Title: Create Maps and Visualize Data in 2D and 3D
Description: Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.37.3 dated 2024-02-21 and 0.41.2 dated 2026-07-19
rayshader-0.37.3/rayshader/R/pipeImport.R |only rayshader-0.37.3/rayshader/R/utils-pipe.R |only rayshader-0.41.2/rayshader/DESCRIPTION | 29 rayshader-0.41.2/rayshader/MD5 | 319 - rayshader-0.41.2/rayshader/NAMESPACE | 2 rayshader-0.41.2/rayshader/NEWS | 843 ++++ rayshader-0.41.2/rayshader/R/add_overlay.R | 107 rayshader-0.41.2/rayshader/R/add_padding.R | 3 rayshader-0.41.2/rayshader/R/add_shadow.R | 91 rayshader-0.41.2/rayshader/R/add_water.R | 140 rayshader-0.41.2/rayshader/R/ambient_shade.R | 142 rayshader-0.41.2/rayshader/R/calculate_normal.R | 28 rayshader-0.41.2/rayshader/R/colorspace_functions.R | 23 rayshader-0.41.2/rayshader/R/constant_shade.R | 46 rayshader-0.41.2/rayshader/R/convert_color.R | 53 rayshader-0.41.2/rayshader/R/convert_path_to_animation_coords.R | 428 +- rayshader-0.41.2/rayshader/R/convert_rgl_to_raymesh.R | 558 +-- rayshader-0.41.2/rayshader/R/create_texture.R | 166 rayshader-0.41.2/rayshader/R/defunct.R |only rayshader-0.41.2/rayshader/R/detect_water.R | 79 rayshader-0.41.2/rayshader/R/flag_obj.R | 12 rayshader-0.41.2/rayshader/R/generate_altitude_overlay.R | 133 rayshader-0.41.2/rayshader/R/generate_compass_overlay.R | 556 ++- rayshader-0.41.2/rayshader/R/generate_contour_overlay.R | 144 rayshader-0.41.2/rayshader/R/generate_dirt_textures.R | 103 rayshader-0.41.2/rayshader/R/generate_label_overlay.R | 383 +- rayshader-0.41.2/rayshader/R/generate_line_overlay.R | 208 - 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rayshader-0.41.2/rayshader/R/render_depth.R | 422 +- rayshader-0.41.2/rayshader/R/render_floating_overlay.R | 192 - rayshader-0.41.2/rayshader/R/render_highquality.R | 1585 +++++--- rayshader-0.41.2/rayshader/R/render_label.R | 558 +-- rayshader-0.41.2/rayshader/R/render_movie.R | 336 - rayshader-0.41.2/rayshader/R/render_multipolygonz.R | 81 rayshader-0.41.2/rayshader/R/render_obj.R | 655 ++- rayshader-0.41.2/rayshader/R/render_path.R | 360 +- rayshader-0.41.2/rayshader/R/render_points.R | 105 rayshader-0.41.2/rayshader/R/render_polygons.R | 326 + rayshader-0.41.2/rayshader/R/render_raymesh.R | 700 ++- rayshader-0.41.2/rayshader/R/render_resize_window.R | 39 rayshader-0.41.2/rayshader/R/render_scalebar.R | 541 +-- rayshader-0.41.2/rayshader/R/render_snapshot.R | 255 - rayshader-0.41.2/rayshader/R/render_snapshot_software.R | 498 +- rayshader-0.41.2/rayshader/R/render_tree.R | 958 ++--- rayshader-0.41.2/rayshader/R/render_water.R | 70 rayshader-0.41.2/rayshader/R/resize_matrix.R | 192 - rayshader-0.41.2/rayshader/R/save_3dprint.R | 56 rayshader-0.41.2/rayshader/R/save_multipolygonz_to_obj.R | 2 rayshader-0.41.2/rayshader/R/save_obj.R | 1770 ++++++---- rayshader-0.41.2/rayshader/R/save_png.R | 144 rayshader-0.41.2/rayshader/R/sphere_shade.R | 209 - rayshader-0.41.2/rayshader/R/texture_shade.R | 201 - rayshader-0.41.2/rayshader/R/transform_into_heightmap_coords.R | 25 rayshader-0.41.2/rayshader/R/transform_sf_to_raycoords.R | 39 rayshader-0.41.2/rayshader/R/tree_obj.R | 12 rayshader-0.41.2/rayshader/R/utils.R | 327 + rayshader-0.41.2/rayshader/R/write_stl.R | 3 rayshader-0.41.2/rayshader/man/add_overlay.Rd | 37 rayshader-0.41.2/rayshader/man/add_shadow.Rd | 26 rayshader-0.41.2/rayshader/man/add_water.Rd | 20 rayshader-0.41.2/rayshader/man/ambient_shade.Rd | 24 rayshader-0.41.2/rayshader/man/calculate_normal.Rd | 4 rayshader-0.41.2/rayshader/man/cloud_shade.Rd | 60 rayshader-0.41.2/rayshader/man/col2rgb_linear.Rd |only rayshader-0.41.2/rayshader/man/constant_shade.Rd | 32 rayshader-0.41.2/rayshader/man/convert_color.Rd | 9 rayshader-0.41.2/rayshader/man/convert_path_to_animation_coords.Rd | 267 - rayshader-0.41.2/rayshader/man/convert_rgl_to_raymesh.Rd | 24 rayshader-0.41.2/rayshader/man/create_texture.Rd | 21 rayshader-0.41.2/rayshader/man/detect_water.Rd | 23 rayshader-0.41.2/rayshader/man/fix_manifold_geometry.Rd | 2 rayshader-0.41.2/rayshader/man/flag_banner_obj.Rd | 4 rayshader-0.41.2/rayshader/man/flag_full_obj.Rd | 4 rayshader-0.41.2/rayshader/man/flag_pole_obj.Rd | 4 rayshader-0.41.2/rayshader/man/generate_altitude_overlay.Rd | 28 rayshader-0.41.2/rayshader/man/generate_compass_overlay.Rd | 171 rayshader-0.41.2/rayshader/man/generate_contour_overlay.Rd | 76 rayshader-0.41.2/rayshader/man/generate_halo_underlay.Rd |only rayshader-0.41.2/rayshader/man/generate_label_overlay.Rd | 129 rayshader-0.41.2/rayshader/man/generate_line_overlay.Rd | 66 rayshader-0.41.2/rayshader/man/generate_point_overlay.Rd | 60 rayshader-0.41.2/rayshader/man/generate_polygon_overlay.Rd | 76 rayshader-0.41.2/rayshader/man/generate_scalebar_overlay.Rd | 151 rayshader-0.41.2/rayshader/man/generate_soil_textures.Rd | 8 rayshader-0.41.2/rayshader/man/generate_surface.Rd | 4 rayshader-0.41.2/rayshader/man/generate_waterline_overlay.Rd | 110 rayshader-0.41.2/rayshader/man/get_ids_with_labels.Rd | 2 rayshader-0.41.2/rayshader/man/height_shade.Rd | 36 rayshader-0.41.2/rayshader/man/lamb_shade.Rd | 28 rayshader-0.41.2/rayshader/man/make_base.Rd | 8 rayshader-0.41.2/rayshader/man/make_base_triangulated.Rd | 4 rayshader-0.41.2/rayshader/man/make_lines.Rd | 14 rayshader-0.41.2/rayshader/man/make_shadow.Rd | 4 rayshader-0.41.2/rayshader/man/make_water.Rd | 10 rayshader-0.41.2/rayshader/man/make_waterlines.Rd | 14 rayshader-0.41.2/rayshader/man/monterey_counties_sf.Rd | 10 rayshader-0.41.2/rayshader/man/monterey_roads_sf.Rd | 8 rayshader-0.41.2/rayshader/man/montereybay.Rd | 4 rayshader-0.41.2/rayshader/man/pipe.Rd | 8 rayshader-0.41.2/rayshader/man/plot_3d.Rd | 146 rayshader-0.41.2/rayshader/man/plot_gg.Rd | 160 rayshader-0.41.2/rayshader/man/plot_map.Rd | 50 rayshader-0.41.2/rayshader/man/raster_to_matrix.Rd | 6 rayshader-0.41.2/rayshader/man/ray_shade.Rd | 48 rayshader-0.41.2/rayshader/man/raymarch_cloud_layer.Rd | 7 rayshader-0.41.2/rayshader/man/rayshader-defunct.Rd |only rayshader-0.41.2/rayshader/man/reduce_matrix_size.Rd | 15 rayshader-0.41.2/rayshader/man/render_beveled_polygons.Rd | 140 rayshader-0.41.2/rayshader/man/render_buildings.Rd | 94 rayshader-0.41.2/rayshader/man/render_camera.Rd | 14 rayshader-0.41.2/rayshader/man/render_clouds.Rd | 78 rayshader-0.41.2/rayshader/man/render_compass.Rd | 54 rayshader-0.41.2/rayshader/man/render_contours.Rd | 44 rayshader-0.41.2/rayshader/man/render_depth.Rd | 125 rayshader-0.41.2/rayshader/man/render_floating_overlay.Rd | 34 rayshader-0.41.2/rayshader/man/render_highquality.Rd | 275 + rayshader-0.41.2/rayshader/man/render_label.Rd | 98 rayshader-0.41.2/rayshader/man/render_movie.Rd | 89 rayshader-0.41.2/rayshader/man/render_multipolygonz.Rd | 54 rayshader-0.41.2/rayshader/man/render_obj.Rd | 80 rayshader-0.41.2/rayshader/man/render_path.Rd | 117 rayshader-0.41.2/rayshader/man/render_points.Rd | 52 rayshader-0.41.2/rayshader/man/render_polygons.Rd | 69 rayshader-0.41.2/rayshader/man/render_raymesh.Rd | 66 rayshader-0.41.2/rayshader/man/render_resize_window.Rd | 10 rayshader-0.41.2/rayshader/man/render_scalebar.Rd | 53 rayshader-0.41.2/rayshader/man/render_snapshot.Rd | 130 rayshader-0.41.2/rayshader/man/render_snapshot_software.Rd | 2 rayshader-0.41.2/rayshader/man/render_tree.Rd | 146 rayshader-0.41.2/rayshader/man/render_water.Rd | 24 rayshader-0.41.2/rayshader/man/resize_matrix.Rd | 24 rayshader-0.41.2/rayshader/man/save_3dprint.Rd | 26 rayshader-0.41.2/rayshader/man/save_multipolygonz_to_obj.Rd | 4 rayshader-0.41.2/rayshader/man/save_obj.Rd | 22 rayshader-0.41.2/rayshader/man/save_png.Rd | 43 rayshader-0.41.2/rayshader/man/sphere_shade.Rd | 40 rayshader-0.41.2/rayshader/man/texture_shade.Rd | 51 rayshader-0.41.2/rayshader/man/transform_into_heightmap_coords.Rd | 2 rayshader-0.41.2/rayshader/man/tree_basic_center_obj.Rd | 4 rayshader-0.41.2/rayshader/man/tree_cone_center_obj.Rd | 4 rayshader-0.41.2/rayshader/man/tree_trunk_obj.Rd | 4 rayshader-0.41.2/rayshader/man/washington_monument_multipolygonz.Rd | 4 164 files changed, 15572 insertions(+), 10196 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.10.0 dated 2026-07-02 and 3.10.1 dated 2026-07-19
gsDesign-3.10.0/gsDesign/inst/slides |only gsDesign-3.10.0/gsDesign/tests/testthat/Rplots.pdf |only gsDesign-3.10.0/gsDesign/vignettes/gsDesignVsProcSeqdesign.html |only gsDesign-3.10.1/gsDesign/DESCRIPTION | 6 gsDesign-3.10.1/gsDesign/MD5 | 51 gsDesign-3.10.1/gsDesign/NEWS.md | 7 gsDesign-3.10.1/gsDesign/R/gsDesign.R | 10 gsDesign-3.10.1/gsDesign/build/vignette.rds |binary gsDesign-3.10.1/gsDesign/inst/doc/ConditionalErrorSpending.html | 351 +-- gsDesign-3.10.1/gsDesign/inst/doc/ConditionalPowerPlot.html | 2 gsDesign-3.10.1/gsDesign/inst/doc/HarmBound.html | 12 gsDesign-3.10.1/gsDesign/inst/doc/MultiSeasonRareEvents.html | 349 +-- gsDesign-3.10.1/gsDesign/inst/doc/PoissonMixtureModel.html | 121 - gsDesign-3.10.1/gsDesign/inst/doc/SelectiveBoundTesting.html | 2 gsDesign-3.10.1/gsDesign/inst/doc/SurvivalOverview.html | 4 gsDesign-3.10.1/gsDesign/inst/doc/VaccineEfficacy.html | 606 +++--- gsDesign-3.10.1/gsDesign/inst/doc/binomialSPRTExample.R | 20 gsDesign-3.10.1/gsDesign/inst/doc/binomialSPRTExample.html | 238 +- gsDesign-3.10.1/gsDesign/inst/doc/binomialTwoSample.R | 44 gsDesign-3.10.1/gsDesign/inst/doc/binomialTwoSample.html | 983 +++++----- gsDesign-3.10.1/gsDesign/inst/doc/gsDesignPackageOverview.html | 2 gsDesign-3.10.1/gsDesign/inst/doc/gsSurvBasicExamples.html | 344 +-- gsDesign-3.10.1/gsDesign/inst/doc/gsSurvPower.html | 2 gsDesign-3.10.1/gsDesign/inst/doc/nNormal.html | 6 gsDesign-3.10.1/gsDesign/tests/testthat/_snaps/independent-test-plot.gsDesign/plottype-power-base-false.svg | 40 gsDesign-3.10.1/gsDesign/tests/testthat/_snaps/independent-test-plot.gsProbability/plottype-power-base-false.svg | 40 gsDesign-3.10.1/gsDesign/tests/testthat/test-selective-bounds.R | 15 gsDesign-3.10.1/gsDesign/vignettes/gsDesignAISkills.html |only 28 files changed, 1674 insertions(+), 1581 deletions(-)
Title: Helper Functions for Printing 'lavaan' Outputs
Description: Helpers for customizing selected outputs from
'lavaan' by Rosseel (2012) <doi:10.18637/jss.v048.i02>
and print them. The functions are intended to be used
by package developers in their packages and so are not
designed to be user-friendly. They are designed to be
let developers customize the tables by other
functions. Currently the parameter estimates tables of a
fitted object are supported.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between lavaan.printer versions 0.1.0 dated 2024-09-15 and 0.1.2 dated 2026-07-19
DESCRIPTION | 12 MD5 | 35 NAMESPACE | 8 NEWS.md | 16 R/lavaan.printer-package.R | 12 R/parameterEstimates_table_list.R | 1142 +++++++++--------- R/parameterEstimates_table_list_helpers.R | 1726 ++++++++++++++-------------- R/print_parameterEstimates_table_list.R | 402 +++--- README.md | 39 build/partial.rdb |binary build/vignette.rds |binary inst/doc/lavaan.printer.Rmd | 590 ++++----- inst/doc/lavaan.printer.html | 2 man/lavaan.printer-package.Rd | 50 man/parameterEstimates_table_list.Rd | 804 ++++++------- tests/testthat/test_est_table_list.R | 606 ++++----- tests/testthat/test_est_table_list_checks.R | 38 tests/testthat/test_est_table_list_sam.R |only vignettes/lavaan.printer.Rmd | 590 ++++----- 19 files changed, 3052 insertions(+), 3020 deletions(-)
More information about lavaan.printer at CRAN
