementation.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-metacyc_reference_data_loading.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-network_plot_detailed.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-pathway_errorbar-comprehensive.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-pathway_errorbar.R | 55 ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-pathway_heatmap.R | 163 ++ ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-picrust-compatibility.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-visualize_gsea_edge_cases.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-visualize_gsea_helper_functions.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test-visualize_gsea_pathway_labels.R |only ggpicrust2-2.5.2/ggpicrust2/tests/testthat/test_examples.R |only 89 files changed, 2626 insertions(+), 353 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.12.2 dated 2025-06-05 and 0.20.0 dated 2025-08-25
future.batchtools-0.12.2/future.batchtools/R/BatchtoolsCustomFuture-class.R |only future.batchtools-0.12.2/future.batchtools/R/BatchtoolsFuture-class.R |only future.batchtools-0.12.2/future.batchtools/R/BatchtoolsMultiprocessFuture-class.R |only future.batchtools-0.12.2/future.batchtools/R/BatchtoolsSSHFuture-class.R |only future.batchtools-0.12.2/future.batchtools/R/BatchtoolsUniprocessFuture-class.R |only future.batchtools-0.12.2/future.batchtools/R/batchtools_template.R |only future.batchtools-0.12.2/future.batchtools/R/with_stealth_rng.R |only future.batchtools-0.12.2/future.batchtools/man/BatchtoolsFuture.Rd |only future.batchtools-0.12.2/future.batchtools/man/batchtools_custom.Rd |only future.batchtools-0.12.2/future.batchtools/man/batchtools_template.Rd |only future.batchtools-0.12.2/future.batchtools/man/future.batchtools.options.Rd |only future.batchtools-0.12.2/future.batchtools/man/nbrOfWorkers.batchtools.Rd |only future.batchtools-0.12.2/future.batchtools/tests/BatchtoolsFuture,gc.R |only future.batchtools-0.12.2/future.batchtools/tests/BatchtoolsFuture.R |only future.batchtools-0.12.2/future.batchtools/tests/BatchtoolsFutureError.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_custom.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_hpc.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_interactive.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_local.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_multicore.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_ssh.R |only future.batchtools-0.12.2/future.batchtools/tests/batchtools_template.R |only future.batchtools-0.12.2/future.batchtools/tests/demo.R |only future.batchtools-0.12.2/future.batchtools/tests/dotdotdot.R |only future.batchtools-0.12.2/future.batchtools/tests/future,labels.R |only future.batchtools-0.12.2/future.batchtools/tests/future,lazy.R |only future.batchtools-0.12.2/future.batchtools/tests/globals,formulas.R |only future.batchtools-0.12.2/future.batchtools/tests/globals,manual.R |only future.batchtools-0.12.2/future.batchtools/tests/globals,subassignment.R |only future.batchtools-0.12.2/future.batchtools/tests/globals,tricky.R |only future.batchtools-0.12.2/future.batchtools/tests/incl |only future.batchtools-0.12.2/future.batchtools/tests/nbrOfWorkers.R |only future.batchtools-0.12.2/future.batchtools/tests/plan.R |only future.batchtools-0.12.2/future.batchtools/tests/resources_OP.R |only future.batchtools-0.12.2/future.batchtools/tests/rng.R |only future.batchtools-0.12.2/future.batchtools/tests/stdout.R |only future.batchtools-0.12.2/future.batchtools/tests/utils.R |only future.batchtools-0.12.2/future.batchtools/tests/zzz,future_lapply.R |only future.batchtools-0.12.2/future.batchtools/tests/zzz.onUnload.R |only future.batchtools-0.20.0/future.batchtools/DESCRIPTION | 12 future.batchtools-0.20.0/future.batchtools/MD5 | 207 +++++--- future.batchtools-0.20.0/future.batchtools/NAMESPACE | 64 +- future.batchtools-0.20.0/future.batchtools/NEWS.md | 170 +++++- future.batchtools-0.20.0/future.batchtools/R/001.import_future_functions.R | 7 future.batchtools-0.20.0/future.batchtools/R/BatchtoolsFutureBackend-class.R |only future.batchtools-0.20.0/future.batchtools/R/BatchtoolsTemplateFutureBackend-class.R |only future.batchtools-0.20.0/future.batchtools/R/batchtools_bash.R | 103 +++- future.batchtools-0.20.0/future.batchtools/R/batchtools_custom.R | 78 +-- future.batchtools-0.20.0/future.batchtools/R/batchtools_interactive.R | 71 ++ future.batchtools-0.20.0/future.batchtools/R/batchtools_local.R | 76 ++- future.batchtools-0.20.0/future.batchtools/R/batchtools_lsf.R |only future.batchtools-0.20.0/future.batchtools/R/batchtools_multicore.R | 109 ++-- future.batchtools-0.20.0/future.batchtools/R/batchtools_openlava.R |only future.batchtools-0.20.0/future.batchtools/R/batchtools_sge.R |only future.batchtools-0.20.0/future.batchtools/R/batchtools_slurm.R |only future.batchtools-0.20.0/future.batchtools/R/batchtools_ssh.R | 94 ++- future.batchtools-0.20.0/future.batchtools/R/batchtools_torque.R |only future.batchtools-0.20.0/future.batchtools/R/future.batchtools-package.R | 9 future.batchtools-0.20.0/future.batchtools/R/nbrOfWorkers.R | 54 +- future.batchtools-0.20.0/future.batchtools/R/options.R | 39 + future.batchtools-0.20.0/future.batchtools/R/temp_registry.R | 21 future.batchtools-0.20.0/future.batchtools/R/testme.R |only future.batchtools-0.20.0/future.batchtools/R/utils.R | 21 future.batchtools-0.20.0/future.batchtools/R/waitForWorker.R | 24 future.batchtools-0.20.0/future.batchtools/build/vignette.rds |binary future.batchtools-0.20.0/future.batchtools/demo/mandelbrot.R | 4 future.batchtools-0.20.0/future.batchtools/inst/WORDLIST | 90 ++- future.batchtools-0.20.0/future.batchtools/inst/doc/future.batchtools.html | 222 ++------ future.batchtools-0.20.0/future.batchtools/inst/doc/future.batchtools.md.rsp | 249 ++-------- future.batchtools-0.20.0/future.batchtools/inst/templates-for-R_CMD_check/batchtools.sge.tmpl | 172 +++++- future.batchtools-0.20.0/future.batchtools/inst/templates-for-R_CMD_check/batchtools.slurm.tmpl |only future.batchtools-0.20.0/future.batchtools/inst/templates-for-R_CMD_check/batchtools.torque.tmpl | 162 ++++-- future.batchtools-0.20.0/future.batchtools/inst/templates-for-R_CMD_check/setup.R | 7 future.batchtools-0.20.0/future.batchtools/inst/templates/bash.tmpl | 72 ++ future.batchtools-0.20.0/future.batchtools/inst/templates/lsf.tmpl |only future.batchtools-0.20.0/future.batchtools/inst/templates/openlava.tmpl |only future.batchtools-0.20.0/future.batchtools/inst/templates/sge.tmpl | 129 +++-- future.batchtools-0.20.0/future.batchtools/inst/templates/slurm.tmpl | 100 +++- future.batchtools-0.20.0/future.batchtools/inst/templates/torque.tmpl | 113 +++- future.batchtools-0.20.0/future.batchtools/inst/testme |only future.batchtools-0.20.0/future.batchtools/man/BatchtoolsFutureBackend.Rd |only future.batchtools-0.20.0/future.batchtools/man/BatchtoolsMulticoreFutureBackend.Rd |only future.batchtools-0.20.0/future.batchtools/man/BatchtoolsTemplateFutureBackend.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_bash.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_interactive.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_local.Rd | 85 +-- future.batchtools-0.20.0/future.batchtools/man/batchtools_lsf.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_multicore.Rd | 89 +-- future.batchtools-0.20.0/future.batchtools/man/batchtools_openlava.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_sge.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_slurm.Rd |only future.batchtools-0.20.0/future.batchtools/man/batchtools_ssh.Rd | 80 +-- future.batchtools-0.20.0/future.batchtools/man/batchtools_torque.Rd |only future.batchtools-0.20.0/future.batchtools/man/delete.BatchtoolsFuture.Rd | 9 future.batchtools-0.20.0/future.batchtools/man/future.batchtools.Rd | 23 future.batchtools-0.20.0/future.batchtools/man/loggedOutput.Rd | 2 future.batchtools-0.20.0/future.batchtools/man/nbrOfWorkers.BatchtoolsFutureBackend.Rd |only future.batchtools-0.20.0/future.batchtools/man/print.BatchtoolsFuture.Rd | 2 future.batchtools-0.20.0/future.batchtools/man/zzz-future.batchtools.options.Rd |only future.batchtools-0.20.0/future.batchtools/tests/test-BatchtoolsFuture,gc.R |only future.batchtools-0.20.0/future.batchtools/tests/test-BatchtoolsFuture.R |only future.batchtools-0.20.0/future.batchtools/tests/test-BatchtoolsFutureError.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_bash.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_custom.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_hpc.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_interactive.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_local.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_multicore.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_ssh.R |only future.batchtools-0.20.0/future.batchtools/tests/test-batchtools_template.R |only future.batchtools-0.20.0/future.batchtools/tests/test-demo.R |only future.batchtools-0.20.0/future.batchtools/tests/test-dotdotdot.R |only future.batchtools-0.20.0/future.batchtools/tests/test-future,labels.R |only future.batchtools-0.20.0/future.batchtools/tests/test-future,lazy.R |only future.batchtools-0.20.0/future.batchtools/tests/test-globals,formulas.R |only future.batchtools-0.20.0/future.batchtools/tests/test-globals,manual.R |only future.batchtools-0.20.0/future.batchtools/tests/test-globals,subassignment.R |only future.batchtools-0.20.0/future.batchtools/tests/test-globals,tricky.R |only future.batchtools-0.20.0/future.batchtools/tests/test-nbrOfWorkers.R |only future.batchtools-0.20.0/future.batchtools/tests/test-plan.R |only future.batchtools-0.20.0/future.batchtools/tests/test-resources_OP.R |only future.batchtools-0.20.0/future.batchtools/tests/test-rng.R |only future.batchtools-0.20.0/future.batchtools/tests/test-stdout.R |only future.batchtools-0.20.0/future.batchtools/tests/test-utils.R |only future.batchtools-0.20.0/future.batchtools/tests/test-zzz,future_lapply.R |only future.batchtools-0.20.0/future.batchtools/tests/test-zzz.onUnload.R |only future.batchtools-0.20.0/future.batchtools/vignettes/future.batchtools.md.rsp | 249 ++-------- 127 files changed, 1836 insertions(+), 1182 deletions(-)
More information about future.batchtools at CRAN
Permanent link
Title: Non-Smooth Regularization for Structural Equation Models
Description: Provides regularized structural equation modeling
(regularized SEM) with non-smooth penalty functions (e.g., lasso) building
on 'lavaan'. The package is heavily inspired by the
['regsem'](<https://github.com/Rjacobucci/regsem>) and
['lslx'](<https://github.com/psyphh/lslx>) packages.
Author: Jannik H. Orzek [aut, cre, cph]
Maintainer: Jannik H. Orzek <jannik.orzek@mailbox.org>
Diff between lessSEM versions 1.5.5 dated 2024-01-22 and 1.5.6 dated 2025-08-25
DESCRIPTION | 22 +++++---- MD5 | 38 ++++++++--------- R/class-regularizedSEM.R | 36 ++++++++++------ R/regularizeSEMInternal.R | 7 ++- R/zzz.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/Definition-Variables-and-Multi-Group-SEM.html | 4 - inst/doc/Estimator-Settings.html | 4 - inst/doc/General-Purpose-Optimization.html | 4 - inst/doc/Mixed-Penalties.html | 4 - inst/doc/Parameter-transformations.html | 8 +-- inst/doc/SCAD-and-MCP.html | 2 inst/doc/The-Structural-Equation-Model.html | 4 - inst/doc/lessSEM.html | 8 +-- inst/doc/log-likelihood-gradients.html | 2 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/lessSEM.Rd | 5 +- man/plot-regularizedSEM-missing-method.Rd | 3 - 20 files changed, 87 insertions(+), 68 deletions(-)
Title: Generalized UniFrac Distances, Distance-Based Multivariate
Methods and Feature-Based Univariate Methods for Microbiome
Data Analysis
Description: A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.
Author: Jun Chen [aut, cre],
Xianyang Zhang [aut],
Lu Yang [aut],
Lujun Zhang [aut]
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between GUniFrac versions 1.8 dated 2023-09-13 and 1.9 dated 2025-08-25
DESCRIPTION | 28 +++++++++--- MD5 | 46 ++++++++++---------- R/GUniFrac.R | 6 -- R/SimMSeq.R | 40 ++++++++++++++---- R/ZicoSeq.R | 93 +++++++++++++++++++++++------------------- build/vignette.rds |binary data/stool.otu.tab.rda |binary data/throat.meta.rda |binary data/throat.otu.tab.rda |binary data/throat.tree.rda |binary data/vaginal.otu.tab.rda |binary inst/doc/ZicoSeq.R | 15 +++--- inst/doc/ZicoSeq.Rmd | 17 +++---- inst/doc/ZicoSeq.html | 76 +++++++++++++++++----------------- man/Rarefy.Rd | 104 +++++++++++++++++++++++------------------------ man/SimulateMSeq.Rd | 5 +- man/SimulateMSeqC.Rd | 9 +++- man/ZicoSeq.plot.Rd | 2 man/adonis3.Rd | 8 +-- man/dICC.Rd | 2 man/dICC.SE.asympt.Rd | 2 man/dICC.SE.bt.Rd | 2 man/dmanova.Rd | 6 +- vignettes/ZicoSeq.Rmd | 17 +++---- 24 files changed, 264 insertions(+), 214 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.9 dated 2025-06-25 and 3.7.0 dated 2025-08-25
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gsDesign-3.7.0/gsDesign/inst/doc/VaccineEfficacy.html | 5313 ++--- gsDesign-3.7.0/gsDesign/inst/doc/binomialSPRTExample.R | 130 gsDesign-3.7.0/gsDesign/inst/doc/binomialSPRTExample.Rmd | 322 gsDesign-3.7.0/gsDesign/inst/doc/binomialSPRTExample.html | 4452 +++- gsDesign-3.7.0/gsDesign/inst/doc/binomialTwoSample.R | 454 gsDesign-3.7.0/gsDesign/inst/doc/binomialTwoSample.Rmd | 782 gsDesign-3.7.0/gsDesign/inst/doc/binomialTwoSample.html | 8997 +++++----- gsDesign-3.7.0/gsDesign/inst/doc/gsDesignPackageOverview.R | 38 gsDesign-3.7.0/gsDesign/inst/doc/gsDesignPackageOverview.Rmd | 142 gsDesign-3.7.0/gsDesign/inst/doc/gsDesignPackageOverview.html | 1417 + gsDesign-3.7.0/gsDesign/inst/doc/gsSurvBasicExamples.R | 508 gsDesign-3.7.0/gsDesign/inst/doc/gsSurvBasicExamples.Rmd | 846 gsDesign-3.7.0/gsDesign/inst/doc/gsSurvBasicExamples.html | 5373 +++-- gsDesign-3.7.0/gsDesign/inst/doc/hGraph.Rmd | 22 gsDesign-3.7.0/gsDesign/inst/doc/hGraph.html | 522 gsDesign-3.7.0/gsDesign/inst/doc/nNormal.R | 162 gsDesign-3.7.0/gsDesign/inst/doc/nNormal.Rmd | 420 gsDesign-3.7.0/gsDesign/inst/doc/nNormal.html | 1747 + gsDesign-3.7.0/gsDesign/inst/doc/toInteger.R | 214 gsDesign-3.7.0/gsDesign/inst/doc/toInteger.Rmd | 402 gsDesign-3.7.0/gsDesign/inst/doc/toInteger.html | 1151 - 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Title: Multivariate Normal Mean Monitoring Through Critical-to-X
Control Chart
Description: A comprehensive set of functions designed for multivariate mean monitoring using the Critical-to-X Control Chart. These functions enable the determination of optimal control limits based on a specified in-control Average Run Length (ARL), the calculation of out-of-control ARL for a given control limit, and post-signal analysis to identify the specific variable responsible for a detected shift in the mean. This suite of tools provides robust support for precise and effective process monitoring and analysis.
Author: Burcu Aytacoglu [aut] ,
Diana Barraza-Barraza [aut, cre] ,
Victor G. Tercero-Gomez [aut] ,
A. Eduardo Cordero-Franco [aut]
Maintainer: Diana Barraza-Barraza <diana.barraza@ujed.mx>
Diff between CTxCC versions 0.2.0 dated 2024-11-08 and 0.3.0 dated 2025-08-25
CTxCC-0.2.0/CTxCC/man/C2.allPerms.Rd |only CTxCC-0.3.0/CTxCC/DESCRIPTION | 27 +++-- CTxCC-0.3.0/CTxCC/MD5 | 10 +- CTxCC-0.3.0/CTxCC/NAMESPACE | 5 - CTxCC-0.3.0/CTxCC/R/Functions.R | 137 +++++++++++++++++++++++++++++- CTxCC-0.3.0/CTxCC/man/CTXoptim.Rd |only CTxCC-0.3.0/CTxCC/man/c2decomp.Rd |only CTxCC-0.3.0/CTxCC/man/contributionplot.Rd |only 8 files changed, 159 insertions(+), 20 deletions(-)
Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate
sensitivity (climate windows) for a given biological response.
Please see van de Pol et al. (2016) <doi:10.1111/2041-210X.12590>
and Bailey and van de Pol (2016) <doi:10.1371/journal.pone.0167980> for details.
Author: Liam D. Bailey [aut, cre],
Martijn van de Pol [aut]
Maintainer: Liam D. Bailey <liam.bailey@liamdbailey.com>
Diff between climwin versions 1.2.31 dated 2025-06-08 and 1.2.32 dated 2025-08-25
DESCRIPTION | 8 +-- MD5 | 43 ++++++++++--------- NEWS.md | 17 +++++++ R/otherfunctions.R | 14 +++--- R/plotall.R | 11 +++-- R/plotbest.R | 2 R/plotbetas.R | 48 +++++++++++----------- R/plotcor.R | 6 +- R/plothist.R | 84 +++++++++++++++++++-------------------- inst/doc/advanced_climwin.html | 4 - inst/doc/climwin.html | 8 +-- man/plotall.Rd | 6 ++ man/plothist.Rd | 5 +- tests/testthat/Rplots.pdf |only tests/testthat/testplotall.R | 27 +++++++++--- tests/testthat/testplotbest.R | 4 - tests/testthat/testplotbetas.R | 4 - tests/testthat/testplotcor.R | 2 tests/testthat/testplotdelta.R | 4 - tests/testthat/testplothist.R | 6 +- tests/testthat/testplotweights.R | 4 - tests/testthat/testplotwin.R | 4 - tests/testthat/testslidingwin.R | 34 +++++++-------- 23 files changed, 197 insertions(+), 148 deletions(-)
Title: Compiler for R
Description: Compile R functions annotated with type and shape
declarations for extremely fast performance and robust runtime
type checking. Supports both just-in-time (JIT) and ahead-of-time
(AOT) compilation. Compilation is performed by lowering R code to
Fortran.
Author: Tomasz Kalinowski [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between quickr versions 0.1.0 dated 2025-06-03 and 0.2.0 dated 2025-08-25
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Title: Streamlining Complex Survey Estimation and Reliability
Assessment in R
Description: Short and understandable commands that generate tabulated,
formatted, and rounded survey estimates. Mostly a wrapper for the
'survey' package (Lumley (2004) <doi:10.18637/jss.v009.i08>
<https://CRAN.R-project.org/package=survey>) that identifies
low-precision estimates using the National Center for Health
Statistics (NCHS) presentation standards (Parker et al. (2017)
<https://www.cdc.gov/nchs/data/series/sr_02/sr02_175.pdf>,
Parker et al. (2023) <doi:10.15620/cdc:124368>).
