Title: Publication-Quality 'ggplot2' Visualisation
Description: Wrapper 'ggplot2' functions for publication-quality visualisation.
Aligned with 'ggplot2' and 'tidyverse'. Covers much of what 'ggplot2' does.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 20.0.0 dated 2026-05-07 and 21.0.0 dated 2026-07-06
DESCRIPTION | 8 MD5 | 159 ++-- NAMESPACE | 2 NEWS.md | 11 R/gg-area.R | 18 R/gg-bar.R | 18 R/gg-bin2d.R | 18 R/gg-blanket-utils.R | 112 +- R/gg-blanket.R | 1184 ++++++++++++++++++------------- R/gg-boxplot.R | 18 R/gg-col.R | 18 R/gg-contour-filled.R | 16 R/gg-contour.R | 16 R/gg-crossbar.R | 18 R/gg-density.R | 18 R/gg-density2d-filled.R | 18 R/gg-density2d.R | 16 R/gg-errorbar.R | 18 R/gg-freqpoly.R | 18 R/gg-hex.R | 18 R/gg-histogram.R | 18 R/gg-jitter.R | 18 R/gg-line.R | 18 R/gg-linerange.R | 18 R/gg-path.R | 18 R/gg-point.R | 18 R/gg-polygon.R | 18 R/gg-qq.R | 18 R/gg-quantile.R | 18 R/gg-raster.R | 18 R/gg-rect.R | 18 R/gg-ribbon.R | 18 R/gg-segment.R | 20 R/gg-sf.R | 16 R/gg-smooth.R | 18 R/gg-spoke.R | 18 R/gg-step.R | 18 R/gg-tile.R | 18 R/gg-violin.R | 18 R/refine.R |only R/set-blanket.R | 194 +++-- README.md | 3 man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/gg_area.Rd | 38 man/gg_bar.Rd | 36 man/gg_bin2d.Rd | 38 man/gg_blanket.Rd | 36 man/gg_boxplot.Rd | 36 man/gg_col.Rd | 38 man/gg_contour.Rd | 34 man/gg_contour_filled.Rd | 36 man/gg_crossbar.Rd | 38 man/gg_density.Rd | 36 man/gg_density2d.Rd | 34 man/gg_density2d_filled.Rd | 38 man/gg_errorbar.Rd | 38 man/gg_freqpoly.Rd | 38 man/gg_hex.Rd | 36 man/gg_histogram.Rd | 36 man/gg_jitter.Rd | 36 man/gg_line.Rd | 38 man/gg_linerange.Rd | 36 man/gg_path.Rd | 36 man/gg_point.Rd | 36 man/gg_polygon.Rd | 36 man/gg_qq.Rd | 36 man/gg_quantile.Rd | 36 man/gg_raster.Rd | 38 man/gg_rect.Rd | 38 man/gg_ribbon.Rd | 36 man/gg_segment.Rd | 38 man/gg_sf.Rd | 36 man/gg_smooth.Rd | 36 man/gg_spoke.Rd | 36 man/gg_step.Rd | 38 man/gg_tile.Rd | 36 man/gg_violin.Rd | 36 man/ggblanket-package.Rd | 7 man/modern_drift.Rd |only man/set_blanket.Rd | 14 man/void_drop.Rd |only 82 files changed, 1910 insertions(+), 1616 deletions(-)
Title: Landscape Connectivity, Habitat, and Protected Area Networks
Description: Given a landscape resistance surface, creates minimum planar graph
(Fall et al. (2007) <doi:10.1007/s10021-007-9038-7>) and grains of connectivity
(Galpern et al. (2012) <doi:10.1111/j.1365-294X.2012.05677.x>) models that can be
used to calculate effective distances for landscape connectivity at multiple scales.
Documentation is provided by several vignettes, and a paper
(Chubaty, Galpern & Doctolero (2020) <doi:10.1111/2041-210X.13350>).
Author: Paul Galpern [aut, cph] ,
Sam Doctolero [aut],
Alex M Chubaty [aut, cre]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between grainscape versions 0.5.0 dated 2025-01-15 and 1.0.0 dated 2026-07-06
grainscape-0.5.0/grainscape/R/grainscape-deprecated.R |only grainscape-0.5.0/grainscape/inst/extdata/issue72_patchID.tif |only grainscape-0.5.0/grainscape/inst/extdata/issue72_resistance.tif |only grainscape-0.5.0/grainscape/inst/extdata/naErrorExample.asc |only grainscape-0.5.0/grainscape/man/grainscape-deprecated.Rd |only grainscape-0.5.0/grainscape/tests/test-all.R |only grainscape-0.5.0/grainscape/tests/testthat/test-examples.R |only grainscape-0.5.0/grainscape/vignettes/figures/HabConnFlowchart.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/cells_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/data_struct_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/engine_class_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/engine_use_snippet.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/typedef_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/grainscape_vignette_files |only grainscape-1.0.0/grainscape/DESCRIPTION | 32 - grainscape-1.0.0/grainscape/MD5 | 234 ++++---- grainscape-1.0.0/grainscape/NAMESPACE | 62 -- grainscape-1.0.0/grainscape/NEWS.md | 107 +++ grainscape-1.0.0/grainscape/R/GOC.R | 94 ++- grainscape-1.0.0/grainscape/R/MPG.R | 112 ++- grainscape-1.0.0/grainscape/R/classes.R | 172 ++--- grainscape-1.0.0/grainscape/R/corridor.R | 120 +--- grainscape-1.0.0/grainscape/R/distance.R | 50 - grainscape-1.0.0/grainscape/R/export.R | 232 +++++-- grainscape-1.0.0/grainscape/R/extract.R | 2 grainscape-1.0.0/grainscape/R/ggGS.R | 22 grainscape-1.0.0/grainscape/R/grain.R | 32 - grainscape-1.0.0/grainscape/R/grainscape-defunct.R |only grainscape-1.0.0/grainscape/R/grainscape-package.R | 81 ++ grainscape-1.0.0/grainscape/R/graphdf.R | 16 grainscape-1.0.0/grainscape/R/habitatConnectivityEngine.R | 23 grainscape-1.0.0/grainscape/R/patchFilter.R | 26 grainscape-1.0.0/grainscape/R/plot.R | 97 +-- grainscape-1.0.0/grainscape/R/plotResistance.R |only grainscape-1.0.0/grainscape/R/point.R | 46 - grainscape-1.0.0/grainscape/R/theme_grainscape.R | 18 grainscape-1.0.0/grainscape/R/zzz.R | 3 grainscape-1.0.0/grainscape/README.md | 6 grainscape-1.0.0/grainscape/build/partial.rdb |binary grainscape-1.0.0/grainscape/build/vignette.rds |binary grainscape-1.0.0/grainscape/inst/WORDLIST | 24 grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.R | 128 +++- grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.Rmd | 220 ++++++- grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.pdf |binary grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.R | 125 ++-- grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.Rmd | 145 ++-- grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.pdf |binary grainscape-1.0.0/grainscape/inst/examples/example_MPG.R | 6 grainscape-1.0.0/grainscape/inst/examples/example_corridor.R | 14 grainscape-1.0.0/grainscape/inst/examples/example_export.R | 4 grainscape-1.0.0/grainscape/inst/examples/example_filter.R | 12 grainscape-1.0.0/grainscape/inst/examples/example_ggGS.R | 30 - grainscape-1.0.0/grainscape/inst/examples/example_grain.R | 11 grainscape-1.0.0/grainscape/inst/examples/example_graphdf.R | 4 grainscape-1.0.0/grainscape/inst/examples/example_plot.R | 7 grainscape-1.0.0/grainscape/inst/examples/example_preamble.R | 6 grainscape-1.0.0/grainscape/inst/include/DataStruct.h | 16 grainscape-1.0.0/grainscape/inst/include/Engine.h | 8 grainscape-1.0.0/grainscape/man/GOC.Rd | 6 grainscape-1.0.0/grainscape/man/MPG.Rd | 32 - grainscape-1.0.0/grainscape/man/corridor-class.Rd | 10 grainscape-1.0.0/grainscape/man/corridor.Rd | 28 grainscape-1.0.0/grainscape/man/distance.Rd | 12 grainscape-1.0.0/grainscape/man/export.Rd | 18 grainscape-1.0.0/grainscape/man/extract.Rd | 2 grainscape-1.0.0/grainscape/man/ggGS.Rd | 48 - grainscape-1.0.0/grainscape/man/goc-class.Rd | 4 grainscape-1.0.0/grainscape/man/grain-class.Rd | 4 grainscape-1.0.0/grainscape/man/grain.Rd | 21 grainscape-1.0.0/grainscape/man/grainscape-defunct.Rd | 36 + grainscape-1.0.0/grainscape/man/grainscape-maps.Rd | 53 + grainscape-1.0.0/grainscape/man/grainscape-package.Rd | 13 grainscape-1.0.0/grainscape/man/graphdf.Rd | 10 grainscape-1.0.0/grainscape/man/habConnEngine.Rd | 2 grainscape-1.0.0/grainscape/man/hce-class.Rd | 4 grainscape-1.0.0/grainscape/man/mpg-class.Rd | 10 grainscape-1.0.0/grainscape/man/patchFilter.Rd | 24 grainscape-1.0.0/grainscape/man/plot.Rd | 19 grainscape-1.0.0/grainscape/man/plotResistance.Rd |only grainscape-1.0.0/grainscape/man/plotWithResistance.Rd |only grainscape-1.0.0/grainscape/man/point.Rd | 10 grainscape-1.0.0/grainscape/man/theme_grainscape.Rd | 6 grainscape-1.0.0/grainscape/man/threshold.Rd | 6 grainscape-1.0.0/grainscape/src/Engine.cpp | 243 +++++--- grainscape-1.0.0/grainscape/tests/testthat.R |only grainscape-1.0.0/grainscape/tests/testthat/_snaps |only grainscape-1.0.0/grainscape/tests/testthat/fixtures |only grainscape-1.0.0/grainscape/tests/testthat/helper-plotdata.R |only grainscape-1.0.0/grainscape/tests/testthat/helper-testdata.R |only grainscape-1.0.0/grainscape/tests/testthat/test-GOC.R |only grainscape-1.0.0/grainscape/tests/testthat/test-MPG.R | 291 +++++++++- grainscape-1.0.0/grainscape/tests/testthat/test-corridor-distance-point.R | 20 grainscape-1.0.0/grainscape/tests/testthat/test-corridor.R |only grainscape-1.0.0/grainscape/tests/testthat/test-defunct.R |only grainscape-1.0.0/grainscape/tests/testthat/test-distance.R |only grainscape-1.0.0/grainscape/tests/testthat/test-export.R | 6 grainscape-1.0.0/grainscape/tests/testthat/test-extract.R |only grainscape-1.0.0/grainscape/tests/testthat/test-ggGS.R |only grainscape-1.0.0/grainscape/tests/testthat/test-grain.R |only grainscape-1.0.0/grainscape/tests/testthat/test-graphdf.R |only grainscape-1.0.0/grainscape/tests/testthat/test-patchFilter.R |only grainscape-1.0.0/grainscape/tests/testthat/test-plot.R |only grainscape-1.0.0/grainscape/tests/testthat/test-plotResistance.R |only grainscape-1.0.0/grainscape/tests/testthat/test-point.R |only grainscape-1.0.0/grainscape/tests/testthat/test-threshold.R |only grainscape-1.0.0/grainscape/tests/testthat/test-voronoi.R |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm.Rmd | 220 ++++++- grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/call_graph_engine_initialize-1.pdf |binary grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/call_graph_engine_start-1.pdf |binary grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/cells_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/data_struct_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/engine_class_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/flowchart-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/typedef_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/figures/partA.png |binary grainscape-1.0.0/grainscape/vignettes/figures/partB.png |binary grainscape-1.0.0/grainscape/vignettes/grainscape_vignette.Rmd | 145 ++-- 117 files changed, 2394 insertions(+), 1256 deletions(-)
Title: Publication-Quality 'ggplot2' Geom Width
Description: Width helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to create geoms such
as bars that have a consistent width appearance across plots.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggwidth versions 0.1.1 dated 2026-05-03 and 0.1.2 dated 2026-07-06
ggwidth-0.1.1/ggwidth/R/get-width.R |only ggwidth-0.1.1/ggwidth/R/set-equiwidth.R |only ggwidth-0.1.1/ggwidth/R/utils.R |only ggwidth-0.1.2/ggwidth/DESCRIPTION | 8 - ggwidth-0.1.2/ggwidth/MD5 | 16 +- ggwidth-0.1.2/ggwidth/NEWS.md | 4 ggwidth-0.1.2/ggwidth/R/width.R |only ggwidth-0.1.2/ggwidth/man/get_width.Rd | 133 ++++------------------ ggwidth-0.1.2/ggwidth/man/ggwidth-package.Rd | 7 - ggwidth-0.1.2/ggwidth/man/set_equiwidth.Rd | 21 --- ggwidth-0.1.2/ggwidth/tests/testthat/test-width.R | 111 ------------------ 11 files changed, 54 insertions(+), 246 deletions(-)
Title: Publication-Quality 'ggplot2' Annotation
Description: Annotation helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to annotate plots in
a way that stays consistent with the set theme.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggscribe versions 0.1.1 dated 2026-05-04 and 0.2.0 dated 2026-07-06
ggscribe-0.1.1/ggscribe/R/axis-bracket.R |only ggscribe-0.1.1/ggscribe/R/axis-line.R |only ggscribe-0.1.1/ggscribe/R/axis-text.R |only ggscribe-0.1.1/ggscribe/R/axis-ticks.R |only ggscribe-0.1.1/ggscribe/R/guide-sec-axis-text.R |only ggscribe-0.1.1/ggscribe/R/panel-shade.R |only ggscribe-0.1.1/ggscribe/R/reference-line.R |only ggscribe-0.1.1/ggscribe/R/theme-sec-axis-text.R |only ggscribe-0.1.1/ggscribe/R/utils.R |only ggscribe-0.1.1/ggscribe/man/theme_sec_axis_text.Rd |only ggscribe-0.2.0/ggscribe/DESCRIPTION | 14 ggscribe-0.2.0/ggscribe/MD5 | 51 - ggscribe-0.2.0/ggscribe/NAMESPACE | 3 ggscribe-0.2.0/ggscribe/NEWS.md | 14 ggscribe-0.2.0/ggscribe/R/aes-contrast.R | 289 ++++++---- ggscribe-0.2.0/ggscribe/R/axis-panel-reference.R |only ggscribe-0.2.0/ggscribe/R/sec-axis-text.R | 154 ++--- ggscribe-0.2.0/ggscribe/README.md | 52 + ggscribe-0.2.0/ggscribe/man/aes_contrast.Rd | 83 -- ggscribe-0.2.0/ggscribe/man/axis_bracket.Rd | 119 +--- ggscribe-0.2.0/ggscribe/man/axis_line.Rd | 62 +- ggscribe-0.2.0/ggscribe/man/axis_text.Rd | 136 +--- ggscribe-0.2.0/ggscribe/man/axis_ticks.Rd | 80 +- ggscribe-0.2.0/ggscribe/man/figures/README-unnamed-chunk-2-1.png |binary ggscribe-0.2.0/ggscribe/man/figures/README-unnamed-chunk-3-1.png |binary ggscribe-0.2.0/ggscribe/man/ggscribe-package.Rd | 7 ggscribe-0.2.0/ggscribe/man/guide_sec_axis_text.Rd | 72 -- ggscribe-0.2.0/ggscribe/man/panel_background.Rd |only ggscribe-0.2.0/ggscribe/man/panel_grid.Rd |only ggscribe-0.2.0/ggscribe/man/panel_shade.Rd | 101 --- ggscribe-0.2.0/ggscribe/man/reference_line.Rd | 109 +-- ggscribe-0.2.0/ggscribe/man/sec_axis_text.Rd | 86 -- ggscribe-0.2.0/ggscribe/tests/spelling.R | 10 33 files changed, 593 insertions(+), 849 deletions(-)
Title: Functions and Data Sets for "That's Weird: Anomaly Detection
Using R" by Rob J Hyndman
Description: All functions and data sets required for the examples in the book
Hyndman (2026) "That's Weird: Anomaly Detection Using R" <https://OTexts.com/weird/>.
All packages needed to run the examples are also loaded.
