Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.52 dated 2025-04-02 and 0.53 dated 2025-08-18
xfun-0.52/xfun/NEWS.md |only xfun-0.53/xfun/DESCRIPTION | 17 +++++++++-------- xfun-0.53/xfun/MD5 | 16 ++++++++-------- xfun-0.53/xfun/R/cache.R | 24 ++++++++++++++++-------- xfun-0.53/xfun/R/record.R | 16 ++++++++++++---- xfun-0.53/xfun/build/vignette.rds |binary xfun-0.53/xfun/inst/NEWS.Rd |only xfun-0.53/xfun/inst/doc/xfun.html | 22 ++++++++++++---------- xfun-0.53/xfun/man/cache_rds.Rd | 6 ++++-- xfun-0.53/xfun/tests/test-cran/test-record.R | 13 +++++++++++++ 10 files changed, 74 insertions(+), 40 deletions(-)
Title: 'AWS S3' Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple
Storage Service ('S3') 'REST' 'API' <https://aws.amazon.com/s3/>.
Author: Thomas J. Leeper [aut] ,
Boettiger Carl [ctb],
Andrew Martin [ctb],
Mark Thompson [ctb],
Tyler Hunt [ctb],
Steven Akins [ctb],
Bao Nguyen [ctb],
Thierry Onkelinx [ctb],
Andrii Degtiarov [ctb],
Dhruv Aggarwal [ctb],
Alyssa Columbus [ctb],
Simon Urbane [...truncated...]
Maintainer: Simon Urbanek <simon.urbanek@R-project.org>
Diff between aws.s3 versions 0.3.21 dated 2020-04-07 and 0.3.22 dated 2025-08-18
aws.s3-0.3.21/aws.s3/inst/CITATION |only aws.s3-0.3.22/aws.s3/DESCRIPTION | 10 - aws.s3-0.3.22/aws.s3/MD5 | 119 ++++++------- aws.s3-0.3.22/aws.s3/NEWS.md | 33 +++ aws.s3-0.3.22/aws.s3/R/accelerate.R | 4 aws.s3-0.3.22/aws.s3/R/acl.R | 4 aws.s3-0.3.22/aws.s3/R/bucket_exists.R | 2 aws.s3-0.3.22/aws.s3/R/bucketlist.R | 2 aws.s3-0.3.22/aws.s3/R/copy_bucket.R | 2 aws.s3-0.3.22/aws.s3/R/cors.R | 6 aws.s3-0.3.22/aws.s3/R/delete_bucket.R | 2 aws.s3-0.3.22/aws.s3/R/delete_object.R | 2 aws.s3-0.3.22/aws.s3/R/encryption.R | 6 aws.s3-0.3.22/aws.s3/R/get_bucket.R | 10 - aws.s3-0.3.22/aws.s3/R/get_location.R | 2 aws.s3-0.3.22/aws.s3/R/get_object.R | 12 - aws.s3-0.3.22/aws.s3/R/head_object.R | 2 aws.s3-0.3.22/aws.s3/R/lifecycle.R | 8 aws.s3-0.3.22/aws.s3/R/notifications.R | 6 aws.s3-0.3.22/aws.s3/R/policy.R | 4 aws.s3-0.3.22/aws.s3/R/print.R | 2 aws.s3-0.3.22/aws.s3/R/put_bucket.R | 2 aws.s3-0.3.22/aws.s3/R/put_object.R | 247 +++++++++++++++++++---------- aws.s3-0.3.22/aws.s3/R/replication.R | 8 aws.s3-0.3.22/aws.s3/R/requestPayment.R | 2 aws.s3-0.3.22/aws.s3/R/s3HTTP.R | 25 +- aws.s3-0.3.22/aws.s3/R/s3save.R | 2 aws.s3-0.3.22/aws.s3/R/s3sync.R | 2 aws.s3-0.3.22/aws.s3/R/tagging.R | 6 aws.s3-0.3.22/aws.s3/R/utils.R | 14 + aws.s3-0.3.22/aws.s3/R/versioning.R | 6 aws.s3-0.3.22/aws.s3/R/website.R | 8 aws.s3-0.3.22/aws.s3/README.md | 10 - aws.s3-0.3.22/aws.s3/man/acceleration.Rd | 4 aws.s3-0.3.22/aws.s3/man/acl.Rd | 6 aws.s3-0.3.22/aws.s3/man/bucket_exists.Rd | 2 aws.s3-0.3.22/aws.s3/man/bucketlist.Rd | 2 aws.s3-0.3.22/aws.s3/man/copyobject.Rd | 2 aws.s3-0.3.22/aws.s3/man/cors.Rd | 6 aws.s3-0.3.22/aws.s3/man/delete_bucket.Rd | 2 aws.s3-0.3.22/aws.s3/man/delete_object.Rd | 2 aws.s3-0.3.22/aws.s3/man/encryption.Rd | 6 aws.s3-0.3.22/aws.s3/man/get_bucket.Rd | 2 aws.s3-0.3.22/aws.s3/man/get_location.Rd | 2 aws.s3-0.3.22/aws.s3/man/get_object.Rd | 10 - aws.s3-0.3.22/aws.s3/man/get_torrent.Rd | 2 aws.s3-0.3.22/aws.s3/man/get_uploads.Rd | 2 aws.s3-0.3.22/aws.s3/man/head_object.Rd | 2 aws.s3-0.3.22/aws.s3/man/lifecycle.Rd | 8 aws.s3-0.3.22/aws.s3/man/notifications.Rd | 6 aws.s3-0.3.22/aws.s3/man/policy.Rd | 4 aws.s3-0.3.22/aws.s3/man/put_bucket.Rd | 4 aws.s3-0.3.22/aws.s3/man/put_object.Rd | 40 ++-- aws.s3-0.3.22/aws.s3/man/replication.Rd | 8 aws.s3-0.3.22/aws.s3/man/requestpayment.Rd | 2 aws.s3-0.3.22/aws.s3/man/s3HTTP.Rd | 2 aws.s3-0.3.22/aws.s3/man/s3save.Rd | 2 aws.s3-0.3.22/aws.s3/man/sync.Rd | 2 aws.s3-0.3.22/aws.s3/man/tagging.Rd | 6 aws.s3-0.3.22/aws.s3/man/versions.Rd | 6 aws.s3-0.3.22/aws.s3/man/website.Rd | 8 61 files changed, 433 insertions(+), 287 deletions(-)
Title: A Framework for Reproducible and Collaborative Data Science
Description: Provides a workflow for your analysis projects by combining
literate programming ('knitr' and 'rmarkdown') and version control
('Git', via 'git2r') to generate a website containing time-stamped,
versioned, and documented results.
Author: John Blischak [aut, cre] ,
Peter Carbonetto [aut] ,
Matthew Stephens [aut] ,
Luke Zappia [ctb] ,
Pierre Formont [ctb] ,
Tim Trice [ctb] ,
Jiaxiang Li [ctb] to create table of contents),
Michael J. Kane [ctb] ,
Anh Tran [ctb] ,
Sydney Purdue [ctb] e [...truncated...]
Maintainer: John Blischak <jdblischak@gmail.com>
Diff between workflowr versions 1.7.1 dated 2023-08-22 and 1.7.2 dated 2025-08-18
DESCRIPTION | 28 LICENSE | 4 MD5 | 362 - NAMESPACE | 82 NEWS.md | 2259 ++++---- R/assertions.R | 350 - R/git.R | 1104 ++-- R/git2r.R | 80 R/infrastructure.R | 460 - R/report.R | 1778 +++--- R/utility.R | 944 +-- R/wflow_build.R | 1096 ++-- R/wflow_git_commit.R | 534 +- R/wflow_git_config.R | 356 - R/wflow_git_pull.R | 686 +- R/wflow_git_push.R | 564 +- R/wflow_git_remote.R | 374 - R/wflow_html.R | 1124 ++-- R/wflow_open.R | 520 - R/wflow_options.R | 226 R/wflow_paths.R | 182 R/wflow_publish.R | 598 +- R/wflow_publish_addin.R | 178 R/wflow_quickstart.R | 590 +- R/wflow_remove.R | 436 - R/wflow_rename.R | 478 - R/wflow_rename_proj.R | 350 - R/wflow_run.R | 148 R/wflow_site.R | 260 R/wflow_start.R | 1044 ++-- R/wflow_start_rstudio.R | 98 R/wflow_status.R | 632 +- R/wflow_toc.R | 270 - R/wflow_use_github.R | 872 +-- R/wflow_use_gitlab.R | 514 - R/wflow_view.R | 422 - R/zzz.R | 314 - build/vignette.rds |binary inst/CITATION | 42 inst/WORDLIST | 285 - inst/doc/wflow-01-getting-started.R | 242 inst/doc/wflow-01-getting-started.Rmd | 1134 ++-- inst/doc/wflow-01-getting-started.html | 1878 ++++--- inst/doc/wflow-02-customization.R | 40 inst/doc/wflow-02-customization.Rmd | 406 - inst/doc/wflow-02-customization.html | 1012 ++- inst/doc/wflow-03-migrating.R | 66 inst/doc/wflow-03-migrating.Rmd | 322 - inst/doc/wflow-03-migrating.html | 932 +-- inst/doc/wflow-04-how-it-works.Rmd | 308 - inst/doc/wflow-04-how-it-works.html | 754 +- inst/doc/wflow-05-faq.R | 74 inst/doc/wflow-05-faq.Rmd | 1191 ++-- inst/doc/wflow-05-faq.html | 1570 +++--- inst/doc/wflow-06-gitlab.R | 12 inst/doc/wflow-06-gitlab.Rmd | 264 - inst/doc/wflow-06-gitlab.html | 932 +-- inst/doc/wflow-07-common-code.R | 14 inst/doc/wflow-07-common-code.Rmd | 442 - inst/doc/wflow-07-common-code.html | 1031 ++- inst/doc/wflow-08-deploy.Rmd | 192 inst/doc/wflow-08-deploy.html | 627 +- inst/doc/wflow-09-workshop.R | 164 inst/doc/wflow-09-workshop.Rmd | 1206 ++-- inst/doc/wflow-09-workshop.html | 1550 +++-- inst/doc/wflow-10-data.R | 6 inst/doc/wflow-10-data.Rmd | 286 - inst/doc/wflow-10-data.html | 713 +- inst/rstudio/addins.dcf | 48 inst/rstudio/templates/project/wflow_start.dcf | 78 man/create_figure_path.Rd | 30 man/extract_commit.Rd | 68 man/is_fig_path_ext.Rd | 30 man/wflow_build.Rd | 492 - man/wflow_git_commit.Rd | 206 man/wflow_git_config.Rd | 152 man/wflow_git_pull.Rd | 216 man/wflow_git_push.Rd | 234 man/wflow_git_remote.Rd | 178 man/wflow_html.Rd | 338 - man/wflow_open.Rd | 166 man/wflow_post_knit.Rd | 80 man/wflow_pre_knit.Rd | 56 man/wflow_pre_processor.Rd | 114 man/wflow_publish.Rd | 272 - man/wflow_quickstart.Rd | 278 - man/wflow_remove.Rd | 128 man/wflow_rename.Rd | 160 man/wflow_rename_proj.Rd | 152 man/wflow_run.Rd | 98 man/wflow_site.Rd | 96 man/wflow_start.Rd | 526 +- man/wflow_status.Rd | 258 man/wflow_toc.Rd | 114 man/wflow_use_github.Rd | 330 - man/wflow_use_gitlab.Rd | 218 man/wflow_view.Rd | 178 man/workflowr-package.Rd | 247 tests/system-info.R | 46 tests/testthat.R | 8 tests/testthat/files/example.Rmd | 56 tests/testthat/files/test-wflow_build/error.Rmd | 20 tests/testthat/files/test-wflow_build/figure-v01.Rmd | 28 tests/testthat/files/test-wflow_build/figure-v02.Rmd | 36 tests/testthat/files/test-wflow_build/global-variable.Rmd | 20 tests/testthat/files/test-wflow_build/local.Rmd | 22 tests/testthat/files/test-wflow_build/seed.Rmd | 22 tests/testthat/files/test-wflow_build/warning.Rmd | 20 tests/testthat/files/test-wflow_html/bib-add.Rmd | 66 tests/testthat/files/test-wflow_html/bib-dont-add-1.Rmd | 70 tests/testthat/files/test-wflow_html/bib-dont-add-2.Rmd | 70 tests/testthat/files/test-wflow_html/cache-all-chunks.Rmd | 48 tests/testthat/files/test-wflow_html/cache-one-chunk.Rmd | 38 tests/testthat/files/test-wflow_html/collapse.Rmd | 20 tests/testthat/files/test-wflow_html/dependson-cache-global.Rmd | 50 tests/testthat/files/test-wflow_html/dependson-cache-local.Rmd | 42 tests/testthat/files/test-wflow_html/dependson-cache-none.Rmd | 42 tests/testthat/files/test-wflow_html/fig-path-all-chunks.Rmd | 46 tests/testthat/files/test-wflow_html/fig-path-one-chunk.Rmd | 38 tests/testthat/files/test-wflow_html/indent.Rmd | 30 tests/testthat/files/test-wflow_html/keep_md.Rmd | 10 tests/testthat/files/test-wflow_html/knit_root_dir.Rmd | 20 tests/testthat/files/test-wflow_html/opts_chunk.Rmd | 24 tests/testthat/files/test-wflow_html/python-figure.Rmd | 56 tests/testthat/files/test-wflow_html/sessioninfo-spacing.Rmd | 24 tests/testthat/files/test-wflow_html/test.bib | 18 tests/testthat/files/test-wflow_quickstart/quickstart.Rmd | 16 tests/testthat/helpers.R | 72 tests/testthat/setup.R | 40 tests/testthat/test-assertions.R | 258 tests/testthat/test-build_rmd.R | 160 tests/testthat/test-build_rmd_external.R | 316 - tests/testthat/test-callr.R | 44 tests/testthat/test-fig_path_ext.R | 220 tests/testthat/test-git.R | 468 - tests/testthat/test-git2r-merge.R | 468 - tests/testthat/test-git2r.R | 266 - tests/testthat/test-glob.R | 344 - tests/testthat/test-integrations.R | 82 tests/testthat/test-knitr.R | 36 tests/testthat/test-obtain_existing_path.R | 184 tests/testthat/test-pkg-options.R | 132 tests/testthat/test-report.R | 2610 ++++------ tests/testthat/test-subdirectories.R | 480 - tests/testthat/test-suppress_report.R | 216 tests/testthat/test-utility.R | 1425 ++--- tests/testthat/test-vig-getting-started.R | 202 tests/testthat/test-vig-gitlab.R | 120 tests/testthat/test-wflow_build.R | 927 +-- tests/testthat/test-wflow_git_commit.R | 622 +- tests/testthat/test-wflow_git_config.R | 244 tests/testthat/test-wflow_git_push_pull.R | 888 +-- tests/testthat/test-wflow_git_remote.R | 310 - tests/testthat/test-wflow_html.R | 1387 ++--- tests/testthat/test-wflow_open.R | 616 +- tests/testthat/test-wflow_options.R | 52 tests/testthat/test-wflow_publish.R | 805 +-- tests/testthat/test-wflow_quickstart.R | 744 +- tests/testthat/test-wflow_remove.R | 646 +- tests/testthat/test-wflow_rename.R | 446 - tests/testthat/test-wflow_rename_proj-external.R | 146 tests/testthat/test-wflow_rename_proj.R | 154 tests/testthat/test-wflow_run.R | 254 tests/testthat/test-wflow_site.R | 128 tests/testthat/test-wflow_start.R | 1332 ++--- tests/testthat/test-wflow_start_rstudio.R | 318 - tests/testthat/test-wflow_status.R | 998 +-- tests/testthat/test-wflow_toc.R | 272 - tests/testthat/test-wflow_use_github.R | 712 +- tests/testthat/test-wflow_use_gitlab.R | 541 +- tests/testthat/test-wflow_view.R | 464 - tests/testthat/test-windows.R | 340 - vignettes/wflow-01-getting-started.Rmd | 1134 ++-- vignettes/wflow-02-customization.Rmd | 406 - vignettes/wflow-03-migrating.Rmd | 322 - vignettes/wflow-04-how-it-works.Rmd | 308 - vignettes/wflow-05-faq.Rmd | 1191 ++-- vignettes/wflow-06-gitlab.Rmd | 264 - vignettes/wflow-07-common-code.Rmd | 442 - vignettes/wflow-08-deploy.Rmd | 192 vignettes/wflow-09-workshop.Rmd | 1206 ++-- vignettes/wflow-10-data.Rmd | 286 - 182 files changed, 36401 insertions(+), 35398 deletions(-)
Title: Continuous Mapping of Genetic Diversity
Description: Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) <doi:10.1111/2041-210X.14090>.
Author: Anusha Bishop [aut, cre] ,
Anne Chambers [aut] ,
Ian Wang [aut]
Maintainer: Anusha Bishop <anusha.bishop@berkeley.edu>
This is a re-admission after prior archival of version 2.1.2 dated 2024-05-16
Diff between wingen versions 2.1.2 dated 2024-05-16 and 2.2.0 dated 2025-08-18
wingen-2.1.2/wingen/tests/testthat/test_krig_gd.R |only wingen-2.2.0/wingen/DESCRIPTION | 27 wingen-2.2.0/wingen/MD5 | 163 wingen-2.2.0/wingen/NAMESPACE | 47 wingen-2.2.0/wingen/NEWS.md | 188 wingen-2.2.0/wingen/R/circle_gd.R | 400 - wingen-2.2.0/wingen/R/convert_vcf.R | 148 wingen-2.2.0/wingen/R/coords_to_raster.R | 120 wingen-2.2.0/wingen/R/coords_to_sf.R | 22 wingen-2.2.0/wingen/R/crs_check.R | 138 wingen-2.2.0/wingen/R/data.R | 148 wingen-2.2.0/wingen/R/dist_gd.R | 276 - wingen-2.2.0/wingen/R/general_gd.R | 1000 ++-- wingen-2.2.0/wingen/R/ggplot_gd.R | 236 - wingen-2.2.0/wingen/R/krig_gd.R | 595 +- wingen-2.2.0/wingen/R/mask_gd.R | 86 wingen-2.2.0/wingen/R/middle_earth.R | 116 wingen-2.2.0/wingen/R/plot_gd.R | 280 - wingen-2.2.0/wingen/R/preview_gd.R | 594 +- wingen-2.2.0/wingen/R/resist_gd.R | 432 - wingen-2.2.0/wingen/R/stats_gd.R | 522 +- wingen-2.2.0/wingen/R/wdim.R | 112 wingen-2.2.0/wingen/R/window_gd.R | 380 - wingen-2.2.0/wingen/R/wkrig_gd.R |only wingen-2.2.0/wingen/README.md | 297 - wingen-2.2.0/wingen/build/partial.rdb |binary wingen-2.2.0/wingen/build/vignette.rds |binary wingen-2.2.0/wingen/data/lotr_lyr.rda |binary wingen-2.2.0/wingen/data/lotr_range.rda |binary wingen-2.2.0/wingen/data/mini_coords.rda |binary wingen-2.2.0/wingen/data/mini_lyr.rda |binary wingen-2.2.0/wingen/data/mini_vcf.rda |binary wingen-2.2.0/wingen/data/mini_vcf_NA.rda |binary wingen-2.2.0/wingen/inst/CITATION | 36 wingen-2.2.0/wingen/inst/doc/wingen-vignette.R | 709 +-- wingen-2.2.0/wingen/inst/doc/wingen-vignette.Rmd | 1829 ++++---- wingen-2.2.0/wingen/inst/doc/wingen-vignette.pdf |binary wingen-2.2.0/wingen/man/circle_gd.Rd | 178 wingen-2.2.0/wingen/man/circle_general.Rd | 168 wingen-2.2.0/wingen/man/coords_to_raster.Rd | 76 wingen-2.2.0/wingen/man/figures/lifecycle-archived.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-defunct.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-deprecated.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-experimental.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-maturing.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-questioning.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-soft-deprecated.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-stable.svg |only wingen-2.2.0/wingen/man/figures/lifecycle-superseded.svg |only wingen-2.2.0/wingen/man/get_geodist.Rd | 68 wingen-2.2.0/wingen/man/get_resdist.Rd | 94 wingen-2.2.0/wingen/man/ggplot_count.Rd | 50 wingen-2.2.0/wingen/man/ggplot_gd.Rd | 56 wingen-2.2.0/wingen/man/krig_gd.Rd | 140 wingen-2.2.0/wingen/man/load_middle_earth_ex.Rd | 40 wingen-2.2.0/wingen/man/load_mini_ex.Rd | 40 wingen-2.2.0/wingen/man/lotr_coords.Rd | 46 wingen-2.2.0/wingen/man/lotr_lyr.Rd | 42 wingen-2.2.0/wingen/man/lotr_range.Rd | 38 wingen-2.2.0/wingen/man/lotr_vcf.Rd | 38 wingen-2.2.0/wingen/man/mask_gd.Rd | 56 wingen-2.2.0/wingen/man/mini_coords.Rd | 46 wingen-2.2.0/wingen/man/mini_lyr.Rd | 42 wingen-2.2.0/wingen/man/mini_vcf.Rd | 38 wingen-2.2.0/wingen/man/mini_vcf_NA.Rd | 38 wingen-2.2.0/wingen/man/plot_count.Rd | 96 wingen-2.2.0/wingen/man/plot_gd.Rd | 102 wingen-2.2.0/wingen/man/preview_gd.Rd | 118 wingen-2.2.0/wingen/man/resist_gd.Rd | 192 wingen-2.2.0/wingen/man/resist_general.Rd | 186 wingen-2.2.0/wingen/man/vcf_to_dosage.Rd | 34 wingen-2.2.0/wingen/man/window_gd.Rd | 176 wingen-2.2.0/wingen/man/window_general.Rd | 162 wingen-2.2.0/wingen/man/wingen-package.Rd | 62 wingen-2.2.0/wingen/man/wkrig_gd.Rd |only wingen-2.2.0/wingen/tests/testthat/test_check_crs.R | 189 wingen-2.2.0/wingen/tests/testthat/test_circle_gd.R | 166 wingen-2.2.0/wingen/tests/testthat/test_convert_vcf.R | 210 wingen-2.2.0/wingen/tests/testthat/test_coords_to_raster.R | 140 wingen-2.2.0/wingen/tests/testthat/test_ggplot_gd.R | 54 wingen-2.2.0/wingen/tests/testthat/test_mask_gd.R | 102 wingen-2.2.0/wingen/tests/testthat/test_middle_earth.R | 30 wingen-2.2.0/wingen/tests/testthat/test_plot_gd.R | 78 wingen-2.2.0/wingen/tests/testthat/test_resist_gd.R | 190 wingen-2.2.0/wingen/tests/testthat/test_wdim.R | 84 wingen-2.2.0/wingen/tests/testthat/test_window_gd.R | 938 ++-- wingen-2.2.0/wingen/tests/testthat/test_wkrig_gd.R |only wingen-2.2.0/wingen/vignettes/wingen-vignette.Rmd | 1829 ++++---- wingen-2.2.0/wingen/vignettes/wingen-vignette.html | 2191 +++++----- 89 files changed, 8945 insertions(+), 8579 deletions(-)
Title: Interface to 'TensorFlow' Estimators
Description: Interface to 'TensorFlow' Estimators
<https://www.tensorflow.org/guide/estimator>, a high-level
API that provides implementations of many different model types
including linear models and deep neural networks.
Author: JJ Allaire [aut],
Yuan Tang [aut] ,
Kevin Ushey [aut],
Kevin Kuo [aut] ,
Tomasz Kalinowski [cre],
Daniel Falbel [ctb, cph],
RStudio [cph, fnd],
Google Inc. [cph]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
This is a re-admission after prior archival of version 1.9.2 dated 2021-08-09
Diff between tfestimators versions 1.9.2 dated 2021-08-09 and 1.9.3 dated 2025-08-18
DESCRIPTION | 12 MD5 | 92 +- NAMESPACE | 9 R/boosted_trees_estimators.R | 4 R/dnn_estimators.R | 4 R/dnn_linear_combined_estimators.R | 4 R/feature_columns.R | 2 R/keras_estimator.R | 2 R/linear_estimators.R | 4 R/package.R | 54 - README.md | 9 build/vignette.rds |binary inst/doc/creating_estimators.Rmd | 23 inst/doc/creating_estimators.html | 883 +++++++++++++------ inst/doc/dataset_api.R | 86 - inst/doc/dataset_api.Rmd | 4 inst/doc/dataset_api.html | 441 +++++++-- inst/doc/estimator_basics.R | 98 +- inst/doc/estimator_basics.html | 534 ++++++++--- inst/doc/feature_columns.R | 48 - inst/doc/feature_columns.html | 422 +++++++-- inst/doc/input_functions.R | 94 +- inst/doc/input_functions.html | 461 +++++++--- inst/doc/parsing_spec.R | 94 +- inst/doc/parsing_spec.html | 436 +++++++-- inst/doc/run_hooks.R | 98 +- inst/doc/run_hooks.html | 492 ++++++++-- inst/doc/tensorboard.R | 10 inst/doc/tensorboard.html | 358 ++++++- inst/doc/tensorflow_layers.Rmd | 35 inst/doc/tensorflow_layers.html | 1215 ++++++++++++++++++--------- man/evaluate.tf_estimator.Rd | 2 man/export_savedmodel.tf_estimator.Rd | 2 man/feature_columns.Rd | 2 man/predict.tf_estimator.Rd | 2 man/session_run_hook.Rd | 15 man/tfestimators.Rd | 30 man/train.tf_estimator.Rd | 2 vignettes/creating_estimators.Rmd | 23 vignettes/dataset_api.Rmd | 4 vignettes/examples/custom_estimator.Rmd | 4 vignettes/examples/iris_custom_decay_dnn.Rmd | 4 vignettes/examples/iris_dnn_classifier.Rmd | 4 vignettes/examples/mnist.Rmd | 4 vignettes/examples/tensorflow_layers.Rmd | 4 vignettes/examples/wide_and_deep.Rmd | 4 vignettes/tensorflow_layers.Rmd | 35 47 files changed, 4335 insertions(+), 1834 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
This is a re-admission after prior archival of version 1.1.8 dated 2025-04-22
Diff between tepr versions 1.1.8 dated 2025-04-22 and 1.1.9 dated 2025-08-18
DESCRIPTION | 6 +- MD5 | 21 +++++---- NAMESPACE | 1 NEWS | 5 ++ R/preprocessing-blacklisthighmap-utils.R | 38 ++++++++++++++++-- R/preprocessing-blacklisthighmap.R | 2 R/preprocessing.R | 1 build/vignette.rds |binary inst/doc/tepr.html | 16 +++---- man/retrievechrom.Rd |only tests/testthat/test-preprocessing-blacklisthighmap.R | 2 tests/testthat/test-preprocessing-createtablescores.R | 2 12 files changed, 67 insertions(+), 27 deletions(-)
Title: Code Storage and Execution Class for 'teal' Applications
Description: Introduction of 'qenv' S4 class, that facilitates code
execution and reproducibility in 'teal' applications.
Author: Dawid Kaledkowski [aut, cre],
Aleksander Chlebowski [aut],
Marcin Kosinski [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Mahmoud Hallal [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
Chendi Liao [rev],
Dony Unardi [rev],
F. [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.code versions 0.6.1 dated 2025-02-14 and 0.7.0 dated 2025-08-18
DESCRIPTION | 16 +- MD5 | 57 ++++--- NAMESPACE | 1 NEWS.md | 17 ++ R/qenv-class.R | 5 R/qenv-eval_code.R | 148 +++++++++---------- R/qenv-get_outputs.R |only R/qenv-get_var.R | 41 ----- R/qenv-join.R | 147 ------------------- R/qenv-within.R | 20 -- R/utils-get_code_dependency.R | 100 ++++++++++++- R/utils.R | 19 ++ build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/qenv.R | 9 - inst/doc/qenv.Rmd | 15 +- inst/doc/qenv.html | 178 ++++++++++++------------ man/eval_code.Rd | 63 +------- man/get_outputs.Rd |only man/get_var.Rd | 22 -- man/get_warn_message_util.Rd | 2 man/join.Rd | 135 ------------------ man/within.qenv.Rd |only tests/testthat/test-get_outputs.R |only tests/testthat/test-qenv_concat.R | 38 +++-- tests/testthat/test-qenv_eval_code.R | 72 ++++----- tests/testthat/test-qenv_get_code.R | 24 ++- tests/testthat/test-qenv_get_var.R | 17 -- tests/testthat/test-qenv_join.R | 38 +++-- tests/testthat/test-qenv_within.R | 23 +++ tests/testthat/test-utils-get_code_dependency.R |only vignettes/qenv.Rmd | 15 +- 32 files changed, 525 insertions(+), 700 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.2.1 dated 2024-08-28 and 0.3.0 dated 2025-08-18
SSN2-0.2.1/SSN2/R/AIC.R |only SSN2-0.2.1/SSN2/inst/doc/introduction.html |only SSN2-0.2.1/SSN2/man/AIC.SSN2.Rd |only SSN2-0.3.0/SSN2/DESCRIPTION | 15 SSN2-0.3.0/SSN2/MD5 | 163 +-- SSN2-0.3.0/SSN2/NAMESPACE | 29 SSN2-0.3.0/SSN2/NEWS.md | 40 SSN2-0.3.0/SSN2/R/AIC_deprecated.R |only SSN2-0.3.0/SSN2/R/AICc.R |only SSN2-0.3.0/SSN2/R/AUROC.R |only SSN2-0.3.0/SSN2/R/SSN2.R | 54 - SSN2-0.3.0/SSN2/R/Torgegram.R | 484 ++++++--- SSN2-0.3.0/SSN2/R/amongObsPredsBigDistMat.R |only SSN2-0.3.0/SSN2/R/amongSitesBigDistMat.R |only SSN2-0.3.0/SSN2/R/amongSitesDistMat.R | 1 SSN2-0.3.0/SSN2/R/anova.R | 511 +++++----- SSN2-0.3.0/SSN2/R/augment.R | 555 +++++----- SSN2-0.3.0/SSN2/R/checks.R | 366 +++---- SSN2-0.3.0/SSN2/R/cov_betahat_adjust.R | 118 ++ SSN2-0.3.0/SSN2/R/cov_matrix.R | 673 +++++++------ SSN2-0.3.0/SSN2/R/cov_vector.R | 566 +++++------ SSN2-0.3.0/SSN2/R/covmatrix.R | 3 SSN2-0.3.0/SSN2/R/createBinaryID.R | 7 SSN2-0.3.0/SSN2/R/data.R | 254 ++--- SSN2-0.3.0/SSN2/R/emmeans.R |only SSN2-0.3.0/SSN2/R/getObsPredsRelationshipsDF.R |only SSN2-0.3.0/SSN2/R/getObsRelationshipsDF.R | 8 SSN2-0.3.0/SSN2/R/getPredRelationshipsDF.R | 2 SSN2-0.3.0/SSN2/R/getSitesRelationshipsDF.R |only SSN2-0.3.0/SSN2/R/get_cov_matrix.R | 26 SSN2-0.3.0/SSN2/R/get_cov_vector.R | 132 +- SSN2-0.3.0/SSN2/R/get_data_object.R | 21 SSN2-0.3.0/SSN2/R/get_data_object_bigdata.R |only SSN2-0.3.0/SSN2/R/get_data_object_bigdata_glm.R |only SSN2-0.3.0/SSN2/R/get_dist_object_bigdata.R |only SSN2-0.3.0/SSN2/R/get_dist_object_bigdata_cross.R |only SSN2-0.3.0/SSN2/R/get_dist_pred_object_bigdata.R |only SSN2-0.3.0/SSN2/R/get_initial_cheap.R |only SSN2-0.3.0/SSN2/R/get_model_stats.R | 20 SSN2-0.3.0/SSN2/R/get_model_stats_bigdata.R |only SSN2-0.3.0/SSN2/R/get_model_stats_bigdata_glm.R |only SSN2-0.3.0/SSN2/R/glance.R | 124 +- SSN2-0.3.0/SSN2/R/glances.R | 210 ++-- SSN2-0.3.0/SSN2/R/gloglik_products.R | 48 SSN2-0.3.0/SSN2/R/initial.R | 633 ++++++------ SSN2-0.3.0/SSN2/R/laploglik_products.R | 241 ++-- SSN2-0.3.0/SSN2/R/local.R | 125 +- SSN2-0.3.0/SSN2/R/logLik.R | 94 + SSN2-0.3.0/SSN2/R/loocv.R | 6 SSN2-0.3.0/SSN2/R/loocv_glm.R | 464 ++++----- SSN2-0.3.0/SSN2/R/partition_vector.R | 76 + SSN2-0.3.0/SSN2/R/plot.R | 563 +++++------ SSN2-0.3.0/SSN2/R/predict.R | 1111 ++++++++++++---------- SSN2-0.3.0/SSN2/R/predict_bigdata.R |only SSN2-0.3.0/SSN2/R/predict_glm.R | 936 ++++++++++-------- SSN2-0.3.0/SSN2/R/predict_terms.R |only SSN2-0.3.0/SSN2/R/randcov_vector.R | 4 SSN2-0.3.0/SSN2/R/restruct_ssn_missing.R | 11 SSN2-0.3.0/SSN2/R/ssn_create_bigdist.R |only SSN2-0.3.0/SSN2/R/ssn_get_stream_distmat.R | 7 SSN2-0.3.0/SSN2/R/ssn_glm.R | 892 +++++++++-------- SSN2-0.3.0/SSN2/R/ssn_import.R | 551 +++++----- SSN2-0.3.0/SSN2/R/ssn_import_predpts.R | 45 SSN2-0.3.0/SSN2/R/ssn_lm.R | 865 +++++++++-------- SSN2-0.3.0/SSN2/R/ssn_simulate.R | 234 ++-- SSN2-0.3.0/SSN2/R/utils.R | 167 +-- SSN2-0.3.0/SSN2/R/zzz.R |only SSN2-0.3.0/SSN2/README.md | 6 SSN2-0.3.0/SSN2/build/vignette.rds |binary SSN2-0.3.0/SSN2/inst/doc/introduction.Rmd | 54 - SSN2-0.3.0/SSN2/inst/doc/introduction.pdf |only SSN2-0.3.0/SSN2/man/MiddleFork04.ssn.Rd | 6 SSN2-0.3.0/SSN2/man/Torgegram.Rd | 17 SSN2-0.3.0/SSN2/man/amongSitesBigDistMat.Rd |only SSN2-0.3.0/SSN2/man/augment.SSN2.Rd | 19 SSN2-0.3.0/SSN2/man/glance.SSN2.Rd | 1 SSN2-0.3.0/SSN2/man/glances.SSN2.Rd | 7 SSN2-0.3.0/SSN2/man/loocv.SSN2.Rd | 17 SSN2-0.3.0/SSN2/man/predict.SSN2.Rd | 79 + SSN2-0.3.0/SSN2/man/reexports.Rd | 3 SSN2-0.3.0/SSN2/man/ssn_create_bigdist.Rd |only SSN2-0.3.0/SSN2/man/ssn_get_stream_distmat.Rd | 2 SSN2-0.3.0/SSN2/man/ssn_glm.Rd | 56 + SSN2-0.3.0/SSN2/man/ssn_import.Rd | 18 SSN2-0.3.0/SSN2/man/ssn_import_predpts.Rd | 8 SSN2-0.3.0/SSN2/man/ssn_initial.Rd | 5 SSN2-0.3.0/SSN2/man/ssn_lm.Rd | 67 + SSN2-0.3.0/SSN2/man/ssn_simulate.Rd | 2 SSN2-0.3.0/SSN2/tests/testthat/helper-data.R | 1 SSN2-0.3.0/SSN2/tests/testthat/test-Torgegram.R | 123 +- SSN2-0.3.0/SSN2/tests/testthat/test-extras.R | 608 ++++++------ SSN2-0.3.0/SSN2/tests/testthat/test-local.R |only SSN2-0.3.0/SSN2/tests/testthat/test-ssn-object.R | 228 ++-- SSN2-0.3.0/SSN2/tests/testthat/test-ssn_glm.R | 597 ++++++----- SSN2-0.3.0/SSN2/tests/testthat/test-ssn_lm.R | 590 +++++------ SSN2-0.3.0/SSN2/vignettes/introduction.Rmd | 54 - 96 files changed, 7702 insertions(+), 6321 deletions(-)
Title: Marker-Based Package for Single-Cell and Spatial-Transcriptomic
Annotation
Description: Annotating single-cell and spatial-transcriptomic (ST) data based on the Marker dataset. It supports the creation of a unified marker list, Markers_list, using sources including: the package's built-in curated species-specific cell type and marker reference databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI'), Seurat objects containing cell label information, or user-provided Excel tables mapping cell types to markers. Based on the Markers_list, 'SlimR' can calculate gene expression of different cell types and predict annotation information and calculate corresponding AUC by 'Celltype_Calculate()', and annotate it by 'Celltype_Annotation()', then verify it by 'Celltype_Verification()'. At the same time, it can calculate gene expression corresponding to the cell type to generate the corresponding annotation reference map for manual annotation (e.g., 'Heatmap', 'Features plot', 'Combined plot'). For more details see Kabacoff (2020, ISBN:9787115420572).
Author: Zhao qing Wang [aut, cre]
Maintainer: Zhao qing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.0.3 dated 2025-07-29 and 1.0.7 dated 2025-08-18
SlimR-1.0.3/SlimR/R/Cellmarker2.R |only SlimR-1.0.3/SlimR/R/Cellmarker2_raw.R |only SlimR-1.0.3/SlimR/R/Cellmarker2_table.R |only SlimR-1.0.3/SlimR/R/Celltype_annotation_Box.R |only SlimR-1.0.3/SlimR/R/Celltype_annotation_Heatmap.R |only SlimR-1.0.3/SlimR/R/Expression_plot.R |only SlimR-1.0.3/SlimR/R/PanglaoDB.R |only SlimR-1.0.3/SlimR/R/PanglaoDB_raw.R |only SlimR-1.0.3/SlimR/R/PanglaoDB_table.R |only SlimR-1.0.3/SlimR/man/Celltype_annotation_Box.Rd |only SlimR-1.0.3/SlimR/man/Celltype_annotation_Heatmap.Rd |only SlimR-1.0.3/SlimR/man/plot_mean_expression.Rd |only SlimR-1.0.3/SlimR/man/read_excel_markers.Rd |only SlimR-1.0.3/SlimR/man/read_seurat_markers.Rd |only SlimR-1.0.7/SlimR/DESCRIPTION | 19 SlimR-1.0.7/SlimR/LICENSE |only SlimR-1.0.7/SlimR/MD5 | 99 +- SlimR-1.0.7/SlimR/NAMESPACE | 38 - SlimR-1.0.7/SlimR/NEWS.md |only SlimR-1.0.7/SlimR/R/Celltype_Annotation.R |only SlimR-1.0.7/SlimR/R/Celltype_Annotation_Combined.R |only SlimR-1.0.7/SlimR/R/Celltype_Annotation_Features.R |only SlimR-1.0.7/SlimR/R/Celltype_Annotation_Heatmap.R |only SlimR-1.0.7/SlimR/R/Celltype_Calculate.R |only SlimR-1.0.7/SlimR/R/Celltype_Verification.R |only SlimR-1.0.7/SlimR/R/Celltype_annotation_Cellmarker2.R | 76 +- SlimR-1.0.7/SlimR/R/Celltype_annotation_Excel.R | 79 +- SlimR-1.0.7/SlimR/R/Celltype_annotation_PanglaoDB.R | 74 +- SlimR-1.0.7/SlimR/R/Celltype_annotation_Seurat.R | 78 +- SlimR-1.0.7/SlimR/R/Database_Cellmarker2.R |only SlimR-1.0.7/SlimR/R/Database_Cellmarker2_raw.R |only SlimR-1.0.7/SlimR/R/Database_Cellmarker2_table.R |only SlimR-1.0.7/SlimR/R/Database_Markers_list_TCellSI.R |only SlimR-1.0.7/SlimR/R/Database_Markers_list_scIBD.R |only SlimR-1.0.7/SlimR/R/Database_PanglaoDB.R |only SlimR-1.0.7/SlimR/R/Database_PanglaoDB_raw.R |only SlimR-1.0.7/SlimR/R/Database_PanglaoDB_table.R |only SlimR-1.0.7/SlimR/R/Expression_calculate.R |only SlimR-1.0.7/SlimR/R/Markers_filter_Cellmarker2.R | 39 - SlimR-1.0.7/SlimR/R/Markers_filter_PanglaoDB.R | 16 SlimR-1.0.7/SlimR/R/Probability_calculate.R | 17 SlimR-1.0.7/SlimR/R/Read_excel_markers.R | 12 SlimR-1.0.7/SlimR/R/Read_seurat_markers.R | 125 ++- SlimR-1.0.7/SlimR/R/globals.R | 2 SlimR-1.0.7/SlimR/R/onattach.R | 10 SlimR-1.0.7/SlimR/README.md | 550 +++++++++++---- SlimR-1.0.7/SlimR/build |only SlimR-1.0.7/SlimR/data/Markers_list_TCellSI.rda |only SlimR-1.0.7/SlimR/data/Markers_list_scIBD.rda |only SlimR-1.0.7/SlimR/man/Cellmarker2.Rd | 13 SlimR-1.0.7/SlimR/man/Cellmarker2_raw.Rd | 13 SlimR-1.0.7/SlimR/man/Cellmarker2_table.Rd | 13 SlimR-1.0.7/SlimR/man/Celltype_Annotation.Rd |only SlimR-1.0.7/SlimR/man/Celltype_Annotation_Combined.Rd |only SlimR-1.0.7/SlimR/man/Celltype_Annotation_Features.Rd |only SlimR-1.0.7/SlimR/man/Celltype_Annotation_Heatmap.Rd |only SlimR-1.0.7/SlimR/man/Celltype_Calculate.Rd |only SlimR-1.0.7/SlimR/man/Celltype_Verification.Rd |only SlimR-1.0.7/SlimR/man/Celltype_annotation_Cellmarker2.Rd | 48 - SlimR-1.0.7/SlimR/man/Celltype_annotation_Excel.Rd | 52 + SlimR-1.0.7/SlimR/man/Celltype_annotation_PanglaoDB.Rd | 50 + SlimR-1.0.7/SlimR/man/Celltype_annotation_Seurat.Rd | 54 + SlimR-1.0.7/SlimR/man/Markers_filter_Cellmarker2.Rd | 40 - SlimR-1.0.7/SlimR/man/Markers_filter_PanglaoDB.Rd | 19 SlimR-1.0.7/SlimR/man/Markers_list_TCellSI.Rd |only SlimR-1.0.7/SlimR/man/Markers_list_scIBD.Rd |only SlimR-1.0.7/SlimR/man/PanglaoDB.Rd | 13 SlimR-1.0.7/SlimR/man/PanglaoDB_raw.Rd | 13 SlimR-1.0.7/SlimR/man/PanglaoDB_table.Rd | 13 SlimR-1.0.7/SlimR/man/Read_excel_markers.Rd |only SlimR-1.0.7/SlimR/man/Read_seurat_markers.Rd |only SlimR-1.0.7/SlimR/man/calculate_expression.Rd |only SlimR-1.0.7/SlimR/man/calculate_probability.Rd | 5 73 files changed, 1143 insertions(+), 437 deletions(-)
Title: Download and Tidy Data from the Reserve Bank of Australia
Description: Download up-to-date data from the Reserve Bank of Australia
in a tidy data frame. Package includes functions to download current and
historical statistical tables
(<https://www.rba.gov.au/statistics/tables/>) and forecasts
(<https://www.rba.gov.au/publications/smp/forecasts-archive.html>). Data
includes a broad range of Australian macroeconomic and financial time
series.
