Title: R Templates from the University of Miami
Description: This holds some r markdown and quarto templates and a template to
create a research project in "R Studio".
Author: Raymond Balise [aut, cre] ,
Gabriel Odom [aut] ,
Kyle Grealis [aut] ,
Francisco Cardozo [aut] ,
Frank Gutierrez [ctb]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between rUM versions 2.0.0 dated 2024-06-02 and 2.1.0 dated 2025-03-21
rUM-2.0.0/rUM/inst/doc/O1_make_research_project.R |only rUM-2.0.0/rUM/inst/doc/O1_make_research_project.Rmd |only rUM-2.0.0/rUM/inst/doc/O1_make_research_project.html |only rUM-2.0.0/rUM/inst/doc/O2_make_research_project_markdown.R |only rUM-2.0.0/rUM/inst/doc/O2_make_research_project_markdown.Rmd |only rUM-2.0.0/rUM/inst/doc/O2_make_research_project_markdown.html |only rUM-2.0.0/rUM/inst/doc/O3_R_Markdown_Templates.R |only rUM-2.0.0/rUM/inst/doc/O3_R_Markdown_Templates.Rmd |only rUM-2.0.0/rUM/inst/doc/O3_R_Markdown_Templates.html |only rUM-2.0.0/rUM/inst/doc/O4_make_a_package.R |only rUM-2.0.0/rUM/inst/doc/O4_make_a_package.Rmd |only rUM-2.0.0/rUM/inst/doc/O4_make_a_package.html |only rUM-2.0.0/rUM/inst/doc/O5_show_example.R |only rUM-2.0.0/rUM/inst/doc/O5_show_example.Rmd |only rUM-2.0.0/rUM/inst/doc/O5_show_example.html |only rUM-2.0.0/rUM/inst/gists/analysis_1_0_2_9001.Rmd |only rUM-2.0.0/rUM/inst/gists/analysis_1_0_2_9001.qmd |only rUM-2.0.0/rUM/inst/gists/analysis_wo_example_1_0_2_9001.Rmd |only rUM-2.0.0/rUM/inst/gists/analysis_wo_example_1_0_2_9001.qmd |only rUM-2.0.0/rUM/inst/gists/quarto_gist.qmd |only rUM-2.0.0/rUM/inst/gists/rmarkdown_gist.Rmd |only rUM-2.0.0/rUM/vignettes/O1_make_research_project.Rmd |only rUM-2.0.0/rUM/vignettes/O2_make_research_project_markdown.Rmd |only rUM-2.0.0/rUM/vignettes/O3_R_Markdown_Templates.Rmd |only rUM-2.0.0/rUM/vignettes/O4_make_a_package.Rmd |only rUM-2.0.0/rUM/vignettes/O5_show_example.Rmd |only rUM-2.1.0/rUM/DESCRIPTION | 20 rUM-2.1.0/rUM/MD5 | 93 +- rUM-2.1.0/rUM/NAMESPACE | 14 rUM-2.1.0/rUM/NEWS.md | 27 rUM-2.1.0/rUM/R/make_project.R | 393 ++++++---- rUM-2.1.0/rUM/R/rUM-package.R | 14 rUM-2.1.0/rUM/R/write_notes.R |only rUM-2.1.0/rUM/R/write_quarto.R |only rUM-2.1.0/rUM/R/write_readme.R |only rUM-2.1.0/rUM/R/write_scss.R |only rUM-2.1.0/rUM/README.md | 17 rUM-2.1.0/rUM/build/vignette.rds |binary rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.R |only rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.Rmd |only rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.html |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.R |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.Rmd |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.html |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.R |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.Rmd |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.html |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.R |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.Rmd |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.html |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.R |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.Rmd |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.html |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.R |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.Rmd |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.html |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.R |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.Rmd |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.html |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.R |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.Rmd |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.html |only rUM-2.1.0/rUM/inst/gists/README.md |only rUM-2.1.0/rUM/inst/gists/aggressive_gitignore.md |only rUM-2.1.0/rUM/inst/gists/analysis_qmd_with_example.qmd |only rUM-2.1.0/rUM/inst/gists/analysis_qmd_wo_example.qmd |only rUM-2.1.0/rUM/inst/gists/analysis_rmd_with_example.Rmd |only rUM-2.1.0/rUM/inst/gists/analysis_rmd_wo_example.Rmd |only rUM-2.1.0/rUM/inst/gists/default_quarto.qmd |only rUM-2.1.0/rUM/inst/gists/packages.bib | 97 -- rUM-2.1.0/rUM/man/make_project.Rd | 8 rUM-2.1.0/rUM/man/rUM-package.Rd | 2 rUM-2.1.0/rUM/man/write_notes.Rd |only rUM-2.1.0/rUM/man/write_quarto.Rd |only rUM-2.1.0/rUM/man/write_readme.Rd |only rUM-2.1.0/rUM/man/write_scss.Rd |only rUM-2.1.0/rUM/vignettes/OO1_using_posit_cloud.Rmd |only rUM-2.1.0/rUM/vignettes/OO2_make_research_project.Rmd |only rUM-2.1.0/rUM/vignettes/OO3_make_research_project_markdown.Rmd |only rUM-2.1.0/rUM/vignettes/OO4_R_Markdown_Templates.Rmd |only rUM-2.1.0/rUM/vignettes/OO5_make_a_package.Rmd |only rUM-2.1.0/rUM/vignettes/OO6_show_example.Rmd |only rUM-2.1.0/rUM/vignettes/OO7_write_scss.Rmd |only rUM-2.1.0/rUM/vignettes/OO8_write_readme.Rmd |only 84 files changed, 442 insertions(+), 243 deletions(-)
Title: Linear Quantile Mixture Models
Description: Estimate linear quantile mixtures based on Time-Constant (TC) and/or Time-Varying (TV), discrete, random coefficients.
Author: Maria Francesca Marino [aut, cre],
Marco Alfo' [aut],
Nicola Salvati [aut],
Maria Giovanna Ranalli [aut]
Maintainer: Maria Francesca Marino <mariafrancesca.marino@unifi.it>
Diff between lqmix versions 1.0 dated 2023-12-07 and 1.1 dated 2025-03-21
DESCRIPTION | 16 MD5 | 70 ++- NAMESPACE | 12 NEWS | 11 R/coef.seach_lqmix.R | 2 R/lqmix.R | 337 +++++++++--------- R/lqmixTC.R | 71 ++- R/lqmixTC.fit.R | 40 +- R/lqmixTCTV.fit_intermittent.R | 43 +- R/lqmixTCTV_intermittent.R | 117 +++--- R/lqmixTV.fit_intermittent.R | 34 + R/lqmixTV_intermittent.R | 125 ++++-- R/lqr.R | 85 ++-- R/lqr.fit.R | 11 R/pain.R | 62 +-- R/plot.lqmix.R | 139 +++---- R/plot.search_lqmix.R | 284 +++++++-------- R/postComputeTCTV_intermittent.R | 4 R/print.lqmix.R | 4 R/print.search_lqmix.R | 7 R/print.summary.lqmix.R | 5 R/print.summary.lqr.R | 3 R/print.summary.search_lqmix.R |only R/search_lqmix.R | 692 +++++++++++++++++++------------------- R/summary.lqmix.R | 388 ++++++++++----------- R/summary.search_lqmix.R |only build/partial.rdb |binary man/coef.search_lqmix.Rd | 2 man/dal.Rd | 3 man/lqmix.Rd | 18 man/lqr.Rd | 5 man/pain.Rd | 2 man/print.summary.lqmix.Rd | 2 man/print.summary.lqr.Rd | 2 man/print.summary.search_lqmix.Rd |only man/search_lqmix.Rd | 5 man/summary.lqmix.Rd | 2 man/summary.search_lqmix.Rd |only 38 files changed, 1371 insertions(+), 1232 deletions(-)
Title: Worldwide or Coordinates-Based Heat Maps
Description: Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.
Author: Luigi Annicchiarico [cre, aut]
Maintainer: Luigi Annicchiarico <luigi.annic@gmail.com>
Diff between WorldMapR versions 1.1.0 dated 2025-01-28 and 1.2.0 dated 2025-03-21
WorldMapR-1.1.0/WorldMapR/tests/testthat/test2.R |only WorldMapR-1.1.0/WorldMapR/tests/testthat/test3.R |only WorldMapR-1.1.0/WorldMapR/tests/testthat/test4.R |only WorldMapR-1.1.0/WorldMapR/tests/testthat/test5.R |only WorldMapR-1.1.0/WorldMapR/tests/testthat/test6.R |only WorldMapR-1.1.0/WorldMapR/tests/testthat/testCat1.R |only WorldMapR-1.2.0/WorldMapR/DESCRIPTION | 16 - WorldMapR-1.2.0/WorldMapR/MD5 | 59 ++-- WorldMapR-1.2.0/WorldMapR/NAMESPACE | 83 ++---- WorldMapR-1.2.0/WorldMapR/NEWS.md | 10 WorldMapR-1.2.0/WorldMapR/R/WorldMapR-package.R | 1 WorldMapR-1.2.0/WorldMapR/R/countrycoord_data.R | 72 +++-- WorldMapR-1.2.0/WorldMapR/R/geometries_data.R | 10 WorldMapR-1.2.0/WorldMapR/R/globals.R | 3 WorldMapR-1.2.0/WorldMapR/R/map_df0.R |only WorldMapR-1.2.0/WorldMapR/R/worldplot.R | 41 +- WorldMapR-1.2.0/WorldMapR/R/worldplotCat.R | 30 -- WorldMapR-1.2.0/WorldMapR/build/vignette.rds |binary WorldMapR-1.2.0/WorldMapR/data/map_df0.RData |only WorldMapR-1.2.0/WorldMapR/inst/doc/WorldMapR_Vignette.R | 53 +-- WorldMapR-1.2.0/WorldMapR/inst/doc/WorldMapR_Vignette.Rmd | 11 WorldMapR-1.2.0/WorldMapR/inst/doc/WorldMapR_Vignette.html | 49 +-- WorldMapR-1.2.0/WorldMapR/man/WorldMapR-package.Rd | 46 +-- WorldMapR-1.2.0/WorldMapR/man/countrycoord_data.Rd | 76 ++--- WorldMapR-1.2.0/WorldMapR/man/geometries_data.Rd | 48 +-- WorldMapR-1.2.0/WorldMapR/man/map_df0.Rd |only WorldMapR-1.2.0/WorldMapR/man/testdata1.Rd | 40 +- WorldMapR-1.2.0/WorldMapR/man/testdata1b.Rd | 40 +- WorldMapR-1.2.0/WorldMapR/man/testdata1c.Rd | 42 +-- WorldMapR-1.2.0/WorldMapR/man/worldplot.Rd | 174 ++++++------ WorldMapR-1.2.0/WorldMapR/man/worldplotCat.Rd | 178 ++++++------- WorldMapR-1.2.0/WorldMapR/tests/testthat.R | 24 - WorldMapR-1.2.0/WorldMapR/tests/testthat/test1.R | 15 - WorldMapR-1.2.0/WorldMapR/tests/testthat/testCat2.R | 8 WorldMapR-1.2.0/WorldMapR/vignettes/WorldMapR_Vignette.Rmd | 11 35 files changed, 579 insertions(+), 561 deletions(-)
Title: Sparse Vectors for Use in Data Frames
Description: Provides sparse vectors powered by ALTREP (Alternative
Representations for R Objects) that behave like regular vectors, and
can thus be used in data frames. Also provides tools to convert
between sparse matrices and data frames with sparse columns and
functions to interact with sparse vectors.
Author: Emil Hvitfeldt [aut, cre] ,
Davis Vaughan [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between sparsevctrs versions 0.3.1 dated 2025-03-17 and 0.3.2 dated 2025-03-21
DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS.md | 6 +++ R/sparsity.R | 2 - src/sparse-arithmatic.c | 81 ++++++++++++++++++++++------------------- src/sparse-utils.c | 9 ++-- tests/testthat/test-sparsity.R | 73 ++++++++++++++++++++++++++++++++++++ 7 files changed, 139 insertions(+), 50 deletions(-)
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
Author: Richard Hanna [aut, cre] ,
Stephan Kadauke [aut] ,
Ezra Porter [aut]
Maintainer: Richard Hanna <hannar1@chop.edu>
Diff between REDCapTidieR versions 1.2.1 dated 2024-12-09 and 1.2.2 dated 2025-03-21
DESCRIPTION | 10 ++--- MD5 | 41 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 5 ++ R/REDCapTidieR-package.R | 1 R/combine_checkboxes.R | 9 ++--- R/labelled.R | 7 ++-- R/read_redcap.R | 64 ++++++++++++++++++++++++++++++++++++ R/write.R | 24 ++++++------- build/vignette.rds |binary man/REDCapTidieR-package.Rd | 2 - man/add_labelled_xlsx_features.Rd | 4 +- man/add_metadata_sheet.Rd | 4 +- man/add_supertbl_toc.Rd | 4 +- man/bind_supertbl_metadata.Rd | 2 - man/check_labelled.Rd | 2 - man/combine_checkboxes.Rd | 5 +- man/supertbl_recode.Rd | 2 - man/update_dag_cols.Rd |only man/write_redcap_xlsx.Rd | 2 - tests/testthat/_snaps/write.md | 26 +++++++------- tests/testthat/test-read_redcap.R | 66 ++++++++++++++++++++++++++++++++++++-- 22 files changed, 209 insertions(+), 72 deletions(-)
Title: Download and Extract Data from US EPA's ECOTOX Database
Description: The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ECOTOXr versions 1.1.1 dated 2024-09-20 and 1.2.0 dated 2025-03-21
ECOTOXr-1.1.1/ECOTOXr/tests/testthat/test_that.r |only ECOTOXr-1.2.0/ECOTOXr/DESCRIPTION | 15 ECOTOXr-1.2.0/ECOTOXr/MD5 | 99 + ECOTOXr-1.2.0/ECOTOXr/NAMESPACE | 7 ECOTOXr-1.2.0/ECOTOXr/NEWS.md | 203 +-- ECOTOXr-1.2.0/ECOTOXr/R/ECOTOXr-package.r | 6 ECOTOXr-1.2.0/ECOTOXr/R/cas_handlers.r | 576 ++++---- ECOTOXr-1.2.0/ECOTOXr/R/database_access.r | 641 +++++---- ECOTOXr-1.2.0/ECOTOXr/R/helpers.r | 783 ++++++------ ECOTOXr-1.2.0/ECOTOXr/R/imports.r | 30 ECOTOXr-1.2.0/ECOTOXr/R/init.r | 978 +++++++-------- ECOTOXr-1.2.0/ECOTOXr/R/online.r | 546 ++++---- ECOTOXr-1.2.0/ECOTOXr/R/process_date.r |only ECOTOXr-1.2.0/ECOTOXr/R/process_numeric.r |only ECOTOXr-1.2.0/ECOTOXr/R/process_unit.r |only ECOTOXr-1.2.0/ECOTOXr/R/sysdata.rda |binary ECOTOXr-1.2.0/ECOTOXr/R/wrappers.r | 325 ++-- ECOTOXr-1.2.0/ECOTOXr/README.md | 140 -- ECOTOXr-1.2.0/ECOTOXr/build/vignette.rds |only ECOTOXr-1.2.0/ECOTOXr/inst/doc |only ECOTOXr-1.2.0/ECOTOXr/inst/ecotox-test.zip |only ECOTOXr-1.2.0/ECOTOXr/inst/openssl.cnf |only ECOTOXr-1.2.0/ECOTOXr/man/ECOTOXr-package.Rd | 6 ECOTOXr-1.2.0/ECOTOXr/man/as_date_ecotox.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/as_numeric_ecotox.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/as_unit_ecotox.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/build_ecotox_sqlite.Rd | 32 ECOTOXr-1.2.0/ECOTOXr/man/cas.Rd | 1 ECOTOXr-1.2.0/ECOTOXr/man/check_ecotox_availability.Rd | 11 ECOTOXr-1.2.0/ECOTOXr/man/check_ecotox_build.Rd | 22 ECOTOXr-1.2.0/ECOTOXr/man/check_ecotox_version.Rd | 28 ECOTOXr-1.2.0/ECOTOXr/man/cite_ecotox.Rd | 17 ECOTOXr-1.2.0/ECOTOXr/man/dbConnectEcotox.Rd | 23 ECOTOXr-1.2.0/ECOTOXr/man/download_ecotox_data.Rd | 17 ECOTOXr-1.2.0/ECOTOXr/man/figures/ecotox-schema.svg |only ECOTOXr-1.2.0/ECOTOXr/man/figures/ecotox-workflow.svg |only ECOTOXr-1.2.0/ECOTOXr/man/figures/graphical-abstract.png |only ECOTOXr-1.2.0/ECOTOXr/man/get_ecotox_info.Rd | 17 ECOTOXr-1.2.0/ECOTOXr/man/get_ecotox_url.Rd | 17 ECOTOXr-1.2.0/ECOTOXr/man/get_path.Rd | 17 ECOTOXr-1.2.0/ECOTOXr/man/list_ecotox_fields.Rd | 11 ECOTOXr-1.2.0/ECOTOXr/man/mixed_to_single_unit.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/process_ecotox_dates.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/process_ecotox_numerics.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/process_ecotox_units.Rd |only ECOTOXr-1.2.0/ECOTOXr/man/search_ecotox.Rd | 5 ECOTOXr-1.2.0/ECOTOXr/man/websearch.Rd | 35 ECOTOXr-1.2.0/ECOTOXr/man/websearch_comptox.Rd | 25 ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_build.r |only ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_cas.r | 130 + ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_exceptions.r |only ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_local.r |only ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_online.r | 256 ++- ECOTOXr-1.2.0/ECOTOXr/tests/testthat/test_sanitation.r |only ECOTOXr-1.2.0/ECOTOXr/vignettes |only 55 files changed, 2609 insertions(+), 2410 deletions(-)
Title: Headless Chrome Web Browser Interface
Description: An implementation of the 'Chrome DevTools Protocol', for
controlling a headless Chrome web browser.
Author: Garrick Aden-Buie [aut, cre] ,
Winston Chang [aut],
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between chromote versions 0.4.0 dated 2025-01-24 and 0.5.0 dated 2025-03-21
DESCRIPTION | 28 MD5 | 111 +- NAMESPACE | 9 NEWS.md | 29 R/browser.R | 30 R/chrome.R | 69 - R/chromote-package.R | 24 R/chromote.R | 78 + R/chromote_session.R | 237 ++++- R/event_manager.R | 56 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/manage.R |only R/protocol.R | 19 R/screenshot.R | 20 R/utils.R | 21 README.md | 1525 +-------------------------------- build |only inst |only man/Browser.Rd | 11 man/ChromeRemote.Rd | 28 man/Chromote.Rd | 37 man/ChromoteSession.Rd | 159 +++ man/chrome_versions.Rd |only man/chrome_versions_list.Rd |only man/chromote-package.Rd | 6 man/figures/lifecycle-experimental.svg |only man/figures/logo.png |only man/fragments |only man/with_chrome_version.Rd |only tests/testthat/_snaps |only tests/testthat/helper.R | 26 tests/testthat/setup.R |only tests/testthat/test-chrome.R |only tests/testthat/test-chromote_session.R | 196 ++++ tests/testthat/test-manage.R |only vignettes |only 37 files changed, 1123 insertions(+), 1596 deletions(-)
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2024)
<doi:10.48550/arXiv.2401.10193> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.0.0 dated 2025-03-13 and 1.0.1 dated 2025-03-21
tinyVAST-1.0.0/tinyVAST/inst/doc/simultaneous_autoregressive_process.R |only tinyVAST-1.0.0/tinyVAST/inst/doc/simultaneous_autoregressive_process.Rmd |only tinyVAST-1.0.0/tinyVAST/inst/doc/simultaneous_autoregressive_process.html |only tinyVAST-1.0.0/tinyVAST/vignettes/simultaneous_autoregressive_process.Rmd |only tinyVAST-1.0.1/tinyVAST/DESCRIPTION | 8 tinyVAST-1.0.1/tinyVAST/MD5 | 63 ++--- tinyVAST-1.0.1/tinyVAST/NEWS.md | 9 tinyVAST-1.0.1/tinyVAST/R/family.R | 4 tinyVAST-1.0.1/tinyVAST/R/fit.R | 22 + tinyVAST-1.0.1/tinyVAST/R/internal.R | 8 tinyVAST-1.0.1/tinyVAST/R/methods.R | 2 tinyVAST-1.0.1/tinyVAST/R/predict.R | 6 tinyVAST-1.0.1/tinyVAST/R/utility.R | 60 +++-- tinyVAST-1.0.1/tinyVAST/build/partial.rdb |binary tinyVAST-1.0.1/tinyVAST/build/vignette.rds |binary tinyVAST-1.0.1/tinyVAST/inst/doc/dsem.html | 2 tinyVAST-1.0.1/tinyVAST/inst/doc/mgcv.Rmd | 2 tinyVAST-1.0.1/tinyVAST/inst/doc/mgcv.html | 4 tinyVAST-1.0.1/tinyVAST/inst/doc/spatial.R | 24 +- tinyVAST-1.0.1/tinyVAST/inst/doc/spatial.Rmd | 26 +- tinyVAST-1.0.1/tinyVAST/inst/doc/spatial.html | 9 tinyVAST-1.0.1/tinyVAST/inst/doc/spatial_factor_analysis.html | 2 tinyVAST-1.0.1/tinyVAST/man/families.Rd | 4 tinyVAST-1.0.1/tinyVAST/man/logLik.tinyVAST.Rd | 42 +-- tinyVAST-1.0.1/tinyVAST/man/print.tinyVAST.Rd | 40 +-- tinyVAST-1.0.1/tinyVAST/man/sample_variable.Rd | 13 - tinyVAST-1.0.1/tinyVAST/man/simulate.tinyVAST.Rd | 116 +++++----- tinyVAST-1.0.1/tinyVAST/man/tinyVASTcontrol.Rd | 7 tinyVAST-1.0.1/tinyVAST/src/tinyVAST.cpp | 18 + tinyVAST-1.0.1/tinyVAST/tests/testthat.R | 1 tinyVAST-1.0.1/tinyVAST/tests/testthat/Rplots.pdf |only tinyVAST-1.0.1/tinyVAST/tests/testthat/test-basic-fits.R | 4 tinyVAST-1.0.1/tinyVAST/tests/testthat/test-index-standardization.R | 4 tinyVAST-1.0.1/tinyVAST/vignettes/mgcv.Rmd | 2 tinyVAST-1.0.1/tinyVAST/vignettes/spatial.Rmd | 26 +- 35 files changed, 289 insertions(+), 239 deletions(-)
Title: An 'Armadillo' Interface
Description: Provides function declarations and inline function definitions that
facilitate communication between R and the 'Armadillo' 'C++' library for
linear algebra and scientific computing. This implementation is detailed
in Vargas Sepulveda and Schneider Malamud (2024)
<doi:10.1016/j.softx.2025.102087>.
Author: Mauricio Vargas Sepulveda [aut, cre]
,
Jonathan Schneider Malamud [ctb],
Conrad Sanderson [aut] )
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between cpp11armadillo versions 0.4.4 dated 2025-02-20 and 0.4.6 dated 2025-03-21
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NEWS.md | 8 +++++++ README.md | 11 +++++----- build/partial.rdb |binary build/vignette.rds |binary configure | 2 - inst/include/wrappers/matrices.hpp | 39 ++++++++++++++++++++++++++++++++----- inst/include/wrappers/vectors.hpp | 2 - 9 files changed, 61 insertions(+), 25 deletions(-)
More information about cpp11armadillo at CRAN
Permanent link
Title: Invariance Partial Pruning Test
Description: An implementation of the Invariance Partial Pruning (IVPP) approach
described in Du, X., Johnson, S. U., Epskamp, S. (2025) The Invariance Partial
Pruning Approach to The Network Comparison in Longitudinal Data. IVPP is a
two-step method that first test for global network structural difference with
invariance test and then inspect specific edge difference with partial pruning.
Author: Xinkai Du [aut, cre, cph]
Maintainer: Xinkai Du <xinkai.du.xd@gmail.com>
Diff between IVPP versions 1.0.0 dated 2025-02-11 and 1.1.0 dated 2025-03-21
IVPP-1.0.0/IVPP/LICENSE |only IVPP-1.1.0/IVPP/DESCRIPTION | 17 IVPP-1.1.0/IVPP/MD5 | 27 - IVPP-1.1.0/IVPP/NEWS.md | 13 IVPP-1.1.0/IVPP/R/IVPP.R | 819 +++++++++++++++++++--------------- IVPP-1.1.0/IVPP/R/dt_gen.R | 6 IVPP-1.1.0/IVPP/R/mod_gen.R | 43 - IVPP-1.1.0/IVPP/README.md | 122 +++-- IVPP-1.1.0/IVPP/man/IVPP-package.Rd | 2 IVPP-1.1.0/IVPP/man/IVPP_panelgvar.Rd | 73 ++- IVPP-1.1.0/IVPP/man/IVPP_tsgvar.Rd | 48 + IVPP-1.1.0/IVPP/man/gen_panelGVAR.Rd | 16 IVPP-1.1.0/IVPP/man/gen_tsGVAR.Rd | 11 IVPP-1.1.0/IVPP/man/sim_panelGVAR.Rd | 3 IVPP-1.1.0/IVPP/man/sim_tsGVAR.Rd | 3 15 files changed, 750 insertions(+), 453 deletions(-)
Title: The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Description: Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Author: Fumio Ishioka [aut, cre]
Maintainer: Fumio Ishioka <fishioka@okayama-u.ac.jp>
Diff between echelon versions 0.3.0 dated 2025-03-03 and 0.3.1 dated 2025-03-20
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/e.echebin.r | 7 ++++--- R/e.echepoi.r | 7 ++++--- R/e_main.monte.r | 8 ++++---- src/e_monteCPP.cpp | 6 ++++++ 7 files changed, 31 insertions(+), 19 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. It is able to detect change points a magnitude faster than
the vanilla Pruned Exact Linear Time(PELT). The package includes
examples of linear regression, logistic regression, Poisson
regression, penalized linear regression data, and whole lot more
examples with custom cost function in case the user wants to use their
own cost function.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li.stat.tamu.edu@lixingchi.com>
Diff between fastcpd versions 0.16.0 dated 2025-03-13 and 0.16.1 dated 2025-03-20
fastcpd-0.16.0/fastcpd/inst/doc/examples-advanced.R |only fastcpd-0.16.0/fastcpd/inst/doc/examples-custom-model.R |only fastcpd-0.16.0/fastcpd/inst/doc/exploration-during-development.R |only fastcpd-0.16.0/fastcpd/man/figures/README-time-comparison-1.png |only fastcpd-0.16.0/fastcpd/tests/testthat/examples/fastcpd_mean.R |only fastcpd-0.16.0/fastcpd/tests/testthat/examples/fastcpd_meanvariance.R |only fastcpd-0.16.0/fastcpd/tests/testthat/examples/fastcpd_variance.R |only fastcpd-0.16.0/fastcpd/tests/testthat/test-examples-fastcpd_mean.R |only fastcpd-0.16.0/fastcpd/tests/testthat/test-examples-fastcpd_meanvariance.R |only fastcpd-0.16.0/fastcpd/tests/testthat/test-examples-fastcpd_variance.R |only fastcpd-0.16.1/fastcpd/DESCRIPTION | 6 fastcpd-0.16.1/fastcpd/MD5 | 98 fastcpd-0.16.1/fastcpd/NEWS.md | 4 fastcpd-0.16.1/fastcpd/R/RcppExports.R | 4 fastcpd-0.16.1/fastcpd/R/fastcpd.R | 152 + fastcpd-0.16.1/fastcpd/R/utilities.R | 119 - fastcpd-0.16.1/fastcpd/README.md | 289 +- fastcpd-0.16.1/fastcpd/build/vignette.rds |binary fastcpd-0.16.1/fastcpd/inst/doc/examples-advanced.Rmd | 533 ++--- fastcpd-0.16.1/fastcpd/inst/doc/examples-advanced.html | 785 ++----- fastcpd-0.16.1/fastcpd/inst/doc/examples-custom-model.Rmd | 120 - fastcpd-0.16.1/fastcpd/inst/doc/examples-custom-model.html | 192 - fastcpd-0.16.1/fastcpd/inst/doc/exploration-during-development.Rmd | 493 ++++ fastcpd-0.16.1/fastcpd/inst/doc/exploration-during-development.html | 1003 +++++----- fastcpd-0.16.1/fastcpd/inst/doc/time-complexity.Rmd | 80 fastcpd-0.16.1/fastcpd/inst/doc/time-complexity.html | 270 +- fastcpd-0.16.1/fastcpd/inst/include/fastcpd.h | 41 fastcpd-0.16.1/fastcpd/inst/include/fastcpd_impl.h | 3 fastcpd-0.16.1/fastcpd/man/fastcpd_mean.Rd | 32 fastcpd-0.16.1/fastcpd/man/fastcpd_meanvariance.Rd | 12 fastcpd-0.16.1/fastcpd/man/fastcpd_variance.Rd | 5 fastcpd-0.16.1/fastcpd/man/figures/README-time-comparison-large-1.png |only fastcpd-0.16.1/fastcpd/man/figures/README-time-comparison-small-1.png |only fastcpd-0.16.1/fastcpd/src/RcppExports.cpp | 11 fastcpd-0.16.1/fastcpd/src/fastcpd_classes.cc | 135 - fastcpd-0.16.1/fastcpd/src/fastcpd_impl.cc | 65 fastcpd-0.16.1/fastcpd/src/fastcpd_test.cc | 50 fastcpd-0.16.1/fastcpd/src/test-fastcpd.cc | 86 fastcpd-0.16.1/fastcpd/tests/testthat.R | 4 fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_mean_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_mean_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_meanvariance_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_meanvariance_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_variance_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/examples/fastcpd_variance_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-check.R | 9 fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_3.R | 2 fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_arma.R | 2 fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_mean_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_mean_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_meanvariance_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_meanvariance_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_variance_1.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-examples-fastcpd_variance_2.R |only fastcpd-0.16.1/fastcpd/tests/testthat/test-vignettes-comparison-pelt-lasso.R | 1 fastcpd-0.16.1/fastcpd/tests/testthat/test-vignettes-comparison-pelt-logistic-regression.R | 3 fastcpd-0.16.1/fastcpd/tests/testthat/test-vignettes-comparison-pelt-poisson-regression.R | 3 fastcpd-0.16.1/fastcpd/vignettes/examples-advanced.Rmd | 533 ++--- fastcpd-0.16.1/fastcpd/vignettes/examples-custom-model.Rmd | 120 - fastcpd-0.16.1/fastcpd/vignettes/exploration-during-development.Rmd | 493 ++++ fastcpd-0.16.1/fastcpd/vignettes/time-complexity.Rmd | 80 fastcpd-0.16.1/fastcpd/vignettes/time-complexity/time-complexity-1.png |binary 62 files changed, 3301 insertions(+), 2537 deletions(-)
Title: Create a Data Dictionary
Description: Creates a data dictionary from any dataframe or tibble in your R environment.
You can opt to add variable labels. You can write the object directly to Excel.
Author: Bethany Jones [aut, cre]
Maintainer: Bethany Jones <r.data.nerd@gmail.com>
Diff between datadictionary versions 1.0.0 dated 2023-03-12 and 1.0.1 dated 2025-03-20
DESCRIPTION | 16 ++--- LICENSE | 4 - MD5 | 30 ++++----- NAMESPACE | 31 ++++------ NEWS.md | 6 + R/create_dictionary.R | 6 - R/summarise_variable.R | 2 R/utils.R | 86 +++++++++++++++------------- README.md | 3 man/create_dictionary.Rd | 82 +++++++++++++------------- man/mode_stat.Rd | 34 +++++------ man/summarise_variable.Rd | 48 +++++++-------- tests/testthat/test-create_dictionary.R | 7 +- tests/testthat/test-summarise_variable.R | 22 ++++++- tests/testthat/testdata/tester.rds |binary tests/testthat/testdata/tester_no_error.rds |binary 16 files changed, 207 insertions(+), 170 deletions(-)
More information about datadictionary at CRAN
Permanent link
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.11 dated 2025-02-05 and 1.1.12 dated 2025-03-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ cleanup | 1 + configure | 10 +++++++++- src/Makevars.in | 8 +++++++- src/cpp11/include/cpp11/R.hpp | 2 +- src/cpp11/include/cpp11/named_arg.hpp | 2 +- 8 files changed, 33 insertions(+), 14 deletions(-)
Title: Lightweight Variable Labels
Description: Assign, extract, or remove variable labels from R vectors.
Lightweight and dependency-free.
Author: Marius Barth [aut, cre]
Maintainer: Marius Barth <marius.barth.uni.koeln@gmail.com>
Diff between tinylabels versions 0.2.4 dated 2023-09-02 and 0.2.5 dated 2025-03-20
tinylabels-0.2.4/tinylabels/R/methods-ggplot2.R |only tinylabels-0.2.5/tinylabels/DESCRIPTION | 11 ++-- tinylabels-0.2.5/tinylabels/MD5 | 23 ++++------ tinylabels-0.2.5/tinylabels/NEWS.md | 7 +++ tinylabels-0.2.5/tinylabels/R/onload.R | 4 - tinylabels-0.2.5/tinylabels/build/vignette.rds |binary tinylabels-0.2.5/tinylabels/inst/CITATION | 13 ++++- tinylabels-0.2.5/tinylabels/inst/doc/specification.R | 2 tinylabels-0.2.5/tinylabels/inst/doc/specification.html | 4 - tinylabels-0.2.5/tinylabels/inst/doc/tinylabels_vignette.R | 5 -- tinylabels-0.2.5/tinylabels/inst/doc/tinylabels_vignette.Rmd | 2 tinylabels-0.2.5/tinylabels/inst/doc/tinylabels_vignette.html | 6 +- tinylabels-0.2.5/tinylabels/vignettes/tinylabels_vignette.Rmd | 2 13 files changed, 42 insertions(+), 37 deletions(-)
Title: High Dimensional Supervised Classification and Clustering
Description: Discriminant analysis and data clustering methods for high
dimensional data, based on the assumption that high-dimensional data live in
different subspaces with low dimensionality proposing a new parametrization of
the Gaussian mixture model which combines the ideas of dimension reduction and
constraints on the model.
Author: Laurent Berge [aut, cre],
Charles Bouveyron [aut],
Stephane Girard [aut]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between HDclassif versions 2.2.1 dated 2023-08-23 and 2.2.2 dated 2025-03-20
DESCRIPTION | 20 ++++++++++++++++---- MD5 | 14 +++++++------- R/hdc.R | 4 ++-- R/mdaHD.R | 17 +++++++++++------ build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ man/hdda.Rd | 22 +++++++++++----------- man/hddc.Rd | 24 ++++++++++++------------ 8 files changed, 65 insertions(+), 42 deletions(-)
Title: Event Prediction
Description: Predicts enrollment and events at the design or analysis stage
using specified enrollment and time-to-event models through
simulations.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between eventPred versions 0.2.7 dated 2025-03-13 and 0.2.8 dated 2025-03-20
DESCRIPTION | 9 +++++---- MD5 | 32 ++++++++++++++++++++------------ NEWS.md | 9 +++++++-- R/eventPred-package.R | 9 ++++++++- R/fitDropout.R | 37 ++++++++++++++++++++----------------- R/fitEvent.R | 38 ++++++++++++++++++++------------------ R/getPrediction.R | 12 +++++------- R/predictEvent.R | 28 ++++++++++++++-------------- inst/shinyApp/app.R | 20 ++++++++++---------- man/eventPred-package.Rd | 9 ++++++++- man/fitDropout.Rd | 20 +++++++++++--------- man/fitEvent.Rd | 21 +++++++++++---------- man/getPrediction.Rd | 8 +++----- tests |only 14 files changed, 142 insertions(+), 110 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 0.1.5 dated 2025-03-12 and 0.1.6 dated 2025-03-20
diceplot-0.1.5/diceplot/tests/test_domino_base.R |only diceplot-0.1.6/diceplot/DESCRIPTION | 8 diceplot-0.1.6/diceplot/MD5 | 15 diceplot-0.1.6/diceplot/NAMESPACE | 7 diceplot-0.1.6/diceplot/R/dominoplot.R | 451 ++++++++---- diceplot-0.1.6/diceplot/R/utils.R | 431 +++++++++++ diceplot-0.1.6/diceplot/man/create_custom_domino_legends.Rd |only diceplot-0.1.6/diceplot/man/domino_plot.Rd | 85 +- diceplot-0.1.6/diceplot/man/geom_dice_sf.Rd |only diceplot-0.1.6/diceplot/tests/test_diceplots.R | 2 10 files changed, 842 insertions(+), 157 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 1.2.0 dated 2025-02-24 and 1.2.1 dated 2025-03-20
cucumber-1.2.0/cucumber/inst/examples/hooks_after_error/tests/testthat/steps |only cucumber-1.2.1/cucumber/DESCRIPTION | 6 cucumber-1.2.1/cucumber/MD5 | 24 +-- cucumber-1.2.1/cucumber/NAMESPACE | 1 cucumber-1.2.1/cucumber/NEWS.md | 4 cucumber-1.2.1/cucumber/R/hooks.R | 3 cucumber-1.2.1/cucumber/R/parse_token.R | 1 cucumber-1.2.1/cucumber/inst/doc/bdd.html | 2 cucumber-1.2.1/cucumber/inst/examples/hooks/tests/testthat/steps/steps.R | 8 - cucumber-1.2.1/cucumber/inst/examples/hooks_after_error/tests/testthat/setup-steps.R |only cucumber-1.2.1/cucumber/inst/examples/hooks_after_error/tests/testthat/test-cucumber.R | 2 cucumber-1.2.1/cucumber/tests/testthat/_snaps/examples.md | 68 ++++++++-- cucumber-1.2.1/cucumber/tests/testthat/test-examples.R | 31 +++- cucumber-1.2.1/cucumber/tests/testthat/test-hooks.R | 23 +++ 14 files changed, 133 insertions(+), 40 deletions(-)
Title: Computation and Visualisation of Atmospheric Convective
Parameters
Description: Allow to compute and visualise convective parameters commonly
used in the operational prediction of severe convective storms. Core algorithm
is based on a highly optimized 'C++' code linked into 'R' via 'Rcpp'. Highly
efficient engine allows to derive thermodynamic and kinematic parameters from
large numerical datasets such as reanalyses or operational Numerical Weather
Prediction models in a reasonable amount of time. Package has been developed
since 2017 by research meteorologists specializing in severe thunderstorms.
The most relevant methods used in the package based on the following publications
Stipanuk (1973) <https://apps.dtic.mil/sti/pdfs/AD0769739.pdf>,
McCann et al. (1994) <doi:10.1175/1520-0434(1994)009%3C0532:WNIFFM%3E2.0.CO;2>,
Bunkers et al. (2000) <doi:10.1175/1520-0434(2000)015%3C0061:PSMUAN%3E2.0.CO;2>,
Corfidi et al. (2003) <doi:10.1175/1520-0434(2003)018%3C0997:CPAMPF%3E2.0.CO;2>,
Showalter (1953) <doi:10.1175/1520-0477-34.6.250>,
Coffe [...truncated...]