Author: Alex Strashny [aut, cre]
Maintainer: Alex Strashny <alex.strashny@gmail.com>
Diff between surveytable versions 0.9.8 dated 2025-05-22 and 0.9.9 dated 2025-08-25
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Title: Single Cell Oriented Reconstruction of PANDA Individual
Optimized Networks
Description: Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Author: Daniel Osorio [aut, cre] ,
Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between SCORPION versions 1.0.2 dated 2024-05-29 and 1.1.0 dated 2025-08-25
DESCRIPTION | 18 - MD5 | 40 +-- NAMESPACE | 46 ++-- R/buildKNN.R | 206 +++++++++--------- R/buildKNND.R | 86 +++---- R/buildNN2.R | 42 +-- R/colSds.R | 12 - R/dFunction.R | 10 R/data-scorpionTest.R | 76 +++--- R/makeSuperCells.R | 550 ++++++++++++++++++++++++------------------------- R/normalizeNetwork.R | 92 ++++---- R/pcNet.R | 188 ++++++++-------- R/prepResult.R | 68 +++--- R/rowSds.R | 12 - R/runPANDA.R | 454 ++++++++++++++++++++-------------------- R/scorpion.R | 281 ++++++++++++------------- R/spreadNet.R | 28 +- R/tanimotoSimilarity.R | 44 +-- R/updateDiagonal.R | 18 - data/datalist | 2 man/scorpion.Rd | 275 ++++++++++++------------ 21 files changed, 1284 insertions(+), 1264 deletions(-)
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] ),
Chao Cheng [ctb]
Maintainer: Doug Hemken <d_hemken@yahoo.com>
This is a re-admission after prior archival of version 0.8.2 dated 2023-03-10
Diff between SASmarkdown versions 0.8.2 dated 2023-03-10 and 0.8.7 dated 2025-08-25
DESCRIPTION | 16 +- MD5 | 22 ++-- R/find_sas.r | 12 +- R/sas_collectcode.r | 37 ++++-- R/sas_output.r | 16 ++ R/saslog.r | 41 +++---- R/sasloghook.r | 13 +- R/saspdf.r | 2 inst/NEWS.Rd | 26 ++++ man/SASmarkdown-package.rd | 82 +++++++-------- man/sas_enginesetup.rd | 246 ++++++++++++++++++++++----------------------- man/saslog_hookset.rd | 178 ++++++++++++++++---------------- 12 files changed, 372 insertions(+), 319 deletions(-)
Title: Bayesian Probit Choice Modeling
Description: Bayes estimation of probit choice models in cross-sectional and panel
settings. The package can analyze binary, multivariate, ordered, and ranked
choices, as well as heterogeneity of choice behavior among deciders. The
main functionality includes model fitting via Gibbs sampling, tools for
convergence diagnostic, choice data simulation, in-sample and out-of-sample
choice prediction, and model selection using information criteria and Bayes
factors. The latent class model extension facilitates preference-based
decider classification, where the number of latent classes can be inferred
via the Dirichlet process or a weight-based updating heuristic. This allows
for flexible modeling of choice behavior without the need to impose
structural constraints. For a reference on the method, see Oelschlaeger and
Bauer (2021) <https://trid.trb.org/view/1759753>.
Author: Lennart Oelschlaeger [aut, cre] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.1.4 dated 2024-02-26 and 1.2.0 dated 2025-08-25
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RprobitB-1.2.0/RprobitB/man/RprobitB_parameter.Rd | 204 RprobitB-1.2.0/RprobitB/man/WAIC.Rd | 92 RprobitB-1.2.0/RprobitB/man/as_cov_names.Rd | 69 RprobitB-1.2.0/RprobitB/man/check_form.Rd | 106 RprobitB-1.2.0/RprobitB/man/check_prior.Rd | 195 RprobitB-1.2.0/RprobitB/man/choice_probabilities.Rd | 76 RprobitB-1.2.0/RprobitB/man/classification.Rd | 82 RprobitB-1.2.0/RprobitB/man/coef.RprobitB_fit.Rd | 51 RprobitB-1.2.0/RprobitB/man/compute_choice_probabilities.Rd | 61 RprobitB-1.2.0/RprobitB/man/compute_p_si.Rd | 55 RprobitB-1.2.0/RprobitB/man/cov_mix.Rd | 42 RprobitB-1.2.0/RprobitB/man/create_lagged_cov.Rd | 92 RprobitB-1.2.0/RprobitB/man/d_to_gamma.Rd | 52 RprobitB-1.2.0/RprobitB/man/draw_from_prior.Rd | 48 RprobitB-1.2.0/RprobitB/man/figures/README-coef-1.png |binary RprobitB-1.2.0/RprobitB/man/figures/README-fit-1.png |only RprobitB-1.2.0/RprobitB/man/figures/logo.png |binary RprobitB-1.2.0/RprobitB/man/filter_gibbs_samples.Rd | 90 RprobitB-1.2.0/RprobitB/man/fit_model.Rd | 200 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| 38 RprobitB-1.2.0/RprobitB/man/pred_acc.Rd | 44 RprobitB-1.2.0/RprobitB/man/predict.RprobitB_fit.Rd | 116 RprobitB-1.2.0/RprobitB/man/preference_flip.Rd | 40 RprobitB-1.2.0/RprobitB/man/prepare_data.Rd | 313 RprobitB-1.2.0/RprobitB/man/sample_allocation.Rd |only RprobitB-1.2.0/RprobitB/man/simulate_choices.Rd | 297 RprobitB-1.2.0/RprobitB/man/sufficient_statistics.Rd | 104 RprobitB-1.2.0/RprobitB/man/train_choice.Rd | 82 RprobitB-1.2.0/RprobitB/man/train_test.Rd | 102 RprobitB-1.2.0/RprobitB/man/transform.Rd | 97 RprobitB-1.2.0/RprobitB/man/transform_gibbs_samples.Rd | 75 RprobitB-1.2.0/RprobitB/man/transform_parameter.Rd | 47 RprobitB-1.2.0/RprobitB/man/update.RprobitB_fit.Rd | 279 RprobitB-1.2.0/RprobitB/man/update_Omega.Rd | 111 RprobitB-1.2.0/RprobitB/man/update_Omega_c.Rd |only RprobitB-1.2.0/RprobitB/man/update_Sigma.Rd | 113 RprobitB-1.2.0/RprobitB/man/update_U.Rd | 84 RprobitB-1.2.0/RprobitB/man/update_U_ranked.Rd | 66 RprobitB-1.2.0/RprobitB/man/update_b.Rd | 112 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RprobitB-1.2.0/RprobitB/tests/testthat/_snaps/model_selection.md | 116 RprobitB-1.2.0/RprobitB/tests/testthat/test-RprobitB_parameter.R | 55 RprobitB-1.2.0/RprobitB/tests/testthat/test-cpp.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-data_management.R | 456 - RprobitB-1.2.0/RprobitB/tests/testthat/test-draw_from_prior.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-mode_approx.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-model_evaluation.R | 162 RprobitB-1.2.0/RprobitB/tests/testthat/test-model_fitting.R | 355 RprobitB-1.2.0/RprobitB/tests/testthat/test-model_selection.R | 54 RprobitB-1.2.0/RprobitB/tests/testthat/test-plotting.R |only RprobitB-1.2.0/RprobitB/vignettes/RprobitB.Rmd | 58 RprobitB-1.2.0/RprobitB/vignettes/img/data-plot-by-choice-1.png |binary RprobitB-1.2.0/RprobitB/vignettes/img/dirichlet-example-plot-1.png |binary RprobitB-1.2.0/RprobitB/vignettes/img/plot-acf-model-train-1.png |binary RprobitB-1.2.0/RprobitB/vignettes/img/plot-coef-model-train-1.png 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Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini [aut, cre]
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between easyPubMed versions 2.13 dated 2019-03-29 and 3.1.6 dated 2025-08-25
easyPubMed-2.13/easyPubMed/R/easyPubMed_scr.R |only easyPubMed-2.13/easyPubMed/data/EPMsamples.rda |only easyPubMed-2.13/easyPubMed/data/PubMed_stopwords.rda |only easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.R |only easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.Rmd |only easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.html |only easyPubMed-2.13/easyPubMed/man/EPMsamples.Rd |only easyPubMed-2.13/easyPubMed/man/PubMed_stopwords.Rd |only easyPubMed-2.13/easyPubMed/man/article_to_df.Rd |only easyPubMed-2.13/easyPubMed/man/articles_to_list.Rd |only easyPubMed-2.13/easyPubMed/man/batch_pubmed_download.Rd |only easyPubMed-2.13/easyPubMed/man/fetch_all_pubmed_ids.Rd |only easyPubMed-2.13/easyPubMed/man/get_pubmed_ids_by_fulltitle.Rd |only easyPubMed-2.13/easyPubMed/man/trim_address.Rd |only easyPubMed-2.13/easyPubMed/vignettes/getting_started_with_easyPubMed.Rmd |only easyPubMed-3.1.6/easyPubMed/DESCRIPTION | 18 + easyPubMed-3.1.6/easyPubMed/MD5 | 96 +++++++--- easyPubMed-3.1.6/easyPubMed/NAMESPACE | 40 +++- easyPubMed-3.1.6/easyPubMed/R/emp_misc.R |only easyPubMed-3.1.6/easyPubMed/R/epm_all_fx.R |only easyPubMed-3.1.6/easyPubMed/R/epm_classes_and_methods.R |only easyPubMed-3.1.6/easyPubMed/R/epm_surrogate_fx.R |only easyPubMed-3.1.6/easyPubMed/build/vignette.rds |binary easyPubMed-3.1.6/easyPubMed/data/epm_samples.rda |only easyPubMed-3.1.6/easyPubMed/data/epm_stopwords.rda |only easyPubMed-3.1.6/easyPubMed/inst/doc/easyPubMed_demo.R |only easyPubMed-3.1.6/easyPubMed/inst/doc/easyPubMed_demo.Rmd |only easyPubMed-3.1.6/easyPubMed/inst/doc/easyPubMed_demo.html |only easyPubMed-3.1.6/easyPubMed/man/EPM_auth_parse.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_check_guide.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_custom_grep.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_date_parse.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_decode_xml_meta.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_detect_pmid.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_efetch_basic_q.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_encode_meta_to_xml.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_esearch_basic_q.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_esearch_efetch_seq.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_esearch_parse.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_init_unique_key.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_job_split.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_mesh_parse.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_prep_outfile.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_read_xml.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_reference_parse.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_retrieve_data.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_submit_q.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_validate_fetch_params.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_validate_parse_params.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_write_to_file.Rd |only easyPubMed-3.1.6/easyPubMed/man/EPM_zerofill.Rd |only easyPubMed-3.1.6/easyPubMed/man/custom_grep.Rd | 14 - 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Title: Prediction and Interpretation in Decision Trees for
Classification and Regression
Description: Optimization of conditional inference trees from the package 'party'
for classification and regression.
For optimization, the model space is searched for the best tree on the full sample by
means of repeated subsampling. Restrictions are allowed so that only trees are accepted
which do not include pre-specified uninterpretable split results (cf. Weihs & Buschfeld, 2021a).
The function PrInDT() represents the basic resampling loop for 2-class classification (cf. Weihs
& Buschfeld, 2021a). The function RePrInDT() (repeated PrInDT()) allows for repeated
applications of PrInDT() for different percentages of the observations of the large and the
small classes (cf. Weihs & Buschfeld, 2021c). The function NesPrInDT() (nested PrInDT())
allows for an extra layer of subsampling for a specific factor variable (cf. Weihs & Buschfeld,
2021b). The functions PrInDTMulev() and PrInDTMulab() deal with multilevel and multilabel
classification. In addition to these PrInDT() variants for c [...truncated...]
Author: Claus Weihs [aut, cre],
Sarah Buschfeld [aut],
Niklas Nitsch [ctb]
Maintainer: Claus Weihs <claus.weihs@tu-dortmund.de>
Diff between PrInDT versions 2.0.0 dated 2025-07-21 and 2.0.1 dated 2025-08-25
DESCRIPTION | 8 +- MD5 | 42 +++++++-------- R/OptPrInDT.R | 38 +++++++++----- R/PrInDT.R | 73 +++++++++++++++------------ R/PrInDTAll.R | 13 +--- R/PrInDTCstruc.R | 139 +++++++++++++++++++++++++++------------------------- R/PrInDTRstruc.R | 12 ++-- R/PrInDTreg.R | 3 - R/PrInDTregAll.R | 1 R/PrInDTstruc1.R | 92 ++++++++++++++++++++++++++-------- R/PrInDTstruc2.R | 127 ++++++++++++++++++++++++++++++++--------------- R/RePrInDT.R | 13 ++-- R/SimRPrInDT.R | 68 ++++++++++++++++--------- man/OptPrInDT.Rd | 11 ++-- man/PrInDT.Rd | 6 +- man/PrInDTAll.Rd | 2 man/PrInDTCstruc.Rd | 21 ++++--- man/PrInDTRstruc.Rd | 12 ++-- man/PrInDTreg.Rd | 3 - man/PrInDTregAll.Rd | 1 man/RePrInDT.Rd | 3 - man/SimRPrInDT.Rd | 13 ++-- 22 files changed, 432 insertions(+), 269 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe, 1992),
a.k.a. log-multiplicative layer effect model (Xie, 1992)
<doi:10.2307/2096242>, and several association models:
Goodman (1979) <doi:10.2307/2286971>
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi (1990) <doi:10.2307/271086>
and by van der Heijden & Mooijaart (1995) <doi:10.1177/0049124195024001002>
Functions allow computing the intrinsic association coefficient
(see Bouchet-Valat (2022) <doi:10.1177/0049124119852389>)
and the Altham (1970) index <doi:10.1111/j.2517-6161.1970.tb00816.x>,
including via the Bayes shrinkage estimator pro [...truncated...]
Author: Milan Bouchet-Valat [aut, cre],
Heather Turner [ctb],
Michael Friendly [ctb],
Jim Lemon [cph],
Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between logmult versions 0.7.4 dated 2022-02-23 and 0.7.5 dated 2025-08-25
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 1 NEWS | 5 build/vignette.rds |binary inst/doc/logmult.html | 400 ++++++++++++++++++++++++++++++++++++++++++------- man/HMSkew-nonlin.Rd | 2 man/RCTrans-nonlin.Rd | 2 man/YRCSkew-nonlin.Rd | 2 man/anoas.Rd | 4 man/assoc.Rd | 4 man/hmskew.Rd | 6 man/hmskewL.Rd | 6 man/rc.Rd | 8 man/rcL.Rd | 10 - man/rcL.trans.Rd | 8 man/summary.unidiff.Rd | 2 man/svyassocmod.Rd | 2 man/svygnm.Rd | 7 man/unidiff.Rd | 18 +- man/yrcskew.Rd | 6 21 files changed, 420 insertions(+), 121 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.0 dated 2025-07-16 and 0.2.1 dated 2025-08-25
getRad-0.2.0/getRad/R/read_vpts_from_url.R |only getRad-0.2.0/getRad/R/utils-rmi.R |only getRad-0.2.1/getRad/DESCRIPTION | 12 +-- getRad-0.2.1/getRad/MD5 | 50 +++++++------ getRad-0.2.1/getRad/NEWS.md | 8 ++ getRad-0.2.1/getRad/R/get_pvol.R | 5 + getRad-0.2.1/getRad/R/get_pvol_cz.R | 58 --------------- getRad-0.2.1/getRad/R/get_pvol_de.R | 61 ++++++++-------- getRad-0.2.1/getRad/R/get_pvol_dk.R | 33 ++++---- getRad-0.2.1/getRad/R/get_pvol_ee.R | 23 +++--- getRad-0.2.1/getRad/R/get_pvol_fi.R | 22 ++--- getRad-0.2.1/getRad/R/get_pvol_nl.R | 68 +++++++++--------- getRad-0.2.1/getRad/R/get_pvol_ro.R |only getRad-0.2.1/getRad/R/get_pvol_se.R |only getRad-0.2.1/getRad/R/get_pvol_us.R | 29 +++---- getRad-0.2.1/getRad/R/get_vpts.R | 18 ++-- getRad-0.2.1/getRad/R/utils.R | 61 ++++++++-------- getRad-0.2.1/getRad/R/utils_pvol.R |only getRad-0.2.1/getRad/R/utils_vpts_aloft.R |only getRad-0.2.1/getRad/R/utils_vpts_rmi.R |only getRad-0.2.1/getRad/R/zzz.R |only getRad-0.2.1/getRad/inst/doc/supported_sources.R | 2 getRad-0.2.1/getRad/inst/doc/supported_sources.Rmd | 4 - getRad-0.2.1/getRad/inst/doc/supported_sources.html | 59 +++++++-------- getRad-0.2.1/getRad/tests/testthat/test-get_pvol.R | 25 ++++++ getRad-0.2.1/getRad/tests/testthat/test-get_pvol_nl.R | 2 getRad-0.2.1/getRad/tests/testthat/test-get_pvol_ro.R |only getRad-0.2.1/getRad/tests/testthat/test-get_pvol_se.R |only getRad-0.2.1/getRad/tests/testthat/test-get_pvol_us.R | 46 ++++++------ getRad-0.2.1/getRad/tests/testthat/test-get_vpts.R | 46 ++++++++++-- getRad-0.2.1/getRad/vignettes/supported_sources.Rmd | 4 - 31 files changed, 340 insertions(+), 296 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between av versions 0.9.4 dated 2025-01-29 and 0.9.5 dated 2025-08-25
DESCRIPTION | 15 ++++++++------- LICENSE | 2 +- MD5 | 28 ++++++++++++++-------------- NEWS | 3 +++ R/capture.R | 2 +- R/encode.R | 2 +- configure | 2 +- man/capturing.Rd | 2 +- man/encoding.Rd | 2 +- src/Makevars.win | 2 +- src/avcompat.h | 6 ++++++ src/fft.c | 7 ++++++- src/video.c | 27 ++++++++++++++++++++------- tests/testthat/test-formats.R | 2 +- tests/testthat/test-video.R | 2 +- 15 files changed, 66 insertions(+), 38 deletions(-)
Title: Pharmacometric and Pharmacokinetic Toolkit
Description: Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given
times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero-
and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008)
<https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf>); parametric simulation from NONMEM-generated parameter estimates
and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).
Author: Justin Wilkins [aut, cre] ,
Bill Denney [aut] ,
Rik Schoemaker [aut],
Satyaprakash Nayak [ctb],
Leonid Gibiansky [ctb],
Andrew Hooker [ctb],
E. Niclas Jonsson [ctb],
Mats O. Karlsson [ctb],
John Johnson [ctb]
Maintainer: Justin Wilkins <justin.wilkins@occams.com>
Diff between pmxTools versions 1.3 dated 2023-02-21 and 1.5 dated 2025-08-25
pmxTools-1.3/pmxTools/tests/testthat/_snaps |only pmxTools-1.5/pmxTools/DESCRIPTION | 24 pmxTools-1.5/pmxTools/MD5 | 163 - pmxTools-1.5/pmxTools/NAMESPACE | 1 pmxTools-1.5/pmxTools/NEWS.md | 14 pmxTools-1.5/pmxTools/R/calc_1cmt.R | 4 pmxTools-1.5/pmxTools/R/calc_2cmt.R | 4 pmxTools-1.5/pmxTools/R/calc_3cmt.R | 4 pmxTools-1.5/pmxTools/R/dgr_table.R | 9 pmxTools-1.5/pmxTools/R/get_est_table.R | 2 pmxTools-1.5/pmxTools/R/get_omega.R | 20 pmxTools-1.5/pmxTools/R/get_probinfo.r | 2 pmxTools-1.5/pmxTools/R/get_shrinkage.R | 2 pmxTools-1.5/pmxTools/R/get_sigma.R | 21 pmxTools-1.5/pmxTools/R/get_theta.R | 15 pmxTools-1.5/pmxTools/R/plot_dist.R | 123 + pmxTools-1.5/pmxTools/R/plot_nmprogress.R | 2 pmxTools-1.5/pmxTools/R/plot_scm.R | 6 pmxTools-1.5/pmxTools/R/pmxTools-package.R |only pmxTools-1.5/pmxTools/R/read_nm.R | 2 pmxTools-1.5/pmxTools/R/read_nmcov.R | 2 pmxTools-1.5/pmxTools/R/read_nmext.R | 2 pmxTools-1.5/pmxTools/R/read_nmtables.R | 2 pmxTools-1.5/pmxTools/R/read_scm.R | 2 pmxTools-1.5/pmxTools/R/rnm.R | 2070 +++++++++++------------ pmxTools-1.5/pmxTools/R/sample_omega.R | 2 pmxTools-1.5/pmxTools/R/sample_sigma.R | 2 pmxTools-1.5/pmxTools/R/sample_uncert.R | 2 pmxTools-1.5/pmxTools/R/statistics.R | 12 pmxTools-1.5/pmxTools/README.md | 4 pmxTools-1.5/pmxTools/build/partial.rdb |binary pmxTools-1.5/pmxTools/build/vignette.rds |binary pmxTools-1.5/pmxTools/inst/doc/pk-curves.R | 2 pmxTools-1.5/pmxTools/inst/doc/pk-curves.Rmd | 4 pmxTools-1.5/pmxTools/inst/doc/pk-curves.html | 475 ++--- pmxTools-1.5/pmxTools/man/blq_trans.Rd | 128 - pmxTools-1.5/pmxTools/man/breaks_blq_general.Rd | 90 - pmxTools-1.5/pmxTools/man/calc_derived.Rd | 340 +-- pmxTools-1.5/pmxTools/man/calc_sd_1cmt.Rd | 154 - pmxTools-1.5/pmxTools/man/calc_sd_2cmt.Rd | 164 - pmxTools-1.5/pmxTools/man/calc_sd_3cmt.Rd | 166 - pmxTools-1.5/pmxTools/man/calc_ss_1cmt.Rd | 160 - pmxTools-1.5/pmxTools/man/calc_ss_2cmt.Rd | 166 - pmxTools-1.5/pmxTools/man/calc_ss_3cmt.Rd | 166 - pmxTools-1.5/pmxTools/man/count_na.Rd | 52 pmxTools-1.5/pmxTools/man/dgr_table.Rd | 101 - pmxTools-1.5/pmxTools/man/estimate_lloq.Rd | 62 pmxTools-1.5/pmxTools/man/fmt_signif.Rd | 56 pmxTools-1.5/pmxTools/man/ftrans_blq_linear.Rd | 82 pmxTools-1.5/pmxTools/man/gcv.Rd | 60 pmxTools-1.5/pmxTools/man/gcv_convert.Rd | 60 pmxTools-1.5/pmxTools/man/get_auc.Rd | 74 pmxTools-1.5/pmxTools/man/get_est_table.Rd | 88 pmxTools-1.5/pmxTools/man/get_omega.Rd | 101 - pmxTools-1.5/pmxTools/man/get_probinfo.Rd | 56 pmxTools-1.5/pmxTools/man/get_shrinkage.Rd | 90 - pmxTools-1.5/pmxTools/man/get_sigma.Rd | 101 - pmxTools-1.5/pmxTools/man/get_theta.Rd | 98 - pmxTools-1.5/pmxTools/man/gm.Rd | 52 pmxTools-1.5/pmxTools/man/itrans_blq_linear.Rd | 74 pmxTools-1.5/pmxTools/man/label_blq.Rd | 62 pmxTools-1.5/pmxTools/man/pcv.Rd | 52 pmxTools-1.5/pmxTools/man/pk_curve.Rd | 90 - pmxTools-1.5/pmxTools/man/plot_dist.Rd | 260 +- pmxTools-1.5/pmxTools/man/plot_nmprogress.Rd | 94 - pmxTools-1.5/pmxTools/man/plot_scm.Rd | 296 +-- pmxTools-1.5/pmxTools/man/pmxTools-package.Rd |only pmxTools-1.5/pmxTools/man/read_nm.Rd | 90 - pmxTools-1.5/pmxTools/man/read_nm_all.Rd | 78 pmxTools-1.5/pmxTools/man/read_nm_multi_table.Rd | 100 - pmxTools-1.5/pmxTools/man/read_nm_std_ext.Rd | 64 pmxTools-1.5/pmxTools/man/read_nmcov.Rd | 96 - pmxTools-1.5/pmxTools/man/read_nmext.Rd | 140 - pmxTools-1.5/pmxTools/man/read_nmtables.Rd | 148 - pmxTools-1.5/pmxTools/man/read_scm.Rd | 112 - pmxTools-1.5/pmxTools/man/rnm.Rd | 176 - pmxTools-1.5/pmxTools/man/sample_omega.Rd | 70 pmxTools-1.5/pmxTools/man/sample_sigma.Rd | 70 pmxTools-1.5/pmxTools/man/sample_uncert.Rd | 72 pmxTools-1.5/pmxTools/man/table_rtf.Rd | 94 - pmxTools-1.5/pmxTools/vignettes/pk-curves.Rmd | 4 81 files changed, 4011 insertions(+), 3897 deletions(-)
Title: Binarization and Trinarization of One-Dimensional Data
Description: Provides methods for the binarization and trinarization of one-dimensional data and some visualization functions.