Author: Rob Hyndman [aut, cre, cph] ,
Torben Tvedebrink [ctb],
Posit Software, PBC [cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between weird versions 2.1.0 dated 2026-05-05 and 3.0.0 dated 2026-07-06
weird-2.1.0/weird/R/gg_density_layer.R |only weird-2.1.0/weird/man/gg_density_layer.Rd |only weird-3.0.0/weird/DESCRIPTION | 31 - weird-3.0.0/weird/MD5 | 140 ++++-- weird-3.0.0/weird/NAMESPACE | 25 + weird-3.0.0/weird/NEWS.md | 18 weird-3.0.0/weird/R/air_quality.R |only weird-3.0.0/weird/R/attach.R | 54 +- weird-3.0.0/weird/R/augment.R |only weird-3.0.0/weird/R/biplot_projection.R |only weird-3.0.0/weird/R/conflicts.R | 39 + weird-3.0.0/weird/R/datasets.R | 19 weird-3.0.0/weird/R/density_df.R |only weird-3.0.0/weird/R/dist_kde.R | 8 weird-3.0.0/weird/R/gg_density.R | 257 ++++++------ weird-3.0.0/weird/R/gmm.R |only weird-3.0.0/weird/R/grubbs.R | 17 weird-3.0.0/weird/R/hampel.R | 2 weird-3.0.0/weird/R/hdr.R | 230 +++++++---- weird-3.0.0/weird/R/interpolation.R | 1 weird-3.0.0/weird/R/kde_bandwidth.R | 10 weird-3.0.0/weird/R/lof_scores.R | 4 weird-3.0.0/weird/R/mvscale.R | 103 +++-- weird-3.0.0/weird/R/outlier_map.R |only weird-3.0.0/weird/R/show_data.R | 14 weird-3.0.0/weird/R/surprisals.R | 2 weird-3.0.0/weird/R/surprisals_models.R | 1 weird-3.0.0/weird/R/utils.R | 27 - weird-3.0.0/weird/R/weird.R | 8 weird-3.0.0/weird/R/wine_reviews.R | 4 weird-3.0.0/weird/R/zzz.R | 18 weird-3.0.0/weird/README.md | 282 -------------- weird-3.0.0/weird/build |only weird-3.0.0/weird/data/gun_deaths.rda |only weird-3.0.0/weird/inst/CITATION | 2 weird-3.0.0/weird/inst/doc |only weird-3.0.0/weird/man/augment.Pca.Rd |only weird-3.0.0/weird/man/biplot_projection.Rd |only weird-3.0.0/weird/man/density_df.Rd |only weird-3.0.0/weird/man/dist_kde.Rd | 2 weird-3.0.0/weird/man/dist_mclust.Rd |only weird-3.0.0/weird/man/fetch_air_quality.Rd |only weird-3.0.0/weird/man/fetch_wine_reviews.Rd | 4 weird-3.0.0/weird/man/figures/README-of-boxplot-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot-2.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot-3.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot2-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot2-2.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot3-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot3-2.png |binary weird-3.0.0/weird/man/figures/README-of-density-1.png |binary weird-3.0.0/weird/man/figures/README-of-density2-1.png |binary weird-3.0.0/weird/man/gg_density.Rd | 6 weird-3.0.0/weird/man/gg_hdrboxplot.Rd | 3 weird-3.0.0/weird/man/gun_deaths.Rd |only weird-3.0.0/weird/man/hampel_anomalies.Rd | 2 weird-3.0.0/weird/man/hdr_table.Rd | 2 weird-3.0.0/weird/man/kde_bandwidth.Rd | 2 weird-3.0.0/weird/man/lof_scores.Rd | 2 weird-3.0.0/weird/man/mvscale.Rd | 40 + weird-3.0.0/weird/man/outlier_map.Rd |only weird-3.0.0/weird/man/reexports.Rd | 3 weird-3.0.0/weird/man/surprisals.Rd | 2 weird-3.0.0/weird/man/surprisals_data.Rd | 2 weird-3.0.0/weird/man/surprisals_model.Rd | 2 weird-3.0.0/weird/man/weird-package.Rd | 1 weird-3.0.0/weird/tests/testthat/_snaps |only weird-3.0.0/weird/tests/testthat/helper_fetch_data.R |only weird-3.0.0/weird/tests/testthat/test_air_quality.R |only weird-3.0.0/weird/tests/testthat/test_augment.R |only weird-3.0.0/weird/tests/testthat/test_bagplot.R | 4 weird-3.0.0/weird/tests/testthat/test_biplot_projection.R |only weird-3.0.0/weird/tests/testthat/test_datasets.R | 44 ++ weird-3.0.0/weird/tests/testthat/test_density_df.R |only weird-3.0.0/weird/tests/testthat/test_dist_kde1.R | 2 weird-3.0.0/weird/tests/testthat/test_dist_mclust.R |only weird-3.0.0/weird/tests/testthat/test_hdr.R | 47 ++ weird-3.0.0/weird/tests/testthat/test_lof_glosh.R | 16 weird-3.0.0/weird/tests/testthat/test_mvscale.R | 105 +++++ weird-3.0.0/weird/tests/testthat/test_outlier_map.R |only weird-3.0.0/weird/tests/testthat/test_stray.R | 14 weird-3.0.0/weird/tests/testthat/test_wine_reviews.R |only weird-3.0.0/weird/vignettes |only 83 files changed, 864 insertions(+), 757 deletions(-)
Title: A Discrete Colour Palette
Description: A discrete colour palette. These colours make it easier to create
relatively accessible and colour-blind safe visualisation.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between jumble versions 0.1.1 dated 2026-05-04 and 0.1.2 dated 2026-07-06
jumble-0.1.1/jumble/R/grey.R |only jumble-0.1.1/jumble/R/navy.R |only jumble-0.1.1/jumble/R/orange.R |only jumble-0.1.1/jumble/R/pink.R |only jumble-0.1.1/jumble/R/red.R |only jumble-0.1.1/jumble/R/slate.R |only jumble-0.1.1/jumble/R/teal.R |only jumble-0.1.2/jumble/DESCRIPTION | 8 - jumble-0.1.2/jumble/MD5 | 33 +++---- jumble-0.1.2/jumble/NEWS.md | 4 jumble-0.1.2/jumble/R/jumble.R | 44 ++++++++++ jumble-0.1.2/jumble/man/grey.Rd | 7 - jumble-0.1.2/jumble/man/jumble.Rd | 2 jumble-0.1.2/jumble/man/navy.Rd | 7 - jumble-0.1.2/jumble/man/orange.Rd | 7 - jumble-0.1.2/jumble/man/pink.Rd | 7 - jumble-0.1.2/jumble/man/red.Rd | 7 - jumble-0.1.2/jumble/man/slate.Rd | 7 - jumble-0.1.2/jumble/man/teal.Rd | 7 - jumble-0.1.2/jumble/tests/spelling.R | 10 +- jumble-0.1.2/jumble/tests/testthat/test-jumble.R | 98 ++++++++++++----------- 21 files changed, 132 insertions(+), 116 deletions(-)
Title: Blend Colours and Palettes
Description: Colour blend functions. These functions make it easier to blend
colours and palettes using digital blend modes such as multiply, screen,
and overlay.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between blends versions 0.1.1 dated 2026-05-04 and 0.1.2 dated 2026-07-06
blends-0.1.1/blends/R/colour-burn.R |only blends-0.1.1/blends/R/colour-dodge.R |only blends-0.1.1/blends/R/darken.R |only blends-0.1.1/blends/R/difference.R |only blends-0.1.1/blends/R/exclusion.R |only blends-0.1.1/blends/R/hard-light.R |only blends-0.1.1/blends/R/lighten.R |only blends-0.1.1/blends/R/multiply.R |only blends-0.1.1/blends/R/overlay.R |only blends-0.1.1/blends/R/screen.R |only blends-0.1.1/blends/R/soft-light.R |only blends-0.1.1/blends/R/utils.R |only blends-0.1.2/blends/DESCRIPTION | 10 +- blends-0.1.2/blends/MD5 | 47 ++++------- blends-0.1.2/blends/NEWS.md | 4 blends-0.1.2/blends/R/blends.R |only blends-0.1.2/blends/man/blends-package.Rd | 7 + blends-0.1.2/blends/man/colour_burn.Rd | 9 +- blends-0.1.2/blends/man/colour_dodge.Rd | 9 +- blends-0.1.2/blends/man/darken.Rd | 9 +- blends-0.1.2/blends/man/difference.Rd | 9 +- blends-0.1.2/blends/man/exclusion.Rd | 9 +- blends-0.1.2/blends/man/figures/README-unnamed-chunk-3-1.png |binary blends-0.1.2/blends/man/figures/README-unnamed-chunk-4-1.png |binary blends-0.1.2/blends/man/hard_light.Rd | 9 +- blends-0.1.2/blends/man/lighten.Rd | 9 +- blends-0.1.2/blends/man/multiply.Rd | 9 +- blends-0.1.2/blends/man/overlay.Rd | 9 +- blends-0.1.2/blends/man/screen.Rd | 17 ++- blends-0.1.2/blends/man/soft_light.Rd | 13 +-- blends-0.1.2/blends/tests/spelling.R | 10 +- 31 files changed, 111 insertions(+), 78 deletions(-)
Title: USGS INL Project Office Publications
Description: Provides bibliographic information and term-frequency text analysis
tools for publications of the U.S. Geological Survey (USGS) Idaho National
Laboratory (INL) Project Office. Includes datasets of publications, authors,
and term frequencies, along with functions to search terms, build word
clouds, and extract text and cover images from publication documents.
Author: Jason C. Fisher [aut, cre] ,
Kerri C. Treinen [aut] ,
Allison R. Trcka [aut]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlpubs versions 1.3.0 dated 2025-06-25 and 1.4.0 dated 2026-07-06
DESCRIPTION | 44 +-- MD5 | 78 +++--- NAMESPACE | 1 NEWS.md | 140 +++++----- R/add_content.R | 225 ++++++++++++----- R/authors.R | 37 +- R/filter_data_list.R | 56 ++-- R/get_pdf_image.R | 149 ++++++++--- R/get_pdf_text.R | 491 +++++++++++++++++++++++++++++++++----- R/get_person.R | 33 +- R/make_webpages.R | 399 ++++++++++++++++++++---------- R/make_wordcloud.R | 142 +++++----- R/mine_text.R | 358 ++++++++++++++------------- R/plot_pubs.R |only R/pubs.R | 59 ++-- R/search_terms.R | 163 ++++++------ R/terms.R | 33 +- README.md | 75 ++--- build/partial.rdb |binary data/authors.rda |binary data/pubs.rda |binary data/terms.rda |binary inst/REFERENCES.bib | 33 ++ inst/extdata/test.pdf |binary inst/tinytest/test_data.R | 132 ++++++++++ inst/tinytest/test_get_pdf.R |only inst/tinytest/test_mine_text.R | 118 ++++++++- inst/tinytest/test_plot_pubs.R |only inst/tinytest/test_search_terms.R |only inst/tinytest/test_utils.R |only man/add_content.Rd | 88 +++++- man/authors.Rd | 38 +- man/filter_data_list.Rd | 29 +- man/get_pdf_image.Rd | 47 ++- man/get_pdf_text.Rd | 96 ++++++- man/get_person.Rd | 17 - man/make_webpages.Rd | 31 +- man/make_wordcloud.Rd | 51 ++- man/mine_text.Rd | 53 ++-- man/plot_pubs.Rd |only man/pubs.Rd | 60 +++- man/search_terms.Rd | 120 ++++----- man/terms.Rd | 34 +- 43 files changed, 2343 insertions(+), 1087 deletions(-)
Title: Bivariate Hurdle Regression with Bayesian Model Averaging
Description: Provides tools for fitting bivariate hurdle negative binomial
models with horseshoe priors, Bayesian Model Averaging (BMA) via stacking,
and comprehensive causal inference methods including G-computation,
transfer entropy, Threshold Vector Autoregressive (TVAR) and Smooth
Transition Autoregressive (STAR) models, Dynamic Bayesian Networks (DBN),
Hidden Markov Models (HMM), and sensitivity analysis.
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between bivarhr versions 0.1.5 dated 2025-12-19 and 0.1.6 dated 2026-07-06
bivarhr-0.1.5/bivarhr/R/export-results.R |only bivarhr-0.1.6/bivarhr/DESCRIPTION | 12 bivarhr-0.1.6/bivarhr/MD5 | 64 +- bivarhr-0.1.6/bivarhr/NAMESPACE | 1 bivarhr-0.1.6/bivarhr/NEWS.md | 51 + bivarhr-0.1.6/bivarhr/R/bivarhr-package.R | 29 - bivarhr-0.1.6/bivarhr/R/bma-selection.R | 51 - bivarhr-0.1.6/bivarhr/R/dbn.R | 96 ++- bivarhr-0.1.6/bivarhr/R/eba.R | 112 +--- bivarhr-0.1.6/bivarhr/R/hmm.R | 513 ++++++++++++++++---- bivarhr-0.1.6/bivarhr/R/hurdle-fit.R | 2 bivarhr-0.1.6/bivarhr/R/io.R | 22 bivarhr-0.1.6/bivarhr/R/placebo.R | 41 - bivarhr-0.1.6/bivarhr/R/rolling-oos.R | 17 bivarhr-0.1.6/bivarhr/R/sensemakr.R | 76 +- bivarhr-0.1.6/bivarhr/R/synthetic-control.R | 72 +- bivarhr-0.1.6/bivarhr/R/transfer-entropy.R | 121 ++-- bivarhr-0.1.6/bivarhr/R/tvar-star.R | 95 +-- bivarhr-0.1.6/bivarhr/man/bivarhr-package.Rd | 5 bivarhr-0.1.6/bivarhr/man/export_results.Rd | 9 bivarhr-0.1.6/bivarhr/man/export_results_xlsx.Rd | 13 bivarhr-0.1.6/bivarhr/man/placebo_temporal.Rd | 39 - bivarhr-0.1.6/bivarhr/man/prewhiten_count_glm.Rd | 11 bivarhr-0.1.6/bivarhr/man/print.bivarhr_hmm.Rd |only bivarhr-0.1.6/bivarhr/man/rolling_oos.Rd | 13 bivarhr-0.1.6/bivarhr/man/run_dbn.Rd | 65 +- bivarhr-0.1.6/bivarhr/man/run_eba.Rd | 110 +--- bivarhr-0.1.6/bivarhr/man/run_hmm.Rd | 173 ++++-- bivarhr-0.1.6/bivarhr/man/run_sensemakr.Rd | 54 -- bivarhr-0.1.6/bivarhr/man/run_synth_bsts.Rd | 69 +- bivarhr-0.1.6/bivarhr/man/run_transfer_entropy.Rd | 71 +- bivarhr-0.1.6/bivarhr/man/run_varx.Rd | 63 +- bivarhr-0.1.6/bivarhr/man/select_by_bma.Rd | 51 - bivarhr-0.1.6/bivarhr/tests/testthat/test-bivarhr.R | 69 +- 34 files changed, 1288 insertions(+), 902 deletions(-)
Title: Functions and Data Sets for 'Applied Predictive Modeling'
Description: A few functions and several data set for the Springer book
'Applied Predictive Modeling'.
Author: Max Kuhn [aut, cre],
Kjell Johnson [aut]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between AppliedPredictiveModeling versions 1.1-7 dated 2018-05-22 and 1.2.0 dated 2026-07-06
AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/R/easyBoundaryFunc.R |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/R/transparentTheme.R |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/AppliedPredictiveModeling-package.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/Hepatic.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/internal.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/jobScheduling.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/segmentationOrignal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/DESCRIPTION | 28 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/MD5 | 64 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/NAMESPACE | 15 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/bookTheme.R | 493 ++++++++-- AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/data.R |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/getPackages.R | 25 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/panels.R | 38 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/permuteRelief.R | 78 + AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/quadBoundaryFunc.R | 78 + AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/scriptLocation.R | 13 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/README.md | 1 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/NEWS.Rd | 7 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/chapters/12_Discriminant_Analysis.R | 2 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/chapters/14_Class_Trees.R | 4 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/AlzheimerDisease.Rd | 56 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/ChemicalManufacturingProcess.Rd | 59 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/FuelEconomy.Rd | 46 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/abalone.Rd | 32 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/apm-internal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/bookTheme.Rd | 54 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/concrete.Rd | 58 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/getPackages.Rd | 34 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/hepatic.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/logisticCreditPredictions.Rd | 28 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/permeability.Rd | 62 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/permuteRelief.Rd | 103 +- AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/quadBoundaryFunc.Rd | 55 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/schedulingData.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/scriptLocation.Rd | 20 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/segmentationOriginal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/solubility.Rd | 60 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/twoClassData.Rd | 31 39 files changed, 1090 insertions(+), 454 deletions(-)
More information about AppliedPredictiveModeling at CRAN
Permanent link
Title: Provides Batch Functions and Visualisation for Basic Statistical
Procedures
Description: Designed to streamline data analysis and statistical testing, reducing the length of R
scripts while generating well-formatted outputs in 'pdf', 'Microsoft Word', and 'Microsoft Excel'
formats. In essence, the package contains functions which are sophisticated wrappers around
existing R functions that are called by using 'f_' (user f_riendly) prefix followed by the normal
function name. This third version of the 'rfriend' package focuses primarily on data exploration,
including tools for creating summary tables, f_summary(), summary figures, f_scan(),
outlier detection and removal, f_outlier() and f_remove_outliers(), performing data transformations,
f_boxcox() in part based on 'MASS/boxcox' and 'rcompanion', and f_bestNormalize()
which wraps and extends functionality from the 'bestNormalize' package. Furthermore, 'rfriend'
can automatically (or on request) generate visualizations such as boxplots, f_boxplot(),
QQ-plots, f_qqnorm(), and histograms f_hist(). Additionally, the package i [...truncated...]
Author: Sander H. van Delden [aut, cre]
Maintainer: Sander H. van Delden <plantmind@proton.me>
Diff between rfriend versions 3.1.0 dated 2026-05-30 and 3.2.0 dated 2026-07-06
DESCRIPTION | 22 MD5 | 98 + NAMESPACE | 14 NEWS.md | 254 ++++ R/data.R |only R/df_to_table.R | 8 R/faov.R | 1392 +++++++++++++++++++------- R/fbestnormalize.R | 15 R/fboxcox.R | 2 R/fboxplot.R | 10 R/fchisq_test.R | 45 R/fcorplot.R | 2 R/fexample_data.R |only R/ffactors.R | 61 + R/ffriedman.R |only R/fglm.R | 1166 +++++++++++++++++++++- R/fkruskal_test.R | 149 ++ R/flm.R |only R/flmer.R | 1994 ++++++++++++++++++++++++++++++++++++-- R/fqqnorm.R | 338 +++--- R/fscan.R | 2 R/fsetwd.R | 17 R/fttest.R | 768 ++++++++++++-- R/fwilcox_test.R | 294 +++++ R/helper_cld_emmeans.R |only R/helper_coef_ref_caption.R |only R/helper_compact_letters.R |only R/helper_contrast_forest.R |only R/helper_forest_plot.R |only R/helper_get_save_path.R | 274 ++--- R/helper_pub_theme.R |only R/helper_rmd_anova_summary.R | 106 +- R/helper_safe_ad.R |only R/helper_safe_shapiro.R | 3 R/import.R | 8 README.md | 322 +++--- build/partial.rdb |binary data |only inst/extdata/plant_trial.csv |only inst/extdata/plant_trial.rds |only inst/extdata/plant_trial.sav |only inst/extdata/plant_trial_raw.csv |only inst/extdata/plant_trial_raw.xlsx |only inst/extdata/plant_trial_wide.csv |only man/f_aov.Rd | 104 + man/f_example_data.Rd |only man/f_factors.Rd | 21 man/f_friedman.Rd |only man/f_glm.Rd | 43 man/f_lm.Rd |only man/f_lmer.Rd | 138 ++ man/f_qqnorm.Rd | 25 man/f_t_test.Rd | 54 - man/f_wilcox_test.Rd | 22 man/plant_trial.Rd |only man/plot.f_friedman.Rd |only tests/testthat/helper-quiet.R | 24 tests/testthat/test-f_aov.R | 444 ++++++++ tests/testthat/test-f_friedman.R |only tests/testthat/test-f_glm.R | 14 tests/testthat/test-f_lm.R |only tests/testthat/test-f_lmer-3.2.R |only tests/testthat/test-f_scan.R | 17 63 files changed, 7048 insertions(+), 1222 deletions(-)
Title: A Toolkit for Nested Sampling
Description: Bayesian evidence estimation and posterior inference with the
nested sampling algorithm, described in Skilling (2006)
<doi:10.1214/06-BA127> and Buchner (2023) <doi:10.1214/23-SS144>,
along with S3 methods for simulating uncertainty and creating
visualisations.
Author: Kyle Dewsnap [aut, cre, cph] ,
TJ Mahr [rev],
Robert Kubinec [rev],
Michael Hughes [cph]
Maintainer: Kyle Dewsnap <kyle.dewsnap@ubc.ca>
Diff between ernest versions 1.2.4 dated 2026-06-30 and 1.2.5 dated 2026-07-06
DESCRIPTION | 6 MD5 | 72 +++++----- NEWS.md | 12 + R/cpp11.R | 4 R/nested_sampling_impl.R | 11 - R/plot.R | 3 README.md | 29 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/more-ernest-runs.R | 14 - inst/doc/more-ernest-runs.html | 49 +++--- inst/doc/nested-sampling-with-ernest.R | 14 - inst/doc/nested-sampling-with-ernest.html | 36 ++--- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/plot-ernest.Rd | 3 src/KMeansRexCore.cpp | 2 src/cpp11.cpp | 18 +- src/ellipsoid.cpp | 25 +-- src/ellipsoid.h | 1 src/exported_utils.cpp | 20 -- src/propose-impl.cpp | 4 src/rectangle.h | 4 src/test-bounding.cpp | 2 src/utils.h | 2 tests/testthat/_snaps/plot/estimate-1-draw.svg | 59 ++++---- tests/testthat/_snaps/plot/estimate-500-draws-no-evidence.svg | 1 tests/testthat/_snaps/plot/estimate-500-draws.svg | 69 +++++---- tests/testthat/_snaps/plot/example-run-no-evidence.svg | 40 ++--- tests/testthat/_snaps/plot/example-run.svg | 59 ++++---- tests/testthat/_snaps/visualize/trace-basic.svg | 1 tests/testthat/_snaps/visualize/trace-x.svg | 1 tests/testthat/_snaps/visualize/trace-yz.svg | 1 tests/testthat/_snaps/visualize/visualize-basic.svg | 7 tests/testthat/_snaps/visualize/visualize-x.svg | 38 ++--- tests/testthat/_snaps/visualize/visualize-yz.svg | 69 ++++----- tests/testthat/test-calculate.R | 19 -- 37 files changed, 345 insertions(+), 350 deletions(-)
Title: Sample Size and Simulation for Negative Binomial Outcomes
Description: Provides tools for planning and simulating recurrent event trials
with overdispersed count endpoints analyzed using negative binomial (or
Poisson) rate models. Implements sample size and power calculations for
fixed designs with variable accrual, dropout, maximum follow-up, and event
gaps, including methods of Zhu and Lakkis (2014) <doi:10.1002/sim.5947> and
Friede and Schmidli (2010) <doi:10.3414/ME09-02-0060> as well as
extensions for score-test sizing and gaps between events. Supports group
sequential monitoring by building on the 'gsDesign' package.