Author: Bartosz Czernecki [aut, cre] ,
Mateusz Taszarek [aut] ,
Piotr Szuster [aut]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between thunder versions 1.1.3 dated 2023-11-10 and 1.1.4 dated 2025-03-20
thunder-1.1.3/thunder/R/wobf.R |only thunder-1.1.4/thunder/DESCRIPTION | 24 thunder-1.1.4/thunder/MD5 | 32 thunder-1.1.4/thunder/NAMESPACE | 1 thunder-1.1.4/thunder/NEWS.md | 6 thunder-1.1.4/thunder/R/get_sounding.R | 14 thunder-1.1.4/thunder/R/radiosonde_utils.R | 1 thunder-1.1.4/thunder/README.md | 3 thunder-1.1.4/thunder/build/vignette.rds |binary thunder-1.1.4/thunder/inst/doc/convective-parameters-and-technical-details.R | 2 thunder-1.1.4/thunder/inst/doc/convective-parameters-and-technical-details.html | 849 +++++++--- thunder-1.1.4/thunder/inst/doc/getstarted.R | 2 thunder-1.1.4/thunder/inst/doc/getstarted.html | 492 +++-- thunder-1.1.4/thunder/inst/doc/miscellaneous.R | 2 thunder-1.1.4/thunder/inst/doc/miscellaneous.html | 77 thunder-1.1.4/thunder/man/get_sounding.Rd | 8 thunder-1.1.4/thunder/src/main.cpp | 8 thunder-1.1.4/thunder/tests/testthat/Rplots.pdf |only 18 files changed, 982 insertions(+), 539 deletions(-)
Title: Network Structural Equation Modeling
Description: Several methods have been developed to integrate structural equation modeling techniques with network data analysis to examine the relationship between network and non-network data. Both node-based and edge-based information can be extracted from the network data to be used as observed variables in structural equation modeling. To facilitate the application of these methods, model specification can be performed in the familiar syntax of the 'lavaan' package, ensuring ease of use for researchers. Technical details and examples can be found at <https://bigsem.psychstat.org>.
Author: Zhiyong Zhang [aut, cre] ,
Ziqian Xu [aut]
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>
Diff between networksem versions 0.2 dated 2025-01-31 and 0.3 dated 2025-03-20
DESCRIPTION | 9 +++++---- MD5 | 9 ++++++--- R/friend_data.R |only R/networkFun_edge.R | 2 +- R/networkFun_edge_LSM.R | 2 +- data |only man/friend_data.Rd |only 7 files changed, 13 insertions(+), 9 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.1.3 dated 2025-03-18 and 1.1.4 dated 2025-03-20
renv-1.1.3/renv/inst/repos/src/contrib/renv_1.1.3.tar.gz |only renv-1.1.4/renv/DESCRIPTION | 6 - renv-1.1.4/renv/MD5 | 39 +++++----- renv-1.1.4/renv/NEWS.md | 15 +++ renv-1.1.4/renv/R/abi.R | 9 +- renv-1.1.4/renv/R/available-packages.R | 3 renv-1.1.4/renv/R/cran.R | 28 +++++++ renv-1.1.4/renv/R/dependencies.R | 10 ++ renv-1.1.4/renv/R/package.R | 6 + renv-1.1.4/renv/R/ppm.R | 8 -- renv-1.1.4/renv/R/repos.R | 33 +++++--- renv-1.1.4/renv/R/snapshot.R | 19 +++- renv-1.1.4/renv/inst/repos/src/contrib/PACKAGES | 4 - renv-1.1.4/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.1.4/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.1.4/renv/inst/repos/src/contrib/renv_1.1.4.tar.gz |only renv-1.1.4/renv/man/sysreqs.Rd | 5 - renv-1.1.4/renv/tests/testthat/resources/empty-yaml-header.Rmd |only renv-1.1.4/renv/tests/testthat/test-dependencies.R | 6 + renv-1.1.4/renv/tests/testthat/test-init.R | 4 - renv-1.1.4/renv/tests/testthat/test-lock.R | 18 ++++ renv-1.1.4/renv/tests/testthat/test-snapshot.R | 25 ++++++ 22 files changed, 184 insertions(+), 54 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.2.0 dated 2024-06-20 and 1.2.1 dated 2025-03-20
epidatr-1.2.0/epidatr/man/cache_epidata_call.Rd |only epidatr-1.2.0/epidatr/man/fetch_tbl.Rd |only epidatr-1.2.1/epidatr/DESCRIPTION | 65 - epidatr-1.2.1/epidatr/MD5 | 60 - epidatr-1.2.1/epidatr/NAMESPACE | 4 epidatr-1.2.1/epidatr/NEWS.md | 5 epidatr-1.2.1/epidatr/R/cache.R | 144 +- epidatr-1.2.1/epidatr/R/covidcast.R | 33 epidatr-1.2.1/epidatr/R/endpoints.R | 6 epidatr-1.2.1/epidatr/R/epidatacall.R | 75 - epidatr-1.2.1/epidatr/R/utils.R | 20 epidatr-1.2.1/epidatr/README.md | 3 epidatr-1.2.1/epidatr/build/vignette.rds |binary epidatr-1.2.1/epidatr/inst/doc/epidatr.R | 77 - epidatr-1.2.1/epidatr/inst/doc/epidatr.Rmd | 24 epidatr-1.2.1/epidatr/inst/doc/epidatr.html | 833 ++++++++-------- epidatr-1.2.1/epidatr/inst/doc/signal-discovery.R | 116 +- epidatr-1.2.1/epidatr/inst/doc/signal-discovery.html | 659 ++++++++---- epidatr-1.2.1/epidatr/inst/doc/versioned-data.R | 18 epidatr-1.2.1/epidatr/inst/doc/versioned-data.html | 497 ++++++--- epidatr-1.2.1/epidatr/man/check_for_cache_warnings.Rd |only epidatr-1.2.1/epidatr/man/check_is_cachable.Rd | 17 epidatr-1.2.1/epidatr/man/clear_cache.Rd | 6 epidatr-1.2.1/epidatr/man/covidcast_epidata.Rd | 12 epidatr-1.2.1/epidatr/man/epidatr-package.Rd | 2 epidatr-1.2.1/epidatr/man/fetch_args_list.Rd | 6 epidatr-1.2.1/epidatr/man/is_cache_enabled.Rd |only epidatr-1.2.1/epidatr/man/pub_covid_hosp_facility.Rd | 4 epidatr-1.2.1/epidatr/man/pvt_norostat.Rd | 2 epidatr-1.2.1/epidatr/tests/testthat/test-cache.R | 62 - epidatr-1.2.1/epidatr/tests/testthat/test-epidatacall.R | 39 epidatr-1.2.1/epidatr/tests/testthat/test-request.R | 1 epidatr-1.2.1/epidatr/vignettes/epidatr.Rmd | 24 33 files changed, 1703 insertions(+), 1111 deletions(-)
Title: Handle Air Quality Data from the European Environment Agency
Data Portal
Description: This software downloads and manages air quality data from the European Environmental Agency (EEA) dataflow (<https://www.eea.europa.eu/data-and-maps/data/aqereporting-9>).
See the web page <https://eeadmz1-downloads-webapp.azurewebsites.net/> for details on the EEA's Air Quality Download Service.
The package allows dynamically mapping the stations, summarising and time aggregating the measurements and building spatial interpolation maps.
See the web page <https://www.eea.europa.eu/en> for further information on EEA activities and history.
Further details, as well as, an extended vignette of the main functions included in the package, are available at the GitHub web page dedicated to the project.
Author: Paolo Maranzano [aut, cre, cph]
,
Riccardo Borgoni [aut, cph] ,
Samir Doghmi [aut, cph],
Agostino Tassan Mazzocco [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Diff between EEAaq versions 1.0.0 dated 2025-02-06 and 1.0.1 dated 2025-03-20
DESCRIPTION | 16 MD5 | 54 +- R/EEAaq_export.R | 66 --- R/EEAaq_get_data.R | 722 ++++++++++++--------------------- R/EEAaq_get_dataframe.R | 15 R/EEAaq_get_stations.R | 26 - R/EEAaq_idw_map.R | 951 ++++++++++++++++++-------------------------- R/EEAaq_import.R | 44 +- R/EEAaq_map_stations.R | 724 +++++++++++++-------------------- R/EEAaq_summary.R | 27 - R/EEAaq_time_aggregate.R | 26 + R/code_extr.R | 4 R/get_LAU.R | 2 R/get_NUTS.R | 1 R/get_pollutant.R | 6 R/get_stations.R | 11 R/handle_dates.R | 1 R/is_EEAaq_df.R | 19 man/EEAaq_export.Rd | 28 - man/EEAaq_get_data.Rd | 82 +-- man/EEAaq_get_dataframe.Rd | 15 man/EEAaq_get_stations.Rd | 4 man/EEAaq_idw_map.Rd | 111 +++-- man/EEAaq_import.Rd | 38 + man/EEAaq_map_stations.Rd | 82 ++- man/EEAaq_summary.Rd | 27 - man/EEAaq_time_aggregate.Rd | 26 + man/is_EEAaq_df.Rd | 19 28 files changed, 1360 insertions(+), 1787 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
Francois Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between questionr versions 0.7.8 dated 2023-01-31 and 0.8.0 dated 2025-03-20
DESCRIPTION | 18 +- MD5 | 39 +++-- NAMESPACE | 3 NEWS.md | 6 R/iorder.R | 10 - R/irec.R | 16 +- R/odds.ratio.R | 101 +++++++-------- R/recode.R | 77 ++++++----- R/table.multi.R | 74 ++++++----- R/tables.R | 280 +++++++++++++++++++++++++++++++++--------- R/tools.R | 8 - R/weighting.R | 209 +++++++++++++++---------------- build/vignette.rds |binary inst/doc/recoding_addins.html | 184 ++++++++++++++++----------- man/cprop.Rd | 8 - man/freq.Rd | 2 man/freqtable.Rd |only man/ltabs.Rd | 2 man/prop.Rd | 8 - man/rprop.Rd | 8 - tests/testthat/test_tables.R | 101 +++++++++++++++ 21 files changed, 734 insertions(+), 420 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.13 dated 2025-02-15 and 1.14 dated 2025-03-20
DESCRIPTION | 6 MD5 | 60 ++++---- NEWS.md | 23 +++ R/RcppExports.R | 4 R/class-workbook-wrappers.R | 48 ++++--- R/class-workbook.R | 92 ++++++++----- R/class-worksheet.R | 2 R/helper-functions.R | 6 R/read.R | 1 R/utils.R | 147 +++++++++++++++------ R/wb_functions.R | 10 + R/wb_load.R | 6 R/write.R | 25 +++ R/write_xlsx.R | 11 + README.md | 9 - build/vignette.rds |binary inst/WORDLIST | 1 man/fmt_txt.Rd | 26 ++- man/wbWorkbook.Rd | 4 man/wb_add_font.Rd | 30 ++-- man/wb_save.Rd | 18 ++ src/RcppExports.cpp | 14 ++ src/strings_xml.cpp | 2 src/write_file.cpp | 195 +++++++++++++++++++++++++++++ tests/testthat/test-formulas.R | 13 + tests/testthat/test-loading_workbook.R | 28 ++++ tests/testthat/test-read_from_created_wb.R | 23 +++ tests/testthat/test-read_sources.R | 12 + tests/testthat/test-strings_xml.R | 2 tests/testthat/test-utils.R | 56 ++++++++ tests/testthat/test-write.R | 16 ++ 31 files changed, 721 insertions(+), 169 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.3 dated 2025-01-13 and 1.0.4 dated 2025-03-20
DESCRIPTION | 8 MD5 | 168 NEWS.md | 102 R/clintrials_gov_convert.R | 140 R/clintrials_gov_upload.R | 186 R/eudract_convert.R | 72 R/incidence_table.R | 100 R/safety.R | 54 R/safety_summary.R | 572 R/simple_safety_xml.R | 120 R/soc_code.R | 28 README.md | 9 build/vignette.rds |binary inst/doc/eudract.R | 18 inst/doc/eudract.Rmd | 286 inst/doc/eudract.html | 10 inst/doc/standard_reporting.R | 8 inst/doc/standard_reporting.Rmd | 182 inst/doc/standard_reporting.html | 6 inst/extdata/1234.xml | 454 inst/extdata/ProtocolRecordSchema.xsd | 1452 +- inst/extdata/RRSUploadSchema.xsd | 1368 +- inst/extdata/adverseEvents.xsd | 570 inst/extdata/ct_safety_upload.xml | 2904 ++-- inst/extdata/find_replace.xslt | 48 inst/extdata/safety__upload.xml | 3676 ++--- inst/extdata/simple.xsd | 386 inst/extdata/simpleToCtGov.xslt | 248 inst/extdata/simpleToEudraCT.xslt | 288 inst/extdata/soc.xml | 276 man/append_xml.Rd | 24 man/clintrials_gov_convert.Rd | 134 man/clintrials_gov_upload.Rd | 170 man/create.safety_summary.Rd | 42 man/df_to_char.Rd | 30 man/dot_plot.Rd | 124 man/eudract_convert.Rd | 116 man/figures/README-report_example-1.png |binary man/incidence_table.Rd | 66 man/plot.dot_plot.Rd | 32 man/print.dot_plot.Rd | 32 man/print.safety_summary.Rd | 34 man/relative_risk.Rd | 156 man/safety.Rd | 66 man/safety_summary.Rd | 134 man/simple_safety_xml.Rd | 104 man/soc_code.Rd | 48 tests/testthat.R | 10 tests/testthat/1234.xml | 454 tests/testthat/GROUP.csv | 8 tests/testthat/NONSERIOUS.csv | 164 tests/testthat/Rplots.pdf |binary tests/testthat/SERIOUS.csv | 164 tests/testthat/_snaps/dotplot/dotplot-1group.svg | 208 tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 772 - tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 488 tests/testthat/_snaps/dotplot/dotplot-ref.svg | 472 tests/testthat/_snaps/dotplot/dotplot.svg | 472 tests/testthat/bak_study_file.xml | 4030 +++--- tests/testthat/ct.xml | 3316 ++--- tests/testthat/data/all_soc.csv | 54 tests/testthat/data/all_soc_v2.csv | 56 tests/testthat/data/events.csv | 3278 ++--- tests/testthat/data/fix_ucl.R | 52 tests/testthat/data/multiple_soc.csv | 6 tests/testthat/data/no_aes.csv | 4 tests/testthat/data/no_saes.csv | 4 tests/testthat/data/output_from_ucl.xml |14114 +++++++++++----------- tests/testthat/data/repeat_occurrences.csv | 8 tests/testthat/data/socless.xml | 9846 +++++++-------- tests/testthat/data/sparse.csv | 6 tests/testthat/events.csv | 3328 ++--- tests/testthat/reference/simple.xml | 2904 ++-- tests/testthat/reference/table_ct.xml | 4016 +++--- tests/testthat/reference/table_eudract.xml | 4972 +++---- tests/testthat/simple.xml | 2904 ++-- tests/testthat/study_file.xml | 4030 +++--- tests/testthat/table_ct.xml | 4016 +++--- tests/testthat/table_eudract.xml | 3894 +++--- tests/testthat/test_append_xml.R | 36 tests/testthat/test_basic.R | 808 - tests/testthat/test_bea.R | 74 tests/testthat/test_errors.R | 566 vignettes/eudract.Rmd | 286 vignettes/standard_reporting.Rmd | 182 85 files changed, 42520 insertions(+), 42533 deletions(-)
Title: Inhomogeneous K- And Pair Correlation Functions Using Global
Estimators
Description: Second-order summary statistics K- and pair-correlation functions describe
interactions in point pattern data. This package provides computations to estimate those
statistics on inhomogeneous point processes, using the methods of
in T Shaw, J Møller, R Waagepetersen, 2020 <doi:10.48550/arXiv.2004.00527>.
Author: Thomas Shaw [aut, cre],
Ege Rubak [ctb],
Adrian Baddeley [ctb],
Rolf Turner [ctb]
Maintainer: Thomas Shaw <tshaw20@utk.edu>
Diff between globalKinhom versions 0.1.9 dated 2024-10-07 and 0.1.10 dated 2025-03-20
DESCRIPTION | 10 ++++++---- MD5 | 6 +++--- R/isotropic_pcf.R | 4 ++++ build/partial.rdb |binary 4 files changed, 13 insertions(+), 7 deletions(-)
Title: REST API Client for the 'PGS' Catalog
Description: Programmatic access to the 'PGS' Catalog.
This package provides easy access to 'PGS' Catalog data by
accessing the REST API <https://www.pgscatalog.org/rest/>.
Author: Ramiro Magno [aut, cre] ,
Isabel Duarte [aut] ,
Ana-Teresa Maia [aut] ,
CINTESIS [cph, fnd],
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between quincunx versions 0.1.7 dated 2023-07-04 and 0.1.9 dated 2025-03-20
quincunx-0.1.7/quincunx/R/utils-pipe.R |only quincunx-0.1.7/quincunx/man/pipe.Rd |only quincunx-0.1.9/quincunx/DESCRIPTION | 31 +-- quincunx-0.1.9/quincunx/MD5 | 76 ++++----- quincunx-0.1.9/quincunx/NAMESPACE | 2 quincunx-0.1.9/quincunx/NEWS.md | 12 + quincunx-0.1.9/quincunx/R/count.R | 4 quincunx-0.1.9/quincunx/R/delay.R |only quincunx-0.1.9/quincunx/R/get.R | 6 quincunx-0.1.9/quincunx/R/get_ancestry_categories.R | 11 - quincunx-0.1.9/quincunx/R/get_cohorts.R | 24 +- quincunx-0.1.9/quincunx/R/get_performance_metrics.R | 18 +- quincunx-0.1.9/quincunx/R/get_publications.R | 36 ++-- quincunx-0.1.9/quincunx/R/get_releases.R | 13 - quincunx-0.1.9/quincunx/R/get_sample_sets.R | 18 +- quincunx-0.1.9/quincunx/R/get_scores.R | 27 ++- quincunx-0.1.9/quincunx/R/get_trait_categories.R | 13 - quincunx-0.1.9/quincunx/R/get_traits.R | 37 ++-- quincunx-0.1.9/quincunx/R/id_mapping.R | 82 ++++------ quincunx-0.1.9/quincunx/R/parse-ancestry_categories.R | 12 - quincunx-0.1.9/quincunx/R/parse-cohorts.R | 50 +++--- quincunx-0.1.9/quincunx/R/parse-performance_metrics.R | 96 +++++------ quincunx-0.1.9/quincunx/R/parse-publications.R | 60 +++---- quincunx-0.1.9/quincunx/R/parse-releases.R | 58 +++---- quincunx-0.1.9/quincunx/R/parse-sample_sets.R | 42 ++--- quincunx-0.1.9/quincunx/R/parse-scores.R | 146 +++++++++--------- quincunx-0.1.9/quincunx/R/parse-trait_categories.R | 24 +- quincunx-0.1.9/quincunx/R/parse-traits.R | 88 +++++----- quincunx-0.1.9/quincunx/R/parse_estimate.R |only quincunx-0.1.9/quincunx/R/remap_id.R | 22 +- quincunx-0.1.9/quincunx/R/request.R | 7 quincunx-0.1.9/quincunx/R/unwrap_cohort.R | 4 quincunx-0.1.9/quincunx/R/unwrap_demographics.R | 30 +-- quincunx-0.1.9/quincunx/R/unwrap_efotrait.R | 4 quincunx-0.1.9/quincunx/R/unwrap_interval.R | 4 quincunx-0.1.9/quincunx/R/unwrap_publication.R | 9 - quincunx-0.1.9/quincunx/R/unwrap_sample.R | 18 +- quincunx-0.1.9/quincunx/README.md | 17 -- quincunx-0.1.9/quincunx/build/partial.rdb |binary quincunx-0.1.9/quincunx/man/request.Rd | 2 quincunx-0.1.9/quincunx/man/request_all.Rd | 2 41 files changed, 589 insertions(+), 516 deletions(-)
Title: Render Barcode Distribution Plots
Description: The function \code{barcode()}
produces a histogram-like plot of a distribution that shows
granularity in the data.
Author: John W. Emerson [aut, cre],
Walton A. Green [aut],
John A. Hartigan [aut],
Liya Xiang [ctb]
Maintainer: John W. Emerson <john.emerson@yale.edu>
Diff between barcode versions 1.3.0 dated 2022-05-10 and 1.4.0 dated 2025-03-20
DESCRIPTION | 30 +++- MD5 | 8 - R/barcode.R | 78 ++++++----- R/barcode.panel.R | 354 +++++++++++++++++++++++++++++++++--------------------- man/barcode.Rd | 4 5 files changed, 289 insertions(+), 185 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Designed for simplicity, a 'mirai' evaluates an R expression
asynchronously in a parallel process, locally or distributed over the
network. The result is automatically available upon completion. Modern
networking and concurrency, built on 'nanonext' and 'NNG' (Nanomsg Next
Gen), ensures reliable and efficient scheduling over fast inter-process
communications or TCP/IP secured by TLS. Distributed computing can launch
remote resources via SSH or cluster managers. An inherently queued
architecture handles many more tasks than available processes, and requires
no storage on the file system. Innovative features include support for
otherwise non-exportable reference objects, event-driven promises, and
asynchronous parallel map.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Hibiki AI Limited [cph],
Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 2.1.0 dated 2025-02-07 and 2.2.0 dated 2025-03-20
mirai-2.1.0/mirai/man/register_cluster.Rd |only mirai-2.1.0/mirai/vignettes/shiny.Rmd.orig |only mirai-2.2.0/mirai/DESCRIPTION | 10 mirai-2.2.0/mirai/MD5 | 120 ++++---- mirai-2.2.0/mirai/NAMESPACE | 4 mirai-2.2.0/mirai/NEWS.md | 29 ++ mirai-2.2.0/mirai/R/daemon.R | 81 ++--- mirai-2.2.0/mirai/R/daemons.R | 303 ++++++++++----------- mirai-2.2.0/mirai/R/dispatcher.R | 37 +- mirai-2.2.0/mirai/R/launchers.R | 252 ++++++++---------- mirai-2.2.0/mirai/R/map.R | 162 ++++++----- mirai-2.2.0/mirai/R/mirai-package.R | 29 +- mirai-2.2.0/mirai/R/mirai.R | 336 +++++++++--------------- mirai-2.2.0/mirai/R/next.R | 57 +--- mirai-2.2.0/mirai/R/parallel.R | 126 +++------ mirai-2.2.0/mirai/R/promises.R | 92 +++++- mirai-2.2.0/mirai/README.md | 8 mirai-2.2.0/mirai/build/vignette.rds |binary mirai-2.2.0/mirai/inst/doc/databases.html | 26 + mirai-2.2.0/mirai/inst/doc/mirai.Rmd | 326 ++++++++++++++--------- mirai-2.2.0/mirai/inst/doc/mirai.html | 364 +++++++++++++++----------- mirai-2.2.0/mirai/inst/doc/parallel.Rmd | 18 - mirai-2.2.0/mirai/inst/doc/parallel.html | 46 +-- mirai-2.2.0/mirai/inst/doc/plumber.html | 26 + mirai-2.2.0/mirai/inst/doc/promises.Rmd | 37 ++ mirai-2.2.0/mirai/inst/doc/promises.html | 56 ++-- mirai-2.2.0/mirai/inst/doc/shiny.Rmd | 137 ++++++++- mirai-2.2.0/mirai/inst/doc/shiny.html | 155 +++++++++-- mirai-2.2.0/mirai/inst/doc/torch.html | 26 + mirai-2.2.0/mirai/man/as.promise.mirai.Rd | 23 - mirai-2.2.0/mirai/man/as.promise.mirai_map.Rd |only mirai-2.2.0/mirai/man/call_mirai.Rd | 65 +--- mirai-2.2.0/mirai/man/call_mirai_.Rd |only mirai-2.2.0/mirai/man/collect_mirai.Rd | 56 +--- mirai-2.2.0/mirai/man/daemon.Rd | 57 ++-- mirai-2.2.0/mirai/man/daemons.Rd | 202 ++++++-------- mirai-2.2.0/mirai/man/dispatcher.Rd | 21 - mirai-2.2.0/mirai/man/dot-flat.Rd | 13 mirai-2.2.0/mirai/man/everywhere.Rd | 57 +--- mirai-2.2.0/mirai/man/host_url.Rd | 40 +- mirai-2.2.0/mirai/man/is_mirai.Rd | 14 - mirai-2.2.0/mirai/man/is_mirai_error.Rd | 33 +- mirai-2.2.0/mirai/man/launch_local.Rd | 59 +--- mirai-2.2.0/mirai/man/make_cluster.Rd | 95 +++--- mirai-2.2.0/mirai/man/mirai-package.Rd | 20 - mirai-2.2.0/mirai/man/mirai.Rd | 108 +++---- mirai-2.2.0/mirai/man/mirai_map.Rd | 72 ++--- mirai-2.2.0/mirai/man/nextstream.Rd | 32 -- mirai-2.2.0/mirai/man/remote_config.Rd | 107 +++---- mirai-2.2.0/mirai/man/serial_config.Rd | 14 - mirai-2.2.0/mirai/man/status.Rd | 40 +- mirai-2.2.0/mirai/man/stop_mirai.Rd | 32 -- mirai-2.2.0/mirai/man/unresolved.Rd | 27 - mirai-2.2.0/mirai/man/with.miraiDaemons.Rd | 14 - mirai-2.2.0/mirai/tests/tests.R | 39 +- mirai-2.2.0/mirai/vignettes/mirai.Rmd | 326 ++++++++++++++--------- mirai-2.2.0/mirai/vignettes/mirai.Rmd.orig | 225 ++++++++++------ mirai-2.2.0/mirai/vignettes/parallel.Rmd | 18 - mirai-2.2.0/mirai/vignettes/parallel.Rmd.orig | 4 mirai-2.2.0/mirai/vignettes/precompile.R | 1 mirai-2.2.0/mirai/vignettes/promises.Rmd | 37 ++ mirai-2.2.0/mirai/vignettes/promises.Rmd.orig | 25 + mirai-2.2.0/mirai/vignettes/shiny.Rmd | 137 ++++++++- 63 files changed, 2742 insertions(+), 2134 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.8.2 dated 2025-01-16 and 0.8.3 dated 2025-03-20
DESCRIPTION | 8 MD5 | 12 NEWS.md | 4 R/addDrugUtilisation.R | 2 R/summariseDrugUtilisation.R | 6 inst/doc/create_cohorts.html | 118 - inst/doc/drug_utilisation.html | 2492 ++++++++++++++++++++--------------------- 7 files changed, 1323 insertions(+), 1319 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling enables to estimate net rainfall from streamflow measurements
following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>.
Resulting net rainfall is then estimated on the ungauged catchments
by spatial interpolation in order to finally simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 1.1.0 dated 2025-02-05 and 1.1.4 dated 2025-03-20
DESCRIPTION | 8 MD5 | 42 ++-- NAMESPACE | 2 R/convolution.R | 3 R/hdist.R | 9 R/mixr.R | 235 +++++++++++++++++++---- R/rsimilarity.R | 194 +++---------------- R/rsimilarity_model.R |only R/weightr.R | 41 ++-- build/partial.rdb |binary build/vignette.rds |binary data/Blavet.rda |binary data/Oudon.rda |binary inst/doc/V01_get_started.html | 11 - inst/doc/V02_inputs_preparation_stars.html | 32 +-- inst/doc/V03_inputs_preparation_whitebox.R | 262 +++++++++++++------------- inst/doc/V03_inputs_preparation_whitebox.html | 15 - man/mixr.Rd | 63 +++++- man/rsimilarity.Rd | 72 +------ man/rsimilarity_model.Rd |only src/convolution.f90 |only src/gdist.f90 | 185 ++++++++---------- src/similarity_module.f90 |only src/transfR.c | 49 +++- 24 files changed, 642 insertions(+), 581 deletions(-)
Title: Measure Memory and CPU Usage for Parallel R Code
Description: Measures memory and CPU usage of R code by regularly taking
snapshots of calls to the system command 'ps'. The package provides an entry
point (albeit coarse) to profile usage of system resources by R code run
in parallel.
Author: Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between syrup versions 0.1.2 dated 2025-03-17 and 0.1.3 dated 2025-03-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/syrup.R | 2 +- man/syrup.Rd | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.4 dated 2024-03-18 and 1.5 dated 2025-03-20
DESCRIPTION | 21 - MD5 | 56 ++-- NAMESPACE | 8 R/CoFAST.R | 2 R/iSCMEB.R | 6 R/main.R | 120 ++++++--- README.md | 10 build/vignette.rds |binary inst/doc/CosMx.R | 2 inst/doc/CosMx.html | 337 ++++++++++++++----------- inst/doc/FASTdlpfc.R | 2 inst/doc/FASTdlpfc.html | 428 ++++++++++++++++++-------------- inst/doc/FASTdlpfc2.R | 2 inst/doc/FASTdlpfc2.html | 613 +++++++++++++++++++++++++++-------------------- inst/doc/FASTsimu.R | 2 inst/doc/FASTsimu.html | 545 ++++++++++++++++++++++++----------------- inst/doc/pbmc3k.R | 2 inst/doc/pbmc3k.html | 345 +++++++++++++++----------- man/AddAdj.Rd | 2 man/AddParSettingFAST.Rd | 2 man/FAST.Rd | 2 man/IntegrateSRTData.Rd | 2 man/RunHarmonyLouvain.Rd | 2 man/RuniSCMEB.Rd | 2 man/iscmeb_run.Rd | 2 man/transferGeneNames.Rd | 10 src/DR_removebatch.cpp | 2 src/alignExp.cpp | 2 src/alignExps.cpp | 2 29 files changed, 1482 insertions(+), 1049 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates to be annotated
to express unspecified date components,
approximate or uncertain date components,
date ranges, and sets of dates.
This is useful for describing and analysing temporal information,
whether historical or recent, where date precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Nathan Werth [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 0.5.2 dated 2025-03-07 and 0.5.3 dated 2025-03-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 10 ++++++++++ R/component_extract.R | 19 ++++++++++++++----- man/component_extract.Rd | 12 ++++++++++++ tests/testthat/test-component_extract.R | 11 +++++++---- 7 files changed, 54 insertions(+), 19 deletions(-)
Title: Visualize Contingency Tables Using Kite-Square Plots
Description: Create a kite-square plot for contingency tables using 'ggplot2', to display their relevant quantities in a single figure (marginal, conditional, expected, observed, chi-squared). The plot resembles a flying kite inside a square if the variables are independent, and deviates from this the more dependence exists.
Author: John Wiedenhoeft [aut, cre, cph]
Maintainer: John Wiedenhoeft <john.wiedenhoeft@medizin.uni-leipzig.de>
Diff between kitesquare versions 0.0.1 dated 2025-03-17 and 0.0.2 dated 2025-03-20
DESCRIPTION | 6 MD5 | 33 +++- NEWS.md | 5 R/kitesquare.R | 7 - README.md | 88 ++++++------ inst/body.qmd |only inst/doc/kitesquare.R | 172 ------------------------ inst/doc/kitesquare.pdf |binary inst/doc/kitesquare.qmd | 321 ---------------------------------------------- man/figures |only vignettes/kitesquare.bib | 6 vignettes/kitesquare.html | 32 ++-- vignettes/kitesquare.md | 5 vignettes/kitesquare.qmd | 321 ---------------------------------------------- 14 files changed, 106 insertions(+), 890 deletions(-)
Title: Access and Harmonize Childfree Demographic Data
Description: Reads demographic data from a variety of public data sources, extracting and harmonizing variables useful for the study of childfree individuals. The identification of childfree individuals and those with other family statuses uses Neal & Neal's (2024) "A Framework for Studying Adults who Neither have Nor Want Children" <doi:10.1177/10664807231198869>; A pre-print is available at <doi:10.31234/osf.io/fa89m>.
Author: Zachary Neal [aut, cre] ,
Jennifer Watling Neal [aut]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between childfree versions 0.0.3 dated 2024-09-04 and 0.0.4 dated 2025-03-20
DESCRIPTION | 11 MD5 | 26 - NEWS.md | 4 R/dhs.R | 58 +-- R/nsfg.R | 735 ++++++++++++++++++++++++++---------------------- R/soss.R | 49 +-- inst/doc/childfree.html | 28 - inst/doc/codebooks.Rmd | 16 - inst/doc/codebooks.html | 36 +- man/childfree.Rd | 3 man/dhs.Rd | 42 +- man/nsfg.Rd | 49 +-- man/soss.Rd | 38 +- vignettes/codebooks.Rmd | 16 - 14 files changed, 604 insertions(+), 507 deletions(-)
Title: Comprehensive Groups of Experiments Analysis for Numerous
Environments
Description: In many cases, experiments must be repeated across multiple seasons or locations to ensure applicability of findings. A single experiment conducted in one location and season may yield limited conclusions, as results can vary under different environmental conditions. In agricultural research, treatment × location and treatment × season interactions play a crucial role. Analyzing a series of experiments across diverse conditions allows for more generalized and reliable recommendations. The 'CANE' package facilitates the pooled analysis of experiments conducted over multiple years, seasons, or locations. It is designed to assess treatment interactions with environmental factors (such as location and season) using various experimental designs. The package supports pooled analysis of variance (ANOVA) for the following designs: (1) 'PooledCRD()': completely randomized design; (2) 'PooledRBD()': randomized block design; (3) 'PooledLSD()': Latin square design; (4) 'PooledSPD()': split plot de [...truncated...]
Author: Vinayaka [aut, cre] ,
T. Lakshmi Pathy [aut, ctb] ,
K. Gopalareddy [aut, ctb] ,
Shweta Kumari [aut, ctb] ,
P. Murali [aut, ctb] ,
P. Govindaraj [aut, ctb],
P. Rama Chandra Prasad [aut, ctb]
,
L.N. Vinaykumar [aut, ctb]
Maintainer: Vinayaka <vinayaka.b3vs@gmail.com>
Diff between CANE versions 0.1.0 dated 2025-03-19 and 0.1.1 dated 2025-03-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/PooledCRD.R | 4 ++-- R/PooledStPD.R | 6 +++--- man/PooledCRD.Rd | 4 ++-- man/PooledStPD.Rd | 6 +++--- 6 files changed, 18 insertions(+), 18 deletions(-)
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.2.5 dated 2025-02-05 and 0.3.0 dated 2025-03-20
shinyscholar-0.2.5/shinyscholar/inst/app_skeleton/helper_functions.R |only shinyscholar-0.2.5/shinyscholar/inst/module_skeleton/skeleton.R |only shinyscholar-0.2.5/shinyscholar/inst/module_skeleton/skeleton_async.R |only shinyscholar-0.3.0/shinyscholar/DESCRIPTION | 6 shinyscholar-0.3.0/shinyscholar/MD5 | 124 +++++--- shinyscholar-0.3.0/shinyscholar/NAMESPACE | 1 shinyscholar-0.3.0/shinyscholar/NEWS.md | 26 + shinyscholar-0.3.0/shinyscholar/R/create_template.R | 113 +++----- shinyscholar-0.3.0/shinyscholar/R/custom_modules.R | 93 +++--- shinyscholar-0.3.0/shinyscholar/R/helper_functions.R | 19 + shinyscholar-0.3.0/shinyscholar/R/metadata.R | 1 shinyscholar-0.3.0/shinyscholar/R/save_and_load.R | 1 shinyscholar-0.3.0/shinyscholar/README.md | 77 +++++ shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/global.Rmd | 6 shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/helper_functions.Rmd |only shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/load.Rmd | 25 + shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/mapping.Rmd | 12 shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/save.Rmd | 1 shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/server.Rmd | 22 + shinyscholar-0.3.0/shinyscholar/inst/app_skeleton/ui.Rmd | 19 - shinyscholar-0.3.0/shinyscholar/inst/extdata/test_test.R | 5 shinyscholar-0.3.0/shinyscholar/inst/module_skeleton/skeletonR.Rmd |only shinyscholar-0.3.0/shinyscholar/inst/module_skeleton/skeleton_asyncR.Rmd |only shinyscholar-0.3.0/shinyscholar/inst/shiny/Rmd/gtext_plot.Rmd | 6 shinyscholar-0.3.0/shinyscholar/inst/shiny/Rmd/references.bib |only shinyscholar-0.3.0/shinyscholar/inst/shiny/Rmd/text_about.Rmd | 2 shinyscholar-0.3.0/shinyscholar/inst/shiny/Rmd/text_intro_tab.Rmd | 4 shinyscholar-0.3.0/shinyscholar/inst/shiny/Rmd/userReport_intro.Rmd | 4 shinyscholar-0.3.0/shinyscholar/inst/shiny/common.R | 15 + shinyscholar-0.3.0/shinyscholar/inst/shiny/global.R | 3 shinyscholar-0.3.0/shinyscholar/inst/shiny/helpers.R | 4 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/core_code.R | 10 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/core_load.R | 23 + shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/core_mapping.R | 16 - shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/core_save.R | 3 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_auto.R |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_auto.Rmd |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_auto.md |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_auto.yml |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_hist.R | 28 +- shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_hist.Rmd | 3 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_scatter.R | 19 - shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_semi.R |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_semi.Rmd |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_semi.md |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/plot_semi.yml |only shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/rep_markdown.R | 32 ++ shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/rep_refPackages.R | 10 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/select_async.R | 4 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/select_query.R | 4 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/select_user.R | 13 shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/template_create.R | 36 +- shinyscholar-0.3.0/shinyscholar/inst/shiny/modules/template_create.md | 2 shinyscholar-0.3.0/shinyscholar/inst/shiny/server.R | 23 + shinyscholar-0.3.0/shinyscholar/inst/shiny/ui.R | 36 +- shinyscholar-0.3.0/shinyscholar/man/create_module.Rd | 6 shinyscholar-0.3.0/shinyscholar/man/create_template.Rd | 2 shinyscholar-0.3.0/shinyscholar/man/metadata.Rd | 1 shinyscholar-0.3.0/shinyscholar/man/register_module.Rd | 1 shinyscholar-0.3.0/shinyscholar/man/reset_data.Rd |only shinyscholar-0.3.0/shinyscholar/man/save_and_load.Rd | 1 shinyscholar-0.3.0/shinyscholar/tests/testthat/helper_plot_auto.R |only shinyscholar-0.3.0/shinyscholar/tests/testthat/helper_plot_semi.R |only shinyscholar-0.3.0/shinyscholar/tests/testthat/helper_save_and_load.R | 5 shinyscholar-0.3.0/shinyscholar/tests/testthat/helper_save_load.R | 1 shinyscholar-0.3.0/shinyscholar/tests/testthat/test-create_template.R | 45 +-- shinyscholar-0.3.0/shinyscholar/tests/testthat/test-downloads.R | 25 + shinyscholar-0.3.0/shinyscholar/tests/testthat/test-metadata.R | 3 shinyscholar-0.3.0/shinyscholar/tests/testthat/test-plot_auto.R |only shinyscholar-0.3.0/shinyscholar/tests/testthat/test-plot_semi.R |only shinyscholar-0.3.0/shinyscholar/tests/testthat/test-save_and_load.R | 138 +++++----- shinyscholar-0.3.0/shinyscholar/tests/testthat/test-save_load.R | 30 ++ shinyscholar-0.3.0/shinyscholar/tests/testthat/test-select_user.R | 12 73 files changed, 737 insertions(+), 384 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.6-2 dated 2025-01-29 and 1.6-3 dated 2025-03-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/R.R | 2 ++ R/mmlt.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 9 +++++++++ 7 files changed, 23 insertions(+), 11 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.12 dated 2025-01-17 and 0.2.13 dated 2025-03-20
lrstat-0.2.12/lrstat/R/runShinyApp.R |only lrstat-0.2.12/lrstat/man/runShinyApp.Rd |only lrstat-0.2.13/lrstat/DESCRIPTION | 8 lrstat-0.2.13/lrstat/MD5 | 71 lrstat-0.2.13/lrstat/NAMESPACE | 5 lrstat-0.2.13/lrstat/NEWS.md | 18 lrstat-0.2.13/lrstat/R/RcppExports.R | 108 + lrstat-0.2.13/lrstat/R/getDesignMeans.R | 813 +++++++++- lrstat-0.2.13/lrstat/R/parameter_descriptions.R | 4 lrstat-0.2.13/lrstat/R/prints.R | 378 +++- lrstat-0.2.13/lrstat/R/runShinyApp_lrstat.R |only lrstat-0.2.13/lrstat/build/vignette.rds |binary lrstat-0.2.13/lrstat/man/covrmst.Rd | 4 lrstat-0.2.13/lrstat/man/getDesignMeanDiffCarryover.Rd | 98 - lrstat-0.2.13/lrstat/man/getDesignMeanDiffCarryoverEquiv.Rd |only lrstat-0.2.13/lrstat/man/kmest.Rd | 7 lrstat-0.2.13/lrstat/man/kmpower1s.Rd | 14 lrstat-0.2.13/lrstat/man/kmpowerequiv.Rd | 4 lrstat-0.2.13/lrstat/man/lrstat1.Rd | 3 lrstat-0.2.13/lrstat/man/natrisk.Rd | 4 lrstat-0.2.13/lrstat/man/nevent.Rd | 4 lrstat-0.2.13/lrstat/man/nevent2.Rd | 4 lrstat-0.2.13/lrstat/man/param_maxFollowupTime.Rd | 4 lrstat-0.2.13/lrstat/man/print.designMeanDiffCarryover.Rd | 6 lrstat-0.2.13/lrstat/man/print.designMeanDiffCarryoverEquiv.Rd |only lrstat-0.2.13/lrstat/man/rmpower1s.Rd | 17 lrstat-0.2.13/lrstat/man/rmpowerequiv.Rd | 2 lrstat-0.2.13/lrstat/man/rmstat.Rd | 6 lrstat-0.2.13/lrstat/man/runShinyApp_lrstat.Rd |only lrstat-0.2.13/lrstat/man/survsplit.Rd |only lrstat-0.2.13/lrstat/src/RcppExports.cpp | 23 lrstat-0.2.13/lrstat/src/kmstat.cpp | 323 +-- lrstat-0.2.13/lrstat/src/logistic_regression.cpp | 63 lrstat-0.2.13/lrstat/src/lrstat.cpp | 81 lrstat-0.2.13/lrstat/src/rmstat.cpp | 306 +-- lrstat-0.2.13/lrstat/src/survival_analysis.cpp | 173 +- lrstat-0.2.13/lrstat/src/survival_analysis.h | 4 lrstat-0.2.13/lrstat/src/utilities.cpp | 47 lrstat-0.2.13/lrstat/tests/testthat/test-kmest.R | 8 lrstat-0.2.13/lrstat/tests/testthat/test-survfit_phregr.R | 61 40 files changed, 1862 insertions(+), 809 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.30 dated 2025-02-21 and 3.33 dated 2025-03-20
modEvA-3.30/modEvA/NEWS |only modEvA-3.33/modEvA/DESCRIPTION | 8 modEvA-3.33/modEvA/MD5 | 32 +-- modEvA-3.33/modEvA/NEWS.md |only modEvA-3.33/modEvA/R/AUC.R | 69 +++++- modEvA-3.33/modEvA/R/MillerCalib.R | 2 modEvA-3.33/modEvA/R/lollipop.R | 2 modEvA-3.33/modEvA/R/mod2obspred.R | 20 + modEvA-3.33/modEvA/R/plotCoeffs.R | 40 ++- modEvA-3.33/modEvA/R/varImp.R | 317 +++++++++++++++++++------------ modEvA-3.33/modEvA/man/AUC.Rd | 9 modEvA-3.33/modEvA/man/MillerCalib.Rd | 2 modEvA-3.33/modEvA/man/lollipop.Rd | 2 modEvA-3.33/modEvA/man/mod2obspred.Rd | 20 + modEvA-3.33/modEvA/man/modEvA-package.Rd | 4 modEvA-3.33/modEvA/man/plotCoeffs.Rd | 23 +- modEvA-3.33/modEvA/man/threshMeasures.Rd | 2 modEvA-3.33/modEvA/man/varImp.Rd | 54 +++-- 18 files changed, 397 insertions(+), 209 deletions(-)
Title: The Free Group
Description: The free group in R; juxtaposition is represented by a
plus. Includes inversion, multiplication by a scalar,
group-theoretic power operation, and Tietze forms. To cite the
package in publications please use Hankin (2022)
<doi:10.48550/ARXIV.2212.05883>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between freegroup versions 1.1-9 dated 2025-01-30 and 1.2-0 dated 2025-03-20
DESCRIPTION | 6 ++-- MD5 | 24 ++++++++--------- NEWS.md | 6 +++- R/freeops.R | 6 ++-- build/partial.rdb |binary build/vignette.rds |binary data/dot.rda |binary inst/doc/freegroup.R | 61 ++++++++++++++++++++++++++++--------------- inst/doc/freegroup.Rnw | 64 +++++++++++++++++++++++++++++++++++----------- inst/doc/freegroup.pdf |binary man/Ops.free.Rd | 8 +++++ tests/testthat/test_aaa.R | 9 +++++- vignettes/freegroup.Rnw | 64 +++++++++++++++++++++++++++++++++++----------- 13 files changed, 175 insertions(+), 73 deletions(-)
Title: Automated Stacked Ensemble Classifier for Severe Class Imbalance
Description: A stacking solution for modeling imbalanced and severely skewed data. It automates the process of building homogeneous or heterogeneous stacked ensemble models by selecting "best" models according to different criteria. In doing so, it strategically searches for and selects diverse, high-performing base-learners to construct ensemble models optimized for skewed data. This package is particularly useful for addressing class imbalance in datasets, ensuring robust and effective model outcomes through advanced ensemble strategies which aim to stabilize the model, reduce its overfitting, and further improve its generalizability.