Author: Stefan Mundus [aut],
Christoph Muessel [aut],
Florian Schmid [aut],
Ludwig Lausser [aut],
Tamara J. Blaette [aut],
Martin Hopfensitz [aut],
Paul Kaftan [ctb],
Hans A. Kestler [aut, cre]
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>
Diff between BiTrinA versions 1.3.1 dated 2023-10-02 and 1.3.2 dated 2025-08-25
DESCRIPTION | 45 +++++++++++++++++++++++++++++++++++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/Vignette.pdf |binary src/binarizeBASCB.c | 32 ++++++++++++++++---------------- 5 files changed, 59 insertions(+), 26 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.5.0 dated 2025-07-29 and 0.5.2 dated 2025-08-25
siera-0.5.0/siera/R/readARS_xl.R |only siera-0.5.0/siera/man/readARS_xl.Rd |only siera-0.5.2/siera/DESCRIPTION | 9 - siera-0.5.2/siera/MD5 | 24 +-- siera-0.5.2/siera/NAMESPACE | 1 siera-0.5.2/siera/NEWS.md | 37 ++-- siera-0.5.2/siera/R/readARS.R | 79 ++++++---- siera-0.5.2/siera/README.md | 2 siera-0.5.2/siera/inst/doc/Getting_started.html | 2 siera-0.5.2/siera/inst/extdata/Common_Safety_Displays_cards.xlsx |binary siera-0.5.2/siera/inst/extdata/cards_constructs.xlsx |binary siera-0.5.2/siera/inst/script/ARD_Out14-1-1.R | 2 siera-0.5.2/siera/man/readARS.Rd | 8 - siera-0.5.2/siera/tests |only 14 files changed, 100 insertions(+), 64 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.2.0 dated 2025-03-31 and 1.2.1 dated 2025-08-25
PlotFTIR-1.2.0/PlotFTIR/man/dot-gg.Rd |only PlotFTIR-1.2.1/PlotFTIR/DESCRIPTION | 9 + PlotFTIR-1.2.1/PlotFTIR/MD5 | 26 ++--- PlotFTIR-1.2.1/PlotFTIR/NAMESPACE | 2 PlotFTIR-1.2.1/PlotFTIR/NEWS.md | 4 PlotFTIR-1.2.1/PlotFTIR/R/io.R | 5 - PlotFTIR-1.2.1/PlotFTIR/R/manipulations.R | 50 +++++++--- PlotFTIR-1.2.1/PlotFTIR/R/plot_ftir.R | 4 PlotFTIR-1.2.1/PlotFTIR/R/utils.R | 2 PlotFTIR-1.2.1/PlotFTIR/R/zzz.R | 2 PlotFTIR-1.2.1/PlotFTIR/inst/doc/plotting_ftir_spectra.html | 16 ++- PlotFTIR-1.2.1/PlotFTIR/man/dot-ggplot.Rd |only PlotFTIR-1.2.1/PlotFTIR/tests/testthat/test-io.R | 10 +- PlotFTIR-1.2.1/PlotFTIR/tests/testthat/test-manipulations.R | 58 +++++++++--- PlotFTIR-1.2.1/PlotFTIR/tests/testthat/test-plot_ftir.R | 40 +++++--- 15 files changed, 150 insertions(+), 78 deletions(-)
Title: Photosynthetic Gas Exchange Analysis
Description: Read, process, fit, and analyze photosynthetic gas exchange
measurements. Documentation is provided by several vignettes; also see
Lochocki, Salesse-Smith, & McGrath (2025) <doi:10.1111/pce.15501>.
Author: Edward B. Lochocki [cre, aut] ,
Coralie E. Salesse-Smith [aut] ,
Justin M. McGrath [aut] ,
PhotoGEA authors [cph]
Maintainer: Edward B. Lochocki <eloch@illinois.edu>
Diff between PhotoGEA versions 1.3.3 dated 2025-06-12 and 1.4.0 dated 2025-08-25
DESCRIPTION | 8 MD5 | 128 ++++++------ NEWS.md | 46 ++++ R/basic_stats.R | 4 R/calculate_c3_assimilation.R | 4 R/calculate_c3_limitations_grassi.R | 4 R/calculate_c3_limitations_warren.R | 4 R/calculate_c4_assimilation.R | 4 R/calculate_gamma_star.R | 4 R/confidence_intervals_c3_aci.R | 2 R/confidence_intervals_c3_variable_j.R | 2 R/confidence_intervals_c4_aci.R | 2 R/error_function_c3_aci.R | 4 R/error_function_c3_variable_j.R | 2 R/error_function_c4_aci.R | 4 R/fit_c3_aci.R | 2 R/fit_c3_variable_j.R | 2 R/fit_c4_aci.R | 2 R/get_oxygen_from_preamble.R | 60 +---- R/identify_tdl_cycles.R | 8 R/initial_guess_c3_aci.R | 2 R/initial_guess_c3_variable_j.R | 2 R/read_licor_6800_Excel.R | 124 ++++++++++- R/read_licor_6800_plaintext.R | 139 +++++++++++-- R/unit_dictionary.R | 2 inst/doc/PhotoGEA.R | 147 -------------- inst/doc/PhotoGEA.Rmd | 187 ----------------- inst/doc/PhotoGEA.html | 189 +----------------- inst/extdata/Rhistory |only inst/extdata/ball_berry_1.csv | 62 ++--- inst/extdata/c3_aci_2.xlsx |binary inst/extdata/plaintext_licor_file | 3 inst/extdata/plaintext_licor_file_v2 | 3 man/calculate_c3_assimilation.Rd | 8 man/calculate_c3_limitations_grassi.Rd | 2 man/calculate_c3_limitations_warren.Rd | 2 man/calculate_c4_assimilation.Rd | 32 +-- man/calculate_gamma_star.Rd | 14 - man/calculate_gm_busch.Rd | 3 man/calculate_gm_ubierna.Rd | 3 man/calculate_leakiness_ubierna.Rd | 3 man/confidence_intervals_c3_aci.Rd | 2 man/confidence_intervals_c3_variable_j.Rd | 2 man/confidence_intervals_c4_aci.Rd | 5 man/error_function_c3_aci.Rd | 2 man/error_function_c3_variable_j.Rd | 2 man/error_function_c4_aci.Rd | 5 man/example_data_files.Rd | 10 man/fit_c3_aci.Rd | 2 man/fit_c3_variable_j.Rd | 2 man/fit_c4_aci.Rd | 4 man/get_oxygen_from_preamble.Rd | 47 +++- man/identify_tdl_cycles.Rd | 6 man/initial_guess_c3_aci.Rd | 2 man/initial_guess_c3_variable_j.Rd | 2 man/read_licor_6800_Excel.Rd | 34 ++- man/read_licor_6800_plaintext.Rd | 37 ++- tests/testthat/test-basic_stats.R | 16 + tests/testthat/test-calculate_c3_assimilation.R | 4 tests/testthat/test-calculate_c3_limitations_grassi.R | 4 tests/testthat/test-calculate_c4_assimilation.R | 4 tests/testthat/test-identify_c3_limiting_processes.R | 4 tests/testthat/test-identify_tdl_cycles.R |only tests/testthat/test-read_licor_6800_Excel.R | 11 + tests/testthat/test-read_licor_6800_plaintext.R | 13 + vignettes/PhotoGEA.Rmd | 187 ----------------- 66 files changed, 642 insertions(+), 988 deletions(-)
Title: Generalized Turnbull's Estimator
Description: Generalized Turnbull's estimator proposed by Dehghan and Duchesne
(2011).
Author: Mohammad Hossein Dehghan [aut],
Thierry Duchesne [aut, cre],
Sophie Baillargeon [aut]
Maintainer: Thierry Duchesne <thierry.duchesne@mat.ulaval.ca>
Diff between gte versions 1.2-3 dated 2022-04-16 and 1.2-4 dated 2025-08-25
DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/gte-package.R | 11 ++++------- R/gte.R | 14 +++++++------- man/gte-package.Rd | 4 ++-- man/gte.Rd | 14 +++++++------- man/simul.Rd | 3 +++ 8 files changed, 57 insertions(+), 37 deletions(-)
Title: Functions Based on Entropic Statistics
Description: Contains methods for data analysis in entropic perspective. These entropic perspective methods are nonparametric, and perform better on non-ordinal data. Currently, the package has a function HeatMap() for visualizing distributional characteristics among multiple populations (groups).
Author: Jialin Zhang [aut, cph, cre]
Maintainer: Jialin Zhang (JZ) <jzhang@math.msstate.edu>
Diff between EntropicStatistics versions 0.1.0 dated 2023-05-29 and 0.1.1 dated 2025-08-25
DESCRIPTION | 13 +-- MD5 | 6 - R/HeatMap.R | 78 +++++++++--------- man/HeatMap.Rd | 246 ++++++++++++++++++++++++++++----------------------------- 4 files changed, 172 insertions(+), 171 deletions(-)
More information about EntropicStatistics at CRAN
Permanent link
Title: Log Execution of Scripts
Description: Logging of scripts suitable for clinical trials using
'Quarto' to create nice human readable logs. 'whirl' enables
execution of scripts in batch, while simultaneously creating logs for
the execution of each script, and providing an overview summary log of
the entire batch execution.
Author: Aksel Thomsen [aut, cre],
Lovemore Gakava [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Michael Svingel [aut],
Skander Mulder [aut],
Oliver Lundsgaard [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between whirl versions 0.3.0 dated 2025-07-08 and 0.3.1 dated 2025-08-25
whirl-0.3.0/whirl/R/pb_script.R |only whirl-0.3.0/whirl/tests/testthat/test-pb_script.R |only whirl-0.3.1/whirl/DESCRIPTION | 10 whirl-0.3.1/whirl/MD5 | 81 ++--- whirl-0.3.1/whirl/NEWS.md | 11 whirl-0.3.1/whirl/R/biocompute.R | 1 whirl-0.3.1/whirl/R/enrich_input.R | 39 +- whirl-0.3.1/whirl/R/log.R | 117 ++++--- whirl-0.3.1/whirl/R/mdformats.R | 13 whirl-0.3.1/whirl/R/progress_bar.R |only whirl-0.3.1/whirl/R/read_glob.R | 47 ++ whirl-0.3.1/whirl/R/run.R | 25 - whirl-0.3.1/whirl/R/run_current_script.R | 13 whirl-0.3.1/whirl/R/utils.R | 17 + whirl-0.3.1/whirl/R/whirl-options.R | 24 + whirl-0.3.1/whirl/R/whirl_queue.R | 34 -- whirl-0.3.1/whirl/R/whirl_r_session.R | 157 ++++------ whirl-0.3.1/whirl/README.md | 16 - whirl-0.3.1/whirl/inst/WORDLIST | 10 whirl-0.3.1/whirl/inst/documents/dummy.qmd | 63 +++- whirl-0.3.1/whirl/inst/documents/files.qmd | 8 whirl-0.3.1/whirl/inst/documents/log.qmd | 96 ++++-- whirl-0.3.1/whirl/inst/documents/python.qmd | 21 + whirl-0.3.1/whirl/inst/documents/python_modules.py | 69 ++-- whirl-0.3.1/whirl/inst/documents/style.css |only whirl-0.3.1/whirl/man/run.Rd | 4 whirl-0.3.1/whirl/man/whirl-options-params.Rd | 7 whirl-0.3.1/whirl/man/whirl-options.Rd | 23 + whirl-0.3.1/whirl/man/whirl-package.Rd | 1 whirl-0.3.1/whirl/tests/testthat/scripts/error_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/packages.R |only whirl-0.3.1/whirl/tests/testthat/scripts/py_dependencies.py |only whirl-0.3.1/whirl/tests/testthat/scripts/py_dependencies_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/py_error_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/py_success_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/py_warning_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/render_error.R |only whirl-0.3.1/whirl/tests/testthat/scripts/success_log.html |only whirl-0.3.1/whirl/tests/testthat/scripts/warning_log.html |only whirl-0.3.1/whirl/tests/testthat/test-biocompute.R | 2 whirl-0.3.1/whirl/tests/testthat/test-errors.R |only whirl-0.3.1/whirl/tests/testthat/test-mdformats.R | 20 + whirl-0.3.1/whirl/tests/testthat/test-progress_bar.R |only whirl-0.3.1/whirl/tests/testthat/test-python.R |only whirl-0.3.1/whirl/tests/testthat/test-run.R | 20 - whirl-0.3.1/whirl/tests/testthat/test-strace.R | 139 +++++++- whirl-0.3.1/whirl/tests/testthat/test-util_queue_summary.R | 5 whirl-0.3.1/whirl/tests/testthat/test-utils.R | 16 - whirl-0.3.1/whirl/tests/testthat/test-whirl_queue.R | 3 whirl-0.3.1/whirl/tests/testthat/test-whirl_r_session.R | 11 50 files changed, 771 insertions(+), 352 deletions(-)
Title: Efficient Computation and Testing of the Bergsma-Dassios Sign
Covariance
Description: Computes the t* statistic corresponding to the tau* population
coefficient introduced by Bergsma and Dassios (2014) <DOI:10.3150/13-BEJ514>
and does so in O(n^2) time following the algorithm of Heller and
Heller (2016) <DOI:10.48550/arXiv.1605.08732> building off of the work of Weihs,
Drton, and Leung (2016) <DOI:10.1007/s00180-015-0639-x>. Also allows for
independence testing using the asymptotic distribution of t* as described by
Nandy, Weihs, and Drton (2016) <DOI:10.1214/16-EJS1166>.
Author: Luca Weihs [aut],
Emin Martinian [ctb] ,
Julian D. Karch [cre]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between TauStar versions 1.1.7 dated 2024-12-12 and 1.1.8 dated 2025-08-25
DESCRIPTION | 12 +++-- MD5 | 24 +++++------ NAMESPACE | 2 NEWS.md | 8 +++ R/Functions.R | 82 ++++++++++++++++++++++++-------------- R/TauStar.R | 2 README.md | 1 man/TauStar-package.Rd | 8 +++ man/binaryQuantileSearch.Rd | 4 - man/isDiscrete.Rd | 26 ++++++++---- man/tStar.Rd | 4 - man/tauStarTest.Rd | 2 tests/testthat/test_tauStarTest.R | 2 13 files changed, 115 insertions(+), 62 deletions(-)
Title: Easy Pie Charts
Description: You only need to type 'why pie charts are bad' on Google to find
thousands of articles full of (valid) reasons why other types of charts
should be preferred over this one.
Therefore, because of the little use due to the reasons already mentioned,
making pie charts (and related) in R is not straightforward, so other
functions are needed to simplify things.
In this R package there are useful functions to make 'tasty' pie charts
immediately by exploiting the many cool templates provided.
Author: Paolo Dalena [aut, cre]
Maintainer: Paolo Dalena <paolodalena97@gmail.com>
Diff between tastypie versions 0.1.1 dated 2023-09-06 and 0.1.2 dated 2025-08-25
DESCRIPTION | 15 +++++---- MD5 | 40 +++++++++++++------------- NEWS.md | 8 +++-- R/bubble_blow.R | 10 +++--- README.md | 46 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/available_templates.R | 8 ++--- inst/doc/available_templates.html | 29 +++++++++++------- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/figures/README-unnamed-chunk-9-2.png |binary tests/testthat/Rplots.pdf |binary tests/testthat/test-addimages.R | 2 - tests/testthat/test-bake.R | 35 ++++++++-------------- tests/testthat/test-bake_pro.R | 27 +++++++---------- tests/testthat/test-bubble.R | 27 +++++++++-------- tests/testthat/test-templates.R | 2 - 21 files changed, 125 insertions(+), 124 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River
Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions:
<https://nrfa.ceh.ac.uk/help/costs-terms-and-conditions>). The package
contains R wrappers to the UK NRFA data temporary-API. There are
functions to retrieve stations falling in a bounding box, to generate
a map and extracting time series and general information. The package
is fully described in Vitolo et al (2016) "rnrfa: An R package to
Retrieve, Filter and Visualize Data from the UK National River Flow
Archive"
<https://journal.r-project.org/archive/2016/RJ-2016-036/RJ-2016-036.pdf>.
Author: Ilaria Prosdocimi [ctb, cre] ,
Claudia Vitolo [aut] ,
Matthew Fry [ctb] ,
Wouter Buytaert [ctb] ,
Michael Spencer [ctb] ,
Tobias Gauster [ctb]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between rnrfa versions 2.1.0.6 dated 2024-06-19 and 2.1.0.7 dated 2025-08-25
rnrfa-2.1.0.6/rnrfa/README.md |only rnrfa-2.1.0.7/rnrfa/DESCRIPTION | 20 +-- rnrfa-2.1.0.7/rnrfa/MD5 | 13 +- rnrfa-2.1.0.7/rnrfa/NEWS.md | 8 + rnrfa-2.1.0.7/rnrfa/build/vignette.rds |binary rnrfa-2.1.0.7/rnrfa/inst/doc/rnrfa-vignette.R | 46 ++++---- rnrfa-2.1.0.7/rnrfa/inst/doc/rnrfa-vignette.html | 132 +++++++++++++---------- rnrfa-2.1.0.7/rnrfa/tests/testthat/test-get_ts.R | 6 - 8 files changed, 126 insertions(+), 99 deletions(-)
Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with
different groups. It uses principal component analysis to convert
multivariate observations into a set of linearly uncorrelated statistical
measures, which are then compared using a number of statistical methods. The
procedure is independent of the distributional properties of samples and
automatically selects features that best explain their differences, avoiding
manual selection of specific points or summary statistics. It is appropriate
for comparing samples of time series, images, spectrometric measures or
similar multivariate observations. This package is described in Fachada et
al. (2016) <doi:10.32614/RJ-2016-055>.