Includes recurrent-event simulation utilities (including seasonal rates),
interim data truncation, Wald and score-test inference for rate ratios,
and information estimation and sample size re-estimation with or without
treatment-group labels.
Author: Keaven Anderson [aut, cre],
Hongtao Zhang [aut],
Andrea Maes [aut],
Nan Xiao [ctb],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesignNB versions 0.2.6 dated 2026-02-16 and 0.3.2 dated 2026-07-06
DESCRIPTION | 36 MD5 | 177 NAMESPACE | 13 NEWS.md | 153 R/calculate_blinded_info.R | 105 R/check_gs_bound.R | 46 R/get_cut_date.R | 24 R/globals.R | 8 R/gsNBCalendar.R | 565 ++- R/multiple_imputation_nb.R |only R/mutze_test.R | 346 + R/preview_pkgdown_site.R |only R/run_ssr_shiny.R |only R/sample_size_nbinom.R | 513 ++ R/sim_gs_nbinom.R | 108 R/sim_ssr_nbinom.R |only R/summarize_gs_sim.R | 66 R/unblinded_ssr.R | 99 README.md | 23 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ai-skills.R |only inst/doc/ai-skills.Rmd |only inst/doc/ai-skills.html |only inst/doc/blinded-info-diagnostics.R | 2 inst/doc/blinded-info-diagnostics.Rmd | 42 inst/doc/blinded-info-diagnostics.html | 206 - inst/doc/completers-interim-example.html | 12 inst/doc/group-sequential-simulation.R | 230 - inst/doc/group-sequential-simulation.Rmd | 245 - inst/doc/group-sequential-simulation.html | 2412 ++++--------- inst/doc/multiple-imputation-nb.R |only inst/doc/multiple-imputation-nb.Rmd |only inst/doc/multiple-imputation-nb.html |only inst/doc/sample-size-nbinom.R | 94 inst/doc/sample-size-nbinom.Rmd | 501 ++ inst/doc/sample-size-nbinom.html | 1344 +++++-- inst/doc/sample-size-skills-example.R |only inst/doc/sample-size-skills-example.Rmd |only inst/doc/sample-size-skills-example.html |only inst/doc/score-vs-wald-simulation.R |only inst/doc/score-vs-wald-simulation.Rmd |only inst/doc/score-vs-wald-simulation.html |only inst/doc/simulation-example.R | 12 inst/doc/simulation-example.Rmd | 85 inst/doc/simulation-example.html | 121 inst/doc/ssr-example.R | 30 inst/doc/ssr-example.Rmd | 65 inst/doc/ssr-example.html | 1240 ++++-- inst/doc/ssr-simulation-study.R |only inst/doc/ssr-simulation-study.Rmd |only inst/doc/ssr-simulation-study.html |only inst/doc/verification-simulation.R | 271 + inst/doc/verification-simulation.Rmd | 373 +- inst/doc/verification-simulation.html | 1989 ++++++++-- inst/extdata/gs_simulation_results.rds |binary inst/extdata/jensen_broad_sweep_results.rds |only inst/extdata/jensen_score_broad_sweep_results.rds |only inst/extdata/null_simulation_results.rds |only inst/extdata/score_sweep_summary.rds |only inst/extdata/simulation_results.rds |binary inst/extdata/ssr_sim_vignette_summary_score.rds |only inst/extdata/ssr_sizing_sensitivity.rds |only inst/shiny-examples |only man/calculate_blinded_info.Rd | 65 man/check_gs_bound.Rd | 16 man/compute_info_at_time.Rd | 41 man/dot-bootstrap_by_cluster.Rd |only man/dot-impute_nb_draw.Rd |only man/fit_nb_glmm.Rd |only man/gsNBCalendar.Rd | 45 man/impute_nb.Rd |only man/impute_nb_composite.Rd |only man/impute_nb_mar.Rd |only man/impute_nb_mnar_ref.Rd |only man/mutze_test.Rd | 56 man/preview_pkgdown_site.Rd |only man/reexports.Rd | 2 man/run_ssr_shiny.Rd |only man/sample_size_nbinom.Rd | 209 - man/sim_gs_nbinom.Rd | 85 man/sim_ssr_nbinom.Rd |only man/summarize_gs_sim.Rd | 11 man/summarize_ssr_sim.Rd |only man/toInteger.Rd | 13 man/unblinded_ssr.Rd | 10 man/update_gsNB.Rd |only tests/testthat/test-calculate_blinded_info.R | 88 tests/testthat/test-check_gs_bound.R |only tests/testthat/test-cut_completers.R | 10 tests/testthat/test-cut_data_by_date.R | 121 tests/testthat/test-estimate_mom.R | 10 tests/testthat/test-get_cut_date.R |only tests/testthat/test-gsNBCalendar.R | 234 + tests/testthat/test-independent-test-simulation-accuracy.R |only tests/testthat/test-mutze_test.R | 282 + tests/testthat/test-nb_sim_seasonal.R |only tests/testthat/test-run_ssr_shiny.R |only tests/testthat/test-sample_size_nbinom.R | 410 ++ tests/testthat/test-sim_gs_nbinom.R |only tests/testthat/test-sim_gs_nbinom_parallel.R |only tests/testthat/test-sim_ssr_nbinom.R |only tests/testthat/test-summarize_gs_sim.R |only tests/testthat/test-unblinded_ssr.R |only vignettes/ai-skills.Rmd |only vignettes/blinded-info-diagnostics.Rmd | 42 vignettes/group-sequential-simulation.Rmd | 245 - vignettes/gsDesignNB.bib | 101 vignettes/multiple-imputation-nb.Rmd |only vignettes/sample-size-nbinom.Rmd | 501 ++ vignettes/sample-size-skills-example.Rmd |only vignettes/score-vs-wald-simulation.Rmd |only vignettes/simulation-example.Rmd | 85 vignettes/ssr-example.Rmd | 65 vignettes/ssr-simulation-study.Rmd |only vignettes/verification-simulation.Rmd | 373 +- 116 files changed, 10228 insertions(+), 4448 deletions(-)
Title: Displaying Changes Between Two Points Using Dumbbell Plots
Description: Creates dumbbell plots to visualize changes between two
measurements for the same observations. The package provides
customization options for labels, colors, arrows, delta values,
and paired statistical test annotations.
Author: Foo Cheung [aut, cre]
Maintainer: Foo Cheung <foocheung@yahoo.com>
Diff between dumbbell versions 0.1 dated 2021-02-25 and 0.2 dated 2026-07-06
DESCRIPTION | 26 MD5 | 26 NAMESPACE | 3 R/dumbbell.R | 557 ++++++-------- R/global.R | 6 README.md |only build/vignette.rds |binary inst/doc/dumbbell.R | 230 +++-- inst/doc/dumbbell.Rmd | 312 +++++--- inst/doc/dumbbell.html | 1888 +++++++++++++++++++++++++++++++++++++++++++------ inst/docs |only man/dumbbell.Rd | 132 +-- man/figures |only vignettes/dumbbell.Rmd | 312 +++++--- 14 files changed, 2594 insertions(+), 898 deletions(-)
Title: Retrieve Time Series Data from 'Banco de España'
Description: Tools for retrieving 'Banco de España' ('BdE') time series
data as 'tibble' objects from bulk CSV files and the 'Statistics web
service (API)'. Bulk CSV functions use stable 'BdE' sequential
numbers, while API functions use API series codes. Catalog functions
support discovery and local caching. Plotting helpers provide
'ggplot2' palettes, scales and themes. 'Banco de España' is the
national central bank and, within the framework of the Single
Supervisory Mechanism ('SSM'), the supervisor of the Spanish banking
system alongside the European Central Bank. This package is not
sponsored, endorsed or administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph] ,
Banco de Espana [cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.6.1 dated 2026-05-21 and 0.7.0 dated 2026-07-06
tidyBdE-0.6.1/tidyBdE/R/bde_check_access.R |only tidyBdE-0.6.1/tidyBdE/R/bde_tidy_palettes.R |only tidyBdE-0.6.1/tidyBdE/R/catalogs.R |only tidyBdE-0.6.1/tidyBdE/R/indicators.R |only tidyBdE-0.6.1/tidyBdE/R/scales.R |only tidyBdE-0.6.1/tidyBdE/R/series.R |only tidyBdE-0.6.1/tidyBdE/R/theme_tidybde.R |only tidyBdE-0.6.1/tidyBdE/man/bde_catalog_load.Rd |only tidyBdE-0.6.1/tidyBdE/man/bde_catalog_search.Rd |only tidyBdE-0.6.1/tidyBdE/man/bde_catalog_update.Rd |only tidyBdE-0.6.1/tidyBdE/man/bde_series_full_load.Rd |only tidyBdE-0.6.1/tidyBdE/man/bde_series_load.Rd |only tidyBdE-0.6.1/tidyBdE/man/chunks |only tidyBdE-0.6.1/tidyBdE/tests/testthat/_snaps/bde_tidy_palettes.md |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-bde_tidy_palettes.R |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-catalogs.R |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-indicators.R |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-parse_dates.R |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-scales.R |only tidyBdE-0.6.1/tidyBdE/tests/testthat/test-series.R |only tidyBdE-0.7.0/tidyBdE/DESCRIPTION | 42 + tidyBdE-0.7.0/tidyBdE/MD5 | 106 ++-- tidyBdE-0.7.0/tidyBdE/NAMESPACE | 3 tidyBdE-0.7.0/tidyBdE/NEWS.md | 35 + tidyBdE-0.7.0/tidyBdE/R/bde-catalogs.R |only tidyBdE-0.7.0/tidyBdE/R/bde-check-access.R |only tidyBdE-0.7.0/tidyBdE/R/bde-indicators.R |only tidyBdE-0.7.0/tidyBdE/R/bde-series-api.R |only tidyBdE-0.7.0/tidyBdE/R/bde-series.R |only tidyBdE-0.7.0/tidyBdE/R/bde-tidy-palettes.R |only tidyBdE-0.7.0/tidyBdE/R/data.R | 44 + tidyBdE-0.7.0/tidyBdE/R/scales-bde.R |only tidyBdE-0.7.0/tidyBdE/R/superseded.R | 28 - tidyBdE-0.7.0/tidyBdE/R/theme-tidybde.R |only tidyBdE-0.7.0/tidyBdE/R/tidyBdE-package.R | 1 tidyBdE-0.7.0/tidyBdE/R/utils.R | 250 +++++++--- tidyBdE-0.7.0/tidyBdE/README.md | 98 ++- tidyBdE-0.7.0/tidyBdE/build/vignette.rds |binary tidyBdE-0.7.0/tidyBdE/data/bde_ind_db.rda |binary tidyBdE-0.7.0/tidyBdE/inst/WORDLIST | 43 + tidyBdE-0.7.0/tidyBdE/inst/doc/csv_manual.html |only tidyBdE-0.7.0/tidyBdE/inst/doc/csv_manual.qmd |only tidyBdE-0.7.0/tidyBdE/inst/doc/tidyBdE.html | 42 - tidyBdE-0.7.0/tidyBdE/inst/doc/tidyBdE.qmd | 72 +- tidyBdE-0.7.0/tidyBdE/inst/schemaorg.json | 30 - tidyBdE-0.7.0/tidyBdE/man/bde_catalogs.Rd |only tidyBdE-0.7.0/tidyBdE/man/bde_check_access.Rd | 6 tidyBdE-0.7.0/tidyBdE/man/bde_ind_db.Rd | 45 + tidyBdE-0.7.0/tidyBdE/man/bde_indicators.Rd | 51 +- tidyBdE-0.7.0/tidyBdE/man/bde_pals.Rd | 1 tidyBdE-0.7.0/tidyBdE/man/bde_parse_dates.Rd | 29 - tidyBdE-0.7.0/tidyBdE/man/bde_series.Rd |only tidyBdE-0.7.0/tidyBdE/man/bde_series_api.Rd |only tidyBdE-0.7.0/tidyBdE/man/bde_tidy_palettes.Rd | 20 tidyBdE-0.7.0/tidyBdE/man/figures/README-chart-1.png |binary tidyBdE-0.7.0/tidyBdE/man/figures/README-macroseries-1.png |binary tidyBdE-0.7.0/tidyBdE/man/roxygen |only tidyBdE-0.7.0/tidyBdE/man/scales_bde.Rd | 24 tidyBdE-0.7.0/tidyBdE/man/theme_tidybde.Rd | 14 tidyBdE-0.7.0/tidyBdE/man/tidyBdE-package.Rd | 9 tidyBdE-0.7.0/tidyBdE/tests/testthat/_snaps/bde-catalogs.md |only tidyBdE-0.7.0/tidyBdE/tests/testthat/_snaps/bde-series-api.md |only tidyBdE-0.7.0/tidyBdE/tests/testthat/_snaps/bde-tidy-palettes.md |only tidyBdE-0.7.0/tidyBdE/tests/testthat/_snaps/scales-bde.md |only tidyBdE-0.7.0/tidyBdE/tests/testthat/_snaps/utils.md |only tidyBdE-0.7.0/tidyBdE/tests/testthat/helpers.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-catalogs.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-check-access.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-indicators.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-series-api.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-series.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-bde-tidy-palettes.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-scales-bde.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-theme-tidybde.R |only tidyBdE-0.7.0/tidyBdE/tests/testthat/test-utils.R |only tidyBdE-0.7.0/tidyBdE/vignettes/chart-1.png |binary tidyBdE-0.7.0/tidyBdE/vignettes/csv_manual.qmd |only tidyBdE-0.7.0/tidyBdE/vignettes/macroseries-1.png |binary tidyBdE-0.7.0/tidyBdE/vignettes/tidyBdE.qmd | 72 +- 79 files changed, 648 insertions(+), 417 deletions(-)
Title: 'SAS'-Style 'PROC FORMAT' for R
Description: Provides 'SAS' 'PROC FORMAT'-like functionality for creating and applying
value formats in R. Supports discrete and range-based mapping of values to labels,
reverse formatting (invalue), date/time/datetime formatting with built-in 'SAS' format
names, multi-label formats, expression labels evaluated at apply-time,
case-insensitive matching, import/export of format definitions, and proper handling
of missing values (NA, NULL, NaN).
Author: Vladimir Larchenko [aut, cre],
Igor Aleschenkov [aut]
Maintainer: Vladimir Larchenko <vladimir.larchenko@keystatsolutions.com>
Diff between ksformat versions 0.7.1 dated 2026-05-21 and 0.8.2 dated 2026-07-06
ksformat-0.7.1/ksformat/inst/doc/ksformat-Cheat-Sheet.pdf |only ksformat-0.8.2/ksformat/DESCRIPTION | 8 ksformat-0.8.2/ksformat/MD5 | 56 ksformat-0.8.2/ksformat/NAMESPACE | 1 ksformat-0.8.2/ksformat/NEWS.md | 50 ksformat-0.8.2/ksformat/R/format_apply.R | 22 ksformat-0.8.2/ksformat/R/format_create.R | 38 ksformat-0.8.2/ksformat/R/format_invalue.R | 21 ksformat-0.8.2/ksformat/R/format_library_app.R | 26 ksformat-0.8.2/ksformat/R/format_parse.R | 765 ------------ ksformat-0.8.2/ksformat/R/format_serialize.R |only ksformat-0.8.2/ksformat/R/utilities.R | 158 ++ ksformat-0.8.2/ksformat/README.md | 2 ksformat-0.8.2/ksformat/build/vignette.rds |binary ksformat-0.8.2/ksformat/inst/doc/ksformat-cheatsheet.pdf |only ksformat-0.8.2/ksformat/inst/doc/usage_examples.R | 41 ksformat-0.8.2/ksformat/inst/doc/usage_examples.Rmd | 66 + ksformat-0.8.2/ksformat/inst/doc/usage_examples.html | 807 +++++++------ ksformat-0.8.2/ksformat/man/dot-cntlout_to_ks_format.Rd | 2 ksformat-0.8.2/ksformat/man/dot-cntlout_to_ks_invalue.Rd | 2 ksformat-0.8.2/ksformat/man/dot-datetime_format_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_date_bound.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_range_bound.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/dot-invalue_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/fexport.Rd | 2 ksformat-0.8.2/ksformat/man/fimport.Rd | 2 ksformat-0.8.2/ksformat/man/finput.Rd | 11 ksformat-0.8.2/ksformat/man/flevels.Rd |only ksformat-0.8.2/ksformat/tests/testthat/test-formats.R | 198 +++ ksformat-0.8.2/ksformat/vignettes/usage_examples.Rmd | 66 + 31 files changed, 1098 insertions(+), 1256 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
Malcolm Barrett [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.3.3 dated 2026-05-29 and 0.3.4 dated 2026-07-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ard_stats_mantelhaen_test.R | 22 ++++++++++++++++------ inst/WORDLIST | 2 ++ 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.5.2 dated 2026-05-20 and 0.5.3 dated 2026-07-06
DESCRIPTION | 13 LICENSE | 4 MD5 | 58 NAMESPACE | 32 NEWS.md | 59 R/ipea_palette.R | 316 +- R/ipeaplot.R | 44 R/save_ipeaplot.R | 356 +-- R/scale_ipea.R | 628 ++--- R/theme_ipea.R | 996 ++++----- README.md | 166 - build/vignette.rds |binary inst/doc/cookbook.R | 710 +++--- inst/doc/cookbook.Rmd | 952 ++++---- inst/doc/cookbook.html | 4048 ++++++++++++++++++------------------- inst/doc/intro_ipeaplot.R | 356 +-- inst/doc/intro_ipeaplot.Rmd | 586 ++--- inst/doc/intro_ipeaplot.html | 1350 ++++++------ man/ipea_pal.Rd | 102 man/ipea_palette.Rd | 108 man/ipeaplot.Rd | 89 man/save_ipeaplot.Rd | 140 - man/scale_color_ipea.Rd | 150 - man/scale_fill_ipea.Rd | 152 - man/theme_ipea.Rd | 166 - tests/tests_pedro_alves/exemplos.R | 540 ++-- tests/tests_pedro_alves/test.R | 400 +-- tests/tests_rafa/test_rafa.R | 264 +- vignettes/cookbook.Rmd | 952 ++++---- vignettes/intro_ipeaplot.Rmd | 586 ++--- 30 files changed, 7164 insertions(+), 7159 deletions(-)
Title: A Comprehensive Toolkit for Clinical HLA Informatics
Description: A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of Genotype List String (GL String, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL String; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL String; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL String. This library is intended for research use. Any application making use of this package in a clinical setting will need to be independently validated according to local regulations.