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between autoEnsemble versions 0.2 dated 2023-05-09 and 0.3 dated 2025-03-20
DESCRIPTION | 20 +++++----------- MD5 | 14 +++++++---- NAMESPACE | 4 +++ R/autoEnsemble.R |only R/ensemble.R | 55 ++++++++++++++++++++++++++++---------------- README.md | 12 +++++---- man/autoEnsemble.Rd |only man/ensemble.Rd | 13 +++++----- man/figures/logo.psd |only man/figures/logo_noname.png |only 10 files changed, 69 insertions(+), 49 deletions(-)
Title: A Spotlight 'React' Widget for 'shiny' Apps
Description: Creates a contextual menu that can be triggered with keyboard shortcuts or programmatically.
This can replace traditional sidebars or navigation bars, thereby enhancing the
user experience with lighter user interfaces.
Author: David Granjon [aut, cre],
Adenekan Wonderful [cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between scoutbaR versions 0.1.0 dated 2025-03-04 and 0.2.0 dated 2025-03-20
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 8 +++++++- R/scoutbar.R | 4 +++- inst/examples/simple/app.R | 7 +++++++ inst/www/scoutbar/scoutbar.js | 2 +- inst/www/scoutbar/scoutbar.js.map | 2 +- man/scoutbar.Rd | 6 ++++-- tests/testthat/_snaps/scoutbar/simple-001.json | 1 + tests/testthat/_snaps/scoutbar/simple-002.json | 1 + tests/testthat/_snaps/scoutbar/simple-002_.png |binary tests/testthat/_snaps/scoutbar/simple-003.json | 1 + tests/testthat/test-scoutbar.R | 2 ++ 13 files changed, 43 insertions(+), 21 deletions(-)
Title: Mental Health Quality of Life Toolkit
Description: Transforms, calculates, and presents results from the Mental Health Quality of Life Questionnaire (MHQoL), a measure of health-related quality of life for individuals with mental health conditions. Provides scoring functions, summary statistics, and visualization tools to facilitate interpretation. For more details see van Krugten et al.(2022) <doi:10.1007/s11136-021-02935-w>.
Author: Stijn Peeters [aut, cre] ,
Frederick Thielen [aut]
Maintainer: Stijn Peeters <s.b.peeters@eshpm.eur.nl>
Diff between MHQoL versions 0.13.0 dated 2025-03-11 and 0.14.0 dated 2025-03-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++-- inst/shiny/app.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper
to make generic calls to the API, plus convenience functions for
specific queries.
Author: Gibran Hemani [aut, cre, cph] ,
Ben Elsworth [aut] ,
Tom Palmer [aut] ,
Rita Rasteiro [aut]
Maintainer: Gibran Hemani <g.hemani@bristol.ac.uk>
Diff between ieugwasr versions 1.0.1 dated 2024-07-01 and 1.0.3 dated 2025-03-20
DESCRIPTION | 10 +++--- MD5 | 25 ++++++++-------- NAMESPACE | 1 NEWS.md | 9 +++++ R/query.R | 26 ++++++++++++++++ build/vignette.rds |binary man/gwasinfo_files.Rd |only man/ieugwasr-package.Rd | 2 - tests/testthat/test_afl2.r | 13 +++++--- tests/testthat/test_api.r | 4 +- tests/testthat/test_check429.r | 3 + tests/testthat/test_ld.r | 29 +++++++++++------- tests/testthat/test_query.r | 64 +++++++++++++++++++++++++++++++++-------- tests/testthat/test_variants.r | 39 +++++++++++++++++------- 14 files changed, 166 insertions(+), 59 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre],
Simon Urbanek [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.10.8 dated 2025-03-06 and 0.10.10 dated 2025-03-20
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 10 ++ R/ModeC.R | 114 ++++++++++++++++++-------------- inst/tinytest/test-or3s.R | 4 + inst/tinytest/test-texParse-internals.R | 96 +++++++++++++------------- man/ModeC.Rd | 2 src/C_Mode.c | 50 ++++++++++++++ src/init.c | 2 tests/tinytest.R | 28 ++++--- 10 files changed, 207 insertions(+), 123 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.1 dated 2025-01-11 and 1.0.2 dated 2025-03-20
BioVizSeq-1.0.1/BioVizSeq/man/figures |only BioVizSeq-1.0.2/BioVizSeq/DESCRIPTION | 6 - BioVizSeq-1.0.2/BioVizSeq/MD5 | 44 +------ BioVizSeq-1.0.2/BioVizSeq/NEWS.md | 3 BioVizSeq-1.0.2/BioVizSeq/R/combi_plot.R | 66 +++++++---- BioVizSeq-1.0.2/BioVizSeq/R/globalvariables.R | 2 BioVizSeq-1.0.2/BioVizSeq/README.md | 6 - BioVizSeq-1.0.2/BioVizSeq/inst/shinyapp/script/mod_advplot.R | 24 +++- BioVizSeq-1.0.2/BioVizSeq/inst/shinyapp/www/html/README.html | 36 +++--- BioVizSeq-1.0.2/BioVizSeq/man/combi_p.Rd | 5 10 files changed, 106 insertions(+), 86 deletions(-)
Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune
several models in one go.The goal is to provide a number of machine learning convenience
functions. It provides the ability to build, tune and obtain predictions of
several models in one function. The models are built using functions from
'caret' with easier to read syntax.
Kuhn(2014) <doi:10.48550/arXiv.1405.6974>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between manymodelr versions 0.3.7 dated 2021-11-15 and 0.3.9 dated 2025-03-20
DESCRIPTION | 16 MD5 | 170 +-- NAMESPACE | 149 +- NEWS.md | 345 +++--- R/add_model_predictions.R | 158 +-- R/agg_by_group.R | 85 - R/data.R | 16 R/extract_model_info.R | 278 ++--- R/fit_model.R | 116 +- R/get_mode.R | 178 +-- R/get_stats.R | 104 +- R/get_var_corr.R | 154 +-- R/get_var_corr_.R | 132 +- R/globals.R |only R/helpers.R | 114 +- R/multi_model_1.R | 160 +-- R/multi_model_2.R | 66 - R/na_replace.R | 102 +- R/na_replace_grouped.R | 64 - R/plot_corr.R | 459 ++++----- R/report_model.R |only R/rowdiff.R | 114 +- R/select_percentile.R | 90 - R/zzz.R | 20 build/vignette.rds |binary inst/doc/correlations.R | 104 +- inst/doc/correlations.html | 814 ++++++++++------ inst/doc/correlations.rmd | 200 +-- inst/doc/manymodelr_vignette.R | 338 +++--- inst/doc/manymodelr_vignette.html | 1418 ++++++++++++++++------------ inst/doc/manymodelr_vignette.rmd | 708 ++++++------- inst/doc/misc.R | 74 - inst/doc/misc.html | 775 +++++++++------ inst/doc/misc.rmd | 152 +-- inst/doc/modeling.R | 195 +-- inst/doc/modeling.html | 1048 ++++++++++++-------- inst/doc/modeling.rmd | 369 +++---- man/add_model_predictions.Rd | 66 - man/add_model_residuals.Rd | 52 - man/agg_by_group.Rd | 54 - man/drop_non_numeric.Rd | 34 man/extract_model_info.Rd | 80 - man/fit_model.Rd | 76 - man/fit_models.Rd | 86 - man/get_data_Stats.Rd | 104 +- man/get_exponent.Rd | 54 - man/get_mode.Rd | 72 - man/get_this.Rd | 58 - man/get_var_corr.Rd | 86 - man/get_var_corr_.Rd | 84 - man/multi_model_1.Rd | 132 +- man/multi_model_2.Rd | 68 - man/na_replace.Rd | 60 - man/na_replace_grouped.Rd | 52 - man/plot_corr.Rd | 224 ++-- man/report_model.Rd |only man/rowdiff.Rd | 98 - man/select_col.Rd | 64 - man/select_percentile.Rd | 62 - man/yields.Rd | 32 tests/testthat.R | 8 tests/testthat/_snaps |only tests/testthat/test_add_model_predictions.R | 66 - tests/testthat/test_agg_by_group.R | 37 tests/testthat/test_extract_model_info.R | 72 - tests/testthat/test_fit_model.R | 67 - tests/testthat/test_get_exponent.R | 47 tests/testthat/test_get_mode.R | 45 tests/testthat/test_get_stats.R | 44 tests/testthat/test_get_this.R | 50 tests/testthat/test_get_var_corr.R | 56 - tests/testthat/test_get_var_corr_.R | 46 tests/testthat/test_multi_model_1.R | 72 - tests/testthat/test_multi_model_2.R | 50 tests/testthat/test_na_replace.R | 81 - tests/testthat/test_percentile.R | 24 tests/testthat/test_plot_corr.R | 105 +- tests/testthat/test_report_model.R |only tests/testthat/test_rowdiff.R | 52 - tests/testthat/test_select_col.R | 14 vignettes/correlations.rmd | 200 +-- vignettes/manymodelr_vignette.rmd | 708 ++++++------- vignettes/misc.rmd | 152 +-- vignettes/modeling.rmd | 369 +++---- 84 files changed, 7130 insertions(+), 6218 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.10.7 dated 2025-01-31 and 1.11.0 dated 2025-03-20
DESCRIPTION | 8 ++-- MD5 | 72 ++++++++++++++++++------------------- NAMESPACE | 2 + NEWS.md | 13 ++++++ R/0nly-internal.R | 45 +++++++++++++++++++++++ R/emm-list.R | 45 ++++++++++++++++++----- R/emmGrid-methods.R | 29 ++++++++++---- R/emmeans.R | 28 ++++++++++++++ R/interfacing.R | 2 - R/summary.R | 2 - R/test.R | 20 ++++++---- inst/doc/AQuickStart.html | 4 +- inst/doc/FAQs.html | 10 ++--- inst/doc/basics.html | 6 +-- inst/doc/comparisons.html | 10 ++--- inst/doc/confidence-intervals.html | 10 ++--- inst/doc/interactions.html | 16 ++++---- inst/doc/messy-data.R | 4 +- inst/doc/messy-data.Rmd | 4 +- inst/doc/messy-data.html | 8 ++-- inst/doc/models.html | 4 +- inst/doc/predictions.html | 4 +- inst/doc/re-engineering-clds.html | 4 +- inst/doc/sophisticated.html | 4 +- inst/doc/transformations.html | 6 +-- inst/doc/utilities.html | 4 +- inst/doc/vignette-topics.html | 4 +- inst/doc/xplanations.html | 4 +- inst/doc/xtending.html | 8 ++-- man/emmGrid-methods.Rd | 16 ++++++-- man/emm_list-object.Rd | 13 ++++-- man/emmeans.Rd | 15 +++++++ man/extending-emmeans.Rd | 2 - man/joint_tests.Rd | 7 +++ man/rbind.emmGrid.Rd | 3 + man/summary.emmGrid.Rd | 4 +- vignettes/messy-data.Rmd | 4 +- 37 files changed, 304 insertions(+), 140 deletions(-)
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.3 dated 2025-02-06 and 0.1.4 dated 2025-03-20
DESCRIPTION | 14 - MD5 | 92 ++++++------ NEWS.md | 9 + R/RcppExports.R | 26 ++- R/ipcw.R | 46 +++--- R/ipe.R | 39 +++-- R/logisregr.R | 6 R/rpsftm.R | 38 +++-- R/trtswitch-package.R | 3 R/tsegest.R | 48 ++++-- R/tsesimp.R | 46 +++--- build/vignette.rds |binary inst/doc/ipcw.html | 14 - inst/doc/ipe.html | 2 inst/doc/rpsftm.html | 2 inst/doc/tsegest.R | 3 inst/doc/tsegest.Rmd | 3 inst/doc/tsegest.html | 41 ++--- man/ipe.Rd | 8 - man/kmest.Rd | 7 man/logisregr.Rd | 6 man/rpsftm.Rd | 8 - man/survsplit.Rd | 2 man/trtswitch-package.Rd | 3 man/tsegest.Rd | 7 man/tsesimp.Rd | 6 src/RcppExports.cpp | 45 +++--- src/ipcw.cpp | 242 +++++++++++++++------------------ src/ipe.cpp | 203 ++++++++++++++++++--------- src/rpsftm.cpp | 158 +++++++++++++++------ src/survival_analysis.cpp | 165 ++++++++++++++-------- src/survival_analysis.h | 4 src/tsegest.cpp | 214 +++++++++++++++-------------- src/tsesimp.cpp | 156 ++++++++++++--------- src/utilities.cpp | 6 src/utilities.h | 2 tests/testthat/test-kmest.R | 24 +-- tests/testthat/test-liferegr.R | 58 +++---- tests/testthat/test-logisregr.R | 58 +++---- tests/testthat/test-lrtest.R | 35 ++-- tests/testthat/test-phregr.R | 60 ++++---- tests/testthat/test-residuals_phregr.R | 210 ++++++++++++++-------------- tests/testthat/test-rmdiff.R | 42 +++-- tests/testthat/test-rmest.R | 28 +-- tests/testthat/test-survfit_phregr.R | 134 +++++++++--------- tests/testthat/test-tsegest.R | 12 - vignettes/tsegest.Rmd | 3 47 files changed, 1355 insertions(+), 983 deletions(-)
Title: Rendering Font into 'data.frame'
Description: Extract glyph information from font data, and translate the
outline curves to flattened paths or tessellated polygons. The converted
data is returned as a 'data.frame' in easy-to-plot format.
Author: Hiroaki Yutani [aut, cre] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>
Diff between string2path versions 0.2.0 dated 2025-02-08 and 0.2.1 dated 2025-03-20
DESCRIPTION | 8 LICENSE.note | 532 +++++++++++++++++++-------------------- MD5 | 24 - NEWS.md | 6 R/main.R | 101 +++++-- inst/AUTHORS | 238 ++++++++--------- man/string2path.Rd | 8 src/Makevars.in | 8 src/Makevars.win.in | 8 src/rust/Cargo.lock | 60 ++-- src/rust/Cargo.toml | 11 src/rust/src/into_fill_stroke.rs | 2 src/rust/vendor.tar.xz |binary 13 files changed, 527 insertions(+), 479 deletions(-)
Title: Spatial and Spatiotemporal Relative Risk
Description: Provides functions to estimate kernel-smoothed spatial and spatio-temporal densities and relative risk functions, and perform subsequent inference. Methodological details can be found in the accompanying tutorial: Davies et al. (2018) <DOI:10.1002/sim.7577>.
Author: Tilman M. Davies [aut, cre],
Jonathan C. Marshall [aut]
Maintainer: Tilman M. Davies <tilman.davies@otago.ac.nz>
Diff between sparr versions 2.3-15 dated 2024-07-07 and 2.3-16 dated 2025-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/tol.classify.R | 19 ++++++++++++++++++- man/sparr-package.Rd | 4 ++-- 4 files changed, 27 insertions(+), 10 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.10 dated 2025-02-05 and 0.5.11 dated 2025-03-19
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 2 NEWS.md | 6 + R/jskm.R | 154 +++++++++++++++++++++++++++++++++++++++++++++++++- R/svyjskm.R | 161 +++++++++++++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/jskm.html | 10 +-- man/jskm.Rd | 12 +++ man/svyjskm.Rd | 13 +++- 10 files changed, 349 insertions(+), 35 deletions(-)
Title: Bayesian Analysis of List Experiments with Prior Information
Description: Estimates Bayesian models of list experiments with informative priors. It includes functionalities to estimate different types of list experiment models with varying prior information. See Lu and Traunmüller (2021) <doi:10.2139/ssrn.3871089> for examples and details of estimation.
Author: Xiao Lu [aut, cre],
Richard Traunmueller [aut]
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Diff between bayeslist versions 0.0.1.4 dated 2024-11-28 and 0.0.1.5 dated 2025-03-19
DESCRIPTION | 6 +-- MD5 | 42 ++++++++++++------------- inst/stan/model_misreport_aux.stan | 14 ++++---- inst/stan/model_misreport_cmp.stan | 10 ++--- inst/stan/model_misreport_doublelist.stan | 18 +++++----- inst/stan/model_misreport_infonorm.stan | 14 ++++---- inst/stan/model_misreport_noaux.stan | 6 +-- inst/stan/model_outcome_aux.stan | 12 +++---- inst/stan/model_outcome_cmp.stan | 8 ++-- inst/stan/model_outcome_doublelist.stan | 12 +++---- inst/stan/model_outcome_infonorm.stan | 8 ++-- inst/stan/model_outcome_noaux.stan | 4 +- inst/stan/model_predict_aux.stan | 14 ++++---- inst/stan/model_predict_aux_linear.stan | 14 ++++---- inst/stan/model_predict_cmp.stan | 10 ++--- inst/stan/model_predict_cmp_linear.stan | 10 ++--- inst/stan/model_predict_doublelist.stan | 18 +++++----- inst/stan/model_predict_doublelist_linear.stan | 18 +++++----- inst/stan/model_predict_infonorm.stan | 10 ++--- inst/stan/model_predict_infonorm_linear.stan | 10 ++--- inst/stan/model_predict_noaux.stan | 6 +-- inst/stan/model_predict_noaux_linear.stan | 6 +-- 22 files changed, 135 insertions(+), 135 deletions(-)
Title: Create Images of Volumetric Brain Data in NIfTI Format Using
'ggplot2' Syntax
Description: A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data.
Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and
themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects,
inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.
Author: Michael Hallquist [aut, cre]
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>
Diff between ggbrain versions 0.8.1 dated 2023-03-21 and 0.9.0 dated 2025-03-19
ggbrain-0.8.1/ggbrain/inst/extdata/Schaefer_200_7networks_2009c_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/abspe_ptfce_fwep_0.05.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/decision_onset_zstat_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/echange_overall_zstat_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/mni_template_2009c_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/pe_ptfce_fwep_0.05.nii.gz |only ggbrain-0.8.1/ggbrain/man/annotate_panel.Rd |only ggbrain-0.9.0/ggbrain/DESCRIPTION | 10 ggbrain-0.9.0/ggbrain/MD5 | 98 ggbrain-0.9.0/ggbrain/NAMESPACE | 13 ggbrain-0.9.0/ggbrain/NEWS.md | 17 ggbrain-0.9.0/ggbrain/R/contrast_parser.R | 48 ggbrain-0.9.0/ggbrain/R/ggb.R | 98 ggbrain-0.9.0/ggbrain/R/ggbrain_images.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_label.R | 6 ggbrain-0.9.0/ggbrain/R/ggbrain_layer.R | 82 ggbrain-0.9.0/ggbrain/R/ggbrain_layer_brain.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_layer_outline.R | 20 ggbrain-0.9.0/ggbrain/R/ggbrain_panel.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_plot.R | 56 ggbrain-0.9.0/ggbrain/R/ggbrain_slices.R | 89 ggbrain-0.9.0/ggbrain/R/sugar.R | 134 - ggbrain-0.9.0/ggbrain/build/vignette.rds |binary ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.R | 44 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.Rmd | 4 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.html | 694 ++--- ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.R | 92 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.Rmd | 169 - ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.html | 1099 +++----- ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.R | 190 + ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.Rmd | 300 ++ ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.html | 1247 +++++++--- ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer2018_200Parcels_7Networks_order_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer_200_7networks_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer_200_7networks_labels.csv | 402 +-- ggbrain-0.9.0/ggbrain/inst/extdata/Yeo2011_7Networks_ColorLUT.txt |only ggbrain-0.9.0/ggbrain/inst/extdata/abspe_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/echange_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/feedback_onset_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/mni_template_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/pe_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/man/annotate_slice.Rd |only ggbrain-0.9.0/ggbrain/man/define.Rd | 12 ggbrain-0.9.0/ggbrain/man/geom_brain.Rd | 10 ggbrain-0.9.0/ggbrain/man/geom_outline.Rd | 6 ggbrain-0.9.0/ggbrain/man/ggb.Rd | 2 ggbrain-0.9.0/ggbrain/man/ggbrain_plot.Rd | 4 ggbrain-0.9.0/ggbrain/man/ggbrain_slices.Rd | 13 ggbrain-0.9.0/ggbrain/man/images.Rd | 2 ggbrain-0.9.0/ggbrain/man/montage.Rd | 2 ggbrain-0.9.0/ggbrain/man/plot.ggb.Rd | 12 ggbrain-0.9.0/ggbrain/man/plot.ggbrain_patchwork.Rd |only ggbrain-0.9.0/ggbrain/man/plus-.ggbrain_images.Rd | 4 ggbrain-0.9.0/ggbrain/man/render.Rd | 35 ggbrain-0.9.0/ggbrain/man/render.ggb.Rd |only ggbrain-0.9.0/ggbrain/man/slices.Rd | 2 ggbrain-0.9.0/ggbrain/vignettes/ggbrain_aesthetics.Rmd | 4 ggbrain-0.9.0/ggbrain/vignettes/ggbrain_introduction.Rmd | 169 - ggbrain-0.9.0/ggbrain/vignettes/ggbrain_labels.Rmd | 300 ++ 59 files changed, 3499 insertions(+), 2047 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features.
All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] ,
Edzer Pebesma [ctb] ,
Roger Bivand [ctb],
Jeroen Ooms [ctb] ,
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@hs-bochum.de>
Diff between gdalcubes versions 0.7.0 dated 2024-03-06 and 0.7.1 dated 2025-03-19
gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/fscache_cube.h |only gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/stream_apply_chunk.cpp |only gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/stream_apply_chunk.h |only gdalcubes-0.7.1/gdalcubes/DESCRIPTION | 12 gdalcubes-0.7.1/gdalcubes/LICENSE | 2 gdalcubes-0.7.1/gdalcubes/MD5 | 253 ++++------ gdalcubes-0.7.1/gdalcubes/NEWS.md | 5 gdalcubes-0.7.1/gdalcubes/R/config.R | 2 gdalcubes-0.7.1/gdalcubes/R/cube.R | 4 gdalcubes-0.7.1/gdalcubes/R/gdalcubes.R | 3 gdalcubes-0.7.1/gdalcubes/R/view.R | 2 gdalcubes-0.7.1/gdalcubes/build/vignette.rds |binary gdalcubes-0.7.1/gdalcubes/configure | 26 - gdalcubes-0.7.1/gdalcubes/configure.ac | 2 gdalcubes-0.7.1/gdalcubes/inst/CITATION | 44 - gdalcubes-0.7.1/gdalcubes/inst/COPYRIGHTS | 92 +-- gdalcubes-0.7.1/gdalcubes/inst/doc/gc01_MODIS.Rmd | 4 gdalcubes-0.7.1/gdalcubes/inst/doc/gc01_MODIS.html | 23 gdalcubes-0.7.1/gdalcubes/inst/formats/CHIRPS_v2_0_daily_p05_tif.json | 34 - gdalcubes-0.7.1/gdalcubes/inst/formats/CHIRPS_v2_0_monthly_p05_tif.json | 34 - gdalcubes-0.7.1/gdalcubes/inst/formats/ESA_CCI_SM_ACTIVE.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/ESA_CCI_SM_PASSIVE.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/GPM_IMERG_3B_DAY_GIS_V06A.json | 80 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/L8_L1TP.json | 120 ++-- gdalcubes-0.7.1/gdalcubes/inst/formats/L8_SR.json | 158 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD09GA.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD10A2.json | 44 - gdalcubes-0.7.1/gdalcubes/inst/formats/MxD11A1.json | 72 +- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD11A2.json | 88 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13A2.json | 84 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13A3.json | 84 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13Q1.json | 104 ++-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD14A2.json | 42 - gdalcubes-0.7.1/gdalcubes/inst/formats/PlanetScope_3B_AnalyticMS_SR.json | 72 +- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L1C.json | 158 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L1C_AWS.json | 160 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L2A.json | 164 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L2A_THEIA.json | 118 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_aggregate_space.R | 120 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_aggregate_time.R | 122 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_apply_pixel.R | 78 +-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_as_json.R | 32 - gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_crop.R | 52 +- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_cube_view.R | 134 ++--- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_rename_bands.R | 24 gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_selection.R | 98 +-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_slice_space.R | 24 gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_slice_time.R | 24 gdalcubes-0.7.1/gdalcubes/man/add_collection_format.Rd | 50 - gdalcubes-0.7.1/gdalcubes/man/add_images.Rd | 74 +- gdalcubes-0.7.1/gdalcubes/man/aggregate_space.Rd | 112 ++-- gdalcubes-0.7.1/gdalcubes/man/aggregate_time.Rd | 100 +-- gdalcubes-0.7.1/gdalcubes/man/animate.Rd | 134 ++--- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.Rd | 100 +-- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.array.Rd | 66 +- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.cube.Rd | 188 +++---- gdalcubes-0.7.1/gdalcubes/man/apply_time.Rd | 130 ++--- gdalcubes-0.7.1/gdalcubes/man/apply_time.array.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/apply_time.cube.Rd | 172 +++--- gdalcubes-0.7.1/gdalcubes/man/as_array.Rd | 80 +-- gdalcubes-0.7.1/gdalcubes/man/as_json.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/bands.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/chunk_apply.Rd | 114 ++-- gdalcubes-0.7.1/gdalcubes/man/collection_formats.Rd | 54 +- gdalcubes-0.7.1/gdalcubes/man/create_image_collection.Rd | 164 +++--- gdalcubes-0.7.1/gdalcubes/man/crop.Rd | 130 ++--- gdalcubes-0.7.1/gdalcubes/man/cube_view.Rd | 158 +++--- gdalcubes-0.7.1/gdalcubes/man/dim.cube.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/dimension_bounds.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/dimension_values.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/dimensions.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/dot-copy_cube.Rd | 42 - gdalcubes-0.7.1/gdalcubes/man/extent.Rd | 66 +- gdalcubes-0.7.1/gdalcubes/man/extract_geom.Rd | 218 ++++---- gdalcubes-0.7.1/gdalcubes/man/fill_time.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/filter_geom.Rd | 126 ++-- gdalcubes-0.7.1/gdalcubes/man/filter_pixel.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/gdalcubes.Rd | 58 +- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdal_has_geos.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdalformats.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdalversion.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_options.Rd | 144 ++--- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_selection.Rd | 180 +++---- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_set_gdal_config.Rd | 46 - gdalcubes-0.7.1/gdalcubes/man/image_collection.Rd | 62 +- gdalcubes-0.7.1/gdalcubes/man/image_mask.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/join_bands.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/json_cube.Rd | 102 ++-- gdalcubes-0.7.1/gdalcubes/man/memsize.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/names.cube.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/nbands.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/ncdf_cube.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/nt.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/nx.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/ny.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/pack_minmax.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/plot.cube.Rd | 218 ++++---- gdalcubes-0.7.1/gdalcubes/man/print.cube.Rd | 62 +- gdalcubes-0.7.1/gdalcubes/man/print.cube_view.Rd | 44 - gdalcubes-0.7.1/gdalcubes/man/print.image_collection.Rd | 60 +- gdalcubes-0.7.1/gdalcubes/man/proj4.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/raster_cube.Rd | 126 ++-- gdalcubes-0.7.1/gdalcubes/man/read_chunk_as_array.Rd | 102 ++-- gdalcubes-0.7.1/gdalcubes/man/reduce_space.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/reduce_space.array.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/reduce_space.cube.Rd | 146 ++--- gdalcubes-0.7.1/gdalcubes/man/reduce_time.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/reduce_time.array.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/reduce_time.cube.Rd | 182 +++---- gdalcubes-0.7.1/gdalcubes/man/rename_bands.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/select_bands.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/select_time.Rd | 90 +-- gdalcubes-0.7.1/gdalcubes/man/size.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/slice_space.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/slice_time.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/srs.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/st_as_stars.cube.Rd | 76 +-- gdalcubes-0.7.1/gdalcubes/man/stac_image_collection.Rd | 112 ++-- gdalcubes-0.7.1/gdalcubes/man/stack_cube.Rd | 160 +++--- gdalcubes-0.7.1/gdalcubes/man/write_chunk_from_array.Rd | 96 +-- gdalcubes-0.7.1/gdalcubes/man/write_ncdf.Rd | 152 +++--- gdalcubes-0.7.1/gdalcubes/man/write_tif.Rd | 158 +++--- gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/build_info.h | 12 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/date.h | 8 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/tinyexpr/tinyexpr.c | 23 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/tinyexpr/tinyexpr.h | 2 gdalcubes-0.7.1/gdalcubes/tests/tinytest.R | 14 gdalcubes-0.7.1/gdalcubes/tools/winlibs.R | 24 gdalcubes-0.7.1/gdalcubes/vignettes/gc01_MODIS.Rmd | 4 129 files changed, 5134 insertions(+), 5097 deletions(-)
Title: '2bit' 'C' Library
Description: A trimmed down copy of the "kent-core source tree"
turned into a 'C' library for manipulation of '.2bit' files.
See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7>
for a quick overview of the '2bit' format. The "kent-core source tree"
can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>.
Only the '.c' and '.h' files from the source tree that are related
to manipulation of '.2bit' files were kept. Note that the package
is primarily useful to developers of other R packages who wish
to use the '2bit' 'C' library in their own 'C'/'C++' code.
Author: Herve Pages [aut, cre],
UC Regents [cph]
Maintainer: Herve Pages <hpages.on.github@gmail.com>
Diff between Rtwobitlib versions 0.3.8 dated 2025-03-18 and 0.3.9 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary src/kent/Makefile.Rtwobitlib | 3 ++- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forth [...truncated...]
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
Kristina Wicke [aut],
John Rhodes [aut, cre]
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 3.1 dated 2025-03-07 and 3.2 dated 2025-03-19
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- R/ToBtoLevel1.R | 2 - R/evonetMisc.R | 63 +++++++++++++++++++++++++-------------------------- build/partial.rdb |binary man/resolveLevel1.Rd | 2 - 6 files changed, 42 insertions(+), 41 deletions(-)
Title: Bayesian Analysis of Dynamic Generalized Linear Models
Description: Provide routines for filtering and smoothing, forecasting, sampling and Bayesian analysis of Dynamic Generalized Linear Models using the methodology described in Alves et al. (2024)<doi:10.48550/arXiv.2201.05387> and dos Santos Jr. et al. (2024)<doi:10.48550/arXiv.2403.13069>.
Author: Silvaneo dos Santos Jr. [aut, cre],
Mariane Branco Alves [aut],
Helio dos Santos Migon [aut]
Maintainer: Silvaneo dos Santos Jr. <silvaneojunior@utexas.edu>
Diff between kDGLM versions 1.2.0 dated 2024-05-25 and 1.2.7 dated 2025-03-19
kDGLM-1.2.0/kDGLM/man/TF_block.Rd |only kDGLM-1.2.7/kDGLM/DESCRIPTION | 16 kDGLM-1.2.7/kDGLM/MD5 | 117 - kDGLM-1.2.7/kDGLM/NAMESPACE | 14 kDGLM-1.2.7/kDGLM/R/func_helper.R | 130 - kDGLM-1.2.7/kDGLM/R/kernel_gamma.R | 24 kDGLM-1.2.7/kDGLM/R/kernel_poisson.R | 3 kDGLM-1.2.7/kDGLM/R/kernels.R | 71 kDGLM-1.2.7/kDGLM/R/main.R | 284 +++ kDGLM-1.2.7/kDGLM/R/plot_helper.R | 10 kDGLM-1.2.7/kDGLM/R/priors.R | 36 kDGLM-1.2.7/kDGLM/R/structure_helper.R | 317 +++ kDGLM-1.2.7/kDGLM/build/partial.rdb |binary kDGLM-1.2.7/kDGLM/build/vignette.rds |binary kDGLM-1.2.7/kDGLM/inst/apalike.csl | 1172 ++++++------- kDGLM-1.2.7/kDGLM/inst/doc/example1.R | 142 - kDGLM-1.2.7/kDGLM/inst/doc/example1.Rmd | 19 kDGLM-1.2.7/kDGLM/inst/doc/example1.html | 2225 ++++++++++++++++++++++++-- kDGLM-1.2.7/kDGLM/inst/doc/fitting.R | 104 - kDGLM-1.2.7/kDGLM/inst/doc/fitting.html | 26 kDGLM-1.2.7/kDGLM/inst/doc/intro.R | 56 kDGLM-1.2.7/kDGLM/inst/doc/intro.Rmd | 75 kDGLM-1.2.7/kDGLM/inst/doc/intro.html | 2144 ++++++++++++++++++++++++- kDGLM-1.2.7/kDGLM/inst/doc/outcomes.R | 37 kDGLM-1.2.7/kDGLM/inst/doc/outcomes.Rmd | 3 kDGLM-1.2.7/kDGLM/inst/doc/outcomes.html | 29 kDGLM-1.2.7/kDGLM/inst/doc/structures.R | 308 +-- kDGLM-1.2.7/kDGLM/inst/doc/structures.Rmd | 22 kDGLM-1.2.7/kDGLM/inst/doc/structures.html | 58 kDGLM-1.2.7/kDGLM/man/CAR_prior.Rd | 11 kDGLM-1.2.7/kDGLM/man/Gamma.Rd | 3 kDGLM-1.2.7/kDGLM/man/analytic_filter.Rd | 4 kDGLM-1.2.7/kDGLM/man/block_mult.Rd | 1 kDGLM-1.2.7/kDGLM/man/block_rename.Rd | 1 kDGLM-1.2.7/kDGLM/man/block_superpos.Rd | 1 kDGLM-1.2.7/kDGLM/man/coef.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/man/eval_dlm_norm_const.Rd | 91 - kDGLM-1.2.7/kDGLM/man/ffs_block.Rd |only kDGLM-1.2.7/kDGLM/man/fit_model.Rd | 322 +-- kDGLM-1.2.7/kDGLM/man/fit_model_single.Rd | 46 kDGLM-1.2.7/kDGLM/man/forecast.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/man/formula.to.structure.Rd |only kDGLM-1.2.7/kDGLM/man/generic_smoother.Rd | 4 kDGLM-1.2.7/kDGLM/man/harmonic_block.Rd | 7 kDGLM-1.2.7/kDGLM/man/intervention.Rd | 1 kDGLM-1.2.7/kDGLM/man/joint_prior.Rd | 96 - kDGLM-1.2.7/kDGLM/man/kdglm.Rd |only kDGLM-1.2.7/kDGLM/man/noise_block.Rd | 6 kDGLM-1.2.7/kDGLM/man/noticeSARI.Rd | 60 kDGLM-1.2.7/kDGLM/man/polynomial_block.Rd | 7 kDGLM-1.2.7/kDGLM/man/reexports.Rd | 40 kDGLM-1.2.7/kDGLM/man/regression_block.Rd | 15 kDGLM-1.2.7/kDGLM/man/simulate.fitted_dlm.Rd | 103 - kDGLM-1.2.7/kDGLM/man/smoothing.Rd | 55 kDGLM-1.2.7/kDGLM/man/specify.dlm_block.Rd | 79 kDGLM-1.2.7/kDGLM/man/summary.dlm_block.Rd | 1 kDGLM-1.2.7/kDGLM/man/tf_block.Rd |only kDGLM-1.2.7/kDGLM/man/update.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/vignettes/example1.Rmd | 19 kDGLM-1.2.7/kDGLM/vignettes/intro.Rmd | 75 kDGLM-1.2.7/kDGLM/vignettes/outcomes.Rmd | 3 kDGLM-1.2.7/kDGLM/vignettes/structures.Rmd | 22 62 files changed, 6705 insertions(+), 1813 deletions(-)
Title: Statistical Combination of Diagnostic Tests
Description: A system for combining two diagnostic tests using various approaches
that include statistical and machine-learning-based methodologies.