Author: Matt Cowgill [aut, cre] ,
Angus Moore [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readrba versions 0.1.11 dated 2024-09-27 and 0.1.12 dated 2025-08-18
DESCRIPTION | 9 - MD5 | 26 +-- NEWS.md | 4 R/check_rba_connection.R | 3 R/get_rba_urls.R | 4 R/sysdata.rda |binary R/tidy_rba.R | 25 +++ README.md | 116 ++++++++++------- build/vignette.rds |binary inst/doc/readrba.html | 206 +++++++++++++++---------------- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary tests/testthat/test-get_rba_urls.R | 4 tests/testthat/test-rba_forecasts.R | 1 14 files changed, 229 insertions(+), 169 deletions(-)
Title: Generate Random Walks Compatible with the 'tidyverse'
Description: Generates random walks of various types by providing a set of functions
that are compatible with the 'tidyverse'. The functions provided in the package
make it simple to create random walks with a variety of properties, such as
how many simulations to run, how many steps to take, and the distribution of
random walk itself.
Author: Steven Sanderson [aut, cre, cph] ,
Antti Rask [aut, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between RandomWalker versions 0.3.0 dated 2025-05-06 and 1.0.0 dated 2025-08-18
RandomWalker-0.3.0/RandomWalker/R/gen-brown-motion-geometric.R |only RandomWalker-0.3.0/RandomWalker/R/gen-brown-motion.R |only RandomWalker-0.3.0/RandomWalker/R/gen-discrete-walk.R |only RandomWalker-1.0.0/RandomWalker/DESCRIPTION | 7 RandomWalker-1.0.0/RandomWalker/MD5 | 149 - RandomWalker-1.0.0/RandomWalker/NAMESPACE | 21 RandomWalker-1.0.0/RandomWalker/NEWS.md | 173 + RandomWalker-1.0.0/RandomWalker/R/00_global_variables.R | 12 RandomWalker-1.0.0/RandomWalker/R/auto-rw30.R | 156 - RandomWalker-1.0.0/RandomWalker/R/gen-random-beta-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-binomial-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-brown-motion-geometric.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-brown-motion.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-cauchy-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-chisquared-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-discrete-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-displacement-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-exponential-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-f-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-gamma-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-geometric-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-hypergeometric-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-logistic-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-lognormal-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-multinom-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-nbinomial-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-normal-walk-drift.R | 336 +- RandomWalker-1.0.0/RandomWalker/R/gen-random-normal-walk.R | 323 +- RandomWalker-1.0.0/RandomWalker/R/gen-random-poisson-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-smirnov-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-t-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-uniform-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-weibull-walk.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-wilcox.R |only RandomWalker-1.0.0/RandomWalker/R/gen-random-wilcoxsr-walk.R |only RandomWalker-1.0.0/RandomWalker/R/helpers.R | 1304 +++++----- RandomWalker-1.0.0/RandomWalker/R/plt-visualize-walks.R | 534 ++-- RandomWalker-1.0.0/RandomWalker/R/stats-walk-summary.R | 212 - RandomWalker-1.0.0/RandomWalker/R/vec-conf-int.R | 108 RandomWalker-1.0.0/RandomWalker/R/vec-cumulative-functions.R | 924 +++---- RandomWalker-1.0.0/RandomWalker/R/vec-distance.R | 112 RandomWalker-1.0.0/RandomWalker/R/vec-running-quantile.R | 300 +- RandomWalker-1.0.0/RandomWalker/README.md | 50 RandomWalker-1.0.0/RandomWalker/build/vignette.rds |binary RandomWalker-1.0.0/RandomWalker/inst/doc/getting-started.Rmd | 196 - RandomWalker-1.0.0/RandomWalker/inst/doc/getting-started.html | 28 RandomWalker-1.0.0/RandomWalker/man/brownian_motion.Rd | 42 RandomWalker-1.0.0/RandomWalker/man/cgmean.Rd | 92 RandomWalker-1.0.0/RandomWalker/man/chmean.Rd | 92 RandomWalker-1.0.0/RandomWalker/man/ckurtosis.Rd | 90 RandomWalker-1.0.0/RandomWalker/man/cmean.Rd | 92 RandomWalker-1.0.0/RandomWalker/man/cmedian.Rd | 90 RandomWalker-1.0.0/RandomWalker/man/confidence_interval.Rd | 91 RandomWalker-1.0.0/RandomWalker/man/convert_snake_to_title_case.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/crange.Rd | 94 RandomWalker-1.0.0/RandomWalker/man/csd.Rd | 92 RandomWalker-1.0.0/RandomWalker/man/cskewness.Rd | 90 RandomWalker-1.0.0/RandomWalker/man/cvar.Rd | 94 RandomWalker-1.0.0/RandomWalker/man/discrete_walk.Rd | 41 RandomWalker-1.0.0/RandomWalker/man/figures/README-random_walk_visual_example-1.png |binary RandomWalker-1.0.0/RandomWalker/man/generate_caption.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/geometric_brownian_motion.Rd | 45 RandomWalker-1.0.0/RandomWalker/man/get_attributes.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/kurtosis_vec.Rd | 100 RandomWalker-1.0.0/RandomWalker/man/rand_walk_column_names.Rd | 36 RandomWalker-1.0.0/RandomWalker/man/rand_walk_helper.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/random_beta_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_binomial_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_cauchy_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_chisquared_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_displacement_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_exponential_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_f_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_gamma_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_geometric_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_hypergeometric_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_logistic_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_lognormal_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_multinomial_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_negbinomial_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_normal_drift_walk.Rd | 43 RandomWalker-1.0.0/RandomWalker/man/random_normal_walk.Rd | 52 RandomWalker-1.0.0/RandomWalker/man/random_poisson_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_smirnov_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_t_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_uniform_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_weibull_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_wilcox_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/random_wilcoxon_sr_walk.Rd |only RandomWalker-1.0.0/RandomWalker/man/running_quantile.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/rw_range.Rd | 92 RandomWalker-1.0.0/RandomWalker/man/skewness_vec.Rd | 100 RandomWalker-1.0.0/RandomWalker/man/std_cum_max_augment.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/std_cum_mean_augment.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/std_cum_min_augment.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/std_cum_prod_augment.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/std_cum_sum_augment.Rd | 3 RandomWalker-1.0.0/RandomWalker/man/subset_walks.Rd |only RandomWalker-1.0.0/RandomWalker/man/visualize_walks.Rd | 2 RandomWalker-1.0.0/RandomWalker/vignettes/getting-started.Rmd | 196 - 100 files changed, 3485 insertions(+), 3156 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.3.1 dated 2025-06-30 and 1.4.0 dated 2025-08-18
insight-1.3.1/insight/R/apply_table_theme.R |only insight-1.3.1/insight/tests/testthat/test-apply_table_theme.R |only insight-1.4.0/insight/DESCRIPTION | 21 insight-1.4.0/insight/MD5 | 90 - insight-1.4.0/insight/NAMESPACE | 21 insight-1.4.0/insight/NEWS.md | 46 insight-1.4.0/insight/R/compute_variances.R | 269 -- insight-1.4.0/insight/R/display.R | 73 insight-1.4.0/insight/R/export_table.R | 549 ++++-- insight-1.4.0/insight/R/find_parameters_other.R | 4 insight-1.4.0/insight/R/find_predictors.R | 32 insight-1.4.0/insight/R/find_random.R | 2 insight-1.4.0/insight/R/find_response.R | 29 insight-1.4.0/insight/R/format_table_glue.R | 35 insight-1.4.0/insight/R/get_datagrid.R | 29 insight-1.4.0/insight/R/get_mixed_info.R |only insight-1.4.0/insight/R/get_modelmatrix.R | 14 insight-1.4.0/insight/R/get_parameters.R | 6 insight-1.4.0/insight/R/get_parameters_others.R | 7 insight-1.4.0/insight/R/get_predicted.R | 27 insight-1.4.0/insight/R/get_predicted_other.R | 14 insight-1.4.0/insight/R/get_statistic.R | 6 insight-1.4.0/insight/R/get_variances.R | 3 insight-1.4.0/insight/R/is_converged.R | 7 insight-1.4.0/insight/R/link_function.R | 5 insight-1.4.0/insight/R/link_inverse.R | 8 insight-1.4.0/insight/R/model_info.R | 16 insight-1.4.0/insight/R/standardize_column_order.R | 9 insight-1.4.0/insight/inst/doc/display.R | 30 insight-1.4.0/insight/inst/doc/display.Rmd | 45 insight-1.4.0/insight/inst/doc/display.html | 898 ++++++++-- insight-1.4.0/insight/man/display.Rd | 6 insight-1.4.0/insight/man/export_table.Rd | 82 insight-1.4.0/insight/man/get_datagrid.Rd | 11 insight-1.4.0/insight/man/get_mixed_info.Rd |only insight-1.4.0/insight/man/get_predicted.Rd | 8 insight-1.4.0/insight/tests/testthat/test-betareg.R | 25 insight-1.4.0/insight/tests/testthat/test-brms.R | 48 insight-1.4.0/insight/tests/testthat/test-coxme.R | 58 insight-1.4.0/insight/tests/testthat/test-display.R | 23 insight-1.4.0/insight/tests/testthat/test-export_table.R | 96 + insight-1.4.0/insight/tests/testthat/test-get_datagrid.R | 37 insight-1.4.0/insight/tests/testthat/test-get_predicted.R | 27 insight-1.4.0/insight/tests/testthat/test-glmmTMB.R | 8 insight-1.4.0/insight/tests/testthat/test-iv_robust.R | 45 insight-1.4.0/insight/tests/testthat/test-lavaan.R |only insight-1.4.0/insight/tests/testthat/test-sdmTMB.R | 6 insight-1.4.0/insight/tests/testthat/test-selection.R |only insight-1.4.0/insight/vignettes/display.Rmd | 45 49 files changed, 2044 insertions(+), 776 deletions(-)
Title: Autodiff for Influence Function Based Estimates
Description: Implements an S7 class for estimates based on influence functions,
with forward mode automatic differentiation defined for standard arithmetic
operations.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between ife versions 0.1.12 dated 2025-02-14 and 0.2.0 dated 2025-08-18
DESCRIPTION | 19 +++++------ MD5 | 12 +++--- NAMESPACE | 3 + NEWS.md | 5 ++ R/influence_func_estimand.R | 27 +++++++++++---- README.md | 76 +++++++++++++++++++++++++++++++------------- tests/testthat/test-Ops.R | 8 ++++ 7 files changed, 106 insertions(+), 44 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-products
matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). It also provides other tools for analysis and graphical display of the models
such as robust methods and homogeneity of variance covariance matrices.
The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Georges Monette [aut] ,
Phil Chalmers [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.7.5 dated 2025-05-24 and 1.7.8 dated 2025-08-18
DESCRIPTION | 14 MD5 | 62 ++- NAMESPACE | 5 NEWS.md | 17 R/boxM.R | 19 - R/colDevs.R | 4 R/datasets.R | 4 R/distancePlot.R |only R/heplot.R | 1 R/plot.boxM.R | 8 R/plot.robmlm.R | 4 R/rel_diff.R |only R/robmlm.R | 16 build/partial.rdb |binary build/vignette.rds |binary inst/doc/HE_manova.html | 8 inst/doc/HE_mmra.html | 8 inst/doc/Robust.R |only inst/doc/Robust.Rmd |only inst/doc/Robust.html |only inst/doc/datasets.html | 496 +++++++++++++--------------- man/Plastic.Rd | 4 man/colDevs.Rd | 4 man/distancePlot.Rd |only man/figures/IRWLS-flowchart.jpg |only man/figures/README-iris-can-1.png |binary man/figures/README-iris4-1.png |binary man/figures/bisquare.jpg |only man/figures/influence-functions.jpg |only man/figures/weight-functions.jpg |only man/plot.boxM.Rd | 6 man/plot.robmlm.Rd | 2 man/rel_diff.Rd |only man/robmlm.Rd | 14 vignettes/Robust.Rmd |only vignettes/fig/robust-pottery-cqplot-1.png |only vignettes/fig/robust-pottery-heplot-1.png |only vignettes/fig/robust-pottery-inflplot-1.png |only vignettes/fig/robust-pottery-pairs-1.png |only vignettes/fig/robust-pottery-weights-1.png |only vignettes/robust.bib |only 41 files changed, 379 insertions(+), 317 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at the country, region, state, and city levels. The package also downloads world-level COVID-19 data from Johns Hopkins University's repository. COVID-19 data is available from the start of follow-up until to May 5, 2023, when the World Health Organization (WHO) declared an end to the Public Health Emergency of International Concern (PHEIC) for COVID-19.
Author: Fabio Demarqui [aut, cre, cph],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
This is a re-admission after prior archival of version 0.1.8 dated 2023-10-15
Diff between covid19br versions 0.1.8 dated 2023-10-15 and 1.0.0 dated 2025-08-18
covid19br-0.1.8/covid19br/tests/testthat/cities.rds |only covid19br-0.1.8/covid19br/tests/testthat/regions.rds |only covid19br-0.1.8/covid19br/tests/testthat/states.rds |only covid19br-0.1.8/covid19br/tests/testthat/world.rds |only covid19br-1.0.0/covid19br/DESCRIPTION | 12 - covid19br-1.0.0/covid19br/MD5 | 35 ++- covid19br-1.0.0/covid19br/NAMESPACE | 3 covid19br-1.0.0/covid19br/NEWS.md | 5 covid19br-1.0.0/covid19br/R/covid19br.R | 3 covid19br-1.0.0/covid19br/R/data_doc_geo.R |only covid19br-1.0.0/covid19br/R/downloadData.R | 96 --------- covid19br-1.0.0/covid19br/R/utils.R | 139 +++++++++++--- covid19br-1.0.0/covid19br/README.md | 2 covid19br-1.0.0/covid19br/data/geocities.rda |only covid19br-1.0.0/covid19br/data/georegions.rda |only covid19br-1.0.0/covid19br/data/geostates.rda |only covid19br-1.0.0/covid19br/data/geoworld.rda |only covid19br-1.0.0/covid19br/man/add_geo.Rd | 3 covid19br-1.0.0/covid19br/man/covid19br.Rd | 2 covid19br-1.0.0/covid19br/man/downloadCovid19.Rd | 2 covid19br-1.0.0/covid19br/man/geocities.Rd |only covid19br-1.0.0/covid19br/man/georegions.Rd |only covid19br-1.0.0/covid19br/man/geostates.Rd |only covid19br-1.0.0/covid19br/man/geoworld.Rd |only covid19br-1.0.0/covid19br/tests/testthat/test_covid19br.R | 8 25 files changed, 161 insertions(+), 149 deletions(-)
Title: Interface to the Google Cloud Machine Learning Platform
Description: Interface to the Google Cloud Machine Learning Platform
<https://cloud.google.com/vertex-ai>, which provides cloud tools for training machine
learning models.
Author: Tomasz Kalinowski [cre],
Daniel Falbel [aut],
Javier Luraschi [aut],
JJ Allaire [aut],
Kevin Ushey [aut],
RStudio [cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
This is a re-admission after prior archival of version 0.6.1 dated 2019-09-03
Diff between cloudml versions 0.6.1 dated 2019-09-03 and 0.7.1 dated 2025-08-18
DESCRIPTION | 24 +- MD5 | 90 +++---- NEWS.md | 12 - R/cloudml-package.R | 14 - R/jobs.R | 12 - R/models.R | 2 build/vignette.rds |binary inst/cloudml/cloudml/deploy.py | 5 inst/doc/deployment.R | 112 ++++----- inst/doc/deployment.Rmd | 8 inst/doc/deployment.html | 300 +++++++++++++++----------- inst/doc/getting_started.R | 54 ++-- inst/doc/getting_started.Rmd | 37 +-- inst/doc/getting_started.html | 339 +++++++++++++++++++---------- inst/doc/storage.R | 116 +++++----- inst/doc/storage.Rmd | 8 inst/doc/storage.html | 348 ++++++++++++++++++------------ inst/doc/training.R | 162 +++++++------- inst/doc/training.Rmd | 22 + inst/doc/training.html | 469 ++++++++++++++++++++++++++--------------- inst/doc/tuning.R | 94 ++++---- inst/doc/tuning.Rmd | 27 +- inst/doc/tuning.html | 466 +++++++++++++++++++++++++++------------- man/cloudml-package.Rd | 26 +- man/cloudml_deploy.Rd | 16 - man/cloudml_predict.Rd | 8 man/cloudml_train.Rd | 22 + man/gcloud_init.Rd | 5 man/gcloud_install.Rd | 5 man/gcloud_terminal.Rd | 5 man/gs_copy.Rd | 6 man/gs_data_dir.Rd | 2 man/gs_data_dir_local.Rd | 2 man/gs_local_dir.Rd | 2 man/gs_rsync.Rd | 16 + man/job_cancel.Rd | 9 man/job_collect.Rd | 18 + man/job_list.Rd | 18 + man/job_status.Rd | 9 man/job_stream_logs.Rd | 16 - man/job_trials.Rd | 9 vignettes/deployment.Rmd | 8 vignettes/getting_started.Rmd | 37 +-- vignettes/storage.Rmd | 8 vignettes/training.Rmd | 22 + vignettes/tuning.Rmd | 27 +- 46 files changed, 1819 insertions(+), 1198 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages
part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.3.1 dated 2024-02-19 and 3.3.2 dated 2025-08-18
DESCRIPTION | 6 +-- MD5 | 40 +++++++++++------------ NEWS.md | 7 ++++ R/AromaUnitSignalBinaryFile.writeDataFrame.R | 2 - R/AromaUnitSignalBinarySet.writeDataFrame.R | 2 - R/AromaUnitTabularBinaryFile.writeDataFrame.R | 2 - man/AbstractCNData.Rd | 2 - man/AbstractPSCNData.Rd | 2 - man/BinnedScatter.Rd | 2 - man/NonPairedPSCNData.Rd | 2 - man/PairedPSCNData.Rd | 2 - man/RawAlleleBFractions.Rd | 2 - man/RawCopyNumbers.Rd | 2 - man/RawGenomicSignals.Rd | 2 - man/RawMirroredAlleleBFractions.Rd | 2 - man/RawSequenceReads.Rd | 2 - man/SegmentedAlleleBFractions.Rd | 2 - man/SegmentedCopyNumbers.Rd | 2 - man/writeDataFrame.AromaUnitSignalBinaryFile.Rd | 2 - man/writeDataFrame.AromaUnitSignalBinarySet.Rd | 2 - man/writeDataFrame.AromaUnitTabularBinaryFile.Rd | 2 - 21 files changed, 48 insertions(+), 41 deletions(-)
Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation
of 'rmarkdown' reports, supporting reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre] ,
Kartikeya Kirar [aut] ,
Marcin Kosinski [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Mahmoud Hallal [aut],
Chendi Liao [rev],
Dony Unardi [rev],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.reporter versions 0.4.0 dated 2025-01-24 and 0.5.0 dated 2025-08-18
teal.reporter-0.4.0/teal.reporter/inst/css/Previewer.css |only teal.reporter-0.4.0/teal.reporter/man/get_bs_version.Rd |only teal.reporter-0.4.0/teal.reporter/man/report_load_srv.Rd |only teal.reporter-0.4.0/teal.reporter/man/report_load_ui.Rd |only teal.reporter-0.5.0/teal.reporter/DESCRIPTION | 25 teal.reporter-0.5.0/teal.reporter/MD5 | 114 - teal.reporter-0.5.0/teal.reporter/NAMESPACE | 2 teal.reporter-0.5.0/teal.reporter/NEWS.md | 15 teal.reporter-0.5.0/teal.reporter/R/AddCardModule.R | 128 -- teal.reporter-0.5.0/teal.reporter/R/DownloadModule.R | 131 +- teal.reporter-0.5.0/teal.reporter/R/FileBlock.R | 15 teal.reporter-0.5.0/teal.reporter/R/LoadReporterModule.R | 113 + teal.reporter-0.5.0/teal.reporter/R/Previewer.R | 584 +++------- teal.reporter-0.5.0/teal.reporter/R/Renderer.R | 9 teal.reporter-0.5.0/teal.reporter/R/ReportCard.R | 2 teal.reporter-0.5.0/teal.reporter/R/Reporter.R | 49 teal.reporter-0.5.0/teal.reporter/R/ResetModule.R | 72 - teal.reporter-0.5.0/teal.reporter/R/SimpleReporter.R | 12 teal.reporter-0.5.0/teal.reporter/R/teal.reporter.R | 1 teal.reporter-0.5.0/teal.reporter/R/utils.R | 128 -- teal.reporter-0.5.0/teal.reporter/R/yaml_utils.R | 8 teal.reporter-0.5.0/teal.reporter/R/zzz.R | 35 teal.reporter-0.5.0/teal.reporter/build/vignette.rds |binary teal.reporter-0.5.0/teal.reporter/inst/WORDLIST | 4 teal.reporter-0.5.0/teal.reporter/inst/css/custom.css | 98 - teal.reporter-0.5.0/teal.reporter/inst/doc/previewerReporter.R | 302 ++--- teal.reporter-0.5.0/teal.reporter/inst/doc/previewerReporter.Rmd | 55 teal.reporter-0.5.0/teal.reporter/inst/doc/previewerReporter.html | 306 ++--- teal.reporter-0.5.0/teal.reporter/inst/doc/simpleReporter.R | 371 +++--- teal.reporter-0.5.0/teal.reporter/inst/doc/simpleReporter.Rmd | 13 teal.reporter-0.5.0/teal.reporter/inst/doc/simpleReporter.html | 15 teal.reporter-0.5.0/teal.reporter/inst/doc/teal-reporter-blocks-overview.html | 8 teal.reporter-0.5.0/teal.reporter/inst/doc/teal-reporter.R | 30 teal.reporter-0.5.0/teal.reporter/inst/doc/teal-reporter.Rmd | 4 teal.reporter-0.5.0/teal.reporter/inst/doc/teal-reporter.html | 2 teal.reporter-0.5.0/teal.reporter/inst/js |only teal.reporter-0.5.0/teal.reporter/man/FileBlock.Rd | 15 teal.reporter-0.5.0/teal.reporter/man/PictureBlock.Rd | 1 teal.reporter-0.5.0/teal.reporter/man/Renderer.Rd | 11 teal.reporter-0.5.0/teal.reporter/man/ReportCard.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/Reporter.Rd | 22 teal.reporter-0.5.0/teal.reporter/man/TableBlock.Rd | 1 teal.reporter-0.5.0/teal.reporter/man/add_card_button.Rd | 6 teal.reporter-0.5.0/teal.reporter/man/as_yaml_auto.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/download_report_button.Rd | 12 teal.reporter-0.5.0/teal.reporter/man/load_report_button.Rd |only teal.reporter-0.5.0/teal.reporter/man/panel_item.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/print.rmd_yaml_header.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/reporter_previewer.Rd | 54 teal.reporter-0.5.0/teal.reporter/man/reporter_previewer_deprecated.Rd |only teal.reporter-0.5.0/teal.reporter/man/reset_report_button.Rd | 5 teal.reporter-0.5.0/teal.reporter/man/rmd_output_arguments.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/rmd_outputs.Rd | 2 teal.reporter-0.5.0/teal.reporter/man/simple_reporter.Rd | 2 teal.reporter-0.5.0/teal.reporter/tests/testthat/test-DownloadModule.R |only teal.reporter-0.5.0/teal.reporter/tests/testthat/test-PreviewerReportModule.R | 70 - teal.reporter-0.5.0/teal.reporter/tests/testthat/test-Reporter.R | 12 teal.reporter-0.5.0/teal.reporter/tests/testthat/test-ResetModule.R | 12 teal.reporter-0.5.0/teal.reporter/tests/testthat/test-utils.R | 4 teal.reporter-0.5.0/teal.reporter/vignettes/previewerReporter.Rmd | 55 teal.reporter-0.5.0/teal.reporter/vignettes/simpleReporter.Rmd | 13 teal.reporter-0.5.0/teal.reporter/vignettes/teal-reporter.Rmd | 4 62 files changed, 1283 insertions(+), 1679 deletions(-)
Title: Fit Robustly Proportional Hazards Regression Model
Description: An implementation of robust estimation in Cox model. Functionality includes fitting efficiently and robustly Cox proportional hazards regression model in its basic form, where explanatory variables are time independent with one event per subject. Method is based on a smooth modification of the partial likelihood.
Author: Tadeusz Bednarski [aut],
Filip Borowicz [aut],
Shana Scogin [cre]
Maintainer: Shana Scogin <shanarscogin@gmail.com>
Diff between coxrobust versions 1.0.1 dated 2022-04-06 and 1.0.2 dated 2025-08-18
DESCRIPTION | 10 ++-- MD5 | 19 ++++----- NEWS.md | 3 + R/coxr.R | 2 R/gen_data.R | 8 +-- R/plot.coxr.R | 8 +-- README.md |only man/coxr.Rd | 2 man/coxr.object.Rd | 108 ++++++++++++++++++++++++++--------------------------- man/gen_data.Rd | 8 +-- man/plot.coxr.Rd | 8 +-- 11 files changed, 90 insertions(+), 86 deletions(-)
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut],
Julia Silge [cre, aut] ,
Posit, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between butcher versions 0.3.5 dated 2025-03-18 and 0.3.6 dated 2025-08-18
DESCRIPTION | 12 +++--- MD5 | 22 ++++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/kknn.R | 16 -------- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/available-axe-methods.html | 66 ++++++++++++++++++------------------ inst/doc/butcher.html | 2 - man/axe-kknn.Rd | 3 - tests/testthat/test-kknn.R | 31 ++++++++-------- tests/testthat/test-weigh.R | 5 +- 12 files changed, 73 insertions(+), 89 deletions(-)
Title: Tools for Spell Checking in R
Description: Spell checking common document formats including latex, markdown, manual pages,
and description files. Includes utilities to automate checking of documentation and
vignettes as a unit test during 'R CMD check'. Both British and American English are
supported out of the box and other languages can be added. In addition, packages may
define a 'wordlist' to allow custom terminology without having to abuse punctuation.
Author: Jeroen Ooms [cre, aut] ,
Jim Hester [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between spelling versions 2.3.1 dated 2024-10-04 and 2.3.2 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ R/spell-check.R | 6 ++++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Power Analysis for Generalised Linear Mixed Models by Simulation
Description: Calculate power for generalised linear mixed models, using
simulation. Designed to work with models fit using the 'lme4' package.
Described in Green and MacLeod, 2016 <doi:10.1111/2041-210X.12504>.
Author: Peter Green [aut, cre] ,
Catriona MacLeod [aut],
Phillip Alday [ctb]
Maintainer: Peter Green <simr.peter@gmail.com>
Diff between simr versions 1.0.7 dated 2023-04-13 and 1.0.8 dated 2025-08-18
DESCRIPTION | 10 ++-- MD5 | 32 ++++++------ NEWS.md | 4 + R/options.R | 2 R/print.R | 6 +- R/testLibrary.R | 10 ++-- README.md | 1 build/vignette.rds |binary inst/doc/examples.R | 6 +- inst/doc/examples.html | 94 +++++++++++++++++++------------------- inst/doc/fromscratch.R | 2 inst/doc/fromscratch.html | 42 ++++++++-------- man/print.powerSim.Rd | 6 +- man/simr-package.Rd | 23 +++++++++ man/simrOptions.Rd | 2 man/tests.Rd | 10 ++-- tests/testthat/test_testLibrary.R | 7 +- 17 files changed, 142 insertions(+), 115 deletions(-)
Title: Analyses of Proportions using Anscombe Transform
Description: Analyses of Proportions can be performed on the Anscombe (arcsine-related) transformed
data. The 'ANOPA' package can analyze proportions obtained from up to
four factors. The factors can be within-subject or between-subject or a mix
of within- and between-subject. The main, omnibus analysis can be followed by
additive decompositions into interaction effects, main effects, simple
effects, contrast effects, etc., mimicking precisely the logic of ANOVA. For
that reason, we call this set of tools 'ANOPA' (Analysis of Proportion
using Anscombe transform) to highlight its similarities with ANOVA.
The 'ANOPA' framework also allows plots of proportions easy to obtain
along with confidence intervals. Finally, effect sizes and planning statistical
power are easily done under this framework. Only particularity, the 'ANOPA' computes
F statistics which have an infinite degree of freedom on the denominator.
See Laurencelle and Cousineau (2023) <doi:10.3389/fpsyg.2022.1045436>.
Author: Denis Cousineau [aut, ctb, cre],
Louis Laurencelle [aut, ctb]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between ANOPA versions 0.1.3 dated 2024-03-22 and 0.2.3 dated 2025-08-18
ANOPA-0.1.3/ANOPA/man/A.Rd |only ANOPA-0.1.3/ANOPA/man/anopa.Rd |only ANOPA-0.1.3/ANOPA/man/anopaN2Power.Rd |only ANOPA-0.1.3/ANOPA/man/anopa_asn_trans1.Rd |only ANOPA-0.1.3/ANOPA/man/conversion.Rd |only ANOPA-0.1.3/ANOPA/man/rBernoulli.Rd |only ANOPA-0.1.3/ANOPA/tests/testthat/test-ANOPA-5-PASFAIT.R |only ANOPA-0.2.3/ANOPA/DESCRIPTION | 16 ANOPA-0.2.3/ANOPA/MD5 | 143 - ANOPA-0.2.3/ANOPA/NAMESPACE | 2 ANOPA-0.2.3/ANOPA/NEWS.md | 24 ANOPA-0.2.3/ANOPA/R/ANOPA-anopa.R | 1235 ++++++------ ANOPA-0.2.3/ANOPA/R/ANOPA-contrastProportions.R | 10 ANOPA-0.2.3/ANOPA/R/ANOPA-convert.R | 78 ANOPA-0.2.3/ANOPA/R/ANOPA-emProportions.R | 337 ++- ANOPA-0.2.3/ANOPA/R/ANOPA-functions.R | 12 ANOPA-0.2.3/ANOPA/R/ANOPA-logicals.R | 31 ANOPA-0.2.3/ANOPA/R/ANOPA-methods.R | 54 ANOPA-0.2.3/ANOPA/R/ANOPA-package.R | 30 ANOPA-0.2.3/ANOPA/R/ANOPA-plot.R | 313 +-- ANOPA-0.2.3/ANOPA/R/ANOPA-posthocProportions.R | 8 ANOPA-0.2.3/ANOPA/R/ANOPA-power.R | 50 ANOPA-0.2.3/ANOPA/R/ANOPA-random.R | 131 - ANOPA-0.2.3/ANOPA/R/ANOPA-unitaryAlpha.R | 14 ANOPA-0.2.3/ANOPA/R/ArringtonEtAll2002.R | 4 ANOPA-0.2.3/ANOPA/R/ArticleExample1.R | 4 ANOPA-0.2.3/ANOPA/R/ArticleExample2.R | 4 ANOPA-0.2.3/ANOPA/R/ArticleExample3.R | 8 ANOPA-0.2.3/ANOPA/R/minimalExamples.R | 17 ANOPA-0.2.3/ANOPA/README.md | 10 ANOPA-0.2.3/ANOPA/build/partial.rdb |binary ANOPA-0.2.3/ANOPA/build/vignette.rds |binary ANOPA-0.2.3/ANOPA/data/minimalMxExampleCompiled.rda |only ANOPA-0.2.3/ANOPA/inst/REFERENCES.bib | 2 ANOPA-0.2.3/ANOPA/inst/doc/A-WhatIsANOPA.Rmd | 38 ANOPA-0.2.3/ANOPA/inst/doc/A-WhatIsANOPA.html | 100 ANOPA-0.2.3/ANOPA/inst/doc/B-DataFormatsForProportions.R | 23 ANOPA-0.2.3/ANOPA/inst/doc/B-DataFormatsForProportions.Rmd | 54 ANOPA-0.2.3/ANOPA/inst/doc/B-DataFormatsForProportions.html | 130 - ANOPA-0.2.3/ANOPA/inst/doc/C-ConfidenceIntervals.Rmd | 7 ANOPA-0.2.3/ANOPA/inst/doc/C-ConfidenceIntervals.html | 24 ANOPA-0.2.3/ANOPA/inst/doc/D-ArringtonExample.R | 49 ANOPA-0.2.3/ANOPA/inst/doc/D-ArringtonExample.Rmd | 94 ANOPA-0.2.3/ANOPA/inst/doc/D-ArringtonExample.html | 114 - ANOPA-0.2.3/ANOPA/inst/doc/E-ArcsineIsAsinine.R | 2 ANOPA-0.2.3/ANOPA/inst/doc/E-ArcsineIsAsinine.Rmd | 10 ANOPA-0.2.3/ANOPA/inst/doc/E-ArcsineIsAsinine.html | 25 ANOPA-0.2.3/ANOPA/inst/doc/F-TestingTypeIError.R | 376 +-- ANOPA-0.2.3/ANOPA/inst/doc/F-TestingTypeIError.Rmd | 8 ANOPA-0.2.3/ANOPA/inst/doc/F-TestingTypeIError.html | 15 ANOPA-0.2.3/ANOPA/man/ANOPA-package.Rd | 14 ANOPA-0.2.3/ANOPA/man/ArringtonEtAl2002.Rd | 2 ANOPA-0.2.3/ANOPA/man/ArticleExample1.Rd | 2 ANOPA-0.2.3/ANOPA/man/ArticleExample2.Rd | 4 ANOPA-0.2.3/ANOPA/man/ArticleExample3.Rd | 6 ANOPA-0.2.3/ANOPA/man/Conversion.Rd |only ANOPA-0.2.3/ANOPA/man/GRP.Rd |only ANOPA-0.2.3/ANOPA/man/PowerComputation.Rd |only ANOPA-0.2.3/ANOPA/man/Transformations.Rd |only ANOPA-0.2.3/ANOPA/man/anopaPlot.Rd |only ANOPA-0.2.3/ANOPA/man/anopafct.Rd |only ANOPA-0.2.3/ANOPA/man/contrastProportions.Rd | 8 ANOPA-0.2.3/ANOPA/man/corrected.Rd | 2 ANOPA-0.2.3/ANOPA/man/emProportions.Rd | 18 ANOPA-0.2.3/ANOPA/man/explain.Rd | 2 ANOPA-0.2.3/ANOPA/man/minimalExamples.Rd | 17 ANOPA-0.2.3/ANOPA/man/posthocProportions.Rd | 6 ANOPA-0.2.3/ANOPA/man/summarize.Rd | 4 ANOPA-0.2.3/ANOPA/man/uncorrected.Rd | 2 ANOPA-0.2.3/ANOPA/man/unitaryAlpha.Rd | 4 ANOPA-0.2.3/ANOPA/tests/testthat/test-ANOPA-1.R | 15 ANOPA-0.2.3/ANOPA/tests/testthat/test-ANOPA-2.R | 53 ANOPA-0.2.3/ANOPA/tests/testthat/test-ANOPA-4.R | 2 ANOPA-0.2.3/ANOPA/tests/testthat/test-ANOPA-5.R |only ANOPA-0.2.3/ANOPA/vignettes/A-WhatIsANOPA.Rmd | 38 ANOPA-0.2.3/ANOPA/vignettes/B-DataFormatsForProportions.Rmd | 54 ANOPA-0.2.3/ANOPA/vignettes/C-ConfidenceIntervals.Rmd | 7 ANOPA-0.2.3/ANOPA/vignettes/D-ArringtonExample.Rmd | 94 ANOPA-0.2.3/ANOPA/vignettes/E-ArcsineIsAsinine.Rmd | 10 ANOPA-0.2.3/ANOPA/vignettes/F-TestingTypeIError.Rmd | 8 80 files changed, 2422 insertions(+), 1556 deletions(-)
Title: Extend the 'copula' Package with Families and Models from
'VineCopula'
Description: Provides new classes for (rotated) BB1, BB6, BB7, BB8, and
Tawn copulas, extends the existing Gumbel and Clayton families with
rotations, and allows to set up a vine copula model using the 'copula' API.
Corresponding objects from the 'VineCopula' API can easily be converted.
Author: Thomas Nagler [aut, cre],
Benedikt Graeler [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between VC2copula versions 0.1.5 dated 2024-02-22 and 0.1.6 dated 2025-08-18
DESCRIPTION | 10 ++--- MD5 | 72 +++++++++++++++++++++--------------------- R/0_wrappers.R | 10 ++--- R/1_generators.R | 2 - R/BB1copula.R | 10 ++--- R/BB6copula.R | 8 ++-- R/BB7copula.R | 10 ++--- R/BB8copula.R | 10 ++--- R/joeBiCopula.R | 12 +++---- R/surClaytonCopula.R | 4 +- R/surGumbelCopula.R | 4 +- R/tawnT1Copula.R | 4 +- R/tawnT2Copula.R | 4 +- R/vineCopulas.R | 7 +--- man/BB1Copula-class.Rd | 6 +-- man/BB1Copula.Rd | 4 +- man/BB6Copula-class.Rd | 6 +-- man/BB6Copula.Rd | 2 - man/BB7Copula-class.Rd | 6 +-- man/BB7Copula.Rd | 4 +- man/BB8Copula-class.Rd | 6 +-- man/BB8Copula.Rd | 4 +- man/BiCop2copula.Rd | 10 ++--- man/VC2copula-package.Rd | 1 man/ddCopula.Rd | 2 - man/joeBiCopula-class.Rd | 6 +-- man/joeBiCopula.Rd | 6 +-- man/surClaytonCopula-class.Rd | 2 - man/surClaytonCopula.Rd | 2 - man/surGumbelCopula-class.Rd | 2 - man/surGumbelCopula.Rd | 2 - man/tawnT1Copula-class.Rd | 2 - man/tawnT1Copula.Rd | 2 - man/tawnT2Copula-class.Rd | 2 - man/tawnT2Copula.Rd | 2 - man/vineCopula-class.Rd | 5 +- man/vineCopula.Rd | 2 - 37 files changed, 125 insertions(+), 128 deletions(-)
Title: Query the 'NHS TRUD API'
Description: Provides a convenient R interface to the 'National Health Service
NHS Technology Reference Update Distribution (TRUD) API', allowing users
to list available releases for their subscribed items, retrieve metadata,
and download release files. For more information on the API, see
<https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.