Author: Nicholas Brown [cre, aut] ,
Busra Coskun [aut]
Maintainer: Nicholas Brown <nicholas.brown@pennmedicine.upenn.edu>
Diff between immunogenetr versions 1.3.0 dated 2026-05-26 and 1.4.0 dated 2026-07-06
DESCRIPTION | 8 MD5 | 139 ++++--- NEWS.md | 24 + R/GLstring_expand_longer.R | 12 R/GLstring_gene_copies_combine.R | 4 R/GLstring_genes.R | 18 - R/GLstring_genes_expanded.R | 8 R/GLstring_genotype_ambiguity.R | 12 R/GLstring_regex.R | 12 R/GLstring_to_ambiguity_table.R | 10 R/HLA_columns_to_GLstring.R | 207 +++++++---- R/HLA_match_number.R | 4 R/HLA_match_summary_HCT.R | 6 R/HLA_mismatch_alleles.R | 8 R/HLA_mismatch_base.R | 46 +- R/HLA_mismatch_logical.R | 4 R/HLA_mismatch_number.R | 10 R/HLA_mismatched_alleles.R | 8 R/HLA_prefix_add.R | 8 R/HLA_prefix_remove.R | 14 R/HLA_truncate.R | 10 R/HLA_typing_synthetic_LIS-data.R |only R/ambiguity_table_to_GLstring.R | 10 R/immunogenetr-package.R | 20 - R/read_HML.R | 12 R/utils-validation.R | 6 README.md | 92 ++--- data/HLA_typing_synthetic_LIS.rda |only inst/doc/immunogenetr.R | 14 inst/doc/immunogenetr.Rmd | 38 +- inst/doc/immunogenetr.html | 233 ++++++------- man/GLstring_expand_longer.Rd | 10 man/GLstring_gene_copies_combine.Rd | 4 man/GLstring_genes.Rd | 6 man/GLstring_genes_expanded.Rd | 6 man/GLstring_genotype_ambiguity.Rd | 6 man/GLstring_regex.Rd | 8 man/GLstring_to_ambiguity_table.Rd | 10 man/HLA_columns_to_GLstring.Rd | 21 - man/HLA_match_number.Rd | 4 man/HLA_match_summary_HCT.Rd | 6 man/HLA_mismatch_alleles.Rd | 8 man/HLA_mismatch_base.Rd | 8 man/HLA_mismatch_logical.Rd | 4 man/HLA_mismatch_number.Rd | 8 man/HLA_mismatched_alleles.Rd | 8 man/HLA_prefix_add.Rd | 4 man/HLA_prefix_remove.Rd | 4 man/HLA_truncate.Rd | 6 man/HLA_typing_synthetic_LIS.Rd |only man/ambiguity_table_to_GLstring.Rd | 8 man/immunogenetr-package.Rd | 2 man/read_HML.Rd | 4 tests/testthat/test-GLstring_expand_longer.R | 2 tests/testthat/test-GLstring_gene_copies_combine.R | 2 tests/testthat/test-GLstring_genes.R | 14 tests/testthat/test-GLstring_genes_expanded.R | 2 tests/testthat/test-GLstring_genotype_ambiguity.R | 6 tests/testthat/test-GLstring_regex.R | 10 tests/testthat/test-HLA_columns_to_GLstring.R | 2 tests/testthat/test-HLA_columns_to_GLstring_nomenclature.R |only tests/testthat/test-HLA_match_number.R | 6 tests/testthat/test-HLA_match_summary_HCT.R | 2 tests/testthat/test-HLA_mismatch_base.R | 26 + tests/testthat/test-HLA_mismatch_logical.R | 6 tests/testthat/test-HLA_mismatch_number.R | 6 tests/testthat/test-HLA_mismatched_alleles.R | 10 tests/testthat/test-HLA_typing_synthetic_LIS-data.R |only tests/testthat/test-ambiguity_table_to_GLstring.R | 2 tests/testthat/test-read_HML.R | 20 - tests/testthat/test-round_trip.R | 2 tests/testthat/test-validation.R | 10 vignettes/immunogenetr.Rmd | 38 +- 73 files changed, 720 insertions(+), 588 deletions(-)
Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes [aut, cre],
Dwayne Tally [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.2.10 dated 2026-01-29 and 1.2.13 dated 2026-07-06
DESCRIPTION | 8 MD5 | 26 +- R/sysdata.rda |binary build/vignette.rds |binary data/cytoData.rda |binary data/cytobandLocations.rda |binary inst/doc/Gallery.html | 434 ++++++++++++++++++++++-------------------- inst/doc/IntroRCytoGPS.Rmd | 4 inst/doc/IntroRCytoGPS.html | 448 ++++++++++++++++++++++++-------------------- man/01-cytobandLocations.Rd | 3 man/02-readLGF.Rd | 4 man/03-CytobandData.Rd | 3 man/07-preclean.Rd | 4 vignettes/IntroRCytoGPS.Rmd | 4 14 files changed, 513 insertions(+), 425 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) <doi:10.18637/jss.v090.c01>.
Author: Guy Brock [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.5.4 dated 2025-04-06 and 1.6.1 dated 2026-07-06
DESCRIPTION | 8 +++---- MD5 | 42 ++++++++++++++++++++++++----------------- NAMESPACE | 2 - R/palettes.R | 15 ++++++++++++++ build/vignette.rds |binary data/Dark24.rda |binary data/Light24.rda |binary data/alphabet.rda |binary data/colorsafe.rda |binary data/glasbey.rda |binary data/iscc.rda |binary data/palette36.rda |binary data/sky-colors.rda |binary data/xkcd.rda |only inst/doc/color-deficits.html | 24 +++++++++++------------ inst/doc/colornames.R |only inst/doc/colornames.Rmd |only inst/doc/colornames.html |only inst/doc/creatingPalettes.html | 20 +++++++++---------- inst/doc/polychrome.html | 22 ++++++++++----------- inst/doc/testgg.html | 8 +++---- inst/extData/rewrite.R | 8 +++++++ inst/extData/xkcdColors.txt |only man/xkcd.Rd |only man/xkcdNames.Rd |only vignettes/colornames.Rmd |only 26 files changed, 90 insertions(+), 59 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph] ,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.1.3 dated 2025-11-18 and 1.2.0 dated 2026-07-06
DESCRIPTION | 15 MD5 | 113 +++-- NAMESPACE | 3 NEWS.md | 11 R/RcppExports.R |only R/backend_cpp.R |only R/data.R | 91 +++- R/draws.R | 27 - R/inputChecks.R | 41 + R/logit.R | 7 R/logit_batched.R |only R/logitr-package.R |only R/logitr.R | 121 ++++- R/methods.R | 10 R/modelInputs.R | 87 +++ R/optimLoop.R | 53 +- README.md | 34 + build/vignette.rds |binary data/loglik_draws.rda |only data/runtimes.rda |binary data/runtimes_draws.rda |only inst/doc/backends.R |only inst/doc/backends.Rmd |only inst/doc/backends.html |only inst/doc/basic_usage.html | 106 ++-- inst/doc/benchmark.R | 103 ++-- inst/doc/benchmark.Rmd | 141 +++--- inst/doc/benchmark.html | 780 ++++++++++++++++++++++++++--------- inst/doc/data_formatting.html | 22 inst/doc/interactions.html | 120 ++--- inst/doc/mnl_models.html | 87 +-- inst/doc/mnl_models_weighted.html | 165 +++---- inst/doc/mxl_models.html | 267 +++++------ inst/doc/predict.html | 89 +-- inst/doc/summarizing_results.Rmd | 2 inst/doc/summarizing_results.html | 432 +++++++++---------- inst/doc/utility_models.Rmd | 2 inst/doc/utility_models.html | 82 +-- inst/example/examples.R | 38 - inst/extdata/mxl_pref.Rds |binary inst/extdata/mxl_pref_cor.Rds |binary inst/extdata/mxl_wtp.Rds |binary man/logitr-package.Rd |only man/logitr.Rd | 67 ++- man/loglik_draws.Rd |only man/rmdchunks/header.Rmd | 16 man/rmdchunks/installation.Rmd | 8 man/rmdchunks/utilityPreference.Rmd | 4 man/rmdchunks/utilityWtp.Rmd | 4 man/runtimes.Rd | 15 man/runtimes_draws.Rd |only src |only tests/testthat/test_backend.R |only tests/testthat/test_batched.R |only tests/testthat/test_cpp.R |only tests/testthat/test_gradients_pref.R | 3 tests/testthat/test_gradients_wtp.R | 3 tests/testthat/test_panel.R |only tests/testthat/test_parallel.R |only tests/testthat/test_sd_signs.R |only vignettes/backends.Rmd |only vignettes/benchmark.Rmd | 141 +++--- vignettes/benchmark.png |binary vignettes/benchmark_draws.png |only vignettes/benchmark_loglik.png |only vignettes/summarizing_results.Rmd | 2 vignettes/utility_models.Rmd | 2 67 files changed, 2110 insertions(+), 1204 deletions(-)
Title: Simplify Access to Brazilian Social Data
Description: Provides tools for downloading and processing microdata from
the PNAD Contínua (PNADC, Continuous National Household Sample Survey),
a rotating panel survey published quarterly by IBGE (Brazilian Institute
of Geography and Statistics). Includes panel identification algorithms
for linking individuals across survey waves.
Author: Laura Tavares Regadas [aut, cre],
DataZoom [fnd],
Igor Rigolon Veiga [aut],
Arthur Lins de Vasconcellos [aut],
Giulia Toscano Imbuzeiro [aut],
Guilherme Jardim [aut],
Pablo Chaves [aut],
Breno Avidos [aut],
Bernardo Sieira [aut]
Maintainer: Laura Tavares Regadas <lauratregadas@gmail.com>
Diff between datazoom.social versions 0.1.0 dated 2026-05-07 and 0.1.1 dated 2026-07-06
DESCRIPTION | 12 LICENSE | 4 MD5 | 48 - NAMESPACE | 13 NEWS.md | 29 R/build_pnadc_panel.R | 523 +++++++++----- R/calculate_panel_attrition.R | 192 ++--- R/cria_df_de_atrito.R | 160 ++-- R/donate_birth_dates.R |only R/load_pnadc.R | 1443 +++++++++++++++++++--------------------- R/pnad_sample.R | 102 +- R/zzz.R | 26 README.md | 834 ++++++++++++----------- build/vignette.rds |binary inst/doc/BUILD_PNADC_PANEL.R | 53 - inst/doc/BUILD_PNADC_PANEL.Rmd | 191 ++--- inst/doc/BUILD_PNADC_PANEL.html | 975 ++++++++++++++------------- inst/doc/LOAD_PNADC.R | 154 ++-- inst/doc/LOAD_PNADC.Rmd | 406 +++++------ inst/doc/LOAD_PNADC.html | 1233 +++++++++++++++++----------------- man/build_pnadc_panel.Rd | 52 - man/cria_df_de_atrito.Rd |only man/load_pnadc.Rd | 182 ++--- man/pnad_sample.Rd | 126 +-- vignettes/BUILD_PNADC_PANEL.Rmd | 191 ++--- vignettes/LOAD_PNADC.Rmd | 406 +++++------ 26 files changed, 3822 insertions(+), 3533 deletions(-)
More information about datazoom.social at CRAN
Permanent link
Title: Render Tables, Listings, and Figures for Clinical Submissions
Description: Render clinical submission tables, listings, and figures to
'RTF', 'LaTeX', 'HTML', 'PDF', and 'DOCX' from pre-summarised data
frames, with no external 'Java' or 'SAS' dependency. Features include
decimal alignment via font metrics, multi-level column headers with
passthrough leaves, predicate-targeted cell styling, footnotes,
group-aware pagination, and figures that wrap a plot or image in the
same page chrome as a table. Built for Clinical Data Interchange Standards
Consortium (CDISC) Analysis Data Model (ADaM) workflows and
regulatory submissions to agencies such as the Food and Drug
Administration (FDA), European Medicines Agency (EMA), and
Pharmaceuticals and Medical Devices Agency (PMDA).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between tabular versions 0.1.0 dated 2026-06-11 and 0.2.0 dated 2026-07-06
tabular-0.1.0/tabular/tests/testthat/testthat-problems.rds |only tabular-0.2.0/tabular/DESCRIPTION | 21 tabular-0.2.0/tabular/MD5 | 319 +-- tabular-0.2.0/tabular/NAMESPACE | 4 tabular-0.2.0/tabular/NEWS.md | 207 ++ tabular-0.2.0/tabular/R/aaa_class.R | 280 ++- tabular-0.2.0/tabular/R/align.R | 19 tabular-0.2.0/tabular/R/as_grid.R | 160 + tabular-0.2.0/tabular/R/backend_docx.R | 778 +++++++- tabular-0.2.0/tabular/R/backend_html.R | 382 +++- tabular-0.2.0/tabular/R/backend_latex.R | 461 ++++- tabular-0.2.0/tabular/R/backend_md.R | 241 ++ tabular-0.2.0/tabular/R/backend_pdf.R | 10 tabular-0.2.0/tabular/R/backend_rtf.R | 546 +++++- tabular-0.2.0/tabular/R/brdr.R | 11 tabular-0.2.0/tabular/R/chrome_style.R | 7 tabular-0.2.0/tabular/R/col_spec.R | 272 +-- tabular-0.2.0/tabular/R/col_width.R | 23 tabular-0.2.0/tabular/R/cols.R | 224 +- tabular-0.2.0/tabular/R/data.R | 98 - tabular-0.2.0/tabular/R/emit.R | 42 tabular-0.2.0/tabular/R/engine_borders.R | 11 tabular-0.2.0/tabular/R/engine_footnotes.R | 82 tabular-0.2.0/tabular/R/engine_format.R | 19 tabular-0.2.0/tabular/R/engine_group_display.R | 221 +- tabular-0.2.0/tabular/R/engine_paginate.R | 185 +- tabular-0.2.0/tabular/R/engine_style.R | 4 tabular-0.2.0/tabular/R/engine_subgroup_split.R | 78 tabular-0.2.0/tabular/R/figure.R |only tabular-0.2.0/tabular/R/figure_raster.R |only tabular-0.2.0/tabular/R/font_metrics.R | 31 tabular-0.2.0/tabular/R/fonts.R | 130 + tabular-0.2.0/tabular/R/footnote.R | 6 tabular-0.2.0/tabular/R/geometry.R | 46 tabular-0.2.0/tabular/R/headers.R | 11 tabular-0.2.0/tabular/R/inline_format.R | 18 tabular-0.2.0/tabular/R/locations.R | 4 tabular-0.2.0/tabular/R/manifest.R | 102 + tabular-0.2.0/tabular/R/page_chrome.R | 12 tabular-0.2.0/tabular/R/paginate.R | 46 tabular-0.2.0/tabular/R/pivot_across.R | 893 +++++++++- tabular-0.2.0/tabular/R/preset.R | 216 +- tabular-0.2.0/tabular/R/preset_minimal.R | 25 tabular-0.2.0/tabular/R/print.R | 105 + tabular-0.2.0/tabular/R/sanity.R | 29 tabular-0.2.0/tabular/R/sort_rows.R | 54 tabular-0.2.0/tabular/R/style.R | 45 tabular-0.2.0/tabular/R/style_template.R | 8 tabular-0.2.0/tabular/R/subgroup.R | 177 + tabular-0.2.0/tabular/R/tabular.R | 102 - tabular-0.2.0/tabular/R/theme.R | 12 tabular-0.2.0/tabular/R/zzz.R | 24 tabular-0.2.0/tabular/README.md | 2 tabular-0.2.0/tabular/data/cdisc_saf_ae.rda |binary tabular-0.2.0/tabular/data/cdisc_saf_demo.rda |binary tabular-0.2.0/tabular/data/cdisc_saf_subgroup.rda |binary tabular-0.2.0/tabular/inst/doc/tabular.R | 2 tabular-0.2.0/tabular/inst/doc/tabular.html | 372 ---- tabular-0.2.0/tabular/inst/doc/tabular.qmd | 2 tabular-0.2.0/tabular/inst/qualification/QUALIFICATION_README.md | 2 tabular-0.2.0/tabular/inst/qualification/qualify_tabular_cdisc.R | 10 tabular-0.2.0/tabular/man/as_grid.Rd | 21 tabular-0.2.0/tabular/man/brdr.Rd | 7 tabular-0.2.0/tabular/man/cdisc_eff_resp.Rd | 5 tabular-0.2.0/tabular/man/cdisc_saf_ae.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_aesocpt.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_aesocpt_ard.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_demo.Rd | 23 tabular-0.2.0/tabular/man/cdisc_saf_subgroup.Rd | 44 tabular-0.2.0/tabular/man/cells.Rd | 4 tabular-0.2.0/tabular/man/check_fonts.Rd | 8 tabular-0.2.0/tabular/man/col_spec.Rd | 181 +- tabular-0.2.0/tabular/man/cols.Rd | 64 tabular-0.2.0/tabular/man/emit.Rd | 23 tabular-0.2.0/tabular/man/figure.Rd |only tabular-0.2.0/tabular/man/figures/README-hero.png |binary tabular-0.2.0/tabular/man/footnote.Rd | 6 tabular-0.2.0/tabular/man/headers.Rd | 11 tabular-0.2.0/tabular/man/html.Rd | 4 tabular-0.2.0/tabular/man/md.Rd | 6 tabular-0.2.0/tabular/man/paginate.Rd | 37 tabular-0.2.0/tabular/man/pivot_across.Rd | 218 ++ tabular-0.2.0/tabular/man/preset.Rd | 156 - tabular-0.2.0/tabular/man/preset_minimal.Rd | 25 tabular-0.2.0/tabular/man/print.tabular_spec.Rd | 2 tabular-0.2.0/tabular/man/set_preset.Rd | 4 tabular-0.2.0/tabular/man/sort_rows.Rd | 54 tabular-0.2.0/tabular/man/style.Rd | 33 tabular-0.2.0/tabular/man/style_template.Rd | 8 tabular-0.2.0/tabular/man/subgroup.Rd | 163 + tabular-0.2.0/tabular/man/tabular-package.Rd | 4 tabular-0.2.0/tabular/man/tabular.Rd | 63 tabular-0.2.0/tabular/man/tabular_classes.Rd | 4 tabular-0.2.0/tabular/man/tabular_predicates.Rd | 8 tabular-0.2.0/tabular/tests/testthat/_problems/test-group_display-1793.R |only tabular-0.2.0/tabular/tests/testthat/_snaps/Total/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_docx/saf_demo_golden.xml | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_html/saf_demo_golden.html | 163 - tabular-0.2.0/tabular/tests/testthat/_snaps/backend_latex/banded_multirange.tex | 10 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_latex/saf_demo_golden.tex | 68 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_md/saf_demo_golden.md | 62 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_rtf/saf_demo_golden.rtf | 705 +------ tabular-0.2.0/tabular/tests/testthat/_snaps/drug_100/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/drug_50/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/engine_decimal.md | 138 - tabular-0.2.0/tabular/tests/testthat/_snaps/engine_headers.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/figure-backends.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/figure.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/headers.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/inline_format.md | 4 tabular-0.2.0/tabular/tests/testthat/_snaps/paginate.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/pivot_across.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/placebo/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/preset.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/set_preset.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/sort_rows.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/subgroup.md | 4 tabular-0.2.0/tabular/tests/testthat/_snaps/tabular.md |only tabular-0.2.0/tabular/tests/testthat/fixtures |only tabular-0.2.0/tabular/tests/testthat/tabular.aux | 6 tabular-0.2.0/tabular/tests/testthat/tabular.log |only tabular-0.2.0/tabular/tests/testthat/test-aaa_class.R | 36 tabular-0.2.0/tabular/tests/testthat/test-align.R | 18 tabular-0.2.0/tabular/tests/testthat/test-as_grid.R | 24 tabular-0.2.0/tabular/tests/testthat/test-backend_docx.R | 150 + tabular-0.2.0/tabular/tests/testthat/test-backend_html.R | 200 +- tabular-0.2.0/tabular/tests/testthat/test-backend_latex.R | 326 +++ tabular-0.2.0/tabular/tests/testthat/test-backend_md.R | 86 tabular-0.2.0/tabular/tests/testthat/test-backend_pdf.R | 48 tabular-0.2.0/tabular/tests/testthat/test-backend_rtf.R | 282 ++- tabular-0.2.0/tabular/tests/testthat/test-col_spec.R | 39 tabular-0.2.0/tabular/tests/testthat/test-col_width.R | 14 tabular-0.2.0/tabular/tests/testthat/test-cols.R | 120 + tabular-0.2.0/tabular/tests/testthat/test-data.R |only tabular-0.2.0/tabular/tests/testthat/test-empty-state.R |only tabular-0.2.0/tabular/tests/testthat/test-engine_borders-table-layers.R | 10 tabular-0.2.0/tabular/tests/testthat/test-engine_decimal.R | 155 + tabular-0.2.0/tabular/tests/testthat/test-engine_footnotes.R | 60 tabular-0.2.0/tabular/tests/testthat/test-engine_format.R | 4 tabular-0.2.0/tabular/tests/testthat/test-engine_headers.R | 8 tabular-0.2.0/tabular/tests/testthat/test-engine_paginate.R | 69 tabular-0.2.0/tabular/tests/testthat/test-engine_style.R | 3 tabular-0.2.0/tabular/tests/testthat/test-engine_subgroup_split.R | 16 tabular-0.2.0/tabular/tests/testthat/test-examples-phantom.R | 3 tabular-0.2.0/tabular/tests/testthat/test-figure-backends.R |only tabular-0.2.0/tabular/tests/testthat/test-figure.R |only tabular-0.2.0/tabular/tests/testthat/test-figure_raster.R |only tabular-0.2.0/tabular/tests/testthat/test-font_metrics.R | 10 tabular-0.2.0/tabular/tests/testthat/test-fonts.R | 118 + tabular-0.2.0/tabular/tests/testthat/test-group_display.R | 625 +++++- tabular-0.2.0/tabular/tests/testthat/test-inline_format.R | 110 - tabular-0.2.0/tabular/tests/testthat/test-page_chrome.R | 4 tabular-0.2.0/tabular/tests/testthat/test-paginate.R | 8 tabular-0.2.0/tabular/tests/testthat/test-pivot_across.R | 678 +++++++ tabular-0.2.0/tabular/tests/testthat/test-preset-extended.R | 4 tabular-0.2.0/tabular/tests/testthat/test-preset.R | 44 tabular-0.2.0/tabular/tests/testthat/test-style.R | 47 tabular-0.2.0/tabular/tests/testthat/test-subgroup.R | 249 ++ tabular-0.2.0/tabular/tests/testthat/test-tabular.R | 36 tabular-0.2.0/tabular/tests/testthat/test-theme.R | 16 tabular-0.2.0/tabular/tests/testthat/test-util_ws.R | 2 tabular-0.2.0/tabular/tests/testthat/test-width_mode.R | 18 tabular-0.2.0/tabular/vignettes/articles/data-in.qmd | 166 + tabular-0.2.0/tabular/vignettes/articles/output.qmd | 31 tabular-0.2.0/tabular/vignettes/articles/presentation.qmd | 69 tabular-0.2.0/tabular/vignettes/articles/recipes.qmd | 77 tabular-0.2.0/tabular/vignettes/articles/structure.qmd | 124 + tabular-0.2.0/tabular/vignettes/tabular.qmd | 2 168 files changed, 10174 insertions(+), 3694 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.42 dated 2026-06-08 and 0.44 dated 2026-07-06
DESCRIPTION | 8 ++-- MD5 | 31 +++++++++------- NAMESPACE | 1 NEWS.md | 22 ++++++++++- R/cluster_util.R | 2 - R/plot_ci.R | 6 ++- R/scan1gen.R |only R/scan1perm.R | 69 +++++++++++++++++++++++++++++++++--- R/scan1perm_gen.R |only README.md | 2 - build/partial.rdb |binary data/CCaltcolors.RData |binary data/CCcolors.RData |binary data/CCorigcolors.RData |binary man/scan1gen.Rd |only man/scan1perm.Rd | 44 ++++++++++++++++++++++ src/linreg_eigen.cpp | 12 ++++-- tests/testthat/test-scan1gen.R |only tests/testthat/test-scan1perm_gen.R |only 19 files changed, 165 insertions(+), 32 deletions(-)
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary B. Abrams [aut],
Greg Gershkowitz [aut],
Anoushka Joglekar [aut],
Chao Liu [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.14 dated 2025-04-08 and 1.1.3 dated 2026-07-06
DESCRIPTION | 8 +-- MD5 | 18 ++++--- R/00-pairedStat.R | 37 +++++++++++---- build/vignette.rds |binary data/GSE6631.rda |binary data/LungPair.rda |binary inst/doc/newmanomics.html | 98 +++++++++++++++++++++--------------------- man/02-pairedStat.Rd | 35 ++++++++++++--- tests/00-pairedTest.Rout.save | 44 +++++++++--------- tests/01-testTeho.R |only tests/01-testTeho.Rout |only 11 files changed, 141 insertions(+), 99 deletions(-)
Title: Reference Data and Helpers for Small Island States and
Territories
Description: A curated reference list of countries and territories with
classifications for Small Island Developing States (SIDS),
sub-national island jurisdictions (SNIJ), World Bank region and
income group, and political association. Sub-sovereign cases such
as Aruba, Curacao, Bonaire, Sint Maarten, the French overseas
territories, and Aaland Islands are represented with disambiguating
codes that standard country-code packages often collapse or omit.