These approaches are divided into four groups: linear combination
methods, non-linear combination methods, mathematical operators,
and machine learning algorithms. See
the <https://biotools.erciyes.edu.tr/dtComb/> website
for more information, documentation, and examples.
Author: Serra Ilayda Yerlitas [aut, ctb],
Serra Bersan Gengec [aut, ctb],
Necla Kochan [aut, ctb],
Gozde Erturk Zararsiz [aut, ctb],
Selcuk Korkmaz [aut, ctb],
Gokmen Zararsiz [aut, ctb, cre]
Maintainer: Gokmen Zararsiz <gokmen.zararsiz@gmail.com>
Diff between dtComb versions 1.0.4 dated 2024-10-11 and 1.0.5 dated 2025-03-19
dtComb-1.0.4/dtComb/data/exampleData1.rda |only dtComb-1.0.4/dtComb/man/exampleData1.Rd |only dtComb-1.0.5/dtComb/DESCRIPTION | 8 dtComb-1.0.5/dtComb/LICENSE | 2 dtComb-1.0.5/dtComb/MD5 | 70 ++-- dtComb-1.0.5/dtComb/R/data.R | 14 dtComb-1.0.5/dtComb/R/linComb.R | 36 +- dtComb-1.0.5/dtComb/R/mathComb.R | 10 dtComb-1.0.5/dtComb/R/mlComb.R | 6 dtComb-1.0.5/dtComb/R/nonlinComb.R | 4 dtComb-1.0.5/dtComb/R/plotComb.R | 278 ++++++++-------- dtComb-1.0.5/dtComb/R/predict.dtComb.R | 6 dtComb-1.0.5/dtComb/R/standardization.R | 304 +++++++++--------- dtComb-1.0.5/dtComb/data/laparoscopy.rda |only dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.R | 14 dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.Rnw | 16 dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.pdf |binary dtComb-1.0.5/dtComb/man/helper_PCL.Rd | 6 dtComb-1.0.5/dtComb/man/helper_PT.Rd | 6 dtComb-1.0.5/dtComb/man/helper_TS.Rd | 6 dtComb-1.0.5/dtComb/man/helper_minimax.Rd | 6 dtComb-1.0.5/dtComb/man/helper_minmax.Rd | 6 dtComb-1.0.5/dtComb/man/laparoscopy.Rd |only dtComb-1.0.5/dtComb/man/linComb.Rd | 6 dtComb-1.0.5/dtComb/man/mathComb.Rd | 6 dtComb-1.0.5/dtComb/man/mlComb.Rd | 6 dtComb-1.0.5/dtComb/man/nonlinComb.Rd | 4 dtComb-1.0.5/dtComb/man/plotComb.Rd | 6 dtComb-1.0.5/dtComb/man/predict.dtComb.Rd | 6 dtComb-1.0.5/dtComb/man/std.train.Rd | 4 dtComb-1.0.5/dtComb/man/transform_math.Rd | 4 dtComb-1.0.5/dtComb/tests/testthat/test-linComb.R | 6 dtComb-1.0.5/dtComb/tests/testthat/test-mathComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-mlComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-nonlinComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-predComb.R | 6 dtComb-1.0.5/dtComb/tests/testthat/test-standardize.R | 6 dtComb-1.0.5/dtComb/vignettes/vignettedtComb.Rnw | 16 38 files changed, 443 insertions(+), 443 deletions(-)
Title: Estimations using Conley Standard Errors
Description: Functions calculating Conley (1999) <doi:10.1016/S0304-4076(98)00084-0> standard errors. The package started by merging and extending multiple packages and
other published scripts on this econometric technique. It strongly emphasizes computational optimization. Details are available in the function documentation and in
the vignette.
Author: Christian Dueben [aut, cre],
Richard Bluhm [cph],
Luis Calderon [cph],
Darin Christensen [cph],
Timothy Conley [cph],
Thiemo Fetzer [cph],
Leander Heldring [cph]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Diff between conleyreg versions 0.1.7 dated 2022-03-03 and 0.1.8 dated 2025-03-19
DESCRIPTION | 16 MD5 | 54 +- NEWS.md | 4 R/conleyreg.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/conleyreg_introduction.R | 8 inst/doc/conleyreg_introduction.html | 670 +++++++++++++++++++++++++++++++---- src/Makevars | 12 src/Makevars.win | 12 src/XeeXhC.cpp | 1 src/XeeXhC.h | 1 src/XeeXhC_R.cpp | 1 src/dist_mat.cpp | 1 src/distance_functions.cpp | 1 src/distance_functions.h | 1 src/distance_matrices.cpp | 1 src/distance_matrices.h | 1 src/isbalanced.cpp | 3 src/lp.cpp | 1 src/lp_filling.cpp | 1 src/lp_filling.h | 1 src/lp_filling_R.cpp | 1 src/lp_vcov.cpp | 1 src/ols.cpp | 1 src/openmp_installed.cpp | 1 src/time_dist.cpp | 1 28 files changed, 646 insertions(+), 155 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Tymoteusz Kwiecinski [aut, cre]
,
Jakub Grzywaczewski [aut],
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>
Diff between SerolyzeR versions 1.0.0 dated 2025-03-07 and 1.1.0 dated 2025-03-19
DESCRIPTION | 11 MD5 | 71 +-- NAMESPACE | 2 R/classes-model.R | 227 +++++++++--- R/classes-plate.R | 37 +- R/classes-plate_builder.R | 42 ++ R/config.R | 2 R/generate_report.R | 404 ++++++++++------------ R/parser-xponent.R | 10 R/parser.R | 125 ++++-- R/plots-standard_curve.R | 6 R/process-dir.R | 151 +++++--- R/process-file.R | 71 ++- R/process-plate.R | 189 ++++------ README.md | 4 build/vignette.rds |binary inst/doc/example_script.R | 23 - inst/doc/example_script.Rmd | 76 +++- inst/doc/example_script.html | 199 ++++++---- inst/img/report_warnings.png |only inst/templates/levey_jennings_report_template.Rmd | 68 ++- inst/templates/plate_report_template.Rmd | 95 +++-- man/Model.Rd | 8 man/Plate.Rd | 38 +- man/PlateBuilder.Rd | 12 man/handle_high_dose_hook.Rd | 4 man/process_dir.Rd | 164 ++++++-- man/process_file.Rd | 95 +++-- man/process_plate.Rd | 154 ++++---- man/read_luminex_data.Rd | 109 ++++- man/translate_sample_names_to_sample_types.Rd | 3 tests/testthat/test-generate_report.R | 1 tests/testthat/test-model.R | 71 +++ tests/testthat/test-parser.R | 9 tests/testthat/test-process-dir.R | 53 ++ tests/testthat/test-process-plate.R | 17 vignettes/example_script.Rmd | 76 +++- 37 files changed, 1733 insertions(+), 894 deletions(-)
Title: Web Scraping and Bibliometric Analysis of MDPI Journals
Description: Provides comprehensive tools to scrape and analyze data from the MDPI journals. It allows users to extract metrics such as submission-to-acceptance times, article types, and whether articles are part of special issues. The package can also visualize this information through plots. Additionally, 'MDPIexploreR' offers tools to explore patterns of self-citations within articles and provides insights into guest-edited special issues.
Author: Pablo Gomez Barreiro [aut, cre]
Maintainer: Pablo Gomez Barreiro <pablogomezbr@hotmail.es>
Diff between MDPIexploreR versions 0.2.0 dated 2024-10-15 and 0.3.0 dated 2025-03-19
MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.R |only MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.Rmd |only MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.html |only MDPIexploreR-0.2.0/MDPIexploreR/vignettes/introduction_MDPIexploreR.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/DESCRIPTION | 11 MDPIexploreR-0.3.0/MDPIexploreR/MD5 | 64 ++- MDPIexploreR-0.3.0/MDPIexploreR/NAMESPACE | 4 MDPIexploreR-0.3.0/MDPIexploreR/NEWS.md | 29 + MDPIexploreR-0.3.0/MDPIexploreR/R/MDPI_journals.R | 7 MDPIexploreR-0.3.0/MDPIexploreR/R/article_find.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/article_info.R | 13 MDPIexploreR-0.3.0/MDPIexploreR/R/global.R | 7 MDPIexploreR-0.3.0/MDPIexploreR/R/guest_editor_info.R | 183 ---------- MDPIexploreR-0.3.0/MDPIexploreR/R/plot_articles.R | 88 ++++ MDPIexploreR-0.3.0/MDPIexploreR/R/selfcite_check.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/special_issue_find.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/special_issue_info.R |only MDPIexploreR-0.3.0/MDPIexploreR/R/topic_find.R |only MDPIexploreR-0.3.0/MDPIexploreR/R/topic_info.R |only MDPIexploreR-0.3.0/MDPIexploreR/README.md | 22 + MDPIexploreR-0.3.0/MDPIexploreR/build/vignette.rds |binary MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.R |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.html |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.R |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.html |only MDPIexploreR-0.3.0/MDPIexploreR/man/MDPI_journals.Rd | 46 +- MDPIexploreR-0.3.0/MDPIexploreR/man/agriculture.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/article_find.Rd | 44 +- MDPIexploreR-0.3.0/MDPIexploreR/man/article_info.Rd | 80 ++-- MDPIexploreR-0.3.0/MDPIexploreR/man/clean_names.Rd | 40 +- MDPIexploreR-0.3.0/MDPIexploreR/man/guest_editor_info.Rd | 85 ++-- MDPIexploreR-0.3.0/MDPIexploreR/man/horticulturae.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/plot_articles.Rd | 50 +- MDPIexploreR-0.3.0/MDPIexploreR/man/selfcite_check.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/special_issue_find.Rd | 56 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/special_issue_info.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/man/topic_find.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/man/topic_info.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/vignettes/article_functions.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/vignettes/plot_articles.Rmd |only 42 files changed, 498 insertions(+), 511 deletions(-)
Title: Robust Bayesian Elastic Net
Description: As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in 'C++' and R.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu@ksu.edu>
Diff between Bayenet versions 0.2 dated 2024-04-05 and 0.3 dated 2025-03-19
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/Bayenet-package.R | 8 ++++---- R/Bayenet.R | 2 +- R/Qenet.R | 2 +- R/Qenetss.R | 2 +- R/robust.R | 4 ++-- man/Bayenet-package.Rd | 8 ++++---- man/Bayenet.Rd | 2 +- 9 files changed, 28 insertions(+), 28 deletions(-)
Title: Vegetation Imaging Spectroscopy Analyzer
Description: Provides easy-to-use tools for data analysis and visualization for hyperspectral remote sensing (also known as imaging spectroscopy), with
a particular focus on vegetation hyperspectral data analysis. It consists of a set of functions, ranging from the organization of hyperspectral data
in the proper data structure for spectral feature selection, calculation of vegetation index, multivariate analysis, as well as to the visualization
of spectra and results of analysis in the 'ggplot2' style.
Author: Kang Yu [aut, cre]
Maintainer: Kang Yu <kang.yu@outlook.com>
Diff between visa versions 0.1.0 dated 2021-04-20 and 1.0.0 dated 2025-03-19
visa-0.1.0/visa/R/data-specdb.R |only visa-0.1.0/visa/R/ggspectra.R |only visa-0.1.0/visa/data/NSpec.DB.rda |only visa-0.1.0/visa/man/NSpec.DB.Rd |only visa-0.1.0/visa/man/SpectraDataFrame-class.Rd |only visa-0.1.0/visa/man/SpectraDataFrame.Rd |only visa-0.1.0/visa/man/SpectraDatabase-class.Rd |only visa-0.1.0/visa/man/SpectraMaxtrix-class.Rd |only visa-0.1.0/visa/man/ggplot.Rd |only visa-0.1.0/visa/man/wavelength-methods.Rd |only visa-1.0.0/visa/DESCRIPTION | 24 visa-1.0.0/visa/MD5 | 96 +- visa-1.0.0/visa/NAMESPACE | 67 + visa-1.0.0/visa/NEWS.md | 10 visa-1.0.0/visa/R/Spectra-class.R | 81 +- visa-1.0.0/visa/R/cm.nsr.R | 112 +-- visa-1.0.0/visa/R/cm.rbd3.R |only visa-1.0.0/visa/R/cm.sr.R | 108 +-- visa-1.0.0/visa/R/data-specdf.R | 6 visa-1.0.0/visa/R/data-speclib.R |only visa-1.0.0/visa/R/find.bestBands.R |only visa-1.0.0/visa/R/ggplot-method.R | 5 visa-1.0.0/visa/R/ggplot.cm.R |only visa-1.0.0/visa/R/ggplot.lmfit.R | 80 +- visa-1.0.0/visa/R/ggplot.spectra.R |only visa-1.0.0/visa/R/nsr.R |only visa-1.0.0/visa/R/plt.2dcm.R |only visa-1.0.0/visa/R/plt.3dcm_best.R |only visa-1.0.0/visa/R/spectra.R | 6 visa-1.0.0/visa/R/sr.R | 47 - visa-1.0.0/visa/R/visa.R | 14 visa-1.0.0/visa/R/wavelength.R | 67 + visa-1.0.0/visa/README.md | 29 visa-1.0.0/visa/build/vignette.rds |binary visa-1.0.0/visa/data/NSpec.Lib.rda |only visa-1.0.0/visa/inst/CITATION | 6 visa-1.0.0/visa/inst/doc/visa.R | 64 + visa-1.0.0/visa/inst/doc/visa.Rmd | 105 ++- visa-1.0.0/visa/inst/doc/visa.html | 707 ++++++++++++++++----- visa-1.0.0/visa/man/NSpec.DF.Rd | 6 visa-1.0.0/visa/man/NSpec.Lib.Rd |only visa-1.0.0/visa/man/Spectra-class.Rd | 124 +-- visa-1.0.0/visa/man/SpectraDataframe-class.Rd |only visa-1.0.0/visa/man/SpectraDataframe.Rd |only visa-1.0.0/visa/man/SpectraLibrary-class.Rd |only visa-1.0.0/visa/man/SpectraMatrix-class.Rd |only visa-1.0.0/visa/man/cm.nsr.Rd | 39 - visa-1.0.0/visa/man/cm.rbd3.Rd |only visa-1.0.0/visa/man/cm.sr.Rd | 36 - visa-1.0.0/visa/man/find.bestBands.Rd |only visa-1.0.0/visa/man/ggplot-method.Rd | 37 - visa-1.0.0/visa/man/ggplot.cm.Rd |only visa-1.0.0/visa/man/ggplot.spectra.Rd |only visa-1.0.0/visa/man/ndvi2.Rd | 2 visa-1.0.0/visa/man/nsr.Rd |only visa-1.0.0/visa/man/plt.2dcm.Rd |only visa-1.0.0/visa/man/plt.3dcm_best.Rd |only visa-1.0.0/visa/man/spectra-methods.Rd | 86 +- visa-1.0.0/visa/man/sr.Rd | 23 visa-1.0.0/visa/man/visa.Rd | 21 visa-1.0.0/visa/man/wavelength.Rd |only visa-1.0.0/visa/tests/testthat.R | 6 visa-1.0.0/visa/tests/testthat/test-ggplot.lmfit.R | 15 visa-1.0.0/visa/vignettes/visa.Rmd | 105 ++- visa-1.0.0/visa/vignettes/visa.txt | 174 ++++- 65 files changed, 1504 insertions(+), 804 deletions(-)
Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the
'bbotk' package. 'miesmuschel' offers both ready-to-use optimization
algorithms, as well as their fundamental building blocks that can be used to
manually construct specialized optimization loops. The Mixed Integer Evolution
Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be
implemented, as well as the multi-objective optimization algorithms NSGA-II
by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre],
Lennart Schneider [ctb] ,
Susanne Dandl [ctb] ,
Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between miesmuschel versions 0.0.4-2 dated 2024-07-09 and 0.0.4-3 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 29 +++++++++++++++-------------- NEWS.md | 10 +++++++--- R/FiltorMaybe.R | 4 ++-- R/FiltorNull.R | 4 ++-- R/FiltorProxy.R | 4 ++-- R/FiltorSurrogateProgressive.R | 4 ++-- R/FiltorSurrogateTournament.R | 4 ++-- R/OperatorCombination.R | 2 +- inst/tinytest/helper_mutators.R | 11 +++++++++++ inst/tinytest/test_mutator_sequential.R |only man/dict_filtors_maybe.Rd | 4 ++-- man/dict_filtors_null.Rd | 4 ++-- man/dict_filtors_proxy.Rd | 4 ++-- man/dict_filtors_surprog.Rd | 4 ++-- man/dict_filtors_surtour.Rd | 4 ++-- 16 files changed, 57 insertions(+), 41 deletions(-)
Title: Client for 'GoFigr.io'
Description: Integrates with your 'RMarkdown' documents to automatically publish
figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive
execution within 'RStudio'.
Author: Maciej Pacula [cre, aut],
Flagstaff Solutions, LLC [cph]
Maintainer: Maciej Pacula <maciej@gofigr.io>
Diff between gofigR versions 0.2.2 dated 2025-02-07 and 0.3.1 dated 2025-03-19
gofigR-0.2.2/gofigR/man/capture.Rd |only gofigR-0.2.2/gofigR/man/plot_interactive.Rd |only gofigR-0.2.2/gofigR/man/plot_knitr.Rd |only gofigR-0.2.2/gofigR/man/plot_rstudio.Rd |only gofigR-0.2.2/gofigR/man/plot_script.Rd |only gofigR-0.3.1/gofigR/DESCRIPTION | 9 gofigR-0.3.1/gofigR/MD5 | 34 - gofigR-0.3.1/gofigR/NAMESPACE | 9 gofigR-0.3.1/gofigR/R/api.R | 3 gofigR-0.3.1/gofigR/R/context.R |only gofigR-0.3.1/gofigR/R/gfconfig.R | 11 gofigR-0.3.1/gofigR/R/integrations.R | 684 ++++++++--------------- gofigR-0.3.1/gofigR/R/watermark.R | 45 + gofigR-0.3.1/gofigR/README.md | 99 +-- gofigR-0.3.1/gofigR/man/CONFIG_PATH.Rd |only gofigR-0.3.1/gofigR/man/check_configured.Rd |only gofigR-0.3.1/gofigR/man/enable.Rd | 8 gofigR-0.3.1/gofigR/man/get_execution_context.Rd |only gofigR-0.3.1/gofigR/man/get_title.Rd |only gofigR-0.3.1/gofigR/man/ggwatermark.Rd |only gofigR-0.3.1/gofigR/man/intercept.Rd | 13 gofigR-0.3.1/gofigR/man/is_intercept_on.Rd |only gofigR-0.3.1/gofigR/man/publish.Rd |only gofigR-0.3.1/gofigR/man/publish_base.Rd |only gofigR-0.3.1/gofigR/man/watermark_generator.Rd | 6 25 files changed, 397 insertions(+), 524 deletions(-)
Title: Download and Processing of Automatic Weather Stations (AWS) Data
of INMET-Brazil
Description: A compilation of functions to download and processing AWS data of INMET-Brazil, with the purpose of reference evapotranspiration (ETo) estimation. The package aims to make meteorological and agricultural data analysis more parsimonious.
Author: Roberto Filgueiras [aut, cre] ,
Luan P. Venancio [aut] ,
Catariny C. Aleman [aut] ,
Fernando F. da Cunha [aut]
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Diff between BrazilMet versions 0.2.0 dated 2022-10-27 and 0.3.0 dated 2025-03-19
BrazilMet-0.2.0/BrazilMet/man/figures/desktop.ini |only BrazilMet-0.3.0/BrazilMet/DESCRIPTION | 12 BrazilMet-0.3.0/BrazilMet/MD5 | 38 BrazilMet-0.3.0/BrazilMet/NAMESPACE | 82 - BrazilMet-0.3.0/BrazilMet/NEWS.md | 11 BrazilMet-0.3.0/BrazilMet/R/atmospheric_parameters.R | 27 BrazilMet-0.3.0/BrazilMet/R/conversion_factor_for_radiations.R | 57 - BrazilMet-0.3.0/BrazilMet/R/daily_download_AWS_INMET.R | 462 +++++----- BrazilMet-0.3.0/BrazilMet/R/daily_eto_FAO56.R | 174 +-- BrazilMet-0.3.0/BrazilMet/R/eto_hs.R | 14 BrazilMet-0.3.0/BrazilMet/R/etp_thorntwaite.R |only BrazilMet-0.3.0/BrazilMet/R/hourly_download_AWS_INMET.R |only BrazilMet-0.3.0/BrazilMet/R/radiation_parameters.R | 355 +++---- BrazilMet-0.3.0/BrazilMet/R/see_stations_info.R | 4 BrazilMet-0.3.0/BrazilMet/R/variables_air_humidity_2.R | 107 +- BrazilMet-0.3.0/BrazilMet/R/wind_speed_variables.R | 4 BrazilMet-0.3.0/BrazilMet/README.md |only BrazilMet-0.3.0/BrazilMet/man/daily_eto_FAO56.Rd | 6 BrazilMet-0.3.0/BrazilMet/man/download_AWS_INMET_daily.Rd | 10 BrazilMet-0.3.0/BrazilMet/man/eto_hs.Rd | 62 - BrazilMet-0.3.0/BrazilMet/man/etp_thorntwaite.Rd |only BrazilMet-0.3.0/BrazilMet/man/hourly_weather_station_download.Rd |only BrazilMet-0.3.0/BrazilMet/man/radiation_conversion.Rd | 6 23 files changed, 763 insertions(+), 668 deletions(-)
Title: Management and Processing of Autonomous Recording Unit (ARU)
Data
Description: Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings.
Extract Metadata from your recordings, select a subset of recordings for
interpretation, and prepare files for processing on the
'WildTrax' <https://wildtrax.ca/> platform. Read and process metadata
from recordings collected using the SongMeter and BAR-LT types of ARUs.
Author: David Hope [aut, cre] ,
Steffi LaZerte [aut] ,
Government of Canada [cph, fnd]
Maintainer: David Hope <david.hope@ec.gc.ca>
Diff between ARUtools versions 0.7.1 dated 2024-10-08 and 0.7.2 dated 2025-03-19
DESCRIPTION | 12 MD5 | 48 +- NEWS.md | 9 R/calc_sun.R | 4 R/checks.R | 3 R/create_dirs.R | 6 README.md | 2 build/vignette.rds |binary inst/doc/ARUtools.R | 6 inst/doc/ARUtools.html | 136 ++++---- inst/doc/Misc.R | 54 +-- inst/doc/SubSample.R | 86 ++--- inst/doc/SubSample.html | 502 +++++++++++++++---------------- inst/doc/customizing.R | 2 inst/doc/customizing.html | 518 ++++++++++++++++---------------- inst/doc/multisampling.html | 436 +++++++++++++------------- inst/doc/spatial.html | 306 +++++++++--------- inst/doc/timezones.html | 92 ++--- man/create_lookaround.Rd | 102 +++--- man/get_pattern.Rd | 44 +- man/guess_ARU_type.Rd | 50 +-- man/meta_clean_logs.Rd | 72 ++-- man/set_pattern.Rd | 58 +-- tests/testthat/_snaps/08_selections.md | 8 tests/testthat/test-02_clean_metadata.R | 8 25 files changed, 1286 insertions(+), 1278 deletions(-)
Title: Convert Digital Images into 'SpatRaster' Objects
Description: Generate 'SpatRaster' objects, as defined by the 'terra'
package, from digital images, using a specified spatial object as a
geographical reference.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rasterpic versions 0.2.6 dated 2024-12-17 and 0.3.0 dated 2025-03-19
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 107 +++---- R/rasterpic_img.R | 576 +++++++++++++++++++-------------------- README.md | 55 +++ build/vignette.rds |binary inst/doc/rasterpic.html | 10 inst/schemaorg.json | 4 tests/testthat/test-fileformat.R | 3 tests/testthat/test-nlayers.R | 1 10 files changed, 420 insertions(+), 360 deletions(-)
Title: Functions for Stochastic Search Variable Selection (SSVS)
Description: Functions for performing stochastic search variable selection (SSVS)
for binary and continuous outcomes and visualizing the results.
SSVS is a Bayesian variable selection method used to estimate the probability
that individual predictors should be included in a regression model.
Using MCMC estimation, the method samples thousands of regression models
in order to characterize the model uncertainty regarding both the predictor
set and the regression parameters. For details see Bainter, McCauley, Wager,
and Losin (2020) Improving practices for selecting a subset of important
predictors in psychology: An application to predicting pain, Advances in
Methods and Practices in Psychological Science 3(1), 66-80
<DOI:10.1177/2515245919885617>.
Author: Sierra Bainter [cre, aut] ,
Thomas McCauley [aut],
Mahmoud Fahmy [aut],
Dean Attali [aut]
Maintainer: Sierra Bainter <sbainter@miami.edu>
Diff between SSVS versions 2.0.0 dated 2022-05-29 and 2.1.0 dated 2025-03-19
DESCRIPTION | 23 +++---- MD5 | 40 ++++++++---- NAMESPACE | 6 + NEWS.md | 4 + R/SSVS.R | 6 + R/SSVS_MI.R |only R/imputed_mtcars.R |only R/plot.R | 19 +++-- R/plot_MI.R |only R/summary.R | 1 R/summary_MI.R |only R/utils-pipe.R |only R/utils.R | 6 + README.md | 112 +++++++++++++++++++++++++++-------- data/imputed_mtcars.RData |only inst/shiny/www/logo.png |binary man/figures/README-binary-plot-1.png |binary man/figures/README-plot-1.png |binary man/figures/logo.png |binary man/imputed_mtcars.Rd |only man/pipe.Rd |only man/plot.ssvs.Rd | 2 man/plot.ssvs_mi.Rd |only man/print.ssvs_mi_summary.Rd |only man/ssvs.Rd | 2 man/ssvs_mi.Rd |only man/summary.ssvs_mi.Rd |only 27 files changed, 158 insertions(+), 63 deletions(-)
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.2.0 dated 2024-12-11 and 1.2.1 dated 2025-03-19
DESCRIPTION | 8 ++-- MD5 | 36 +++++++++--------- NEWS.md | 6 +++ R/convert_time.R | 11 +++++ R/convert_units.R | 11 +++++ R/fipscounty.R | 11 +++++ R/grid.R | 22 ++++++++++- R/keywords.R | 12 +++++- R/servers.R | 11 +++++ R/table.R | 22 ++++++++++- R/version.R | 11 +++++ R/zzz.r | 12 +++++- build/vignette.rds |binary inst/doc/Using_rerddap.R | 43 ++++----------------- inst/doc/Using_rerddap.Rmd | 50 ++++++------------------- inst/doc/Using_rerddap.html | 87 +++++++++++++++----------------------------- inst/doc/rerddap.html | 5 +- vignettes/Using_rerddap.Rmd | 50 ++++++------------------- vignettes/ifrPSA.png |binary 19 files changed, 206 insertions(+), 202 deletions(-)
Title: The Fill-Mask Association Test
Description: The Fill-Mask Association Test ('FMAT')
<doi:10.1037/pspa0000396>
is an integrative and probability-based method using
Masked Language Models to measure conceptual associations
(e.g., attitudes, biases, stereotypes, social norms, cultural values)
as propositions in natural language.
Supported language models include 'BERT'
<doi:10.48550/arXiv.1810.04805> and its variants available at 'Hugging Face'
<https://huggingface.co/models?pipeline_tag=fill-mask>.
Methodological references and installation guidance are provided at
<https://psychbruce.github.io/FMAT/>.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between FMAT versions 2024.7 dated 2024-07-29 and 2025.3 dated 2025-03-19
DESCRIPTION | 14 +- MD5 | 20 ++- NAMESPACE | 5 NEWS.md | 8 + R/FMAT.R | 251 +++++++++++++++++++++++++++++++++++++++--------- README.md | 33 +++--- man/BERT_download.Rd | 5 man/BERT_info.Rd | 14 +- man/BERT_info_date.Rd |only man/FMAT_load.Rd | 2 man/FMAT_run.Rd | 2 man/set_cache_folder.Rd |only 12 files changed, 276 insertions(+), 78 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.9.0 dated 2024-11-23 and 0.10.0 dated 2025-03-19
DESCRIPTION | 15 +- MD5 | 120 +++++++++++----------- NEWS.md | 5 R/LearnerClassifCVGlmnet.R | 15 ++ R/LearnerClassifGlmnet.R | 14 +- R/LearnerClassifKKNN.R | 2 R/LearnerClassifLogReg.R | 58 +++++++--- R/LearnerClassifNnet.R | 2 R/LearnerClassifRanger.R | 12 +- R/LearnerClassifXgboost.R | 61 +++++++---- R/LearnerRegrCVGlmnet.R | 12 +- R/LearnerRegrGlmnet.R | 12 +- R/LearnerRegrKKNN.R | 2 R/LearnerRegrKM.R | 4 R/LearnerRegrLM.R | 45 +++++++- R/LearnerRegrNnet.R | 2 R/LearnerRegrRanger.R | 12 +- R/LearnerRegrXgboost.R | 38 ++++-- R/helpers_glmnet.R | 32 +++++ R/helpers_ranger.R | 23 ++++ build/partial.rdb |binary inst/paramtest/test_paramtest_classif.cv_glmnet.R | 6 - inst/paramtest/test_paramtest_classif.glmnet.R | 7 - inst/paramtest/test_paramtest_classif.logreg.R | 6 - inst/paramtest/test_paramtest_classif.xgboost.R | 2 inst/paramtest/test_paramtest_regr.cv_glmnet.R | 6 - inst/paramtest/test_paramtest_regr.glmnet.R | 7 - inst/paramtest/test_paramtest_regr.lm.R | 6 - inst/paramtest/test_paramtest_regr.xgboost.R | 2 man/mlr3learners-package.Rd | 1 man/mlr_learners_classif.cv_glmnet.Rd | 10 + man/mlr_learners_classif.glmnet.Rd | 11 +- man/mlr_learners_classif.kknn.Rd | 2 man/mlr_learners_classif.lda.Rd | 2 man/mlr_learners_classif.log_reg.Rd | 13 ++ man/mlr_learners_classif.multinom.Rd | 2 man/mlr_learners_classif.naive_bayes.Rd | 2 man/mlr_learners_classif.nnet.Rd | 2 man/mlr_learners_classif.qda.Rd | 2 man/mlr_learners_classif.ranger.Rd | 15 ++ man/mlr_learners_classif.svm.Rd | 2 man/mlr_learners_classif.xgboost.Rd | 12 +- man/mlr_learners_regr.cv_glmnet.Rd | 10 + man/mlr_learners_regr.glmnet.Rd | 11 +- man/mlr_learners_regr.kknn.Rd | 2 man/mlr_learners_regr.km.Rd | 4 man/mlr_learners_regr.lm.Rd | 13 ++ man/mlr_learners_regr.nnet.Rd | 2 man/mlr_learners_regr.ranger.Rd | 15 ++ man/mlr_learners_regr.svm.Rd | 2 man/mlr_learners_regr.xgboost.Rd | 12 +- tests/testthat/test_classif_glmnet.R | 41 +++++++ tests/testthat/test_classif_kknn.R | 2 tests/testthat/test_classif_log_reg.R | 55 ++++++++++ tests/testthat/test_classif_ranger.R | 11 +- tests/testthat/test_classif_xgboost.R | 69 ++++++++---- tests/testthat/test_regr_glmnet.R | 38 ++++++ tests/testthat/test_regr_kknn.R | 2 tests/testthat/test_regr_lm.R | 48 ++++++++ tests/testthat/test_regr_ranger.R | 10 + tests/testthat/test_regr_xgboost.R | 43 +++++-- 61 files changed, 787 insertions(+), 207 deletions(-)
Title: Mathijs Deen's Miscellaneous Auxiliaries
Description: Provides a variety of functions useful for data analysis,
selection, manipulation, and graphics.
Author: Mathijs Deen [aut, cre]
Maintainer: Mathijs Deen <dev@mathijsdeen.com>
Diff between MDMA versions 1.1.0 dated 2024-04-25 and 2.0.0 dated 2025-03-19
MDMA-1.1.0/MDMA/R/posteriorModelOdds.R |only MDMA-1.1.0/MDMA/man/posteriorModelOdds.Rd |only MDMA-2.0.0/MDMA/DESCRIPTION | 14 MDMA-2.0.0/MDMA/MD5 | 127 ++- MDMA-2.0.0/MDMA/NAMESPACE | 169 +++-- MDMA-2.0.0/MDMA/NEWS |only MDMA-2.0.0/MDMA/R/CEA.R |only MDMA-2.0.0/MDMA/R/CEAC.R |only MDMA-2.0.0/MDMA/R/QIDS-data.R | 30 MDMA-2.0.0/MDMA/R/R2.vglm.R |only MDMA-2.0.0/MDMA/R/auc.R | 42 - MDMA-2.0.0/MDMA/R/check.R | 264 ++++---- MDMA-2.0.0/MDMA/R/coefsLogReg.R | 62 - MDMA-2.0.0/MDMA/R/corList.R | 44 - MDMA-2.0.0/MDMA/R/currency2unicode.R |only MDMA-2.0.0/MDMA/R/dPPC2.R | 150 ++-- MDMA-2.0.0/MDMA/R/f2Local.R |only MDMA-2.0.0/MDMA/R/frequencies.R | 46 - MDMA-2.0.0/MDMA/R/gnomes-data.R |only MDMA-2.0.0/MDMA/R/inRange.R | 108 +-- MDMA-2.0.0/MDMA/R/keep.R | 62 - MDMA-2.0.0/MDMA/R/m.R | 56 - MDMA-2.0.0/MDMA/R/ni.R | 32 MDMA-2.0.0/MDMA/R/pMM.R |only MDMA-2.0.0/MDMA/R/plotDistribution.R | 138 ++-- MDMA-2.0.0/MDMA/R/probeInteraction.R | 366 +++++------ MDMA-2.0.0/MDMA/R/rci.R | 42 - MDMA-2.0.0/MDMA/R/roc.R | 368 +++++------ MDMA-2.0.0/MDMA/R/tTest.R | 460 +++++++------- MDMA-2.0.0/MDMA/R/wtp.R |only MDMA-2.0.0/MDMA/R/zzz.R |only MDMA-2.0.0/MDMA/data/QIDS.rda |binary MDMA-2.0.0/MDMA/data/gnomes.rda |only MDMA-2.0.0/MDMA/man/CEA.Rd |only MDMA-2.0.0/MDMA/man/CEAC.Rd |only MDMA-2.0.0/MDMA/man/QIDS.Rd | 50 - MDMA-2.0.0/MDMA/man/R2.vglm.Rd |only MDMA-2.0.0/MDMA/man/auc.Rd | 56 - MDMA-2.0.0/MDMA/man/check.Rd | 150 ++-- MDMA-2.0.0/MDMA/man/coefsLogReg.Rd | 62 - MDMA-2.0.0/MDMA/man/corList.Rd | 56 - MDMA-2.0.0/MDMA/man/currency2unicode.Rd |only MDMA-2.0.0/MDMA/man/dPPC2.Rd | 104 +-- MDMA-2.0.0/MDMA/man/f2Local.Rd |only MDMA-2.0.0/MDMA/man/figures/lifecycle-archived.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-defunct.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-deprecated.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-experimental.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-maturing.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-questioning.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-soft-deprecated.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-stable.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-superseded.svg | 44 - MDMA-2.0.0/MDMA/man/frequencies.Rd | 50 - MDMA-2.0.0/MDMA/man/gnomes.Rd |only MDMA-2.0.0/MDMA/man/grapes-inRange-grapes.Rd | 74 +- MDMA-2.0.0/MDMA/man/grapes-ni-grapes.Rd | 60 - MDMA-2.0.0/MDMA/man/grapes-withinRange-grapes.Rd | 76 +- MDMA-2.0.0/MDMA/man/keep.Rd | 74 +- MDMA-2.0.0/MDMA/man/m.Rd | 68 +- MDMA-2.0.0/MDMA/man/pMM.Rd |only MDMA-2.0.0/MDMA/man/plot.CEA.Rd |only MDMA-2.0.0/MDMA/man/plot.CEAC.Rd |only MDMA-2.0.0/MDMA/man/plot.probeInteraction.Rd | 108 +-- MDMA-2.0.0/MDMA/man/plot.roc.Rd | 150 ++-- MDMA-2.0.0/MDMA/man/plotDistribution.Rd | 140 ++-- MDMA-2.0.0/MDMA/man/print.check.lm.Rd | 64 - MDMA-2.0.0/MDMA/man/print.probeInteraction.Rd | 62 - MDMA-2.0.0/MDMA/man/print.tTest.Rd | 60 - MDMA-2.0.0/MDMA/man/print.wtp.Rd |only MDMA-2.0.0/MDMA/man/probeInteraction.Rd | 114 +-- MDMA-2.0.0/MDMA/man/rci.Rd | 72 +- MDMA-2.0.0/MDMA/man/roc.Rd | 82 +- MDMA-2.0.0/MDMA/man/summary.tTest.Rd | 68 +- MDMA-2.0.0/MDMA/man/tTest.Rd | 152 ++-- MDMA-2.0.0/MDMA/man/wtp.Rd |only MDMA-2.0.0/MDMA/tests |only 77 files changed, 2496 insertions(+), 2432 deletions(-)
Title: Generating Features for a Cohort
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Author: Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Jenna Reps [aut],
Anthony Sena [aut],
Ger Inberg [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between FeatureExtraction versions 3.7.2 dated 2024-10-18 and 3.8.0 dated 2025-03-19
FeatureExtraction-3.7.2/FeatureExtraction/inst/java/SqlRender-1.15.0.jar |only FeatureExtraction-3.7.2/FeatureExtraction/inst/java/featureExtraction-3.7.1-SNAPSHOT.jar |only FeatureExtraction-3.8.0/FeatureExtraction/DESCRIPTION | 10 FeatureExtraction-3.8.0/FeatureExtraction/MD5 | 95 +- FeatureExtraction-3.8.0/FeatureExtraction/NEWS.md | 8 FeatureExtraction-3.8.0/FeatureExtraction/R/Aggregation.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/CompareCohorts.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/CovariateData.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultTemporalCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultTemporalSequenceCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DetailedCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/FeatureExtraction.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariates.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariatesFromCohortAttributes.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariatesFromOtherCohorts.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetDefaultCovariates.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/HelperFunctions.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/Normalization.R | 5 FeatureExtraction-3.8.0/FeatureExtraction/R/Table1.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/UnitTestHelperFunctions.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/build/vignette.rds |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/csv/PrespecTemporalAnnualAnalysis.csv |only FeatureExtraction-3.8.0/FeatureExtraction/inst/csv/jarChecksum.txt | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.R | 160 ++-- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.R | 112 +-- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.R | 216 +++--- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.R | 224 +++--- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.R | 236 +++---- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.R | 232 +++---- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/java/SqlRender-1.19.1.jar |only FeatureExtraction-3.8.0/FeatureExtraction/inst/java/featureExtraction-3.8.0-SNAPSHOT.jar |only FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/DomainConcept.sql | 20 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/GetAttrCovariates.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/GetHdpsCovariates.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/IncludeDescendants.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/RemoveCovariateTempTables.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/FeatureExtraction.java | 326 +++++----- FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/ReadCSVFile.java | 2 FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCohortAttrCovariatesData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCohortBasedCovariatesData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCovariateData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbDefaultCovariateData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/tests/testthat/test-DetailedCovariateSettings.R | 2 51 files changed, 892 insertions(+), 816 deletions(-)
More information about FeatureExtraction at CRAN
Permanent link
Title: Apply Transformations to Data
Description: Provides a set of functions for data transformations.
