Title: Flexible, Interactive 'shiny' Modules for Almost Any Plot
Description: Offers a core selection of interactivity-first 'shiny' modules for many
plot types meant to serve as flexible building blocks for applications and
as the base for more complex modules. These modules
allow for the rapid and convenient construction of 'shiny' apps with very few lines
of code and decouple plotting from the underlying data. These modules allow
for full plot aesthetic customization by the end user through UI inputs. Utility
functions for simple UI organization, automated UI tooltips, and additional
plot enhancements are also provided. Includes a multi-panel figure builder app
for arranging multiple modules together in a free-form layout.
Author: Jared Andrews [aut, cre] ,
Jacob Martin [aut]
Maintainer: Jared Andrews <jared.andrews07@gmail.com>
Diff between VizModules versions 0.1.1 dated 2026-04-08 and 0.2.0 dated 2026-06-16
VizModules-0.1.1/VizModules/R/plot_mods.R |only VizModules-0.1.1/VizModules/R/sysdata.rda |only VizModules-0.1.1/VizModules/man/INTERNAL_apply_stat_annotations.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_compute_pairwise_stats.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_create_download_handler.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_create_stat_annotations.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_empty_plot.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_generate_pair_strings.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_parse_pair_strings.Rd |only VizModules-0.1.1/VizModules/man/INTERNAL_write_stats_csv.Rd |only VizModules-0.2.0/VizModules/DESCRIPTION | 17 VizModules-0.2.0/VizModules/MD5 | 316 +- VizModules-0.2.0/VizModules/NAMESPACE | 21 VizModules-0.2.0/VizModules/NEWS.md | 41 VizModules-0.2.0/VizModules/R/createModuleApp.R | 13 VizModules-0.2.0/VizModules/R/data.R | 61 VizModules-0.2.0/VizModules/R/dittoViz_ScatterPlot_module_server.R | 145 VizModules-0.2.0/VizModules/R/dittoViz_ScatterPlot_module_ui.R | 130 VizModules-0.2.0/VizModules/R/dittoViz_yPlot_module_app.R | 3 VizModules-0.2.0/VizModules/R/dittoViz_yPlot_module_server.R | 144 VizModules-0.2.0/VizModules/R/dittoViz_yPlot_module_ui.R | 111 VizModules-0.2.0/VizModules/R/dumbbellPlot.R | 20 VizModules-0.2.0/VizModules/R/dumbbellPlot_module_server.R | 48 VizModules-0.2.0/VizModules/R/dumbbellPlot_module_ui.R | 46 VizModules-0.2.0/VizModules/R/globals.R |only VizModules-0.2.0/VizModules/R/linePlot.R | 101 VizModules-0.2.0/VizModules/R/linePlot_module_server.R | 75 VizModules-0.2.0/VizModules/R/linePlot_module_ui.R | 59 VizModules-0.2.0/VizModules/R/parallelCoordinatesPlot.R | 112 VizModules-0.2.0/VizModules/R/parallelCoordinatesPlot_module_server.R | 111 VizModules-0.2.0/VizModules/R/parallelCoordinatesPlot_module_ui.R | 50 VizModules-0.2.0/VizModules/R/parse_utils.R | 9 VizModules-0.2.0/VizModules/R/piePlot_module_server.R | 36 VizModules-0.2.0/VizModules/R/piePlot_module_ui.R | 61 VizModules-0.2.0/VizModules/R/plot_axis.R |only VizModules-0.2.0/VizModules/R/plot_boxplot.R |only VizModules-0.2.0/VizModules/R/plot_facets.R |only VizModules-0.2.0/VizModules/R/plot_fit_lines.R |only VizModules-0.2.0/VizModules/R/plot_helpers.R |only VizModules-0.2.0/VizModules/R/plot_legend.R |only VizModules-0.2.0/VizModules/R/plot_reference_lines.R |only VizModules-0.2.0/VizModules/R/plot_source_data.R |only VizModules-0.2.0/VizModules/R/plotthis_AreaPlot_module_server.R | 67 VizModules-0.2.0/VizModules/R/plotthis_AreaPlot_module_ui.R | 47 VizModules-0.2.0/VizModules/R/plotthis_BarPlot_module_server.R | 78 VizModules-0.2.0/VizModules/R/plotthis_BarPlot_module_ui.R | 44 VizModules-0.2.0/VizModules/R/plotthis_BoxPlot_module_server.R | 106 VizModules-0.2.0/VizModules/R/plotthis_BoxPlot_module_ui.R | 86 VizModules-0.2.0/VizModules/R/plotthis_DensityPlot_module_server.R | 68 VizModules-0.2.0/VizModules/R/plotthis_DensityPlot_module_ui.R | 40 VizModules-0.2.0/VizModules/R/plotthis_DotPlot_module_app.R |only VizModules-0.2.0/VizModules/R/plotthis_DotPlot_module_server.R |only VizModules-0.2.0/VizModules/R/plotthis_DotPlot_module_ui.R |only VizModules-0.2.0/VizModules/R/plotthis_Histogram_module_server.R | 70 VizModules-0.2.0/VizModules/R/plotthis_Histogram_module_ui.R | 40 VizModules-0.2.0/VizModules/R/plotthis_SplitBarPlot_module_server.R | 74 VizModules-0.2.0/VizModules/R/plotthis_SplitBarPlot_module_ui.R | 240 - VizModules-0.2.0/VizModules/R/plotthis_ViolinPlot_module_server.R | 114 VizModules-0.2.0/VizModules/R/plotthis_ViolinPlot_module_ui.R | 80 VizModules-0.2.0/VizModules/R/radarPlot_module_server.R | 36 VizModules-0.2.0/VizModules/R/radarPlot_module_ui.R | 69 VizModules-0.2.0/VizModules/R/reset_uniform_ui_inputs.R | 35 VizModules-0.2.0/VizModules/R/stat_helper.R | 997 +++--- VizModules-0.2.0/VizModules/R/ternaryPlot_module_server.R | 36 VizModules-0.2.0/VizModules/R/ternaryPlot_module_ui.R | 47 VizModules-0.2.0/VizModules/R/ui_utils.R | 277 + VizModules-0.2.0/VizModules/R/uniform_ui_inputs.R | 139 VizModules-0.2.0/VizModules/README.md | 77 VizModules-0.2.0/VizModules/build/vignette.rds |binary VizModules-0.2.0/VizModules/data/example_markers.rda |only VizModules-0.2.0/VizModules/data/example_mtcars.rda |binary VizModules-0.2.0/VizModules/data/example_rnaseq.rda |only VizModules-0.2.0/VizModules/inst/apps/figure-builder |only VizModules-0.2.0/VizModules/inst/apps/module-gallery/app.R | 48 VizModules-0.2.0/VizModules/inst/apps/rnaseq-showcase |only VizModules-0.2.0/VizModules/inst/apps/test_dotPlot |only VizModules-0.2.0/VizModules/inst/doc/adding-a-new-module.Rmd | 18 VizModules-0.2.0/VizModules/inst/doc/adding-a-new-module.html | 34 VizModules-0.2.0/VizModules/inst/doc/quick-start.R | 50 VizModules-0.2.0/VizModules/inst/doc/quick-start.Rmd | 64 VizModules-0.2.0/VizModules/inst/doc/quick-start.html | 62 VizModules-0.2.0/VizModules/man/INTERNAL_add_ablines.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_add_fit_lines_to_subplots.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_add_hlines.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_add_multi_axis_traces.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_add_plot_config.Rd | 9 VizModules-0.2.0/VizModules/man/INTERNAL_add_reference_lines.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_add_vlines.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_adjusted_axis_label.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_axis_title_to_annotations.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_apply_facet_subplot_spacing.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_legend_styling.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_plotly_newshape.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_apply_render_margins.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_subplot_axis_styling.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_apply_title_layout.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_axis_titles_as_annotations.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_build_facet_annotations.Rd | 24 VizModules-0.2.0/VizModules/man/INTERNAL_build_facet_panel_borders.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_calculate_range.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_clean_facet_dim.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_compute_linear_fit.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_compute_loess_fit.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_create_axis_styles.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_create_ggplot_axis_style.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_custom_legend.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_extract_marker_sizes.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_fix_boxplot_facet_positions.Rd | 2 VizModules-0.2.0/VizModules/man/INTERNAL_hide_jitter_from_legend.Rd | 2 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VizModules-0.2.0/VizModules/man/createModuleApp.Rd | 10 VizModules-0.2.0/VizModules/man/create_source_download_handler.Rd |only VizModules-0.2.0/VizModules/man/create_stat_annotations.Rd |only VizModules-0.2.0/VizModules/man/dittoViz_scatterPlotInputsUI.Rd | 33 VizModules-0.2.0/VizModules/man/dittoViz_scatterPlotOutputUI.Rd | 7 VizModules-0.2.0/VizModules/man/dittoViz_yPlotInputsUI.Rd | 27 VizModules-0.2.0/VizModules/man/dittoViz_yPlotOutputUI.Rd | 45 VizModules-0.2.0/VizModules/man/dumbbellPlot.Rd | 7 VizModules-0.2.0/VizModules/man/dumbbellPlotInputsUI.Rd | 17 VizModules-0.2.0/VizModules/man/dumbbellPlotOutputUI.Rd | 7 VizModules-0.2.0/VizModules/man/empty_plot.Rd |only VizModules-0.2.0/VizModules/man/example_markers.Rd |only VizModules-0.2.0/VizModules/man/example_rnaseq.Rd |only VizModules-0.2.0/VizModules/man/figures/DotPlot.png |only VizModules-0.2.0/VizModules/man/generate_pair_strings.Rd |only VizModules-0.2.0/VizModules/man/is_pure_type.Rd | 2 VizModules-0.2.0/VizModules/man/linePlot.Rd | 22 VizModules-0.2.0/VizModules/man/linePlotInputsUI.Rd | 5 VizModules-0.2.0/VizModules/man/linePlotOutputUI.Rd | 45 VizModules-0.2.0/VizModules/man/module_tack_ui.Rd | 9 VizModules-0.2.0/VizModules/man/organize_inputs.Rd | 22 VizModules-0.2.0/VizModules/man/parallelCoordinatesPlot.Rd | 19 VizModules-0.2.0/VizModules/man/parallelCoordinatesPlotInputsUI.Rd | 11 VizModules-0.2.0/VizModules/man/parallelCoordinatesPlotOutputUI.Rd | 7 VizModules-0.2.0/VizModules/man/parse_pair_strings.Rd |only VizModules-0.2.0/VizModules/man/piePlotInputsUI.Rd | 175 - VizModules-0.2.0/VizModules/man/piePlotOutputUI.Rd | 45 VizModules-0.2.0/VizModules/man/plotthis_AreaPlotInputsUI.Rd | 15 VizModules-0.2.0/VizModules/man/plotthis_AreaPlotOutputUI.Rd | 45 VizModules-0.2.0/VizModules/man/plotthis_BarPlotApp.Rd | 2 VizModules-0.2.0/VizModules/man/plotthis_BarPlotInputsUI.Rd | 14 VizModules-0.2.0/VizModules/man/plotthis_BarPlotOutputUI.Rd | 45 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VizModules-0.2.0/VizModules/man/plotthis_ViolinPlotApp.Rd | 2 VizModules-0.2.0/VizModules/man/plotthis_ViolinPlotInputsUI.Rd | 60 VizModules-0.2.0/VizModules/man/plotthis_ViolinPlotOutputUI.Rd | 45 VizModules-0.2.0/VizModules/man/radarPlotInputsUI.Rd | 11 VizModules-0.2.0/VizModules/man/radarPlotOutputUI.Rd | 7 VizModules-0.2.0/VizModules/man/ternaryPlotInputsUI.Rd | 1 VizModules-0.2.0/VizModules/man/ternaryPlotOutputUI.Rd | 7 VizModules-0.2.0/VizModules/tests/testthat/test-dumbbellPlot.R | 17 VizModules-0.2.0/VizModules/tests/testthat/test-linePlot.R | 532 ++- VizModules-0.2.0/VizModules/tests/testthat/test-multiColorPicker.R | 114 VizModules-0.2.0/VizModules/tests/testthat/test-parallelCoordinatesPlot.R | 53 VizModules-0.2.0/VizModules/tests/testthat/test-piePlot.R | 196 - VizModules-0.2.0/VizModules/tests/testthat/test-plot_mods.R | 1456 ++++++---- VizModules-0.2.0/VizModules/tests/testthat/test-scatterPlot.R |only VizModules-0.2.0/VizModules/tests/testthat/test-stat_helper.R | 178 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Title: Estimate and Forecast Real-Time Infection Dynamics
Description: Estimates the time-varying reproduction number, rate of
spread, and doubling time using a renewal equation approach combined
with Bayesian inference via Stan. Supports Gaussian process and
random walk priors for modelling changes in
transmission over time. Accounts for delays between infection and
observation (incubation period, reporting delays), right-truncation
in recent data, day-of-week effects, and observation overdispersion.
Can estimate relationships between primary and secondary outcomes
(e.g., cases to hospitalisations or deaths) and forecast both. Runs
across multiple regions in parallel. Based on
Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and
Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Adrian Lison [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Mun [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.8.0 dated 2026-02-04 and 1.9.0 dated 2026-06-16
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EpiNow2-1.9.0/EpiNow2/R/extract.R | 33 EpiNow2-1.9.0/EpiNow2/R/fit.R | 4 EpiNow2-1.9.0/EpiNow2/R/format.R | 25 EpiNow2-1.9.0/EpiNow2/R/get.R | 99 EpiNow2-1.9.0/EpiNow2/R/opts.R | 197 EpiNow2-1.9.0/EpiNow2/R/plot.R | 38 EpiNow2-1.9.0/EpiNow2/R/preprocessing.R | 25 EpiNow2-1.9.0/EpiNow2/R/regional_epinow.R | 22 EpiNow2-1.9.0/EpiNow2/R/report.R | 4 EpiNow2-1.9.0/EpiNow2/R/setup.R | 10 EpiNow2-1.9.0/EpiNow2/R/simulate_infections.R | 44 EpiNow2-1.9.0/EpiNow2/R/simulate_secondary.R | 34 EpiNow2-1.9.0/EpiNow2/R/stan.R | 5 EpiNow2-1.9.0/EpiNow2/R/stanmodels.R | 3 EpiNow2-1.9.0/EpiNow2/R/summarise.R | 161 EpiNow2-1.9.0/EpiNow2/R/utilities.R | 94 EpiNow2-1.9.0/EpiNow2/README.md | 7 EpiNow2-1.9.0/EpiNow2/build/partial.rdb |binary EpiNow2-1.9.0/EpiNow2/build/vignette.rds |binary EpiNow2-1.9.0/EpiNow2/data/example_truncated.rda |binary EpiNow2-1.9.0/EpiNow2/inst/WORDLIST | 1 EpiNow2-1.9.0/EpiNow2/inst/doc/EpiNow2.Rmd | 82 EpiNow2-1.9.0/EpiNow2/inst/doc/EpiNow2.html | 111 EpiNow2-1.9.0/EpiNow2/inst/doc/case-studies.Rmd | 41 EpiNow2-1.9.0/EpiNow2/inst/doc/case-studies.html | 73 EpiNow2-1.9.0/EpiNow2/inst/doc/delays.Rmd |only EpiNow2-1.9.0/EpiNow2/inst/doc/delays.html |only EpiNow2-1.9.0/EpiNow2/inst/doc/epinow.Rmd | 37 EpiNow2-1.9.0/EpiNow2/inst/doc/epinow.html | 58 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_dist.R |only EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_dist.Rmd |only EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_dist.html |only EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_dist_workflow.Rmd |only EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_dist_workflow.html |only EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections.Rmd | 2 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections.html | 4 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections_options.Rmd | 183 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections_options.html | 246 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections_workflow.Rmd | 92 EpiNow2-1.9.0/EpiNow2/inst/doc/estimate_infections_workflow.html | 264 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EpiNow2-1.9.0/EpiNow2/tests/testthat/test-checks.R | 28 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-delays.R | 322 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-dist.R | 24 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-dist_spec.R | 129 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-epinow.R | 124 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-estimate_dist.R |only EpiNow2-1.9.0/EpiNow2/tests/testthat/test-estimate_infections.R | 273 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-estimate_secondary.R | 67 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-estimate_truncation.R | 193 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-forecast-infections.R | 35 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-obs_opts.R | 1 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-regional_epinow.R | 51 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-regional_summary.R | 18 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-rt_opts.R | 6 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-convole.R | 12 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-delays.R | 39 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-generated_quantities.R | 34 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-guassian-process.R | 12 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-infections.R | 24 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-observation_model.R | 11 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-pmfs.R | 22 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-rt.R | 114 EpiNow2-1.9.0/EpiNow2/tests/testthat/test-stan-secondary.R | 8 EpiNow2-1.9.0/EpiNow2/vignettes/EpiNow2-plot_estimates-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/EpiNow2-plot_regional_epinow_summary-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/EpiNow2.Rmd | 82 EpiNow2-1.9.0/EpiNow2/vignettes/EpiNow2.Rmd.orig | 12 EpiNow2-1.9.0/EpiNow2/vignettes/case-studies.Rmd | 41 EpiNow2-1.9.0/EpiNow2/vignettes/delays-convolution-1.png |only EpiNow2-1.9.0/EpiNow2/vignettes/delays-plot-distributions-1.png |only EpiNow2-1.9.0/EpiNow2/vignettes/delays-plot-distributions-2.png |only 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|only EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections.Rmd | 2 EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-bp-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-default-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-fixed-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-gp_projection-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-lower_accuracy-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-no_delays-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-nonparametric-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-susceptible_depletion-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-truncation-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options-weekly_rw-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/estimate_infections_options.Rmd | 183 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|only EpiNow2-1.9.0/EpiNow2/vignettes/prior_choice_guide-workflow-step3-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/prior_choice_guide-workflow-step3-2.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/prior_choice_guide-workflow-step4-1.png |binary EpiNow2-1.9.0/EpiNow2/vignettes/prior_choice_guide.Rmd | 183 339 files changed, 24424 insertions(+), 10288 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.3.1 dated 2026-05-16 and 1.3.2 dated 2026-06-16
DESCRIPTION | 6 MD5 | 109 NAMESPACE | 9 NEWS.md | 64 R/any_table.R | 6483 ++++++++++++++++----------------- R/code_statistics.R |only R/compute.R | 1073 ++--- R/create_format.R | 13 R/crosstabs.R | 2762 +++++++------- R/dummy_data.R | 777 +-- R/excel_helpers.R | 4133 ++++++++++----------- R/export_with_style.R | 934 ++-- R/frequencies.R | 3451 ++++++++--------- R/globals.R | 191 R/if_else.R | 2096 +++++----- R/import_export.R | 1205 +++--- R/loading.R | 35 R/messages.R | 3373 ++++++++--------- R/options.R | 1976 +++++----- R/qol.R | 268 - R/recode.R | 18 R/retain.R | 986 ++--- R/small_helpers.R | 22 R/sort_plus.R | 10 R/statistics.R | 1278 +++--- R/strings.R | 45 R/summarise_plus.R | 260 - README.md | 2 inst/tinytest/test-any_table.R | 1850 ++++----- inst/tinytest/test-code_statistics.R |only inst/tinytest/test-compute.R | 258 - inst/tinytest/test-export_with_style.R | 199 - inst/tinytest/test-if_else.R | 828 ++-- inst/tinytest/test-options.R | 535 +- inst/tinytest/test-retain.R | 464 +- inst/tinytest/test-summarise_plus.R | 2007 +++++----- man/any_table.Rd | 2 man/code_statistics.Rd |only man/concat.Rd | 125 man/crosstabs.Rd | 2 man/drop_type_vars.Rd | 87 man/excel_output_style.Rd | 6 man/export_with_style.Rd | 9 man/frequencies.Rd | 2 man/if_else.Rd | 3 man/import_export.Rd | 2 man/libname.Rd | 5 man/modify_number_formats.Rd | 2 man/modify_output_style.Rd | 2 man/number_format_style.Rd | 2 man/qol-package.Rd | 14 man/qol_options.Rd | 14 man/recode.Rd | 5 man/retain.Rd | 56 man/round_values.Rd | 14 man/style_options.Rd | 78 man/summarise_plus.Rd | 13 57 files changed, 19408 insertions(+), 18755 deletions(-)
Title: Tools for Multilayer and Single Layer Network Modeling
Description: Estimation and bootstrap utilities for single layer and multilayer
Mixed Graphical Models, including functions for centrality, bridge metrics,
membership stability, and plotting (De Martino et al. (2026) <doi:10.48550/arXiv.2602.05716>).
Author: Maria De Martino [aut, cre],
Caterina Gregorio [aut],
Adrien Perigord [ctb],
Hudson Golino [ctb],
Jonas Haslbeck [ctb]
Maintainer: Maria De Martino <maria.demartino@uniud.it>
Diff between MixMashNet versions 1.0.0 dated 2026-04-30 and 1.1.0 dated 2026-06-16
DESCRIPTION | 6 MD5 | 36 ++--- NAMESPACE | 2 NEWS.md | 12 + R/community_scores.R | 67 +++++++++- R/get_centrality.R | 275 ++++++++++++++++++++++++++++++++++++--------- R/get_edges.R | 257 +++++++++++++++++++++++++++++++++--------- R/infer_mgm_spec.R | 27 +++- R/layouts.R | 141 +++++++++++++++-------- R/mixMN.R | 33 +++-- R/mixMN_from_wadj.R | 3 R/multimixMN.R | 37 ++++-- R/plot-network.R | 54 ++++++-- R/plot.R | 31 ++++- man/get_centrality.Rd | 4 man/get_edges.Rd | 4 man/mixMN.Rd | 2 man/plot.mixMN_fit.Rd | 12 + man/plot.multimixMN_fit.Rd | 19 ++- 19 files changed, 790 insertions(+), 232 deletions(-)
Title: Download Time Series Data from the U.S. Bureau of Labor
Statistics
Description: These functions provide a convenient interface for downloading data from the U.S. Bureau of Labor Statistics <https://www.bls.gov>. The functions in this package utilize flat files produced by the Bureau of Labor Statistics, which contain full series history. These files include employment, unemployment, wages, prices, industry and occupational data at a national, state, and sub-state level, depending on the series. Individual functions are included for those programs which have data available at the state level. The core functions provide direct access to the Current Employment Statistics (CES) <https://www.bls.gov/ces/>, Local Area Unemployment Statistics (LAUS) <https://www.bls.gov/lau/>, Occupational Employment and Wage Statistics (OEWS) <https://www.bls.gov/oes/> and Alternative Measures of Labor Underutilization (SALT) <https://www.bls.gov/lau/stalt.htm> data produced by the Bureau of Labor Statistics.
Author: Nevada Department of Employment, Training, and Rehabilitation [cph],
David Schmidt [aut, cre],
Mark Rembert [aut]
Maintainer: David Schmidt <deschmidt@detr.nv.gov>
Diff between BLSloadR versions 0.4.5 dated 2026-04-23 and 0.4.6 dated 2026-06-16
DESCRIPTION |only LICENSE |only MD5 | 8 ++++---- NAMESPACE |only NEWS.md |only R/download_helpers.R | 1 - README.md |only build |only data/area_lookup.rda |only data/ind_lookup.rda |binary inst |only man |only 12 files changed, 4 insertions(+), 5 deletions(-)
More information about GenerateIndexPedigree at CRAN
Permanent link
Title: Bayesian Inference for Neyman-Scott Point Processes
Description: The Bayesian MCMC estimation of parameters for Thomas-type cluster
point process with various inhomogeneities. It allows for inhomogeneity in
(i) distribution of parent points, (ii) mean number of points in a cluster,
(iii) cluster spread. The package also allows for the Bayesian MCMC
algorithm for the homogeneous generalized Thomas process. The cluster size
is allowed to have a variance that is greater or less than the expected
value (cluster sizes are over or under dispersed). Details are described in
Dvořák, Remeš, Beránek & Mrkvička (2022) <arXiv: 10.48550/arXiv.2205.07946>.
Author: Mrkvicka Tomas [aut],
Dvorak Jiri [aut],
Beranek Ladislav [aut],
Remes Radim [aut, cre],
Park Jaewoo [ctb],
Lee Sujeong [ctb]
Maintainer: Remes Radim <inrem@jcu.cz>
Diff between binspp versions 0.2.3 dated 2025-12-03 and 0.2.4 dated 2026-06-16
DESCRIPTION | 9 MD5 | 59 R/C_prep.R | 44 R/C_prep_naive.R | 54 R/binspp_auxiliary.R | 2987 ++++++++++++++++++++-------------------- R/estgtp.R | 612 ++++---- R/estgtpr.R | 230 +-- R/estinternsp.R | 1183 ++++++++------- R/rgenp.R | 72 R/rgtp.R | 225 +-- R/trees_N4.R | 2 build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/estgtp.Rd | 75 - man/estgtpr.Rd | 81 - man/estinternsp.Rd | 77 - man/estintp.Rd | 20 man/first_step.Rd | 4 man/plot.output_estintp.Rd | 8 man/plot_conn.Rd | 10 man/print.output_estinternsp.Rd | 77 - man/print.output_estintp.Rd | 8 man/rThomasInhom.Rd | 28 man/rawMCMCoutput.Rd | 8 man/re_estimate.Rd | 8 man/rgtp.Rd | 10 man/simulate.output_estintp.Rd | 8 man/trees_N4.Rd | 2 tests |only vignettes |only 31 files changed, 3114 insertions(+), 2787 deletions(-)
Title: Regression, Inference, and General Data Analysis Tools in R
Description: A set of tools to streamline data analysis. Learning both R and introductory statistics at the same time can be challenging, and so we created 'rigr' to facilitate common data analysis tasks and enable learners to focus on statistical concepts. We provide easy-to-use interfaces for descriptive statistics, one- and two-sample inference, and regression analyses. 'rigr' output includes key information while omitting unnecessary details that can be confusing to beginners. Heteroscedasticity-robust ("sandwich") standard errors are returned by default, and multiple partial F-tests and tests for contrasts are easy to specify. A single regression function can fit both linear and generalized linear models, allowing students to more easily make connections between different classes of models.
Author: Amy D Willis [aut, cre] ,
Taylor Okonek [aut],
Charles J Wolock [aut],
Brian D Williamson [aut],
Scott S Emerson [aut],
Andrew J Spieker [aut],
Yiqun T Chen [aut],
Travis Y Hee Wai [ctb],
James P Hughes [ctb],
R Core Team [ctb],
Akhil S Bhel [ctb],
T [...truncated...]
Maintainer: Amy D Willis <adwillis@uw.edu>
Diff between rigr versions 1.0.9 dated 2026-04-03 and 1.0.10 dated 2026-06-16
DESCRIPTION | 6 MD5 | 12 build/vignette.rds |binary inst/doc/descrip_intro.html | 396 +++------------------ inst/doc/one_and_two_sample_inference.html | 467 ++++--------------------- inst/doc/regress_intro.html | 539 +++++------------------------ tests/testthat/test_wilcoxon.R | 110 +++-- 7 files changed, 342 insertions(+), 1188 deletions(-)
Title: Empirical Bayes Methods for Pharmacovigilance
Description: A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.1002/sim.70195>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.
Author: Yihao Tan [aut, cre] ,
Marianthi Markatou [aut] ,
Saptarshi Chakraborty [aut] ,
Raktim Mukhopadhyay [aut]
Maintainer: Yihao Tan <yihaotan@buffalo.edu>
Diff between pvEBayes versions 0.2.2 dated 2026-03-13 and 0.3.0 dated 2026-06-16
DESCRIPTION | 15 MD5 | 54 +-- NAMESPACE | 2 R/data.R | 55 +++ R/pvEBayes-package.R | 61 ++- R/pvEBayes_main_function.R | 461 ++++++++++++++++++-------- R/pvEBayes_object_S3_methods.R | 261 +++++++++++++- R/r_contin_table_gen.R | 476 +++++++++++++-------------- R/srr-stats-standards.R | 203 ++++++----- README.md | 56 ++- data/faers_opioid_mental.rda |only data/vigi_opioid_mental.rda |only inst/CITATION | 13 inst/doc/pvEBayes-introduction.R | 43 ++ inst/doc/pvEBayes-introduction.Rmd | 85 ++++ inst/doc/pvEBayes-introduction.html | 372 +++++++++++++++------ man/dot-KM_fit.Rd | 17 man/faers_opioid_mental.Rd |only man/get_posterior_prob.Rd |only man/plot.pvEBayes.Rd | 3 man/posterior_draws.Rd | 5 man/pvEBayes-package.Rd | 5 man/pvEBayes.Rd | 105 +++-- man/pvEBayes_tune.Rd | 4 man/summary.pvEBayes.Rd | 25 + man/summary_table_pvEBayes.Rd |only man/tuning_efron.Rd | 2 man/vigi_opioid_mental.Rd |only tests/testthat/test-correctness.R | 274 +++++++++++++-- tests/testthat/test-pvEBayes_main_function.R | 42 +- vignettes/pvEBayes-introduction.Rmd | 85 ++++ 31 files changed, 1917 insertions(+), 807 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 1.0.1 dated 2026-02-06 and 1.1.0 dated 2026-06-16
DESCRIPTION | 8 MD5 | 79 ++--- NEWS.md | 19 + R/plotObservationPeriod.R | 45 ++ R/plotPerson.R | 32 +- R/plotTrend.R | 8 R/summariseClinicalRecords.R | 232 ++++++++++----- R/summariseConceptIdCounts.R | 19 - R/summariseConceptSetCounts.R | 5 R/summariseInternal.R | 46 +- R/summariseMissingData.R | 27 + R/summariseObservationPeriod.R | 23 + R/summarisePerson.R | 59 +++ R/summariseTrend.R | 80 ++++- R/tableClinicalRecords.R | 8 R/tableConceptIdCounts.R | 26 - R/tableMissingData.R | 15 R/tableTopConceptCounts.R | 12 README.md | 42 ++ inst/brand/readme.yml | 136 ++++---- inst/doc/database_characteristics.html | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.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-14-1.png |only man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/plotObservationPeriod.Rd | 4 man/plotTrend.Rd | 2 man/summariseTrend.Rd | 3 man/tableClinicalRecords.Rd | 3 tests/testthat/test-summariseClinicalRecords.R | 139 ++++++++ tests/testthat/test-summariseConceptIdCounts.R | 2 tests/testthat/test-summariseObservationPeriod.R | 18 + tests/testthat/test-summariseTrend.R | 62 ++-- vignettes/articles/summarise_clinical_tables_records.Rmd | 46 +- vignettes/articles/summarise_concept_id_counts.Rmd | 49 ++- vignettes/articles/summarise_person.Rmd | 106 ++++-- vignettes/articles/summarise_trend.Rmd | 105 ++++-- 41 files changed, 1064 insertions(+), 398 deletions(-)
Title: A Collection of ML Tools for Species Detection and
Classification in Camera Trap Images and Videos
Description: Functions required to classify subjects within camera trap field data. The package can handle both images and videos. The authors recommend a two-step approach using Microsoft's 'MegaDector' model and then a second model trained on the classes of interest.
Author: Kyra Swanson [aut, cre] ,
Mathias Tobler [aut]
Maintainer: Kyra Swanson <tswanson@sdzwa.org>
Diff between animl versions 3.2.0 dated 2026-02-03 and 3.3.0 dated 2026-06-16
animl-3.2.0/animl/R/split.R |only animl-3.2.0/animl/man/test_main.Rd |only animl-3.2.0/animl/man/train_main.Rd |only animl-3.2.0/animl/man/train_val_test.Rd |only animl-3.3.0/animl/DESCRIPTION | 15 animl-3.3.0/animl/LICENSE | 2 animl-3.3.0/animl/MD5 | 145 ++- animl-3.3.0/animl/NAMESPACE | 105 +- animl-3.3.0/animl/NEWS.md |only animl-3.3.0/animl/R/classification.R | 259 +++--- animl-3.3.0/animl/R/detection.R | 238 ++++-- animl-3.3.0/animl/R/export.R | 472 ++++++++---- animl-3.3.0/animl/R/file_management.R | 556 +++++++++----- animl-3.3.0/animl/R/install.R | 579 ++++++++------- animl-3.3.0/animl/R/reid.R | 259 +++--- animl-3.3.0/animl/R/sequence_classification.R | 494 ++++++------ animl-3.3.0/animl/R/train.R | 102 +- animl-3.3.0/animl/R/video_processing.R | 97 +- animl-3.3.0/animl/R/visualization.R | 140 ++- animl-3.3.0/animl/R/zzz.R | 56 - animl-3.3.0/animl/README.md | 328 ++++---- animl-3.3.0/animl/man/WorkingDirectory.Rd | 48 - animl-3.3.0/animl/man/active_times.Rd |only animl-3.3.0/animl/man/animl_install.Rd | 44 - animl-3.3.0/animl/man/animl_install_instructions.Rd | 22 animl-3.3.0/animl/man/build_file_manifest.Rd | 86 +- animl-3.3.0/animl/man/check_animl_py.Rd |only animl-3.3.0/animl/man/check_file.Rd | 50 - animl-3.3.0/animl/man/check_python.Rd | 44 - animl-3.3.0/animl/man/classify.Rd | 104 +- animl-3.3.0/animl/man/compute_batched_distance_matrix.Rd | 66 - animl-3.3.0/animl/man/compute_distance_matrix.Rd | 48 - animl-3.3.0/animl/man/cosine_distance.Rd | 44 - animl-3.3.0/animl/man/create_pyenv.Rd | 38 animl-3.3.0/animl/man/delete_pyenv.Rd | 40 - animl-3.3.0/animl/man/detect.Rd | 113 +- animl-3.3.0/animl/man/download_model.Rd | 50 - animl-3.3.0/animl/man/euclidean_squared_distance.Rd | 44 - animl-3.3.0/animl/man/export_camptrapdp.Rd |only animl-3.3.0/animl/man/export_camtrapR.Rd | 93 +- animl-3.3.0/animl/man/export_coco.Rd | 56 - animl-3.3.0/animl/man/export_folders.Rd | 90 +- animl-3.3.0/animl/man/export_megadetector.Rd | 62 - animl-3.3.0/animl/man/export_timelapse.Rd | 48 - animl-3.3.0/animl/man/export_train_val_test.Rd |only animl-3.3.0/animl/man/export_yolo.Rd |only animl-3.3.0/animl/man/extract_frames.Rd | 90 +- animl-3.3.0/animl/man/extract_miew_embeddings.Rd | 74 - animl-3.3.0/animl/man/get_animals.Rd | 44 - animl-3.3.0/animl/man/get_empty.Rd | 44 - animl-3.3.0/animl/man/get_frame_as_image.Rd | 44 - animl-3.3.0/animl/man/list_models.Rd | 40 - animl-3.3.0/animl/man/load_animl.Rd | 46 - animl-3.3.0/animl/man/load_class_list.Rd | 40 - animl-3.3.0/animl/man/load_classifier.Rd | 65 - animl-3.3.0/animl/man/load_data.Rd | 44 - animl-3.3.0/animl/man/load_detector.Rd | 53 - animl-3.3.0/animl/man/load_json.Rd | 44 - animl-3.3.0/animl/man/load_miew.Rd | 44 - animl-3.3.0/animl/man/load_yaml.Rd |only animl-3.3.0/animl/man/parse_detections.Rd | 72 - animl-3.3.0/animl/man/plot_all_bounding_boxes.Rd | 97 +- animl-3.3.0/animl/man/plot_box.Rd | 95 +- animl-3.3.0/animl/man/remove_diagonal.Rd | 40 - animl-3.3.0/animl/man/remove_link.Rd | 48 - animl-3.3.0/animl/man/save_classifier.Rd | 88 -- animl-3.3.0/animl/man/save_data.Rd | 52 - animl-3.3.0/animl/man/save_json.Rd | 52 - animl-3.3.0/animl/man/save_yaml.Rd |only animl-3.3.0/animl/man/sequence_calculation.Rd |only animl-3.3.0/animl/man/sequence_classification.Rd | 143 +-- animl-3.3.0/animl/man/single_classification.Rd | 77 + animl-3.3.0/animl/man/test_classifier.Rd |only animl-3.3.0/animl/man/train_classifier.Rd |only animl-3.3.0/animl/man/update_animl_py.Rd | 40 - animl-3.3.0/animl/man/update_labels_from_folders.Rd | 52 - animl-3.3.0/animl/tests |only 77 files changed, 3613 insertions(+), 2952 deletions(-)
Title: Additional Documentation and Regression Tests for
'stats::free1way()'
Description: Function 'stats::free1way()' implements semiparametrically
efficient population- and permutation-based inference in
distribution-free stratified K-sample oneway layouts. This package
provides additional documentation, including a detailed description
of the implementation, and serves as a home for extensive regression tests.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Frank E Harrell Jr [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between free1way.docreg versions 1.0-0 dated 2026-05-22 and 1.0-1 dated 2026-06-16
free1way.docreg-1.0-0/free1way.docreg/build/partial.rdb |only free1way.docreg-1.0-0/free1way.docreg/vignettes/free1way.Rout.save |only free1way.docreg-1.0-1/free1way.docreg/DESCRIPTION | 9 free1way.docreg-1.0-1/free1way.docreg/MD5 | 22 free1way.docreg-1.0-1/free1way.docreg/NAMESPACE | 31 free1way.docreg-1.0-1/free1way.docreg/build/vignette.rds |binary free1way.docreg-1.0-1/free1way.docreg/cleanup | 2 free1way.docreg-1.0-1/free1way.docreg/inst/NEWS.Rd | 10 free1way.docreg-1.0-1/free1way.docreg/inst/doc/free1way.R | 14 free1way.docreg-1.0-1/free1way.docreg/inst/doc/free1way.Rnw | 731 +++++----- free1way.docreg-1.0-1/free1way.docreg/inst/doc/free1way.pdf |binary free1way.docreg-1.0-1/free1way.docreg/inst/nuweb |only free1way.docreg-1.0-1/free1way.docreg/tests/bugfixes.R |only free1way.docreg-1.0-1/free1way.docreg/vignettes/free1way.Rnw | 731 +++++----- 14 files changed, 825 insertions(+), 725 deletions(-)
More information about free1way.docreg at CRAN
Permanent link
Title: Community Niche Position and Width Estimation Tools
Description: Provides methods for estimating species niche position and niche
breadth under continuous environmental gradients. The package implements
canonical correspondence analysis (CCA), partial CCA (pCCA), generalized
additive models (GAM), and Levins' niche breadth metrics for species-level
and community-level analyses. Methods are based on ter Braak (1986)
<doi:10.2307/1938672>, Okie et al. (2015) <doi:10.1098/rspb.2014.2630>,
Feng et al. (2020) <doi:10.1111/mec.15441>, Wood (2017)
<doi:10.1201/9781315370279>, and Levins (1968, ISBN:978-0691080628).
Author: Shuotao Zhou [aut, cre],
Kai Feng [aut],
Ye Deng [aut]
Maintainer: Shuotao Zhou <zhoushuotao@stu.hunau.edu.cn>
Diff between EcoNiche versions 1.0.2 dated 2026-03-10 and 1.0.3 dated 2026-06-16
DESCRIPTION | 8 - MD5 | 27 ++-- NEWS.md | 15 +- R/cca.R | 35 ++--- R/data.R |only README.md | 157 ++++++++++++------------- build/vignette.rds |binary data |only inst/doc/coniche-workflow.R | 90 ++++++++++++-- inst/doc/coniche-workflow.Rmd | 159 ++++++++++++++++++++------ inst/doc/coniche-workflow.html | 248 ++++++++++++++++++++++++++++++++++++++++- man/cca_workflow.Rd | 23 +-- man/plant_env.Rd |only man/plant_group.Rd |only man/plant_otu.Rd |only vignettes/coniche-workflow.Rmd | 159 ++++++++++++++++++++------ 16 files changed, 700 insertions(+), 221 deletions(-)
Title: Dependency Coefficients
Description: Functions to compute coefficients measuring the dependence of two or more than two variables. The functions can be deployed to gain information about functional dependencies of the variables with emphasis on monotone functions. The statistics describe how well one response variable can be approximated by a monotone function of other variables. In regression analysis the variable selection is an important issue. In this framework the functions could be useful tools in modeling the regression function. Detailed explanations on the subject can be found in papers Liebscher (2014) <doi:10.2478/demo-2014-0004>; Liebscher (2017) <doi:10.1515/demo-2017-0012>; Liebscher (2021): <https://arfjournals.com/image/catalog/Journals%20Papers/AJSS/No%202%20(2021)/4-AJSS_123-150.pdf>; Liebscher (2021): Kendall regression coefficient. Computational Statistics and Data Analysis 157. 107140.
Author: Eckhard Liebscher [aut, cre]
Maintainer: Eckhard Liebscher <eckhard.liebscher@hs-merseburg.de>
Diff between depcoeff versions 0.1.1 dated 2026-01-20 and 1.0.1 dated 2026-06-16
depcoeff-0.1.1/depcoeff/inst |only depcoeff-1.0.1/depcoeff/DESCRIPTION | 10 depcoeff-1.0.1/depcoeff/MD5 | 25 - depcoeff-1.0.1/depcoeff/NAMESPACE | 5 depcoeff-1.0.1/depcoeff/NEWS.md |only depcoeff-1.0.1/depcoeff/R/packdepcoeff.R | 716 +++++++++++++++++++++++++------ depcoeff-1.0.1/depcoeff/man/kendr.Rd | 31 - depcoeff-1.0.1/depcoeff/man/kendrm.Rd |only depcoeff-1.0.1/depcoeff/man/kendrs.Rd | 21 depcoeff-1.0.1/depcoeff/man/kendtaum.Rd |only depcoeff-1.0.1/depcoeff/man/spearr.Rd | 14 depcoeff-1.0.1/depcoeff/man/spearrs.Rd | 25 - depcoeff-1.0.1/depcoeff/man/xic.Rd |only depcoeff-1.0.1/depcoeff/man/zetac.Rd | 20 depcoeff-1.0.1/depcoeff/man/zetaci.Rd | 18 depcoeff-1.0.1/depcoeff/man/zetapm.Rd | 21 16 files changed, 701 insertions(+), 205 deletions(-)
Title: Toolkit for Analyzing Curricular Complexity
Description: Enables educational researchers and practitioners to calculate the curricular complexity of a plan of study, visualize its prerequisite structure at scale, and conduct customizable analyses. The original tool can be found at <https://curricularanalytics.org>. Additional functions to explore curriculum complexity from the literature are also included.
Author: David Reeping [aut, cre]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexity versions 1.0.1 dated 2026-01-08 and 1.0.2 dated 2026-06-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/deferment_factor.R | 2 +- inst/doc/CurricularComplexity-demo.Rmd | 2 +- inst/doc/CurricularComplexity-demo.html | 10 +++++----- vignettes/CurricularComplexity-demo.Rmd | 2 +- 6 files changed, 16 insertions(+), 16 deletions(-)
More information about CurricularComplexity at CRAN
Permanent link
Title: Conditionally Symmetric Multidimensional Gaussian Mixture Model
Description: Implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (Journal of the American Statistical Association 2025, <doi:10.1080/01621459.2024.2422124>).
Author: Ryan Sun [aut, cre],
Emily Kim [aut]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between csmGmm versions 0.4.0 dated 2025-09-16 and 0.5.0 dated 2026-06-16
DESCRIPTION | 21 +++++++++------ MD5 | 48 ++++++++++++++++++++++-------------- NAMESPACE | 18 ++++++++++++- R/check_incongruous.R | 24 +++++++++++++++++- R/create_plots.R |only R/generate_init_lists.R |only R/globals.R | 3 +- R/prepare_csmgmm_data.R |only R/process_lfdr_results.R |only R/read_gwas.R |only R/symm_fit_cor.R | 5 +-- R/symm_fit_cor_fulllik.R | 5 +-- R/symm_fit_cor_noAssumption.R | 5 +-- R/symm_fit_cor_rho.R | 5 +-- R/symm_fit_ind.R | 5 +-- R/symm_fit_ind_noAssumption.R | 5 +-- build/vignette.rds |binary inst/doc/csmGmm_tutorial.html | 7 +++-- man/create_plots.Rd |only man/find_4d.Rd |only man/generate_init_lists.Rd |only man/prepare_csmgmm_data.Rd |only man/process_lfdr_results.Rd |only man/read_gwas_one.Rd |only man/read_gwas_set.Rd |only man/symm_fit_cor_EM.Rd | 2 - man/symm_fit_cor_EM_fulllik.Rd | 2 - man/symm_fit_cor_EM_noAssumption.Rd | 2 - man/symm_fit_cor_EM_rho.Rd | 2 - man/symm_fit_ind_EM.Rd | 2 - man/symm_fit_ind_EM_noAssumption.Rd | 2 - 31 files changed, 107 insertions(+), 56 deletions(-)
Title: Easily Install and Load 'tesselle' Packages
Description: Easy install and load key packages from the 'tesselle' suite
in a single step. The 'tesselle' suite is a collection of packages for
research and teaching in archaeology. These packages focus on
quantitative analysis methods developed for archaeology. The
'tesselle' packages are designed to work seamlessly together and to
complement general-purpose and other specialized statistical packages.
These packages can be used to explore and analyze common data types in
archaeology: count data, compositional data and chronological data.
Learn more about 'tesselle' at <https://www.tesselle.org>.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tesselle versions 1.6.0 dated 2025-04-28 and 1.7.0 dated 2026-06-16
DESCRIPTION | 28 +++++++++++++++------------- MD5 | 13 +++++++------ NEWS.md | 10 ++++++++++ R/tesselle-package.R | 25 +++++++------------------ README.md | 31 ++++++++++++++++++++----------- build |only inst/CITATION | 2 +- man/tesselle-package.Rd | 38 +++++++++++++++++++++----------------- 8 files changed, 81 insertions(+), 66 deletions(-)
Title: Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).
Author: Dominic Gruen [aut, cre]
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.4.1 dated 2026-06-12 and 0.4.2 dated 2026-06-16
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 + R/VarID_functions.R | 15 +++++++-------- inst/doc/RaceID.html | 4 ++-- man/pruneKnn.Rd | 2 +- 6 files changed, 22 insertions(+), 22 deletions(-)
Title: Extreme Value Analysis for Circular Data
Description: General functions for performing extreme value analysis on a circular
domain as part of the statistical methodology in the paper by Konzen, E.,
Neves, C., and Jonathan, P. (2021). Modeling nonstationary extremes of storm
severity: Comparing parametric and semiparametric inference.
Environmetrics, 32(4), e2667 <doi:10.1002/env.2667>.
Author: Evandro Konzen [aut, cre]
Maintainer: Evandro Konzen <circularev.r@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2022-05-13
Diff between circularEV versions 0.1.1 dated 2022-05-13 and 0.1.2 dated 2026-06-16
DESCRIPTION | 26 LICENSE |only MD5 | 58 - R/LocalEstim.R | 12 R/PlotParamEstim.R | 4 R/PolarPlotData.R | 82 - R/PolarPlotRL.R | 72 - R/SplineML.R | 11 R/ThrSelection.R | 21 R/auxFunctions.R | 10 R/thresholdExamplesML.R | 4 R/thresholdExamplesMom.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/localMethods.R | 70 - inst/doc/localMethods.Rmd | 63 - inst/doc/localMethods.html | 2113 +++----------------------------------------- inst/doc/splineML.R | 70 - inst/doc/splineML.Rmd | 63 - inst/doc/splineML.html | 2125 +++------------------------------------------ man/HsSP.Rd | 4 man/LocalEstim.Rd | 12 man/PolarPlotData.Rd | 14 man/SplineML.Rd | 11 man/ThrSelection.Rd | 4 man/circularEV-package.Rd | 13 man/drc.Rd | 4 man/thresholdExampleML.Rd | 8 man/thresholdExampleMom.Rd | 6 vignettes/localMethods.Rmd | 63 - vignettes/splineML.Rmd | 63 - 31 files changed, 797 insertions(+), 4211 deletions(-)
Title: Phylogenetic Tree Statistics
Description: Collection of phylogenetic tree statistics,
collected throughout the literature. All functions have been
written to maximize computation speed. The package includes
umbrella functions to calculate all statistics, all balance
associated statistics, or all branching time related statistics.
Furthermore, the 'treestats' package supports summary statistic
calculations on Ltables, provides speed-improved coding of
branching times, Ltable conversion and includes algorithms to
create intermediately balanced trees. Full description can be
found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.
Author: Thijs Janzen [cre, aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between treestats versions 1.70.11 dated 2026-05-20 and 1.71.12 dated 2026-06-16
treestats-1.70.11/treestats/inst/include/branch_colless.h |only treestats-1.71.12/treestats/DESCRIPTION | 11 - treestats-1.71.12/treestats/MD5 | 50 +++---- treestats-1.71.12/treestats/NAMESPACE | 1 treestats-1.71.12/treestats/NEWS.md | 9 + treestats-1.71.12/treestats/R/RcppExports.R | 8 - treestats-1.71.12/treestats/R/calc_all_stats.R | 4 treestats-1.71.12/treestats/R/calc_brts_stats.R | 4 treestats-1.71.12/treestats/R/crown_age.R | 2 treestats-1.71.12/treestats/R/inv_branch_dist.R |only treestats-1.71.12/treestats/R/list_statistics.R | 2 treestats-1.71.12/treestats/inst/doc/Correlations.html | 8 - treestats-1.71.12/treestats/inst/doc/Getting_started.html | 50 +++---- treestats-1.71.12/treestats/inst/doc/Speed_improvement.html | 4 treestats-1.71.12/treestats/inst/doc/Tree_size.Rmd | 9 + treestats-1.71.12/treestats/inst/doc/Tree_size.html | 20 ++- treestats-1.71.12/treestats/inst/include/crown_age.h | 66 ++-------- treestats-1.71.12/treestats/man/calc_all_stats.Rd | 1 treestats-1.71.12/treestats/man/calc_brts_stats.Rd | 1 treestats-1.71.12/treestats/man/inv_branch_dist.Rd |only treestats-1.71.12/treestats/src/RcppExports.cpp | 25 --- treestats-1.71.12/treestats/src/brts.cpp | 45 +----- treestats-1.71.12/treestats/src/laplacian.cpp | 27 ---- treestats-1.71.12/treestats/src/phylo.cpp | 9 - treestats-1.71.12/treestats/tests/testthat/test-allstats.R | 4 treestats-1.71.12/treestats/tests/testthat/test-brts_stats.R | 2 treestats-1.71.12/treestats/tests/testthat/test-inv_branch_dist.R |only treestats-1.71.12/treestats/vignettes/Tree_size.Rmd | 9 + 28 files changed, 140 insertions(+), 231 deletions(-)
Title: Stylometric Multivariate Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/articles/RJ-2016-007/index.html>. You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.
Author: Maciej Eder [aut, cre],
Jan Rybicki [aut],
Mike Kestemont [aut],
Steffen Pielstroem [aut]
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.7.7 dated 2026-05-12 and 0.7.71 dated 2026-06-16
stylo-0.7.7/stylo/R/rolling.classify.r |only stylo-0.7.71/stylo/DESCRIPTION | 12 ++++++------ stylo-0.7.71/stylo/MD5 | 24 ++++++++++++------------ stylo-0.7.71/stylo/NAMESPACE | 2 ++ stylo-0.7.71/stylo/NEWS.md | 7 +++++++ stylo-0.7.71/stylo/R/classify.R | 6 ++++-- stylo-0.7.71/stylo/R/gui.support.R | 1 + stylo-0.7.71/stylo/R/make.samples.R | 6 ++++-- stylo-0.7.71/stylo/R/oppose.R | 2 +- stylo-0.7.71/stylo/R/rolling.classify.R |only stylo-0.7.71/stylo/R/rolling.delta.R | 2 +- stylo-0.7.71/stylo/R/stylo.R | 8 +++++--- stylo-0.7.71/stylo/R/txt.to.words.ext.R | 30 +++++++++++++++++++++++++----- stylo-0.7.71/stylo/man/delete.markup.Rd | 2 +- 14 files changed, 69 insertions(+), 33 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
This is a re-admission after prior archival of version 10.1.8 dated 2026-05-29
Diff between rswipl versions 10.1.8 dated 2026-05-29 and 10.1.9 dated 2026-06-16
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Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut],
Manuel Munoz-Marquez [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrMisc versions 2.10.1 dated 2026-01-08 and 2.10.2 dated 2026-06-16
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/RcmdrMisc-package.R | 18 ++++++------------ R/cv.R | 3 ++- R/numSummary.R | 6 +++--- man/RcmdrMisc-package.Rd | 18 ++++++------------ man/cv.Rd | 4 +++- man/numSummary.Rd | 4 ++-- man/reexports.Rd | 2 +- 10 files changed, 41 insertions(+), 46 deletions(-)
Title: Multivariate Bias Correction of Climate Model Outputs
Description: Calibrate and apply multivariate bias correction algorithms
for climate model simulations of multiple climate variables. Three methods
described by Cannon (2016) <doi:10.1175/JCLI-D-15-0679.1> and
Cannon (2018) <doi:10.1007/s00382-017-3580-6> are implemented --
(i) MBC Pearson correlation (MBCp), (ii) MBC rank correlation (MBCr),
and (iii) MBC N-dimensional PDF transform (MBCn) -- as is the Rank
Resampling for Distributions and Dependences (R2D2) method. An additional
multivariate rescaling method based on the linear Monge-Kantorovich map
for Gaussian optimal transport of dependence structure is also included.
Author: Alex J. Cannon [aut, cre]
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between MBC versions 0.10-7 dated 2024-11-12 and 0.10-8 dated 2026-06-16
DESCRIPTION | 21 ++++++++++++--------- MD5 | 16 +++++++++------- NAMESPACE | 3 ++- R/MRSmk.R |only README.md | 46 ++-------------------------------------------- inst/CITATION | 34 +++++++--------------------------- man/MBC-package.Rd | 18 +++++++++++++++--- man/MRSmk.Rd |only man/QDM.Rd | 2 +- man/R2D2.Rd | 2 +- 10 files changed, 49 insertions(+), 93 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to read, write and validate geographic metadata
defined with ISO TC211 / OGC ISO geographic information metadata standards, and
encoded using the ISO 19139 and ISO 19115-3 (XML) standard technical specifications.