Provides predicate helpers and a tidy joiner intended to extend
rather than replace 'countrycode'. Source data is maintained at
<https://github.com/University-of-Aruba/island-research-reference-data>
and licensed CC BY 4.0.
Author: Rendell de Kort [aut, cre] ,
University of Aruba [cph, fnd] Network)
Maintainer: Rendell de Kort <rendell.dekort@ua.aw>
Diff between islandcodes versions 0.1.1 dated 2026-05-15 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 +-- MD5 | 33 ++++++++++------- NAMESPACE | 2 + NEWS.md | 7 +++ R/coords.R |only R/data.R | 15 +++++++ R/distance.R |only README.md | 15 ++++++- data/islands.rda |binary inst/CITATION | 7 ++- inst/doc/islandcodes.R | 23 +++++++++++- inst/doc/islandcodes.Rmd | 43 ++++++++++++++++++++++ inst/doc/islandcodes.html | 77 ++++++++++++++++++++++++++++++++++++++++- man/figures |only man/island_coords.Rd |only man/island_distance.Rd |only man/islands.Rd | 15 +++++++ tests/testthat/test-coords.R |only tests/testthat/test-distance.R |only tests/testthat/test-lookup.R | 9 +++- vignettes/islandcodes.Rmd | 43 ++++++++++++++++++++++ 21 files changed, 267 insertions(+), 28 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots require some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'-based publication ready plots.
This version includes modern R ecosystem compatibility updates and customizable
p-value formatting presets (APA, AMA, NEJM, Lancet, GraphPad, and scientific
notation) for publication workflows, plus robust sparse-subset handling in
statistical annotation layers such as 'stat_compare_means()' and 'geom_pwc()',
with informative per-group skip diagnostics for non-comparable subsets.
Author: Alboukadel Kassambara [aut, cre],
Laszlo Erdey [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.6.3 dated 2026-02-24 and 1.0.0 dated 2026-07-06
DESCRIPTION | 49 MD5 | 454 ++- NAMESPACE | 7 NEWS.md | 811 +++++-- R/add_summary.R | 236 +- R/annotate_figure.R | 155 + R/as_ggplot.R | 37 R/as_npc.R | 50 R/axis_scale.R | 136 - R/background_image.R | 40 R/bgcolor.R | 26 R/border.R | 36 R/compare_means.R | 582 +++-- R/create_aes.R | 64 R/desc_statby.R | 54 R/diff_express.R | 40 R/facet.R | 154 - R/font.R | 137 - R/gene_citation.R | 33 R/gene_expression.R | 26 R/geom_bracket.R | 518 +++- R/geom_exec.R | 83 R/geom_pwc.R | 979 +++++--- R/get_breaks.R | 38 R/get_coord.R | 22 R/get_legend.R | 40 R/get_palette.R | 101 R/ggadd.R | 180 - R/ggadjust_pvalue.R | 113 R/ggarrange.R | 267 +- R/ggballoonplot.R | 223 + R/ggbarplot.R | 584 +++-- R/ggboxplot.R | 245 +- R/ggdensity.R | 133 - R/ggdonutchart.R | 139 - R/ggdotchart.R | 265 +- R/ggdotplot.R | 148 - R/ggecdf.R | 78 R/ggerrorplot.R | 168 - R/ggexport.R | 78 R/gghistogram.R | 205 + R/ggline.R | 329 +- R/ggmaplot.R | 312 +- R/ggpaired.R | 174 - R/ggpar.R | 141 - R/ggparagraph.R | 81 R/ggpie.R | 182 - R/ggpubr-package.R | 21 R/ggpubr_args.R | 36 R/ggpubr_options.R | 4 R/ggqqplot.R | 211 + R/ggscatter.R | 412 ++- R/ggscatterhist.R | 333 +- R/ggstripchart.R | 182 - R/ggsummarystats.R | 85 R/ggtext.R | 219 - R/ggtexttable.R | 1137 +++++----- R/ggviolin.R | 306 +- R/gradient_color.R | 26 R/grids.R | 51 R/npc_to_data_coord.R | 4 R/p_format_utils.R |only R/rotate.R | 32 R/rotate_axis_text.R | 75 R/rremove.R | 85 R/set_palette.R | 105 R/shared_docs.R | 10 R/show_line_types.R | 27 R/show_point_shapes.R | 25 R/stat_anova_test.R | 523 ++-- R/stat_central_tendency.R | 70 R/stat_chull.R | 17 R/stat_compare_means.R | 720 ++++-- R/stat_conf_ellipse.R | 73 R/stat_cor.R | 536 +++- R/stat_friedman_test.R | 79 R/stat_kruskal_test.R | 66 R/stat_mean.R | 28 R/stat_overlay_normal_density.R | 36 R/stat_pvalue_manual.R | 389 ++- R/stat_regline_equation.R | 251 +- R/stat_stars.R | 34 R/stat_welch_anova_test.R | 67 R/text_grob.R | 36 R/theme_pubr.R | 149 - R/theme_transparent.R | 33 R/utilities.R | 1030 +++++---- R/utilities_base.R | 82 R/utilities_color.R | 193 + R/utilities_label.R | 146 - R/utils-aes.R | 6 R/utils-tidyr.R | 2 R/utils_stat_test_label.R | 264 +- R/zzz.R |only README.md | 71 inst/CITATION |only man/add_summary.Rd | 5 man/annotate_figure.Rd | 49 man/as_ggplot.Rd | 10 man/as_npc.Rd | 2 man/axis_scale.Rd | 2 man/background_image.Rd | 15 man/bgcolor.Rd | 2 man/build_symnum_args.Rd |only man/clean_lock_files.Rd |only man/compare_means.Rd | 140 + man/create_aes.Rd | 8 man/create_p_label.Rd |only man/desc_statby.Rd | 6 man/diff_express.Rd | 40 man/facet.Rd | 18 man/font.Rd | 28 man/format_p_value.Rd |only man/format_single_p.Rd |only man/gene_citation.Rd | 17 man/gene_expression.Rd | 14 man/geom_bracket.Rd | 73 man/geom_exec.Rd | 13 man/geom_pwc.Rd | 131 - man/get_breaks.Rd | 12 man/get_legend.Rd | 8 man/get_p_format_style.Rd |only man/get_palette.Rd | 48 man/ggadjust_pvalue.Rd | 70 man/ggarrange.Rd | 61 man/ggballoonplot.Rd | 88 man/ggbarplot.Rd | 133 - man/ggboxplot.Rd | 66 man/ggdensity.Rd | 38 man/ggdonutchart.Rd | 41 man/ggdotchart.Rd | 50 man/ggdotplot.Rd | 46 man/ggecdf.Rd | 17 man/ggerrorplot.Rd | 71 man/ggexport.Rd | 16 man/gghistogram.Rd | 46 man/ggline.Rd | 93 man/ggmaplot.Rd | 76 man/ggpaired.Rd | 36 man/ggpar.Rd | 58 man/ggparagraph.Rd | 23 man/ggpie.Rd | 37 man/ggpubr-common-params.Rd | 8 man/ggpubr-package.Rd | 22 man/ggpubr_args.Rd | 2 man/ggpubr_options.Rd | 2 man/ggqqplot.Rd | 15 man/ggscatter.Rd | 62 man/ggscatterhist.Rd | 34 man/ggstripchart.Rd | 80 man/ggsummarystats.Rd | 31 man/ggtext.Rd | 21 man/ggtexttable.Rd | 131 - man/ggviolin.Rd | 118 - man/gradient_color.Rd | 8 man/list_p_format_styles.Rd |only man/npc_to_data_coord.Rd | 2 man/p_format_styles.Rd |only man/resolve_p_format_params.Rd |only man/rotate.Rd | 6 man/rremove.Rd | 6 man/set_palette.Rd | 6 man/show_line_types.Rd | 4 man/show_point_shapes.Rd | 4 man/stat_anova_test.Rd | 102 man/stat_central_tendency.Rd | 23 man/stat_chull.Rd | 16 man/stat_compare_means.Rd | 189 + man/stat_conf_ellipse.Rd | 16 man/stat_cor.Rd | 136 + man/stat_friedman_test.Rd | 91 man/stat_kruskal_test.Rd | 85 man/stat_mean.Rd | 16 man/stat_overlay_normal_density.Rd | 12 man/stat_pvalue_manual.Rd | 116 - man/stat_regline_equation.Rd | 64 man/stat_stars.Rd | 18 man/stat_welch_anova_test.Rd | 85 man/text_grob.Rd | 10 man/theme_pubr.Rd | 13 man/theme_transparent.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-add_stat_label.R | 155 + tests/testthat/test-annotate-figure-label.R |only tests/testthat/test-annotate-figure-titles.R |only tests/testthat/test-as_npc.R | 2 tests/testthat/test-check_data.R | 94 tests/testthat/test-clean_lock_files.R |only tests/testthat/test-colour-alias.R |only tests/testthat/test-compare-means-comparisons-note.R |only tests/testthat/test-compare-means-family.R |only tests/testthat/test-compare-means-padjust-group.R |only tests/testthat/test-compare-means-paired-id.R |only tests/testthat/test-compare-means-spaced-names.R |only tests/testthat/test-compare_means.R | 124 - tests/testthat/test-convert_label_dotdot_notation_to_after_stat.R | 81 tests/testthat/test-create_aes.R | 1 tests/testthat/test-facet-panel-labs.R |only tests/testthat/test-facet.R | 6 tests/testthat/test-geom-bracket-horizontal.R |only tests/testthat/test-geom-bracket-tip-collapse.R |only tests/testthat/test-geom-bracket-vertical.R |only tests/testthat/test-geom-exec-linewidth.R |only tests/testthat/test-geom-pwc-p-adjust-n.R |only tests/testthat/test-geom_pwc.R | 277 ++ tests/testthat/test-get-breaks-anchor.R |only tests/testthat/test-get_coord.R | 3 tests/testthat/test-ggadjust_pvalue.R | 27 tests/testthat/test-ggarrange-byrow.R |only tests/testthat/test-ggarrange-common-legend.R |only tests/testthat/test-ggarrange-spacing.R |only tests/testthat/test-ggballoonplot.R |only tests/testthat/test-ggbarplot-alpha-errorbar.R |only tests/testthat/test-ggbarplot-dodge2-errorbar.R |only tests/testthat/test-ggbarplot-facet-summary.R |only tests/testthat/test-ggbarplot-numeric-x.R |only tests/testthat/test-ggbarplot-stacked-posneg.R |only tests/testthat/test-ggboxplot-coef.R |only tests/testthat/test-ggboxplot.R | 100 tests/testthat/test-ggexport.R |only tests/testthat/test-ggline-jitter-dodge.R |only tests/testthat/test-ggline-multi-group.R |only tests/testthat/test-ggmaplot-facet.R |only tests/testthat/test-ggmaplot-ns-order.R |only tests/testthat/test-ggmaplot.R |only tests/testthat/test-ggpaired-jitter.R |only tests/testthat/test-ggpar-element-markdown.R |only tests/testthat/test-ggpar-legend-title.R |only tests/testthat/test-ggpie-donut-repel.R |only tests/testthat/test-ggscatter.R | 4 tests/testthat/test-ggscatterhist.R |only tests/testthat/test-ggstripchart.R | 37 tests/testthat/test-ggsummarystats.R |only tests/testthat/test-ggtext.R | 12 tests/testthat/test-ggtheme-null.R |only tests/testthat/test-ggviolin-align.R |only tests/testthat/test-ggviolin-scales.R |only tests/testthat/test-ggviolin.R |only tests/testthat/test-group-coord-zero-id.R |only tests/testthat/test-legend-direction.R |only tests/testthat/test-named-palette.R |only tests/testthat/test-null-default-import.R |only tests/testthat/test-orientation-axis-limits.R |only tests/testthat/test-p_format_utils.R |only tests/testthat/test-parse_font.R |only tests/testthat/test-regline-digits.R |only tests/testthat/test-set-ticksby.R |only tests/testthat/test-show-n.R |only tests/testthat/test-stat-compare-means-id.R |only tests/testthat/test-stat-cor-conf-int.R |only tests/testthat/test-stat-cor-label-anchor.R |only tests/testthat/test-stat-cor-rmse.R |only tests/testthat/test-stat-pvalue-manual-pdigits.R |only tests/testthat/test-stat-pvalue-manual-pformat.R |only tests/testthat/test-stat_anova_test.R | 214 + tests/testthat/test-stat_compare_means.R | 317 ++ tests/testthat/test-stat_cor.R |only tests/testthat/test-stat_friedman_test.R | 10 tests/testthat/test-stat_kruskal_test.R | 6 tests/testthat/test-stat_pvalue_manual.R | 153 + tests/testthat/test-stat_welch_anova_test.R | 6 tests/testthat/test-tab-add-title-just.R |only tests/testthat/test-table-cell-header-font.R |only tests/testthat/test-theme-pubr-ticks.R |only tests/testthat/test-utilities_color.R |only tests/testthat/test-utils-tidyr.R | 22 266 files changed, 14123 insertions(+), 8037 deletions(-)
More information about deckglgeoarrow at CRAN
Permanent link
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut] ,
Davide Garolini [aut] ,
Malan Bosman [aut] ,
F. Hoffmann-La Roche AG [cph, fnd],
Alanah Jonas [aut],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.8.0 dated 2026-05-28 and 0.8.1 dated 2026-07-06
DESCRIPTION | 11 ++- MD5 | 40 ++++++------ NEWS.md | 8 ++ R/ard_summary.R | 100 +++++++++++++++---------------- R/ard_tabulate.R | 57 ++++++++++++----- R/ard_tabulate_value.R | 23 ++++--- R/ard_total_n.R | 23 ++++--- R/bind_ard.R | 7 +- R/get_ard_statistics.R | 10 ++- R/rename_ard_columns.R | 14 +++- R/tidy_ard_order.R | 90 ++++++++++++++++----------- R/unlist_ard_columns.R | 6 + inst/WORDLIST | 1 man/cards-package.Rd | 2 man/rename_ard_columns.Rd | 4 - man/unlist_ard_columns.Rd | 2 tests/testthat/_snaps/tidy_as_ard.md | 98 ------------------------------ tests/testthat/test-bind_ard.R | 6 + tests/testthat/test-rename_ard_columns.R | 19 +++++ tests/testthat/test-tidy_as_ard.R | 48 +++++++++----- tests/testthat/test-unlist_ard_columns.R | 9 ++ 21 files changed, 309 insertions(+), 269 deletions(-)
Title: Work with 'BIDS' (Brain Imaging Data Structure) Projects
Description: Tools for working with 'BIDS' (Brain Imaging Data Structure)
formatted neuroimaging datasets. The package provides functionality for
reading and querying 'BIDS'-compliant projects, creating mock 'BIDS'
datasets for testing, and extracting preprocessed data from 'fMRIPrep'
derivatives. It supports searching and filtering 'BIDS' files by various
entities such as subject, session, task, and run to streamline
neuroimaging data workflows. See Gorgolewski et al. (2016)
<doi:10.1038/sdata.2016.44> for the 'BIDS' specification.