Author: Nuno Fachada [aut, cre]
Maintainer: Nuno Fachada <faken@fakenmc.com>
Diff between micompr versions 1.2.0 dated 2025-06-28 and 1.3.0 dated 2025-08-25
DESCRIPTION | 8 +- MD5 | 20 +++--- NEWS.md | 8 ++ R/cmpoutput.R | 7 +- R/util.R | 129 ++++++++++++++++++++++++++++++++++------ inst/doc/paper.pdf |binary inst/doc/tolatex-examples.pdf |binary man/centerscale.Rd | 63 +++++++++++++++++-- tests/testthat/test_cmpoutput.R | 12 ++- tests/testthat/test_micomp.R | 7 +- tests/testthat/test_util.R | 85 +++++++++++++++++++++++++- 11 files changed, 293 insertions(+), 46 deletions(-)
Title: Stratified Randomized Experiments
Description: Estimate average treatment effects (ATEs) in stratified randomized experiments. `sreg` supports a wide range of stratification designs, including matched pairs, n-tuple designs, and larger strata with many units — possibly of unequal size across strata. 'sreg' is designed to accommodate scenarios with multiple treatments and cluster-level treatment assignments, and accommodates optimal linear covariate adjustment based on baseline observable characteristics. 'sreg' computes estimators and standard errors based on Bugni, Canay, Shaikh (2018) <doi:10.1080/01621459.2017.1375934>; Bugni, Canay, Shaikh, Tabord-Meehan (2024+) <doi:10.48550/arXiv.2204.08356>; Jiang, Linton, Tang, Zhang (2023+) <doi:10.48550/arXiv.2201.13004>; Bai, Jiang, Romano, Shaikh, and Zhang (2024) <doi:10.1016/j.jeconom.2024.105740>; Bai (2022) <doi:10.1257/aer.20201856>; Bai, Romano, and Shaikh (2022) <doi:10.1080/01621459.2021.1883437>; Liu (2024+) <doi:10.48550/arXiv.2301.09016& [...truncated...]
Author: Juri Trifonov [aut, cre, cph],
Yuehao Bai [aut],
Azeem Shaikh [aut],
Max Tabord-Meehan [aut]
Maintainer: Juri Trifonov <jutrifonov@u.northwestern.edu>
Diff between sreg versions 2.0.1 dated 2025-08-19 and 2.0.2 dated 2025-08-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 2 ++ R/core.R | 4 ++++ README.md | 2 +- inst/doc/intro-to-sreg.html | 2 +- man/sreg.Rd | 6 +++++- 7 files changed, 23 insertions(+), 13 deletions(-)
Title: Specific Correspondence Analysis for the Social Sciences
Description: Specific and class specific multiple correspondence analysis on
survey-like data. Soc.ca is optimized to the needs of the social scientist and
presents easily interpretable results in near publication ready quality.
Author: Anton Grau Larsen [aut, cre],
Jacob Lunding [aut],
Stefan Andrade [aut]
Maintainer: Anton Grau Larsen <agraul@ruc.dk>
This is a re-admission after prior archival of version 0.8.0 dated 2021-09-02
Diff between soc.ca versions 0.8.0 dated 2021-09-02 and 0.8.1 dated 2025-08-25
soc.ca-0.8.0/soc.ca/man/extract_ind.Rd |only soc.ca-0.8.0/soc.ca/man/extract_mod.Rd |only soc.ca-0.8.1/soc.ca/DESCRIPTION | 33 +- soc.ca-0.8.1/soc.ca/MD5 | 86 +++-- soc.ca-0.8.1/soc.ca/NAMESPACE | 15 soc.ca-0.8.1/soc.ca/NEWS.md | 2 soc.ca-0.8.1/soc.ca/R/data_documentation.r | 39 +- soc.ca-0.8.1/soc.ca/R/dev_tables.R |only soc.ca-0.8.1/soc.ca/R/functions_analysis.r | 165 +++++++--- soc.ca-0.8.1/soc.ca/R/functions_array.r | 4 soc.ca-0.8.1/soc.ca/R/functions_build_plot.r | 315 ++++++++++++++++++-- soc.ca-0.8.1/soc.ca/R/functions_convert_from.R |only soc.ca-0.8.1/soc.ca/R/functions_description.r | 103 ++++++ soc.ca-0.8.1/soc.ca/R/functions_ellipse.r | 168 ++++++++-- soc.ca-0.8.1/soc.ca/R/functions_plot.r | 48 +-- soc.ca-0.8.1/soc.ca/R/functions_tools.r | 185 +++++++++++ soc.ca-0.8.1/soc.ca/R/functions_triads.r | 234 ++++++++++++++ soc.ca-0.8.1/soc.ca/R/globals.R |only soc.ca-0.8.1/soc.ca/R/zzz.r | 3 soc.ca-0.8.1/soc.ca/man/add.cases.Rd |only soc.ca-0.8.1/soc.ca/man/add.categories.Rd |only soc.ca-0.8.1/soc.ca/man/add.category.relations.Rd |only soc.ca-0.8.1/soc.ca/man/add.density.Rd |only soc.ca-0.8.1/soc.ca/man/add.ellipse.Rd |only soc.ca-0.8.1/soc.ca/man/add.quadrant.labels.Rd |only soc.ca-0.8.1/soc.ca/man/ellipses.Rd |only soc.ca-0.8.1/soc.ca/man/extract_cases.Rd |only soc.ca-0.8.1/soc.ca/man/extract_cats.Rd |only soc.ca-0.8.1/soc.ca/man/extract_sup.Rd | 2 soc.ca-0.8.1/soc.ca/man/get.category.relations.Rd |only soc.ca-0.8.1/soc.ca/man/indicator.Rd | 5 soc.ca-0.8.1/soc.ca/man/indicator.to.long.Rd |only soc.ca-0.8.1/soc.ca/man/map.active.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.add.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.ca.base.Rd | 11 soc.ca-0.8.1/soc.ca/man/map.csa.mca.Rd | 4 soc.ca-0.8.1/soc.ca/man/map.ctr.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.ellipse.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.ind.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.mod.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.path.Rd | 4 soc.ca-0.8.1/soc.ca/man/map.select.Rd | 6 soc.ca-0.8.1/soc.ca/man/map.sup.Rd | 6 soc.ca-0.8.1/soc.ca/man/mca.eigen.check.Rd | 5 soc.ca-0.8.1/soc.ca/man/moschidis.Rd | 18 - soc.ca-0.8.1/soc.ca/man/political_space97.Rd | 14 soc.ca-0.8.1/soc.ca/man/prune.mca.Rd |only soc.ca-0.8.1/soc.ca/man/randomize.mca.Rd |only soc.ca-0.8.1/soc.ca/man/rename_aes.Rd |only soc.ca-0.8.1/soc.ca/man/soc.ca.Rd | 18 + soc.ca-0.8.1/soc.ca/man/soc.csa.Rd | 1 soc.ca-0.8.1/soc.ca/man/soc.mca.Rd | 4 soc.ca-0.8.1/soc.ca/man/supplementary.categories.Rd |only soc.ca-0.8.1/soc.ca/man/what.is.x.Rd | 10 54 files changed, 1308 insertions(+), 236 deletions(-)
Title: Integrated Text Mining Solution
Description: An integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, lexical summary, terms
co-occurrences and documents similarity measures, graphs of terms,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files,
as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut],
Antoine Chollet [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
This is a re-admission after prior archival of version 0.1.3 dated 2021-05-12
Diff between R.temis versions 0.1.3 dated 2021-05-12 and 0.1.4 dated 2025-08-25
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- NEWS | 3 +++ R/graph.R | 6 +++--- man/terms_graph.Rd | 6 +++--- 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Integration-Based Coefficients of Variation
Description: Estimate coefficient of variation percent (CV%) for any arbitrary distribution, including some built-in estimates for commonly-used transformations in pharmacometrics. Methods are described in various sources, but applied here as summarized in: Prybylski, (2024) <doi:10.1007/s40262-023-01343-2>.
Author: John Prybylski [aut, cre, cph]
Maintainer: John Prybylski <jprybylski@gmail.com>
Diff between pmxcv versions 0.0.1.0 dated 2024-03-26 and 0.0.2 dated 2025-08-25
DESCRIPTION | 19 +- LICENSE | 4 MD5 | 59 ++++---- NAMESPACE | 28 +-- R/dist.intcv.R | 76 +++++----- R/dist.moment.R | 70 +++++---- R/globals.R | 2 R/intcv.R | 27 +-- R/invcv.R | 64 ++++----- R/moment.R | 25 +-- R/moment_f.R | 47 +++--- R/nonmemboxcox.R | 70 +++++---- R/numcv.R | 34 ++-- README.md | 12 + build |only inst/CITATION | 2 man/dist.intcv.Rd | 66 ++++----- man/dist.moment.Rd | 60 ++++---- man/intcv.Rd | 37 ++--- man/invcv.Rd | 50 +++---- man/moment.Rd | 37 ++--- man/moment_f.Rd | 57 ++++---- man/nonmemboxcox.Rd | 58 ++++---- man/numcv.Rd | 48 +++--- tests/testthat.R | 24 +-- tests/testthat/test-dist_builtins.R | 254 ++++++++++++++++++------------------ tests/testthat/test-integral_cv.R | 60 ++++---- tests/testthat/test-inverse_cv.R | 36 ++--- tests/testthat/test-moments.R | 70 ++++----- tests/testthat/test-nm_boxcox.R | 104 +++++++------- tests/testthat/test-numeric_cv.R | 76 +++++----- 31 files changed, 810 insertions(+), 766 deletions(-)
Title: Add Smoothing Spline Modelling Capability to `nlme`
Description: Adds smoothing spline modelling capability to nlme. Fits
smoothing spline terms in Gaussian linear and nonlinear
mixed-effects models.
Author: Rod Ball [aut],
Andrzej Galecki [cre]
Maintainer: Andrzej Galecki <agalecki@umich.edu>
Diff between lmeSplines versions 1.1-12 dated 2022-05-02 and 1.1.15 dated 2025-08-25
DESCRIPTION | 23 ++- MD5 | 15 +- NAMESPACE | 12 + R/lmeSplines.R | 359 ++++++++++++++++++++++++++++++++++++++--------------- R/smSplineEx1.R |only README.md | 44 +++--- man/approx.Z.Rd | 65 +++++---- man/smSplineEx1.Rd | 60 ++++++-- man/smspline.Rd | 218 +++++++++++++++----------------- 9 files changed, 495 insertions(+), 301 deletions(-)
Title: Supervised Dimensional Reduction by Guided Partial Least Squares
Description: Guided partial least squares (guided-PLS) is the combination of partial least squares by singular value decomposition (PLS-SVD) and guided principal component analysis (guided-PCA). This package provides implementations of PLS-SVD, guided-PLS, and guided-PCA for supervised dimensionality reduction. The guided-PCA function (new in v1.1.0) automatically handles mixed data types (continuous and categorical) in the supervision matrix and provides detailed contribution analysis for interpretability. For the details of the methods, see the reference section of GitHub README.md <https://github.com/rikenbit/guidedPLS>.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between guidedPLS versions 1.0.0 dated 2023-05-11 and 1.1.0 dated 2025-08-25
DESCRIPTION | 12 +- MD5 | 27 ++--- NAMESPACE | 5 R/guidedPCA.R |only R/guidedPLS.R | 111 ++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 12 ++ inst/doc/guidedPLS-1.html | 202 +++++++++++++++++++--------------------- inst/doc/guidedPLS-2.html | 188 +++++++++++++++++-------------------- man/PLSSVD.Rd | 2 man/guidedPCA.Rd |only man/guidedPLS.Rd | 10 + man/sPLSDA.Rd | 2 tests/testthat/test_guidedPCA.R |only tests/testthat/test_guidedPLS.R | 41 ++++++++ 16 files changed, 369 insertions(+), 243 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.3 dated 2025-08-18 and 1.5.4 dated 2025-08-25
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 1 NEWS.md | 4 R/create_mean_sd_matrices.R | 4 R/twoway_simultesting.R | 138 ++++++++++++++---------- inst/doc/eSp_balanced_design_powertest.html | 44 +++---- man/calculate_mean_matrix.Rd | 4 tests/testthat/test-twoway_simulation_testing.R | 2 9 files changed, 130 insertions(+), 91 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Bayesian MI-LASSO for Variable Selection on Multiply-Imputed
Datasets
Description: Provides a suite of Bayesian MI-LASSO for variable selection methods for multiply-imputed datasets. The package includes four Bayesian MI-LASSO models using shrinkage (Multi-Laplace, Horseshoe, ARD) and Spike-and-Slab (Spike-and-Laplace) priors, along with tools for model fitting via MCMC, four-step projection predictive variable selection, and hyperparameter calibration. Methods are suitable for both continuous and binary covariates under missing-at-random or missing-completely-at-random assumptions. See Zou, J., Wang, S. and Chen, Q. (2025), Bayesian MI-LASSO for Variable Selection on Multiply-Imputed Data. ArXiv, 2211.00114. <doi:10.48550/arXiv.2211.00114> for more details. We also provide the frequentist`s MI-LASSO function.
Author: Jungang Zou [aut, cre],
Sijian Wang [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between BMIselect versions 1.0.2 dated 2025-08-20 and 1.0.3 dated 2025-08-25
DESCRIPTION | 9 +++-- MD5 | 11 +++++-- R/bmiselect.R | 83 +++++++++++++++++++++++++++---------------------------- build |only inst |only man/BMI_LASSO.Rd | 20 ++++++------- vignettes |only 7 files changed, 65 insertions(+), 58 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.0 dated 2025-07-02 and 0.8.1 dated 2025-08-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/common.R | 8 ++++---- build/vignette.rds |binary inst/include/vcfpp.h | 13 ------------- src/htslib-1.21/config.status | 2 +- 7 files changed, 18 insertions(+), 27 deletions(-)
Title: Tests for Variance Homogeneity
Description: Performs 20 omnibus tests for testing the composite hypothesis of variance homogeneity.
Author: Gozde Cosar [aut],
Merve Kasikci [aut],
Osman Dag [aut, cre]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between vartest versions 1.2 dated 2024-05-07 and 1.3 dated 2025-08-25
DESCRIPTION | 12 +++--- MD5 | 90 ++++++++++++++++++++++++---------------------- NAMESPACE | 3 + R/adjusted.taha.test.R | 19 +-------- R/ansari.test.R | 19 +-------- R/bartletts.test.R | 19 +-------- R/capon.test.R | 19 +-------- R/cochrans.test.R | 20 +--------- R/david.barton.test.R | 19 +-------- R/duran.test.R | 19 +-------- R/f.test.R | 21 +--------- R/fk.test.R | 19 +-------- R/g.test.R | 21 +--------- R/hartley.test.R | 20 +--------- R/klotz.test.R | 19 +-------- R/levene.test.R | 20 +--------- R/mood.test.R | 19 +-------- R/mzv.test.R | 20 +--------- R/obrien.test.R | 20 +--------- R/print.summary.vht.R |only R/siegel.tukey.test.R | 19 +-------- R/summary.vht.R |only R/taha.test.R | 19 +-------- R/talwar.gentle.test.R | 19 +-------- R/zv.test.R | 20 +--------- man/adjusted.taha.test.Rd | 7 ++- man/ansari.test.Rd | 6 ++- man/bartletts.test.Rd | 4 +- man/capon.test.Rd | 7 ++- man/cochrans.test.Rd | 5 +- man/david.barton.test.Rd | 6 ++- man/duran.test.Rd | 7 ++- man/f.test.Rd | 5 +- man/fk.test.Rd | 7 ++- man/g.test.Rd | 5 +- man/hartley.test.Rd | 7 ++- man/klotz.test.Rd | 7 ++- man/levene.test.Rd | 7 ++- man/mood.test.Rd | 7 ++- man/mzv.test.Rd | 4 +- man/obrien.test.Rd | 6 ++- man/print.summary.vht.Rd |only man/siegel.tukey.test.Rd | 7 ++- man/summary.vht.Rd |only man/taha.test.Rd | 7 ++- man/talwar.gentle.test.Rd | 7 ++- man/zv.test.Rd | 4 +- tests |only 48 files changed, 192 insertions(+), 425 deletions(-)
Title: Add More 'AdminLTE2' Components to 'shinydashboard'
Description: Extend 'shinydashboard' with 'AdminLTE2' components.
'AdminLTE2' is a free 'Bootstrap 3' dashboard template available
at <https://adminlte.io>. Customize boxes, add timelines and a lot more.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] ,
Guang Yang [ctb, cph] ,
Winston Chang [ctb, cph] ,
Victor Perrier [ctb]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between shinydashboardPlus versions 2.0.5 dated 2024-08-18 and 2.0.6 dated 2025-08-25
shinydashboardPlus-2.0.5/shinydashboardPlus/inst/shinydashboardPlus-2.0.5 |only shinydashboardPlus-2.0.6/shinydashboardPlus/DESCRIPTION | 6 shinydashboardPlus-2.0.6/shinydashboardPlus/MD5 | 76 shinydashboardPlus-2.0.6/shinydashboardPlus/NEWS.md | 107 - shinydashboardPlus-2.0.6/shinydashboardPlus/R/useful-items.R | 274 ++- shinydashboardPlus-2.0.6/shinydashboardPlus/R/utils.R | 271 ++- shinydashboardPlus-2.0.6/shinydashboardPlus/R/zzz.R |only shinydashboardPlus-2.0.6/shinydashboardPlus/README.md | 37 shinydashboardPlus-2.0.6/shinydashboardPlus/build/stage23.rdb |binary shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/box-elements.R | 90 - shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/box-elements.html | 31 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/controlbar.R | 256 +-- shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/controlbar.html | 31 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/css-preloader.R | 42 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/css-preloader.html | 31 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/enhanced-header.R | 206 +- shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/enhanced-header.html | 31 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/extra-elements.R | 278 +-- shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/extra-elements.html | 29 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/improved-boxes.R | 776 +++++----- shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/improved-boxes.html | 43 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/more-skins.R | 262 +-- shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/more-skins.html | 41 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/shinydashboardPlus.R | 32 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/doc/shinydashboardPlus.html | 29 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/examples/box_elements/timeline.R | 8 shinydashboardPlus-2.0.6/shinydashboardPlus/inst/placeholders |only shinydashboardPlus-2.0.6/shinydashboardPlus/inst/shinydashboardPlus-2.0.6 |only shinydashboardPlus-2.0.6/shinydashboardPlus/man/messageItem.Rd | 2 shinydashboardPlus-2.0.6/shinydashboardPlus/man/notificationItem.Rd | 2 shinydashboardPlus-2.0.6/shinydashboardPlus/man/timeline.Rd | 8 31 files changed, 1605 insertions(+), 1394 deletions(-)
More information about shinydashboardPlus at CRAN
Permanent link
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.4 dated 2025-04-28 and 1.0.5 dated 2025-08-25
shapr-1.0.4/shapr/R/asymmetric_and_casual_Shapley.R |only shapr-1.0.4/shapr/R/print_iter.R |only shapr-1.0.4/shapr/inst/extdata |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/Asymmetric_ordering.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/Causal_ordering.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/compare_plots-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_asym_cau_SV-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_asym_cau_beeswarm-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_asym_con_beeswarm-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_sym_cau_beeswarm-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_sym_con_SV-1.png |only shapr-1.0.4/shapr/vignettes/figure_asymmetric_causal/explanation_sym_con_beeswarm-1.png |only 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shapr-1.0.5/shapr/R/RcppExports.R | 590 shapr-1.0.5/shapr/R/approach.R | 14 shapr-1.0.5/shapr/R/approach_categorical.R | 505 shapr-1.0.5/shapr/R/approach_copula.R | 346 shapr-1.0.5/shapr/R/approach_ctree.R | 610 shapr-1.0.5/shapr/R/approach_empirical.R | 1222 - shapr-1.0.5/shapr/R/approach_gaussian.R | 346 shapr-1.0.5/shapr/R/approach_independence.R | 8 shapr-1.0.5/shapr/R/approach_regression_separate.R | 1018 - shapr-1.0.5/shapr/R/approach_regression_surrogate.R | 4 shapr-1.0.5/shapr/R/approach_vaeac.R | 5844 ++++---- shapr-1.0.5/shapr/R/approach_vaeac_torch_modules.R | 4098 ++--- shapr-1.0.5/shapr/R/asymmetric_and_causal_Shapley.R |only shapr-1.0.5/shapr/R/check_convergence.R | 6 shapr-1.0.5/shapr/R/cli.R | 566 shapr-1.0.5/shapr/R/compute_estimates.R | 33 shapr-1.0.5/shapr/R/compute_vS.R | 610 shapr-1.0.5/shapr/R/documentation.R | 15 shapr-1.0.5/shapr/R/explain.R | 1286 - shapr-1.0.5/shapr/R/explain_forecast.R | 916 - shapr-1.0.5/shapr/R/finalize_explanation.R | 461 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|only shapr-1.0.5/shapr/vignettes/figure_vaeac/continue-training-2-2.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/continue-training-2.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/continue-training-3.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/continue-training-4.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/continue-training-5.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/early-stopping-1-1.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/early-stopping-2-1.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/early-stopping-3-1.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/early-stopping-3-2.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/first-vaeac-plots-1.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/paired-sampling-plotting-1.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/paired-sampling-plotting-2.webp |only shapr-1.0.5/shapr/vignettes/figure_vaeac/vaeac-grouping-of-features-1.webp |only 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Title: Functions and Data Supporting 'Linear Mixed-Effects Models: A
Step-by-Step Approach'
Description: Provides functions and datasets to support the book
by Galecki and Burzykowski (2013),
'Linear Mixed-Effects Models: A Step-by-Step Approach',
Springer. Includes functions for power calculations,
log-likelihood contributions, and data simulation
for linear mixed-effects models.
Author: Andrzej Galecki [aut, cre] ,
Tomasz Burzykowski [aut]
Maintainer: Andrzej Galecki <agalecki@umich.edu>
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Title: Easy Graphs for Data Visualisation and Linear Models for ANOVA
Description: Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify.shenoylab.com/>. Citation: <doi:10.5281/zenodo.5136508>.