This includes ISO 19110 (Feature cataloguing), 19115 (dataset metadata), 19119 (service metadata)
and 19136 (GML). Other interoperable schemas from the OGC are progressively supported
as well, such as the Sensor Web Enablement (SWE) Common Data Model, the OGC GML
Coverage Implementation Schema (GMLCOV), or the OGC GML Referenceable Grid (GMLRGRID).
Author: Emmanuel Blondel [aut, cre] ,
R Consortium [fnd]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.9.3 dated 2025-11-22 and 0.10.0 dated 2026-06-16
DESCRIPTION | 14 MD5 | 1012 ++++++++++++------------ NAMESPACE | 2 R/ISOAbstractAcquisitionInformation.R | 3 R/ISOAbstractApplicationSchemaInformation.R | 3 R/ISOAbstractCatalogue.R | 5 R/ISOAbstractCitation.R | 3 R/ISOAbstractConstraints.R | 3 R/ISOAbstractContentInformation.R | 3 R/ISOAbstractDataEvaluation.R | 3 R/ISOAbstractDataQuality.R | 3 R/ISOAbstractDistribution.R | 3 R/ISOAbstractExtent.R | 3 R/ISOAbstractFeatureCatalogue.R | 3 R/ISOAbstractFeatureType.R | 3 R/ISOAbstractFormat.R | 3 R/ISOAbstractGenericName.R | 3 R/ISOAbstractLineageInformation.R | 3 R/ISOAbstractMaintenanceInformation.R | 3 R/ISOAbstractMetadata.R | 3 R/ISOAbstractMetadataExtension.R | 3 R/ISOAbstractMetaquality.R | 12 R/ISOAbstractObject.R | 10 R/ISOAbstractOnlineResource.R | 3 R/ISOAbstractParameter.R | 3 R/ISOAbstractPlatform.R | 3 R/ISOAbstractPortrayalCatalogueInformation.R | 3 R/ISOAbstractPropertyType.R | 3 R/ISOAbstractQualityElement.R | 3 R/ISOAbstractReferenceSystem.R | 3 R/ISOAbstractResourceDescription.R | 3 R/ISOAbstractResponsibility.R | 3 R/ISOAbstractResult.R | 5 R/ISOAbstractSpatialRepresentation.R | 3 R/ISOAbstractSpatialResolution.R | 3 R/ISOAbstractStandardOrderProcess.R | 3 R/ISOAbstractTemporalQuality.R | 3 R/ISOAbstractTypedDate.R | 3 R/ISOAddress.R | 5 R/ISOAnchor.R | 5 R/ISOAngle.R | 5 R/ISOApplicationSchemaInformation.R | 5 R/ISOAssociatedResource.R | 3 R/ISOAssociationType.R | 5 R/ISOAttributeGroup.R | 3 R/ISOBand.R | 5 R/ISOBaseBoolean.R | 5 R/ISOBaseCharacterString.R | 5 R/ISOBaseDate.R | 5 R/ISOBaseDateTime.R | 5 R/ISOBaseDecimal.R | 5 R/ISOBaseInteger.R | 5 R/ISOBaseReal.R | 5 R/ISOBinary.R | 5 R/ISOBoundingPolygon.R | 5 R/ISOBrowseGraphic.R | 5 R/ISOCTCodelistValue.R | 6 R/ISOCellGeometry.R | 5 R/ISOCharacterSet.R | 5 R/ISOCitation.R | 5 R/ISOClassification.R | 5 R/ISOCodelist.R | 121 ++ R/ISOCodelistCatalogue.R | 5 R/ISOConformanceResult.R | 5 R/ISOConstraints.R | 5 R/ISOContact.R | 6 R/ISOContentInformation.R | 5 R/ISOCountry.R | 5 R/ISOCoupledResource.R | 5 R/ISOCouplingType.R | 5 R/ISOCoverageContentType.R | 12 R/ISOCoverageDescription.R | 5 R/ISODCPList.R | 5 R/ISODataIdentification.R | 5 R/ISODataIdentification19115_3.R | 3 R/ISODataIdentification19139.R | 3 R/ISODataQualityAbstractElement.R | 5 R/ISODataQualityCompleteness.R | 15 R/ISODataQualityLogicalConsistency.R | 25 R/ISODataQualityPositionalAccuracy.R | 20 R/ISODataQualityScope.R | 3 R/ISODataQualityTemporalAccuracy.R | 20 R/ISODataQualityThematicAccuracy.R | 23 R/ISODate.R | 5 R/ISODateType.R | 5 R/ISODescriptiveResult.R | 3 R/ISODigitalTransferOptions.R | 5 R/ISODimension.R | 5 R/ISODimensionNameType.R | 5 R/ISODistance.R | 5 R/ISODistribution.R | 5 R/ISODistributor.R | 5 R/ISOEvaluationMethod.R | 18 R/ISOEvaluationMethodType.R | 5 R/ISOExtent.R | 5 R/ISOFeatureCatalogueDescription.R | 5 R/ISOFeatureType.R | 5 R/ISOFeatureType19115_3.R | 2 R/ISOFeatureType19139.R | 3 R/ISOFeatureTypeInfo.R | 3 R/ISOFileName.R | 5 R/ISOFormat.R | 5 R/ISOFreeText.R | 5 R/ISOGeographicBoundingBox.R | 5 R/ISOGeographicDescription.R | 5 R/ISOGeographicExtent.R | 5 R/ISOGeometricObjectType.R | 5 R/ISOGeometricObjects.R | 5 R/ISOGeorectified.R | 5 R/ISOGeoreferenceable.R | 5 R/ISOGridSpatialRepresentation.R | 5 R/ISOIdentification.R | 5 R/ISOIdentification19115_3.R | 3 R/ISOIdentification19139.R | 3 R/ISOImageDescription.R | 5 R/ISOImageryAcquisitionInformation.R | 5 R/ISOImageryAlgorithm.R | 5 R/ISOImageryBand.R | 5 R/ISOImageryBandDefinition.R | 5 R/ISOImageryContext.R | 5 R/ISOImageryCoverageDescription.R | 5 R/ISOImageryCoverageResult.R | 5 R/ISOImageryEnvironmentalRecord.R | 5 R/ISOImageryEvent.R | 5 R/ISOImageryGCP.R | 5 R/ISOImageryGCPCollection.R | 5 R/ISOImageryGeolocationInformation.R | 5 R/ISOImageryGeometryType.R | 5 R/ISOImageryGeorectified.R | 5 R/ISOImageryGeoreferenceable.R | 5 R/ISOImageryImageDescription.R | 5 R/ISOImageryInstrument.R | 5 R/ISOImageryMetadata.R | 5 R/ISOImageryNominalResolution.R | 5 R/ISOImageryObjective.R | 5 R/ISOImageryObjectiveType.R | 5 R/ISOImageryOperation.R | 5 R/ISOImageryOperationType.R | 5 R/ISOImageryPlan.R | 5 R/ISOImageryPlatform.R | 5 R/ISOImageryPlatformPass.R | 5 R/ISOImageryPolarisationOrientation.R | 5 R/ISOImageryPriority.R | 5 R/ISOImageryProcessStep.R | 5 R/ISOImageryProcessStepReport.R | 5 R/ISOImageryProcessing.R | 5 R/ISOImageryRangeElementDescription.R | 5 R/ISOImageryRequestedDate.R | 5 R/ISOImageryRequirement.R | 5 R/ISOImageryRevision.R | 3 R/ISOImagerySensor.R | 3 R/ISOImagerySensorType.R | 5 R/ISOImagerySequence.R | 5 R/ISOImagerySource.R | 5 R/ISOImageryTransferFunctionType.R | 5 R/ISOImageryTrigger.R | 5 R/ISOImagingCondition.R | 5 R/ISOIndividual.R | 3 R/ISOInitiativeType.R | 5 R/ISOInstrumentationEvent.R | 3 R/ISOInstrumentationEventList.R | 3 R/ISOInstrumentationEventType.R | 4 R/ISOKeywordClass.R | 3 R/ISOKeywordType.R | 5 R/ISOKeywords.R | 5 R/ISOLanguage.R | 5 R/ISOLegalConstraints.R | 5 R/ISOLength.R | 5 R/ISOLineage.R | 5 R/ISOLocalName.R | 3 R/ISOLocale.R | 5 R/ISOLocaleContainer.R | 5 R/ISOLocalisedCharacterString.R | 5 R/ISOMDFeatureCatalogue.R | 3 R/ISOMaintenanceFrequency.R | 5 R/ISOMaintenanceInformation.R | 5 R/ISOMeasure.R | 5 R/ISOMeasureReference.R | 3 R/ISOMedium.R | 5 R/ISOMediumFormat.R | 5 R/ISOMemberName.R | 5 R/ISOMetaIdentifier.R | 5 R/ISOMetadata.R | 5 R/ISOMetadataScope.R | 4 R/ISOMimeFileType.R | 5 R/ISOMultiplicity.R | 5 R/ISOMultiplicityRange.R | 5 R/ISOOnLineFunction.R | 5 R/ISOOnlineResource.R | 5 R/ISOOperationChainMetadata.R | 5 R/ISOOperationMetadata.R | 5 R/ISOOrganisation.R | 3 R/ISOParameterDirection.R | 3 R/ISOPeriodDuration.R | 5 R/ISOPixelOrientation.R | 5 R/ISOPortrayalCatalogueReference.R | 5 R/ISOPresentationForm.R | 5 R/ISOProcessParameter.R | 3 R/ISOProcessStep.R | 5 R/ISOProgress.R | 5 R/ISOQualityResultFile.R | 3 R/ISOQuantitativeResult.R | 5 R/ISORangeDimension.R | 5 R/ISORecordType.R | 5 R/ISOReferenceSystem.R | 5 R/ISOReferenceSystemType.R | 3 R/ISOReleasability.R | 3 R/ISORepresentativeFraction.R | 5 R/ISOResolution.R | 5 R/ISOResponsibility.R | 3 R/ISORestriction.R | 5 R/ISORole.R | 5 R/ISOSRVParameter.R | 5 R/ISOSRVParameterDirection.R | 5 R/ISOSampleDimension.R | 3 R/ISOScale.R | 5 R/ISOScope.R | 3 R/ISOScopeCode.R | 5 R/ISOScopeDescription.R | 5 R/ISOScopedName.R | 5 R/ISOSecurityConstraints.R | 5 R/ISOSeries.R | 5 R/ISOServiceIdentification.R | 5 R/ISOSource.R | 5 R/ISOSpatialRepresentation.R | 5 R/ISOSpatialRepresentationType.R | 5 R/ISOSpatialTemporalExtent.R | 5 R/ISOStandaloneQualityReportInformation.R | 3 R/ISOStandardOrderProcess.R | 5 R/ISOTelephone.R | 5 R/ISOTelephoneType.R | 4 R/ISOTemporalExtent.R | 5 R/ISOTopicCategory.R | 5 R/ISOTopologyLevel.R | 5 R/ISOTypeName.R | 5 R/ISOURI.R | 3 R/ISOUnlimitedInteger.R | 5 R/ISOUomIdentifier.R | 3 R/ISOUsabilityElement.R | 5 R/ISOUsage.R | 5 R/ISOVectorSpatialRepresentation.R | 5 R/ISOVerticalExtent.R | 5 R/data_codelists.R |only README.md | 2 data |only man/ISOAbsoluteExternalPositionalAccuracy.Rd | 7 man/ISOAbstractAcquisitionInformation.Rd | 3 man/ISOAbstractApplicationSchemaInformation.Rd | 3 man/ISOAbstractCatalogue.Rd | 5 man/ISOAbstractCitation.Rd | 3 man/ISOAbstractCompleteness.Rd | 5 man/ISOAbstractConstraints.Rd | 3 man/ISOAbstractContentInformation.Rd | 3 man/ISOAbstractDataEvaluation.Rd | 3 man/ISOAbstractDataQuality.Rd | 3 man/ISOAbstractDistribution.Rd | 3 man/ISOAbstractExtent.Rd | 3 man/ISOAbstractFeatureCatalogue.Rd | 3 man/ISOAbstractFeatureType.Rd | 3 man/ISOAbstractFormat.Rd | 3 man/ISOAbstractGenericName.Rd | 3 man/ISOAbstractLineageInformation.Rd | 3 man/ISOAbstractLogicalConsistency.Rd | 5 man/ISOAbstractMDContentInformation.Rd | 5 man/ISOAbstractMaintenanceInformation.Rd | 3 man/ISOAbstractMetadata.Rd | 3 man/ISOAbstractMetadataExtension.Rd | 3 man/ISOAbstractMetaquality.Rd | 3 man/ISOAbstractOnlineResource.Rd | 3 man/ISOAbstractParameter.Rd | 3 man/ISOAbstractPlatform.Rd | 3 man/ISOAbstractPortrayalCatalogueInformation.Rd | 3 man/ISOAbstractPositionalAccuracy.Rd | 5 man/ISOAbstractPropertyType.Rd | 3 man/ISOAbstractQualityElement.Rd | 3 man/ISOAbstractReferenceSystem.Rd | 3 man/ISOAbstractResourceDescription.Rd | 3 man/ISOAbstractResponsibility.Rd | 3 man/ISOAbstractResult.Rd | 5 man/ISOAbstractSpatialRepresentation.Rd | 3 man/ISOAbstractSpatialResolution.Rd | 3 man/ISOAbstractStandardOrderProcess.Rd | 3 man/ISOAbstractTemporalAccuracy.Rd | 5 man/ISOAbstractTemporalQuality.Rd | 3 man/ISOAbstractThematicAccuracy.Rd | 5 man/ISOAbstractTypedDate.Rd | 3 man/ISOAccuracyOfATimeMeasurement.Rd | 7 man/ISOAddress.Rd | 7 man/ISOAggregationDerivation.Rd | 3 man/ISOAnchor.Rd | 5 man/ISOAngle.Rd | 5 man/ISOApplicationSchemaInformation.Rd | 5 man/ISOAssociatedResource.Rd | 3 man/ISOAssociationType.Rd | 7 man/ISOAttributeGroup.Rd | 3 man/ISOBand.Rd | 5 man/ISOBaseBoolean.Rd | 5 man/ISOBaseCharacterString.Rd | 5 man/ISOBaseDate.Rd | 5 man/ISOBaseDateTime.Rd | 5 man/ISOBaseDecimal.Rd | 5 man/ISOBaseInteger.Rd | 5 man/ISOBaseReal.Rd | 5 man/ISOBinary.Rd | 7 man/ISOBoundingPolygon.Rd | 5 man/ISOBrowseGraphic.Rd | 5 man/ISOCTCodelistValue.Rd | 6 man/ISOCellGeometry.Rd | 7 man/ISOCharacterSet.Rd | 5 man/ISOCitation.Rd | 7 man/ISOClassification.Rd | 7 man/ISOCodelist.Rd | 18 man/ISOCodelistCatalogue.Rd | 5 man/ISOCompletenessCommission.Rd | 7 man/ISOCompletenessOmission.Rd | 7 man/ISOConceptualConsistency.Rd | 7 man/ISOConfidence.Rd | 3 man/ISOConformanceResult.Rd | 5 man/ISOConstraints.Rd | 5 man/ISOContact.Rd | 8 man/ISOCountry.Rd | 5 man/ISOCoupledResource.Rd | 5 man/ISOCouplingType.Rd | 5 man/ISOCoverageContentType.Rd | 14 man/ISOCoverageDescription.Rd | 7 man/ISODCPList.Rd | 7 man/ISODataIdentification.Rd | 5 man/ISODataIdentification19115_3.Rd | 3 man/ISODataIdentification19139.Rd | 5 man/ISODataInspection.Rd | 3 man/ISODataQualityAbstractElement.Rd | 5 man/ISODataQualityScope.Rd | 5 man/ISODate.Rd | 5 man/ISODateType.Rd | 7 man/ISODescriptiveResult.Rd | 3 man/ISODigitalTransferOptions.Rd | 7 man/ISODimension.Rd | 7 man/ISODimensionNameType.Rd | 7 man/ISODistance.Rd | 5 man/ISODistribution.Rd | 7 man/ISODistributor.Rd | 7 man/ISODomainConsistency.Rd | 7 man/ISOEvaluationMethod.Rd | 3 man/ISOEvaluationMethodType.Rd | 7 man/ISOExtent.Rd | 5 man/ISOFeatureCatalogueDescription.Rd | 7 man/ISOFeatureType.Rd | 7 man/ISOFeatureType19115_3.Rd | 4 man/ISOFeatureType19139.Rd | 5 man/ISOFeatureTypeInfo.Rd | 3 man/ISOFileName.Rd | 5 man/ISOFormat.Rd | 7 man/ISOFormatConsistency.Rd | 7 man/ISOFreeText.Rd | 7 man/ISOFullInspection.Rd | 3 man/ISOGeographicBoundingBox.Rd | 5 man/ISOGeographicDescription.Rd | 5 man/ISOGeographicExtent.Rd | 5 man/ISOGeometricObjectType.Rd | 5 man/ISOGeometricObjects.Rd | 5 man/ISOGeorectified.Rd | 5 man/ISOGeoreferenceable.Rd | 5 man/ISOGridSpatialRepresentation.Rd | 5 man/ISOGriddedDataPositionalAccuracy.Rd | 7 man/ISOHomogeneity.Rd | 3 man/ISOIdentification.Rd | 5 man/ISOIdentification19115_3.Rd | 3 man/ISOIdentification19139.Rd | 3 man/ISOImageDescription.Rd | 7 man/ISOImageryAbstractGeolocationInformation.Rd | 5 man/ISOImageryAcquisitionInformation.Rd | 5 man/ISOImageryAlgorithm.Rd | 5 man/ISOImageryBand.Rd | 5 man/ISOImageryBandDefinition.Rd | 5 man/ISOImageryContext.Rd | 5 man/ISOImageryCoverageDescription.Rd | 5 man/ISOImageryCoverageResult.Rd | 5 man/ISOImageryEnvironmentalRecord.Rd | 5 man/ISOImageryEvent.Rd | 5 man/ISOImageryGCP.Rd | 5 man/ISOImageryGCPCollection.Rd | 5 man/ISOImageryGeometryType.Rd | 5 man/ISOImageryGeorectified.Rd | 5 man/ISOImageryGeoreferenceable.Rd | 5 man/ISOImageryImageDescription.Rd | 5 man/ISOImageryInstrument.Rd | 5 man/ISOImageryMetadata.Rd | 5 man/ISOImageryNominalResolution.Rd | 5 man/ISOImageryObjective.Rd | 5 man/ISOImageryObjectiveType.Rd | 5 man/ISOImageryOperation.Rd | 5 man/ISOImageryOperationType.Rd | 5 man/ISOImageryPlan.Rd | 5 man/ISOImageryPlatform.Rd | 5 man/ISOImageryPlatformPass.Rd | 5 man/ISOImageryPolarisationOrientation.Rd | 5 man/ISOImageryPriority.Rd | 5 man/ISOImageryProcessStep.Rd | 5 man/ISOImageryProcessStepReport.Rd | 5 man/ISOImageryProcessing.Rd | 5 man/ISOImageryRangeElementDescription.Rd | 5 man/ISOImageryRequestedDate.Rd | 7 man/ISOImageryRequirement.Rd | 5 man/ISOImageryRevision.Rd | 3 man/ISOImagerySensor.Rd | 3 man/ISOImagerySensorType.Rd | 5 man/ISOImagerySequence.Rd | 5 man/ISOImagerySource.Rd | 5 man/ISOImageryTransferFunctionType.Rd | 5 man/ISOImageryTrigger.Rd | 5 man/ISOImagingCondition.Rd | 5 man/ISOIndirectEvaluation.Rd | 3 man/ISOIndividual.Rd | 3 man/ISOInitiativeType.Rd | 7 man/ISOInstrumentationEvent.Rd | 3 man/ISOInstrumentationEventList.Rd | 3 man/ISOInstrumentationEventType.Rd | 6 man/ISOKeywordClass.Rd | 3 man/ISOKeywordType.Rd | 7 man/ISOKeywords.Rd | 7 man/ISOLanguage.Rd | 7 man/ISOLegalConstraints.Rd | 7 man/ISOLength.Rd | 5 man/ISOLineage.Rd | 7 man/ISOLocalName.Rd | 3 man/ISOLocale.Rd | 7 man/ISOLocaleContainer.Rd | 5 man/ISOLocalisedCharacterString.Rd | 5 man/ISOMDFeatureCatalogue.Rd | 3 man/ISOMaintenanceFrequency.Rd | 7 man/ISOMaintenanceInformation.Rd | 7 man/ISOMeasure.Rd | 5 man/ISOMeasureReference.Rd | 3 man/ISOMedium.Rd | 7 man/ISOMediumFormat.Rd | 5 man/ISOMemberName.Rd | 5 man/ISOMetaIdentifier.Rd | 7 man/ISOMetadata.Rd | 5 man/ISOMetadataScope.Rd | 6 man/ISOMimeFileType.Rd | 5 man/ISOMultiplicity.Rd | 5 man/ISOMultiplicityRange.Rd | 5 man/ISONonQuantitativeAttributeAccuracy.Rd | 7 man/ISONonQuantitativeAttributeCorrectness.Rd | 3 man/ISOOnLineFunction.Rd | 7 man/ISOOnlineResource.Rd | 7 man/ISOOperationChainMetadata.Rd | 5 man/ISOOperationMetadata.Rd | 5 man/ISOOrganisation.Rd | 3 man/ISOParameterDirection.Rd | 3 man/ISOPeriodDuration.Rd | 5 man/ISOPixelOrientation.Rd | 5 man/ISOPortrayalCatalogueReference.Rd | 7 man/ISOPresentationForm.Rd | 7 man/ISOProcessParameter.Rd | 3 man/ISOProcessStep.Rd | 7 man/ISOQualityResultFile.Rd | 3 man/ISOQuantitativeAttributeAccuracy.Rd | 7 man/ISOQuantitativeResult.Rd | 7 man/ISORangeDimension.Rd | 7 man/ISORecordType.Rd | 5 man/ISOReferenceSystem.Rd | 7 man/ISOReferenceSystemType.Rd | 5 man/ISORelativeInternalPositionalAccuracy.Rd | 7 man/ISOReleasability.Rd | 3 man/ISORepresentativeFraction.Rd | 7 man/ISORepresentativity.Rd | 3 man/ISOResolution.Rd | 5 man/ISOResponsibility.Rd | 3 man/ISORestriction.Rd | 7 man/ISORole.Rd | 7 man/ISOSRVParameter.Rd | 4 man/ISOSRVParameterDirection.Rd | 5 man/ISOSRVServiceIdentification.Rd | 6 man/ISOSampleBasedInspection.Rd | 3 man/ISOSampleDimension.Rd | 3 man/ISOScale.Rd | 5 man/ISOScope.Rd | 3 man/ISOScopeCode.Rd | 5 man/ISOScopeDescription.Rd | 5 man/ISOScopedName.Rd | 5 man/ISOSecurityConstraints.Rd | 7 man/ISOSeries.Rd | 5 man/ISOSource.Rd | 7 man/ISOSpatialRepresentation.Rd | 5 man/ISOSpatialRepresentationType.Rd | 5 man/ISOSpatialTemporalExtent.Rd | 7 man/ISOStandaloneQualityReportInformation.Rd | 3 man/ISOStandardOrderProcess.Rd | 5 man/ISOStatus.Rd | 5 man/ISOTelephone.Rd | 7 man/ISOTelephoneType.Rd | 6 man/ISOTemporalConsistency.Rd | 7 man/ISOTemporalExtent.Rd | 5 man/ISOTemporalValidity.Rd | 7 man/ISOThematicClassificationCorrectness.Rd | 7 man/ISOTopicCategory.Rd | 7 man/ISOTopologicalConsistency.Rd | 7 man/ISOTopologyLevel.Rd | 7 man/ISOTypeName.Rd | 5 man/ISOURI.Rd | 3 man/ISOUnlimitedInteger.Rd | 5 man/ISOUomIdentifier.Rd | 3 man/ISOUsabilityElement.Rd | 5 man/ISOUsage.Rd | 5 man/ISOVectorSpatialRepresentation.Rd | 7 man/ISOVerticalExtent.Rd | 7 man/codelists.Rd |only man/parseISOCodelists.Rd |only 509 files changed, 716 insertions(+), 2939 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Ger Inberg [aut, cre] ,
Adam Black [aut] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between CDMConnector versions 2.5.1 dated 2026-04-03 and 2.6.0 dated 2026-06-16
CDMConnector-2.5.1/CDMConnector/tests/testthat/_problems |only CDMConnector-2.5.1/CDMConnector/tests/testthat/testthat-problems.rds |only CDMConnector-2.6.0/CDMConnector/DESCRIPTION | 17 CDMConnector-2.6.0/CDMConnector/MD5 | 35 - CDMConnector-2.6.0/CDMConnector/NAMESPACE | 6 CDMConnector-2.6.0/CDMConnector/NEWS.md | 8 CDMConnector-2.6.0/CDMConnector/R/cdm.R | 126 +++- CDMConnector-2.6.0/CDMConnector/R/cohdSimilarConcepts.R | 12 CDMConnector-2.6.0/CDMConnector/R/dbSource.R | 62 ++ CDMConnector-2.6.0/CDMConnector/R/utils.R | 74 +- CDMConnector-2.6.0/CDMConnector/build/partial.rdb |binary CDMConnector-2.6.0/CDMConnector/build/vignette.rds |binary CDMConnector-2.6.0/CDMConnector/inst/doc/a01_getting-started.html | 72 +- CDMConnector-2.6.0/CDMConnector/inst/doc/a02_cohorts.R | 294 +++++----- CDMConnector-2.6.0/CDMConnector/inst/doc/a02_cohorts.html | 249 +------- CDMConnector-2.6.0/CDMConnector/inst/doc/a03_dbplyr.html | 4 CDMConnector-2.6.0/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 4 CDMConnector-2.6.0/CDMConnector/man/cdmFromCon.Rd | 4 CDMConnector-2.6.0/CDMConnector/man/insertTableSpark.Rd |only CDMConnector-2.6.0/CDMConnector/tests/testthat/test-02-db-cdm.R | 33 + 20 files changed, 512 insertions(+), 488 deletions(-)
Title: Spatial Concentration and Radius-Based Risk Calculations
Description: Provides methods for spatial concentration and radius-based risk
calculations. The package focuses on efficient determination of the sum of
observations within a given radius, identifying areas of high local
concentration, and aggregating point data to polygon geometries. These
methods are useful for applications such as insurance, urban analytics,
environmental exposure analysis, and other spatial point pattern workflows.
The underlying maximum covering problem is described by Church (1974)
<doi:10.1007/BF01942293>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.8.0 dated 2026-05-04 and 0.8.1 dated 2026-06-16
spatialrisk-0.8.0/spatialrisk/man/spatialrisk-deprecated.Rd |only spatialrisk-0.8.1/spatialrisk/DESCRIPTION | 14 spatialrisk-0.8.1/spatialrisk/MD5 | 50 +- spatialrisk-0.8.1/spatialrisk/NAMESPACE | 7 spatialrisk-0.8.1/spatialrisk/NEWS.md | 18 spatialrisk-0.8.1/spatialrisk/R/concentration_hotspot_pair_refine.R | 154 +++++-- spatialrisk-0.8.1/spatialrisk/R/deprecated-aliases.R | 93 +++- spatialrisk-0.8.1/spatialrisk/R/highest_concentration_terra.R | 86 ++-- spatialrisk-0.8.1/spatialrisk/R/hotspot-workflow.R |only spatialrisk-0.8.1/spatialrisk/build/vignette.rds |binary spatialrisk-0.8.1/spatialrisk/inst/doc/fixed-radius-concentration.R | 8 spatialrisk-0.8.1/spatialrisk/inst/doc/fixed-radius-concentration.Rmd | 72 +++ spatialrisk-0.8.1/spatialrisk/inst/doc/fixed-radius-concentration.html | 193 ++++++---- spatialrisk-0.8.1/spatialrisk/inst/doc/visualisation.html | 2 spatialrisk-0.8.1/spatialrisk/man/choropleth_ggplot2.Rd | 1 spatialrisk-0.8.1/spatialrisk/man/concentration.Rd |only spatialrisk-0.8.1/spatialrisk/man/concentration_hotspot.Rd | 23 + spatialrisk-0.8.1/spatialrisk/man/find_highest_concentration.Rd |only spatialrisk-0.8.1/spatialrisk/man/interpolate_spline.Rd | 1 spatialrisk-0.8.1/spatialrisk/man/map_points.Rd | 24 - spatialrisk-0.8.1/spatialrisk/man/plot_points.Rd |only spatialrisk-0.8.1/spatialrisk/man/points_in_circle.Rd |only spatialrisk-0.8.1/spatialrisk/man/points_to_polygon.Rd |only spatialrisk-0.8.1/spatialrisk/man/points_within_radius.Rd | 19 spatialrisk-0.8.1/spatialrisk/man/prepare_spatialrisk.Rd |only spatialrisk-0.8.1/spatialrisk/man/radius_sum.Rd | 49 -- spatialrisk-0.8.1/spatialrisk/man/summarise_points_by_polygon.Rd | 26 - spatialrisk-0.8.1/spatialrisk/tests/testthat/test-concentration-hotspot-pair-refine.R | 15 spatialrisk-0.8.1/spatialrisk/tests/testthat/test_concentration_hotspot.R | 105 +++++ spatialrisk-0.8.1/spatialrisk/vignettes/fixed-radius-concentration.Rmd | 72 +++ 30 files changed, 715 insertions(+), 317 deletions(-)
Title: Analyzing Multiple Omics Data with an Offset Approach
Description: Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block. Also offers options to deal with block-wise missingness in multi-omics data.
Author: Simon Klau [aut],
Roman Hornung [aut, cre],
Alina Bauer [aut],
Jonas Hagenberg [aut]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between prioritylasso versions 0.3.1 dated 2023-04-10 and 0.4.0 dated 2026-06-16
DESCRIPTION | 29 +++++++-- MD5 | 22 +++---- NEWS | 8 ++ R/predict.prioritylasso.R | 6 +- R/prioritylasso.R | 83 ++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/explanation_blockwise_missing.R | 8 +- inst/doc/explanation_blockwise_missing.html | 6 +- inst/doc/prioritylasso_vignette.R | 4 - inst/doc/prioritylasso_vignette.html | 66 +++++++++++----------- man/pl_data.Rd | 2 man/prioritylasso.Rd | 8 ++ 12 files changed, 159 insertions(+), 83 deletions(-)
Title: Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre] ,
Maurice Goodman [ctb] ,
Wouter van der Bijl [ctb] ,
Giovanni M. Marchetti [ctr]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 2.0.1 dated 2026-05-14 and 3.0.0 dated 2026-06-16
DESCRIPTION | 10 - MD5 | 71 ++++++---- NAMESPACE | 13 + NEWS.md | 11 + R/dsem.R | 166 ++++++++++++++++++++----- R/family.R |only R/make_dsem_ram.R | 32 +++- R/make_msv.R |only R/utility.R | 12 - README.md | 10 - build/vignette.rds |binary inst/doc/MGARCH.R |only inst/doc/MGARCH.Rmd |only inst/doc/MGARCH.html |only inst/doc/features.R | 4 inst/doc/features.Rmd | 6 inst/doc/features.html | 12 - inst/doc/model-description.R | 5 inst/doc/model-description.Rmd | 11 - inst/doc/model-description.html | 13 - inst/doc/nonlinear.Rmd | 2 inst/doc/nonlinear.html | 4 inst/doc/random_slopes.html | 2 man/dsem.Rd | 34 +++-- man/dsemRTMB.Rd | 22 ++- man/dsem_control.Rd | 7 - man/fixed.Rd |only man/gaussian_fixed_sd.Rd |only man/lognormal.Rd |only man/loo_residuals.Rd | 8 - man/make_msv.Rd |only man/tweedie.Rd |only src/dsem.cpp | 123 +++++++++++++++--- tests/testthat/test-distributions.R | 36 ++++- tests/testthat/test-gmrf-versions.R | 35 ++--- tests/testthat/test-platform.R | 98 ++++++++++---- tests/testthat/test-priors.R | 16 +- vignettes/MGARCH.Rmd |only vignettes/features.Rmd | 6 vignettes/model-description.Rmd | 11 - vignettes/nonlinear.Rmd | 2 vignettes/web_only/dynamic_factor_analysis.Rmd | 16 +- 42 files changed, 554 insertions(+), 244 deletions(-)
Title: Hierarchical Piecewise Regression with Smoothed Change-Points
Description: Fits Bayesian hierarchical piecewise regression models with
multiple logistic-smoothed change-points. Non-linear parameters (change-point
locations and transition sharpness) and linear parameters can each be
conditioned on covariates and factors via flexible design matrices.
A random-intercept structure is supported for any parameter. Spike-and-slab
regularization is supported for selecting the number of breakpoints.
Posterior inference uses a Metropolis-within-Gibbs sampler implemented
in 'Rust' for speed. Methods are based on the smooth transition
piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389>
and variable selection spike-and-slab priors of Kuo and Mallick (1998)
<https://www.jstor.org/stable/25053023>.
Author: Aidan D Bindoff [aut, cre]
Maintainer: Aidan D Bindoff <aidan.bindoff@utas.edu.au>
Diff between smoothbp versions 0.2.4 dated 2026-06-14 and 0.2.7 dated 2026-06-16
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 3 +++ NEWS.md | 22 ++++++++++++++++++++++ R/derivative.R |only man/derivative.Rd |only src/Makevars.in | 5 +---- src/Makevars.win.in | 7 +------ src/rust/Cargo.toml | 3 +-- 9 files changed, 40 insertions(+), 22 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. See Li and Zhang (2026) <doi:10.18637/jss.v116.i06> for details.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li.stat.tamu.edu@lixingchi.com>
Diff between fastcpd versions 0.16.2 dated 2025-04-25 and 1.0.0 dated 2026-06-16
fastcpd-0.16.2/fastcpd/inst/include |only fastcpd-0.16.2/fastcpd/src/fastcpd_classes.cc |only fastcpd-0.16.2/fastcpd/src/fastcpd_test.cc |only fastcpd-0.16.2/fastcpd/src/ref_fastglm_fit_glm.cc |only fastcpd-0.16.2/fastcpd/src/ref_fastglm_fit_glm_dense.cc |only fastcpd-0.16.2/fastcpd/src/ref_r_family.c |only fastcpd-0.16.2/fastcpd/src/ref_tseries.cc |only fastcpd-0.16.2/fastcpd/src/ref_tseries_cfuncs.f90 |only fastcpd-0.16.2/fastcpd/src/ref_tseries_dsumsl.f |only fastcpd-0.16.2/fastcpd/src/ref_tseries_formats.c |only fastcpd-0.16.2/fastcpd/src/ref_tseries_garch.c |only fastcpd-0.16.2/fastcpd/src/test-fastcpd.cc |only fastcpd-1.0.0/fastcpd/DESCRIPTION | 26 fastcpd-1.0.0/fastcpd/MD5 | 162 +++--- fastcpd-1.0.0/fastcpd/NAMESPACE | 2 fastcpd-1.0.0/fastcpd/NEWS.md | 44 + fastcpd-1.0.0/fastcpd/R/fastcpd.R | 85 +++ fastcpd-1.0.0/fastcpd/R/utilities.R | 42 + fastcpd-1.0.0/fastcpd/README.md | 233 ++------ fastcpd-1.0.0/fastcpd/build/partial.rdb |only fastcpd-1.0.0/fastcpd/build/vignette.rds |binary fastcpd-1.0.0/fastcpd/configure |only fastcpd-1.0.0/fastcpd/configure.win |only fastcpd-1.0.0/fastcpd/inst/CITATION | 17 fastcpd-1.0.0/fastcpd/inst/doc/comparison-packages.html | 38 - fastcpd-1.0.0/fastcpd/inst/doc/comparison-pelt.html | 2 fastcpd-1.0.0/fastcpd/inst/doc/examples-advanced.html | 2 fastcpd-1.0.0/fastcpd/inst/doc/examples-custom-model.Rmd | 100 +++ fastcpd-1.0.0/fastcpd/inst/doc/examples-custom-model.html | 172 ++++-- fastcpd-1.0.0/fastcpd/inst/doc/exploration-during-development.html | 2 fastcpd-1.0.0/fastcpd/inst/doc/time-complexity.html | 4 fastcpd-1.0.0/fastcpd/man/fastcpd.Rd | 109 +++- fastcpd-1.0.0/fastcpd/man/fastcpd_ar.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_arima.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_arma.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_binomial.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_exponential.Rd |only fastcpd-1.0.0/fastcpd/man/fastcpd_garch.Rd | 40 + fastcpd-1.0.0/fastcpd/man/fastcpd_lasso.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_lm.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_mean.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_meanvariance.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_poisson.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_ts.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_var.Rd | 2 fastcpd-1.0.0/fastcpd/man/fastcpd_variance.Rd | 2 fastcpd-1.0.0/fastcpd/man/figures/README-ar3-1.png |binary fastcpd-1.0.0/fastcpd/man/figures/README-time-comparison-large-1.png |binary fastcpd-1.0.0/fastcpd/man/figures/README-time-comparison-small-1.png |binary fastcpd-1.0.0/fastcpd/man/figures/logo.png |only fastcpd-1.0.0/fastcpd/man/plot.Rd | 6 fastcpd-1.0.0/fastcpd/man/print.Rd | 8 fastcpd-1.0.0/fastcpd/man/show.Rd | 8 fastcpd-1.0.0/fastcpd/man/summary.Rd | 8 fastcpd-1.0.0/fastcpd/src/Makevars | 2 fastcpd-1.0.0/fastcpd/src/Makevars.win | 2 fastcpd-1.0.0/fastcpd/src/RcppExports.cpp | 54 -- fastcpd-1.0.0/fastcpd/src/codegen |only fastcpd-1.0.0/fastcpd/src/families |only fastcpd-1.0.0/fastcpd/src/fastcpd_arma.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_binomial.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_custom.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_exponential.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_family.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_garch.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_garch.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_gaussian.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_glm.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_impl.cc | 268 +++++----- fastcpd-1.0.0/fastcpd/src/fastcpd_impl.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_lasso.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_ma.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_mean.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_mean_1d.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_meanvariance.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_meanvariance_1d.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_mgaussian.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_optim.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_poisson.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_template.h |only fastcpd-1.0.0/fastcpd/src/fastcpd_variance.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_variance_1d.cc |only fastcpd-1.0.0/fastcpd/src/fastcpd_xptr.h |only fastcpd-1.0.0/fastcpd/tests/__pycache__ |only fastcpd-1.0.0/fastcpd/tests/testthat/examples/fastcpd_custom_xptr.txt |only fastcpd-1.0.0/fastcpd/tests/testthat/examples/fastcpd_exponential_1.R |only fastcpd-1.0.0/fastcpd/tests/testthat/examples/fastcpd_garch_2.txt |only fastcpd-1.0.0/fastcpd/tests/testthat/examples/fastcpd_garch_3.txt |only fastcpd-1.0.0/fastcpd/tests/testthat/test-check.R | 3 fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_4.R | 2 fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_custom_xptr.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_exponential_1.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_garch.R | 8 fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_garch_2.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-examples-fastcpd_garch_3.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-fastcpd-custom-xptr.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-fastcpd-glm-irls.R |only fastcpd-1.0.0/fastcpd/tests/testthat/test-pvalue-distribution.R |only fastcpd-1.0.0/fastcpd/tools |only fastcpd-1.0.0/fastcpd/vignettes/examples-custom-model.Rmd | 100 +++ 100 files changed, 1055 insertions(+), 518 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
The multilevel GSEA algorithm is derived from the 'fgsea' package.
Methods are described in Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.1.4 dated 2026-04-08 and 0.1.5 dated 2026-06-16
DESCRIPTION | 8 - MD5 | 20 ++-- NAMESPACE | 2 NEWS.md | 14 ++- R/bayes_enrich.R |only R/gsea.R | 152 ++++++++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/enrichit.html | 18 ++-- man/bayes_enrich.Rd |only man/bayes_summary.Rd |only man/enrichit-package.Rd | 5 + tests/testthat/test-bayes-enrich.R |only 13 files changed, 119 insertions(+), 100 deletions(-)
Title: Numeric Matrices K-NN and PCA Imputation
Description: Fast k-nearest neighbors (K-NN) and principal component
analysis (PCA) imputation algorithms for missing values in epigenetic
data or other high-dimensional numeric matrices. For PCA, a locally
optimal block preconditioned conjugate gradient (LOBPCG) eigensolver
with warm starts of both the eigenblock and search direction is also
supported. Two complementary imputation strategies are available.
Group-wise imputation (e.g., by chromosome) is recommended for
Illumina DNA methylation microarrays (e.g., 450K, EPIC) and other
matrices with groupable columns. A sliding window approach for K-NN or
PCA imputation is recommended only for whole-genome methylation data
such as whole-genome bisulfite sequencing (WGBS) or Enzymatic
Methyl-seq (EM-seq). The package also supports hyperparameter tuning
via repeated cross-validation. The K-NN algorithm is described in:
Hastie, T., Tibshirani, R., Sherlock, G., Eisen, M., Brown, P. and
Botstein, D. (1999) "Imputing Missing Data for Gene Expression
Arra [...truncated...]
Author: Hung Pham [aut, cre, cph] ,
Posit Software, PBC [cph]
Maintainer: Hung Pham <amser.hoanghung@gmail.com>
Diff between slideimp versions 1.1.0 dated 2026-05-01 and 1.2.0 dated 2026-06-16
slideimp-1.1.0/slideimp/src/impute_knn_mlpack.cpp |only slideimp-1.2.0/slideimp/DESCRIPTION | 54 +- slideimp-1.2.0/slideimp/MD5 | 87 ++- slideimp-1.2.0/slideimp/NEWS.md | 26 + slideimp-1.2.0/slideimp/R/RcppExports.R | 8 slideimp-1.2.0/slideimp/R/col_vars.R | 26 - slideimp-1.2.0/slideimp/R/crate.R |only slideimp-1.2.0/slideimp/R/group_imp.R | 193 +++++--- slideimp-1.2.0/slideimp/R/knn_imp.R | 89 +--- slideimp-1.2.0/slideimp/R/mat_miss.R | 7 slideimp-1.2.0/slideimp/R/mean_imp_col.R | 6 slideimp-1.2.0/slideimp/R/pca_imp.R | 157 ++++--- slideimp-1.2.0/slideimp/R/print.R | 57 +- slideimp-1.2.0/slideimp/R/sim_mat.R | 3 slideimp-1.2.0/slideimp/R/slide_imp.R | 172 +++++-- slideimp-1.2.0/slideimp/R/tune_imp.R | 356 ++++++++-------- slideimp-1.2.0/slideimp/R/utils.R | 51 +- slideimp-1.2.0/slideimp/README.md | 168 +++---- slideimp-1.2.0/slideimp/inst/CITATION |only slideimp-1.2.0/slideimp/inst/LICENSE.note |only slideimp-1.2.0/slideimp/man/col_vars.Rd | 19 slideimp-1.2.0/slideimp/man/group_imp.Rd | 95 +--- slideimp-1.2.0/slideimp/man/knn_imp.Rd | 23 - slideimp-1.2.0/slideimp/man/pca_imp.Rd | 110 ++-- slideimp-1.2.0/slideimp/man/slide_imp.Rd | 94 ++-- slideimp-1.2.0/slideimp/man/slideimp-package.Rd | 10 slideimp-1.2.0/slideimp/man/slideimp_resolve_group.Rd | 3 slideimp-1.2.0/slideimp/man/tune_imp.Rd | 71 +-- slideimp-1.2.0/slideimp/src/RcppExports.cpp | 35 - slideimp-1.2.0/slideimp/src/armaSVD.cpp | 234 +++++++--- slideimp-1.2.0/slideimp/src/find_windows.cpp | 70 ++- slideimp-1.2.0/slideimp/src/find_windows_flank.cpp | 78 ++- slideimp-1.2.0/slideimp/src/hybrid_topk_eig.h | 38 - slideimp-1.2.0/slideimp/src/impute_knn_brute.cpp | 74 ++- slideimp-1.2.0/slideimp/src/imputed_value.h | 1 slideimp-1.2.0/slideimp/src/lobpcg_warm.h | 55 ++ slideimp-1.2.0/slideimp/src/mat_stats.cpp | 113 ++++- slideimp-1.2.0/slideimp/tests/testthat/helper.R | 13 slideimp-1.2.0/slideimp/tests/testthat/test-col_vars.R | 6 slideimp-1.2.0/slideimp/tests/testthat/test-crate.R |only slideimp-1.2.0/slideimp/tests/testthat/test-group_imp.R | 141 ++++-- slideimp-1.2.0/slideimp/tests/testthat/test-knn_imp.R | 66 -- slideimp-1.2.0/slideimp/tests/testthat/test-mat_miss.R | 8 slideimp-1.2.0/slideimp/tests/testthat/test-pca_imp.R | 274 +++++++++--- slideimp-1.2.0/slideimp/tests/testthat/test-sim_mat.R | 16 slideimp-1.2.0/slideimp/tests/testthat/test-slide_imp.R | 123 +++-- slideimp-1.2.0/slideimp/tests/testthat/test-tune_imp.R | 184 ++++++-- 47 files changed, 2123 insertions(+), 1291 deletions(-)
Title: Easily Build, Simulate, and Explore Stock-and-Flow Models
Description: Stock-and-flow models are a computational method from the
field of system dynamics. They represent how systems change over time
and are mathematically equivalent to ordinary differential equations.
'sdbuildR' (system dynamics builder) provides an intuitive interface
for constructing stock-and-flow models without requiring extensive
domain knowledge. Models can quickly be simulated and revised,
supporting iterative development. 'sdbuildR' simulates models in 'R'
and 'Julia', and supports computationally intensive ensemble
simulations. Additionally, 'sdbuildR' can import models created in
'Insight Maker' (<https://insightmaker.com/>).
Author: Kyra Caitlin Evers [aut, cre, cph]
Maintainer: Kyra Caitlin Evers <kyra.c.evers@gmail.com>
Diff between sdbuildR versions 1.0.8 dated 2025-11-19 and 2.0.0 dated 2026-06-16
sdbuildR-1.0.8/sdbuildR/R/build_xmile.R |only sdbuildR-1.0.8/sdbuildR/R/custom_func.R |only sdbuildR-1.0.8/sdbuildR/R/globals.R |only sdbuildR-1.0.8/sdbuildR/R/helpers.R |only sdbuildR-1.0.8/sdbuildR/R/insightmaker_to_sfm.R |only sdbuildR-1.0.8/sdbuildR/R/julia_func.R |only sdbuildR-1.0.8/sdbuildR/R/julia_setup.R |only sdbuildR-1.0.8/sdbuildR/R/solvers.R |only sdbuildR-1.0.8/sdbuildR/R/template.R |only sdbuildR-1.0.8/sdbuildR/R/units.R |only sdbuildR-1.0.8/sdbuildR/R/visualise.R |only sdbuildR-1.0.8/sdbuildR/man/as.data.frame.sdbuildR_sim.Rd |only sdbuildR-1.0.8/sdbuildR/man/as.data.frame.sdbuildR_xmile.Rd |only sdbuildR-1.0.8/sdbuildR/man/build.Rd |only sdbuildR-1.0.8/sdbuildR/man/convert_u.Rd |only sdbuildR-1.0.8/sdbuildR/man/debugger.Rd |only sdbuildR-1.0.8/sdbuildR/man/drop_u.Rd |only sdbuildR-1.0.8/sdbuildR/man/find_dependencies.Rd |only sdbuildR-1.0.8/sdbuildR/man/get_build_code.Rd |only sdbuildR-1.0.8/sdbuildR/man/get_regex_time_units.Rd |only 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sdbuildR-1.0.8/sdbuildR/man/xmile.Rd |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-assemble_script_julia.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-assemble_script_r.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-build.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-conv_r.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-ensemble.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-helpers.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-insightmaker_to_sfm.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-julia_vs_r.R |only sdbuildR-1.0.8/sdbuildR/tests/testthat/test-visualise.R |only sdbuildR-2.0.0/sdbuildR/DESCRIPTION | 50 sdbuildR-2.0.0/sdbuildR/MD5 | 382 + sdbuildR-2.0.0/sdbuildR/NAMESPACE | 95 sdbuildR-2.0.0/sdbuildR/NEWS.md | 120 sdbuildR-2.0.0/sdbuildR/R/aaa.R |only sdbuildR-2.0.0/sdbuildR/R/assemble_helpers.R |only sdbuildR-2.0.0/sdbuildR/R/assemble_script_julia.R | 1730 ------ sdbuildR-2.0.0/sdbuildR/R/assemble_script_r.R | 776 --- sdbuildR-2.0.0/sdbuildR/R/compile_script.R |only sdbuildR-2.0.0/sdbuildR/R/conv_julia_distributions.R |only sdbuildR-2.0.0/sdbuildR/R/conv_julia_helpers.R |only sdbuildR-2.0.0/sdbuildR/R/conv_julia_statements.R |only sdbuildR-2.0.0/sdbuildR/R/ensemble.R |only sdbuildR-2.0.0/sdbuildR/R/ensemble_julia.R |only sdbuildR-2.0.0/sdbuildR/R/ensemble_r.R |only sdbuildR-2.0.0/sdbuildR/R/export_model.R |only sdbuildR-2.0.0/sdbuildR/R/export_psychomodels.R |only sdbuildR-2.0.0/sdbuildR/R/import_desolve.R |only sdbuildR-2.0.0/sdbuildR/R/import_insightmaker.R |only sdbuildR-2.0.0/sdbuildR/R/insightmaker_conv.R | 2535 ++++++---- sdbuildR-2.0.0/sdbuildR/R/insightmaker_conv_eqn.R | 1587 +----- sdbuildR-2.0.0/sdbuildR/R/interpret_unit_test.R |only sdbuildR-2.0.0/sdbuildR/R/julia_conv_ast.R |only sdbuildR-2.0.0/sdbuildR/R/julia_conv_calls.R |only sdbuildR-2.0.0/sdbuildR/R/julia_conv_eqn.R | 1532 ------ sdbuildR-2.0.0/sdbuildR/R/julia_conv_fallback.R |only sdbuildR-2.0.0/sdbuildR/R/julia_conv_validate.R |only sdbuildR-2.0.0/sdbuildR/R/lang_adapter.R |only sdbuildR-2.0.0/sdbuildR/R/order_equations.R |only sdbuildR-2.0.0/sdbuildR/R/plot.R |only sdbuildR-2.0.0/sdbuildR/R/plot_helpers.R |only sdbuildR-2.0.0/sdbuildR/R/scripts.R |only sdbuildR-2.0.0/sdbuildR/R/sdbuildR_custom_func.R |only sdbuildR-2.0.0/sdbuildR/R/sim_methods.R |only sdbuildR-2.0.0/sdbuildR/R/sim_settings.R |only sdbuildR-2.0.0/sdbuildR/R/simulate.R | 1678 ++---- sdbuildR-2.0.0/sdbuildR/R/stockflow.R |only sdbuildR-2.0.0/sdbuildR/R/summary_stockflow.R |only sdbuildR-2.0.0/sdbuildR/R/sysdata.rda |binary sdbuildR-2.0.0/sdbuildR/R/templates.R |only sdbuildR-2.0.0/sdbuildR/R/update.R |only sdbuildR-2.0.0/sdbuildR/R/use_julia.R |only sdbuildR-2.0.0/sdbuildR/R/utils.R |only sdbuildR-2.0.0/sdbuildR/R/verify.R |only sdbuildR-2.0.0/sdbuildR/R/zzz.R | 30 sdbuildR-2.0.0/sdbuildR/README.md | 175 sdbuildR-2.0.0/sdbuildR/inst/CITATION |only sdbuildR-2.0.0/sdbuildR/inst/Project.toml | 64 sdbuildR-2.0.0/sdbuildR/inst/init.jl | 45 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sdbuildR-2.0.0/sdbuildR/tests/testthat/test-cache-invalidation.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-change_name.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-compare_models.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-conv_julia.R | 747 +- sdbuildR-2.0.0/sdbuildR/tests/testthat/test-conv_julia_distributions.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-custom_func-nse.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-custom_func.R | 573 -- sdbuildR-2.0.0/sdbuildR/tests/testthat/test-edge-cases.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-ensemble-jl.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-ensemble-r.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-export_model.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-export_psychomodels.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-import_desolve.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-insightmaker.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-insightmaker_conv_eqn.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-interpret_unit_test.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-julia_conv_ast.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-language-switching.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-layout-invariants.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-meta.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-nse.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-order_equations.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-plot_ensemble_stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-plot_helpers.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-plot_simulate_stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-plot_stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-plot_verify_stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-prep-functions.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-print_simulate_stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-sdbuildR_custom_func.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-sim_methods.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-sim_settings.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-simulate.R | 438 + sdbuildR-2.0.0/sdbuildR/tests/testthat/test-stockflow.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-summary.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-templates.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-update.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-use_julia.R | 119 sdbuildR-2.0.0/sdbuildR/tests/testthat/test-utils.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/test-verify.R |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/abm |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/Balancing_an_Inverted_Pendulum.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/C_N_bacteria_DOM.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/Kepler_Ellipsen.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/Spring_Mass_Model.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/Stanford_Prison_Experiment.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/cld.InsightMaker |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/cld.json |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/population.InsightMaker |only sdbuildR-2.0.0/sdbuildR/tests/testthat/testdata/insightmaker/cran/population.json |only 225 files changed, 5010 insertions(+), 8080 deletions(-)
Title: Unicode and Punycode Domain Name Processing
Description: High-performance Unicode and Punycode encoding/decoding for
internationalized domain names. Provides RFC 3492 compliant conversion
functions with a focus on URL processing and data analysis workflows.