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between bidser versions 0.2.0 dated 2026-02-19 and 0.5.0 dated 2026-07-06
DESCRIPTION | 19 MD5 | 254 ++- NAMESPACE | 77 - NEWS.md | 132 + R/all_generic.R | 470 +++++- R/bids.R | 949 +++++++++--- R/bids_uri.R |only R/bidsio.R | 184 +- R/check.R | 42 R/confounds.R | 413 +++++ R/dataset_description.R |only R/datatype_registry.R |only R/entity_filters.R |only R/events.R | 151 + R/index_dt.R |only R/matchers.R | 43 R/mock_bids.R | 281 ++- R/pack_bids.R | 164 +- R/plot_bids.R | 237 ++- R/plot_bids_project.R | 2 R/project_extensions.R |only R/query.R |only R/regex_parsers.R | 159 +- R/schema.R |only R/sidecar.R | 240 ++- R/specs.R | 120 + R/tabulars.R |only R/zzz.R |only README.md | 35 build/vignette.rds |binary inst/CITATION | 9 inst/bids-schema |only inst/doc/confounds-and-variables.R |only inst/doc/confounds-and-variables.Rmd |only inst/doc/confounds-and-variables.html |only inst/doc/derivatives.R |only inst/doc/derivatives.Rmd |only inst/doc/derivatives.html |only inst/doc/mock-bids.R |only inst/doc/mock-bids.Rmd |only inst/doc/mock-bids.html |only inst/doc/quickstart.R | 179 ++ inst/doc/quickstart.Rmd | 275 ++- inst/doc/quickstart.html | 1665 +++++++++++++++++----- man/as_bids_uri.Rd |only man/bids_check_compliance.Rd | 15 man/bids_datatype_spec.Rd |only man/bids_entities.Rd |only man/bids_heatmap.Rd | 2 man/bids_index.Rd |only man/bids_parser.Rd | 3 man/bids_project.Rd | 43 man/bids_report.Rd |only man/bids_report_data.Rd |only man/bids_schema.Rd |only man/bids_schema_versions.Rd |only man/bids_subject.Rd | 2 man/bids_summary.Rd | 2 man/bids_transform.Rd | 8 man/bids_uri.Rd |only man/bids_version.Rd |only man/bidser_pkg_env.Rd | 2 man/brain_mask.Rd | 2 man/build_subject_graph.Rd | 2 man/check_confounds.Rd |only man/check_func_scans.Rd | 2 man/confound_files-method.Rd | 2 man/confound_set.Rd | 14 man/create_preproc_mask.Rd | 2 man/create_preproc_mask.bids_project.Rd | 2 man/dataset_description.Rd |only man/dataset_name.Rd |only man/derivative_files.Rd |only man/derivative_pipelines.Rd |only man/dot-bids_schema_entities.Rd |only man/dot-bids_schema_suffixes.Rd |only man/dot-bids_schema_validate_filename.Rd |only man/dot-bidser_schema_check_tree.Rd |only man/event_files-method.Rd | 4 man/file_pairs.Rd | 2 man/flat_list-method.Rd | 2 man/func_scans.Rd | 2 man/func_scans.bids_project.Rd | 2 man/gen_parser.Rd |only man/get_metadata.Rd |only man/get_repetition_time.Rd | 2 man/is_bids_uri.Rd |only man/list_datatypes.Rd |only man/list_pack_bids.Rd | 2 man/load_all_events-method.Rd | 2 man/mask_files.Rd | 2 man/n_volumes.Rd |only man/pack_bids.Rd | 2 man/participants-method.Rd | 31 man/participants.mock_bids_project.Rd | 6 man/plot.bids_project.Rd | 2 man/plot_bids.Rd | 2 man/preproc_scans-method.Rd | 2 man/preproc_scans.bids_project.Rd | 2 man/query_files.Rd |only man/read_confounds-method.Rd | 10 man/read_confounds.Rd | 38 man/read_confounds.bids_project.Rd | 52 man/read_dataset_description.Rd |only man/read_events.Rd | 15 man/read_events.bids_project.Rd | 2 man/read_func_scans.Rd | 2 man/read_participants.Rd |only man/read_preproc_scans.bids_project.Rd | 9 man/read_scans_tsv.Rd |only man/read_sessions_tsv.Rd |only man/read_sidecar.Rd | 27 man/register_datatype.Rd |only man/resolve_bids_uri.Rd |only man/search_files.Rd | 14 man/sidecar.Rd |only man/surface_files.Rd | 2 man/tasks-method.Rd | 2 man/transform_files.Rd | 2 man/unregister_datatype.Rd |only man/variables_table.Rd |only tests/testthat/helper-bids-examples.R | 9 tests/testthat/test_bids_core.R |only tests/testthat/test_bids_remaining.R |only tests/testthat/test_bids_subject.R | 6 tests/testthat/test_bids_subject_local.R |only tests/testthat/test_bids_uri.R |only tests/testthat/test_bidsio_coverage.R |only tests/testthat/test_build_subject_graph.R | 2 tests/testthat/test_check_func.R |only tests/testthat/test_confounds.R | 140 + tests/testthat/test_coverage_boost.R |only tests/testthat/test_coverage_final.R |only tests/testthat/test_coverage_sessions.R |only tests/testthat/test_dataset_description.R |only tests/testthat/test_datatype_registry.R |only tests/testthat/test_dwi_datatype.R |only tests/testthat/test_formula_filters.R |only tests/testthat/test_index_dt.R |only tests/testthat/test_infer_tr.R |only tests/testthat/test_metadata_inheritance.R |only tests/testthat/test_mock_bids.R | 66 tests/testthat/test_mock_bids_methods.R |only tests/testthat/test_n_volumes.R |only tests/testthat/test_pack_bids.R | 49 tests/testthat/test_pack_bids_coverage.R |only tests/testthat/test_plot_bids.R | 8 tests/testthat/test_plot_bids_coverage.R |only tests/testthat/test_plot_internals.R |only tests/testthat/test_preproc_mask.R | 39 tests/testthat/test_preproc_scans_sessions_runs.R | 2 tests/testthat/test_project_ext_helpers.R |only tests/testthat/test_project_extensions.R |only tests/testthat/test_query_files.R |only tests/testthat/test_query_helpers.R |only tests/testthat/test_read_confounds.R | 250 +++ tests/testthat/test_read_preproc_scans.R |only tests/testthat/test_regression_fixes.R |only tests/testthat/test_schema.R |only tests/testthat/test_sidecar.R | 4 tests/testthat/test_summary_compliance.R | 3 tests/testthat/test_tabulars.R |only tools |only vignettes/albers.css | 1039 +++++++++++-- vignettes/albers.js | 321 +++- vignettes/confounds-and-variables.Rmd |only vignettes/derivatives.Rmd |only vignettes/mock-bids.Rmd |only vignettes/quickstart.Rmd | 275 ++- 169 files changed, 7118 insertions(+), 1540 deletions(-)
Title: Five Novel Stochastic Regression Models with Arvind-Distributed
Errors and Effects
Description: Implements the 'Arvind' distribution and five novel stochastic
regression models that replace the traditional Gaussian error assumption
with 'Arvind'-distributed errors. The 'Arvind' distribution is a flexible
single-parameter continuous distribution on the positive real line
characterised by a polynomial numerator with Gaussian-type decay. The
package provides complete distribution functions (darvind(), parvind(),
qarvind(), rarvind()), maximum likelihood estimation via
fit_arvind_mle(), and five model-fitting routines: Random Walk on
Coefficients via fit_rw1(), Time-Varying Coefficient Linear Model via
fit_tvlm(), Simulation-Extrapolation via fit_simex(), Mixed-Effects
Regression via fit_mixed(), and Regime-Switching Hidden Markov Model via
fit_hmm(). Additionally provides Monte Carlo forecasting with prediction
intervals via forecast_arvind(), comprehensive goodness-of-fit
diagnostics (21 metrics and 25 plots) via diagnostics_arvind() and
plot_arvind(), k-fold and rolling-window cro [...truncated...]
Author: Shikhar Tyagi [aut, cre] ,
Arvind Pandey [aut]
Maintainer: Shikhar Tyagi <shikhar1093tyagi@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2026-05-11
Diff between ArvindSt versions 1.0.0 dated 2026-05-11 and 1.1.0 dated 2026-07-06
ArvindSt-1.0.0/ArvindSt/build |only ArvindSt-1.0.0/ArvindSt/vignettes |only ArvindSt-1.1.0/ArvindSt/DESCRIPTION | 15 - ArvindSt-1.1.0/ArvindSt/MD5 | 12 ArvindSt-1.1.0/ArvindSt/R/model_hmm.R | 155 +++++++++--- ArvindSt-1.1.0/ArvindSt/inst/WORDLIST | 1 ArvindSt-1.1.0/ArvindSt/inst/doc/ArvindSt-introduction.html | 4 ArvindSt-1.1.0/ArvindSt/man/fit_hmm.Rd | 8 8 files changed, 147 insertions(+), 48 deletions(-)
Title: Sequential Threshold-Spatial-Quantile Panel Estimation
Description: Implements a sequential panel estimation protocol for regional
economic panels that combines three estimation layers in a fixed order.
The first layer applies a two-way fixed effects baseline. The second
layer applies the panel threshold regression method of Hansen (1999)
<doi:10.1016/S0304-4076(99)00025-1> to identify structural breaks at an
unknown threshold of a moderating variable, with bootstrap inference
following Hansen (2000) <doi:10.1111/1468-0262.00124>. The third layer
applies a spatial Durbin model with an impact decomposition following
LeSage and Pace (2009, ISBN:978-1-4200-6424-7) to quantify direct and
indirect spillover effects. The fourth layer applies the two-step panel
quantile estimator of Canay (2011) <doi:10.1111/j.1368-423X.2011.00349.x>
to document distributional heterogeneity in the outcome. The threshold
identified in the second layer defines a subsample used as structured
input to the fourth layer, and a consistency check evaluates whether t [...truncated...]
Author: Prakash Vhankade [aut, cre]
Maintainer: Prakash Vhankade <prakash.vhankade@gipe.ac.in>
Diff between tsqr versions 0.1.2 dated 2026-06-22 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 MD5 | 39 ++--- NAMESPACE | 9 + R/canay_quantile.R | 243 +++++++++++++++----------------- R/data.R | 40 ++--- R/ptr_hansen.R | 264 +++++++++++++++++------------------ R/sdm_impact.R | 187 +++++++++++------------- R/tsq_consistency.R | 87 ++++------- R/tsq_panel.R | 95 ++++++------ R/tsq_plot.R | 103 +++++-------- build |only man/canay_quantile.Rd | 51 ++---- man/maharashtra_panel.Rd | 38 ++--- man/ptr_hansen.Rd | 49 ++---- man/sdm_impact.Rd | 43 +---- man/tsq_consistency_check.Rd | 24 +-- man/tsq_panel.Rd | 27 +-- man/tsq_plot.Rd | 8 - tests/testthat/test-canay_quantile.R | 25 +-- tests/testthat/test-consistency.R | 18 -- tests/testthat/test-ptr_hansen.R | 55 ++----- 21 files changed, 640 insertions(+), 771 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized linear
models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [aut] ,
Anthony Williams [cph],
Boost developers [cph],
Tom Palmer [aut, cre]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between parglm versions 0.1.10 dated 2026-05-22 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- NEWS.md | 8 +++++++ R/parglm.R | 14 +++++++++++++ build/vignette.rds |binary src/family.cpp | 2 - src/parallel_glm.cpp | 16 ++++++++++++++- src/parallel_qr.cpp | 7 ------ src/parallel_qr.h | 2 - tests/testthat/test_misc.R | 46 +++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 96 insertions(+), 23 deletions(-)
Title: Smooth L0 Penalty Approximations for Gaussian Graphical Models
Description: Provides smooth approximations to the L0 norm penalty for
estimating sparse Gaussian graphical models (GGMs). Network estimation
is performed using the Local Linear Approximation (LLA) framework
(Fan & Li, 2001 <doi:10.1198/016214501753382273>;
Zou & Li, 2008 <doi:10.1214/009053607000000802>) with five penalty
functions: arctangent (Wang & Zhu, 2016 <doi:10.1155/2016/6495417>),
EXP (Wang, Fan, & Zhu, 2018 <doi:10.1007/s10463-016-0588-3>), Gumbel,
Log (Candes, Wakin, & Boyd, 2008 <doi:10.1007/s00041-008-9045-x>),
and Weibull. Adaptive penalty parameters for EXP, Gumbel, and Weibull
are estimated via maximum likelihood, and model selection uses
information criteria including AIC, BIC, and EBIC (Extended BIC).
Simulation functions generate multivariate normal data from GGMs with
stochastic block model or small-world (Watts-Strogatz) network structures.
Author: Alexander Christensen [aut, cre] ,
Jeongwon Choi [ctb] ,
John Fox [cph, ctb] ,
Yves Rosseel [cph, ctb] ,
Alexander Robitzsch [cph, ctb] ,
David Blackman [ctb] ,
Sebastiano Vigna [ctb] ,
John Burkardt [cph, ctb]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between L0ggm versions 0.1.0 dated 2026-05-15 and 0.1.1 dated 2026-07-06
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------ NEWS | 12 ++++++++++ R/edge_confusion.R | 2 - R/network_estimation.R | 51 +++++++++++++++++++++++++++++++-------------- R/polychoric_matrix.R | 2 + R/proxswap_lattice.R | 4 +-- R/simulate_smallworld.R | 5 +--- R/smallworldness.R | 2 - R/weibull_parameters.R | 9 ++++--- man/network_estimation.Rd | 24 +++++++++++++-------- man/polychoric_matrix.Rd | 2 + man/proxswap_lattice.Rd | 4 +-- man/simulate_smallworld.Rd | 5 +--- man/weibull_parameters.Rd | 9 ++++--- 15 files changed, 105 insertions(+), 62 deletions(-)
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dio [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.8.7 dated 2026-05-11 and 0.9.0 dated 2026-07-06
DESCRIPTION | 6 MD5 | 73 +++++----- NAMESPACE | 6 NEWS.md | 3 R/2kyears_temp.R | 6 R/carbon.R | 254 ++++++++++++++++++------------------ R/daily_temp.R | 12 + R/emissions.R | 5 R/fires.R |only R/globalvars.R | 7 R/hurricanes.R | 2 R/icecurves.R | 6 R/instrumental_temp.R | 6 R/methane.R | 6 R/paleo.R | 12 + R/seaice.R | 6 R/sealevel.R | 13 + README.md | 34 +++- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/usinghockeystick.R | 32 ++-- inst/doc/usinghockeystick.html | 44 ++++-- inst/doc/usinghockeystick.qmd | 9 + man/figures/README-carbon-1.png |binary man/figures/README-dailytemp-1.png |binary man/figures/README-fires-1.png |only man/figures/README-fires-2.png |only man/figures/README-grid-1.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/get_fires_area.Rd |only man/get_fires_emissions.Rd |only man/plot_fires_area.Rd |only man/plot_fires_emissions.Rd |only tests/testthat/test-functions.R | 107 +++++++++++++++ vignettes/usinghockeystick.qmd | 9 + 41 files changed, 441 insertions(+), 221 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9.3 dated 2026-07-01 and 1.0.9.4 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/Overview_HTP.html | 4 ++-- inst/tinytest/test_detectSerieOut.R | 3 ++- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Spatial Component Analysis for Spatial Sequencing Data
Description: Spatial components offer tools for dimension reduction and
spatially variable gene detection for high dimensional spatial transcriptomics
data. Construction of a projection onto low-dimensional feature space of
spatially dependent metagenes offers pre-processing to clustering, testing for
spatial variability and denoising of spatial expression patterns. For more
details, see Koehler et al. (2026) <doi:10.1093/bioinformatics/btag052>.
Author: David Koehler [aut, cre]
Maintainer: David Koehler <koehler@imbie.uni-bonn.de>
Diff between SPACO versions 1.0.0 dated 2026-03-31 and 1.0.2 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/EvalFunctions.R | 33 +++++++++++++++++++++++---------- src/Rcpp_Functions.cpp | 3 +++ tests/testthat/test-SCA.R | 13 +++++++++---- 5 files changed, 43 insertions(+), 22 deletions(-)
Title: Assessing Package Risk Metrics
Description: A reliable and validated tool that captures detailed risk metrics
such as R 'CMD' check, test coverage, traceability matrix, documentation, dependencies,
reverse dependencies, suggested dependency analysis, repository data,
and enhanced reporting for R packages that are local or stored
on remote repositories such as GitHub, CRAN, and Bioconductor.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between risk.assessr versions 4.1.0 dated 2026-06-11 and 4.1.1 dated 2026-07-06
DESCRIPTION | 6 MD5 | 82 ++++--- NAMESPACE | 5 NEWS.md | 11 + R/assess_pkg.R | 3 R/create_empty_results.R | 3 R/generate_html_report.R | 65 +++++ R/get_frugal_metrics.R |only R/get_risk_analysis.R | 83 +++++-- R/get_security_vulnerabilities.R |only R/setup_rcmdcheck_args.R | 93 +++++--- R/write_summary_report.R | 29 ++ build/vignette.rds |binary inst/config/risk-definition.json | 31 ++ inst/doc/Popularity_metric.html | 22 -- inst/doc/Pubmed_data.Rmd | 2 inst/doc/Pubmed_data.html | 2 inst/doc/dependency_tree.html | 186 ++++++++++------- inst/doc/security_vulnerabilities.R |only inst/doc/security_vulnerabilities.Rmd |only inst/doc/security_vulnerabilities.html |only inst/report_templates/risk_report_template.Rmd | 50 ++++ inst/report_templates/summary.Rmd | 5 man/convert_number_to_abbreviation.Rd | 2 man/convert_number_to_percent.Rd | 2 man/fetch_osv_data.Rd |only man/generate_vulnerabilities_section.Rd |only man/get_frugal_metrics.Rd |only man/get_risk_analysis.Rd | 6 man/get_security_vulnerabilities.Rd |only man/init_frugal_covr_list.Rd |only man/init_frugal_results.Rd |only man/risk.assessr-package.Rd | 1 man/safe_value.Rd | 2 man/setup_rcmdcheck_args.Rd | 6 tests/testthat/test-assess_pkg.R | 53 ++++ tests/testthat/test-check_suggested_exp_funcs.R | 64 +++-- tests/testthat/test-create_empty_results.R | 2 tests/testthat/test-generate_html_report.R | 68 +++++- tests/testthat/test-get_frugal_metrics.R |only tests/testthat/test-get_github_data.R | 130 +++++++++++ tests/testthat/test-get_risk_analysis.R | 228 +++++++++++++++++++++ tests/testthat/test-get_security_vulnerabilities.R |only tests/testthat/test-parse_dcf_dependencies.R | 22 +- tests/testthat/test-risk_assess_pkg.R | 32 ++ tests/testthat/test-setup_rcmdcheck_args.R | 146 ++++++++----- tests/testthat/test-write_summary_report.R | 113 +++++++++- vignettes/Pubmed_data.Rmd | 2 vignettes/security_vulnerabilities.Rmd |only 49 files changed, 1237 insertions(+), 320 deletions(-)
Title: Bayes Factor Design for Two-Arm Binomial Trials
Description: Design and analysis of one- and two-stage binomial
clinical phase II trials using Bayes factors. Implements Bayes factors
for point-null and directional hypotheses, predictive densities under
different hypotheses, and power and sample size calibration. Both one-arm
trials with only a single treatment arm and two-arm trials with treatment
and control arm are implemented for the one- and two-stage designs.