Author: Alasdair Warwick [aut, cre, cph] ,
Robert Luben [aut] ,
Abraham Olvera-Barrios [aut] ,
Chuin Ying Ung [aut] ,
Jon Clayden [rev] ,
Alexandros Kouretsis [rev]
Maintainer: Alasdair Warwick <alasdair.warwick.19@ucl.ac.uk>
Diff between trud versions 0.1.0 dated 2024-07-22 and 0.2.0 dated 2025-08-18
trud-0.1.0/trud/R/utils-pipe.R |only trud-0.1.0/trud/man/pipe.Rd |only trud-0.2.0/trud/DESCRIPTION | 51 +- trud-0.2.0/trud/MD5 | 54 +- trud-0.2.0/trud/NAMESPACE | 2 trud-0.2.0/trud/NEWS.md | 32 + trud-0.2.0/trud/R/download_item.R | 183 ++++--- trud-0.2.0/trud/R/get_item_metadata.R | 70 +- trud-0.2.0/trud/R/get_subscribed_metadata.R | 61 +- trud-0.2.0/trud/R/sysdata.rda |only trud-0.2.0/trud/R/trud_items.R | 75 ++ trud-0.2.0/trud/R/utils.R | 209 ++++++-- trud-0.2.0/trud/README.md | 253 +++++----- trud-0.2.0/trud/build |only trud-0.2.0/trud/inst |only trud-0.2.0/trud/man/download_item.Rd | 91 ++- trud-0.2.0/trud/man/get_item_metadata.Rd | 56 +- trud-0.2.0/trud/man/get_subscribed_metadata.Rd | 33 - trud-0.2.0/trud/man/rmd |only trud-0.2.0/trud/man/trud-package.Rd | 14 trud-0.2.0/trud/man/trud_items.Rd | 26 - trud-0.2.0/trud/tests/spelling.R |only trud-0.2.0/trud/tests/testthat.R | 5 trud-0.2.0/trud/tests/testthat/test-download_item.R | 134 ++++- trud-0.2.0/trud/tests/testthat/test-get_item_metadata.R | 157 ++++-- trud-0.2.0/trud/tests/testthat/test-get_subscribed_metadata.R | 29 - trud-0.2.0/trud/tests/testthat/test-trud_items.R | 116 ++++ trud-0.2.0/trud/tests/testthat/test-utils.R | 114 ++-- trud-0.2.0/trud/vignettes |only 29 files changed, 1233 insertions(+), 532 deletions(-)
Title: Plant Phenotyping and Bayesian Statistics
Description: Analyse common types of plant phenotyping data, provide a simplified interface
to longitudinal growth modeling and select Bayesian statistics,
and streamline use of 'PlantCV' output.
Several Bayesian methods and reporting guidelines for Bayesian methods are described in
Kruschke (2018) <doi:10.1177/2515245918771304>,
Kruschke (2013) <doi:10.1037/a0029146>, and Kruschke (2021) <doi:10.1038/s41562-021-01177-7>.
Author: Josh Sumner [aut, cre] ,
Jeffrey Berry [aut] ,
Noah Fahlgren [rev] ,
Donald Danforth Plant Science Center [cph]
Maintainer: Josh Sumner <jsumner@danforthcenter.org>
Diff between pcvr versions 1.2.0 dated 2025-04-16 and 1.3.1 dated 2025-08-18
pcvr-1.2.0/pcvr/inst/doc/bellwether.R |only pcvr-1.2.0/pcvr/inst/doc/bellwether.Rmd |only pcvr-1.2.0/pcvr/inst/doc/bellwether.html |only pcvr-1.2.0/pcvr/man/bw.outliers.Rd |only pcvr-1.2.0/pcvr/man/bw.time.Rd |only pcvr-1.2.0/pcvr/man/bw.water.Rd |only pcvr-1.2.0/pcvr/vignettes/bellwether.Rmd |only pcvr-1.3.1/pcvr/DESCRIPTION | 12 pcvr-1.3.1/pcvr/MD5 | 128 - pcvr-1.3.1/pcvr/NAMESPACE | 6 pcvr-1.3.1/pcvr/NEWS.md | 34 pcvr-1.3.1/pcvr/R/brmPlot.R | 2 pcvr-1.3.1/pcvr/R/brmSS.R | 51 pcvr-1.3.1/pcvr/R/brmSSHelpers.R | 67 pcvr-1.3.1/pcvr/R/brms_segmentedForm.R | 209 + pcvr-1.3.1/pcvr/R/bwoutliers.R | 31 pcvr-1.3.1/pcvr/R/bwtime.R | 14 pcvr-1.3.1/pcvr/R/bwwater.R | 4 pcvr-1.3.1/pcvr/R/combineDraws.R | 26 pcvr-1.3.1/pcvr/R/conjugate.R | 27 pcvr-1.3.1/pcvr/R/cumulativePheno.R | 6 pcvr-1.3.1/pcvr/R/distPlot.R | 65 pcvr-1.3.1/pcvr/R/frem.R | 106 pcvr-1.3.1/pcvr/R/growthSS.R | 22 pcvr-1.3.1/pcvr/R/growthSS_generalHelpers.R | 13 pcvr-1.3.1/pcvr/R/growthSim.R | 233 + pcvr-1.3.1/pcvr/R/nlmeSS.R | 93 pcvr-1.3.1/pcvr/R/nlrqSS.R | 108 pcvr-1.3.1/pcvr/R/pcvjoyplot.R | 9 pcvr-1.3.1/pcvr/R/pcvtheme.R | 1 pcvr-1.3.1/pcvr/R/relativeTolerance.R | 4 pcvr-1.3.1/pcvr/R/testGrowth.R | 2 pcvr-1.3.1/pcvr/R/wue.R | 7 pcvr-1.3.1/pcvr/build/vignette.rds |binary pcvr-1.3.1/pcvr/inst/doc/longitudinal.Rmd | 2 pcvr-1.3.1/pcvr/inst/doc/longitudinal.html | 1789 ++++++++------ pcvr-1.3.1/pcvr/inst/doc/pcvr.R |only pcvr-1.3.1/pcvr/inst/doc/pcvr.Rmd |only pcvr-1.3.1/pcvr/inst/doc/pcvr.html |only pcvr-1.3.1/pcvr/inst/doc/roots.Rmd | 2 pcvr-1.3.1/pcvr/inst/doc/roots.html | 1118 ++++---- pcvr-1.3.1/pcvr/man/combineDraws.Rd | 16 pcvr-1.3.1/pcvr/man/conjugate.Rd | 2 pcvr-1.3.1/pcvr/man/cumulativePheno.Rd | 6 pcvr-1.3.1/pcvr/man/distributionPlot.Rd | 12 pcvr-1.3.1/pcvr/man/frem.Rd | 15 pcvr-1.3.1/pcvr/man/growthSS.Rd | 20 pcvr-1.3.1/pcvr/man/growthSim.Rd | 42 pcvr-1.3.1/pcvr/man/pcv.joyplot.Rd | 3 pcvr-1.3.1/pcvr/man/pcv.outliers.Rd |only pcvr-1.3.1/pcvr/man/pcv.time.Rd |only pcvr-1.3.1/pcvr/man/pcv.water.Rd |only pcvr-1.3.1/pcvr/man/pwue.Rd | 9 pcvr-1.3.1/pcvr/man/relativeTolerance.Rd | 4 pcvr-1.3.1/pcvr/tests/testthat/test-brmSSHelpers.R | 54 pcvr-1.3.1/pcvr/tests/testthat/test-brmsInterceptModels.R | 4 pcvr-1.3.1/pcvr/tests/testthat/test-brmsModels.R | 1718 +++++++------ pcvr-1.3.1/pcvr/tests/testthat/test-conjugate_helpers.R | 11 pcvr-1.3.1/pcvr/tests/testthat/test-growthModels.R | 68 pcvr-1.3.1/pcvr/tests/testthat/test-growthSS_helpers.R | 119 pcvr-1.3.1/pcvr/tests/testthat/test-initializers.R | 22 pcvr-1.3.1/pcvr/tests/testthat/test-long_mv_workflow.R | 30 pcvr-1.3.1/pcvr/tests/testthat/test-long_sv_workflow.R | 8 pcvr-1.3.1/pcvr/tests/testthat/test-mvSSModels.R | 38 pcvr-1.3.1/pcvr/tests/testthat/test-nlmeSS_helpers.R | 45 pcvr-1.3.1/pcvr/tests/testthat/test-survSS_helpers.R | 3 pcvr-1.3.1/pcvr/tests/testthat/test-sv-conjugate.R | 4 pcvr-1.3.1/pcvr/tests/testthat/test-wide_mv_workflow.R | 25 pcvr-1.3.1/pcvr/tests/testthat/test-wide_sv_workflow.R | 28 pcvr-1.3.1/pcvr/vignettes/longitudinal.Rmd | 2 pcvr-1.3.1/pcvr/vignettes/pcvr.Rmd |only pcvr-1.3.1/pcvr/vignettes/roots.Rmd | 2 72 files changed, 4129 insertions(+), 2372 deletions(-)
Title: Multi-Objective Optimal Design of Experiments
Description: Provides functionality to generate compound optimal designs for targeting the multiple experimental objectives directly, ensuring that the full set of research questions is answered as economically as possible. Designs can be found using point or coordinate exchange algorithms combining estimation, inference and lack-of-fit criteria that account for model inadequacy. Details and examples are given by Koutra et al. (2024) <doi:10.48550/arXiv.2412.17158>.
Author: Vasiliki Koutra [aut, cre, cph] ,
Olga Egorova [aut, cph],
Steven Gilmour [aut, cph],
Luzia Trinca [aut, cph]
Maintainer: Vasiliki Koutra <vasiliki.koutra@kcl.ac.uk>
Diff between MOODE versions 1.0.1 dated 2025-01-08 and 1.1.0 dated 2025-08-18
MOODE-1.0.1/MOODE/R/print.settings.R |only MOODE-1.0.1/MOODE/man/print.settings.Rd |only MOODE-1.1.0/MOODE/DESCRIPTION | 11 ++++++----- MOODE-1.1.0/MOODE/MD5 | 27 +++++++++++++-------------- MOODE-1.1.0/MOODE/NAMESPACE | 2 +- MOODE-1.1.0/MOODE/NEWS.md | 8 +++++++- MOODE-1.1.0/MOODE/R/Search.R | 10 +++++++--- MOODE-1.1.0/MOODE/R/mood.R | 12 +++++++----- MOODE-1.1.0/MOODE/R/pointexchange.R | 3 ++- MOODE-1.1.0/MOODE/R/print.mood.R |only MOODE-1.1.0/MOODE/R/spheric.R | 10 ++++++---- MOODE-1.1.0/MOODE/README.md | 18 +++++++++--------- MOODE-1.1.0/MOODE/build/partial.rdb |binary MOODE-1.1.0/MOODE/man/Search.Rd | 4 ++-- MOODE-1.1.0/MOODE/man/mood.Rd | 2 +- MOODE-1.1.0/MOODE/man/point.swap.Rd | 1 + 16 files changed, 62 insertions(+), 46 deletions(-)
Title: Multivariate Kernel Density Estimation with Vine Copulas
Description: Implements the vine copula based kernel density estimator of
Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does
not suffer from the curse of dimensionality and is therefore well suited for
high-dimensional applications.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kdevine versions 0.4.5 dated 2024-06-13 and 0.4.6 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/contour.kdevinecop.R | 2 +- R/kdevinecop.R | 2 +- man/contour.kdevinecop.Rd | 2 +- man/kdevinecop.Rd | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Estimation, forecasting, and simulation of generalized
autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013)
<doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>.
Model specification allows for various data types and distributions,
different parametrizations, exogenous variables, joint and separate modeling
of exogenous variables and dynamics, higher score and autoregressive orders,
custom and unconditional initial values of time-varying parameters, fixed
and bounded values of coefficients, and missing values. Model estimation is
performed by the maximum likelihood method.
Author: Vladimir Holy [aut, cre]
Maintainer: Vladimir Holy <vladimir.holy@vse.cz>
Diff between gasmodel versions 0.6.1 dated 2025-06-12 and 0.6.2 dated 2025-08-18
DESCRIPTION | 6 MD5 | 76 ++++--- NEWS.md | 5 R/distr_ged_meanscale.R |only R/helper_bootstrap.R |only R/helper_load.R |only R/helper_silent.R | 33 ++- R/main_bootstrap.R | 328 +++----------------------------- R/main_estimate.R | 130 ++++-------- R/main_filter.R | 75 ++----- R/main_forecast.R | 82 ++------ R/main_simulate.R | 68 +----- R/sysdata.rda |binary README.md | 12 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/case_durations.Rmd | 15 - inst/doc/case_durations.html | 63 ++++-- inst/doc/case_rankings.Rmd | 154 ++++++--------- inst/doc/case_rankings.html | 231 +++++++++++++--------- inst/doc/compare_gas.Rmd | 19 - inst/doc/compare_gas.html | 70 ++++-- inst/doc/customization.Rmd |only inst/doc/customization.html |only inst/doc/distributions.Rmd | 39 +++ inst/doc/distributions.html | 111 ++++++++-- man/distr.Rd | 10 man/gas.Rd | 85 +++++--- man/gas_bootstrap.Rd | 78 +++---- man/gas_filter.Rd | 72 ++----- man/gas_forecast.Rd | 49 ++-- man/gas_simulate.Rd | 42 +--- man/wrappers_optim.Rd | 20 + tests/manual/test_distr_ged_meanscale.r |only vignettes/case_durations.Rmd | 15 - vignettes/case_durations.Rmd.orig | 15 - vignettes/case_rankings.Rmd | 154 ++++++--------- vignettes/case_rankings.Rmd.orig | 26 -- vignettes/compare_gas.Rmd | 19 - vignettes/compare_gas.Rmd.orig | 14 - vignettes/customization.Rmd |only vignettes/distributions.Rmd | 39 +++ vignettes/library.bib |only 43 files changed, 973 insertions(+), 1182 deletions(-)
Title: Generate Postestimation Quantities for Bayesian MCMC Estimation
Description: An implementation of functions to generate and plot postestimation quantities after estimating Bayesian regression models using Markov chain Monte Carlo (MCMC). Functionality includes the estimation of the Precision-Recall curves (see Beger, 2016 <doi:10.2139/ssrn.2765419>), the implementation of the observed values method of calculating predicted probabilities by Hanmer and Kalkan (2013) <doi:10.1111/j.1540-5907.2012.00602.x>, the implementation of the average value method of calculating predicted probabilities (see King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>), and the generation and plotting of first differences to summarize typical effects across covariates (see Long 1997, ISBN:9780803973749; King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>). This package can be used with MCMC output generated by any Bayesian estimation tool including 'JAGS', 'BUGS', 'MCMCpack', and 'Stan'.
Author: Johannes Karreth [aut] ,
Shana Scogin [aut, cre] ,
Rob Williams [aut] ,
Andreas Beger [aut] ,
Myunghee Lee [ctb],
Neil Williams [ctb]
Maintainer: Shana Scogin <shanarscogin@gmail.com>
Diff between BayesPostEst versions 0.3.2 dated 2021-11-11 and 0.4.0 dated 2025-08-18
BayesPostEst-0.3.2/BayesPostEst/R/BayesPostEst.R |only BayesPostEst-0.3.2/BayesPostEst/R/data.R |only BayesPostEst-0.3.2/BayesPostEst/data |only BayesPostEst-0.3.2/BayesPostEst/man/jags_interactive.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/jags_interactive_cat.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/jags_logit.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/jags_probit.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/sim_data.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/sim_data_interactive.Rd |only BayesPostEst-0.3.2/BayesPostEst/man/sim_data_interactive_cat.Rd |only BayesPostEst-0.3.2/BayesPostEst/tests/testdata |only BayesPostEst-0.3.2/BayesPostEst/tests/testdata-raw |only BayesPostEst-0.4.0/BayesPostEst/DESCRIPTION | 30 BayesPostEst-0.4.0/BayesPostEst/MD5 | 102 - BayesPostEst-0.4.0/BayesPostEst/NEWS.md | 5 BayesPostEst-0.4.0/BayesPostEst/R/BayesPostEst-package.R |only BayesPostEst-0.4.0/BayesPostEst/R/imports.R |only BayesPostEst-0.4.0/BayesPostEst/R/mcmcFD.R | 3 BayesPostEst-0.4.0/BayesPostEst/R/mcmcReg.R | 15 BayesPostEst-0.4.0/BayesPostEst/README.md | 196 +-- BayesPostEst-0.4.0/BayesPostEst/build/partial.rdb |binary BayesPostEst-0.4.0/BayesPostEst/inst/doc/getting_started.html | 584 ++++++++-- BayesPostEst-0.4.0/BayesPostEst/man/BayesPostEst.Rd | 28 BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-38-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-40-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-42-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-44-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-47-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-48-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-49-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-53-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-54-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-56-1.png |binary BayesPostEst-0.4.0/BayesPostEst/man/figures/README-unnamed-chunk-57-1.png |binary BayesPostEst-0.4.0/BayesPostEst/tests/testthat/helper-libs.R | 6 BayesPostEst-0.4.0/BayesPostEst/tests/testthat/setup-data |only BayesPostEst-0.4.0/BayesPostEst/tests/testthat/setup.R |only BayesPostEst-0.4.0/BayesPostEst/tests/testthat/teardown.R |only BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcAveProb.R | 24 BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcCoefPlot.R | 180 +-- BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcFD.R | 59 - BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcMargEff.R | 43 BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcObsProb.R | 40 BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcReg.R | 196 ++- BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcRocPrc.R | 326 ++++- BayesPostEst-0.4.0/BayesPostEst/tests/testthat/test_mcmcTab.R | 81 - 46 files changed, 1408 insertions(+), 510 deletions(-)
Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superb(), return a plot. It can
also be used to obtain a dataframe with the statistics and their precision intervals
so that other plotting environments (e.g., Excel)
can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109>
or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001> for specific references.
The documentation is available at <https://dcousin3.github.io/superb/> .
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 0.95.19 dated 2024-11-10 and 1.0.0 dated 2025-08-18
DESCRIPTION | 30 MD5 | 332 +- NAMESPACE | 2 NEWS.md | 567 ++- R/CousineauLaurencelleLambda.R | 4 R/TMB1964r.R | 8 R/WelchDegreeOfFreedom.R | 2 R/dataFigure1.R | 16 R/dataFigure2.R | 16 R/dataFigure3.R | 16 R/dataFigure4.R | 18 R/functionsLogical.R | 41 R/functionsPlotting_advanced.R | 4 R/functionsPlotting_base.R | 6 R/functionsPlotting_boxplot.R | 10 R/functionsPlotting_circular.R | 10 R/functionsPlotting_corset.R | 31 R/functionsPlotting_moderate.R | 38 R/functionsPlotting_ribbon.R | 2 R/functionsStatistical.R | 31 R/functionsTransformation.R | 13 R/geom_flat_violin.R | 19 R/geom_superberrorbar.R | 36 R/grd.R | 173 - R/makeTransparent.R | 7 R/runDebug.R | 11 R/showSignificance.R | 2 R/superb-package.R | 13 R/superb.R | 131 R/superbData.R | 2 R/superbPlot.R | 1500 +++++----- R/superbShiny.R | 23 R/superbToWide.R | 80 README.md | 157 - build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 13 inst/doc/CustomizingSuperbPlots.R | 24 inst/doc/CustomizingSuperbPlots.Rmd | 8 inst/doc/CustomizingSuperbPlots.html | 53 inst/doc/TheMakingOf.R | 56 inst/doc/TheMakingOf.Rmd | 34 inst/doc/TheMakingOf.html | 51 inst/doc/Vignette1.R | 25 inst/doc/Vignette1.Rmd | 25 inst/doc/Vignette1.html | 77 inst/doc/Vignette2.R | 16 inst/doc/Vignette2.Rmd | 20 inst/doc/Vignette2.html | 23 inst/doc/Vignette3.R | 22 inst/doc/Vignette3.Rmd | 30 inst/doc/Vignette3.html | 204 - inst/doc/Vignette4.R | 16 inst/doc/Vignette4.Rmd | 16 inst/doc/Vignette4.html | 145 inst/doc/Vignette5.R | 36 inst/doc/Vignette5.Rmd | 18 inst/doc/Vignette5.html | 43 inst/doc/Vignette6.R | 24 inst/doc/Vignette6.Rmd | 24 inst/doc/Vignette6.html | 57 inst/doc/Vignette7.R | 14 inst/doc/Vignette7.Rmd | 14 inst/doc/Vignette7.html | 51 inst/doc/Vignette8.R | 6 inst/doc/Vignette8.Rmd | 6 inst/doc/Vignette8.html | 15 inst/doc/Vignette9.R | 6 inst/doc/Vignette9.Rmd | 6 inst/doc/Vignette9.html | 208 - inst/doc/VignetteA.R | 42 inst/doc/VignetteA.Rmd | 18 inst/doc/VignetteA.html | 53 inst/doc/VignetteB.R | 8 inst/doc/VignetteB.Rmd | 16 inst/doc/VignetteB.html | 26 inst/doc/VignetteC.R | 4 inst/doc/VignetteC.Rmd | 4 inst/doc/VignetteC.html | 9 inst/doc/VignetteD.R | 24 inst/doc/VignetteD.Rmd | 10 inst/doc/VignetteD.html | 52 inst/doc/VignetteE.R | 30 inst/doc/VignetteE.Rmd | 22 inst/doc/VignetteE.html | 45 inst/doc/VignetteF.R | 2 inst/doc/VignetteF.Rmd | 2 inst/doc/VignetteF.html | 21 inst/doc/VignetteG.R | 16 inst/doc/VignetteG.Rmd | 22 inst/doc/VignetteG.html | 96 inst/doc/VignetteH.R | 34 inst/doc/VignetteH.Rmd | 24 inst/doc/VignetteH.html | 47 inst/superbShiny/App.R | 35 inst/superbShiny/rsconnect/shinyapps.io/dcousin3/superbshiny.dcf | 2 man/CousineauLaurencelleLambda.Rd | 4 man/GRD.Rd | 36 man/TMB1964r.Rd | 8 man/WelchDegreeOfFreedom.Rd | 2 man/biasCorrectionTransform.Rd | 4 man/dataFigure1.Rd | 16 man/dataFigure2.Rd | 16 man/dataFigure3.Rd | 16 man/dataFigure4.Rd | 18 man/geom_flat_violin.Rd | 17 man/geom_superberrorbar.Rd | 31 man/makeTransparent.Rd | 7 man/measuresWithMissingData.Rd | 3 man/poolSDTransform.Rd | 2 man/precisionMeasureWithCustomDF.Rd | 24 man/runDebug.Rd | 11 man/showSignificance.Rd | 2 man/subjectCenteringTransform.Rd | 2 man/summaryStatistics.Rd | 4 man/superb-package.Rd | 4 man/superb.Rd | 76 man/superbData.Rd | 2 man/superbPlot.Rd | 26 man/superbPlot.bar.Rd | 2 man/superbPlot.boxplot.Rd | 10 man/superbPlot.circularline.Rd | 2 man/superbPlot.circularlineBand.Rd | 2 man/superbPlot.circularpoint.Rd | 2 man/superbPlot.circularpointjitter.Rd | 2 man/superbPlot.circularpointlinejitter.Rd | 2 man/superbPlot.corset.Rd | 13 man/superbPlot.halfwidthline.Rd | 2 man/superbPlot.line.Rd | 2 man/superbPlot.lineBand.Rd | 2 man/superbPlot.point.Rd | 2 man/superbPlot.pointindividualline.Rd | 8 man/superbPlot.pointjitter.Rd | 2 man/superbPlot.pointjitterviolin.Rd | 2 man/superbPlot.pointlinejitter.Rd | 2 man/superbPlot.raincloud.Rd | 2 man/superbShiny.Rd | 18 man/superbToWide.Rd | 11 man/twoStepTransform.Rd | 4 tests/testthat/test_GRD.R | 42 tests/testthat/test_compatibility.R | 2 tests/testthat/test_deprecated.R |only tests/testthat/test_experimental.R |only tests/testthat/test_geom_superberrorbar.R | 2 tests/testthat/test_showSignificance.R | 2 tests/testthat/test_superb.R | 62 tests/testthat/test_superbData.R | 4 tests/testthat/test_superbPlot.R | 74 tests/testthat/test_superbToWide.R | 48 vignettes/CustomizingSuperbPlots.Rmd | 8 vignettes/TheMakingOf.Rmd | 34 vignettes/Vignette1.Rmd | 25 vignettes/Vignette2.Rmd | 20 vignettes/Vignette3.Rmd | 30 vignettes/Vignette4.Rmd | 16 vignettes/Vignette5.Rmd | 18 vignettes/Vignette6.Rmd | 24 vignettes/Vignette7.Rmd | 14 vignettes/Vignette8.Rmd | 6 vignettes/Vignette9.Rmd | 6 vignettes/VignetteA.Rmd | 18 vignettes/VignetteB.Rmd | 16 vignettes/VignetteC.Rmd | 4 vignettes/VignetteD.Rmd | 10 vignettes/VignetteE.Rmd | 22 vignettes/VignetteF.Rmd | 2 vignettes/VignetteG.Rmd | 22 vignettes/VignetteH.Rmd | 24 168 files changed, 3605 insertions(+), 2774 deletions(-)
Title: Sweave Drivers with Extra Tricks Up their Sleeve
Description: Weave and tangle drivers for Sweave extending the
standard drivers. RweaveExtraLatex and RtangleExtra provide options
to completely ignore code chunks on weaving, tangling, or both.
Chunks ignored on weaving are not parsed, yet are written out
verbatim on tangling. Chunks ignored on tangling may be evaluated as
usual on weaving, but are completely left out of the tangled
scripts. The driver RtangleExtra also provides options to control
the separation between code chunks in the tangled script, and to
specify the extension of the file name (or remove it entirely) when
splitting is selected.
Author: Vincent Goulet [cre, aut],
R Core Team [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between RweaveExtra versions 1.2-0 dated 2025-03-14 and 1.2-1 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SweaveGetSourceName.R | 5 +++-- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++++++++ 5 files changed, 21 insertions(+), 10 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.11.0 dated 2025-06-05 and 2.11.1 dated 2025-08-18
redcapAPI-2.11.0/redcapAPI/NEWS |only redcapAPI-2.11.1/redcapAPI/DESCRIPTION | 6 redcapAPI-2.11.1/redcapAPI/MD5 | 51 redcapAPI-2.11.1/redcapAPI/NAMESPACE | 2 redcapAPI-2.11.1/redcapAPI/NEWS.md |only redcapAPI-2.11.1/redcapAPI/R/exportSAS.R |only redcapAPI-2.11.1/redcapAPI/R/importRecords.R | 8 redcapAPI-2.11.1/redcapAPI/R/makeApiCall.R | 26 redcapAPI-2.11.1/redcapAPI/R/unlockREDCap.R | 26 redcapAPI-2.11.1/redcapAPI/R/validateImport_methods.R | 226 +- redcapAPI-2.11.1/redcapAPI/build/vignette.rds |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-best-practices.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-casting-data.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-data-validation.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-faq.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-getting-started-connecting.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-missing-data-detection.pdf |binary redcapAPI-2.11.1/redcapAPI/inst/doc/redcapAPI-offline-connection.pdf |binary redcapAPI-2.11.1/redcapAPI/man/exportSAS.Rd |only redcapAPI-2.11.1/redcapAPI/man/makeApiCall.Rd | 6 redcapAPI-2.11.1/redcapAPI/man/unlockREDCap.Rd | 5 redcapAPI-2.11.1/redcapAPI/tests/testthat/test-024-unlockREDCap-ArgumentValidation.R | 1 redcapAPI-2.11.1/redcapAPI/tests/testthat/test-024-unlockREDCap.R | 26 redcapAPI-2.11.1/redcapAPI/tests/testthat/test-050-makeApiCall.R | 150 - redcapAPI-2.11.1/redcapAPI/tests/testthat/test-150-importDeleteRecords-Functionality.R | 29 redcapAPI-2.11.1/redcapAPI/tests/testthat/test-210-exportSAS.R |only redcapAPI-2.11.1/redcapAPI/tests/testthat/test-352-savePurgeRestoreProject-Functionality.R | 142 - redcapAPI-2.11.1/redcapAPI/tests/testthat/test-903-validateImport_methods.R | 874 +++++----- redcapAPI-2.11.1/redcapAPI/tests/testthat/testdata/test_redcapAPI_Data.Rdata |binary 29 files changed, 837 insertions(+), 741 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of maximally distinct qualitative color palettes,
optionally tailored to color deficiency. A list of colors or a subspace
of a color space is used as input and then projected to the DIN99d color space,
where colors that are maximally distinct are chosen algorithmically.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <jolars@posteo.com>
Diff between qualpalr versions 0.4.4 dated 2023-09-13 and 1.0.0 dated 2025-08-18
qualpalr-0.4.4/qualpalr/R/color-conversion.R |only qualpalr-0.4.4/qualpalr/R/cvd-simulation.R |only qualpalr-0.4.4/qualpalr/R/sysdata.rda |only qualpalr-0.4.4/qualpalr/man/autopal.Rd |only qualpalr-0.4.4/qualpalr/src/Makevars.win |only qualpalr-0.4.4/qualpalr/src/qualpal.cpp |only qualpalr-0.4.4/qualpalr/tests/testthat/rgb_hsl.RData |only qualpalr-0.4.4/qualpalr/tests/testthat/setup.R |only qualpalr-0.4.4/qualpalr/tests/testthat/teardown.R |only qualpalr-0.4.4/qualpalr/tests/testthat/test_color.R |only qualpalr-0.4.4/qualpalr/tools |only qualpalr-1.0.0/qualpalr/DESCRIPTION | 39 - qualpalr-1.0.0/qualpalr/MD5 | 110 ++- qualpalr-1.0.0/qualpalr/NAMESPACE | 6 qualpalr-1.0.0/qualpalr/NEWS.md | 202 ++++-- qualpalr-1.0.0/qualpalr/R/RcppExports.R | 37 + qualpalr-1.0.0/qualpalr/R/analyze_palette.R |only qualpalr-1.0.0/qualpalr/R/autopal.R | 61 + qualpalr-1.0.0/qualpalr/R/get_palette.R |only qualpalr-1.0.0/qualpalr/R/list_palettes.R |only qualpalr-1.0.0/qualpalr/R/plotting.R | 10 qualpalr-1.0.0/qualpalr/R/qualpal-deprecated.R |only qualpalr-1.0.0/qualpalr/R/qualpal.R | 385 ++++++------ qualpalr-1.0.0/qualpalr/R/qualpalr.R | 1 qualpalr-1.0.0/qualpalr/R/utils.R | 67 ++ qualpalr-1.0.0/qualpalr/README.md | 32 qualpalr-1.0.0/qualpalr/build/vignette.rds |binary qualpalr-1.0.0/qualpalr/inst/CITATION | 48 + qualpalr-1.0.0/qualpalr/inst/doc/comparisons.R |only qualpalr-1.0.0/qualpalr/inst/doc/comparisons.Rmd |only qualpalr-1.0.0/qualpalr/inst/doc/comparisons.html |only qualpalr-1.0.0/qualpalr/inst/doc/introduction.R | 37 - qualpalr-1.0.0/qualpalr/inst/doc/introduction.Rmd | 121 ++- qualpalr-1.0.0/qualpalr/inst/doc/introduction.html | 308 +++++---- qualpalr-1.0.0/qualpalr/inst/include |only qualpalr-1.0.0/qualpalr/man/analyze_palette.Rd |only qualpalr-1.0.0/qualpalr/man/autopal-deprecated.Rd |only qualpalr-1.0.0/qualpalr/man/convert_colors.Rd |only qualpalr-1.0.0/qualpalr/man/figures |only qualpalr-1.0.0/qualpalr/man/get_palette.Rd |only qualpalr-1.0.0/qualpalr/man/list_palettes.Rd |only qualpalr-1.0.0/qualpalr/man/pairs.qualpal.Rd | 4 qualpalr-1.0.0/qualpalr/man/plot.qualpal.Rd | 2 qualpalr-1.0.0/qualpalr/man/print.qualpal.Rd | 2 qualpalr-1.0.0/qualpalr/man/qualpal-deprecated.Rd |only qualpalr-1.0.0/qualpalr/man/qualpal.Rd | 192 ++--- qualpalr-1.0.0/qualpalr/src/Makevars | 25 qualpalr-1.0.0/qualpalr/src/RcppExports.cpp | 95 ++ qualpalr-1.0.0/qualpalr/src/convert.h |only qualpalr-1.0.0/qualpalr/src/qualpal |only qualpalr-1.0.0/qualpalr/src/qualpalr.cpp |only qualpalr-1.0.0/qualpalr/tests/testthat/helper_dont_plot.R | 2 qualpalr-1.0.0/qualpalr/tests/testthat/test_analyze.R |only qualpalr-1.0.0/qualpalr/tests/testthat/test_autopal.R | 13 qualpalr-1.0.0/qualpalr/tests/testthat/test_get_palette.R |only qualpalr-1.0.0/qualpalr/tests/testthat/test_list_palettes.R |only qualpalr-1.0.0/qualpalr/tests/testthat/test_plotting.R | 1 qualpalr-1.0.0/qualpalr/tests/testthat/test_qualpal.R | 71 +- qualpalr-1.0.0/qualpalr/vignettes/comparisons.Rmd |only qualpalr-1.0.0/qualpalr/vignettes/introduction.Rmd | 121 ++- qualpalr-1.0.0/qualpalr/vignettes/qualpal.bib | 133 +++- 61 files changed, 1334 insertions(+), 791 deletions(-)
Title: Run Multiple Large Language Model Predictions Against a Table,
or Vectors
Description: Run multiple 'Large Language Model' predictions against a table. The
predictions run row-wise over a specified column. It works using a
one-shot prompt, along with the current row's content. The prompt that is used
will depend of the type of analysis needed.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between mall versions 0.1.0 dated 2024-10-24 and 0.2.0 dated 2025-08-18
DESCRIPTION | 13 +- MD5 | 55 ++++---- NAMESPACE | 4 NEWS.md | 7 + R/llm-use.R | 39 +++++- R/m-backend-prompt.R | 184 ++++++++++++------------------ R/m-backend-submit.R | 109 ++++++++++++++++- R/m-cache.R | 12 - R/m-defaults.R | 6 R/m-vec-prompt.R | 16 -- R/mall.R | 5 README.md | 3 man/llm_use.Rd | 10 + tests/testthat/_snaps/llm-classify.md | 4 tests/testthat/_snaps/llm-custom.md | 2 tests/testthat/_snaps/llm-extract.md | 10 - tests/testthat/_snaps/llm-summarize.md | 8 - tests/testthat/_snaps/llm-translate.md | 8 - tests/testthat/_snaps/llm-use.md | 30 ++++ tests/testthat/_snaps/llm-verify.md | 4 tests/testthat/_snaps/m-backend-prompt.md |only tests/testthat/_snaps/m-backend-submit.md |only tests/testthat/_snaps/m-defaults.md |only tests/testthat/helper-ellmer.R |only tests/testthat/helper-ollama.R | 6 tests/testthat/test-llm-classify.R | 2 tests/testthat/test-llm-use.R | 42 ++++++ tests/testthat/test-m-backend-prompt.R | 20 ++- tests/testthat/test-m-backend-submit.R | 87 ++++++++++++++ tests/testthat/test-m-defaults.R |only tests/testthat/test-zzz-cache.R | 8 - 31 files changed, 487 insertions(+), 207 deletions(-)
Title: Extended Legends and Axes for 'ggplot2'
Description: A 'ggplot2' extension that focusses on expanding the
plotter's arsenal of guides. Guides in 'ggplot2' include axes and
legends. 'legendry' offers new axes and annotation options, as well as
new legends and colour displays.
Author: Teun van den Brand [aut, cre, cph]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between legendry versions 0.2.2 dated 2025-05-30 and 0.2.3 dated 2025-08-18
DESCRIPTION | 6 MD5 | 32 - NEWS.md | 8 R/compose-crux.R | 494 ++++++++++++++-------------- R/compose-sandwich.R | 238 +++++++------ R/gizmo-barcap.R | 6 R/gizmo-density.R | 666 +++++++++++++++++++------------------- R/guide-circles.R | 792 +++++++++++++++++++++++----------------------- R/guide-colbar.R | 13 R/guide-colsteps.R | 8 R/utils-ggplot2.R | 560 ++++++++++++++++---------------- R/utils.R | 12 R/zzz.R | 26 - man/compose_sandwich.Rd | 5 man/guide_colbar.Rd | 5 man/guide_colsteps.Rd | 5 tests/testthat/Rplots.pdf |binary 17 files changed, 1469 insertions(+), 1407 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras versions 2.15.0 dated 2024-04-20 and 2.16.0 dated 2025-08-18
DESCRIPTION | 14 MD5 | 82 ++-- NAMESPACE | 2 NEWS.md | 11 R/callbacks.R | 2 R/constraints.R | 2 R/install.R | 34 + R/layer-custom.R | 2 R/layers-core.R | 1 R/package.R | 44 ++ R/wrapper_custom.R | 2 build/vignette.rds |binary inst/doc/applications.R | 178 ++++----- inst/doc/applications.html | 3 inst/doc/custom_layers.R | 474 ++++++++++++------------ inst/doc/custom_layers.html | 3 inst/doc/custom_models.R | 98 ++--- inst/doc/custom_models.html | 3 inst/doc/faq.R | 502 +++++++++++++------------- inst/doc/faq.html | 3 inst/doc/functional_api.R | 538 ++++++++++++++-------------- inst/doc/functional_api.html | 5 inst/doc/guide_keras.R | 486 ++++++++++++------------- inst/doc/guide_keras.html | 3 inst/doc/index.R | 78 ++-- inst/doc/index.Rmd | 2 inst/doc/index.html | 14 inst/doc/saving_serializing.R | 310 ++++++++-------- inst/doc/saving_serializing.html | 3 inst/doc/sequential_model.R | 664 +++++++++++++++++------------------ inst/doc/sequential_model.html | 5 inst/doc/training_callbacks.R | 126 +++--- inst/doc/training_callbacks.html | 3 inst/doc/training_visualization.R | 96 ++--- inst/doc/training_visualization.html | 9 man/KerasCallback.Rd | 2 man/KerasConstraint.Rd | 2 man/KerasLayer.Rd | 2 man/KerasWrapper.Rd | 2 man/install_keras.Rd | 41 +- man/keras-package.Rd | 4 vignettes/index.Rmd | 2 42 files changed, 1994 insertions(+), 1863 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.4 dated 2025-07-07 and 2.3.5 dated 2025-08-18
GitStats-2.3.4/GitStats/R/error_handlers.R |only GitStats-2.3.4/GitStats/inst/roche |only GitStats-2.3.5/GitStats/DESCRIPTION | 6 GitStats-2.3.5/GitStats/MD5 | 58 +++----- GitStats-2.3.5/GitStats/NEWS.md | 5 GitStats-2.3.5/GitStats/R/EngineGraphQL.R | 58 +++++++- GitStats-2.3.5/GitStats/R/EngineGraphQLGitHub.R | 20 +- GitStats-2.3.5/GitStats/R/EngineGraphQLGitLab.R | 32 +--- GitStats-2.3.5/GitStats/R/EngineRest.R | 57 ++++---- GitStats-2.3.5/GitStats/R/EngineRestGitLab.R | 4 GitStats-2.3.5/GitStats/R/GitHost.R | 48 +++--- GitStats-2.3.5/GitStats/R/GitHostGitLab.R | 5 GitStats-2.3.5/GitStats/build/vignette.rds |binary GitStats-2.3.5/GitStats/inst/doc/get_repos_with_code.html | 4 GitStats-2.3.5/GitStats/inst/doc/set_hosts.html | 4 GitStats-2.3.5/GitStats/inst/get_storage_workflow.R | 2 GitStats-2.3.5/GitStats/tests/testthat/_snaps/00-api-requests.md |only GitStats-2.3.5/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 4 GitStats-2.3.5/GitStats/tests/testthat/_snaps/02-get_commits-GitHub.md | 4 GitStats-2.3.5/GitStats/tests/testthat/_snaps/helpers.md | 9 + GitStats-2.3.5/GitStats/tests/testthat/helper-error-fixtures.R |only GitStats-2.3.5/GitStats/tests/testthat/helper-fixtures.R | 41 ----- GitStats-2.3.5/GitStats/tests/testthat/test-00-api-requests.R | 71 +++++++++- GitStats-2.3.5/GitStats/tests/testthat/test-00-get_orgs-GitLab.R | 10 - GitStats-2.3.5/GitStats/tests/testthat/test-00-graphql_errors.R |only GitStats-2.3.5/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 53 ------- GitStats-2.3.5/GitStats/tests/testthat/test-02-get_commits-GitHub.R | 13 - GitStats-2.3.5/GitStats/tests/testthat/test-helpers.R | 27 ++- 28 files changed, 273 insertions(+), 262 deletions(-)
Title: Emulation of Dynamic Simulators via One-Step-Ahead Approach
Description: Performs emulation of dynamic simulators using Gaussian process via one-step ahead approach. The package implements a flexible framework for approximating time-dependent outputs from computationally expensive dynamic systems. It is specifically designed for nonlinear dynamic systems where full simulations may be costly. The underlying Gaussian process model accounts for temporal dependency through the one-step-ahead formulation, allowing for accurate emulation of complex dynamics. Hyperparameters are estimated via maximum likelihood. For methodological details, see Heo (2025, <doi:10.48550/arXiv.2503.20250>) for exact method, and Mohammadi, Challenor, and Goodfellow (2019, <doi:10.1016/j.csda.2019.05.006>) for Monte Carlo method.