Addresses limitations in existing R packages for handling international
domain names in web scraping and URL parsing applications.
Author: Bart Turczynski [aut, cre]
Maintainer: Bart Turczynski <bartek+punycoder@turczynski.pl>
Diff between punycoder versions 1.0.0 dated 2026-06-11 and 1.1.0 dated 2026-06-16
DESCRIPTION | 9 +- MD5 | 40 +++++---- NAMESPACE | 2 NEWS.md | 23 +++-- R/RcppExports.R | 8 + R/normalize.R |only R/validators.R | 6 - README.md | 17 ++- inst/doc/punycoder-intro.R | 10 +- inst/doc/punycoder-intro.Rmd | 10 +- inst/doc/punycoder-intro.html | 14 +-- man/host_normalize.Rd |only man/normalization_profile_info.Rd |only man/punycoder-package.Rd | 1 src/RcppExports.cpp | 22 +++++ src/exports.cpp | 35 ++++++++ src/init.c | 4 src/punycoder_nfc.cpp |only src/punycoder_nfc.h |only src/punycoder_normalize.cpp |only src/punycoder_normalize.h |only src/unicode_tables_16_0_0.cpp |only src/unicode_tables_16_0_0.h |only tests/testthat/test-backends.R | 165 ++++++++++++++++++++++++++++++-------- tests/testthat/test-normalize.R |only vignettes/punycoder-intro.Rmd | 10 +- 26 files changed, 290 insertions(+), 86 deletions(-)
Title: Demographic Modelling Using Projection Matrices
Description: Tools for modelling populations and demography using matrix projection models,
with deterministic and stochastic model implementations. Includes population projection,
indices of short- and long-term population size and growth, perturbation analysis,
convergence to stability or stationarity, and diagnostic and manipulation tools.
Author: Iain Stott [aut, cre],
Dave Hodgson [aut],
Stuart Townley [aut],
Stephen Ellner [ctb]
Maintainer: Iain Stott <iainmstott@gmail.com>
Diff between popdemo versions 1.3-3 dated 2026-03-09 and 1.3-4 dated 2026-06-16
ChangeLog | 1 DESCRIPTION | 6 +- MD5 | 16 +++--- R/popdemo-onAttach.R | 2 inst/doc/popdemo.R | 4 - inst/doc/popdemo.Rmd | 4 - inst/doc/popdemo.html | 132 +++++++++++++++++++++++++------------------------- vignettes/imgs |only vignettes/popdemo.Rmd | 4 - 9 files changed, 86 insertions(+), 83 deletions(-)
Title: Multivariate Outlier Detection Methods
Description: Provides methods for detecting multivariate outliers in numeric datasets. The package implements classical Mahalanobis distance, robust Minimum Covariance Determinant (MCD), and Principal Component Analysis (PCA)-based approaches for outlier detection. The methodology is informed by Aggarwal (2017) <doi:10.1007/978-3-319-47578-3> and Grentzelos, Caroni and Barranco-Chamorro (2020) <doi:10.1002/cmm4.1129>. Visualization functions are included to aid interpretation of detected outliers. Mahalanobis distance calculations are accelerated using 'C++' through 'Rcpp'.
Author: Senuri Yasara [aut, cre],
Pavanthi Sudasinghe [aut]
Maintainer: Senuri Yasara <senuriyasara@gmail.com>
Diff between MOutliers versions 0.1.1 dated 2026-06-15 and 0.1.2 dated 2026-06-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot_outliers.R | 3 +++ man/plot_outliers.Rd | 4 ++++ 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding
Description: Methods for analyzing DNA methylation data via Most Recurrent Methylation Patterns (MRMPs). Supports cell-type annotation, spatial deconvolution, unsupervised clustering, and cancer cell-of-origin inference. Includes C-backed summaries for YAME “.cg/.cm” files (overlap counts, log2 odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS deconvolution, and plotting utilities. Scales to large spatial and single-cell methylomes and is robust to extreme sparsity.
Author: Hongxiang Fu [aut, cre] ,
Wanding Zhou [cph, fnd],
The SAMtools/HTSlib authors [ctb, cph] ,
Attractive Chaos [ctb, cph] )
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Diff between MethScope versions 1.0.2 dated 2026-06-13 and 1.0.3 dated 2026-06-16
DESCRIPTION | 6 +-- MD5 | 14 ++++---- README.md | 18 +++++++++++ inst/doc/MethScope-Tutorial.R | 10 +++++- inst/doc/MethScope-Tutorial.Rmd | 13 ++++++-- inst/doc/MethScope-Tutorial.html | 62 +++++++++++++++++++++------------------ src/Makevars | 2 - vignettes/MethScope-Tutorial.Rmd | 13 ++++++-- 8 files changed, 91 insertions(+), 47 deletions(-)
Title: Classifications for Statistics Norway
Description: Functions to search, retrieve, apply and update classification
standards and code lists using Statistics Norway's API
<https://www.ssb.no/klass> from the system 'KLASS'. Retrieves classifications
by date with options to choose language, hierarchical level and formatting.
Author: Susie Jentoft [aut],
Diana-Cristina Iancu [aut],
Lisa Li [aut],
Oeyvind I. Berntsen [aut, cre],
Statistics Norway [cph]
Maintainer: Oeyvind I. Berntsen <Oyvind.Berntsen@ssb.no>
Diff between klassR versions 1.0.5 dated 2026-02-26 and 1.0.6 dated 2026-06-16
DESCRIPTION | 20 LICENSE | 2 MD5 | 130 +-- NAMESPACE | 36 NEWS.md | 91 +- R/Convert_table.R | 42 - R/Hent_data.R | 880 +++++++++++------------ R/KLASS.R | 444 +++++------ R/Klass_list.R | 682 ++++++++--------- R/Levels.R | 92 +- R/UpdateKlass-graph-build.R | 868 +++++++++++----------- R/UpdateKlass-graph-navigate.R | 412 +++++----- R/UpdateKlass.R | 415 +++++----- R/checkLevel.R | 38 R/data.R | 72 - R/find_equivalents.R |only R/format.R | 152 +-- man/CheckDate.Rd | 30 man/ConvertTable.Rd | 58 - man/GetBaseUrl.Rd | 30 man/GetNums.Rd | 36 man/GetUrl.Rd | 36 man/GetUrl2.Rd | 40 - man/Levels.Rd | 44 - man/MakeChar.Rd | 36 man/MakeUrl.Rd | 84 +- man/apply_klass.Rd | 134 +-- man/check_connect.Rd | 40 - man/correspond_list.Rd | 62 - man/count_neighbors.Rd | 50 - man/find_dates.Rd | 64 - man/find_equivalent_codes.Rd |only man/find_equivalent_nodes.Rd |only man/find_name.Rd | 48 - man/find_variant_from.Rd | 52 - man/find_variant_to.Rd | 52 - man/formattering.Rd | 44 - man/formattering_kommune.Rd | 38 man/formattering_nace.Rd | 36 man/get_family.Rd | 50 - man/get_klass.Rd | 146 +-- man/get_name.Rd | 46 - man/get_variant_name.Rd | 34 man/get_version.Rd | 62 - man/is_combined.Rd | 80 +- man/is_split.Rd | 54 - man/klass_131_1964_graph.Rd | 32 man/klass_131_2020_graph.Rd | 32 man/klass_131_graph.Rd | 32 man/klass_graph.Rd | 76 - man/klass_node.Rd | 74 - man/klassdata.Rd | 50 - man/levelCheck.Rd | 49 - man/list_family.Rd | 58 - man/list_klass.Rd | 54 - man/search_klass.Rd | 54 - man/stop_quietly.Rd | 28 man/update_code.Rd | 140 +-- man/update_klass.Rd | 218 ++--- man/update_klass_node.Rd | 70 - tests/testthat.R | 8 tests/testthat/test-UpdateKlass-graph-navigate.R | 88 +- tests/testthat/test-UpdateKlass.R | 414 +++++----- tests/testthat/test_ApplyKlass.R | 412 +++++----- tests/testthat/test_GetKlass.R | 336 ++++---- tests/testthat/test_ListKlass.R | 50 - tests/testthat/test_find_equivalent_codes.R |only tests/testthat/test_formattering.R | 44 - 68 files changed, 4101 insertions(+), 4080 deletions(-)
Title: Discrete Choice and Competitive Reactions: End-to-End Simulation
Description: Although discrete choice (choice-based conjoint) analysis has become a widely used
technique for the elicitation of consumer preferences and hence a foundation for product
design, to the best of our knowledge, there exists neither free and open-source nor
commercial software that covers the game-theoretic simulation of competitive reactions among
firms based on discrete choice models to improve decision making beyond traditional product
(line) optimization. The package does not only provide functions to fill this gap but
comprises an entire simulation pipeline including the upstream processes of discrete choice
analysis itself. It ranges from preference generation, choice design, design assessment,
error and response simulation, through hierarchical Bayesian estimation of mixed logit models
as well as convergence and model assessment, to Nash equilibrium computation. Doing so, it
partly draws from established packages concerned with discrete choice analysis. While its
structure general [...truncated...]
Author: Jan H. R. Dressler [aut, cre, cph],
Peter Kurz [ths],
Winfried J. Steiner [ths]
Maintainer: Jan H. R. Dressler <jhrd13@tu-clausthal.de>
Diff between cash versions 1.0.2 dated 2026-06-09 and 1.0.3 dated 2026-06-16
DESCRIPTION | 9 +++++---- MD5 | 35 ++++++++++++++++++----------------- R/B_prefgen.R | 3 +++ R/C_choicedes.R | 13 ++++++++----- R/D_responsesim.R | 3 +++ R/E_hbmxlest.R | 3 +++ R/F_designeval.R | 3 +++ R/G_modeleval.R | 35 ++++++++++++++++++++--------------- R/H_precomputeM.R | 5 ++++- R/I_preoptandnashgame.R | 3 +++ inst |only man/B_prefgen.Rd | 3 +++ man/C_choicedes.Rd | 3 +++ man/D_responsesim.Rd | 3 +++ man/E_hbmxlest.Rd | 3 +++ man/F_designeval.Rd | 3 +++ man/G_modeleval.Rd | 3 +++ man/H_precomputeM.Rd | 3 +++ man/I_preoptandnashgame.Rd | 3 +++ 19 files changed, 94 insertions(+), 42 deletions(-)
Title: Forecasting with Bayesian Panel Vector Autoregressions
Description: Provides Bayesian estimation and forecasting of dynamic panel data using
Bayesian Panel Vector Autoregressions with hierarchical prior distributions
following the specification by Sanchez-Martinez & Woźniak (2026) <doi:10.48550/arXiv.2606.14143>.
The models include country-specific Vector Autoregressions (VARs) that share a global prior
distribution that extend the model by Jarociński (2010) <doi:10.1002/jae.1082>.
Under this prior expected value, each country's system follows
a global VAR with country-invariant parameters. Further flexibility is
provided by the hierarchical prior structure that retains the Minnesota prior
interpretation for the global VAR and features estimated prior covariance
matrices, shrinkage, and persistence levels. Bayesian forecasting is developed
for models including exogenous variables, allowing conditional forecasts given
the future trajectories of some variables and restricted forecasts assuring
that rates are forecasted to stay positive an [...truncated...]
Author: Tomasz Wozniak [aut, cre] ,
Miguel Sanchez-Martinez [ctb],
International Labour Organization [cph]
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between bpvars versions 1.0 dated 2025-12-11 and 2.0 dated 2026-06-16
bpvars-1.0/bpvars/src/rtmvtnorm.cpp |only bpvars-1.0/bpvars/src/rtmvtnorm.h |only bpvars-2.0/bpvars/DESCRIPTION | 40 - bpvars-2.0/bpvars/MD5 | 197 +++-- bpvars-2.0/bpvars/NAMESPACE | 2 bpvars-2.0/bpvars/NEWS.md | 5 bpvars-2.0/bpvars/R/bpvars-package.R | 25 bpvars-2.0/bpvars/R/compute_forecast_performance.R | 8 bpvars-2.0/bpvars/R/compute_variance_decompositions.R | 18 bpvars-2.0/bpvars/R/country_grouping_incomegroup.R | 2 bpvars-2.0/bpvars/R/country_grouping_region.R | 2 bpvars-2.0/bpvars/R/country_grouping_subregionbroad.R | 2 bpvars-2.0/bpvars/R/country_grouping_subregiondetailed.R | 2 bpvars-2.0/bpvars/R/estimate.BVARGROUPPANEL.R | 7 bpvars-2.0/bpvars/R/estimate.BVARGROUPPRIORPANEL.R | 7 bpvars-2.0/bpvars/R/estimate.bvarPANEL.R | 7 bpvars-2.0/bpvars/R/estimate.bvars.R | 7 bpvars-2.0/bpvars/R/forecast.R | 28 bpvars-2.0/bpvars/R/forecast_performance.R | 7 bpvars-2.0/bpvars/R/ilo_conditional_forecasts.R |only bpvars-2.0/bpvars/R/ilo_dynamic_panel.R | 2 bpvars-2.0/bpvars/R/ilo_dynamic_panel_missing.R | 2 bpvars-2.0/bpvars/R/ilo_exogenous_forecasts.R | 10 bpvars-2.0/bpvars/R/ilo_exogenous_variables.R | 2 bpvars-2.0/bpvars/R/ilo_exogenous_variables_missing.R | 2 bpvars-2.0/bpvars/R/plot.R | 2 bpvars-2.0/bpvars/R/summary.R | 4 bpvars-2.0/bpvars/README.md | 82 +- bpvars-2.0/bpvars/build/partial.rdb |binary bpvars-2.0/bpvars/build/vignette.rds |only bpvars-2.0/bpvars/data/country_grouping_incomegroup.rda |binary bpvars-2.0/bpvars/data/country_grouping_region.rda |binary bpvars-2.0/bpvars/data/country_grouping_subregionbroad.rda |binary bpvars-2.0/bpvars/data/country_grouping_subregiondetailed.rda |binary bpvars-2.0/bpvars/data/ilo_conditional_forecasts.rda |only bpvars-2.0/bpvars/data/ilo_dynamic_panel.rda |binary bpvars-2.0/bpvars/data/ilo_dynamic_panel_missing.rda |binary bpvars-2.0/bpvars/data/ilo_exogenous_forecasts.rda |binary bpvars-2.0/bpvars/data/ilo_exogenous_variables.rda |binary bpvars-2.0/bpvars/data/ilo_exogenous_variables_missing.rda |binary bpvars-2.0/bpvars/inst/CITATION |only bpvars-2.0/bpvars/inst/doc |only bpvars-2.0/bpvars/inst/include/bpvars_RcppExports.h | 4 bpvars-2.0/bpvars/inst/tinytest/test_forecast.R | 5 bpvars-2.0/bpvars/man/bpvars-package.Rd | 23 bpvars-2.0/bpvars/man/compute_forecast_performance.ForecastsPANELpoos.Rd | 7 bpvars-2.0/bpvars/man/compute_forecast_performance.Rd | 7 bpvars-2.0/bpvars/man/compute_variance_decompositions.PosteriorBVARGROUPPANEL.Rd | 6 bpvars-2.0/bpvars/man/compute_variance_decompositions.PosteriorBVARPANEL.Rd | 6 bpvars-2.0/bpvars/man/compute_variance_decompositions.PosteriorBVARs.Rd | 6 bpvars-2.0/bpvars/man/country_grouping_incomegroup.Rd | 2 bpvars-2.0/bpvars/man/country_grouping_region.Rd | 2 bpvars-2.0/bpvars/man/country_grouping_subregionbroad.Rd | 2 bpvars-2.0/bpvars/man/country_grouping_subregiondetailed.Rd | 2 bpvars-2.0/bpvars/man/estimate.BVARGROUPPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.BVARGROUPPRIORPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.BVARPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.BVARs.Rd | 7 bpvars-2.0/bpvars/man/estimate.PosteriorBVARGROUPPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.PosteriorBVARGROUPPRIORPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.PosteriorBVARPANEL.Rd | 7 bpvars-2.0/bpvars/man/estimate.PosteriorBVARs.Rd | 7 bpvars-2.0/bpvars/man/forecast.PosteriorBVARGROUPPANEL.Rd | 10 bpvars-2.0/bpvars/man/forecast.PosteriorBVARGROUPPRIORPANEL.Rd | 10 bpvars-2.0/bpvars/man/forecast.PosteriorBVARPANEL.Rd | 10 bpvars-2.0/bpvars/man/forecast.PosteriorBVARs.Rd | 10 bpvars-2.0/bpvars/man/forecast_poos_recursively.BVARGROUPPANEL.Rd | 7 bpvars-2.0/bpvars/man/forecast_poos_recursively.BVARGROUPPRIORPANEL.Rd | 7 bpvars-2.0/bpvars/man/forecast_poos_recursively.BVARPANEL.Rd | 7 bpvars-2.0/bpvars/man/forecast_poos_recursively.BVARs.Rd | 7 bpvars-2.0/bpvars/man/forecast_poos_recursively.Rd | 7 bpvars-2.0/bpvars/man/ilo_conditional_forecasts.Rd |only bpvars-2.0/bpvars/man/ilo_dynamic_panel.Rd | 2 bpvars-2.0/bpvars/man/ilo_dynamic_panel_missing.Rd | 2 bpvars-2.0/bpvars/man/ilo_exogenous_forecasts.Rd | 10 bpvars-2.0/bpvars/man/ilo_exogenous_variables.Rd | 2 bpvars-2.0/bpvars/man/ilo_exogenous_variables_missing.Rd | 2 bpvars-2.0/bpvars/man/plot.ForecastsPANEL.Rd | 2 bpvars-2.0/bpvars/man/reexports.Rd | 2 bpvars-2.0/bpvars/man/specify_bvarGroupPANEL.Rd | 177 ++--- bpvars-2.0/bpvars/man/specify_bvarGroupPriorPANEL.Rd | 316 ++++----- bpvars-2.0/bpvars/man/specify_bvarPANEL.Rd | 335 ++++------ bpvars-2.0/bpvars/man/specify_bvars.Rd | 335 ++++------ bpvars-2.0/bpvars/man/specify_panel_data_matrices.Rd | 128 +-- bpvars-2.0/bpvars/man/specify_poosf_exercise.Rd | 119 +-- bpvars-2.0/bpvars/man/specify_posterior_bvarGroupPANEL.Rd | 99 +- bpvars-2.0/bpvars/man/specify_posterior_bvarGroupPriorPANEL.Rd | 99 +- bpvars-2.0/bpvars/man/specify_posterior_bvarPANEL.Rd | 145 ++-- bpvars-2.0/bpvars/man/specify_posterior_bvars.Rd | 145 ++-- bpvars-2.0/bpvars/man/specify_prior_bvarPANEL.Rd | 160 ++-- bpvars-2.0/bpvars/man/specify_prior_bvars.Rd | 154 ++-- bpvars-2.0/bpvars/man/specify_starting_values_bvarGroupPANEL.Rd | 219 +++--- bpvars-2.0/bpvars/man/specify_starting_values_bvarGroupPriorPANEL.Rd | 208 +++--- bpvars-2.0/bpvars/man/specify_starting_values_bvarPANEL.Rd | 198 ++--- bpvars-2.0/bpvars/man/specify_starting_values_bvars.Rd | 192 ++--- bpvars-2.0/bpvars/man/summary.ForecastsPANEL.Rd | 4 bpvars-2.0/bpvars/src/Makevars | 2 bpvars-2.0/bpvars/src/Makevars.win | 2 bpvars-2.0/bpvars/src/RcppExports.cpp | 144 ++-- bpvars-2.0/bpvars/src/forecast_panel.cpp | 36 - bpvars-2.0/bpvars/src/forecast_panel.h | 10 bpvars-2.0/bpvars/src/forecast_performance.cpp | 1 bpvars-2.0/bpvars/vignettes |only 103 files changed, 2042 insertions(+), 1883 deletions(-)
Title: Bayesian Aggregate Treatment Effects
Description: Running and comparing meta-analyses of data with hierarchical
Bayesian models in Stan, including convenience functions for formatting
data, plotting and pooling measures specific to meta-analysis. This implements many models
from Meager (2019) <doi:10.1257/app.20170299>.
Author: Witold Wiecek [cre, aut],
Rachael Meager [aut],
Brice Green [ctb] ,
Danny Toomey [ctb] ,
Trustees of Columbia University [cph]
Maintainer: Witold Wiecek <witold.wiecek@gmail.com>
Diff between baggr versions 0.8 dated 2026-02-10 and 0.8.2 dated 2026-06-16
baggr-0.8.2/baggr/DESCRIPTION | 8 baggr-0.8.2/baggr/MD5 | 164 - baggr-0.8.2/baggr/NAMESPACE | 2 baggr-0.8.2/baggr/NEWS.md | 33 baggr-0.8.2/baggr/R/auto_prior.R | 72 baggr-0.8.2/baggr/R/baggr-package.R | 4 baggr-0.8.2/baggr/R/baggr.R | 96 baggr-0.8.2/baggr/R/baggr_compare.R | 8 baggr-0.8.2/baggr/R/binary_to_individual.R | 4 baggr-0.8.2/baggr/R/check_cols.R | 22 baggr-0.8.2/baggr/R/convert_inputs.R | 169 + baggr-0.8.2/baggr/R/effect_draw.R | 26 baggr-0.8.2/baggr/R/fixed_effects.R | 2 baggr-0.8.2/baggr/R/forest_plot.R | 2 baggr-0.8.2/baggr/R/funnel.R | 11 baggr-0.8.2/baggr/R/group_effects.R | 68 baggr-0.8.2/baggr/R/helpers.R | 10 baggr-0.8.2/baggr/R/labbe.R | 2 baggr-0.8.2/baggr/R/loocv.R | 6 baggr-0.8.2/baggr/R/pooling_metrics.R | 10 baggr-0.8.2/baggr/R/predict.R |only baggr-0.8.2/baggr/R/prepare_ma.R | 6 baggr-0.8.2/baggr/R/print_baggr.R | 4 baggr-0.8.2/baggr/R/prior_dist.R | 4 baggr-0.8.2/baggr/R/selection.R | 17 baggr-0.8.2/baggr/R/trt_effects.R | 4 baggr-0.8.2/baggr/R/vitamin_a.R |only baggr-0.8.2/baggr/build/vignette.rds |binary baggr-0.8.2/baggr/data/vitamin_a.rda |only baggr-0.8.2/baggr/inst/doc/baggr.R | 8 baggr-0.8.2/baggr/inst/doc/baggr.Rmd | 33 baggr-0.8.2/baggr/inst/doc/baggr.html | 257 +- baggr-0.8.2/baggr/inst/doc/baggr_binary.Rmd | 7 baggr-0.8.2/baggr/inst/doc/baggr_binary.html | 38 baggr-0.8.2/baggr/inst/doc/baggr_selection.Rmd |only baggr-0.8.2/baggr/inst/doc/baggr_selection.html |only baggr-0.8.2/baggr/inst/stan/functions/selection.stan | 121 - baggr-0.8.2/baggr/inst/stan/logit.stan | 5 baggr-0.8.2/baggr/inst/stan/mutau.stan | 26 baggr-0.8.2/baggr/inst/stan/mutau_full.stan | 5 baggr-0.8.2/baggr/inst/stan/rubin.stan | 70 baggr-0.8.2/baggr/inst/stan/rubin_full.stan | 8 baggr-0.8.2/baggr/man/baggr-package.Rd | 4 baggr-0.8.2/baggr/man/baggr.Rd | 69 baggr-0.8.2/baggr/man/baggr_compare.Rd | 8 baggr-0.8.2/baggr/man/binary_to_individual.Rd | 4 baggr-0.8.2/baggr/man/convert_inputs.Rd | 158 - baggr-0.8.2/baggr/man/effect_draw.Rd | 20 baggr-0.8.2/baggr/man/effect_plot.Rd | 6 baggr-0.8.2/baggr/man/fixed_effects.Rd | 2 baggr-0.8.2/baggr/man/forest_plot.Rd | 2 baggr-0.8.2/baggr/man/funnel_plot.Rd | 9 baggr-0.8.2/baggr/man/labbe.Rd | 2 baggr-0.8.2/baggr/man/loocv.Rd | 4 baggr-0.8.2/baggr/man/mutau_cor.Rd | 2 baggr-0.8.2/baggr/man/pooling.Rd | 10 baggr-0.8.2/baggr/man/predict.baggr.Rd |only baggr-0.8.2/baggr/man/prepare_ma.Rd | 6 baggr-0.8.2/baggr/man/prepare_prior.Rd | 18 baggr-0.8.2/baggr/man/print.baggr.Rd | 2 baggr-0.8.2/baggr/man/priors.Rd | 4 baggr-0.8.2/baggr/man/selection.Rd | 18 baggr-0.8.2/baggr/man/treatment_effect.Rd | 2 baggr-0.8.2/baggr/man/vitamin_a.Rd |only baggr-0.8.2/baggr/src/Makevars |only baggr-0.8.2/baggr/src/stanExports_logit.h | 15 baggr-0.8.2/baggr/src/stanExports_mutau.h | 463 ++-- baggr-0.8.2/baggr/src/stanExports_rubin.h | 1116 ++++++---- baggr-0.8.2/baggr/src/stanExports_rubin_full.h | 33 baggr-0.8.2/baggr/tests/testthat/Rplots.pdf |binary baggr-0.8.2/baggr/tests/testthat/test_binary.R | 837 ++++--- baggr-0.8.2/baggr/tests/testthat/test_full.R | 195 + baggr-0.8.2/baggr/tests/testthat/test_group_effects_meta_regression_full.R |only baggr-0.8.2/baggr/tests/testthat/test_helpers.R | 6 baggr-0.8.2/baggr/tests/testthat/test_mutau.R | 32 baggr-0.8.2/baggr/tests/testthat/test_mutau_logpd.R |only baggr-0.8.2/baggr/tests/testthat/test_onerow.R | 8 baggr-0.8.2/baggr/tests/testthat/test_prior.R | 59 baggr-0.8.2/baggr/tests/testthat/test_rubin.R | 923 ++++---- baggr-0.8.2/baggr/tests/testthat/test_selection_and_validation.R | 137 + baggr-0.8.2/baggr/tests/testthat/test_vitamin_a.R |only baggr-0.8.2/baggr/tools |only baggr-0.8.2/baggr/vignettes/baggr.Rmd | 33 baggr-0.8.2/baggr/vignettes/baggr.bib | 65 baggr-0.8.2/baggr/vignettes/baggr_binary.Rmd | 7 baggr-0.8.2/baggr/vignettes/baggr_binary.Rmd.orig | 7 baggr-0.8.2/baggr/vignettes/baggr_selection.Rmd |only baggr-0.8.2/baggr/vignettes/baggr_selection.Rmd.orig |only baggr-0.8.2/baggr/vignettes/fig/selection-unnamed-chunk-3-1.png |only baggr-0.8.2/baggr/vignettes/recompute_vigs.R | 1 baggr-0.8/baggr/R/prior_summary.R |only 91 files changed, 3566 insertions(+), 2053 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.59 dated 2026-03-28 and 0.60 dated 2026-06-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/install.R | 10 +++++++++- R/platforms.R | 4 ++-- 4 files changed, 17 insertions(+), 9 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre] ,
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb],
Romain Lesur [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.32 dated 2024-10-04 and 0.33 dated 2026-06-16
DESCRIPTION | 15 +++-- MD5 | 12 ++-- R/static.R | 130 ++++++++++++++++++--------------------------------- R/utils.R | 34 ------------- man/create_server.Rd | 9 +-- man/httd.Rd | 5 - man/server_config.Rd | 6 +- 7 files changed, 70 insertions(+), 141 deletions(-)
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre] ,
Syoyo Fujita [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.38.10 dated 2025-02-28 and 0.41.3 dated 2026-06-16
rayrender-0.38.10/rayrender/R/save_png.R |only rayrender-0.38.10/rayrender/R/utils-pipe.R |only rayrender-0.38.10/rayrender/configure.ac |only rayrender-0.38.10/rayrender/man/pipe.Rd |only rayrender-0.38.10/rayrender/man/run_documentation.Rd |only rayrender-0.38.10/rayrender/man/save_png.Rd |only rayrender-0.38.10/rayrender/src/Makevars.win |only rayrender-0.38.10/rayrender/src/PreviewDisplay.cpp |only rayrender-0.38.10/rayrender/src/PreviewDisplay.h |only rayrender-0.38.10/rayrender/src/RayMatrix.cpp |only rayrender-0.38.10/rayrender/src/RayMatrix.h |only rayrender-0.38.10/rayrender/src/aabb.cpp |only rayrender-0.38.10/rayrender/src/aabb.h |only rayrender-0.38.10/rayrender/src/adaptivesampler.cpp |only rayrender-0.38.10/rayrender/src/adaptivesampler.h |only rayrender-0.38.10/rayrender/src/animatedtransform.cpp |only rayrender-0.38.10/rayrender/src/animatedtransform.h |only rayrender-0.38.10/rayrender/src/assert.cpp |only rayrender-0.38.10/rayrender/src/assert.h |only rayrender-0.38.10/rayrender/src/bounds.h |only rayrender-0.38.10/rayrender/src/box.cpp |only rayrender-0.38.10/rayrender/src/box.h |only rayrender-0.38.10/rayrender/src/buildscene.cpp |only rayrender-0.38.10/rayrender/src/buildscene.h |only rayrender-0.38.10/rayrender/src/bvh.cpp |only rayrender-0.38.10/rayrender/src/bvh.h |only rayrender-0.38.10/rayrender/src/calcnormals.cpp |only rayrender-0.38.10/rayrender/src/calcnormals.h |only rayrender-0.38.10/rayrender/src/calctangents.cpp |only rayrender-0.38.10/rayrender/src/calctangents.h |only rayrender-0.38.10/rayrender/src/camera.cpp |only rayrender-0.38.10/rayrender/src/camera.h |only rayrender-0.38.10/rayrender/src/color.cpp |only rayrender-0.38.10/rayrender/src/color.h |only rayrender-0.38.10/rayrender/src/constant.cpp |only rayrender-0.38.10/rayrender/src/constant.h |only rayrender-0.38.10/rayrender/src/csg.cpp |only rayrender-0.38.10/rayrender/src/csg.h |only rayrender-0.38.10/rayrender/src/curve.cpp |only 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Title: National Emergency Medical Service Quality Alliance Measure
Calculations
Description: Designed to automate the calculation of Emergency Medical
Service (EMS) quality metrics, 'nemsqar' implements measures defined
by the National EMS Quality Alliance (NEMSQA). By providing reliable,
evidence-based quality assessments, the package supports EMS agencies,
healthcare providers, and researchers in evaluating and improving
patient outcomes. Users can find details on all approved NEMSQA
measures at <https://www.nemsqa.org/measures>. Full technical
specifications, including documentation and pseudocode used to develop
'nemsqar', are available on the NEMSQA website after creating a user
profile at <https://www.nemsqa.org>.
Author: Nicolas Foss [aut, cre],
Samuel Kordik [aut] ,
Alyssa Green [ctb],
Iowa Department of Health and Human Services [cph]
Maintainer: Nicolas Foss <nicolas.foss@hhs.iowa.gov>
Diff between nemsqar versions 1.2.0 dated 2026-05-12 and 1.2.1 dated 2026-06-16
DESCRIPTION | 15 ++++++------ MD5 | 58 ++++++++++++++++++++++++----------------------- NEWS.md | 12 ++++++++- R/airway_01.R | 56 ++++++++++++++++++++++++--------------------- R/airway_05.R | 56 ++++++++++++++++++++++++--------------------- R/airway_18.R | 52 +++++++++++++++++++++--------------------- R/airway_18_population.R | 34 +++++++++++++-------------- R/asthma_01.R | 56 ++++++++++++++++++++++++--------------------- R/constants.R | 2 - R/globalVariables.R | 6 ++-- R/hypoglycemia_01.R | 56 ++++++++++++++++++++++++--------------------- R/pediatrics_03b.R | 56 ++++++++++++++++++++++++--------------------- R/respiratory_01.R | 56 ++++++++++++++++++++++++--------------------- R/respiratory_02.R | 56 ++++++++++++++++++++++++--------------------- R/safety_01.R | 56 ++++++++++++++++++++++++--------------------- R/safety_02.R | 56 ++++++++++++++++++++++++--------------------- R/safety_04.R | 56 ++++++++++++++++++++++++--------------------- R/seizure_02.R | 56 ++++++++++++++++++++++++--------------------- R/stroke_01.R | 56 ++++++++++++++++++++++++--------------------- R/syncope_01.R | 56 ++++++++++++++++++++++++--------------------- R/tbi_01.R | 56 ++++++++++++++++++++++++--------------------- R/tbi_01_population.R | 6 ++-- R/trauma_01.R | 56 ++++++++++++++++++++++++--------------------- R/trauma_03.R | 56 ++++++++++++++++++++++++--------------------- R/trauma_04.R | 56 ++++++++++++++++++++++++--------------------- R/trauma_08.R | 56 ++++++++++++++++++++++++--------------------- R/trauma_14.R | 56 ++++++++++++++++++++++++--------------------- R/ttr_01.R | 56 ++++++++++++++++++++++++--------------------- README.md | 2 - inst/WORDLIST |only tests/spelling.R |only 31 files changed, 699 insertions(+), 608 deletions(-)
Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models.
Author: Jose Augusto Fiorucci [aut, cre, cph] ,
Francisco Louzada [aut, cph] ,
Igor De Oliveira Barros Faluhelyi [aut, ctb]
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>
Diff between forecTheta versions 3.0 dated 2025-05-20 and 3.0.3 dated 2026-06-16
ChangeLog | 8 +++++++ DESCRIPTION | 6 ++--- MD5 | 10 ++++----- R/forecastFunctions.R | 49 +++++++++++++++++++++------------------------- man/baggedThetaModels.Rd | 12 ++++------- man/forecTheta-package.Rd | 4 +-- 6 files changed, 46 insertions(+), 43 deletions(-)
Title: Scientific Content and Citation Analysis from PDF Documents
Description: Provides comprehensive tools for extracting and analyzing scientific
content from PDF documents, including citation extraction, reference matching,
text analysis, and bibliometric indicators. Supports multi-column PDF layouts,
'CrossRef' API <https://www.crossref.org/documentation/retrieve-metadata/rest-api/> integration, and advanced citation parsing.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between contentanalysis versions 1.1.0 dated 2026-05-19 and 1.1.1 dated 2026-06-16
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 2 + README.md | 2 - inst/doc/introduction.html | 38 +++++++++++++++--------------- man/figures/README-unnamed-chunk-10-1.png |binary 6 files changed, 30 insertions(+), 28 deletions(-)
More information about contentanalysis at CRAN
Permanent link
Title: A Collection of Database, Data Structure, Visualization, and
Utility Functions for R
Description: The caroline R library contains dozens of functions useful
for: database migration (dbWriteTable2), database style joins &
aggregation (nerge, groupBy, & bestBy), data structure
conversion (nv, tab2df), legend table making (sstable & leghead),
automatic legend positioning for scatter and box plots (),
plot annotation (labsegs & mvlabs), data visualization
(pies, sparge, confound.grid & raPlot), character string manipulation (m & pad),
file I/O (write.delim), batch scripting, data exploration, and more.
The package's greatest contributions lie in the database style merge,
aggregation and interface functions as well as in it's extensive
use and propagation of row, column and vector names in most functions.
Author: David Schruth [aut, cre]
Maintainer: David Schruth <code@anthropoidea.org>
Diff between caroline versions 0.9.9 dated 2024-10-21 and 1.0.0 dated 2026-06-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.sparge.R | 35 ++++++++++++++++++++--------------- R/string.R | 5 ++++- man/plot.sparge.Rd | 7 ++++--- 5 files changed, 36 insertions(+), 27 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.46 dated 2025-12-05 and 0.47 dated 2026-06-16
DESCRIPTION | 10 - MD5 | 52 +++++----- R/bs4_book.R | 4 R/gitbook.R | 2 R/html.R | 3 R/publish.R | 17 --- R/render.R | 4 R/skeleton.R | 18 ++- R/utils.R | 4 README.md | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/bookdown.R | 4 inst/doc/bookdown.Rmd | 34 +++--- inst/doc/bookdown.html | 45 ++++---- inst/rstudio/templates/project/resources/common/05-blocks.Rmd | 4 inst/rstudio/templates/project/resources/common/06-share.Rmd | 2 inst/rstudio/templates/project/resources/common/README.md | 2 inst/rstudio/templates/project/resources/common/index.Rmd | 2 man/bookdown-package.Rd | 5 man/bs4_book.Rd | 4 man/fence_theorems.Rd | 4 man/gitbook.Rd | 2 man/html_document2.Rd | 2 man/render_book.Rd | 4 tests/testthat/helper-validate_html.R | 17 ++- vignettes/bookdown.Rmd | 34 +++--- 27 files changed, 148 insertions(+), 137 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.4.0 dated 2026-05-16 and 5.4.1 dated 2026-06-16
bibliometrix-5.4.0/bibliometrix/tests/testthat/Rplots.pdf |only bibliometrix-5.4.1/bibliometrix/DESCRIPTION | 8 bibliometrix-5.4.1/bibliometrix/MD5 | 37 - bibliometrix-5.4.1/bibliometrix/NEWS | 7 bibliometrix-5.4.1/bibliometrix/R/apply_citation_matching.R | 270 +++++++++- bibliometrix-5.4.1/bibliometrix/R/convert2df.R | 7 bibliometrix-5.4.1/bibliometrix/R/plotThematicEvolution.R | 30 + bibliometrix-5.4.1/bibliometrix/R/summary.bibliometrix.R | 2 bibliometrix-5.4.1/bibliometrix/R/thematicMap.R | 22 bibliometrix-5.4.1/bibliometrix/R/zzz.R | 12 bibliometrix-5.4.1/bibliometrix/build/partial.rdb |binary bibliometrix-5.4.1/bibliometrix/inst/CITATION | 12 bibliometrix-5.4.1/bibliometrix/inst/biblioshiny/biblioAI.R | 163 +++++- bibliometrix-5.4.1/bibliometrix/inst/biblioshiny/contentAnalysisServer.R | 2 bibliometrix-5.4.1/bibliometrix/inst/biblioshiny/server.R | 118 ---- bibliometrix-5.4.1/bibliometrix/inst/biblioshiny/ui.R | 126 +++- bibliometrix-5.4.1/bibliometrix/inst/biblioshiny/utils.R | 6 bibliometrix-5.4.1/bibliometrix/man/applyCitationMatching.Rd | 42 + bibliometrix-5.4.1/bibliometrix/man/applyReferenceMatching.Rd | 42 + bibliometrix-5.4.1/bibliometrix/man/normalize_citations.Rd | 55 +- 20 files changed, 749 insertions(+), 212 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-11 0.2.1
2026-02-14 0.1.6
2026-01-25 0.1.5
2026-01-21 0.1.4
2026-01-09 0.1.3
2025-11-17 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-24 0.1.1
2024-07-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-28 2.1.1
2020-06-06 2.1.0
2020-05-05 2.0.0
2020-03-16 1.2.0
2018-04-09 1.1.1
2018-02-20 1.0.0
Title: Collapsible 'HTML' Tables from Hierarchical Data
Description: Creates collapsible, expandable 'HTML' tables from hierarchical
data. Supports data frame input with multi-level grouping, custom column
formatters, bottom-up rollup aggregation, and CSS-variable-based theming.
Works in 'Shiny' applications, R Markdown, 'Quarto', and the 'RStudio' Viewer.
Author: Derek Underwood [aut, cre]
Maintainer: Derek Underwood <dereku@gmail.com>
Diff between nestable versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-06-15
DESCRIPTION | 8 +++++--- MD5 | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-)
Title: Krippendorff's Alpha for Multi-Valued Data
Description: Calculate Krippendorff's alpha for multi-valued data using the methods
introduced by Krippendorff and Craggs (2016) <doi:10.1080/19312458.2016.1228863>.
Nominal, ordinal, interval, and ratio data types are supported, with option to
create bootstrapped estimates of alpha.
Author: Corie Drake [aut, cre, cph]
Maintainer: Corie Drake <therealcfdrake@gmail.com>
Diff between mvalpha versions 0.5.1 dated 2025-10-17 and 0.6.0 dated 2026-06-15
DESCRIPTION | 19 ++-- MD5 | 29 +++++- NAMESPACE | 11 ++ NEWS.md | 8 + R/RcppExports.R |only R/mvalpha.R | 175 +++++++++++++++++++++++------------------ build/partial.rdb |binary man/examples/mvalpha_example.R | 28 +++--- man/generate_mv_data.Rd |only man/mvalpha.Rd | 44 +++------- src |only tests |only 12 files changed, 180 insertions(+), 134 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <https://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Mike Malecki [aut],
Neal Richardson [aut],
Gordon Shotwell [aut],
Aljaz Sluga [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunch versions 1.31.1 dated 2025-08-19 and 1.31.2 dated 2026-06-15
crunch-1.31.1/crunch/man/dataset-owner.Rd |only crunch-1.31.1/crunch/man/owners.Rd |only crunch-1.31.1/crunch/tests/testthat/test-share.R |only crunch-1.31.2/crunch/DESCRIPTION | 8 - crunch-1.31.2/crunch/MD5 | 91 +++++------- crunch-1.31.2/crunch/NAMESPACE | 4 crunch-1.31.2/crunch/R/AllClasses.R | 18 +- crunch-1.31.2/crunch/R/AllGenerics.R | 7 crunch-1.31.2/crunch/R/dataset-catalog.R | 12 - crunch-1.31.2/crunch/R/dataset.R | 29 --- crunch-1.31.2/crunch/R/misc.R | 1 crunch-1.31.2/crunch/R/permissions.R | 35 ++-- crunch-1.31.2/crunch/R/show.R | 68 ++++++-- crunch-1.31.2/crunch/R/subvariables.R | 7 crunch-1.31.2/crunch/R/zcl.R | 17 +- crunch-1.31.2/crunch/build/vignette.rds |binary crunch-1.31.2/crunch/inst/doc/abstract-categories.html | 5 crunch-1.31.2/crunch/inst/doc/analyze.html | 5 crunch-1.31.2/crunch/inst/doc/array-variables.html | 5 crunch-1.31.2/crunch/inst/doc/crunch.html | 11 - crunch-1.31.2/crunch/inst/doc/deck-cookbook.html | 5 crunch-1.31.2/crunch/inst/doc/derive.html | 5 crunch-1.31.2/crunch/inst/doc/export.html | 5 crunch-1.31.2/crunch/inst/doc/filters.html | 5 crunch-1.31.2/crunch/inst/doc/fork-and-merge.html | 5 crunch-1.31.2/crunch/inst/doc/projects.html | 5 crunch-1.31.2/crunch/inst/doc/subtotals.html | 7 crunch-1.31.2/crunch/inst/doc/variable-order.html | 5 crunch-1.31.2/crunch/inst/doc/variables.html | 5 crunch-1.31.2/crunch/inst/mocks.tgz |binary crunch-1.31.2/crunch/man/crunch-extract.Rd | 2 crunch-1.31.2/crunch/man/envOrOption.Rd | 1 crunch-1.31.2/crunch/tests/testthat/helper-expectations.R | 56 +++++++ crunch-1.31.2/crunch/tests/testthat/helper.R | 3 crunch-1.31.2/crunch/tests/testthat/test-api.R | 1 crunch-1.31.2/crunch/tests/testthat/test-append-debug.R | 5 crunch-1.31.2/crunch/tests/testthat/test-dataset-catalog.R | 18 -- crunch-1.31.2/crunch/tests/testthat/test-dataset-stream.R | 2 crunch-1.31.2/crunch/tests/testthat/test-decks.R | 5 crunch-1.31.2/crunch/tests/testthat/test-exclusion-filter.R | 12 - crunch-1.31.2/crunch/tests/testthat/test-expressions.R | 40 +++++ crunch-1.31.2/crunch/tests/testthat/test-filters.R | 17 -- crunch-1.31.2/crunch/tests/testthat/test-fork.R | 1 crunch-1.31.2/crunch/tests/testthat/test-multitables.R | 23 +-- crunch-1.31.2/crunch/tests/testthat/test-new-dataset.R | 2 crunch-1.31.2/crunch/tests/testthat/test-projects.R | 7 crunch-1.31.2/crunch/tests/testthat/test-shoji.R | 15 + crunch-1.31.2/crunch/tests/testthat/test-zcl.R | 18 ++ 48 files changed, 358 insertions(+), 240 deletions(-)
Title: Robust Principal Component Analysis Using the Cauchy
Distribution
Description: A new robust principal component analysis algorithm is implemented that relies upon the Cauchy Distribution. The algorithm is suitable for high dimensional data even if the sample size is less than the number of variables. The methodology is described in this paper: Fayomi A., Pantazis Y., Tsagris M. and Wood A.T.A. (2024). "Cauchy robust principal component analysis with applications to high-dimensional data sets". Statistics and Computing, 34: 26. <doi:10.1007/s11222-023-10328-x>.
Author: Michail Tsagris [aut, cre],
Aisha Fayomi [ctb],
Yannis Pantazis [ctb],
Andrew T.A. Wood [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cauchypca versions 1.3 dated 2024-01-24 and 1.4 dated 2026-06-15
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 1 - R/cauchy.pca.R | 22 ++++++++-------------- man/cauchypca-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 26 deletions(-)
Title: Constrained Delaunay Triangulation Meshes for Spatial 'SPDE'
Models
Description: Generate constrained Delaunay triangulation meshes for use with
stochastic partial differential equation (SPDE) spatial models
(Lindgren, Rue and Lindstroem 2011 <doi:10.1111/j.1467-9868.2011.00777.x>).
Provides automatic mesh generation from point coordinates with boundary
constraints, Ruppert refinement for mesh quality, finite element method
(FEM) matrix assembly (mass, stiffness, projection), barrier models,
spherical meshes via icosahedral subdivision, and metric graph meshes for
network geometries. Built on the 'CDT' header-only C++ library
(Amirkhanov 2024 <https://github.com/artem-ogre/CDT>). Designed as the
mesh backend for the 'tulpa' Bayesian hierarchical modelling engine but
usable standalone for any spatial triangulation task.
Author: Gilles Colling [aut, cre, cph] ,
Artem Amirkhanov [ctb, cph] ),
William C. Lenthe [ctb, cph] )
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between tulpaMesh versions 0.1.1 dated 2026-04-03 and 0.1.3 dated 2026-06-15
tulpaMesh-0.1.1/tulpaMesh/src/Makevars.win |only tulpaMesh-0.1.3/tulpaMesh/DESCRIPTION | 8 tulpaMesh-0.1.3/tulpaMesh/LICENSE | 4 tulpaMesh-0.1.3/tulpaMesh/MD5 | 138 - tulpaMesh-0.1.3/tulpaMesh/NAMESPACE | 66 tulpaMesh-0.1.3/tulpaMesh/NEWS.md | 86 tulpaMesh-0.1.3/tulpaMesh/R/barrier.R | 154 - tulpaMesh-0.1.3/tulpaMesh/R/convert.R | 120 - tulpaMesh-0.1.3/tulpaMesh/R/crs.R | 68 tulpaMesh-0.1.3/tulpaMesh/R/diagnostics.R | 360 +-- tulpaMesh-0.1.3/tulpaMesh/R/fem_p2.R | 184 - tulpaMesh-0.1.3/tulpaMesh/R/graph.R | 354 +- tulpaMesh-0.1.3/tulpaMesh/R/mesh.R | 1193 +++++----- tulpaMesh-0.1.3/tulpaMesh/R/mesh1d.R | 208 - tulpaMesh-0.1.3/tulpaMesh/R/mesh_ops.R | 462 +-- tulpaMesh-0.1.3/tulpaMesh/R/nonstationary.R | 156 - tulpaMesh-0.1.3/tulpaMesh/R/refine.R | 284 +- tulpaMesh-0.1.3/tulpaMesh/R/sphere.R | 442 +-- tulpaMesh-0.1.3/tulpaMesh/R/tulpaMesh-package.R | 20 tulpaMesh-0.1.3/tulpaMesh/README.md | 172 - tulpaMesh-0.1.3/tulpaMesh/build/partial.rdb |binary tulpaMesh-0.1.3/tulpaMesh/build/vignette.rds |binary tulpaMesh-0.1.3/tulpaMesh/configure.win | 16 tulpaMesh-0.1.3/tulpaMesh/inst/CITATION | 16 tulpaMesh-0.1.3/tulpaMesh/inst/COPYRIGHTS | 56 tulpaMesh-0.1.3/tulpaMesh/inst/WORDLIST | 64 tulpaMesh-0.1.3/tulpaMesh/inst/doc/advanced.Rmd | 510 ++-- tulpaMesh-0.1.3/tulpaMesh/inst/doc/advanced.html | 12 tulpaMesh-0.1.3/tulpaMesh/inst/doc/quickstart.html | 66 tulpaMesh-0.1.3/tulpaMesh/inst/doc/workflows.Rmd | 338 +- tulpaMesh-0.1.3/tulpaMesh/inst/doc/workflows.html | 39 tulpaMesh-0.1.3/tulpaMesh/man/as_tulpa_mesh.Rd | 54 tulpaMesh-0.1.3/tulpaMesh/man/barrier_triangles.Rd | 46 tulpaMesh-0.1.3/tulpaMesh/man/fem_matrices.Rd | 102 tulpaMesh-0.1.3/tulpaMesh/man/fem_matrices_nonstationary.Rd | 70 tulpaMesh-0.1.3/tulpaMesh/man/fem_matrices_p2.Rd | 60 tulpaMesh-0.1.3/tulpaMesh/man/mesh_components.Rd | 38 tulpaMesh-0.1.3/tulpaMesh/man/mesh_crs.Rd | 52 tulpaMesh-0.1.3/tulpaMesh/man/mesh_quality.Rd | 90 tulpaMesh-0.1.3/tulpaMesh/man/mesh_summary.Rd | 46 tulpaMesh-0.1.3/tulpaMesh/man/plot.tulpa_mesh.Rd | 96 tulpaMesh-0.1.3/tulpaMesh/man/refine_mesh.Rd | 84 tulpaMesh-0.1.3/tulpaMesh/man/subdivide_mesh.Rd | 38 tulpaMesh-0.1.3/tulpaMesh/man/subset_mesh.Rd | 44 tulpaMesh-0.1.3/tulpaMesh/man/tulpaMesh-package.Rd | 63 tulpaMesh-0.1.3/tulpaMesh/man/tulpa_mesh.Rd | 170 - tulpaMesh-0.1.3/tulpaMesh/man/tulpa_mesh_1d.Rd | 86 tulpaMesh-0.1.3/tulpaMesh/man/tulpa_mesh_graph.Rd | 94 tulpaMesh-0.1.3/tulpaMesh/man/tulpa_mesh_sphere.Rd | 76 tulpaMesh-0.1.3/tulpaMesh/src/mesh.cpp | 67 tulpaMesh-0.1.3/tulpaMesh/tests/testthat.R | 8 tulpaMesh-0.1.3/tulpaMesh/tests/testthat/Rplots.pdf |binary tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-barrier.R | 168 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-convert.R | 84 tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-crs.R | 118 tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-diagnostics.R | 208 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-fem-p2.R | 174 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-fmesher-comparison.R | 312 +- tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-graph.R | 196 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-mesh-ops.R | 278 +- tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-mesh.R | 170 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-mesh1d.R | 154 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-nonstationary.R | 172 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-parallel.R | 116 tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-refine.R | 132 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-ruppert.R | 236 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-sf-boundary.R | 166 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-sphere.R | 182 - tulpaMesh-0.1.3/tulpaMesh/tests/testthat/test-zero-triangles.R |only tulpaMesh-0.1.3/tulpaMesh/vignettes/advanced.Rmd | 510 ++-- tulpaMesh-0.1.3/tulpaMesh/vignettes/workflows.Rmd | 338 +- 71 files changed, 5389 insertions(+), 5305 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.2.5 dated 2026-03-03 and 0.2.7 dated 2026-06-15
DESCRIPTION | 6 +- MD5 | 8 +-- NEWS.md | 51 +++++++++++++++++++++ R/Ganttify.R | 134 +++++++++++++++++++++++++++++++++++++++----------------- man/Ganttify.Rd | 23 +++++++-- 5 files changed, 172 insertions(+), 50 deletions(-)
Title: Statistical Analysis of Textual Data
Description: Provides a set of functions devoted to multivariate exploratory statistics on textual data. Classical methods such as correspondence analysis and agglomerative hierarchical clustering are available. Chronologically constrained agglomerative hierarchical clustering enriched with labelled-by-words trees is offered. Given a division of the corpus into parts, their characteristic words and documents are identified. Further, accessing to 'FactoMineR' functions is very easy. Two of them are relevant in textual domain. MFA() addresses multiple lexical table allowing applications such as dealing with multilingual corpora as well as simultaneously analyzing both open-ended and closed questions in surveys. See <http://xplortext.unileon.es> for examples.