Permanent link
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 3.1.0 dated 2026-06-29 and 3.2.0 dated 2026-07-19
mizer-3.1.0/mizer/man/is.ArrayResourceBySize.Rd |only mizer-3.1.0/mizer/man/is.ArraySpeciesBySize.Rd |only mizer-3.1.0/mizer/man/is.ArrayTimeByResourceBySize.Rd |only mizer-3.1.0/mizer/man/is.ArrayTimeBySpecies.Rd |only mizer-3.1.0/mizer/man/is.ArrayTimeBySpeciesBySize.Rd |only mizer-3.1.0/mizer/vignettes/.install_extras |only mizer-3.1.0/mizer/vignettes/_quarto.yml |only mizer-3.1.0/mizer/vignettes/diffusion_references.bib |only mizer-3.2.0/mizer/DESCRIPTION | 10 mizer-3.2.0/mizer/MD5 | 340 +++--- mizer-3.2.0/mizer/NAMESPACE | 34 mizer-3.2.0/mizer/NEWS.md | 236 ++++ mizer-3.2.0/mizer/R/ArrayResourceBySize-class.R | 136 +- mizer-3.2.0/mizer/R/ArraySpeciesBySize-class.R | 242 +++- mizer-3.2.0/mizer/R/ArrayTimeBySpecies-class.R | 86 + mizer-3.2.0/mizer/R/ArrayTimeBySpeciesBySize-class.R | 89 + mizer-3.2.0/mizer/R/MizerParams-class.R | 16 mizer-3.2.0/mizer/R/calibrate.R | 2 mizer-3.2.0/mizer/R/compareParams.R | 77 + mizer-3.2.0/mizer/R/generic_methods.R | 151 ++- mizer-3.2.0/mizer/R/helpers.R | 87 + mizer-3.2.0/mizer/R/manipulate_species.R | 362 +++++-- mizer-3.2.0/mizer/R/mizer-package.R | 2 mizer-3.2.0/mizer/R/newMultispeciesParams.R | 14 mizer-3.2.0/mizer/R/newSingleSpeciesParams.R | 17 mizer-3.2.0/mizer/R/plots.R | 77 + mizer-3.2.0/mizer/R/project.R | 17 mizer-3.2.0/mizer/R/project_n.R | 15 mizer-3.2.0/mizer/R/rate_functions.R | 9 mizer-3.2.0/mizer/R/registerExtensions.R | 65 + mizer-3.2.0/mizer/R/resource_dynamics.R | 45 mizer-3.2.0/mizer/R/resource_logistic.R | 39 mizer-3.2.0/mizer/R/resource_semichemostat.R | 37 mizer-3.2.0/mizer/R/saveParams.R | 40 mizer-3.2.0/mizer/R/setColours.R | 46 mizer-3.2.0/mizer/R/setExtDiffusion.R | 8 mizer-3.2.0/mizer/R/setExtEncounter.R | 8 mizer-3.2.0/mizer/R/setExtMort.R | 8 mizer-3.2.0/mizer/R/setFishing.R | 221 ++++ mizer-3.2.0/mizer/R/setInteraction.R | 8 mizer-3.2.0/mizer/R/setMaxIntakeRate.R | 8 mizer-3.2.0/mizer/R/setMetabolicRate.R | 36 mizer-3.2.0/mizer/R/setMetadata.R | 21 mizer-3.2.0/mizer/R/setPredKernel.R | 9 mizer-3.2.0/mizer/R/setReproduction.R | 30 mizer-3.2.0/mizer/R/setResource.R | 219 +++- mizer-3.2.0/mizer/R/setSearchVolume.R | 7 mizer-3.2.0/mizer/R/species_params.R | 501 +++++++++- mizer-3.2.0/mizer/R/steady.R | 15 mizer-3.2.0/mizer/R/summary_methods.R | 6 mizer-3.2.0/mizer/R/transport.R | 161 ++- mizer-3.2.0/mizer/R/validSpeciesParams.R | 173 --- mizer-3.2.0/mizer/R/wrapper_functions.R | 22 mizer-3.2.0/mizer/R/zzz.R |only mizer-3.2.0/mizer/README.md | 10 mizer-3.2.0/mizer/build/vignette.rds |binary mizer-3.2.0/mizer/data/NS_params.rda |binary mizer-3.2.0/mizer/data/NS_sim.rda |binary mizer-3.2.0/mizer/data/NS_species_params.rda |binary mizer-3.2.0/mizer/data/NS_species_params_gears.rda |binary mizer-3.2.0/mizer/inst/WORDLIST | 38 mizer-3.2.0/mizer/inst/doc/celtic_gear_params.csv |only mizer-3.2.0/mizer/inst/doc/celtic_interaction.csv |only mizer-3.2.0/mizer/inst/shiny/selectivity_effects/app.R | 2 mizer-3.2.0/mizer/man/ArrayResourceBySize.Rd | 9 mizer-3.2.0/mizer/man/ArraySpeciesBySize.Rd | 9 mizer-3.2.0/mizer/man/ArrayTimeByResourceBySize.Rd | 9 mizer-3.2.0/mizer/man/ArrayTimeBySpecies.Rd | 9 mizer-3.2.0/mizer/man/ArrayTimeBySpeciesBySize.Rd | 9 mizer-3.2.0/mizer/man/MizerParams.Rd | 4 mizer-3.2.0/mizer/man/addPlot.Rd | 2 mizer-3.2.0/mizer/man/adjustSizeGrid.Rd |only mizer-3.2.0/mizer/man/animate.Rd | 4 mizer-3.2.0/mizer/man/as.data.frame.Rd | 5 mizer-3.2.0/mizer/man/completeSpeciesParams.Rd | 30 mizer-3.2.0/mizer/man/dispatchExtensions.Rd | 6 mizer-3.2.0/mizer/man/expandSizeGrid.Rd | 11 mizer-3.2.0/mizer/man/gear_params.Rd | 25 mizer-3.2.0/mizer/man/getFluxGradient.Rd | 1 mizer-3.2.0/mizer/man/get_f0_default.Rd | 4 mizer-3.2.0/mizer/man/get_gamma_default.Rd | 5 mizer-3.2.0/mizer/man/get_h_default.Rd | 5 mizer-3.2.0/mizer/man/get_ks_default.Rd | 5 mizer-3.2.0/mizer/man/get_steady_state_n.Rd | 6 mizer-3.2.0/mizer/man/l2w.Rd | 3 mizer-3.2.0/mizer/man/newCommunityParams.Rd | 11 mizer-3.2.0/mizer/man/newMultispeciesParams.Rd | 25 mizer-3.2.0/mizer/man/newSingleSpeciesParams.Rd | 9 mizer-3.2.0/mizer/man/newTraitParams.Rd | 9 mizer-3.2.0/mizer/man/plot.ArrayResourceBySize.Rd |only mizer-3.2.0/mizer/man/plot.ArraySpeciesBySize.Rd |only mizer-3.2.0/mizer/man/plot.ArrayTimeByResourceBySize.Rd |only mizer-3.2.0/mizer/man/plot.ArrayTimeBySpecies.Rd |only mizer-3.2.0/mizer/man/plot.ArrayTimeBySpeciesBySize.Rd |only mizer-3.2.0/mizer/man/plot.Rd | 86 - mizer-3.2.0/mizer/man/plot2.Rd | 2 mizer-3.2.0/mizer/man/plotBiomass.Rd | 2 mizer-3.2.0/mizer/man/plotCDF.Rd | 2 mizer-3.2.0/mizer/man/plotCDF2.Rd | 2 mizer-3.2.0/mizer/man/plotDiet.Rd | 2 mizer-3.2.0/mizer/man/plotFMort.Rd | 2 mizer-3.2.0/mizer/man/plotFeedingLevel.Rd | 2 mizer-3.2.0/mizer/man/plotGrowthCurves.Rd | 2 mizer-3.2.0/mizer/man/plotM2.Rd | 2 mizer-3.2.0/mizer/man/plotMizerParams.Rd | 2 mizer-3.2.0/mizer/man/plotMizerSim.Rd | 2 mizer-3.2.0/mizer/man/plotPredMort.Rd | 2 mizer-3.2.0/mizer/man/plotRelative.Rd | 2 mizer-3.2.0/mizer/man/plotSpectra.Rd | 2 mizer-3.2.0/mizer/man/plotSpectra2.Rd | 2 mizer-3.2.0/mizer/man/plotSpectraRelative.Rd | 14 mizer-3.2.0/mizer/man/plotYield.Rd | 2 mizer-3.2.0/mizer/man/plotYieldGear.Rd | 15 mizer-3.2.0/mizer/man/plotting_functions.Rd | 7 mizer-3.2.0/mizer/man/print.Rd | 27 mizer-3.2.0/mizer/man/project.Rd | 6 mizer-3.2.0/mizer/man/providesDispatchMethods.Rd |only mizer-3.2.0/mizer/man/recordExtension.Rd | 7 mizer-3.2.0/mizer/man/resource_logistic.Rd | 4 mizer-3.2.0/mizer/man/resource_params.Rd | 25 mizer-3.2.0/mizer/man/resource_semichemostat.Rd | 4 mizer-3.2.0/mizer/man/saveParams.Rd | 46 mizer-3.2.0/mizer/man/scaleModel.Rd | 2 mizer-3.2.0/mizer/man/setColours.Rd | 14 mizer-3.2.0/mizer/man/setExtDiffusion.Rd | 8 mizer-3.2.0/mizer/man/setExtEncounter.Rd | 8 mizer-3.2.0/mizer/man/setExtMort.Rd | 8 mizer-3.2.0/mizer/man/setMaxIntakeRate.Rd | 8 mizer-3.2.0/mizer/man/setMetabolicRate.Rd | 21 mizer-3.2.0/mizer/man/setMetadata.Rd | 7 mizer-3.2.0/mizer/man/setParams.Rd | 21 mizer-3.2.0/mizer/man/setPredKernel.Rd | 10 mizer-3.2.0/mizer/man/setReproduction.Rd | 19 mizer-3.2.0/mizer/man/setResource.Rd | 26 mizer-3.2.0/mizer/man/setSearchVolume.Rd | 7 mizer-3.2.0/mizer/man/set_multispecies_model.Rd | 4 mizer-3.2.0/mizer/man/species_params.Rd | 79 + mizer-3.2.0/mizer/man/steady.Rd | 6 mizer-3.2.0/mizer/man/str.Rd | 7 mizer-3.2.0/mizer/man/summary.Rd | 7 mizer-3.2.0/mizer/man/validSpeciesParams.Rd | 30 mizer-3.2.0/mizer/tests/testthat/Rplots.pdf |only mizer-3.2.0/mizer/tests/testthat/_snaps/backwards_compatibility.md | 6 mizer-3.2.0/mizer/tests/testthat/_snaps/project.md | 6 mizer-3.2.0/mizer/tests/testthat/_snaps/summary_methods.md | 32 mizer-3.2.0/mizer/tests/testthat/helper.R | 13 mizer-3.2.0/mizer/tests/testthat/test-ArrayResourceBySize.R |only mizer-3.2.0/mizer/tests/testthat/test-ArraySpeciesBySize.R | 17 mizer-3.2.0/mizer/tests/testthat/test-ArrayTimeBySpecies.R | 15 mizer-3.2.0/mizer/tests/testthat/test-ArrayTimeBySpeciesBySize.R | 6 mizer-3.2.0/mizer/tests/testthat/test-backwards_compatibility.R | 7 mizer-3.2.0/mizer/tests/testthat/test-calc-selectivity.R | 2 mizer-3.2.0/mizer/tests/testthat/test-calibrate.R | 3 mizer-3.2.0/mizer/tests/testthat/test-compareParams.R | 23 mizer-3.2.0/mizer/tests/testthat/test-extension-dispatch.R | 72 + mizer-3.2.0/mizer/tests/testthat/test-extension-versions.R | 22 mizer-3.2.0/mizer/tests/testthat/test-get_steady_state_n.R | 45 mizer-3.2.0/mizer/tests/testthat/test-helpers.R | 47 mizer-3.2.0/mizer/tests/testthat/test-manipulate_species.R | 85 + mizer-3.2.0/mizer/tests/testthat/test-newSingleSpeciesParams.R | 4 mizer-3.2.0/mizer/tests/testthat/test-plotBiomassObservedVsModel.R | 9 mizer-3.2.0/mizer/tests/testthat/test-plotYieldObservedVsModel.R | 9 mizer-3.2.0/mizer/tests/testthat/test-plots.R | 41 mizer-3.2.0/mizer/tests/testthat/test-project.R | 15 mizer-3.2.0/mizer/tests/testthat/test-resource_dynamics.R | 1 mizer-3.2.0/mizer/tests/testthat/test-resource_logistic.R | 2 mizer-3.2.0/mizer/tests/testthat/test-setBevertonHolt.R | 22 mizer-3.2.0/mizer/tests/testthat/test-setColours.R | 27 mizer-3.2.0/mizer/tests/testthat/test-setExtDiffusion.R | 13 mizer-3.2.0/mizer/tests/testthat/test-setExtEncounter.R | 13 mizer-3.2.0/mizer/tests/testthat/test-setExtMort.R | 3 mizer-3.2.0/mizer/tests/testthat/test-setFishing.R | 106 +- mizer-3.2.0/mizer/tests/testthat/test-setMetabolicRate.R | 52 - mizer-3.2.0/mizer/tests/testthat/test-setReproduction.R | 8 mizer-3.2.0/mizer/tests/testthat/test-setResource.R | 162 ++- mizer-3.2.0/mizer/tests/testthat/test-species_params.R | 197 +++ mizer-3.2.0/mizer/tests/testthat/test-steady.R | 48 mizer-3.2.0/mizer/tests/testthat/test-steadySingleSpecies.R | 19 mizer-3.2.0/mizer/tests/testthat/test-validSpeciesParams.R | 65 - mizer-3.2.0/mizer/tests/testthat/test-wrapper_functions.R | 7 mizer-3.2.0/mizer/tests/testthat/test-zzz.R |only mizer-3.2.0/mizer/vignettes/reflib.bib | 22 182 files changed, 4515 insertions(+), 1313 deletions(-)
Title: (Double) Generalized Linear Models for Spatio-Temporal Data
Description: Fit spatio-temporal models within a (double) generalized linear modelling framework. The package includes functions for estimation, simulation and inference.
Author: Steffen Maletz [aut, cre] ,
Konstantinos Fokianos [aut] ,
Roland Fried [aut] ,
Valerie Weismann [ctb]
Maintainer: Steffen Maletz <maletz@statistik.tu-dortmund.de>
Diff between glmSTARMA versions 1.0.0 dated 2026-01-26 and 1.1.0 dated 2026-07-19
DESCRIPTION | 10 MD5 | 100 ++- NEWS.md |only R/control.R | 22 R/dglmstarma.R | 16 R/family.R | 44 - R/fitted_glmstarma.R | 6 R/glmstarma.R | 6 R/glmstarma_package.R | 2 R/load_data.R | 7 R/predict_glmstarma.R | 8 R/print_summary_glmstarma.R | 65 +- R/residuals_glmstarma.R | 8 R/simulation.R | 11 R/sst.R | 2 build/partial.rdb |binary inst |only man/dglmstarma.Rd | 1 man/dglmstarma.control.Rd | 5 man/glmSTARMA-package.Rd | 2 man/glmstarma.Rd | 1 man/glmstarma_sim.control.Rd | 5 man/sst.Rd | 2 man/stfamily.Rd | 2 src/covariates.cpp | 32 - src/covariates.h | 28 - src/dglmstarma.cpp | 47 + src/family.h | 16 src/family_binomial.cpp | 83 --- src/family_gamma.cpp | 114 ---- src/family_inverse_gauss.cpp | 117 ---- src/family_negative_binomial.cpp | 120 ---- src/family_normal.cpp | 87 --- src/family_poisson.cpp | 65 -- src/family_quasibinomial.cpp | 158 ------ src/family_quasipoisson.cpp | 131 ----- src/fitting.cpp | 40 - src/fitting.h | 15 src/glmstarma.cpp | 4 src/model.cpp | 24 src/model.h | 2 src/predict.cpp | 30 - tests/testthat/test-S3.R | 334 ++++++++++++ tests/testthat/test-control.R |only tests/testthat/test-covariates.R | 18 tests/testthat/test-data.R | 96 +++ tests/testthat/test-dglmstarma.R | 7 tests/testthat/test-dglmstarma_sim.R | 92 ++- tests/testthat/test-family.R | 902 ++++++++++++++++++++++++++++++++++- tests/testthat/test-generateW.R | 5 tests/testthat/test-glmstarma.R | 38 + tests/testthat/test-glmstarma_sim.R | 10 tests/testthat/test-predict.R |only 53 files changed, 1833 insertions(+), 1107 deletions(-)
Title: Healthcare Antitrust Analysis
Description: Antitrust analysis of
healthcare markets. Contains functions to implement the
semiparametric estimation technique described in Raval, Rosenbaum,
and Tenn (2017) "A Semiparametric Discrete Choice Model: An Application
to Hospital Mergers" <doi:10.1111/ecin.12454>.