Author: Avinash R Shenoy [cre, aut]
Maintainer: Avinash R Shenoy <a.shenoy@imperial.ac.uk>
Diff between grafify versions 5.0.0.1 dated 2025-03-10 and 5.1.0 dated 2025-08-25
DESCRIPTION | 11 MD5 | 26 +- NAMESPACE | 2 NEWS.md | 18 + R/graf_colour_list.R | 2 R/plot_xy_CatGroup.R | 355 +++++++++++++++++++++-------- R/plot_xy_Group.R |only build/partial.rdb |binary man/graf_colours.Rd | 2 man/plot_xy_CatGroup.Rd | 21 + man/plot_xy_Group.Rd |only tests/testthat/test-plot_3d_scatterbar.R | 29 +- tests/testthat/test-plot_3d_scatterbox.R | 29 +- tests/testthat/test-plot_befafter_colors.R | 28 +- tests/testthat/test-plot_qqline.R | 27 +- 15 files changed, 404 insertions(+), 146 deletions(-)
Title: Fixed Effects Counterfactual Estimators
Description: Provides tools for estimating causal effects in panel data using counterfactual methods, as well as other modern DID estimators. It is designed for causal panel analysis with binary treatments under the parallel trends assumption. The package supports scenarios where treatments can switch on and off and allows for limited carryover effects. It includes several imputation estimators, such as Gsynth (Xu 2017), linear factor models, and the matrix completion method. Detailed methodology is described in Liu, Wang, and Xu (2024) <doi:10.48550/arXiv.2107.00856> and Chiu et al. (2025) <doi:10.48550/arXiv.2309.15983>. Optionally integrates with the "HonestDiDFEct" package for sensitivity analyses compatible with imputation estimators. "HonestDiDFEct" is not on CRAN but can be obtained from <https://github.com/lzy318/HonestDiDFEct>.
Author: Licheng Liu [aut],
Ziyi Liu [aut],
Ye Wang [aut],
Yiqing Xu [aut, cre],
Tianzhu Qin [aut],
Shiyun Hu [aut],
Rivka Lipkovitz [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between fect versions 1.0.0 dated 2022-10-14 and 2.0.5 dated 2025-08-25
fect-1.0.0/fect/NEWS.md |only fect-1.0.0/fect/R/get_cohort.r |only fect-1.0.0/fect/README.md |only fect-1.0.0/fect/man/simdata1.Rd |only fect-2.0.5/fect/DESCRIPTION | 48 fect-2.0.5/fect/MD5 | 108 fect-2.0.5/fect/NAMESPACE | 68 fect-2.0.5/fect/R/RcppExports.R | 48 fect-2.0.5/fect/R/boot.R | 4474 +++++++++++++++--------- fect-2.0.5/fect/R/cv.R | 1251 +++--- fect-2.0.5/fect/R/cv_binary.R | 2 fect-2.0.5/fect/R/default.R | 892 ++-- fect-2.0.5/fect/R/diagtest.R | 203 - fect-2.0.5/fect/R/did_wrapper.R |only fect-2.0.5/fect/R/effect.R |only fect-2.0.5/fect/R/esplot.R |only fect-2.0.5/fect/R/fe.R | 586 ++- fect-2.0.5/fect/R/fect_gsynth.R | 2396 ++++++------ fect-2.0.5/fect/R/fect_sens.R |only fect-2.0.5/fect/R/fittest.R | 10 fect-2.0.5/fect/R/getcohort.R |only fect-2.0.5/fect/R/interFE.R | 169 fect-2.0.5/fect/R/mc.R | 484 +- fect-2.0.5/fect/R/permutation.R | 190 - fect-2.0.5/fect/R/plot.R | 6478 +++++++++++++++++++++-------------- fect-2.0.5/fect/R/polynomial.R | 606 ++- fect-2.0.5/fect/R/print.R | 24 fect-2.0.5/fect/R/support.R | 419 +- fect-2.0.5/fect/data/datalist |only fect-2.0.5/fect/data/fect.RData |binary fect-2.0.5/fect/data/gs2020.rda |only fect-2.0.5/fect/data/hh2019.rda |only fect-2.0.5/fect/data/simdata.rda |only fect-2.0.5/fect/data/simgsynth.rda |only fect-2.0.5/fect/data/turnout.rda |only fect-2.0.5/fect/man/att.cumu.Rd | 61 fect-2.0.5/fect/man/did_wrapper.Rd |only fect-2.0.5/fect/man/effect.rd |only fect-2.0.5/fect/man/esplot.Rd |only fect-2.0.5/fect/man/fect-internal.Rd | 6 fect-2.0.5/fect/man/fect-package.Rd | 56 fect-2.0.5/fect/man/fect.Rd | 335 - fect-2.0.5/fect/man/fect_sens.Rd |only fect-2.0.5/fect/man/get.cohort.Rd | 44 fect-2.0.5/fect/man/gs2020.Rd |only fect-2.0.5/fect/man/hh2019.Rd |only fect-2.0.5/fect/man/interFE.Rd | 91 fect-2.0.5/fect/man/plot.fect.Rd | 405 +- fect-2.0.5/fect/man/print.fect.Rd | 43 fect-2.0.5/fect/man/print.interFE.Rd | 24 fect-2.0.5/fect/man/simdata.Rd | 23 fect-2.0.5/fect/man/simgsynth.Rd |only fect-2.0.5/fect/man/turnout.Rd | 33 fect-2.0.5/fect/src/Makevars | 2 fect-2.0.5/fect/src/Makevars.win | 2 fect-2.0.5/fect/src/RcppExports.cpp | 136 fect-2.0.5/fect/src/auxiliary.cpp | 56 fect-2.0.5/fect/src/fe_sub.cpp | 497 +- fect-2.0.5/fect/src/fect.h | 20 fect-2.0.5/fect/src/ife.cpp | 862 ++-- fect-2.0.5/fect/src/ife_sub.cpp | 983 +++-- fect-2.0.5/fect/src/mc.cpp | 127 fect-2.0.5/fect/tests |only 63 files changed, 13367 insertions(+), 8895 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.5.0 dated 2025-07-11 and 1.6.2 dated 2025-08-25
DESCRIPTION | 16 ++++++++-------- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + NEWS.md | 28 ++++++++++++++++++++++++++-- R/draw_spectralslice.R |only R/pitch_overlay.R | 2 -- R/praatpicture.R | 7 +++++-- R/waveplot.R | 32 ++++++++++++++++++++++---------- man/draw_spectralslice.Rd |only man/praatpicture.Rd | 5 +++++ man/waveplot.Rd | 5 +++++ 11 files changed, 82 insertions(+), 32 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C. Sachs [aut, cre],
Robert W. Corty [ctb],
Luis Crouch [ctb]
Maintainer: Michael C. Sachs <sachsmc@gmail.com>
Diff between plotROC versions 2.3.1 dated 2023-10-06 and 2.3.3 dated 2025-08-25
DESCRIPTION | 11 MD5 | 40 NEWS | 11 R/calculate_roc.R | 122 R/geom_roc.R | 2 R/geom_rocci.R | 2 R/style_roc.R | 10 build/vignette.rds |binary inst/doc/examples.R | 43 inst/doc/examples.Rmd | 30 inst/doc/examples.html | 9430 ++++++++++++++++++++++----------------------- man/calc_auc.Rd | 2 man/geom_roc.Rd | 56 man/geom_rocci.Rd | 56 man/plotROC.Rd | 2 man/stat_roc.Rd | 73 man/stat_rocci.Rd | 73 man/style_roc.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test-calc.R | 41 vignettes/examples.Rmd | 30 21 files changed, 5196 insertions(+), 4841 deletions(-)
Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre, cph] ,
Henrik Singmann [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between gratia versions 0.11.0 dated 2025-08-18 and 0.11.1 dated 2025-08-25
DESCRIPTION | 8 MD5 | 119 NAMESPACE | 8 NEWS.md | 45 R/conditional-values.R | 7 R/derivatives.R | 48 R/diagnose.R | 79 R/distribution-helpers.R | 17 R/family-utils.R | 3 R/fix-family.R | 87 R/residuals.R | 10 R/utililties.R | 38 man/appraise.Rd | 13 man/theta.Rd | 3 tests/Examples/gratia-Ex.Rout.save | 21 tests/testthat/_snaps/basis/draw-basis-works-with-a-bivariate-te-contour.svg | 18 tests/testthat/_snaps/basis/draw-basis-works-with-a-bivariate-te.svg | 18 tests/testthat/_snaps/basis/draw-basis-works-with-a-bivariate-tprs-contour.svg | 18 tests/testthat/_snaps/basis/draw-basis-works-with-a-bivariate-tprs.svg | 18 tests/testthat/_snaps/compare-smooths/compare-smooths-all-smooths.svg | 4 tests/testthat/_snaps/compare-smooths/compare-smooths-bottom-legend.svg | 4 tests/testthat/_snaps/compare-smooths/compare-smooths-set-nrow-ncol.svg | 4 tests/testthat/_snaps/concurvity/draw-concurvity-pairwise.svg | 150 - tests/testthat/_snaps/diagnostic-plots/appraise-lm.svg | 2 tests/testthat/_snaps/diagnostic-plots/qq-plot-glm-uniform.svg | 2 tests/testthat/_snaps/diagnostic-plots/qq-plot-lm-uniform.svg | 2 tests/testthat/_snaps/draw-gam/draw-gam-rm1.svg | 2 tests/testthat/_snaps/draw-gam/draw-gam-rm2.svg | 2 tests/testthat/_snaps/draw-gam/grouped-by-gam.svg | 6 tests/testthat/_snaps/draw-gam/ordered-grouped-by-gam.svg | 6 tests/testthat/_snaps/draw-methods/draw-gam-model-with-ranef-smooth-factor-by.svg | 2 tests/testthat/_snaps/draw-methods/draw-gam-model-with-ranef-smooth.svg | 2 tests/testthat/_snaps/draw-methods/draw-works-for-sos-smooths.svg | 384 +-- tests/testthat/_snaps/draw-methods/issue-22-draw-with-mixed-random-effects.svg | 2 tests/testthat/_snaps/draw-parametric-effects/issue-219-parametric-effects.svg | 8 tests/testthat/_snaps/draw-smooth-estimates/draw-gam-for-su-m-trivar-t22.svg | 18 tests/testthat/_snaps/draw-smooth-estimates/draw-gam-for-su-m-trivar-te2.svg | 18 tests/testthat/_snaps/draw-smooth-estimates/draw-gam-sos-chlorophyll-with-crs.svg | 1250 +++++----- tests/testthat/_snaps/draw-smooth-estimates/draw-gam-sos-chlorophyll.svg | 1250 +++++----- tests/testthat/_snaps/draw-smooth-estimates/draw-sm-est-grouped-by-true-ordered.svg | 22 tests/testthat/_snaps/draw-smooth-estimates/draw-sm-est-grouped-by-true.svg | 6 tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-sz-factor-smooth.svg | 6 tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-sz-two-factor-smooth.svg | 22 tests/testthat/_snaps/hgam-paper/hgam-paper-zoop-model-5.svg | 2 tests/testthat/_snaps/partial-derivatives.md |only tests/testthat/_snaps/qq-plot/qq-plot-uniform-randomisation-pearson-residuals.svg | 2 tests/testthat/_snaps/qq-plot/qq-plot-uniform-randomisation-response-residuals.svg | 2 tests/testthat/_snaps/qq-plot/qq-plot-uniform-randomisation.svg | 2 tests/testthat/_snaps/quantile-residuals.md | 8 tests/testthat/setup.R | 11 tests/testthat/test-basis.R | 2 tests/testthat/test-compare-smooths.R | 5 tests/testthat/test-concurvity.R | 1 tests/testthat/test-diagnostic-plots.R | 3 tests/testthat/test-draw-gam.R | 3 tests/testthat/test-draw-methods.R | 4 tests/testthat/test-draw-parametric-effects.R | 1 tests/testthat/test-draw-smooth-estimates.R | 6 tests/testthat/test-partial-derivatives.R | 67 tests/testthat/test-qq-plot.R | 3 tests/testthat/test-quantile-residuals.R | 4 61 files changed, 2033 insertions(+), 1845 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Jonas Lindblad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 1.1.0 dated 2025-06-26 and 1.1.5 dated 2025-08-25
DESCRIPTION | 12 - MD5 | 33 ++-- NEWS.md | 14 + R/FixRiskyIntervals.R | 54 +++++- R/GaussSuppressionFromData.R | 133 ++++++++++++++++- R/Intervals.R | 97 ++++++++++-- R/SuppressLinkedTables.R | 178 +++++++++++++++++++---- R/gaussSuppression_linked.R | 247 +++++++++++++++++++++++++++++++- R/interval_suppression.R |only build/vignette.rds |binary inst/doc/Linked_table_suppression.R |only inst/doc/Linked_table_suppression.Rmd |only inst/doc/Linked_table_suppression.html |only man/ComputeIntervals.Rd | 9 + man/FixRiskyIntervals.Rd | 9 + man/GaussSuppressionFromData.Rd | 35 ++++ man/SuppressLinkedTables.Rd | 97 ++++++++++-- tests/testthat/test-LinkedSuppression.R | 142 ++++++++++++------ tests/testthat/test-Wrappers.R | 4 vignettes/Linked_table_suppression.Rmd |only 20 files changed, 909 insertions(+), 155 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Quantify the Relationship Between Development Rate and
Temperature in Ectotherms
Description: A set of functions to quantify the relationship between development
rate and temperature and to build phenological models. The package comprises
a set of models and estimated parameters borrowed from a literature review
in ectotherms. The methods and literature review are described in Rebaudo
et al. (2018) <doi:10.1111/2041-210X.12935>, Rebaudo and Rabhi (2018)
<doi:10.1111/eea.12693>, and Regnier et al. (2021) <doi:10.1093/ee/nvab115>.
An example can be found in Rebaudo et al. (2017)
<doi:10.1007/s13355-017-0480-5>.
Author: Francois Rebaudo [aut, cre] ,
Baptiste Regnier [aut] ,
Camila Benavides [ctb] ,
Tanusson Selvarajah [ctb] ,
Nicolas Bonnal [ctb] ,
Badre Rabhi [ctb] ,
Quentin Struelens [ctb]
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>
Diff between devRate versions 0.2.4 dated 2023-08-24 and 0.2.5 dated 2025-08-25
DESCRIPTION | 14 +-- MD5 | 126 +++++++++++++++++-------------- NAMESPACE | 11 ++ NEWS.md | 7 + R/data.R | 2 R/devRate_harmigera.R |only R/devRate_phenoBDD.R | 146 ++++++++++++++++++++++++++++-------- README.md | 20 +++- build/partial.rdb |binary build/vignette.rds |binary data/analytis_77.RData |binary data/bayoh_03.RData |binary data/beta_16.RData |binary data/beta_95.RData |binary data/bieri1_83.RData |binary data/briere1_99.RData |binary data/briere2_99.RData |binary data/campbell_74.RData |binary data/damos_08.RData |binary data/damos_11.RData |binary data/davidson_44.RData |binary data/devRateEqList.RData |binary data/harcourtYee_82.RData |binary data/hilbertLogan_83.RData |binary data/janisch_32.RData |binary data/kontodimas_04.RData |binary data/lactin1_95.RData |binary data/lactin2_95.RData |binary data/lamb_92.RData |binary data/logan10_76.RData |binary data/logan6_76.RData |binary data/perf2_11.RData |binary data/poly2.RData |binary data/poly4.RData |binary data/ratkowsky_82.RData |binary data/ratkowsky_83.RData |binary data/regniere_12.RData |binary data/rootsq_82.RData |binary data/schoolfieldHigh_81.RData |binary data/schoolfieldLow_81.RData |binary data/schoolfield_81.RData |binary data/sharpeDeMichele_77.RData |binary data/shi_11.RData |binary data/stinner_74.RData |binary data/taylor_81.RData |binary data/wagner_88.RData |binary data/wang_82.RData |binary data/wangengel_98.RData |binary inst/doc/guiaDelUsuario.R | 10 +- inst/doc/guiaDelUsuario.html | 150 ++++++++++++++++++------------------- inst/doc/helicoverpa_armigera.R |only inst/doc/helicoverpa_armigera.Rmd |only inst/doc/helicoverpa_armigera.html |only inst/doc/modelEvaluation.R | 18 ++-- inst/doc/modelEvaluation.html | 14 +-- inst/doc/quickUserGuide.R | 6 - inst/doc/quickUserGuide.html | 146 ++++++++++++++++++------------------ man/devRate.Rd | 26 ++++++ man/devRateIBMparam.Rd | 66 +++++++++++++++- man/ha_ahmad2024_ls.Rd |only man/ha_bartekova2006.Rd |only man/ha_foley1981.Rd |only man/ha_jallow2001.Rd |only man/ha_kay1981_ls.Rd |only man/ha_kay1981_nls.Rd |only man/ha_mironidis2008_ls.Rd |only man/ha_mironidis2008_nls.Rd |only man/ha_noorulane2018_ls.Rd |only man/ha_noorulane2018_nls.Rd |only man/ha_qureshi1999_ls.Rd |only man/kontodimas_04.Rd | 2 vignettes/helicoverpa_armigera.Rmd |only 72 files changed, 489 insertions(+), 275 deletions(-)
Title: A 'Bootstrap 4' Version of 'shinydashboard'
Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power of
'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
<https://github.com/ColorlibHQ/AdminLTE>.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between bs4Dash versions 2.3.4 dated 2024-09-03 and 2.3.5 dated 2025-08-25
bs4Dash-2.3.4/bs4Dash/inst/bs4Dash-2.3.4 |only bs4Dash-2.3.5/bs4Dash/DESCRIPTION | 44 bs4Dash-2.3.5/bs4Dash/MD5 | 233 - bs4Dash-2.3.5/bs4Dash/NAMESPACE | 1 bs4Dash-2.3.5/bs4Dash/NEWS.md | 164 bs4Dash-2.3.5/bs4Dash/R/aliases.R | 138 bs4Dash-2.3.5/bs4Dash/R/auto-color.R | 10 bs4Dash-2.3.5/bs4Dash/R/bs4Dash-package.r | 13 bs4Dash-2.3.5/bs4Dash/R/bs4DashGallery.R | 17 bs4Dash-2.3.5/bs4Dash/R/cards.R | 710 ++- bs4Dash-2.3.5/bs4Dash/R/dashboardBody.R | 6 bs4Dash-2.3.5/bs4Dash/R/dashboardControlbar.R | 64 bs4Dash-2.3.5/bs4Dash/R/dashboardFooter.R | 3 bs4Dash-2.3.5/bs4Dash/R/dashboardHeader.R | 499 +- bs4Dash-2.3.5/bs4Dash/R/dashboardPage.R | 35 bs4Dash-2.3.5/bs4Dash/R/dashboardSidebar.R | 300 + bs4Dash-2.3.5/bs4Dash/R/deps.R | 25 bs4Dash-2.3.5/bs4Dash/R/feedbacks.R | 84 bs4Dash-2.3.5/bs4Dash/R/grid.R | 23 bs4Dash-2.3.5/bs4Dash/R/import-standalone-obj-type.R |only bs4Dash-2.3.5/bs4Dash/R/import-standalone-types-check.R |only bs4Dash-2.3.5/bs4Dash/R/inputs.R | 158 bs4Dash-2.3.5/bs4Dash/R/render-functions.R | 29 bs4Dash-2.3.5/bs4Dash/R/skinSelector.R | 24 bs4Dash-2.3.5/bs4Dash/R/tabs.R | 159 bs4Dash-2.3.5/bs4Dash/R/useful-items.R | 1843 ++++------ bs4Dash-2.3.5/bs4Dash/R/utils.R | 703 ++- bs4Dash-2.3.5/bs4Dash/R/zzz.R |only bs4Dash-2.3.5/bs4Dash/README.md | 12 bs4Dash-2.3.5/bs4Dash/build/stage23.rdb |binary bs4Dash-2.3.5/bs4Dash/inst/bs4Dash-2.3.5 |only bs4Dash-2.3.5/bs4Dash/inst/doc/bs4Dash.html | 20 bs4Dash-2.3.5/bs4Dash/inst/doc/css-preloader.html | 22 bs4Dash-2.3.5/bs4Dash/inst/doc/extra-elements.R | 30 bs4Dash-2.3.5/bs4Dash/inst/doc/extra-elements.html | 29 bs4Dash-2.3.5/bs4Dash/inst/doc/improved-boxes.R | 22 bs4Dash-2.3.5/bs4Dash/inst/doc/improved-boxes.html | 35 bs4Dash-2.3.5/bs4Dash/inst/doc/more-skins.html | 24 bs4Dash-2.3.5/bs4Dash/inst/doc/step-by-step.R | 688 +-- bs4Dash-2.3.5/bs4Dash/inst/doc/step-by-step.Rmd | 4 bs4Dash-2.3.5/bs4Dash/inst/doc/step-by-step.html | 265 - bs4Dash-2.3.5/bs4Dash/inst/examples/showcase/app.R | 234 - bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/accordions/app.R | 6 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/box-api/app.R | 18 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/box-dropdown/app.R | 12 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/box-sidebar/app.R | 17 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/controlbar-api/app.R | 35 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/dashboardUser/app.R | 6 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/descriptionBlock/app.R | 18 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/fresh-theming/app.R | 8 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/preloader/app.R | 5 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/scrollToTop/app.R | 2 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/skinSelector/app.R | 2 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/socialBox/app.R | 3 bs4Dash-2.3.5/bs4Dash/inst/examples/vignettes-demos/userMessages/app.R | 24 bs4Dash-2.3.5/bs4Dash/inst/placeholders |only bs4Dash-2.3.5/bs4Dash/inst/shinylive/tools.R | 3 bs4Dash-2.3.5/bs4Dash/inst/tests/test-gallery.R | 16 bs4Dash-2.3.5/bs4Dash/man/accordion.Rd | 48 bs4Dash-2.3.5/bs4Dash/man/actionButton.Rd | 38 bs4Dash-2.3.5/bs4Dash/man/alert.Rd | 14 bs4Dash-2.3.5/bs4Dash/man/appButton.Rd | 46 bs4Dash-2.3.5/bs4Dash/man/attachmentBlock.Rd | 2 bs4Dash-2.3.5/bs4Dash/man/badge.Rd | 26 bs4Dash-2.3.5/bs4Dash/man/box.Rd | 203 - 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Title: Create Panels of Independent States
Description: Create panel data consisting of independent states from 1816 to
the present. The package includes the Gleditsch & Ward (G&W) and Correlates
of War (COW) lists of independent states, as well as helper functions for
working with state panel data and standardizing other data sources to
create country-year/month/etc. data.