Author: Ramon Alvarez-Esteban [aut, cre] ,
Monica Becue-Bertaut [aut] ,
Josep-Anton Sanchez-Espigares [ctb] ,
Belchin Adriyanov Kostov [ctb]
Maintainer: Ramon Alvarez-Esteban <ramon.alvarez@unileon.es>
Diff between Xplortext versions 1.6 dated 2026-05-14 and 1.6.1 dated 2026-06-15
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/LexCA.R | 20 +++++++++++++------- build/partial.rdb |binary inst/Xplortext.pdf |binary man/Xplortext-package.Rd | 4 ++-- 6 files changed, 27 insertions(+), 21 deletions(-)
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surfaces, least-cost paths, least-cost corridors, least-cost networks, ranked alternative paths, cost allocation and cost boundaries, using a number of human-movement-related cost functions that can be selected by the user. The package is built around a compute-once design: a single cost surface object is created first and then reused by every analysis function, avoiding redundant computation. Visualisation is fully decoupled from computation and is provided through 'ggplot2' methods that can be invoked, customised, and re-invoked at any time without re-running any analysis. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 2.2 dated 2026-04-29 and 3.0.0 dated 2026-06-15
movecost-2.2/movecost/R/Etna_boundary.r |only movecost-2.2/movecost/R/Etna_end_location.r |only movecost-2.2/movecost/R/Etna_start_location.r |only movecost-2.2/movecost/R/create_barrier_cs.R |only movecost-2.2/movecost/R/destin.loc.r |only movecost-2.2/movecost/R/malta_dtm_40.r |only movecost-2.2/movecost/R/movealloc.r |only movecost-2.2/movecost/R/movebound.r |only movecost-2.2/movecost/R/movecomp.r |only movecost-2.2/movecost/R/movecorr.r |only movecost-2.2/movecost/R/movecost.r |only movecost-2.2/movecost/R/movenetw.r |only movecost-2.2/movecost/R/moverank.r |only movecost-2.2/movecost/R/springs.r |only movecost-2.2/movecost/R/volc.loc.r |only movecost-2.2/movecost/R/volc.r |only movecost-2.2/movecost/data |only movecost-2.2/movecost/man/Etna_boundary.Rd |only movecost-2.2/movecost/man/Etna_end_location.Rd |only movecost-2.2/movecost/man/Etna_start_location.Rd |only movecost-2.2/movecost/man/create_barrier_cs.Rd |only movecost-2.2/movecost/man/destin.loc.Rd |only movecost-2.2/movecost/man/malta_dtm_40.Rd |only movecost-2.2/movecost/man/movealloc.Rd |only movecost-2.2/movecost/man/movebound.Rd |only movecost-2.2/movecost/man/movecomp.Rd |only movecost-2.2/movecost/man/movecorr.Rd |only movecost-2.2/movecost/man/movecost.Rd |only movecost-2.2/movecost/man/movenetw.Rd |only movecost-2.2/movecost/man/moverank.Rd |only movecost-2.2/movecost/man/springs.Rd |only movecost-2.2/movecost/man/volc.Rd |only movecost-2.2/movecost/man/volc.loc.Rd |only movecost-3.0.0/movecost/DESCRIPTION | 21 - movecost-3.0.0/movecost/MD5 | 114 ++++-- movecost-3.0.0/movecost/NAMESPACE | 91 ++--- movecost-3.0.0/movecost/NEWS.md | 306 +++++++++++++++++- movecost-3.0.0/movecost/R/cost_functions.R |only movecost-3.0.0/movecost/R/data.R |only movecost-3.0.0/movecost/R/mc_accum.R |only movecost-3.0.0/movecost/R/mc_alloc.R |only movecost-3.0.0/movecost/R/mc_boundary.R |only movecost-3.0.0/movecost/R/mc_comp.R |only movecost-3.0.0/movecost/R/mc_corridor.R |only movecost-3.0.0/movecost/R/mc_dtm.R |only movecost-3.0.0/movecost/R/mc_export.R |only movecost-3.0.0/movecost/R/mc_network.R |only movecost-3.0.0/movecost/R/mc_paths.R |only movecost-3.0.0/movecost/R/mc_rank.R |only movecost-3.0.0/movecost/R/mc_surface.R |only movecost-3.0.0/movecost/R/movecost-defunct.R |only movecost-3.0.0/movecost/R/plot_methods.R |only movecost-3.0.0/movecost/R/utils.R |only movecost-3.0.0/movecost/README.md | 234 +++++-------- movecost-3.0.0/movecost/build |only movecost-3.0.0/movecost/inst |only movecost-3.0.0/movecost/man/mc_accum.Rd |only movecost-3.0.0/movecost/man/mc_alloc.Rd |only movecost-3.0.0/movecost/man/mc_boundary.Rd |only movecost-3.0.0/movecost/man/mc_comp.Rd |only movecost-3.0.0/movecost/man/mc_corridor.Rd |only movecost-3.0.0/movecost/man/mc_cost_functions.Rd |only movecost-3.0.0/movecost/man/mc_dtm.Rd |only movecost-3.0.0/movecost/man/mc_export.Rd |only movecost-3.0.0/movecost/man/mc_network.Rd |only movecost-3.0.0/movecost/man/mc_paths.Rd |only movecost-3.0.0/movecost/man/mc_rank.Rd |only movecost-3.0.0/movecost/man/mc_save.Rd |only movecost-3.0.0/movecost/man/mc_surface.Rd |only movecost-3.0.0/movecost/man/movecost-data.Rd |only movecost-3.0.0/movecost/man/movecost-defunct.Rd |only movecost-3.0.0/movecost/man/movecost-internals.Rd |only movecost-3.0.0/movecost/man/movecost-methods.Rd |only movecost-3.0.0/movecost/man/movecost-package.Rd |only movecost-3.0.0/movecost/man/movecost-plots.Rd |only movecost-3.0.0/movecost/man/plot.movecost_accum.Rd |only movecost-3.0.0/movecost/man/plot.movecost_alloc.Rd |only movecost-3.0.0/movecost/man/plot.movecost_boundary.Rd |only movecost-3.0.0/movecost/man/plot.movecost_comp.Rd |only movecost-3.0.0/movecost/man/plot.movecost_corridor.Rd |only movecost-3.0.0/movecost/man/plot.movecost_network.Rd |only movecost-3.0.0/movecost/man/plot.movecost_paths.Rd |only movecost-3.0.0/movecost/man/plot.movecost_rank.Rd |only movecost-3.0.0/movecost/man/plot.movecost_surface.Rd |only movecost-3.0.0/movecost/tests |only movecost-3.0.0/movecost/vignettes |only 86 files changed, 533 insertions(+), 233 deletions(-)
Title: Fitting Shared Atoms Nested Models via MCMC or Variational Bayes
Description: An efficient tool for fitting nested mixture models based on a shared set of
atoms via Markov Chain Monte Carlo and variational inference algorithms.
Specifically, the package implements the common atoms model (Denti et al., 2023),
its finite version (similar to D'Angelo et al., 2023), and a hybrid finite-infinite
model (D'Angelo and Denti, 2026). All models implement univariate nested mixtures
with Gaussian kernels equipped with a normal-inverse gamma prior distribution
on the parameters. Additional functions are provided to help analyze the
results of the fitting procedure.
References:
Denti, Camerlenghi, Guindani, Mira (2023) <doi:10.1080/01621459.2021.1933499>,
D’Angelo, Canale, Yu, Guindani (2023) <doi:10.1111/biom.13626>,
D’Angelo, Denti (2026) <doi:10.1214/24-BA1458>.
Author: Francesco Denti [aut, cre, cph] ,
Laura D'Angelo [aut]
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Diff between sanba versions 0.0.3 dated 2025-09-24 and 0.0.4 dated 2026-06-15
DESCRIPTION | 12 +++---- MD5 | 65 +++++++++++++++++++------------------- NAMESPACE | 5 ++ NEWS.md | 11 +++++- R/00_CAM.R | 38 +++++++++++++++------- R/00_fSAN.R | 29 +++++++++++----- R/00_fiSAN.R | 31 ++++++++++++------ R/01_MCMC_mcmc_CAM.R | 3 - R/01_MCMC_mcmc_fiSAN.R | 2 - R/01_VI_variational_fSAN.R | 1 R/02_SANBA_printing.R | 27 ++++++++++++++- R/02_SANBA_summary.R | 16 +++++---- R/03_SANBA_estimate_partitions.R | 8 ++-- R/04_MCMC_compute_postdens.R |only R/04_MCMC_compute_psm.R | 2 - R/04_VI_estimate_G.R | 25 ++++++++------ R/05_getfunctions.R | 2 - README.md | 27 ++++++++------- build/partial.rdb |binary man/compute_postdens.Rd |only man/compute_psm.Rd | 2 - man/estimate_G.Rd | 8 ++-- man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |binary man/figures/README-example2-1.png |binary man/figures/README-example2-2.png |binary man/fit_CAM.Rd | 13 +++++-- man/fit_fSAN.Rd | 11 ++++-- man/fit_fiSAN.Rd | 11 ++++-- man/get_accessors.Rd | 2 - man/plot.SANmcmc_postdens.Rd |only man/sanba-package.Rd | 3 + man/summary.SANmcmc.Rd | 2 - src/MCMC_FSAN_MAIN.cpp | 2 - src/SAN_FUNS.cpp | 2 - 35 files changed, 224 insertions(+), 136 deletions(-)
Title: Pricing Equity Derivatives with Extensions of Black-Scholes
Description: Algorithms to price American and European equity options,
convertible bonds and a variety of other financial derivatives. It
uses an extension of the usual Black-Scholes model in which jump to
default may occur at a probability specified by a power-law link
between stock price and hazard rate as found in the paper by
Takahashi, Kobayashi, and Nakagawa (2001)
<doi:10.3905/jfi.2001.319302>. We use ideas and techniques from
Andersen and Buffum (2002) <doi:10.2139/ssrn.355308> and Linetsky
(2006) <doi:10.1111/j.1467-9965.2006.00271.x>.
Author: Brian K. Boonstra [aut, cre]
Maintainer: Brian K. Boonstra <ragtop@boonstra.org>
Diff between ragtop versions 1.2.0 dated 2025-07-10 and 1.2.1 dated 2026-06-15
ragtop-1.2.0/ragtop/man/ragtop.Rd |only ragtop-1.2.1/ragtop/DESCRIPTION | 55 +-- ragtop-1.2.1/ragtop/MD5 | 135 ++++----- ragtop-1.2.1/ragtop/NAMESPACE | 4 ragtop-1.2.1/ragtop/NEWS.md | 6 ragtop-1.2.1/ragtop/R/american_options.R | 8 ragtop-1.2.1/ragtop/R/blackscholes.R | 17 - ragtop-1.2.1/ragtop/R/calibration.R | 98 +++--- ragtop-1.2.1/ragtop/R/cashflows.R | 23 - ragtop-1.2.1/ragtop/R/cc_code.R | 6 ragtop-1.2.1/ragtop/R/checkinputs.R |only ragtop-1.2.1/ragtop/R/data.R | 18 - ragtop-1.2.1/ragtop/R/implicit.R | 40 +- ragtop-1.2.1/ragtop/R/instruments.R | 8 ragtop-1.2.1/ragtop/R/ragtop.R | 5 ragtop-1.2.1/ragtop/R/term_structures.R | 64 ++-- ragtop-1.2.1/ragtop/R/util.R | 6 ragtop-1.2.1/ragtop/README.md | 143 +++++----- ragtop-1.2.1/ragtop/build/vignette.rds |binary ragtop-1.2.1/ragtop/inst/doc/ragtop_convertibles_in_r.R | 84 +++-- ragtop-1.2.1/ragtop/inst/doc/ragtop_convertibles_in_r.Rmd | 84 +++-- ragtop-1.2.1/ragtop/inst/doc/ragtop_convertibles_in_r.html | 93 +++--- ragtop-1.2.1/ragtop/man/CALL.Rd | 5 ragtop-1.2.1/ragtop/man/PUT.Rd | 5 ragtop-1.2.1/ragtop/man/TIME_RESOLUTION_FACTOR.Rd | 5 ragtop-1.2.1/ragtop/man/TIME_RESOLUTION_SIGNIF_DIGITS.Rd | 5 ragtop-1.2.1/ragtop/man/TSLAMarket.Rd | 23 - ragtop-1.2.1/ragtop/man/accelerated_coupon_value.Rd | 10 ragtop-1.2.1/ragtop/man/adjust_for_dividends.Rd | 6 ragtop-1.2.1/ragtop/man/american.Rd | 30 +- ragtop-1.2.1/ragtop/man/american_implied_volatility.Rd | 50 +-- ragtop-1.2.1/ragtop/man/black_scholes_on_term_structures.Rd | 36 +- ragtop-1.2.1/ragtop/man/blackscholes.Rd | 36 +- ragtop-1.2.1/ragtop/man/check_discount_factor_fcn.Rd |only ragtop-1.2.1/ragtop/man/check_survival_probability_fcn.Rd |only ragtop-1.2.1/ragtop/man/check_variance_cumulation_fcn.Rd |only ragtop-1.2.1/ragtop/man/construct_implicit_grid_structure.Rd | 16 - ragtop-1.2.1/ragtop/man/control_variate_pairs.Rd | 8 ragtop-1.2.1/ragtop/man/coupon_value_at_exercise.Rd | 10 ragtop-1.2.1/ragtop/man/detail_from_AnnivDates.Rd | 2 ragtop-1.2.1/ragtop/man/equivalent_bs_vola_to_jump.Rd | 38 +- ragtop-1.2.1/ragtop/man/equivalent_jump_vola_to_bs.Rd | 38 +- ragtop-1.2.1/ragtop/man/find_present_value.Rd | 26 - ragtop-1.2.1/ragtop/man/fit_to_option_market_df.Rd | 12 ragtop-1.2.1/ragtop/man/fit_variance_cumulation.Rd | 28 - ragtop-1.2.1/ragtop/man/form_present_value_grid.Rd | 26 - ragtop-1.2.1/ragtop/man/implied_jump_process_volatility.Rd | 28 - ragtop-1.2.1/ragtop/man/implied_volatilities.Rd | 56 +-- ragtop-1.2.1/ragtop/man/implied_volatilities_with_rates_struct.Rd | 56 +-- ragtop-1.2.1/ragtop/man/implied_volatility.Rd | 56 +-- ragtop-1.2.1/ragtop/man/implied_volatility_with_term_struct.Rd | 56 +-- ragtop-1.2.1/ragtop/man/infer_conforming_time_grid.Rd | 16 - ragtop-1.2.1/ragtop/man/integrate_pde.Rd | 16 - ragtop-1.2.1/ragtop/man/is.blank.Rd | 6 ragtop-1.2.1/ragtop/man/iterate_grid_from_timestep.Rd | 18 - ragtop-1.2.1/ragtop/man/ragtop-package.Rd |only ragtop-1.2.1/ragtop/man/shift_for_dividends.Rd | 6 ragtop-1.2.1/ragtop/man/take_implicit_timestep.Rd | 20 - ragtop-1.2.1/ragtop/man/time_adj_dividends.Rd | 6 ragtop-1.2.1/ragtop/man/timestep_instruments.Rd | 16 - ragtop-1.2.1/ragtop/man/value_from_prior_coupons.Rd | 6 ragtop-1.2.1/ragtop/man/warn_once_negative_default_intensity.Rd |only ragtop-1.2.1/ragtop/tests/testthat.R | 1 ragtop-1.2.1/ragtop/tests/testthat/test_blackscholes.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_calibration.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_cashflows.R | 13 ragtop-1.2.1/ragtop/tests/testthat/test_convertibles.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_grid_solver.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_options.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_payoffs.R | 4 ragtop-1.2.1/ragtop/tests/testthat/test_term_structures.R | 4 ragtop-1.2.1/ragtop/vignettes/ragtop_convertibles_in_r.Rmd | 84 +++-- 72 files changed, 891 insertions(+), 909 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Joan Maspons [aut, cre] ,
Mark Padgham [aut],
Bob Rudis [aut],
Robin Lovelace [aut],
Maelle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Anthony North [ctb],
Martin Machyna [ctb],
Marcin Kalicinsk [...truncated...]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmdata versions 0.3.0 dated 2025-08-23 and 0.4.0 dated 2026-06-15
DESCRIPTION | 9 MD5 | 153 +++-- NAMESPACE | 3 NEWS.md | 47 + R/RcppExports.R | 49 - R/elevation.R | 6 R/features.R | 7 R/get-osmdata-df.R | 10 R/get-osmdata-sc.R | 2 R/get-osmdata-sf.R | 41 + R/get-osmdata-sp.R | 4 R/get-osmdata-xml.R | 11 R/get-osmdata.R | 41 - R/getbb.R | 242 +++++++-- R/opq.R | 172 ++++-- R/osm-extract.R | 36 - R/osmdata-package.R | 46 - R/overpass-query.R | 6 R/trim-osmdata.R | 2 R/unique-osmdata.R | 8 R/wkt4326.R | 2 R/zzz.R | 2 README.md | 310 ++++++++++- build/vignette.rds |binary inst/doc/osm-sf-translation.html | 4 inst/doc/osmdata-sc.html | 4 inst/doc/osmdata.html | 13 inst/doc/query-split.html | 4 inst/httptest2/redact.R | 19 man/add_osm_feature.Rd | 35 - man/add_osm_features.Rd | 31 - man/available_features.Rd | 4 man/available_tags.Rd | 4 man/bbox_to_string.Rd | 25 man/filter_osm_user.Rd |only man/get_overpass_url.Rd | 6 man/getbb.Rd | 60 +- man/opq.Rd | 39 - man/opq_around.Rd | 27 - man/opq_csv.Rd | 27 - man/opq_enclosing.Rd | 27 - man/opq_osm_id.Rd | 31 - man/opq_string.Rd | 23 man/osm_elevation.Rd | 14 man/osm_lines.Rd | 10 man/osm_multilines.Rd | 10 man/osm_multipolygons.Rd | 10 man/osm_points.Rd | 10 man/osm_poly2line.Rd | 10 man/osm_polygons.Rd | 10 man/osmdata-package.Rd | 42 - man/osmdata_data_frame.Rd | 16 man/osmdata_sc.Rd | 15 man/osmdata_sf.Rd | 25 man/osmdata_sp.Rd | 15 man/osmdata_xml.Rd | 15 man/overpass_status.Rd | 23 man/set_overpass_url.Rd | 4 man/trim_osmdata.Rd | 10 man/unique_osmdata.Rd | 10 man/unname_osmdata_sf.Rd | 10 src/osmdata-data_frame.cpp | 23 src/osmdata-sf.cpp | 197 +++++-- src/osmdata.h | 2 tests/testthat/fixtures/osm-meta_geom.osm |only tests/testthat/mock_bb_df_viewbox |only tests/testthat/mock_bb_typo_pol |only tests/testthat/mock_bb_wikidata |only tests/testthat/mock_bb_wikidata_NULL |only tests/testthat/setup.R | 4 tests/testthat/test-c.R | 2 tests/testthat/test-extract.R | 2 tests/testthat/test-getbb.R | 201 +++++++ tests/testthat/test-opq.R | 107 +++- tests/testthat/test-osmdata.R | 185 +++--- tests/testthat/test-sf-construction.R | 797 ++++++++++++++---------------- tests/testthat/test-sf-osm.R | 38 + tests/testthat/test-trim.R | 5 tests/testthat/test-unique.R | 2 tests/testthat/test-unname.R | 9 80 files changed, 2218 insertions(+), 1207 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). Supporting publication: Blaauw, M., Reimer, P.J., in press. An open-source toolkit for radiocarbon dating and calibration. Radiocarbon. The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre] ,
Paula Reimer [ctb] ,
Vegard Martinsen [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 2.1.0 dated 2026-04-09 and 2.2.0 dated 2026-06-15
DESCRIPTION | 13 - MD5 | 94 +++++----- NAMESPACE | 3 NEWS.md | 16 + R/calibrate.R | 152 +++++++---------- R/plots.R | 260 +++++++++++++---------------- R/rice-package.R | 4 R/rice.R | 334 +++++++++++++++++++++++++++++++++++--- R/sources.R | 24 +- R/timescales.R | 161 +++++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/rice.R | 30 ++- inst/doc/rice.Rmd | 44 +++-- inst/doc/rice.html | 391 ++++++++++++++++++++++++--------------------- man/BCADtoC14.Rd | 3 man/BCADtoDelta14C.Rd | 3 man/BCADtoF14C.Rd | 3 man/BCADtopMC.Rd | 3 man/C14tocalBP.Rd | 3 man/b2ktoC14.Rd | 3 man/b2ktoDelta14C.Rd | 3 man/b2ktoF14C.Rd | 3 man/b2ktopMC.Rd | 3 man/calBPtoC14.Rd | 3 man/calBPtoDelta14C.Rd | 3 man/calBPtoF14C.Rd | 3 man/calBPtopMC.Rd | 3 man/caldist.Rd | 2 man/calib.t.Rd | 3 man/calibratable.Rd | 4 man/calibrate.Rd | 4 man/draw.ccurve.Rd | 6 man/draw.dates.Rd | 13 + man/fromto.Rd | 2 man/howmuchC14.Rd | 20 +- man/l.calib.Rd | 3 man/older.Rd | 3 man/p.range.Rd | 3 man/r.calib.Rd | 3 man/radio.Rd |only man/rice-package.Rd | 12 + man/rice.Rd | 12 + man/smooth.curve.Rd | 3 man/younger.Rd | 3 tests/testthat/test-rice.R | 2 vignettes/radio.png |only vignettes/rice.Rmd | 44 +++-- 49 files changed, 1106 insertions(+), 603 deletions(-)
Title: UNHCR Refugee Population Statistics Database
Description: The Refugee Population Statistics Database published by
The Office of The United Nations High Commissioner for Refugees (UNHCR)
contains information about forcibly displaced populations
spanning more than 70 years of statistical activities.
It covers displaced populations such as refugees, asylum-seekers and
internally displaced people, including their demographics.
Stateless people are also included, most of who have never been displaced.
The database also reflects the different types of solutions
for displaced populations such as repatriation or resettlement.
More information on the data and methodology can be found on
the UNHCR Refugee Data Finder <https://www.unhcr.org/refugee-statistics/>.
Author: Hisham Galal [aut],
Ahmadou Dicko [aut],
Janis Kreuder [cre],
UNHCR [cph]
Maintainer: Janis Kreuder <kreuder@unhcr.org>
Diff between refugees versions 2025.06.1 dated 2026-03-30 and 2025.12.0 dated 2026-06-15
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ data/asylum_applications.rda |binary data/asylum_decisions.rda |binary data/demographics.rda |binary data/flows.rda |binary data/idmc.rda |binary data/population.rda |binary data/solutions.rda |binary data/unrwa.rda |binary 11 files changed, 17 insertions(+), 13 deletions(-)
Title: Primary Event Censored Distributions
Description: Provides functions for working with primary
event censored distributions and 'Stan' implementations for use in Bayesian
modeling. Primary event censored distributions are useful for modeling
delayed reporting scenarios in epidemiology and other fields (Charniga et
al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for
arbitrary delay distributions, a range of common primary distributions, and
allows for truncation and secondary event censoring to be accounted for
(Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of
common distributions also have analytical solutions implemented, allowing
for faster computation. In addition, it provides multiple methods for
fitting primary event censored distributions to data via optional
dependencies.
Author: Sam Abbott [aut, cre, cph] ,
Sam Brand [aut] ,
Adam Howes [ctb] ,
James Mba Azam [aut] ,
Carl Pearson [aut] ,
Sebastian Funk [aut] ,
Kelly Charniga [aut]
Maintainer: Sam Abbott <contact@samabbott.co.uk>
Diff between primarycensored versions 1.5.0 dated 2026-06-04 and 1.5.1 dated 2026-06-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 11 +++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/primarycensored.html | 5 ++--- inst/stan/functions/primarycensored.stan | 18 ++++++++++++------ 7 files changed, 34 insertions(+), 18 deletions(-)
More information about primarycensored at CRAN
Permanent link
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.5.2 dated 2026-04-22 and 1.5.3 dated 2026-06-15
DESCRIPTION | 6 +-- MD5 | 16 +++++----- NEWS.md | 9 +++++ R/load.R | 18 ++++++++++- R/run-loadhooks.R | 26 ++++++++++++++++ man/load_all.Rd | 6 +++ tests/testthat/test-load-hooks.R | 57 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-po.R | 1 tests/testthat/testLoadHooks/R/a.r | 5 +++ 9 files changed, 130 insertions(+), 14 deletions(-)
Title: Interface to the HAL Open Archive API
Description: An interface to the search API of 'HAL'
<https://hal.science/>, the French open archive for scholarly
documents from all academic fields. This package provides programmatic
access to the API <https://api.archives-ouvertes.fr/docs> and allows
to search for records and download documents.
Author: Nicolas Frerebeau [aut, cre] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between odyssey versions 1.0.0 dated 2026-01-08 and 1.0.1 dated 2026-06-15
DESCRIPTION | 17 ++++---- MD5 | 56 +++++++++++++-------------- NAMESPACE | 1 NEWS.md | 7 +++ R/AllGenerics.R | 14 +++--- R/hal_count.R | 2 R/hal_download.R | 26 +++++++++--- R/hal_facet.R | 11 ++++- R/hal_group.R | 7 ++- R/hal_parse.R | 22 ++++++++-- R/hal_search.R | 32 +++++++++++---- R/odyssey-package.R | 3 - README.md | 93 +++++++++++++++++++++++++++------------------ inst/CITATION | 5 +- inst/examples/ex-facet.R | 11 ++++- inst/tinytest/test_facet.R | 3 - inst/tinytest/test_group.R | 3 - man/as.data.frame.Rd | 2 man/hal_count.Rd | 6 +- man/hal_download.Rd | 10 ++-- man/hal_facet.Rd | 23 +++++++---- man/hal_filter.Rd | 12 ++--- man/hal_group.Rd | 12 ++--- man/hal_query.Rd | 12 ++--- man/hal_search.Rd | 16 +++---- man/hal_select.Rd | 12 ++--- man/hal_sort.Rd | 12 ++--- man/odyssey-package.Rd | 8 +++ man/operators.Rd | 14 +++--- 29 files changed, 282 insertions(+), 170 deletions(-)
Title: Download Weather Station Data from GHCNd
Description: The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.
Author: Emilio Berti [aut, cre]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between GHCNr versions 1.4.6 dated 2025-10-27 and 1.4.7 dated 2026-06-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/daily.R | 1 + 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Quantitative Chronology in Archaeology
Description: Simple radiocarbon calibration and chronological analysis.
This package allows the calibration of radiocarbon ages and modern
carbon fraction values using multiple calibration curves. It allows
the calculation of highest density region intervals and credible
intervals. The package also provides tools for visualising results and
estimating statistical summaries.
Author: Nicolas Frerebeau [aut, cre] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between ananke versions 0.2.0 dated 2026-05-07 and 0.3.0 dated 2026-06-15
DESCRIPTION | 14 MD5 | 77 ++- NAMESPACE | 2 NEWS.md | 8 R/AllGenerics.R | 53 ++ R/ananke-package.R | 2 R/c14_calibrate.R | 36 + R/coerce.R | 4 R/describe.R | 2 R/plot.R | 30 - R/radialplot.R |only README.md | 154 ++++--- inst/bibliography.bib | 299 ++++++++------- inst/examples/ex-14c-plot.R | 11 inst/examples/ex-14c-ridgelines.R | 3 inst/examples/ex-radialplot.R |only inst/po/fr/LC_MESSAGES/R-ananke.mo |binary inst/tinytest/_tinysnapshot/plot_cal_cred_decr.svg | 6 inst/tinytest/_tinysnapshot/plot_cal_cred_incr.svg | 6 inst/tinytest/_tinysnapshot/plot_cal_hdr_decr.svg | 26 - inst/tinytest/_tinysnapshot/plot_cal_hdr_incr.svg | 26 - inst/tinytest/_tinysnapshot/radialplot_bar.svg |only inst/tinytest/_tinysnapshot/radialplot_log.svg |only inst/tinytest/_tinysnapshot/radialplot_nolog.svg |only inst/tinytest/_tinysnapshot/ridge_cal_decr.svg | 54 +- inst/tinytest/_tinysnapshot/ridge_cal_fixed_color.svg |only inst/tinytest/_tinysnapshot/ridge_cal_incr.svg | 54 +- inst/tinytest/_tinysnapshot/ridge_cal_position_color.svg |only inst/tinytest/test_c14_plot.R | 14 inst/tinytest/test_radialplot.R |only man/ananke-package.Rd | 2 man/c14_calibrate.Rd | 4 man/c14_plot.Rd | 20 - man/figures/README-calibration-1.png |binary man/figures/README-calibration-2.png |binary man/interval_credible.Rd | 3 man/interval_hdr.Rd | 3 man/mean.Rd | 3 man/median.Rd | 3 man/quantile.Rd | 3 man/radialplot.Rd |only man/ridgelines.Rd | 10 po/R-ananke.pot | 24 + po/R-fr.po | 24 + 44 files changed, 583 insertions(+), 397 deletions(-)
Title: Create Randomization Lists
Description: Randomization lists are an integral component of randomized clinical trials. 'randotools' provides tools to easily create such lists.
Author: Alan G Haynes [aut, cre]
Maintainer: Alan G Haynes <alan.haynes@unibe.ch>
Diff between randotools versions 0.2.6 dated 2026-03-11 and 0.2.8 dated 2026-06-15
DESCRIPTION | 8 +- MD5 | 30 ++++----- NEWS.md | 97 +++++++++++++++++-------------- R/blockrand.R | 16 +++++ R/randolist.R | 37 +++++++++++- README.md | 8 -- build/vignette.rds |binary inst/doc/imbalance.html | 12 +-- inst/doc/randotools.R | 15 ++++ inst/doc/randotools.Rmd | 31 ++++++++++ inst/doc/randotools.html | 122 +++++++++++++++++++++++++--------------- man/figures/imbseq-1.png |binary man/figures/imbtest-1.png |binary man/randolist.Rd | 26 ++++++++ tests/testthat/test-randolist.R | 6 + vignettes/randotools.Rmd | 31 ++++++++++ 16 files changed, 319 insertions(+), 120 deletions(-)
Title: Calculation of 22 CAnonical Time-Series CHaracteristics
Description: Calculate 22 summary statistics coded in C on time-series vectors to enable
pattern detection, classification, and regression applications in the
feature space as proposed by Lubba et al. (2019) <doi:10.1007/s10618-019-00647-x>.
Author: Trent Henderson [cre, aut],
Carl Lubba [ctb],
Maximilian Muecke [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between Rcatch22 versions 0.2.3 dated 2024-10-02 and 0.2.5 dated 2026-06-15
DESCRIPTION | 23 +- MD5 | 14 - README.md | 29 +-- build/vignette.rds |binary inst/doc/Rcatch22.R | 10 - inst/doc/Rcatch22.html | 392 ++++++++++++++++++------------------------------- src/SP_Summaries.c | 4 src/catch22.cpp | 50 +----- 8 files changed, 199 insertions(+), 323 deletions(-)
Title: 3D Software Rasterizer
Description: Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Author: Tyler Morgan-Wall [aut, cph, cre] ,
Syoyo Fujita [ctb, cph],
Vilya Harvey [ctb, cph],
G-Truc Creation [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayvertex versions 0.12.0 dated 2025-02-03 and 0.15.0 dated 2026-06-15
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rayvertex-0.15.0/rayvertex/src/rayraster.cpp | 491 +++++- rayvertex-0.15.0/rayvertex/src/shaders.cpp | 374 ++++ rayvertex-0.15.0/rayvertex/src/shaders.h | 104 + rayvertex-0.15.0/rayvertex/tests |only 104 files changed, 4563 insertions(+), 2781 deletions(-)
Title: Network Meta-Analysis of Multiple Diagnostic Tests
Description: Provides statistical methods for network meta-analysis
of diagnostic tests to simultaneously compare multiple tests within a
missing data framework, including:
- Bayesian hierarchical model for network meta-analysis of multiple
diagnostic tests
(Ma, Lian, Chu, Ibrahim, and Chen (2018) <doi:10.1093/biostatistics/kxx025>)
- Bayesian Hierarchical Summary Receiver Operating Characteristic Model
for Network Meta-Analysis of Diagnostic Tests
(Lian, Hodges, and Chu (2019) <doi:10.1080/01621459.2018.1476239>).
Author: Xing Xing [aut, cre] ,
Boyang Lu [aut],
Lifeng Lin [aut],
Qinshu Lian [aut],
James S. Hodges [aut],
Yong Chen [aut],
Haitao Chu [aut]
Maintainer: Xing Xing <xxing@arizona.edu>
Diff between NMADTA versions 0.1.3 dated 2026-04-15 and 0.1.4 dated 2026-06-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Fitting and Testing Generalized Logistic Distributions
Description: Tools for the generalized logistic distribution (Type I,
also known as skew-logistic distribution), encompassing
basic distribution functions (p, q, d, r, score), maximum
likelihood estimation, and structural change methods.
Author: Achim Zeileis [aut, cre] ,
Thomas Windberger [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glogis versions 1.0-2 dated 2022-04-19 and 1.0-3 dated 2026-06-15
glogis-1.0-2/glogis/NEWS |only glogis-1.0-3/glogis/DESCRIPTION | 18 ++++++++-------- glogis-1.0-3/glogis/MD5 | 18 ++++++++-------- glogis-1.0-3/glogis/NEWS.md |only glogis-1.0-3/glogis/R/glogisfit.R | 2 - glogis-1.0-3/glogis/README.md |only glogis-1.0-3/glogis/build/partial.rdb |binary glogis-1.0-3/glogis/inst/CITATION | 19 ++++++++--------- glogis-1.0-3/glogis/man/HICP.Rd | 2 - glogis-1.0-3/glogis/man/figures |only glogis-1.0-3/glogis/man/glogis.Rd | 2 - glogis-1.0-3/glogis/tests/Examples/glogis-Ex.Rout.save | 2 - 12 files changed, 34 insertions(+), 29 deletions(-)
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association.
Author: Giampiero Marra [aut, cre],
Rosalba Radice [aut]
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.2-6.8 dated 2025-06-23 and 0.2-6.9 dated 2026-06-15
GJRM-0.2-6.8/GJRM/R/Reg2Copost.r |only GJRM-0.2-6.8/GJRM/R/int.rescheck.R |only GJRM-0.2-6.9/GJRM/ChangeLog | 3 GJRM-0.2-6.9/GJRM/DESCRIPTION | 13 GJRM-0.2-6.9/GJRM/MD5 | 285 - GJRM-0.2-6.9/GJRM/NAMESPACE | 44 GJRM-0.2-6.9/GJRM/R/CopulaCLM.r | 8 GJRM-0.2-6.9/GJRM/R/SemiParBIV.fit.R | 23 GJRM-0.2-6.9/GJRM/R/SemiParBIV.fit.post.r | 8 GJRM-0.2-6.9/GJRM/R/SemiParBIV.r | 8 GJRM-0.2-6.9/GJRM/R/SemiParROY.r | 17 GJRM-0.2-6.9/GJRM/R/SemiParTRIV.r | 2 GJRM-0.2-6.9/GJRM/R/ass.dp.r | 38 GJRM-0.2-6.9/GJRM/R/bCopulaCLMgHsCont.R | 103 GJRM-0.2-6.9/GJRM/R/bCopulaCLMgHsOrd.R | 97 GJRM-0.2-6.9/GJRM/R/bcont.R | 71 GJRM-0.2-6.9/GJRM/R/bcont23.R | 66 GJRM-0.2-6.9/GJRM/R/bcont23twoParC.R | 4 GJRM-0.2-6.9/GJRM/R/bcont3.R | 64 GJRM-0.2-6.9/GJRM/R/bcont32.R | 66 GJRM-0.2-6.9/GJRM/R/bcont32twoParC.R | 4 GJRM-0.2-6.9/GJRM/R/bcont3twoParC.R | 4 GJRM-0.2-6.9/GJRM/R/bcontROB.R | 9 GJRM-0.2-6.9/GJRM/R/bcontSurv.R | 69 GJRM-0.2-6.9/GJRM/R/bcontSurvG.R | 88 GJRM-0.2-6.9/GJRM/R/bcontSurvGBIN.R | 83 GJRM-0.2-6.9/GJRM/R/bcontSurvGBINROY.R | 21 GJRM-0.2-6.9/GJRM/R/bcontSurvGBINss.R | 20 GJRM-0.2-6.9/GJRM/R/bcontSurvGDep.R | 86 GJRM-0.2-6.9/GJRM/R/bcontSurvGDepA.R | 82 GJRM-0.2-6.9/GJRM/R/bcontSurvG_extended.R | 381 +- GJRM-0.2-6.9/GJRM/R/bcontSurvGcont2Surv.R | 82 GJRM-0.2-6.9/GJRM/R/bcontSurvGuniv.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivI.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivI_ExcessHazard.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivInform.r | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivL.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivL_ExcessHazard.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivMIXED.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivMIXED_ExcessHazard.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivMIXED_ExcessHazard_LeftTruncation.R | 2 GJRM-0.2-6.9/GJRM/R/bcontSurvGunivMIXED_LeftTruncation.R | 4 GJRM-0.2-6.9/GJRM/R/bcontSurvGuniv_ExcessHazard.R | 4 GJRM-0.2-6.9/GJRM/R/bcontThetaOnly.R | 248 - GJRM-0.2-6.9/GJRM/R/bconttwoParC.R | 3 GJRM-0.2-6.9/GJRM/R/bcorrecDiscr.R | 6 GJRM-0.2-6.9/GJRM/R/bcorrecFuncs.R | 1534 +++++++++- GJRM-0.2-6.9/GJRM/R/bcountThetaOnly.R |only GJRM-0.2-6.9/GJRM/R/bdiscrcont.R | 122 GJRM-0.2-6.9/GJRM/R/bdiscrcont12.R | 110 GJRM-0.2-6.9/GJRM/R/bdiscrcont13.R | 100 GJRM-0.2-6.9/GJRM/R/bdiscrcont23.R | 103 GJRM-0.2-6.9/GJRM/R/bdiscrcontThetaOnly.R |only GJRM-0.2-6.9/GJRM/R/bdiscrdiscr.R | 82 GJRM-0.2-6.9/GJRM/R/bdiscrdiscr11.R | 84 GJRM-0.2-6.9/GJRM/R/bdiscrdiscr12.R | 78 GJRM-0.2-6.9/GJRM/R/bprobgHs.r | 67 GJRM-0.2-6.9/GJRM/R/bprobgHsBinROY.r | 9 GJRM-0.2-6.9/GJRM/R/bprobgHsCont.r | 79 GJRM-0.2-6.9/GJRM/R/bprobgHsCont2ROY.r | 16 GJRM-0.2-6.9/GJRM/R/bprobgHsCont3.r | 76 GJRM-0.2-6.9/GJRM/R/bprobgHsCont3ROY.r | 14 GJRM-0.2-6.9/GJRM/R/bprobgHsCont3SS.r | 5 GJRM-0.2-6.9/GJRM/R/bprobgHsCont3binTW.r | 74 GJRM-0.2-6.9/GJRM/R/bprobgHsCont3binTWSS.R | 5 GJRM-0.2-6.9/GJRM/R/bprobgHsContSS.r | 5 GJRM-0.2-6.9/GJRM/R/bprobgHsContUniv.r | 26 GJRM-0.2-6.9/GJRM/R/bprobgHsContUniv3.r | 22 GJRM-0.2-6.9/GJRM/R/bprobgHsContUnivBIN.r | 4 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr1.r | 72 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr1ROY.r | 13 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr1SS.r | 5 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr2.r | 71 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr2ROY.r | 14 GJRM-0.2-6.9/GJRM/R/bprobgHsDiscr2SS.r | 5 GJRM-0.2-6.9/GJRM/R/bprobgHsPO.r | 3 GJRM-0.2-6.9/GJRM/R/bprobgHsPO0.r | 1 GJRM-0.2-6.9/GJRM/R/bprobgHsSS.r | 7 GJRM-0.2-6.9/GJRM/R/bprobgHstwoParC.r | 5 GJRM-0.2-6.9/GJRM/R/cond.mv.R | 604 +++ GJRM-0.2-6.9/GJRM/R/cond.mv.pcc.R |only GJRM-0.2-6.9/GJRM/R/copgHs.r | 14 GJRM-0.2-6.9/GJRM/R/copgHsAT.r | 164 + GJRM-0.2-6.9/GJRM/R/copgHsCont.r | 14 GJRM-0.2-6.9/GJRM/R/copgHsContFM.r |only GJRM-0.2-6.9/GJRM/R/copgHsCountFM.r |only GJRM-0.2-6.9/GJRM/R/copula.prob.r | 145 GJRM-0.2-6.9/GJRM/R/copulaReg.fit.post.r | 10 GJRM-0.2-6.9/GJRM/R/copulaSampleSel.r | 10 GJRM-0.2-6.9/GJRM/R/distrHsATDiscr.r | 9 GJRM-0.2-6.9/GJRM/R/distrHsATDiscr2.r | 14 GJRM-0.2-6.9/GJRM/R/distrHsDiscr.r | 59 GJRM-0.2-6.9/GJRM/R/edf.loop.r | 6 GJRM-0.2-6.9/GJRM/R/eta.tr.R | 2 GJRM-0.2-6.9/GJRM/R/form.eq12.r | 7 GJRM-0.2-6.9/GJRM/R/func.OPT.r | 8 GJRM-0.2-6.9/GJRM/R/gamlss.R | 6 GJRM-0.2-6.9/GJRM/R/gjrm.pcc.r |only GJRM-0.2-6.9/GJRM/R/gjrm.r | 78 GJRM-0.2-6.9/GJRM/R/hfunc.R |only GJRM-0.2-6.9/GJRM/R/jc.probs1.r | 531 --- GJRM-0.2-6.9/GJRM/R/jc.probs2.r | 268 - GJRM-0.2-6.9/GJRM/R/jc.probs3.r | 105 GJRM-0.2-6.9/GJRM/R/jc.probs4.r | 214 - GJRM-0.2-6.9/GJRM/R/jc.probs5.r | 158 - GJRM-0.2-6.9/GJRM/R/jc.probs7.r | 44 GJRM-0.2-6.9/GJRM/R/jc.probs8.r | 56 GJRM-0.2-6.9/GJRM/R/jc.probs9.r |only GJRM-0.2-6.9/GJRM/R/k.tau.R | 7 GJRM-0.2-6.9/GJRM/R/marg.mv.r | 20 GJRM-0.2-6.9/GJRM/R/numch.r | 2 GJRM-0.2-6.9/GJRM/R/numgh.r | 8 GJRM-0.2-6.9/GJRM/R/plot.SemiParBIV.r | 16 GJRM-0.2-6.9/GJRM/R/pp.r | 40 GJRM-0.2-6.9/GJRM/R/ppROY.r | 8 GJRM-0.2-6.9/GJRM/R/pream.wm.r | 31 GJRM-0.2-6.9/GJRM/R/predict.SemiParBIV.r | 13 GJRM-0.2-6.9/GJRM/R/print.gjrm.pcc.r |only GJRM-0.2-6.9/GJRM/R/print.gjrm.r | 23 GJRM-0.2-6.9/GJRM/R/print.summary.gjrm.pcc.r |only GJRM-0.2-6.9/GJRM/R/print.summary.gjrm.r | 43 GJRM-0.2-6.9/GJRM/R/pscr0.r | 12 GJRM-0.2-6.9/GJRM/R/r.resp.R | 8 GJRM-0.2-6.9/GJRM/R/rIC.R | 2 GJRM-0.2-6.9/GJRM/R/res.check.R | 761 +++- GJRM-0.2-6.9/GJRM/R/resp.check.R | 79 GJRM-0.2-6.9/GJRM/R/rob.const.R | 4 GJRM-0.2-6.9/GJRM/R/sim.resp.R | 7 GJRM-0.2-6.9/GJRM/R/startsn.r | 62 GJRM-0.2-6.9/GJRM/R/summary.gjrm.pcc.r |only GJRM-0.2-6.9/GJRM/R/summary.gjrm.r | 3 GJRM-0.2-6.9/GJRM/R/susu.r | 14 GJRM-0.2-6.9/GJRM/R/susutsn.r | 73 GJRM-0.2-6.9/GJRM/R/teta.tr.R | 42 GJRM-0.2-6.9/GJRM/R/theta2tau.r | 131 GJRM-0.2-6.9/GJRM/man/GJRM-package.Rd | 4 GJRM-0.2-6.9/GJRM/man/bprobgHsContUniv.Rd | 14 GJRM-0.2-6.9/GJRM/man/cond.mv.Rd | 16 GJRM-0.2-6.9/GJRM/man/cond.mv.pcc.Rd |only GJRM-0.2-6.9/GJRM/man/copgHs.Rd | 2 GJRM-0.2-6.9/GJRM/man/copula.prob.Rd | 28 GJRM-0.2-6.9/GJRM/man/gamlss.Rd | 12 GJRM-0.2-6.9/GJRM/man/gjrm.Rd | 68 GJRM-0.2-6.9/GJRM/man/gjrm.pcc.Rd |only GJRM-0.2-6.9/GJRM/man/hfunc.Rd |only GJRM-0.2-6.9/GJRM/man/marg.mv.Rd | 7 GJRM-0.2-6.9/GJRM/man/mc.copula.prob.Rd |only GJRM-0.2-6.9/GJRM/man/print.gjrm.Rd | 13 GJRM-0.2-6.9/GJRM/man/res.check.Rd | 9 GJRM-0.2-6.9/GJRM/man/rob.const.Rd | 1 GJRM-0.2-6.9/GJRM/man/rob.int.Rd | 1 GJRM-0.2-6.9/GJRM/man/rpcc.Rd |only GJRM-0.2-6.9/GJRM/man/summary.gjrm.pcc.Rd |only 153 files changed, 6150 insertions(+), 2919 deletions(-)
Title: Echo State Networks for Time Series Modeling and Forecasting
Description: Provides a lightweight implementation of functions and methods for
fast and fully automatic time series modeling and forecasting using Echo
State Networks (ESNs).
Author: Alexander Haeusser [aut, cre, cph]
Maintainer: Alexander Haeusser <alexander-haeusser@gmx.de>
Diff between echos versions 1.0.3 dated 2026-02-21 and 1.0.4 dated 2026-06-15
DESCRIPTION | 6 - MD5 | 56 ++++++++------- NEWS.md | 10 ++ R/data.R | 129 ++++++++++++++++++++++++------------ R/methods-fable.R | 15 +++- R/train_esn.R | 30 ++++++++ R/tune_esn.R | 32 ++++++++ README.md | 30 +++++++- data/m4_data.rda |binary data/m4_monthly_subset.rda |only inst/doc/vignette_01_baseR.Rmd | 13 +++ inst/doc/vignette_01_baseR.html | 40 ++++++++++- inst/doc/vignette_02_tidyR.R | 2 inst/doc/vignette_02_tidyR.Rmd | 8 -- inst/doc/vignette_02_tidyR.html | 8 +- inst/doc/vignette_03_datasets.R | 4 - inst/doc/vignette_03_datasets.Rmd | 8 +- inst/doc/vignette_03_datasets.html | 12 +-- man/ESN.Rd | 15 +++- man/figures/README-base-1.svg | 4 - man/figures/logo.png |binary man/m4_data.Rd | 30 ++------ man/m4_monthly_subset.Rd |only man/synthetic_data.Rd | 54 +++++++++------ man/train_esn.Rd | 31 ++++++++ man/tune_esn.Rd | 37 ++++++++-- tests/testthat/test-methods-fable.R | 4 - vignettes/vignette_01_baseR.Rmd | 13 +++ vignettes/vignette_02_tidyR.Rmd | 8 -- vignettes/vignette_03_datasets.Rmd | 8 +- 30 files changed, 435 insertions(+), 172 deletions(-)
Title: Extension to 'tmap' for Creating Network Visualizations
Description: Provides functions for visualizing networks with 'tmap'. It supports 'sfnetworks' objects natively but is not limited to them. Useful for adding network layers such as edges and nodes to 'tmap' maps. More features may be added in future versions.
Author: Martijn Tennekes [aut, cre],
Andrea Gilardi [aut] ,
Robin Lovelace [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap.networks versions 0.2 dated 2026-05-09 and 0.2-1 dated 2026-06-15
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NEWS | 3 ++ R/tm_layers_edges.R | 71 ++++++++++++++++++++++++++++++---------------------- R/tm_layers_nodes.R | 42 ++++++++++++++---------------- man/tm_edges.Rd | 58 +++++++++++++++++++++++++----------------- man/tm_network.Rd | 2 - man/tm_nodes.Rd | 62 +++++++++++++++++++++++++++------------------ 8 files changed, 148 insertions(+), 110 deletions(-)
Title: Extensions to 'tmap' with Two New Modes: 'mapbox' and 'maplibre'
Description: The 'tmap' package provides two plotting modes for static and interactive thematic maps. This package extends 'tmap' with two additional modes based on 'Mapbox GL JS' and 'MapLibre GL JS'. These modes feature interactive vector tiles, globe views, and other modern web-mapping capabilities, while maintaining a consistent 'tmap' interface across all plotting modes.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap.mapgl versions 0.2-1 dated 2026-05-09 and 0.3 dated 2026-06-15
tmap.mapgl-0.2-1/tmap.mapgl/R/mapgl_arrange.R |only tmap.mapgl-0.2-1/tmap.mapgl/R/mapgl_shiny.R |only tmap.mapgl-0.3/tmap.mapgl/DESCRIPTION | 8 tmap.mapgl-0.3/tmap.mapgl/MD5 | 43 tmap.mapgl-0.3/tmap.mapgl/NAMESPACE | 15 tmap.mapgl-0.3/tmap.mapgl/NEWS | 10 tmap.mapgl-0.3/tmap.mapgl/R/mapgl_aux.R | 32 tmap.mapgl-0.3/tmap.mapgl/R/mapgl_init.R | 88 - tmap.mapgl-0.3/tmap.mapgl/R/mapgl_layers.R | 1131 +++++++++++++------- tmap.mapgl-0.3/tmap.mapgl/R/mapgl_legend.R | 228 +++- tmap.mapgl-0.3/tmap.mapgl/R/mapgl_misc.R | 25 tmap.mapgl-0.3/tmap.mapgl/R/mapgl_providers.R | 48 tmap.mapgl-0.3/tmap.mapgl/R/mapgl_run.R | 159 ++ tmap.mapgl-0.3/tmap.mapgl/R/mapgl_shape.R | 114 +- tmap.mapgl-0.3/tmap.mapgl/R/onload.R | 57 - tmap.mapgl-0.3/tmap.mapgl/R/shiny.R |only tmap.mapgl-0.3/tmap.mapgl/R/tm_layers_polygons_3d.R | 19 tmap.mapgl-0.3/tmap.mapgl/R/tm_mapbox.R | 6 tmap.mapgl-0.3/tmap.mapgl/R/tmapMapboxDataPlot.R | 8 tmap.mapgl-0.3/tmap.mapgl/R/tmapMaplibreDataPlot.R | 8 tmap.mapgl-0.3/tmap.mapgl/man/tm_mapbox.Rd | 4 tmap.mapgl-0.3/tmap.mapgl/man/tm_maplibre.Rd | 4 tmap.mapgl-0.3/tmap.mapgl/man/tm_polygons_3d.Rd | 15 tmap.mapgl-0.3/tmap.mapgl/man/tmapMapbox.Rd | 120 +- 24 files changed, 1571 insertions(+), 571 deletions(-)
Title: Extension to 'tmap' for Creating Glyphs
Description: Provides new layer functions to 'tmap' for drawing glyphs. A glyph is a small chart (e.g., donut chart) shown at specific map locations to visualize multivariate or time-series data. The functions work with the syntax of 'tmap' and allow flexible control over size, layout, and appearance.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap.glyphs versions 0.1-1 dated 2026-05-09 and 0.2 dated 2026-06-15
DESCRIPTION | 14 ++++--- MD5 | 26 ++++++------- NAMESPACE | 4 ++ NEWS | 3 + R/grob_functions.R | 14 ++++++- R/tm_layer_donuts.R | 44 ++++++++++++++++++----- R/tm_layer_flowers.R | 44 ++++++++++++++++++----- R/tmapGridDonuts.R | 29 ++++++++++++++- R/tmapGridFlowers.R | 25 ++++++++++++- R/tmapScaleComposition.R | 2 - R/tmapScaleMulti.R | 6 ++- man/internals_glyphs.Rd | 88 +++++++++++++++++++++++++++++++++++++++++++++++ man/tm_donuts.Rd | 30 +++++++++------- man/tm_flowers.Rd | 40 +++++++++++++++------ 14 files changed, 298 insertions(+), 71 deletions(-)
Title: List-Processing à La 'SRFI-1'
Description: Provides list-processing utilities inspired by the
'SRFI-1' list library for Scheme
(<https://srfi.schemers.org/srfi-1/srfi-1.html>), including
car/cdr family accessors, zip, pairwise, for.each,
pair.fold.right and friends. Higher-order helpers that are
orthogonal to list processing are deferred to the 'functional'
package; this package is freely a mixture of implementation and
API.
Author: Peter Danenberg [aut, cre]
Maintainer: Peter Danenberg <pcd@roxygen.org>
This is a re-admission after prior archival of version 0.1 dated 2012-01-12
Diff between lisp versions 0.1 dated 2012-01-12 and 0.2 dated 2026-06-15
lisp-0.1/lisp/TODO |only lisp-0.1/lisp/package.R |only lisp-0.2/lisp/DESCRIPTION | 33 ++++++++++++++++++++++----------- lisp-0.2/lisp/MD5 | 15 +++++++-------- lisp-0.2/lisp/NAMESPACE | 1 + lisp-0.2/lisp/R/lisp.R | 6 ++++++ lisp-0.2/lisp/inst |only lisp-0.2/lisp/man/last.Rd | 3 +++ lisp-0.2/lisp/man/pair.fold.right.Rd | 4 ++++ lisp-0.2/lisp/man/zip.with.names.Rd | 4 ++++ 10 files changed, 47 insertions(+), 19 deletions(-)
Title: Reconstruct Animal Paths from Solar Geolocation Loggers Data
Description: Spatio-temporal locations of an animal are computed
from annotated data with a hidden Markov model via particle
filter algorithm. The package is relatively robust to varying
degrees of shading.
The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>,
general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765>
and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.