Author: Matthew T Panhans [aut, cre]
Maintainer: Matthew T Panhans <mpanhans@gmail.com>
Diff between healthcare.antitrust versions 0.1.5 dated 2026-02-07 and 0.1.6 dated 2026-07-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/impliedshare_calc.R | 2 +- inst/doc/semipar_example.html | 4 ++-- 5 files changed, 14 insertions(+), 10 deletions(-)
More information about healthcare.antitrust at CRAN
Permanent link
Title: Simplex Regression Models with Parametric or Fixed Mean Link
Functions
Description: Fits and analyzes simplex regression models with either
fixed or parametric mean link functions. Implements the simplex
probability density function, cumulative distribution function,
quantile function, random number generation, and variance evaluation.
Offers several fixed and parametric link functions for the mean
submodel, tools for residual analysis and diagnostic plotting,
hypothesis testing procedures, and influence measures such as Cook's
distance and leverage (hat values). Includes the Scout Score (SS)
criterion for model selection, enabling comprehensive inference and
diagnostic analysis within the simplex regression framework.
For more details see Barndorff-Nielsen and Jorgensen (1991)
<doi:10.1016/0047-259X(91)90008-P> and Justino and Cribari-Neto (2026)
<doi:10.1016/j.apm.2025.116713>.
Author: Maria Eduarda da Cruz Justino [aut, cre] ,
Francisco Cribari-Neto [ctb, ths]
Maintainer: Maria Eduarda da Cruz Justino <eueduardacruz@gmail.com>
Diff between SimplexRegression versions 0.1.4 dated 2026-07-08 and 0.1.5 dated 2026-07-19
DESCRIPTION | 13 - MD5 | 115 +++++----- NAMESPACE | 2 NEWS.md | 66 ++---- R/abortionopposition.R | 115 +++++----- R/aisrowing.R |only R/biomass.R | 72 +++--- R/readingskills.R | 41 +-- R/relativehumidity.R | 47 ++-- R/simplexreg_deviance.R | 6 R/simplexreg_dist.R | 37 ++- R/simplexreg_fit.R | 151 +++++++------ R/simplexreg_influence.R | 351 ++++++++++++++++++++++---------- R/simplexreg_links.R | 22 +- R/simplexreg_methods.R | 41 +-- R/simplexreg_penalized_ic.R | 34 +-- R/simplexreg_plots.R | 64 ++--- R/simplexreg_press.R | 30 +- R/simplexreg_r2.R |only R/simplexreg_resettest.R | 32 +- R/simplexreg_residuals.R | 81 +++---- R/simplexreg_scoretest.R | 43 ++- R/simplexreg_sscriteria.R | 91 ++++---- R/simplexreg_var.R | 5 build/vignette.rds |binary data/AISRowing.rda |only data/AbortionOpposition.rda |binary data/Biomass.rda |binary data/RelativeHumidity.rda |binary inst/WORDLIST | 43 +++ inst/doc/relative-humidity.R | 24 -- inst/doc/relative-humidity.Rmd | 41 +-- inst/doc/relative-humidity.html | 208 ++++++++---------- man/AISRowing.Rd |only man/AbortionOpposition.Rd | 115 +++++----- man/Biomass.Rd | 72 +++--- man/ReadingSkills.Rd | 41 +-- man/RelativeHumidity.Rd | 45 ++-- man/cooks.distance.simplexregression.Rd |only man/dev.unit.simplex.Rd | 6 man/diag.distances.Rd | 85 +++++-- man/diag.im.Rd | 121 +++++++---- man/gleverage.Rd | 10 man/halfnormal.plot.Rd | 12 - man/local.influence.Rd | 14 - man/penalized.ic.Rd | 30 +- man/penalized.ss.Rd | 77 +++---- man/plot.simplexregression.Rd | 16 - man/press.Rd | 30 +- man/r2.Rd |only man/resettest.Rd | 30 +- man/residuals.simplexregression.Rd | 79 +++---- man/scoretest.Rd | 32 +- man/simplex_opt.Rd | 36 ++- man/simplexreg.control.Rd | 29 +- man/simplexreg.fit.Rd | 97 ++++---- man/simplexreg.methods.Rd | 23 -- man/simplexreg.nul.Rd | 6 man/variance.simplex.Rd | 7 tests/testthat/test-simplexreg_fit.R | 6 tests/testthat/test-simplexreg_r2.R |only vignettes/relative-humidity.Rmd | 41 +-- 62 files changed, 1601 insertions(+), 1234 deletions(-)
More information about SimplexRegression at CRAN
Permanent link
Title: Name-Blind Variable-Role Detection by Data Signature
Description: Deterministic, name-blind detection of variable roles (group,
outcome, survival time and event, paired and agreement measurements,
repeated measures, scale items, subject identifier, covariate) in tabular
data. Roles are assigned from each column's information-theoretic signature
-- Shannon entropy, normalized mutual information, and distributional shape
-- rather than from column names, so renaming columns to 'col_1', 'col_2',
... does not change the result ("Data inspice, non nomen"). An optional,
capped name-based hint and automatic header-row detection are also provided.
No large language models and no external data transmission. Extracted from
the 'MDStatR' biostatistics engine; see Boynukara (2026)
<doi:10.5281/zenodo.20707791>.
Author: Can Boynukara [aut, cre, cph] ,
M. Yasir Ceyhan [ctb]
Maintainer: Can Boynukara <canboynukara1@gmail.com>
Diff between rolescry versions 0.1.0 dated 2026-06-22 and 0.2.0 dated 2026-07-19
DESCRIPTION | 6 MD5 | 76 +- NAMESPACE | 18 NEWS.md |only R/anm.R |only R/classify.R | 198 +++--- R/dependency.R |only R/detect.R | 1024 ++++++++++++++++++++++++----------- R/detect_roles.R | 275 ++++----- R/header.R | 326 +++++------ R/mdl.R |only R/name_bonus.R | 112 +-- R/nmi.R | 126 ++-- R/read_data.R | 236 ++++---- R/rolescry-package.R | 38 - R/signatures.R | 656 +++++++++++----------- R/utils.R | 145 +++- R/var_info.R | 84 +- README.md | 207 +++---- inst/CITATION | 38 - inst/WORDLIST | 53 + inst/doc/rolescry.R | 19 inst/doc/rolescry.Rmd | 257 ++++---- inst/doc/rolescry.html | 95 +-- man/compute_nmi.Rd | 72 +- man/detect_header.Rd | 82 +- man/detect_roles.Rd | 162 ++--- man/read_data.Rd | 108 +-- man/rolescry-package.Rd | 84 +- man/rolescry_default_name_bonus.Rd | 76 +- tests/testthat.R | 8 tests/testthat/helper-dgp.R | 92 +-- tests/testthat/test-baseline-equiv.R | 104 +-- tests/testthat/test-classify.R | 24 tests/testthat/test-detect-roles.R | 54 - tests/testthat/test-header.R | 74 +- tests/testthat/test-name-blind.R | 91 +-- tests/testthat/test-nmi.R | 36 - tests/testthat/test-read-data.R | 46 - tests/testthat/test-turnusol.R | 104 +-- vignettes/rolescry.Rmd | 257 ++++---- 41 files changed, 3002 insertions(+), 2461 deletions(-)
Title: Unicode and Punycode Domain Name Processing
Description: High-performance Unicode and Punycode processing for
internationalized domain names. The 'puny_encode()' / 'puny_decode()'
helpers are a low-level, RFC 3492 compliant Punycode codec for domain
labels (the 'xn--' ASCII-Compatible Encoding of RFC 5890/5891); they
perform the raw transform plus letter-digit-hyphen checks and do not
apply Unicode IDNA normalization. 'host_normalize()' is the Unicode
Technical Standard #46 host-normalization entry point, mapping a host
name to a canonical lowercase ASCII comparison form (non-transitional
profile, pinned Unicode version). The 'url_encode()' / 'url_decode()' /
'parse_url()' helpers do best-effort host extraction and rewriting in
URL-shaped strings and are deliberately not RFC 3986 / WHATWG URL
parsers or canonicalizers; they are deprecated in favor of dedicated
URL packages. Aimed at host normalization and data analysis workflows.
Used as the Punycode and IDNA engine by the 'pslr' and 'rurl' packages.
Author: Bart Turczynski [aut, cre]
Maintainer: Bart Turczynski <bartek@turczynski.pl>
Diff between punycoder versions 1.1.0 dated 2026-06-16 and 1.2.1 dated 2026-07-19
DESCRIPTION | 46 ++- MD5 | 111 ++++----- NEWS.md | 52 ++++ R/RcppExports.R | 4 R/normalize.R | 102 +++++++- R/punycoder-package.R |only R/punycoder.R | 55 ++-- R/results.R | 9 R/url-utils.R | 110 +++++++-- R/validators.R | 3 README.md | 208 +++++++++++++---- inst/CITATION |only inst/WORDLIST | 79 ++++++ inst/doc/punycoder-intro.R | 21 + inst/doc/punycoder-intro.Rmd | 43 ++- inst/doc/punycoder-intro.html | 79 ++++-- inst/testdata/IdnaTestV2.txt |only man/host_normalize.Rd | 63 +++-- man/is_idn.Rd | 8 man/is_punycode.Rd | 6 man/normalization_profile_info.Rd | 36 ++ man/parse_url.Rd | 55 +++- man/print.punycoder_parsed_url.Rd | 7 man/print.punycoder_validation.Rd | 4 man/puny_decode.Rd | 27 +- man/puny_encode.Rd | 30 +- man/punycoder-package.Rd | 30 +- man/url_decode.Rd | 38 ++- man/url_encode.Rd | 42 ++- man/validate_domain.Rd | 19 - src/RcppExports.cpp | 10 src/exports.cpp | 51 +++- src/init.c | 4 src/punycoder_algorithm.cpp | 16 - src/punycoder_backend.cpp | 15 - src/punycoder_core.h | 12 src/punycoder_domain.cpp | 40 ++- src/punycoder_errors.cpp | 92 +++++++ src/punycoder_nfc.h | 2 src/punycoder_normalize.cpp | 77 ++++-- src/punycoder_normalize.h | 27 +- src/punycoder_service.cpp | 34 +- src/punycoder_url.cpp | 8 src/punycoder_utf8.cpp | 8 tests/testthat/helper-idna.R |only tests/testthat/helper-validation.R | 22 + tests/testthat/test-backends.R | 49 +++- tests/testthat/test-contracts.R | 83 ++++-- tests/testthat/test-encoding.R | 96 +++++-- tests/testthat/test-idna-conformance.R |only tests/testthat/test-lifecycle.R | 17 - tests/testthat/test-normalize.R | 137 ++++++++++- tests/testthat/test-osv.R |only tests/testthat/test-performance.R | 33 +- tests/testthat/test-rfc3492.R | 43 +++ tests/testthat/test-security.R |only tests/testthat/test-unicode.R | 6 tests/testthat/test-urls.R | 403 ++++++++++++++++++++++----------- tests/testthat/test-validators.R | 184 ++++++++++++--- vignettes/punycoder-intro.Rmd | 43 ++- 60 files changed, 2104 insertions(+), 695 deletions(-)
Title: Builds the 'TinyCC' Command-Line Interface and Library for 'C'
Scripting in 'R'
Description: Builds the 'TinyCC' (Tiny 'C' Compiler) command-line interface
and library for package use in 'R'. The package compiles 'TinyCC' from source and
provides R functions to interact with the compiler. 'TinyCC' can be
used for header preprocessing, just-in-time compilation of 'C' code in
'R', and lightweight 'C' scripting workflows.
Author: Sounkou Mahamane Toure [aut, cre],
Mike Cheng [cph] ,
Adam Dunkels [ctb] ,
Swedish Institute of Computer Science [cph] ,
Fabrice Bellard and TinyCC authors [cph]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rtinycc versions 0.1.9 dated 2026-04-27 and 0.1.12 dated 2026-07-19
Rtinycc-0.1.12/Rtinycc/DESCRIPTION | 23 Rtinycc-0.1.12/Rtinycc/MD5 | 117 Rtinycc-0.1.12/Rtinycc/NAMESPACE | 2 Rtinycc-0.1.12/Rtinycc/NEWS.md | 36 Rtinycc-0.1.12/Rtinycc/R/aaa.R | 19 Rtinycc-0.1.12/Rtinycc/R/aaa_ffi_codegen_matrix.R | 87 Rtinycc-0.1.12/Rtinycc/R/aaa_ffi_codegen_rules.R | 100 Rtinycc-0.1.12/Rtinycc/R/callbacks.R | 200 + Rtinycc-0.1.12/Rtinycc/R/ffi.R | 342 +- Rtinycc-0.1.12/Rtinycc/R/ffi_codegen.R | 168 - Rtinycc-0.1.12/Rtinycc/R/ffi_types.R | 13 Rtinycc-0.1.12/Rtinycc/R/tinycc.R | 151 Rtinycc-0.1.12/Rtinycc/R/treesitter_helpers.R | 4 Rtinycc-0.1.12/Rtinycc/README.md | 858 +++++ Rtinycc-0.1.12/Rtinycc/TODO | 5 Rtinycc-0.1.12/Rtinycc/build/vignette.rds |binary Rtinycc-0.1.12/Rtinycc/configure | 23 Rtinycc-0.1.12/Rtinycc/inst/LICENSE.note | 41 Rtinycc-0.1.12/Rtinycc/inst/c_examples/simd_bytecode.c |only Rtinycc-0.1.12/Rtinycc/inst/c_examples/simd_bytecode_demo.R |only Rtinycc-0.1.12/Rtinycc/inst/doc/compilation-and-call-overhead.Rmd | 2 Rtinycc-0.1.12/Rtinycc/inst/doc/compilation-and-call-overhead.html | 218 - Rtinycc-0.1.12/Rtinycc/inst/doc/ffi-boundary-semantics.Rmd | 45 Rtinycc-0.1.12/Rtinycc/inst/doc/ffi-boundary-semantics.html | 53 Rtinycc-0.1.12/Rtinycc/inst/doc/ffi-helpers.html | 8 Rtinycc-0.1.12/Rtinycc/inst/doc/getting-started.html | 13 Rtinycc-0.1.12/Rtinycc/inst/doc/internals.Rmd | 10 Rtinycc-0.1.12/Rtinycc/inst/doc/internals.html | 8 Rtinycc-0.1.12/Rtinycc/inst/include |only Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_callback_invoke_runtime.R | 450 ++ Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_callbacks.R | 9 Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_ffi_types.R | 59 Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_libtcc.R | 184 + Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_safety_regressions.R |only Rtinycc-0.1.12/Rtinycc/inst/tinytest/test_simd_bytecode_examples.R |only Rtinycc-0.1.12/Rtinycc/man/figures/README-io_uring-demo-1.png |binary Rtinycc-0.1.12/Rtinycc/man/tcc_bind.Rd | 7 Rtinycc-0.1.12/Rtinycc/man/tcc_call_symbol.Rd | 56 Rtinycc-0.1.12/Rtinycc/man/tcc_callback.Rd | 26 Rtinycc-0.1.12/Rtinycc/man/tcc_callback_async_drain.Rd | 7 Rtinycc-0.1.12/Rtinycc/man/tcc_callback_async_schedule.Rd | 4 Rtinycc-0.1.12/Rtinycc/man/tcc_get_symbol.Rd | 5 Rtinycc-0.1.12/Rtinycc/man/tcc_global.Rd | 6 Rtinycc-0.1.12/Rtinycc/man/tcc_include_paths.Rd | 3 Rtinycc-0.1.12/Rtinycc/man/tcc_list_symbols.Rd |only Rtinycc-0.1.12/Rtinycc/man/tcc_map_c_type_to_ffi.Rd | 4 Rtinycc-0.1.12/Rtinycc/man/tcc_output.Rd | 9 Rtinycc-0.1.12/Rtinycc/man/tcc_output_file.Rd |only Rtinycc-0.1.12/Rtinycc/man/tcc_relocate.Rd | 5 Rtinycc-0.1.12/Rtinycc/man/tcc_state.Rd | 5 Rtinycc-0.1.12/Rtinycc/man/tcc_struct.Rd | 5 Rtinycc-0.1.12/Rtinycc/man/tcc_union.Rd | 3 Rtinycc-0.1.12/Rtinycc/src/RC_libtcc.c | 1603 +++++++--- Rtinycc-0.1.12/Rtinycc/src/init.c | 19 Rtinycc-0.1.12/Rtinycc/src/platform_async.c | 273 + Rtinycc-0.1.12/Rtinycc/src/platform_async.h | 18 Rtinycc-0.1.12/Rtinycc/src/tinycc-e273cf4.tar.gz |only Rtinycc-0.1.12/Rtinycc/tools/vendortinycc.R | 7 Rtinycc-0.1.12/Rtinycc/vignettes/compilation-and-call-overhead.Rmd | 2 Rtinycc-0.1.12/Rtinycc/vignettes/ffi-boundary-semantics.Rmd | 45 Rtinycc-0.1.12/Rtinycc/vignettes/internals.Rmd | 10 Rtinycc-0.1.9/Rtinycc/src/tinycc-34eed88.tar.gz |only 62 files changed, 4286 insertions(+), 1084 deletions(-)
Title: Plausible Naive Bayes Classifier Using PDE
Description: Provides a nonparametric, multicore-capable plausible naive Bayes classifier based on Pareto density estimation (PDE). It addresses low-evidence cases through a plausibility correction. To enhance the interpretability of the flexible naive Bayes classifier by revealing its posterior structure and feature-wise, class-specific evidence, posterior probabilities can be visualized as class-wise line plots for one-dimensional data or color-coded Voronoi diagrams for pairwise feature projections, and class-conditional PDE likelihoods as overlaid, mirrored density profiles resembling violin plots. Methodological details are provided by Stier, Q., Hoffmann, J. and Thrun, M. C. (2026) "Classifying with the Fine Structure of Distributions: Leveraging Distributional Information for Robust and Plausible Naive Bayes" <DOI:10.3390/make8010013>. For multicore computations, the implementation applies the general memory-sharing approach described by Thrun, M. C. and Märte, J. (2026) "memshare: Mem [...truncated...]