Author: Junoh Heo [aut, cre]
Maintainer: Junoh Heo <heojunoh@msu.edu>
Diff between dynemu versions 1.0.0 dated 2025-03-28 and 1.0.2 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/GP.R | 10 +++++----- R/dyn_solve.R | 3 ++- R/dynemu_GP.R | 8 +++++--- R/dynemu_exact.R | 51 ++++++++++++++++++++++++++++++--------------------- R/dynemu_pred.R | 24 ++++++++++++++++++++---- man/dyn_solve.Rd | 3 ++- man/dynemu_GP.Rd | 4 +++- man/dynemu_exact.Rd | 4 ++-- man/dynemu_pred.Rd | 6 +++--- 11 files changed, 86 insertions(+), 55 deletions(-)
Title: Create Demographic Table
Description: To create demographic table with simple summary statistics,
with optional comparison(s) over one or more groups.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.2.2 dated 2025-06-13 and 0.2.3 dated 2025-08-18
DemographicTable-0.2.2/DemographicTable/man/Sprintf.DemographicTable.Rd |only DemographicTable-0.2.3/DemographicTable/DESCRIPTION | 6 DemographicTable-0.2.3/DemographicTable/MD5 | 27 DemographicTable-0.2.3/DemographicTable/NAMESPACE | 5 DemographicTable-0.2.3/DemographicTable/R/0PACKAGE.R | 3 DemographicTable-0.2.3/DemographicTable/R/DemographicTable.R | 36 - DemographicTable-0.2.3/DemographicTable/R/as_flextable.R | 51 + DemographicTable-0.2.3/DemographicTable/R/onLoad.R | 10 DemographicTable-0.2.3/DemographicTable/build/vignette.rds |binary DemographicTable-0.2.3/DemographicTable/inst/doc/intro.R | 54 - DemographicTable-0.2.3/DemographicTable/inst/doc/intro.html | 348 ++++++++-- DemographicTable-0.2.3/DemographicTable/inst/doc/intro.qmd | 86 +- DemographicTable-0.2.3/DemographicTable/man/as_flextable.DemographicTable.Rd | 6 DemographicTable-0.2.3/DemographicTable/man/print.DemographicTable.Rd |only DemographicTable-0.2.3/DemographicTable/vignettes/DemographicTable.bib |only DemographicTable-0.2.3/DemographicTable/vignettes/intro.qmd | 86 +- 16 files changed, 484 insertions(+), 234 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Advanced and Fast Data Transformation
Description: A large C/C++-based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust, and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R, fast
functions for data transformation and common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data. It
seamlessly supports base R objects/cla [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
Alina Cherkas [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999- [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.1.2 dated 2025-05-24 and 2.1.3 dated 2025-08-18
collapse-2.1.2/collapse/tests/testthat/test-fhdbetween-fhdwithin-HDB-HDW.R |only collapse-2.1.2/collapse/tests/testthat/test-fnobs-fndistinct.R |only collapse-2.1.3/collapse/DESCRIPTION | 8 - collapse-2.1.3/collapse/MD5 | 56 +++++----- collapse-2.1.3/collapse/NEWS.md | 4 collapse-2.1.3/collapse/R/GRP.R | 2 collapse-2.1.3/collapse/R/global_macros.R | 2 collapse-2.1.3/collapse/R/join.R | 12 +- collapse-2.1.3/collapse/R/pivot.R | 2 collapse-2.1.3/collapse/R/small_helper.R | 4 collapse-2.1.3/collapse/R/zzz.R | 1 collapse-2.1.3/collapse/inst/WORDLIST |only collapse-2.1.3/collapse/inst/doc/collapse_documentation.html | 4 collapse-2.1.3/collapse/inst/doc/collapse_for_tidyverse_users.html | 26 ++++ collapse-2.1.3/collapse/inst/doc/collapse_object_handling.html | 4 collapse-2.1.3/collapse/inst/doc/developing_with_collapse.Rmd | 4 collapse-2.1.3/collapse/inst/doc/developing_with_collapse.html | 7 - collapse-2.1.3/collapse/man/collapse-package.Rd | 2 collapse-2.1.3/collapse/man/fslice.Rd | 2 collapse-2.1.3/collapse/src/collapse_c.h | 1 collapse-2.1.3/collapse/src/data.table.h | 6 + collapse-2.1.3/collapse/src/fbstats.cpp | 14 +- collapse-2.1.3/collapse/src/match.c | 21 ++- collapse-2.1.3/collapse/src/small_helper.c | 19 +++ collapse-2.1.3/collapse/tests/testthat/test-GRP.R | 1 collapse-2.1.3/collapse/tests/testthat/test-data.table.R | 3 collapse-2.1.3/collapse/tests/testthat/test-fHDbetween-fHDwithin-HDB-HDW.R |only collapse-2.1.3/collapse/tests/testthat/test-fNobs-fNdistinct.R |only collapse-2.1.3/collapse/tests/testthat/test-join.R | 10 + collapse-2.1.3/collapse/tests/testthat/test-miscellaneous-issues.R | 3 collapse-2.1.3/collapse/tests/testthat/testthat-problems.rds |only collapse-2.1.3/collapse/vignettes/developing_with_collapse.Rmd | 4 32 files changed, 154 insertions(+), 68 deletions(-)
Title: A Tool for Rating Text/Image Stimuli
Description: Evaluates stimuli using Large Language Models APIs with URL support.
Author: Shiyang Zheng [aut, cre]
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Diff between chatRater versions 1.1.0 dated 2025-03-03 and 1.2.0 dated 2025-08-18
chatRater-1.1.0/chatRater/man/chatRater-package.Rd |only chatRater-1.1.0/chatRater/man/get_levenshtein_d.Rd |only chatRater-1.1.0/chatRater/man/get_lexical_coverage.Rd |only chatRater-1.1.0/chatRater/man/get_semantic_transparency.Rd |only chatRater-1.1.0/chatRater/man/get_word_frequency.Rd |only chatRater-1.1.0/chatRater/man/get_zipf_metric.Rd |only chatRater-1.1.0/chatRater/man/llm_api_call.Rd |only chatRater-1.2.0/chatRater/DESCRIPTION | 24 chatRater-1.2.0/chatRater/MD5 | 21 chatRater-1.2.0/chatRater/NAMESPACE | 11 chatRater-1.2.0/chatRater/R/chatRater.R | 824 +++---------- chatRater-1.2.0/chatRater/README.md | 137 +- chatRater-1.2.0/chatRater/man/generate_ratings.Rd | 55 chatRater-1.2.0/chatRater/man/generate_ratings_for_all.Rd | 51 chatRater-1.2.0/chatRater/tests/testthat.R | 14 15 files changed, 350 insertions(+), 787 deletions(-)
Title: Bayesian Sparse Estimation of a Covariance Matrix
Description: Bayesian estimations of a covariance matrix for multivariate
normal data. Assumes that the covariance matrix is sparse or band
matrix and positive-definite. Methods implemented include the beta-mixture
shrinkage prior (Lee et al. (2022) <doi:10.1016/j.jmva.2022.105067>),
screened beta-mixture prior (Lee et al. (2024) <doi:10.1214/24-BA1495>),
and post-processed posteriors for banded and sparse covariances
(Lee et al. (2023) <doi:10.1214/22-BA1333>; Lee and Lee (2023)
<doi:10.1016/j.jeconom.2023.105475>). This software has been developed using
funding supported by Basic Science Research Program through the National
Research Foundation of Korea ('NRF') funded by the Ministry of Education
('RS-2023-00211979', 'NRF-2022R1A5A7033499', 'NRF-2020R1A4A1018207'
and 'NRF-2020R1C1C1A01013338').
Author: Kwangmin Lee [aut],
Kyeongwon Lee [aut, cre],
Kyoungjae Lee [aut],
Seongil Jo [aut],
Jaeyong Lee [ctb]
Maintainer: Kyeongwon Lee <kwlee1718@gmail.com>
Diff between bspcov versions 1.0.2 dated 2025-07-02 and 1.0.3 dated 2025-08-18
bspcov-1.0.2/bspcov/R/estimate.R |only bspcov-1.0.3/bspcov/DESCRIPTION | 11 + bspcov-1.0.3/bspcov/MD5 | 49 ++++---- bspcov-1.0.3/bspcov/NAMESPACE | 19 +++ bspcov-1.0.3/bspcov/R/bmspcov.R | 106 ++++++++++++++++-- bspcov-1.0.3/bspcov/R/data.SP500.R | 2 bspcov-1.0.3/bspcov/R/data.colon.R | 2 bspcov-1.0.3/bspcov/R/data.tissues.R | 2 bspcov-1.0.3/bspcov/R/estimate.bspcov.R |only bspcov-1.0.3/bspcov/R/globals.R | 2 bspcov-1.0.3/bspcov/R/plot.bspcov.R | 50 +++++++- bspcov-1.0.3/bspcov/R/plot.postmean.bspcov.R | 112 +++++++++++++++---- bspcov-1.0.3/bspcov/R/plot.quantile.bspcov.R |only bspcov-1.0.3/bspcov/R/quantile.bspcov.R |only bspcov-1.0.3/bspcov/R/sbmspcov.R | 139 ++++++++++++++++++++---- bspcov-1.0.3/bspcov/R/summary.bspcov.R | 105 ++++++++++++++++-- bspcov-1.0.3/bspcov/README.md | 8 + bspcov-1.0.3/bspcov/man/SP500.Rd | 2 bspcov-1.0.3/bspcov/man/bmspcov.Rd | 36 +++++- bspcov-1.0.3/bspcov/man/colon.Rd | 2 bspcov-1.0.3/bspcov/man/estimate.Rd | 7 - bspcov-1.0.3/bspcov/man/plot.bspcov.Rd | 7 - bspcov-1.0.3/bspcov/man/plot.postmean.bspcov.Rd | 56 ++++++++- bspcov-1.0.3/bspcov/man/plot.quantile.bspcov.Rd |only bspcov-1.0.3/bspcov/man/quantile.bspcov.Rd |only bspcov-1.0.3/bspcov/man/save_quantile_plot.Rd |only bspcov-1.0.3/bspcov/man/sbmspcov.Rd | 43 ++++++- bspcov-1.0.3/bspcov/man/summary.bspcov.Rd | 15 +- bspcov-1.0.3/bspcov/man/tissues.Rd | 2 29 files changed, 640 insertions(+), 137 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.3.0 dated 2024-12-21 and 1.4.0 dated 2025-08-18
SVEMnet-1.3.0/SVEMnet/R/svemnet_sim_mixture.R |only SVEMnet-1.4.0/SVEMnet/DESCRIPTION | 11 SVEMnet-1.4.0/SVEMnet/MD5 | 65 SVEMnet-1.4.0/SVEMnet/NAMESPACE | 8 SVEMnet-1.4.0/SVEMnet/NEWS | 7 SVEMnet-1.4.0/SVEMnet/R/SVEMnet-package.R | 4 SVEMnet-1.4.0/SVEMnet/R/SVEMnet.R | 376 - SVEMnet-1.4.0/SVEMnet/R/coef.R | 58 SVEMnet-1.4.0/SVEMnet/R/glmnet_with_cv.R | 359 - SVEMnet-1.4.0/SVEMnet/R/globals.R | 2 SVEMnet-1.4.0/SVEMnet/R/plot.svemnet.R | 25 SVEMnet-1.4.0/SVEMnet/R/predict.cv.R |only SVEMnet-1.4.0/SVEMnet/R/predict.svem_lasso.R | 28 SVEMnet-1.4.0/SVEMnet/R/svem_random_table.R |only SVEMnet-1.4.0/SVEMnet/R/svem_significance_test.R | 498 - SVEMnet-1.4.0/SVEMnet/R/svem_significance_test_parallel.R | 496 - SVEMnet-1.4.0/SVEMnet/build/partial.rdb |binary SVEMnet-1.4.0/SVEMnet/build/vignette.rds |binary SVEMnet-1.4.0/SVEMnet/inst/doc/SVEMnet_vignette.R | 34 SVEMnet-1.4.0/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 227 SVEMnet-1.4.0/SVEMnet/inst/doc/SVEMnet_vignette.html | 3108 +++++++--- SVEMnet-1.4.0/SVEMnet/man/SVEMnet-package.Rd | 4 SVEMnet-1.4.0/SVEMnet/man/SVEMnet.Rd | 67 SVEMnet-1.4.0/SVEMnet/man/predict_cv.Rd | 37 SVEMnet-1.4.0/SVEMnet/man/svem_random_table.Rd |only SVEMnet-1.4.0/SVEMnet/man/svem_significance_test.Rd | 182 SVEMnet-1.4.0/SVEMnet/man/svem_significance_test_parallel.Rd | 114 SVEMnet-1.4.0/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 227 SVEMnet-1.4.0/SVEMnet/vignettes/debias_aicc.R |only SVEMnet-1.4.0/SVEMnet/vignettes/debias_aicc_c2.R |only SVEMnet-1.4.0/SVEMnet/vignettes/debias_aicc_cvglm.R |only SVEMnet-1.4.0/SVEMnet/vignettes/debias_and_objective.R |only SVEMnet-1.4.0/SVEMnet/vignettes/figures/14AUG25.png |only SVEMnet-1.4.0/SVEMnet/vignettes/figures/AICc_debias_glmnet.png |only SVEMnet-1.4.0/SVEMnet/vignettes/figures/waicc_vs_waic.png |only SVEMnet-1.4.0/SVEMnet/vignettes/svem_vs_lassoCV.R |only SVEMnet-1.4.0/SVEMnet/vignettes/svem_vs_lassoCV_par_v2.R |only SVEMnet-1.4.0/SVEMnet/vignettes/svemnet_sim.R | 218 SVEMnet-1.4.0/SVEMnet/vignettes/svemnet_sim_identity.R | 289 SVEMnet-1.4.0/SVEMnet/vignettes/svemnet_sim_mixture_v2.R | 364 - 40 files changed, 4021 insertions(+), 2787 deletions(-)
Title: Uniformity Tests on the Circle, Sphere, and Hypersphere
Description: Implementation of uniformity tests on the circle and
(hyper)sphere. The main function of the package is unif_test(), which
conveniently collects more than 35 tests for assessing uniformity on
S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are
implemented in the unif_stat() function, which allows computing several
statistics for different samples within a single call, thus facilitating
Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows
parallelizing them in a simple way. The asymptotic null distributions of
the statistics are available through the function unif_stat_distr(). The
core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package.
The package also provides several novel datasets and gives the replicability
for the data applications/simulations in García-Portugués et al. (2021)
<doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023)
<doi:10.3150/21-BEJ1454>, Fernández-de-Marcos and
García-Portugués (2024) <d [...truncated...]
Author: Eduardo Garcia-Portugues [aut, cre] ,
Thomas Verdebout [aut] ,
Alberto Fernandez-de-Marcos [ctb],
Paula Navarro [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between sphunif versions 1.4.1 dated 2025-07-27 and 1.4.2 dated 2025-08-18
DESCRIPTION | 14 +- MD5 | 14 +- NEWS.md | 2 R/sphunif-package.R | 10 - inst/WORDLIST | 1 inst/doc/sphunif.html | 263 +++++++++++++++++++++---------------------------- man/sphunif-package.Rd | 10 - vignettes/sphunif.bib | 9 + 8 files changed, 147 insertions(+), 176 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <stuartt@a-star.edu.sg>
Diff between Signac versions 1.14.0 dated 2024-08-21 and 1.15.0 dated 2025-08-18
DESCRIPTION | 22 +++---- MD5 | 45 ++++++++------- NAMESPACE | 1 NEWS.md | 18 ++++++ R/fragments.R | 6 +- R/heatmaps.R | 1 R/objects.R | 101 +++++++++++++++++++++++++++++++---- R/quantification.R | 35 ++++++++++-- R/utilities.R | 53 ++++++++++-------- R/visualization.R | 35 +++++++++++- README.md | 6 -- build/partial.rdb |binary data/blacklist_hg38_unified.rda |binary inst/extdata/chr1_start.fa |only inst/extdata/chr1_start.fa.fai |only man/CreateChromatinAssay.Rd | 9 ++- man/CreateMotifObject.Rd | 1 man/FeatureMatrix.Rd | 12 +++- man/RegionHeatmap.Rd | 4 + man/RegionPlot.Rd | 4 + man/SetMotifData.Rd | 5 + man/as.ChromatinAssay.Rd | 9 ++- tests/testdata/pwm_2motifs.rds |only tests/testthat/test-motifs.R |only tests/testthat/test-preprocessing.R | 21 +++++++ tests/testthat/test-quantification.R |only 26 files changed, 302 insertions(+), 86 deletions(-)
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharche [...truncated...]
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Rasmus Rydbirk [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between pagoda2 versions 1.0.12 dated 2024-02-26 and 1.0.13 dated 2025-08-18
DESCRIPTION | 8 +- MD5 | 12 ++-- R/p1app4p2.R | 10 --- README.md | 2 man/Pagoda2.Rd | 132 ++++++++++++++++++++++++------------------------- man/p2ViewPagodaApp.Rd | 24 ++++---- src/RcppExports.cpp | 6 +- 7 files changed, 96 insertions(+), 98 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.6.0 dated 2025-03-05 and 5.7.0 dated 2025-08-18
huxtable-5.6.0/huxtable/R/properties-aaa-setup.R |only huxtable-5.6.0/huxtable/R/properties-border-generics.R |only huxtable-5.6.0/huxtable/R/properties-border.R |only huxtable-5.6.0/huxtable/tests/testthat/filecec5332acc3.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec53854bfe2.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec567db13c6.log |only huxtable-5.6.0/huxtable/tests/testthat/setup-add-colnames.R |only huxtable-5.6.0/huxtable/tests/testthat/table-tester-2.log |only huxtable-5.6.0/huxtable/tests/testthat/teardown-add_colnames.R |only huxtable-5.6.0/huxtable/tests/testthat/test-attributes.R |only huxtable-5.6.0/huxtable/tests/testthat/test-zz-fuzz.R |only huxtable-5.7.0/huxtable/DESCRIPTION | 10 huxtable-5.7.0/huxtable/MD5 | 534 +++-- huxtable-5.7.0/huxtable/NAMESPACE | 121 - huxtable-5.7.0/huxtable/NEWS.md | 25 huxtable-5.7.0/huxtable/R/Workbook.R | 193 +- huxtable-5.7.0/huxtable/R/aaa-utils.R | 248 +- huxtable-5.7.0/huxtable/R/bind-insert-internal.R | 136 - huxtable-5.7.0/huxtable/R/bind-insert.R | 164 - huxtable-5.7.0/huxtable/R/bookdown.R | 33 huxtable-5.7.0/huxtable/R/border-utils.R |only huxtable-5.7.0/huxtable/R/brdr.R | 57 huxtable-5.7.0/huxtable/R/clean-contents.R | 283 ++ huxtable-5.7.0/huxtable/R/column-to-header.R | 36 huxtable-5.7.0/huxtable/R/creation-internal.R | 10 huxtable-5.7.0/huxtable/R/creation.R | 124 - huxtable-5.7.0/huxtable/R/dimnames.R | 37 huxtable-5.7.0/huxtable/R/doc-helpers.R |only huxtable-5.7.0/huxtable/R/dplyr.R | 41 huxtable-5.7.0/huxtable/R/edit-defaults.R | 24 huxtable-5.7.0/huxtable/R/flextable.R | 120 - huxtable-5.7.0/huxtable/R/get-multiple.R | 9 huxtable-5.7.0/huxtable/R/html.R | 286 ++- huxtable-5.7.0/huxtable/R/huxreg.R | 496 +++-- huxtable-5.7.0/huxtable/R/knitr.R | 106 - huxtable-5.7.0/huxtable/R/latex-dependencies.R | 68 huxtable-5.7.0/huxtable/R/latex.R | 295 +-- huxtable-5.7.0/huxtable/R/mapping-functions.R | 305 +-- huxtable-5.7.0/huxtable/R/markdown.R | 269 +- huxtable-5.7.0/huxtable/R/md.R | 39 huxtable-5.7.0/huxtable/R/merge.R | 17 huxtable-5.7.0/huxtable/R/misc.R | 76 huxtable-5.7.0/huxtable/R/number-format-functions.R | 37 huxtable-5.7.0/huxtable/R/package-docs.R | 1 huxtable-5.7.0/huxtable/R/package-utils.R |only huxtable-5.7.0/huxtable/R/properties-border-get.R |only huxtable-5.7.0/huxtable/R/properties-border-set-map.R |only huxtable-5.7.0/huxtable/R/properties-cell.R | 947 +++++++--- huxtable-5.7.0/huxtable/R/properties-padding.R | 109 - huxtable-5.7.0/huxtable/R/properties-row-col.R | 138 + huxtable-5.7.0/huxtable/R/properties-table.R | 329 ++- huxtable-5.7.0/huxtable/R/property-helpers.R |only huxtable-5.7.0/huxtable/R/quick-functions.R | 392 +++- huxtable-5.7.0/huxtable/R/restack-split.R | 110 - huxtable-5.7.0/huxtable/R/row-col-fns.R | 53 huxtable-5.7.0/huxtable/R/roxygen-functions.R | 12 huxtable-5.7.0/huxtable/R/rtf.R | 201 +- huxtable-5.7.0/huxtable/R/screen.R | 698 ++++--- huxtable-5.7.0/huxtable/R/set-multiple.R | 51 huxtable-5.7.0/huxtable/R/set-outer.R | 42 huxtable-5.7.0/huxtable/R/string-utils.R |only huxtable-5.7.0/huxtable/R/stripes.R | 6 huxtable-5.7.0/huxtable/R/style-cells.R | 26 huxtable-5.7.0/huxtable/R/subset-extract-internal.R | 131 - huxtable-5.7.0/huxtable/R/subset-extract.R | 53 huxtable-5.7.0/huxtable/R/themes.R | 179 - huxtable-5.7.0/huxtable/R/typst.R |only huxtable-5.7.0/huxtable/R/zzz.R | 33 huxtable-5.7.0/huxtable/README.md | 225 +- huxtable-5.7.0/huxtable/build/vignette.rds |binary huxtable-5.7.0/huxtable/inst/doc/design-principles-html.html | 100 - huxtable-5.7.0/huxtable/inst/doc/design-principles-pdf.pdf |binary huxtable-5.7.0/huxtable/inst/doc/huxreg-html.html | 563 +++-- huxtable-5.7.0/huxtable/inst/doc/huxreg-pdf.pdf |binary huxtable-5.7.0/huxtable/inst/doc/huxtable-html.html | 796 ++++---- huxtable-5.7.0/huxtable/inst/doc/huxtable-pdf.pdf |binary huxtable-5.7.0/huxtable/inst/doc/themes-html.html | 192 +- huxtable-5.7.0/huxtable/man/add_colnames.Rd | 22 huxtable-5.7.0/huxtable/man/add_footnote.Rd | 6 huxtable-5.7.0/huxtable/man/add_rows.Rd | 9 huxtable-5.7.0/huxtable/man/align.Rd | 48 huxtable-5.7.0/huxtable/man/as_Workbook.Rd | 16 huxtable-5.7.0/huxtable/man/as_flextable.Rd | 13 huxtable-5.7.0/huxtable/man/as_huxtable.Rd | 20 huxtable-5.7.0/huxtable/man/background_color.Rd | 25 huxtable-5.7.0/huxtable/man/bold.Rd | 32 huxtable-5.7.0/huxtable/man/border-colors.Rd | 78 huxtable-5.7.0/huxtable/man/border-styles.Rd | 78 huxtable-5.7.0/huxtable/man/borders.Rd | 85 huxtable-5.7.0/huxtable/man/by_cases.Rd | 10 huxtable-5.7.0/huxtable/man/by_colorspace.Rd | 17 huxtable-5.7.0/huxtable/man/by_function.Rd | 10 huxtable-5.7.0/huxtable/man/by_quantiles.Rd | 38 huxtable-5.7.0/huxtable/man/by_ranges.Rd | 54 huxtable-5.7.0/huxtable/man/by_regex.Rd | 10 huxtable-5.7.0/huxtable/man/by_rows.Rd | 12 huxtable-5.7.0/huxtable/man/by_values.Rd | 12 huxtable-5.7.0/huxtable/man/caption.Rd | 14 huxtable-5.7.0/huxtable/man/caption_pos.Rd | 12 huxtable-5.7.0/huxtable/man/caption_width.Rd | 12 huxtable-5.7.0/huxtable/man/cbind.huxtable.Rd | 12 huxtable-5.7.0/huxtable/man/col_width.Rd | 19 huxtable-5.7.0/huxtable/man/column_to_header.Rd | 13 huxtable-5.7.0/huxtable/man/description-colors.Rd |only huxtable-5.7.0/huxtable/man/dplyr-verbs.Rd | 6 huxtable-5.7.0/huxtable/man/escape_contents.Rd | 24 huxtable-5.7.0/huxtable/man/fmt-numbers.Rd |only huxtable-5.7.0/huxtable/man/fmt_percent.Rd | 12 huxtable-5.7.0/huxtable/man/fmt_pretty.Rd | 12 huxtable-5.7.0/huxtable/man/font.Rd | 36 huxtable-5.7.0/huxtable/man/font_size.Rd | 43 huxtable-5.7.0/huxtable/man/guess_knitr_output_format.Rd | 4 huxtable-5.7.0/huxtable/man/header_cols.Rd | 20 huxtable-5.7.0/huxtable/man/height.Rd | 16 huxtable-5.7.0/huxtable/man/hux_prop_params.Rd |only huxtable-5.7.0/huxtable/man/huxreg.Rd | 15 huxtable-5.7.0/huxtable/man/huxtable-news.Rd | 25 huxtable-5.7.0/huxtable/man/huxtable.Rd | 16 huxtable-5.7.0/huxtable/man/insert_column.Rd | 28 huxtable-5.7.0/huxtable/man/knit_print.data.frame.Rd | 25 huxtable-5.7.0/huxtable/man/knit_print.huxtable.Rd | 3 huxtable-5.7.0/huxtable/man/label.Rd | 12 huxtable-5.7.0/huxtable/man/latex_float.Rd | 12 huxtable-5.7.0/huxtable/man/mapping-functions.Rd | 56 huxtable-5.7.0/huxtable/man/mapping-params.Rd |only huxtable-5.7.0/huxtable/man/markdown-note.Rd |only huxtable-5.7.0/huxtable/man/markdown.Rd | 15 huxtable-5.7.0/huxtable/man/merge_repeated_rows.Rd | 3 huxtable-5.7.0/huxtable/man/na_string.Rd | 16 huxtable-5.7.0/huxtable/man/number_format.Rd | 48 huxtable-5.7.0/huxtable/man/padding.Rd | 54 huxtable-5.7.0/huxtable/man/position.Rd | 12 huxtable-5.7.0/huxtable/man/print.huxtable.Rd | 11 huxtable-5.7.0/huxtable/man/quick-output.Rd | 83 huxtable-5.7.0/huxtable/man/report_latex_dependencies.Rd | 5 huxtable-5.7.0/huxtable/man/restack-across-down.Rd | 6 huxtable-5.7.0/huxtable/man/rotation.Rd | 43 huxtable-5.7.0/huxtable/man/row_height.Rd | 16 huxtable-5.7.0/huxtable/man/rowspecs.Rd | 18 huxtable-5.7.0/huxtable/man/sanitize.Rd | 6 huxtable-5.7.0/huxtable/man/set_contents.Rd | 11 huxtable-5.7.0/huxtable/man/set_default_properties.Rd | 6 huxtable-5.7.0/huxtable/man/set_markdown_contents.Rd | 6 huxtable-5.7.0/huxtable/man/span-overwrites-shadows.Rd |only huxtable-5.7.0/huxtable/man/spans.Rd | 14 huxtable-5.7.0/huxtable/man/stripe.Rd | 16 huxtable-5.7.0/huxtable/man/style-functions.Rd | 6 huxtable-5.7.0/huxtable/man/t.huxtable.Rd | 10 huxtable-5.7.0/huxtable/man/table_environment.Rd | 12 huxtable-5.7.0/huxtable/man/tabular_environment.Rd | 12 huxtable-5.7.0/huxtable/man/text_color.Rd | 25 huxtable-5.7.0/huxtable/man/themes.Rd | 15 huxtable-5.7.0/huxtable/man/tidy_override.Rd | 7 huxtable-5.7.0/huxtable/man/to_html.Rd | 22 huxtable-5.7.0/huxtable/man/to_latex.Rd | 16 huxtable-5.7.0/huxtable/man/to_md.Rd | 8 huxtable-5.7.0/huxtable/man/to_rtf.Rd | 10 huxtable-5.7.0/huxtable/man/to_screen.Rd | 16 huxtable-5.7.0/huxtable/man/to_typst.Rd |only huxtable-5.7.0/huxtable/man/valign.Rd | 34 huxtable-5.7.0/huxtable/man/width.Rd | 12 huxtable-5.7.0/huxtable/man/wrap.Rd | 24 huxtable-5.7.0/huxtable/tests/testthat.R | 1 huxtable-5.7.0/huxtable/tests/testthat/_snaps |only huxtable-5.7.0/huxtable/tests/testthat/echo-true-latex-test.Rmd | 8 huxtable-5.7.0/huxtable/tests/testthat/quarto-test-tex-labels-out.pdf |binary huxtable-5.7.0/huxtable/tests/testthat/quarto-test-tex-labels.qmd | 1 huxtable-5.7.0/huxtable/tests/testthat/quarto-typst.qmd |only huxtable-5.7.0/huxtable/tests/testthat/setup-functions.R | 13 huxtable-5.7.0/huxtable/tests/testthat/table-tester-2.Rmd | 11 huxtable-5.7.0/huxtable/tests/testthat/test-as-html.R |only huxtable-5.7.0/huxtable/tests/testthat/test-column-to-header.R | 19 huxtable-5.7.0/huxtable/tests/testthat/test-dplyr.R | 66 huxtable-5.7.0/huxtable/tests/testthat/test-flextable.R | 10 huxtable-5.7.0/huxtable/tests/testthat/test-html-builders.R |only huxtable-5.7.0/huxtable/tests/testthat/test-huxreg-helpers.R |only huxtable-5.7.0/huxtable/tests/testthat/test-huxreg.R | 99 - huxtable-5.7.0/huxtable/tests/testthat/test-huxtable-creation.R | 66 huxtable-5.7.0/huxtable/tests/testthat/test-knit-print.R | 13 huxtable-5.7.0/huxtable/tests/testthat/test-latex-dependencies.R | 25 huxtable-5.7.0/huxtable/tests/testthat/test-manipulation-helpers.R | 112 - huxtable-5.7.0/huxtable/tests/testthat/test-map-interface.R | 137 - huxtable-5.7.0/huxtable/tests/testthat/test-mapping-functions.R | 102 - huxtable-5.7.0/huxtable/tests/testthat/test-markdown.R | 4 huxtable-5.7.0/huxtable/tests/testthat/test-merge.R | 60 huxtable-5.7.0/huxtable/tests/testthat/test-miscellaneous.R | 40 huxtable-5.7.0/huxtable/tests/testthat/test-new-borders.R | 243 +- huxtable-5.7.0/huxtable/tests/testthat/test-number-format-functions.R | 6 huxtable-5.7.0/huxtable/tests/testthat/test-number-formatting.R | 184 + huxtable-5.7.0/huxtable/tests/testthat/test-object-manipulation.R | 90 huxtable-5.7.0/huxtable/tests/testthat/test-openxlsx.R | 17 huxtable-5.7.0/huxtable/tests/testthat/test-print.R | 57 huxtable-5.7.0/huxtable/tests/testthat/test-properties.R |only huxtable-5.7.0/huxtable/tests/testthat/test-quick-output.R | 91 huxtable-5.7.0/huxtable/tests/testthat/test-restack-split.R | 44 huxtable-5.7.0/huxtable/tests/testthat/test-row-col-functions.R | 26 huxtable-5.7.0/huxtable/tests/testthat/test-set-interface.R | 80 huxtable-5.7.0/huxtable/tests/testthat/test-set-multiple.R | 243 +- huxtable-5.7.0/huxtable/tests/testthat/test-stripes.R | 20 huxtable-5.7.0/huxtable/tests/testthat/test-style.R | 28 huxtable-5.7.0/huxtable/tests/testthat/test-subset-replace.R | 102 - huxtable-5.7.0/huxtable/tests/testthat/test-subset-spans.R | 20 huxtable-5.7.0/huxtable/tests/testthat/test-thead-html.R |only huxtable-5.7.0/huxtable/tests/testthat/test-themes.R | 4 huxtable-5.7.0/huxtable/tests/testthat/test-typst-markdown.R |only huxtable-5.7.0/huxtable/tests/testthat/test-typst.R |only huxtable-5.7.0/huxtable/tests/testthat/test-validate-outputs.R |only huxtable-5.7.0/huxtable/tests/testthat/test-yy-end-to-end.R | 173 + 208 files changed, 8099 insertions(+), 5362 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.8.13 dated 2025-03-28 and 0.9.0 dated 2025-08-18
DESCRIPTION | 8 - MD5 | 244 +++++++++++++++--------------- NEWS.md | 7 R/annotate_interactive.R | 4 R/annotation_raster_interactive.R | 5 R/default.R | 98 ++++++------ R/dsvg.R | 28 ++- R/dsvg_view.R | 23 +- R/element_interactive.R | 37 ++-- R/facet_interactive.R | 183 +++++++++++++++++----- R/fonts.R | 42 +++-- R/geom_abline_interactive.R | 25 ++- R/geom_bar_interactive.R | 14 + R/geom_bin_2d_interactive.R | 3 R/geom_boxplot_interactive.R | 234 ++++++++++++++++++----------- R/geom_col_interactive.R | 15 + R/geom_contour_interactive.R | 6 R/geom_count_interactive.R | 3 R/geom_crossbar_interactive.R | 95 ++++++++--- R/geom_curve_interactive.R | 3 R/geom_density_2d_interactive.R | 6 R/geom_density_interactive.R | 3 R/geom_dotplot_interactive.R | 3 R/geom_errorbar_interactive.R | 46 ++++- R/geom_errorbarh_interactive.R | 45 ++++- R/geom_freqpoly_interactive.R | 3 R/geom_hex_interactive.R | 3 R/geom_histogram_interactive.R | 3 R/geom_hline_interactive.R | 14 + R/geom_jitter_interactive.R | 3 R/geom_label_interactive.R | 9 - R/geom_linerange_interactive.R | 28 ++- R/geom_map_interactive.R | 32 +++- R/geom_path_interactive.R | 76 ++++++--- R/geom_point_interactive.R | 12 + R/geom_pointrange_interactive.R | 54 +++++- R/geom_polygon_interactive.R | 31 ++- R/geom_quantile_interactive.R | 3 R/geom_raster_interactive.R | 5 R/geom_rect_interactive.R | 31 +++ R/geom_ribbon_interactive.R | 50 +++--- R/geom_segment_interactive.R | 42 +++-- R/geom_sf_interactive.R | 52 +++--- R/geom_smooth_interactive.R | 37 +++- R/geom_spoke_interactive.R | 3 R/geom_text_interactive.R | 3 R/geom_text_repel_interactive.R | 12 + R/geom_tile_interactive.R | 24 ++- R/geom_violin_interactive.R | 37 +++- R/geom_vline_interactive.R | 14 + R/ggiraph.R | 4 R/girafe.R | 70 ++++++-- R/girafe_options.R | 280 ++++++++++++++++++++--------------- R/grob_interactive.R | 12 - R/guide_bins_interactive.R | 15 + R/guide_colourbar_interactive.R | 20 ++ R/guide_coloursteps_interactive.R | 29 ++- R/guide_interactive.R | 65 +++++--- R/guide_legend_interactive.R | 27 ++- R/interactive_curve_grob.R | 5 R/interactive_polyline_grob.R | 6 R/ipar.R | 77 +++++---- R/labeller_interactive.R | 6 R/layer_interactive.R | 36 +++- R/scale_alpha_interactive.R | 21 +- R/scale_brewer_interactive.R | 18 +- R/scale_colour_interactive.R | 42 +++-- R/scale_gradient_interactive.R | 19 +- R/scale_interactive.R | 74 ++++++--- R/scale_linetype_interactive.R | 12 + R/scale_manual_interactive.R | 21 +- R/scale_shape_interactive.R | 15 + R/scale_size_interactive.R | 30 ++- R/scale_steps_interactive.R | 18 +- R/scale_viridis_interactive.R | 24 ++- R/tracers.R | 10 - R/utils.R | 38 ++-- R/utils_css.R | 49 +++--- R/utils_ggplot2.R | 56 +++++-- R/utils_ggplot2_performance.R | 8 - build/vignette.rds |binary inst/tinytest/setup.R | 4 inst/tinytest/test-utils.R | 14 - man/annotate_interactive.Rd | 21 +- man/annotation_raster_interactive.Rd | 26 ++- man/element_interactive.Rd | 34 +++- man/geom_abline_interactive.Rd | 102 ++++++++---- man/geom_bar_interactive.Rd | 46 +++-- man/geom_bin_2d_interactive.Rd | 8 - man/geom_boxplot_interactive.Rd | 52 ++++-- man/geom_contour_interactive.Rd | 24 +-- man/geom_count_interactive.Rd | 17 +- man/geom_crossbar_interactive.Rd | 34 +++- man/geom_density_2d_interactive.Rd | 55 ++++-- man/geom_density_interactive.Rd | 36 +++- man/geom_dotplot_interactive.Rd | 27 ++- man/geom_errorbarh_interactive.Rd | 27 ++- man/geom_hex_interactive.Rd | 4 man/geom_histogram_interactive.Rd | 17 +- man/geom_jitter_interactive.Rd | 10 - man/geom_map_interactive.Rd | 25 +-- man/geom_path_interactive.Rd | 139 ++++++++++------- man/geom_point_interactive.Rd | 44 ++++- man/geom_polygon_interactive.Rd | 107 ++++++++++--- man/geom_quantile_interactive.Rd | 24 +-- man/geom_raster_interactive.Rd | 8 - man/geom_rect_interactive.Rd | 95 +++++++---- man/geom_ribbon_interactive.Rd | 42 +++-- man/geom_segment_interactive.Rd | 73 ++++++--- man/geom_sf_interactive.Rd | 39 +++- man/geom_smooth_interactive.Rd | 32 ++-- man/geom_spoke_interactive.Rd | 24 ++- man/geom_text_interactive.Rd | 59 +++++-- man/geom_text_repel_interactive.Rd | 34 ++-- man/geom_violin_interactive.Rd | 14 + man/guide_bins_interactive.Rd | 162 ++++++++++---------- man/guide_colourbar_interactive.Rd | 131 +++++++++------- man/guide_coloursteps_interactive.Rd | 67 ++++---- man/guide_legend_interactive.Rd | 240 +++++++++++++++++++----------- man/labeller_interactive.Rd | 137 +++++++++-------- man/scale_gradient_interactive.Rd | 131 +++++++++------- man/scale_manual_interactive.Rd | 133 +++++++++++----- man/scale_viridis_interactive.Rd | 107 +++++++------ 123 files changed, 3438 insertions(+), 1855 deletions(-)
Title: Automatically Search Errors or Warnings
Description: Provides environment hooks that obtain errors and warnings which
occur during the execution of code to automatically search for solutions.
Author: James Balamuta [aut, cre, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between errorist versions 0.1.2 dated 2023-11-14 and 0.1.3 dated 2025-08-18
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/handlers.R | 2 +- build/vignette.rds |binary inst/doc/working-with-errorist.html | 7 ++++--- man/errorist_init.Rd | 2 +- man/shims.Rd | 2 +- 8 files changed, 27 insertions(+), 19 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such
as queues, stacks, deques, dicts and ordered dicts. Benchmarks
<https://randy3k.github.io/collections/articles/benchmark.html> have
shown that these containers are asymptotically more efficient than
those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] ,
Yann Collet [cph]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.3.8 dated 2025-05-08 and 0.3.9 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/deque.R | 3 ++- R/queue.R | 3 ++- R/stack.R | 4 +++- README.md | 2 +- src/deque.c | 6 ++++++ src/dict.c | 2 +- src/queue.c | 3 +++ src/stack.c | 2 ++ 10 files changed, 33 insertions(+), 18 deletions(-)
Title: Selecting General Circulation Models for Species Distribution
Modeling
Description: Methods to help selecting General Circulation Models (GCMs)
in the context of projecting models to future scenarios. It is provided
clusterization algorithms, distance and correlation metrics, as well as
a tailor-made algorithm to detect the optimum subset of GCMs that recreate
the environment of all GCMs as proposed in Esser et al. (2025) <doi:10.1111/gcb.70008>.