Transformations are performed on character and numeric data. As the scope of the package is
within Student Analytics, there are functions focused around the academic year.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvconverter versions 0.5.10 dated 2024-06-11 and 0.7.0 dated 2025-03-19
vvconverter-0.5.10/vvconverter/tests/testthat/test-month_name.R |only vvconverter-0.5.10/vvconverter/tests/testthat/test-test-yes-no.R |only vvconverter-0.5.10/vvconverter/tests/testthat/test-transform-logical-yes-no.R |only vvconverter-0.7.0/vvconverter/DESCRIPTION | 6 +-- vvconverter-0.7.0/vvconverter/MD5 | 12 ++---- vvconverter-0.7.0/vvconverter/R/month_name.R | 10 ++++- vvconverter-0.7.0/vvconverter/R/test_yes_no.R | 7 +++ vvconverter-0.7.0/vvconverter/R/transform_logical_yes_no.R | 20 +++++++++- vvconverter-0.7.0/vvconverter/tests/testthat/test_clean_multiple_underscores.R |only 9 files changed, 41 insertions(+), 14 deletions(-)
Title: 'Rcpp' Implementation of Dirichlet Process Regression
Description: 'Rcpp' reimplementation of the the Bayesian non-parametric Dirichlet Process Regression model for penalized regression first published in Zeng and Zhou (2017) <doi:10.1038/s41467-017-00470-2>. A full Bayesian version is implemented with Gibbs sampling, as well as a faster but less accurate variational Bayes approximation.
Author: Mohammad Abu Gazala [cre, aut],
Daniel Nachun [ctb],
Ping Zeng [ctb]
Maintainer: Mohammad Abu Gazala <abugazalamohammad@gmail.com>
Diff between RcppDPR versions 0.1.9 dated 2025-03-15 and 0.1.10 dated 2025-03-19
RcppDPR-0.1.10/RcppDPR/DESCRIPTION | 6 ++--- RcppDPR-0.1.10/RcppDPR/MD5 | 11 +++------- RcppDPR-0.1.10/RcppDPR/NEWS.md | 2 + RcppDPR-0.1.10/RcppDPR/src/ldr.cpp | 13 +++--------- RcppDPR-0.1.10/RcppDPR/src/root_solver.cpp | 2 - RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.bed |only RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.bim |only RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.fam |only 8 files changed, 14 insertions(+), 20 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the
'pedsuite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.9.4 dated 2024-05-08 and 0.9.5 dated 2025-03-19
DESCRIPTION | 16 ++-- MD5 | 42 +++++------ NEWS.md | 19 ++++- R/genoCombinations.R | 4 - R/likelihood.R | 11 +-- R/likelihood2.R | 3 R/merlin.R | 2 R/oneMarkerDistribution.R | 131 +++++++++++++++++++++++++++--------- R/startdata.R | 26 ++++--- R/twoMarkerDistribution.R | 62 +++++++++-------- R/utils.R | 18 +--- README.md | 55 ++++++++++----- build/partial.rdb |binary man/genoCombinations.Rd | 4 - man/likelihood.Rd | 10 -- man/merlin.Rd | 2 man/oneMarkerDistribution.Rd | 69 +++++++++++------- man/pedprobr-package.Rd | 2 man/twoMarkerDistribution.Rd | 44 +++++------- tests/testthat/test-likelihood.R | 14 ++- tests/testthat/test-oneMarkerDist.R | 77 ++++++++++++--------- tests/testthat/test-twoMarkerDist.R | 92 ++++++++++++------------- 22 files changed, 424 insertions(+), 279 deletions(-)
Title: Processing Force-Plate Data
Description: Process raw force-plate data (txt-files) by segmenting them into trials and, if needed, calculating (user-defined) descriptive
statistics of variables for user-defined time bins (relative to trigger onsets) for each trial. When segmenting the data a baseline
correction, a filter, and a data imputation can be applied if needed. Experimental data can also be processed and combined with the
segmented force-plate data. This procedure is suggested by Johannsen et al. (2023) <doi:10.6084/m9.figshare.22190155> and some of the
options (e.g., choice of low-pass filter) are also suggested by Winter (2009) <doi:10.1002/9780470549148>.
Author: Raphael Hartmann [aut, cre] ,
Anton Koger [aut, ctb] ,
Leif Johannsen [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between forceplate versions 1.1-3 dated 2024-03-12 and 1.1-4 dated 2025-03-19
DESCRIPTION | 14 ++-- MD5 | 6 +- R/segment_fp_data.R | 138 ++++++++++++++++++++++++++++++++++--------------- man/segment_fp_data.Rd | 74 +++++++++++++++----------- 4 files changed, 150 insertions(+), 82 deletions(-)
Title: Execute Pharmacometric Models Using 'shiny'
Description: Execute Nonlinear Mixed Effects (NLME) models for pharmacometrics using a 'shiny'
interface. Specify engine parameters and select from different run options, including
simple estimation, stepwise covariate search, bootstrapping, simulation, visual predictive
check, and more. Models are executed using the 'Certara.RsNLME' package.
Author: James Craig [aut, cre],
Mike Talley [aut],
Vitalii Nazarov [aut],
Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.RsNLME.ModelExecutor versions 3.0.1 dated 2025-01-07 and 3.0.2 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 5 ++++- R/modelExecutorUI.R | 6 ++---- 4 files changed, 12 insertions(+), 11 deletions(-)
More information about Certara.RsNLME.ModelExecutor at CRAN
Permanent link
Title: Calculate Indices of Dynamic Interaction for Wildlife Tracking
Data
Description: Dynamic interaction refers to spatial-temporal associations in the movements of two (or more) animals. This package provides tools for calculating a suite of indices used for quantifying dynamic interaction with wildlife telemetry data. For more information on each of the methods employed see the references within. The package (as of version >= 0.3) also has new tools for automating contact analysis in large tracking datasets. The package (as of version 1.0) uses the 'move2' class of objects for working with tracking dataset.
Author: Jed Long [aut, cre, cph]
Maintainer: Jed Long <jed.long@uwo.ca>
Diff between wildlifeDI versions 1.0.0 dated 2024-03-22 and 1.0.1 dated 2025-03-19
DESCRIPTION | 14 +- MD5 | 22 +-- NEWS | 4 R/Prox.R | 2 R/checkTO.R | 2 R/conProcess.R | 6 - R/wildlifeDI-package.r | 5 README.md | 118 +++++++-------------- build/vignette.rds |binary inst/doc/wildlifeDI-vignette-contact_analysis.html | 80 +++++++------- inst/doc/wildlifeDI-vignette.html | 18 +-- man/wildlifeDI-package.Rd | 9 + 12 files changed, 131 insertions(+), 149 deletions(-)
Title: Programmatic Access to the European Central Bank's Data Portal
Description: Provides an interface to the European Central Bank's Data
Portal API, allowing for programmatic retrieval of a vast quantity
of statistical data.
Author: Eric Persson [aut, cre],
Franz X. Mohr [ctb]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ecb versions 0.4.2 dated 2023-04-20 and 0.4.3 dated 2025-03-19
ecb-0.4.2/ecb/inst/doc/ecb_sdw.R |only ecb-0.4.2/ecb/inst/doc/ecb_sdw.Rmd |only ecb-0.4.2/ecb/inst/doc/ecb_sdw.html |only ecb-0.4.2/ecb/vignettes/ecb_sdw.Rmd |only ecb-0.4.2/ecb/vignettes/phillips_plot-1.png |only ecb-0.4.3/ecb/DESCRIPTION | 30 - ecb-0.4.3/ecb/MD5 | 39 -- ecb-0.4.3/ecb/NAMESPACE | 14 ecb-0.4.3/ecb/R/get_historical_sdw.R | 96 ++--- ecb-0.4.3/ecb/R/main.R | 533 +++++++++++++--------------- ecb-0.4.3/ecb/build/vignette.rds |binary ecb-0.4.3/ecb/inst/doc/ecb_edp.R |only ecb-0.4.3/ecb/inst/doc/ecb_edp.Rmd |only ecb-0.4.3/ecb/inst/doc/ecb_edp.html |only ecb-0.4.3/ecb/man/convert_dates.Rd | 44 +- ecb-0.4.3/ecb/man/get_data.Rd | 134 +++---- ecb-0.4.3/ecb/man/get_dataflows.Rd | 42 +- ecb-0.4.3/ecb/man/get_description.Rd | 40 +- ecb-0.4.3/ecb/man/get_dimensions.Rd | 46 +- ecb-0.4.3/ecb/tests/testthat.R | 8 ecb-0.4.3/ecb/tests/testthat/tests.R | 116 +++--- ecb-0.4.3/ecb/vignettes/ecb_edp.Rmd |only ecb-0.4.3/ecb/vignettes/hicp_plot-1.png |binary ecb-0.4.3/ecb/vignettes/screenshot.png |binary ecb-0.4.3/ecb/vignettes/screenshot2.png |binary 25 files changed, 567 insertions(+), 575 deletions(-)
Title: Fitting (Exponential/Diffusion) RT-MPT Models
Description: Fit (exponential or diffusion) response-time extended multinomial processing tree (RT-MPT) models
by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003> and Klauer, Hartmann, and Meyer-Grant (submitted).
The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models,
but also latencies. This enables it to estimate process completion times and encoding plus motor execution times
next to the process probabilities of traditional MPTs. 'rtmpt' is a hierarchical Bayesian framework and posterior
samples are sampled using a Metropolis-within-Gibbs sampler (for exponential RT-MPTs) or Hamiltonian-within-Gibbs
sampler (for diffusion RT-MPTs).
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Constantin G. Meyer-Grant [aut, ctb],
Henrik Singmann [ctb, aut],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 2.0-2 dated 2025-01-23 and 2.0-3 dated 2025-03-19
DESCRIPTION | 6 +- MD5 | 28 ++++++------ R/call_rtmpt.R | 95 +++++++++++++++++++++++++++--------------- R/get_indices.R | 1 R/get_infofile.R | 2 R/make_mcmc.R | 4 - R/print_rtmpt.R | 2 R/simulate_rtmpt.R | 2 R/simulate_rtmpt_SBC.R | 2 inst/doc/rtmpt_guideline.html | 4 - man/fit_drtmpt.Rd | 2 man/fit_ertmpt.Rd | 2 src/diagnosis.cpp | 60 +++++++++++++++----------- src/main.cpp | 6 ++ src/r_wrapper.cpp | 43 ++++++++++--------- 15 files changed, 157 insertions(+), 102 deletions(-)
Title: Calculate Surface/Image Texture Indexes
Description: Methods for the computation of surface/image texture indices using a geostatistical based approach (Trevisani et al. (2023) <doi:10.1016/j.geomorph.2023.108838>). It provides various functions for the computation of surface texture indices (e.g., omnidirectional roughness and roughness anisotropy), including the ones based on the robust MAD estimator. The kernels included in the software permit also to calculate the surface/image texture indices directly from the input surface (i.e., without de-trending) using increments of order 2. It also provides the new radial roughness index (RRI), representing the improvement of the popular topographic roughness index (TRI). The framework can be easily extended with ad-hoc surface/image texture indices.
Author: Sebastiano Trevisani [aut, cre]
,
Ilich Alexander [ctb] ,
Zakharko Taras [ctb]
Maintainer: Sebastiano Trevisani <strevisani@iuav.it>
Diff between SurfRough versions 0.0.1.0 dated 2024-08-30 and 0.0.1.1 dated 2025-03-19
DESCRIPTION | 15 + MD5 | 29 ++- NAMESPACE | 14 + R/GeostTextureLibrarySharedRoxy.R | 336 +++++++++++++++++++++++++++++++++++--- R/RcppExports.R |only R/package.R |only README.md | 8 man/Madscan.Rd | 91 +++++----- man/Meanscan.Rd | 73 ++++---- man/RRI.Rd | 99 ++++++----- man/RRIK3.Rd |only man/RRIMax.Rd |only man/RRIMin.Rd |only man/Trik2.Rd | 91 +++++----- man/Trik2.SpatRaster.Rd |only man/Trik2.numeric.Rd |only man/circularDispersionGV.Rd | 53 +++-- man/circularDispersionNV.Rd | 55 +++--- src |only 19 files changed, 602 insertions(+), 262 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.63.0 dated 2025-03-01 and 0.64.0 dated 2025-03-19
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------ NAMESPACE | 6 +++ NEWS.md | 34 ++++++++++++++---- R/anova.R | 92 +++++++++++++++++++++++++++++++++++++++++++------ R/fetch.R |only R/mplm.R | 6 +-- R/plm.R | 7 +++ R/plm_contrasts.R | 4 +- R/print-export-plm.R | 16 +++++--- R/private-regression.R | 33 ++++++++--------- R/private_options.R | 2 - R/scan.R | 2 + man/anova.sc_plm.Rd | 52 +++++++++++++++++++++++---- man/fetch.Rd |only 15 files changed, 219 insertions(+), 69 deletions(-)
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elemental indexes are first calculated for a collection
of elemental aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.8.1 dated 2024-09-12 and 0.8.2 dated 2025-03-19
DESCRIPTION | 15 MD5 | 207 ++- NAMESPACE | 14 NEWS.md | 47 R/aggregate.piar_index.R | 301 +++-- R/aggregation_structure-class.R | 10 R/aggregation_structure.R | 20 R/as_aggregation_structure.R | 3 R/as_index.R | 65 - R/chain.R | 19 R/coerce-aggregation_structure.R | 60 - R/coerce-index.R | 47 R/contrib.R | 94 + R/cut.piar_aggregation_structure.R |only R/elemental_index.R | 132 -- R/expand_classification.R | 33 R/extract.piar_index.R | 187 +-- R/head.piar_index.R | 2 R/helpers.R |only R/impute_prices.R | 58 R/index-class.R | 41 R/is.na.piar_index.R | 2 R/levels.piar_aggregation_structure.R | 10 R/levels.piar_index.R | 10 R/mean.piar_index.R | 155 +- R/merge.piar_index.R | 6 R/price_relative.R | 18 R/split.piar_index.R | 27 R/split_classification.R |only R/stack.piar_index.R | 10 R/time.piar_index.R | 8 R/update.aggregation_structure.R | 17 R/weights.piar_aggregation_structure.R | 22 R/window.piar_index.R | 46 README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/adjust-weights.R |only inst/doc/adjust-weights.Rmd |only inst/doc/adjust-weights.html |only inst/doc/contributions.R |only inst/doc/contributions.Rmd |only inst/doc/contributions.html |only inst/doc/imputation.R |only inst/doc/imputation.Rmd |only inst/doc/imputation.html |only inst/doc/index-number-formulas.R |only inst/doc/index-number-formulas.Rmd |only inst/doc/index-number-formulas.html |only inst/doc/matrix-aggregation.R |only inst/doc/matrix-aggregation.Rmd |only inst/doc/matrix-aggregation.html |only inst/doc/multiple-baskets.R |only inst/doc/multiple-baskets.Rmd |only inst/doc/multiple-baskets.html |only inst/doc/multiple-data-sources.R |only inst/doc/multiple-data-sources.Rmd |only inst/doc/multiple-data-sources.html |only inst/doc/multiple-dimensions.R |only inst/doc/multiple-dimensions.Rmd |only inst/doc/multiple-dimensions.html |only inst/doc/piar.R | 314 ----- inst/doc/piar.Rmd | 575 +-------- inst/doc/piar.html | 992 +++-------------- inst/doc/spatial-price-index.R |only inst/doc/spatial-price-index.Rmd |only inst/doc/spatial-price-index.html |only inst/doc/subperiods.R |only inst/doc/subperiods.Rmd |only inst/doc/subperiods.html |only inst/doc/superlative-aggregation.R |only inst/doc/superlative-aggregation.Rmd |only inst/doc/superlative-aggregation.html |only man/aggregate.piar_index.Rd | 27 man/aggregation_structure.Rd | 5 man/as.data.frame.piar_index.Rd | 20 man/as.matrix.piar_aggregation_structure.Rd | 33 man/as.ts.piar_index.Rd |only man/as_aggregation_structure.Rd | 3 man/as_index.Rd | 14 man/chain.Rd | 1 man/contrib.Rd | 23 man/cut.piar_aggregation_structure.Rd |only man/elemental_index.Rd | 15 man/expand_classification.Rd | 7 man/head.piar_index.Rd | 1 man/impute_prices.Rd | 12 man/is.na.piar_index.Rd | 1 man/levels.piar_aggregation_structure.Rd | 1 man/levels.piar_index.Rd | 5 man/mean.piar_index.Rd | 5 man/merge.piar_index.Rd | 1 man/split.piar_index.Rd | 5 man/split_classification.Rd |only man/stack.piar_index.Rd | 1 man/sub-.piar_index.Rd | 1 man/time.piar_index.Rd | 6 man/update.piar_aggregation_structure.Rd | 5 man/weights.piar_aggregation_structure.Rd | 9 man/window.piar_index.Rd | 1 tests/Examples/piar-Ex.Rout.save | 160 ++ tests/test-making-price-indexes.R | 2 tests/test-making-price-indexes.Rout.save | 2 tests/testthat/test-aggregate.R | 49 tests/testthat/test-aggregation-structure-attributes.R | 40 tests/testthat/test-aggregation_structure.R | 28 tests/testthat/test-as.ts.R |only tests/testthat/test-as_index.R | 32 tests/testthat/test-coerce-aggregation-structure.R | 11 tests/testthat/test-coerce-index.R | 23 tests/testthat/test-contrib.R | 51 tests/testthat/test-cut.R |only tests/testthat/test-expand_classification.R | 3 tests/testthat/test-extract-index.R | 23 tests/testthat/test-split.R | 6 tests/testthat/test-split_classification.R |only tests/testthat/test-stack.R | 2 tests/testthat/test-update.R | 36 vignettes/adjust-weights.Rmd |only vignettes/contributions.Rmd |only vignettes/imputation.Rmd |only vignettes/index-number-formulas.Rmd |only vignettes/matrix-aggregation.Rmd |only vignettes/multiple-baskets.Rmd |only vignettes/multiple-data-sources.Rmd |only vignettes/multiple-dimensions.Rmd |only vignettes/piar.Rmd | 575 +-------- vignettes/spatial-price-index.Rmd |only vignettes/subperiods.Rmd |only vignettes/superlative-aggregation.Rmd |only 131 files changed, 2002 insertions(+), 2819 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 10.0.0 dated 2025-03-12 and 10.0.1 dated 2025-03-19
DESCRIPTION | 11 +++--- LICENSE | 2 - MD5 | 22 ++++++------ NAMESPACE | 2 + NEWS.md | 4 ++ R/msigdbr-check-data.R | 55 +++++++++++++++++++------------- R/msigdbr-package.R | 3 + R/msigdbr.R | 68 ++++++++++++++++++++++----------------- README.md | 8 ---- build/partial.rdb |binary man/msigdbr_check_data.Rd | 5 ++ tests/testthat/test-msigdbr.R | 72 +++++++++++------------------------------- 12 files changed, 122 insertions(+), 130 deletions(-)
Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a
C API that can be used to write high-performance C and C++
geometry operations using R as an interface. Headers are provided
to make linking to and using these functions from C++ code as
easy and as safe as possible. This package contains an internal
copy of the 'GEOS' library to guarantee the best possible
consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] ,
GEOS authors [aut],
Martin Davis [ctb, cph],
Benjamin Campbell [ctb, cph],
Tomasz Sowa [ctb, cph],
Christian Kaiser [ctb, cph],
David Skea [ctb, cph],
Daniel Baston [ctb, cph],
Sandro Santilli [ctb, cph],
Mateusz Loskot [...truncated...]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between libgeos versions 3.11.1-2 dated 2023-11-29 and 3.11.1-3 dated 2025-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 10 +++++++--- src/geos_include/nlohmann_json.hpp | 4 ++-- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.9.2 dated 2025-03-12 and 0.10.1 dated 2025-03-19
DESCRIPTION | 16 ++++++++-------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 5 +++++ NEWS.md | 15 ++++++++++++--- R/countTokens.R |only R/gemini.R | 8 +++++--- R/gemini_audio.R | 19 +++++++++++-------- R/gemini_chat.R | 16 +++++++++++----- R/gemini_image.R | 16 +++++++++++----- R/gen_docs.R | 2 -- R/setEnv.R |only R/vertex.R | 2 +- man/countTokens.Rd |only man/gemini.Rd | 2 +- man/gemini_audio.Rd | 2 +- man/gemini_chat.Rd | 2 +- man/gemini_image.Rd | 2 +- man/setEnv.Rd |only 18 files changed, 85 insertions(+), 52 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.3-2 dated 2024-09-18 and 3.3-3 dated 2025-03-18
DESCRIPTION | 16 +++++------ MD5 | 18 ++++++------ NEWS | 13 +++++++++ R/random.R | 63 ++++++++++++++++++++++++++++++++++++++++++++- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/macros/defns.Rd | 4 ++ man/rpoispp.Rd | 39 ++++++++++++++++++++------- man/rpoistrunc.Rd | 5 +++ tests/Random.R | 11 +++++++ 10 files changed, 140 insertions(+), 31 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs. The methods are described in Leifeld, Cranmer and Desmarais (2018), JStatSoft <doi:10.18637/jss.v083.i06>.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between btergm versions 1.10.12 dated 2024-03-31 and 1.11.1 dated 2025-03-18
DESCRIPTION | 20 +- MD5 | 32 +-- NAMESPACE | 14 - R/btergm.R | 116 ++++++------- R/chemnet.R | 7 R/gofmethods.R | 18 -- R/gofstatistics.R | 141 ++++++---------- R/knecht.R | 3 R/mtergm.R | 7 build/partial.rdb |binary man/btergm.Rd | 12 + man/chemnet.Rd | 7 man/knecht.Rd | 3 man/mtergm.Rd | 5 tests/testthat/test-btergm.R | 13 - tests/testthat/test-data.R | 2 tests/testthat/test-gof.R | 366 ++++++++++++++++++++++++++++++++++++++++++- 17 files changed, 543 insertions(+), 223 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre],
Michael https://github.com/MichaelChirico [ctb],
R Core Team [cph]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.21 dated 2024-05-18 and 1.4.22 dated 2025-03-18
DESCRIPTION | 14 ++++++++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 10 +++++----- NEWS.md | 7 +++++++ R/conditions.R | 16 ++++++++++++++-- R/deparse.R | 4 +++- R/item.sub.R | 2 +- R/load.R | 2 ++ R/state.compare.R | 9 ++++++--- R/unitizer-package.R | 3 +-- build/vignette.rds |binary inst/doc/u1_intro.R | 18 +++++++++--------- inst/doc/u1_intro.html | 7 ++++--- man/all.equal.condition.Rd | 4 ++-- man/all_eq.Rd | 2 +- man/unitizer.Rd | 18 ++++++++++++++++++ 16 files changed, 98 insertions(+), 48 deletions(-)
Title: Weighted Mean SHAP and CI for Robust Feature Assessment in ML
Grid
Description: This R package introduces Weighted Mean SHapley Additive exPlanations (WMSHAP), an innovative method for calculating SHAP values for a grid of fine-tuned base-learner machine learning models as well as stacked ensembles, a method not previously available due to the common reliance on single best-performing models. By integrating the weighted mean SHAP values from individual base-learners comprising the ensemble or individual base-learners in a tuning grid search, the package weights SHAP contributions according to each model's performance, assessed by multiple either R squared (for both regression and classification models). alternatively, this software also offers weighting SHAP values based on the area under the precision-recall curve (AUCPR), the area under the curve (AUC), and F2 measures for binary classifiers. It further extends this framework to implement weighted confidence intervals for weighted mean SHAP values, offering a more comprehensive and robust feature importance eval [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between shapley versions 0.4 dated 2024-10-22 and 0.5 dated 2025-03-18
shapley-0.4/shapley/R/shapley.feature.selection.R |only shapley-0.4/shapley/R/shapley.test.R |only shapley-0.4/shapley/R/test.R |only shapley-0.4/shapley/man/figures/best.png |only shapley-0.4/shapley/man/figures/logo.png |only shapley-0.4/shapley/man/figures/logo2.png |only shapley-0.4/shapley/man/figures/logocopy.png |only shapley-0.4/shapley/man/figures/shap.png |only shapley-0.4/shapley/man/figures/shapleylow.png |only shapley-0.4/shapley/man/figures/waffle.png |only shapley-0.4/shapley/man/shapley.feature.selection.Rd |only shapley-0.4/shapley/man/shapley.test.Rd |only shapley-0.4/shapley/man/test.Rd |only shapley-0.5/shapley/DESCRIPTION | 45 ----- shapley-0.5/shapley/MD5 | 49 ++--- shapley-0.5/shapley/NAMESPACE | 5 shapley-0.5/shapley/R/feature.selection.R |only shapley-0.5/shapley/R/feature.test.R |only shapley-0.5/shapley/R/shapley.R | 159 +++++++++--------- shapley-0.5/shapley/R/shapley.domain.R | 46 +---- shapley-0.5/shapley/R/shapley.feature.test.R |only shapley-0.5/shapley/R/shapley.plot.R | 42 +--- shapley-0.5/shapley/R/shapley.table.R |only shapley-0.5/shapley/R/shapley.top.R | 33 ++- shapley-0.5/shapley/README.md | 21 +- shapley-0.5/shapley/man/feature.selection.Rd |only shapley-0.5/shapley/man/feature.test.Rd |only shapley-0.5/shapley/man/figures/best.jpeg |only shapley-0.5/shapley/man/figures/shap.jpeg |only shapley-0.5/shapley/man/figures/shapley.png |binary shapley-0.5/shapley/man/figures/shapley_algorithm.jpg |only shapley-0.5/shapley/man/figures/waffle.jpg |only shapley-0.5/shapley/man/shapley.Rd | 134 +++++++-------- shapley-0.5/shapley/man/shapley.domain.Rd | 28 +-- shapley-0.5/shapley/man/shapley.feature.test.Rd |only shapley-0.5/shapley/man/shapley.plot.Rd | 27 +-- shapley-0.5/shapley/man/shapley.table.Rd |only shapley-0.5/shapley/man/shapley.top.Rd | 23 +- 38 files changed, 284 insertions(+), 328 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 1.0.0 dated 2025-03-10 and 1.0.1 dated 2025-03-18
DESCRIPTION | 22 +++++++++++----------- MD5 | 8 ++++---- R/file_loaders.R | 1 + build/vignette.rds |binary tests/testthat/test-file_loaders.R | 4 ++-- 5 files changed, 18 insertions(+), 17 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert [aut, cre, cph]
,
ZeroMQ authors [aut, cph]
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.9.7 dated 2025-02-09 and 0.9.8 dated 2025-03-18
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/qsys_local.r | 4 +++- R/qsys_lsf.r | 4 +++- R/qsys_multicore.r | 4 +++- R/qsys_multiprocess.r | 4 +++- R/qsys_sge.r | 12 +++++++++--- R/qsys_slurm.r | 4 +++- R/qsys_ssh.r | 4 +++- build/vignette.rds |binary src/cppzmq/zmq.hpp | 8 ++++---- 12 files changed, 50 insertions(+), 27 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 0.3.4 dated 2024-04-11 and 0.3.5 dated 2025-03-18
butcher-0.3.4/butcher/R/nested_model_fit.R |only butcher-0.3.4/butcher/build/butcher.pdf |only butcher-0.3.4/butcher/man/axe-nested_model_fit.Rd |only butcher-0.3.4/butcher/tests/testthat/test-nested_model_fit.R |only butcher-0.3.5/butcher/DESCRIPTION | 19 - butcher-0.3.5/butcher/MD5 | 34 +-- butcher-0.3.5/butcher/NAMESPACE | 5 butcher-0.3.5/butcher/NEWS.md | 26 +- butcher-0.3.5/butcher/R/utilities.R | 4 butcher-0.3.5/butcher/README.md | 10 butcher-0.3.5/butcher/build/stage23.rdb |binary butcher-0.3.5/butcher/build/vignette.rds |binary butcher-0.3.5/butcher/inst/doc/adding-models-to-butcher.R | 118 +++++------ butcher-0.3.5/butcher/inst/doc/adding-models-to-butcher.html | 3 butcher-0.3.5/butcher/inst/doc/available-axe-methods.R | 6 butcher-0.3.5/butcher/inst/doc/available-axe-methods.Rmd | 6 butcher-0.3.5/butcher/inst/doc/available-axe-methods.html | 76 +++---- butcher-0.3.5/butcher/inst/doc/butcher.R | 4 butcher-0.3.5/butcher/inst/doc/butcher.html | 5 butcher-0.3.5/butcher/vignettes/available-axe-methods.Rmd | 6 20 files changed, 153 insertions(+), 169 deletions(-)
Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible!
The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation.
The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup. The diagram may show thousands of them. The position of the dot in the diagram is determined by the
sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore, the diagram shows the line of no effect and the overall study results. For small subgroups, which are found on the left side of the plot, larger random deviations from the mean study effect are expected, while for larger subgroups only small deviations from the study mean can be expected to be chance findings.
So for a study with no conspicuous subgroup ef [...truncated...]
Author: Bodo Kirsch [aut, cre],
Steffen Jeske [aut],
Julia Eichhorn [aut],
Susanne Lippert [aut],
Thomas Schmelter [aut],
Christoph Muysers [aut],
Hermann Kulmann [aut]
Maintainer: Bodo Kirsch <kirschbodo@gmail.com>
Diff between subscreen versions 3.0.7 dated 2022-05-12 and 4.0.1 dated 2025-03-18
DESCRIPTION | 68 MD5 | 118 NAMESPACE | 24 NEWS.md | 330 R/fct_createColorVector.R |only R/fct_createFilteredTable.R |only R/fct_createParentTable.R |only R/fct_createPlot_points_data_complement.R |only R/fct_displayOptionsPanel.R |only R/fct_subscreen_interactionPlot.R |only R/fct_subscreen_mosaicPlot.R |only R/fct_subscreen_parents.R |only R/fct_variableOptionsPanel.R |only R/importance.R |only R/mod_asmus_v2.R |only R/mod_bubble.R |only R/mod_color.R |only R/mod_comparer.R |only R/mod_graph.R |only R/mod_legend.R |only R/mod_mosaic.R |only R/mod_upload_tab.R |only R/mod_variable_importance.R |only R/results.R |only R/results_complement_true.R |only R/results_factorial_complement_true.R |only R/results_factorial_true.R |only R/subscreencalc.R | 912 +- R/subscreenshow.R | 168 R/subscreenvi.R | 231 R/utils_createCombinationMatrix.R |only R/utils_different_hues.R |only R/utils_font_color.R |only R/utils_is_integer0.R |only R/utils_pseudo_contexts.R |only R/utils_pseudo_func.R |only R/utils_roundDownNice.R |only R/utils_roundUpNice.R |only R/utils_shinyInput.R |only R/utils_shinyInput_remove.R |only README.md |only build/vignette.rds |binary data |only inst/doc/subscreen.html | 1562 +++ inst/doc/subscreen.rmd | 886 ++ inst/shiny-app/subscreen/app.R | 7774 ++++--------------- inst/www/SubgroupExplorer_Logo_final.png |only inst/www/SubgroupExplorer_Logo_final_inverted.png |only inst/www/sge_style.css |only inst/www/sge_style_dark.css |only inst/www/subscreen_asmus_multiplicity_0.1.png |only inst/www/subscreen_asmus_multiplicity_0.25.png |only inst/www/subscreen_asmus_multiplicity_0.5.png |only inst/www/subscreen_logo_inverted.png |only inst/www/subscreencalc_verbose.png |only inst/www/subscreenshow_ASMUS.png |only inst/www/subscreenshow_ASMUS_include_option.png |only inst/www/subscreenshow_ASMUS_page2.png |only inst/www/subscreenshow_ASMUS_rel_rem_options.png |only inst/www/subscreenshow_ASMUS_w_text.png |only inst/www/subscreenshow_Explorer_Graph.png |only inst/www/subscreenshow_Explorer_Plot_gold.png |only inst/www/subscreenshow_Explorer_Plot_green.png |only inst/www/subscreenshow_Explorer_Plot_red.png |only inst/www/subscreenshow_Explorer_Plot_red_hover.png |only inst/www/subscreenshow_Explorer_filter_green.png |only inst/www/subscreenshow_Explorer_interaction_plot.png |only inst/www/subscreenshow_Explorer_table_selected.png |only inst/www/subscreenshow_Upload_demo_info.png |only inst/www/subscreenshow_Upload_start.png |only inst/www/subscreenshow_colourOptions.png |only inst/www/subscreenshow_comparer.png |only inst/www/subscreenshow_comparer_clicked.png |only inst/www/subscreenshow_displayOptions.png |only inst/www/subscreenshow_importance.png |only inst/www/subscreenshow_mosaic.png |only inst/www/subscreenshow_mosaic_2f.png |only inst/www/subscreenshow_mosaic_2factors.png |only inst/www/subscreenshow_mosaic_3f.png |only inst/www/subscreenshow_mosaic_3factors.png |only inst/www/subscreenshow_variableOptions.png |only man/createFilteredTable.Rd |only man/createParentTable.Rd |only man/createPlot_points_data_complement.Rd |only man/displayOptionsPanel.Rd |only man/importance.Rd |only man/interaction_plot2.Rd |only man/parents.Rd |only man/pseudo_contexts.Rd |only man/pseudo_func.Rd |only man/results.Rd |only man/results_complement_true.Rd |only man/results_factorial_complement_true.Rd |only man/results_factorial_true.Rd |only man/subscreen_mosaicPlot.Rd |only man/subscreencalc.Rd | 295 man/subscreenshow.Rd | 19 man/subscreenvi.Rd | 128 man/variableOptionsPanel.Rd |only vignettes/subscreen.rmd | 886 ++ 100 files changed, 6428 insertions(+), 6973 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.2.0 dated 2025-01-24 and 5.2.1 dated 2025-03-18
DESCRIPTION | 8 +++--- MD5 | 52 ++++++++++++++++++++++---------------------- NAMESPACE | 3 +- NEWS | 11 +++++++++ R/fastsecrloglik.R | 20 +++++++++++++--- R/generalsecrloglik.R | 18 ++++++++++----- R/secr.fit.R | 51 ++++++++++++++++++++++++++++++++++++------- R/secr.refit.R |only R/sim.detect.R | 27 +++++++++++++++------- R/utility.R | 32 ++++++++++++++++++++++++--- inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.pdf |binary man/AIC.secr.Rd | 6 ++--- man/MCgof.Rd | 4 +-- man/RSE.Rd | 2 - man/circular.Rd | 2 - man/derivedMS.Rd | 6 ++--- man/details.Rd | 17 +++++++++++++- man/detectfn.Rd | 4 +-- man/empirical.Rd | 14 +++++------ man/esaPlot.Rd | 2 - man/fxi.Rd | 4 +-- man/modelAverage.Rd | 4 +-- man/rbind.capthist.Rd | 2 - man/secr-package.Rd | 4 +-- man/secr.fit.Rd | 7 ++++- man/secr.refit.Rd |only man/utility.Rd | 4 +-- 28 files changed, 212 insertions(+), 92 deletions(-)
Title: Meta-Analysis of Medians
Description: Implements several methods to meta-analyze studies that report the
sample median of the outcome. The methods described by
McGrath et al. (2019) <doi:10.1002/sim.8013>,
Ozturk and Balakrishnan (2020) <doi:10.1002/sim.8738>, and
McGrath et al. (2020a) <doi:10.1002/bimj.201900036> can be
applied to directly meta-analyze the median or difference of medians between
groups. Additionally, a number of methods (e.g., McGrath et al. (2020b)
<doi:10.1177/0962280219889080>, Cai et al. (2021)
<doi:10.1177/09622802211047348>, and McGrath et al. (2023)
<doi:10.1177/09622802221139233>) are implemented to estimate
study-specific (difference of) means and their standard errors in order to
estimate the pooled (difference of) means. Methods for meta-analyzing median
survival times (McGrath et al. (2025) <doi:10.48550/arXiv.2503.03065>) are
also implemented. See McGrath et al. (2024) <doi:10.1002/jrsm.1686> for a
detailed guide on using the package.
Author: Sean McGrath [aut, cre] ,
XiaoFei Zhao [aut],
Stephan Katzenschlager [aut],
Omer Ozturk [aut],
Renata Iskander [ctb],
Russell Steele [aut],
Andrea Benedetti [aut]
Maintainer: Sean McGrath <sean.mcgrath514@gmail.com>
Diff between metamedian versions 1.1.1 dated 2023-12-13 and 1.2.1 dated 2025-03-18
metamedian-1.1.1/metamedian/R/print.qe.fit.R |only metamedian-1.1.1/metamedian/R/qe.fit.R |only metamedian-1.2.1/metamedian/DESCRIPTION | 33 + metamedian-1.2.1/metamedian/MD5 | 41 +- metamedian-1.2.1/metamedian/NAMESPACE | 1 metamedian-1.2.1/metamedian/NEWS.md | 11 metamedian-1.2.1/metamedian/R/data.R | 27 + metamedian-1.2.1/metamedian/R/describe_studies.R | 8 metamedian-1.2.1/metamedian/R/metamean.R | 5 metamedian-1.2.1/metamedian/R/metamedian.R | 2 metamedian-1.2.1/metamedian/R/metamedian_survival.R |only metamedian-1.2.1/metamedian/R/qe.R | 2 metamedian-1.2.1/metamedian/R/qe.study.level.R | 8 metamedian-1.2.1/metamedian/README.md | 172 +++++++++- metamedian-1.2.1/metamedian/data/dat.lung.rda |only metamedian-1.2.1/metamedian/inst |only metamedian-1.2.1/metamedian/man/dat.lung.Rd |only metamedian-1.2.1/metamedian/man/describe_studies.Rd | 8 metamedian-1.2.1/metamedian/man/figures |only metamedian-1.2.1/metamedian/man/metamean.Rd | 2 metamedian-1.2.1/metamedian/man/metamedian-defunct.Rd | 4 metamedian-1.2.1/metamedian/man/metamedian.Rd | 2 metamedian-1.2.1/metamedian/man/metamedian_survival.Rd |only metamedian-1.2.1/metamedian/man/qe.Rd | 2 metamedian-1.2.1/metamedian/man/qe.study.level.Rd | 8 metamedian-1.2.1/metamedian/tests/testthat/test-metamedian_survival.R |only 26 files changed, 266 insertions(+), 70 deletions(-)
Title: Tools for Exploring Multivariate Data via ICS/ICA
Description: Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009,
<doi:10.1111/j.1467-9868.2009.00706.x>) and Oja, Sirkia and Eriksson's
(AJS, 2006, <https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different
scatter matrices to obtain an invariant coordinate system or independent
components, depending on the underlying assumptions.