Author: Michael Thrun [aut, cph, cre] ,
Quirin Stier [aut, rev] ,
Tim Robin Neldner [ctr, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between PDEnaiveBayes versions 0.3.0 dated 2026-06-21 and 0.4.0 dated 2026-07-19
DESCRIPTION | 10 MD5 | 44 ++-- NAMESPACE | 70 +++--- R/ApplyBayesTheorem4Likelihoods.R | 70 +++++- R/CenterEstimate.R | 5 R/GetLikelihoodFunction.R | 5 R/GetLikelihoods.R | 15 + R/KernelPlausibleLikelihoods.R | 2 R/PlausibleLikelihoods.R | 14 - R/PlotBayesianDecision2D.R | 390 +++++++++++++++++++----------------- R/PlotLikelihoods.R | 3 R/PlotNaiveBayes.R | 396 +++++++++++++++++++++++-------------- R/PlotPosteriors.R | 141 ++++++++++--- R/Predict_naiveBayes.R | 23 +- R/Train_naiveBayes.R | 20 + R/defineOrEstimateDistribution.R | 6 R/densityEstimation4smallNoCases.R | 27 +- R/fitParameters.R | 3 R/likelihoodsArray2List.R | 7 build/partial.rdb |binary inst/doc/PDEnaiveBayes.html | 25 +- man/PlotNaiveBayes.Rd | 6 man/PlotPosteriors.Rd | 138 ++++++------ 23 files changed, 878 insertions(+), 542 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.4.1 dated 2026-05-23 and 1.5.0 dated 2026-07-19
couplr-1.4.1/couplr/man/greedy_couples.Rd |only couplr-1.4.1/couplr/man/greedy_couples_blocked.Rd |only couplr-1.4.1/couplr/man/greedy_couples_from_distance.Rd |only couplr-1.4.1/couplr/man/greedy_couples_single.Rd |only couplr-1.5.0/couplr/DESCRIPTION | 8 couplr-1.5.0/couplr/MD5 | 303 couplr-1.5.0/couplr/NAMESPACE | 1 couplr-1.5.0/couplr/NEWS.md | 188 couplr-1.5.0/couplr/R/RcppExports.R | 12 couplr-1.5.0/couplr/R/lap_solve.R | 8 couplr-1.5.0/couplr/R/lap_solve_batch.R | 10 couplr-1.5.0/couplr/R/matching_blocks.R | 702 - couplr-1.5.0/couplr/R/matching_core.R | 2723 +++---- couplr-1.5.0/couplr/R/matching_diagnostics.R | 1665 ++-- couplr-1.5.0/couplr/R/matching_distance_cache.R | 723 +- couplr-1.5.0/couplr/R/matching_join.R | 684 - couplr-1.5.0/couplr/R/matching_propensity.R | 4 couplr-1.5.0/couplr/R/matching_sensitivity.R | 23 couplr-1.5.0/couplr/R/matching_subclass.R | 12 couplr-1.5.0/couplr/R/morph_pixel.R | 754 -- couplr-1.5.0/couplr/R/morph_tiling.R | 132 couplr-1.5.0/couplr/R/morph_utils.R | 52 couplr-1.5.0/couplr/R/trace_auction.R | 35 couplr-1.5.0/couplr/R/trace_auction_scaled.R | 45 couplr-1.5.0/couplr/R/trace_bottleneck.R | 41 couplr-1.5.0/couplr/R/trace_bruteforce.R | 43 couplr-1.5.0/couplr/R/trace_gabow_tarjan.R | 42 couplr-1.5.0/couplr/R/trace_helpers_frame.R | 60 couplr-1.5.0/couplr/R/trace_hungarian.R | 20 couplr-1.5.0/couplr/R/trace_jv.R | 39 couplr-1.5.0/couplr/R/trace_munkres.R | 44 couplr-1.5.0/couplr/R/trace_ssap_bucket.R | 37 couplr-1.5.0/couplr/R/trace_stub.R | 10 couplr-1.5.0/couplr/README.md | 489 - couplr-1.5.0/couplr/inst/doc/algorithms.Rmd | 2500 +++--- couplr-1.5.0/couplr/inst/doc/algorithms.html | 4 couplr-1.5.0/couplr/inst/doc/comparison.R | 4 couplr-1.5.0/couplr/inst/doc/comparison.Rmd | 1666 ++-- couplr-1.5.0/couplr/inst/doc/comparison.html | 8 couplr-1.5.0/couplr/inst/doc/getting-started.R | 4 couplr-1.5.0/couplr/inst/doc/getting-started.Rmd | 972 +- couplr-1.5.0/couplr/inst/doc/getting-started.html | 17 couplr-1.5.0/couplr/inst/doc/matching-workflows.R | 14 couplr-1.5.0/couplr/inst/doc/matching-workflows.Rmd | 3600 +++++----- couplr-1.5.0/couplr/inst/doc/matching-workflows.html | 76 couplr-1.5.0/couplr/inst/doc/pixel-morphing.Rmd | 2108 ++--- couplr-1.5.0/couplr/inst/doc/pixel-morphing.html | 9 couplr-1.5.0/couplr/inst/doc/troubleshooting.R | 8 couplr-1.5.0/couplr/inst/doc/troubleshooting.Rmd | 1382 +-- couplr-1.5.0/couplr/inst/doc/troubleshooting.html | 24 couplr-1.5.0/couplr/man/BIG_COST.Rd | 1 couplr-1.5.0/couplr/man/balance_diagnostics.Rd | 8 couplr-1.5.0/couplr/man/calculate_var_balance.Rd | 14 couplr-1.5.0/couplr/man/compute_distances.Rd | 7 couplr-1.5.0/couplr/man/couplr-package.Rd | 5 couplr-1.5.0/couplr/man/dot-couples_blocked.Rd | 2 couplr-1.5.0/couplr/man/dot-couples_from_distance.Rd | 2 couplr-1.5.0/couplr/man/dot-couples_single.Rd | 2 couplr-1.5.0/couplr/man/example_costs.Rd | 2 couplr-1.5.0/couplr/man/example_df.Rd | 2 couplr-1.5.0/couplr/man/join_matched.Rd | 2 couplr-1.5.0/couplr/man/match_couples.Rd | 31 couplr-1.5.0/couplr/man/match_couples_blocked.Rd | 1 couplr-1.5.0/couplr/man/match_couples_from_distance.Rd | 1 couplr-1.5.0/couplr/man/match_couples_single.Rd | 1 couplr-1.5.0/couplr/man/matchmaker.Rd | 2 couplr-1.5.0/couplr/man/pixel_morph.Rd | 6 couplr-1.5.0/couplr/man/pixel_morph_animate.Rd | 6 couplr-1.5.0/couplr/man/sensitivity_analysis.Rd | 3 couplr-1.5.0/couplr/man/standardized_difference.Rd | 2 couplr-1.5.0/couplr/src/RcppExports.cpp | 39 couplr-1.5.0/couplr/src/core/lap_utils_rcpp.cpp | 35 couplr-1.5.0/couplr/src/core/lap_utils_rcpp.h | 17 couplr-1.5.0/couplr/src/gabow_tarjan/solve_gabow_tarjan.cpp | 34 couplr-1.5.0/couplr/src/gabow_tarjan/utils_gabow_tarjan.cpp | 31 couplr-1.5.0/couplr/src/interface/prepare_cost_matrix.cpp | 9 couplr-1.5.0/couplr/src/morph/morph_pixel_level.cpp | 30 couplr-1.5.0/couplr/src/rcpp_interface.cpp | 23 couplr-1.5.0/couplr/src/solvers/greedy_matching.cpp | 30 couplr-1.5.0/couplr/src/solvers/greedy_matching_rcpp.cpp | 260 couplr-1.5.0/couplr/src/solvers/network_simplex/ns_graph.h | 16 couplr-1.5.0/couplr/src/solvers/network_simplex/solve_network_simplex.cpp | 6 couplr-1.5.0/couplr/src/solvers/network_simplex/solve_network_simplex_rcpp.cpp | 106 couplr-1.5.0/couplr/src/solvers/orlin_ahuja/orlin_solve_rcpp.cpp | 35 couplr-1.5.0/couplr/src/solvers/solve_auction.cpp | 693 - couplr-1.5.0/couplr/src/solvers/solve_auction.h | 5 couplr-1.5.0/couplr/src/solvers/solve_auction_rcpp.cpp | 585 - couplr-1.5.0/couplr/src/solvers/solve_bottleneck.cpp | 4 couplr-1.5.0/couplr/src/solvers/solve_bottleneck_rcpp.cpp | 227 couplr-1.5.0/couplr/src/solvers/solve_bruteforce.cpp | 15 couplr-1.5.0/couplr/src/solvers/solve_bruteforce_rcpp.cpp | 81 couplr-1.5.0/couplr/src/solvers/solve_csa.cpp | 59 couplr-1.5.0/couplr/src/solvers/solve_csa_rcpp.cpp | 238 couplr-1.5.0/couplr/src/solvers/solve_csflow_rcpp.cpp | 213 couplr-1.5.0/couplr/src/solvers/solve_cycle_cancel_rcpp.cpp | 345 couplr-1.5.0/couplr/src/solvers/solve_full_matching.cpp | 7 couplr-1.5.0/couplr/src/solvers/solve_hk01.cpp | 30 couplr-1.5.0/couplr/src/solvers/solve_hk01_rcpp.cpp | 242 couplr-1.5.0/couplr/src/solvers/solve_hungarian_rcpp.cpp | 17 couplr-1.5.0/couplr/src/solvers/solve_jv_duals_rcpp.cpp | 18 couplr-1.5.0/couplr/src/solvers/solve_jv_rcpp.cpp | 35 couplr-1.5.0/couplr/src/solvers/solve_lapmod.cpp | 10 couplr-1.5.0/couplr/src/solvers/solve_lapmod_rcpp.cpp | 35 couplr-1.5.0/couplr/src/solvers/solve_line_metric.cpp | 38 couplr-1.5.0/couplr/src/solvers/solve_line_metric_rcpp.cpp | 6 couplr-1.5.0/couplr/src/solvers/solve_munkres.cpp | 13 couplr-1.5.0/couplr/src/solvers/solve_munkres_rcpp.cpp | 17 couplr-1.5.0/couplr/src/solvers/solve_push_relabel_rcpp.cpp | 250 couplr-1.5.0/couplr/src/solvers/solve_ramshaw_tarjan_rcpp.cpp | 35 couplr-1.5.0/couplr/src/solvers/solve_sinkhorn.cpp | 11 couplr-1.5.0/couplr/src/solvers/solve_sinkhorn_rcpp.cpp | 18 couplr-1.5.0/couplr/src/solvers/solve_ssap_bucket.cpp | 90 couplr-1.5.0/couplr/src/solvers/solve_ssap_bucket_rcpp.cpp | 374 - couplr-1.5.0/couplr/src/solvers/solve_ssp_rcpp.cpp | 163 couplr-1.5.0/couplr/tests/testthat/test-assignment-csa.R | 16 couplr-1.5.0/couplr/tests/testthat/test-assignment-push_relabel.R | 2 couplr-1.5.0/couplr/tests/testthat/test-assignment-ssap-bucket.R | 54 couplr-1.5.0/couplr/tests/testthat/test-autoplot.R | 194 couplr-1.5.0/couplr/tests/testthat/test-coverage-90-boost.R | 682 - couplr-1.5.0/couplr/tests/testthat/test-coverage-90-final.R | 732 +- couplr-1.5.0/couplr/tests/testthat/test-coverage-90-target.R | 1108 +-- couplr-1.5.0/couplr/tests/testthat/test-coverage-95.R | 1274 +-- couplr-1.5.0/couplr/tests/testthat/test-coverage-boost.R | 420 - couplr-1.5.0/couplr/tests/testthat/test-coverage-push-90.R | 664 - couplr-1.5.0/couplr/tests/testthat/test-distance-cache-coverage.R | 718 - couplr-1.5.0/couplr/tests/testthat/test-error-handling.R | 834 +- couplr-1.5.0/couplr/tests/testthat/test-line-metric.R | 39 couplr-1.5.0/couplr/tests/testthat/test-matching-blocks.R | 932 +- couplr-1.5.0/couplr/tests/testthat/test-matching-core-coverage-2.R | 388 - couplr-1.5.0/couplr/tests/testthat/test-matching-core-coverage-3.R | 496 - couplr-1.5.0/couplr/tests/testthat/test-matching-core-coverage-4.R | 1010 +- couplr-1.5.0/couplr/tests/testthat/test-matching-core-coverage.R | 1018 +- couplr-1.5.0/couplr/tests/testthat/test-matching-core-extended.R | 1018 +- couplr-1.5.0/couplr/tests/testthat/test-matching-mahalanobis.R | 326 couplr-1.5.0/couplr/tests/testthat/test-matching-parallel-coverage-2.R | 838 +- couplr-1.5.0/couplr/tests/testthat/test-matching-ratio.R | 162 couplr-1.5.0/couplr/tests/testthat/test-matching-replace.R | 140 couplr-1.5.0/couplr/tests/testthat/test-matching.R | 2732 +++---- couplr-1.5.0/couplr/tests/testthat/test-morph-coverage-final.R | 468 - couplr-1.5.0/couplr/tests/testthat/test-morph-pixel.R | 12 couplr-1.5.0/couplr/tests/testthat/test-morph-tiling-coverage.R | 78 couplr-1.5.0/couplr/tests/testthat/test-morph-tiling-extended.R | 38 couplr-1.5.0/couplr/tests/testthat/test-morph-tiling.R | 46 couplr-1.5.0/couplr/tests/testthat/test-print-methods.R | 2 couplr-1.5.0/couplr/tests/testthat/test-rcpp-interface-coverage.R | 598 - couplr-1.5.0/couplr/tests/testthat/test-solver-csa.R | 56 couplr-1.5.0/couplr/tests/testthat/test-statistical-recovery.R |only couplr-1.5.0/couplr/tests/testthat/test-summary-enhanced.R | 134 couplr-1.5.0/couplr/tests/testthat/test-trace-parity.R | 12 couplr-1.5.0/couplr/vignettes/algorithms.Rmd | 2500 +++--- couplr-1.5.0/couplr/vignettes/comparison.Rmd | 1666 ++-- couplr-1.5.0/couplr/vignettes/getting-started.Rmd | 972 +- couplr-1.5.0/couplr/vignettes/matching-workflows.Rmd | 3600 +++++----- couplr-1.5.0/couplr/vignettes/pixel-morphing.Rmd | 2108 ++--- couplr-1.5.0/couplr/vignettes/troubleshooting.Rmd | 1382 +-- 155 files changed, 25817 insertions(+), 29602 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc. From this
version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all,
see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb],
Patrick [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 2.2-1 dated 2026-02-13 and 2.2-3 dated 2026-07-19
DESCRIPTION | 6 MD5 | 26 +- R/spplot.R | 8 build/vignette.rds |binary inst/doc/csdacm.R | 2 inst/doc/csdacm.pdf |binary inst/doc/intro_sp.R | 2 inst/doc/intro_sp.pdf |binary inst/doc/retiring_rgdal_geos_1.html | 2 inst/doc/sp_gallery.html | 434 +++++++++++++++--------------------- man/Line-class.Rd | 22 - man/Lines-class.Rd | 27 +- man/bbox.Rd | 1 src/sp_xports.c | 10 14 files changed, 241 insertions(+), 299 deletions(-)
Title: Publication-Ready Tables for 'manymome' Results
Description: Converts results from the 'manymome' package,
presented in Cheung and Cheung (2024)
<doi:10.3758/s13428-023-02224-z>, to publication-ready
tables.