Author: Dayani Bailly [aut] ,
Reginaldo Re [aut] ,
Marcos R. Lima [aut] ,
Luiz Esser [aut, cre, cph]
Maintainer: Luiz Esser <luizesser@gmail.com>
Diff between chooseGCM versions 1.0.2 dated 2025-01-16 and 1.1 dated 2025-08-18
chooseGCM-1.0.2/chooseGCM/build |only chooseGCM-1.0.2/chooseGCM/inst/doc |only chooseGCM-1.0.2/chooseGCM/vignettes |only chooseGCM-1.1/chooseGCM/DESCRIPTION | 21 chooseGCM-1.1/chooseGCM/MD5 | 27 chooseGCM-1.1/chooseGCM/NEWS.md | 6 chooseGCM-1.1/chooseGCM/README.md | 954 ---------- chooseGCM-1.1/chooseGCM/tests/testthat/test-closestdist_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-compare_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-cor_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-dist_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-env_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-flatten_gcms.R | 15 chooseGCM-1.1/chooseGCM/tests/testthat/test-hclust_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-import_gcms.R | 51 chooseGCM-1.1/chooseGCM/tests/testthat/test-kmeans_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-montecarlo_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-optk_gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-summary-gcms.R |only chooseGCM-1.1/chooseGCM/tests/testthat/test-transform_gcms.R | 14 20 files changed, 153 insertions(+), 935 deletions(-)
Title: Interact with Large Language Models in 'RStudio'
Description: Enables user interactivity with large-language models ('LLM') inside
the 'RStudio' integrated development environment (IDE). The user can
interact with the model using the 'shiny' app included in this package, or
directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub'
'Copilot', and 'LlamaGPT'.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between chattr versions 0.3.0 dated 2025-05-28 and 0.3.1 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/backend-ellmer.R | 2 +- README.md | 5 ++--- tests/testthat/_snaps/app-ui.md | 12 ++++++------ tests/testthat/_snaps/chattr-use.md | 4 ++-- tests/testthat/test-app-server.R | 2 +- 8 files changed, 27 insertions(+), 24 deletions(-)
Title: Bias Diagnostic for Linear Mixed Models
Description: Provides a function to perform bias diagnostics on linear mixed models fitted with lmer() from the 'lme4' package. Implements permutation tests for assessing the bias of fixed effects, as described in Karl and Zimmerman (2021) <doi:10.1016/j.jspi.2020.06.004>. Karl and Zimmerman (2020) <doi:10.17632/tmynggddfm.1> provide R code for implementing the test using 'mvglmmRank' output. Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mixedbiastest versions 0.3.0 dated 2024-12-13 and 0.4.1 dated 2025-08-18
DESCRIPTION | 11 - MD5 | 20 +- R/list_fixed.R | 32 +--- R/mixedbiastest-package.R | 2 R/mixedbiastest.R | 287 +++++++++++++++++-------------------------- R/plot.R | 47 +++---- build/partial.rdb |binary man/list_fixed_effects.Rd | 26 +-- man/mixedbiastest-package.Rd | 2 man/mixedbiastest.Rd | 22 +-- man/plot.mixedbiastest.Rd | 6 11 files changed, 189 insertions(+), 266 deletions(-)
Title: Introduction to Sports Analytics using R (ISAR) Data
Description: We provide data sets used in the textbook "Introduction to Sports Analytics using R" by Elmore and Urbaczweski (2025).
Author: Ryan Elmore [cre, aut]
Maintainer: Ryan Elmore <Ryan.Elmore@du.edu>
Diff between ISAR versions 1.0.0 dated 2025-07-21 and 1.0.1 dated 2025-08-18
DESCRIPTION | 6 +++--- MD5 | 23 +++++++++++++++++++---- R/epl_gk_stats_2025.R |only R/epl_player_stats_2024.R | 2 +- R/epl_player_stats_2025.R |only R/epl_team_stats_2025.R |only R/nwsl_player_stats_2023.R |only R/nwsl_player_stats_2024.R |only data/epl_gk_stats_2025.rda |only data/epl_player_stats_2024.rda |binary data/epl_player_stats_2025.rda |only data/epl_team_stats_2025.rda |only data/nwsl_player_stats_2023.rda |only data/nwsl_player_stats_2024.rda |only man/epl_gk_stats_2025.Rd |only man/epl_player_stats_2024.Rd | 2 +- man/epl_player_stats_2025.Rd |only man/epl_team_stats_2025.Rd |only man/nwsl_player_stats_2023.Rd |only man/nwsl_player_stats_2024.Rd |only 20 files changed, 24 insertions(+), 9 deletions(-)
Title: Functions and Datasets for the Data Science Course at IBAW
Description: A collection of useful functions and datasets for the Data Science
Course at IBAW.
Author: Stefan Lanz [aut, cre]
Maintainer: Stefan Lanz <slanz1137@gmail.com>
Diff between ibawds versions 1.1.0 dated 2025-03-07 and 1.2.0 dated 2025-08-18
DESCRIPTION | 17 -- MD5 | 55 ++++--- NAMESPACE | 1 R/checks.R | 105 ++++++++++++- R/evaluate_casestudy.R |only R/grading_tables.R | 112 +++++++++++--- R/install.R | 20 ++ R/slide_tools.R | 6 README.md | 1 build/partial.rdb |binary data/cran_history.rda |binary inst/WORDLIST | 3 inst/extdata/evaluation_wordlist | 31 +++- inst/extdata/slides_wordlist | 103 ++++++++++++- man/cran_history.Rd | 2 man/define_latex_stats.Rd | 6 man/evaluate_casestudy.Rd |only man/grading_tables.Rd | 27 ++- man/spell_check_evaluation.Rd | 8 - tests/testthat/data/01_Rmd/test.Rmd | 1 tests/testthat/data/01_Rmd/test.qmd | 1 tests/testthat/data/Beurteilung/Beurteilung_Reto.Rmd | 15 + tests/testthat/data/Beurteilung/Beurteilung_Sandro.qmd | 5 tests/testthat/data/casestudy |only tests/testthat/test-checks.R | 130 ++++++++++++++--- tests/testthat/test-evaluate_casestudy.R |only tests/testthat/test-grading_tables.R | 86 +++++++++-- tests/testthat/test-install.R | 46 +++++- 28 files changed, 639 insertions(+), 142 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.17-2 dated 2025-04-17 and 2.17-3 dated 2025-08-18
BiodiversityR-2.17-2/BiodiversityR/R/spatialsample.R |only BiodiversityR-2.17-2/BiodiversityR/man/spatialsample.Rd |only BiodiversityR-2.17-3/BiodiversityR/DESCRIPTION | 20 +- BiodiversityR-2.17-3/BiodiversityR/MD5 | 12 - BiodiversityR-2.17-3/BiodiversityR/NAMESPACE | 2 BiodiversityR-2.17-3/BiodiversityR/R/ensemble.blockCV.R | 19 + BiodiversityR-2.17-3/BiodiversityR/inst/ChangeLog | 8 BiodiversityR-2.17-3/BiodiversityR/man/ensemble.blockCV.Rd | 126 ++++++------- 8 files changed, 101 insertions(+), 86 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 21.0.0 dated 2025-07-24 and 21.0.0.1 dated 2025-08-18
arrow-21.0.0.1/arrow/DESCRIPTION | 6 +- arrow-21.0.0.1/arrow/MD5 | 25 +++------- arrow-21.0.0.1/arrow/NEWS.md | 12 ++++ arrow-21.0.0.1/arrow/tools/cpp/CMakeLists.txt | 2 arrow-21.0.0.1/arrow/tools/cpp/cmake_modules/ThirdpartyToolchain.cmake | 21 ++++++++ arrow-21.0.0.1/arrow/tools/cpp/cmake_modules/thrift-3187.patch |only arrow-21.0.0.1/arrow/tools/cpp/meson.build | 2 arrow-21.0.0.1/arrow/tools/cpp/src/arrow/util/tracing_internal.h | 17 +++--- arrow-21.0.0.1/arrow/tools/cpp/vcpkg.json | 2 arrow-21.0.0.1/arrow/tools/nixlibs.R | 6 ++ arrow-21.0.0/arrow/tools/checksums |only 11 files changed, 62 insertions(+), 31 deletions(-)
Title: A Collection of Tools and Helpers Extending the Tidyverse
Description: A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages.
This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of
'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count,
various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks,
saving to PDF and PNG from a pipe and various small utilities.
Author: Marcel Wiesweg [aut, cre]
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>
Diff between tidytidbits versions 0.3.2 dated 2022-03-16 and 0.3.3 dated 2025-08-18
DESCRIPTION | 8 +++---- MD5 | 44 +++++++++++++++++++++---------------------- NEWS.md | 5 ++++ R/dplyr-like.R | 10 ++++----- R/forcats-like.R | 8 +++---- R/na.R | 24 ++++++++++++++--------- R/purrr-like.R | 12 +++++------ man/are_true.Rd | 2 - man/categorical_test_by.Rd | 2 - man/count_by.Rd | 2 - man/first_non_nas_at.Rd | 2 - man/first_which_non_na_at.Rd | 2 - man/format_numbers_at.Rd | 2 - man/format_p_values_at.Rd | 2 - man/invalid.Rd | 4 +-- man/lump_rows.Rd | 2 - man/order_factor_by.Rd | 4 +-- man/pluck_vector.Rd | 4 +-- man/rename_factor.Rd | 2 - man/rename_reorder_factor.Rd | 2 - man/truthy.Rd | 4 +-- man/with_name.Rd | 4 +-- man/with_value_containing.Rd | 4 +-- 23 files changed, 83 insertions(+), 72 deletions(-)
Title: Luck-Corrected Peer Performance Analysis in R
Description: Provides functions to perform the peer performance
analysis of funds' returns as described in Ardia and Boudt (2018) <doi:10.1016/j.jbankfin.2017.10.014>.
Author: David Ardia [aut, cre] ,
Kris Boudt [aut] ,
Nabil Bouamara [ctb],
Sebastien Legros [ctb],
Benjamin Seguin [ctb]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between PeerPerformance versions 2.3.1 dated 2024-11-13 and 2.3.2 dated 2025-08-18
PeerPerformance-2.3.1/PeerPerformance/COPYING |only PeerPerformance-2.3.1/PeerPerformance/NEWS |only PeerPerformance-2.3.1/PeerPerformance/README.md |only PeerPerformance-2.3.2/PeerPerformance/DESCRIPTION | 32 +++++----- PeerPerformance-2.3.2/PeerPerformance/MD5 | 30 ++++----- PeerPerformance-2.3.2/PeerPerformance/NEWS.md |only PeerPerformance-2.3.2/PeerPerformance/R/alphaScreening.R | 14 ++-- PeerPerformance-2.3.2/PeerPerformance/R/msharpeScreening.R | 2 PeerPerformance-2.3.2/PeerPerformance/R/sharpeBlockSize.R | 5 - PeerPerformance-2.3.2/PeerPerformance/R/sharpeScreening.R | 2 PeerPerformance-2.3.2/PeerPerformance/R/sharpeTesting.R | 2 PeerPerformance-2.3.2/PeerPerformance/build/partial.rdb |binary PeerPerformance-2.3.2/PeerPerformance/inst/CITATION | 4 - PeerPerformance-2.3.2/PeerPerformance/man/alphaScreening.Rd | 2 PeerPerformance-2.3.2/PeerPerformance/man/msharpeScreening.Rd | 2 PeerPerformance-2.3.2/PeerPerformance/man/sharpeScreening.Rd | 2 PeerPerformance-2.3.2/PeerPerformance/man/sharpeTesting.Rd | 2 PeerPerformance-2.3.2/PeerPerformance/tests/testthat/test_testing.R | 4 - 18 files changed, 53 insertions(+), 50 deletions(-)
More information about PeerPerformance at CRAN
Permanent link
Title: Functions to Efficiently Simulate and Evaluate NFL Seasons
Description: A set of functions to simulate National Football League
seasons including the sophisticated tie-breaking procedures.
Author: Sebastian Carl [cre, aut, cph],
Lee Sharpe [aut]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflseedR versions 2.0.0 dated 2025-03-24 and 2.0.1 dated 2025-08-18
DESCRIPTION | 6 +- MD5 | 24 +++++------ NEWS.md | 7 +++ R/simulations_utils.R | 4 - R/standings.R | 3 - R/standings_add_draft_ranks.R | 15 ++++--- R/standings_prettify.R | 14 +++++- R/standings_utils.R | 14 ++++++ man/nfl_simulations.Rd | 3 - man/nfl_standings.Rd | 3 - tests/testthat/_snaps/sims/simulations.md | 57 ++++++++++++++------------- tests/testthat/_snaps/standings/standings.md | 4 - tests/testthat/test-standings.R | 7 +++ 13 files changed, 104 insertions(+), 57 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.3.2 dated 2025-07-17 and 0.4.0 dated 2025-08-18
DESCRIPTION | 8 MD5 | 47 +++-- NAMESPACE | 14 + NEWS.md | 10 + R/legends.R | 215 ++++++++++++++++-------- R/legends_compare.R |only R/plugins.R | 12 + R/turf.R |only README.md | 2 inst/htmlwidgets/lib/maptiler-geocoding-control |only inst/htmlwidgets/lib/turf |only inst/htmlwidgets/mapboxgl.js | 72 ++++++-- inst/htmlwidgets/mapboxgl.yaml | 12 + inst/htmlwidgets/mapboxgl_compare.js | 72 +++++++- inst/htmlwidgets/mapboxgl_compare.yaml | 6 inst/htmlwidgets/maplibregl.js | 72 ++++++-- inst/htmlwidgets/maplibregl.yaml | 13 + inst/htmlwidgets/maplibregl_compare.js | 94 +++++++++- inst/htmlwidgets/turf-operations.js |only man/map_legends.Rd | 80 ++++++++ man/turf_area.Rd |only man/turf_buffer.Rd |only man/turf_center_of_mass.Rd |only man/turf_centroid.Rd |only man/turf_concave_hull.Rd |only man/turf_convex_hull.Rd |only man/turf_difference.Rd |only man/turf_distance.Rd |only man/turf_filter.Rd |only man/turf_intersect.Rd |only man/turf_union.Rd |only man/turf_voronoi.Rd |only 32 files changed, 595 insertions(+), 134 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.5 dated 2025-07-07 and 1.3.6 dated 2025-08-18
DESCRIPTION | 8 MD5 | 84 +++--- R/diagnostic.lsirm.R | 433 ++++++++++++++++++++++++++++++++--- R/lsirm.R | 101 +++++--- R/lsirm1pl_fixed_gamma.R | 2 R/lsirm1pl_fixed_gamma_mar.R | 2 R/lsirm1pl_fixed_gamma_mcar.R | 2 R/lsirm1pl_mar.R | 2 R/lsirm1pl_mar_ss.R | 2 R/lsirm1pl_mcar.R | 2 R/lsirm1pl_mcar_ss.R | 2 R/lsirm1pl_normal_fixed_gamma.R | 2 R/lsirm1pl_normal_fixed_gamma_mar.R | 2 R/lsirm1pl_normal_fixed_gamma_mcar.R | 2 R/lsirm1pl_normal_mar.R | 2 R/lsirm1pl_normal_mar_ss.R | 2 R/lsirm1pl_normal_mcar.R | 2 R/lsirm1pl_normal_mcar_ss.R | 2 R/lsirm1pl_normal_o.R | 2 R/lsirm1pl_normal_ss.R | 2 R/lsirm1pl_o.R | 2 R/lsirm1pl_ss.R | 2 R/lsirm2pl_fixed_gamma.R | 2 R/lsirm2pl_fixed_gamma_mar.R | 2 R/lsirm2pl_fixed_gamma_mcar.R | 2 R/lsirm2pl_mar.R | 2 R/lsirm2pl_mar_ss.R | 2 R/lsirm2pl_mcar.R | 2 R/lsirm2pl_mcar_ss.R | 2 R/lsirm2pl_normal_fixed_gamma.R | 2 R/lsirm2pl_normal_fixed_gamma_mar.R | 2 R/lsirm2pl_normal_fixed_gamma_mcar.R | 2 R/lsirm2pl_normal_mar.R | 2 R/lsirm2pl_normal_mar_ss.R | 2 R/lsirm2pl_normal_mcar.R | 2 R/lsirm2pl_normal_mcar_ss.R | 2 R/lsirm2pl_normal_o.R | 2 R/lsirm2pl_normal_ss.R | 2 R/lsirm2pl_o.R | 2 R/lsirm2pl_ss.R | 2 man/diagnostic.Rd | 6 man/lsirm1pl.Rd | 12 man/lsirm2pl.Rd | 12 43 files changed, 571 insertions(+), 157 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [ctb],
Denes Toth [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 2.3.2 dated 2024-07-29 and 2.3.3 dated 2025-08-18
DESCRIPTION | 10 +- MD5 | 172 +++++++++++++++++++-------------------- NEWS.md | 7 + R/anyInfinite.R | 2 R/anyMissing.R | 2 R/anyNaN.R | 2 R/asInteger.R | 2 R/assert.R | 4 R/checkCharacter.R | 2 R/checkNamed.R | 2 R/checkNames.R | 2 R/checkOS.R | 2 R/coalesce.R | 6 - R/helper.R | 4 R/matchArg.R | 6 - R/qassert.R | 2 R/vname.R | 2 README.md | 18 ++-- build/vignette.rds |binary inst/doc/checkmate.R | 28 +++--- inst/doc/checkmate.html | 110 ++++++++++++------------ inst/doc/tinytest.R | 6 - inst/doc/tinytest.html | 9 +- man/anyInfinite.Rd | 2 man/anyMissing.Rd | 2 man/anyNaN.Rd | 2 man/asInteger.Rd | 2 man/assert.Rd | 2 man/checkAccess.Rd | 2 man/checkArray.Rd | 2 man/checkAtomic.Rd | 2 man/checkAtomicVector.Rd | 2 man/checkCharacter.Rd | 4 man/checkChoice.Rd | 2 man/checkClass.Rd | 2 man/checkComplex.Rd | 2 man/checkCount.Rd | 2 man/checkDataFrame.Rd | 2 man/checkDataTable.Rd | 2 man/checkDate.Rd | 2 man/checkDirectoryExists.Rd | 2 man/checkDisjunct.Rd | 2 man/checkDouble.Rd | 2 man/checkEnvironment.Rd | 2 man/checkFALSE.Rd | 2 man/checkFactor.Rd | 2 man/checkFileExists.Rd | 2 man/checkFlag.Rd | 2 man/checkFormula.Rd | 2 man/checkFunction.Rd | 2 man/checkInt.Rd | 2 man/checkInteger.Rd | 2 man/checkIntegerish.Rd | 2 man/checkList.Rd | 2 man/checkLogical.Rd | 2 man/checkMatrix.Rd | 2 man/checkMultiClass.Rd | 2 man/checkNamed.Rd | 4 man/checkNames.Rd | 2 man/checkNull.Rd | 2 man/checkNumber.Rd | 2 man/checkNumeric.Rd | 2 man/checkOS.Rd | 2 man/checkPOSIXct.Rd | 2 man/checkPathForOutput.Rd | 2 man/checkPermutation.Rd | 2 man/checkR6.Rd | 2 man/checkRaw.Rd | 2 man/checkScalar.Rd | 2 man/checkScalarNA.Rd | 2 man/checkSetEqual.Rd | 2 man/checkString.Rd | 4 man/checkSubset.Rd | 2 man/checkTRUE.Rd | 2 man/checkTibble.Rd | 2 man/checkVector.Rd | 2 man/coalesce.Rd | 4 man/makeAssertion.Rd | 2 man/makeExpectation.Rd | 2 man/matchArg.Rd | 6 - man/qassert.Rd | 2 man/vname.Rd | 2 src/all_missing.c | 4 src/any_missing.c | 2 src/backports.h | 5 + src/helper.c | 6 - tests/testthat/test_anyMissing.R | 15 +++ 87 files changed, 295 insertions(+), 267 deletions(-)
Title: Visualization of Clonal Expansion for Single Cell Immune
Profiles
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Author: Qile Yang [cre, aut, cph]
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Diff between APackOfTheClones versions 1.2.4 dated 2024-11-18 and 1.3.0 dated 2025-08-18
APackOfTheClones-1.2.4/APackOfTheClones/R/typecheck.R |only APackOfTheClones-1.2.4/APackOfTheClones/tests/testthat/_snaps |only APackOfTheClones-1.2.4/APackOfTheClones/tests/testthat/test-typecheck.R |only APackOfTheClones-1.3.0/APackOfTheClones/DESCRIPTION | 17 APackOfTheClones-1.3.0/APackOfTheClones/MD5 | 125 +- APackOfTheClones-1.3.0/APackOfTheClones/NAMESPACE | 10 APackOfTheClones-1.3.0/APackOfTheClones/R/APOTCPlot.R | 356 +++---- APackOfTheClones-1.3.0/APackOfTheClones/R/APackOfTheClones-package.R | 4 APackOfTheClones-1.3.0/APackOfTheClones/R/AdjustAPOTC.R | 375 ++++---- APackOfTheClones-1.3.0/APackOfTheClones/R/ApotcClonalNetwork.R | 65 - APackOfTheClones-1.3.0/APackOfTheClones/R/ApotcData.R | 446 +++++----- APackOfTheClones-1.3.0/APackOfTheClones/R/ApotcGGPlot.R |only APackOfTheClones-1.3.0/APackOfTheClones/R/ApotcIndexing.R | 33 APackOfTheClones-1.3.0/APackOfTheClones/R/RcppExports.R | 4 APackOfTheClones-1.3.0/APackOfTheClones/R/Repulsion.R | 152 +-- APackOfTheClones-1.3.0/APackOfTheClones/R/RunAPOTC.R | 18 APackOfTheClones-1.3.0/APackOfTheClones/R/asserts.R |only APackOfTheClones-1.3.0/APackOfTheClones/R/cluster_labels.R | 36 APackOfTheClones-1.3.0/APackOfTheClones/R/deprecated_functions.R | 52 - APackOfTheClones-1.3.0/APackOfTheClones/R/get_clone_sizes.R | 2 APackOfTheClones-1.3.0/APackOfTheClones/R/ggplot2_functions.R | 82 + APackOfTheClones-1.3.0/APackOfTheClones/R/insert_legend.R | 33 APackOfTheClones-1.3.0/APackOfTheClones/R/plot_API.R | 179 ++-- APackOfTheClones-1.3.0/APackOfTheClones/R/scRepertoire_v2_functions.R | 46 - APackOfTheClones-1.3.0/APackOfTheClones/R/seurat_command.R | 2 APackOfTheClones-1.3.0/APackOfTheClones/R/showCloneHighlight.R | 35 APackOfTheClones-1.3.0/APackOfTheClones/R/updateApotc.R |only APackOfTheClones-1.3.0/APackOfTheClones/R/utils.R | 76 - APackOfTheClones-1.3.0/APackOfTheClones/R/vizAPOTC.R | 4 APackOfTheClones-1.3.0/APackOfTheClones/build/partial.rdb |binary APackOfTheClones-1.3.0/APackOfTheClones/build/vignette.rds |binary APackOfTheClones-1.3.0/APackOfTheClones/data/combined_pbmc.rda |binary APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.R | 100 +- APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.Rmd | 2 APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.html | 38 APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.html | 6 APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones-utils.html | 2 APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones.R | 92 +- APackOfTheClones-1.3.0/APackOfTheClones/inst/doc/APackOfTheClones.html | 6 APackOfTheClones-1.3.0/APackOfTheClones/man/APOTCPlot.Rd | 6 APackOfTheClones-1.3.0/APackOfTheClones/man/APackOfTheClones-package.Rd | 4 APackOfTheClones-1.3.0/APackOfTheClones/man/AdjustAPOTC.Rd | 4 APackOfTheClones-1.3.0/APackOfTheClones/man/clonal_expansion_plot.Rd | 2 APackOfTheClones-1.3.0/APackOfTheClones/man/count_clone_sizes.Rd | 2 APackOfTheClones-1.3.0/APackOfTheClones/man/getApotcDataIds.Rd | 3 APackOfTheClones-1.3.0/APackOfTheClones/man/getLastApotcDataId.Rd | 3 APackOfTheClones-1.3.0/APackOfTheClones/man/integrate_tcr.Rd | 2 APackOfTheClones-1.3.0/APackOfTheClones/man/mergeCloneSizes.Rd | 2 APackOfTheClones-1.3.0/APackOfTheClones/man/updateApotc.Rd |only APackOfTheClones-1.3.0/APackOfTheClones/man/vizAPOTC.Rd | 8 APackOfTheClones-1.3.0/APackOfTheClones/src/CloneLinkHelpers.cpp | 195 ---- APackOfTheClones-1.3.0/APackOfTheClones/src/LineLinkDataFrameFactory.h |only APackOfTheClones-1.3.0/APackOfTheClones/src/RcppExports.cpp | 9 APackOfTheClones-1.3.0/APackOfTheClones/tests/spelling.R | 9 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/helper-testFunctions.R | 11 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-APOTCPlot.R | 1 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-ApotcClonalNetwork.R | 32 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-ApotcIndexing.R | 25 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-Repulsion.R | 8 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-colors.R | 64 - APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-insert_legend.R | 72 - APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-noscript-defaultApotcPlot.R | 2 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-showCloneHighlight.R | 3 APackOfTheClones-1.3.0/APackOfTheClones/tests/testthat/test-vizAPOTC.R | 5 APackOfTheClones-1.3.0/APackOfTheClones/vignettes/APackOfTheClones-runs.Rmd | 2 65 files changed, 1409 insertions(+), 1463 deletions(-)
More information about APackOfTheClones at CRAN
Permanent link
Title: The Voigt Distribution
Description: Random generation, density function and parameter estimation for the Voigt distribution. The main objective of this package is to provide R users with efficient estimation of Voigt parameters using classic iid data in a Bayesian framework. The estimating function allows flexible prior specification, specification of fixed parameters and several options for Markov Chain Monte Carlo posterior simulation. A basic version of the algorithm is described in: Cannas M. and Piras, N. (2025) <doi:10.1007/978-3-031-96303-2_53>.
Author: Massimo Cannas [aut, cre],
Nicola Piras [aut],
Daniele Chiriu [ctb]
Maintainer: Massimo Cannas <massimo.cannas@unica.it>
Diff between voigt versions 1.0 dated 2025-07-05 and 2.0 dated 2025-08-18
DESCRIPTION | 17 ++++++++----- MD5 | 14 ++++++----- NAMESPACE | 4 +-- R/voigt.R | 66 +++++++++++++++--------------------------------------- build/partial.rdb |binary data |only man/Voigt.Rd | 14 ++++------- man/evoigt.Rd | 18 +++++++++++++- man/raman.Rd |only 9 files changed, 60 insertions(+), 73 deletions(-)
Title: Spatial Early Warning Signals of Ecosystem Degradation
Description: Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation. EWS are spatial metrics derived from raster data -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Author: Alain Danet [aut],
Alexandre Genin [aut, cre] ,
Vishwesha Guttal [aut],
Sonia Kefi [aut],
Sabiha Majumder [aut],
Sumithra Sankaran [aut],
Florian Schneider [aut]
Maintainer: Alexandre Genin <alexandre.genin@sete.cnrs.fr>
Diff between spatialwarnings versions 3.1.0 dated 2024-09-06 and 3.1.1 dated 2025-08-18
spatialwarnings-3.1.0/spatialwarnings/man/spatialwarnings.Rd |only spatialwarnings-3.1.1/spatialwarnings/DESCRIPTION | 30 +-- spatialwarnings-3.1.1/spatialwarnings/MD5 | 43 ++-- spatialwarnings-3.1.1/spatialwarnings/NAMESPACE | 5 spatialwarnings-3.1.1/spatialwarnings/NEWS | 14 + spatialwarnings-3.1.1/spatialwarnings/R/checks.R | 2 spatialwarnings-3.1.1/spatialwarnings/R/fitpsd.R | 12 - spatialwarnings-3.1.1/spatialwarnings/R/helpers.R | 43 +++- spatialwarnings-3.1.1/spatialwarnings/R/roxygen-tags.R | 2 spatialwarnings-3.1.1/spatialwarnings/R/spatialwarnings.R | 14 - spatialwarnings-3.1.1/spatialwarnings/R/task_kbdm.R | 9 spatialwarnings-3.1.1/spatialwarnings/R/task_variogram_indic.R | 11 - spatialwarnings-3.1.1/spatialwarnings/build/partial.rdb |binary spatialwarnings-3.1.1/spatialwarnings/man/display_size_info.Rd |only spatialwarnings-3.1.1/spatialwarnings/man/spatialwarnings-package.Rd |only spatialwarnings-3.1.1/spatialwarnings/src/variogram.cpp | 12 - spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-display_matrix.R | 2 spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-kbdm.R | 2 spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-lsw.R | 6 spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-patches.R | 9 spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-psd-predict.R | 23 +- spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-spectrum.R | 2 spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-tplnorm.R | 95 +++++----- spatialwarnings-3.1.1/spatialwarnings/tests/testthat/test-variogram.R | 9 24 files changed, 199 insertions(+), 146 deletions(-)
More information about spatialwarnings at CRAN
Permanent link
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results), can
handle (and impute) missing values and is delivered with a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre] ,
Elise Maigne [aut],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SOMbrero versions 1.4-3 dated 2025-06-19 and 1.4.4 dated 2025-08-18
DESCRIPTION | 8 - MD5 | 58 ++++++------ NAMESPACE | 3 NEWS.md | 10 ++ R/data.R | 2 R/graph_som.R | 2 R/grids.R | 4 R/parameters.R | 2 R/plots.R | 4 R/prediction.R | 2 R/prototype_initialization.R | 3 R/quality.R | 2 R/som.R | 4 R/sombreroGUI.R | 5 - R/superclasses.R | 157 +++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/a-doc-SOMbrero-package.html | 16 +-- man/initGrid.Rd | 2 man/initSOM.Rd | 2 man/myGrid.Rd | 2 man/plot.somRes.Rd | 2 man/predict.somRes.Rd | 2 man/presidentielles2002.Rd | 2 man/projectIGraph.Rd | 2 man/protoDist.Rd | 2 man/quality.Rd | 2 man/somRes.plotting.Rd | 2 man/sombreroGUI.Rd | 5 - man/superClass.Rd | 122 ++++++++++++++------------- man/trainSOM.Rd | 2 30 files changed, 248 insertions(+), 183 deletions(-)
Title: Sensitivity Analysis for Irregular Assessment Times
Description: Sensitivity analysis for trials with irregular and informative
assessment times, based on a new influence function-based, augmented
inverse intensity-weighted estimator.
Author: Andrew Redd [aut, cre] ,
Yujing Gao [aut],
Shu Yang [aut],
Bonnie Smith [aut],
Ravi Varadhan [aut],
Agatha Mallett [ctb, ctr],
Daniel Scharfstein [pdr, aut] ,
University of Utah [cph]
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between SensIAT versions 0.1.1 dated 2024-11-17 and 0.2.0 dated 2025-08-18
SensIAT-0.1.1/SensIAT/R/pcori_conditional_means.R |only SensIAT-0.1.1/SensIAT/man/pcori_conditional_means.Rd |only SensIAT-0.2.0/SensIAT/DESCRIPTION | 25 SensIAT-0.2.0/SensIAT/MD5 | 103 - SensIAT-0.2.0/SensIAT/NAMESPACE | 169 +- SensIAT-0.2.0/SensIAT/NEWS.md | 6 SensIAT-0.2.0/SensIAT/R/PCORI_example_data.R | 42 SensIAT-0.2.0/SensIAT/R/PCORI_fulldata_model.R | 91 - SensIAT-0.2.0/SensIAT/R/PCORI_within_group_model.R | 412 ++--- SensIAT-0.2.0/SensIAT/R/RcppExports.R | 10 SensIAT-0.2.0/SensIAT/R/SIDRnew.R | 812 ++++------ SensIAT-0.2.0/SensIAT/R/SensIAT-package.R | 136 - SensIAT-0.2.0/SensIAT/R/SensIAT_prepare_data.R |only SensIAT-0.2.0/SensIAT/R/SensIAT_sim_outcome_modeler_mave.R |only SensIAT-0.2.0/SensIAT/R/add_class.R |only SensIAT-0.2.0/SensIAT/R/add_terminal_observations.R |only SensIAT-0.2.0/SensIAT/R/autoplot.R |only SensIAT-0.2.0/SensIAT/R/compute_influence_for_one_alpha_and_one_patient.R | 268 +-- SensIAT-0.2.0/SensIAT/R/compute_slope.R |only SensIAT-0.2.0/SensIAT/R/data_transform.R |only SensIAT-0.2.0/SensIAT/R/estimate_baseline_intensity.R | 107 - SensIAT-0.2.0/SensIAT/R/fit_marginal_model.R |only SensIAT-0.2.0/SensIAT/R/influence.R | 430 ----- SensIAT-0.2.0/SensIAT/R/influence_sim.R |only SensIAT-0.2.0/SensIAT/R/jackknife.R | 121 + SensIAT-0.2.0/SensIAT/R/predict_within_group.R | 86 - SensIAT-0.2.0/SensIAT/R/prune.R | 59 SensIAT-0.2.0/SensIAT/R/sensitivity_expected_values.R |only SensIAT-0.2.0/SensIAT/R/sim_outcome_modeler.R | 610 ++++--- SensIAT-0.2.0/SensIAT/R/util-match.names.R |only SensIAT-0.2.0/SensIAT/README.md | 3 SensIAT-0.2.0/SensIAT/data/SensIAT_example_fulldata.rda |only SensIAT-0.2.0/SensIAT/inst/WORDLIST | 10 SensIAT-0.2.0/SensIAT/inst/examples |only SensIAT-0.2.0/SensIAT/man/SensIAT-package.Rd | 2 SensIAT-0.2.0/SensIAT/man/SensIAT_example_data.Rd | 19 SensIAT-0.2.0/SensIAT/man/SensIAT_fit_marginal_model.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_jackknife.Rd | 26 SensIAT-0.2.0/SensIAT/man/SensIAT_prepare_data.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler.Rd | 46 SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler_mave.Rd |only SensIAT-0.2.0/SensIAT/man/add_class.Rd |only SensIAT-0.2.0/SensIAT/man/add_terminal_observations.Rd |only SensIAT-0.2.0/SensIAT/man/autoplot.SensIAT_fulldata_jackknife_results.Rd |only SensIAT-0.2.0/SensIAT/man/autoplot.SensIAT_fulldata_model.Rd |only SensIAT-0.2.0/SensIAT/man/autoplot.SensIAT_within_group_model.Rd |only SensIAT-0.2.0/SensIAT/man/autoplot.SensIAT_withingroup_jackknife_results.Rd |only SensIAT-0.2.0/SensIAT/man/compute_influence_terms.Rd |only SensIAT-0.2.0/SensIAT/man/fit_SensIAT_within_group_model.Rd | 86 - SensIAT-0.2.0/SensIAT/man/jackknife.Rd |only SensIAT-0.2.0/SensIAT/man/pcoriaccel_estimate_pmf.Rd | 48 SensIAT-0.2.0/SensIAT/man/pcoriaccel_evaluate_basis_mat.Rd |only SensIAT-0.2.0/SensIAT/man/predict.SensIAT_within_group_model.Rd | 8 SensIAT-0.2.0/SensIAT/man/sensitivity_expected_values.Rd |only SensIAT-0.2.0/SensIAT/src/RcppExports.cpp | 13 SensIAT-0.2.0/SensIAT/src/spline_basis.cpp | 16 SensIAT-0.2.0/SensIAT/src/spline_basis.h | 20 SensIAT-0.2.0/SensIAT/tests/testthat/test-NW.R | 214 +- SensIAT-0.2.0/SensIAT/tests/testthat/test-PCORI_within_group_model.R |only SensIAT-0.2.0/SensIAT/tests/testthat/test-SensIAT_sim_outcome_modeler_mave.R |only SensIAT-0.2.0/SensIAT/tests/testthat/test-common.R | 38 SensIAT-0.2.0/SensIAT/tests/testthat/test-estimate_baseline_intensity.R |only SensIAT-0.2.0/SensIAT/tests/testthat/test-influence_term1.R | 210 +- SensIAT-0.2.0/SensIAT/tests/testthat/test-influence_term2-fixed.R | 26 SensIAT-0.2.0/SensIAT/tests/testthat/test-influence_term2.R | 218 +- SensIAT-0.2.0/SensIAT/tests/testthat/test-sim_outcome_modeler.R | 57 SensIAT-0.2.0/SensIAT/tests/testthat/test-splinebasis.R | 6 SensIAT-0.2.0/SensIAT/tests/testthat/test-util-match.names.R |only 68 files changed, 2294 insertions(+), 2259 deletions(-)
Title: Chart Generation for 'Microsoft Word' and 'Microsoft PowerPoint'
Documents
Description: Create native charts for 'Microsoft PowerPoint' and 'Microsoft Word' documents.
These can then be edited and annotated. Functions are provided to let users create charts, modify
and format their content. The chart's underlying data is automatically saved within the
'Word' document or 'PowerPoint' presentation. It extends package 'officer' that does
not contain any feature for 'Microsoft' native charts production.
Author: David Gohel [aut, cre],
ArData [cph],
YouGov [fnd],
Jan Marvin Garbuszus [ctb] ,
Stefan Moog [ctb] ,
Eli Daniels [ctb],
Marlon Molina [ctb] ,
Rokas Klydzia [ctb] ,
David Camposeco [ctb] ,
Dan Joplin [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between mschart versions 0.4.0 dated 2022-11-30 and 0.4.1 dated 2025-08-18
DESCRIPTION | 14 ++++++++---- MD5 | 35 ++++++++++++++++++------------- NAMESPACE | 14 ++++++++++++ NEWS.md | 14 ++++++++++++ R/chart_data_labels.R | 2 + R/chart_data_styles.R | 4 +-- R/excel_series.R | 11 +++------ R/ms_chart.R | 9 +++++++- R/ph_with_chart.R | 3 +- R/series.R | 8 +++++++ R/sppr_codes.R |only R/theme.R | 42 ++++++++++++++++++++++++++++++-------- R/themes.R |only R/to_pml.R | 17 +++++++++++---- man/chart_fill_ggplot2.Rd |only man/chart_labels_text.Rd | 4 +-- man/figures/fig_theme_ggplot2.png |only man/mschart.Rd | 4 ++- man/ph_with.ms_chart.Rd | 2 - man/set_theme.Rd | 32 +++++++++++++++++++++------- man/theme_ggplot2.Rd |only 21 files changed, 160 insertions(+), 55 deletions(-)
Title: Probabilistic Record Linkage Using Pretrained Text Embeddings
Description: Links datasets through fuzzy string matching using pretrained text embeddings. Produces more accurate record linkage when lexical string distance metrics are a poor guide to match quality (e.g., "Patricia" is more lexically similar to "Patrick" than it is to "Trish"). Capable of performing multilingual record linkage. Methods are described in Ornstein (2025) <https://joeornstein.github.io/publications/fuzzylink.pdf>.
Author: Joe Ornstein [aut, cre, cph]
Maintainer: Joe Ornstein <jornstein@uga.edu>
Diff between fuzzylink versions 0.2.1 dated 2025-06-14 and 0.2.4 dated 2025-08-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 12 ++++++++++++ R/fuzzylink.R | 28 ++++++++++++++++++++++++++++ R/get_embeddings.R | 10 ++++++++-- 5 files changed, 55 insertions(+), 9 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.2.0 dated 2025-06-24 and 0.2.1 dated 2025-08-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dominoplot.R | 7 ++++++- 3 files changed, 11 insertions(+), 6 deletions(-)
Title: 'shiny' Application for Statistical Test Assumption Checking and
Guidance
Description: A 'shiny' application to assess statistical assumptions and guide users toward appropriate tests. The app is designed for researchers with minimal statistical training and provides diagnostics, plots, and test recommendations for a wide range of analyses. Many statistical assumptions are implemented using the package 'rstatix' (Kassambara, 2019) <doi:10.32614/CRAN.package.rstatix> and 'performance' (Lüdecke et al., 2021) <doi:10.21105/joss.03139>.