Author: Eldar Rakhimberdiev [aut, cre],
Anatoly Saveliev [aut],
Julia Karagicheva [aut],
Simeon Lisovski [ctb],
Johannes de Groeve [ctb]
Maintainer: Eldar Rakhimberdiev <eldar.rakhimberdiev@uva.nl>
Diff between FLightR versions 0.5.5 dated 2024-07-04 and 0.5.6 dated 2026-06-15
DESCRIPTION | 12 MD5 | 55 NEWS.md | 24 R/data_import.R | 37 R/data_preparation.R | 6 R/new_plotting_functions.R | 28 R/run_particle_filter.R | 805 ++++++++-- R/summary_functions.R | 2 R/validation_metrics.R |only README.md | 9 build/vignette.rds |binary inst/CITATION | 2 inst/doc/FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.R | 82 - inst/doc/FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.html | 481 ++++- man/find.stationary.location.Rd | 2 man/get.tags.data.Rd | 6 man/map.FLightR.ggmap.Rd | 10 man/match_gps_to_twilights.Rd |only man/plot_slopes_by_location.Rd | 2 man/plot_util_distr.Rd | 16 man/posterior_point_distribution.Rd |only man/read_gps_track.Rd |only man/read_validation_config.Rd |only man/run.particle.filter.Rd | 36 man/validation_summary.Rd |only tests/testthat/helper-source-checkout.R |only tests/testthat/test-cached-propagation.R |only tests/testthat/test-partial-cached-propagation.R |only tests/testthat/test-run-particle-filter-directions.R |only tests/testthat/test-run-particle-filter-threads.R |only tests/testthat/test-run-particle-filter-verbosity.R |only tests/testthat/test-transition-encoding.R |only tests/testthat/test-validation-metrics.R |only tests/testthat/test-weight-stack.R |only tests/testthat/test_data_processing.R | 30 tests/testthat/test_data_result_summary_and_plotting.R | 2 36 files changed, 1286 insertions(+), 361 deletions(-)
Title: Download Stats of R Packages
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages.
Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>.
'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between dlstats versions 0.1.7 dated 2023-05-24 and 0.1.8 dated 2026-06-15
DESCRIPTION | 8 - MD5 | 20 ++-- NAMESPACE | 6 + R/bioc_stats.R | 59 ++++++++++--- R/cran_stats.R | 76 +++++++++++------ R/dlstats-package.R |only R/plot_bioc_stats.R | 21 ++-- build/vignette.rds |binary inst/doc/dlstats.html | 219 ++++++++++++++++++++++++++++++++++++++++--------- man/bioc_stats.Rd | 9 +- man/cran_stats.Rd | 21 +--- man/dlstats-package.Rd |only 12 files changed, 324 insertions(+), 115 deletions(-)
Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has
already an implementation in package 'Synth') are implemented: first,
'MSCMT' allows for using multiple outcome variables, second, time series
can be supplied as economic predictors, and third, a well-defined
cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
A detailed description of the main algorithms is given in
Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] ,
Stefan Kloessner [aut],
Karline Soetaert [com],
Jack Dongarra [cph],
R.J. Hanson [cph],
K.H. Haskell [cph],
Cleve Moler [cph],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.4.3 dated 2026-05-26 and 1.4.4 dated 2026-06-15
DESCRIPTION | 8 MD5 | 14 - NEWS | 7 build/partial.rdb |binary inst/doc/CheckingSynth.html | 313 ++++++++-------------- inst/doc/UsingTimeSeries.html | 302 ++++++++------------- inst/doc/WorkingWithMSCMT.html | 572 ++++++++++++++--------------------------- src/solve.f | 4 8 files changed, 455 insertions(+), 765 deletions(-)
Title: Panel Evaluation in Forensic Kinship Analysis
Description: Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
Author: Guanju Ma [aut, cre],
Shujin Li [ctb]
Maintainer: Guanju Ma <guanjuma@hebmu.edu.cn>
Diff between KINSIMU versions 0.1.3 dated 2025-12-19 and 0.1.3-2 dated 2026-06-15
KINSIMU-0.1.3-2/KINSIMU/DESCRIPTION | 10 +++++----- KINSIMU-0.1.3-2/KINSIMU/MD5 | 14 +++++--------- KINSIMU-0.1.3-2/KINSIMU/NEWS.md | 5 ++++- KINSIMU-0.1.3-2/KINSIMU/man/FortytwoSTR.Rd | 1 - KINSIMU-0.1.3-2/KINSIMU/man/KINSIMU-package.Rd | 7 ++++++- KINSIMU-0.1.3-2/KINSIMU/man/pediexample.Rd | 1 - KINSIMU-0.1.3/KINSIMU/build |only KINSIMU-0.1.3/KINSIMU/inst/doc |only KINSIMU-0.1.3/KINSIMU/vignettes |only 9 files changed, 20 insertions(+), 18 deletions(-)
Title: Fast and Memory Efficient Fitting of Linear Models with
High-Dimensional Fixed Effects
Description: Fast and user-friendly estimation of generalized linear
models with multiple fixed effects and cluster the standard errors.
The method to obtain the estimated fixed-effects coefficients is based
on Stammann (2018) <doi:10.48550/arXiv.1707.01815>, Gaure (2013)
<doi:10.1016/j.csda.2013.03.024>, Berge (2018)
<https://ideas.repec.org/p/luc/wpaper/18-13.html>, and Correia et al.
(2020) <doi: 10.1177/1536867X20909691>. This implementation is
described in Vargas Sepulveda (2025)
<doi:10.1371/journal.pone.0331178>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Joao Santos Silva [ths],
Yoto Yotov [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between capybara versions 1.8.0 dated 2025-08-27 and 2.0.0 dated 2026-06-15
capybara-1.8.0/capybara/R/apes.R |only capybara-1.8.0/capybara/R/apes_bias_helpers.R |only capybara-1.8.0/capybara/R/bias_corr.R |only capybara-1.8.0/capybara/R/cpp11.R |only capybara-1.8.0/capybara/data/trade_panel.rda |only capybara-1.8.0/capybara/man/apes.Rd |only capybara-1.8.0/capybara/man/bias_corr.Rd |only capybara-1.8.0/capybara/man/trade_panel.Rd |only capybara-1.8.0/capybara/src/01_center.h |only capybara-1.8.0/capybara/src/02_beta.h |only capybara-1.8.0/capybara/src/03_alpha.h |only capybara-1.8.0/capybara/src/04_lm.h |only capybara-1.8.0/capybara/src/05_glm_helpers.h |only capybara-1.8.0/capybara/src/06_glm.h |only capybara-1.8.0/capybara/src/07_negbin.h |only capybara-1.8.0/capybara/src/08_sums.h |only capybara-1.8.0/capybara/src/cpp11.cpp |only capybara-1.8.0/capybara/tests/testthat |only capybara-1.8.0/capybara/tests/testthat.R |only capybara-2.0.0/capybara/DESCRIPTION | 57 capybara-2.0.0/capybara/MD5 | 202 - capybara-2.0.0/capybara/NAMESPACE | 28 capybara-2.0.0/capybara/NEWS.md | 50 capybara-2.0.0/capybara/R/autoplot.R | 109 capybara-2.0.0/capybara/R/capybara-package.R | 149 capybara-2.0.0/capybara/R/cpp4r.R |only capybara-2.0.0/capybara/R/fe_table.R |only capybara-2.0.0/capybara/R/feglm.R | 484 +-- capybara-2.0.0/capybara/R/feglm_helpers.R | 694 +--- capybara-2.0.0/capybara/R/feglm_offset.R | 69 capybara-2.0.0/capybara/R/felm.R | 347 +- capybara-2.0.0/capybara/R/felm_helpers.R | 52 capybara-2.0.0/capybara/R/fenegbin.R | 378 +- capybara-2.0.0/capybara/R/fepoisson.R | 135 capybara-2.0.0/capybara/R/fepoisson_asymmetric.R |only capybara-2.0.0/capybara/R/fit_control.R | 402 +- capybara-2.0.0/capybara/R/fit_helpers.R | 641 +++- capybara-2.0.0/capybara/R/generics_augment.R | 75 capybara-2.0.0/capybara/R/generics_coef.R | 53 capybara-2.0.0/capybara/R/generics_confint.R | 76 capybara-2.0.0/capybara/R/generics_fitted.R | 27 capybara-2.0.0/capybara/R/generics_formula.R |only capybara-2.0.0/capybara/R/generics_glance.R | 64 capybara-2.0.0/capybara/R/generics_predict.R | 343 +- capybara-2.0.0/capybara/R/generics_print.R | 361 +- capybara-2.0.0/capybara/R/generics_summary.R | 130 capybara-2.0.0/capybara/R/generics_tidy.R | 43 capybara-2.0.0/capybara/R/generics_vcov.R | 488 +-- capybara-2.0.0/capybara/R/summary_table.R | 640 ++-- capybara-2.0.0/capybara/README.md | 124 capybara-2.0.0/capybara/build/vignette.rds |binary capybara-2.0.0/capybara/configure | 90 capybara-2.0.0/capybara/data/correia2019.rda |only capybara-2.0.0/capybara/data/ross2004.rda |only capybara-2.0.0/capybara/inst/CITATION |only capybara-2.0.0/capybara/inst/doc/asymmetric.R |only capybara-2.0.0/capybara/inst/doc/asymmetric.Rmd |only capybara-2.0.0/capybara/inst/doc/asymmetric.html |only capybara-2.0.0/capybara/inst/doc/intro.Rmd | 77 capybara-2.0.0/capybara/inst/doc/intro.html | 102 capybara-2.0.0/capybara/inst/doc/separation.R |only capybara-2.0.0/capybara/inst/doc/separation.Rmd |only capybara-2.0.0/capybara/inst/doc/separation.html |only capybara-2.0.0/capybara/inst/doc/variance-covariance.R |only capybara-2.0.0/capybara/inst/doc/variance-covariance.Rmd |only capybara-2.0.0/capybara/inst/doc/variance-covariance.html |only capybara-2.0.0/capybara/inst/templates |only capybara-2.0.0/capybara/inst/tinytest |only capybara-2.0.0/capybara/man/autoplot.Rd | 31 capybara-2.0.0/capybara/man/broom.Rd | 30 capybara-2.0.0/capybara/man/capybara-package.Rd | 24 capybara-2.0.0/capybara/man/correia2019.Rd |only capybara-2.0.0/capybara/man/fe_table.Rd |only capybara-2.0.0/capybara/man/feglm.Rd | 109 capybara-2.0.0/capybara/man/felm.Rd | 82 capybara-2.0.0/capybara/man/fenegbin.Rd | 70 capybara-2.0.0/capybara/man/fepoisson.Rd | 59 capybara-2.0.0/capybara/man/fepoisson_asymmetric.Rd |only capybara-2.0.0/capybara/man/fit_control.Rd | 240 - capybara-2.0.0/capybara/man/reexports.Rd | 4 capybara-2.0.0/capybara/man/ross2004.Rd |only capybara-2.0.0/capybara/man/sandwich_vcov.Rd |only capybara-2.0.0/capybara/man/summary_table.Rd | 20 capybara-2.0.0/capybara/man/update.feglm.Rd |only capybara-2.0.0/capybara/man/update.felm.Rd |only capybara-2.0.0/capybara/man/update.felm_formula.Rd |only capybara-2.0.0/capybara/man/vcov.feglm.Rd | 46 capybara-2.0.0/capybara/man/vcov.felm.Rd | 44 capybara-2.0.0/capybara/src/01_01_center_helpers.h |only capybara-2.0.0/capybara/src/01_02_center_acceleration.h |only capybara-2.0.0/capybara/src/01_03_center_stammann.h |only capybara-2.0.0/capybara/src/01_04_center_berge.h |only capybara-2.0.0/capybara/src/01_05_center.h |only capybara-2.0.0/capybara/src/02_chol.h |only capybara-2.0.0/capybara/src/03_beta.h |only capybara-2.0.0/capybara/src/04_alpha.h |only capybara-2.0.0/capybara/src/05_01_separation_helpers.h |only capybara-2.0.0/capybara/src/05_02_separation_relu.h |only capybara-2.0.0/capybara/src/05_03_separation_simplex.h |only capybara-2.0.0/capybara/src/05_04_separation.h |only capybara-2.0.0/capybara/src/06_01_fit_helpers.h |only capybara-2.0.0/capybara/src/06_02_fit_deviance.h |only capybara-2.0.0/capybara/src/06_03_fit_links.h |only capybara-2.0.0/capybara/src/06_04_fit_drop.h |only capybara-2.0.0/capybara/src/06_05_fit_vcov.h |only capybara-2.0.0/capybara/src/06_06_fit_sums.h |only capybara-2.0.0/capybara/src/07_lm.h |only capybara-2.0.0/capybara/src/08_glm.h |only capybara-2.0.0/capybara/src/09_negbin.h |only capybara-2.0.0/capybara/src/10_fepoisson_asymmetric.h |only capybara-2.0.0/capybara/src/11_formula_parser.h |only capybara-2.0.0/capybara/src/Makevars.in | 11 capybara-2.0.0/capybara/src/capybara.cpp | 2206 ++++++++++++-- capybara-2.0.0/capybara/src/cpp4r.cpp |only capybara-2.0.0/capybara/tests/tinytest.R |only capybara-2.0.0/capybara/vignettes/asymmetric.Rmd |only capybara-2.0.0/capybara/vignettes/intro.Rmd | 77 capybara-2.0.0/capybara/vignettes/separation.Rmd |only capybara-2.0.0/capybara/vignettes/variance-covariance.Rmd |only 119 files changed, 6178 insertions(+), 3365 deletions(-)
Title: Functional Utilities for Data Processing
Description: Covers several areas of data processing: batch-splitting, reading and writing of large
data files, data tiling, one-hot encoding and decoding of data tiles, stratified proportional
(random or probabilistic) data sampling, data normalization and thresholding, substring location
and commonalities inside strings, and location and tabulation of amino acids, modifications or
associated monoisotopic masses inside modified peptides. The extractor implements code from
'Matrix.utils', Varrichio C (2020), <https://cran.r-project.org/package=Matrix.utils>.
Author: Dragos Bandur [aut, cre]
Maintainer: Dragos Bandur <dbandur@sympatico.ca>
Diff between akin versions 0.3.6 dated 2026-06-07 and 0.3.7 dated 2026-06-15
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ NEWS.md | 8 ++++++++ R/cover.R | 6 +++--- R/fcommon.R | 28 +++++++++++----------------- R/utils.R | 18 ++++++++++++++++-- R/zzz.R | 1 + man/cover.Rd | 2 +- man/fcommon.Rd | 8 ++++---- 10 files changed, 61 insertions(+), 41 deletions(-)
Title: Clinical Trial Simulator
Description: Simulate phase II and/or phase III clinical trials. It supports various types of endpoints and adaptive strategies. Tools for carrying out graphical testing procedure and combination test under group sequential design are also provided.
Author: Han Zhang [cre, aut]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between TrialSimulator versions 1.18.4 dated 2026-05-13 and 1.20.1 dated 2026-06-15
DESCRIPTION | 6 MD5 | 62 ++- NAMESPACE | 1 NEWS.md | 23 + R/Arms.R | 2 R/Endpoint.R | 33 ++ R/Endpoints.R | 36 +- R/Regimens.R | 95 +++++- R/Trials.R | 442 +++++++++++++++++++++------- R/crossover.R |only R/regimen.R | 35 +- README.md | 2 build/vignette.rds |binary inst/doc/crossoverAtMilestone.R |only inst/doc/crossoverAtMilestone.Rmd |only inst/doc/crossoverAtMilestone.html |only inst/doc/crossoverWashout.html | 8 inst/doc/defineNonTimeToEventEndpoints.R | 12 inst/doc/defineNonTimeToEventEndpoints.Rmd | 21 + inst/doc/defineNonTimeToEventEndpoints.html | 278 +++++++++-------- inst/doc/dynamicTreatmentSwitching.R | 37 -- inst/doc/dynamicTreatmentSwitching.Rmd | 55 +-- inst/doc/dynamicTreatmentSwitching.html | 84 ++--- man/Endpoints.Rd | 7 man/Regimens.Rd | 90 ++++- man/Trials.Rd | 57 +++ man/crossover.Rd |only man/endpoint.Rd | 10 man/regimen.Rd | 30 + tests/testthat/test-crossover.R |only tests/testthat/test-endpoint.R |only tests/testthat/test-parallel.R | 6 tests/testthat/test-regimen.R | 5 vignettes/crossoverAtMilestone.Rmd |only vignettes/defineNonTimeToEventEndpoints.Rmd | 21 + vignettes/dynamicTreatmentSwitching.Rmd | 55 +-- 36 files changed, 1027 insertions(+), 486 deletions(-)
More information about TrialSimulator at CRAN
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Title: A Glimpse at the Diversity of Peru's Endemic Plants
Description: Provides an updated database of accepted endemic plant taxa from Peru. The current collection contains over 8,000 taxonomic records at species and infraspecific ranks. Data are derived from Govaerts, R., Nic Lughadha, E., Black, N. et al., 'The World Checklist of Vascular Plants: A continuously updated resource for exploring global plant diversity', published in Sci Data 8, 215 (2021) <doi:10.1038/s41597-021-00997-6>.
Author: Paul E. Santos Andrade [aut, cre] ,
Lucely L. Vilca Bustamante [aut]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between ppendemic versions 0.2.1 dated 2026-02-26 and 0.2.2 dated 2026-06-15
DESCRIPTION | 11 - MD5 | 45 +++-- R/direct_match.R | 3 R/fuzzy_match_genus.R | 9 - R/fuzzy_match_infraspp_within_species.R | 31 ++- R/fuzzy_match_spp_within_genus.R | 6 R/internal.R | 57 ++++-- R/is_ppendemic.R | 4 R/matching_ppendemic.R | 13 + R/ppendemic_data.R | 151 ++++++++++++++--- R/suffix_match_spp_within_genus.R | 6 README.md | 44 ++-- build |only data/ppendemic_tab16.rda |only inst/doc |only man/figures/README-unnamed-chunk-2-1.png |binary man/is_ppendemic.Rd | 4 man/matching_ppendemic.Rd | 10 + man/ppendemic_tab14.Rd | 36 ++-- man/ppendemic_tab15.Rd | 6 man/ppendemic_tab16.Rd |only tests/testthat/test_matching_ppendemic.R | 8 tests/testthat/test_matching_ppendemic_normalization.R | 15 + tests/testthat/test_matching_regressions.R |only tests/testthat/test_progress_option.R |only vignettes |only 26 files changed, 329 insertions(+), 130 deletions(-)
Title: Prescribe Sub-Symptom Exercise for Adolescent Concussion
Description: A clinical decision support system for sub-symptom threshold
aerobic exercise (SSTAE) prescription in adolescents with persistent
post-concussion symptoms (PPCS). Implements an evidence-based protocol
derived from a systematic review of seven studies (Li, 2026; <doi:10.17605/osf.io/kvuf6>),
encoding safety screening, Buffalo Concussion Treadmill Test (BCTT)-guided
heart rate prescription, session-level progress tracking, and evidence
disclosure using the Grading of Recommendations, Assessment, Development
and Evaluation (GRADE) framework into an open-source tool for athletic
trainers and clinicians. Designed to support implementation in
resource-limited settings where BCTT equipment may be unavailable.
GRADE certainty of evidence: LOW. For clinician use only; not a
substitute for clinical judgement.
Author: Guang Li [aut, cre]
Maintainer: Guang Li <contact@guanglab.org>
Diff between PPCSexRx versions 0.1.0 dated 2026-06-01 and 0.1.1 dated 2026-06-15
DESCRIPTION | 17 +++++++------ MD5 | 6 +++- NEWS.md |only README.md | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++- inst/CITATION |only 5 files changed, 85 insertions(+), 11 deletions(-)
Title: Fast Interactive Data Analysis Pipelines
Description: A lightweight and intuitive framework for building interactive data
analysis pipelines. You add R functions one by one, and 'pipeflow'
wires them into a pipeline that stays consistent as you go. Modify,
remove, or insert steps at any stage, manage all parameters in one
place, fast execution (C++-powered DAG) for interactive use and Shiny
backends.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between pipeflow versions 0.2.3 dated 2025-07-26 and 0.3.0 dated 2026-06-15
pipeflow-0.2.3/pipeflow/R/pkgname.R |only pipeflow-0.2.3/pipeflow/inst/doc/v05-split-and-combine.R |only pipeflow-0.2.3/pipeflow/inst/doc/v05-split-and-combine.Rmd |only pipeflow-0.2.3/pipeflow/inst/doc/v05-split-and-combine.html |only pipeflow-0.2.3/pipeflow/tests/testthat/test_pkgname.R |only pipeflow-0.2.3/pipeflow/vignettes/v05-split-and-combine.Rmd |only pipeflow-0.3.0/pipeflow/DESCRIPTION | 39 pipeflow-0.3.0/pipeflow/LICENSE |only pipeflow-0.3.0/pipeflow/MD5 | 183 pipeflow-0.3.0/pipeflow/NAMESPACE | 29 pipeflow-0.3.0/pipeflow/NEWS.md | 60 pipeflow-0.3.0/pipeflow/R/RcppExports.R |only pipeflow-0.3.0/pipeflow/R/aliases.R | 431 pipeflow-0.3.0/pipeflow/R/log.R | 28 pipeflow-0.3.0/pipeflow/R/param.R | 345 pipeflow-0.3.0/pipeflow/R/pipeflow-package.R |only pipeflow-0.3.0/pipeflow/R/pipeline.R | 4304 +++---- pipeflow-0.3.0/pipeflow/R/pipelineR6.R |only pipeflow-0.3.0/pipeflow/R/pipeline_helpers.R |only pipeflow-0.3.0/pipeflow/R/utils.R | 39 pipeflow-0.3.0/pipeflow/R/zzz.R |only pipeflow-0.3.0/pipeflow/build/vignette.rds |binary pipeflow-0.3.0/pipeflow/inst/doc/v01-get-started.R | 91 pipeflow-0.3.0/pipeflow/inst/doc/v01-get-started.Rmd | 225 pipeflow-0.3.0/pipeflow/inst/doc/v01-get-started.html | 535 pipeflow-0.3.0/pipeflow/inst/doc/v02-modify-pipeline.R | 148 pipeflow-0.3.0/pipeflow/inst/doc/v02-modify-pipeline.Rmd | 157 pipeflow-0.3.0/pipeflow/inst/doc/v02-modify-pipeline.html | 168 pipeflow-0.3.0/pipeflow/inst/doc/v03-combine-pipelines.R | 122 pipeflow-0.3.0/pipeflow/inst/doc/v03-combine-pipelines.Rmd | 224 pipeflow-0.3.0/pipeflow/inst/doc/v03-combine-pipelines.html | 381 pipeflow-0.3.0/pipeflow/inst/doc/v04-collect-output.R | 199 pipeflow-0.3.0/pipeflow/inst/doc/v04-collect-output.Rmd | 293 pipeflow-0.3.0/pipeflow/inst/doc/v04-collect-output.html | 489 pipeflow-0.3.0/pipeflow/inst/doc/v05-split-map-reduce.R |only pipeflow-0.3.0/pipeflow/inst/doc/v05-split-map-reduce.Rmd |only pipeflow-0.3.0/pipeflow/inst/doc/v05-split-map-reduce.html |only pipeflow-0.3.0/pipeflow/inst/doc/v06-self-modify-pipeline.R | 295 pipeflow-0.3.0/pipeflow/inst/doc/v06-self-modify-pipeline.Rmd | 484 pipeflow-0.3.0/pipeflow/inst/doc/v06-self-modify-pipeline.html | 765 - pipeflow-0.3.0/pipeflow/man/Extract.pipeflow_pip.Rd |only pipeflow-0.3.0/pipeflow/man/Pipeline.Rd | 2068 +-- pipeflow-0.3.0/pipeflow/man/length.pipeflow.Rd |only pipeflow-0.3.0/pipeflow/man/pip_add.Rd |only pipeflow-0.3.0/pipeflow/man/pip_add_from.Rd |only pipeflow-0.3.0/pipeflow/man/pip_bind.Rd |only pipeflow-0.3.0/pipeflow/man/pip_clone.Rd |only pipeflow-0.3.0/pipeflow/man/pip_collect_out.Rd |only pipeflow-0.3.0/pipeflow/man/pip_get_graph.Rd |only pipeflow-0.3.0/pipeflow/man/pip_get_params.Rd |only pipeflow-0.3.0/pipeflow/man/pip_has_step.Rd |only pipeflow-0.3.0/pipeflow/man/pip_lock.Rd |only pipeflow-0.3.0/pipeflow/man/pip_new.Rd |only pipeflow-0.3.0/pipeflow/man/pip_remove.Rd |only pipeflow-0.3.0/pipeflow/man/pip_rename.Rd |only pipeflow-0.3.0/pipeflow/man/pip_replace.Rd |only pipeflow-0.3.0/pipeflow/man/pip_run.Rd |only pipeflow-0.3.0/pipeflow/man/pip_set_params.Rd |only pipeflow-0.3.0/pipeflow/man/pip_tag.Rd |only pipeflow-0.3.0/pipeflow/man/pip_unlock.Rd |only pipeflow-0.3.0/pipeflow/man/pip_untag.Rd |only pipeflow-0.3.0/pipeflow/man/pip_view.Rd |only pipeflow-0.3.0/pipeflow/man/pipe_add.Rd | 19 pipeflow-0.3.0/pipeflow/man/pipe_append.Rd | 13 pipeflow-0.3.0/pipeflow/man/pipe_append_to_step_names.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_clone.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_collect_out.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_discard_steps.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_get_data.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_get_depends.Rd | 12 pipeflow-0.3.0/pipeflow/man/pipe_get_graph.Rd | 7 pipeflow-0.3.0/pipeflow/man/pipe_get_out.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_get_params.Rd | 14 pipeflow-0.3.0/pipeflow/man/pipe_insert.Rd | 9 pipeflow-0.3.0/pipeflow/man/pipe_length.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_lock_unlock.Rd | 7 pipeflow-0.3.0/pipeflow/man/pipe_new.Rd | 19 pipeflow-0.3.0/pipeflow/man/pipe_pop_step.Rd | 12 pipeflow-0.3.0/pipeflow/man/pipe_print.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_remove_step.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_rename_step.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_replace_step.Rd | 7 pipeflow-0.3.0/pipeflow/man/pipe_reset.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_run.Rd | 9 pipeflow-0.3.0/pipeflow/man/pipe_run_step.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_set_data.Rd | 14 pipeflow-0.3.0/pipeflow/man/pipe_set_data_split.Rd | 21 pipeflow-0.3.0/pipeflow/man/pipe_set_keep_out.Rd | 14 pipeflow-0.3.0/pipeflow/man/pipe_set_params.Rd | 5 pipeflow-0.3.0/pipeflow/man/pipe_set_params_at_step.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipe_split.Rd | 6 pipeflow-0.3.0/pipeflow/man/pipeflow-package.Rd |only pipeflow-0.3.0/pipeflow/man/print.Rd |only pipeflow-0.3.0/pipeflow/man/step_info.Rd | 14 pipeflow-0.3.0/pipeflow/src |only pipeflow-0.3.0/pipeflow/tests/testthat.R | 5 pipeflow-0.3.0/pipeflow/tests/testthat/helper_dag.R |only pipeflow-0.3.0/pipeflow/tests/testthat/helper_general.R | 20 pipeflow-0.3.0/pipeflow/tests/testthat/helper_test_data.R | 4 pipeflow-0.3.0/pipeflow/tests/testthat/test_RcppExports.R |only pipeflow-0.3.0/pipeflow/tests/testthat/test_aliases.R | 1163 - pipeflow-0.3.0/pipeflow/tests/testthat/test_log.R | 83 pipeflow-0.3.0/pipeflow/tests/testthat/test_param.R | 201 pipeflow-0.3.0/pipeflow/tests/testthat/test_pipeflow-package.R |only pipeflow-0.3.0/pipeflow/tests/testthat/test_pipeline.R | 6106 +++------- pipeflow-0.3.0/pipeflow/tests/testthat/test_pipelineR6.R |only pipeflow-0.3.0/pipeflow/tests/testthat/test_pipeline_helper.R |only pipeflow-0.3.0/pipeflow/tests/testthat/test_utils.R | 167 pipeflow-0.3.0/pipeflow/vignettes/articles |only pipeflow-0.3.0/pipeflow/vignettes/v01-get-started.Rmd | 225 pipeflow-0.3.0/pipeflow/vignettes/v02-modify-pipeline.Rmd | 157 pipeflow-0.3.0/pipeflow/vignettes/v03-combine-pipelines.Rmd | 224 pipeflow-0.3.0/pipeflow/vignettes/v04-collect-output.Rmd | 293 pipeflow-0.3.0/pipeflow/vignettes/v05-split-map-reduce.Rmd |only pipeflow-0.3.0/pipeflow/vignettes/v06-self-modify-pipeline.Rmd | 484 115 files changed, 9852 insertions(+), 11655 deletions(-)
Title: Joint Covariance and Treatment-Effect Tests for Multiple
Outcomes
Description: Fits generalized linear models, Cox proportional-hazards
models, log-rank tests, generalized estimating equations, mixed models
with repeated measures, Kaplan-Meier curves, quantile differences, and
hierarchical net-benefit (win-difference) and log win-ratio statistics
jointly across multiple endpoints, and returns the full asymptotic
covariance matrix linking them. Implements PATED (Prognostic Assisted
Treatment Effect Detection), a randomized-trial method that exploits
balanced prognostic covariates to tighten standard errors and increase
statistical power without introducing bias.
Author: Han Zhang [aut, cre]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between multipleOutcomes versions 0.16.2 dated 2026-05-18 and 0.18.1 dated 2026-06-15
DESCRIPTION | 24 ++++++------ MD5 | 43 +++++++++++++++------- NAMESPACE | 5 ++ NEWS.md | 31 +++++++++++++++ R/NetBenefitAdapter.R |only R/WinRatioAdapter.R |only R/computeNetBenefit.R |only R/jointCovariance.R | 5 +- R/make_adapter.R | 8 ++++ R/nb_endpoint.R |only R/netbenefit_.R |only R/oak.R |only R/pated.R | 7 ++- R/poplar.R |only R/winratio_.R |only data/oak.rda |only data/poplar.rda |only man/jointCovariance.Rd | 4 +- man/nb_endpoint.Rd |only man/netbenefit_.Rd |only man/oak.Rd |only man/pated.Rd | 7 ++- man/poplar.Rd |only man/winratio_.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/helper-sim-data.R | 29 ++++++++++++++ tests/testthat/test-inplace-formula.R |only tests/testthat/test-mc-cross-engine.R | 36 ++++++++++++++++++ tests/testthat/test-netbenefit-vs-fit_win_ratio.R |only tests/testthat/test-netbenefit.R |only tests/testthat/test-validation.R | 3 + tests/testthat/test-winratio.R |only 32 files changed, 168 insertions(+), 34 deletions(-)
More information about multipleOutcomes at CRAN
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Title: Multidimensional Poverty Index (MPI) via the Alkire-Foster
Method
Description: Estimate Multidimensional Poverty Index (MPI) measures from household
survey microdata using the Alkire-Foster dual-cutoff counting method (Alkire
and Foster, 2011). Load indicator
specifications from CSV, Excel, JSON, or plain-text files; compute the
headcount ratio (H), intensity (A), and MPI = H x A across any subgroup;
and export results to formatted Excel reports. Supports complex survey
designs — stratification, clustering, and probability weights — and
optionally appends design-based standard errors and confidence intervals.
Author: Bhas Abdulsamad [aut, cre, cph]
Maintainer: Bhas Abdulsamad <aeabdulsamad@gmail.com>
Diff between mpindex versions 0.2.1 dated 2024-01-09 and 0.3.0 dated 2026-06-15
mpindex-0.2.1/mpindex/R/data-df_household.R |only mpindex-0.2.1/mpindex/R/data-df_household_roster.R |only mpindex-0.2.1/mpindex/R/helpers.R |only mpindex-0.2.1/mpindex/R/save_mpi.R |only mpindex-0.2.1/mpindex/R/write-as-excel.R |only mpindex-0.3.0/mpindex/DESCRIPTION | 31 mpindex-0.3.0/mpindex/MD5 | 98 mpindex-0.3.0/mpindex/NAMESPACE | 6 mpindex-0.3.0/mpindex/NEWS.md | 41 mpindex-0.3.0/mpindex/R/compute-contribution.R | 55 mpindex-0.3.0/mpindex/R/compute-headcount-ratio-adjusted.R | 72 mpindex-0.3.0/mpindex/R/compute-headcount-ratio.R | 64 mpindex-0.3.0/mpindex/R/compute-mpi-from-profile.R |only mpindex-0.3.0/mpindex/R/compute-mpi.R | 386 - mpindex-0.3.0/mpindex/R/create-deprivation-matrix.R | 63 mpindex-0.3.0/mpindex/R/data-df-household-roster.R |only mpindex-0.3.0/mpindex/R/data-df-household.R |only mpindex-0.3.0/mpindex/R/data-helpers.R |only mpindex-0.3.0/mpindex/R/define-deprivation.R | 198 mpindex-0.3.0/mpindex/R/define-mpi-specs.R | 258 - mpindex-0.3.0/mpindex/R/save-mpi.R |only mpindex-0.3.0/mpindex/R/survey-helpers.R |only mpindex-0.3.0/mpindex/R/utils.R | 100 mpindex-0.3.0/mpindex/R/zzz.R |only mpindex-0.3.0/mpindex/README.md | 9 mpindex-0.3.0/mpindex/build/vignette.rds |binary mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.R |only mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.Rmd |only mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.html |only mpindex-0.3.0/mpindex/inst/doc/mpindex.R | 643 +-- mpindex-0.3.0/mpindex/inst/doc/mpindex.Rmd | 793 +-- mpindex-0.3.0/mpindex/inst/doc/mpindex.html | 2057 ++++------ mpindex-0.3.0/mpindex/inst/doc/survey-weights.R |only mpindex-0.3.0/mpindex/inst/doc/survey-weights.Rmd |only mpindex-0.3.0/mpindex/inst/doc/survey-weights.html |only mpindex-0.3.0/mpindex/man/compute_mpi.Rd | 204 mpindex-0.3.0/mpindex/man/compute_mpi_from_profile.Rd |only mpindex-0.3.0/mpindex/man/define_deprivation.Rd | 60 mpindex-0.3.0/mpindex/man/define_mpi_specs.Rd | 57 mpindex-0.3.0/mpindex/man/deprived.Rd |only mpindex-0.3.0/mpindex/man/df_household.Rd | 2 mpindex-0.3.0/mpindex/man/df_household_roster.Rd | 2 mpindex-0.3.0/mpindex/man/global_mpi_specs.Rd |only mpindex-0.3.0/mpindex/man/save_mpi.Rd | 43 mpindex-0.3.0/mpindex/man/use_global_mpi_specs.Rd | 12 mpindex-0.3.0/mpindex/tests/deprivation-profile-simple.R | 12 mpindex-0.3.0/mpindex/tests/deprivation-profile.R | 68 mpindex-0.3.0/mpindex/tests/testthat/helper-deprivation-profile-simple.R |only mpindex-0.3.0/mpindex/tests/testthat/helper-deprivation-profile.R |only mpindex-0.3.0/mpindex/tests/testthat/helper-survey.R |only mpindex-0.3.0/mpindex/tests/testthat/test-arg-rename.R |only mpindex-0.3.0/mpindex/tests/testthat/test-by-and-extra-cols.R |only mpindex-0.3.0/mpindex/tests/testthat/test-compute-contribution.R | 32 mpindex-0.3.0/mpindex/tests/testthat/test-compute-headcount-ratio-adjusted.R | 23 mpindex-0.3.0/mpindex/tests/testthat/test-compute-headcount-ratio.R | 23 mpindex-0.3.0/mpindex/tests/testthat/test-compute-mpi-with.R |only mpindex-0.3.0/mpindex/tests/testthat/test-compute-mpi.R | 128 mpindex-0.3.0/mpindex/tests/testthat/test-create-deprivation-matrix.R | 39 mpindex-0.3.0/mpindex/tests/testthat/test-define-deprivation.R | 53 mpindex-0.3.0/mpindex/tests/testthat/test-define-mpi-specs.R | 84 mpindex-0.3.0/mpindex/tests/testthat/test-overall.R |only mpindex-0.3.0/mpindex/tests/testthat/test-save-mpi.R |only mpindex-0.3.0/mpindex/tests/testthat/test-survey.R |only mpindex-0.3.0/mpindex/vignettes/migrating-to-0-3-0.Rmd |only mpindex-0.3.0/mpindex/vignettes/mpindex.Rmd | 793 +-- mpindex-0.3.0/mpindex/vignettes/survey-weights.Rmd |only 66 files changed, 3124 insertions(+), 3385 deletions(-)
Title: OECD PISA Datasets from 2000-2022 in an Easy-to-Use Format
Description: The Programme for International Student Assessment (PISA) is a global study conducted by the Organization for Economic Cooperation and Development (OECD) in member and non-member countries to assess educational systems by assessing 15-year-old school students academic performance in mathematics, science, and reading. This datasets contains information on their scores and other socioeconomic characteristics, information about their school and its infrastructure, as well as the countries that are taking part in the program.
Author: Kevin Wang [aut, cre],
Paul Yacobellis [aut],
Erika Siregar [aut],
Sarah Romanes [aut],
Kim Fitter [aut],
Giulio Valentino Dalla Riva [aut],
Dianne Cook [aut],
Nick Tierney [aut],
Priya Dingorkar [aut],
Shabarish Sai Subramanian [aut],
Guan Ru Chen [ [...truncated...]
Maintainer: Kevin Wang <kevinwangstats@gmail.com>
Diff between learningtower versions 1.1.0 dated 2024-12-21 and 1.1.1 dated 2026-06-15
DESCRIPTION | 8 +- MD5 | 36 +++++------ NEWS.md | 4 + R/data.R | 2 R/load_student.R | 21 ++++++ README.md | 23 +++++-- build/vignette.rds |binary inst/doc/learningtower_school.R | 4 + inst/doc/learningtower_school.Rmd | 4 + inst/doc/learningtower_school.html | 11 +-- inst/doc/learningtower_student.R | 4 + inst/doc/learningtower_student.Rmd | 6 + inst/doc/learningtower_student.html | 99 ++++++++++++++++---------------- man/countrycode.Rd | 2 tests/testthat/test-merge.R | 3 tests/testthat/test-student-col-types.R | 1 tests/testthat/test-test-load.R | 13 +++- vignettes/learningtower_school.Rmd | 4 + vignettes/learningtower_student.Rmd | 6 + 19 files changed, 161 insertions(+), 90 deletions(-)
Title: Species Distribution Modeling with H3 Grids
Description: Provides tools for species distribution modeling using H3
hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>).
Facilitates retrieval of species occurrence records, generation of H3 grids,
computation of landscape metrics, and preparation of spatial data for modern
species distribution models workflows. Designed for biodiversity and landscape ecology research.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between h3sdm versions 0.1.5 dated 2026-06-12 and 0.1.6 dated 2026-06-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 2 ++ NEWS.md | 19 +++++++++++++++++++ R/h3sdm_filter_range.R |only R/h3sdm_pa.R | 4 ++++ R/h3sdm_pres_from_sf.R |only man/h3sdm_filter_range.Rd |only man/h3sdm_pres_from_sf.Rd |only 9 files changed, 37 insertions(+), 8 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.2.3 dated 2026-04-06 and 2.2.4 dated 2026-06-15
DESCRIPTION | 8 MD5 | 76 - R/GeoCompositeLik2.R | 592 ++++++----- R/GeoCovariogram.r | 25 R/GeoFit.r | 49 R/GeoFit2.R | 2 R/GeoKrig.r | 281 ++--- R/GeoKrigloc.R | 530 +++++---- R/GeoLik.r | 2389 ++++++++++++++++++++++----------------------- R/GeoNeighIndex.R | 1323 +++++++++++++++--------- R/GeoNeighbSelect.R | 4 R/GeoScores.R | 196 ++- R/GeoVarestbootstrap.R | 328 +++--- R/GeoWls.r | 2 R/Utility_cov.R | 43 build/partial.rdb |binary data/anomalies.rda |binary data/madagascartemp.rda |binary data/rainNLD.rda |binary data/spanish_wind.rda |binary data/winds.coords.rda |binary data/winds.rda |binary man/GeoCovariogram.Rd | 2 man/GeoFit.Rd | 9 man/GeoFit2.Rd | 7 man/GeoNeighIndex.Rd | 137 +- man/GeoNeighbSelect.Rd | 3 man/GeoScatterplot.Rd | 10 man/GeoScores.Rd | 324 ++++-- man/GeoVariogram.Rd | 9 man/GeoWls.Rd | 3 man/StartParam.Rd | 2 man/WlsStart.Rd | 2 src/CompositeLikelihood2.c | 196 ++- src/CorrelationFunction.c | 393 +++---- src/Distributions.c | 573 ++++++---- src/GeoModels_init.c | 24 src/TB.c | 22 src/header.h | 2 39 files changed, 4374 insertions(+), 3192 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-26 0.2.1
2021-05-04 0.2.0
2021-01-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-16 0.3.4
2024-10-30 0.3.3
2022-10-10 0.3.1
2022-10-05 0.3.0
2022-03-21 0.2.0
2021-11-12 0.1.3
2021-05-04 0.1.2
2021-01-29 0.1.1
2020-12-18 0.1.0
Title: Compositional Data Analysis
Description: Methods for analysis of compositional data including robust
methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace
rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>),
count zeros (<doi:10.1177/1471082X14535524>),
methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>),
contingency (<doi:10.1080/03610926.2013.824980>)
and compositional tables (<doi:10.1111/sjos.12326>, <doi: [...truncated...]
Author: Matthias Templ [aut, cre] ,
Karel Hron [aut] ,
Peter Filzmoser [aut] ,
Kamila Facevicova [ctb],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb],
Dominika Miksova [ctb],
Bernhard Meindl [ctb],
Alessandra Menafoglio [ct [...truncated...]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.4.2 dated 2025-08-22 and 2.6.0 dated 2026-06-15
robCompositions-2.4.2/robCompositions/R/gm_backup.R |only robCompositions-2.4.2/robCompositions/R/impRZilr.R |only robCompositions-2.4.2/robCompositions/R/imputeBDLs.R |only robCompositions-2.4.2/robCompositions/man/impRZilr.Rd |only robCompositions-2.4.2/robCompositions/man/imputeBDLs.Rd |only robCompositions-2.4.2/robCompositions/tests/testthat/imp_test.R |only robCompositions-2.4.2/robCompositions/tests/testthat/importFood.R |only robCompositions-2.4.2/robCompositions/tests/testthat/rz.R |only robCompositions-2.4.2/robCompositions/tests/testthat/test_iris.r |only robCompositions-2.6.0/robCompositions/DESCRIPTION | 28 - robCompositions-2.6.0/robCompositions/MD5 | 196 +++++----- robCompositions-2.6.0/robCompositions/NAMESPACE | 22 - robCompositions-2.6.0/robCompositions/NEWS | 46 ++ robCompositions-2.6.0/robCompositions/R/cellNetCoDa.R |only robCompositions-2.6.0/robCompositions/R/cellPcaCoDa.R |only robCompositions-2.6.0/robCompositions/R/clustCoDa.R | 23 - robCompositions-2.6.0/robCompositions/R/contaminate_simplex.R |only robCompositions-2.6.0/robCompositions/R/daFisher.R | 2 robCompositions-2.6.0/robCompositions/R/dataSets.R | 15 robCompositions-2.6.0/robCompositions/R/impAll.R | 8 robCompositions-2.6.0/robCompositions/R/impRZalr.R | 2 robCompositions-2.6.0/robCompositions/R/imputeBDL-deprecated.R |only robCompositions-2.6.0/robCompositions/R/imputeBDL.R |only robCompositions-2.6.0/robCompositions/R/imputeUDLs.R | 5 robCompositions-2.6.0/robCompositions/R/plot.cellNetCoDa.R |only robCompositions-2.6.0/robCompositions/R/plot.cellPcaCoDa.R |only robCompositions-2.6.0/robCompositions/R/plot.imp.R | 9 robCompositions-2.6.0/robCompositions/R/plot.pcaCoDa.R | 6 robCompositions-2.6.0/robCompositions/R/pls_pb.R | 5 robCompositions-2.6.0/robCompositions/R/spca_logrs.R | 3 robCompositions-2.6.0/robCompositions/R/utils.R | 26 - robCompositions-2.6.0/robCompositions/build/partial.rdb |binary robCompositions-2.6.0/robCompositions/build/vignette.rds |binary robCompositions-2.6.0/robCompositions/data/GDPsatis.rda |binary robCompositions-2.6.0/robCompositions/data/ageCatWorld.rda |binary robCompositions-2.6.0/robCompositions/data/alcohol.rda |binary robCompositions-2.6.0/robCompositions/data/alcoholreg.rda |binary robCompositions-2.6.0/robCompositions/data/arcticLake.rda |binary robCompositions-2.6.0/robCompositions/data/cancer.rda |binary robCompositions-2.6.0/robCompositions/data/cancerMN.rda |binary robCompositions-2.6.0/robCompositions/data/chorizonDL.rda |binary robCompositions-2.6.0/robCompositions/data/coffee.rda |binary robCompositions-2.6.0/robCompositions/data/economy.rda |binary robCompositions-2.6.0/robCompositions/data/educFM.rda |binary robCompositions-2.6.0/robCompositions/data/efsa.rda |binary robCompositions-2.6.0/robCompositions/data/election.rda |binary robCompositions-2.6.0/robCompositions/data/electionATbp.rda |binary robCompositions-2.6.0/robCompositions/data/employment.rda |binary robCompositions-2.6.0/robCompositions/data/employment2.rda |binary robCompositions-2.6.0/robCompositions/data/employment_df.rda |binary robCompositions-2.6.0/robCompositions/data/expenditures.rda |binary robCompositions-2.6.0/robCompositions/data/expendituresEU.rda |binary robCompositions-2.6.0/robCompositions/data/foodbalance.rda |binary robCompositions-2.6.0/robCompositions/data/gemas.rda |binary robCompositions-2.6.0/robCompositions/data/gjovik.rda |binary robCompositions-2.6.0/robCompositions/data/govexp.rda |binary robCompositions-2.6.0/robCompositions/data/haplogroups.rda |binary robCompositions-2.6.0/robCompositions/data/honey.rda |binary robCompositions-2.6.0/robCompositions/data/instw.rda |binary robCompositions-2.6.0/robCompositions/data/isic32.rda |binary robCompositions-2.6.0/robCompositions/data/laborForce.rda |binary robCompositions-2.6.0/robCompositions/data/landcover.rda |binary robCompositions-2.6.0/robCompositions/data/lifeExpGdp.rda |binary robCompositions-2.6.0/robCompositions/data/machineOperators.rda |binary robCompositions-2.6.0/robCompositions/data/manu_abs.rda |binary robCompositions-2.6.0/robCompositions/data/mcad.rda |binary robCompositions-2.6.0/robCompositions/data/mortality.rda |binary robCompositions-2.6.0/robCompositions/data/mortality_tab.rda |binary robCompositions-2.6.0/robCompositions/data/nutrients.rda |binary robCompositions-2.6.0/robCompositions/data/nutrients_branded.rda |binary robCompositions-2.6.0/robCompositions/data/payments.rda |binary robCompositions-2.6.0/robCompositions/data/phd.rda |binary robCompositions-2.6.0/robCompositions/data/phd_totals.rda |binary robCompositions-2.6.0/robCompositions/data/precipitation.rda |binary robCompositions-2.6.0/robCompositions/data/production.rda |binary robCompositions-2.6.0/robCompositions/data/rcodes.rda |binary robCompositions-2.6.0/robCompositions/data/saffron.rda |binary robCompositions-2.6.0/robCompositions/data/skyeLavas.rda |binary robCompositions-2.6.0/robCompositions/data/socExp.rda |binary robCompositions-2.6.0/robCompositions/data/teachingStuff.rda |binary robCompositions-2.6.0/robCompositions/data/trondelagC.rda |binary robCompositions-2.6.0/robCompositions/data/trondelagO.rda |binary robCompositions-2.6.0/robCompositions/data/unemployed.rda |binary robCompositions-2.6.0/robCompositions/inst/doc/imputation.Rnw | 6 robCompositions-2.6.0/robCompositions/inst/doc/imputation.pdf |binary robCompositions-2.6.0/robCompositions/inst/doc/robCompositions-overview.Rnw | 8 robCompositions-2.6.0/robCompositions/inst/doc/robCompositions-overview.pdf |binary robCompositions-2.6.0/robCompositions/man/bootnComp.Rd | 2 robCompositions-2.6.0/robCompositions/man/cellNetCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/cellPcaCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/contaminate_simplex.Rd |only robCompositions-2.6.0/robCompositions/man/govexp.Rd | 5 robCompositions-2.6.0/robCompositions/man/impAll.Rd | 4 robCompositions-2.6.0/robCompositions/man/impRZalr.Rd | 2 robCompositions-2.6.0/robCompositions/man/imputeBDL.Rd |only robCompositions-2.6.0/robCompositions/man/plot.cellNetCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/plot.cellPcaCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/print.cellNetCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/print.cellPcaCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/robCompositions-package.Rd | 7 robCompositions-2.6.0/robCompositions/man/spca_logrs.Rd | 3 robCompositions-2.6.0/robCompositions/man/summary.cellNetCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/summary.cellPcaCoDa.Rd |only robCompositions-2.6.0/robCompositions/man/teachingStuff.Rd | 5 robCompositions-2.6.0/robCompositions/man/unemployed.Rd | 5 robCompositions-2.6.0/robCompositions/src/sandia_rules.h | 2 robCompositions-2.6.0/robCompositions/tests/testthat/test_cellNetCoDa.R |only robCompositions-2.6.0/robCompositions/tests/testthat/test_cellPcaCoDa.R |only robCompositions-2.6.0/robCompositions/tests/testthat/test_imputation.R |only robCompositions-2.6.0/robCompositions/tests/testthat/test_propagation.R |only robCompositions-2.6.0/robCompositions/vignettes/imputation.Rnw | 6 robCompositions-2.6.0/robCompositions/vignettes/refPCS.bib | 6 robCompositions-2.6.0/robCompositions/vignettes/refPCSn.bib | 5 robCompositions-2.6.0/robCompositions/vignettes/robCompositions-overview.Rnw | 8 114 files changed, 258 insertions(+), 212 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide Type II and Type III SS. However, the results of nested and complex designs are often different from those of 'SAS'. Different results do not necessarily mean incorrectness. However, many want the same results as 'SAS'. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.8 dated 2026-03-08 and 1.0.0 dated 2026-06-15
sasLM-0.10.8/sasLM/inst/doc/Report-Different-Simplest2603082306.pdf |only sasLM-0.10.8/sasLM/inst/doc/Report-NOT-OKs2603082307.pdf |only sasLM-0.10.8/sasLM/inst/doc/Validation-Report-GLM-2603082308.pdf |only sasLM-1.0.0/sasLM/DESCRIPTION | 10 sasLM-1.0.0/sasLM/MD5 | 240 +++++----- sasLM-1.0.0/sasLM/R/BasicUtil.R | 34 - sasLM-1.0.0/sasLM/R/Diffogram.R | 11 sasLM-1.0.0/sasLM/R/EMS.R | 3 sasLM-1.0.0/sasLM/R/GLM.R | 26 - sasLM-1.0.0/sasLM/R/LSM.R | 6 sasLM-1.0.0/sasLM/R/ORinv.R | 6 sasLM-1.0.0/sasLM/R/ORmn.R | 151 +++--- sasLM-1.0.0/sasLM/R/PDIFF.R | 9 sasLM-1.0.0/sasLM/R/RDmn.R | 14 sasLM-1.0.0/sasLM/R/REG.R | 28 - sasLM-1.0.0/sasLM/R/RRmn.R | 7 sasLM-1.0.0/sasLM/R/RanTest.R | 5 sasLM-1.0.0/sasLM/R/T3MS.R | 3 sasLM-1.0.0/sasLM/R/T3test.R | 4 sasLM-1.0.0/sasLM/R/UNIV.R | 6 sasLM-1.0.0/sasLM/R/e2.R | 16 sasLM-1.0.0/sasLM/R/e3.R | 17 sasLM-1.0.0/sasLM/R/lr0.R | 2 sasLM-1.0.0/sasLM/inst/NEWS.Rd | 19 sasLM-1.0.0/sasLM/inst/doc/Report-Different-Simplest2606121557.pdf |only sasLM-1.0.0/sasLM/inst/doc/Report-NOT-OKs2606121557.pdf |only sasLM-1.0.0/sasLM/inst/doc/Validation-Report-GLM-2606121701.pdf |only sasLM-1.0.0/sasLM/inst/doc/bioequivalence-with-sasLM.R |only sasLM-1.0.0/sasLM/inst/doc/bioequivalence-with-sasLM.Rmd |only sasLM-1.0.0/sasLM/inst/doc/bioequivalence-with-sasLM.html |only sasLM-1.0.0/sasLM/inst/doc/index.html |only sasLM-1.0.0/sasLM/inst/doc/sasLM-for-SAS-users.R |only sasLM-1.0.0/sasLM/inst/doc/sasLM-for-SAS-users.Rmd |only sasLM-1.0.0/sasLM/inst/doc/sasLM-for-SAS-users.html |only sasLM-1.0.0/sasLM/inst/doc/stratified-2x2-tables.R |only sasLM-1.0.0/sasLM/inst/doc/stratified-2x2-tables.Rmd |only sasLM-1.0.0/sasLM/inst/doc/stratified-2x2-tables.html |only sasLM-1.0.0/sasLM/man/BEdata.Rd | 6 sasLM-1.0.0/sasLM/man/BY.Rd | 8 sasLM-1.0.0/sasLM/man/CIest.Rd | 14 sasLM-1.0.0/sasLM/man/CONTR.Rd | 12 sasLM-1.0.0/sasLM/man/Coll.Rd | 6 sasLM-1.0.0/sasLM/man/Cor.test.Rd | 14 sasLM-1.0.0/sasLM/man/CumAlpha.Rd | 14 sasLM-1.0.0/sasLM/man/Diffogram.Rd | 6 sasLM-1.0.0/sasLM/man/DoEdata.Rd | 2 sasLM-1.0.0/sasLM/man/Drift.Rd | 6 sasLM-1.0.0/sasLM/man/EMS.Rd | 4 sasLM-1.0.0/sasLM/man/ESTM.Rd | 14 sasLM-1.0.0/sasLM/man/ExitP.Rd | 8 sasLM-1.0.0/sasLM/man/G2SWEEP.Rd | 14 sasLM-1.0.0/sasLM/man/GLM.Rd | 25 - sasLM-1.0.0/sasLM/man/LCL.Rd | 4 sasLM-1.0.0/sasLM/man/LSM.Rd | 28 - sasLM-1.0.0/sasLM/man/Max.Rd | 4 sasLM-1.0.0/sasLM/man/Mean.Rd | 4 sasLM-1.0.0/sasLM/man/Median.Rd | 4 sasLM-1.0.0/sasLM/man/Min.Rd | 4 sasLM-1.0.0/sasLM/man/ModelMatrix.Rd | 8 sasLM-1.0.0/sasLM/man/N.Rd | 6 sasLM-1.0.0/sasLM/man/OBFBound.Rd | 16 sasLM-1.0.0/sasLM/man/OR.Rd | 16 sasLM-1.0.0/sasLM/man/ORcmh.Rd | 17 sasLM-1.0.0/sasLM/man/ORinv.Rd | 17 sasLM-1.0.0/sasLM/man/ORmn.Rd | 14 sasLM-1.0.0/sasLM/man/ORmn1.Rd | 12 sasLM-1.0.0/sasLM/man/PDIFF.Rd | 16 sasLM-1.0.0/sasLM/man/Pcor.test.Rd | 10 sasLM-1.0.0/sasLM/man/PocockBound.Rd | 12 sasLM-1.0.0/sasLM/man/QuartileRange.Rd | 8 sasLM-1.0.0/sasLM/man/RD.Rd | 10 sasLM-1.0.0/sasLM/man/RDinv.Rd | 17 sasLM-1.0.0/sasLM/man/RDmn.Rd | 10 sasLM-1.0.0/sasLM/man/RDmn1.Rd | 12 sasLM-1.0.0/sasLM/man/REG.Rd | 32 - sasLM-1.0.0/sasLM/man/RR.Rd | 10 sasLM-1.0.0/sasLM/man/RRinv.Rd | 17 sasLM-1.0.0/sasLM/man/RRmn.Rd | 10 sasLM-1.0.0/sasLM/man/RRmn1.Rd | 12 sasLM-1.0.0/sasLM/man/RanTest.Rd | 14 sasLM-1.0.0/sasLM/man/Range.Rd | 2 sasLM-1.0.0/sasLM/man/SLICE.Rd | 16 sasLM-1.0.0/sasLM/man/SS.Rd | 6 sasLM-1.0.0/sasLM/man/ScoreCI.Rd | 12 sasLM-1.0.0/sasLM/man/SkewnessSE.Rd | 2 sasLM-1.0.0/sasLM/man/T3MS.Rd | 6 sasLM-1.0.0/sasLM/man/T3test.Rd | 8 sasLM-1.0.0/sasLM/man/TTEST.Rd | 4 sasLM-1.0.0/sasLM/man/UCL.Rd | 4 sasLM-1.0.0/sasLM/man/UNIV.Rd | 23 sasLM-1.0.0/sasLM/man/WhiteTest.Rd | 6 sasLM-1.0.0/sasLM/man/af.Rd | 2 sasLM-1.0.0/sasLM/man/aov1.Rd | 18 sasLM-1.0.0/sasLM/man/aov2.Rd | 18 sasLM-1.0.0/sasLM/man/aov3.Rd | 18 sasLM-1.0.0/sasLM/man/aspirinCHD.Rd | 8 sasLM-1.0.0/sasLM/man/bk.Rd | 6 sasLM-1.0.0/sasLM/man/cSS.Rd | 16 sasLM-1.0.0/sasLM/man/corFisher.Rd | 6 sasLM-1.0.0/sasLM/man/e1.Rd | 10 sasLM-1.0.0/sasLM/man/e2.Rd | 10 sasLM-1.0.0/sasLM/man/e3.Rd | 10 sasLM-1.0.0/sasLM/man/est.Rd | 22 sasLM-1.0.0/sasLM/man/estmb.Rd | 8 sasLM-1.0.0/sasLM/man/g2inv.Rd | 6 sasLM-1.0.0/sasLM/man/geoCV.Rd | 2 sasLM-1.0.0/sasLM/man/geoMean.Rd | 2 sasLM-1.0.0/sasLM/man/is.cor.Rd | 6 sasLM-1.0.0/sasLM/man/lfit.Rd | 16 sasLM-1.0.0/sasLM/man/lr.Rd | 10 sasLM-1.0.0/sasLM/man/lr0.Rd | 8 sasLM-1.0.0/sasLM/man/mtest.Rd | 4 sasLM-1.0.0/sasLM/man/pB.Rd | 10 sasLM-1.0.0/sasLM/man/pD.Rd | 6 sasLM-1.0.0/sasLM/man/pResD.Rd | 6 sasLM-1.0.0/sasLM/man/regD.Rd | 8 sasLM-1.0.0/sasLM/man/sasLM-package.Rd | 4 sasLM-1.0.0/sasLM/man/satt.Rd | 10 sasLM-1.0.0/sasLM/man/seqBound.Rd | 18 sasLM-1.0.0/sasLM/man/seqCI.Rd | 10 sasLM-1.0.0/sasLM/man/tmtest.Rd | 8 sasLM-1.0.0/sasLM/man/trimmedMean.Rd | 4 sasLM-1.0.0/sasLM/man/tsum.Rd | 10 sasLM-1.0.0/sasLM/man/tsum0.Rd | 10 sasLM-1.0.0/sasLM/man/tsum1.Rd | 16 sasLM-1.0.0/sasLM/man/tsum2.Rd | 20 sasLM-1.0.0/sasLM/man/tsum3.Rd | 22 sasLM-1.0.0/sasLM/man/vtest.Rd | 8 sasLM-1.0.0/sasLM/man/ztest.Rd | 8 129 files changed, 811 insertions(+), 776 deletions(-)
Title: Visualization of 'exametrika' Output Using 'ggplot2'
Description: Provides 'ggplot2'-based visualization functions for output objects
from the 'exametrika' package, which implements test data engineering methods
described in Shojima (2022, ISBN:978-981-16-9547-1). Supports a wide range of
psychometric models including Item Response Theory, Latent Class Analysis,
Latent Rank Analysis, Biclustering (binary, ordinal, and nominal),
Bayesian Network Models, and related network models. All plot functions
return 'ggplot2' objects that can be further customized by the user.