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome.table versions 0.4.0 dated 2024-12-10 and 0.4.1 dated 2026-07-19
DESCRIPTION | 15 ++++++----- MD5 | 20 +++++++-------- NEWS.md | 8 +++++- README.md | 24 +++++++++++------- build/vignette.rds |binary inst/doc/manymome.table.Rmd | 2 - inst/doc/manymome.table.html | 40 ++++++++++++++++-------------- man/as_flextable.cond_indirect_effects.Rd | 2 - man/as_flextable.indirect_list.Rd | 2 - man/reexports.Rd | 2 - vignettes/manymome.table.Rmd | 2 - 11 files changed, 67 insertions(+), 50 deletions(-)
More information about manymome.table at CRAN
Permanent link
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] ,
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.2-16 dated 2026-05-03 and 0.2-17 dated 2026-07-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/liblwgeom/gbox.c | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut] ),
Tom Palmer [aut, cre] ,
Philipp Lepert [ctb]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between Statamarkdown versions 0.9.6 dated 2025-10-07 and 0.9.7 dated 2026-07-19
Statamarkdown-0.9.6/Statamarkdown/inst/README.md |only Statamarkdown-0.9.7/Statamarkdown/DESCRIPTION | 19 Statamarkdown-0.9.7/Statamarkdown/LICENSE | 2 Statamarkdown-0.9.7/Statamarkdown/MD5 | 40 Statamarkdown-0.9.7/Statamarkdown/NAMESPACE | 12 Statamarkdown-0.9.7/Statamarkdown/NEWS.md |only Statamarkdown-0.9.7/Statamarkdown/R/engine_output.R | 56 Statamarkdown-0.9.7/Statamarkdown/R/find_stata.r | 152 - Statamarkdown-0.9.7/Statamarkdown/R/misc.r | 39 Statamarkdown-0.9.7/Statamarkdown/R/spinstata.R | 423 ++-- Statamarkdown-0.9.7/Statamarkdown/R/stata_collectcode.r | 132 - Statamarkdown-0.9.7/Statamarkdown/R/stata_engine.r | 152 - Statamarkdown-0.9.7/Statamarkdown/R/stata_engine_output.r | 141 - Statamarkdown-0.9.7/Statamarkdown/R/utils.R | 96 - Statamarkdown-0.9.7/Statamarkdown/README.md | 58 Statamarkdown-0.9.7/Statamarkdown/inst/doc/1_Basic_Use_of_Statamarkdown.html | 846 ++++----- Statamarkdown-0.9.7/Statamarkdown/inst/doc/2_Linking_Stata_Code_Chunks.html | 846 ++++----- Statamarkdown-0.9.7/Statamarkdown/inst/doc/3_Combining_Stata_and_R.html | 862 +++++----- Statamarkdown-0.9.7/Statamarkdown/man/Statamarkdown-package.rd | 18 Statamarkdown-0.9.7/Statamarkdown/man/find_stata.Rd | 114 - Statamarkdown-0.9.7/Statamarkdown/man/spinstata.Rd | 166 - Statamarkdown-0.9.7/Statamarkdown/man/stata_engine.rd | 2 22 files changed, 2086 insertions(+), 2090 deletions(-)
Title: Robust Test Statistics for Structural Equation Models
Description: Computes robust p-values for overall fit and nested comparisons of
structural equation models fitted with 'lavaan'. Implements penalized
eigenvalue block averaging and penalized regression (Foldnes, Moss,
Grønneberg, 2025) <doi:10.1080/10705511.2024.2372028>, including their
extension to nested models (Foldnes, Grønneberg, Moss, 2026)
<doi:10.3758/s13428-026-02968-4>, alongside familiar corrections such as
Satorra-Bentler. Supported settings include complete-data ML, GLS, and ULS,
categorical DWLS and ULS, and full-information maximum likelihood with one
or several groups.
Author: Jonas Moss [aut, cre] ,
Njal Foldnes [ctb] ,
Steffen Groenneberg [ctb]
Maintainer: Jonas Moss <jonas.moss.statistics@gmail.com>
This is a re-admission after prior archival of version 0.9.0 dated 2026-06-09
Diff between semTests versions 0.9.0 dated 2026-06-09 and 1.0.0 dated 2026-07-19
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semTests-1.0.0/semTests/tests/testthat/test-utility.R | 84 - semTests-1.0.0/semTests/tools |only semTests-1.0.0/semTests/vignettes/categorical-data.Rmd |only semTests-1.0.0/semTests/vignettes/continuous-data.Rmd |only semTests-1.0.0/semTests/vignettes/fiml-missing-data.Rmd |only semTests-1.0.0/semTests/vignettes/latent-growth.Rmd |only semTests-1.0.0/semTests/vignettes/measurement-invariance.Rmd |only semTests-1.0.0/semTests/vignettes/semTests.Rmd | 173 +- 105 files changed, 3095 insertions(+), 1683 deletions(-)
Title: Log-Gaussian Cox Process Models with Approximations
Description: Supports modelling case data to facilitate. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Monte Carlo maximum likelihood is the main fitting method with a low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and a stochastic partial differential equation approximation. Bayesian methods
are also provided for some methods. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 1.0.3 dated 2026-06-07 and 1.0.4 dated 2026-07-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/griddata_class.R | 6 +++--- build/partial.rdb |binary src/region_model.cpp | 18 +++++++++++++----- 5 files changed, 24 insertions(+), 16 deletions(-)
Title: R Client for 'iRODS'
Description: The open sourced data management software 'Integrated
Rule-Oriented Data System' ('iRODS') offers solutions for the whole
data life cycle (<https://irods.org/>). The loosely constructed and
highly configurable architecture of 'iRODS' frees the user from strict
formatting constraints and single-vendor solutions. This package
provides an interface to the 'iRODS' HTTP API, allowing you to manage
your data and metadata in 'iRODS' with R. Storage of annotated files
and R objects in 'iRODS' ensures findability, accessibility,
interoperability, and reusability of data.
Author: iRODS Consortium [cre, cph],
Martin Schobben [aut] ,
Mariana Montes [aut],
Terrell Russell [ctb],
Christine Staiger [ctb],
Ton Smeele [ctb],
Alan King [ctb]
Maintainer: iRODS Consortium <support@irods.org>
Diff between rirods versions 0.2.0 dated 2024-03-15 and 0.3.0 dated 2026-07-19
rirods-0.2.0/rirods/inst/irods_demo/irods_catalog_provider/setup-4.3.1.input |only rirods-0.2.0/rirods/inst/irods_demo/irods_client_rest_cpp |only rirods-0.3.0/rirods/DESCRIPTION | 15 rirods-0.3.0/rirods/MD5 | 79 +-- rirods-0.3.0/rirods/NEWS.md | 7 rirods-0.3.0/rirods/README.md | 217 +++------ rirods-0.3.0/rirods/build/partial.rdb |binary rirods-0.3.0/rirods/inst/WORDLIST | 4 rirods-0.3.0/rirods/inst/doc/demo.R | 24 - rirods-0.3.0/rirods/inst/doc/demo.Rmd | 2 rirods-0.3.0/rirods/inst/doc/demo.html | 11 rirods-0.3.0/rirods/inst/doc/develop.R | 28 - rirods-0.3.0/rirods/inst/doc/develop.html | 2 rirods-0.3.0/rirods/inst/doc/icommands.R | 188 +++---- rirods-0.3.0/rirods/inst/doc/icommands.html | 6 rirods-0.3.0/rirods/inst/doc/local-irods.R | 148 +++--- rirods-0.3.0/rirods/inst/doc/local-irods.html | 6 rirods-0.3.0/rirods/inst/doc/metadata.R | 240 +++++----- rirods-0.3.0/rirods/inst/doc/metadata.html | 6 rirods-0.3.0/rirods/inst/irods_demo/README.md | 10 rirods-0.3.0/rirods/inst/irods_demo/dependencies.dot |only rirods-0.3.0/rirods/inst/irods_demo/dependencies.png |only rirods-0.3.0/rirods/inst/irods_demo/docker-compose.yml | 54 +- rirods-0.3.0/rirods/inst/irods_demo/grafana |only rirods-0.3.0/rirods/inst/irods_demo/irods_catalog/Dockerfile | 2 rirods-0.3.0/rirods/inst/irods_demo/irods_catalog/init-user-db.sh | 1 rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_consumer |only rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_provider/Dockerfile | 33 + rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_provider/entrypoint.sh | 35 + rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_provider/install_transfer_totals.sh |only rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_provider/s3.keypair |only rirods-0.3.0/rirods/inst/irods_demo/irods_catalog_provider/unattended_install.json |only rirods-0.3.0/rirods/inst/irods_demo/irods_client_http_api/config.json | 2 rirods-0.3.0/rirods/inst/irods_demo/irods_client_icommands/Dockerfile | 24 - rirods-0.3.0/rirods/inst/irods_demo/irods_client_s3_api |only rirods-0.3.0/rirods/inst/irods_demo/nginx |only rirods-0.3.0/rirods/inst/irods_demo/prometheus |only rirods-0.3.0/rirods/inst/irods_demo/sql_exporter |only rirods-0.3.0/rirods/man/imeta.Rd | 2 rirods-0.3.0/rirods/man/iquery.Rd | 2 rirods-0.3.0/rirods/vignettes/demo.Rmd | 2 41 files changed, 598 insertions(+), 552 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.8 dated 2025-03-03 and 0.3.10 dated 2026-07-19
DESCRIPTION | 10 MD5 | 60 ++-- NEWS.md | 11 R/genetrack_ly.R | 5 R/genetracks.R | 35 +- R/genetracks_grob.R | 13 R/gg_genetracks.R | 4 R/gg_scatter.R | 666 ++++++++++++++++++++++++++--------------------- R/locus.R | 4 R/locus_ggplot.R | 4 R/locus_plot.R | 5 R/locus_plotly.R | 5 R/scatter_plot.R | 1 R/set_layers.R | 6 README.md | 1 build/vignette.rds |binary inst/doc/locuszoomr.R | 106 +------ inst/doc/locuszoomr.Rmd | 100 ------- inst/doc/locuszoomr.html | 44 +-- man/eqtl_plot.Rd | 2 man/genetrack_ly.Rd | 5 man/genetracks.Rd | 9 man/genetracks_grob.Rd | 5 man/gg_genetracks.Rd | 5 man/gg_scatter.Rd | 15 - man/locus_ggplot.Rd | 5 man/locus_plot.Rd | 7 man/locus_plotly.Rd | 5 man/overlay_plot.Rd | 2 man/set_layers.Rd | 6 vignettes/locuszoomr.Rmd | 100 ------- 31 files changed, 596 insertions(+), 650 deletions(-)
Title: Implementation of Case-Control Optimal Matching
Description: Cases are matched to controls in an efficient, optimal and computationally flexible way. It uses
the idea of sub-sampling in the level of the case, by creating pseudo-observations of controls. The
user can select between replacement and without replacement, the number of controls, and several covariates
to match upon. See Mamouris (2021) <doi:10.1186/s12874-021-01256-3> for an overview.