Author: Ahmed Bargheet [aut, cre]
Maintainer: Ahmed Bargheet <ahmed.bargheet@yahoo.com>
Diff between AssumpSure versions 1.0.0 dated 2025-07-15 and 1.1.0 dated 2025-08-18
DESCRIPTION | 11 MD5 | 5 NEWS.md |only inst/app/app.R | 5044 ++++++++++++++++++++++++++++++++++++++++++++------------- 4 files changed, 3983 insertions(+), 1077 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] ,
Posit Software, PBC [cph, fnd],
Alessandro Gasparini [ctb] ,
Benjie Gillam [ctb],
Claus Thorn Ekstroem [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] ,
Inaki Ucar [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.30 dated 2024-03-23 and 0.31 dated 2025-08-18
DESCRIPTION | 44 ++++++----- LICENSE | 2 MD5 | 22 ++--- R/render.R | 170 ++++++++++++++++++++++------------------------ R/utils.R | 7 - build/vignette.rds |binary inst/doc/intro-en_US.html | 4 - inst/doc/intro-zh_CN.html | 4 - man/decktape.Rd | 24 +++--- man/inf_mr.Rd | 8 +- man/moon_reader.Rd | 126 +++++++++++++++------------------- man/summon_remark.Rd | 5 - 12 files changed, 200 insertions(+), 216 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.14 dated 2025-07-22 and 0.0.15 dated 2025-08-18
smoothemplik-0.0.14/smoothemplik/man/weightedEL.Rd |only smoothemplik-0.0.14/smoothemplik/man/weightedEL0.Rd |only smoothemplik-0.0.14/smoothemplik/man/weightedEuL.Rd |only smoothemplik-0.0.14/smoothemplik/src/weightedEL.cpp |only smoothemplik-0.0.14/smoothemplik/src/weightedEuL.cpp |only smoothemplik-0.0.14/smoothemplik/tests/testthat/Rplots.pdf |only smoothemplik-0.0.14/smoothemplik/tests/testthat/test-weightedEL.R |only smoothemplik-0.0.14/smoothemplik/tests/testthat/test-weightedEL0.R |only smoothemplik-0.0.14/smoothemplik/tests/testthat/test-weightedEuL.R |only smoothemplik-0.0.15/smoothemplik/DESCRIPTION | 6 smoothemplik-0.0.15/smoothemplik/MD5 | 76 +++---- smoothemplik-0.0.15/smoothemplik/NAMESPACE | 6 smoothemplik-0.0.15/smoothemplik/NEWS.md | 15 - smoothemplik-0.0.15/smoothemplik/R/RcppExports.R | 16 - smoothemplik-0.0.15/smoothemplik/R/elfunctions.R | 101 +++++----- smoothemplik-0.0.15/smoothemplik/R/helpers.R | 2 smoothemplik-0.0.15/smoothemplik/R/selfunctions.R | 10 smoothemplik-0.0.15/smoothemplik/R/smoothers.R | 65 +++--- smoothemplik-0.0.15/smoothemplik/R/zzz.R | 4 smoothemplik-0.0.15/smoothemplik/build/partial.rdb |binary smoothemplik-0.0.15/smoothemplik/inst/CITATION | 6 smoothemplik-0.0.15/smoothemplik/inst/REFERENCES.bib | 11 + smoothemplik-0.0.15/smoothemplik/inst/doc/choice-of-SEL-weights.R | 6 smoothemplik-0.0.15/smoothemplik/inst/doc/choice-of-SEL-weights.Rmd | 8 smoothemplik-0.0.15/smoothemplik/inst/doc/choice-of-SEL-weights.html | 29 +- smoothemplik-0.0.15/smoothemplik/inst/doc/non-parametric-rcpp.html | 16 - smoothemplik-0.0.15/smoothemplik/man/DCV.Rd | 4 smoothemplik-0.0.15/smoothemplik/man/EL.Rd |only smoothemplik-0.0.15/smoothemplik/man/EL0.Rd |only smoothemplik-0.0.15/smoothemplik/man/EuL.Rd |only smoothemplik-0.0.15/smoothemplik/man/bw.CV.Rd | 5 smoothemplik-0.0.15/smoothemplik/man/ctracelr.Rd | 8 smoothemplik-0.0.15/smoothemplik/man/interpTwo.Rd | 2 smoothemplik-0.0.15/smoothemplik/man/kernelSmooth.Rd | 6 smoothemplik-0.0.15/smoothemplik/man/smoothEmplik.Rd | 4 smoothemplik-0.0.15/smoothemplik/src/EL.cpp |only smoothemplik-0.0.15/smoothemplik/src/EuL.cpp |only smoothemplik-0.0.15/smoothemplik/src/RcppExports.cpp | 98 ++++----- smoothemplik-0.0.15/smoothemplik/src/kernelsm.h | 3 smoothemplik-0.0.15/smoothemplik/src/kernelsmoothers.cpp | 5 smoothemplik-0.0.15/smoothemplik/tests/testthat/test-EL.R |only smoothemplik-0.0.15/smoothemplik/tests/testthat/test-EL0.R |only smoothemplik-0.0.15/smoothemplik/tests/testthat/test-EuL.R |only smoothemplik-0.0.15/smoothemplik/tests/testthat/test-bw.CV.R | 66 +----- smoothemplik-0.0.15/smoothemplik/tests/testthat/test-interpTwo.R | 2 smoothemplik-0.0.15/smoothemplik/tests/testthat/test-kernelDensity.R |only smoothemplik-0.0.15/smoothemplik/tests/testthat/test-kernelSmooth.R | 17 + smoothemplik-0.0.15/smoothemplik/vignettes/choice-of-SEL-weights.Rmd | 8 48 files changed, 294 insertions(+), 311 deletions(-)
Title: Utilities to Fit Paired Comparison Models for Preferences
Description: Generates design matrix for analysing real paired comparisons and derived paired comparison data (Likert type items/ratings or rankings) using a loglinear approach. Fits loglinear Bradley-Terry model (LLBT) exploiting an eliminate feature. Computes pattern models for paired comparisons, rankings, and ratings. Some treatment of missing values (MCAR and MNAR). Fits latent class (mixture) models for paired comparison, rating and ranking patterns using a non-parametric ML approach.
Author: Reinhold Hatzinger [aut],
Marco Johannes Maier [cre]
Maintainer: Marco Johannes Maier <marco_maier@posteo.de>
Diff between prefmod versions 0.8-36 dated 2023-09-30 and 0.8-37 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++++++++ build/partial.rdb |binary man/issp2000.Rd | 4 ++-- man/llbt.fit.Rd | 2 +- man/llbt.worth.Rd | 2 +- 7 files changed, 22 insertions(+), 14 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data handling (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and resid [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.7.3 dated 2025-07-07 and 0.7.4 dated 2025-08-18
misty-0.7.3/misty/R/robust.coef.R |only misty-0.7.3/misty/R/rwg.lindell.R |only misty-0.7.3/misty/R/std.coef.R |only misty-0.7.3/misty/man/as.na.Rd |only misty-0.7.3/misty/man/robust.coef.Rd |only misty-0.7.3/misty/man/rwg.lindell.Rd |only misty-0.7.3/misty/man/std.coef.Rd |only misty-0.7.4/misty/DESCRIPTION | 10 misty-0.7.4/misty/MD5 | 304 ++--- misty-0.7.4/misty/NAMESPACE | 26 misty-0.7.4/misty/NEWS.md | 49 misty-0.7.4/misty/R/aov.b.R | 16 misty-0.7.4/misty/R/aov.w.R | 14 misty-0.7.4/misty/R/blimp.bayes.R | 2 misty-0.7.4/misty/R/center.R | 14 misty-0.7.4/misty/R/check.collin.R | 51 misty-0.7.4/misty/R/check.resid.R | 543 +++++++--- misty-0.7.4/misty/R/ci.cor.R | 14 misty-0.7.4/misty/R/ci.mean.R | 14 misty-0.7.4/misty/R/ci.mean.w.R | 73 - misty-0.7.4/misty/R/ci.prop.R | 34 misty-0.7.4/misty/R/ci.prop.diff.R | 21 misty-0.7.4/misty/R/ci.var.R | 37 misty-0.7.4/misty/R/clear.R | 2 misty-0.7.4/misty/R/cluster.rwg.R |only misty-0.7.4/misty/R/cluster.scores.R | 12 misty-0.7.4/misty/R/coding.R | 6 misty-0.7.4/misty/R/coeff.robust.R |only misty-0.7.4/misty/R/coeff.std.R |only misty-0.7.4/misty/R/cohens.d.R | 84 - misty-0.7.4/misty/R/cor.matrix.R | 35 misty-0.7.4/misty/R/crosstab.R | 12 misty-0.7.4/misty/R/descript.R | 92 - misty-0.7.4/misty/R/df.check.R | 6 misty-0.7.4/misty/R/df.duplicated.R | 19 misty-0.7.4/misty/R/df.head.R | 6 misty-0.7.4/misty/R/df.long.R |only misty-0.7.4/misty/R/df.merge.R | 31 misty-0.7.4/misty/R/df.move.R | 13 misty-0.7.4/misty/R/df.rbind.R | 15 misty-0.7.4/misty/R/df.rename.R | 4 misty-0.7.4/misty/R/df.sort.R | 4 misty-0.7.4/misty/R/df.subset.R | 59 - misty-0.7.4/misty/R/dominance.R | 2 misty-0.7.4/misty/R/dominance.manual.R | 2 misty-0.7.4/misty/R/effsize.R | 20 misty-0.7.4/misty/R/freq.R | 10 misty-0.7.4/misty/R/item.alpha.R | 20 misty-0.7.4/misty/R/item.cfa.R | 10 misty-0.7.4/misty/R/item.invar.R | 8 misty-0.7.4/misty/R/item.omega.R | 32 misty-0.7.4/misty/R/item.reverse.R | 8 misty-0.7.4/misty/R/item.scores.R | 8 misty-0.7.4/misty/R/lagged.R | 8 misty-0.7.4/misty/R/mplus.print.R | 2 misty-0.7.4/misty/R/multilevel.cfa.R | 10 misty-0.7.4/misty/R/multilevel.cor.R | 226 ++-- misty-0.7.4/misty/R/multilevel.descript.R | 40 misty-0.7.4/misty/R/multilevel.icc.R | 37 misty-0.7.4/misty/R/multilevel.invar.R | 8 misty-0.7.4/misty/R/multilevel.omega.R | 8 misty-0.7.4/misty/R/multilevel.r2.R | 748 +------------- misty-0.7.4/misty/R/na.as.R | 4 misty-0.7.4/misty/R/na.auxiliary.R | 309 ++++- misty-0.7.4/misty/R/na.coverage.R | 12 misty-0.7.4/misty/R/na.descript.R | 22 misty-0.7.4/misty/R/na.indicator.R | 10 misty-0.7.4/misty/R/na.pattern.R | 12 misty-0.7.4/misty/R/na.prop.R | 10 misty-0.7.4/misty/R/na.test.R | 16 misty-0.7.4/misty/R/print.misty.object.R | 1437 +++++++++++++++++++-------- misty-0.7.4/misty/R/read.data.R | 38 misty-0.7.4/misty/R/read.dta.R | 6 misty-0.7.4/misty/R/read.mplus.R | 6 misty-0.7.4/misty/R/read.sav.R | 7 misty-0.7.4/misty/R/read.xlsx.R | 6 misty-0.7.4/misty/R/rec.R | 8 misty-0.7.4/misty/R/restart.R | 2 misty-0.7.4/misty/R/skewness.R | 10 misty-0.7.4/misty/R/summa.R |only misty-0.7.4/misty/R/test.levene.R | 17 misty-0.7.4/misty/R/test.t.R | 12 misty-0.7.4/misty/R/test.welch.R | 2 misty-0.7.4/misty/R/test.z.R | 37 misty-0.7.4/misty/R/uniq.R | 97 + misty-0.7.4/misty/R/utils.R | 1012 +++++++++++++++++-- misty-0.7.4/misty/R/write.data.R |only misty-0.7.4/misty/R/write.dta.R | 6 misty-0.7.4/misty/R/write.mplus.R | 5 misty-0.7.4/misty/R/write.result.R | 305 +++++ misty-0.7.4/misty/R/write.sav.R | 57 - misty-0.7.4/misty/R/write.xlsx.R | 4 misty-0.7.4/misty/man/aov.b.Rd | 3 misty-0.7.4/misty/man/center.Rd | 4 misty-0.7.4/misty/man/check.collin.Rd | 6 misty-0.7.4/misty/man/check.resid.Rd | 85 + misty-0.7.4/misty/man/ci.cor.Rd | 2 misty-0.7.4/misty/man/ci.mean.Rd | 2 misty-0.7.4/misty/man/ci.mean.w.Rd | 2 misty-0.7.4/misty/man/ci.prop.Rd | 2 misty-0.7.4/misty/man/ci.var.Rd | 2 misty-0.7.4/misty/man/cluster.rwg.Rd |only misty-0.7.4/misty/man/cluster.scores.Rd | 2 misty-0.7.4/misty/man/coeff.robust.Rd |only misty-0.7.4/misty/man/coeff.std.Rd |only misty-0.7.4/misty/man/cor.matrix.Rd | 6 misty-0.7.4/misty/man/crosstab.Rd | 5 misty-0.7.4/misty/man/descript.Rd | 33 misty-0.7.4/misty/man/df.check.Rd | 6 misty-0.7.4/misty/man/df.duplicated.Rd | 7 misty-0.7.4/misty/man/df.head.Rd | 7 misty-0.7.4/misty/man/df.long.Rd |only misty-0.7.4/misty/man/df.merge.Rd | 7 misty-0.7.4/misty/man/df.move.Rd | 10 misty-0.7.4/misty/man/df.rbind.Rd | 5 misty-0.7.4/misty/man/df.rename.Rd | 7 misty-0.7.4/misty/man/df.sort.Rd | 7 misty-0.7.4/misty/man/df.subset.Rd | 52 misty-0.7.4/misty/man/dominance.Rd | 2 misty-0.7.4/misty/man/dominance.manual.Rd | 2 misty-0.7.4/misty/man/effsize.Rd | 7 misty-0.7.4/misty/man/freq.Rd | 5 misty-0.7.4/misty/man/item.alpha.Rd | 16 misty-0.7.4/misty/man/item.cfa.Rd | 5 misty-0.7.4/misty/man/item.invar.Rd | 2 misty-0.7.4/misty/man/item.omega.Rd | 23 misty-0.7.4/misty/man/item.reverse.Rd | 2 misty-0.7.4/misty/man/item.scores.Rd | 2 misty-0.7.4/misty/man/lagged.Rd | 2 misty-0.7.4/misty/man/multilevel.cfa.Rd | 2 misty-0.7.4/misty/man/multilevel.cor.Rd | 16 misty-0.7.4/misty/man/multilevel.descript.Rd | 2 misty-0.7.4/misty/man/multilevel.icc.Rd | 2 misty-0.7.4/misty/man/multilevel.invar.Rd | 2 misty-0.7.4/misty/man/multilevel.omega.Rd | 2 misty-0.7.4/misty/man/na.as.Rd |only misty-0.7.4/misty/man/na.auxiliary.Rd | 103 + misty-0.7.4/misty/man/na.coverage.Rd | 7 misty-0.7.4/misty/man/na.descript.Rd | 11 misty-0.7.4/misty/man/na.indicator.Rd | 4 misty-0.7.4/misty/man/na.pattern.Rd | 7 misty-0.7.4/misty/man/na.prop.Rd | 4 misty-0.7.4/misty/man/na.test.Rd | 8 misty-0.7.4/misty/man/print.misty.object.Rd | 4 misty-0.7.4/misty/man/read.data.Rd | 20 misty-0.7.4/misty/man/read.dta.Rd | 6 misty-0.7.4/misty/man/read.mplus.Rd | 6 misty-0.7.4/misty/man/read.sav.Rd | 6 misty-0.7.4/misty/man/read.xlsx.Rd | 6 misty-0.7.4/misty/man/rec.Rd | 2 misty-0.7.4/misty/man/skewness.Rd | 2 misty-0.7.4/misty/man/summa.Rd |only misty-0.7.4/misty/man/test.levene.Rd | 3 misty-0.7.4/misty/man/test.t.Rd | 9 misty-0.7.4/misty/man/test.welch.Rd | 3 misty-0.7.4/misty/man/test.z.Rd | 9 misty-0.7.4/misty/man/uniq.Rd | 51 misty-0.7.4/misty/man/write.data.Rd |only misty-0.7.4/misty/man/write.dta.Rd | 6 misty-0.7.4/misty/man/write.mplus.Rd | 5 misty-0.7.4/misty/man/write.result.Rd | 16 misty-0.7.4/misty/man/write.sav.Rd | 4 misty-0.7.4/misty/man/write.xlsx.Rd | 4 163 files changed, 4386 insertions(+), 2574 deletions(-)
Title: Process and Report 'GreenFeed' Data
Description: Provides tools for downloading, processing, and reporting daily and finalized 'GreenFeed' data.
Author: Guillermo Martinez-Boggio [cre, aut, cph] ,
Meredith Harrison [ctb],
Patrick Lutz [ctb]
Maintainer: Guillermo Martinez-Boggio <gmartinezboggio@ucdavis.edu>
Diff between greenfeedr versions 1.2.1 dated 2025-04-17 and 1.3.0 dated 2025-08-18
DESCRIPTION | 16 +- MD5 | 56 ++++--- NAMESPACE | 4 NEWS.md | 2 R/compare_gfdata.R | 3 R/get_gfdata.R | 104 -------------- R/pellin.R | 162 +++++++++++---------- R/process_gfdata.R | 54 +++++-- R/report_gfdata.R | 62 +------- R/run_app.R |only R/run_gfapp.R |only R/utils.R | 319 ++++++++++++++++++++++++++++++++----------- R/viseat.R | 49 +----- README.md | 61 +++++--- inst/doc/greenfeedr.R | 10 - inst/doc/greenfeedr.Rmd | 10 - inst/doc/greenfeedr.html | 73 +++++++-- inst/md |only inst/shinyapp |only man/download_data.Rd |only man/eval_gfparam.Rd | 7 man/get_gfdata.Rd | 2 man/process_gfdata.Rd | 2 man/report_gfdata.Rd | 4 man/run_app.Rd |only man/run_gfapp.Rd |only man/transform_gases.Rd |only tests/testthat/test-viseat.R | 4 vignettes/greenfeedr.Rmd | 10 - 29 files changed, 565 insertions(+), 449 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.11 dated 2025-04-02 and 1.1.12 dated 2025-08-18
DESCRIPTION | 52 +-- MD5 | 116 +++--- NAMESPACE | 28 + R/VarCorr.R | 387 +++++++++++++++------- R/glmmTMB.R | 74 ++-- R/methods.R | 354 ++++++++++++++++++++ R/predict.R | 554 ++++++++++++++++---------------- R/utils.R | 186 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 42 ++ inst/doc/covstruct.R | 1 inst/doc/covstruct.html | 27 - inst/doc/covstruct.rmd | 3 inst/doc/glmmTMB.Rnw | 2 inst/doc/glmmTMB.pdf |binary inst/doc/hacking.html | 4 inst/doc/mcmc.html | 4 inst/doc/miscEx.html | 4 inst/doc/model_evaluation.R | 24 + inst/doc/model_evaluation.Rnw | 63 +++ inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 4 inst/doc/priors.html | 6 inst/doc/sim.html | 10 inst/doc/troubleshooting.R | 28 + inst/doc/troubleshooting.html | 31 - inst/doc/troubleshooting.rmd | 48 +- inst/test_data/make_ex.R | 24 + inst/test_data/models.rda |binary inst/test_data/old_fit.rds |only inst/vignette_data/model_evaluation.rda |binary man/bread.glmmTMB.Rd |only man/estfun.glmmTMB.Rd |only man/formatVC.Rd | 11 man/format_sdvar.Rd |only man/getGroups.glmmTMB.Rd |only man/getReStruc.Rd | 12 man/glmmTMB.Rd | 1 man/glmmTMBControl.Rd | 5 man/gt_load.Rd | 4 man/meatHC.Rd |only man/predict.glmmTMB.Rd | 4 man/sandwich.Rd |only man/vcov.glmmTMB.Rd | 13 man/vcovHC.glmmTMB.Rd |only src/glmmTMB.cpp | 201 +++++++---- tests/testthat/setup_makeex.R | 2 tests/testthat/test-VarCorr.R | 16 tests/testthat/test-basics.R | 10 tests/testthat/test-downstream.R | 7 tests/testthat/test-env.R | 15 tests/testthat/test-families.R | 2 tests/testthat/test-methods.R | 262 ++++++++++++++- tests/testthat/test-predict.R | 72 +++- tests/testthat/test-simulate_new.R | 73 ++++ tests/testthat/test-smooths.R | 2 tests/testthat/test-utils.R | 7 tests/testthat/test-varstruc.R | 43 +- vignettes/covstruct.rmd | 3 vignettes/glmmTMB.Rnw | 2 vignettes/model_evaluation.Rnw | 63 +++ vignettes/troubleshooting.rmd | 48 +- 63 files changed, 2157 insertions(+), 797 deletions(-)
Title: Equations to 'XML'
Description: Provides function to transform latex math expressions
into format 'HTML' or 'Office Open XML Math'. The 'XML'
result can then be included in 'HTML', 'Microsoft Word'
documents or 'Microsoft PowerPoint' presentations by using
a 'Markdown' document or the R package 'officer'.
Author: David Gohel [aut, cre],
ArData [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between equatags versions 0.2.1 dated 2024-05-24 and 0.2.2 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/write_mathjax.R | 10 +++++++--- man/transform_mathjax.Rd | 6 +++++- 5 files changed, 24 insertions(+), 12 deletions(-)
Title: Document Conversion to 'PDF' or 'PNG'
Description: It provides the ability to generate images from documents
of different types. Three main features are provided: functions for
generating document thumbnails, functions for performing visual tests
of documents and a function for updating fields and table of contents
of a 'Microsoft Word' or 'RTF' document. In order to work, 'LibreOffice' must be
installed on the machine and or 'Microsoft Word'. If the latter is
available, it can be used to produce PDF documents or images
identical to the originals; otherwise, 'LibreOffice' is used and
the rendering can be sometimes different from the original
documents.
Author: David Gohel [aut, cre],
ArData [cph],
David Hajage [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between doconv versions 0.3.2 dated 2023-02-09 and 0.3.3 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/docx2pdf.R | 46 +++++++++++++++++++++++++++++----------------- R/expect_snapshot_doc.R | 1 + R/to_miniature.R | 8 ++++---- R/to_pdf.R | 2 +- R/utils.R | 19 +++++++++++++++++++ man/to_miniature.Rd | 8 ++++---- 9 files changed, 77 insertions(+), 38 deletions(-)
Title: Analyze System Scalability with the Universal Scalability Law
Description: The Universal Scalability Law (Gunther 2007)
<doi:10.1007/978-3-540-31010-5> is a model to predict hardware and
software scalability. It uses system capacity as a function of load to
forecast the scalability for the system.
Author: Neil J. Gunther [aut],
Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding <stm@moeding.net>
Diff between usl versions 3.0.3 dated 2022-08-28 and 3.0.4 dated 2025-08-18
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS | 5 +++++ R/usl-package.R | 3 +-- R/usl.R | 4 ++-- README.md | 2 +- build/vignette.rds |binary inst/doc/usl.pdf |binary man/usl-package.Rd | 9 +++++++++ man/usl.Rd | 2 +- man/usl.solve.nlxb.Rd | 2 +- 11 files changed, 35 insertions(+), 22 deletions(-)
Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments
that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut] ,
Benjamin D. Schalet [ctb],
Aaron J. Kaat [ctb],
David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between PROsetta versions 0.4.1 dated 2023-02-03 and 0.4.2 dated 2025-08-18
PROsetta-0.4.1/PROsetta/vignettes/PROsetta_cache |only PROsetta-0.4.1/PROsetta/vignettes/PROsetta_files |only PROsetta-0.4.2/PROsetta/DESCRIPTION | 17 PROsetta-0.4.2/PROsetta/MD5 | 128 PROsetta-0.4.2/PROsetta/NAMESPACE | 1 PROsetta-0.4.2/PROsetta/NEWS.md | 26 PROsetta-0.4.2/PROsetta/R/core_functions.R | 322 +- PROsetta-0.4.2/PROsetta/R/import.R | 2 PROsetta-0.4.2/PROsetta/R/linking_functions.R | 76 PROsetta-0.4.2/PROsetta/R/loading_functions.R | 65 PROsetta-0.4.2/PROsetta/R/parameterization_functions.R |only PROsetta-0.4.2/PROsetta/R/plot_functions.R | 14 PROsetta-0.4.2/PROsetta/R/post_functions.R | 29 PROsetta-0.4.2/PROsetta/R/preanalysis_functions.r | 6 PROsetta-0.4.2/PROsetta/README.md | 2 PROsetta-0.4.2/PROsetta/build/vignette.rds |binary PROsetta-0.4.2/PROsetta/data/anchor_asq.rda |binary PROsetta-0.4.2/PROsetta/data/anchor_dep.rda |binary PROsetta-0.4.2/PROsetta/data/data_asq.rda |binary PROsetta-0.4.2/PROsetta/data/data_dep.rda |binary PROsetta-0.4.2/PROsetta/data/itemmap_asq.rda |binary PROsetta-0.4.2/PROsetta/data/itemmap_dep.rda |binary PROsetta-0.4.2/PROsetta/data/response_asq.rda |binary PROsetta-0.4.2/PROsetta/data/response_dep.rda |binary PROsetta-0.4.2/PROsetta/inst/data-raw/anchor_AxMASQ.csv | 60 PROsetta-0.4.2/PROsetta/inst/data-raw/anchor_DeCESD.csv | 58 PROsetta-0.4.2/PROsetta/inst/data-raw/datasets.R | 12 PROsetta-0.4.2/PROsetta/inst/data-raw/imap_AxMASQ.csv | 82 PROsetta-0.4.2/PROsetta/inst/data-raw/imap_DeCESD.csv | 98 PROsetta-0.4.2/PROsetta/inst/doc/PROsetta.R | 229 - PROsetta-0.4.2/PROsetta/inst/doc/PROsetta.Rmd | 473 +-- PROsetta-0.4.2/PROsetta/inst/doc/PROsetta.html | 1375 ++++------ PROsetta-0.4.2/PROsetta/man/computeResponseProbability.Rd | 10 PROsetta-0.4.2/PROsetta/man/detectParameterization.Rd | 11 PROsetta-0.4.2/PROsetta/man/getRSSS.Rd | 7 PROsetta-0.4.2/PROsetta/man/getTheta.Rd | 3 PROsetta-0.4.2/PROsetta/man/loadData.Rd | 3 PROsetta-0.4.2/PROsetta/man/plotInfo-methods.Rd | 2 PROsetta-0.4.2/PROsetta/man/runCalibration.Rd | 2 PROsetta-0.4.2/PROsetta/man/runEquateObserved.Rd | 2 PROsetta-0.4.2/PROsetta/tests/testthat/test_getAnchorDimension.R | 2 PROsetta-0.4.2/PROsetta/tests/testthat/test_loadData.r | 44 PROsetta-0.4.2/PROsetta/tests/testthat/test_mixed_models.r |only PROsetta-0.4.2/PROsetta/tests/testthat/test_runCalibration.r | 31 PROsetta-0.4.2/PROsetta/tests/testthat/test_runLinking.R | 68 PROsetta-0.4.2/PROsetta/tests/testthat/test_runRSSS.R | 40 PROsetta-0.4.2/PROsetta/vignettes/PROsetta.Rmd | 473 +-- PROsetta-0.4.2/PROsetta/vignettes/styles.css | 1 48 files changed, 1957 insertions(+), 1817 deletions(-)
Title: Multiple Administrations Adaptive Testing
Description: Provides an extension of the shadow-test approach to computerized adaptive
testing (CAT) implemented in the 'TestDesign' package for the assessment framework
involving multiple tests administered periodically throughout the year. This framework
is referred to as the Multiple Administrations Adaptive Testing (MAAT) and supports
multiple item pools vertically scaled and multiple phases (stages) of CAT within each test.
Between phases and tests, transitioning from one item pool (and associated constraints)
to another is allowed as deemed necessary to enhance the quality of measurement.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut] ,
Luping Niu [aut] ,
Sooyong Lee [aut] ,
M. Christina Schneider [ctb],
Jay Lee [ctb],
Garron Gianopulos [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between maat versions 1.1.0 dated 2022-05-18 and 1.1.1 dated 2025-08-18
DESCRIPTION | 18 MD5 | 60 NEWS.md | 10 R/administered_functions.R | 6 R/examinee_class.R | 4 R/examinee_updaters.R | 4 R/module_class.R | 2 R/module_functions.R | 8 R/package.R | 12 R/routing_functions.R | 6 R/sim_functions.R | 55 build/vignette.rds |binary inst/doc/maat.R | 43 inst/doc/maat.Rmd | 20 inst/doc/maat.html | 2679 +++++++++++++++++++++++++++++++++----- man/createModule.Rd | 8 man/examinee-class.Rd | 4 man/excludeAdministeredItems.Rd | 6 man/maat-package.Rd | 38 man/maat.Rd | 2 man/module-class.Rd | 2 man/output_maat-class.Rd | 2 man/simTheta.Rd | 2 man/updateAssessmentLevelTheta.Rd | 2 man/updateGrade.Rd | 2 man/updateItemData.Rd | 4 man/updateThetaUsingCombined.Rd | 2 vignettes/Routing_scenario_1.pptx |binary vignettes/bibliography.bib | 21 vignettes/maat.Rmd | 20 vignettes/routing_T1T2.svg | 2 31 files changed, 2558 insertions(+), 486 deletions(-)
Title: A Test Environment for Database Requests
Description: Testing and documenting code that communicates with remote
databases can be painful. Although the interaction with R is usually relatively
simple (e.g. data(frames) passed to and from a database), because they rely on
a separate service and the data there, testing them can be difficult to set up,
unsustainable in a continuous integration environment, or impossible without
replicating an entire production cluster. This package addresses that by
allowing you to make recordings from your database interactions and then play
them back while testing (or in other contexts) all without needing to spin up
or have access to the database your code would typically connect to.
Author: Jonathan Keane [aut, cre] ,
Mauricio Vargas [aut] ,
Helen Miller [rev] ,
Etienne Racine [rev]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between dittodb versions 0.1.8 dated 2024-04-08 and 0.1.9 dated 2025-08-18
DESCRIPTION | 13 +-- MD5 | 26 +++---- NEWS.md | 3 R/connection.R | 12 +-- R/mock-db.R | 2 build/vignette.rds |binary inst/doc/developing-dittodb.html | 4 - inst/doc/dittodb.R | 144 +++++++++++++++++++-------------------- inst/doc/dittodb.Rmd | 2 inst/doc/dittodb.html | 25 +++--- inst/doc/nycflights.html | 6 - man/mock-db-methods.Rd | 12 +-- man/mockdb.Rd | 2 vignettes/dittodb.Rmd | 2 14 files changed, 129 insertions(+), 124 deletions(-)
Title: Signature Analyzer for Targeted Sequencing (SATS)
Description: Performs mutational signature analysis for targeted sequenced tumors. Unlike the canonical analysis of mutational signatures, SATS factorizes the mutation counts matrix into a panel context matrix (measuring the size of the targeted sequenced genome for each tumor in the unit of million base pairs (Mb)), a signature profile matrix, and a signature activity matrix. SATS also calculates the expected number of mutations attributed by a signature, namely signature burden, for each targeted sequenced tumor. For more details see Lee et al. (2024) <doi:10.1101/2023.05.18.23290188>.
Author: DongHyuk Lee [aut],
Bin Zhu [aut],
Bill Wheeler [cre]
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Diff between SATS versions 1.0.4 dated 2025-07-05 and 1.0.6 dated 2025-08-18
SATS-1.0.4/SATS/man/GereratePanelSize.Rd |only SATS-1.0.6/SATS/DESCRIPTION | 12 - SATS-1.0.6/SATS/MD5 | 31 ++-- SATS-1.0.6/SATS/NAMESPACE | 6 SATS-1.0.6/SATS/R/L_matrix_Generation.R | 123 +++++++++++++++- SATS-1.0.6/SATS/R/mappingSignature.R | 40 +++-- SATS-1.0.6/SATS/R/source_check.R | 65 ++++++++ SATS-1.0.6/SATS/data/RefTMB.rda |binary SATS-1.0.6/SATS/data/SimData.rda |binary SATS-1.0.6/SATS/man/CalculateSigExpectancy.Rd | 14 + SATS-1.0.6/SATS/man/EstimateSigActivity.Rd | 14 + SATS-1.0.6/SATS/man/GenerateLMatrix.Rd |only SATS-1.0.6/SATS/man/GeneratePanelSize.Rd |only SATS-1.0.6/SATS/man/MappingSignature.Rd | 15 + SATS-1.0.6/SATS/man/RefTMB.Rd | 6 SATS-1.0.6/SATS/man/SATS-package.Rd | 9 - SATS-1.0.6/SATS/man/SimData.Rd | 5 SATS-1.0.6/SATS/tests/testthat/test-GeneratePanelSize.R | 4 18 files changed, 276 insertions(+), 68 deletions(-)
Title: Safetensors File Format
Description: A file format for storing tensors that is secure (doesn't allow for
code execution), fast and simple to implement. 'safetensors' also enables cross
language and cross frameworks compatibility making it an ideal format for
storing machine learning model weights.
Author: Daniel Falbel [aut, cre],
Sebastian Fischer [ctb],
Posit [cph]
Maintainer: Daniel Falbel <daniel@posit.co>
Diff between safetensors versions 0.1.2 dated 2023-09-12 and 0.2.0 dated 2025-08-18
DESCRIPTION | 16 +++--- MD5 | 27 ++++++---- NAMESPACE | 5 + NEWS.md | 8 +++ R/safetensors.R | 82 +++++++++++-------------------- R/torch.R |only R/write.R | 100 +++++++++++++++++++------------------- R/zzz.R |only README.md | 11 ++-- man/safe_load_file.Rd | 10 +-- man/safe_save_file.Rd | 2 man/safe_tensor_buffer.Rd |only man/safe_tensor_meta.Rd |only man/safetensors.Rd | 14 ++--- man/safetensors_frameworks.Rd |only tests/testthat/test-safetensors.R | 33 +++++++++++- tests/testthat/test-write.R | 35 ++++++------- 17 files changed, 185 insertions(+), 158 deletions(-)
Title: Functional-Based Chain Ladder for Claims Reserving
Description: Functional claims reserving methods based on aggregated chain-ladder data, also known as a run-off triangle, implemented in three nonparametric algorithms (PARALLAX, REACT, and MACRAME) proposed in Maciak, Mizera, and Pešta (2022) <doi:10.1017/asb.2022.4>. Additional methods including permutation bootstrap for completed run-off triangles are also provided.
Author: Matus Maciak [aut, cre],
Rastislav Matus [ctb],
Ivan Mizera [aut],
Michal Pesta [aut]
Maintainer: Matus Maciak <maciak@karlin.mff.cuni.cz>
Diff between ProfileLadder versions 0.1.3 dated 2025-07-23 and 0.1.4 dated 2025-08-18
DESCRIPTION | 12 +-- MD5 | 85 +++++++++++----------- NAMESPACE | 2 R/CameronMutual.R | 8 +- R/GFCIB.R | 6 - R/NevadaGeneral.R | 6 - R/as.profileLadder.R | 21 ++--- R/covid19CZ.R | 2 R/incrExplor.R | 24 +++--- R/mcBreaks.R | 26 ++++-- R/mcReserve.R | 36 ++++----- R/mcStates.R | 18 +++- R/mcTrans.R | 13 +++ R/observed.R | 25 +++--- R/parallelReserve.R | 34 ++++---- R/permuteReserve.R | 157 ++++++++++++++++++++++++++++------------- R/plot.mcSetup.R | 21 ++++- R/plot.permutedReserve.R | 83 +++++++++++---------- R/plot.profileLadder.R | 66 +++++++++-------- R/print.mcSetup.R | 58 +++++++++++---- R/print.permutedReserve.R | 13 ++- R/print.profileLadder.R | 128 +++++++++++++++++++++++++++++++-- R/set.fancy.print.R |only R/summary.mcSetup.R | 16 ++-- R/summary.permutedReserve.R | 51 +++++++++---- R/summary.profileLadder.R | 22 +++-- R/zzz.R |only man/CameronMutual.Rd | 6 - man/GFCIB.Rd | 6 - man/NevadaGeneral.Rd | 6 - man/as.profileLadder.Rd | 16 ++-- man/covid19CZ.Rd | 2 man/incrExplor.Rd | 24 +++--- man/mcBreaks.Rd | 26 ++++-- man/mcReserve.Rd | 32 ++++---- man/mcStates.Rd | 18 +++- man/observed.Rd | 17 ++-- man/parallelReserve.Rd | 30 +++---- man/permuteReserve.Rd | 59 ++++++++++----- man/plot.mcSetup.Rd | 14 ++- man/plot.permutedReserve.Rd | 12 +-- man/plot.profileLadder.Rd | 17 +++- man/print.profileLadder.Rd | 15 +++ man/set.fancy.print.Rd |only man/summary.permutedReserve.Rd | 15 ++- 45 files changed, 813 insertions(+), 435 deletions(-)
Title: A Collection of R Functions by the Petersen Lab
Description: A collection of R functions that are widely used by the Petersen
Lab. Included are functions for various purposes, including evaluating the
accuracy of judgments and predictions, performing scoring of assessments,
generating correlation matrices, conversion of data between various types,
data management, psychometric evaluation, extensions related to latent
variable modeling, various plotting capabilities, and other miscellaneous
useful functions. By making the package available, we hope to make our
methods reproducible and replicable by others and to help others perform
their data processing and analysis methods more easily and efficiently. The
codebase is provided in Petersen (2025) <doi:10.5281/zenodo.7602890> and on
'CRAN': <doi: 10.32614/CRAN.package.petersenlab>. The package is described
in "Principles of Psychological Assessment: With Applied Examples in R"
(Petersen, 2024, 2025a) <doi:10.1201/9781003357421>,
<doi:10.25820/work.007199>, <doi:10.5281/ze [...truncated...]
Author: Isaac T. Petersen [aut, cre] ,
Developmental Psychopathology Lab at the University of Iowa [ctb],
Angela D. Staples [ctb] ,
Johanna Caskey [ctb] ,
Philipp Doebler [ctb] ,
Loreen Sabel [ctb]
Maintainer: Isaac T. Petersen <isaac-t-petersen@uiowa.edu>
Diff between petersenlab versions 1.1.0 dated 2025-02-03 and 1.2.0 dated 2025-08-18
DESCRIPTION | 32 ++--- LICENSE | 2 MD5 | 56 +++++---- NAMESPACE | 6 R/accuracyAtCutoff.R | 152 ++++++++++++++++--------- R/accuracyAtEachCutoff.R | 4 R/accuracyOverall.R | 87 +++++++++----- R/bayesTheorem.R | 2 R/lm.beta.lmer.R |only R/pValues.R | 5 R/partialCorrelationMatrix.R | 3 R/personMonths.R | 2 R/robust_load.R |only R/semPlotInteraction.R | 13 +- R/simulateAUC.R | 12 - R/sourdoughRecipeTimes.R |only R/vwReg.R | 4 README.md | 8 - build/partial.rdb |binary inst/CITATION | 4 man/accuracyAtCutoff.Rd | 259 ++++++++++++++++++++++--------------------- man/accuracyAtEachCutoff.Rd | 230 +++++++++++++++++++------------------- man/accuracyOverall.Rd | 6 man/adjust_sourdough_time.Rd |only man/bayesTheorem.Rd | 2 man/lm.beta.lmer.Rd |only man/lmeSummary.Rd | 4 man/personMonths.Rd | 2 man/robust_load.Rd |only man/semPlotInteraction.Rd | 5 man/simulateAUC.Rd | 12 - man/vwReg.Rd | 4 32 files changed, 522 insertions(+), 394 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre] ,
Campos Nicolas [ctb] ,
Pino Nicolas [ctb] ,
Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.1.1 dated 2025-07-21 and 1.1.2 dated 2025-08-18
DESCRIPTION | 6 +-- MD5 | 89 ++++++++++++++++++++++++++++++++------------------ NAMESPACE | 9 +++++ R/assigncl.r |only R/data-education.r |only R/data-idahohd.r | 14 +++++-- R/data-idahohd2.r | 14 +++++-- R/data-leafw2.r |only R/data-llancahue.r | 26 +++++++------- R/data-llancahue2.r | 24 ++++++------- R/data-maple.r |only R/data-papersdocstu.r | 2 - R/data-pspLlancahue.r | 34 +++++-------------- R/data-pspruca.r | 14 ++++++- R/data-pspruca2.r | 16 ++++++-- R/descstat.r | 74 ++++++++++++++++++++++++++++++++--------- R/modresults.r |only R/plotrend.r |only R/pressind.r |only R/rankmod.r |only R/singleupp.r |only R/smoothfit.r |only R/tabtexdescstat.r | 36 +++++++++++++------- R/tabtexregre.r | 42 +++++++---------------- R/valesta.r | 47 ++++++++++++++++---------- R/valestamod.r |only R/vifx.r |only data/education.rda |only data/idahohd.rda |binary data/idahohd2.rda |binary data/leafw2.rda |only data/maple.rda |only data/pspruca.rda |binary data/pspruca2.rda |binary inst/CITATION | 4 +- man/assigncl.Rd |only man/descstat.Rd | 21 ++++++++++- man/education.Rd |only man/idahohd.Rd | 14 +++++-- man/idahohd2.Rd | 14 +++++-- man/leafw2.Rd |only man/llancahue.Rd | 22 ++++++------ man/llancahue2.Rd | 22 ++++++------ man/maple.Rd |only man/modresults.Rd |only man/papersdocstu.Rd | 2 - man/plotrend.Rd |only man/pressind.Rd |only man/pspLlancahue.Rd | 34 +++++-------------- man/pspruca.Rd | 14 ++++++- man/pspruca2.Rd | 16 ++++++-- man/rankmod.Rd |only man/singleupp.Rd |only man/smoothfit.Rd |only man/tabtexdescstat.Rd | 18 +++++++--- man/tabtexregre.Rd | 4 +- man/valesta.Rd | 32 +++++++++++------ man/valestamod.Rd |only man/vifx.Rd |only 59 files changed, 399 insertions(+), 265 deletions(-)
Title: Read bigWig and bigBed Files
Description: Read bigWig and bigBed files using "libBigWig"
<https://github.com/dpryan79/libBigWig>. Provides lightweight access
to the binary bigWig and bigBed formats developed by the UCSC Genome
Browser group.