Author: Koji Kosugi [aut, cre] ,
Daichi Kamimura [aut]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between ggExametrika versions 1.1.0 dated 2026-04-17 and 1.1.1 dated 2026-06-15
DESCRIPTION | 8 +- MD5 | 34 +++++------ NAMESPACE | 1 NEWS.md | 39 +++++++++++++ R/Biclustering.R | 10 +-- R/GRM.R | 3 - R/IRPtoCMPRMP.R | 3 - R/LRAordinal.R | 9 +-- R/PolyBiclustering.R | 4 - R/ScoreRank.R | 3 - R/arraytoLDPSR.R | 90 +++++++++++++++++++++---------- R/plotDistractor_gg.R | 3 - R/plotFCBR_gg.R | 3 - R/plotLDPSR_gg.R | 4 - man/plotArray_gg.Rd | 29 ++++++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-Biclustering-plots.R | 55 ++++++++++++++++++ tests/testthat/test-plotArray_gg.R | 8 +- 18 files changed, 217 insertions(+), 89 deletions(-)
Title: Representation of DET Curve with Confidence Intervals
Description: Builds both ROC (Receiver Operating Characteristic) and DET (Detection Error Tradeoff) curves from a set of predictors that are the
results of a binary classification system. The curves give a general view of classifier performance
and are useful for comparing different systems.
Author: Garcia-Rodenas, Alvaro [aut],
Franco, Manuel [aut],
Vivo, Juana-Maria [aut],
Fernandez-Breis, Jesualdo T. [aut],
Font, Roberto [aut],
Curran, James [cre]
Maintainer: "Curran, James" <j.curran@auckland.ac.nz>
Diff between DET versions 3.0.2 dated 2025-08-28 and 3.0.3 dated 2026-06-15
DET-3.0.2/DET/data/ovarianCancer.RData |only DET-3.0.2/DET/data/speaker.RData |only DET-3.0.3/DET/DESCRIPTION | 16 DET-3.0.3/DET/MD5 | 55 - DET-3.0.3/DET/NAMESPACE | 3 DET-3.0.3/DET/NEWS.md | 44 - DET-3.0.3/DET/R/detc.R | 424 +++++----- DET-3.0.3/DET/R/internalFunctions.R | 299 +++---- DET-3.0.3/DET/R/measures.R | 105 +- DET-3.0.3/DET/R/ovarianCancer-data.R | 4 DET-3.0.3/DET/R/plot.R | 1061 ++++++++++++++------------- DET-3.0.3/DET/R/show.R | 72 + DET-3.0.3/DET/R/speaker-data.R | 12 DET-3.0.3/DET/README.md | 113 ++ DET-3.0.3/DET/build/partial.rdb |binary DET-3.0.3/DET/man/EER.Rd | 6 DET-3.0.3/DET/man/detc.Rd | 35 DET-3.0.3/DET/man/detc.ci.Rd | 21 DET-3.0.3/DET/man/minDcf.Rd | 14 DET-3.0.3/DET/man/ovarianCancer.Rd | 4 DET-3.0.3/DET/man/plot.DET.Rd | 2 DET-3.0.3/DET/man/plot.DETs.Rd | 18 DET-3.0.3/DET/man/plotROC.Rd | 4 DET-3.0.3/DET/man/plotROCs.Rd | 18 DET-3.0.3/DET/man/pointsEER.Rd | 4 DET-3.0.3/DET/man/show-DETs-method.Rd |only DET-3.0.3/DET/man/speaker.Rd | 10 DET-3.0.3/DET/tests/testthat.R |only DET-3.0.3/DET/tests/testthat/test-detc.R | 16 DET-3.0.3/DET/tests/testthat/test-measures.R |only DET-3.0.3/DET/tests/testthat/test-plots.R |only DET-3.0.3/DET/tests/testthat/test-show.R |only 32 files changed, 1282 insertions(+), 1078 deletions(-)
Title: Making "Deduplicated" Functions
Description: Contains one main function deduped() which speeds up slow,
vectorized functions by only performing computations on the unique values
of the input and expanding the results at the end.
Author: Or Gadish [aut, cre, cph]
Maintainer: Or Gadish <orgadish@gmail.com>
Diff between deduped versions 0.4.0 dated 2026-04-02 and 0.5.0 dated 2026-06-15
deduped-0.4.0/deduped/R/deduped_map.R |only deduped-0.4.0/deduped/man/deduped_map.Rd |only deduped-0.4.0/deduped/tests/testthat/test-deduped_map.R |only deduped-0.5.0/deduped/DESCRIPTION | 10 - deduped-0.5.0/deduped/MD5 | 26 +- deduped-0.5.0/deduped/NAMESPACE | 1 deduped-0.5.0/deduped/NEWS.md | 23 ++ deduped-0.5.0/deduped/R/deduped.R | 99 +++++++++-- deduped-0.5.0/deduped/R/with_deduped.R | 59 ++++-- deduped-0.5.0/deduped/R/zzz.R |only deduped-0.5.0/deduped/README.md | 58 +++++- deduped-0.5.0/deduped/inst/WORDLIST | 3 deduped-0.5.0/deduped/man/deduped.Rd | 16 + deduped-0.5.0/deduped/man/with_deduped.Rd | 134 ++++++++------- deduped-0.5.0/deduped/tests/testthat/test-deduped.R | 134 ++++++++++++--- deduped-0.5.0/deduped/tests/testthat/test-with_deduped.R | 46 ++++- 16 files changed, 469 insertions(+), 140 deletions(-)
Title: Visualizing Decomposition of Differences in Rate Metrics
Description: Provides tools for decomposing differences in rate metrics
between two groups into contributions from individual subgroups and
visualizing them as a "Theseus Plot". Inspired by the story of the
Ship of Theseus, the method replaces subgroup data from one group with
that of another step by step, recalculating the overall metric at each
stage to quantify subgroup contributions. A Theseus Plot combines the
stepwise progression of a waterfall plot with the comparative bars of
a bar chart, offering an intuitive way to understand subgroup-level
effects.
Author: Koji Makiyama [aut, cre, cph],
Kazuyuki Sano [ctb, wdc],
Shinichi Takayanagi [med],
Daisuke Ichikawa [exp],
LY Corporation Analytics Solution Enhancement Team [spn]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Diff between TheseusPlot versions 0.2.0 dated 2026-04-09 and 0.3.0 dated 2026-06-14
TheseusPlot-0.2.0/TheseusPlot/man/figures/README-prot_carrier_n-1.png |only TheseusPlot-0.2.0/TheseusPlot/tests/testthat/test-test-table-missing-and-asymmetric-categories.R |only TheseusPlot-0.3.0/TheseusPlot/DESCRIPTION | 10 TheseusPlot-0.3.0/TheseusPlot/MD5 | 33 - TheseusPlot-0.3.0/TheseusPlot/NEWS.md | 20 TheseusPlot-0.3.0/TheseusPlot/R/create_ship.R | 22 TheseusPlot-0.3.0/TheseusPlot/R/ship_of_theseus.R | 284 +++++----- TheseusPlot-0.3.0/TheseusPlot/README.md | 138 ++-- TheseusPlot-0.3.0/TheseusPlot/man/ShipOfTheseus.Rd | 267 ++++----- TheseusPlot-0.3.0/TheseusPlot/man/create_ship.Rd | 20 TheseusPlot-0.3.0/TheseusPlot/man/figures/README-factor_column-1.png |binary TheseusPlot-0.3.0/TheseusPlot/man/figures/README-no_factor_column-1.png |only TheseusPlot-0.3.0/TheseusPlot/man/figures/README-overview-1.png |binary TheseusPlot-0.3.0/TheseusPlot/man/figures/README-plot_carrier-1.png |binary TheseusPlot-0.3.0/TheseusPlot/man/figures/README-plot_carrier_n-1.png |only TheseusPlot-0.3.0/TheseusPlot/man/figures/README-plot_dep_delay-1.png |binary TheseusPlot-0.3.0/TheseusPlot/man/figures/README-plot_dep_delay_n-1.png |binary TheseusPlot-0.3.0/TheseusPlot/man/figures/README-plot_origin-1.png |binary TheseusPlot-0.3.0/TheseusPlot/tests/testthat/test-factor-order.R |only TheseusPlot-0.3.0/TheseusPlot/tests/testthat/test-plot-waterfalls-compatibility.R |only TheseusPlot-0.3.0/TheseusPlot/tests/testthat/test-table-missing-and-asymmetric-categories.R |only 21 files changed, 423 insertions(+), 371 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.13.1 dated 2026-05-17 and 1.14.0 dated 2026-06-14
DESCRIPTION | 6 - MD5 | 43 +++---- NEWS.md | 103 ++++++++++++++++++ R/00_exametrikaPlot.R | 59 ++++++---- R/00_plot_biclustering.R | 77 +++++++++++-- R/00_plot_irt.R | 112 +++++++++++--------- R/00_plot_lca_lra.R | 222 ++++++++++++++++++++++++---------------- R/00_plot_network.R | 42 ++++--- R/00_plot_poly_biclustering.R | 166 ++++++++++++++++++----------- R/02_TestItemFunctions.R | 2 R/04C_ParameterEstimation.R | 2 R/07_IRM.R | 4 R/09_LDLRA.R | 2 R/10_LDB.R | 2 R/22_GlassoUnit.R | 57 +++++++++- inst/doc/biclustering.html | 6 - inst/doc/irt.html | 24 ++-- inst/doc/network-models.html | 4 man/plot.exametrika.Rd | 9 + tests/testthat/Rplots.pdf |binary tests/testthat/test-glasso.R | 56 ++++++++++ tests/testthat/test-irm.R | 27 ++++ tests/testthat/test-plot-dots.R |only 23 files changed, 726 insertions(+), 299 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced "picture"), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Diogo Bezerra [aut],
Marcos Wasilew [aut],
Carlos Amorin [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 1.1.0 dated 2026-04-07 and 1.1.1 dated 2026-06-14
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS.md | 13 +++++ R/pikchrWrappers.R | 12 ++--- build/vignette.rds |binary inst/doc/Examples.html | 36 +++++++-------- inst/doc/userman.html | 104 +++++++++++++++++++++++----------------------- man/figures/logo.png |binary man/figures/pikchrHex.svg | 59 ++++++++++++-------------- man/pikchr.Rd | 10 ++-- src/pikchr.c | 17 ++++--- 11 files changed, 147 insertions(+), 132 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and other studies from <https://www.iea.nl/>.
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.4.0 dated 2026-03-11 and 1.4.2 dated 2026-06-14
DESCRIPTION | 25 +--- MD5 | 71 ++++++------ NEWS.md | 8 + R/ILSAdownload.R | 43 +++++-- R/ILSAmerge.R | 32 +++-- R/ILSAready.R | 62 ++++++---- R/ILSArename.R | 32 +++-- R/addSchools.R | 32 +++-- R/availableILSA.R | 43 ++++--- R/checkavailable.R |only R/combineStudents.R | 27 +++- R/justload.R | 29 +++- R/sysdata.rda |binary README.md | 10 - build/vignette.rds |binary inst/doc/Download.R | 14 +- inst/doc/Download.html | 50 ++++---- inst/doc/IdentifyILSAfiles.html | 13 +- inst/doc/Load.R | 33 +++++ inst/doc/Load.Rmd | 52 ++++++++ inst/doc/Load.html | 211 +++++++++++++++++++++++++++--------- inst/doc/Merge.R | 6 - inst/doc/Merge.html | 171 ++++++++++++++--------------- inst/doc/Onestep.html | 121 ++++++++++---------- inst/doc/Rename.html | 25 ++-- inst/extdata/ilsainfo/ILSAlinks.csv | 2 inst/extdata/ilsainfo/ILSApops.csv | 16 ++ man/ILSAdownload.Rd | 11 + man/ILSAmerge.Rd | 4 man/ILSAready.Rd | 6 - man/ILSArename.Rd | 4 man/availableILSA.Rd | 2 man/justload.Rd | 4 man/readILSA.Rd | 2 man/untibble.Rd | 2 man/whichcol.Rd | 26 +++- vignettes/Load.Rmd | 52 ++++++++ 37 files changed, 816 insertions(+), 425 deletions(-)
Title: Dynamic Shrinkage Process and Change Point Detection
Description: Provides efficient Markov chain Monte Carlo (MCMC) algorithms for
dynamic shrinkage processes, which extend global-local shrinkage priors to
the time series setting by allowing shrinkage to depend on its own past.
These priors yield locally adaptive estimates, useful for time series and
regression functions with irregular features. The package includes full MCMC
implementations for trend filtering using dynamic shrinkage on signal differences,
producing locally constant or linear fits with adaptive credible bands.
Also included are models with static shrinkage and normal-inverse-Gamma priors for comparison.
Additional tools cover dynamic regression with time-varying coefficients and
B-spline models with shrinkage on basis differences, allowing for flexible
curve-fitting with unequally spaced data. Some support for heteroscedastic errors,
outlier detection, and change point estimation.
Methods in this package are described in Kowal et al. (2019) <doi:10.1111/rssb.12325>,
Wu et al. [...truncated...]
Author: Daniel R. Kowal [aut, cph],
Haoxuan Wu [aut],
Toryn Schafer [aut, cre] ,
Jason B. Cho [aut],
David S. Matteson [aut]
Maintainer: Toryn Schafer <toryn27@gmail.com>
Diff between dsp versions 1.4.0 dated 2026-05-12 and 1.5.0 dated 2026-06-14
DESCRIPTION | 6 ++-- MD5 | 40 ++++++++++++++++----------------- NEWS.md | 8 ++++++ R/ASV.R | 5 ++-- R/abco.R | 63 ++++++++++++++++++++++++++++++++++++++-------------- R/dsp_model.R | 27 +++++++++++++--------- R/mcmc_samplers.R | 48 ++++++++++++++++++--------------------- R/nb_btf.R | 12 +++++++-- R/plotmethods.R | 4 +-- R/predict.R | 6 ++-- R/print.R | 4 +-- man/abco.Rd | 12 +++++++-- man/btf.Rd | 5 +--- man/btf0.Rd | 5 +--- man/btf_bspline.Rd | 2 - man/btf_bspline0.Rd | 2 - man/btf_nb.Rd | 2 - man/btf_reg.Rd | 5 +--- man/btf_sparse.Rd | 5 +--- man/dsp_fit.Rd | 5 +--- man/fit_ASV.Rd | 2 - 21 files changed, 158 insertions(+), 110 deletions(-)
Title: Extracts Risk Neutral Densities of Prices, Money Market Rates
and Government Bond Yields from Interest Rates Futures Options
Prices
Description: Provides with parametric Risk Neutral Densities (RNDs) and cumulative densities of futures prices on fixed-income products. It relies on options on Short Term Interest Rate futures or options on government bond futures. It models the futures price as a mixture of lognormal densities. It also provides with the RNDs and cumulative densities of the money market rate or the government bond yield inferred from the futures price, using the RND of the futures price. It eventually provides with the probability attached to each bond in the delivery basket of a government bond futures to be the cheapest at maturity, using the RND of the bond futures price. The package leverages on the works of Melick, W. R. and Thomas, C. P. (1997) <doi:10.2307/2331318> and B. Bahra (1998) <doi:10.2139/ssrn.77429>.
Author: William Arrata [aut, cre]
Maintainer: William Arrata <william.arrata@gmail.com>
Diff between yrnd versions 0.1.3 dated 2026-05-15 and 0.1.4 dated 2026-06-14
DESCRIPTION | 8 MD5 | 46 NAMESPACE | 2 R/bond_future_charac_bbg.R | 29 R/bond_future_price.R | 292 R/ctd_bond_yield.R | 402 R/deliv_bonds_charac_bbg.R |only R/globals.R | 3 R/option_prices_bbg.R | 4 R/proba_ctd.R |only R/stir_future_charac_bbg.R | 2 R/stir_future_price.R | 286 R/stir_rate.R | 341 inst/doc/yrnd_functions.R | 33 inst/doc/yrnd_functions.Rmd | 42 inst/doc/yrnd_functions.html |132029 +++++++++++++++++++++++++----------------- man/bond_future_charac_bbg.Rd | 2 man/bond_future_price.Rd | 4 man/ctd_bond_yield.Rd | 14 man/deliv_bonds_charac_bbg.Rd |only man/option_prices_bbg.Rd | 4 man/proba_ctd.Rd |only man/stir_future_charac_bbg.Rd | 2 man/stir_future_price.Rd | 2 man/stir_rate.Rd | 2 vignettes/yrnd_functions.Rmd | 42 26 files changed, 80093 insertions(+), 53498 deletions(-)
Title: Easy, Fast, and Pretty Specification Curve Analysis
Description: Making specification curve analysis easy, fast, and pretty. It
improves upon existing offerings with additional features and 'tidyverse'
integration. Users can easily visualize and evaluate how their models behave
under different specifications with a high degree of customization. For a
description and applications of specification curve analysis see Simonsohn,
Simmons, and Nelson (2020) <doi:10.1038/s41562-020-0912-z>.
Author: Zayne Sember [aut, cre, cph]
Maintainer: Zayne Sember <zayne@mit.edu>
Diff between speccurvieR versions 0.4.2 dated 2024-10-09 and 0.5.0 dated 2026-06-14
DESCRIPTION | 16 LICENSE | 4 MD5 | 81 NAMESPACE | 86 - NEWS.md | 67 R/data.R | 148 - R/functions.R | 2567 +++++++++++++----------------- R/globals.R | 10 R/helpers.R | 744 ++++---- R/speccurvieR-package.R | 42 build/partial.rdb |binary man/bottles.Rd | 172 +- man/controlExtractor.Rd | 62 man/duplicate_remover.Rd | 46 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.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-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/formula_builder.Rd | 64 man/paste_factory.Rd | 50 man/plotAIC.Rd | 92 - man/plotControlDistributions.Rd | 92 - man/plotCurve.Rd | 134 - man/plotDeviance.Rd | 94 - man/plotR2Adj.Rd | 98 - man/plotRMSE.Rd | 84 man/plotVars.Rd | 88 - man/sca.Rd | 184 +- man/scp.Rd | 48 man/se_boot.Rd | 100 - man/se_compare.Rd | 250 +- man/speccurvieR-package.Rd | 46 man/unAsIs.Rd | 42 tests |only 40 files changed, 2670 insertions(+), 2841 deletions(-)
Title: Resolution, Conversion, Linking and Metadata for Scholarly
Identifiers
Description: Enables querying of scholarly identifier services to
verify identifier existence, convert identifiers across systems,
retrieve bibliographic metadata, and discover linked identifiers.
Supports identifier types including DOI, PMID, PMCID, arXiv,
ORCID, OpenAlex, ROR, UniProt, and selected NCBI accessions
(GEO, BioProject, RefSeq, SRA, and genome assembly).
Author: Thomas Rauter [aut, cre, fnd]
Maintainer: Thomas Rauter <rauterthomas0@gmail.com>
Diff between scholidonline versions 0.1.1 dated 2026-05-14 and 0.2.0 dated 2026-06-14
scholidonline-0.1.1/scholidonline/R/provider_epmc_helpers.R |only scholidonline-0.1.1/scholidonline/R/providers_ncbi_helpers.R |only scholidonline-0.2.0/scholidonline/DESCRIPTION | 13 scholidonline-0.2.0/scholidonline/MD5 | 125 +- scholidonline-0.2.0/scholidonline/NEWS.md | 16 scholidonline-0.2.0/scholidonline/R/dispatcher_helpers.R |only scholidonline-0.2.0/scholidonline/R/dispatchers_convert.R | 598 ++++------ scholidonline-0.2.0/scholidonline/R/dispatchers_exists.R | 488 ++++++-- scholidonline-0.2.0/scholidonline/R/dispatchers_link.R | 167 +- scholidonline-0.2.0/scholidonline/R/dispatchers_metadata.R | 448 ++++++- scholidonline-0.2.0/scholidonline/R/engine_binary.R | 102 - scholidonline-0.2.0/scholidonline/R/engine_helpers.R | 84 + scholidonline-0.2.0/scholidonline/R/engine_unary.R | 131 -- scholidonline-0.2.0/scholidonline/R/http_helpers.R |only scholidonline-0.2.0/scholidonline/R/id_convert.R | 72 - scholidonline-0.2.0/scholidonline/R/id_exists.R | 55 scholidonline-0.2.0/scholidonline/R/id_links.R | 74 - scholidonline-0.2.0/scholidonline/R/id_metadata.R | 85 - scholidonline-0.2.0/scholidonline/R/input_validation.R | 135 +- scholidonline-0.2.0/scholidonline/R/provider_arxiv_helpers.R | 163 -- scholidonline-0.2.0/scholidonline/R/provider_ncbi_accession_helpers.R |only scholidonline-0.2.0/scholidonline/R/provider_ncbi_accession_types_helpers.R |only scholidonline-0.2.0/scholidonline/R/provider_ncbi_geo_helpers.R |only scholidonline-0.2.0/scholidonline/R/provider_openalex_helpers.R |only scholidonline-0.2.0/scholidonline/R/provider_ror_helpers.R |only scholidonline-0.2.0/scholidonline/R/provider_uniprot_helpers.R |only scholidonline-0.2.0/scholidonline/R/providers_arxiv.R | 244 ---- scholidonline-0.2.0/scholidonline/R/providers_crossref.R | 117 - scholidonline-0.2.0/scholidonline/R/providers_doi.R | 87 - scholidonline-0.2.0/scholidonline/R/providers_epmc.R | 305 +---- scholidonline-0.2.0/scholidonline/R/providers_ncbi.R | 528 ++------ scholidonline-0.2.0/scholidonline/R/providers_ncbi_accessions.R |only scholidonline-0.2.0/scholidonline/R/providers_ncbi_geo.R |only scholidonline-0.2.0/scholidonline/R/providers_openalex.R |only scholidonline-0.2.0/scholidonline/R/providers_orcid.R | 129 -- scholidonline-0.2.0/scholidonline/R/providers_ror.R |only scholidonline-0.2.0/scholidonline/R/providers_uniprot.R |only scholidonline-0.2.0/scholidonline/R/rate_limit.R |only scholidonline-0.2.0/scholidonline/R/registry.R | 194 ++- scholidonline-0.2.0/scholidonline/README.md | 103 + scholidonline-0.2.0/scholidonline/inst/WORDLIST | 12 scholidonline-0.2.0/scholidonline/inst/doc/batching_and_throttling.R | 3 scholidonline-0.2.0/scholidonline/inst/doc/batching_and_throttling.Rmd | 23 scholidonline-0.2.0/scholidonline/inst/doc/batching_and_throttling.html | 55 scholidonline-0.2.0/scholidonline/inst/doc/get_started.R | 7 scholidonline-0.2.0/scholidonline/inst/doc/get_started.Rmd | 57 scholidonline-0.2.0/scholidonline/inst/doc/get_started.html | 415 +++++- scholidonline-0.2.0/scholidonline/inst/doc/online_resolution.Rmd | 18 scholidonline-0.2.0/scholidonline/inst/doc/online_resolution.html | 20 scholidonline-0.2.0/scholidonline/man/id_convert.Rd | 6 scholidonline-0.2.0/scholidonline/man/id_exists.Rd | 9 scholidonline-0.2.0/scholidonline/man/id_links.Rd | 10 scholidonline-0.2.0/scholidonline/man/id_metadata.Rd | 19 scholidonline-0.2.0/scholidonline/man/scholidonline_types.Rd | 6 scholidonline-0.2.0/scholidonline/tests/testthat/test-dispatchers_geo-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-dispatchers_ncbi_accessions-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-dispatchers_openalex-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-dispatchers_ror-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-dispatchers_uniprot-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-engine_binary-offline.R | 127 -- scholidonline-0.2.0/scholidonline/tests/testthat/test-engine_helpers-offline.R | 112 + scholidonline-0.2.0/scholidonline/tests/testthat/test-engine_unary-offline.R | 89 - scholidonline-0.2.0/scholidonline/tests/testthat/test-http_wrappers-offline.R | 25 scholidonline-0.2.0/scholidonline/tests/testthat/test-input_validation-offline.R | 46 scholidonline-0.2.0/scholidonline/tests/testthat/test-provider_arxiv_helpers-offline.R | 49 scholidonline-0.2.0/scholidonline/tests/testthat/test-provider_ncbi_accession_helpers-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-provider_ncbi_rate_limit-offline.R | 32 scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_arxiv-offline.R | 3 scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_ncbi_accessions-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_ncbi_geo-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_openalex-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_ror-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-providers_uniprot-offline.R |only scholidonline-0.2.0/scholidonline/tests/testthat/test-scholidonline_capabilities-offline.R | 5 scholidonline-0.2.0/scholidonline/vignettes/batching_and_throttling.Rmd | 23 scholidonline-0.2.0/scholidonline/vignettes/get_started.Rmd | 57 scholidonline-0.2.0/scholidonline/vignettes/online_resolution.Rmd | 18 77 files changed, 3031 insertions(+), 2678 deletions(-)
Title: Benchmarking Routine for R
Description: Benchmarking of arbitrary R code, inspired by similar functionality
in a Perl module, is implemented via a simple wrapper around system.time().
Given a specification of the benchmarking process (counts of replications,
evaluation environment) and an arbitrary number of expressions, the function
evaluates each of the expressions in the specified environment, replicating the
evaluation as many times as specified, and returning the results conveniently
wrapped into a data frame.
Author: Wacek Kusnierczyk [aut],
Dirk Eddelbuettel [aut, cre] ,
Berend Hasselman [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
This is a re-admission after prior archival of version 1.0.0 dated 2012-08-30
Diff between rbenchmark versions 1.0.0 dated 2012-08-30 and 1.0.1 dated 2026-06-14
rbenchmark-1.0.0/rbenchmark/man/benchmark-package.Rd |only rbenchmark-1.0.1/rbenchmark/ChangeLog | 32 ++- rbenchmark-1.0.1/rbenchmark/DESCRIPTION | 47 ++--- rbenchmark-1.0.1/rbenchmark/MD5 | 13 - rbenchmark-1.0.1/rbenchmark/R/benchmark.R | 86 ++++----- rbenchmark-1.0.1/rbenchmark/build |only rbenchmark-1.0.1/rbenchmark/demo/benchmark.R | 25 +- rbenchmark-1.0.1/rbenchmark/man/benchmark.Rd | 169 ++++++++++-------- rbenchmark-1.0.1/rbenchmark/man/rbenchmark-package.Rd |only 9 files changed, 211 insertions(+), 161 deletions(-)
Title: A Client for 'Evolution Cloud API'
Description: Provides an 'R' interface to the 'Evolution API'
<https://evoapicloud.com>, enabling sending and receiving 'WhatsApp'
messages directly from 'R'. Functions include sending text, media
(image/video/document), audio, stickers, geographic locations, contacts,
polls, interactive lists and button messages. Also includes number
verification and structured CLI logging for debugging.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between evolution versions 0.1.0 dated 2026-02-27 and 0.1.1 dated 2026-06-14
DESCRIPTION | 11 ++++--- LICENSE | 4 +- MD5 | 34 +++++++++++++---------- NEWS.md | 41 +++++++++++++++++++++++++++- R/evolution.R | 63 +++++++++++++++++++++++++++++++++++++------- R/zzz.R | 4 ++ README.md | 7 ++-- man/dot-normalize_number.Rd |only man/send_buttons.Rd | 4 ++ man/send_list.Rd | 4 ++ man/send_location.Rd | 4 ++ man/send_media.Rd | 4 ++ man/send_poll.Rd | 4 ++ man/send_sticker.Rd | 4 ++ man/send_text.Rd | 4 ++ man/send_whatsapp_audio.Rd | 4 ++ tests |only 17 files changed, 154 insertions(+), 42 deletions(-)
Title: Migrate Installed R Packages Between R Versions
Description: Detects all R installations on the current machine and migrates
installed R packages between them. Provides find_routes() to discover R
versions, manifest() to scan package libraries in a child R process, inventory()
to compare two libraries, and ship() to install packages into a target R
version using 'pak'. Includes a Shiny dashboard (open_hub()) for interactive
source-to-target migration.
Author: Lennon Li [aut, cre] ,
Claude Fable [ctb] ),
Claude Opus [ctb] ),
Claude Sonnet [ctb] ),
OpenAI Codex [ctb] )
Maintainer: Lennon Li <yeli@biostats.ai>
Diff between courieR versions 0.2.2 dated 2026-06-04 and 0.3.1 dated 2026-06-14
courieR-0.2.2/courieR/inst/app/modules/mod_receipt.R |only courieR-0.2.2/courieR/inst/app/modules/mod_update.R |only courieR-0.3.1/courieR/DESCRIPTION | 40 courieR-0.3.1/courieR/MD5 | 118 courieR-0.3.1/courieR/NAMESPACE | 43 courieR-0.3.1/courieR/NEWS.md | 217 courieR-0.3.1/courieR/R/app-imports.R |only courieR-0.3.1/courieR/R/copy_packages.R |only courieR-0.3.1/courieR/R/courieR-package.R | 28 courieR-0.3.1/courieR/R/dispatch.R | 100 courieR-0.3.1/courieR/R/estimate.R |only courieR-0.3.1/courieR/R/find_routes.R | 589 +- courieR-0.3.1/courieR/R/inspect_shipment.R | 108 courieR-0.3.1/courieR/R/inventory.R | 297 - courieR-0.3.1/courieR/R/manifest.R | 330 - courieR-0.3.1/courieR/R/migrate.R |only courieR-0.3.1/courieR/R/open_hub.R | 85 courieR-0.3.1/courieR/R/report_issue.R |only courieR-0.3.1/courieR/R/rig.R | 84 courieR-0.3.1/courieR/R/ship.R | 604 +- courieR-0.3.1/courieR/R/utils.R | 102 courieR-0.3.1/courieR/R/wrap.R | 74 courieR-0.3.1/courieR/README.md | 246 courieR-0.3.1/courieR/build/vignette.rds |binary courieR-0.3.1/courieR/inst/WORDLIST | 18 courieR-0.3.1/courieR/inst/app/global.R | 52 courieR-0.3.1/courieR/inst/app/modules/mod_depot_ship.R |only courieR-0.3.1/courieR/inst/app/modules/mod_error_reporter.R | 133 courieR-0.3.1/courieR/inst/app/modules/mod_migrate.R | 448 - courieR-0.3.1/courieR/inst/app/modules/mod_origin.R | 392 + courieR-0.3.1/courieR/inst/app/modules/mod_sync.R | 2445 +++++++-- courieR-0.3.1/courieR/inst/app/server.R | 178 courieR-0.3.1/courieR/inst/app/ui.R | 110 courieR-0.3.1/courieR/inst/app/www/styles.css | 2482 ++++++---- courieR-0.3.1/courieR/inst/doc/get-started.R | 73 courieR-0.3.1/courieR/inst/doc/get-started.Rmd | 698 +- courieR-0.3.1/courieR/inst/doc/get-started.html | 395 + courieR-0.3.1/courieR/inst/doc/testing.R |only courieR-0.3.1/courieR/inst/doc/testing.Rmd |only courieR-0.3.1/courieR/inst/doc/testing.html |only courieR-0.3.1/courieR/inst/report_template.Rmd | 32 courieR-0.3.1/courieR/man/copy_packages.Rd |only courieR-0.3.1/courieR/man/courieR-package.Rd | 57 courieR-0.3.1/courieR/man/dispatch.Rd | 84 courieR-0.3.1/courieR/man/figures |only courieR-0.3.1/courieR/man/find_routes.Rd | 166 courieR-0.3.1/courieR/man/find_target_lib.Rd |only courieR-0.3.1/courieR/man/inventory.Rd | 27 courieR-0.3.1/courieR/man/manifest.Rd | 24 courieR-0.3.1/courieR/man/migrate.Rd |only courieR-0.3.1/courieR/man/open_hub.Rd | 61 courieR-0.3.1/courieR/man/report_issue.Rd |only courieR-0.3.1/courieR/man/rig_install.Rd | 48 courieR-0.3.1/courieR/man/ship.Rd | 159 courieR-0.3.1/courieR/tests/testthat.R | 6 courieR-0.3.1/courieR/tests/testthat/DESCRIPTION | 6 courieR-0.3.1/courieR/tests/testthat/test-app-refresh.R |only courieR-0.3.1/courieR/tests/testthat/test-copy-packages.R |only courieR-0.3.1/courieR/tests/testthat/test-depot-ship-batches.R |only courieR-0.3.1/courieR/tests/testthat/test-e2e-ship.R |only courieR-0.3.1/courieR/tests/testthat/test-eligible-targets.R |only courieR-0.3.1/courieR/tests/testthat/test-estimate.R |only courieR-0.3.1/courieR/tests/testthat/test-find_routes.R | 110 courieR-0.3.1/courieR/tests/testthat/test-inventory.R | 210 courieR-0.3.1/courieR/tests/testthat/test-manifest.R | 91 courieR-0.3.1/courieR/tests/testthat/test-migrate.R |only courieR-0.3.1/courieR/tests/testthat/test-rig.R | 10 courieR-0.3.1/courieR/tests/testthat/test-ship.R | 483 + courieR-0.3.1/courieR/tests/testthat/test-wrap.R | 62 courieR-0.3.1/courieR/vignettes/figures |only courieR-0.3.1/courieR/vignettes/get-started.Rmd | 698 +- courieR-0.3.1/courieR/vignettes/testing.Rmd |only 72 files changed, 8490 insertions(+), 4333 deletions(-)
Title: Generate SVG Information Cards with Embedded Fonts and Badges
Description: Create self-contained SVG information cards with embedded 'Google
Fonts', shields-style badges, and custom logos. Cards are fully
portable SVG files ideal for dashboards, reports, and web applications.
Includes functions to export cards to PNG format and display them in
'R Markdown' and 'Quarto' documents.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between cardargus versions 0.2.3 dated 2026-06-14 and 0.2.4 dated 2026-06-14
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NEWS.md | 14 +++++++++++++- R/fonts.R | 28 ++++++++++++++++++++++++++-- man/font_cache_dir.Rd | 7 ++++++- man/running_under_check.Rd |only tests/testthat/test-fonts.R |only 7 files changed, 55 insertions(+), 12 deletions(-)
Title: A 'ggplot2' Extension to Make Normal Violin Plots
Description: Uses 'ggplot2' to create normally distributed violin plots
with specified means and standard deviations. This function can be
useful in showing hypothetically normal distributions and confidence
intervals.
Author: W. Joel Schneider [aut, cre]
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between ggnormalviolin versions 0.2.1 dated 2025-03-29 and 0.3.0 dated 2026-06-14
ggnormalviolin-0.2.1/ggnormalviolin/R/utils-pipe.R |only ggnormalviolin-0.2.1/ggnormalviolin/man/pipe.Rd |only ggnormalviolin-0.3.0/ggnormalviolin/DESCRIPTION | 13 ggnormalviolin-0.3.0/ggnormalviolin/MD5 | 30 - ggnormalviolin-0.3.0/ggnormalviolin/NAMESPACE | 3 ggnormalviolin-0.3.0/ggnormalviolin/NEWS.md | 7 ggnormalviolin-0.3.0/ggnormalviolin/R/main.R | 253 +++++----- ggnormalviolin-0.3.0/ggnormalviolin/build/vignette.rds |binary ggnormalviolin-0.3.0/ggnormalviolin/inst/WORDLIST | 2 ggnormalviolin-0.3.0/ggnormalviolin/inst/doc/ggnormalviolin.R | 52 +- ggnormalviolin-0.3.0/ggnormalviolin/inst/doc/ggnormalviolin.html | 147 ++--- ggnormalviolin-0.3.0/ggnormalviolin/inst/doc/ggnormalviolin.qmd | 58 +- ggnormalviolin-0.3.0/ggnormalviolin/man/GeomNormalViolin.Rd | 4 ggnormalviolin-0.3.0/ggnormalviolin/man/StatNormalViolin.Rd | 4 ggnormalviolin-0.3.0/ggnormalviolin/man/geom_normalviolin.Rd | 10 ggnormalviolin-0.3.0/ggnormalviolin/tests/testthat/test-main.R | 9 ggnormalviolin-0.3.0/ggnormalviolin/vignettes/ggnormalviolin.qmd | 58 +- 17 files changed, 378 insertions(+), 272 deletions(-)
More information about ggnormalviolin at CRAN
Permanent link
Title: Non-Negative Matrix Factorization with Kernel Covariates
Description: Performs Non-negative Matrix Factorization (NMF)
with Kernel Covariates. Given an observation matrix and kernel
covariates, it optimizes both a basis matrix and a parameter matrix.
Notably, if the kernel matrix is an identity matrix, the method
simplifies to standard NMF. Also provides NMF with Random Effects
(NMF-RE) via nmfre(), which estimates a mixed-effects model combining
covariate-driven scores with unit-specific random effects together
with wild bootstrap inference, and NMF-based Structural Equation
Modeling (NMF-SEM) via nmf.sem(), which fits a two-block input-output
model for blind source separation and path analysis.
References: Satoh (2025) <doi:10.48550/arXiv.2403.05359>;
Satoh (2025) <doi:10.48550/arXiv.2510.10375>;
Satoh (2025) <doi:10.48550/arXiv.2512.18250>;
Satoh (2026) <doi:10.48550/arXiv.2603.01468>;
Satoh (2026) <doi:10.1007/s42081-025-00314-0>.
Author: Kenichi Satoh [aut, cre]
Maintainer: Kenichi Satoh <kenichi-satoh@biwako.shiga-u.ac.jp>
Diff between nmfkc versions 0.7.3 dated 2026-05-13 and 0.8.2 dated 2026-06-14
DESCRIPTION | 11 MD5 | 94 + NAMESPACE | 21 NEWS.md | 388 ++++++ R/nmf.sem.R | 2 R/nmfae.R | 175 +- R/nmfae.signed.R | 148 +- R/nmfkc.R | 1863 ++++++++++++++++++++--------- R/nmfkc.ard.R |only R/nmfkc.bicv.R |only R/nmfkc.consensus.R |only R/nmfkc.net.R | 172 +- R/nmfkc.signed.R | 126 + R/nmfkc.signed.rff.R |only R/nmfre.R | 56 R/s3methods.R | 29 build/vignette.rds |binary inst/doc/network-community-with-nmfkc.R |only inst/doc/network-community-with-nmfkc.Rmd |only inst/doc/network-community-with-nmfkc.html |only inst/doc/nmf-re-with-nmfkc.html | 32 inst/doc/rank-selection-with-nmfkc.R |only inst/doc/rank-selection-with-nmfkc.Rmd |only inst/doc/rank-selection-with-nmfkc.html |only inst/doc/timeseries-with-nmfkc.html | 24 inst/doc/topic-modeling-with-nmfkc.Rmd | 2 inst/doc/topic-modeling-with-nmfkc.html | 188 +- man/nmf.cluster.criteria.Rd |only man/nmf.cluster.flow.Rd |only man/nmfae.Rd | 4 man/nmfae.rank.Rd |only man/nmfae.signed.Rd | 5 man/nmfae.signed.rank.Rd |only man/nmfkc.Rd | 52 man/nmfkc.ard.Rd |only man/nmfkc.bicv.Rd |only man/nmfkc.consensus.Rd |only man/nmfkc.criterion.Rd | 12 man/nmfkc.ecv.Rd | 120 + man/nmfkc.net.DOT.Rd | 10 man/nmfkc.net.rank.Rd |only man/nmfkc.rank.Rd | 157 +- man/nmfkc.signed.Rd | 4 man/nmfkc.signed.rank.Rd |only man/nmfkc.signed.rff.Rd |only man/nmfre.Rd | 16 man/plot.nmf.cluster.criteria.Rd |only man/plot.nmf.cluster.flow.Rd |only man/plot.nmf.rank.Rd |only man/plot.nmfkc.ard.Rd |only man/plot.nmfkc.consensus.Rd |only man/print.nmf.cluster.criteria.Rd |only man/print.nmf.cluster.flow.Rd |only man/print.nmf.rank.Rd |only man/print.nmfkc.ard.Rd |only man/print.nmfkc.consensus.Rd |only man/print.summary.nmf.sem.Rd |only man/summary.nmf.sem.Rd | 10 tests/testthat/test-nmf.cluster.criteria.R |only tests/testthat/test-nmf.cluster.flow.R |only tests/testthat/test-nmfkc.ard.R |only tests/testthat/test-nmfkc.bicv.R |only tests/testthat/test-nmfkc.consensus.R |only tests/testthat/test-nmfkc.net.R | 27 vignettes/network-community-with-nmfkc.Rmd |only vignettes/rank-selection-with-nmfkc.Rmd |only vignettes/topic-modeling-with-nmfkc.Rmd | 2 67 files changed, 2588 insertions(+), 1162 deletions(-)
Title: Convolution-Closed Models for Count Time Series
Description: Useful tools for fitting, validating, and forecasting of practical convolution-closed time series models for low counts are provided. Marginal distributions of the data can be modelled via Poisson and Generalized Poisson innovations. Regression effects can be incorporated through time varying innovation rates. The models are described in Jung and Tremayne (2011) <doi:10.1111/j.1467-9892.2010.00697.x> and the model assessment tools are presented in Czado et al. (2009) <doi:10.1111/j.1541-0420.2009.01191.x> and, Tsay (1992) <doi:10.2307/2347612>.
Author: Manuel Huth [aut, cre],
Robert C. Jung [aut],
Andy Tremayne [aut]
Maintainer: Manuel Huth <manuel.huth@yahoo.com>
Diff between coconots versions 2.0.2 dated 2025-08-22 and 2.0.3 dated 2026-06-14
DESCRIPTION | 10 ++++----- MD5 | 20 +++++++++--------- NAMESPACE | 4 +++ NEWS.md | 9 ++++++++ R/cocoReg.R | 12 ++++++---- R/cocoReg_cov.R | 4 +-- R/predict.coco.R | 57 ++++++++++++++++++++++++++++++++++++++++++---------- build/partial.rdb |binary man/cocoReg.Rd | 10 +++++---- man/predict.coco.Rd | 2 - src/cfunctions.cpp | 2 + 11 files changed, 93 insertions(+), 37 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data
distributions are visualized. This package offers a flexible,
layer-based, and easy to use approach to create thematic maps, such as
choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Jakub Nowosad [ctb],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb],
John Clouse [ctb],
Robin Lovelace [ctb],
Jannes Muenchow [ctb],
Olivier Roy [ctb],
Edzer Pebesma [ctb],
Hugh [...truncated...]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 4.3 dated 2026-04-20 and 4.4 dated 2026-06-14
DESCRIPTION | 16 +- MD5 | 282 ++++++++++++++++++------------------ NAMESPACE | 32 ++++ NEWS.md | 15 + R/basemap_equivalents.R |only R/doc_units.R |only R/docs.R | 140 +++++++++++++++++ R/messages.R | 15 + R/misc_crs.R | 2 R/misc_text.R | 29 +++ R/process_breaks.R | 4 R/process_meta.R | 38 +++- R/qtm.R | 9 + R/shiny.R | 55 +------ R/shiny_dispatch.R |only R/shiny_grid.R |only R/shiny_leaflet.R |only R/spatial_sf.R | 14 + R/spatial_stars.R | 18 ++ R/spatial_terra.R | 39 ++++ R/step1_helper_facets.R | 18 ++ R/step2_data.R | 19 ++ R/step4_plot.R | 49 ++++-- R/tm_add_legend.R | 1 R/tm_animate.R | 3 R/tm_chart.R | 2 R/tm_component_functions.R | 30 ++- R/tm_components.R | 7 R/tm_crs.R | 10 - R/tm_facets.R | 2 R/tm_group.R | 2 R/tm_inset.R | 1 R/tm_label_format.R | 1 R/tm_layers_aux.R | 31 +-- R/tm_layers_circles.R |only R/tm_layers_iso.R | 4 R/tm_layers_lines.R | 53 ++++-- R/tm_layers_polygons.R | 144 +++++++++++++++--- R/tm_layers_raster.R | 10 + R/tm_layers_rgb.R | 8 - R/tm_layers_sf.R | 43 +++-- R/tm_layers_symbols.R | 69 +++++++- R/tm_layers_text.R | 29 ++- R/tm_layout.R | 16 +- R/tm_legend.R | 6 R/tm_options.R | 4 R/tm_popup.R |only R/tm_pos.R | 2 R/tm_scale_.R | 17 +- R/tm_scale_bivariate.R | 2 R/tm_shape.R | 17 +- R/tm_vars.R | 1 R/tmapChart.R | 14 + R/tmapGridAux_tiles.R | 10 + R/tmapGridComp.R | 17 +- R/tmapGridComp_funs.R | 21 +- R/tmapGridDataPlot_circles.R |only R/tmapGridDataPlot_polygons.R | 12 - R/tmapGridDataPlot_raster.R | 10 + R/tmapGridDataPlot_text.R | 10 - R/tmapGridRun.R | 22 ++ R/tmapGridShape.R | 2 R/tmapGrid_misc.R | 13 + R/tmapLeaflet.R | 10 + R/tmapLeafletArrange.R | 25 +-- R/tmapLeafletAux.R | 22 ++ R/tmapLeafletComp.R | 4 R/tmapLeafletComp_funs.R | 7 R/tmapLeafletDataPlot_circles.R |only R/tmapLeafletDataPlot_lines.R | 18 +- R/tmapLeafletDataPlot_polygons.R | 30 +++ R/tmapLeafletDataPlot_raster.R | 1 R/tmapLeafletDataPlot_symbols.R | 179 +++++++++++++++++++--- R/tmapLeafletDataPlot_text.R | 2 R/tmapOnLoad.R | 37 +--- R/tmapScaleContinuous.R | 4 R/tmapScaleDiscrete.R | 2 R/tmapScaleIntervals.R | 4 R/tmapScale_.R | 12 + R/tmapScale_defaults.R | 13 + R/tmapShape_misc.R | 39 ++++ R/tmapTrans.R | 1 R/tmap_arrange.R | 98 ++++++------ R/tmap_export.R | 11 + R/tmap_mode.R | 141 ++++++++++++------ R/tmap_options.R | 17 +- R/tmap_options_defaults.R | 6 R/tmap_providers.R | 36 +++- R/tmap_save.R | 44 +++++ R/view_format_popups.R | 86 ++++++---- build/partial.rdb |binary man/qtm.Rd | 10 + man/renderTmap.Rd | 18 ++ man/tm_add_legend.Rd | 3 man/tm_animate.Rd | 17 ++ man/tm_basemap.Rd | 18 +- man/tm_chart.Rd | 4 man/tm_circles.Rd |only man/tm_compass.Rd | 4 man/tm_components.Rd | 9 - man/tm_credits.Rd | 4 man/tm_crs.Rd | 10 - man/tm_facets.Rd | 2 man/tm_grid.Rd | 18 +- man/tm_group.Rd | 2 man/tm_inset.Rd | 5 man/tm_iso.Rd | 4 man/tm_label_format.Rd | 3 man/tm_layout.Rd | 20 ++ man/tm_legend.Rd | 12 + man/tm_lines.Rd | 157 +++++++++++++++----- man/tm_logo.Rd | 4 man/tm_minimap.Rd | 4 man/tm_mouse_coordinates.Rd | 4 man/tm_options.Rd | 11 - man/tm_plot.Rd | 5 man/tm_polygons.Rd | 137 ++++++++++++++--- man/tm_popup.Rd |only man/tm_pos.Rd | 2 man/tm_raster.Rd | 103 +++++++++++-- man/tm_rgb.Rd | 8 - man/tm_scale.Rd | 2 man/tm_scale_asis.Rd | 2 man/tm_scale_bivariate.Rd | 2 man/tm_scale_categorical.Rd | 2 man/tm_scale_continuous.Rd | 2 man/tm_scale_discrete.Rd | 2 man/tm_scale_intervals.Rd | 4 man/tm_scale_rank.Rd | 2 man/tm_scale_rgb.Rd | 2 man/tm_scalebar.Rd | 22 +- man/tm_sf.Rd | 114 ++++++++++++-- man/tm_shape.Rd | 14 + man/tm_symbols.Rd | 105 +++++++++---- man/tm_text.Rd | 123 ++++++++++++--- man/tm_title.Rd | 4 man/tm_vars.Rd | 3 man/tm_view.Rd | 12 - man/tmapGridLeaflet.Rd | 55 ++++++- man/tmapSubmitBasemapEquivalents.Rd |only man/tmap_animation.Rd | 62 ++----- man/tmap_arrange.Rd | 8 - man/tmap_internal.Rd | 22 +- man/tmap_leaflet.Rd | 8 - man/tmap_mode.Rd | 62 +++---- man/tmap_options.Rd | 21 +- man/tmap_providers.Rd | 42 +++-- man/tmap_save.Rd | 56 +++++-- 148 files changed, 2645 insertions(+), 995 deletions(-)
Title: R Package for the Smoking History Generator
Description: Efficient R interface to the Cancer Intervention and Surveillance
Modeling Network (CISNET) Smoking History Generator microsimulation
engine, which synthesizes individual smoking histories
(initiation, cessation, intensity) and ages at death from calibrated
initiation, cessation, cigarettes-per-day, and mortality tables. The
wrapper exposes fixed-cohort and population data-frame simulation,
multi-threaded segmentation, reproducible pseudo-random streams
(L'Ecuyer RngStream MRG32k3a or Matsumoto--Nishimura Mersenne Twister),
legacy CLI-style configuration files, and portable YAML configuration
save/load with optional split smoking and mortality parameter bundles.