Author: Riko Kelter [aut, cre]
Maintainer: Riko Kelter <rkelter@uni-koeln.de>
Diff between bfbin2arm versions 0.1.4 dated 2026-06-23 and 0.1.5 dated 2026-07-06
bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.R |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.Rmd |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.html |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.R |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.Rmd |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.html |only bfbin2arm-0.1.4/bfbin2arm/vignettes/bfbin2arm-rope-singlearm-onestage-calibration.Rmd |only bfbin2arm-0.1.4/bfbin2arm/vignettes/bfbin2arm-rope-singlearm-onestage-design.Rmd |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig10.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig11.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig12.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig5.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig6.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig7.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig8.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig9.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario1.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario2.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario3.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario4.png |only bfbin2arm-0.1.5/bfbin2arm/DESCRIPTION | 8 bfbin2arm-0.1.5/bfbin2arm/MD5 | 126 +-- bfbin2arm-0.1.5/bfbin2arm/NAMESPACE | 11 bfbin2arm-0.1.5/bfbin2arm/R/design_singlearm_onestage_bf.R | 2 bfbin2arm-0.1.5/bfbin2arm/R/design_singlearm_twostage_rope.R |only bfbin2arm-0.1.5/bfbin2arm/R/helpers_singlearm_bf.R | 55 + bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_bf_onestage_design.R | 393 ++++++---- bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_rope_onestage.R | 2 bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_rope_twostage.R |only bfbin2arm-0.1.5/bfbin2arm/R/utils_rope_twostage.R |only bfbin2arm-0.1.5/bfbin2arm/build/vignette.rds |binary bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-overview.html | 22 bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.R | 74 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.Rmd | 79 -- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.html | 334 ++++---- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-twostage_bayesian.html | 63 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_frequentist.html | 18 bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_full.html | 73 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_hybrid.html | 250 ++++-- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-twoarm-twostage_Bayesian.html | 243 +++--- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-twoarm_onestage_Bayesian.html | 34 bfbin2arm-0.1.5/bfbin2arm/man/as.data.frame.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/coef.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/design_singlearm_twostage_rope.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/plot.singlearm_onestage_bf_design.Rd | 32 bfbin2arm-0.1.5/bfbin2arm/man/plot.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/print.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/print.summary.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/summary.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/vignettes/bfbin2arm-singlearm-onestage.Rmd | 79 -- bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/algorithm_bayes.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-single_arm_two_stage_bayes_fig3fig.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-more-inf-des-priors-no-ce.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-riociguat-more-informative-design-priors.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-riociguat.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-twoarm-twostage-vignette-fixed-design-ss-reduc.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-twoarm-twostage-vignette-twostage-opt-des-ss-reduc.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig3.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig4.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_flowchart_rootfinding.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_full_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_hybrid_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_hybrid_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig1.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig2.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig3.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig4.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig5.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig6.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-bayes.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-frequentist.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-full.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-hybrid.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm_twostage_freq_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm-onestage-design.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig3.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig4.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig5.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/references.bib | 50 + 82 files changed, 1143 insertions(+), 805 deletions(-)
Title: Coefficient of Variation (CV) with Confidence Intervals (CI)
Description: Provides some easy-to-use functions and classes to calculate
variability measures such as coefficient of variation with confidence
intervals provided with all available methods. References are
'Panichkitkosolkul' (2013) <doi:10.1155/2013/324940>,
'Altunkaynak' & 'Gamgam' (2018) <doi:10.1080/03610918.2018.1435800>,
'Albatineh', 'Kibria', Wilcox & 'Zogheib' (2014) <doi:10.1080/02664763.2013.847405>.
Author: Maani Beigy [aut, cre]
Maintainer: Maani Beigy <manibeygi@gmail.com>
Diff between cvcqv versions 1.0.3 dated 2026-05-21 and 1.0.4 dated 2026-07-06
DESCRIPTION | 10 MD5 | 83 NEWS.md | 24 R/BootCoefQuartVar.R | 314 +- R/BootCoefVar.R | 323 +- R/CoefQuartVar.R | 282 +- R/CoefQuartVarCI.R | 637 ++-- R/CoefVar.R | 136 - R/CoefVarCI.R | 3479 ++++++++++++++------------- R/SampleQuantiles.R | 197 - R/aak_helpers.R |only R/cqv_versatile.R | 644 ++-- R/cv_versatile.R | 2571 +++++++++++-------- R/zzz.R |only README.md | 9 inst/doc/cqv_versatile.R | 655 ++--- inst/doc/cqv_versatile.Rmd | 655 ++--- inst/doc/cqv_versatile.html | 38 inst/doc/cv_versatile.R | 2422 +++++++++--------- inst/doc/cv_versatile.Rmd | 2422 +++++++++--------- inst/doc/cv_versatile.html | 132 - man/CoefVarCI.Rd | 21 man/cv_versatile.Rd | 18 tests/testthat/test_state_BootCoefQuartVar.R | 265 +- tests/testthat/test_state_BootCoefVar.R | 243 - tests/testthat/test_state_CoefQuartVar.R | 337 +- tests/testthat/test_state_CoefQuartVarCI.R | 344 +- tests/testthat/test_state_CoefVar.R | 52 tests/testthat/test_state_CoefVarCI.R | 2131 ++++++++-------- tests/testthat/test_state_R.R | 94 tests/testthat/test_state_SampleQuantiles.R | 79 tests/testthat/test_state_aak_adj.R |only tests/testthat/test_state_aak_als.R |only tests/testthat/test_state_aak_ls.R |only tests/testthat/test_state_alpha.R | 117 tests/testthat/test_state_cqv_versatile.R | 620 ++-- tests/testthat/test_state_cv_versatile.R | 1846 +++++++------- tests/testthat/test_state_digits.R | 425 +-- tests/testthat/test_state_na_rm.R | 168 - tests/testthat/test_state_names.R | 53 tests/testthat/test_state_probs.R | 119 tests/testthat/test_state_type.R | 26 tests/testthat/test_state_x.R | 393 +-- vignettes/cqv_versatile.Rmd | 655 ++--- vignettes/cv_versatile.Rmd | 2422 +++++++++--------- 45 files changed, 13250 insertions(+), 12211 deletions(-)
Title: 'Galaxy' API Implementation
Description: On 'Galaxy' platforms like 'Galaxy Europe' <https://usegalaxy.eu>, many tools and workflows can run directly on a high-performance computer. 'GalaxyR' connects R with 'Galaxy' platforms API <https://usegalaxy.eu/api/docs> and allows credential management, uploading data, invoking workflows or tools, checking their status, and downloading results.
Author: Julian Frey [aut, cre] ,
Zoe Schindler [ctb]
Maintainer: Julian Frey <julian.frey@wwd.uni-freiburg.de>
Diff between GalaxyR versions 0.1.1 dated 2026-02-17 and 0.1.2 dated 2026-07-06
DESCRIPTION | 9 MD5 | 32 +-- NAMESPACE | 5 NEWS.md | 7 R/2025-10-27_JF_R_Galaxy_functions.R | 124 ++++++------ R/2026-01-21_s4_class_methods.R | 349 ++++++++++++++++++++++++++++++++++- README.md | 340 +++++++++++++++++----------------- inst/examples |only man/galaxy_delete_dataset.Rd | 2 man/galaxy_delete_history.Rd |only man/galaxy_get_file_info.Rd | 82 ++++---- man/galaxy_get_tool.Rd | 76 +++---- man/galaxy_get_tool_id.Rd | 108 +++++----- man/galaxy_get_workflow_inputs.Rd | 70 +++---- man/galaxy_history_size.Rd | 86 ++++---- man/galaxy_list_files.Rd |only man/galaxy_list_histories.Rd | 48 ++-- man/galaxy_list_invocations.Rd | 42 ++-- man/galaxy_print_tool_inputs.Rd |only 19 files changed, 879 insertions(+), 501 deletions(-)
Title: Spatial Machine Learning
Description: Implements a spatial extension of the random forest algorithm
(Georganos et al. (2019) <doi:10.1080/10106049.2019.1595177>). Provides
a Geographically Weighted Random Forest regression and a routine to
find the optimal bandwidth (Georganos and Kalogirou (2022)
<doi:10.3390/ijgi11090471>). A lightweight cross-validation helper for
tuning the 'mtry' parameter of a random forest and a generator of
synthetic spatial test data are also included. The package depends on
'ranger' as its single random-forest back-end.
Author: Stamatis Kalogirou [aut, cre, cph] ,
Stefanos Georganos [aut]
Maintainer: Stamatis Kalogirou <stamatis.science@gmail.com>
This is a re-admission after prior archival of version 0.1.7 dated 2024-04-01
Diff between SpatialML versions 0.1.7 dated 2024-04-01 and 1.8.2 dated 2026-07-06
DESCRIPTION | 43 ++- MD5 | 42 ++- NAMESPACE | 18 + NEWS.md |only R/grf.R | 531 +++++++++++++++++++++++++++-------------------- R/grf.bw.R | 172 +++++++++------ R/predict.grf.R | 91 +++++--- R/random.test.data.R | 78 ++++-- R/rf.mtry.optim.R | 184 +++++++++++++--- R/utils-internal.R |only build |only inst |only man/Income.Rd | 95 ++++---- man/SpatialML-package.Rd |only man/grf.Rd | 269 +++++++++++++++-------- man/grf.bw.Rd | 224 +++++++++++-------- man/predict.grf.Rd | 159 ++++++++------ man/random.test.data.Rd | 75 ++++-- man/rf.mtry.optim.Rd | 156 +++++++++---- tests |only vignettes |only 21 files changed, 1370 insertions(+), 767 deletions(-)
Title: Access Data from Marineregions.org: Gazetteer & Data Products
Description: Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.
Author: Michelle Guevara [aut, cre] ,
Salvador Jesus Fernandez Bejarano [aut] ,
Lotte Pohl [aut] ,
Julia Gustavsen [rev],
Muralidhar M.A. [rev],
Sheila M. Saia [rev],
LifeWatch Belgium [fnd]
Maintainer: Michelle Guevara <michelle.guevara@vliz.be>
Diff between mregions2 versions 1.1.2 dated 2025-03-21 and 1.3.0 dated 2026-07-06
DESCRIPTION | 38 LICENSE | 4 MD5 | 252 NAMESPACE | 126 NEWS.md | 4 R/00_gaz_geom.R | 722 +- R/01_gaz_search.R | 1096 +-- R/02_gaz_relations.R | 236 R/03_gaz_sources.R | 454 - R/04_gaz_types.R | 368 - R/05_gaz_wmses.R | 68 R/07_mrp_view.R | 528 - R/08_mrp_get.R | 700 +- R/data.R | 88 R/mregions2-package.R | 172 R/utils-pipe.R | 28 R/utils.R | 410 - README.md | 802 +- build/vignette.rds |binary inst/CITATION | 14 inst/doc/mregions2.R | 332 - inst/doc/mregions2.Rmd | 808 +- inst/doc/mregions2.html | 2521 +++---- inst/mrp_list.csv | 44 inst/mrp_ontology.csv | 750 +- inst/pkgdown.yml | 26 man/MRGID.Rd | 108 man/gaz_geometry.Rd | 128 man/gaz_relations.Rd | 118 man/gaz_rest.Rd | 62 man/gaz_rest_geometries.Rd | 90 man/gaz_rest_names_by_mrgid.Rd | 48 man/gaz_rest_record_by_mrgid.Rd | 62 man/gaz_rest_records_by_lat_long.Rd | 78 man/gaz_rest_records_by_name.Rd | 88 man/gaz_rest_records_by_names.Rd | 76 man/gaz_rest_records_by_source.Rd | 54 man/gaz_rest_records_by_type.Rd | 56 man/gaz_rest_relations_by_mrgid.Rd | 82 man/gaz_rest_source_by_sourceid.Rd | 52 man/gaz_rest_sources.Rd | 68 man/gaz_rest_types.Rd | 62 man/gaz_rest_wmses.Rd | 66 man/gaz_search.Rd | 142 man/gaz_search_by_source.Rd | 88 man/gaz_search_by_type.Rd | 92 man/gaz_sources.Rd | 68 man/gaz_types.Rd | 62 man/mregions2-package.Rd | 74 man/mrp_col_unique.Rd | 86 man/mrp_colnames.Rd | 72 man/mrp_get.Rd | 212 man/mrp_list.Rd | 78 man/mrp_ontology.Rd | 62 man/mrp_view.Rd | 294 man/pipe.Rd | 40 tests/testthat.R | 16 tests/testthat/gaz/api/mrgid/14.R | 866 +- tests/testthat/gaz/api/mrgid/17.json | 32 tests/testthat/gaz/api/mrgid/30666.json | 32 tests/testthat/gaz/api/mrgid/49243.json | 32 tests/testthat/gaz/api/mrgid/8399.json | 32 tests/testthat/gaz/api/mrgid/999999999.R | 16 tests/testthat/gaz/api/rest/1geom/58-c83a0d.R | 34 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-0a955a.R | 18 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-2c70ba.R | 18 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-ae5945.json | 68 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-aff46e.json | 1732 ++--- tests/testthat/gaz/api/rest/byname/Belgie-09a3d0.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-773121.json | 100 tests/testthat/gaz/api/rest/byname/Belgium-965816.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-ef9d65.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-f42f5c.R | 18 tests/testthat/gaz/api/rest/byname/Belgiun-505272.R | 16 tests/testthat/gaz/api/rest/byname/Belgiun-773121.json | 132 tests/testthat/gaz/api/rest/byname/Belgiun-965816.R | 16 tests/testthat/gaz/api/rest/byname/test_like_is_false-bd74f7.R | 18 tests/testthat/gaz/api/rest/byname/test_not_found-773121.R | 18 tests/testthat/gaz/api/rest/bynames/true/true/Belgique/Framce.json | 172 tests/testthat/gaz/api/rest/bysource/Belgian+Sea+Fisheries.json | 964 +- tests/testthat/gaz/api/rest/bysource/This+is+not+a+source.R | 16 tests/testthat/gaz/api/rest/bysource/Victor+Scarabino.json | 10 tests/testthat/gaz/api/rest/bytype/diving+spot-0cae27.R | 16 tests/testthat/gaz/api/rest/bytype/diving+spot-95f866.json | 580 - tests/testthat/gaz/api/rest/bytype/this+is+not+a+type-95f866.R | 16 tests/testthat/gaz/api/rest/bytype/wreck-0cae27.R | 16 tests/testthat/gaz/api/rest/bytype/wreck-95f866.json | 164 tests/testthat/gaz/api/rest/geom/30666.R | 18 tests/testthat/gaz/api/rest/geom/4280.R | 64 tests/testthat/gaz/api/rest/geom/49243.R | 46 tests/testthat/gaz/api/rest/geom/58.R | 50 tests/testthat/gaz/api/rest/relations/49243-8ef451.R | 18 tests/testthat/gaz/api/rest/relations/49243-e78ab2.json | 36 tests/testthat/gaz/api/rest/sourceid/53.json | 12 tests/testthat/gaz/api/rest/sourceid/77.json | 12 tests/testthat/gaz/api/rest/sources/-0cae27.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-2642ef.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-5fcbb3.R | 16 tests/testthat/gaz/api/rest/sources/-95f866.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-b71d9d.json | 234 tests/testthat/gaz/api/rest/sources/-e6f0e7.json | 1004 +-- tests/testthat/gaz/api/rest/toname/3293.json | 8 tests/testthat/gaz/api/rest/toname/49243.json | 6 tests/testthat/gaz/api/rest/toname/999999999.R | 18 tests/testthat/gaz/api/rest/types.json | 3254 +++++----- tests/testthat/gaz/api/rest/wms/3293.json | 20 tests/testthat/prod/fail/geo/eez-13c29b58.zip | 10 tests/testthat/prod/fail/geo/eez-419caace.zip | 12 tests/testthat/prod/fail/geo/eez-58a78801.zip | 10 tests/testthat/prod/fail/geo/eez-713ad0ad.zip | 12 tests/testthat/prod/fail/geo/ows-38243e.R | 12 tests/testthat/prod/fail/geo/ows-4cb98d.R | 12 tests/testthat/prod/fail/geo/ows-85ca5a.R | 12 tests/testthat/prod/fail/geo/ows-8d68a6.R | 12 tests/testthat/prod/fail/geo/ows-9545b5.R | 12 tests/testthat/prod/ok/geo/ows-10d21b.R | 12 tests/testthat/prod/ok/geo/ows-1af2a2.R | 12 tests/testthat/prod/ok/geo/ows-62a7cf.R | 12 tests/testthat/prod/ok/geo/ows-b0edf4.R | 12 tests/testthat/prod/ok/geo/ows-bca3eb.R | 12 tests/testthat/prod/ok/geo/ows-db8988.R | 940 +- tests/testthat/setup.R | 52 tests/testthat/test-gaz.R | 559 - tests/testthat/test-mrp_view_helpers.R | 46 tests/testthat/test-prod.R | 709 +- tests/testthat/test-utils.R | 274 vignettes/mregions2.Rmd | 808 +- 127 files changed, 14940 insertions(+), 14915 deletions(-)
Title: Read Spectrometric Data and Metadata
Description: Parse various reflectance/transmittance/absorbance spectra file
formats to extract spectral data and metadata, as described in Gruson, White
& Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import
files from 'Avantes' <https://www.avantes.com/>, 'CRAIC'
<https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight'
<https://www.oceanoptics.com/> brands.
Author: Hugo Gruson [cre, aut, cph] ,
Rafael Maia [aut, cph] ,
Thomas White [aut, cph] ,
Kotya Karapetyan [ctb, cph] )
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between lightr versions 2.0.0 dated 2026-04-11 and 2.1.0 dated 2026-07-06
DESCRIPTION | 8 ++-- MD5 | 48 ++++++++++++------------ NEWS.md | 15 +++++++ R/compute_processed.R | 2 - R/convert_tocsv.R | 6 ++- R/deprecated.R | 6 ++- R/get_metadata.R | 6 ++- R/get_spec.R | 25 +++++++++++- R/parse_avantes_binary.R | 17 +++----- R/parse_csv.R | 2 - R/parse_generic.R | 3 - R/parse_jdx.R | 75 +++++++++++--------------------------- R/parse_oceanoptics_converted.R | 44 +++++++++++++++------- R/utils.R | 2 - inst/doc/batch_import.html | 4 +- inst/doc/renormalise.html | 7 +-- inst/doc/true_example.html | 4 +- man/lightr-package.Rd | 3 + man/lr_convert_tocsv.Rd | 23 +++++++++++ man/lr_get_metadata.Rd | 23 +++++++++++ man/lr_get_spec.Rd | 23 +++++++++++ man/lr_parse_csv.Rd | 2 - tests/testthat/_snaps/metadata.md | 14 +++++++ tests/testthat/test_dispatch.R | 5 ++ tests/testthat/test_metadata.R | 15 +++++++ 25 files changed, 255 insertions(+), 127 deletions(-)
Title: Scale Space Multiresolution Analysis of Random Signals
Description: A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features.
mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales.
To infer which of the captured features are credible, Bayesian analysis is used.
The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction.
(2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found.
(3) Posterior credibility analysis of the differences of smooths created.
The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011> and extended in Flury, Gerber, Schmid and Furrer (2021) <DOI:10.1016/j.spasta.2020.100483>.