Author: Pavlos Mamouris [aut, cre],
Vahid Nassiri [aut, ctb]
Maintainer: Pavlos Mamouris <pavlos.mamouris@rwdatasolutions.com>
Diff between ccoptimalmatch versions 0.1.0 dated 2021-04-21 and 0.1.1 dated 2026-07-19
DESCRIPTION | 12 MD5 | 18 R/being_processed_data.R | 27 - R/not_processed_data.R | 25 - build/vignette.rds |binary inst/doc/ccoptimalmatching_vignette.R | 28 - inst/doc/ccoptimalmatching_vignette.html | 774 +++++++++++++++++-------------- man/being_processed.Rd | 24 man/ccoptimalmatch.Rd | 4 man/not_processed.Rd | 22 10 files changed, 526 insertions(+), 408 deletions(-)
More information about ccoptimalmatch at CRAN
Permanent link
Title: Bayesian Generalized Linear Models (IID Samples)
Description: Provides Bayesian linear and generalized linear model fitting
with independent and identically distributed (iid) posterior samples. The
main functions mirror R's lm() and glm() interfaces while adding prior
family specifications for Gaussian, Poisson, binomial, and Gamma models
with log-concave likelihoods. Sampling for supported non-conjugate models
uses accept-reject methods based on likelihood subgradients as in Nygren
and Nygren (2006) <doi:10.1198/016214506000000357>. The package also
includes tools for prior setup, posterior summaries, prediction,
diagnostics, simulation, vignettes, and optional 'OpenCL' acceleration for
larger models.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between glmbayes versions 0.9.6 dated 2026-06-21 and 0.9.7 dated 2026-07-19
glmbayes-0.9.6/glmbayes/R/load_kernel_library.R |only glmbayes-0.9.6/glmbayes/man/load_kernel_source.Rd |only glmbayes-0.9.6/glmbayes/src/nmath |only glmbayes-0.9.7/glmbayes/DESCRIPTION | 19 glmbayes-0.9.7/glmbayes/MD5 | 292 glmbayes-0.9.7/glmbayes/NAMESPACE | 36 glmbayes-0.9.7/glmbayes/NEWS.md | 58 glmbayes-0.9.7/glmbayes/R/RcppExports.R | 8 glmbayes-0.9.7/glmbayes/R/bayestestR-methods.R |only glmbayes-0.9.7/glmbayes/R/glmbayes-package.R | 168 glmbayes-0.9.7/glmbayes/R/gpu_diagnostics.R | 5 glmbayes-0.9.7/glmbayes/R/insight-methods.R |only glmbayes-0.9.7/glmbayes/R/lmb.R | 1 glmbayes-0.9.7/glmbayes/R/pfamily.R | 25 glmbayes-0.9.7/glmbayes/R/prior_simfunction.R |only glmbayes-0.9.7/glmbayes/R/rcpp_wrappers.R | 17 glmbayes-0.9.7/glmbayes/R/reexports.R |only glmbayes-0.9.7/glmbayes/R/rglmb.R | 618 - glmbayes-0.9.7/glmbayes/R/simfunction.R | 13 glmbayes-0.9.7/glmbayes/README.md | 30 glmbayes-0.9.7/glmbayes/build/partial.rdb |binary glmbayes-0.9.7/glmbayes/inst/COPYRIGHTS | 5 glmbayes-0.9.7/glmbayes/inst/WORDLIST | 5 glmbayes-0.9.7/glmbayes/inst/cl/README.md | 121 glmbayes-0.9.7/glmbayes/inst/cl/R_ext_internals/R_ext_internals.cl | 52 glmbayes-0.9.7/glmbayes/inst/cl/System/stdint.cl | 56 glmbayes-0.9.7/glmbayes/inst/cl/libR_shims/libR.cl | 82 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-01.html | 12 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-02-S01.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-02-S02.html | 246 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-02-S03.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-02-S04.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-02-S05.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-03.html | 1590 --- glmbayes-0.9.7/glmbayes/inst/doc/Chapter-04.html | 287 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-05.html | 162 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-06.html | 168 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-07.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-08.html | 50 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-09.html | 80 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-10.html | 80 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-11.html | 56 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-13.html | 12 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-14.html | 34 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-17.html | 196 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-18.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A01.html | 65 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A02.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A03.html | 137 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A04.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A05.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A06.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A07.Rmd | 5241 +++++----- glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A07.html | 145 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A08.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A09.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A10.Rmd | 38 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A10.html | 82 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A11.html | 4 glmbayes-0.9.7/glmbayes/inst/doc/Chapter-A12.html | 4 glmbayes-0.9.7/glmbayes/inst/examples/Ex_glmbayes_bayestestR_prior_methods.R |only glmbayes-0.9.7/glmbayes/inst/examples/Ex_glmbayes_insight_methods.R |only glmbayes-0.9.7/glmbayes/inst/examples/Ex_load_kernel_source.R | 38 glmbayes-0.9.7/glmbayes/man/glmbayes-package.Rd | 3 glmbayes-0.9.7/glmbayes/man/glmbayes_bayestestR_prior_methods.Rd |only glmbayes-0.9.7/glmbayes/man/glmbayes_insight_methods.Rd |only glmbayes-0.9.7/glmbayes/man/gpu_diagnostics.Rd | 30 glmbayes-0.9.7/glmbayes/man/pfamily.Rd | 7 glmbayes-0.9.7/glmbayes/man/prior_simfuncs.Rd |only glmbayes-0.9.7/glmbayes/man/reexports.Rd |only glmbayes-0.9.7/glmbayes/src/EnvelopeDispersionBuild.cpp | 253 glmbayes-0.9.7/glmbayes/src/RcppExports.cpp | 27 glmbayes-0.9.7/glmbayes/src/backup |only glmbayes-0.9.7/glmbayes/src/export_wrappers.cpp | 24 glmbayes-0.9.7/glmbayes/src/famfuncs_Gamma.cpp | 10 glmbayes-0.9.7/glmbayes/src/famfuncs_binomial.cpp | 22 glmbayes-0.9.7/glmbayes/src/famfuncs_gaussian.cpp | 6 glmbayes-0.9.7/glmbayes/src/kernel_loader.cpp | 416 glmbayes-0.9.7/glmbayes/src/kernel_wrappers.cpp | 13 glmbayes-0.9.7/glmbayes/src/opencl.h | 7 glmbayes-0.9.7/glmbayes/src/openclPort.h | 36 glmbayes-0.9.7/glmbayes/src/rIndepNormalGammaReg.cpp | 5 glmbayes-0.9.7/glmbayes/src/rng_utils.cpp | 35 glmbayes-0.9.7/glmbayes/tests/testthat/test-bayestestR-methods.R |only glmbayes-0.9.7/glmbayes/tests/testthat/test-insight-methods.R |only glmbayes-0.9.7/glmbayes/tests/testthat/test-lmb-non-zellner.R | 37 glmbayes-0.9.7/glmbayes/tests/testthat/test-prior_simfunction.R |only glmbayes-0.9.7/glmbayes/vignettes/Chapter-A07.Rmd | 5241 +++++----- glmbayes-0.9.7/glmbayes/vignettes/Chapter-A10.Rmd | 38 89 files changed, 7406 insertions(+), 9190 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre] ,
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-8 dated 2026-07-02 and 1.0-9 dated 2026-07-19
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- inst/doc/FDRenvelopes.pdf |binary inst/doc/GET.pdf |binary inst/doc/QuantileRegression.pdf |binary inst/doc/QuantileRegression.tex.rsp | 4 ++-- inst/doc/pointpatterns.pdf |binary inst/doc/pointpatterns.tex.rsp | 8 ++++---- vignettes/QuantileRegression.Rnw.orig | 4 ++-- vignettes/QuantileRegression.tex.rsp | 4 ++-- vignettes/pointpatterns.Rnw.orig | 8 ++++---- vignettes/pointpatterns.tex.rsp | 8 ++++---- 12 files changed, 33 insertions(+), 33 deletions(-)
Title: Microbiome Mixture Analysis
Description: Evaluate whether a microbiome sample is a mixture of two
samples, by fitting a model for the number of read counts as a
function of single nucleotide polymorphism (SNP) allele and the
genotypes of two potential source samples.
Lobo et al. (2021) <doi:10.1093/g3journal/jkab308>.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between mbmixture versions 0.6 dated 2024-11-27 and 0.8 dated 2026-07-19
DESCRIPTION | 13 +- LICENSE | 2 MD5 | 23 ++-- NEWS.md | 9 + R/cluster_util.R | 4 R/mbmixture-package.R |only README.md | 21 +++- build/partial.rdb |only build/vignette.rds |binary data/mbmixdata.RData |binary inst/doc/mbmixture.Rmd | 3 inst/doc/mbmixture.html | 217 +++++++++++++++++++++++++++-------------------- man/mbmixture-package.Rd |only vignettes/mbmixture.Rmd | 3 14 files changed, 180 insertions(+), 115 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-22 1.0.1
Title: Likelihood Ratio Test P-Values for Structural Equation Models
Description: Computes likelihood ratio test (LRT) p-values
for free parameters in a structural equation model.
Currently supports models fitted by the 'lavaan' package by
Rosseel (2012) <doi:10.18637/jss.v048.i02>.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlrtp versions 0.1.1 dated 2024-06-20 and 0.1.2 dated 2026-07-19
DESCRIPTION | 16 - MD5 | 18 - NEWS.md | 18 + R/fix_to_zero.R | 20 + R/semlrtp-package.R |only README.md | 8 build/partial.rdb |only build/vignette.rds |binary inst/doc/semlrtp.html | 276 ++++++++++++------------- man/lrt.Rd | 2 man/semlrtp-package.Rd |only tests/testthat/test_fix_to_zero_start_values.R |only 12 files changed, 201 insertions(+), 157 deletions(-)
Title: Public Suffix List Engine
Description: A focused implementation of the Public Suffix List (PSL). Bundles a
reproducible, pinned PSL snapshot and implements the official prevailing-rule
algorithm to answer public-suffix (eTLD) and registrable-domain (eTLD+1)
queries. Distinguishes ICANN and PRIVATE rule sections, accepts Unicode and
ASCII hostnames via 'punycoder' canonicalization, and supports an explicit,
validated offline refresh path. The matcher is compiled with 'cpp11' and
requires no external system library. Used as the PSL engine by the 'rurl'
package.
Author: Bart Turczynski [aut, cre]
Maintainer: Bart Turczynski <bartek@turczynski.pl>
Diff between pslr versions 1.0.1 dated 2026-06-22 and 1.1.1 dated 2026-07-19
DESCRIPTION | 33 - MD5 | 100 ++-- NAMESPACE | 5 NEWS.md | 129 +++++ R/benchmark-fixtures.R |only R/cache.R | 206 +++++++-- R/canonicalize.R | 100 ++-- R/duplicates.R | 20 R/matcher.R | 620 ++++++++++++++++++++-------- R/metadata.R | 114 ++++- R/parser.R | 303 ++++++++----- R/query.R | 473 +++++++++++++-------- R/refresh.R | 517 +++++++++++++++++------ README.md | 145 ++++++ inst/CITATION |only inst/WORDLIST | 54 ++ inst/doc/introduction.R | 13 inst/doc/introduction.Rmd | 55 ++ inst/doc/introduction.html | 99 +++- man/is_public_suffix.Rd | 12 man/psl_cache_prune.Rd |only man/psl_engine.Rd |only man/psl_outdated.Rd |only man/psl_refresh.Rd | 6 man/psl_rules.Rd | 2 man/psl_use.Rd | 8 man/psl_version.Rd | 2 man/pslr-package.Rd | 6 man/public_suffix.Rd | 14 man/public_suffix_rule.Rd | 12 man/registrable_domain.Rd | 14 man/suffix_extract.Rd | 14 src/matcher.cpp | 257 ++++++++--- tests/testthat/fixtures/oracle-baseline.rds |only tests/testthat/helper-active.R | 15 tests/testthat/helper-oracle.R |only tests/testthat/test-benchmark-fixtures.R |only tests/testthat/test-bundled-data.R | 22 tests/testthat/test-cache-prune.R |only tests/testthat/test-cache.R | 125 ++++- tests/testthat/test-canonicalize.R | 49 ++ tests/testthat/test-dedup.R | 55 +- tests/testthat/test-duplicates.R | 25 - tests/testthat/test-engine.R |only tests/testthat/test-extract.R | 77 ++- tests/testthat/test-freshness-corpus.R |only tests/testthat/test-matcher.R | 232 ++++++++-- tests/testthat/test-oracle.R |only tests/testthat/test-osv.R |only tests/testthat/test-parser.R | 119 ++++- tests/testthat/test-profile-rebuild.R | 16 tests/testthat/test-psl-vectors.R | 12 tests/testthat/test-query.R | 50 +- tests/testthat/test-refresh.R | 250 ++++++++++- tests/testthat/test-security.R |only tests/testthat/test-use.R | 46 +- tests/testthat/test-version-rules.R | 95 +++- vignettes/introduction.Rmd | 55 ++ 58 files changed, 3521 insertions(+), 1055 deletions(-)
Title: Bayesian Error Propagation and Forecast Uncertainty
Decomposition
Description: Provides a full pipeline from regularized or standard regression
models (elastic net, linear models, generalized linear models, random
forests) to informed Bayesian priors, structured forecast uncertainty
decomposition (parameter / environmental / residual, plus a temporal
component when the model carries an autocorrelation term), and forecast
shelf life analysis (the quantification of when a forecast becomes
uninformative). Designed for ecological and genomic forecasting with
climate or environmental covariates. Methods build on Bürkner (2017)
<doi:10.18637/jss.v080.i01> for Bayesian regression via 'Stan',
Friedman, Hastie, and Tibshirani (2010) <doi:10.18637/jss.v033.i01>
for elastic net regularization, Wright and Ziegler (2017)
<doi:10.18637/jss.v077.i01> for random forests, and Vehtari, Gelman,
and Gabry (2017) <doi:10.1007/s11222-016-9696-4> for leave-one-out
cross-validation.
Author: Luis Javier Madrigal-Roca [aut, cre],
John Kelly [aut]
Maintainer: Luis Javier Madrigal-Roca <madrigalrocalj@yahoo.com>
This is a re-admission after prior archival of version 1.1.0 dated 2026-05-25
Diff between ErrorTracer versions 1.1.0 dated 2026-05-25 and 1.2.1 dated 2026-07-19
DESCRIPTION | 8 MD5 | 59 ++-- NAMESPACE | 11 NEWS.md | 163 +++++++++++ R/calibrate.R | 104 +++++++ R/decompose.R | 37 +- R/fit.R | 61 ++++ R/plot.R | 47 +++ R/predict.R | 471 +++++++++++++++++++++++++++++----- R/priors.R | 95 +++++- R/sensitivity.R | 10 R/shelf_life.R | 114 +++++++- R/skill.R |only R/sobol.R |only README.md | 2 build/vignette.rds |binary inst/doc/introduction.html | 16 - inst/doc/worked_example.html | 16 - man/decompose_uncertainty.Rd | 37 +- man/et_fit.Rd | 32 ++ man/et_pit.Rd |only man/et_plot_pit.Rd |only man/et_predict.Rd | 45 ++- man/et_sensitivity_profile.Rd | 7 man/et_skill_score.Rd |only man/et_sobol.Rd |only man/extract_priors.Rd | 53 +++ man/shelf_life.Rd | 28 +- tests/testthat/test-decompose.R | 73 ++++- tests/testthat/test-env-ensemble.R |only tests/testthat/test-integration.R | 89 ++++++ tests/testthat/test-pit.R |only tests/testthat/test-priors.R | 63 ++++ tests/testthat/test-skill.R |only tests/testthat/test-v-env-stability.R | 114 ++++++++ 35 files changed, 1540 insertions(+), 215 deletions(-)
Title: Scalable Statistical Computing with HDF5-Backed Matrices
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, and QR decomposition) written in C++ and R, along with building
blocks from which higher-level multivariate methods such as canonical
correlation analysis can be constructed. These building blocks are designed
not only for direct use, but also as foundational components for developing
new statistical methods that must operate on datasets too large to fit in
memory. The package supports data provided either as 'HDF5' files or
standard R objects, and is intended for high-dimensional applications such
as 'omics' and precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 2.0.3 dated 2026-07-06 and 2.0.4 dated 2026-07-19
DESCRIPTION | 8 MD5 | 170 ++++++++-------- NEWS.md | 32 +++ R/S3_arithmetic.R | 47 +++- R/S3_bind.R | 12 - R/S3_diagonal.R | 62 ----- R/S3_matvec.R | 1 README.md | 10 inst/doc/BigDataStatMeth.html | 56 ++--- inst/include/Utilities/Utilities.hpp | 12 - inst/include/hdf5Algebra/crossprod.hpp | 2 inst/include/hdf5Algebra/matrixAggregations.hpp | 92 ++++---- inst/include/hdf5Algebra/matrixCorrelation.hpp | 24 +- inst/include/hdf5Algebra/matrixDiagonal.hpp | 6 inst/include/hdf5Algebra/matrixEigenDecomposition.hpp | 22 +- inst/include/hdf5Algebra/matrixEquationSolver.hpp | 10 inst/include/hdf5Algebra/matrixInvCholesky.hpp | 46 ++-- inst/include/hdf5Algebra/matrixNormalization.hpp | 38 +-- inst/include/hdf5Algebra/matrixPCA.hpp | 30 +- inst/include/hdf5Algebra/matrixQR.hpp | 24 +- inst/include/hdf5Algebra/matrixSdMean.hpp | 12 - inst/include/hdf5Algebra/matrixSubstract.hpp | 20 - inst/include/hdf5Algebra/matrixSum.hpp | 20 - inst/include/hdf5Algebra/matrixSvd.hpp | 16 - inst/include/hdf5Algebra/matrixSvdBlock.hpp | 46 ++-- inst/include/hdf5Algebra/matrixTriangular.hpp | 12 - inst/include/hdf5Algebra/multiplication.hpp | 10 inst/include/hdf5Algebra/multiplicationSparse.hpp | 2 inst/include/hdf5Algebra/tcrossprod.hpp | 2 inst/include/hdf5Algebra/vectorOperations.hpp | 32 +-- inst/include/hdf5Algebra/vectormatrix.hpp | 12 - inst/include/hdf5Omics/hdf5RemoveMAF.hpp | 12 - inst/include/hdf5Utilities/hdf5ApplytoDatasets.hpp | 10 inst/include/hdf5Utilities/hdf5BindDatasets.hpp | 20 - inst/include/hdf5Utilities/hdf5Datasets.hpp | 190 +++++++++--------- inst/include/hdf5Utilities/hdf5DatasetsInternal.hpp | 80 +++---- inst/include/hdf5Utilities/hdf5Diagonal.hpp | 4 inst/include/hdf5Utilities/hdf5Dims.hpp | 30 +- inst/include/hdf5Utilities/hdf5Files.hpp | 36 +-- inst/include/hdf5Utilities/hdf5Groups.hpp | 26 +- inst/include/hdf5Utilities/hdf5ImportFiles.hpp | 6 inst/include/hdf5Utilities/hdf5ImputeData.hpp | 20 - inst/include/hdf5Utilities/hdf5Methods.hpp | 14 - inst/include/hdf5Utilities/hdf5ReduceDataset.hpp | 20 - inst/include/hdf5Utilities/hdf5RemoveElements.hpp | 12 - inst/include/hdf5Utilities/hdf5RemoveLowData.hpp | 14 - inst/include/hdf5Utilities/hdf5SortDataset.hpp | 10 inst/include/hdf5Utilities/hdf5SplitDataset.hpp | 20 - inst/include/hdf5Utilities/hdf5Utilities.hpp | 60 ++--- inst/include/memAlgebra/memMultiplication.hpp | 6 inst/include/memAlgebra/memSubstract.hpp | 2 inst/include/memAlgebra/memSum.hpp | 2 man/Ops.HDF5Matrix.Rd | 6 man/cbind.HDF5Matrix.Rd | 5 man/diag-replace.Rd | 3 src/hdf5_applyFunction.cpp | 10 src/hdf5_createGroup.cpp | 10 src/hdf5_createMatrix.cpp | 14 - src/hdf5_getDatasetList.cpp | 8 src/hdf5_importFile.cpp | 10 src/hdf5_pseudoinverse.cpp | 12 - src/hdf5_r6_bind.cpp | 6 src/hdf5_r6_cholesky.cpp | 12 - src/hdf5_r6_correlation.cpp | 6 src/hdf5_r6_eigen.cpp | 6 src/hdf5_r6_matvec.cpp | 22 +- src/hdf5_r6_normalize.cpp | 8 src/hdf5_r6_omics.cpp | 18 - src/hdf5_r6_pca.cpp | 8 src/hdf5_r6_pseudoinv.cpp | 6 src/hdf5_r6_qr.cpp | 6 src/hdf5_r6_reduce_apply.cpp | 12 - src/hdf5_r6_sparse.cpp | 6 src/hdf5_r6_split.cpp | 6 src/hdf5_r6_svd.cpp | 6 src/hdf5_r6_write.cpp | 2 src/hdf5_reduceDataset.cpp | 8 src/hdf5_writeDimnames.cpp | 6 src/mem_blockmult.cpp | 4 src/mem_blocksubstract.cpp | 2 src/mem_blocksum.cpp | 2 src/mem_correlation.cpp | 22 +- src/mem_crossprod.cpp | 4 src/mem_scalarprod.cpp | 4 src/mem_tcrossprod.cpp | 4 src/mem_weightprod.cpp | 4 86 files changed, 883 insertions(+), 867 deletions(-)
More information about BigDataStatMeth at CRAN
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Title: Automatic Phylogenetic Tree Generator
Description: Generates phylogenetic trees and distance matrices from a list
of taxon names, or from a higher taxon expanded down to a chosen lower
rank. Trees are obtained as induced subtrees of the Open Tree of Life
synthetic tree using the 'rotl' package (Michonneau, Brown and Winter,
2016, <doi:10.1111/2041-210X.12593>). Expansion of a higher taxon to its
descendants uses 'taxize' (Chamberlain and Szocs, 2013,
<doi:10.12688/f1000research.2-191.v2>).