Methods follow Jeon et al. (2012) <doi:10.1111/j.1539-6924.2011.01775.x>.
Random number generators: Matsumoto and Nishimura (1998)
<doi:10.1145/272991.272995>; L'Ecuyer (1999) <doi:10.1287/opre.47.1.159>;
L'Ecuyer et al. (2002) <doi:10.1287/opre.50.6.1073.358>.
Author: John Clarke [aut, cre] ,
Ben Racine [aut] ,
Martin Krapcho [aut] ,
Alexander Gaenko [aut] ,
Makoto Matsumoto [ctb, cph] ; copyright notice in source),
Takuji Nishimura [ctb, cph] ; copyright notice in source),
Pierre L'Ecuyer [ctb, cph] ;
copyright n [...truncated...]
Maintainer: John Clarke <john.clarke@cornerstonenw.com>
Diff between SmokingHistoryGenerator versions 6.5.3-1.0.1 dated 2026-06-12 and 7.0.0 dated 2026-06-14
SmokingHistoryGenerator-6.5.3-1.0.1/SmokingHistoryGenerator/inst/extdata/2018/mortality |only SmokingHistoryGenerator-6.5.3-1.0.1/SmokingHistoryGenerator/inst/extdata/2018/smoking |only SmokingHistoryGenerator-6.5.3-1.0.1/SmokingHistoryGenerator/tests/testdata/NHIS-1965-2018 |only SmokingHistoryGenerator-6.5.3-1.0.1/SmokingHistoryGenerator/tools |only SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/DESCRIPTION | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/MD5 | 119 +++----- SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/NEWS.md | 36 ++ SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/R/load_params.R | 69 +++- SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/README.md | 48 --- SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/build/partial.rdb |binary SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/inst/extdata/2018/mort |only SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/inst/extdata/2018/smok |only SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/man/SmokingHistoryGenerator-package.Rd | 2 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/man/shg_load_params.Rd | 2 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/src/main.cpp | 73 +---- SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/src/smoking_sim.cpp | 146 ++++++++-- SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/src/version.h | 4 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/src/wrapper.cpp | 22 - SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/src/wrapper.h | 12 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/fixtures/2018/MT/yob_1950_cessation_0.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/fixtures/2018/MT/yob_2010_cessation_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/fixtures/2018/RS/yob_1950_cessation_0.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/fixtures/2018/RS/yob_2010_cessation_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/inputs/test_input_MersenneTwister_1950_0.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/inputs/test_input_MersenneTwister_2010_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/inputs/test_input_RngStream_1950_0.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/inputs/test_input_RngStream_2010_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/outputs/test_output_MersenneTwister_2010_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/outputs/test_output_RngStream_1950_0.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/outputs/test_output_RngStream_2010_2050.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/templates/test_input_example.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testdata/2018 |only SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testdata/legacy-web-examples/test_input_example_MersenneTwister.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testdata/legacy-web-examples/test_input_example_RngStream.txt | 8 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-basic.R | 22 - SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-config-bundle.R | 14 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-load-params.R | 12 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-nhis-partial-inputs.R | 20 - SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-race-default.R |only SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-rs-segment-remainder.R | 6 SmokingHistoryGenerator-7.0.0/SmokingHistoryGenerator/tests/testthat/test-sim-bundle-config.R | 2 41 files changed, 416 insertions(+), 313 deletions(-)
More information about SmokingHistoryGenerator at CRAN
Permanent link
Title: Processing METAR Weather Reports
Description: Allows to download current and historical METAR weather reports
extract and parse basic parameters and present main weather information.
Current reports are downloaded from Aviation Weather Center
<https://aviationweather.gov/data/metar/> and historical reports from
Iowa Environmental Mesonet web page of Iowa State University
ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>.
Author: Pawel Cwiek [aut, cre],
David Megginson [ctb] ,
Greg Thompson [ctb]
Maintainer: Pawel Cwiek <prc.altodato@gmail.com>
Diff between pmetar versions 0.7.0 dated 2026-01-15 and 0.7.1 dated 2026-06-14
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- R/metar_get.R | 9 ++++ R/metar_get_historical.R | 58 ++++++++++++++++++++++++----- build/vignette.rds |binary data/ourairports.rda |binary inst/doc/pmetar.html | 18 ++++----- man/metar_get_historical.Rd | 3 - man/pmetar-package.Rd | 5 ++ tests/testthat/test_metar_get_historical.R | 2 - tests/testthat/test_metar_location.R | 4 +- 11 files changed, 89 insertions(+), 38 deletions(-)
Title: Análisis Computacional de Eventos de Protesta
Description: La librería 'ACEP' contiene funciones específicas para
desarrollar análisis computacional de eventos de protesta. Asimismo,
contiene bases de datos con colecciones de notas sobre protestas y
diccionarios de palabras conflictivas. La colección de diccionarios
reune diccionarios de diferentes orígenes.
The 'ACEP' library contains specific functions to perform computational
analysis of protest events. It also contains a database with collections
of notes on protests and dictionaries of conflicting words. Collection
of dictionaries that brings together dictionaries from different sources.
Author: Agustin Nieto [aut, cre]
Maintainer: Agustin Nieto <agustin.nieto77@gmail.com>
Diff between ACEP versions 0.1.1 dated 2026-05-14 and 0.1.2 dated 2026-06-14
ACEP-0.1.1/ACEP/man/proteger_arrays_schema.Rd |only ACEP-0.1.1/ACEP/vignettes/geocode_cache.json |only ACEP-0.1.2/ACEP/DESCRIPTION | 15 ACEP-0.1.2/ACEP/LICENSE | 4 ACEP-0.1.2/ACEP/MD5 | 243 - ACEP-0.1.2/ACEP/NAMESPACE | 131 ACEP-0.1.2/ACEP/NEWS.md | 299 + ACEP-0.1.2/ACEP/R/acep_bases.R | 96 ACEP-0.1.2/ACEP/R/acep_classes.R | 406 +- ACEP-0.1.2/ACEP/R/acep_claude.R | 487 +- ACEP-0.1.2/ACEP/R/acep_clean.R | 273 - ACEP-0.1.2/ACEP/R/acep_context.R | 210 - ACEP-0.1.2/ACEP/R/acep_count.R | 207 - ACEP-0.1.2/ACEP/R/acep_db.R | 96 ACEP-0.1.2/ACEP/R/acep_detect.R | 78 ACEP-0.1.2/ACEP/R/acep_diccionarios.R | 74 ACEP-0.1.2/ACEP/R/acep_extract.R | 119 ACEP-0.1.2/ACEP/R/acep_frec.R | 42 ACEP-0.1.2/ACEP/R/acep_gemini.R | 413 +- ACEP-0.1.2/ACEP/R/acep_gpt.R | 1052 ++--- ACEP-0.1.2/ACEP/R/acep_int.R | 54 ACEP-0.1.2/ACEP/R/acep_load_base.R | 88 ACEP-0.1.2/ACEP/R/acep_may.R | 66 ACEP-0.1.2/ACEP/R/acep_min.R | 66 ACEP-0.1.2/ACEP/R/acep_ollama.R | 682 +-- ACEP-0.1.2/ACEP/R/acep_openrouter.R | 986 ++--- ACEP-0.1.2/ACEP/R/acep_pipeline.R | 458 +- ACEP-0.1.2/ACEP/R/acep_plot_rst.R | 92 ACEP-0.1.2/ACEP/R/acep_plot_st.R | 136 ACEP-0.1.2/ACEP/R/acep_postag.R | 790 ++-- ACEP-0.1.2/ACEP/R/acep_postag_hibrido.R | 778 ++-- ACEP-0.1.2/ACEP/R/acep_prompt_gpt.R | 62 ACEP-0.1.2/ACEP/R/acep_rs.R | 53 ACEP-0.1.2/ACEP/R/acep_sst.R | 168 ACEP-0.1.2/ACEP/R/acep_svo.R | 550 +-- ACEP-0.1.2/ACEP/R/acep_together.R | 528 +- ACEP-0.1.2/ACEP/R/acep_token.R | 72 ACEP-0.1.2/ACEP/R/acep_token_plot.R | 166 ACEP-0.1.2/ACEP/R/acep_token_table.R | 75 ACEP-0.1.2/ACEP/R/acep_upos.R | 135 ACEP-0.1.2/ACEP/R/globals.R | 2 ACEP-0.1.2/ACEP/R/utils_dependencies.R | 40 ACEP-0.1.2/ACEP/R/utils_provider.R | 367 +- ACEP-0.1.2/ACEP/R/utils_validation.R | 352 - ACEP-0.1.2/ACEP/README.md | 666 +-- ACEP-0.1.2/ACEP/build/partial.rdb |binary ACEP-0.1.2/ACEP/build/vignette.rds |binary ACEP-0.1.2/ACEP/data/acep_bases.rda |binary ACEP-0.1.2/ACEP/inst/doc/conflictividad_soip.R | 392 +- ACEP-0.1.2/ACEP/inst/doc/conflictividad_soip.Rmd | 520 +- ACEP-0.1.2/ACEP/inst/doc/conflictividad_soip.html | 1326 +++---- ACEP-0.1.2/ACEP/inst/doc/extraccion_de_svo_con_acep.R | 220 - ACEP-0.1.2/ACEP/inst/doc/extraccion_de_svo_con_acep.Rmd | 566 +-- ACEP-0.1.2/ACEP/inst/doc/extraccion_de_svo_con_acep.html | 2162 ++++++------ ACEP-0.1.2/ACEP/inst/doc/extraccion_palabras_clave.R | 146 ACEP-0.1.2/ACEP/inst/doc/extraccion_palabras_clave.Rmd | 222 - ACEP-0.1.2/ACEP/inst/doc/extraccion_palabras_clave.html | 1044 ++--- ACEP-0.1.2/ACEP/inst/doc/limpieza_de_texto_con_acep.R | 772 ++-- ACEP-0.1.2/ACEP/inst/doc/limpieza_de_texto_con_acep.Rmd | 1012 ++--- ACEP-0.1.2/ACEP/inst/doc/limpieza_de_texto_con_acep.html | 1698 ++++----- ACEP-0.1.2/ACEP/inst/doc/tokenizar_con_acep.R | 64 ACEP-0.1.2/ACEP/inst/doc/tokenizar_con_acep.Rmd | 232 - ACEP-0.1.2/ACEP/inst/doc/tokenizar_con_acep.html | 949 ++--- ACEP-0.1.2/ACEP/man/acep_bases.Rd | 126 ACEP-0.1.2/ACEP/man/acep_claude.Rd | 6 ACEP-0.1.2/ACEP/man/acep_clean.Rd | 4 ACEP-0.1.2/ACEP/man/acep_count.Rd | 75 ACEP-0.1.2/ACEP/man/acep_db.Rd | 72 ACEP-0.1.2/ACEP/man/acep_detect.Rd | 74 ACEP-0.1.2/ACEP/man/acep_diccionarios.Rd | 106 ACEP-0.1.2/ACEP/man/acep_frec.Rd | 52 ACEP-0.1.2/ACEP/man/acep_gemini.Rd | 6 ACEP-0.1.2/ACEP/man/acep_gpt.Rd | 11 ACEP-0.1.2/ACEP/man/acep_int.Rd | 68 ACEP-0.1.2/ACEP/man/acep_load_base.Rd | 62 ACEP-0.1.2/ACEP/man/acep_min.Rd | 56 ACEP-0.1.2/ACEP/man/acep_openrouter.Rd | 6 ACEP-0.1.2/ACEP/man/acep_plot_rst.Rd | 58 ACEP-0.1.2/ACEP/man/acep_plot_st.Rd | 102 ACEP-0.1.2/ACEP/man/acep_prompt_gpt.Rd | 6 ACEP-0.1.2/ACEP/man/acep_rs.Rd | 75 ACEP-0.1.2/ACEP/man/acep_svo.Rd | 102 ACEP-0.1.2/ACEP/man/acep_together.Rd | 6 ACEP-0.1.2/ACEP/man/acep_token.Rd | 52 ACEP-0.1.2/ACEP/man/acep_token_plot.Rd | 62 ACEP-0.1.2/ACEP/man/acep_token_table.Rd | 58 ACEP-0.1.2/ACEP/man/acep_upos.Rd | 78 ACEP-0.1.2/ACEP/man/dot-acep_count_cache_key.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_count_pattern.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_escape_regex.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_provider_http_error_message.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_provider_post.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_provider_strip_key.Rd |only ACEP-0.1.2/ACEP/man/dot-acep_regex_cache_max.Rd |only ACEP-0.1.2/ACEP/man/figures/logo.svg | 188 - ACEP-0.1.2/ACEP/tests/testthat.R | 8 ACEP-0.1.2/ACEP/tests/testthat/helper-fixtures.R | 90 ACEP-0.1.2/ACEP/tests/testthat/test-acep-fixes.R |only ACEP-0.1.2/ACEP/tests/testthat/test-acep-ollama.R | 19 ACEP-0.1.2/ACEP/tests/testthat/test-acep-provider-post.R |only ACEP-0.1.2/ACEP/tests/testthat/test-acep_claude.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_clean.R | 284 - ACEP-0.1.2/ACEP/tests/testthat/test-acep_context.R | 18 ACEP-0.1.2/ACEP/tests/testthat/test-acep_count.R | 24 ACEP-0.1.2/ACEP/tests/testthat/test-acep_db.R | 48 ACEP-0.1.2/ACEP/tests/testthat/test-acep_detect.R | 70 ACEP-0.1.2/ACEP/tests/testthat/test-acep_extract.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_frec.R | 38 ACEP-0.1.2/ACEP/tests/testthat/test-acep_gemini.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_gpt.R | 17 ACEP-0.1.2/ACEP/tests/testthat/test-acep_int.R | 36 ACEP-0.1.2/ACEP/tests/testthat/test-acep_load_base.R | 24 ACEP-0.1.2/ACEP/tests/testthat/test-acep_may.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_min.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_openrouter.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_sst.R | 212 - ACEP-0.1.2/ACEP/tests/testthat/test-acep_svo.R | 12 ACEP-0.1.2/ACEP/tests/testthat/test-acep_together.R | 16 ACEP-0.1.2/ACEP/tests/testthat/test-acep_token.R | 54 ACEP-0.1.2/ACEP/tests/testthat/test-acep_token_plot.R | 62 ACEP-0.1.2/ACEP/tests/testthat/test-acep_token_table.R | 40 ACEP-0.1.2/ACEP/tests/testthat/test-acep_upos.R | 13 ACEP-0.1.2/ACEP/tests/testthat/test-optimization-safety.R | 1110 +++--- ACEP-0.1.2/ACEP/vignettes/conflictividad_soip.Rmd | 520 +- ACEP-0.1.2/ACEP/vignettes/extraccion_de_svo_con_acep.Rmd | 566 +-- ACEP-0.1.2/ACEP/vignettes/extraccion_palabras_clave.Rmd | 222 - ACEP-0.1.2/ACEP/vignettes/limpieza_de_texto_con_acep.Rmd | 1012 ++--- ACEP-0.1.2/ACEP/vignettes/tokenizar_con_acep.Rmd | 232 - 128 files changed, 14885 insertions(+), 14471 deletions(-)
Title: Native and Extensible R Driver for 'Zarr'
Description: The 'Zarr' specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native 'Zarr' implementation in R with support for all required features of 'Zarr' version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between zarr versions 0.4.0 dated 2026-05-28 and 0.4.1 dated 2026-06-14
DESCRIPTION | 8 MD5 | 85 ++--- NEWS.md | 7 R/api.R | 4 R/array.R | 21 - R/array_builder.R | 13 R/group.R | 18 - R/node.R | 223 +++++++++++-- R/sharding.R | 4 R/zarr.R | 2 README.md | 8 man/array_builder.Rd | 208 ++++++------ man/chunk_grid_regular.Rd | 174 +++++----- man/chunk_grid_regular_IO.Rd | 148 ++++---- man/chunk_grid_sharded.Rd | 150 ++++---- man/chunk_grid_sharded_IO.Rd | 96 ++--- man/chunking.Rd | 78 ++-- man/zarr-package.Rd | 5 man/zarr.Rd | 314 +++++++++--------- man/zarr_array.Rd | 216 ++++++------ man/zarr_codec.Rd | 191 +++++------ man/zarr_codec_blosc.Rd | 165 +++++---- man/zarr_codec_bytes.Rd | 178 +++++----- man/zarr_codec_crc32c.Rd | 139 ++++---- man/zarr_codec_gzip.Rd | 154 ++++----- man/zarr_codec_sharding.Rd | 80 ++-- man/zarr_codec_transpose.Rd | 159 ++++----- man/zarr_codec_ucs4.Rd | 143 ++++---- man/zarr_codec_vlenutf8.Rd | 146 ++++---- man/zarr_codec_zstd.Rd | 154 ++++----- man/zarr_conv_ref.Rd | 122 +++---- man/zarr_conv_uom.Rd | 88 ++--- man/zarr_convention.Rd | 141 ++++---- man/zarr_data_type.Rd | 99 +++-- man/zarr_domain.Rd | 103 +++--- man/zarr_extension.Rd | 72 ++-- man/zarr_group.Rd | 364 +++++++++++---------- man/zarr_httpstore.Rd | 561 +++++++++++++++++---------------- man/zarr_localstore.Rd | 581 +++++++++++++++++----------------- man/zarr_memorystore.Rd | 493 +++++++++++++++-------------- man/zarr_node.Rd | 264 ++++++++++----- man/zarr_store.Rd | 662 ++++++++++++++++++++------------------- tests/testthat/test-attributes.R |only tests/testthat/test-sharding.R | 4 44 files changed, 3674 insertions(+), 3171 deletions(-)
Title: Hierarchical Piecewise Regression with Smoothed Change-Points
Description: Fits Bayesian hierarchical piecewise regression models with
multiple logistic-smoothed change-points. Non-linear parameters (change-point
locations and transition sharpness) and linear parameters can each be
conditioned on covariates and factors via flexible design matrices.
A random-intercept structure is supported for any parameter. Spike-and-slab
regularization is supported for selecting the number of breakpoints.
Posterior inference uses a Metropolis-within-Gibbs sampler implemented
in 'Rust' for speed. Methods are based on the smooth transition
piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389>
and variable selection spike-and-slab priors of Kuo and Mallick (1998)
<https://www.jstor.org/stable/25053023>.
Author: Aidan D Bindoff [aut, cre]
Maintainer: Aidan D Bindoff <aidan.bindoff@utas.edu.au>
Diff between smoothbp versions 0.2.2 dated 2026-06-02 and 0.2.4 dated 2026-06-14
DESCRIPTION | 8 MD5 | 97 NAMESPACE | 4 NEWS.md | 13 R/extendr-wrappers.R | 4 R/methods_text.R |only R/postprocess.R | 2 R/priors.R | 13 R/recovery.R | 8 R/results_text.R |only R/simulate.R | 361 +-- R/smoothbp.R | 141 + R/smoothbp_ss.R | 113 - R/tab_model.R | 3 R/utils.R | 16 README.md | 36 build/partial.rdb |only inst/WORDLIST |only inst/doc/advanced-modeling.Rmd | 2 inst/doc/advanced-modeling.html | 2 inst/doc/brms-comparison.R | 116 + inst/doc/brms-comparison.Rmd | 2200 ++++++++++---------- inst/doc/brms-comparison.html | 1342 ++++++------ inst/doc/getting-started.R | 12 inst/doc/getting-started.Rmd | 871 ++++--- inst/doc/getting-started.html | 61 man/figures |only man/model_methods.Rd |only man/model_results.Rd |only man/simulate_smoothbp.Rd | 64 man/smoothbp.Rd | 18 man/smoothbp_priors.Rd | 8 man/smoothbp_ss.Rd | 7 man/update.smoothbp_fit.Rd | 5 src/Makevars.in | 6 src/Makevars.win.in | 6 src/rust/src/bridge.rs | 4 src/rust/src/lib.rs | 242 +- src/rust/src/model.rs | 26 src/rust/src/sampler.rs | 56 src/rust/src/sampler_re.rs | 1218 +++++++++-- tests/testthat/test-b0-bounds.R | 2 tests/testthat/test-brms-comparison.R | 2 tests/testthat/test-hierarchical.R | 6 tests/testthat/test-linear-bounds.R | 8 tests/testthat/test-smoothbp.R | 12 tests/testthat/test-spike-slab.R | 8 tests/testthat/test-update-recovery-hypothesis-bf.R |only tools/config.R | 8 tools/test_vignette_params.R |only tools/verify_mixing_changes.R | 8 vignettes/advanced-modeling.Rmd | 2 vignettes/brms-comparison.Rmd | 2200 ++++++++++---------- vignettes/getting-started.Rmd | 871 ++++--- 54 files changed, 6160 insertions(+), 4052 deletions(-)
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at <http://www.phidot.org/software/mark/downloads/>
but is not open source.
Author: Jeff Laake [cre, aut],
Eldar Rakhimberdiev [ctb],
Ben Augustine [ctb],
Daniel Turek [ctb],
Brett McClintock [ctb],
Jim Hines [ctb],
analysis from Bret Collier [ctb],
Jay Rotella [ctb],
David Pavlacky [ctb],
Andrew Paul [aut],
Luke Eberhart- Phillips [...truncated...]
Maintainer: Jeff Laake <jefflaake@gmail.com>
Diff between RMark versions 3.0.7 dated 2026-01-31 and 3.0.8 dated 2026-06-14
DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/mark.R | 6 ++---- R/zzz.R | 14 +++++++------- 5 files changed, 28 insertions(+), 20 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project was funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut] ,
Pete Philipson [aut] ,
Andrea Jorgensen [ctb] ,
Ruwanthi Kolamunnage-Dona [aut] ,
Paula Williamson [ctb] ,
Dimitris Rizopoulos [ctb, dtc] ,
Alessandro Gasparini [aut] ,
Medical Research Council [fnd]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between joineRML versions 0.4.7 dated 2025-02-04 and 0.4.8 dated 2026-06-14
joineRML-0.4.7/joineRML/tests/testthat/Rplots.pdf |only joineRML-0.4.8/joineRML/DESCRIPTION | 34 ++++---- joineRML-0.4.8/joineRML/MD5 | 67 ++++++++-------- joineRML-0.4.8/joineRML/NAMESPACE | 1 joineRML-0.4.8/joineRML/NEWS.md | 26 ++++++ joineRML-0.4.8/joineRML/R/bootSE.R | 6 - joineRML-0.4.8/joineRML/R/dynLong.R | 4 joineRML-0.4.8/joineRML/R/dynSurv.R | 8 - joineRML-0.4.8/joineRML/R/hessian.R | 6 - joineRML-0.4.8/joineRML/R/initsSurv.R | 4 joineRML-0.4.8/joineRML/R/joineRML.R | 2 joineRML-0.4.8/joineRML/R/mjoint.R | 17 ++-- joineRML-0.4.8/joineRML/R/plot.ranef.mjoint.R | 5 - joineRML-0.4.8/joineRML/R/sampleData.R | 4 joineRML-0.4.8/joineRML/R/sigma.mjoint.R | 2 joineRML-0.4.8/joineRML/R/simData.R | 8 - joineRML-0.4.8/joineRML/R/vcov.mjoint.R | 5 - joineRML-0.4.8/joineRML/README.md | 22 +++-- joineRML-0.4.8/joineRML/build/partial.rdb |binary joineRML-0.4.8/joineRML/build/vignette.rds |binary joineRML-0.4.8/joineRML/inst/doc/joineRML-tidy.html | 13 +-- joineRML-0.4.8/joineRML/inst/doc/joineRML.html | 21 ++--- joineRML-0.4.8/joineRML/inst/doc/technical.pdf |binary joineRML-0.4.8/joineRML/man/dynLong.Rd | 2 joineRML-0.4.8/joineRML/man/dynSurv.Rd | 2 joineRML-0.4.8/joineRML/man/joineRML.Rd | 2 joineRML-0.4.8/joineRML/man/mjoint.Rd | 4 joineRML-0.4.8/joineRML/tests/testthat/helper-fits.R |only joineRML-0.4.8/joineRML/tests/testthat/test-#59.R | 1 joineRML-0.4.8/joineRML/tests/testthat/test-ancillary.R | 23 ++--- joineRML-0.4.8/joineRML/tests/testthat/test-boot.R | 21 +++-- joineRML-0.4.8/joineRML/tests/testthat/test-dynplot.R |only joineRML-0.4.8/joineRML/tests/testthat/test-dynpred.R |only joineRML-0.4.8/joineRML/tests/testthat/test-inputs.R | 5 - joineRML-0.4.8/joineRML/tests/testthat/test-methods.R |only joineRML-0.4.8/joineRML/tests/testthat/test-models.R | 36 ++++---- joineRML-0.4.8/joineRML/tests/testthat/test-tidy.R | 1 37 files changed, 206 insertions(+), 146 deletions(-)
Title: 'DataTables' 2.x for R
Description: A modern R binding for 'DataTables' V2 with modular
extension loading, 'Bootstrap 5' styling, 'Shiny' integration (proxy, events,
inline inputs), server-side processing helpers, and standalone (non-Shiny)
support. Configure 'DataTables' options directly via R lists, a 1:1 mapping
to the 'JavaScript' API.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorin [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between DT2 versions 0.1.1 dated 2026-05-04 and 0.1.2 dated 2026-06-14
DT2-0.1.1/DT2/man/figures/diagrama-2025-09-11-2.pik |only DT2-0.1.1/DT2/man/figures/diagrama-2025-09-11.svg |only DT2-0.1.2/DT2/DESCRIPTION | 10 - DT2-0.1.2/DT2/MD5 | 69 +++++---- DT2-0.1.2/DT2/NEWS.md |only DT2-0.1.2/DT2/R/dt2.R | 15 ++ DT2-0.1.2/DT2/R/dt2_buttons.R | 6 DT2-0.1.2/DT2/R/dt2_formats.R | 40 ++--- DT2-0.1.2/DT2/R/dt2_html.R | 4 DT2-0.1.2/DT2/R/dt2_inputs.R | 4 DT2-0.1.2/DT2/R/dt2_options.R | 48 +++++- DT2-0.1.2/DT2/R/dt2_server_processing.R | 7 DT2-0.1.2/DT2/R/dt2_utils.R | 38 ++++- DT2-0.1.2/DT2/README.md | 14 + DT2-0.1.2/DT2/build/vignette.rds |binary DT2-0.1.2/DT2/inst/doc/extensions-guide.html | 28 +-- DT2-0.1.2/DT2/inst/doc/formatting.Rmd | 8 + DT2-0.1.2/DT2/inst/doc/formatting.html | 44 +++--- DT2-0.1.2/DT2/inst/doc/getting-started.Rmd | 4 DT2-0.1.2/DT2/inst/doc/getting-started.html | 143 ++++++++++---------- DT2-0.1.2/DT2/inst/doc/js-config.html | 52 +++---- DT2-0.1.2/DT2/inst/doc/shiny-integration.html | 4 DT2-0.1.2/DT2/man/dt2.Rd | 2 DT2-0.1.2/DT2/man/dt2_buttons.Rd | 8 + DT2-0.1.2/DT2/man/dt2_cols_escape.Rd | 6 DT2-0.1.2/DT2/man/dt2_language.Rd | 9 + DT2-0.1.2/DT2/man/dt2_order.Rd | 5 DT2-0.1.2/DT2/man/dt2_search_global.Rd | 4 DT2-0.1.2/DT2/man/dt2_theme.Rd | 2 DT2-0.1.2/DT2/man/dt2_use_buttons.Rd | 8 + DT2-0.1.2/DT2/man/figures/logo.pik |only DT2-0.1.2/DT2/man/figures/logo.svg |only DT2-0.1.2/DT2/man/render_dt2.Rd | 2 DT2-0.1.2/DT2/tests |only DT2-0.1.2/DT2/vignettes/formatting.Rmd | 8 + DT2-0.1.2/DT2/vignettes/getting-started.Rmd | 4 36 files changed, 382 insertions(+), 214 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: An interactive HTML widget of the perspective plot for generalized additive models. An alternative solution of the function mgcv::vis.gam(). The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.
Author: Tingting Zhan [aut, cre] ,
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.3.0 dated 2026-05-17 and 0.3.1 dated 2026-06-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/widget_gam.R | 22 +++++----------------- man/hyper.gam-package.Rd | 2 +- man/widget_gam.Rd | 11 ++++------- 5 files changed, 19 insertions(+), 34 deletions(-)
Title: Grouped Hyper Data Frame
Description: To aggregate a hyper data frame, defined in the package 'spatstat.geom', according to a grouping structure. To facilitate downstream analysis based on a "grouped" hyper data frame. The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.4.1 dated 2026-05-19 and 0.4.2 dated 2026-06-13
groupedHyperframe-0.4.1/groupedHyperframe/R/Defunct.R |only groupedHyperframe-0.4.1/groupedHyperframe/R/aggregate_FUN.R |only groupedHyperframe-0.4.1/groupedHyperframe/man/aggregate_FUN.Rd |only groupedHyperframe-0.4.1/groupedHyperframe/man/defunct.Rd |only groupedHyperframe-0.4.2/groupedHyperframe/DESCRIPTION | 10 ++--- groupedHyperframe-0.4.2/groupedHyperframe/MD5 | 17 ++++------ groupedHyperframe-0.4.2/groupedHyperframe/NAMESPACE | 2 - groupedHyperframe-0.4.2/groupedHyperframe/R/aggregate.hyperframe.R | 16 ++++++--- groupedHyperframe-0.4.2/groupedHyperframe/R/int.R |only groupedHyperframe-0.4.2/groupedHyperframe/R/pppBy.R | 2 - groupedHyperframe-0.4.2/groupedHyperframe/man/aggregate.hyperframe.Rd | 11 ++++++ groupedHyperframe-0.4.2/groupedHyperframe/man/groupedHyperframe-package.Rd | 2 - 12 files changed, 36 insertions(+), 24 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Byte Pair Encoding Text Tokenization
Description: Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
VK.com [cph],
Gregory Popovitch [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Ivan Belonogov [ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between tokenizers.bpe versions 0.1.5 dated 2026-05-20 and 0.1.6 dated 2026-06-13
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 src/parallel_hashmap/phmap.h | 279 +++++++++++++++---------------- src/parallel_hashmap/phmap_base.h | 323 ++++++++++++++++++------------------ src/parallel_hashmap/phmap_bits.h | 6 src/parallel_hashmap/phmap_config.h | 8 7 files changed, 328 insertions(+), 310 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Triple-Difference Estimators
Description: Implements triple-difference (DDD) estimators for both average
treatment effects and event-study parameters. Methods include regression
adjustment, inverse-probability weighting, and doubly-robust estimators,
all of which rely on a conditional DDD parallel-trends assumption and
allow covariate adjustment across multiple pre- and post-treatment
periods. The methodology is detailed in Ortiz-Villavicencio and
Sant'Anna (2025) <doi:10.48550/arXiv.2505.09942>.
Author: Marcelo Ortiz-Villavicencio [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Marcelo Ortiz-Villavicencio <marcelo.ortiz@emory.edu>
Diff between triplediff versions 0.2.0 dated 2026-01-15 and 0.2.4 dated 2026-06-13
DESCRIPTION | 8 MD5 | 35 NEWS.md | 21 R/agg_ddd.R | 3 R/att_gt.R | 45 R/compute_aggregations.R | 65 - R/compute_nuisances.R | 224 ++- R/ddd.R | 12 R/mboot.R | 37 R/preprocess.R | 189 ++ README.md | 2 man/agg_ddd.Rd | 3 man/compute_se_agg.Rd | 7 man/ddd.Rd | 10 man/figures/README-unnamed-chunk-10-1.png |binary tests/testthat/test-aggte-clustervars-override.R |only tests/testthat/test-cluster-alignment-correctness.R |only tests/testthat/test-cluster-analytic.R |only tests/testthat/test-cluster-unbalanced-bootstrap.R |only tests/testthat/test-mboot-cluster.R |only tests/testthat/test-preprocess.R | 1295 +++++++++++++++++++- 21 files changed, 1804 insertions(+), 152 deletions(-)
Title: Switzerland's Data Series in One Place
Description: Download and import open Swiss economic time series from
'dataseries.org' <https://dataseries.org>, a comprehensive and
up-to-date collection of public data from Switzerland. Series are
retrieved through the public 'dataseries.org' API and imported as a
'data.frame' or 'ts' object.
Author: Christoph Sax [aut, cre],
Jannes Muenchow [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between dataseries versions 0.2.0 dated 2017-04-29 and 1.0.0 dated 2026-06-13
dataseries-0.2.0/dataseries/NEWS |only dataseries-0.2.0/dataseries/R/as_ts.R |only dataseries-0.2.0/dataseries/R/inventory.R |only dataseries-1.0.0/dataseries/DESCRIPTION | 34 +- dataseries-1.0.0/dataseries/MD5 | 28 + dataseries-1.0.0/dataseries/NAMESPACE | 7 dataseries-1.0.0/dataseries/NEWS.md |only dataseries-1.0.0/dataseries/R/api.R |only dataseries-1.0.0/dataseries/R/catalog.R |only dataseries-1.0.0/dataseries/R/dataseries-package.R |only dataseries-1.0.0/dataseries/R/ds.R | 258 +++++++++++------- dataseries-1.0.0/dataseries/R/utils.R |only dataseries-1.0.0/dataseries/README.md | 89 +++++- dataseries-1.0.0/dataseries/man/cache_ls.Rd |only dataseries-1.0.0/dataseries/man/dataseries-package.Rd |only dataseries-1.0.0/dataseries/man/ds.Rd | 79 +++-- dataseries-1.0.0/dataseries/man/ds_catalog.Rd |only dataseries-1.0.0/dataseries/man/ds_meta.Rd |only dataseries-1.0.0/dataseries/man/ds_search.Rd |only dataseries-1.0.0/dataseries/man/inventory.Rd | 27 - dataseries-1.0.0/dataseries/tests |only 21 files changed, 346 insertions(+), 176 deletions(-)
Title: Model Cumulative Growing Degree-Days for Pest Monitoring
Description: Pest monitoring is crucial, especially during the early season, to understand the distribution and the proliferation of the target pest. Raw count data from pest monitoring/traps can be coupled with environmental variables such as temperature, growing degree-day ('GDD') etc. to get useful insights about the pest phenology. This package pulls temperature data from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), the 'Daymet' application programming interface ('API', <https://daymet.ornl.gov>), or 'Open Meteo' ('API', <https://open-meteo.com/>) sequentially for a user-specified time period and calculates cumulative growing degree-days. Users provide pest development thresholds (lower and upper temperatures), pest of concern, and the geographic coordinates of the trap location to track emergence and phenology.
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 0.1.0 dated 2026-05-20 and 1.0.0 dated 2026-06-13
TrackTrap-0.1.0/TrackTrap/man/plot_phenology_trend.Rd |only TrackTrap-1.0.0/TrackTrap/DESCRIPTION | 26 - TrackTrap-1.0.0/TrackTrap/LICENSE | 2 TrackTrap-1.0.0/TrackTrap/MD5 | 27 - TrackTrap-1.0.0/TrackTrap/NAMESPACE | 8 TrackTrap-1.0.0/TrackTrap/NEWS.md |only TrackTrap-1.0.0/TrackTrap/R/TrackTrap-package.R |only TrackTrap-1.0.0/TrackTrap/R/data.R | 1 TrackTrap-1.0.0/TrackTrap/R/globals.R |only TrackTrap-1.0.0/TrackTrap/R/phenology.R | 350 +++++++++++------- TrackTrap-1.0.0/TrackTrap/R/utils-pipe.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.rda |binary TrackTrap-1.0.0/TrackTrap/man/calc_pest_phenology.Rd | 84 +--- TrackTrap-1.0.0/TrackTrap/man/fetch_open_meteo.Rd |only TrackTrap-1.0.0/TrackTrap/man/pest_thresholds.Rd | 48 +- TrackTrap-1.0.0/TrackTrap/man/pipe.Rd |only TrackTrap-1.0.0/TrackTrap/man/plot_trap_phenology.Rd |only TrackTrap-1.0.0/TrackTrap/tests |only 19 files changed, 333 insertions(+), 213 deletions(-)
Title: Geographically-Conscious Taxonomic Assignment for Metabarcoding
Description: A bioinformatics pipeline for performing taxonomic
assignment of DNA metabarcoding sequence data while considering
geographic location. A detailed tutorial is available at
<https://urodelan.github.io/LocaTT_Tutorial/>.
A manuscript describing these methods is in preparation.
Author: Kenen B Goodwin [aut, cre] ,
Christopher Cousins [ctb],
Taal Levi [ctb],
Tiffany S Garcia [ths]
Maintainer: Kenen B Goodwin <urodelan@gmail.com>
Diff between LocaTT versions 1.2.0 dated 2026-03-27 and 1.3.0 dated 2026-06-13
DESCRIPTION | 9 ++--- MD5 | 55 +++++++++++++++++++++++++++++-- NAMESPACE | 20 +++++++++++ R/cor2cov.R |only R/dcopula.R |only R/ddirmult.R |only R/dissimilarity.R |only R/diversity.R |only R/djsdm.R |only R/dmWAIC.R |only R/dmpredict.R |only R/dmreg.R |only R/dmvlogis.R |only R/mlWAIC.R |only R/mlcoef.R |only R/mlcor.R |only R/mlformat.R |only R/mlpredict.R |only R/mlreg.R |only R/normalize.R |only R/richness.R |only R/softmax.R |only R/waic.R |only inst/CITATION | 4 +- inst/extdata/example_mvlogistic_data.rds |only inst/extdata/example_regression_data.rds |only inst/intdata |only man/cor2cov.Rd |only man/dcopula.Rd |only man/ddirmult.Rd |only man/dissimilarity.Rd |only man/diversity.Rd |only man/djsdm.Rd |only man/dmWAIC.Rd |only man/dmpredict.Rd |only man/dmreg.Rd |only man/dmvlogis.Rd |only man/mlWAIC.Rd |only man/mlcoef.Rd |only man/mlcor.Rd |only man/mlformat.Rd |only man/mlpredict.Rd |only man/mlreg.Rd |only man/normalize.Rd |only man/richness.Rd |only man/softmax.Rd |only man/waic.Rd |only 47 files changed, 79 insertions(+), 9 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.70 dated 2026-02-16 and 1.0 dated 2026-06-13
DESCRIPTION | 6 MD5 | 38 - NAMESPACE | 1 NEWS.md | 21 R/0_globals.R | 3 R/2_1_1_topicsModel_Pred.R | 89 ++- R/2_2_topicsGrams.R | 6 R/4_1_topicsPlot.R | 234 +++++++- README.md | 13 inst/doc/extended_installation_guide.Rmd | 3 inst/doc/extended_installation_guide.html | 2 man/topicsModel.Rd | 12 man/topicsPlot.Rd | 30 - man/topicsPlotOverview.Rd | 53 + tests/testthat/_snaps/1_6_topicsPlot/2-ngram-negative.svg | 44 - tests/testthat/_snaps/1_6_topicsPlot/3-ngram-positive.svg | 66 +- tests/testthat/_snaps/1_6_topicsPlot/topics-overview-plot.svg | 108 +-- tests/testthat/_snaps/1_6_topicsPlot/topics2-overview-plot.svg | 272 +++++----- tests/testthat/test_1_6_topicsPlot.R | 29 - vignettes/extended_installation_guide.Rmd | 3 20 files changed, 687 insertions(+), 346 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Corrections are supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.5 dated 2026-06-04 and 1.0.6 dated 2026-06-13
TmCalculator-1.0.5/TmCalculator/R/plot_circos_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_karyotype_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_linear_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_genome_tracks.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_heatmap.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_interactive.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_linear.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.Rmd |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.html |only TmCalculator-1.0.5/TmCalculator/man/plot_circos_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_karyotype_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_linear_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_genome_tracks.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_heatmap.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_interactive.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_linear.Rd |only TmCalculator-1.0.5/TmCalculator/vignettes/TmCalculator.Rmd |only TmCalculator-1.0.6/TmCalculator/DESCRIPTION | 26 TmCalculator-1.0.6/TmCalculator/MD5 | 58 TmCalculator-1.0.6/TmCalculator/NAMESPACE | 105 - TmCalculator-1.0.6/TmCalculator/R/coor_to_genomic_ranges.R | 3 TmCalculator-1.0.6/TmCalculator/R/ecoli_rep_hotspots.R | 50 TmCalculator-1.0.6/TmCalculator/R/integrate_granges.R | 8 TmCalculator-1.0.6/TmCalculator/R/make_genomiccoord.R | 5 TmCalculator-1.0.6/TmCalculator/R/plot_genome_track.R |only TmCalculator-1.0.6/TmCalculator/R/plot_tm.R |only TmCalculator-1.0.6/TmCalculator/R/to_genomic_ranges.R | 4 TmCalculator-1.0.6/TmCalculator/build/vignette.rds |binary TmCalculator-1.0.6/TmCalculator/data/ecoli_rep_hotspots.rda |binary TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.R | 469 +++-- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.Rmd | 406 ++--- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.html | 782 +++++----- TmCalculator-1.0.6/TmCalculator/inst/scripts |only TmCalculator-1.0.6/TmCalculator/inst/vignette-source |only TmCalculator-1.0.6/TmCalculator/man/TmCalculator-package.Rd | 2 TmCalculator-1.0.6/TmCalculator/man/ecoli_rep_hotspots.Rd | 49 TmCalculator-1.0.6/TmCalculator/man/integrate_granges.Rd | 8 TmCalculator-1.0.6/TmCalculator/man/plot_genome_track.Rd |only TmCalculator-1.0.6/TmCalculator/man/plot_tm.Rd |only TmCalculator-1.0.6/TmCalculator/vignettes/genome_wide_tm_ecoli.Rmd | 406 ++--- 41 files changed, 1267 insertions(+), 1114 deletions(-)
Title: Tidy Intensive Longitudinal Data Analysis
Description: A reproducible, tidyverse-style framework for intensive longitudinal
data analysis in R, with built-in methodological safeguards, provenance
tracking, and reporting tools. Encodes time structure, enforces
within-between decomposition, provides spacing-aware lags, and integrates
diagnostics and visualization. Use ild_prepare(), ild_center(), ild_lag(),
and related functions for a unified pipeline from raw EMA/diary data to
interpretable models.
Author: Alex Litovchenko [aut, cre]
Maintainer: Alex Litovchenko <al4877@columbia.edu>
This is a re-admission after prior archival of version 0.4.0 dated 2026-04-17
Diff between tidyILD versions 0.4.0 dated 2026-04-17 and 0.4.1 dated 2026-06-13
DESCRIPTION | 28 +++-- LICENSE | 2 MD5 | 54 +++++----- NEWS.md | 16 +++ R/ild_prepare.R | 59 +++++++++++ R/ild_prepare_wide.R |only README.md | 2 inst/CITATION | 4 inst/doc/benchmark-simulation-recovery.html | 8 - inst/doc/brms-dynamics-recipes.html | 4 inst/doc/ctsem-continuous-time-dynamics.html | 4 inst/doc/ild-analysis-report.html | 4 inst/doc/ild-decomposition-and-spacing.html | 4 inst/doc/ild-glossary-and-quickstart.R | 17 +++ inst/doc/ild-glossary-and-quickstart.Rmd | 29 +++++ inst/doc/ild-glossary-and-quickstart.html | 133 ++++++++++++++++++++++++++- inst/doc/ild-provenance.html | 34 +++--- inst/doc/ild-specialist-backends.html | 8 - inst/doc/kfas-choosing-backend.html | 4 inst/doc/kfas-irregular-timing-spacing.html | 4 inst/doc/kfas-state-space-modeling.html | 4 inst/doc/temporal-dynamics-model-choice.html | 8 - inst/doc/tidyILD-workflow.html | 4 inst/doc/tsibble-interoperability.html | 4 man/ild_prepare.Rd | 29 +++++ tests/testthat/helper-contract-fixtures.R | 15 ++- tests/testthat/test-heterogeneity-lmer.R | 17 ++- tests/testthat/test-ild_prepare_wide.R |only vignettes/ild-glossary-and-quickstart.Rmd | 29 +++++ 29 files changed, 429 insertions(+), 99 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.8.1 dated 2026-02-16 and 1.9 dated 2026-06-13
DESCRIPTION | 6 ++--- MD5 | 42 ++++++++++++++++++----------------- NAMESPACE | 4 +++ NEWS.md | 6 +++++ R/0_0_text_install.R | 11 +++++---- R/4_4_textWordPrediction.R |only R/7_1_textTopics.R | 31 +++++++++++++++++++++++-- R/7_2_textTopicsAnalysis.R | 16 +++++++++++++ README.md | 7 +++++ inst/doc/LBAM.html | 4 +-- inst/doc/ext_install_guide.Rmd | 2 - inst/doc/ext_install_guide.html | 2 - inst/doc/huggingface_in_r.R | 2 - inst/doc/huggingface_in_r.Rmd | 2 - inst/doc/huggingface_in_r.html | 3 -- inst/python/bert_topic.py | 2 + man/textTopics.Rd | 41 ++++++++++++++++++++++++++++++++-- man/textTopicsWordcloud.Rd | 11 ++++++++- man/textWordPrediction.Rd |only tests/testthat/test_6_textFineTune.R | 2 - tests/testthat/test_7_textTopics.R | 2 - vignettes/ext_install_guide.Rmd | 2 - vignettes/huggingface_in_r.Rmd | 2 - 23 files changed, 154 insertions(+), 46 deletions(-)
Title: Panel VAR Models with Interactive Fixed Effects
Description: Implements the estimator of Tugan (2021) <doi:10.1093/ectj/utaa021>
for panel vector autoregression (VAR) models with interactive fixed effects.
Provides joint estimation of VAR coefficients, latent common factors, and
factor loadings via an iterative algorithm that alternates between principal
component estimation of the factors and least squares estimation of the VAR
coefficients, following the approach of Bai (2009) <doi:10.3982/ECTA6135>.
Supports
impulse response functions under recursive (Cholesky) identification,
parametric confidence bands from the joint asymptotic distribution of the
estimator (Theorem 2.3), and a classical residual bootstrap for robustness
checks.
Author: Binzhi Chen [aut, cre]
Maintainer: Binzhi Chen <Binzhi.Chen9@gmail.com>
Diff between pvarife versions 0.1.1 dated 2026-06-11 and 0.1.2 dated 2026-06-13
DESCRIPTION | 9 +- MD5 | 33 ++++---- R/asymptotic.R | 53 ++++++++++-- R/confidence_bands.R | 143 ++++++++++++++++++++++++----------- R/estimate_pvarife.R | 32 +++++-- R/initial_step.R | 9 ++ R/irf.R | 15 ++- R/simulate.R | 18 ++-- R/utils.R | 7 + man/asymptotic_var.Rd | 18 +++- man/bootstrap_irf_bands.Rd | 38 +++++++-- man/irf_bands.Rd | 15 +++ man/pvarife.Rd | 12 ++ tests/testthat/test-asymptotic.R | 26 ++++++ tests/testthat/test-estimate.R | 18 ++++ tests/testthat/test-generalization.R |only tests/testthat/test-irf.R | 28 ++++++ tests/testthat/test-simulate.R | 18 ++++ 18 files changed, 381 insertions(+), 111 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.8.2 dated 2026-06-12 and 0.8.3 dated 2026-06-13
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 14 R/backends.R | 10 R/join_explain.R | 19 README.md | 2 inst/doc/backends.R | 128 ++ inst/doc/backends.Rmd | 954 ++++++++++++++------ inst/doc/backends.html | 635 ++++++++++--- inst/doc/common-issues.R | 180 +++ inst/doc/common-issues.Rmd | 512 +++++++++-- inst/doc/common-issues.html | 1645 ++++++++++++++++++++++++----------- inst/doc/production.R | 155 +++ inst/doc/production.Rmd | 1306 +++++++++++++++++++--------- inst/doc/production.html | 1206 ++++++++++++++++++-------- inst/doc/quickstart.R | 182 +++ inst/doc/quickstart.Rmd | 1317 +++++++++++++++++----------- inst/doc/quickstart.html | 1748 ++++++++++++++++++++++++++++---------- inst/doc/why-keys-dont-match.R | 67 + inst/doc/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- inst/doc/why-keys-dont-match.html | 785 +++++++++++++---- tests/testthat/Rplots.pdf |binary vignettes/backends.Rmd | 954 ++++++++++++++------ vignettes/common-issues.Rmd | 512 +++++++++-- vignettes/production.Rmd | 1306 +++++++++++++++++++--------- vignettes/quickstart.Rmd | 1317 +++++++++++++++++----------- vignettes/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- 27 files changed, 12128 insertions(+), 5022 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.1.0 dated 2026-06-11 and 3.1.2 dated 2026-06-13
DESCRIPTION | 8 +- MD5 | 32 +++++----- NEWS.md | 40 ++++++++++++ inst/doc/ggRandomForests-regression.html | 34 +++++----- inst/doc/ggRandomForests-survival.html | 40 ++++++------ inst/doc/ggRandomForests.html | 4 - inst/doc/varpro.R | 81 +++++++++++++++++++------ inst/doc/varpro.html | 97 ++++++++++++++++++++++--------- inst/doc/varpro.qmd | 81 +++++++++++++++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/helper-varpro-fixtures.R | 6 + tests/testthat/test_gg_isopro.R | 9 ++ tests/testthat/test_gg_udependent.R | 3 tests/testthat/test_gg_varpro.R | 2 vignettes/precompute_varpro.R | 95 +++++++++++++++++++++++++----- vignettes/varpro.qmd | 81 +++++++++++++++++++------ vignettes/varpro_precomputed.rds |binary 17 files changed, 454 insertions(+), 159 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption [...truncated...]
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.3.0 dated 2025-12-13 and 2.5.0 dated 2026-06-13
did-2.3.0/did/vignettes/TWFE_cache |only did-2.5.0/did/DESCRIPTION | 21 did-2.5.0/did/MD5 | 208 +-- did-2.5.0/did/NAMESPACE | 30 did-2.5.0/did/NEWS.md | 132 + did-2.5.0/did/R/AGGTEobj.R | 8 did-2.5.0/did/R/DIDparams.R | 2 did-2.5.0/did/R/DIDparams2.R | 4 did-2.5.0/did/R/MP.R | 16 did-2.5.0/did/R/aggte.R | 24 did-2.5.0/did/R/att_gt.R | 473 +++++-- did-2.5.0/did/R/compute.aggte.R | 221 ++- did-2.5.0/did/R/compute.att_gt.R | 1067 ++++++++++++---- did-2.5.0/did/R/compute.att_gt2.R | 708 ++++++++-- did-2.5.0/did/R/conditional_did_pretest.R | 224 ++- did-2.5.0/did/R/data.R | 11 did-2.5.0/did/R/ggdid.R | 32 did-2.5.0/did/R/gplot.R | 14 did-2.5.0/did/R/imports.R | 15 did-2.5.0/did/R/mboot.R | 137 +- did-2.5.0/did/R/pre_process_did.R | 298 +++- did-2.5.0/did/R/pre_process_did2.R | 393 +++-- did-2.5.0/did/R/process_attgt.R | 21 did-2.5.0/did/R/simulate_data.R | 15 did-2.5.0/did/R/tidy.R | 130 + did-2.5.0/did/R/utility_functions.R | 116 + did-2.5.0/did/README.md | 56 did-2.5.0/did/build/partial.rdb |binary did-2.5.0/did/build/vignette.rds |binary did-2.5.0/did/inst/CITATION | 2 did-2.5.0/did/inst/doc/TWFE.R | 10 did-2.5.0/did/inst/doc/TWFE.Rmd | 34 did-2.5.0/did/inst/doc/TWFE.html | 59 did-2.5.0/did/inst/doc/did-basics.R | 7 did-2.5.0/did/inst/doc/did-basics.Rmd | 13 did-2.5.0/did/inst/doc/did-basics.html | 82 - did-2.5.0/did/inst/doc/extensions.html | 6 did-2.5.0/did/inst/doc/multi-period-did.Rmd | 2 did-2.5.0/did/inst/doc/multi-period-did.html | 11 did-2.5.0/did/inst/doc/pre-testing.R | 8 did-2.5.0/did/inst/doc/pre-testing.Rmd | 12 did-2.5.0/did/inst/doc/pre-testing.html | 34 did-2.5.0/did/man/AGGTEobj.Rd | 2 did-2.5.0/did/man/DIDparams.Rd | 110 + did-2.5.0/did/man/MP.Rd | 8 did-2.5.0/did/man/aggte.Rd | 24 did-2.5.0/did/man/att_gt.Rd | 150 +- did-2.5.0/did/man/compute.aggte.Rd | 14 did-2.5.0/did/man/compute.att_gt2.Rd | 4 did-2.5.0/did/man/conditional_did_pretest.Rd | 64 did-2.5.0/did/man/did-package.Rd | 3 did-2.5.0/did/man/figures/README-unnamed-chunk-12-1.png |binary did-2.5.0/did/man/figures/README-unnamed-chunk-9-1.png |binary did-2.5.0/did/man/ggdid.AGGTEobj.Rd | 2 did-2.5.0/did/man/ggdid.MP.Rd | 2 did-2.5.0/did/man/ggdid.Rd | 19 did-2.5.0/did/man/mboot.Rd | 9 did-2.5.0/did/man/mpdta.Rd | 11 did-2.5.0/did/man/nobs.AGGTEobj.Rd |only did-2.5.0/did/man/nobs.MP.Rd |only did-2.5.0/did/man/pre_process_did.Rd | 112 + did-2.5.0/did/man/pre_process_did2.Rd | 112 + did-2.5.0/did/man/reexports.Rd | 2 did-2.5.0/did/man/test.mboot.Rd | 8 did-2.5.0/did/man/tidy.AGGTEobj.Rd | 35 did-2.5.0/did/man/tidy.MP.Rd | 25 did-2.5.0/did/man/trimmer.Rd | 4 did-2.5.0/did/tests |only did-2.5.0/did/vignettes/TWFE.Rmd | 34 did-2.5.0/did/vignettes/did-basics.Rmd | 13 did-2.5.0/did/vignettes/multi-period-did.Rmd | 2 did-2.5.0/did/vignettes/pre-testing.Rmd | 12 72 files changed, 4021 insertions(+), 1416 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-12 0.1.0
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding
Description: Methods for analyzing DNA methylation data via Most Recurrent Methylation Patterns (MRMPs). Supports cell-type annotation, spatial deconvolution, unsupervised clustering, and cancer cell-of-origin inference. Includes C-backed summaries for YAME “.cg/.cm” files (overlap counts, log2 odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS deconvolution, and plotting utilities. Scales to large spatial and single-cell methylomes and is robust to extreme sparsity.