Author: Thimo Schuster [aut],
Roman Flury [cre, aut],
Leena Pasanen [ctb],
Reinhard Furrer [ctb]
Maintainer: Roman Flury <fluryro@gmail.com>
Diff between mrbsizeR versions 1.3 dated 2024-02-13 and 1.3.1 dated 2026-07-06
mrbsizeR-1.3.1/mrbsizeR/DESCRIPTION | 16 mrbsizeR-1.3.1/mrbsizeR/MD5 | 74 mrbsizeR-1.3.1/mrbsizeR/NEWS.md | 87 - mrbsizeR-1.3.1/mrbsizeR/R/RcppExports.R | 94 - mrbsizeR-1.3.1/mrbsizeR/R/mrbsizeR.R | 211 +- mrbsizeR-1.3.1/mrbsizeR/build/vignette.rds |binary mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.R | 320 +-- mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.Rmd | 982 ++++++------ mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.pdf |binary mrbsizeR-1.3.1/mrbsizeR/man/CImap.Rd | 82 - mrbsizeR-1.3.1/mrbsizeR/man/HPWmap.Rd | 90 - mrbsizeR-1.3.1/mrbsizeR/man/MinLambda.Rd | 148 - mrbsizeR-1.3.1/mrbsizeR/man/TaperingPlot.Rd | 136 - mrbsizeR-1.3.1/mrbsizeR/man/dctMatrix.Rd | 74 mrbsizeR-1.3.1/mrbsizeR/man/dftMatrix.Rd | 70 mrbsizeR-1.3.1/mrbsizeR/man/eigenLaplace.Rd | 50 mrbsizeR-1.3.1/mrbsizeR/man/eigenQsphere.Rd | 70 mrbsizeR-1.3.1/mrbsizeR/man/fftshift.Rd | 94 - mrbsizeR-1.3.1/mrbsizeR/man/ifftshift.Rd | 88 - mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeR-package.Rd |only mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeRgrid.Rd | 166 +- mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeRsphere.Rd | 136 - mrbsizeR-1.3.1/mrbsizeR/man/plot.CImapGrid.Rd | 150 - mrbsizeR-1.3.1/mrbsizeR/man/plot.CImapSphere.Rd | 152 - mrbsizeR-1.3.1/mrbsizeR/man/plot.HPWmapGrid.Rd | 164 +- mrbsizeR-1.3.1/mrbsizeR/man/plot.HPWmapSphere.Rd | 168 +- mrbsizeR-1.3.1/mrbsizeR/man/plot.minLambda.Rd | 76 mrbsizeR-1.3.1/mrbsizeR/man/plot.smMeanGrid.Rd | 124 - mrbsizeR-1.3.1/mrbsizeR/man/plot.smMeanSphere.Rd | 128 - mrbsizeR-1.3.1/mrbsizeR/man/rmvtDCT.Rd | 100 - mrbsizeR-1.3.1/mrbsizeR/man/tridiag.Rd | 62 mrbsizeR-1.3.1/mrbsizeR/man/turnmat.Rd | 52 mrbsizeR-1.3.1/mrbsizeR/src/rcpp_helper.cpp | 4 mrbsizeR-1.3.1/mrbsizeR/tests/testthat.R | 8 mrbsizeR-1.3.1/mrbsizeR/tests/testthat/test-rcpp.R | 410 ++--- mrbsizeR-1.3.1/mrbsizeR/tests/testthat/test-trigonometric.R | 22 mrbsizeR-1.3.1/mrbsizeR/vignettes/bibliography.bib | 147 - mrbsizeR-1.3.1/mrbsizeR/vignettes/mrbsizeR.Rmd | 982 ++++++------ mrbsizeR-1.3/mrbsizeR/man/mrbsizeR.Rd |only 39 files changed, 2871 insertions(+), 2866 deletions(-)
Title: Kernel-Based Regularized Least Squares
Description: Implements Kernel-based Regularized Least Squares (KRLS), a
machine learning method to fit multidimensional functions y = f(x) for
regression and classification problems without relying on linearity or
additivity assumptions. KRLS finds the best fitting function by
minimizing the squared loss of a Tikhonov regularization problem,
using Gaussian kernels as radial basis functions. For further details
see Hainmueller and Hazlett (2014, <doi:10.1093/pan/mpt019>).
Author: Jens Hainmueller [aut, cre],
Chad Hazlett [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between KRLS versions 1.7-0 dated 2026-06-05 and 1.7-1 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 18 ++++++++++++++++++ inst/doc/krls-nystrom-scaling.html | 8 ++++---- inst/doc/krls-quickstart.html | 2 +- tests/testthat/test-krls.R | 12 +++++++++++- 6 files changed, 43 insertions(+), 15 deletions(-)
Title: VCG Sampling using Energy-Based Covariate Balancing
Description: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing. The package offers visualization tools to assess covariate balance and includes a permutation test to evaluate the statistical significance of observed deviations.
Author: Andreas Schulz [aut, cre] ,
Sanofi [cph, fnd]
Maintainer: Andreas Schulz <andreas.schulz2@sanofi.com>
Diff between eVCGsampler versions 1.0.0 dated 2026-03-10 and 1.1.0 dated 2026-07-06
DESCRIPTION | 8 +- MD5 | 21 +++++- man/combine_data.Rd | 78 ++++++++++++------------- man/combine_variables.Rd | 98 +++++++++++++++---------------- man/find_outliers.Rd | 144 +++++++++++++++++++++++------------------------ man/multiSampler.Rd | 104 ++++++++++++++++----------------- tests |only 7 files changed, 232 insertions(+), 221 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.1.1 dated 2026-06-22 and 0.1.2 dated 2026-07-06
DESCRIPTION | 26 ++++---- MD5 | 47 +++++++++++---- NAMESPACE | 14 ++++ R/latex-output.R |only R/mixed-models.R |only R/paper.R | 48 +++++++++++++-- R/reporting.R | 108 ++++++++++++++++++++--------------- R/utils.R | 112 ++++++++++++++++++++++++++++++++++++- R/zzz-aliases.R | 12 +++ build/vignette.rds |binary inst/WORDLIST | 22 +++++++ inst/colleyRstats.sty |only inst/doc/choosing-a-test.R |only inst/doc/choosing-a-test.Rmd |only inst/doc/choosing-a-test.html |only inst/doc/getting-started.html | 6 - inst/doc/overleaf.R |only inst/doc/overleaf.Rmd |only inst/doc/overleaf.html |only man/classify_outcome.Rd |only man/define_result_macro.Rd |only man/emit_name_macros.Rd |only man/emit_overleaf.Rd |only man/expand_latex_macros.Rd |only man/latex_escape.Rd |only man/latex_preamble.Rd | 5 + man/recommend_test.Rd |only man/reportArtConTable.Rd | 6 + man/reportCLMM.Rd |only man/reportDunnTestTable.Rd | 7 ++ man/reportGLMM.Rd |only man/use_colleyrstats_sty.Rd |only tests/testthat/test-latex-output.R |only tests/testthat/test-mixed-models.R |only vignettes/choosing-a-test.Rmd |only vignettes/overleaf.Rmd |only 36 files changed, 326 insertions(+), 87 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 2.0.2 dated 2026-06-08 and 2.0.3 dated 2026-07-06
BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_eigen_pseudoinv.R |only BigDataStatMeth-2.0.3/BigDataStatMeth/DESCRIPTION | 23 ++--- BigDataStatMeth-2.0.3/BigDataStatMeth/MD5 | 45 ++++------ BigDataStatMeth-2.0.3/BigDataStatMeth/NAMESPACE | 1 BigDataStatMeth-2.0.3/BigDataStatMeth/NEWS.md | 31 ++++++ BigDataStatMeth-2.0.3/BigDataStatMeth/R/HDF5Matrix_op_factorizations.R | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/R/RcppExports.R | 28 +++--- BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_decompositions.R | 19 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_factorizations.R | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_pseudoinverse.R | 44 +++++++-- BigDataStatMeth-2.0.3/BigDataStatMeth/README.md | 4 BigDataStatMeth-2.0.3/BigDataStatMeth/inst/doc/BigDataStatMeth.html | 28 +++--- BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixCorrelation.hpp | 6 - BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixPseudoinverse.hpp | 16 ++- BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixQR.hpp | 21 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/man/bdpseudoinv_hdf5.Rd | 25 ++--- BigDataStatMeth-2.0.3/BigDataStatMeth/man/chol.HDF5Matrix.Rd | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/man/prcomp.HDF5Matrix.Rd | 19 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/man/pseudoinverse.Rd | 40 +++++++- BigDataStatMeth-2.0.3/BigDataStatMeth/src/hdf5_pseudoinverse.cpp | 44 +++++---- BigDataStatMeth-2.0.3/BigDataStatMeth/src/hdf5_r6_cholesky.cpp | 12 +- BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_crossprod.cpp | 14 ++- BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_tcrossprod.cpp | 4 BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_weightprod.cpp | 45 ++++++---- 24 files changed, 331 insertions(+), 162 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Factor and Autoregressive Models for Tensor Time Series
Description: Factor and autoregressive models for matrix and tensor valued time series. We provide functions for estimation, simulation and prediction. The models are discussed in
Li et al (2021) <doi:10.48550/arXiv.2110.00928>, Chen et al (2020) <DOI:10.1080/01621459.2021.1912757>,
Chen et al (2020) <DOI:10.1016/j.jeconom.2020.07.015>, and Xiao et al (2020) <doi:10.48550/arXiv.2006.02611>.
Author: Zebang Li [aut, cre],
Ruofan Yu [aut],
Rong Chen [aut],
Yuefeng Han [aut],
Han Xiao [aut],
Dan Yang [aut]
Maintainer: Zebang Li <zebangmail@gmail.com>
Diff between tensorTS versions 1.0.2 dated 2024-04-27 and 1.0.3 dated 2026-07-06
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Monte Carlo and Bayesian Stop-Signal Reaction Time Estimation
Description: Estimates stop-signal reaction time (SSRT) in the stop-signal
task using the integration and mean methods described by Verbruggen and
colleagues (2019) <doi:10.7554/eLife.46323>. In addition to point
estimates, the package provides Monte Carlo tools (nonparametric bootstrap
confidence intervals, parametric ex-Gaussian simulation, minimum-trial-count
and power analysis, and sensitivity analysis under violations of the
horse-race assumptions) and Bayesian estimation via 'Stan', including
single-subject and hierarchical ex-Gaussian horse-race models with an
optional trigger-failure parameter following Matzke and colleagues (2013)
<doi:10.1037/a0030543>, posterior inhibition functions, and posterior
predictive checks. The Bayesian layer works with either the 'cmdstanr' or
'rstan' backend.
Author: Anton Leontyev [aut, cre]
Maintainer: Anton Leontyev <antonleontyev@missouristate.edu>
Diff between SSRTcalc versions 0.3.3 dated 2021-04-19 and 2.1.1 dated 2026-07-06
SSRTcalc-0.3.3/SSRTcalc/R/adaptive-data.R |only SSRTcalc-0.3.3/SSRTcalc/R/fixed-data.R |only SSRTcalc-0.3.3/SSRTcalc/R/integration_adaptiveSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/integration_fixedSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/mean_adaptiveSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/mean_fixedSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/plotInhFunc.R |only SSRTcalc-0.3.3/SSRTcalc/data/adaptive.RData |only SSRTcalc-0.3.3/SSRTcalc/data/fixed.RData |only SSRTcalc-0.3.3/SSRTcalc/man/plotInhFunc.Rd |only SSRTcalc-2.1.1/SSRTcalc/DESCRIPTION | 46 +++- SSRTcalc-2.1.1/SSRTcalc/MD5 | 60 ++++-- SSRTcalc-2.1.1/SSRTcalc/NAMESPACE | 48 ++++- SSRTcalc-2.1.1/SSRTcalc/NEWS.md | 126 ++++++++----- SSRTcalc-2.1.1/SSRTcalc/R/SSRTcalc-package.R |only SSRTcalc-2.1.1/SSRTcalc/R/core_ssrt.R |only SSRTcalc-2.1.1/SSRTcalc/R/data.R |only SSRTcalc-2.1.1/SSRTcalc/R/helpers.R |only SSRTcalc-2.1.1/SSRTcalc/R/mc_extensions.R |only SSRTcalc-2.1.1/SSRTcalc/R/stan_extensions.R |only SSRTcalc-2.1.1/SSRTcalc/README.md | 161 +++++++++++++---- SSRTcalc-2.1.1/SSRTcalc/build/partial.rdb |binary SSRTcalc-2.1.1/SSRTcalc/data/adaptive.rda |only SSRTcalc-2.1.1/SSRTcalc/data/fixed.rda |only SSRTcalc-2.1.1/SSRTcalc/inst |only SSRTcalc-2.1.1/SSRTcalc/man/SSRTcalc-package.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/adaptive.Rd | 42 ++-- SSRTcalc-2.1.1/SSRTcalc/man/fixed.Rd | 98 ++++++---- SSRTcalc-2.1.1/SSRTcalc/man/integration_adaptiveSSD.Rd | 47 +++- SSRTcalc-2.1.1/SSRTcalc/man/integration_fixedSSD.Rd | 44 +++- SSRTcalc-2.1.1/SSRTcalc/man/mean_adaptiveSSD.Rd | 39 ++-- SSRTcalc-2.1.1/SSRTcalc/man/mean_fixedSSD.Rd | 39 ++-- SSRTcalc-2.1.1/SSRTcalc/man/ranef.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ranef.ssrt_stan.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/run_all_mc.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_boot.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_power.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_robustness.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_simulate.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_compare.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_inhibition_fn.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_loo.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_pp_check.Rd |only SSRTcalc-2.1.1/SSRTcalc/tests |only 45 files changed, 533 insertions(+), 217 deletions(-)
Title: An Interface to IMF (International Monetary Fund) Data
Description: Provides low-level access to the International Monetary Fund
Statistical Data and Metadata eXchange ('SDMX') 3.0 API, available at
<https://data.imf.org/>, and a concise workflow for discovering datasets,
inspecting dimensions, and downloading observations as tidy data frames.
Author: Pedro Baltazar [aut, cre, cph]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between imf.data versions 0.1.7 dated 2024-09-14 and 0.2.0 dated 2026-07-06
imf.data-0.1.7/imf.data/R/database.R |only imf.data-0.1.7/imf.data/R/methods.R |only imf.data-0.1.7/imf.data/R/package.R |only imf.data-0.1.7/imf.data/R/request.R |only imf.data-0.1.7/imf.data/R/settings.R |only imf.data-0.1.7/imf.data/R/zzz.R |only imf.data-0.1.7/imf.data/man/imf.data-package.Rd |only imf.data-0.1.7/imf.data/man/load_datasets.Rd |only imf.data-0.1.7/imf.data/man/mt_compact_data.Rd |only imf.data-0.1.7/imf.data/man/mt_data_structure.Rd |only imf.data-0.1.7/imf.data/man/mt_dataflow.Rd |only imf.data-0.2.0/imf.data/DESCRIPTION | 34 ++++----- imf.data-0.2.0/imf.data/LICENSE | 2 imf.data-0.2.0/imf.data/MD5 | 70 ++++++++++++++----- imf.data-0.2.0/imf.data/NAMESPACE | 16 ++-- imf.data-0.2.0/imf.data/NEWS.md | 5 + imf.data-0.2.0/imf.data/R/imf_api.R |only imf.data-0.2.0/imf.data/R/sdmx_api.R |only imf.data-0.2.0/imf.data/README.md |only imf.data-0.2.0/imf.data/build |only imf.data-0.2.0/imf.data/inst |only imf.data-0.2.0/imf.data/man/get_data.Rd |only imf.data-0.2.0/imf.data/man/list_datasets.Rd | 20 +++-- imf.data-0.2.0/imf.data/man/list_dimension_values.Rd |only imf.data-0.2.0/imf.data/man/list_dimensions.Rd |only imf.data-0.2.0/imf.data/man/sdmx_api.Rd |only imf.data-0.2.0/imf.data/man/sdmx_availability.Rd |only imf.data-0.2.0/imf.data/man/sdmx_data.Rd |only imf.data-0.2.0/imf.data/man/sdmx_metadata.Rd |only imf.data-0.2.0/imf.data/man/sdmx_structure.Rd |only imf.data-0.2.0/imf.data/man/set_imf_proxy.Rd |only imf.data-0.2.0/imf.data/tests |only imf.data-0.2.0/imf.data/vignettes |only 33 files changed, 96 insertions(+), 51 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, and KCF format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.6.1 dated 2026-06-20 and 0.7.0 dated 2026-07-06
DESCRIPTION | 16 MD5 | 65 +-- NAMESPACE | 4 NEWS.md | 24 + R/auto-parse.R | 34 + R/parse-glycam-iupac.R |only R/parse-glycoct.R | 629 ++++++++++++++++++++++++++++-- R/parse-iupac-compact.R |only R/parse-iupac-condensed.R | 10 R/parse-iupac-extended.R | 10 R/parse-iupac-short.R | 10 R/parse-kcf.R |only R/parse-linear-code.R | 10 R/parse-linucs.R |only R/parse-pglyco.R | 10 R/parse-strucgp.R | 10 R/parse-wurcs.R | 263 +++++++++++- R/struc-parser-wrapper.R | 35 + man/auto_parse.Rd | 8 man/parse_glycam_iupac.Rd |only man/parse_glycoct.Rd | 7 man/parse_iupac_compact.Rd |only man/parse_iupac_condensed.Rd | 4 man/parse_iupac_extended.Rd | 4 man/parse_iupac_short.Rd | 4 man/parse_kcf.Rd |only man/parse_linear_code.Rd | 4 man/parse_linucs.Rd |only man/parse_pglyco_struc.Rd | 4 man/parse_strucgp_struc.Rd | 4 man/parse_wurcs.Rd | 6 tests/testthat/test-auto-parse.R | 51 ++ tests/testthat/test-na-support.R | 13 tests/testthat/test-parse-glycam-iupac.R |only tests/testthat/test-parse-glycoct.R | 297 ++++++++++++++ tests/testthat/test-parse-iupac-compact.R |only tests/testthat/test-parse-kcf.R |only tests/testthat/test-parse-linucs.R |only tests/testthat/test-parse-wurcs.R | 153 +++++++ tests/testthat/test-progress.R |only 40 files changed, 1576 insertions(+), 113 deletions(-)
Title: A Collection of Database, Data Structure, Visualization, and
Utility Functions for R
Description: The caroline R library contains dozens of functions useful
for: database migration (dbWriteTable2), database style joins &
aggregation (nerge, groupBy, & bestBy), data structure
conversion (nv, tab2df), legend table making (sstable & leghead),
automatic legend positioning for scatter and box plots (legend.position),
plot annotation (labsegs & mvlabs), data visualization
(pies & raPlot), character string manipulation (m & pad),
file I/O (write.delim), batch scripting, data exploration, and more.
The package's greatest contributions stem from its database style merge,
aggregation and interface functions as well as in it's extensive
use and propagation of row, column and vector names in most functions.
The latest additions are plotting functions (confound.grid & sparge)
that intake a dataframe & formulas to visually resolve variable confounding.
Author: David Schruth [aut, cre]
Maintainer: David Schruth <code@anthropoidea.org>
Diff between caroline versions 1.0.0 dated 2026-06-16 and 1.1.1 dated 2026-07-06
DESCRIPTION | 18 +- MD5 | 55 ++++-- NAMESPACE | 5 NEWS.md |only R/aggregate.R | 62 ------- R/convert.R | 48 ++++- R/database.R | 84 ++++++++++ R/models.R | 11 + R/plot.sparge.R | 437 ++++++++++++++++++++++++++++++++++++++--------------- R/plots.R | 19 +- R/string.R | 4 R/zzz.R |only README.md |only build |only inst |only man/bestBy.Rd | 12 + man/heatmatrix.Rd | 7 man/nerge.Rd | 47 ++++- man/nv.Rd | 12 + man/nv2df.Rd |only man/pct.Rd | 10 - man/plot.sparge.Rd | 135 ++++++++++++---- man/tab2df.Rd | 3 vignettes |only 24 files changed, 692 insertions(+), 277 deletions(-)