Author: Christophe Benjamin [aut, cre]
Maintainer: Christophe Benjamin <christophe.benjamin@protonmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2021-01-10
Diff between aptg versions 0.1.1 dated 2021-01-10 and 0.4.0 dated 2026-07-19
DESCRIPTION | 32 ++- LICENSE | 2 MD5 | 32 ++- NAMESPACE | 21 +- NEWS.md |only R/aptg-internal.R |only R/downto.tree.R | 122 +++++++----- R/region.tree.R |only R/taxa.tree.R | 152 +++++++++++---- README.md |only build/vignette.rds |binary inst/doc/aptg.R | 75 ++++++- inst/doc/aptg.Rmd | 184 ++++++++++++++++-- inst/doc/aptg.html | 522 +++++++++++++++++++++++++++++++++++++++++++++-------- man/downto.tree.Rd | 91 ++++++--- man/region.tree.Rd |only man/taxa.tree.Rd | 95 +++++++-- tests |only vignettes/aptg.Rmd | 184 ++++++++++++++++-- 19 files changed, 1227 insertions(+), 285 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
Daniel Kaschek [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel St [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.2 dated 2026-06-02 and 5.1.3 dated 2026-07-19
DESCRIPTION | 40 MD5 | 849 + NAMESPACE | 56 NEWS.md | 352 R/DollarNames.R | 17 R/RcppExports.R | 58 R/adjoint.R |only R/adjointDiscrete.R |only R/assert.R | 44 R/d.R | 10 R/dde.R |only R/dsl.R | 79 R/err-foceiBase.R | 167 R/err-sim.R | 163 R/err.R | 151 R/et.R | 11 R/etTran.R | 2 R/eventSens.R |only R/evidPush.R | 41 R/fixef.R | 91 R/indLin.R |only R/intern.R | 9 R/mu.R | 35 R/odeToLin.R |only R/omegaVarCov.R |only R/parseFuns.R | 85 R/piping.R | 10 R/reexport.R | 5 R/rstudio.R | 2 R/rxIndLin.R | 5 R/rxJacobian.R | 286 R/rxMemoryEstimate.R | 108 R/rxOom.R |only R/rxOptExpr.R | 368 R/rxPrune.R | 28 R/rxResidualError.R | 7 R/rxSyntaxFunctions.R | 2 R/rxUiGet.R | 3 R/rxValidate.R | 27 R/rxode-options.R | 30 R/rxode2.R | 418 R/rxode2_md5.R | 2 R/rxsolve.R | 1613 +++ R/symengine.R | 361 R/tran.R | 2 R/ui-bind.R | 12 R/ui-fix.R | 7 R/ui.R | 4 R/utils.R | 11 build/partial.rdb |binary build/vendor-sundials.R |only build/vignette.rds |binary cleanup | 3 cleanup.win | 1 configure | 1 configure.win | 1 data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/COPYRIGHTS | 74 inst/doc/rxode2-syntax.html | 136 inst/include/rxMemoryCalc.h | 44 inst/include/rxode2.h | 188 inst/include/rxode2EventTranslate.h | 6 inst/include/rxode2_RcppExports.h | 24 inst/include/rxode2_control.h | 15 inst/include/rxode2_model_shared.c | 212 inst/include/rxode2_model_shared.h | 38 inst/include/rxode2parseHandleEvid.h | 1389 ++ inst/include/rxode2parseStruct.h | 70 inst/include/rxode2parseVer.h | 4 inst/include/rxode2parse_control.h | 16 inst/include/rxode2ptr.h | 98 inst/tools/workaround.R | 450 inst/tran.g | 10 man/as.arrow.Rd |only man/assertRxUi.Rd | 6 man/binomProbs.Rd | 2 man/coef.rxUi.Rd |only man/delay.Rd |only man/dot-handleSingleErrTypeNormOrTFoceiBase.Rd | 7 man/dot-rxAdjoint.Rd |only man/dot-rxAdjointExpand.Rd |only man/dot-rxAdjointGrad.Rd |only man/dot-rxAdjointGradBuild.Rd |only man/dot-rxAdjointGradEval.Rd |only man/dot-rxAdjointGradEvalC.Rd |only man/dot-rxAdjointGradPop.Rd |only man/dot-rxAdjointMethodStiff.Rd |only man/dot-rxAdjointModel.Rd |only man/dot-rxAdjointSolve.Rd |only man/dot-rxAdjointSolveBuild.Rd |only man/dot-rxAdjointSolveEvalC.Rd |only man/dot-rxDelaySensJumpMap.Rd |only man/dot-rxDiscreteAdjointBuild.Rd |only man/dot-rxDiscreteAdjointGrad.Rd |only man/dot-rxDiscreteForwardSens.Rd |only man/dot-rxFwdSensJacBlock.Rd |only man/dot-rxInjectMatExpOdes.Rd |only man/dot-rxMemoisedFns.Rd |only man/dot-rxPastBaseLinesFromEnv.Rd |only man/dot-rxSens.Rd | 2 man/dot-rxSensStrippable.Rd |only man/fixef.rxUi.Rd |only man/head.rxSolveOom.Rd |only man/indLin.Rd |only man/meanProbs.Rd | 2 man/odeMethodToInt.Rd | 362 man/odeToLin.Rd |only man/reexports.Rd | 4 man/rmdhunks/rxode2-syntax-hunk.Rmd | 23 man/rxAppendModel.Rd | 2 man/rxCompile.Rd | 12 man/rxEventSensDeactivate.Rd |only man/rxEventSensLoadModel.Rd |only man/rxEventTableFile.Rd |only man/rxExpandSens3_.Rd |only man/rxForget.Rd | 7 man/rxGetModel.Rd | 53 man/rxHasAr.Rd |only man/rxIsAutoSwitch.Rd |only man/rxIsDense.Rd |only man/rxIsImplicit.Rd |only man/rxIsNonStiff.Rd |only man/rxIsStiff.Rd |only man/rxMemoryEstimate.Rd | 2 man/rxOmegaVarCovDeriv.Rd |only man/rxOmegaVarCovDeriv_.Rd |only man/rxOptExpr.Rd | 59 man/rxResidualError.Rd | 8 man/rxSensMatExp.Rd |only man/rxSolve.Rd | 589 + man/rxSolveAdjoint.Rd |only man/rxSolveAdjointRk4.Rd |only man/rxSolveChunked.Rd |only man/rxSyntaxFunctions.Rd | 2 man/rxTrans.Rd | 12 man/rxValidate.Rd | 4 man/rxode2.Rd | 76 man/setCvodeLinearSolver.Rd |only src/Makevars.in | 7 src/RcppExports.cpp | 64 src/ab.cpp |only src/ab_adjoint.cpp |only src/abm.cpp |only src/adjoint.cpp |only src/approx.cpp | 9 src/bs.cpp |only src/ck54.cpp |only src/codegen.c | 416 src/codegen.h | 196 src/codegen2.h | 218 src/common.h | 11 src/cvPost.cpp | 4 src/cvode.cpp |only src/cvode_dense.cpp |only src/cvode_diag_impl.h |only src/cvode_impl.h |only src/cvode_ls_impl.h |only src/cvode_proj_impl.h |only src/cvode_r.cpp |only src/cvode_solver.cpp |only src/cvode_solver.h |only src/cvodes_adjoint.cpp |only src/dlsode.f |only src/dop5.cpp |only src/dop54.cpp |only src/dop853.c | 43 src/dop853.h | 5 src/dop87.cpp |only src/dverk65.cpp |only src/dverk78.cpp |only src/dvode.f |only src/dvode_support.c |only src/em.cpp |only src/etTran.cpp | 7 src/euler.cpp |only src/expandGrid.cpp | 97 src/expm.cpp | 150 src/genModelVars.c | 22 src/genModelVars.h | 49 src/grk4a.cpp |only src/heun.cpp |only src/iem.cpp |only src/implicit_euler_rxode2.hpp |only src/implicit_solvers.cpp |only src/init.c | 122 src/intdy.c | 6 src/linCmt.cpp | 47 src/linCmt.h | 311 src/linCmtSensType.h |only src/lsoda.c | 34 src/lsoda_adjoint.cpp |only src/macros2micros.h | 128 src/matexp.f | 2 src/midpoint.cpp |only src/mm.cpp |only src/ode |only src/ode_dop54_bridge.h |only src/ode_dop87_bridge.h |only src/ode_dverk65.cpp |only src/ode_dverk65_bridge.h |only src/ode_dverk78.cpp |only src/ode_dverk78_bridge.h |only src/ode_euler_bridge.h |only src/ode_grk4a_bridge.h |only src/ode_heun_bridge.h |only src/ode_impl.cpp |only src/ode_implicit_bridge.h |only src/ode_midpoint_bridge.h |only src/ode_rk3_bridge.h |only src/ode_rk43_bridge.h |only src/ode_rk5_bridge.h |only src/ode_rk7_bridge.h |only src/ode_rk8_10_bridge.h |only src/ode_rk8_12_bridge.h |only src/ode_rkb109.cpp |only src/ode_rkb109_bridge.h |only src/ode_rkb6_bridge.h |only src/ode_rkbs32.cpp |only src/ode_rkbs32_bridge.h |only src/ode_rkbs54.cpp |only src/ode_rkbs54_bridge.h |only src/ode_rkc108.cpp |only src/ode_rkc108_bridge.h |only src/ode_rkc5_bridge.h |only src/ode_rkc65.cpp |only src/ode_rkc65_bridge.h |only src/ode_rkcv8_bridge.h |only src/ode_rkdp65.cpp |only src/ode_rkdp65_bridge.h |only src/ode_rkdp85.cpp |only src/ode_rkdp85_bridge.h |only src/ode_rkev87.cpp |only src/ode_rkev87_bridge.h |only src/ode_rkf108.cpp |only src/ode_rkf108_bridge.h |only src/ode_rkf1210.cpp |only src/ode_rkf1210_bridge.h |only src/ode_rkf1412.cpp |only src/ode_rkf1412_bridge.h |only src/ode_rkf32_bridge.h |only src/ode_rkf45.cpp |only src/ode_rkf45_bridge.h |only src/ode_rkf89.cpp |only src/ode_rkf89_bridge.h |only src/ode_rkh10_bridge.h |only src/ode_rkk87.cpp |only src/ode_rkk87_bridge.h |only src/ode_rkl5_bridge.h |only src/ode_rklk5a_bridge.h |only src/ode_rklk5b_bridge.h |only src/ode_rkls44_bridge.h |only src/ode_rkls54_bridge.h |only src/ode_rko10_bridge.h |only src/ode_rko129.cpp |only src/ode_rko129_bridge.h |only src/ode_rkpp54.cpp |only src/ode_rkpp54_bridge.h |only src/ode_rkpp54b.cpp |only src/ode_rkpp54b_bridge.h |only src/ode_rkr4_bridge.h |only src/ode_rks10_bridge.h |only src/ode_rks1110a.cpp |only src/ode_rks1110a_bridge.h |only src/ode_rks4_bridge.h |only src/ode_rks54.cpp |only src/ode_rks54_bridge.h |only src/ode_rks5_bridge.h |only src/ode_rks98.cpp |only src/ode_rks98_bridge.h |only src/ode_rkss54.cpp |only src/ode_rkss54_bridge.h |only src/ode_rkss76.cpp |only src/ode_rkss76_bridge.h |only src/ode_rkssp22_bridge.h |only src/ode_rkssp43.cpp |only src/ode_rkssp43_bridge.h |only src/ode_rkssp53_bridge.h |only src/ode_rkssp54_bridge.h |only src/ode_rkt54.cpp |only src/ode_rkt54_bridge.h |only src/ode_rkt98a.cpp |only src/ode_rkt98a_bridge.h |only src/ode_rktf65.cpp |only src/ode_rktf65_bridge.h |only src/ode_rktmy7.cpp |only src/ode_rktmy7_bridge.h |only src/ode_rktmy7s.cpp |only src/ode_rktmy7s_bridge.h |only src/ode_rktp64.cpp |only src/ode_rktp64_bridge.h |only src/ode_rktp75.cpp |only src/ode_rktp75_bridge.h |only src/ode_rktp86.cpp |only src/ode_rktp86_bridge.h |only src/ode_rkv65.cpp |only src/ode_rkv65_bridge.h |only src/ode_rkv65r.cpp |only src/ode_rkv65r_bridge.h |only src/ode_rkv76r.cpp |only src/ode_rkv76r_bridge.h |only src/ode_rkv78.cpp |only src/ode_rkv78_bridge.h |only src/ode_rkv87e.cpp |only src/ode_rkv87e_bridge.h |only src/ode_rkv87r.cpp |only src/ode_rkv87r_bridge.h |only src/ode_rkv89.cpp |only src/ode_rkv89_bridge.h |only src/ode_rkv98r.cpp |only src/ode_rkv98r_bridge.h |only src/ode_rkz10_bridge.h |only src/ode_ssp3_bridge.h |only src/ode_trapz_bridge.h |only src/ode_vern65_bridge.h |only src/ode_vern76_bridge.h |only src/ode_vern98_bridge.h |only src/odeint_bsd.h |only src/odeinter.h |only src/omegaVarCov.cpp |only src/par_solve.cpp | 2545 ++++- src/par_solve.h | 135 src/parseCmtProperties.h | 57 src/parseDdt.h | 18 src/parseDfdy.h | 14 src/parseFuns.h | 25 src/parseFunsDiff.h | 11 src/parseFunsDosing.h | 69 src/parseIdentifier.h | 7 src/parseLogical.h | 5 src/parseStatements.h | 5 src/print_node.h | 5 src/qs.cpp | 4 src/rk3.cpp |only src/rk4.cpp |only src/rk43.cpp |only src/rk4s.cpp |only src/rk5.cpp |only src/rk7.cpp |only src/rk8_10.cpp |only src/rk8_12.cpp |only src/rkb109.cpp |only src/rkb6.cpp |only src/rkbs32.cpp |only src/rkbs54.cpp |only src/rkc108.cpp |only src/rkc5.cpp |only src/rkc65.cpp |only src/rkcv8.cpp |only src/rkdp65.cpp |only src/rkdp85.cpp |only src/rkev87.cpp |only src/rkf108.cpp |only src/rkf1210.cpp |only src/rkf1412.cpp |only src/rkf32.cpp |only src/rkf45.cpp |only src/rkf78.cpp |only src/rkf89.cpp |only src/rkh10.cpp |only src/rkk87.cpp |only src/rkl5.cpp |only src/rklk5a.cpp |only src/rklk5b.cpp |only src/rkls44.cpp |only src/rkls54.cpp |only src/rko10.cpp |only src/rko129.cpp |only src/rkpp54.cpp |only src/rkpp54b.cpp |only src/rkr4.cpp |only src/rks10.cpp |only src/rks1110a.cpp |only src/rks4.cpp |only src/rks5.cpp |only src/rks54.cpp |only src/rks98.cpp |only src/rkss54.cpp |only src/rkss76.cpp |only src/rkssp22.cpp |only src/rkssp43.cpp |only src/rkssp53.cpp |only src/rkssp54.cpp |only src/rkt54.cpp |only src/rkt98a.cpp |only src/rktf65.cpp |only src/rktmy7.cpp |only src/rktmy7s.cpp |only src/rktp64.cpp |only src/rktp75.cpp |only src/rktp86.cpp |only src/rkv65.cpp |only src/rkv65r.cpp |only src/rkv76r.cpp |only src/rkv78.cpp |only src/rkv87e.cpp |only src/rkv87r.cpp |only src/rkv89.cpp |only src/rkv98r.cpp |only