Author: Hongxiang Fu [aut, cre] ,
Wanding Zhou [cph, fnd],
The SAMtools/HTSlib authors [ctb, cph] ,
Attractive Chaos [ctb, cph] )
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Diff between MethScope versions 1.0.1 dated 2026-02-26 and 1.0.2 dated 2026-06-13
DESCRIPTION | 11 ++++++----- MD5 | 33 ++++++++++++++++++++------------- NAMESPACE | 2 ++ R/ModelTraining.R | 28 +++++++++++++++++++--------- R/PredictCellType.R | 38 +++++++++++++++++++++++++++++--------- R/PretrainedModels.R |only R/sysdata.rda |binary README.md | 4 +++- inst/doc/MethScope-Tutorial.R | 3 ++- inst/doc/MethScope-Tutorial.Rmd | 5 +++-- inst/doc/MethScope-Tutorial.html | 8 ++++---- inst/extdata/models |only inst/extdata/toy.cm |binary man/Input_training.Rd | 2 +- man/Liu2021_MouseBrain_P1000.Rd |only man/PredictCellType.Rd | 3 ++- man/Zhou2025_HumanAtlas_P1000.Rd |only tests/testthat |only tests/testthat.R |only vignettes/MethScope-Tutorial.Rmd | 5 +++-- 20 files changed, 94 insertions(+), 48 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using STAN
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.0 dated 2026-05-27 and 1.0.1 dated 2026-06-13
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 3 +++ R/bvar.R | 2 ++ R/zzz.R |only README.md | 21 ++++++++++++++++++--- inst/CITATION | 2 +- 7 files changed, 33 insertions(+), 12 deletions(-)
Title: Computes Diversity Indices for Archaeological Data
Description: Companion package of Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>. It computes Diversity Indices, decomposes several of them and computes bootstrap confidence intervals.
Author: Andreu Sanso [aut, cre],
Arnaud Barat [aut],
Jordi Rosell [aut]
Maintainer: Andreu Sanso <andreu.sanso@uib.eu>
Diff between diversityArch versions 0.3.0 dated 2026-05-04 and 0.4.0 dated 2026-06-13
DESCRIPTION | 12 +++---- MD5 | 72 +++++++++++++++++++++---------------------- NEWS.md | 11 ++++++ R/all_indices.R | 87 ++++++++++++++++++++++++++++++++-------------------- R/bs.R | 6 +-- R/bs_dec.R | 10 ++--- R/bs_frag.R | 4 +- R/check_x.R | 11 +----- R/dec_equit.R | 4 +- R/dec_shannon.R | 7 +--- R/dominance.R | 4 +- R/equitability.R | 4 +- R/evenness.R | 4 +- R/margalef.R | 4 +- R/menhinick.R | 4 +- R/shannon.R | 4 +- R/shannon_frag.R | 2 - R/simpson_D.R | 4 +- R/simpson_E.R | 4 +- man/Qesem_f.Rd | 9 ++--- man/Qesem_s.Rd | 9 ++--- man/all_indices.Rd | 8 ++-- man/bs.Rd | 4 +- man/bs_dec.Rd | 4 +- man/bs_frag.Rd | 4 +- man/check_x.Rd | 5 -- man/dec_equit.Rd | 4 +- man/dec_shannon.Rd | 4 +- man/dominance.Rd | 4 +- man/equitability.Rd | 4 +- man/evenness.Rd | 4 +- man/margalef.Rd | 4 +- man/menhinick.Rd | 4 +- man/shannon.Rd | 4 +- man/shannon_frag.Rd | 2 - man/simpson_D.Rd | 4 +- man/simpson_E.Rd | 4 +- 37 files changed, 183 insertions(+), 160 deletions(-)
Title: Canonical Correlation Analysis via Reduced Rank Regression
Description: Canonical correlation analysis (CCA) via reduced-rank regression with support for regularization and cross-validation. Several methods for estimating CCA in high-dimensional settings are implemented. The first set of methods, cca_rrr() (and variants: cca_group_rrr() and cca_graph_rrr()), assumes that one dataset is high-dimensional and the other is low-dimensional, while the second, ecca() (for Efficient CCA) assumes that both datasets are high-dimensional. For both methods, standard l1 regularization as well as group-lasso regularization are available. cca_graph_rrr further supports total variation regularization when there is a known graph structure among the variables of the high-dimensional dataset. In this case, the loadings of the canonical directions of the high-dimensional dataset are assumed to be smooth on the graph. For more details see Donnat and Tuzhilina (2024) <doi:10.48550/arXiv.2405.19539> and Wu, Tuzhilina and Donnat (2025) <doi:10.48550/arXiv.2507.11160> [...truncated...]
Author: Claire Donnat [aut, cre] ,
Elena Tuzhilina [aut] ,
Zixuan Wu [aut]
Maintainer: Claire Donnat <cdonnat@uchicago.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2026-04-29
Diff between ccar3 versions 0.1.1 dated 2026-04-29 and 0.1.2 dated 2026-06-13
DESCRIPTION | 10 ++--- MD5 | 25 ++++++------- R/ecca.r | 1 R/graph_reduced_rank_regression.R | 1 R/group_reduced_rank_regression.R | 15 +++++++ R/reduced_rank_regression.R | 11 +++++ R/utils.R | 62 ++++++++++++++++++++++++++++++++- tests/testthat/helper-cran.R |only tests/testthat/test-cca_graph_rrr_cv.R | 2 + tests/testthat/test-cca_group_rrr.R | 2 - tests/testthat/test-cca_group_rrr_cv.R | 1 tests/testthat/test-cca_rrr.R | 2 - tests/testthat/test-cca_rrr_cv.R | 4 +- tests/testthat/test-ecca.R | 2 - 14 files changed, 114 insertions(+), 24 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.5 dated 2026-04-23 and 0.2.6 dated 2026-06-13
DESCRIPTION | 10 MD5 | 157 +- NAMESPACE | 212 +-- NEWS.md | 128 +- R/BayesERtools-package.R | 12 R/build_spec_coveff.R | 842 ++++++------- R/coveff.R | 903 +++++++------- R/dev_ermod_emax.R | 688 +++++------ R/dev_ermod_lin.R | 1658 +++++++++++++-------------- R/ermod-class.R | 730 ++++++------ R/ermod-methods.R | 750 ++++++------ R/ersim-class.R | 152 +- R/ersim-methods.R | 220 +-- R/eval_ermod.R | 278 ++-- R/loo_kfold.R | 496 ++++---- R/p_direction.R | 164 +- R/plot_ermod.R | 1940 ++++++++++++++++---------------- R/plot_ermod_exp_cov_sel.R | 346 ++--- R/s3_generics.R | 108 - R/sim_ermod.R | 967 ++++++++------- R/utils-draws.R |only R/yyy.R | 356 ++--- README.md | 448 +++---- build/vignette.rds |binary inst/doc/overview_of_the_package.R | 120 - inst/doc/overview_of_the_package.Rmd | 266 ++-- inst/doc/overview_of_the_package.html | 1566 ++++++++++++------------- man/BayesERtools-package.Rd | 72 - man/as_draws.Rd | 104 - man/build_spec_coveff.Rd | 172 +- man/calc_ersim_med_qi.Rd | 40 man/combine_er_components.Rd | 90 - man/d_sim_binom_cov.Rd | 116 - man/d_sim_emax.Rd | 78 - man/d_sim_lin.Rd | 70 - man/d_sim_placebo.Rd | 84 - man/dev_ermod_bin.Rd | 172 +- man/dev_ermod_bin_cov_functions.Rd | 180 +- man/dev_ermod_bin_cov_sel.Rd | 236 +-- man/dev_ermod_bin_exp_sel.Rd | 164 +- man/dev_ermod_emax.Rd | 256 ++-- man/dev_ermod_emax_exp_sel.Rd | 214 +-- man/edit_spec_coveff.Rd | 210 +-- man/ermod_cov_sel_method.Rd | 50 man/ermod_exp_sel_method.Rd | 50 man/ermod_method.Rd | 84 - man/ersim_method.Rd | 56 man/eval_ermod.Rd | 146 +- man/extract_coef_exp_ci.Rd | 54 man/extract_ermod.Rd | 104 - man/extract_ersim.Rd | 104 - man/extract_method.Rd | 104 - man/figures/logo_svg.svg | 1870 +++++++++++++++--------------- man/kfold.Rd | 126 +- man/loo.Rd | 56 man/p_direction.Rd | 146 +- man/plot_cov_sel.Rd | 102 - man/plot_coveff.Rd | 154 +- man/plot_er.Rd | 346 ++--- man/plot_er_exp_sel.Rd | 74 - man/plot_er_gof.Rd | 280 ++-- man/print_coveff.Rd | 150 +- man/prior_summary.Rd | 44 man/sim_coveff.Rd | 142 +- man/sim_er.Rd | 172 +- man/sim_er_new_exp.Rd | 226 +-- man/sim_er_new_exp_marg.Rd | 224 +-- tests/testthat.R | 24 tests/testthat/test-build_spec_coveff.R | 166 +- tests/testthat/test-coveff.R | 346 ++--- tests/testthat/test-dev_ermod_emax.R | 456 +++---- tests/testthat/test-dev_ermod_lin.R | 930 +++++++-------- tests/testthat/test-ermod-methods.R | 298 ++-- tests/testthat/test-eval_ermod.R | 268 ++-- tests/testthat/test-loo_kfold.R | 289 ++-- tests/testthat/test-p_direction.R | 104 - tests/testthat/test-plot_ermod.R | 672 +++++------ tests/testthat/test-sim_ermod.R | 374 +++--- vignettes/data/supported_models.csv | 16 vignettes/overview_of_the_package.Rmd | 266 ++-- 80 files changed, 12438 insertions(+), 12410 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.9 dated 2025-02-17 and 0.1.10 dated 2026-06-13
rstanemax-0.1.10/rstanemax/DESCRIPTION | 16 - rstanemax-0.1.10/rstanemax/MD5 | 19 - rstanemax-0.1.10/rstanemax/NEWS.md | 7 rstanemax-0.1.10/rstanemax/R/posterior_predict.R | 4 rstanemax-0.1.10/rstanemax/build/vignette.rds |binary rstanemax-0.1.10/rstanemax/inst/doc/emaxmodel.html | 117 +++++----- rstanemax-0.1.10/rstanemax/man/posterior_predict.Rd | 4 rstanemax-0.1.10/rstanemax/src/stanExports_emax.cc | 34 +- rstanemax-0.1.10/rstanemax/src/stanExports_emax_binary.cc | 34 +- rstanemax-0.1.10/rstanemax/tests/testthat/test-posterior_integration.R |only rstanemax-0.1.9/rstanemax/src/Makevars.win |only rstanemax-0.1.9/rstanemax/tests/testthat/test-tidybayes_integration.R |only 12 files changed, 121 insertions(+), 114 deletions(-)
Title: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description: An interface to integrate 'igraph' and 'ggplot2' graphics within
a normalized coordinate system. 'RGraphSpace' extends 'ggplot2' with
graph-aware geometries optimized for large networks. The 'GraphSpace' class
integrates directly with 'ggplot2' through specialized 'geoms' and lazy
resolution of node attributes, supporting customization of aesthetics and
visual styles. These 'geoms' use a dual-anchor normalization approach to
align layers, particularly useful for analyses in which network elements
must be spatially aligned with reference maps and images.
Author: Sysbiolab Team [aut],
Flavio Kessler [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.3.0 dated 2026-05-22 and 1.4.0 dated 2026-06-13
RGraphSpace-1.3.0/RGraphSpace/R/inject-nodespace.R |only RGraphSpace-1.4.0/RGraphSpace/DESCRIPTION | 35 - RGraphSpace-1.4.0/RGraphSpace/MD5 | 73 +- RGraphSpace-1.4.0/RGraphSpace/NAMESPACE | 26 RGraphSpace-1.4.0/RGraphSpace/R/annotation-gspace.R |only RGraphSpace-1.4.0/RGraphSpace/R/geom-edgespace.R | 263 ++++--- RGraphSpace-1.4.0/RGraphSpace/R/geom-graphspace.R | 34 RGraphSpace-1.4.0/RGraphSpace/R/geom-nodespace.R | 165 +++- RGraphSpace-1.4.0/RGraphSpace/R/gspace-checks.R | 15 RGraphSpace-1.4.0/RGraphSpace/R/gspace-classes.R | 104 ++ RGraphSpace-1.4.0/RGraphSpace/R/gspace-coercion.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-constructor.R | 18 RGraphSpace-1.4.0/RGraphSpace/R/gspace-features.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-generics.R | 42 + RGraphSpace-1.4.0/RGraphSpace/R/gspace-ggplot-constructor.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-methods.R | 261 +++++-- RGraphSpace-1.4.0/RGraphSpace/R/gspace-normalize.R | 349 +++++----- RGraphSpace-1.4.0/RGraphSpace/R/gspace-supplements.R | 2 RGraphSpace-1.4.0/RGraphSpace/R/gspace-themes.R | 173 ++-- RGraphSpace-1.4.0/RGraphSpace/data/gtoy1.RData |binary RGraphSpace-1.4.0/RGraphSpace/inst/NEWS.Rd | 7 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.R | 10 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.html | 52 - RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-accessors.Rd | 90 +- RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-class.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-methods.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/RGraphSpace-package.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/annotation_gspace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/as.GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/geom_edgespace.Rd | 28 RGraphSpace-1.4.0/RGraphSpace/man/geom_graphspace.Rd | 17 RGraphSpace-1.4.0/RGraphSpace/man/geom_nodespace.Rd | 26 RGraphSpace-1.4.0/RGraphSpace/man/getGraphSpace-methods.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/ggplot-GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/gs_features-utils.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/inject_nodespace.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/normalizeGraphSpace-methods.Rd | 65 + RGraphSpace-1.4.0/RGraphSpace/man/plotGraphSpace-methods.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/theme_gspace.Rd | 42 - RGraphSpace-1.4.0/RGraphSpace/vignettes/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/vignettes/bibliography.bib | 33 42 files changed, 1300 insertions(+), 696 deletions(-)
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Alexander Tedeschi [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael N [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.11.0 dated 2025-08-29 and 0.12.0 dated 2026-06-13
DESCRIPTION | 14 MD5 | 135 ++--- NAMESPACE | 6 NEWS.md | 45 + R/add_param.R |only R/apply_mistnet.R | 6 R/beam.R | 63 +- R/bioRad-deprecated.R | 4 R/calculate_vp.R | 132 ++++- R/clean_mixture.R | 6 R/color_scale.R | 22 R/dbz_eta.R | 2 R/filter_precip.R | 39 + R/integrate_to_ppi.R | 130 ++++ R/project_as_ppi.R | 7 R/read_pvolfile.R | 12 R/s3.R | 2 R/scan_convert.R | 12 R/select.R | 4 R/sunrise_sunset.R | 52 - R/utils.R | 72 ++ R/validate_vpts.R | 18 R/vpts.R | 2 README.md | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/bioRad.Rmd | 2 inst/doc/bioRad.html | 7 inst/doc/rad_aero_22.R | 868 ++++++++++++++++----------------- inst/doc/rad_aero_22.Rmd | 2 inst/doc/rad_aero_22.html | 7 inst/doc/range_correction.html | 41 - man/add_expected_eta_to_scan.Rd | 11 man/add_param.Rd |only man/apply_mistnet.Rd | 4 man/beam_distance.Rd | 14 man/beam_height.Rd | 14 man/beam_profile.Rd | 26 man/beam_profile_overlap.Rd | 26 man/beam_range.Rd | 14 man/beam_width.Rd | 38 - man/bioRad-package.Rd | 1 man/calculate_vp.Rd | 82 ++- man/check_night.Rd | 2 man/clean_mixture.Rd | 4 man/composite_ppi.Rd | 8 man/doy_noy.Rd | 2 man/figures/README-plot_ppi-1.png |binary man/filter_precip.Rd | 10 man/gaussian_beam_profile.Rd | 26 man/integrate_to_ppi.Rd | 63 +- man/is.nan.data.frame.Rd | 20 man/map.Rd | 2 man/min_package_version.Rd |only man/plot.vp.Rd | 2 man/plot.vpi.Rd | 4 man/project_as_ppi.Rd | 4 man/read_pvolfile.Rd | 3 man/scan_to_raster.Rd | 10 man/sunrise_sunset.Rd | 49 - man/tidyverse.Rd | 3 tests/testthat/test-add_param.R |only tests/testthat/test-apply_mistnet.R | 2 tests/testthat/test-beam.R | 31 - tests/testthat/test-filter_precip.R |only tests/testthat/test-integrate_to_ppi.R | 122 ++++ tests/testthat/test-project_as_ppi.R | 11 tests/testthat/test-s3.R | 10 tests/testthat/test-scan_convert.R | 9 vignettes/bioRad.Rmd | 2 vignettes/rad_aero_22.Rmd | 2 71 files changed, 1465 insertions(+), 902 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.10.0 dated 2026-04-08 and 1.10.1 dated 2026-06-13
bbotk-1.10.0/bbotk/inst |only bbotk-1.10.0/bbotk/src/is_dominated.c |only bbotk-1.10.1/bbotk/DESCRIPTION | 10 bbotk-1.10.1/bbotk/MD5 | 173 ++-- bbotk-1.10.1/bbotk/NAMESPACE | 4 bbotk-1.10.1/bbotk/NEWS.md | 7 bbotk-1.10.1/bbotk/R/OptimInstanceAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchFocusSearch.R | 16 bbotk-1.10.1/bbotk/R/OptimizerBatchIrace.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchNLoptr.R | 4 bbotk-1.10.1/bbotk/R/TerminatorStagnationHypervolume.R | 10 bbotk-1.10.1/bbotk/R/helper.R | 6 bbotk-1.10.1/bbotk/R/zzz.R | 2 bbotk-1.10.1/bbotk/build/partial.rdb |binary bbotk-1.10.1/bbotk/man/Archive.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/ArchiveAsync.Rd | 403 +++++----- bbotk-1.10.1/bbotk/man/ArchiveAsyncFrozen.Rd | 313 +++---- bbotk-1.10.1/bbotk/man/ArchiveBatch.Rd | 247 +++--- bbotk-1.10.1/bbotk/man/CallbackAsync.Rd | 79 - bbotk-1.10.1/bbotk/man/CallbackBatch.Rd | 71 - bbotk-1.10.1/bbotk/man/Codomain.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ContextAsync.Rd | 119 +- bbotk-1.10.1/bbotk/man/ContextBatch.Rd | 113 +- bbotk-1.10.1/bbotk/man/EvalInstance.Rd | 185 ++-- bbotk-1.10.1/bbotk/man/Objective.Rd | 307 +++---- bbotk-1.10.1/bbotk/man/ObjectiveRFun.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ObjectiveRFunDt.Rd | 187 ++-- bbotk-1.10.1/bbotk/man/ObjectiveRFunMany.Rd | 162 ++-- bbotk-1.10.1/bbotk/man/ObjectiveTestFunction.Rd | 121 +-- bbotk-1.10.1/bbotk/man/OptimInstance.Rd | 202 ++--- bbotk-1.10.1/bbotk/man/OptimInstanceAsync.Rd | 170 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncMultiCrit.Rd | 154 +-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncSingleCrit.Rd | 153 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatch.Rd | 199 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchMultiCrit.Rd | 152 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchSingleCrit.Rd | 140 +-- bbotk-1.10.1/bbotk/man/OptimInstanceMultiCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/OptimInstanceSingleCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/Optimizer.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/OptimizerAsync.Rd | 91 +- bbotk-1.10.1/bbotk/man/OptimizerBatch.Rd | 88 +- bbotk-1.10.1/bbotk/man/Progressor.Rd | 116 +- bbotk-1.10.1/bbotk/man/Terminator.Rd | 261 +++--- bbotk-1.10.1/bbotk/man/bb_optimize.Rd | 3 bbotk-1.10.1/bbotk/man/bbotk-package.Rd | 1 bbotk-1.10.1/bbotk/man/bbotk_reflections.Rd | 1 bbotk-1.10.1/bbotk/man/branin.Rd | 3 bbotk-1.10.1/bbotk/man/is_dominated.Rd | 5 bbotk-1.10.1/bbotk/man/local_search.Rd | 10 bbotk-1.10.1/bbotk/man/mlr_optimizers.Rd | 5 bbotk-1.10.1/bbotk/man/mlr_optimizers_async_design_points.Rd | 98 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_grid_search.Rd | 101 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_chain.Rd | 88 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_cmaes.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_design_points.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_focus_search.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_gensa.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_grid_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_irace.Rd | 71 - bbotk-1.10.1/bbotk/man/mlr_optimizers_local_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_nloptr.Rd | 69 - bbotk-1.10.1/bbotk/man/mlr_optimizers_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_terminators.Rd | 4 bbotk-1.10.1/bbotk/man/mlr_terminators_clock_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_combo.Rd | 220 ++--- bbotk-1.10.1/bbotk/man/mlr_terminators_evals.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_none.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_perf_reached.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_run_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_batch.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_hypervolume.Rd | 107 +- bbotk-1.10.1/bbotk/man/mlr_test_functions.Rd | 2 bbotk-1.10.1/bbotk/man/reexports.Rd | 2 bbotk-1.10.1/bbotk/man/shrink_ps.Rd | 8 bbotk-1.10.1/bbotk/src/init.c | 4 bbotk-1.10.1/bbotk/src/local_search.c | 2 bbotk-1.10.1/bbotk/tests/testthat/helper.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_Objective.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_OptimInstanceBatchMultiCrit.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchFocusSearch.R | 12 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchLocalSearch.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationBatch.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationHypervolume.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_c_functions.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_helper.R |only bbotk-1.10.1/bbotk/tests/testthat/test_nds_selection.R | 20 89 files changed, 3704 insertions(+), 3561 deletions(-)
Title: Develop Hybridization Probes
Description: Hybridization probes for target sequences can be made based on melting temperature value calculated by R package 'TmCalculator' <https://CRAN.R-project.org/package=TmCalculator> and methods extended from Beliveau, B. J.,(2018) <doi:10.1073/pnas.1714530115>, and those hybridization probes can be used to capture specific target regions in fluorescence in situ hybridization and next generation sequence experiments.
Author: Junhui Li [cre, aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ProbeDeveloper versions 1.1.1 dated 2026-03-23 and 1.1.2 dated 2026-06-13
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- R/ProbeMake.R | 8 ++++---- README.md |only 4 files changed, 12 insertions(+), 11 deletions(-)
More information about ProbeDeveloper at CRAN
Permanent link
Title: An R Interface to the California Academy of Sciences Eschmeyer's
Catalog of Fishes
Description: Accesses the California Academy of Sciences Eschmeyer's Catalog of Fishes in R using web requests. The Catalog of fishes is the leading authority in fish taxonomy. Functions in the package allow users to search for fish taxa and valid names, retrieve taxonomic references, retrieve monthly taxonomic changes, obtain natural history collection information, and see the number of species by taxonomic group. For more information on the Catalog: Fricke, R., Eschmeyer, W. N. & R. van der Laan (eds) 2025. ESCHMEYER'S CATALOG OF FISHES <https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp>.
Author: Samuel R. Borstein [aut, cre],
Brandon Dominy [aut],
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between rcatfish versions 1.0.2 dated 2026-02-19 and 1.0.3 dated 2026-06-12
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 ++--- build/vignette.rds |binary inst/doc/rcatfish-vignette.html | 2 +- tests/testthat/test_rcatfish_updates.R | 2 +- 6 files changed, 14 insertions(+), 15 deletions(-)
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Description: Implementation of the Harmony algorithm for single cell integration, described in Patikas, Yao, et al. <doi:10.64898/2026.03.16.711825>. Package includes a standalone Harmony function and interfaces to external frameworks.
Author: Nikolaos Patikas [aut, ctb] ,
Hongcheng Yao [aut, ctb] ,
Ilya Korsunsky [cre, aut] ,
Martin Hemberg [aut] ,
Nghia Millard [aut] ,
Jean Fan [aut, ctb] ,
Kamil Slowikowski [aut, ctb] ,
Miles Smith [ctb],
Soumya Raychaudhuri [aut]
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>
This is a re-admission after prior archival of version 2.0.4 dated 2026-06-04
Diff between harmony versions 2.0.4 dated 2026-06-04 and 2.0.5 dated 2026-06-12
DESCRIPTION | 6 +- MD5 | 16 ++--- R/zzz.R | 36 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Seurat.html | 108 ++++++++++++++++++------------------- inst/doc/detailedWalkthrough.html | 102 +++++++++++++++++----------------- inst/doc/quickstart.html | 84 ++++++++++++++-------------- tests/testthat/test_two_variable.R | 106 ++++++++++++++++++------------------ 9 files changed, 230 insertions(+), 228 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut],
Idris A. Eckley [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.6 dated 2026-06-09 and 0.1.7 dated 2026-06-12
DESCRIPTION | 9 +++++---- MD5 | 8 +++++--- src/ChangepointResult.h | 4 ++-- src/Costs.h | 36 +++++++++++++++++++----------------- tests |only 5 files changed, 31 insertions(+), 26 deletions(-)
Title: Utilities for Importing Data from Plain Text Accounting Files
Description: Utilities for querying plain text accounting files from 'Ledger', 'HLedger', and 'Beancount'.
Author: Trevor L. Davis [aut, cre] ,
Jenya Sovetkin [ctb],
Chris Lloyd [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ledger versions 2.0.13 dated 2026-03-30 and 2.1.1 dated 2026-06-12
DESCRIPTION | 11 MD5 | 30 NAMESPACE | 2 NEWS.md | 14 R/net_worth.R | 22 R/prune_coa.R | 6 R/register.R | 85 +- README.md | 969 +++++++++++++++++-------------- man/figures/README-income_chart-1.png |binary man/figures/README-net_worth_chart-1.png |binary man/figures/logo.png |only man/figures/logo.svg |only man/net_worth.Rd | 2 man/prune_coa.Rd | 6 man/register.Rd | 15 tests/testthat/test-net_worth.R | 4 tests/testthat/test-register.R | 18 17 files changed, 686 insertions(+), 498 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.8.0 dated 2026-03-31 and 0.8.2 dated 2026-06-12
DESCRIPTION | 8 MD5 | 182 ++--- NAMESPACE | 76 +- NEWS.md | 23 R/JoinReport.R | 8 R/addin.R | 6 R/advanced_patterns.R | 49 - R/backends.R | 239 +++--- R/join_explain.R | 26 R/join_repair.R | 49 - R/join_spy.R | 41 - R/join_strict.R | 66 - R/joinspy-package.R | 2 R/key_check.R | 36 - R/logging.R | 29 R/string_diagnostics.R | 30 R/utils-keys.R |only README.md | 104 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/backends.Rmd | 612 ++++++++--------- inst/doc/backends.html | 4 inst/doc/common-issues.R | 2 inst/doc/common-issues.Rmd | 983 +++++++++++++-------------- inst/doc/common-issues.html | 25 inst/doc/production.R | 8 inst/doc/production.Rmd | 853 ++++++++++++------------ inst/doc/production.html | 134 +-- inst/doc/quickstart.Rmd | 1029 ++++++++++++++--------------- inst/doc/quickstart.html | 68 + inst/doc/why-keys-dont-match.Rmd | 721 ++++++++++---------- inst/doc/why-keys-dont-match.html | 61 - man/addin_join_inspector.Rd | 32 man/analyze_join_chain.Rd | 84 +- man/check_cartesian.Rd | 72 +- man/detect_cardinality.Rd | 72 +- man/dot-analyze_match.Rd | 44 - man/dot-analyze_multicolumn_keys.Rd | 48 - man/dot-check_cols.Rd |only man/dot-classify_cardinality.Rd |only man/dot-detect_backend.Rd | 40 - man/dot-detect_case_mismatch.Rd | 48 - man/dot-detect_empty_strings.Rd | 36 - man/dot-detect_encoding_issues.Rd | 48 - man/dot-detect_factor_mismatch.Rd | 48 - man/dot-detect_near_matches.Rd | 48 - man/dot-detect_numeric_precision.Rd | 36 - man/dot-detect_type_mismatch.Rd | 48 - man/dot-detect_whitespace.Rd | 48 - man/dot-format_bytes.Rd | 36 - man/dot-join_spy_impl.Rd | 64 - man/dot-json_escape.Rd |only man/dot-levenshtein.Rd | 40 - man/dot-make_key.Rd |only man/dot-perform_join.Rd | 60 - man/dot-predict_row_counts.Rd | 44 - man/dot-report_to_list.Rd | 40 - man/dot-report_to_text.Rd | 40 - man/dot-resolve_by.Rd |only man/dot-summarize_keys.Rd | 40 - man/dot-to_json.Rd | 36 - man/dot-validate_df.Rd |only man/full_join_spy.Rd | 74 +- man/get_log_file.Rd | 34 man/inner_join_spy.Rd | 74 +- man/is_join_report.Rd | 34 man/join_diff.Rd | 66 - man/join_explain.Rd | 86 +- man/join_repair.Rd | 126 +-- man/join_spy.Rd | 136 +-- man/join_strict.Rd | 128 +-- man/joinspy-package.Rd | 53 - man/key_check.Rd | 82 +- man/key_duplicates.Rd | 92 +- man/last_report.Rd | 60 - man/left_join_spy.Rd | 106 +- man/log_report.Rd | 92 +- man/new_join_report.Rd | 70 - man/plot.JoinReport.Rd | 86 +- man/print.JoinReport.Rd | 38 - man/right_join_spy.Rd | 74 +- man/set_log_file.Rd | 66 - man/suggest_repairs.Rd | 56 - man/summary.JoinReport.Rd | 60 - tests/testthat/Rplots.pdf |binary tests/testthat/test-backends-integration.R | 166 ++-- tests/testthat/test-backends.R | 344 ++++----- tests/testthat/test-bugfixes.R |only tests/testthat/test-coverage-boost.R | 24 tests/testthat/test-join_strict.R | 28 tests/testthat/test-phase3-6.R | 12 vignettes/backends.Rmd | 612 ++++++++--------- vignettes/common-issues.Rmd | 983 +++++++++++++-------------- vignettes/production.Rmd | 853 ++++++++++++------------ vignettes/quickstart.Rmd | 1029 ++++++++++++++--------------- vignettes/why-keys-dont-match.Rmd | 721 ++++++++++---------- 96 files changed, 6546 insertions(+), 6545 deletions(-)
Title: Species Distribution Modeling with H3 Grids
Description: Provides tools for species distribution modeling using H3
hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>).
Facilitates retrieval of species occurrence records, generation of H3 grids,
computation of landscape metrics, and preparation of spatial data for modern
species distribution models workflows. Designed for biodiversity and landscape ecology research.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between h3sdm versions 0.1.4 dated 2026-05-29 and 0.1.5 dated 2026-06-12
DESCRIPTION | 16 - MD5 | 42 ++-- NAMESPACE | 2 NEWS.md | 63 ++++++ R/data-doc.R | 122 +++++++++++- R/h3sdm_aoa.R | 16 - R/h3sdm_filter_outliers.R |only R/h3sdm_pa.R | 197 +++++++++++-------- R/h3sdm_pa_from_records.R | 72 ++++++- R/h3sdm_pres.R |only data/cr_outline.rda |only data/cr_outline_c.rda |binary inst/doc/h3sdm.R | 34 ++- inst/doc/h3sdm.Rmd | 103 ++++++---- inst/doc/h3sdm.html | 280 ++++++++++++++-------------- man/bioclim_current.Rd | 2 man/bioclim_future.Rd | 4 man/cr_outline.Rd |only man/cr_outline_c.Rd | 42 +++- man/h3sdm_filter_outliers.Rd |only man/h3sdm_pa.Rd | 77 ++++--- man/h3sdm_pa_from_records.Rd | 17 + man/h3sdm_pres.Rd |only vignettes/articles/multi_model_workflow.Rmd | 248 +++++++++++------------- vignettes/h3sdm.Rmd | 103 ++++++---- 25 files changed, 915 insertions(+), 525 deletions(-)
Title: NASA 'EarthData' Access Utilities
Description: Providing easy, portable access to NASA 'EarthData' products
through the use of bearer tokens. Much of NASA's public data catalogs hosted
and maintained by its 12 Distributed Active Archive Centers ('DAACs') are
now made available on the Amazon Web Services 'S3' storage. However,
accessing this data through the standard 'S3' API is restricted to only to
compute resources running inside 'us-west-2' Data Center in Portland, Oregon,
which allows NASA to avoid being charged data egress rates. This package
provides public access to the data from any networked device by using the
'EarthData' login application programming interface (API),
<https://www.earthdata.nasa.gov/data/earthdata-login>,
providing convenient authentication and access to cloud-hosted NASA 'EarthData'
products. This makes access to a wide range of earth observation data from
any location straight forward and compatible with R packages that are
widely used with cloud native earth observation data (such as 'terra',
's [...truncated...]
Author: Carl Boettiger [aut, cre, cph] ,
Luis Lopez [aut] ,
Yuvi Panda [aut],
Bri Lind [aut] ,
Andy Teucher [ctb] ,
Openscapes [fnd]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between earthdatalogin versions 0.0.3 dated 2025-07-11 and 0.0.4 dated 2026-06-12
earthdatalogin-0.0.3/earthdatalogin/inst/vignette-sources/gdalcubes-stac-cog-explore.Rmd |only earthdatalogin-0.0.4/earthdatalogin/DESCRIPTION | 6 +- earthdatalogin-0.0.4/earthdatalogin/MD5 | 23 ++++------ earthdatalogin-0.0.4/earthdatalogin/NEWS.md | 7 +++ earthdatalogin-0.0.4/earthdatalogin/R/edl_search.R | 3 - earthdatalogin-0.0.4/earthdatalogin/build/vignette.rds |binary earthdatalogin-0.0.4/earthdatalogin/inst/doc/data-formats.html | 4 - earthdatalogin-0.0.4/earthdatalogin/inst/doc/gdalcubes-stac-cog.html | 6 +- earthdatalogin-0.0.4/earthdatalogin/inst/doc/legacy-formats.html | 6 +- earthdatalogin-0.0.4/earthdatalogin/inst/doc/non-egressed.html | 2 earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-edl_netrc.R | 3 + earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-edl_search.R | 15 ++++++ earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-list-nasa-stacs.R | 10 ++++ 13 files changed, 59 insertions(+), 26 deletions(-)
More information about earthdatalogin at CRAN
Permanent link
Title: A Collection of Tools for Network Analysis
Description: Provides a collection of network analytic (convenience) functions which are missing in other standard packages. This includes triad census with attributes <doi:10.1016/j.socnet.2019.04.003>, core-periphery models <doi:10.1016/S0378-8733(99)00019-2>, and several graph generators. Most functions are build upon 'igraph'.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between netUtils versions 0.8.5 dated 2026-04-14 and 0.8.6 dated 2026-06-12
DESCRIPTION | 6 MD5 | 25 +- NEWS.md | 6 R/dyad_census_attr.R | 11 - R/fast_cliques.R | 4 R/graph_structures.R | 6 R/graphs.R | 8 R/print_igraph.R | 18 +- R/qap.R | 4 R/sample_kcores.R | 4 R/structural_equivalence.R | 2 R/triad_census_attr.R | 316 ++++--------------------------------- R/utils.R | 16 + tests/testthat/test-print_igraph.R |only 14 files changed, 103 insertions(+), 323 deletions(-)
More information about SmokingHistoryGenerator at CRAN
Permanent link
Title: Markov Decision Processes (MDPs)
Description: Create and optimize (semi) MDPs with discrete time steps and
state space. Both hierarchical and ordinary-traditional MDPs can be
modeled.
Author: Lars Relund Nielsen [aut, cre]
Maintainer: Lars Relund Nielsen <lars@relund.dk>
This is a re-admission after prior archival of version 2.1.2 dated 2023-01-31
Diff between MDP2 versions 2.1.2 dated 2023-01-31 and 2.2.2.0 dated 2026-06-12
MDP2-2.1.2/MDP2/R/binary.R |only MDP2-2.1.2/MDP2/R/hmpMDPWriter.R |only MDP2-2.1.2/MDP2/src/matalg.h |only MDP2-2.1.2/MDP2/src/matrix.h |only MDP2-2.2.2.0/MDP2/DESCRIPTION | 26 MDP2-2.2.2.0/MDP2/MD5 | 115 MDP2-2.2.2.0/MDP2/NAMESPACE | 1 MDP2-2.2.2.0/MDP2/NEWS.md | 12 MDP2-2.2.2.0/MDP2/R/convert.R | 3 MDP2-2.2.2.0/MDP2/R/mdp.R | 149 - MDP2-2.2.2.0/MDP2/R/plot.R | 724 ++++- MDP2-2.2.2.0/MDP2/R/writer.R |only MDP2-2.2.2.0/MDP2/build/vignette.rds |binary MDP2-2.2.2.0/MDP2/inst/WORDLIST | 4 MDP2-2.2.2.0/MDP2/inst/doc/building.R | 18 MDP2-2.2.2.0/MDP2/inst/doc/building.Rmd | 16 MDP2-2.2.2.0/MDP2/inst/doc/building.html | 457 +-- MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.R | 10 MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.Rmd | 4 MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.html | 93 MDP2-2.2.2.0/MDP2/inst/doc/infinite-hmdp.R | 14 MDP2-2.2.2.0/MDP2/inst/doc/infinite-hmdp.html | 189 - MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.R | 8 MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.Rmd | 6 MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.html | 113 MDP2-2.2.2.0/MDP2/inst/doc/mdp2.html | 4 MDP2-2.2.2.0/MDP2/inst/examples/convert-ex.R | 13 MDP2-2.2.2.0/MDP2/inst/examples/memoryMDPWriter-ex.R |only MDP2-2.2.2.0/MDP2/inst/examples/plot-ex.R | 76 MDP2-2.2.2.0/MDP2/man/MDP2-package.Rd | 5 MDP2-2.2.2.0/MDP2/man/binaryActionWriter.Rd | 84 MDP2-2.2.2.0/MDP2/man/binaryMDPWriter.Rd | 183 - MDP2-2.2.2.0/MDP2/man/convertBinary2HMP.Rd | 15 MDP2-2.2.2.0/MDP2/man/convertHMP2Binary.Rd | 13 MDP2-2.2.2.0/MDP2/man/getBinInfoActions.Rd | 2 MDP2-2.2.2.0/MDP2/man/getBinInfoStates.Rd | 2 MDP2-2.2.2.0/MDP2/man/getHypergraph.Rd | 83 MDP2-2.2.2.0/MDP2/man/getPolicy.Rd | 4 MDP2-2.2.2.0/MDP2/man/getRPO.Rd | 7 MDP2-2.2.2.0/MDP2/man/hmpMDPWriter.Rd | 59 MDP2-2.2.2.0/MDP2/man/loadMDP.Rd | 3 MDP2-2.2.2.0/MDP2/man/memoryMDPWriter.Rd |only MDP2-2.2.2.0/MDP2/man/plot.HMDP.Rd | 91 MDP2-2.2.2.0/MDP2/man/plotHypergraph.Rd | 145 - MDP2-2.2.2.0/MDP2/man/runCalcWeights.Rd | 2 MDP2-2.2.2.0/MDP2/man/runPolicyIteAve.Rd | 13 MDP2-2.2.2.0/MDP2/man/runPolicyIteDiscount.Rd | 5 MDP2-2.2.2.0/MDP2/man/runValueIte.Rd | 10 MDP2-2.2.2.0/MDP2/src/RcppExports.cpp | 1 MDP2-2.2.2.0/MDP2/src/basicdt.h | 62 MDP2-2.2.2.0/MDP2/src/hmdp.cpp | 2580 +++++++++++++++++-- MDP2-2.2.2.0/MDP2/src/hmdp.h | 1759 +++++++++--- MDP2-2.2.2.0/MDP2/src/modules.cpp | 104 MDP2-2.2.2.0/MDP2/src/timer.h | 172 - MDP2-2.2.2.0/MDP2/tests/testthat/files/cow.csv |only MDP2-2.2.2.0/MDP2/tests/testthat/test_building.R | 519 +++ MDP2-2.2.2.0/MDP2/tests/testthat/test_convert.R | 1 MDP2-2.2.2.0/MDP2/tests/testthat/test_criteria.R | 395 ++ MDP2-2.2.2.0/MDP2/tests/testthat/test_plot.R |only MDP2-2.2.2.0/MDP2/tests/testthat/test_steady.R | 1 MDP2-2.2.2.0/MDP2/vignettes/building.Rmd | 16 MDP2-2.2.2.0/MDP2/vignettes/finite-mdp.Rmd | 4 MDP2-2.2.2.0/MDP2/vignettes/infinite-mdp.Rmd | 6 63 files changed, 6585 insertions(+), 1816 deletions(-)
Title: Computation of the Double-Entry Intraclass Correlation
Description: The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Author: Christian Bloetner [aut, cre],
Michael Paul Grosz [aut]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between iccde versions 0.3.8 dated 2025-04-23 and 0.3.9 dated 2026-06-12
DESCRIPTION | 6 +- MD5 | 16 ++--- NAMESPACE | 3 - R/iccde.R | 163 +++++++++++++++++++++++++++++++++++++++++++++++++++---- R/iccdeboot.R | 69 +++++++++++++++++------ R/iccdemat.R | 40 +++++++++++-- man/iccde.Rd | 42 ++++++++++++-- man/iccdeboot.Rd | 21 ++++--- man/iccdemat.Rd | 8 ++ 9 files changed, 307 insertions(+), 61 deletions(-)
Title: Temporal Parametric Hazard Modeling
Description: Provides native R implementations of the multiphase parametric
hazard model of Blackstone, Naftel, and Turner (1986)
<doi:10.1080/01621459.1986.10478314> with a focus on behavioral parity,
transparent numerics, and reproducible validation against reference
outputs from the original 'C'/'SAS' HAZARD program, originally developed at
the University of Alabama at Birmingham (UAB). The 'SAS'/'C' code and this R
package are currently developed and maintained at The Cleveland Clinic
Foundation, and the R code was wholly developed at The Cleveland Clinic
Foundation. The generalized temporal
decomposition family extends to longitudinal mixed-effects settings
(Rajeswaran et al. 2018 <doi:10.1177/0962280215623583>). The package is
intentionally implemented in pure R first; performance-critical paths may
later be accelerated with 'Rcpp' without changing the public interface.
Author: John Ehrlinger [aut, cre, cph]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between TemporalHazard versions 1.0.3 dated 2026-05-30 and 1.1.0 dated 2026-06-12
DESCRIPTION | 6 MD5 | 173 ++-- NEWS.md | 359 +++++++++ R/TemporalHazard-package.R |only R/argument_mapping.R | 3 R/decomposition.R | 44 + R/diagnostics.R | 221 +++-- R/hazard_api.R | 266 ++++++- R/hessian-invert.R |only R/hessian-multiphase.R |only R/likelihood-exponential.R | 68 + R/likelihood-loglogistic.R | 77 ++ R/likelihood-lognormal.R | 97 ++ R/likelihood-multiphase.R | 212 +++++ R/likelihood-weibull.R | 183 ++++ R/math_primitives.R | 41 + R/optimizer.R | 67 + R/phase-spec.R | 70 + R/predict-cl.R | 243 ++++-- R/stepwise-formula.R | 43 + R/stepwise.R | 57 + R/weights-fixture.R |only README.md | 8 inst/doc/clinical-analysis-walkthrough.html | 301 +++++--- inst/doc/fitting-hazard-models.R | 145 +++ inst/doc/fitting-hazard-models.html | 371 +++++++++- inst/doc/fitting-hazard-models.qmd | 327 ++++++++ inst/doc/getting-started.html | 36 inst/doc/inference-diagnostics.html | 56 - inst/doc/inference-diagnostics.qmd | 6 inst/doc/mf-mathematical-foundations.html | 2 inst/doc/mf-mathematical-foundations.qmd | 15 inst/doc/prediction-visualization.html | 4 inst/doc/sas-to-r-migration.html | 50 - inst/extdata/stepwise-fixtures/avc-forward-wald.sas |only inst/extdata/stepwise-fixtures/parse-hazard-lst.R |only inst/extdata/stepwise-fixtures/payload |only inst/extdata/weights-fixtures |only inst/fixtures/mp_synthetic_3phase.rds |binary inst/fixtures/stepwise-avc-forward-wald.rds |only man/TemporalHazard-package.Rd |only man/dot-hzr_conserve_events.Rd | 10 man/dot-hzr_free_vcov.Rd |only man/dot-hzr_predict_jacobian_multiphase.Rd | 10 man/dot-hzr_predict_with_se.Rd | 7 man/dot-hzr_predict_with_se_decomposed.Rd |only man/dot-hzr_select_fixmu_phase.Rd | 20 man/figures/readme-hazard-phases.png |binary man/figures/readme-survival.png |binary man/hazard.Rd | 78 ++ man/hzr_argument_mapping.Rd | 5 man/hzr_clamp_prob.Rd | 11 man/hzr_competing_risks.Rd | 16 man/hzr_deciles.Rd | 37 man/hzr_decompos.Rd | 26 man/hzr_kaplan.Rd | 8 man/hzr_log1mexp.Rd | 20 man/hzr_log1pexp.Rd | 18 man/hzr_nelson.Rd | 8 man/hzr_phase.Rd | 74 + man/hzr_stepwise.Rd | 62 + man/predict.hazard.Rd | 31 man/print.summary.hazard.Rd | 5 man/stepwise_trace.Rd | 3 man/vcov.hazard.Rd | 14 tests/testthat/helper-invariants.R |only tests/testthat/helper-sas-parity.R | 333 ++++++++ tests/testthat/test-coe-left-truncation.R |only tests/testthat/test-conservation-of-events.R | 222 +++++ tests/testthat/test-decompos-boundary.R |only tests/testthat/test-diagnostics.R | 158 +++- tests/testthat/test-exponential-hessian.R |only tests/testthat/test-hazard-api.R | 64 + tests/testthat/test-hessian-invert.R |only tests/testthat/test-hessian-stability.R |only tests/testthat/test-interval-censoring-multiphase.R |only tests/testthat/test-interval-censoring-weibull.R | 74 + tests/testthat/test-invariants.R |only tests/testthat/test-loglogistic-hessian.R |only tests/testthat/test-lognormal-hessian.R |only tests/testthat/test-multiphase-api.R | 28 tests/testthat/test-multiphase-gradient.R | 4 tests/testthat/test-multiphase-hessian.R |only tests/testthat/test-multiphase-likelihood.R | 5 tests/testthat/test-phase-specific-covariates.R |only tests/testthat/test-predict-cl.R | 208 +++++ tests/testthat/test-predict-hazard-multiphase.R |only tests/testthat/test-sas-parity.R | 742 +++++++++++++++++++- tests/testthat/test-stepwise-parity.R | 174 ++-- tests/testthat/test-weibull-event-hazard.R |only tests/testthat/test-weibull-hessian.R |only tests/testthat/test-weights-sas-parity.R |only tests/testthat/test-weights.R | 311 ++++++++ vignettes/fitting-hazard-models.qmd | 327 ++++++++ vignettes/inference-diagnostics.qmd | 6 vignettes/mf-mathematical-foundations.qmd | 15 96 files changed, 5924 insertions(+), 761 deletions(-)
More information about TemporalHazard at CRAN
Permanent link
Title: Datasets from the Hello Data Science Book
Description: Provides datasets used for analysis
and visualizations in the open-access Hello Data Science book.
Author: Mine Dogucu [aut, cre] ,
Catalina Medina [aut] ,
Alma Castro [aut]
Maintainer: Mine Dogucu <mdogucu@gmail.com>
Diff between hellodatascience versions 0.1.0 dated 2026-01-19 and 0.1.1 dated 2026-06-12
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++++++++-- NEWS.md | 4 ++++ R/data-confederations.R |only R/data-country-capital.R |only R/data-country-rank.R |only R/data-mx-us-wc-ranks.R |only data/confederations.rda |only data/country_capital.rda |only data/country_rank.rda |only data/mx_us_wc_ranks.rda |only man/confederations.Rd |only man/country_capital.Rd |only man/country_rank.Rd |only man/mx_us_wc_ranks.Rd |only 15 files changed, 22 insertions(+), 6 deletions(-)
More information about hellodatascience at CRAN
Permanent link
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymization methods are included. Note that the package
includes a graphical user interface published in Meindl and Templ (2019) <doi:10.3390/a12090191> that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] ,
Bernhard Meindl [aut],
Alexander Kowarik [aut] ,
Johannes Gussenbauer [aut],
Organisation For Economic Co-Operation And Development [cph] code code for rank swapping,
mdav-microaggregation, suda2 and other risk
measures [...truncated...]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.8.1 dated 2026-03-10 and 5.8.2 dated 2026-06-12
DESCRIPTION | 19 MD5 | 35 - NAMESPACE | 2 NEWS | 13 R/AI_applyAnonymization.R | 33 R/ai_access_utilities.R | 11 R/measure_risk.R | 117 ++- R/recordLinkage.R |only inst/doc/ai_assisted_anonymization.Rmd | 285 ++++---- inst/doc/ai_assisted_anonymization.html | 397 ++++++----- inst/doc/sdcMicro.html | 4 man/AI_applyAnonymization.Rd | 12 man/query_llm.Rd | 3 man/recordLinkage.Rd |only src/Measure_Risk.h | 1081 +++++++++----------------------- tests/testthat/test_ai_early_stopping.R |only tests/testthat/test_ldiversity.R |only tests/testthat/test_pram.R | 490 ++------------ tests/testthat/test_recordLinkage.R |only vignettes/ai_assisted.bib | 93 ++ vignettes/ai_assisted_anonymization.Rmd | 285 ++++---- 21 files changed, 1194 insertions(+), 1686 deletions(-)
Title: Image Processing for Simulated Cameras
Description: Uses convolution-based techniques to generate simulated camera bokeh, depth of field, and other camera effects, using an image and an optional depth map. Accepts both filename inputs and in-memory array representations of images and matrices, including common raster formats such as 'JPEG', 'PNG', 'TIFF', 'TGA', 'BMP', 'PSD', 'GIF', 'HDR', 'PIC', 'PNM', 'DNG', and 'EXR'. Includes functions to perform 2D convolutions, color correction, colorspace conversion, image/matrix reorientation and resizing, image and text overlays, exposure adjustment, camera vignette effects, and image titles.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayimage versions 0.15.1 dated 2025-02-01 and 0.26.1 dated 2026-06-12
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Title: Sparse Principal Component Analysis with Multiple Principal
Components
Description: Implements an algorithm for computing multiple sparse principal
components of a dataset. The method is based on Cory-Wright and Pauphilet
"Sparse PCA with Multiple Principal Components" (2026)
<doi:10.48550/arXiv.2209.14790>. The algorithm uses an iterative deflation
heuristic with a truncated power method applied at each iteration to compute
sparse principal components with controlled sparsity.
Author: Ryan Cory-Wright [aut, cph] ,
Jean Pauphilet [aut, cre, cph]
Maintainer: Jean Pauphilet <jpauphilet@london.edu>
Diff between msPCA versions 0.4.0 dated 2026-05-22 and 0.4.1 dated 2026-06-12
DESCRIPTION | 10 - MD5 | 28 ++-- NEWS.md | 7 + R/main.R | 50 ++----- README.md | 204 +++++++++++++++++++++---------- build |only inst/CITATION |only inst/doc |only man/feasibility_violation_off.Rd | 3 man/fraction_variance_explained.Rd | 3 man/fraction_variance_explained_perPC.Rd | 2 man/mspca.Rd | 1 man/print_mspca.Rd | 9 - man/tpm.Rd | 1 man/variance_explained_perPC.Rd | 2 vignettes |only 16 files changed, 201 insertions(+), 119 deletions(-)