Author: Andreas Beger [cre, aut]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between states versions 0.3.2 dated 2023-09-05 and 0.3.3 dated 2025-08-25
DESCRIPTION | 11 +- MD5 | 24 +++--- NEWS.md | 3 R/plot-missing.R | 4 - R/states-package.R | 3 README.md | 4 - build/vignette.rds |binary inst/doc/differences-gw-cow.html | 4 - inst/doc/statelists.R | 2 inst/doc/statelists.html | 118 +++++++++++++++++++++---------- man/figures/README-unnamed-chunk-4-1.png |binary man/states.Rd | 13 +++ tests/testthat/test-plot-missing.R | 33 ++++---- 13 files changed, 141 insertions(+), 78 deletions(-)
Title: R Commander Plugin for Teaching Statistical Methods
Description: R Commander plugin for teaching statistical methods.
It adds a new menu for making easier the teaching of the main concepts about the main statistical methods.
Author: Tomas R. Cotos Yanez [aut] ,
Manuel A. Mosquera Rodriguez [aut, cre] ,
Ana Perez Gonzalez [aut] ,
Benigno Reguengo Lareo [aut]
Maintainer: Manuel A. Mosquera Rodriguez <mamrguez@uvigo.es>
Diff between RcmdrPlugin.TeachStat versions 1.1.3 dated 2023-11-14 and 1.1.4 dated 2025-08-25
DESCRIPTION | 16 +++++++++------- MD5 | 20 ++++++++++---------- NEWS | 9 +++++++++ build/partial.rdb |binary man/GUI_RandomANOVA.Rd | 2 +- man/RcmdrPlugin.TeachStat-package.Rd | 6 +++--- man/Utilities.Rd | 6 +++--- man/aovreml.Rd | 2 +- man/aovremm.Rd | 2 +- man/characRV.Rd | 4 ++-- man/priceIndexNum.Rd | 6 +++--- 11 files changed, 42 insertions(+), 31 deletions(-)
More information about RcmdrPlugin.TeachStat at CRAN
Permanent link
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the
tree in various orders. Aggregate, cumulate, print, plot, convert to and from
data.frame and more. Useful for decision trees, machine learning, finance,
conversion from and to JSON, and many other applications.
Author: Russ Hyde [ctb] ,
Chris Hammill [ctb] ,
Facundo Munoz [ctb] ,
Markus Wamser [ctb] ,
Pierre Formont [ctb] ,
Kent Russel [ctb] ,
Noam Ross [ctb] ,
Duncan Garmonsway [ctb] ,
Christoph Glur [aut, cre]
Maintainer: Christoph Glur <christoph.glur@powerpartners.pro>
Diff between data.tree versions 1.1.0 dated 2023-11-12 and 1.2.0 dated 2025-08-25
DESCRIPTION | 11 +- MD5 | 34 ++++---- NEWS | 41 ++++++++++ R/node.R | 16 ---- R/node_conversion_dataframe.R | 23 +++++ R/node_conversion_rpart.R | 4 - R/node_methods.R | 2 build/vignette.rds |binary data/acme.rda |binary data/mushroom.rda |binary inst/doc/applications.R | 156 +++++++++++++++++++-------------------- inst/doc/applications.html | 74 +++++++++--------- inst/doc/data.tree.R | 46 +++++------ inst/doc/data.tree.html | 89 +++++++++++++--------- man/NODE_RESERVED_NAMES_CONST.Rd | 2 man/Node.Rd | 6 - man/as.Node.data.frame.Rd | 5 + man/as.Node.rpart.Rd | 6 - 18 files changed, 289 insertions(+), 226 deletions(-)
Title: Generate CRediT Author Statements
Description: A tiny package to generate CRediT author statements (<https://credit.niso.org/>).
It provides three functions: create a template, read it back and generate the CRediT author statement in a text file.
Author: Josep Pueyo-Ros [aut, cre] ,
Marcelo S. Perlin [rev] ,
Joao Martins [rev]
Maintainer: Josep Pueyo-Ros <josep.pueyo@udg.edu>
Diff between CRediTas versions 0.2.0 dated 2023-04-13 and 0.3.0 dated 2025-08-25
DESCRIPTION | 18 +++--- MD5 | 23 ++++---- NEWS.md | 7 ++ R/cras_write.R | 35 +++++------- R/roles_get.R | 2 README.md | 72 +++++++++++++++++++------- build/vignette.rds |binary inst/CITATION |only inst/doc/get_started.R | 34 ++++++------ inst/doc/get_started.Rmd | 8 ++ inst/doc/get_started.html | 106 ++++++++++++++++++++------------------- tests/testthat/test-cras_write.R | 6 +- vignettes/get_started.Rmd | 8 ++ 13 files changed, 189 insertions(+), 130 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-19 6.3.3
Title: Analyzes Real-World Treatment Patterns of a Study Population of
Interest
Description: Computes treatment patterns within a given cohort using the Observational
Medical Outcomes Partnership (OMOP) common data model (CDM). As described
in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] ,
Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between TreatmentPatterns versions 3.1.0 dated 2025-06-03 and 3.1.1 dated 2025-08-25
DESCRIPTION | 6 +- MD5 | 26 ++++---- NEWS.md | 7 ++ R/CDMInterface.R | 6 +- R/constructPathways.R | 47 +++++----------- inst/doc/a000_bestPractices.html | 6 +- inst/doc/a001_DefiningCohorts.html | 16 ++--- inst/doc/a010_Computing_Pathways.html | 32 +++++----- inst/doc/a030_Evaluating_Output.R | 23 ++++--- inst/doc/a030_Evaluating_Output.Rmd | 23 ++++--- inst/doc/a030_Evaluating_Output.html | 85 ++++++++++++++++------------- tests/testthat/test-computePathways.R | 14 ++-- tests/testthat/test-multipleCohortTables.R | 9 ++- vignettes/a030_Evaluating_Output.Rmd | 23 ++++--- 14 files changed, 173 insertions(+), 150 deletions(-)
More information about TreatmentPatterns at CRAN
Permanent link
Title: Prompt Large Language Models and Enhance Their Functionality
Description: Easily construct prompts and associated logic for interacting with
large language models (LLMs).
'tidyprompt' introduces the concept of prompt wraps, which are building
blocks that you can use to quickly turn a simple prompt into a complex
one. Prompt wraps do not just modify the prompt text, but also add
extraction and validation functions that will be applied to the response
of the LLM. This ensures that the user gets the desired output.
'tidyprompt' can add various features to prompts and their evaluation
by LLMs, such as structured output, automatic feedback, retries, reasoning
modes, autonomous R function calling, and R code generation and evaluation.
It is designed to be compatible with any LLM provider that offers
chat completion.
Author: Luka Koning [aut, cre, cph],
Tjark Van de Merwe [aut, cph],
Kennispunt Twente [fnd]
Maintainer: Luka Koning <l.koning@kennispunttwente.nl>
Diff between tidyprompt versions 0.1.0 dated 2025-08-18 and 0.2.0 dated 2025-08-25
DESCRIPTION | 10 MD5 | 89 NAMESPACE | 3 NEWS.md | 117 R/answer_as_category.R | 418 +-- R/answer_as_json.R | 667 +++-- R/answer_using_tools.R | 2822 ++++++++++++------------ R/helper_ellmer_json_compatibility.R |only R/helper_ellmer_tool_compatibility.R |only R/internal_request_llm_provider.R | 754 ++++-- R/internal_test_helpers.R | 49 R/llm_provider.R | 756 +++--- R/llm_providers.R | 1671 +++++++------- R/prompt_wrap.R | 682 +++-- R/send_prompt.R | 877 +++---- R/tidyprompt-package.R | 2 R/tidyprompt.R | 28 README.md | 88 build/vignette.rds |binary inst/doc/getting_started.R |only inst/doc/getting_started.Rmd | 64 inst/doc/getting_started.html | 71 inst/examples/answer_as_json.R | 250 +- inst/examples/answer_using_tools.R | 224 + inst/examples/provider_prompt_wrap.R |only man/answer_as_category.Rd | 7 man/answer_as_json.Rd | 305 +- man/answer_as_multi_category.Rd | 7 man/answer_using_tools.Rd | 205 + man/llm_provider-class.Rd | 70 man/llm_provider_ellmer.Rd | 6 man/llm_provider_google_gemini.Rd | 9 man/llm_provider_openai.Rd | 7 man/prompt_wrap.Rd | 4 man/provider_prompt_wrap.Rd |only man/r_json_schema_to_example.Rd | 250 +- man/send_prompt.Rd | 14 man/tidyprompt-class.Rd | 18 man/tools_add_docs.Rd | 144 + man/tools_get_docs.Rd | 144 + tests/testthat/test-answer-as-json.R | 674 +++-- tests/testthat/test-answer_as_key_value.R | 6 tests/testthat/test-answer_using_tools.R | 288 +- tests/testthat/test-ellmer_json_compatibility.R |only tests/testthat/test-ellmer_tool_compatibility.R |only tests/testthat/test-openai_request.R |only tests/testthat/test-provider_prompt_wraps.R |only tests/testthat/test-send_prompt.R | 73 vignettes/getting_started.Rmd | 64 vignettes/getting_started.Rmd.orig | 66 50 files changed, 7115 insertions(+), 4888 deletions(-)
Title: Temporal Empirical Dynamic Modeling
Description: Inferring causation from time series data through empirical dynamic modeling (EDM), with methods such as convergent cross mapping from Sugihara et al. (2012) <doi:10.1126/science.1227079>, partial cross mapping as outlined in Leng et al. (2020) <doi:10.1038/s41467-020-16238-0>, and cross mapping cardinality as described in Tao et al. (2023) <doi:10.1016/j.fmre.2023.01.007>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between tEDM versions 1.0 dated 2025-07-15 and 1.1 dated 2025-08-25
tEDM-1.0/tEDM/man/figures/edm/fig1-1.png |only tEDM-1.0/tEDM/man/figures/edm/fig2-1.png |only tEDM-1.0/tEDM/man/figures/edm/fig3-1.png |only tEDM-1.0/tEDM/man/figures/edm/hk-cvd.png |only tEDM-1.1/tEDM/DESCRIPTION | 6 tEDM-1.1/tEDM/MD5 | 131 - tEDM-1.1/tEDM/NAMESPACE | 42 tEDM-1.1/tEDM/NEWS.md | 24 tEDM-1.1/tEDM/R/RcppExports.R | 68 tEDM-1.1/tEDM/R/ccm.R | 11 tEDM-1.1/tEDM/R/cmc.R | 9 tEDM-1.1/tEDM/R/embedded.R | 2 tEDM-1.1/tEDM/R/fnn.R | 63 tEDM-1.1/tEDM/R/formatoutput.R | 350 +-- tEDM-1.1/tEDM/R/globals.R | 8 tEDM-1.1/tEDM/R/ic.R | 74 tEDM-1.1/tEDM/R/internal_utility.R | 252 +- tEDM-1.1/tEDM/R/logostic_map.R | 10 tEDM-1.1/tEDM/R/multispatialccm.R | 120 - tEDM-1.1/tEDM/R/pcm.R | 10 tEDM-1.1/tEDM/R/simplex.R | 16 tEDM-1.1/tEDM/R/smap.R | 7 tEDM-1.1/tEDM/README.md | 15 tEDM-1.1/tEDM/inst/case/cvd.csv | 2066 ++++++++++---------- tEDM-1.1/tEDM/inst/doc/tEDM.Rmd | 532 ++--- tEDM-1.1/tEDM/inst/doc/tEDM.html | 849 ++++---- tEDM-1.1/tEDM/man/ccm.Rd | 10 tEDM-1.1/tEDM/man/cmc.Rd | 143 - tEDM-1.1/tEDM/man/embedded.Rd | 2 tEDM-1.1/tEDM/man/figures/edm/cvds_hk.png |only tEDM-1.1/tEDM/man/figures/edm/cvds_hk.rds |only tEDM-1.1/tEDM/man/figures/edm/fig_case2-1.png |binary tEDM-1.1/tEDM/man/figures/edm/fig_case3-1.png |binary tEDM-1.1/tEDM/man/figures/edm/fig_cvds_ts-1.png |only tEDM-1.1/tEDM/man/figures/edm/fig_pcm-1.png |only tEDM-1.1/tEDM/man/figures/edm/fig_simplex_cvd-1.png |only tEDM-1.1/tEDM/man/fnn.Rd | 107 - tEDM-1.1/tEDM/man/ic.Rd | 125 - tEDM-1.1/tEDM/man/multispatialccm.Rd | 158 - tEDM-1.1/tEDM/man/pcm.Rd | 176 - tEDM-1.1/tEDM/man/simplex.Rd | 150 - tEDM-1.1/tEDM/man/smap.Rd | 128 - tEDM-1.1/tEDM/src/CCM.cpp | 54 tEDM-1.1/tEDM/src/CCM.h | 26 tEDM-1.1/tEDM/src/CMC.cpp | 13 tEDM-1.1/tEDM/src/CMC.h | 2 tEDM-1.1/tEDM/src/CppDistances.cpp | 8 tEDM-1.1/tEDM/src/CppDistances.h | 3 tEDM-1.1/tEDM/src/CppStats.cpp | 29 tEDM-1.1/tEDM/src/CppStats.h | 6 tEDM-1.1/tEDM/src/EDMExp.cpp | 177 + tEDM-1.1/tEDM/src/Embed.cpp | 61 tEDM-1.1/tEDM/src/Embed.h | 13 tEDM-1.1/tEDM/src/Forecast4TS.cpp | 82 tEDM-1.1/tEDM/src/Forecast4TS.h | 54 tEDM-1.1/tEDM/src/IntersectionCardinality.cpp | 48 tEDM-1.1/tEDM/src/IntersectionCardinality.h | 8 tEDM-1.1/tEDM/src/MVE.cpp | 14 tEDM-1.1/tEDM/src/MVE.h | 10 tEDM-1.1/tEDM/src/MultispatialCCM.cpp | 29 tEDM-1.1/tEDM/src/MultispatialCCM.h | 10 tEDM-1.1/tEDM/src/PCM.cpp | 88 tEDM-1.1/tEDM/src/PCM.h | 24 tEDM-1.1/tEDM/src/RcppExports.cpp | 162 - tEDM-1.1/tEDM/src/SMap.cpp | 138 - tEDM-1.1/tEDM/src/SMap.h | 49 tEDM-1.1/tEDM/src/SimplexProjection.cpp | 153 - tEDM-1.1/tEDM/src/SimplexProjection.h | 50 tEDM-1.1/tEDM/src/StatsExp.cpp | 17 tEDM-1.1/tEDM/vignettes/tEDM.Rmd | 532 ++--- tEDM-1.1/tEDM/vignettes/tEDM.Rmd.orig | 288 +- 71 files changed, 4176 insertions(+), 3636 deletions(-)
Title: The Composer of Plots
Description: The 'ggplot2' package provides a strong API for sequentially
building up a plot, but does not concern itself with composition of multiple
plots. 'patchwork' is a package that expands the API to allow for
arbitrarily complex composition of plots by, among others, providing
mathematical operators for combining multiple plots. Other packages that try
to address this need (but with a different approach) are 'gridExtra' and
'cowplot'.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between patchwork versions 1.3.1 dated 2025-06-21 and 1.3.2 dated 2025-08-25
patchwork-1.3.1/patchwork/tests/testthat/_snaps/arithmetic/add-base-graphics-p1-plot-1-10-1-10.svg |only patchwork-1.3.2/patchwork/DESCRIPTION | 6 - patchwork-1.3.2/patchwork/MD5 | 37 ++++----- patchwork-1.3.2/patchwork/NAMESPACE | 4 - patchwork-1.3.2/patchwork/NEWS.md | 4 + patchwork-1.3.2/patchwork/R/aaa.R | 4 - patchwork-1.3.2/patchwork/R/add_plot.R | 6 - patchwork-1.3.2/patchwork/R/arithmetic.R | 6 - patchwork-1.3.2/patchwork/R/free.R | 4 - patchwork-1.3.2/patchwork/R/inset_element.R | 4 - patchwork-1.3.2/patchwork/R/plot_annotation.R | 29 ++++--- patchwork-1.3.2/patchwork/R/plot_layout.R | 2 patchwork-1.3.2/patchwork/R/plot_multipage.R | 6 - patchwork-1.3.2/patchwork/R/plot_patchwork.R | 2 patchwork-1.3.2/patchwork/R/wrap_plots.R | 6 - patchwork-1.3.2/patchwork/tests/testthat/_snaps/layout/basic-inset-works.svg | 4 + patchwork-1.3.2/patchwork/tests/testthat/_snaps/layout/insets-can-be-changed.svg | 38 ++++++--- patchwork-1.3.2/patchwork/tests/testthat/_snaps/layout/other-alignments-work.svg | 4 + patchwork-1.3.2/patchwork/tests/testthat/_snaps/layout/patchworks-can-be-inset.svg | 8 ++ patchwork-1.3.2/patchwork/tests/testthat/helper-setup.R | 39 +++++----- 20 files changed, 129 insertions(+), 84 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. Kriging models, are
applied to global multi-objective optimization of black-box functions.