Author: Jay Hesselberth [aut, cre],
RNA Bioscience Initiative [fnd, cph],
Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between cpp11bigwig versions 0.1.1 dated 2025-01-19 and 0.1.2 dated 2025-08-18
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- NEWS.md | 4 +++ R/read.r | 19 ++++++++++++-- README.md | 6 ++-- src/cpp11bigwig.cpp | 2 - tests/testthat/test-read.R | 59 +++++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 92 insertions(+), 16 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.2 dated 2025-06-16 and 1.0.3 dated 2025-08-18
DESCRIPTION | 6 MD5 | 46 NAMESPACE | 1 NEWS.md | 8 R/addCohortSurvival.R | 31 R/estimateSurvival.R | 191 -- R/inputValidation.R | 11 R/mockCohortSurvival.R |only R/plotSurvival.R | 41 R/tableSurvival.R | 6 build/vignette.rds |binary inst/doc/a01_Single_event_of_interest.R | 5 inst/doc/a01_Single_event_of_interest.Rmd | 19 inst/doc/a01_Single_event_of_interest.html | 2414 ++++++++++++++++------------ inst/doc/a02_Competing_risk_survival.html | 308 +-- inst/doc/a03_Further_survival_analyses.html | 48 man/availableSurvivalGrouping.Rd |only man/estimateCompetingRiskSurvival.Rd | 13 man/estimateSingleEventSurvival.Rd | 7 man/riskTable.Rd | 3 man/tableSurvival.Rd | 3 tests/testthat/test-addCohortSurvival.R | 198 -- tests/testthat/test-estimateSurvival.R | 501 ++--- tests/testthat/test-plotSurvival.R | 47 vignettes/a01_Single_event_of_interest.Rmd | 19 25 files changed, 2147 insertions(+), 1779 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between tree versions 1.0-44 dated 2024-12-11 and 1.0-45 dated 2025-08-18
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- R/treemisc.R | 18 +++++++++++++++++- man/snip.tree.Rd | 3 ++- man/text.tree.Rd | 3 ++- tests/digits.R |only 6 files changed, 31 insertions(+), 12 deletions(-)
Title: Temporal Encoder-Masked Probabilistic Ensemble Regressor
Description: Implements a probabilistic ensemble time-series forecaster that combines an auto-encoder with a neural decision forest whose split variables are learned through a differentiable feature-mask layer. Functions are written with 'torch' tensors and provide CRPS (Continuous Ranked Probability Scores) training plus mixture-distribution post-processing.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between temper versions 1.0.0 dated 2025-07-15 and 1.1.0 dated 2025-08-18
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NAMESPACE | 3 +- NEWS.md | 4 +++ R/main.R | 73 ++++++++++++++++++++++++++++++++++++++++++++---------------- 5 files changed, 68 insertions(+), 28 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 3.1-6 dated 2025-03-17 and 3.1-8 dated 2025-08-18
DESCRIPTION | 15 ++-- MD5 | 136 ++++++++++++++++++++++----------------------- NEWS | 17 +++++ data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/btb.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/concrete.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/meningitis.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/shelling.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/stonetools.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/macros/defns.Rd | 25 ++++---- man/murchison.Rd | 14 ++-- man/simba.Rd | 5 + 69 files changed, 123 insertions(+), 91 deletions(-)
Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.
Author: Maja Pohar Perme [aut],
Damjan Manevski [aut, cre]
Maintainer: Damjan Manevski <damjan.manevski@mf.uni-lj.si>
Diff between relsurv versions 2.3-2 dated 2025-01-28 and 2.3-3 dated 2025-08-18
relsurv-2.3-2/relsurv/R/predict.aalen.relsurv.R |only relsurv-2.3-3/relsurv/DESCRIPTION | 8 relsurv-2.3-3/relsurv/MD5 | 39 - relsurv-2.3-3/relsurv/NAMESPACE | 3 relsurv-2.3-3/relsurv/R/Rcode.r | 17 relsurv-2.3-3/relsurv/R/predict.aalen.model.R |only relsurv-2.3-3/relsurv/R/predict.rsadd.R | 80 ++- relsurv-2.3-3/relsurv/R/rformulate.r | 138 ++--- relsurv-2.3-3/relsurv/R/rsaalen.R | 29 - relsurv-2.3-3/relsurv/R/rssurvrsadd.r | 86 +-- relsurv-2.3-3/relsurv/R/survaalen.R | 21 relsurv-2.3-3/relsurv/R/survfitrsadd.r | 71 +- relsurv-2.3-3/relsurv/R/zzz.R | 1 relsurv-2.3-3/relsurv/inst/news.Rd | 11 relsurv-2.3-3/relsurv/man/predict.aalen.model.Rd |only relsurv-2.3-3/relsurv/man/predict.rsadd.Rd | 18 relsurv-2.3-3/relsurv/man/rs.surv.Rd | 2 relsurv-2.3-3/relsurv/man/rs.surv.rsadd.Rd | 4 relsurv-2.3-3/relsurv/man/rsaalen.Rd | 7 relsurv-2.3-3/relsurv/man/survaalen.Rd | 6 relsurv-2.3-3/relsurv/man/survfit.rsadd.Rd | 3 relsurv-2.3-3/relsurv/src/netfastpinter2.c | 608 +++++++++++------------ 22 files changed, 650 insertions(+), 502 deletions(-)
Title: Install the 'Natverse' Packages from Scratch
Description: Provides streamlined installation for packages from the 'natverse',
a suite of R packages for computational neuroanatomy built on top of the
'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete
'natverse' suite requires a 'GitHub' user account and personal access token
'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.
Author: Sridhar Jagannathan [aut] ,
Gregory Jefferis [aut, cre]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natmanager versions 0.5.1 dated 2023-09-11 and 0.5.2 dated 2025-08-18
DESCRIPTION | 14 ++++++++------ MD5 | 12 ++++++------ NEWS.md | 5 ++++- R/install.R | 4 ++-- README.md | 4 ++-- man/install.Rd | 4 ++-- man/selfupdate.Rd | 4 ++-- 7 files changed, 26 insertions(+), 21 deletions(-)
Title: NeuroAnatomy Toolbox ('nat') Extension for Handling Template
Brains
Description: Extends package 'nat' (NeuroAnatomy Toolbox) by
providing objects and functions for handling template brains.
Author: Gregory Jefferis [aut, cre] ,
James Manton [aut]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat.templatebrains versions 1.1 dated 2023-06-14 and 1.2.1 dated 2025-08-18
DESCRIPTION | 18 ++++++++++-------- MD5 | 29 +++++++++++++++-------------- NEWS.md | 10 ++++++++++ R/PACKAGE.R | 3 +-- R/fit-xform.R | 16 ++++++++++------ R/reg_repos.R | 4 ++-- R/regtemplate.R | 6 +++--- R/transformation.R | 7 ++++--- R/utils.R |only README.md | 2 +- inst/WORDLIST | 32 ++++++++++++++++++-------------- man/fit_xform.Rd | 16 ++++++++++------ man/fit_xform_brain.Rd | 2 +- man/guess_templatebrain.Rd | 6 +++--- man/local_reg_dir_for_url.Rd | 4 ++-- man/xform_brain.Rd | 7 ++++--- 16 files changed, 94 insertions(+), 68 deletions(-)
More information about nat.templatebrains at CRAN
Permanent link
Title: NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron
Similarity and Clustering
Description: Extends package 'nat' (NeuroAnatomy Toolbox) by providing a
collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).
Author: Gregory Jefferis [aut, cre] ,
James Manton [aut]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat.nblast versions 1.6.7 dated 2023-06-14 and 1.6.8 dated 2025-08-18
DESCRIPTION | 15 MD5 | 100 +- NAMESPACE | 92 +- NEWS.md | 142 ++-- R/DATA.r | 120 +-- R/clustering.r | 298 ++++---- R/nat.nblast.r | 195 ++--- R/neuriteblast.r | 1148 ++++++++++++++++------------------ R/scoremats.r | 610 +++++++++--------- R/similarity.r | 148 ++-- R/smat.r | 485 +++++++------- R/spam.r | 148 ++-- R/zzz.r | 24 README.md | 173 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 136 ++-- inst/doc/NBLAST-Clustering.R | 52 - inst/doc/NBLAST-Clustering.Rmd | 122 +-- inst/doc/NBLAST-Clustering.html | 814 ++++++++++++------------ man/NeuriteBlast.Rd | 108 +-- man/WeightedNNBasedLinesetMatching.Rd | 130 +-- man/calc_dists_dotprods.Rd | 86 +- man/calc_prob_mat.Rd | 80 +- man/calc_score_matrix.Rd | 62 - man/create_scoringmatrix.Rd | 230 +++--- man/diagonal.Rd | 70 +- man/extract-methods.Rd | 78 +- man/fctraces20.Rd | 66 - man/fill_in_sparse_score_mat.Rd | 46 - man/fill_pairs_sparse_score_mat.Rd | 74 +- man/nat.nblast-package.Rd | 233 +++--- man/nblast.Rd | 382 +++++------ man/nblast_allbyall.Rd | 132 +-- man/neuron_pairs.Rd | 61 - man/nhclust.Rd | 132 +-- man/plot3d.hclust.Rd | 140 ++-- man/show_similarity.Rd | 140 ++-- man/smat.fcwb.Rd | 68 +- man/sparse_score_mat.Rd | 68 +- man/sub_dist_mat.Rd | 88 +- man/sub_score_mat.Rd | 78 +- man/subset.hclust.Rd | 56 - tests/spelling.R | 6 tests/test-all.R | 8 tests/testthat/test-NBLAST1.r | 54 - tests/testthat/test-NBLAST2.r | 204 +++--- tests/testthat/test-clustering.r | 120 +-- tests/testthat/test-scoremats.r | 106 +-- tests/testthat/test-smat.r | 98 +- vignettes/NBLAST-Clustering.Rmd | 122 +-- 51 files changed, 4082 insertions(+), 4066 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] ,
James Manton [aut] ,
Dominik Krzeminski [ctb]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.24 dated 2024-02-05 and 1.8.25 dated 2025-08-18
nat-1.8.24/nat/tests/testthat/Rplots.pdf |only nat-1.8.24/nat/tests/testthat/testdata/neuroml/level1/CablesIncluded.swc |only nat-1.8.24/nat/tests/testthat/testdata/neuroml/level1/Simple.morph.swc |only nat-1.8.24/nat/tests/testthat/testdata/neuron/EBT7R.CNG.swc |only nat-1.8.24/nat/tests/testthat/testdata/neuron/XT6L2.CNG.swc |only nat-1.8.24/nat/tests/testthat/testdata/neuron/unfitted.swc |only nat-1.8.24/nat/tests/testthat/testdata/summary_cell07pns.rda |only nat-1.8.25/nat/DESCRIPTION | 16 nat-1.8.25/nat/MD5 | 143 - nat-1.8.25/nat/NAMESPACE | 5 nat-1.8.25/nat/NEWS | 7 nat-1.8.25/nat/R/alphashape3d.R | 2 nat-1.8.25/nat/R/cmtk-reformat.R | 43 nat-1.8.25/nat/R/graph-nodes.R | 12 nat-1.8.25/nat/R/im3d.R | 4 nat-1.8.25/nat/R/nat-package.R | 11 nat-1.8.25/nat/R/ndigest.R | 6 nat-1.8.25/nat/R/neuron-io-amira.R | 3 nat-1.8.25/nat/R/neuron-plot.R | 8 nat-1.8.25/nat/R/neuron.R | 6 nat-1.8.25/nat/R/neuronlist_interactive_3d.R | 30 nat-1.8.25/nat/R/ngraph.R | 25 nat-1.8.25/nat/R/potential_synapses.R | 2 nat-1.8.25/nat/R/seglist.R | 2 nat-1.8.25/nat/build/partial.rdb |binary nat-1.8.25/nat/build/vignette.rds |binary nat-1.8.25/nat/data/Cell07PNs.rda |binary nat-1.8.25/nat/inst/doc/Installation.html | 8 nat-1.8.25/nat/inst/doc/neurons-intro.R | 44 nat-1.8.25/nat/inst/doc/neurons-intro.html | 1053 ---------- nat-1.8.25/nat/man/as.im3d.Rd | 2 nat-1.8.25/nat/man/as.mesh3d.Rd | 2 nat-1.8.25/nat/man/boundingbox.Rd | 4 nat-1.8.25/nat/man/cmtk.extract_affine.Rd | 6 nat-1.8.25/nat/man/cmtk.reformatx.Rd | 39 nat-1.8.25/nat/man/find.neuron.Rd | 17 nat-1.8.25/nat/man/find.soma.Rd | 15 nat-1.8.25/nat/man/graph.nodes.Rd | 10 nat-1.8.25/nat/man/im3d-coords.Rd | 2 nat-1.8.25/nat/man/im3d-io.Rd | 2 nat-1.8.25/nat/man/imexpand.grid.Rd | 2 nat-1.8.25/nat/man/imslice.Rd | 2 nat-1.8.25/nat/man/is.im3d.Rd | 2 nat-1.8.25/nat/man/is.neuronlist.Rd | 2 nat-1.8.25/nat/man/mask.Rd | 2 nat-1.8.25/nat/man/nat-package.Rd | 22 nat-1.8.25/nat/man/ndigest.Rd | 6 nat-1.8.25/nat/man/neuron.Rd | 6 nat-1.8.25/nat/man/neuronlist-arithmetic.Rd | 2 nat-1.8.25/nat/man/neuronlist-dataframe-methods.Rd | 6 nat-1.8.25/nat/man/neuronlistfh.Rd | 2 nat-1.8.25/nat/man/ngraph.Rd | 2 nat-1.8.25/nat/man/nlapply.Rd | 2 nat-1.8.25/nat/man/nopen3d.Rd | 2 nat-1.8.25/nat/man/nview3d.Rd | 2 nat-1.8.25/nat/man/origin.Rd | 2 nat-1.8.25/nat/man/pan3d.Rd | 4 nat-1.8.25/nat/man/projection.Rd | 2 nat-1.8.25/nat/man/read.cmtk.Rd | 4 nat-1.8.25/nat/man/read.cmtkreg.Rd | 4 nat-1.8.25/nat/man/read.neurons.Rd | 2 nat-1.8.25/nat/man/seglist.Rd | 2 nat-1.8.25/nat/man/threshold.Rd | 2 nat-1.8.25/nat/man/unmask.Rd | 2 nat-1.8.25/nat/man/voxdims.Rd | 2 nat-1.8.25/nat/man/write.cmtk.Rd | 2 nat-1.8.25/nat/man/write.cmtkreg.Rd | 2 nat-1.8.25/nat/man/write.neurons.Rd | 2 nat-1.8.25/nat/tests/testthat/setup.R |only nat-1.8.25/nat/tests/testthat/teardown.R |only nat-1.8.25/nat/tests/testthat/test-neuroml-io.R | 4 nat-1.8.25/nat/tests/testthat/test-ngraph.R | 4 nat-1.8.25/nat/tests/testthat/test-seglist.R | 24 nat-1.8.25/nat/tests/testthat/test-summary.R | 2 nat-1.8.25/nat/tests/testthat/testdata/neuroml/level1/CablesIncluded.swc.txt |only nat-1.8.25/nat/tests/testthat/testdata/neuroml/level1/Simple.morph.swc.txt |only nat-1.8.25/nat/tests/testthat/testdata/neuron/EBT7R.CNG.swc.txt |only nat-1.8.25/nat/tests/testthat/testdata/neuron/XT6L2.CNG.swc.txt |only nat-1.8.25/nat/tests/testthat/testdata/neuron/unfitted.swc.txt |only nat-1.8.25/nat/tests/testthat/testdata/summary_cell07pns.rds |only 80 files changed, 354 insertions(+), 1303 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.22 dated 2025-06-14 and 1.1.23 dated 2025-08-18
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++------------- NEWS | 3 ++ R/map.feature.R | 2 - R/providers.R | 2 - inst/doc/lingtypology_creating_maps.Rmd | 2 - inst/doc/lingtypology_creating_maps.html | 6 ++--- inst/doc/lingtypology_db_API.html | 4 +-- inst/doc/lingtypology_dplyr.html | 4 +-- inst/doc/lingtypology_glottolog_functions.html | 4 +-- inst/doc/lingtypology_intro.html | 4 +-- man/map.feature.Rd | 2 - man/providers.Rd | 2 - tests/testthat/test-mapfeature.R | 12 +++++----- vignettes/lingtypology_creating_maps.Rmd | 2 - 15 files changed, 43 insertions(+), 40 deletions(-)
Title: Lean Analytics and Robust Exploration Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.3.1 dated 2025-07-04 and 5.3.2 dated 2025-08-18
lares-5.3.1/lares/NEWS |only lares-5.3.1/lares/inst/_pkgdown.yml |only lares-5.3.2/lares/DESCRIPTION | 6 +- lares-5.3.2/lares/MD5 | 38 ++++++------- lares-5.3.2/lares/R/cache.R | 10 +++ lares-5.3.2/lares/R/currency.R | 89 ++++++++++++++++-------------- lares-5.3.2/lares/R/dont_sleep.R | 14 ++-- lares-5.3.2/lares/R/facebook.R | 2 lares-5.3.2/lares/R/lares.R | 2 lares-5.3.2/lares/R/maze.R | 2 lares-5.3.2/lares/R/scrabble.R | 5 - lares-5.3.2/lares/R/sudoku.R | 1 lares-5.3.2/lares/R/wordle.R | 1 lares-5.3.2/lares/README.md | 96 ++++++++++++++++----------------- lares-5.3.2/lares/man/cache_write.Rd | 10 +++ lares-5.3.2/lares/man/fb_creatives.Rd | 2 lares-5.3.2/lares/man/lares.Rd | 2 lares-5.3.2/lares/man/maze_solve.Rd | 8 ++ lares-5.3.2/lares/man/scrabble.Rd | 8 ++ lares-5.3.2/lares/man/sudoku_solver.Rd | 7 ++ lares-5.3.2/lares/man/wordle.Rd | 7 ++ 21 files changed, 181 insertions(+), 129 deletions(-)
Title: Delete or Merge Regressors Algorithms for Linear and Logistic
Model Selection and High-Dimensional Data
Description: Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Szymon Nowakowski, Piotr Pokarowski, Wojciech Rejchel and Agnieszka Sołtys, 2023. Improving Group Lasso for High-Dimensional Categorical Data. In: Computational Science – ICCS 2023. Lecture Notes in Computer Science, vol 14074, p. 455-470. Springer, Cham. <doi:10.1007/978-3-031-36021-3_47>. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/vo [...truncated...]
Author: Agnieszka Prochenka-Soltys [aut] ,
Piotr Pokarowski [aut],
Szymon Nowakowski [aut, cre]
Maintainer: Szymon Nowakowski <s.nowakowski@mimuw.edu.pl>
Diff between DMRnet versions 0.4.0 dated 2023-08-07 and 0.4.1 dated 2025-08-18
DESCRIPTION | 13 MD5 | 52 +-- NEWS.md | 10 R/DMRnet-package.R | 4 R/coef.cv.DMR.R | 6 R/cv.DMR.R | 3 R/cv.DMRnet.R | 3 R/cv_GIC_indexed.R | 101 +++++-- R/cv_MD_indexed.R | 69 +++-- R/cv_compute_model.R | 5 R/plot.cv.DMR.R | 61 ++-- R/predict.cv.DMR.R | 6 R/promoter.R | 116 ++++---- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.R | 6 inst/doc/getting-started.Rmd | 14 - inst/doc/getting-started.html | 559 +++++++++++++++++++++--------------------- man/DMRnet-package.Rd | 8 man/coef.cv.DMR.Rd | 4 man/cv.DMR.Rd | 3 man/cv.DMRnet.Rd | 3 man/plot.cv.DMR.Rd | 2 man/predict.cv.DMR.Rd | 4 man/promoter.Rd | 116 ++++---- vignettes/getting-started.Rmd | 14 - 27 files changed, 649 insertions(+), 535 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations. It makes it possible to
easily perform routine tasks when exploring correlation matrices such
as ignoring the diagonal, focusing on the correlations of certain
variables against others, or rearranging and visualizing the matrix in
terms of the strength of the correlations.
Author: Max Kuhn [aut, cre],
Simon Jackson [aut],
Jorge Cimentada [aut]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between corrr versions 0.4.4 dated 2022-08-16 and 0.4.5 dated 2025-08-18
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 4 R/output.R | 2 README.md | 59 +++--- build/vignette.rds |binary inst/doc/databases.html | 182 +++++++++--------- inst/doc/using-corrr.R | 10 - inst/doc/using-corrr.Rmd | 2 inst/doc/using-corrr.html | 341 +++++++++++++++++------------------ man/figures/README-combination-1.png |binary man/figures/README-combination-2.png |binary man/rplot.Rd | 2 vignettes/using-corrr.Rmd | 2 14 files changed, 327 insertions(+), 311 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.6 dated 2025-06-22 and 7.7 dated 2025-08-18
DESCRIPTION | 10 +++--- MD5 | 54 +++++++++++++++++----------------- NAMESPACE | 2 - R/akern.reg.R | 12 +++---- R/bic.alfamixnorm.R | 3 + R/bic.mixcompnorm.R | 6 +-- R/frechet2.R | 68 ++++++++++++++++++++++++------------------- man/Compositional-package.Rd | 4 +- man/akernreg.tune.Rd | 8 ++--- man/aknnreg.tune.Rd | 8 ++--- man/alfaknnreg.tune.Rd | 8 ++--- man/alfapcr.tune.Rd | 2 - man/alfarda.tune.Rd | 10 +++--- man/alfaridge.tune.Rd | 10 +++--- man/cv.ascls.Rd | 4 +- man/cv.atflr.Rd | 4 +- man/cv.comp.reg.Rd | 8 ++--- man/cv.lasso.compreg.Rd | 4 +- man/cv.lasso.klcompreg.Rd | 4 +- man/cv.tflr.Rd | 8 ++--- man/glmpcr.tune.Rd | 4 +- man/kernreg.tune.Rd | 8 ++--- man/klalfapcr.tune.Rd | 6 +-- man/makefolds.Rd | 2 - man/mkde.tune.Rd | 10 +++--- man/rda.Rd | 2 - man/rda.tune.Rd | 6 +-- man/ridge.tune.Rd | 10 +++--- 28 files changed, 147 insertions(+), 138 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 6.0.5 dated 2025-07-31 and 6.0.6 dated 2025-08-18
DESCRIPTION | 11 +++++------ MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/V8.R | 4 ++-- build/partial.rdb |binary inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- inst/js/wasm-feature-detect.js | 2 +- src/bindings.cpp | 4 +++- tests/testthat/test_serialize.R | 2 +- 10 files changed, 31 insertions(+), 25 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast
cumulative residuals, excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling. PLS for the
additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike [aut, cre],
Torben Martinussen [aut],
Jeremy Silver [ctb],
Klaus K. Holst [ctb]
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 2.0.6 dated 2024-09-06 and 2.0.7 dated 2025-08-18
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- R/mgresid.r | 2 - R/recurrent.r | 43 ++++++++++++++++++-------------------- man/recurrent.marginal.coxmean.Rd | 33 +++++++++++++++-------------- man/recurrent.marginal.mean.Rd | 10 +++----- src/cox-aalen.c | 7 ++++-- 7 files changed, 58 insertions(+), 57 deletions(-)
Title: Bayesian Mixtures with an Unknown Number of Components
Description: Fits Bayesian finite mixtures with an unknown number of components using the telescoping sampler and different component distributions. For more details see Frühwirth-Schnatter et al. (2021) <doi:10.1214/21-BA1294>.
Author: Gertraud Malsiner-Walli [aut, cre] ,
Bettina Gruen [aut] ,
Sylvia Fruehwirth-Schnatter [aut]
Maintainer: Gertraud Malsiner-Walli <Gertraud.Malsiner-Walli@wu.ac.at>
Diff between telescope versions 0.2-0 dated 2025-01-23 and 0.2-1 dated 2025-08-18
DESCRIPTION | 16 MD5 | 62 +- NAMESPACE | 46 +- R/identifyLCAMixture.R | 5 R/identifyMixture.R | 5 R/plotBubble.R | 3 R/plotScatter.R | 6 R/priorOnK_spec.R | 8 R/prior_alpha_e0.R | 5 R/sampleK.R | 3 R/sampleLCA.R | 4 R/sampleLCAMixture.R | 2 R/sampleMultNormMixture.R | 6 R/samplePoisMixture.R | 3 R/sampleUniNormMixture.R | 5 R/sample_e0_alpha.R | 4 build/vignette.rds |binary inst/NEWS.Rd | 10 inst/doc/Bayesian_LCA.html | 388 +++++++++--------- inst/doc/Bayesian_LCA_mixtures.html | 546 +++++++++++++------------- inst/doc/Bayesian_Poisson_mixtures.html | 360 ++++++++--------- inst/doc/Bayesian_mult_Gaussian_mixtures.html | 368 ++++++++--------- inst/doc/Bayesian_univ_Gaussian_mixtures.html | 366 ++++++++--------- man/priorOnK_spec.Rd | 4 man/sampleAlpha.Rd | 1 man/sampleE0.Rd | 1 man/sampleK_alpha.Rd | 1 man/sampleK_e0.Rd | 1 man/sampleLCA.Rd | 1 man/sampleMultNormMixture.Rd | 1 man/samplePoisMixture.Rd | 1 man/sampleUniNormMixture.Rd | 1 32 files changed, 1141 insertions(+), 1092 deletions(-)
Title: Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM), Tenenhaus, Esposito Vinzi, Chatelin, Lauro (2005) <doi:10.1016/j.csda.2004.03.005>,
analysis for both metric and non-metric data, as well as REBUS analysis, Esposito Vinzi, Trinchera, Squillacciotti, and Tenenhaus (2008) <doi:10.1002/asmb.728>.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plspm versions 0.5.1 dated 2024-01-23 and 0.5.2 dated 2025-08-18
DESCRIPTION | 11 +++--- MD5 | 22 ++++++------- NEWS | 7 +++- R/innerplot.R | 4 +- R/outerplot.R | 4 +- R/plot.plspm.R | 4 +- build/vignette.rds |binary inst/doc/plspm_introduction.R | 64 ++++++++++++++++++++-------------------- inst/doc/plspm_introduction.pdf |binary man/innerplot.Rd | 4 +- man/outerplot.Rd | 4 +- man/plot.plspm.Rd | 4 +- 12 files changed, 67 insertions(+), 61 deletions(-)
Title: 'OpenStreetMap' API
Description: Interface to 'OpenStreetMap API' for fetching and saving data
from/to the 'OpenStreetMap' database
(<https://wiki.openstreetmap.org/wiki/API_v0.6>).
Author: Joan Maspons [aut, cre, cph] ,
Jon Harmon [rev] ,
Carlos Camara [rev]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmapiR versions 0.2.3 dated 2025-04-15 and 0.2.4 dated 2025-08-18
DESCRIPTION | 13 +- MD5 | 64 +++++----- NEWS.md | 9 + R/R_to_xml.R | 2 R/osm_get_changesets.R | 6 R/osm_get_gpx_metadata.R | 15 +- R/osm_get_notes.R | 6 R/osm_get_objects.R | 16 +- R/osm_get_user_blocks.R | 6 R/osm_get_user_details.R | 6 R/osmapi_changesets.R | 13 -- R/osmapi_elements.R | 46 +++---- R/osmapi_gps_traces.R | 31 +++- R/osmapi_map_notes.R | 10 - R/osmapi_user_blocks.R | 4 R/osmapi_user_data.R | 8 - R/osmchange.R | 4 build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/osmapiR.html | 6 man/osm_create_changeset.Rd | 2 man/osm_create_gpx.Rd | 2 man/osm_get_gpx_metadata.Rd | 6 man/osm_search_notes.Rd | 4 tests/testthat/mock_get_metadata_gpx/osm.org/api/0.6/gpx/3458743.json.json |only tests/testthat/mock_get_metadata_gpx/osm.org/api/0.6/gpx/3790367.json.json |only tests/testthat/test-changesets.R | 2 tests/testthat/test-elements.R | 8 - tests/testthat/test-gps_traces.R | 13 +- tests/testthat/test-map_notes.R | 46 +++++-- tests/testthat/test-osmapiR_request.R | 2 tests/testthat/test-tags_list-wide.R | 12 - tests/testthat/test-user_blocks.R | 2 tests/testthat/test-user_data.R | 4 34 files changed, 215 insertions(+), 155 deletions(-)
Title: Model Species Distributions by Estimating the Probability of
Occurrence Using Presence-Only Data
Description: Provides a likelihood-based approach to modeling species distributions using presence-only data. In contrast to the popular software program MAXENT, this approach yields estimates of the probability of occurrence, which is a natural descriptor of a species' distribution.
Author: Richard Chandler [aut],
Andy Royle [aut],
Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between maxlike versions 0.1-11 dated 2024-03-19 and 0.1-12 dated 2025-08-18
DESCRIPTION | 24 +++++++++++++++++++----- MD5 | 10 +++++----- NEWS | 4 ++++ man/carw.Rd | 8 +++----- man/maxlike-package.Rd | 2 +- man/maxlike.Rd | 16 ++++++++-------- 6 files changed, 40 insertions(+), 24 deletions(-)
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.4.2 dated 2025-03-05 and 2.4.4 dated 2025-08-18
DESCRIPTION | 9 +++++---- MD5 | 22 +++++++++++----------- NEWS.md | 9 ++++++++- R/hbam.R | 7 +++++-- R/hbam_cv.R | 6 ++++-- R/prep_data.R | 2 +- inst/doc/hbamr.R | 1 + inst/doc/hbamr.Rmd | 1 + man/hbam.Rd | 2 +- man/hbam_cv.Rd | 5 ++++- man/prep_data.Rd | 2 +- vignettes/hbamr.Rmd | 1 + 12 files changed, 43 insertions(+), 24 deletions(-)
Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre, cph] ,
Henrik Singmann [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between gratia versions 0.10.0 dated 2024-12-19 and 0.11.0 dated 2025-08-18
gratia-0.10.0/gratia/inst/doc/data-slices.R |only gratia-0.10.0/gratia/inst/doc/data-slices.Rmd |only gratia-0.10.0/gratia/inst/doc/data-slices.html |only gratia-0.10.0/gratia/tests/testthat/_snaps/draw-methods/draw-simple-partial-residuals.svg |only gratia-0.10.0/gratia/vignettes/data-slices.Rmd |only gratia-0.11.0/gratia/DESCRIPTION | 21 gratia-0.11.0/gratia/MD5 | 333 +-- gratia-0.11.0/gratia/NAMESPACE | 42 gratia-0.11.0/gratia/NEWS.md | 178 + gratia-0.11.0/gratia/R/add-methods.R | 25 gratia-0.11.0/gratia/R/assemble.R |only gratia-0.11.0/gratia/R/basis-funs.R | 249 +- gratia-0.11.0/gratia/R/by-variable-utilities.R | 2 gratia-0.11.0/gratia/R/compare-smooths.R | 2 gratia-0.11.0/gratia/R/concurvity.R | 11 gratia-0.11.0/gratia/R/conditional-values.R | 4 gratia-0.11.0/gratia/R/confint-methods.R | 4 gratia-0.11.0/gratia/R/data-sim.R | 41 gratia-0.11.0/gratia/R/data-slice.R | 67 gratia-0.11.0/gratia/R/datasets.R | 4 gratia-0.11.0/gratia/R/derivatives.R | 89 gratia-0.11.0/gratia/R/diagnose.R | 169 + gratia-0.11.0/gratia/R/difference-smooths.R | 153 + gratia-0.11.0/gratia/R/distribution-helpers.R | 9 gratia-0.11.0/gratia/R/draw-gam.R | 361 --- gratia-0.11.0/gratia/R/draw-methods.R | 8 gratia-0.11.0/gratia/R/edf.R | 17 gratia-0.11.0/gratia/R/evenly.R | 2 gratia-0.11.0/gratia/R/family-utils.R | 33 gratia-0.11.0/gratia/R/fderiv.R | 2 gratia-0.11.0/gratia/R/fitted_values.R | 169 + gratia-0.11.0/gratia/R/fix-family.R |only gratia-0.11.0/gratia/R/ggplot-functions.R |only gratia-0.11.0/gratia/R/gjrm-methods.R | 15 gratia-0.11.0/gratia/R/nested-functions.R | 52 gratia-0.11.0/gratia/R/overview.R | 50 gratia-0.11.0/gratia/R/parametric-effects.R | 32 gratia-0.11.0/gratia/R/posterior-samples.R | 511 ++++- gratia-0.11.0/gratia/R/rd-helpers.R |only gratia-0.11.0/gratia/R/residuals.R | 132 + gratia-0.11.0/gratia/R/samplers.R | 8 gratia-0.11.0/gratia/R/simulate-methods.R | 67 gratia-0.11.0/gratia/R/smooth-data.R | 50 gratia-0.11.0/gratia/R/smooth-estimates.R | 200 +- gratia-0.11.0/gratia/R/subsetting.R | 10 gratia-0.11.0/gratia/R/utililties.R | 104 + gratia-0.11.0/gratia/R/variance-components.R | 7 gratia-0.11.0/gratia/README.md | 112 - gratia-0.11.0/gratia/build/partial.rdb |binary gratia-0.11.0/gratia/build/vignette.rds |binary gratia-0.11.0/gratia/inst/CITATION | 53 gratia-0.11.0/gratia/inst/WORDLIST |only gratia-0.11.0/gratia/inst/doc/gratia.Rmd | 1 gratia-0.11.0/gratia/inst/doc/gratia.html | 44 gratia-0.11.0/gratia/man/add_fitted_samples.Rd | 2 gratia-0.11.0/gratia/man/add_sizer.Rd | 2 gratia-0.11.0/gratia/man/appraise.Rd | 2 gratia-0.11.0/gratia/man/assemble.Rd |only gratia-0.11.0/gratia/man/assemble.gam.Rd |only gratia-0.11.0/gratia/man/basis.Rd | 14 gratia-0.11.0/gratia/man/confint.gam.Rd | 4 gratia-0.11.0/gratia/man/data_combos.Rd | 2 gratia-0.11.0/gratia/man/data_sim.Rd | 8 gratia-0.11.0/gratia/man/data_slice.Rd | 12 gratia-0.11.0/gratia/man/derivative_samples.Rd | 19 gratia-0.11.0/gratia/man/derivatives.Rd | 2 gratia-0.11.0/gratia/man/difference_smooths.Rd | 25 gratia-0.11.0/gratia/man/draw.gam.Rd | 4 gratia-0.11.0/gratia/man/edf.Rd | 19 gratia-0.11.0/gratia/man/eval_smooth.Rd | 7 gratia-0.11.0/gratia/man/fderiv.Rd | 2 gratia-0.11.0/gratia/man/figures/README-appraise-figure-1.png |binary gratia-0.11.0/gratia/man/figures/README-draw-gam-figure-1.png |binary gratia-0.11.0/gratia/man/figures/README-draw-gam-figure-2d-1.png |binary gratia-0.11.0/gratia/man/fitted_samples.Rd | 20 gratia-0.11.0/gratia/man/get_by_smooth.Rd | 2 gratia-0.11.0/gratia/man/gw_functions.Rd | 4 gratia-0.11.0/gratia/man/is_by_smooth.Rd | 2 gratia-0.11.0/gratia/man/is_mgcv_family.Rd |only gratia-0.11.0/gratia/man/is_multivariate_y.Rd |only gratia-0.11.0/gratia/man/model_concurvity.Rd | 2 gratia-0.11.0/gratia/man/nested_rug_values.Rd | 2 gratia-0.11.0/gratia/man/overview.Rd | 3 gratia-0.11.0/gratia/man/partial_residuals.Rd | 2 gratia-0.11.0/gratia/man/post_draws.Rd | 2 gratia-0.11.0/gratia/man/posterior_samples.Rd | 20 gratia-0.11.0/gratia/man/predicted_samples.Rd | 6 gratia-0.11.0/gratia/man/qq_plot.Rd | 6 gratia-0.11.0/gratia/man/quantile_residuals.Rd |only gratia-0.11.0/gratia/man/residuals_hist_plot.Rd | 19 gratia-0.11.0/gratia/man/residuals_linpred_plot.Rd | 19 gratia-0.11.0/gratia/man/response_derivatives.Rd | 18 gratia-0.11.0/gratia/man/rtw.Rd |only gratia-0.11.0/gratia/man/scale_fill_partial_effect.Rd |only gratia-0.11.0/gratia/man/seq_min_max_eps.Rd | 2 gratia-0.11.0/gratia/man/shift_values.Rd | 2 gratia-0.11.0/gratia/man/simulate.Rd | 4 gratia-0.11.0/gratia/man/smooth_estimates.Rd | 14 gratia-0.11.0/gratia/man/smooth_samples.Rd | 2 gratia-0.11.0/gratia/man/spline_values.Rd | 2 gratia-0.11.0/gratia/man/spline_values2.Rd | 2 gratia-0.11.0/gratia/man/worm_plot.Rd | 4 gratia-0.11.0/gratia/man/zooplankton.Rd | 4 gratia-0.11.0/gratia/tests/Examples/gratia-Ex.Rout.save | 123 + gratia-0.11.0/gratia/tests/testthat/_snaps/assemble.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/backward/response-derivatives.md | 20 gratia-0.11.0/gratia/tests/testthat/_snaps/basis.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/basis/draw-basis-works-ok-with-weighted-basis-funs.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/basis/draw-basis-works-with-a-scam-single-smooth.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/central/response-derivatives.md | 20 gratia-0.11.0/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-all-smooths.svg | 112 - gratia-0.11.0/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-bottom-legend.svg | 112 - gratia-0.11.0/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-set-nrow-ncol.svg | 114 - gratia-0.11.0/gratia/tests/testthat/_snaps/conditional-values.md | 53 gratia-0.11.0/gratia/tests/testthat/_snaps/data-slice.md | 31 gratia-0.11.0/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-complex-factor-by.svg | 4 gratia-0.11.0/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg | 8 gratia-0.11.0/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivs-for-ordered-factor-by.svg | 4 gratia-0.11.0/gratia/tests/testthat/_snaps/derivatives/draw-issue-57-derivatives-for-factor-by.svg | 70 gratia-0.11.0/gratia/tests/testthat/_snaps/diagnostic-plots/appraise-for-mvn-model.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/diagnostic-plots/appraise-for-twlss-model.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/diagnostic-plots/r-hist-plot-qresids-poisson-model.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/diagnostic-plots/r-linpred-plot-pit-resids-poisson-model.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gamm.svg | 16 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-gam.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/draw-gam/draw-gam-dlnm-m.svg | 45 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gamm4.svg | 8 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gaulss.svg | 16 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam-rotated-labels.svg | 4 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam-with-fixed-scales-rotated.svg | 4 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-fs-smooth-with-discrete-plasma-palette.svg | 323 +-- gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-fs-smooth.svg | 323 +-- gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-non-standard-names.svg | 42 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-model-with-fs-smooth-fixed-scales.svg | 132 - gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-works-for-sos-smooths.svg | 942 ++++----- gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/draw-ziplss-parametric-terms-issue-45.svg | 6 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/nb-rootogram-plot-hanging.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/nb-rootogram-plot-standing.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/draw-methods/nb-rootogram-plot-suspended.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-peff-preserves-factor-levels.svg | 215 +- gratia-0.11.0/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-gam-for-su-m-quadvar-t22.svg | 2 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gamm4.svg | 2 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gaulss.svg | 4 gratia-0.11.0/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-t22.svg | 2 gratia-0.11.0/gratia/tests/testthat/_snaps/fderiv.md | 142 - gratia-0.11.0/gratia/tests/testthat/_snaps/fitted-values.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/fitted/posterior-samples.md | 40 gratia-0.11.0/gratia/tests/testthat/_snaps/fix-family.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/forward/response-derivatives.md | 20 gratia-0.11.0/gratia/tests/testthat/_snaps/gjrm-methods/draw-simple-gjrm-gamlss.svg | 6 gratia-0.11.0/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-2.svg | 853 ++++---- gratia-0.11.0/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-2.svg | 82 gratia-0.11.0/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-4.svg | 54 gratia-0.11.0/gratia/tests/testthat/_snaps/overview.md | 90 gratia-0.11.0/gratia/tests/testthat/_snaps/posterior/posterior-samples.md | 80 gratia-0.11.0/gratia/tests/testthat/_snaps/quantile-residuals.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/rfoo.md |only gratia-0.11.0/gratia/tests/testthat/_snaps/scales |only gratia-0.11.0/gratia/tests/testthat/_snaps/soap-films.md | 64 gratia-0.11.0/gratia/tests/testthat/_snaps/soap-films/draw-gam-so-soap-film.svg | 956 ++++------ gratia-0.11.0/gratia/tests/testthat/_snaps/soap-films/draw-smooth-estimates-so-nested-soap-film.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/soap-films/draw-smooth-estimates-so-soap-film-bndry.svg |only gratia-0.11.0/gratia/tests/testthat/_snaps/soap-films/draw-smooth-estimates-so-soap-film.svg | 152 - gratia-0.11.0/gratia/tests/testthat/_snaps/utilities.md |only gratia-0.11.0/gratia/tests/testthat/setup.R | 227 ++ gratia-0.11.0/gratia/tests/testthat/test-assemble.R |only gratia-0.11.0/gratia/tests/testthat/test-basis.R | 31 gratia-0.11.0/gratia/tests/testthat/test-conditional-values.R | 45 gratia-0.11.0/gratia/tests/testthat/test-data-slice.R | 23 gratia-0.11.0/gratia/tests/testthat/test-diagnostic-plots.R | 49 gratia-0.11.0/gratia/tests/testthat/test-difference-smooths.R | 10 gratia-0.11.0/gratia/tests/testthat/test-draw-gam.R | 10 gratia-0.11.0/gratia/tests/testthat/test-draw-methods.R | 20 gratia-0.11.0/gratia/tests/testthat/test-family-utils.R | 34 gratia-0.11.0/gratia/tests/testthat/test-fitted-values.R | 33 gratia-0.11.0/gratia/tests/testthat/test-fix-family.R |only gratia-0.11.0/gratia/tests/testthat/test-gfam.R | 36 gratia-0.11.0/gratia/tests/testthat/test-hgam-paper.R | 45 gratia-0.11.0/gratia/tests/testthat/test-parallel.R |only gratia-0.11.0/gratia/tests/testthat/test-parametric-effects.R | 14 gratia-0.11.0/gratia/tests/testthat/test-posterior-samples.R | 42 gratia-0.11.0/gratia/tests/testthat/test-quantile-residuals.R |only gratia-0.11.0/gratia/tests/testthat/test-rfoo.R |only gratia-0.11.0/gratia/tests/testthat/test-samplers.R | 8 gratia-0.11.0/gratia/tests/testthat/test-scales.R |only gratia-0.11.0/gratia/tests/testthat/test-simulate-methods.R | 42 gratia-0.11.0/gratia/tests/testthat/test-soap-films.R | 73 gratia-0.11.0/gratia/tests/testthat/test-utilities.R | 52 gratia-0.11.0/gratia/vignettes/gratia.Rmd | 1 189 files changed, 6129 insertions(+), 3692 deletions(-)
Title: Difference-in-Differences in Heterogeneous Adoption Designs with
Quasi Untreated Groups
Description: Estimation of Difference-in-Differences (DiD) estimators from de Chaisemartin et al. (2025) <doi:10.48550/arXiv.2405.04465> in Heterogeneous Adoption Designs with Quasi Untreated Groups.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut],
Xavier D'Haultfoeuille [aut]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between DIDHAD versions 1.0.1 dated 2024-07-23 and 2.0.0 dated 2025-08-18
DIDHAD-1.0.1/DIDHAD/R/cross_validation.R |only DIDHAD-2.0.0/DIDHAD/DESCRIPTION | 14 +++--- DIDHAD-2.0.0/DIDHAD/MD5 | 18 ++++---- DIDHAD-2.0.0/DIDHAD/NAMESPACE | 11 +++-- DIDHAD-2.0.0/DIDHAD/R/did_had.R | 27 ++++++------ DIDHAD-2.0.0/DIDHAD/R/did_had_est.R | 18 ++++++-- DIDHAD-2.0.0/DIDHAD/R/did_had_graph.R | 4 - DIDHAD-2.0.0/DIDHAD/R/did_het_adoption_main.R | 56 ++++++++++++++------------ DIDHAD-2.0.0/DIDHAD/R/print.R | 51 ++++++++++++++++++----- DIDHAD-2.0.0/DIDHAD/build |only DIDHAD-2.0.0/DIDHAD/man/did_had.Rd | 26 ++++++------ 11 files changed, 139 insertions(+), 86 deletions(-)
Title: Breaks for Additive Season and Trend
Description: Decomposition of time series into
trend, seasonal, and remainder components with methods for detecting and
characterizing abrupt changes within the trend and seasonal components. 'BFAST'
can be used to analyze different types of satellite image time series and can
be applied to other disciplines dealing with seasonal or non-seasonal time
series, such as hydrology, climatology, and econometrics. The algorithm can be
extended to label detected changes with information on the parameters of the
fitted piecewise linear models. 'BFAST' monitoring functionality is described
in Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor'
provides functionality to detect disturbance in near real-time based on 'BFAST'-
type models, and is described in Verbesselt et al. (2012) <doi:10.1016/j.rse.2012.02.022>.