Author: Klaus Nordhausen [aut, cre] ,
Andreas Alfons [aut] ,
Aurore Archimbaud [aut] ,
Hannu Oja [aut] ,
Anne Ruiz-Gazen [aut] ,
David E. Tyler [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICS versions 1.4-1 dated 2023-09-21 and 1.4-2 dated 2025-03-18
DESCRIPTION | 8 MD5 | 20 NEWS | 5 R/ICS_S3.R | 2561 ++++++++++++++++++------------------- R/covW.R | 130 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/ICS.pdf |binary inst/doc/paper |only man/ICS-S3.Rd | 3 tests/testthat/test-ICS_S3_tests.R | 332 ++-- 11 files changed, 1536 insertions(+), 1523 deletions(-)
Title: Split-Apply-Combine with Dynamic Groups
Description: Estimate group aggregates, where one can set user-defined conditions
that each group of records must satisfy to be suitable for aggregation. If
a group of records is not suitable, it is expanded using a collapsing scheme
defined by the user. A paper on this package was published in the Journal
of Statistical Software <doi:10.18637/jss.v112.i04>.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between accumulate versions 0.9.3 dated 2023-09-22 and 1.0.0 dated 2025-03-18
DESCRIPTION | 11 MD5 | 15 - NEWS | 3 R/accumulate.R | 5 build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.html | 651 +++++++++++++++++++++++++-------------------- man/accumulate.Rd | 4 vignettes/style.css | 39 -- 9 files changed, 406 insertions(+), 322 deletions(-)
Title: Access Data from the Oregon State Prism Climate Project
Description: Allows users to access the Oregon State Prism climate data
(<https://prism.nacse.org/>). Using the web service API data
can easily downloaded in bulk and loaded into R for spatial analysis.
Some user friendly visualizations are also provided.
Author: Hart Edmund [aut, ccp],
Kendon Bell [aut],
Alan Butler [ctb, cre]
Maintainer: Alan Butler <rabutler@usbr.gov>
Diff between prism versions 0.2.1 dated 2023-10-18 and 0.2.2 dated 2025-03-18
DESCRIPTION | 8 MD5 | 92 ++-- NEWS.md | 15 R/get_prism_annual.R | 36 - R/get_prism_dailys.R | 17 R/get_prism_monthlys.R | 33 - R/get_prism_normals.R | 113 ++++- R/pd_get.R | 68 ++- R/pd_get_md.R | 9 R/pd_get_station_md.R | 15 R/pd_stack.R | 4 R/prism_archive_clean.R | 6 R/prism_archive_ls.R | 2 R/prism_archive_subset.R | 76 ++- R/prism_archive_verify.R | 9 R/prism_set_dl_dir.R | 15 R/prism_webservice.R | 44 +- R/utility_functions.R | 85 ++-- README.md | 93 +++- build/vignette.rds |binary inst/doc/prism.R | 212 +++++----- inst/doc/prism.html | 4 man/figures/README-quick_plot-1.png |binary man/figures/README-raster_math-1.png |binary man/get_prism_data.Rd | 39 + man/pd_get.Rd | 35 + man/pd_get_md.Rd | 9 man/pd_get_station_md.Rd | 7 man/pd_stack.Rd | 5 man/prism_archive_clean.Rd | 11 man/prism_archive_subset.Rd | 9 man/prism_archive_verify.Rd | 12 man/prism_set_dl_dir.Rd | 15 tests/testthat/prism_test/PRISM_ppt_30yr_normal_4kmD1_0301_bil.zip |only tests/testthat/prism_test/README.md | 5 tests/testthat/setup-prism.R | 4 tests/testthat/teardown-prism.R | 4 tests/testthat/test-files_download.R | 67 ++- tests/testthat/test-gen_dates.R | 87 ++-- tests/testthat/test-get_prism_.R |only tests/testthat/test-get_prism_normals.R | 62 ++ tests/testthat/test-pd_get.R | 26 + tests/testthat/test-pd_get_md.R | 16 tests/testthat/test-pd_get_station_md.R | 5 tests/testthat/test-prism_archive_clean.R | 10 tests/testthat/test-prism_archive_ls.R | 2 tests/testthat/test-prism_archive_subset.R | 91 +++- tests/testthat/test-prism_archive_verify.R | 2 48 files changed, 1062 insertions(+), 417 deletions(-)
Title: Visualize Simon's Two-Stage Design
Description: To visualize the probabilities of early termination, fail
and success of Simon's two-stage design. To evaluate and
visualize the operating characteristics of Simon's two-stage
design.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between VisualizeSimon2Stage versions 0.1.6 dated 2024-10-27 and 0.1.7 dated 2025-03-18
VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/R/Simon_oc.R |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/R/Simon_pr.R |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/R/autoplot.ph2simon.R |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/R/ph2simon_etc.R |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/Simon_oc.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/Simon_pr.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/Sprintf.Simon_oc.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/Sprintf.ph2simon.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/autoplot.ph2simon.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/show-Simon_oc-method.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/show-Simon_pr-method.Rd |only VisualizeSimon2Stage-0.1.6/VisualizeSimon2Stage/man/summary.ph2simon.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/DESCRIPTION | 29 ++-- VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/MD5 | 50 ++++---- VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/NAMESPACE | 52 +++++--- VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/NEWS.md | 2 VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/0PACKAGE.R | 27 ++++ VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/0S4.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/Sprintf.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/autoplot.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/ph2simon4.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/print.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/r_simon.R | 59 +++++++--- VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/show.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/simon_oc.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/simon_pr.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/R/summary.R |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/README.md |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/build/partial.rdb |binary VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/inst |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/Sprintf.simon_oc.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/Sprintf_ph2simon.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/VisualizeSimon2Stage-package.Rd | 29 ++++ VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/gg_ph2simon.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/ph2simon4.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/print_ph2simon.Rd | 9 - VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/r_simon.Rd | 47 +++++-- VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/show_simon.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/simon_oc.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/simon_pr.Rd |only VisualizeSimon2Stage-0.1.7/VisualizeSimon2Stage/man/summary_ph2simon.Rd |only 41 files changed, 209 insertions(+), 95 deletions(-)
More information about VisualizeSimon2Stage at CRAN
Permanent link
Title: Parsimonious Gaussian Mixture Models
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
Author: Paul D. McNicholas [aut, cre] ,
Aisha ElSherbiny [aut],
K. Raju Jampani [ctb],
Aaron F. McDaid [aut],
T. Brendan Murphy [aut],
Larry Banks [ctb]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between pgmm versions 1.2.7 dated 2023-09-25 and 1.2.8 dated 2025-03-18
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/pgmmEM.R | 6 +++--- man/pgmm.Rd | 4 ++-- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: A General Framework for Combining Ecosystem Models
Description: Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<doi:10.1111/faf.12310>.
Author: Michael A. Spence [aut, cre] ,
James A. Martindale [aut] ,
Michael J. Thomson [aut] ,
Thomas I. J. Bartos [aut]
Maintainer: Michael A. Spence <michael.spence@cefas.gov.uk>
Diff between EcoEnsemble versions 1.1.0 dated 2024-08-19 and 1.1.2 dated 2025-03-18
DESCRIPTION | 14 MD5 | 48 +- NEWS.md | 40 +- R/EcoEnsemble-package.R | 54 +- R/EnsembleData-class.R | 2 R/fit_ensemble.R | 27 + build/vignette.rds |binary inst/doc/BetaConjugatePrior.R | 28 - inst/doc/BetaConjugatePrior.html | 260 ++++++------- inst/doc/EcoEnsemble.R | 14 inst/doc/EcoEnsemble.html | 114 +++--- inst/doc/ExploringPriors.R | 2 inst/doc/ExploringPriors.html | 268 +++++++------- inst/doc/IncludingDrivers.R | 16 inst/doc/SyntheticData.R | 2 inst/doc/SyntheticData.html | 318 ++++++++--------- inst/stan/ensemble_model_hierarchical_withdrivers.stan | 4 inst/stan/ensemble_model_withdrivers.stan | 4 inst/stan/ensemble_prior_hierarchical_withdrivers.stan | 4 inst/stan/ensemble_prior_withdrivers.stan | 4 man/EnsembleData.Rd | 2 man/fit_ensemble_model.Rd | 2 man/get_mcmc_ensemble_model.Rd | 4 man/sample_prior.Rd | 2 tests/testthat/test-get_stanmodel.R | 5 25 files changed, 636 insertions(+), 602 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 2.1.1 dated 2025-03-10 and 2.1.2 dated 2025-03-18
DESCRIPTION | 8 +- MD5 | 8 +- R/corrplot.r | 13 ++-- R/rare_multiplot.r | 168 ++++++++++++++++++++++++++--------------------------- R/write_biom.r | 8 +- 5 files changed, 106 insertions(+), 99 deletions(-)
Title: Extra 'Recipes' for Text Processing
Description: Converting text to numerical features requires specifically
created procedures, which are implemented as steps according to the
'recipes' package. These steps allows for tokenization, filtering,
counting (tf and tfidf) and feature hashing.
Author: Emil Hvitfeldt [aut, cre] ,
Michael W. Kearney [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between textrecipes versions 1.0.7 dated 2025-01-23 and 1.1.0 dated 2025-03-18
DESCRIPTION | 12 MD5 | 140 ++-- NAMESPACE | 5 NEWS.md | 10 R/aaa.R | 10 R/clean_levels.R | 28 R/clean_names.R | 24 R/count_functions.R | 99 ++- R/dummy_hash.R | 99 ++- R/import-standalone-obj-type.R | 107 +-- R/import-standalone-types-check.R | 293 +++++----- R/lda.R | 59 +- R/lemma.R | 28 R/ngram-c.R | 6 R/ngram.R | 43 - R/pos_filter.R | 20 R/sequence_onehot.R | 72 +- R/show_tokens.R | 2 R/stem.R | 30 - R/stopwords.R | 46 + R/text_normalization.R | 29 R/textfeature.R | 51 + R/texthash.R | 106 ++- R/textrecipes-package.R | 1 R/tf.R | 159 ++++- R/tfidf.R | 130 +++- R/tokenfilter.R | 75 +- R/tokenize.R | 79 +- R/tokenize_bpe.R | 49 + R/tokenize_sentencepiece.R | 55 + R/tokenize_wordpiece.R | 37 - R/tokenizer-sentencepiece.R | 3 R/tokenizer-udpipe.R | 3 R/tokenlist.R | 30 - R/tokenmerge.R | 46 - R/untokenize.R | 20 R/word_embeddings.R | 71 +- inst/doc/cookbook---using-more-complex-recipes-involving-text.html | 4 man/step_dummy_hash.Rd | 19 man/step_texthash.Rd | 19 man/step_tf.Rd | 26 man/step_tfidf.Rd | 19 tests/embeddings/embeddings-references.R | 34 - tests/testthat/_snaps/tokenmerge.md | 8 tests/testthat/test-clean_levels.R | 42 - tests/testthat/test-clean_names.R | 36 - tests/testthat/test-dummy_hash.R | 199 ++++-- tests/testthat/test-lda.R | 101 +-- tests/testthat/test-lemma.R | 44 - tests/testthat/test-ngram.R | 89 ++- tests/testthat/test-pos_filter.R | 46 - tests/testthat/test-s3-methods.R | 14 tests/testthat/test-sequence_onehot.R | 192 ++++-- tests/testthat/test-stem.R | 46 - tests/testthat/test-stopwords.R | 50 - tests/testthat/test-text_normalization.R | 28 tests/testthat/test-textfeature.R | 123 ++-- tests/testthat/test-texthash.R | 147 +++-- tests/testthat/test-tf.R | 264 ++++++--- tests/testthat/test-tfidf.R | 189 +++++- tests/testthat/test-tokenfilter.R | 48 - tests/testthat/test-tokenize.R | 51 - tests/testthat/test-tokenize_bpe.R | 116 ++- tests/testthat/test-tokenize_sentencepiece.R | 136 +++- tests/testthat/test-tokenize_wordpiece.R | 34 - tests/testthat/test-tokenizer-spacyr.R | 20 tests/testthat/test-tokenizer-tokenizersbpe.R | 91 ++- tests/testthat/test-tokenlist.R | 65 +- tests/testthat/test-tokenmerge.R | 54 - tests/testthat/test-untokenize.R | 42 - tests/testthat/test-word_embeddings.R | 140 ++-- 71 files changed, 3017 insertions(+), 1596 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library for reliable, high-performance messaging over in-process,
IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability
Protocols', a standard for common communications patterns including
publish/subscribe, request/reply and service discovery. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing. Intuitive 'aio' objects resolve automatically when
asynchronous operations complete, and synchronisation primitives allow R to
wait upon events signalled by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.5.1 dated 2025-02-16 and 1.5.2 dated 2025-03-18
nanonext-1.5.1/nanonext/src/nng-110.tar.xz |only nanonext-1.5.2/nanonext/DESCRIPTION | 6 nanonext-1.5.2/nanonext/MD5 | 174 +-- nanonext-1.5.2/nanonext/NAMESPACE | 2 nanonext-1.5.2/nanonext/NEWS.md | 10 nanonext-1.5.2/nanonext/R/aio.R | 189 +-- nanonext-1.5.2/nanonext/R/context.R | 85 - nanonext-1.5.2/nanonext/R/docs.R | 504 ++++------ nanonext-1.5.2/nanonext/R/listdial.R | 77 - nanonext-1.5.2/nanonext/R/messenger.R | 18 nanonext-1.5.2/nanonext/R/nano.R | 75 - nanonext-1.5.2/nanonext/R/nanonext-package.R | 54 - nanonext-1.5.2/nanonext/R/ncurl.R | 143 +- nanonext-1.5.2/nanonext/R/opts.R | 78 - nanonext-1.5.2/nanonext/R/sendrecv.R | 106 +- nanonext-1.5.2/nanonext/R/socket.R | 66 - nanonext-1.5.2/nanonext/R/stream.R | 24 nanonext-1.5.2/nanonext/R/sync.R | 126 +- nanonext-1.5.2/nanonext/R/tls.R | 57 - nanonext-1.5.2/nanonext/R/utils.R | 137 +- nanonext-1.5.2/nanonext/README.md | 15 nanonext-1.5.2/nanonext/build/vignette.rds |binary nanonext-1.5.2/nanonext/configure | 34 nanonext-1.5.2/nanonext/configure.win | 4 nanonext-1.5.2/nanonext/inst/doc/nanonext.html | 26 nanonext-1.5.2/nanonext/man/as.promise.ncurlAio.Rd | 12 nanonext-1.5.2/nanonext/man/as.promise.recvAio.Rd | 12 nanonext-1.5.2/nanonext/man/call_aio.Rd | 41 nanonext-1.5.2/nanonext/man/close.Rd | 7 nanonext-1.5.2/nanonext/man/collect_aio.Rd | 8 nanonext-1.5.2/nanonext/man/context.Rd | 13 nanonext-1.5.2/nanonext/man/cv.Rd | 47 nanonext-1.5.2/nanonext/man/dial.Rd | 27 nanonext-1.5.2/nanonext/man/dot-advance.Rd | 6 nanonext-1.5.2/nanonext/man/dot-context.Rd | 10 nanonext-1.5.2/nanonext/man/dot-interrupt.Rd | 7 nanonext-1.5.2/nanonext/man/dot-keep.Rd | 8 nanonext-1.5.2/nanonext/man/dot-mark.Rd | 7 nanonext-1.5.2/nanonext/man/dot-unresolved.Rd | 22 nanonext-1.5.2/nanonext/man/grapes-twiddle-greater-than-grapes.Rd | 26 nanonext-1.5.2/nanonext/man/is_aio.Rd | 18 nanonext-1.5.2/nanonext/man/is_error_value.Rd | 5 nanonext-1.5.2/nanonext/man/listen.Rd | 25 nanonext-1.5.2/nanonext/man/messenger.Rd | 10 nanonext-1.5.2/nanonext/man/monitor.Rd | 10 nanonext-1.5.2/nanonext/man/msleep.Rd | 10 nanonext-1.5.2/nanonext/man/nano.Rd | 86 - nanonext-1.5.2/nanonext/man/nanonext-package.Rd | 40 nanonext-1.5.2/nanonext/man/ncurl.Rd | 44 nanonext-1.5.2/nanonext/man/ncurl_aio.Rd | 56 - nanonext-1.5.2/nanonext/man/ncurl_session.Rd | 47 nanonext-1.5.2/nanonext/man/nng_error.Rd | 6 nanonext-1.5.2/nanonext/man/nng_version.Rd | 4 nanonext-1.5.2/nanonext/man/opt.Rd | 370 +++---- nanonext-1.5.2/nanonext/man/parse_url.Rd | 37 nanonext-1.5.2/nanonext/man/pipe_notify.Rd | 31 nanonext-1.5.2/nanonext/man/protocols.Rd | 164 +-- nanonext-1.5.2/nanonext/man/random.Rd | 10 nanonext-1.5.2/nanonext/man/reap.Rd | 6 nanonext-1.5.2/nanonext/man/recv.Rd | 49 nanonext-1.5.2/nanonext/man/recv_aio.Rd | 43 nanonext-1.5.2/nanonext/man/reply.Rd | 42 nanonext-1.5.2/nanonext/man/request.Rd | 65 - nanonext-1.5.2/nanonext/man/send.Rd | 63 - nanonext-1.5.2/nanonext/man/send_aio.Rd | 49 nanonext-1.5.2/nanonext/man/serial_config.Rd | 18 nanonext-1.5.2/nanonext/man/socket.Rd | 61 - nanonext-1.5.2/nanonext/man/start.Rd | 12 nanonext-1.5.2/nanonext/man/stat.Rd | 42 nanonext-1.5.2/nanonext/man/status_code.Rd | 6 nanonext-1.5.2/nanonext/man/stop_aio.Rd | 17 nanonext-1.5.2/nanonext/man/stream.Rd | 16 nanonext-1.5.2/nanonext/man/subscribe.Rd | 8 nanonext-1.5.2/nanonext/man/survey_time.Rd | 12 nanonext-1.5.2/nanonext/man/tls_config.Rd | 17 nanonext-1.5.2/nanonext/man/transports.Rd | 336 +++--- nanonext-1.5.2/nanonext/man/unresolved.Rd | 14 nanonext-1.5.2/nanonext/man/write_cert.Rd | 23 nanonext-1.5.2/nanonext/src/aio.c | 70 + nanonext-1.5.2/nanonext/src/core.c | 90 - nanonext-1.5.2/nanonext/src/init.c | 3 nanonext-1.5.2/nanonext/src/mbedtls-362.tar.xz |binary nanonext-1.5.2/nanonext/src/nanonext.h | 21 nanonext-1.5.2/nanonext/src/ncurl.c | 22 nanonext-1.5.2/nanonext/src/nng-110-2.tar.xz |only nanonext-1.5.2/nanonext/src/proto.c | 14 nanonext-1.5.2/nanonext/src/sync.c | 20 nanonext-1.5.2/nanonext/src/thread.c | 2 nanonext-1.5.2/nanonext/tests/tests.R | 7 89 files changed, 2109 insertions(+), 2275 deletions(-)
Title: Weekly Hass Avocado Sales Summary
Description: Provides a weekly summary of Hass Avocado sales for the
contiguous US from January 2017 through December 20204.
See the package website for more information, documentation,
and examples. Data source: Haas Avocado Board
<https://hassavocadoboard.com/category-data/>.
Author: Nikhil Agarwal [aut, cre]
Maintainer: Nikhil Agarwal <gitnik@niks.me>
Diff between avocado versions 0.1.0 dated 2020-12-18 and 0.2.0 dated 2025-03-18
avocado-0.1.0/avocado/data/hass.rda |only avocado-0.1.0/avocado/inst/doc/a_intro.R |only avocado-0.1.0/avocado/inst/doc/a_intro.Rmd |only avocado-0.1.0/avocado/inst/doc/a_intro.html |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass-region.R |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass-region.Rmd |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass-region.html |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass.R |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass.Rmd |only avocado-0.1.0/avocado/inst/doc/b_analyze-hass.html |only avocado-0.1.0/avocado/man/hass.Rd |only avocado-0.1.0/avocado/vignettes/a_intro.Rmd |only avocado-0.1.0/avocado/vignettes/b_analyze-hass-region.Rmd |only avocado-0.1.0/avocado/vignettes/b_analyze-hass.Rmd |only avocado-0.2.0/avocado/DESCRIPTION | 18 avocado-0.2.0/avocado/MD5 | 48 - avocado-0.2.0/avocado/NEWS.md | 10 avocado-0.2.0/avocado/R/data.R | 92 +-- avocado-0.2.0/avocado/README.md | 89 ++- avocado-0.2.0/avocado/build/vignette.rds |binary avocado-0.2.0/avocado/data/hass_market.rda |only avocado-0.2.0/avocado/data/hass_region.rda |binary avocado-0.2.0/avocado/data/hass_usa.rda |binary avocado-0.2.0/avocado/inst/doc/avocado.R |only avocado-0.2.0/avocado/inst/doc/avocado.Rmd |only avocado-0.2.0/avocado/inst/doc/avocado.html |only avocado-0.2.0/avocado/inst/doc/b_analyze-hass-cntry.R | 83 --- avocado-0.2.0/avocado/inst/doc/b_analyze-hass-cntry.Rmd | 93 --- avocado-0.2.0/avocado/inst/doc/b_analyze-hass-cntry.html | 365 +++++--------- avocado-0.2.0/avocado/man/figures |only avocado-0.2.0/avocado/man/hass_market.Rd |only avocado-0.2.0/avocado/man/hass_region.Rd | 28 - avocado-0.2.0/avocado/man/hass_usa.Rd | 28 - avocado-0.2.0/avocado/vignettes/avocado.Rmd |only avocado-0.2.0/avocado/vignettes/b_analyze-hass-cntry.Rmd | 93 --- 35 files changed, 373 insertions(+), 574 deletions(-)
Title: Markdown-Based Surveys Using 'Quarto' and 'shiny'
Description: Generate surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph]
,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.8.0 dated 2025-01-27 and 0.9.0 dated 2025-03-18
surveydown-0.8.0/surveydown/inst/examples/sd_skip_if.qmd |only surveydown-0.8.0/surveydown/man/figures/technologies_old.png |only surveydown-0.9.0/surveydown/DESCRIPTION | 6 surveydown-0.9.0/surveydown/MD5 | 41 - surveydown-0.9.0/surveydown/NAMESPACE | 2 surveydown-0.9.0/surveydown/NEWS.md | 28 surveydown-0.9.0/surveydown/R/config.R | 36 - surveydown-0.9.0/surveydown/R/dashboard.R | 11 surveydown-0.9.0/surveydown/R/db.R | 145 ++-- surveydown-0.9.0/surveydown/R/server.R | 326 ++++++++-- surveydown-0.9.0/surveydown/R/ui.R | 293 ++++++-- surveydown-0.9.0/surveydown/README.md | 11 surveydown-0.9.0/surveydown/inst/examples/sd_skip_forward.qmd |only surveydown-0.9.0/surveydown/inst/template/app.R | 40 - surveydown-0.9.0/surveydown/inst/template/survey.qmd | 6 surveydown-0.9.0/surveydown/man/figures/technologies.svg | 2 surveydown-0.9.0/surveydown/man/sd_db_config.Rd | 3 surveydown-0.9.0/surveydown/man/sd_db_connect.Rd | 8 surveydown-0.9.0/surveydown/man/sd_question.Rd | 95 +- surveydown-0.9.0/surveydown/man/sd_reactive.Rd |only surveydown-0.9.0/surveydown/man/sd_server.Rd | 2 surveydown-0.9.0/surveydown/man/sd_show_if.Rd | 2 surveydown-0.9.0/surveydown/man/sd_skip_forward.Rd |only surveydown-0.9.0/surveydown/man/sd_skip_if.Rd | 45 - 24 files changed, 753 insertions(+), 349 deletions(-)
Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA
and related models. The aim of the package is to provide consistent
interface for the user. For example, a single function autocorrelations()
computes various kinds of theoretical and sample autocorrelations. This is
work in progress, see the documentation and vignettes for the current
functionality. Function sarima() fits extended multiplicative seasonal
ARIMA models with trends, exogenous variables and arbitrary roots on the
unit circle, which can be fixed or estimated (for the algebraic basis for
this see <doi:10.48550/arXiv.2208.05055>, a paper on the methodology is being prepared).
Author: Georgi N. Boshnakov [aut, cre],
Jamie Halliday [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between sarima versions 0.9.3 dated 2024-03-26 and 0.9.4 dated 2025-03-18
DESCRIPTION | 13 MD5 | 43 NEWS.md | 962 ++++++------- R/RcppExports.R | 62 R/fitTools.R | 1870 +++++++++++++------------- R/zzz.R | 32 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 236 +-- inst/auto/REFERENCES.el | 2 inst/doc/garch_tests_example.R | 196 +- inst/doc/garch_tests_example.pdf |binary inst/doc/white_noise_tests.R | 218 +-- inst/doc/white_noise_tests.pdf |binary man/FisherInformation-methods.Rd | 200 +- man/tsdiag.Sarima.Rd | 298 ++-- tests/testthat/d_ex_InformationMatrixARMA.rds |only tests/testthat/im_ar1.rds |only tests/testthat/im_ar2.rds |only tests/testthat/im_arma1p1.rds |only tests/testthat/im_arma1p2.rds |only tests/testthat/im_arma2p1.rds |only tests/testthat/im_arma2p2.rds |only tests/testthat/im_ma1.rds |only tests/testthat/im_ma2.rds |only tests/testthat/test-armacalc.R | 428 +++-- tests/testthat/test-sarima-uar.R | 68 27 files changed, 2350 insertions(+), 2278 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 0.2.0 dated 2025-01-13 and 0.2.1 dated 2025-03-18
DESCRIPTION | 8 MD5 | 61 NAMESPACE | 7 NEWS.md | 10 R/controls.R | 383 ++++-- R/h3j-h3t.R |only R/layers.R | 26 R/legends.R | 88 + R/plugins.R | 435 +++++- R/shiny.R | 232 ++- R/sources.R | 496 +++++-- R/storymaps.R | 40 R/views.R | 137 +- inst/htmlwidgets/lib/h3j-h3t |only inst/htmlwidgets/mapboxgl.js | 221 +++ inst/htmlwidgets/mapboxgl.yaml | 2 inst/htmlwidgets/mapboxgl_compare.js | 1644 +++++++++++++++++++++++++ inst/htmlwidgets/mapboxgl_compare.yaml | 46 inst/htmlwidgets/maplibregl.js | 575 ++++++--- inst/htmlwidgets/maplibregl.yaml | 5 inst/htmlwidgets/maplibregl_compare.js | 1834 ++++++++++++++++++++++++++++- inst/htmlwidgets/maplibregl_compare.yaml | 58 inst/htmlwidgets/styles/layers-control.css | 80 + man/add_categorical_legend.Rd | 17 man/add_continuous_legend.Rd | 17 man/add_h3j_source.Rd |only man/add_layers_control.Rd | 27 man/add_legend.Rd | 17 man/compare.Rd | 86 + man/mapboxglCompareOutput.Rd |only man/mapboxgl_compare_proxy.Rd |only man/maplibreCompareOutput.Rd |only man/maplibre_compare_proxy.Rd |only man/renderMapboxglCompare.Rd |only man/renderMaplibreCompare.Rd |only man/story_section.Rd | 4 36 files changed, 5713 insertions(+), 843 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <https://spark.apache.org/>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] ,
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut] ,
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] ,
Wil Davis [ctb],
Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr versions 1.8.6 dated 2024-04-29 and 1.9.0 dated 2025-03-18
sparklyr-1.8.6/sparklyr/inst/java/sparklyr-2.4-2.11.jar |only sparklyr-1.8.6/sparklyr/inst/java/sparklyr-master-2.12.jar |only sparklyr-1.9.0/sparklyr/DESCRIPTION | 10 sparklyr-1.9.0/sparklyr/MD5 | 96 +- sparklyr-1.9.0/sparklyr/NAMESPACE | 2 sparklyr-1.9.0/sparklyr/NEWS.md | 22 sparklyr-1.9.0/sparklyr/R/avro_utils.R | 15 sparklyr-1.9.0/sparklyr/R/config_spark.R | 10 sparklyr-1.9.0/sparklyr/R/core_invoke.R | 6 sparklyr-1.9.0/sparklyr/R/core_worker_config.R | 5 sparklyr-1.9.0/sparklyr/R/data_interface.R | 9 sparklyr-1.9.0/sparklyr/R/dplyr_spark.R | 1 sparklyr-1.9.0/sparklyr/R/dplyr_sql.R | 8 sparklyr-1.9.0/sparklyr/R/install_spark.R | 72 - sparklyr-1.9.0/sparklyr/R/install_spark_versions.R | 155 +-- sparklyr-1.9.0/sparklyr/R/install_spark_windows.R | 6 sparklyr-1.9.0/sparklyr/R/livy_connection.R | 2 sparklyr-1.9.0/sparklyr/R/ml_persistence.R | 15 sparklyr-1.9.0/sparklyr/R/shell_connection.R | 13 sparklyr-1.9.0/sparklyr/R/spark_apply.R | 102 +- sparklyr-1.9.0/sparklyr/R/spark_compile.R | 34 sparklyr-1.9.0/sparklyr/R/spark_extensions.R | 17 sparklyr-1.9.0/sparklyr/R/spark_gen_embedded_sources.R | 9 sparklyr-1.9.0/sparklyr/R/spark_invoke.R | 6 sparklyr-1.9.0/sparklyr/R/tables_spark.R | 6 sparklyr-1.9.0/sparklyr/R/utils.R | 29 sparklyr-1.9.0/sparklyr/R/worker_apply.R | 19 sparklyr-1.9.0/sparklyr/R/worker_main.R | 1 sparklyr-1.9.0/sparklyr/README.md | 69 - sparklyr-1.9.0/sparklyr/build/partial.rdb |binary sparklyr-1.9.0/sparklyr/inst/extdata/versions-next.json | 6 sparklyr-1.9.0/sparklyr/inst/extdata/versions.json | 442 ----------- sparklyr-1.9.0/sparklyr/inst/java/sparklyr-2.4-2.12.jar |binary sparklyr-1.9.0/sparklyr/inst/java/sparklyr-3.0-2.12.jar |binary sparklyr-1.9.0/sparklyr/inst/java/sparklyr-3.5-2.12.jar |only sparklyr-1.9.0/sparklyr/inst/java/sparklyr-master-2.13.jar |only sparklyr-1.9.0/sparklyr/java/embedded_sources.R | 37 sparklyr-1.9.0/sparklyr/java/spark-3.0.0/utils.scala |only sparklyr-1.9.0/sparklyr/java/spark-3.5.0/sparksqlutils.scala | 100 ++ sparklyr-1.9.0/sparklyr/java/spark-3.5.0/utils.scala |only sparklyr-1.9.0/sparklyr/java/spark-4.0.0 |only sparklyr-1.9.0/sparklyr/man/invoke.Rd | 7 sparklyr-1.9.0/sparklyr/man/jarray.Rd | 2 sparklyr-1.9.0/sparklyr/man/jfloat.Rd | 2 sparklyr-1.9.0/sparklyr/man/jfloat_array.Rd | 2 sparklyr-1.9.0/sparklyr/man/spark_versions.Rd | 4 sparklyr-1.9.0/sparklyr/man/src_databases.Rd | 5 sparklyr-1.9.0/sparklyr/tools/readme/dplyr-ggplot2-1.png |binary 48 files changed, 624 insertions(+), 722 deletions(-)
Title: Univariate GARCH-MIDAS, Double-Asymmetric GARCH-MIDAS and
MEM-MIDAS
Description: Adds the MIxing-Data Sampling (MIDAS, Ghysels et al. (2007) <doi:10.1080/07474930600972467>) components to a variety of GARCH and MEM (Engle (2002) <doi:10.1002/jae.683>, Engle and Gallo (2006) <doi:10.1016/j.jeconom.2005.01.018>, and Amendola et al. (2024) <doi:10.1016/j.seps.2023.101764>) models, with the aim of predicting the volatility with additional low-frequency (that is, MIDAS) terms. The estimation takes place through simple functions, which provide in-sample and (if present) and out-of-sample evaluations. 'rumidas' also offers a summary tool, which synthesizes the main information of the estimated model. There is also the possibility of generating one-step-ahead and multi-step-ahead forecasts.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between rumidas versions 0.1.2 dated 2024-02-17 and 0.1.3 dated 2025-03-18
DESCRIPTION | 6 MD5 | 28 - NAMESPACE | 6 NEWS.md | 5 R/functions.R | 1 R/midas_functions.R | 1007 +++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/CITATION | 2 man/GM_2M_cond_vol.Rd |only man/GM_2M_cond_vol_no_skew.Rd |only man/GM_2M_loglik.Rd |only man/GM_2M_loglik_no_skew.Rd |only man/GM_2M_long_run_vol.Rd |only man/GM_2M_long_run_vol_no_skew.Rd |only man/MEM_X_loglik.Rd | 6 man/MEM_X_loglik_no_skew.Rd | 4 man/mv_into_mat.Rd | 1 man/ugmfit.Rd | 2 18 files changed, 1034 insertions(+), 34 deletions(-)
Title: Enhanced 'R Markdown' Format for 'Word' and 'PowerPoint'
Description: Allows production of 'Microsoft' corporate documents from 'R Markdown' by
reusing formatting defined in 'Microsoft Word' documents. You can reuse table styles,
list styles but also add column sections, landscape oriented pages. Table and image
captions as well as cross-references are transformed into 'Microsoft Word' fields,
allowing documents edition and merging without issue with references; the syntax
conforms to the 'bookdown' cross-reference definition. Objects generated by
the 'officer' package are also supported in the 'knitr' chunks.
'Microsoft PowerPoint' presentations also benefit from this as well as the
ability to produce editable vector graphics in 'PowerPoint' and also to
define placeholder where content is to be added.
Author: David Gohel [aut, cre, cph],
ArData [cph],
Institut fuer Qualitaetssicherung und Transparenz im Gesundheitswesen
[fnd],
Noam Ross [aut] ,
ArData [cph],
Martin Camitz [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officedown versions 0.3.3 dated 2024-07-16 and 0.4.0 dated 2025-03-18
officedown-0.3.3/officedown/tests/testthat/utils.R |only officedown-0.4.0/officedown/DESCRIPTION | 14 ++-- officedown-0.4.0/officedown/MD5 | 28 ++++---- officedown-0.4.0/officedown/NEWS.md | 20 +++++- officedown-0.4.0/officedown/R/hooks.R | 33 ++++++++++ officedown-0.4.0/officedown/R/rdocx_document.R | 7 +- officedown-0.4.0/officedown/build/vignette.rds |binary officedown-0.4.0/officedown/man/rdocx_document.Rd | 7 ++ officedown-0.4.0/officedown/tests/testthat/helper-utils.R |only officedown-0.4.0/officedown/tests/testthat/test-rdocx-lists.R | 2 officedown-0.4.0/officedown/tests/testthat/test-rdocx-par-settings.R | 2 officedown-0.4.0/officedown/tests/testthat/test-rdocx-plots.R | 17 ----- officedown-0.4.0/officedown/tests/testthat/test-rdocx-sections.R | 2 officedown-0.4.0/officedown/tests/testthat/test-rdocx-tables.R | 2 officedown-0.4.0/officedown/tests/testthat/test-render-r.R | 2 officedown-0.4.0/officedown/tests/testthat/test-rpptx.R | 22 +++--- 16 files changed, 100 insertions(+), 58 deletions(-)
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and visualize linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
The methods and the package are explained in detail in Adämmer (2019) <doi:10.32614/RJ-2019-052>.