Multi-objective Expected Improvement and Step-wise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois [aut, cre] ,
Victor Picheny [aut]
Maintainer: Mickael Binois <mickael.binois@inria.fr>
Diff between GPareto versions 1.1.8 dated 2024-01-26 and 1.1.9 dated 2025-08-25
DESCRIPTION | 26 ++++++++++++++++++-------- MD5 | 38 +++++++++++++++++++------------------- NEWS | 10 ++++++++-- R/GPareto-package.R | 2 +- R/GParetoptim.R | 2 +- R/crit_EHI.R | 4 ++-- R/crit_EMI.R | 2 +- R/crit_optimizer.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GPareto_vignette.R | 9 +++++---- inst/doc/GPareto_vignette.Rnw | 9 +++++---- inst/doc/GPareto_vignette.pdf |binary man/GPareto-package.Rd | 2 +- man/GParetoptim.Rd | 2 +- man/crit_EHI.Rd | 2 +- man/crit_EMI.Rd | 2 +- man/crit_optimizer.Rd | 2 +- man/crit_qEHI.Rd | 2 +- vignettes/GPareto_vignette.Rnw | 9 +++++---- 20 files changed, 72 insertions(+), 53 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/products/category/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureStor versions 3.7.0 dated 2022-05-25 and 3.7.1 dated 2025-08-25
DESCRIPTION | 10 MD5 | 78 ++--- NAMESPACE | 18 + NEWS.md | 9 R/add_methods.R | 10 R/az_storage.R | 12 R/azcopy.R | 8 R/azcopy_auth.R | 9 R/blob_client_funcs.R | 2 R/blob_lease.R | 4 R/client_endpoint.R | 2 R/download_dest.R | 6 R/sas.R | 15 - R/sign_request.R | 1 R/storage_utils.R | 2 R/transfer_utils.R | 3 README.md | 4 build/vignette.rds |binary inst/doc/aad.html | 302 +++++++++++++++-------- inst/doc/aad.rmd | 2 inst/doc/generics.html | 288 +++++++++++++--------- inst/doc/intro.html | 548 ++++++++++++++++++++++++------------------ inst/doc/intro.rmd | 4 man/adls_filesystem.Rd | 3 man/az_storage.Rd | 42 +-- man/azcopy.Rd | 2 man/blob.Rd | 2 man/blob_container.Rd | 3 man/create_storage_account.Rd | 12 man/delete_storage_account.Rd | 8 man/file_share.Rd | 3 man/generics.Rd | 15 - man/get_storage_account.Rd | 8 man/lease.Rd | 4 man/metadata.Rd | 12 man/properties.Rd | 3 man/sas.Rd | 19 - man/storage_endpoint.Rd | 2 vignettes/aad.rmd | 2 vignettes/intro.rmd | 4 40 files changed, 912 insertions(+), 569 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.10.0 dated 2025-08-22 and 2.10.1 dated 2025-08-25
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 537 +++++++++++++++++++++---------------------- R/RcppExports.R | 200 ++++++++-------- build/partial.rdb |binary inst/doc/Using-TreeDist.html | 6 inst/doc/landscapes.html | 4 src/tree_distances.cpp | 35 +- 8 files changed, 411 insertions(+), 393 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Facilitate the evaluation of forecasts in a convenient
framework based on data.table. It allows user to to check their forecasts
and diagnose issues, to visualise forecasts and missing data, to transform
data before scoring, to handle missing forecasts, to aggregate scores, and
to visualise the results of the evaluation. The package mostly focuses on
the evaluation of probabilistic forecasts and allows evaluating several
different forecast types and input formats. Find more information about the
package in the Vignettes as well as in the accompanying paper,
<doi:10.48550/arXiv.2205.07090>.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Toshiaki Asakura [ctb] ,
James Mba Azam [ctb] ,
Sebastian Funk [aut],
Michael Chirico [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 2.1.1 dated 2025-06-25 and 2.1.2 dated 2025-08-25
DESCRIPTION | 6 MD5 | 32 +- NEWS.md | 5 R/class-forecast-quantile.R | 14 R/get-pit-histogram.R | 4 README.md | 17 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Deprecated-functions.html | 5 inst/doc/Deprecated-visualisations.html | 11 inst/doc/scoring-rules.html | 9 inst/manuscript/manuscript.Rmd | 2 inst/manuscript/manuscript.tex | 110 +++---- man/get_pit_histogram.Rd | 4 tests/testthat/test-class-forecast-quantile.R | 20 + vignettes/scoring-multivariate-forecasts.R | 10 vignettes/scoring-multivariate-forecasts.html | 395 +++++++++++--------------- 17 files changed, 330 insertions(+), 314 deletions(-)
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
This is a re-admission after prior archival of version 1.5.3 dated 2024-07-26
Diff between nser versions 1.5.3 dated 2024-07-26 and 1.5.6 dated 2025-08-25
nser-1.5.3/nser/inst/nseoption.py |only nser-1.5.6/nser/DESCRIPTION | 10 +-- nser-1.5.6/nser/MD5 | 93 +++++++++++++++-------------- nser-1.5.6/nser/NAMESPACE | 1 nser-1.5.6/nser/R/bhav1.R | 2 nser-1.5.6/nser/R/bhavtoday.R | 31 ++++----- nser-1.5.6/nser/R/fobhav.R | 54 +++++----------- nser-1.5.6/nser/R/fobhav1.R |only nser-1.5.6/nser/R/fobhavtoday.R | 36 +++++------ nser-1.5.6/nser/build/vignette.rds |binary nser-1.5.6/nser/inst/doc/bhavfos.R | 2 nser-1.5.6/nser/inst/doc/bhavfos.html | 8 +- nser-1.5.6/nser/inst/doc/bhavpr.R | 2 nser-1.5.6/nser/inst/doc/bhavpr.html | 4 - nser-1.5.6/nser/inst/doc/bhavs.R | 2 nser-1.5.6/nser/inst/doc/bhavs.html | 4 - nser-1.5.6/nser/inst/doc/bhavtoday.R | 2 nser-1.5.6/nser/inst/doc/bhavtoday.html | 4 - nser-1.5.6/nser/inst/doc/dailydata.R | 2 nser-1.5.6/nser/inst/doc/dailydata.html | 4 - nser-1.5.6/nser/inst/doc/daytomonth.R | 2 nser-1.5.6/nser/inst/doc/daytoweek.R | 2 nser-1.5.6/nser/inst/doc/fdii.R | 2 nser-1.5.6/nser/inst/doc/fobhav.R | 8 -- nser-1.5.6/nser/inst/doc/fobhav.Rmd | 6 - nser-1.5.6/nser/inst/doc/fobhav.html | 33 +--------- nser-1.5.6/nser/inst/doc/fobhav1.R |only nser-1.5.6/nser/inst/doc/fobhav1.Rmd |only nser-1.5.6/nser/inst/doc/fobhav1.html |only nser-1.5.6/nser/inst/doc/fobhavtoday.R | 2 nser-1.5.6/nser/inst/doc/fobhavtoday.html | 4 - nser-1.5.6/nser/inst/doc/nseindex.R | 2 nser-1.5.6/nser/inst/doc/nseipo.R | 2 nser-1.5.6/nser/inst/doc/nselive.R | 2 nser-1.5.6/nser/inst/doc/nselive.html | 4 - nser-1.5.6/nser/inst/doc/nseopen.R | 2 nser-1.5.6/nser/inst/doc/nseopen.html | 4 - nser-1.5.6/nser/inst/doc/nsetree.R | 2 nser-1.5.6/nser/inst/doc/nsetree.html | 4 - nser-1.5.6/nser/inst/doc/optbanknifty.R | 2 nser-1.5.6/nser/inst/doc/optbanknifty.html | 4 - nser-1.5.6/nser/inst/doc/optnifty.R | 2 nser-1.5.6/nser/inst/doc/optnifty.html | 4 - nser-1.5.6/nser/inst/nlive.py | 18 ----- nser-1.5.6/nser/inst/npo.py | 2 nser-1.5.6/nser/man/bhav1.Rd | 2 nser-1.5.6/nser/man/fobhav.Rd | 5 - nser-1.5.6/nser/man/fobhav1.Rd |only nser-1.5.6/nser/tests |only nser-1.5.6/nser/vignettes/fobhav.Rmd | 6 - nser-1.5.6/nser/vignettes/fobhav1.Rmd |only 51 files changed, 167 insertions(+), 220 deletions(-)
Title: Toolkit for Analysis of Genomic Data
Description: A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Eitan Yaffe [aut],
Amos Tanay [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between misha versions 4.3.6 dated 2025-03-06 and 4.3.11 dated 2025-08-25
DESCRIPTION | 7 MD5 | 113 ++++----- NAMESPACE | 1 NEWS.md | 22 + R/db.R | 4 R/intervals.R | 24 +- R/track-2d.R | 4 R/track-array.R | 1 R/track.R | 319 ++++++++++++++++++++++++--- build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/Genomes.R | 158 ++++++------- inst/doc/Genomes.html | 2 inst/doc/Manual.R | 62 ++--- inst/doc/Manual.html | 2 man/gintervals.mapply.Rd | 17 + man/gtrack.create_dense.Rd |only man/gtrack.import.Rd | 76 +++++- src/BinsManager.cpp | 3 src/GIntervalsBigSet.cpp | 2 src/GIntervalsBigSet1D.cpp | 5 src/GIntervalsBigSet2D.cpp | 5 src/GIntervalsMeta.cpp | 9 src/GIntervalsMeta1D.cpp | 22 - src/GIntervalsMeta2D.cpp | 20 - src/GTrackIntervalsFetcher.cpp | 2 src/GenomeCisDecay.cpp | 10 src/GenomeComputeStrandAutocorr.cpp | 23 + src/GenomeTrackApply.cpp | 41 ++- src/GenomeTrackArrayExtract.cpp | 17 - src/GenomeTrackArrayImport.cpp | 7 src/GenomeTrackBinnedTransform.cpp | 13 - src/GenomeTrackCreateDense.cpp |only src/GenomeTrackDistribution.cpp | 32 +- src/GenomeTrackExtract.cpp | 34 +- src/GenomeTrackFindNeighbors.cpp | 6 src/GenomeTrackInfo.cpp | 16 - src/GenomeTrackPartition.cpp | 11 src/GenomeTrackQuantiles.cpp | 30 +- src/GenomeTrackSampler.cpp | 3 src/GenomeTrackSummary.cpp | 46 ++- src/GenomeTrackWilcox.cpp | 7 src/IntervalsLiftover.cpp | 10 src/Makevars | 1 src/TrackExpressionScanner.cpp | 31 +- src/TrackExpressionScanner.h | 5 src/TrackExpressionVars.cpp | 119 +++++----- src/TrackExpressionVars.h | 3 src/TrackVars.cpp | 12 - src/misha-init.cpp | 10 src/rdbinterval.cpp | 59 ++--- src/rdbutils.cpp | 48 +--- src/rdbutils.h | 72 ++++++ tests/testthat/test-gintervals.mapply.R | 18 + tests/testthat/test-gtrack.create_dense.R |only tests/testthat/test-gtrack.import.R | 249 +++++++++++++++++++++ tests/testthat/test-kmer.R | 226 +++++++++++++++++++ tests/testthat/test-pwm.R | 354 ++++++++++++++++++++++++++++++ tests/testthat/test-track.attrs.R | 14 - 59 files changed, 1879 insertions(+), 531 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currently it works with GFS <https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast>, MeteoGalicia <https://www.meteogalicia.gal/web/modelos/threddsIndex.action>, NAM <https://www.ncei.noaa.gov/products/weather-climate-models/north-american-mesoscale>, and RAP <https://www.ncei.noaa.gov/products/weather-climate-models/rapid-refresh-update>.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@upm.es>
Diff between meteoForecast versions 0.56 dated 2023-03-08 and 0.57 dated 2025-08-25
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------ R/composeURL.R | 72 ++++++++++----------------------------------------- R/pointGFS.R | 52 ++++++++++++++++++++++-------------- README.md | 10 ++----- inst/CITATION | 2 - man/getPoint.Rd | 4 +- man/getRaster.Rd | 8 ++--- man/meteo-package.Rd | 4 +- man/vars.Rd | 4 +- 10 files changed, 75 insertions(+), 109 deletions(-)
Title: Extra Appenders for 'lgr'
Description: Additional appenders for the logging package 'lgr' that
support logging to 'Elasticsearch', 'Dynatrace', 'AWSCloudWatchLog',
databases, 'syslog', email- and push notifications, and more.
Author: Stefan Fleck [aut, cre] ,
Jimmy Briggs [ctb, rev]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgrExtra versions 0.2.0 dated 2025-07-23 and 0.2.1 dated 2025-08-25
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NEWS.md | 20 +++++++++++++------- R/AppenderElasticSearch.R | 2 +- R/LayoutDynatrace.R |only man/AppenderElasticSearch.Rd | 2 +- man/lgrExtra-package.Rd | 2 +- tests/testthat/test_DynatraceLayout.R | 4 ++-- 8 files changed, 31 insertions(+), 24 deletions(-)
Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.
Author: Benjamin M. Taylor [aut, cre],
Tilman M. Davies [aut],
Barry S. Rowlingson [aut],
Peter J. Diggle [aut],
Edzer Pebesma [ctb],
Dominic Schumacher. [ctb]
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Diff between lgcp versions 2.0 dated 2023-10-03 and 2.0-1 dated 2025-08-25
DESCRIPTION | 38 ++++++++++--- MD5 | 72 +++++++++++++------------- R/AggregateSpatialOnlyPlusParameters.R | 2 R/MultitypeSpatialOnlyPlusParameters.R | 2 R/SpatialOnlyPlusParameters.R | 2 R/SpatioTemporalPlusParameters.R | 2 R/adaptiveSchemes.R | 4 - R/lgcp.R | 9 ++- R/lgcpStructures.R | 4 - R/minimumContrast.R | 4 - R/parameterEstimation.R | 4 - R/spatialAtRiskClassDef.R | 18 +++--- build/partial.rdb |binary build/vignette.rds |binary data/wpopdata.rda |binary data/wtowncoords.rda |binary data/wtowns.rda |binary inst/doc/lgcp.pdf |binary man/GaussianPrior.Rd | 2 man/LogGaussianPrior.Rd | 2 man/density.stppp.Rd | 4 - man/initialiseAMCMC.Rd | 2 man/lgcp-package.Rd | 29 ++++++---- man/lgcpPredictAggregateSpatialPlusPars.Rd | 2 man/lgcpPredictMultitypeSpatialPlusPars.Rd | 2 man/lgcpPredictSpatialPlusPars.Rd | 2 man/lgcpPredictSpatioTemporalPlusPars.Rd | 2 man/spatialAtRisk.Rd | 2 man/spatialAtRisk.SpatialGridDataFrame.Rd | 2 man/spatialAtRisk.SpatialPolygonsDataFrame.Rd | 2 man/spatialAtRisk.bivden.Rd | 2 man/spatialAtRisk.default.Rd | 2 man/spatialAtRisk.fromXYZ.Rd | 2 man/spatialAtRisk.function.Rd | 2 man/spatialAtRisk.im.Rd | 2 man/spatialAtRisk.lgcpgrid.Rd | 2 man/updateAMCMC.Rd | 2 37 files changed, 129 insertions(+), 99 deletions(-)
Title: Gaussian Process Panel Modeling
Description: Provides an implementation of Gaussian process panel modeling (GPPM).
GPPM is described in Karch, Brandmaier & Voelkle (2020; <DOI:10.3389/fpsyg.2020.00351>) and Karch (2016; <DOI:10.18452/17641>).
Essentially, GPPM is Gaussian process based modeling of longitudinal panel data.
'gppm' also supports regular Gaussian process regression (with a focus on flexible model specification), and multi-task learning.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
This is a re-admission after prior archival of version 0.2.0 dated 2018-07-05
Diff between gppm versions 0.2.0 dated 2018-07-05 and 0.3.0 dated 2025-08-25
gppm-0.2.0/gppm/man/covf.Rd |only gppm-0.2.0/gppm/man/datas.Rd |only gppm-0.2.0/gppm/man/maxnObs.Rd |only gppm-0.2.0/gppm/man/meanf.Rd |only gppm-0.3.0/gppm/DESCRIPTION | 24 - gppm-0.3.0/gppm/MD5 | 142 +++---- gppm-0.3.0/gppm/NAMESPACE | 42 +- gppm-0.3.0/gppm/R/FitRes.R | 77 ++-- gppm-0.3.0/gppm/R/GPPM.R | 136 +++---- gppm-0.3.0/gppm/R/GPPMControl.R | 8 gppm-0.3.0/gppm/R/LongData.R | 48 +- gppm-0.3.0/gppm/R/ParsedModel.R | 160 ++++---- gppm-0.3.0/gppm/R/StanData.R | 128 +++--- gppm-0.3.0/gppm/R/cross_validation.R | 105 ++--- gppm-0.3.0/gppm/R/data.R | 3 gppm-0.3.0/gppm/R/extractors.R | 252 +++++++------ gppm-0.3.0/gppm/R/fit.R | 74 ++- gppm-0.3.0/gppm/R/plotLong.R | 34 + gppm-0.3.0/gppm/R/predict.R | 277 ++++++++------ gppm-0.3.0/gppm/R/simulate.R | 100 ++--- gppm-0.3.0/gppm/R/stanmodels.R |only gppm-0.3.0/gppm/R/summary.R | 152 ++++---- gppm-0.3.0/gppm/R/toStan.R | 30 - gppm-0.3.0/gppm/R/zzz.R |only gppm-0.3.0/gppm/configure |only gppm-0.3.0/gppm/configure.win |only gppm-0.3.0/gppm/data/demoLGCM.rda |binary gppm-0.3.0/gppm/data/trueParas.rda |binary gppm-0.3.0/gppm/demo/00Index | 6 gppm-0.3.0/gppm/demo/example1linearModel.R | 28 - gppm-0.3.0/gppm/demo/example2LGCM.R | 44 +- gppm-0.3.0/gppm/demo/example3AR1.R | 28 - gppm-0.3.0/gppm/inst/demo_helpers.R | 412 +++++++++++----------- gppm-0.3.0/gppm/inst/stan |only gppm-0.3.0/gppm/inst/stanTemplate.stan | 4 gppm-0.3.0/gppm/man/SE.Rd | 34 + gppm-0.3.0/gppm/man/accuracy.Rd | 19 - gppm-0.3.0/gppm/man/coef.GPPM.Rd | 36 + gppm-0.3.0/gppm/man/confint.GPPM.Rd | 36 + gppm-0.3.0/gppm/man/covFun.Rd |only gppm-0.3.0/gppm/man/createLeavePersonsOutFolds.Rd | 8 gppm-0.3.0/gppm/man/crossvalidate.Rd | 16 gppm-0.3.0/gppm/man/demoLGCM.Rd | 6 gppm-0.3.0/gppm/man/fit.GPPM.Rd | 29 + gppm-0.3.0/gppm/man/fit.Rd | 44 +- gppm-0.3.0/gppm/man/fitted.GPPM.Rd | 34 + gppm-0.3.0/gppm/man/getData.Rd |only gppm-0.3.0/gppm/man/getIntern.Rd | 36 + gppm-0.3.0/gppm/man/gppm.Rd | 8 gppm-0.3.0/gppm/man/gppmControl.Rd | 42 +- gppm-0.3.0/gppm/man/logLik.GPPM.Rd | 34 + gppm-0.3.0/gppm/man/maxNObs.Rd |only gppm-0.3.0/gppm/man/meanFun.Rd |only gppm-0.3.0/gppm/man/nObs.Rd | 36 + gppm-0.3.0/gppm/man/nPars.Rd | 34 + gppm-0.3.0/gppm/man/nPers.Rd | 34 + gppm-0.3.0/gppm/man/nPreds.Rd | 34 + gppm-0.3.0/gppm/man/parEsts.Rd | 34 + gppm-0.3.0/gppm/man/pars.Rd | 34 + gppm-0.3.0/gppm/man/plot.GPPMPred.Rd | 18 gppm-0.3.0/gppm/man/plot.LongData.Rd | 6 gppm-0.3.0/gppm/man/predict.GPPM.Rd | 14 gppm-0.3.0/gppm/man/preds.Rd | 34 + gppm-0.3.0/gppm/man/simulate.GPPM.Rd | 24 - gppm-0.3.0/gppm/man/summary.GPPM.Rd | 10 gppm-0.3.0/gppm/man/trueParas.Rd | 4 gppm-0.3.0/gppm/man/vcov.GPPM.Rd | 34 + gppm-0.3.0/gppm/tests/long/fullPipeline.R |only gppm-0.3.0/gppm/tests/long/test-simulate-long.R | 53 +- gppm-0.3.0/gppm/tests/testthat/setup-global.R | 14 gppm-0.3.0/gppm/tests/testthat/setup-gppm.R | 16 gppm-0.3.0/gppm/tests/testthat/test-cv.R | 39 +- gppm-0.3.0/gppm/tests/testthat/test-extractors.R | 54 +- gppm-0.3.0/gppm/tests/testthat/test-fit.R | 30 + gppm-0.3.0/gppm/tests/testthat/test-gppm.R | 79 +--- gppm-0.3.0/gppm/tests/testthat/test-plotLong.R | 6 gppm-0.3.0/gppm/tests/testthat/test-predict.R | 77 ++-- gppm-0.3.0/gppm/tests/testthat/test-simulate.R | 24 - gppm-0.3.0/gppm/tests/testthat/test-summary.R | 7 79 files changed, 1918 insertions(+), 1527 deletions(-)
Title: Functions for 'Ecdat'
Description: Functions and vignettes to update
data sets in 'Ecdat' and to create, manipulate,
plot, and analyze those and similar data sets.