'BFAST Lite' approach is a flexible approach that handles missing data
without interpolation, and will be described in an upcoming paper.
Furthermore, different mode [...truncated...]
Author: Jan Verbesselt [aut],
Dainius Masiliūnas [aut, cre] ,
Achim Zeileis [aut],
Rob Hyndman [ctb],
Marius Appel [aut],
Martin Jung [ctb],
Andrei Mîrț [ctb] ,
Paulo Negri Bernardino [ctb],
Dongdong Kong [ctb]
Maintainer: Dainius Masiliūnas <pastas4@gmail.com>
Diff between bfast versions 1.7.0 dated 2024-10-22 and 1.7.1 dated 2025-08-18
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS | 5 +++++ R/bfastpp.R | 2 +- build/partial.rdb |binary 5 files changed, 17 insertions(+), 11 deletions(-)
Title: AI Screening Tools in R for Systematic Reviewing
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://platform.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2025) <DOI:10.1037/met0000769>.
Author: Mikkel H. Vembye [aut, cre, cph] ,
Thomas Olsen [aut]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Diff between AIscreenR versions 0.1.1 dated 2024-11-26 and 0.2.0 dated 2025-08-18
DESCRIPTION | 24 +-- MD5 | 47 +++--- NAMESPACE | 2 NEWS.md | 7 R/api_key_functions.R | 2 R/data.R | 4 R/fine_tune_data.R |only R/misc.func.hidden.price.R | 160 ++++++++++---------- R/screen_analyzer.R | 8 - R/screen_errors.R | 178 +++++++++++------------ R/tabscreen_gpt.R | 6 R/tabscreen_gpt.original.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/model_prizes.rda |binary inst/doc/Using-GPT-API-Models-For-Screening.Rmd | 17 +- inst/doc/Using-GPT-API-Models-For-Screening.html | 28 ++- man/AIscreenR-package.Rd | 7 man/create_fine_tune_data.Rd |only man/model_prizes.Rd | 4 man/save_fine_tune_data.Rd |only man/screen_analyzer.Rd | 8 - man/tabscreen_gpt.original.Rd | 4 man/tabscreen_gpt.tools.Rd | 4 tests/testthat/test-approximate_price_gpt.R | 6 vignettes/Using-GPT-API-Models-For-Screening.Rmd | 17 +- 26 files changed, 287 insertions(+), 250 deletions(-)
Title: Prompt Large Language Models and Enhance Their Functionality
Description: Easily construct prompts and associated logic for interacting with
large language models (LLMs).
'tidyprompt' introduces the concept of prompt wraps, which are building
blocks that you can use to quickly turn a simple prompt into a complex
one. Prompt wraps do not just modify the prompt text, but also add
extraction and validation functions that will be applied to the response
of the LLM. This ensures that the user gets the desired output.
'tidyprompt' can add various features to prompts and their evaluation
by LLMs, such as structured output, automatic feedback, retries, reasoning
modes, autonomous R function calling, and R code generation and evaluation.
It is designed to be compatible with any LLM provider that offers
chat completion.
Author: Luka Koning [aut, cre, cph],
Tjark Van de Merwe [aut, cph],
Kennispunt Twente [fnd]
Maintainer: Luka Koning <l.koning@kennispunttwente.nl>
Diff between tidyprompt versions 0.0.1 dated 2025-01-08 and 0.1.0 dated 2025-08-18
DESCRIPTION | 17 MD5 | 245 +- NAMESPACE | 5 NEWS.md | 30 R/answer_as_boolean.R | 22 R/answer_as_category.R |only R/answer_as_integer.R | 62 R/answer_as_json.R | 555 +++--- R/answer_as_key_value.R | 355 ++- R/answer_as_list.R | 94 - R/answer_as_named_list.R | 91 R/answer_as_regex_match.R | 6 R/answer_as_text.R | 36 R/answer_by_chain_of_thought.R | 16 R/answer_by_react.R | 166 - R/answer_using_r.R | 948 +++++----- R/answer_using_sql.R | 562 +++--- R/answer_using_tools.R | 2561 ++++++++++++++-------------- R/chat_history.R | 442 ++-- R/helper_other_extract_from_return_list.R | 6 R/helper_other_r_json_schema.R | 114 - R/helper_text_df_to_string.R | 1 R/helper_text_skim_with_labels_and_levels.R | 19 R/helper_text_vector_list_to_string.R | 10 R/internal_extraction.R | 69 R/internal_request_llm_provider.R | 497 ++--- R/internal_test_helpers.R | 10 R/llm_break.R | 64 R/llm_feedback.R | 24 R/llm_provider.R | 583 +++--- R/llm_providers.R | 1364 ++++++++------ R/misc_add_text.R | 6 R/misc_llm_verify.R | 261 +- R/misc_quit_if.R | 48 R/misc_user_verify.R | 4 R/persistent_chat.R | 199 +- R/print.R | 155 - R/prompt_wrap.R | 90 R/send_prompt.R | 826 ++++----- R/tidyprompt-package.R | 1 R/tidyprompt.R | 1093 ++++++----- R/zzz.R | 33 README.md | 40 inst/doc/creating_prompt_wraps.Rmd | 348 +-- inst/doc/creating_prompt_wraps.html | 5 inst/doc/getting_started.Rmd | 721 +++---- inst/doc/getting_started.html | 34 inst/doc/sentiment_analysis.html | 5 inst/examples/answer_as_boolean.R | 24 inst/examples/answer_as_category.R |only inst/examples/answer_as_integer.R | 24 inst/examples/answer_as_json.R | 542 ++--- inst/examples/answer_as_key_value.R | 72 inst/examples/answer_as_list.R | 70 inst/examples/answer_as_multi_category.R |only inst/examples/answer_as_text.R | 24 inst/examples/answer_by_chain_of_thought.R | 106 - inst/examples/answer_by_react.R | 84 inst/examples/answer_using_r.R | 104 - inst/examples/answer_using_sql.R | 200 +- inst/examples/answer_using_tools.R | 112 - inst/examples/chat_history.R | 98 - inst/examples/df_to_string.R | 14 inst/examples/extract_from_return_list.R | 16 inst/examples/llm_break.R | 62 inst/examples/llm_break_soft.R |only inst/examples/llm_feedback.R | 44 inst/examples/llm_provider.R | 114 - inst/examples/llm_providers.R | 47 inst/examples/llm_verify.R | 124 - inst/examples/persistent_chat.R | 90 inst/examples/quit_if.R | 26 inst/examples/skim_with_labels_and_levels.R | 16 inst/examples/tidyprompt.R | 124 - inst/examples/user_verify.R | 78 inst/examples/vector_list_to_string.R | 10 man/add_text.Rd | 2 man/answer_as_boolean.Rd | 4 man/answer_as_category.Rd |only man/answer_as_integer.Rd | 4 man/answer_as_json.Rd | 4 man/answer_as_key_value.Rd | 176 - man/answer_as_list.Rd | 4 man/answer_as_multi_category.Rd |only man/answer_as_named_list.Rd | 4 man/answer_as_regex_match.Rd | 4 man/answer_as_text.Rd | 4 man/answer_by_chain_of_thought.Rd | 2 man/answer_by_react.Rd | 2 man/answer_using_r.Rd | 2 man/answer_using_sql.Rd | 2 man/answer_using_tools.Rd | 2 man/llm_break.Rd | 4 man/llm_break_soft.Rd |only man/llm_provider-class.Rd | 597 +++--- man/llm_provider_ellmer.Rd |only man/llm_provider_google_gemini.Rd | 204 +- man/llm_provider_groq.Rd | 48 man/llm_provider_mistral.Rd | 48 man/llm_provider_ollama.Rd | 62 man/llm_provider_openai.Rd | 48 man/llm_provider_openrouter.Rd | 48 man/llm_provider_xai.Rd | 48 man/prompt_wrap.Rd | 64 man/quit_if.Rd | 2 man/set_system_prompt.Rd | 2 man/tidyprompt-class.Rd | 602 +++--- man/tidyprompt-package.Rd | 6 tests/testthat/test-answer-as-boolean.R | 43 tests/testthat/test-answer-as-json.R | 387 ++-- tests/testthat/test-answer_as_integer.R | 49 tests/testthat/test-answer_as_key_value.R | 85 tests/testthat/test-answer_as_list.R | 6 tests/testthat/test-answer_using_r.R | 50 tests/testthat/test-answer_using_tools.R | 157 - tests/testthat/test-chat_history.R | 29 tests/testthat/test-df_to_string.R | 10 tests/testthat/test-llm_provider.R | 43 tests/testthat/test-prompt_wrap.R | 45 tests/testthat/test-send_prompt.R | 68 tests/testthat/test-set_sytem_prompt.R | 20 tests/testthat/test-tidyprompt.R | 177 - vignettes/creating_prompt_wraps.Rmd | 348 +-- vignettes/example_usage.R |only vignettes/getting_started.Rmd | 721 +++---- vignettes/getting_started.Rmd.orig | 472 ++--- vignettes/readme_example.Rmd.example | 182 - vignettes/readme_example.Rmd.orig | 136 - 128 files changed, 10580 insertions(+), 9515 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 3.4.0 dated 2025-06-11 and 3.5.0 dated 2025-08-18
DESCRIPTION | 10 MD5 | 43 ++- NAMESPACE | 5 NEWS.md | 7 R/fit_svs.R | 53 +++- R/fitting.R | 40 +++ R/fmrs.R | 420 +++++++++++++++++++++++++++++++++--- R/mrs_data_proc.R | 133 +++++++++++ R/mrs_read_ima.R | 4 R/rats.R | 15 - R/utils.R | 4 inst/cli_scripts/spant_fit_svs | 8 inst/doc/spant-intro.html | 120 +++++----- inst/doc/spant-preprocessing.html | 4 inst/rmd/dataset_summary_svs_qa.Rmd | 32 ++ inst/rmd/spec_glm_results.Rmd | 15 + man/auto_phase_bl.Rd |only man/comb_fit_list_dyns.Rd |only man/fit_svs.Rd | 11 man/gen_numeric_reg.Rd |only man/glm_spec_fmrs_fl.Rd | 6 man/mr_data2bids.Rd |only man/mrs_data2list.Rd |only man/phase_ref_1h_brain.Rd | 19 + man/segment_t1_fsl.Rd | 4 25 files changed, 806 insertions(+), 147 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc_node_en.html> for more information).
Choose observational time series from meteorological stations with 'selectDWD()'.
Find raster data from radar and interpolation according to <https://bookdown.org/brry/rdwd/raster-data.html>.
Download (multiple) data sets with progress bars and no re-downloads through 'dataDWD()'.
Read both tabular observational data and binary gridded datasets with 'readDWD()'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.8.0 dated 2023-06-17 and 1.9.3 dated 2025-08-18
DESCRIPTION | 23 - MD5 | 96 ++-- NAMESPACE | 1 NEWS.md | 15 R/checkIndex.R | 45 + R/checkUpdates.R |only R/createIndex.R | 47 +- R/dataDWD.R | 32 - R/dirDWD.R | 4 R/fileType.R | 15 R/indexFTP.R | 89 +-- R/locdir.R | 4 R/nearbyStations.R | 27 - R/projectRasterDWD.R | 228 +++++----- R/rdwd-package.R | 2 R/readDWD.R | 175 ++++++- R/readMeta.R | 3 R/runLocalTests.R | 33 - R/selectDWD.R | 12 R/updateIndexes.R | 36 + README.md | 20 build/vignette.rds |binary data/fileIndex.rda |binary data/formatIndex.rda |binary data/geoIndex.rda |binary data/gridIndex.rda |binary data/metaIndex.rda |binary inst/doc/rdwd.html | 2 inst/shinyapps/compare_years/app.R | 24 - inst/shinyapps/compare_years/rsconnect/shinyapps.io/brry/wetter.dcf | 24 - man/checkIndex.Rd | 2 man/checkUpdates.Rd |only man/createIndex.Rd | 7 man/dataDWD.Rd | 13 man/dirDWD.Rd | 4 man/fileType.Rd | 9 man/indexFTP.Rd | 37 - man/locdir.Rd | 4 man/nearbyStations.Rd | 18 man/rdwd.Rd | 12 man/readDWD.asczip.Rd |only man/readDWD.data.Rd | 7 man/readDWD.grib2.Rd | 8 man/readDWD.hyras.Rd |only man/readDWD.meta.Rd | 2 man/readDWD.multia.Rd | 14 man/readDWD.nc.Rd | 12 man/readDWD.pdf.Rd | 13 man/selectDWD.Rd | 3 man/updateIndexes.Rd | 26 + man/validFileTypes.Rd | 2 51 files changed, 729 insertions(+), 421 deletions(-)
Title: Partial Least Squares Regression for Beta Regression Models
Description: Provides Partial least squares Regression for (weighted) beta regression models (Bertrand 2013, <https://ojs-test.apps.ocp.math.cnrs.fr/index.php/J-SFdS/article/view/215>) and k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plsRbeta versions 0.3.0 dated 2023-03-15 and 0.3.1 dated 2025-08-18
DESCRIPTION | 18 MD5 | 92 ++-- R/PLS_beta.R | 2 R/PLS_beta_formula.R | 2 R/PLS_beta_kfoldcv.R | 2 R/PLS_beta_kfoldcv_formula.R | 2 R/PLS_beta_wvc.R | 6 R/bootplsbeta.R | 2 R/coefs.plsRbeta.R | 2 R/coefs.plsRbeta.raw.R | 2 R/kfolds2CVinfos_beta.R | 2 R/kfolds2Chisq.R | 2 R/kfolds2Chisqind.R | 2 R/permcoefs.plsRbeta.R | 2 R/permcoefs.plsRbeta.raw.R | 2 R/plsRbeta-package.R | 36 - R/plsRbeta.R | 2 R/print.plsRbetamodel.R | 2 R/print.summary.plsRbetamodel.R | 2 R/simul_data_UniYX_beta.R | 2 R/summary.plsRbetamodel.R | 2 R/tilt.bootplsbeta.R | 2 README.md | 130 ++---- build/vignette.rds |binary inst/CITATION | 2 inst/doc/tn_Insights.R | 183 -------- inst/doc/tn_Insights.html | 771 ++++++++++++++++++------------------- man/PLS_beta.Rd | 2 man/PLS_beta_formula.Rd | 2 man/PLS_beta_kfoldcv.Rd | 2 man/PLS_beta_kfoldcv_formula.Rd | 2 man/PLS_beta_wvc.Rd | 6 man/bootplsbeta.Rd | 2 man/coefs.plsRbeta.Rd | 2 man/coefs.plsRbeta.raw.Rd | 2 man/kfolds2CVinfos_beta.Rd | 2 man/kfolds2Chisq.Rd | 2 man/kfolds2Chisqind.Rd | 2 man/permcoefs.plsRbeta.Rd | 2 man/permcoefs.plsRbeta.raw.Rd | 2 man/plsRbeta-package.Rd | 46 +- man/plsRbeta.Rd | 377 +++++++++++++----- man/print.plsRbetamodel.Rd | 2 man/print.summary.plsRbetamodel.Rd | 2 man/simul_data_UniYX_beta.Rd | 2 man/summary.plsRbetamodel.Rd | 2 man/tilt.bootplsbeta.Rd | 2 47 files changed, 840 insertions(+), 897 deletions(-)
Title: Some Utilities for Developing Data Science Software
Description: A collection of general-purpose helper functions that I (and maybe
others) find useful when developing data science software. Includes tools
for simulation, data transformation, input validation, and more.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between oeli versions 0.7.4 dated 2025-06-27 and 0.7.5 dated 2025-08-18
oeli-0.7.4/oeli/src/dirichlet.h |only oeli-0.7.4/oeli/src/mvnorm.h |only oeli-0.7.4/oeli/src/tnorm.h |only oeli-0.7.4/oeli/src/wishart.h |only oeli-0.7.5/oeli/DESCRIPTION | 19 oeli-0.7.5/oeli/MD5 | 99 +- oeli-0.7.5/oeli/NAMESPACE | 11 oeli-0.7.5/oeli/NEWS.md | 16 oeli-0.7.5/oeli/R/RcppExports.R | 28 oeli-0.7.5/oeli/R/equidistant_vectors.R |only oeli-0.7.5/oeli/R/gaussian_tv.R |only oeli-0.7.5/oeli/R/mixnorm.R |only oeli-0.7.5/oeli/R/mvnorm.R | 62 + oeli-0.7.5/oeli/R/oeli-package.R | 1 oeli-0.7.5/oeli/R/wishart.R | 16 oeli-0.7.5/oeli/README.md | 72 - oeli-0.7.5/oeli/inst |only oeli-0.7.5/oeli/man/Simulator.Rd | 2 oeli-0.7.5/oeli/man/check_numeric_vector.Rd | 1 oeli-0.7.5/oeli/man/check_probability_vector.Rd | 1 oeli-0.7.5/oeli/man/chunk_vector.Rd | 1 oeli-0.7.5/oeli/man/correlated_regressors.Rd | 2 oeli-0.7.5/oeli/man/ddirichlet.Rd | 2 oeli-0.7.5/oeli/man/dmixnorm.Rd |only oeli-0.7.5/oeli/man/dmvnorm.Rd | 40 oeli-0.7.5/oeli/man/dtnorm.Rd | 2 oeli-0.7.5/oeli/man/dwishart.Rd | 18 oeli-0.7.5/oeli/man/equidistant_vectors.Rd |only oeli-0.7.5/oeli/man/figures/README-mixnorm-1.png |only oeli-0.7.5/oeli/man/figures/README-package_logo-1.png |binary oeli-0.7.5/oeli/man/gaussian_tv.Rd |only oeli-0.7.5/oeli/man/insert_vector_entry.Rd | 1 oeli-0.7.5/oeli/man/map_indices.Rd | 101 +- oeli-0.7.5/oeli/man/match_numerics.Rd | 1 oeli-0.7.5/oeli/man/permutations.Rd | 1 oeli-0.7.5/oeli/man/simulate_markov_chain.Rd | 4 oeli-0.7.5/oeli/man/split_vector_at.Rd | 89 - oeli-0.7.5/oeli/man/subsets.Rd | 83 - oeli-0.7.5/oeli/man/vector_occurrence.Rd | 1 oeli-0.7.5/oeli/src/RcppExports.cpp | 643 +++++++++++++- oeli-0.7.5/oeli/src/dirichlet.cpp | 14 oeli-0.7.5/oeli/src/internal.cpp |only oeli-0.7.5/oeli/src/internal.h |only oeli-0.7.5/oeli/src/mixnorm.cpp |only oeli-0.7.5/oeli/src/mvnorm.cpp | 84 + oeli-0.7.5/oeli/src/test-dirichlet.cpp | 2 oeli-0.7.5/oeli/src/test-mixnorm.cpp |only oeli-0.7.5/oeli/src/test-mvnorm.cpp | 46 - oeli-0.7.5/oeli/src/test-tnorm.cpp | 2 oeli-0.7.5/oeli/src/test-wishart.cpp | 2 oeli-0.7.5/oeli/src/tnorm.cpp | 34 oeli-0.7.5/oeli/src/wishart.cpp | 40 oeli-0.7.5/oeli/tests/testthat/test-equidistant_vectors.R |only oeli-0.7.5/oeli/tests/testthat/test-gaussian_tv.R |only oeli-0.7.5/oeli/tests/testthat/test-mixnorm.R |only oeli-0.7.5/oeli/tests/testthat/test-mvnorm.R | 32 oeli-0.7.5/oeli/tests/testthat/test-wishart.R | 1 57 files changed, 1234 insertions(+), 340 deletions(-)
Title: Reads Raw Files from Li-COR Gas Analyzers
Description: Reads raw files from Li-COR gas analyzers and produces a dataframe that can directly be used with 'fluxible' <https://cran.r-project.org/package=fluxible>.
Author: Joseph Gaudard [aut, cre]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between licoread versions 0.2.0 dated 2025-05-08 and 0.3.0 dated 2025-08-18
DESCRIPTION | 10 ++--- MD5 | 49 ++++++++++++++++++++++---- NAMESPACE | 8 ++++ NEWS.md | 4 ++ R/import7500.R |only R/import7500_new_oneobs.R |only R/import7500_old_oneobs.R |only build/vignette.rds |binary inst/doc/licoread.R | 21 +++++++++++ inst/doc/licoread.Rmd | 36 +++++++++++++++++++ inst/doc/licoread.html | 67 ++++++++++++++++++++++++++++++++++++ inst/extdata/co2fluxtent |only inst/extdata/pftc5 |only inst/extdata/pftc7 |only man/import7500.Rd |only man/import7500_new_oneobs.Rd |only man/import7500_old_oneobs.Rd |only tests/testthat/_snaps/import7500.md |only tests/testthat/co2fluxtent |only tests/testthat/pftc5 |only tests/testthat/pftc7 |only tests/testthat/test-import7500.R |only vignettes/biblio_phd_zot.bib |only vignettes/emerald-harvard.csl |only vignettes/licoread.Rmd | 36 +++++++++++++++++++ 25 files changed, 218 insertions(+), 13 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.2 dated 2025-07-24 and 1.5.3 dated 2025-08-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/independent_twoway_generation.R | 2 +- inst/doc/eSp_balanced_design_powertest.html | 8 ++++---- 5 files changed, 16 insertions(+), 12 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Streamlined Export of Graphs and Data Tables
Description: Easily export 'R' graphs and statistical output to 'Microsoft
Office' / 'LibreOffice', 'Latex' and 'HTML' Documents, using sensible defaults
that result in publication-quality output with simple, straightforward commands.
Output to 'Microsoft Office' is in editable 'DrawingML' vector format for
graphs, and can use corporate template documents for styling. This enables
the production of standardized reports and also allows for manual tidy-up
of the layout of 'R' graphs in 'Powerpoint' before final publication. Export
of graphs is flexible, and functions enable the currently showing R graph
or the currently showing 'R' stats object to be exported, but also allow the
graphical or tabular output to be passed as objects. The package relies on package
'officer' for export to 'Office' documents,and output files are also fully compatible
with 'LibreOffice'. Base 'R', 'ggplot2' and 'lattice' plots are supported, as
well as a wide variety of 'R' stats objects, via wrappers to xtable(), broom::ti [...truncated...]
Author: Tom Wenseleers [aut, cre],
Christophe Vanderaa [aut]
Maintainer: Tom Wenseleers <tom.wenseleers@kuleuven.be>
Diff between export versions 0.3.1 dated 2025-07-28 and 0.3.2 dated 2025-08-18
DESCRIPTION | 6 ++-- MD5 | 4 +- R/graph2office.R | 75 +++++++++++++++++++++++++------------------------------ 3 files changed, 40 insertions(+), 45 deletions(-)
Title: Easy Interface to the Statistical Disclosure Control Package
'sdcTable' Extended with Own Implementation of
'GaussSuppression'
Description: The main function, ProtectTable(), performs table suppression according to a
frequency rule with a data set as the only required input. Within this function,
protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called.
Lists of level-hierarchy (parameter 'dimList') and other required input to these functions
are created automatically.
The suppression method Gauss (default) is implemented independently of 'sdcTable'.
The function, PTgui(), starts a graphical user interface based on the 'shiny' package.
Author: Oeyvind Langsrud [aut, cre]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between easySdcTable versions 1.1.1 dated 2025-03-17 and 1.1.2 dated 2025-08-18
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- NEWS.md | 4 ++ build/vignette.rds |binary inst/doc/easySdcTableVignette.R | 4 +- inst/doc/easySdcTableVignette.Rmd | 8 ++-- inst/doc/easySdcTableVignette.html | 66 +++++++++++++++++-------------------- inst/doc/singletonsAndZeros.html | 54 +++++++++++++++--------------- vignettes/easySdcTableVignette.Rmd | 8 ++-- 9 files changed, 85 insertions(+), 83 deletions(-)
Title: Add Logging to Functions
Description: Decorate functions to make them return enhanced output. The
enhanced output consists in an object of type 'chronicle' containing
the result of the function applied to its arguments, as well as a log
detailing when the function was run, what were its inputs, what were
the errors (if the function failed to run) and other useful
information. Tools to handle decorated functions are included, such as
a forward pipe operator that makes chaining decorated functions
possible.
Author: Bruno Rodrigues [aut, cre, cph] ,
Matous Eibich [ctb]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between chronicler versions 0.2.2 dated 2024-03-20 and 0.3.0 dated 2025-08-18
chronicler-0.2.2/chronicler/R/chronicle.R |only chronicler-0.2.2/chronicler/R/data.R |only chronicler-0.2.2/chronicler/inst/doc/advanced-topics.R |only chronicler-0.2.2/chronicler/inst/doc/advanced-topics.Rmd |only chronicler-0.2.2/chronicler/inst/doc/advanced-topics.html |only chronicler-0.2.2/chronicler/inst/doc/maybe-monad.R |only chronicler-0.2.2/chronicler/inst/doc/maybe-monad.Rmd |only chronicler-0.2.2/chronicler/inst/doc/maybe-monad.html |only chronicler-0.2.2/chronicler/inst/doc/real-world-example.R |only chronicler-0.2.2/chronicler/inst/doc/real-world-example.Rmd |only chronicler-0.2.2/chronicler/inst/doc/real-world-example.html |only chronicler-0.2.2/chronicler/man/make_log_df.Rd |only chronicler-0.2.2/chronicler/man/pick.Rd |only chronicler-0.2.2/chronicler/tests/testthat/test-run_time.R |only chronicler-0.2.2/chronicler/tests/testthat/test-test_chronicler.R |only chronicler-0.2.2/chronicler/tests/testthat/test-test_purely.R |only chronicler-0.2.2/chronicler/vignettes/advanced-topics.Rmd |only chronicler-0.2.2/chronicler/vignettes/maybe-monad.Rmd |only chronicler-0.2.2/chronicler/vignettes/real-world-example.Rmd |only chronicler-0.3.0/chronicler/DESCRIPTION | 44 +- chronicler-0.3.0/chronicler/MD5 | 99 +++-- chronicler-0.3.0/chronicler/NAMESPACE | 23 + chronicler-0.3.0/chronicler/NEWS.md | 16 chronicler-0.3.0/chronicler/R/as_data_fr.R |only chronicler-0.3.0/chronicler/R/bind_record.R |only chronicler-0.3.0/chronicler/R/ggplot_fun.R |only chronicler-0.3.0/chronicler/R/included-datasets.R |only chronicler-0.3.0/chronicler/R/pipe.R |only chronicler-0.3.0/chronicler/R/purely.R |only chronicler-0.3.0/chronicler/R/record.R |only chronicler-0.3.0/chronicler/R/write_chronicle.R |only chronicler-0.3.0/chronicler/R/zap_log.R |only chronicler-0.3.0/chronicler/R/zzz.R | 5 chronicler-0.3.0/chronicler/README.md | 173 ++++++---- chronicler-0.3.0/chronicler/build/vignette.rds |binary chronicler-0.3.0/chronicler/data/avia.rda |binary chronicler-0.3.0/chronicler/inst/doc/a-non-mathematician-s-introduction-to-monads.R |only chronicler-0.3.0/chronicler/inst/doc/a-non-mathematician-s-introduction-to-monads.Rmd |only chronicler-0.3.0/chronicler/inst/doc/a-non-mathematician-s-introduction-to-monads.html |only chronicler-0.3.0/chronicler/inst/doc/a-real-world-example.R |only chronicler-0.3.0/chronicler/inst/doc/a-real-world-example.Rmd |only chronicler-0.3.0/chronicler/inst/doc/a-real-world-example.html |only chronicler-0.3.0/chronicler/inst/doc/recording-ggplot.R |only chronicler-0.3.0/chronicler/inst/doc/recording-ggplot.Rmd |only chronicler-0.3.0/chronicler/inst/doc/recording-ggplot.html |only chronicler-0.3.0/chronicler/inst/doc/the-maybe-monad.R |only chronicler-0.3.0/chronicler/inst/doc/the-maybe-monad.Rmd |only chronicler-0.3.0/chronicler/inst/doc/the-maybe-monad.html |only chronicler-0.3.0/chronicler/man/as.data.frame.chronicle.Rd |only chronicler-0.3.0/chronicler/man/as_chronicle.Rd | 2 chronicler-0.3.0/chronicler/man/avia.Rd | 9 chronicler-0.3.0/chronicler/man/bind_record.Rd | 2 chronicler-0.3.0/chronicler/man/check_diff.Rd | 6 chronicler-0.3.0/chronicler/man/check_g.Rd | 6 chronicler-0.3.0/chronicler/man/figures/README-unnamed-chunk-27-1.png |only chronicler-0.3.0/chronicler/man/flatten_record.Rd | 4 chronicler-0.3.0/chronicler/man/fmap_record.Rd | 6 chronicler-0.3.0/chronicler/man/grapes-greater-than-equals-grapes.Rd | 2 chronicler-0.3.0/chronicler/man/is_chronicle.Rd | 2 chronicler-0.3.0/chronicler/man/print.chronicle.Rd | 18 - chronicler-0.3.0/chronicler/man/purely.Rd | 10 chronicler-0.3.0/chronicler/man/read_log.Rd | 45 ++ chronicler-0.3.0/chronicler/man/record.Rd | 25 - chronicler-0.3.0/chronicler/man/record_ggplot.Rd |only chronicler-0.3.0/chronicler/man/record_many.Rd | 8 chronicler-0.3.0/chronicler/man/unveil.Rd |only chronicler-0.3.0/chronicler/man/write_chronicle_df.Rd |only chronicler-0.3.0/chronicler/man/zap_log.Rd |only chronicler-0.3.0/chronicler/tests/testthat.R | 8 chronicler-0.3.0/chronicler/tests/testthat/test-ggplot_fun.R |only chronicler-0.3.0/chronicler/tests/testthat/test-pipe.R |only chronicler-0.3.0/chronicler/tests/testthat/test-purely.R |only chronicler-0.3.0/chronicler/tests/testthat/test-record.R |only chronicler-0.3.0/chronicler/tests/testthat/test-write_chronicle_df.R |only chronicler-0.3.0/chronicler/vignettes/a-non-mathematician-s-introduction-to-monads.Rmd |only chronicler-0.3.0/chronicler/vignettes/a-real-world-example.Rmd |only chronicler-0.3.0/chronicler/vignettes/recording-ggplot.Rmd |only chronicler-0.3.0/chronicler/vignettes/the-maybe-monad.Rmd |only 78 files changed, 326 insertions(+), 187 deletions(-)
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and
Generalized Linear Models
Description: The c060 package provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models.
Author: Martin Sill [aut],
Thomas Hielscher [aut],
Manuela Zucknick [aut],
Natalia Becker. [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between c060 versions 0.3-0 dated 2023-03-23 and 0.3-1 dated 2025-08-18
DESCRIPTION | 33 ++++++++++++++++++++++++++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ README.md | 4 ++-- build/partial.rdb |binary man/balancedFolds.Rd | 2 +- man/coef.intsearch.Rd | 2 +- man/plot.summary.int.Rd | 4 ++-- man/stabpath.Rd | 2 +- man/summary.intsearch.Rd | 2 +- 10 files changed, 49 insertions(+), 22 deletions(-)
Title: Distributional Semantic Models in R
Description: An interactive laboratory for research on distributional semantic models ('DSM',
see <https://en.wikipedia.org/wiki/Distributional_semantics> for more information).
Author: Stephanie Evert [cre, aut]
Maintainer: Stephanie Evert <stephanie.evert@fau.de>
Diff between wordspace versions 0.2-8 dated 2022-08-22 and 0.2-9 dated 2025-08-18
DESCRIPTION | 13 MD5 | 58 +- NEWS | 4 build/vignette.rds |binary data/DSM_GoodsMatrix.rda |binary data/DSM_HieroglyphsMatrix.rda |binary data/DSM_SingularValues.rda |binary data/DSM_TermContext.rda |binary data/DSM_TermContextMatrix.rda |binary data/DSM_TermTerm.rda |binary data/DSM_TermTermMatrix.rda |binary data/DSM_Vectors.rda |binary data/DSM_VerbNounTriples_BNC.rda |binary data/ESSLLI08_Nouns.rda |binary data/RG65.rda |binary data/SemCorWSD.rda |binary data/WordSim353.rda |binary inst/doc/wordspace-intro.R | 14 inst/doc/wordspace-intro.Rmd | 4 inst/doc/wordspace-intro.html | 989 +++++++++++---------------------------- man/DSM_TermContextMatrix.Rd | 2 man/WordSim353.Rd | 2 man/as_distmat.Rd | 2 man/dsm.Rd | 4 man/dsm_canonical_matrix.Rd | 8 man/dsm_projection.Rd | 2 man/rsvd.Rd | 2 man/signcount.Rd | 4 man/wordspace-package.Rd | 16 vignettes/wordspace-intro.Rmd | 4 30 files changed, 369 insertions(+), 759 deletions(-)
Title: Algorithms and Tools for Tabular Statistics and Hierarchical
Computations
Description: Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.8.0 dated 2025-06-19 and 1.8.1 dated 2025-08-18
DESCRIPTION | 8 ++--- MD5 | 15 +++++---- NAMESPACE | 1 NEWS.md | 15 +++++++++ R/DummyDuplicated.R | 45 +++++++++++++++++++++++++++- R/GaussSuppression.R | 31 ++++++++++++------- R/RowGroups.R | 70 +++++++++++++++++++++++++++++++++++++++++++-- man/GaussSuppression.Rd | 5 +++ man/any_duplicated_rows.Rd |only 9 files changed, 164 insertions(+), 26 deletions(-)
Title: Sparse Truncated Singular Value Decomposition (from 'SVDLIBC')
Description: Wrapper around the 'SVDLIBC' library for (truncated) singular value decomposition of a sparse matrix.
Currently, only sparse real matrices in Matrix package format are supported.
Author: Doug Rohde [aut],
Michael Berry [aut],
Theresa Do [aut],
Gavin O'Brien [aut],
Vijay Krishna [aut],
Sowmini Varadhan [aut],
University of Tennessee Research Foundation [cph] ,
Stephanie Evert [cre, aut, cph]
Maintainer: Stephanie Evert <stephanie.evert@fau.de>
Diff between sparsesvd versions 0.2-2 dated 2023-01-14 and 0.2-3 dated 2025-08-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ man/sparsesvd.Rd | 4 ++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Meta-CART: A Flexible Approach to Identify Moderators in
Meta-Analysis
Description: Meta-CART integrates classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The method is described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.
Author: Xinru Li [aut],
Elise Dusseldorp [aut, cph],
Kaihua Liu [ctb] ,
Juan Claramunt [aut, cre],
Jacqueline Meulman [ctb]
Maintainer: Juan Claramunt <j.claramunt.gonzalez@fsw.leidenuniv.nl>
Diff between metacart versions 3.0.0 dated 2025-04-17 and 3.0.4 dated 2025-08-18
DESCRIPTION | 6 MD5 | 20 - NAMESPACE | 1 R/PlottingPV.R |only R/REmrt_SSS.R | 585 +++++++++++++++++++++++---------------------- R/REmrt_main.R | 78 +++--- R/plotSupport.R | 363 +++++++++++++++++++++------ R/re_cross_valid_Support.R | 12 man/REmrt.Rd | 17 - man/computetable.Rd |only man/computetableIT.Rd |only man/oval_draw.Rd | 4 man/plotPV.Rd |only 13 files changed, 660 insertions(+), 426 deletions(-)
Title: Create Simple Predictive Models on Bayesian Belief Networks
Description: A system to build, visualise and evaluate Bayesian belief networks. The methods are described in Stafford et al. (2015) <doi:10.12688/f1000research.5981.1>.
Author: Victoria Dominguez Almela [cre, aut] ,
Richard Stafford [cph, aut]
Maintainer: Victoria Dominguez Almela <vda1r22@soton.ac.uk>
Diff between bbnet versions 1.2.0 dated 2025-07-31 and 1.2.1 dated 2025-08-18
DESCRIPTION | 6 - MD5 | 18 ++-- NEWS.md | 7 + R/bbn.predict.R | 4 R/bbn.sensitivity.R | 4 README.md | 123 +++++++++++++++--------------- inst/doc/bbnet.html | 121 ++++++++++++++--------------- man/figures/README-unnamed-chunk-11-3.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary 10 files changed, 145 insertions(+), 138 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-02 3.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-22 1.1.8