Author: Philipp Adaemmer [aut, cre] ,
James P. LeSage [ctb],
Mehmet Balcilar [ctb],
Jon Danielsson [ctb]
Maintainer: Philipp Adaemmer <philipp.adaemmer@uni-greifswald.de>
Diff between lpirfs versions 0.2.3 dated 2023-07-06 and 0.2.4 dated 2025-03-18
DESCRIPTION | 12 ++++----- MD5 | 48 +++++++++++++++++++-------------------- NEWS.md | 6 ++++ R/data-documentation.R | 8 +++--- R/lp_lin_panel.R | 6 +++- R/lp_nl.R | 34 +++++++++++++-------------- R/lp_nl_iv.R | 8 +++--- R/lp_nl_panel.R | 4 +-- R/package.R | 3 -- README.md | 4 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lpirfs_vignette.R | 22 ++++++++--------- inst/doc/lpirfs_vignette.html | 22 ++++++++--------- man/ag_data.Rd | 4 +-- man/interest_rules_var_data.Rd | 2 - man/lp_lin_panel.Rd | 6 +++- man/lp_nl.Rd | 32 +++++++++++++------------- man/lp_nl_iv.Rd | 8 +++--- man/lp_nl_panel.Rd | 7 +++-- man/lpirfs-package.Rd | 8 ++++++ man/monetary_var_data.Rd | 2 - src/newey_west.cpp | 4 --- src/newey_west_tsls.cpp | 13 ++++------ tests/testthat/test-newey_west.R | 29 +++++++++++++++++++++-- 25 files changed, 164 insertions(+), 128 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: A unified interface to interact with various Large Language Model (LLM) APIs such as 'OpenAI' (see <https://platform.openai.com/docs/overview> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), 'Gemini' (see <https://aistudio.google.com> for details), and 'Voyage AI' (see <https://docs.voyageai.com/docs/introduction> for details). Allows users to use and switch between various APIs seamlessly within R, and define LLM agents.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.2.3 dated 2025-03-13 and 0.2.5 dated 2025-03-18
DESCRIPTION | 10 MD5 | 20 + NAMESPACE | 4 R/LLMR.R | 7 R/LLM_robust_utils.R |only R/Zagent.R | 573 +----------------------------------------------- man/Agent.Rd | 2 man/cache_llm_call.Rd |only man/call_llm.Rd | 65 ----- man/call_llm_robust.Rd |only man/llm_config.Rd | 52 ---- man/log_llm_error.Rd |only man/parse_embeddings.Rd | 25 -- 13 files changed, 46 insertions(+), 712 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme-value and other copula families, as well as their rotations,
mixtures and asymmetrizations. Nested Archimedean copulas, related
tools and special functions. Methods for density, distribution, random
number generation, bivariate dependence measures, Rosenblatt transform,
Kendall distribution function, perspective and contour plots. Fitting of
copula models with potentially partly fixed parameters, including
standard errors. Serial independence tests, copula specification tests
(independence, exchangeability, radial symmetry, extreme-value
dependence, goodness-of-fit) and model selection based on
cross-validation. Empirical copula, smoothed versions, and
non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] ,
Ivan Kojadinovic [aut] ,
Martin Maechler [aut, cre] ,
Jun Yan [aut] ,
Johanna G. Neslehova [ctb] ,
<https://orcid.org/0000-0001-9634-4796>),
Rebecca Morger [ctb] : code for free mixCopula weight
parameters)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 1.1-5 dated 2025-02-09 and 1.1-6 dated 2025-03-18
DESCRIPTION | 11 +++++---- MD5 | 38 ++++++++++++++++---------------- R/AllClass.R | 6 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++ inst/doc/AC_Liouville.html | 4 +-- inst/doc/AR_Clayton.html | 4 +-- inst/doc/Frank-Rmpfr.pdf |binary inst/doc/GIG.html | 14 +++++------ inst/doc/HAXC.html | 4 +-- inst/doc/NALC.html | 8 +++--- inst/doc/copula_GARCH.html | 4 +-- inst/doc/dNAC.html | 4 +-- inst/doc/empiricial_copulas.html | 4 +-- inst/doc/logL_visualization.html | 46 +++++++++++++++++++-------------------- inst/doc/nacopula-pkg.pdf |binary inst/doc/qrng.html | 4 +-- inst/doc/rhoAMH-dilog.pdf |binary inst/doc/wild_animals.html | 32 +++++++++++++-------------- 20 files changed, 101 insertions(+), 91 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 4.3.2 dated 2025-01-27 and 4.3.3 dated 2025-03-18
DESCRIPTION | 11 +- MD5 | 31 +++--- NAMESPACE | 2 NEWS | 6 + R/conceptualStructure.R | 30 +----- R/plotThematicEvolution.R | 190 ++++++++++++++++++++++-------------------- R/tableTag.R | 12 +- R/thematicEvolution.R | 18 +++ R/thematicMap.R | 6 - R/zzz.R | 3 build/partial.rdb |binary inst/biblioshiny/biblioShot.R |only inst/biblioshiny/libraries.R | 19 ---- inst/biblioshiny/server.R | 65 ++++++++------ inst/biblioshiny/ui.R | 23 ++++- inst/biblioshiny/utils.R | 31 ++++-- man/plotThematicEvolution.Rd | 32 +++++-- 17 files changed, 270 insertions(+), 209 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep' and 'HCP' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.2.1 dated 2025-03-09 and 1.3.0 dated 2025-03-18
DESCRIPTION | 8 - MD5 | 22 +-- NAMESPACE | 2 NEWS.md | 10 + R/otherfunc.R | 11 - R/vertmixedTFCE.R | 52 +++----- inst/doc/VertexWiseR_Example_2.html | 207 +++++++++++------------------------ vignettes/FINK_tstatmaps.png |binary vignettes/Python_troubleshooting.Rmd | 2 vignettes/SPRENG_tstatmaps.png |binary vignettes/VertexWiseR_Example_2.Rmd | 27 ---- vignettes/traj.png |binary 12 files changed, 121 insertions(+), 220 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.3.0 dated 2024-12-05 and 1.4 dated 2025-03-18
text-1.3.0/text/man/figures/text_logo_animation.gif |only text-1.4/text/DESCRIPTION | 8 text-1.4/text/MD5 | 128 +- text-1.4/text/NAMESPACE | 16 text-1.4/text/NEWS.md | 21 text-1.4/text/R/0_0_text_install.R | 6 text-1.4/text/R/0_1_globals.R | 11 text-1.4/text/R/1_1_textEmbed.R | 443 +++++++ text-1.4/text/R/2_2_textTrainRegression.R | 558 ++++++++-- text-1.4/text/R/2_3_textTrainRandomForest.R | 62 - text-1.4/text/R/2_4_0_textPredict_Assess_Classify.R | 7 text-1.4/text/R/2_4_1_textPredictTextTrained.R | 6 text-1.4/text/R/2_5_textTrainPredictExamples.R |only text-1.4/text/R/4_0_textPlot.R | 355 ++++-- text-1.4/text/R/4_3_textPlotProjection.R | 184 +-- text-1.4/text/R/5_2_textGeneration.R | 17 text-1.4/text/R/7_2_textTopicsAnalysis.R | 83 - text-1.4/text/R/ExampleDataDescription.R | 10 text-1.4/text/README.md | 107 + text-1.4/text/build/vignette.rds |binary text-1.4/text/inst/CITATION | 2 text-1.4/text/inst/doc/LBAM.R | 6 text-1.4/text/inst/doc/LBAM.Rmd | 6 text-1.4/text/inst/doc/LBAM.html | 8 text-1.4/text/inst/doc/huggingface_in_r.Rmd | 2 text-1.4/text/inst/doc/huggingface_in_r.html | 2 text-1.4/text/inst/doc/implicit_motives_tutorial.R | 16 text-1.4/text/inst/doc/implicit_motives_tutorial.Rmd | 16 text-1.4/text/inst/doc/implicit_motives_tutorial.html | 28 text-1.4/text/inst/doc/text.Rmd | 8 text-1.4/text/inst/doc/text.html | 11 text-1.4/text/inst/extdata/The_L-BAM_Library.csv | 12 text-1.4/text/inst/python/huggingface_Interface3.py | 44 text-1.4/text/inst/python/requirements.txt | 6 text-1.4/text/man/DP_projections_HILS_SWLS_100.Rd | 3 text-1.4/text/man/Language_based_assessment_data_3_100.Rd | 3 text-1.4/text/man/Language_based_assessment_data_8.Rd | 2 text-1.4/text/man/figures/README-DPP_plot-1.png |binary text-1.4/text/man/figures/harmony_logo_all.png |only text-1.4/text/man/figures/logo.png |binary text-1.4/text/man/figures/logo_old.png |only text-1.4/text/man/figures/talk_text_topics.svg |only text-1.4/text/man/raw_embeddings_1.Rd | 3 text-1.4/text/man/textEmbed.Rd | 5 text-1.4/text/man/textGeneration.Rd | 12 text-1.4/text/man/textPlot.Rd | 18 text-1.4/text/man/textProjectionPlot.Rd | 9 text-1.4/text/man/textTopicsTest.Rd | 21 text-1.4/text/man/textTrainExamples.Rd |only text-1.4/text/man/textTrainRandomForest.Rd | 5 text-1.4/text/man/textTrainRegression.Rd | 19 text-1.4/text/man/word_embeddings_4.Rd | 3 text-1.4/text/tests/testthat/_snaps |only text-1.4/text/tests/testthat/test_0_install_test.R | 2 text-1.4/text/tests/testthat/test_1_1_Analyses_flow.R | 5 text-1.4/text/tests/testthat/test_1_2_textEmbed.R | 2 text-1.4/text/tests/testthat/test_2_2_textTrainRandomForest.R | 49 text-1.4/text/tests/testthat/test_2_3_textTrain_strata.R | 53 text-1.4/text/tests/testthat/test_2_6_textPredict_implicitmotives.R | 166 +- text-1.4/text/tests/testthat/test_2_9_textTrainExamples.R |only text-1.4/text/tests/testthat/test_4_textPlot.R | 71 + text-1.4/text/tests/testthat/test_5_Tasks.R | 126 ++ text-1.4/text/tests/testthat/test_7_textTopics.R | 29 text-1.4/text/tests/testthat/test_PM_tutorial.R | 13 text-1.4/text/vignettes/LBAM.Rmd | 6 text-1.4/text/vignettes/huggingface_in_r.Rmd | 2 text-1.4/text/vignettes/implicit_motives_tutorial.Rmd | 16 text-1.4/text/vignettes/text.Rmd | 8 68 files changed, 2044 insertions(+), 796 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.3-5 dated 2025-01-18 and 3.3-6 dated 2025-03-18
DESCRIPTION | 18 ++++--- MD5 | 32 ++++++------ NAMESPACE | 11 ++++ NEWS | 32 ++++++++++++ R/diagram.R | 105 +++++++++++++++++++++++++++++++----------- R/tess.R | 18 ------- R/tessfun.R |only R/window.R | 5 +- inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/as.function.tess.Rd | 8 ++- man/distfun.Rd | 11 ++++ man/integral.tessfun.Rd |only man/macros/defns.Rd | 4 + man/methods.funxy.Rd | 6 ++ man/plot.yardstick.Rd | 55 +++++++++++++++++----- man/spatstat.geom-internal.Rd | 10 +++- man/spatstat.geom-package.Rd | 8 +++ 18 files changed, 242 insertions(+), 85 deletions(-)
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
Author: Jan Grau [aut, cre],
Jens Keilwagen [aut]
Maintainer: Jan Grau <grau@informatik.uni-halle.de>
Diff between PRROC versions 1.3.1 dated 2018-06-19 and 1.4 dated 2025-03-18
DESCRIPTION | 21 +++++++-- MD5 | 25 ++++++----- NAMESPACE | 5 +- R/PRROC.R | 97 +++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/CITATION | 8 +-- inst/doc/PRROC.R | 54 ++++++++++++++++++++++--- inst/doc/PRROC.Rnw | 36 +++++++++++++++++ inst/doc/PRROC.pdf |binary man/PRROC-package.Rd | 4 - man/ggprroc.Rd |only tests/testthat/test-PR.R | 20 ++++++--- tests/testthat/test-ROC.R | 20 ++++++--- vignettes/PRROC.Rnw | 36 +++++++++++++++++ 14 files changed, 280 insertions(+), 46 deletions(-)
Title: Soil Iron Oxides via Diffuse Reflectance
Description: Calculate the ratio of iron oxides, hematite and goethite, in
soil using the diffuse reflectance technique. The Kubelka-Munk theory,
second derivative analysis, and spectral region amplitudes related to
hematite and goethite content are used for quantification (Torrent,
J., & Barron, V. (2008) <doi:10.2136/sssabookser5.5.c13>).
Additionally, the package calculates soil color in the visible
spectrum using Munsell and RGB color spaces, based on color theory
(Viscarra et al. (2006) <doi:10.1016/j.geoderma.2005.07.017>).
Author: Gustavo Frosi [aut, cre] ,
Vidal Barron [aut] ,
Alberto Inda [aut] ,
Kayn Bastiani [aut]
Maintainer: Gustavo Frosi <gustavofrosi@hotmail.com>
Diff between OxSR versions 1.0.0 dated 2025-03-11 and 1.0.1 dated 2025-03-18
DESCRIPTION | 36 ++++++++++++++++---------- MD5 | 17 +++++++----- NEWS.md | 2 + R/relacion_hm_gt.R | 16 ++++++----- README.md | 47 ++++++++++------------------------- inst/WORDLIST | 10 ++----- man/figures |only man/relation_hm_gt.Rd | 4 +- tests/testthat/test-relacion_hm_gt.R | 5 --- 9 files changed, 63 insertions(+), 74 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Provides a suite of helper functions and a collection of datasets used in the book <https://uncovering-data-science.netlify.app>. It is designed to make data science techniques accessible to individuals with minimal coding experience. Inspired by an ancient Persian idiom, the package likens this learning process to "eating the liver of data science," symbolizing deep and immersive engagement with the field.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.18 dated 2024-11-22 and 1.19 dated 2025-03-18
DESCRIPTION | 12 +-- MD5 | 50 ++++++++------- NAMESPACE | 7 +- NEWS.md | 16 ++++ R/accuracy.R | 1 R/conf.mat.R | 79 ++++++++++++++++-------- R/conf.mat.plot.R | 3 R/kNN.R | 142 ++++++++++++++++++++++++-------------------- R/kNN.plot.R | 95 +++++++++++++++++++++++------ R/minmax.R | 129 +++++++++++++++++++++------------------ R/one.hot.R |only R/scaler.R | 19 +++-- R/zscore.R | 120 +++++++++++++++++++++---------------- README.md | 9 +- inst/doc/liver-example.Rmd | 4 - inst/doc/liver-example.html | 43 +++++++------ man/conf.mat.Rd | 2 man/conf.mat.plot.Rd | 2 man/figures/logo.png |binary man/kNN.Rd | 7 -- man/kNN.plot.Rd | 14 ++-- man/liver-package.Rd | 3 man/minmax.Rd | 8 +- man/one.hot.Rd |only man/scaler.Rd | 14 ++-- man/zscore.Rd | 7 +- vignettes/liver-example.Rmd | 4 - 27 files changed, 474 insertions(+), 316 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <https://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Mike Malecki [aut],
Neal Richardson [aut],
Gordon Shotwell [aut],
Aljaz Sluga [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunch versions 1.30.4 dated 2024-01-17 and 1.31.0 dated 2025-03-18
crunch-1.30.4/crunch/R/gadgets.R |only crunch-1.30.4/crunch/inst/rstudio |only crunch-1.30.4/crunch/man/copyOrderGroup.Rd |only crunch-1.30.4/crunch/man/listDatasetGadget.Rd |only crunch-1.30.4/crunch/man/makeArrayGadget.Rd |only crunch-1.30.4/crunch/tests/testthat/test-gadgets.R |only crunch-1.30.4/crunch/vignettes/crunch/0/api/datasets-03e1cd-POST.R |only crunch-1.30.4/crunch/vignettes/crunch/0/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/0/api/datasets/c25696.json |only crunch-1.30.4/crunch/vignettes/crunch/0/api/public |only crunch-1.30.4/crunch/vignettes/crunch/1/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/1/api/datasets/c25696-7931d8-PATCH.204 |only crunch-1.30.4/crunch/vignettes/crunch/2/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/3/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/3/api/datasets/c25696.json |only crunch-1.30.4/crunch/vignettes/crunch/4/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/5/api/datasets/c25696 |only crunch-1.30.4/crunch/vignettes/crunch/5/api/datasets/c25696.json |only crunch-1.30.4/crunch/vignettes/crunch/5/api/logout.204 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/datasets-cc4309-POST.R |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/datasets/5b6c9f.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/datasets/9540f6 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/datasets/9540f6.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/0/api/public |only crunch-1.30.4/crunch/vignettes/fork-and-merge/1/api/datasets/9540f6 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/1/api/datasets/9540f6.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/2/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/2/api/datasets/5b6c9f.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/3/api/datasets-2ea7ca-POST.R |only crunch-1.30.4/crunch/vignettes/fork-and-merge/3/api/datasets/25c7c7 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/3/api/datasets/25c7c7.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/4/api/datasets/25c7c7 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/4/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/4/api/datasets/d04628 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/4/api/datasets/d04628.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/5/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/5/api/datasets/5b6c9f.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets-b06465-POST.R |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets/91e745 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets/91e745.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets/b5a775 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/6/api/datasets/b5a775.json |only crunch-1.30.4/crunch/vignettes/fork-and-merge/7/api/datasets/91e745 |only crunch-1.30.4/crunch/vignettes/fork-and-merge/8/api/datasets/5b6c9f |only crunch-1.30.4/crunch/vignettes/fork-and-merge/8/api/datasets/5b6c9f.json |only crunch-1.30.4/crunch/vignettes/subtotals/0/api/datasets/17173f |only crunch-1.30.4/crunch/vignettes/subtotals/0/api/datasets/17173f.json |only crunch-1.30.4/crunch/vignettes/subtotals/0/api/datasets/by_name |only crunch-1.30.4/crunch/vignettes/subtotals/1/api/datasets/17173f |only crunch-1.30.4/crunch/vignettes/subtotals/2/api/datasets/17173f |only crunch-1.30.4/crunch/vignettes/subtotals/3/api/datasets/17173f |only crunch-1.30.4/crunch/vignettes/subtotals/3/api/logout.204 |only crunch-1.31.0/crunch/DESCRIPTION | 16 crunch-1.31.0/crunch/MD5 | 665 +++++----- crunch-1.31.0/crunch/NAMESPACE | 2 crunch-1.31.0/crunch/R/AllGenerics.R | 10 crunch-1.31.0/crunch/R/R-to-variable.R | 20 crunch-1.31.0/crunch/R/SO-survey.R | 2 crunch-1.31.0/crunch/R/api.R | 5 crunch-1.31.0/crunch/R/append-dataset.R | 4 crunch-1.31.0/crunch/R/archive-and-publish.R | 2 crunch-1.31.0/crunch/R/as-data-frame.R | 182 ++ crunch-1.31.0/crunch/R/auth.R | 3 crunch-1.31.0/crunch/R/automation.R | 66 crunch-1.31.0/crunch/R/cut.R | 4 crunch-1.31.0/crunch/R/dataset.R | 9 crunch-1.31.0/crunch/R/datetime.R | 14 crunch-1.31.0/crunch/R/delete.R | 7 crunch-1.31.0/crunch/R/filters.R | 13 crunch-1.31.0/crunch/R/folders.R | 10 crunch-1.31.0/crunch/R/fork-and-merge.R | 20 crunch-1.31.0/crunch/R/get-datasets.R | 79 - crunch-1.31.0/crunch/R/hide-variables.R | 8 crunch-1.31.0/crunch/R/make-array.R | 6 crunch-1.31.0/crunch/R/misc.R | 4 crunch-1.31.0/crunch/R/new-dataset.R | 61 crunch-1.31.0/crunch/R/ordering.R | 83 - crunch-1.31.0/crunch/R/search.R | 10 crunch-1.31.0/crunch/R/sliding-categories.R | 2 crunch-1.31.0/crunch/R/variable-derivation.R | 5 crunch-1.31.0/crunch/R/variable-metadata.R | 1 crunch-1.31.0/crunch/R/variable-type.R | 2 crunch-1.31.0/crunch/R/variable-update.R | 10 crunch-1.31.0/crunch/R/variable.R | 1 crunch-1.31.0/crunch/R/weight.R | 13 crunch-1.31.0/crunch/R/zcl.R | 2 crunch-1.31.0/crunch/build/vignette.rds |binary crunch-1.31.0/crunch/inst/crunch-test.R | 27 crunch-1.31.0/crunch/inst/doc/abstract-categories.R | 2 crunch-1.31.0/crunch/inst/doc/abstract-categories.html | 4 crunch-1.31.0/crunch/inst/doc/analyze.R | 134 +- crunch-1.31.0/crunch/inst/doc/analyze.html | 8 crunch-1.31.0/crunch/inst/doc/array-variables.R | 106 - crunch-1.31.0/crunch/inst/doc/array-variables.html | 4 crunch-1.31.0/crunch/inst/doc/crunch.R | 41 crunch-1.31.0/crunch/inst/doc/crunch.Rmd | 31 crunch-1.31.0/crunch/inst/doc/crunch.html | 128 + crunch-1.31.0/crunch/inst/doc/deck-cookbook.R | 648 ++++----- crunch-1.31.0/crunch/inst/doc/deck-cookbook.html | 6 crunch-1.31.0/crunch/inst/doc/derive.R | 57 crunch-1.31.0/crunch/inst/doc/derive.Rmd | 19 crunch-1.31.0/crunch/inst/doc/derive.html | 50 crunch-1.31.0/crunch/inst/doc/export.R | 92 - crunch-1.31.0/crunch/inst/doc/export.html | 4 crunch-1.31.0/crunch/inst/doc/filters.R | 108 - crunch-1.31.0/crunch/inst/doc/filters.html | 4 crunch-1.31.0/crunch/inst/doc/fork-and-merge.R | 68 - crunch-1.31.0/crunch/inst/doc/fork-and-merge.Rmd | 62 crunch-1.31.0/crunch/inst/doc/fork-and-merge.html | 30 crunch-1.31.0/crunch/inst/doc/projects.html | 4 crunch-1.31.0/crunch/inst/doc/subtotals.R | 30 crunch-1.31.0/crunch/inst/doc/subtotals.Rmd | 24 crunch-1.31.0/crunch/inst/doc/subtotals.html | 6 crunch-1.31.0/crunch/inst/doc/variable-order.R | 14 crunch-1.31.0/crunch/inst/doc/variable-order.html | 4 crunch-1.31.0/crunch/inst/doc/variables.R | 144 +- crunch-1.31.0/crunch/inst/doc/variables.html | 4 crunch-1.31.0/crunch/inst/httptest/redact.R | 9 crunch-1.31.0/crunch/inst/httptest/start-vignette.R | 17 crunch-1.31.0/crunch/inst/junit_fix.R |only crunch-1.31.0/crunch/inst/mocks.tgz |binary crunch-1.31.0/crunch/man/SO_survey.Rd | 2 crunch-1.31.0/crunch/man/SubtotalsHeadings.Rd | 4 crunch-1.31.0/crunch/man/Transforms.Rd | 4 crunch-1.31.0/crunch/man/analysis-methods.Rd | 2 crunch-1.31.0/crunch/man/appendDataset.Rd | 4 crunch-1.31.0/crunch/man/archive-and-publish.Rd | 2 crunch-1.31.0/crunch/man/catalog-dataframes.Rd | 2 crunch-1.31.0/crunch/man/cd.Rd | 2 crunch-1.31.0/crunch/man/createDataset.Rd | 7 crunch-1.31.0/crunch/man/crunch-extract.Rd | 22 crunch-1.31.0/crunch/man/cut-DatetimeVariable-method.Rd | 2 crunch-1.31.0/crunch/man/cut-NumericVariable-method.Rd | 2 crunch-1.31.0/crunch/man/dataset-to-R.Rd | 18 crunch-1.31.0/crunch/man/datasets.Rd | 2 crunch-1.31.0/crunch/man/deleteDataset.Rd | 6 crunch-1.31.0/crunch/man/derivations.Rd | 2 crunch-1.31.0/crunch/man/describe-entity.Rd | 2 crunch-1.31.0/crunch/man/envOrOption.Rd | 2 crunch-1.31.0/crunch/man/folder.Rd | 2 crunch-1.31.0/crunch/man/forkDataset.Rd | 24 crunch-1.31.0/crunch/man/geo.Rd | 2 crunch-1.31.0/crunch/man/hide.Rd | 6 crunch-1.31.0/crunch/man/listDatasets.Rd | 9 crunch-1.31.0/crunch/man/loadDataset.Rd | 28 crunch-1.31.0/crunch/man/makeWeight.Rd | 2 crunch-1.31.0/crunch/man/mergeFork.Rd | 2 crunch-1.31.0/crunch/man/mv.Rd | 2 crunch-1.31.0/crunch/man/newDataset.Rd | 11 crunch-1.31.0/crunch/man/newExampleDataset.Rd | 7 crunch-1.31.0/crunch/man/ordering.Rd | 6 crunch-1.31.0/crunch/man/prepareDataForCrunch.Rd | 7 crunch-1.31.0/crunch/man/rmdir.Rd | 2 crunch-1.31.0/crunch/man/shojifyDatasetMetadata.Rd | 12 crunch-1.31.0/crunch/man/slideCategories.Rd | 2 crunch-1.31.0/crunch/man/toVariable.Rd | 8 crunch-1.31.0/crunch/man/weight.Rd | 2 crunch-1.31.0/crunch/tests/testthat/helper-contexts.R | 14 crunch-1.31.0/crunch/tests/testthat/helper.R | 3 crunch-1.31.0/crunch/tests/testthat/setup.R | 2 crunch-1.31.0/crunch/tests/testthat/test-append-debug.R | 56 crunch-1.31.0/crunch/tests/testthat/test-append-subvariables.R | 178 +- crunch-1.31.0/crunch/tests/testthat/test-as-data-frame.R | 158 ++ crunch-1.31.0/crunch/tests/testthat/test-auth.R | 5 crunch-1.31.0/crunch/tests/testthat/test-automation.R | 18 crunch-1.31.0/crunch/tests/testthat/test-case-variables.R | 3 crunch-1.31.0/crunch/tests/testthat/test-categories.R | 2 crunch-1.31.0/crunch/tests/testthat/test-combine-categories.R | 2 crunch-1.31.0/crunch/tests/testthat/test-combine-responses.R | 1 crunch-1.31.0/crunch/tests/testthat/test-compare.R | 2 crunch-1.31.0/crunch/tests/testthat/test-crunchbox.R | 2 crunch-1.31.0/crunch/tests/testthat/test-cube-subset.R | 25 crunch-1.31.0/crunch/tests/testthat/test-cube-transforms.R | 18 crunch-1.31.0/crunch/tests/testthat/test-cut.R | 7 crunch-1.31.0/crunch/tests/testthat/test-dataset-entity.R | 9 crunch-1.31.0/crunch/tests/testthat/test-dataset-stream.R | 6 crunch-1.31.0/crunch/tests/testthat/test-datetime.R | 28 crunch-1.31.0/crunch/tests/testthat/test-derive-array.R | 20 crunch-1.31.0/crunch/tests/testthat/test-derive-debug.R | 444 +++--- crunch-1.31.0/crunch/tests/testthat/test-derive.R | 183 +- crunch-1.31.0/crunch/tests/testthat/test-export-dataset.R | 6 crunch-1.31.0/crunch/tests/testthat/test-expressions.R | 8 crunch-1.31.0/crunch/tests/testthat/test-filters.R | 14 crunch-1.31.0/crunch/tests/testthat/test-folders.R | 4 crunch-1.31.0/crunch/tests/testthat/test-fork.R | 23 crunch-1.31.0/crunch/tests/testthat/test-get-datasets.R | 59 crunch-1.31.0/crunch/tests/testthat/test-make-array.R | 8 crunch-1.31.0/crunch/tests/testthat/test-multitables.R | 17 crunch-1.31.0/crunch/tests/testthat/test-new-dataset.R | 112 + crunch-1.31.0/crunch/tests/testthat/test-palettes.R | 5 crunch-1.31.0/crunch/tests/testthat/test-private-variables.R | 2 crunch-1.31.0/crunch/tests/testthat/test-progress.R | 155 +- crunch-1.31.0/crunch/tests/testthat/test-project-folder.R | 8 crunch-1.31.0/crunch/tests/testthat/test-projects.R | 7 crunch-1.31.0/crunch/tests/testthat/test-share.R | 4 crunch-1.31.0/crunch/tests/testthat/test-slides.R | 6 crunch-1.31.0/crunch/tests/testthat/test-update-with-missing.R | 2 crunch-1.31.0/crunch/tests/testthat/test-variable-as-methods.R | 13 crunch-1.31.0/crunch/tests/testthat/test-variable-folders.R | 4 crunch-1.31.0/crunch/tests/testthat/test-variable-order.R | 336 ----- crunch-1.31.0/crunch/tests/testthat/test-variables.R | 2 crunch-1.31.0/crunch/tests/testthat/test-versioning.R | 21 crunch-1.31.0/crunch/tests/testthat/test-weighting.R | 2 crunch-1.31.0/crunch/vignettes/crunch.Rmd | 31 crunch-1.31.0/crunch/vignettes/crunch/0/api.json | 29 crunch-1.31.0/crunch/vignettes/crunch/0/api/datasets-68f2e9-POST.R |only crunch-1.31.0/crunch/vignettes/crunch/0/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/0/api/datasets/0e7d58.json |only crunch-1.31.0/crunch/vignettes/crunch/0/api/progress.json | 17 crunch-1.31.0/crunch/vignettes/crunch/0/api/projects |only crunch-1.31.0/crunch/vignettes/crunch/0/api/projects.json |only crunch-1.31.0/crunch/vignettes/crunch/0/api/sources-POST.R | 41 crunch-1.31.0/crunch/vignettes/crunch/1/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/1/api/datasets/0e7d58-7931d8-PATCH.204 |only crunch-1.31.0/crunch/vignettes/crunch/2/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/3/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/3/api/datasets/0e7d58.json |only crunch-1.31.0/crunch/vignettes/crunch/4/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/5/api/datasets/0e7d58 |only crunch-1.31.0/crunch/vignettes/crunch/5/api/datasets/0e7d58.json |only crunch-1.31.0/crunch/vignettes/derive.Rmd | 19 crunch-1.31.0/crunch/vignettes/fork-and-merge.Rmd | 62 crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api.json | 31 crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/datasets-33ab07-POST.R |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/datasets/44c194 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/datasets/44c194.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/datasets/5af735.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/projects |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/projects.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/0/api/sources-POST.R | 35 crunch-1.31.0/crunch/vignettes/fork-and-merge/1/api/datasets/44c194 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/1/api/datasets/44c194.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/2/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/2/api/datasets/5af735.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/3/api/datasets-797056-POST.R |only crunch-1.31.0/crunch/vignettes/fork-and-merge/3/api/datasets/093bf8 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/3/api/datasets/093bf8.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/3/api/progress.json | 17 crunch-1.31.0/crunch/vignettes/fork-and-merge/3/api/sources-POST.R | 35 crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/datasets/093bf8 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/datasets/3e463e |only crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/datasets/3e463e.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/progress.json | 17 crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/projects |only crunch-1.31.0/crunch/vignettes/fork-and-merge/4/api/projects.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/5/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/5/api/datasets/5af735.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets-923fde-POST.R |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets/37cc49 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets/37cc49.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets/55d13a |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets/55d13a.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/projects |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/projects.json |only crunch-1.31.0/crunch/vignettes/fork-and-merge/6/api/sources-POST.R | 35 crunch-1.31.0/crunch/vignettes/fork-and-merge/7/api/datasets/37cc49 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/8/api/datasets/5af735 |only crunch-1.31.0/crunch/vignettes/fork-and-merge/8/api/datasets/5af735.json |only crunch-1.31.0/crunch/vignettes/subtotals.Rmd | 24 crunch-1.31.0/crunch/vignettes/subtotals/0/api.json | 8 crunch-1.31.0/crunch/vignettes/subtotals/0/api/datasets/ba16ac |only crunch-1.31.0/crunch/vignettes/subtotals/0/api/datasets/ba16ac.json |only crunch-1.31.0/crunch/vignettes/subtotals/0/api/projects |only crunch-1.31.0/crunch/vignettes/subtotals/0/api/projects.json |only crunch-1.31.0/crunch/vignettes/subtotals/1/api/datasets/ba16ac |only crunch-1.31.0/crunch/vignettes/subtotals/2/api/datasets/ba16ac |only crunch-1.31.0/crunch/vignettes/subtotals/3/api/datasets/ba16ac |only 272 files changed, 3177 insertions(+), 2679 deletions(-)
Title: A 'dplyr' Interface for Crunch
Description: In order to facilitate analysis of datasets hosted on the Crunch
data platform <https://crunch.io/>, the 'crplyr' package implements 'dplyr'
methods on top of the Crunch backend. The usual methods 'select', 'filter',
'group_by', 'summarize', and 'collect' are implemented in such a way as to
perform as much computation on the server and pull as little data locally
as possible.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Neal Richardson [aut],
Mike Malecki [aut],
Gordon Shotwell [aut],
Aljaz Sluga [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crplyr versions 0.4.0 dated 2023-03-21 and 0.4.2 dated 2025-03-18
DESCRIPTION | 8 +- MD5 | 53 ++++++++++---- NAMESPACE | 6 + NEWS.md | 2 R/as-tibble.R | 17 ++-- build/vignette.rds |binary inst/doc/plotting.R | 10 +- inst/doc/plotting.html | 120 ++++++++++++++++---------------- tests/testthat/_snaps |only tests/testthat/helper.R | 6 + tests/testthat/test-as-tibble.R | 24 +++--- tests/testthat/test-collect.R | 10 +- tests/testthat/test-filter.R | 10 +- tests/testthat/test-group-by.R | 6 - tests/testthat/test-mutate.R | 2 tests/testthat/test-select.R | 4 - tests/testthat/test-variable-autoplot.R | 2 17 files changed, 161 insertions(+), 119 deletions(-)
Title: Estimation of Censored AI/QUAI Demand System via Maximum
Likelihood Estimation (MLE)
Description: Tools for estimating censored Almost Ideal (AI) and Quadratic Almost Ideal (QUAI) demand systems using Maximum Likelihood Estimation (MLE). It includes functions for calculating demand share equations and the truncated log-likelihood function for a system of equations, incorporating demographic variables. The package is designed to handle censored data, where some observations may be zero due to non-purchase of certain goods. Package also contains a procedure to approximate demand elasticities numerically and estimate standard errors via Delta Method. It is particularly useful for applied researchers analyzing household consumption data.
Author: Noe J Nava [aut, cre]
Maintainer: Noe J Nava <noejnava2@gmail.com>
Diff between censoredAIDS versions 0.1.0 dated 2025-03-13 and 1.0.0 dated 2025-03-18
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++++------ NAMESPACE | 1 + R/aidsCalculate.R | 11 ++++++----- R/censoredElasticity.R |only R/censoredaidsLoglike.R | 8 +++----- R/muaidsCalculate.R |only inst |only man/aidsCalculate.Rd | 3 ++- man/censoredElasticity.Rd |only man/censoredaidsLoglike.Rd | 4 ++-- man/muaidsCalculate.Rd |only tests/testthat/test-censoredElasticity.R |only 13 files changed, 31 insertions(+), 24 deletions(-)
Title: Shared Memory Atomic Operations
Description: Implements named semaphores from the 'boost' 'C++' library
<https://www.boost.org/>. A semaphore object is shared amongst several
processes. This integer value can be safely incremented or decremented by
each process. Processes can also wait (blocking) for the value to become
positive.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between semaphore versions 1.0.2 dated 2024-11-13 and 1.1.0 dated 2025-03-18
DESCRIPTION | 12 ++--- MD5 | 20 ++++----- NEWS.md | 5 ++ R/RcppExports.R | 4 - R/semaphore.r | 82 ++++++++++++++++++++++++++-------------- R/zzz.r | 2 README.md | 8 +-- man/semaphores.Rd | 20 +++++++-- src/RcppExports.cpp | 9 ++-- src/semaphore.cpp | 15 +++++-- tests/testthat/test-semaphore.r | 7 +-- 11 files changed, 120 insertions(+), 64 deletions(-)
Title: '2bit' 'C' Library
Description: A trimmed down copy of the "kent-core source tree"
turned into a 'C' library for manipulation of '.2bit' files.
See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7>
for a quick overview of the '2bit' format. The "kent-core source tree"
can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>.
Only the '.c' and '.h' files from the source tree that are related
to manipulation of '.2bit' files were kept. Note that the package
is primarily useful to developers of other R packages who wish
to use the '2bit' 'C' library in their own 'C'/'C++' code.
Author: Herve Pages [aut, cre],
UC Regents [cph]
Maintainer: Herve Pages <hpages.on.github@gmail.com>
Diff between Rtwobitlib versions 0.3.6 dated 2024-04-24 and 0.3.8 dated 2025-03-18
DESCRIPTION | 6 +- MD5 | 14 +++--- build/vignette.rds |binary inst/doc/Rtwobitlib.Rmd | 4 - inst/doc/Rtwobitlib.html | 106 ++++++++++++++++++++++------------------------- src/kent/NOTES.txt | 18 +++++++ src/kent/common.c | 35 ++++----------- vignettes/Rtwobitlib.Rmd | 4 - 8 files changed, 92 insertions(+), 95 deletions(-)
Title: Implements Pseudo-R2D2 Prior for Ordinal Regression
Description: Implements the pseudo-R2D2 prior for ordinal regression from the paper "Psuedo-R2D2 prior for high-dimensional ordinal regression" by Yanchenko (2025) <doi:10.48550/arXiv.2502.17491>. In particular, it provides code to evaluate the probability distribution function for the cut-points, compute the log-likelihood, calculate the hyper-parameters for the global variance parameter, find the distribution of McFadden's coefficient-of-determination, and fit the model in 'rstan'. Please cite the paper if you use these codes.
Author: Eric Yanchenko [aut, cre]
Maintainer: Eric Yanchenko <eyanchenko@aiu.ac.jp>
Diff between R2D2ordinal versions 1.0.0 dated 2025-02-27 and 1.0.1 dated 2025-03-18
DESCRIPTION | 6 - MD5 | 14 +- inst/doc/overview.html | 8 - inst/stan/r2d2ord.stan | 6 - src/stanExports_r2d2ord.h | 72 ++++++------- vignettes/overview_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/overview_files/figure-html/unnamed-chunk-4-2.png |binary vignettes/overview_files/figure-html/unnamed-chunk-4-3.png |binary 8 files changed, 54 insertions(+), 52 deletions(-)
Title: Routines for L1 Estimation
Description: L1 estimation for linear regression using Barrodale and Roberts' method
<doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
Estimation of mean and covariance matrix using the multivariate Laplace distribution,
density, distribution function, quantile function and random number generation
for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
Implementation of Naik and Plungpongpun <doi:10.1007/0-8176-4487-3_7> for the
Generalized spatial median estimator is included.
Author: Felipe Osorio [aut, cre] ,
Tymoteusz Wolodzko [aut]
Maintainer: Felipe Osorio <faosorios.stat@gmail.com>
Diff between L1pack versions 0.50 dated 2024-09-08 and 0.52 dated 2025-03-18
ChangeLog | 3 +++ DESCRIPTION | 14 +++++++------- MD5 | 10 ++++++---- NAMESPACE | 8 ++++++-- R/plot.R |only inst/CITATION | 6 +++--- man/envelope.Rd |only 7 files changed, 25 insertions(+), 16 deletions(-)
Title: Highest Quality GIF Encoder
Description: Multi-threaded GIF encoder written in Rust: <https://gif.ski/>.
Converts images to GIF animations using pngquant's efficient cross-frame
palettes and temporal dithering with thousands of colors per frame.
Author: Jeroen Ooms [aut, cre] ,
Kornel Lesinski [aut] ,
Authors of the dependency Rust crates [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gifski versions 1.32.0-1 dated 2024-10-13 and 1.32.0-2 dated 2025-03-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ inst/AUTHORS | 2 +- src/Makevars | 7 ++++--- src/Makevars.ucrt | 6 +++--- src/myrustlib/vendor.tar.xz |binary 7 files changed, 20 insertions(+), 16 deletions(-)
Title: Summarise and Visualise Characteristics of Patients in the OMOP
CDM
Description: Summarise and visualise the characteristics of patients in data
mapped to the Observational Medical Outcomes Partnership (OMOP) common data
model (CDM).
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [ctb] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between CohortCharacteristics versions 0.4.0 dated 2024-11-26 and 0.5.0 dated 2025-03-18
DESCRIPTION | 23 MD5 | 68 - NEWS.md | 18 R/benchmarkCohortCharacteristics.R | 4 R/plotCohortAttrition.R | 546 +++++++------ R/plotCohortOverlap.R | 63 + R/summariseCharacteristics.R | 216 +++-- R/summariseCohortOverlap.R | 2 R/summariseCohortTiming.R | 2 R/summariseLargeScaleCharacteristics.R | 44 - R/table.R | 11 R/tableLargeScaleCharacteristics.R | 2 inst/doc/summarise_characteristics.R | 3 inst/doc/summarise_characteristics.Rmd | 3 inst/doc/summarise_characteristics.html | 602 +++++++-------- inst/doc/summarise_cohort_overlap.R | 3 inst/doc/summarise_cohort_overlap.Rmd | 3 inst/doc/summarise_cohort_overlap.html | 224 ++--- inst/doc/summarise_cohort_timing.R | 3 inst/doc/summarise_cohort_timing.Rmd | 3 inst/doc/summarise_cohort_timing.html | 220 ++--- inst/doc/summarise_large_scale_characteristics.R | 3 inst/doc/summarise_large_scale_characteristics.Rmd | 3 inst/doc/summarise_large_scale_characteristics.html | 742 ++++--------------- man/plotCohortAttrition.Rd | 4 man/summariseCharacteristics.Rd | 6 tests/testthat/test-benchmarkCohortCharacteristics.R | 14 tests/testthat/test-plotCohortAttrition.R | 3 tests/testthat/test-plotCohortOverlap.R | 20 tests/testthat/test-summariseCharacteristics.R | 120 ++- tests/testthat/test-tableLargeScaleCharacteristics.R | 31 vignettes/summarise_characteristics.Rmd | 3 vignettes/summarise_cohort_overlap.Rmd | 3 vignettes/summarise_cohort_timing.Rmd | 3 vignettes/summarise_large_scale_characteristics.Rmd | 3 35 files changed, 1448 insertions(+), 1573 deletions(-)
More information about CohortCharacteristics at CRAN
Permanent link
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination
of the LZ77 algorithm and Huffman coding <https://www.rfc-editor.org/rfc/rfc7932>.