src/rkz10.cpp |only src/ros4.cpp |only src/rx2api.c | 119 src/rx2api.h | 6 src/rxData.cpp | 490 - src/rxData.h | 2 src/rxDerived.cpp | 3 src/rxGlobals.h | 9 src/rxMemAvail.h | 6 src/rxRamBytes.c |only src/rxSerialize.cpp | 129 src/rxode2_df.cpp | 36 src/rxode2_sundials_stan_compat.h |only src/rxomp.h | 16 src/rxthreefry.cpp | 34 src/sb3a.cpp |only src/sb3am4.cpp |only src/sem.cpp |only src/solveWarn.cpp |only src/solveWarn.h |only src/ssp3.cpp |only src/stl |only src/sundials_adiak_metadata.h |only src/sundials_cli.h |only src/sundials_cvode.c |only src/sundials_cvode_diag.c |only src/sundials_cvode_io.c |only src/sundials_cvode_ls.c |only src/sundials_cvode_nls.c |only src/sundials_cvode_proj.c |only src/sundials_datanode.h |only src/sundials_debug.h |only src/sundials_hashmap_impl.h |only src/sundials_iterative_impl.h |only src/sundials_logger_impl.h |only src/sundials_macros.h |only src/sundials_nvector_serial.c |only src/sundials_profiler_impl.h |only src/sundials_sundials_band.c |only src/sundials_sundials_cli.c |only src/sundials_sundials_context.c |only src/sundials_sundials_dense.c |only src/sundials_sundials_direct.c |only src/sundials_sundials_errors.c |only src/sundials_sundials_hashmap.c |only src/sundials_sundials_iterative.c |only src/sundials_sundials_linearsolver.c |only src/sundials_sundials_logger.c |only src/sundials_sundials_math.c |only src/sundials_sundials_matrix.c |only src/sundials_sundials_memory.c |only src/sundials_sundials_nonlinearsolver.c |only src/sundials_sundials_nvector.c |only src/sundials_sundials_profiler.c |only src/sundials_sundials_version.c |only src/sundials_sunlinsol_band.c |only src/sundials_sunlinsol_dense.c |only src/sundials_sunmatrix_band.c |only src/sundials_sunmatrix_dense.c |only src/sundials_sunmatrix_sparse.c |only src/sundials_sunnonlinsol_fixedpoint.c |only src/sundials_sunnonlinsol_newton.c |only src/sundials_system_memory.c |only src/sundials_utils.h |only src/sunlinsol_spbcgs.c |only src/sunlinsol_spgmr.c |only src/sunlinsol_sptfqmr.c |only src/tran.c | 62 src/tran.g.d_parser.h |11677 ++++++++++++------------ src/tran.h | 101 src/trapz.cpp |only src/utilc.cpp | 1 src/vern65.cpp |only src/vern76.cpp |only src/vern98.cpp |only src/vv.cpp |only tests/testthat.R | 14 tests/testthat/helper-methods.R |only tests/testthat/test-100-cmt.R | 2 tests/testthat/test-adjoint-discrete.R |only tests/testthat/test-adjoint-sens.R |only tests/testthat/test-alag.R | 6 tests/testthat/test-altrep-output.R | 20 tests/testthat/test-ar.R |only tests/testthat/test-autoswitch-jacobian.R |only tests/testthat/test-backward.R | 8 tests/testthat/test-bioavailibility.R | 2 tests/testthat/test-capture-adaptive-dosing.R |only tests/testthat/test-cmt-order.R | 1 tests/testthat/test-cov.R | 956 + tests/testthat/test-cvode.R |only tests/testthat/test-cvpost.R | 17 tests/testthat/test-dde-past.R |only tests/testthat/test-dde-sens.R |only tests/testthat/test-dde.R |only tests/testthat/test-dfdy.R | 53 tests/testthat/test-dsl.R | 65 tests/testthat/test-et-r.R | 4 tests/testthat/test-et.R | 30 tests/testthat/test-etTrans.R | 21 tests/testthat/test-event-sensitivities.R |only tests/testthat/test-evid-push.R | 610 - tests/testthat/test-example-3-1.R | 2 tests/testthat/test-example-3-2.R | 2 tests/testthat/test-example-3-3.R | 2 tests/testthat/test-fixef.R | 56 tests/testthat/test-geom-cens.R | 2 tests/testthat/test-implicit-time.R |only tests/testthat/test-ind-lin.R | 45 tests/testthat/test-ini.R | 8 tests/testthat/test-issue-999.R | 4 tests/testthat/test-keep.R | 27 tests/testthat/test-lhs-lag.R |only tests/testthat/test-lhs-param.R | 1 tests/testthat/test-lincmt-cmt-ref.R |only tests/testthat/test-lincmt-solve-sens.R | 31 tests/testthat/test-lincmt-solve.R | 3 tests/testthat/test-logical.R | 2 tests/testthat/test-mdv.R | 1 tests/testthat/test-mexp-nonmem.R |only tests/testthat/test-missing-evid.R | 2 tests/testthat/test-mix.R | 6 tests/testthat/test-mu.R | 36 tests/testthat/test-multisim-shared-event-oob.R |only tests/testthat/test-named-id.R | 2 tests/testthat/test-newind.R | 2 tests/testthat/test-nmtest.R | 55 tests/testthat/test-null-assign.R | 1 tests/testthat/test-occ.R | 45 tests/testthat/test-odeToLin.R |only tests/testthat/test-off.R | 2 tests/testthat/test-omega-varcov.R |only tests/testthat/test-oom.R |only tests/testthat/test-opt-expr.R | 306 tests/testthat/test-par-dop853.R | 3 tests/testthat/test-par-solve.R | 2 tests/testthat/test-pkg-exported-funs.R | 30 tests/testthat/test-reset.R | 2 tests/testthat/test-rk-decay.R |only tests/testthat/test-rk-order.R |only tests/testthat/test-rk4.R |only tests/testthat/test-rxFix.R | 30 tests/testthat/test-rxMemoryEstimate.R | 17 tests/testthat/test-rxode-issue-007.R | 2 tests/testthat/test-sens3.R |only tests/testthat/test-serialize.R | 6 tests/testthat/test-solver-basic.R |only tests/testthat/test-state-dep-dur.R | 28 tests/testthat/test-state-dep-f.R | 16 tests/testthat/test-state-dep-lag.R | 14 tests/testthat/test-state-dep-rate.R | 24 tests/testthat/test-state-dep-sort.R | 2 tests/testthat/test-steady-state.R | 2 tests/testthat/test-sticky-vars.R | 4 tests/testthat/test-symplectic-solvers.R |only tests/testthat/test-syncidx-dose-index-oob.R |only tests/testthat/test-tad.R | 115 tests/testthat/test-ui-mod-functions.R | 2 tests/testthat/test-ui-mv.R | 8 tests/testthat/test-ui-solve.R | 4 tests/testthat/test-zzzz-rxUse.R | 2 561 files changed, 22038 insertions(+), 7851 deletions(-)
Title: Pakistan Spatial Data Toolkit
Description: Provides a tidy interface to Pakistan's official administrative
boundary data from the United Nations Office for the Coordination of
Humanitarian Affairs (OCHA). Spatial data at country, province, district,
and tehsil levels are embedded in the package as 'sf' objects compatible
with the 'tidyverse' and geospatial ecosystem. Includes utilities for
geographic dictionary lookup, coordinate reference system selection,
spatial measurement, and neighbour structure construction for use with
'spdep', 'ggplot2', 'leaflet', and related packages.
Author: Abdullah Umer [aut, cre]
Maintainer: Abdullah Umer <abdullahumer1101@gmail.com>
Diff between pkmapr versions 1.2.1 dated 2026-05-13 and 1.4.0 dated 2026-07-19
DESCRIPTION | 29 MD5 | 65 +- NAMESPACE | 1 NEWS.md | 105 ++- R/crs_suggest.R | 112 +-- R/join.R | 112 +-- R/metadata.R | 106 +-- R/neighbors.R | 286 +++++---- R/search.R | 365 ++++++------ R/spatial_ops.R | 216 +++---- R/visualise.R | 288 ++++----- README.md | 104 ++- build/vignette.rds |binary inst/CITATION |only inst/doc/epidemiology-pkmapr.R | 24 inst/doc/epidemiology-pkmapr.Rmd | 362 +++++++----- inst/doc/epidemiology-pkmapr.html | 1019 +++++++++++++++++----------------- inst/doc/intro-to-pkmapr.R | 20 inst/doc/intro-to-pkmapr.Rmd | 195 +++--- inst/doc/intro-to-pkmapr.html | 845 ++++++++++++++-------------- inst/doc/spatial-analysis-pkmapr.R | 22 inst/doc/spatial-analysis-pkmapr.Rmd | 238 ++++--- inst/doc/spatial-analysis-pkmapr.html | 885 ++++++++++++++--------------- inst/figures/code.R | 8 man/pk_basemap.Rd | 2 man/pk_dictionary.Rd | 5 man/pk_map.Rd | 12 man/pk_neighbors.Rd | 99 +-- man/pkmapr.Rd | 5 tests/testthat/test-deprecated.R | 2 tests/testthat/test-neighbors.R | 20 vignettes/epidemiology-pkmapr.Rmd | 362 +++++++----- vignettes/intro-to-pkmapr.Rmd | 195 +++--- vignettes/spatial-analysis-pkmapr.Rmd | 238 ++++--- 34 files changed, 3346 insertions(+), 3001 deletions(-)
Title: Collection of Artistic and Nature-Inspired Color Palettes
Description: Offers a variety of color palettes inspired by art, nature, and personal
inspirations. Each palette is accompanied by a unique backstory, enriching the
understanding and significance of the colors.
Author: Loukas Theodosiou [aut, cre]
Maintainer: Loukas Theodosiou <theodosiou@evolbio.mpg.de>
Diff between ltc versions 0.3.0 dated 2026-01-16 and 0.4.0 dated 2026-07-19
DESCRIPTION | 18 ++++++++---------- MD5 | 12 +++++++----- NAMESPACE | 9 +++++++++ NEWS.md | 22 ++++++++++++++++++++++ R/ltc_cvd.R |only R/ltc_functions.R | 10 +++++++--- inst/WORDLIST | 2 -- man/ltc_cvd.Rd |only 8 files changed, 53 insertions(+), 20 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.8.1 dated 2026-06-05 and 0.9.1 dated 2026-07-19
DESCRIPTION | 6 MD5 | 44 ++++-- NAMESPACE | 13 ++ R/gridtable.R |only R/io_tablet.R | 4 R/tablet.R | 184 +++-------------------------- inst/doc/tablet-introduction-html.R | 14 +- inst/doc/tablet-introduction-html.Rmd | 26 ++-- inst/doc/tablet-introduction-html.html | 32 ++--- inst/doc/tablet-introduction-pdf.R | 14 +- inst/doc/tablet-introduction-pdf.Rmd | 26 ++-- inst/doc/tablet-introduction-pdf.pdf |binary man/as.data.frame.gridtable.Rd |only man/as_calibrated.Rd |only man/as_calibrated.data.frame.Rd |only man/as_gridtable.Rd |only man/as_gridtable.character.Rd |only man/as_gridtable.data.frame.Rd |only man/as_kable.tablet.Rd | 4 man/io_tablet.Rd | 4 man/kbl.Rd |only man/kbl.calibrated.Rd |only man/kbl.default.Rd |only man/kbl.gridtable.Rd |only man/kbl.tablet.Rd |only man/print.gridtable.Rd |only man/tablet.data.frame.Rd | 6 tests/testthat/test-gridtable-calibrated.R |only vignettes/tablet-introduction-html.Rmd | 26 ++-- vignettes/tablet-introduction-pdf.Rmd | 26 ++-- 30 files changed, 160 insertions(+), 269 deletions(-)
Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
approximate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.6.3 dated 2025-11-18 and 0.6.4 dated 2026-07-19
sps-0.6.3/sps/inst/doc/sps.qmd |only sps-0.6.3/sps/inst/doc/take-all.qmd |only sps-0.6.3/sps/tests/testthat |only sps-0.6.3/sps/tests/testthat.R |only sps-0.6.3/sps/vignettes/sps.qmd |only sps-0.6.3/sps/vignettes/take-all.qmd |only sps-0.6.4/sps/DESCRIPTION | 13 sps-0.6.4/sps/MD5 | 66 +- sps-0.6.4/sps/NEWS.md | 6 sps-0.6.4/sps/R/expected_coverage.R | 3 sps-0.6.4/sps/R/inclusion_prob.R | 13 sps-0.6.4/sps/R/prop_allocation.R | 23 sps-0.6.4/sps/R/sps.R | 48 + sps-0.6.4/sps/R/sps_iterator.R | 25 sps-0.6.4/sps/R/sps_repweights.R | 30 - sps-0.6.4/sps/README.md | 24 sps-0.6.4/sps/build/partial.rdb |binary sps-0.6.4/sps/build/vignette.rds |binary sps-0.6.4/sps/inst/CITATION | 4 sps-0.6.4/sps/inst/doc/sps.R | 42 - sps-0.6.4/sps/inst/doc/sps.Rmd |only sps-0.6.4/sps/inst/doc/sps.html | 918 +++++++++++++++++---------------- sps-0.6.4/sps/inst/doc/take-all.R | 17 sps-0.6.4/sps/inst/doc/take-all.Rmd |only sps-0.6.4/sps/inst/doc/take-all.html | 717 +++++++++---------------- sps-0.6.4/sps/inst/tinytest |only sps-0.6.4/sps/man/expected_coverage.Rd | 18 sps-0.6.4/sps/man/inclusion_prob.Rd | 19 sps-0.6.4/sps/man/prop_allocation.Rd | 24 sps-0.6.4/sps/man/sps-package.Rd | 5 sps-0.6.4/sps/man/sps.Rd | 38 - sps-0.6.4/sps/man/sps_iterator.Rd | 23 sps-0.6.4/sps/man/sps_repweights.Rd | 24 sps-0.6.4/sps/tests/tinytest.R |only sps-0.6.4/sps/vignettes/sps.Rmd |only sps-0.6.4/sps/vignettes/take-all.Rmd |only 36 files changed, 971 insertions(+), 1129 deletions(-)