Author: Spencer Graves [aut, cre]
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.3-6 dated 2024-11-12 and 0.4.0 dated 2025-08-25
Ecfun-0.3-6/Ecfun/R/findCountry.R |only Ecfun-0.3-6/Ecfun/man/findCountry.Rd |only Ecfun-0.4.0/Ecfun/DESCRIPTION | 10 Ecfun-0.4.0/Ecfun/MD5 | 36 - Ecfun-0.4.0/Ecfun/NAMESPACE | 4 Ecfun-0.4.0/Ecfun/NEWS.md | 4 Ecfun-0.4.0/Ecfun/R/grepInTable.R |only Ecfun-0.4.0/Ecfun/README.md | 16 Ecfun-0.4.0/Ecfun/build/vignette.rds |binary Ecfun-0.4.0/Ecfun/inst/WORDLIST | 2 Ecfun-0.4.0/Ecfun/inst/doc/UpdatingUSGDPpresidents.R | 282 ++++++++- Ecfun-0.4.0/Ecfun/inst/doc/UpdatingUSGDPpresidents.Rmd | 405 +++++++++++-- Ecfun-0.4.0/Ecfun/inst/doc/UpdatingUSGDPpresidents.html | 352 +++++++++-- Ecfun-0.4.0/Ecfun/inst/doc/nuclearArmageddon.Rmd | 12 Ecfun-0.4.0/Ecfun/inst/doc/nuclearArmageddon.html | 117 +-- Ecfun-0.4.0/Ecfun/inst/doc/updateOCC1950.html | 208 ++---- Ecfun-0.4.0/Ecfun/inst/doc/update_nuclearWeaponStates.html | 13 Ecfun-0.4.0/Ecfun/man/asNumericDF.Rd | 6 Ecfun-0.4.0/Ecfun/man/grepInTable.Rd |only Ecfun-0.4.0/Ecfun/vignettes/UpdatingUSGDPpresidents.Rmd | 405 +++++++++++-- Ecfun-0.4.0/Ecfun/vignettes/nuclearArmageddon.Rmd | 12 21 files changed, 1504 insertions(+), 380 deletions(-)
Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from major central
bank APIs. It supports access to the 'Bundesbank SDMX Web Service API'
(<https://www.bundesbank.de/en/statistics/time-series-databases/help-for-sdmx-web-service/web-service-interface-data>),
the 'Swiss National Bank Data Portal' (<https://data.snb.ch/en>), the
'European Central Bank Data Portal API'
(<https://data.ecb.europa.eu/help/api/overview>), the 'Bank of England
Interactive Statistical Database'
(<https://www.bankofengland.co.uk/boeapps/database>), the 'Banco de
España API'
(<https://www.bde.es/webbe/en/estadisticas/recursos/api-estadisticas-bde.html>),
and the 'Banque de France Web Service'
(<https://webstat.banque-france.fr/en/pages/guide-migration-api/>).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.6.0 dated 2025-02-02 and 0.7.0 dated 2025-08-25
DESCRIPTION | 23 +- MD5 | 73 +++++-- NAMESPACE | 14 + NEWS.md | 9 R/assertions.R | 60 ++---- R/bbk-package.R | 6 R/bbk.R | 184 ++++++++++--------- R/bde.R |only R/bdf.R |only R/boe.R |only R/ecb-euro-rates.R | 54 ++--- R/ecb.R | 198 ++++++++++----------- R/onb.R |only R/snb.R | 78 ++++---- R/utils.R | 7 README.md | 64 ++---- man/bbk-package.Rd | 2 man/bbk_data.Rd | 57 +++--- man/bbk_metadata.Rd | 28 +- man/bbk_series.Rd | 13 + man/bde_data.Rd |only man/bdf_codelist.Rd |only man/bdf_data.Rd |only man/bdf_dataset.Rd |only man/boe_data.Rd |only man/ecb_data.Rd | 59 +++--- man/ecb_euro_rates.Rd | 12 - man/ecb_metadata.Rd | 25 +- man/figures/README-plotting-1.png |binary man/onb_data.Rd |only man/onb_dimension.Rd |only man/onb_frequency.Rd |only man/onb_hierarchy.Rd |only man/onb_metadata.Rd |only man/onb_toc.Rd |only man/snb_data.Rd | 27 +- tests/testthat/fixtures/bde-data.rds |only tests/testthat/fixtures/boe-data.xml |only tests/testthat/fixtures/onb-content-hierid-pos.xml |only tests/testthat/fixtures/onb-content-hierid.xml |only tests/testthat/fixtures/onb-content.xml |only tests/testthat/fixtures/onb-data.xml |only tests/testthat/fixtures/onb-freq.xml |only tests/testthat/fixtures/onb-metadata.xml |only tests/testthat/test-bbk.R | 32 ++- tests/testthat/test-bde.R |only tests/testthat/test-boe.R |only tests/testthat/test-ecb-euro-rates.R | 8 tests/testthat/test-ecb.R | 8 tests/testthat/test-snb.R | 4 50 files changed, 593 insertions(+), 452 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-22 1.2.2
2023-01-05 1.2.0
2020-08-14 1.1.0
2017-12-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 1.2.1
2023-09-21 1.2-0
2022-01-12 1.1-0
2021-09-15 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-22 0.4.1
2021-07-06 0.2.1
2019-09-22 0.1.0
2019-09-19 0.0.1
Title: (Precipitation) Frequency Analysis and Variability with
L-Moments from 'lmom'
Description: It is an extension of 'lmom' R package: 'pel...()','cdf...()',qua...()' function
families are lumped and called from one function per each family respectively in order to
create robust automatic tools to fit data with different probability
distributions and then to estimate probability values and return periods. The implemented functions are able to manage time series with constant and/or missing values without stopping
the execution with error messages. The package also contains tools to calculate several indices based on variability (e.g. 'SPI' , Standardized
Precipitation Index, see <https://climatedataguide.ucar.edu/climate-data/standardized-precipitation-index-spi> and <http://spei.csic.es/>) for multiple time series or spatially gridded values.
Author: Emanuele Cordano [aut, cre]
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between lmomPi versions 0.6.6 dated 2023-08-15 and 0.6.7 dated 2025-08-25
lmomPi-0.6.6/lmomPi/man/lmomPi-Package.Rd |only lmomPi-0.6.7/lmomPi/DESCRIPTION | 16 ++++---- lmomPi-0.6.7/lmomPi/MD5 | 17 ++++---- lmomPi-0.6.7/lmomPi/R/cdf.R | 4 +- lmomPi-0.6.7/lmomPi/R/lmomPi-package.R | 57 ++++++++++++------------------ lmomPi-0.6.7/lmomPi/R/pel.R | 14 +++---- lmomPi-0.6.7/lmomPi/R/qua.R | 6 +-- lmomPi-0.6.7/lmomPi/man/cdf.Rd | 4 +- lmomPi-0.6.7/lmomPi/man/pel.Rd | 14 +++---- lmomPi-0.6.7/lmomPi/man/qua.Rd | 6 +-- 10 files changed, 65 insertions(+), 73 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-22 1.1.2
2025-01-19 1.1
2024-04-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-24 3.0.0
2024-07-09 2.0.9
2023-10-30 2.0.5
2023-02-24 2.0.0
2022-03-25 1.4.1
2021-10-25 1.4.0
2021-10-14 1.3.7
2021-10-12 1.3.6
2021-03-20 1.3.5
2020-11-18 1.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-23 0.9-2.1
2025-07-22 0.9-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-30 0.1.4
2023-03-16 0.1.3
2022-07-17 0.1.2
2022-04-25 0.1.1
2021-12-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-29 0.1.1
2020-06-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-03 2.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-26 1.2.0
2024-11-26 1.2.1
2024-09-23 1.1.0
2024-05-28 1.0.3
2024-03-21 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-02 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-15 1.2.0
2025-01-07 1.0.0
2024-12-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-08 1.1.0
2025-01-14 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-04 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-07 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-17 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-24 2.3.6
2024-10-13 2.3.4
2024-06-17 2.3.3
2022-10-12 2.3.2
2022-06-30 2.3.1
2022-01-04 2.3.0
2021-09-02 2.2.1
2021-08-18 2.2.0
2021-05-13 2.1.0
2021-04-25 2.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-13 1.1-1
2022-03-22 1.1
2021-07-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-16 2.0.1
2025-03-11 2.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-10 2.3.3
2024-11-29 2.3.2
2024-04-17 2.3.1
2024-01-22 2.3.0
2023-10-24 2.2.0
2023-05-24 2.1.0
2022-11-18 2.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-17 1.0-0
2024-10-25 0.1-0
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.18 dated 2025-07-29 and 1.19 dated 2025-08-25
openxlsx2-1.18/openxlsx2/R/utils-pipe.R |only openxlsx2-1.18/openxlsx2/man/pipe.Rd |only openxlsx2-1.19/openxlsx2/DESCRIPTION | 8 openxlsx2-1.19/openxlsx2/MD5 | 152 ++++----- openxlsx2-1.19/openxlsx2/NAMESPACE | 2 openxlsx2-1.19/openxlsx2/NEWS.md | 19 + openxlsx2-1.19/openxlsx2/R/class-comment.R | 6 openxlsx2-1.19/openxlsx2/R/class-style_mgr.R | 99 ++--- openxlsx2-1.19/openxlsx2/R/class-workbook-wrappers.R | 127 ++++--- openxlsx2-1.19/openxlsx2/R/class-workbook.R | 136 +++++--- openxlsx2-1.19/openxlsx2/R/class-worksheet.R | 12 openxlsx2-1.19/openxlsx2/R/helper-functions.R | 2 openxlsx2-1.19/openxlsx2/R/openxlsx2-package.R | 5 openxlsx2-1.19/openxlsx2/R/read.R | 8 openxlsx2-1.19/openxlsx2/R/utils.R | 104 ++++-- openxlsx2-1.19/openxlsx2/R/wb_load.R | 47 ++ openxlsx2-1.19/openxlsx2/R/write.R | 2 openxlsx2-1.19/openxlsx2/inst/WORDLIST | 2 openxlsx2-1.19/openxlsx2/inst/doc/Update-from-openxlsx.R | 35 +- openxlsx2-1.19/openxlsx2/inst/doc/Update-from-openxlsx.Rmd | 35 +- openxlsx2-1.19/openxlsx2/inst/doc/Update-from-openxlsx.html | 26 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2.R | 29 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2.Rmd | 33 + openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2.html | 26 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_charts_manual.R | 17 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_charts_manual.Rmd | 19 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_charts_manual.html | 31 - openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_read_to_df.R | 2 openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_read_to_df.Rmd | 2 openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_read_to_df.html | 2 openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_style_manual.R | 117 +++---- openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 117 +++---- openxlsx2-1.19/openxlsx2/inst/doc/openxlsx2_style_manual.html | 167 ++++------ openxlsx2-1.19/openxlsx2/inst/extdata/colors.R | 2 openxlsx2-1.19/openxlsx2/inst/extdata/themes.R | 6 openxlsx2-1.19/openxlsx2/man/dims_helper.Rd | 5 openxlsx2-1.19/openxlsx2/man/openxlsx2-package.Rd | 4 openxlsx2-1.19/openxlsx2/man/wbWorkbook.Rd | 14 openxlsx2-1.19/openxlsx2/man/wb_add_border.Rd | 4 openxlsx2-1.19/openxlsx2/man/wb_add_cell_style.Rd | 10 openxlsx2-1.19/openxlsx2/man/wb_add_data.Rd | 2 openxlsx2-1.19/openxlsx2/man/wb_add_dxfs_style.Rd | 7 openxlsx2-1.19/openxlsx2/man/wb_add_fill.Rd | 15 openxlsx2-1.19/openxlsx2/man/wb_add_font.Rd | 6 openxlsx2-1.19/openxlsx2/man/wb_add_form_control.Rd | 5 openxlsx2-1.19/openxlsx2/man/wb_add_mschart.Rd | 15 openxlsx2-1.19/openxlsx2/man/wb_add_numfmt.Rd | 6 openxlsx2-1.19/openxlsx2/man/wb_add_pivot_table.Rd | 13 openxlsx2-1.19/openxlsx2/man/wb_add_sparklines.Rd | 8 openxlsx2-1.19/openxlsx2/man/wb_add_style.Rd | 3 openxlsx2-1.19/openxlsx2/man/wb_add_thread.Rd | 7 openxlsx2-1.19/openxlsx2/man/wb_cell_style.Rd | 8 openxlsx2-1.19/openxlsx2/man/wb_data.Rd | 6 openxlsx2-1.19/openxlsx2/man/wb_dims.Rd | 7 openxlsx2-1.19/openxlsx2/man/wb_set_bookview.Rd | 18 - openxlsx2-1.19/openxlsx2/src/helper_functions.cpp | 85 ++--- openxlsx2-1.19/openxlsx2/tests/testthat/test-class-color.R | 16 openxlsx2-1.19/openxlsx2/tests/testthat/test-class-comment.R | 37 +- openxlsx2-1.19/openxlsx2/tests/testthat/test-class-workbook-wrappers.R | 6 openxlsx2-1.19/openxlsx2/tests/testthat/test-class-workbook.R | 54 +-- openxlsx2-1.19/openxlsx2/tests/testthat/test-class-worksheet.R | 24 - openxlsx2-1.19/openxlsx2/tests/testthat/test-cloneWorksheet.R | 26 - openxlsx2-1.19/openxlsx2/tests/testthat/test-conditional_formatting.R | 23 + openxlsx2-1.19/openxlsx2/tests/testthat/test-helper-functions.R | 8 openxlsx2-1.19/openxlsx2/tests/testthat/test-loading_workbook.R | 8 openxlsx2-1.19/openxlsx2/tests/testthat/test-read_xlsb.R | 2 openxlsx2-1.19/openxlsx2/tests/testthat/test-read_xlsx_correct_sheet.R | 2 openxlsx2-1.19/openxlsx2/tests/testthat/test-save.R | 6 openxlsx2-1.19/openxlsx2/tests/testthat/test-tables.R | 8 openxlsx2-1.19/openxlsx2/tests/testthat/test-utils.R | 12 openxlsx2-1.19/openxlsx2/tests/testthat/test-wb_functions.R | 10 openxlsx2-1.19/openxlsx2/tests/testthat/test-wb_styles.R | 86 ++--- openxlsx2-1.19/openxlsx2/tests/testthat/test-write.R | 76 ++-- openxlsx2-1.19/openxlsx2/vignettes/Update-from-openxlsx.Rmd | 35 +- openxlsx2-1.19/openxlsx2/vignettes/openxlsx2.Rmd | 33 + openxlsx2-1.19/openxlsx2/vignettes/openxlsx2_charts_manual.Rmd | 19 - openxlsx2-1.19/openxlsx2/vignettes/openxlsx2_read_to_df.Rmd | 2 openxlsx2-1.19/openxlsx2/vignettes/openxlsx2_style_manual.Rmd | 117 +++---- 78 files changed, 1222 insertions(+), 1033 deletions(-)
Title: Tools for Tensor Analysis and Decomposition
Description: A set of tools for creation, manipulation, and modeling
of tensors with arbitrary number of modes. A tensor in the context of data
analysis is a multidimensional array. rTensor does this by providing a S4
class 'Tensor' that wraps around the base 'array' class. rTensor
provides common tensor operations as methods, including matrix unfolding,
summing/averaging across modes, calculating the Frobenius norm, and taking
the inner product between two tensors. Familiar array operations are
overloaded, such as index subsetting via '[' and element-wise operations.
rTensor also implements various tensor decomposition, including CP, GLRAM,
MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements
transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some
auxiliary functions include the Khatri-Rao product, Kronecker product, and
the Hadamard product for a list of matrices.
Author: James Li [aut],
Jacob Bien [aut],
Martin Wells [aut],
Koki Tsuyuzaki [cre, ctb]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between rTensor versions 1.4.8 dated 2021-05-15 and 1.4.9 dated 2025-08-25
DESCRIPTION | 30 +++++++++++++++++++++++------- LICENSE |only MD5 | 11 ++++++----- NEWS | 12 ++++++++---- man/khatri_rao.Rd | 2 +- man/kronecker_list.Rd | 2 +- man/load_orl.Rd | 2 +- 7 files changed, 40 insertions(+), 19 deletions(-)
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models, and
it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel,
RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr'
dynamic documents. Details can be found in Arel-Bundock (2022)
<doi:10.18637/jss.v103.i01>.
Author: Vincent Arel-Bundock [aut, cre] ,
Joachim Gassen [ctb] ,
Nathan Eastwood [ctb],
Nick Huntington-Klein [ctb] ,
Moritz Schwarz [ctb] ,
Benjamin Elbers [ctb] ,
Grant McDermott [ctb] ,
Lukas Wallrich [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 2.4.0 dated 2025-06-08 and 2.5.0 dated 2025-08-25
modelsummary-2.4.0/modelsummary/inst/tinytest |only modelsummary-2.4.0/modelsummary/man/tidy_custom_internal.default.Rd |only modelsummary-2.4.0/modelsummary/tests/tinytest |only modelsummary-2.5.0/modelsummary/DESCRIPTION | 30 - modelsummary-2.5.0/modelsummary/MD5 | 264 +--------- modelsummary-2.5.0/modelsummary/NAMESPACE | 1 modelsummary-2.5.0/modelsummary/NEWS.md | 24 modelsummary-2.5.0/modelsummary/R/datasummary_df.R | 25 modelsummary-2.5.0/modelsummary/R/datasummary_skim.R | 3 modelsummary-2.5.0/modelsummary/R/dvnames.R | 5 modelsummary-2.5.0/modelsummary/R/factory_flextable.R | 59 +- modelsummary-2.5.0/modelsummary/R/factory_huxtable.R | 7 modelsummary-2.5.0/modelsummary/R/factory_tinytable.R | 3 modelsummary-2.5.0/modelsummary/R/fmt_factory.R | 5 modelsummary-2.5.0/modelsummary/R/format_estimates.R | 7 modelsummary-2.5.0/modelsummary/R/get_estimates.R | 30 - modelsummary-2.5.0/modelsummary/R/get_gof.R | 25 modelsummary-2.5.0/modelsummary/R/map_estimates.R | 45 - modelsummary-2.5.0/modelsummary/R/modelsummary.R | 36 - modelsummary-2.5.0/modelsummary/R/modelsummary_cbind.R | 41 + modelsummary-2.5.0/modelsummary/R/sanitize_output.R | 2 modelsummary-2.5.0/modelsummary/R/themes.R | 2 modelsummary-2.5.0/modelsummary/R/tidy_custom.R | 2 modelsummary-2.5.0/modelsummary/man/datasummary.Rd | 2 modelsummary-2.5.0/modelsummary/man/datasummary_balance.Rd | 2 modelsummary-2.5.0/modelsummary/man/datasummary_correlation.Rd | 2 modelsummary-2.5.0/modelsummary/man/datasummary_crosstab.Rd | 2 modelsummary-2.5.0/modelsummary/man/datasummary_skim.Rd | 6 modelsummary-2.5.0/modelsummary/man/dsummary.Rd | 2 modelsummary-2.5.0/modelsummary/man/dvnames.Rd | 5 modelsummary-2.5.0/modelsummary/man/fmt_sprintf.Rd | 9 modelsummary-2.5.0/modelsummary/man/get_estimates.Rd | 13 modelsummary-2.5.0/modelsummary/man/get_gof.Rd | 11 modelsummary-2.5.0/modelsummary/man/map_estimates.Rd | 9 modelsummary-2.5.0/modelsummary/man/modelplot.Rd | 11 modelsummary-2.5.0/modelsummary/man/modelsummary.Rd | 18 modelsummary-2.5.0/modelsummary/man/msummary.Rd | 18 modelsummary-2.5.0/modelsummary/tests/tinytest.R | 12 38 files changed, 371 insertions(+), 367 deletions(-)
Title: CUR/CX Tensor Decomposition
Description: CUR/CX decomposition factorizes a matrix into two factor matrices and Multidimensional CX Decomposition factorizes a tensor into a core tensor and some factor matrices. See the reference section of GitHub README.md <https://github.com/rikenbit/ccTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between ccTensor versions 1.0.2 dated 2021-08-12 and 1.0.3 dated 2025-08-25
ccTensor-1.0.2/ccTensor/README.md |only ccTensor-1.0.3/ccTensor/DESCRIPTION | 10 +++++----- ccTensor-1.0.3/ccTensor/LICENSE |only ccTensor-1.0.3/ccTensor/MD5 | 14 +++++++------- ccTensor-1.0.3/ccTensor/build/partial.rdb |binary ccTensor-1.0.3/ccTensor/inst/NEWS | 4 ++++ ccTensor-1.0.3/ccTensor/man/CUR.Rd | 6 +++--- ccTensor-1.0.3/ccTensor/man/CX.Rd | 4 ++-- ccTensor-1.0.3/ccTensor/man/MultiCX.Rd | 2 +- 9 files changed, 22 insertions(+), 18 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.7 dated 2025-07-25 and 0.2.8 dated 2025-08-25
autoslider.core-0.2.7/autoslider.core/man/adding_ai_footnotes.Rd |only autoslider.core-0.2.8/autoslider.core/DESCRIPTION | 10 - autoslider.core-0.2.8/autoslider.core/MD5 | 54 +++++----- autoslider.core-0.2.8/autoslider.core/NAMESPACE | 3 autoslider.core-0.2.8/autoslider.core/NEWS.md | 6 + autoslider.core-0.2.8/autoslider.core/R/ai.R | 11 +- autoslider.core-0.2.8/autoslider.core/R/decorate.R | 3 autoslider.core-0.2.8/autoslider.core/R/drtable.R | 2 autoslider.core-0.2.8/autoslider.core/R/g_mean_general.R | 2 autoslider.core-0.2.8/autoslider.core/R/package.R | 2 autoslider.core-0.2.8/autoslider.core/R/to_slides.R | 11 +- autoslider.core-0.2.8/autoslider.core/inst/WORDLIST | 1 autoslider.core-0.2.8/autoslider.core/inst/doc/adding_templates.html | 4 autoslider.core-0.2.8/autoslider.core/inst/doc/autoslideR.html | 30 +++-- autoslider.core-0.2.8/autoslider.core/inst/doc/generate_placeholder_slides.html | 4 autoslider.core-0.2.8/autoslider.core/inst/doc/tlg_templates.html | 4 autoslider.core-0.2.8/autoslider.core/inst/doc/use_LLM.R | 2 autoslider.core-0.2.8/autoslider.core/inst/doc/use_LLM.Rmd | 8 - autoslider.core-0.2.8/autoslider.core/inst/doc/use_LLM.html | 23 ++-- autoslider.core-0.2.8/autoslider.core/inst/doc/using_formats.html | 4 autoslider.core-0.2.8/autoslider.core/inst/templates/g_mean_general.R | 2 autoslider.core-0.2.8/autoslider.core/man/g_mean_general.Rd | 2 autoslider.core-0.2.8/autoslider.core/man/get_ai_notes.Rd |only autoslider.core-0.2.8/autoslider.core/man/table_to_slide.Rd | 3 autoslider.core-0.2.8/autoslider.core/tests/testthat/_snaps/save_output.md | 3 autoslider.core-0.2.8/autoslider.core/tests/testthat/test-data_snapshot.R | 2 autoslider.core-0.2.8/autoslider.core/tests/testthat/test-srep_outputs.R | 2 autoslider.core-0.2.8/autoslider.core/tests/testthat/test_ai.R | 26 ++-- autoslider.core-0.2.8/autoslider.core/vignettes/use_LLM.Rmd | 8 - 29 files changed, 137 insertions(+), 95 deletions(-)
More information about autoslider.core at CRAN
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