Brotli is similar in speed to deflate (gzip) but offers more dense compression.
Author: Jeroen Ooms [aut, cre] ,
Google, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between brotli versions 1.3.1 dated 2024-10-04 and 1.3.2 dated 2025-03-18
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS | 3 ++ build/vignette.rds |binary inst/doc/benchmarks.R | 52 +++++++++++++++++++++++------------------------ inst/doc/benchmarks.html | 15 +++++-------- src/Makevars | 6 ++--- 7 files changed, 47 insertions(+), 47 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.1.2 dated 2025-03-02 and 1.1.3 dated 2025-03-18
renv-1.1.2/renv/inst/repos/src/contrib/renv_1.1.2.tar.gz |only renv-1.1.3/renv/DESCRIPTION | 6 renv-1.1.3/renv/MD5 | 89 ++++++------ renv-1.1.3/renv/NEWS.md | 33 ++++ renv-1.1.3/renv/R/available-packages.R | 68 +++++++++ renv-1.1.3/renv/R/bootstrap.R | 35 +++- renv-1.1.3/renv/R/cache.R | 4 renv-1.1.3/renv/R/config.R | 41 ++--- renv-1.1.3/renv/R/data_frame.R | 2 renv-1.1.3/renv/R/dependencies.R | 50 +++++- renv-1.1.3/renv/R/description.R | 10 - renv-1.1.3/renv/R/hash.R | 27 --- renv-1.1.3/renv/R/hydrate.R | 18 +- renv-1.1.3/renv/R/install.R | 32 ++-- renv-1.1.3/renv/R/json-read.R | 60 ++++---- renv-1.1.3/renv/R/mask.R | 5 renv-1.1.3/renv/R/md5sum.R |only renv-1.1.3/renv/R/platform.R | 3 renv-1.1.3/renv/R/remotes.R | 5 renv-1.1.3/renv/R/renvignore.R | 80 ++++++++++- renv-1.1.3/renv/R/retrieve.R | 25 ++- renv-1.1.3/renv/R/settings.R | 8 - renv-1.1.3/renv/R/snapshot.R | 14 - renv-1.1.3/renv/R/sysreqs.R | 109 +++++++++++---- renv-1.1.3/renv/R/update.R | 15 +- renv-1.1.3/renv/R/utils.R | 3 renv-1.1.3/renv/README.md | 7 renv-1.1.3/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.1.3/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.1.3/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.1.3/renv/inst/repos/src/contrib/renv_1.1.3.tar.gz |only renv-1.1.3/renv/inst/resources/activate.R | 95 +++++++------ renv-1.1.3/renv/inst/sysreqs/sysreqs.json | 38 ++++- renv-1.1.3/renv/man/dependencies.Rd | 22 +++ renv-1.1.3/renv/man/install.Rd | 6 renv-1.1.3/renv/man/settings.Rd | 8 - renv-1.1.3/renv/man/update.Rd | 5 renv-1.1.3/renv/tests/testthat/_snaps/sysreqs.md |only renv-1.1.3/renv/tests/testthat/helper-setup.R | 2 renv-1.1.3/renv/tests/testthat/test-dependencies.R | 7 renv-1.1.3/renv/tests/testthat/test-enumerate.R | 34 ++-- renv-1.1.3/renv/tests/testthat/test-hydrate.R | 22 +++ renv-1.1.3/renv/tests/testthat/test-json.R | 15 ++ renv-1.1.3/renv/tests/testthat/test-md5.R |only renv-1.1.3/renv/tests/testthat/test-paths.R | 2 renv-1.1.3/renv/tests/testthat/test-renvignore.R | 37 +++++ renv-1.1.3/renv/tests/testthat/test-sysreqs.R | 57 +++++++ renv-1.1.3/renv/tests/testthat/test-update.R | 24 +++ 48 files changed, 831 insertions(+), 296 deletions(-)
Title: Machine Learning Model Evaluation for 'h2o' Package
Description: Enhances the H2O platform by providing tools for detailed evaluation of machine learning models. It includes functions for bootstrapped performance evaluation, extended F-score calculations, and various other metrics, aimed at improving model assessment.
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between h2otools versions 0.3 dated 2023-05-04 and 0.4 dated 2025-03-18
DESCRIPTION | 19 ++++++++----------- MD5 | 12 +++++++++--- NAMESPACE | 5 +++++ R/bootImportance.R |only R/capture.R |only R/h2o.get_ids.R |only README.md | 22 ++++++++++++++++++---- man/bootImportance.Rd |only man/capture.Rd |only man/h2o.get_ids.Rd |only 10 files changed, 40 insertions(+), 18 deletions(-)
Title: A Fast, Easy-to-Use Database Interface
Description: Provides select, insert, update, upsert, and delete database operations. Supports 'PostgreSQL', 'MySQL', 'SQLite', and more, and plays nicely with the 'DBI' package.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Diff between dbx versions 0.3.2 dated 2024-06-03 and 0.4.0 dated 2025-03-18
DESCRIPTION | 10 ++-- LICENSE | 2 MD5 | 43 ++++++++++---------- NEWS.md | 8 +++ R/connect.R | 2 R/delete.R | 2 R/helpers.R | 59 +++++++++++++++++----------- R/insert.R | 2 R/select.R | 15 ++++++- R/upsert.R | 11 ++++- README.md | 52 ++++++++++++++++++++++-- tests/testthat/helper-is.R | 12 +++++ tests/testthat/helper-run-data-type-tests.R | 26 ++++++++---- tests/testthat/helper-run-execute-tests.R | 2 tests/testthat/helper-run-insert-tests.R | 8 ++- tests/testthat/helper-run-upsert-tests.R | 54 ++++++++++++++++++++++++- tests/testthat/test-duckdb.R |only tests/testthat/test-mariadb.R | 2 tests/testthat/test-mysql.R | 3 - tests/testthat/test-odbc-mysql.R | 17 ++++++-- tests/testthat/test-odbc-postgres.R | 14 +++++- tests/testthat/test-odbc-sqlserver.R | 16 ++++++- tests/testthat/test-postgresql.R | 6 +- 23 files changed, 276 insertions(+), 90 deletions(-)
Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut],
Song Wu [aut],
Jie Yang [aut]
Maintainer: Junying Wang <junying.wang@stonybrook.edu>
Diff between crm12Comb versions 0.1.9 dated 2024-12-09 and 0.1.10 dated 2025-03-18
DESCRIPTION | 6 MD5 | 16 +- R/est.R | 8 - inst/doc/crm12Comb.R | 40 +++++ inst/doc/crm12Comb.Rmd | 61 ++++++++ inst/doc/crm12Comb.html | 351 ++++++++++++++++++++++++++++++++++-------------- man/efficacy_est.Rd | 2 man/toxicity_est.Rd | 2 vignettes/crm12Comb.Rmd | 61 ++++++++ 9 files changed, 429 insertions(+), 118 deletions(-)
Title: Sitree Extensions
Description: Provides extensions for package 'sitree' for allometric variables, growth, mortality, recruitment, management, tree removal and external modifiers functions.
Author: Clara Anton Fernandez [aut] ,
Ignacio Sevillano [cre]
Maintainer: Ignacio Sevillano <ignacio.sevillano@nibio.no>
Diff between sitreeE versions 0.0-8 dated 2021-11-23 and 0.0-9 dated 2025-03-18
DESCRIPTION | 22 +++++--- MD5 | 6 +- R/Biomass_sitree.R | 138 ++++++++++++++++++++++++++--------------------------- R/Volume_sitree.R | 118 ++++++++++++++++++++++----------------------- 4 files changed, 145 insertions(+), 139 deletions(-)
Title: Gaussian Model Invariant by Permutation Symmetry
Description: Find the permutation symmetry group such that the covariance
matrix of the given data is approximately invariant under it.
Discovering such a permutation decreases the number of observations
needed to fit a Gaussian model, which is of great use when it is
smaller than the number of variables. Even if that is not the case,
the covariance matrix found with 'gips' approximates the actual
covariance with less statistical error. The methods implemented in
this package are described in Graczyk et al. (2022)
<doi:10.1214/22-AOS2174>. Documentation about 'gips' is
provided via its website at <https://przechoj.github.io/gips/> and
the paper by Chojecki, Morgen, Kołodziejek
(2025, <doi:10.18637/jss.v112.i07>).
Author: Adam Przemyslaw Chojecki [aut, cre],
Pawel Morgen [aut],
Bartosz Kolodziejek [aut]
Maintainer: Adam Przemyslaw Chojecki <adam.prze.choj@gmail.com>
Diff between gips versions 1.2.1 dated 2023-08-12 and 1.2.3 dated 2025-03-18
DESCRIPTION | 13 - MD5 | 86 +++---- NAMESPACE | 1 NEWS.md | 26 ++ R/calculate_gamma_function.R | 14 - R/estimate_probabilities.R | 17 - R/find_MAP.R | 77 +++--- R/get_structure_constants.R | 65 +++-- R/gips_class.R | 295 +++++++++++++++++++------ R/log_posteriori_of_gips.R | 6 R/project_matrix.R | 8 R/utils.R | 13 + README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 3 inst/doc/Optimizers.R | 88 +++---- inst/doc/Optimizers.Rmd | 10 inst/doc/Optimizers.html | 58 ++-- inst/doc/Theory.R | 10 inst/doc/Theory.Rmd | 8 inst/doc/Theory.html | 35 +- inst/doc/gips.R | 2 inst/doc/gips.Rmd | 8 inst/doc/gips.html | 35 +- man/AIC.gips.Rd | 4 man/calculate_gamma_function.Rd | 4 man/figures/README-example_mean_known1_1-1.png |binary man/figures/README-example_mean_known3_1-1.png |binary man/figures/README-example_mean_known6-1.png |binary man/figures/README-example_mean_unknown2-1.png |binary man/figures/README-example_mean_unknown4-1.png |binary man/find_MAP.Rd | 12 - man/gips.Rd | 2 man/logLik.gips.Rd | 20 + man/plot.gips.Rd | 11 man/summary.gips.Rd | 32 ++ tests/testthat/Rplots.pdf |only tests/testthat/test-find_MAP.R | 4 tests/testthat/test-get_structure_constants.R | 16 - tests/testthat/test-gips_class.R | 44 ++- vignettes/Optimizers.Rmd | 10 vignettes/Theory.Rmd | 8 vignettes/gips.Rmd | 8 45 files changed, 669 insertions(+), 390 deletions(-)
Title: Sudoku as an Experimental Design
Description: Sudoku designs (Bailey et al., 2008<doi:10.1080/00029890.2008.11920542>) can be used as experimental designs which tackle one extra source of variation than conventional Latin square designs. Although Sudoku designs are similar to Latin square designs, only addition is the region concept. Some very important functions related to row-column designs as well as block designs along with basic functions are included in this package.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between SudokuDesigns versions 1.1.0 dated 2024-11-28 and 1.2.0 dated 2025-03-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Check_MP_Inverse.R | 46 +++++++++++++++++++++++++++++----------------- 3 files changed, 34 insertions(+), 22 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.2.3-1 dated 2025-02-06 and 14.4.0-1 dated 2025-03-18
ChangeLog | 49 DESCRIPTION | 8 MD5 | 152 +- R/RcppArmadillo.package.skeleton.R | 19 build/partial.rdb |binary build/vignette.rds |binary configure | 18 configure.ac | 2 inst/NEWS.Rd | 29 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/CubeToMatOp_bones.hpp | 4 inst/include/armadillo_bits/Cube_meat.hpp | 48 inst/include/armadillo_bits/GenCube_bones.hpp | 6 inst/include/armadillo_bits/Gen_bones.hpp | 4 inst/include/armadillo_bits/Mat_meat.hpp | 64 + inst/include/armadillo_bits/OpCube_bones.hpp | 10 inst/include/armadillo_bits/Op_bones.hpp | 8 inst/include/armadillo_bits/Proxy.hpp | 106 +- inst/include/armadillo_bits/ProxyCube.hpp | 20 inst/include/armadillo_bits/SpOp_bones.hpp | 8 inst/include/armadillo_bits/SpProxy.hpp | 68 - inst/include/armadillo_bits/SpToDOp_bones.hpp | 8 inst/include/armadillo_bits/arma_forward.hpp | 1 inst/include/armadillo_bits/arma_rng.hpp | 30 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/arrayops_meat.hpp | 11 inst/include/armadillo_bits/auxlib_meat.hpp | 4 inst/include/armadillo_bits/diagview_bones.hpp | 2 inst/include/armadillo_bits/eGlueCube_bones.hpp | 6 inst/include/armadillo_bits/eGlue_bones.hpp | 4 inst/include/armadillo_bits/eOpCube_bones.hpp | 11 inst/include/armadillo_bits/eOp_bones.hpp | 9 inst/include/armadillo_bits/field_bones.hpp | 24 inst/include/armadillo_bits/field_meat.hpp | 246 +++- inst/include/armadillo_bits/fn_accu.hpp | 186 +++ inst/include/armadillo_bits/fn_conv_to.hpp | 23 inst/include/armadillo_bits/fn_dot.hpp | 2 inst/include/armadillo_bits/fn_elem.hpp | 184 +-- inst/include/armadillo_bits/fn_reshape.hpp | 49 inst/include/armadillo_bits/fn_resize.hpp | 52 + inst/include/armadillo_bits/glue_solve_meat.hpp | 7 inst/include/armadillo_bits/glue_times_meat.hpp | 158 +-- inst/include/armadillo_bits/memory.hpp | 6 inst/include/armadillo_bits/mtGlueCube_bones.hpp | 6 inst/include/armadillo_bits/mtGlue_bones.hpp | 6 inst/include/armadillo_bits/mtOpCube_bones.hpp | 14 inst/include/armadillo_bits/mtOp_bones.hpp | 12 inst/include/armadillo_bits/mtSpOp_bones.hpp | 10 inst/include/armadillo_bits/mtSpReduceOp_bones.hpp | 6 inst/include/armadillo_bits/op_all_bones.hpp | 6 inst/include/armadillo_bits/op_all_meat.hpp | 153 +- inst/include/armadillo_bits/op_any_bones.hpp | 6 inst/include/armadillo_bits/op_any_meat.hpp | 126 +- inst/include/armadillo_bits/op_htrans_meat.hpp | 54 - inst/include/armadillo_bits/op_mean_meat.hpp | 4 inst/include/armadillo_bits/op_misc_meat.hpp | 22 inst/include/armadillo_bits/op_reshape_meat.hpp | 47 inst/include/armadillo_bits/op_resize_meat.hpp | 36 inst/include/armadillo_bits/op_sort_bones.hpp | 10 inst/include/armadillo_bits/op_sort_index_bones.hpp | 23 inst/include/armadillo_bits/op_sort_index_meat.hpp | 71 - inst/include/armadillo_bits/op_sort_meat.hpp | 229 ++-- inst/include/armadillo_bits/op_sp_sum_bones.hpp | 3 inst/include/armadillo_bits/op_sp_sum_meat.hpp | 82 + inst/include/armadillo_bits/op_strans_meat.hpp | 54 - inst/include/armadillo_bits/op_sum_bones.hpp | 27 inst/include/armadillo_bits/op_sum_meat.hpp | 290 ++++- inst/include/armadillo_bits/op_trimat_bones.hpp | 4 inst/include/armadillo_bits/op_trimat_meat.hpp | 112 +- inst/include/armadillo_bits/op_vectorise_meat.hpp | 63 - inst/include/armadillo_bits/spdiagview_bones.hpp | 2 inst/include/armadillo_bits/spop_misc_meat.hpp | 16 inst/include/armadillo_bits/traits.hpp | 20 inst/include/armadillo_bits/unwrap.hpp | 1034 -------------------- man/RcppArmadillo.package.skeleton.Rd | 45 vignettes/pdf/RcppArmadillo-sparseMatrix.pdf |binary 77 files changed, 2116 insertions(+), 2129 deletions(-)
Title: Triangle Meshes and Related Geometry Tools
Description: Generate planar and spherical triangle meshes,
compute finite element calculations for 1- and 2-dimensional flat and curved
manifolds with associated basis function spaces, methods for lines and
polygons, and transparent handling of coordinate reference systems and
coordinate transformation, including 'sf' and 'sp' geometries. The core
'fmesher' library code was originally part of the 'INLA' package, and
implements parts of "Triangulations and Applications" by
Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Author: Finn Lindgren [aut, cre, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb] ,
Fabian E. Bachl [ctb]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between fmesher versions 0.2.0 dated 2024-11-06 and 0.3.0 dated 2025-03-18
fmesher-0.2.0/fmesher/man/fm_evaluator_helpers.Rd |only fmesher-0.3.0/fmesher/DESCRIPTION | 21 fmesher-0.3.0/fmesher/MD5 | 215 - fmesher-0.3.0/fmesher/NAMESPACE | 104 fmesher-0.3.0/fmesher/NEWS.md | 54 fmesher-0.3.0/fmesher/R/RcppExports.R | 47 fmesher-0.3.0/fmesher/R/bary.R | 841 +++++ fmesher-0.3.0/fmesher/R/basis.R |only fmesher-0.3.0/fmesher/R/bbox.R | 66 fmesher-0.3.0/fmesher/R/crs.R | 125 fmesher-0.3.0/fmesher/R/diameter.R | 34 fmesher-0.3.0/fmesher/R/evaluator.R | 1601 ----------- fmesher-0.3.0/fmesher/R/fem.R | 118 fmesher-0.3.0/fmesher/R/fm.R | 19 fmesher-0.3.0/fmesher/R/fmesher.R | 66 fmesher-0.3.0/fmesher/R/ggplot.R | 29 fmesher-0.3.0/fmesher/R/integration.R | 208 - fmesher-0.3.0/fmesher/R/lattice_2d.R | 24 fmesher-0.3.0/fmesher/R/lattice_Nd.R |only fmesher-0.3.0/fmesher/R/list.R | 10 fmesher-0.3.0/fmesher/R/manifold.R | 23 fmesher-0.3.0/fmesher/R/matern.R | 3 fmesher-0.3.0/fmesher/R/mesh.R | 50 fmesher-0.3.0/fmesher/R/mesh_1d.R | 47 fmesher-0.3.0/fmesher/R/mesh_2d.R | 43 fmesher-0.3.0/fmesher/R/mesh_3d.R |only fmesher-0.3.0/fmesher/R/mesh_assessment.R |only fmesher-0.3.0/fmesher/R/nonconvex_hull.R | 4 fmesher-0.3.0/fmesher/R/print.R | 182 + fmesher-0.3.0/fmesher/R/segm.R | 9 fmesher-0.3.0/fmesher/R/sf_mesh.R | 19 fmesher-0.3.0/fmesher/R/sf_utils.R | 2 fmesher-0.3.0/fmesher/R/split_lines.R | 12 fmesher-0.3.0/fmesher/R/utils.R | 26 fmesher-0.3.0/fmesher/README.md | 2 fmesher-0.3.0/fmesher/build/vignette.rds |binary fmesher-0.3.0/fmesher/inst/doc/articles.html | 4 fmesher-0.3.0/fmesher/inst/doc/basic_use.R | 11 fmesher-0.3.0/fmesher/inst/doc/basic_use.Rmd | 11 fmesher-0.3.0/fmesher/inst/doc/basic_use.html | 130 fmesher-0.3.0/fmesher/inst/doc/custom_classes.R |only fmesher-0.3.0/fmesher/inst/doc/custom_classes.Rmd |only fmesher-0.3.0/fmesher/inst/doc/custom_classes.html |only fmesher-0.3.0/fmesher/inst/doc/inla_conversion.R | 75 fmesher-0.3.0/fmesher/inst/doc/inla_conversion.Rmd | 84 fmesher-0.3.0/fmesher/inst/doc/inla_conversion.html | 162 - fmesher-0.3.0/fmesher/man/as.triangles3d.fm_mesh_3d.Rd |only fmesher-0.3.0/fmesher/man/figures/README-example2-plot-1.png |binary fmesher-0.3.0/fmesher/man/fm_CRS_sp.Rd | 9 fmesher-0.3.0/fmesher/man/fm_as_fm.Rd | 11 fmesher-0.3.0/fmesher/man/fm_as_lattice_2d.Rd | 3 fmesher-0.3.0/fmesher/man/fm_as_lattice_Nd.Rd |only fmesher-0.3.0/fmesher/man/fm_as_mesh_1d.Rd | 3 fmesher-0.3.0/fmesher/man/fm_as_mesh_2d.Rd | 13 fmesher-0.3.0/fmesher/man/fm_as_mesh_3d.Rd |only fmesher-0.3.0/fmesher/man/fm_as_segm.Rd | 3 fmesher-0.3.0/fmesher/man/fm_as_sfc.Rd | 15 fmesher-0.3.0/fmesher/man/fm_as_tensor.Rd | 3 fmesher-0.3.0/fmesher/man/fm_assess.Rd |only fmesher-0.3.0/fmesher/man/fm_bary.Rd | 96 fmesher-0.3.0/fmesher/man/fm_bary_loc.Rd |only fmesher-0.3.0/fmesher/man/fm_bary_simplex.Rd |only fmesher-0.3.0/fmesher/man/fm_basis.Rd | 94 fmesher-0.3.0/fmesher/man/fm_basis_helpers.Rd | 6 fmesher-0.3.0/fmesher/man/fm_bbox.Rd | 30 fmesher-0.3.0/fmesher/man/fm_block.Rd | 9 fmesher-0.3.0/fmesher/man/fm_centroids.Rd | 2 fmesher-0.3.0/fmesher/man/fm_contains.Rd | 2 fmesher-0.3.0/fmesher/man/fm_cprod.Rd | 10 fmesher-0.3.0/fmesher/man/fm_crs.Rd | 15 fmesher-0.3.0/fmesher/man/fm_diameter.Rd | 21 fmesher-0.3.0/fmesher/man/fm_dof.Rd | 9 fmesher-0.3.0/fmesher/man/fm_evaluate.Rd | 44 fmesher-0.3.0/fmesher/man/fm_fem.Rd | 12 fmesher-0.3.0/fmesher/man/fm_gmrf.Rd | 3 fmesher-0.3.0/fmesher/man/fm_int.Rd | 31 fmesher-0.3.0/fmesher/man/fm_int_mesh_2d.Rd | 5 fmesher-0.3.0/fmesher/man/fm_int_mesh_2d_core.Rd | 2 fmesher-0.3.0/fmesher/man/fm_is_within.Rd | 12 fmesher-0.3.0/fmesher/man/fm_lattice_2d.Rd | 9 fmesher-0.3.0/fmesher/man/fm_lattice_Nd.Rd |only fmesher-0.3.0/fmesher/man/fm_manifold.Rd | 6 fmesher-0.3.0/fmesher/man/fm_mesh_1d.Rd | 3 fmesher-0.3.0/fmesher/man/fm_mesh_2d.Rd | 9 fmesher-0.3.0/fmesher/man/fm_mesh_3d.Rd |only fmesher-0.3.0/fmesher/man/fm_nonconvex_hull_inla.Rd | 2 fmesher-0.3.0/fmesher/man/fm_qinv.Rd | 27 fmesher-0.3.0/fmesher/man/fm_raw_basis.Rd | 2 fmesher-0.3.0/fmesher/man/fm_segm.Rd | 6 fmesher-0.3.0/fmesher/man/fm_simplify.Rd | 3 fmesher-0.3.0/fmesher/man/fm_split_lines.Rd | 5 fmesher-0.3.0/fmesher/man/fm_tensor.Rd | 3 fmesher-0.3.0/fmesher/man/fm_transform.Rd | 9 fmesher-0.3.0/fmesher/man/fm_vertex_projection.Rd | 8 fmesher-0.3.0/fmesher/man/fmesher-deprecated.Rd | 27 fmesher-0.3.0/fmesher/man/fmesher-print.Rd | 12 fmesher-0.3.0/fmesher/man/fmesher_bary.Rd | 3 fmesher-0.3.0/fmesher/man/fmesher_bary3d.Rd |only fmesher-0.3.0/fmesher/man/fmesher_mesh3d.Rd |only fmesher-0.3.0/fmesher/man/geom_fm.Rd | 12 fmesher-0.3.0/fmesher/src/RcppExports.cpp | 29 fmesher-0.3.0/fmesher/src/Rcpp_interface.cc | 620 ++-- fmesher-0.3.0/fmesher/src/fmesher.h | 1 fmesher-0.3.0/fmesher/src/fmesher_helpers.cc | 25 fmesher-0.3.0/fmesher/src/fmesher_helpers.h | 11 fmesher-0.3.0/fmesher/src/locator.cc | 84 fmesher-0.3.0/fmesher/src/locator.h | 26 fmesher-0.3.0/fmesher/src/mesh.cc | 2 fmesher-0.3.0/fmesher/src/mesh.h | 5 fmesher-0.3.0/fmesher/src/mesh3.cc |only fmesher-0.3.0/fmesher/src/mesh3.h |only fmesher-0.3.0/fmesher/src/meshc.cc | 6 fmesher-0.3.0/fmesher/src/vector.h | 222 + fmesher-0.3.0/fmesher/tests/testthat/test-barycentric.R | 16 fmesher-0.3.0/fmesher/tests/testthat/test-integration.R | 14 fmesher-0.3.0/fmesher/tests/testthat/test-rcdt_2d.R | 57 fmesher-0.3.0/fmesher/vignettes/basic_use.Rmd | 11 fmesher-0.3.0/fmesher/vignettes/custom_classes.Rmd |only fmesher-0.3.0/fmesher/vignettes/inla_conversion.Rmd | 84 119 files changed, 3391 insertions(+), 2912 deletions(-)
Title: Ecological Inference Applying Entropy
Description: Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.
Author: Alberto Diaz-Dapena [aut, cph],
Esteban Fernandez-Vazquez [aut, cph],
Silvia Maria Franco Anaya [aut, cre, cph]
Maintainer: Silvia Maria Franco Anaya <sfrana@unileon.es>
Diff between EIEntropy versions 0.0.1.3 dated 2024-11-04 and 0.0.1.4 dated 2025-03-17
DESCRIPTION | 10 MD5 | 22 NEWS.md | 14 R/ei_gce.R | 169 +- R/ei_gme.R | 133 +- inst/doc/EIVignette.R | 18 inst/doc/EIVignette.Rmd | 164 -- inst/doc/EIVignette.html | 3000 ++++++++++++++++++++++++++--------------------- man/ei_gce.Rd | 49 man/ei_gme.Rd | 43 man/summary.kl.Rd | 2 vignettes/EIVignette.Rmd | 164 -- 12 files changed, 2043 insertions(+), 1745 deletions(-)
Title: Export Data Frames to Excel 'xlsx' Format
Description: Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'
<https://libxlsxwriter.github.io>. Fast and no Java or Excel required.
Author: Jeroen Ooms [aut, cre] ,
John McNamara [cph] )
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between writexl versions 1.5.1 dated 2024-10-04 and 1.5.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/write_xlsx.R | 5 +++-- src/Makevars | 12 ++++++++---- 5 files changed, 21 insertions(+), 13 deletions(-)
Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] ,
Kaio Dias [aut, cph] ,
Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>
Diff between ProbBreed versions 1.0.4.5 dated 2025-02-02 and 1.0.4.6 dated 2025-03-17
DESCRIPTION | 6 +- MD5 | 40 ++++++------- NEWS.md | 4 + inst/stan/IBD1.stan | 10 +-- inst/stan/IBD2.stan | 10 +-- inst/stan/IBD3.stan | 10 +-- inst/stan/IBD4.stan | 10 +-- inst/stan/IBD5.stan | 6 +- inst/stan/IBD6.stan | 6 +- inst/stan/IBD7.stan | 6 +- inst/stan/IBD8.stan | 6 +- inst/stan/RCBD1.stan | 10 +-- inst/stan/RCBD2.stan | 10 +-- inst/stan/RCBD3.stan | 10 +-- inst/stan/RCBD4.stan | 10 +-- inst/stan/RCBD5.stan | 6 +- inst/stan/RCBD6.stan | 6 +- inst/stan/RCBD7.stan | 6 +- inst/stan/RCBD8.stan | 6 +- inst/stan/entrymean1.stan | 138 +++++++++++++++++++++++----------------------- inst/stan/entrymean2.stan | 130 +++++++++++++++++++++---------------------- 21 files changed, 225 insertions(+), 221 deletions(-)
Title: Run R Scripts if Needed
Description: Automation tool to run R scripts if needed, based on last modified
time. It comes with no package dependencies, organizational overhead, or
structural requirements. In short: run an R script if underlying files have
changed, otherwise do nothing.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between makeit versions 1.0.1 dated 2023-10-27 and 1.0.2 dated 2025-03-17
DESCRIPTION | 16 - MD5 | 16 - NEWS.md | 7 R/make.R | 9 build/vignette.rds |binary inst/doc/makeit.Rmd | 16 - inst/doc/makeit.html | 469 ++++++++++++++++++++++++++++----------------------- man/make.Rd | 9 vignettes/makeit.Rmd | 16 - 9 files changed, 321 insertions(+), 237 deletions(-)
Title: Preprocessing and Feature Engineering Steps for Modeling
Description: A recipe prepares your data for modeling. We provide an
extensible framework for pipeable sequences of feature engineering
steps provides preprocessing tools to be applied to data. Statistical
parameters for the steps can be estimated from an initial data set and
then applied to other data sets. The resulting processed output can
then be used as inputs for statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Emil Hvitfeldt [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between recipes versions 1.1.1 dated 2025-02-12 and 1.2.0 dated 2025-03-17
DESCRIPTION | 8 MD5 | 679 +++++++++++----------- NAMESPACE | 25 NEWS.md | 43 + R/BoxCox.R | 29 R/YeoJohnson.R | 39 - R/aaa.R | 63 +- R/arrange.R | 22 R/bin2factor.R | 21 R/bs.R | 46 + R/case_weights.R | 27 R/center.R | 32 - R/class.R | 95 +-- R/classdist.R | 63 +- R/classdist_shrunken.R | 226 ++++--- R/colcheck.R | 24 R/corr.R | 72 +- R/count.R | 99 ++- R/cut.R | 23 R/date.R | 75 +- R/deprec-impute_bag.R | 26 R/deprec-impute_knn.R | 26 R/deprec-impute_lower.R | 18 R/deprec-impute_median.R | 18 R/deprec-impute_mena.R | 22 R/deprec-impute_mode.R | 22 R/deprec-impute_roll.R | 24 R/deprec-terms_select.R | 2 R/depth.R | 57 + R/developer.R | 16 R/discretize.R | 80 +- R/dummy.R | 101 +-- R/dummy_extract.R | 127 +++- R/dummy_multi_choice.R | 119 ++- R/extension_check.R | 17 R/extract_parameter.R | 9 R/factor2string.R | 17 R/filter.R | 22 R/filter_missing.R | 58 + R/format.R | 6 R/geodist.R | 90 +- R/get_types_recipes.R | 7 R/harmonic.R | 80 +- R/holiday.R | 108 ++- R/hyperbolic.R | 27 R/ica.R | 64 +- R/import-standalone-obj-type.R | 107 +-- R/import-standalone-types-check.R | 293 +++++---- R/impute_bag.R | 39 - R/impute_knn.R | 60 + R/impute_linear.R | 43 - R/impute_lower.R | 26 R/impute_mean.R | 53 + R/impute_median.R | 46 + R/impute_mode.R | 40 - R/impute_roll.R | 21 R/indicate_na.R | 62 +- R/integer.R | 38 - R/interact.R | 48 - R/intercept.R | 16 R/inverse.R | 18 R/invlogit.R | 11 R/isomap.R | 57 + R/kpca.R | 62 +- R/kpca_poly.R | 67 +- R/kpca_rbf.R | 54 + R/lag.R | 59 + R/lincomb.R | 32 - R/log.R | 22 R/logit.R | 18 R/misc.R | 78 +- R/missing.R | 16 R/mutate.R | 20 R/mutate_at.R | 17 R/naomit.R | 19 R/newvalues.R | 33 - R/nnmf.R | 72 +- R/nnmf_sparse.R | 79 +- R/normalize.R | 43 - R/novel.R | 21 R/ns.R | 43 - R/num2factor.R | 22 R/nzv.R | 60 + R/ordinalscore.R | 47 - R/other.R | 88 +- R/pca.R | 87 +- R/percentile.R | 50 + R/pls.R | 129 +++- R/poly.R | 45 - R/poly_bernstein.R | 44 - R/printing.R | 39 - R/profile.R | 47 - R/ptype.R | 115 +-- R/range.R | 29 R/range_check.R | 66 +- R/ratio.R | 42 - R/recipe.R | 232 ++++--- R/recipes-package.R | 1 R/reexports.R | 5 R/regex.R | 90 ++ R/relevel.R | 22 R/relu.R | 38 - R/rename.R | 22 R/rename_at.R | 24 R/rm.R | 24 R/roles.R | 80 +- R/sample.R | 49 + R/scale.R | 50 + R/select.R | 21 R/selections.R | 36 - R/shuffle.R | 23 R/slice.R | 22 R/sparsevctrs.R | 59 + R/spatialsign.R | 30 R/spline_b.R | 45 - R/spline_convex.R | 45 - R/spline_helpers.R | 28 R/spline_monotone.R | 45 - R/spline_natural.R | 76 +- R/spline_nonnegative.R | 45 - R/sqrt.R | 27 R/steps_and_checks.R | 64 +- R/string2factor.R | 20 R/testthat_helper.R | 16 R/time.R | 45 - R/tune_args.R | 21 R/unknown.R | 21 R/unorder.R | 17 R/update-role-requirements.R | 47 - R/update.R | 5 R/window.R | 61 + R/zv.R | 33 - inst/boilerplate.R | 54 + inst/doc/Dummies.html | 5 inst/doc/Roles.html | 5 inst/doc/Selecting_Variables.html | 5 inst/doc/Skipping.html | 5 inst/doc/recipes.html | 5 inst/old-get_types.R | 10 inst/pls_test_references.R | 33 - man/dot-recipes_preserve_sparsity.Rd |only man/recipes_ptype.Rd | 2 man/reexports.Rd | 2 man/rmd/non-standard-roles.Rmd | 10 man/roles.Rd | 11 man/sparse_data.Rd | 4 man/step_arrange.Rd | 7 man/step_count.Rd | 19 man/step_dummy.Rd | 19 man/step_dummy_extract.Rd | 19 man/step_dummy_multi_choice.Rd | 19 man/step_filter.Rd | 7 man/step_filter_missing.Rd | 7 man/step_holiday.Rd | 19 man/step_impute_mean.Rd | 7 man/step_impute_median.Rd | 7 man/step_indicate_na.Rd | 19 man/step_lag.Rd | 7 man/step_naomit.Rd | 7 man/step_regex.Rd | 19 man/step_rename.Rd | 7 man/step_rename_at.Rd | 7 man/step_rm.Rd | 7 man/step_sample.Rd | 7 man/step_scale.Rd | 9 man/step_select.Rd | 7 man/step_shuffle.Rd | 7 man/step_slice.Rd | 7 man/step_sqrt.Rd | 7 man/step_zv.Rd | 7 tests/testthat/_snaps/BoxCox.md | 2 tests/testthat/_snaps/basics.md | 56 + tests/testthat/_snaps/bs.md | 4 tests/testthat/_snaps/classdist.md | 2 tests/testthat/_snaps/classdist_shrunken.md | 2 tests/testthat/_snaps/corr.md | 2 tests/testthat/_snaps/date.md | 2 tests/testthat/_snaps/depth.md | 2 tests/testthat/_snaps/discretize.md | 2 tests/testthat/_snaps/dummy.md | 14 tests/testthat/_snaps/factor2string.md | 4 tests/testthat/_snaps/filter_missing.md | 2 tests/testthat/_snaps/geodist.md | 6 tests/testthat/_snaps/hyperbolic.md | 4 tests/testthat/_snaps/ica.md | 6 tests/testthat/_snaps/impute_knn.md | 4 tests/testthat/_snaps/impute_lower.md | 4 tests/testthat/_snaps/mutate_at.md | 2 tests/testthat/_snaps/nnmf_sparse.md | 4 tests/testthat/_snaps/normalize.md | 4 tests/testthat/_snaps/ns.md | 4 tests/testthat/_snaps/nzv.md | 5 tests/testthat/_snaps/other.md | 4 tests/testthat/_snaps/pca.md | 4 tests/testthat/_snaps/percentile.md | 8 tests/testthat/_snaps/poly.md | 4 tests/testthat/_snaps/poly_bernstein.md | 4 tests/testthat/_snaps/range.md | 4 tests/testthat/_snaps/ratio.md | 2 tests/testthat/_snaps/rename_at.md | 2 tests/testthat/_snaps/scale.md | 4 tests/testthat/_snaps/spatialsign.md | 12 tests/testthat/_snaps/spline_b.md | 4 tests/testthat/_snaps/spline_convex.md | 4 tests/testthat/_snaps/spline_monotone.md | 4 tests/testthat/_snaps/spline_natural.md | 4 tests/testthat/_snaps/spline_nonnegative.md | 4 tests/testthat/_snaps/sqrt.md | 4 tests/testthat/_snaps/string2factor.md | 4 tests/testthat/_snaps/unknown.md | 4 tests/testthat/_snaps/unorder.md | 2 tests/testthat/helper-case-weights.R | 1 tests/testthat/helper-extract_parameter_set.R | 7 tests/testthat/test-BoxCox.R | 138 +++- tests/testthat/test-YeoJohnson.R | 148 +++- tests/testthat/test-arrange.R | 41 - tests/testthat/test-bake.R | 2 tests/testthat/test-basics.R | 142 ++-- tests/testthat/test-bin2factor.R | 13 tests/testthat/test-bs.R | 56 + tests/testthat/test-case-weight-functions.R | 20 tests/testthat/test-center.R | 31 - tests/testthat/test-class.R | 45 - tests/testthat/test-classdist.R | 66 +- tests/testthat/test-classdist_shrunken.R | 116 ++- tests/testthat/test-colcheck.R | 49 - tests/testthat/test-column_order.R | 52 - tests/testthat/test-corr.R | 22 tests/testthat/test-count.R | 120 +++ tests/testthat/test-cut.R | 66 +- tests/testthat/test-data.frame.R | 12 tests/testthat/test-date.R | 91 +- tests/testthat/test-deprec-impute_bag.R | 7 tests/testthat/test-deprec-impute_knn.R | 7 tests/testthat/test-deprec-impute_lower.R | 5 tests/testthat/test-deprec-impute_median.R | 7 tests/testthat/test-deprec-impute_mena.R | 7 tests/testthat/test-deprec-impute_mode.R | 5 tests/testthat/test-deprec-impute_roll.R | 5 tests/testthat/test-depth.R | 34 - tests/testthat/test-discretize.R | 34 - tests/testthat/test-dummy.R | 160 +++-- tests/testthat/test-dummy_extract.R | 139 +++- tests/testthat/test-dummy_multi_choice.R | 126 +++- tests/testthat/test-extract-dials.R | 46 - tests/testthat/test-factor2string.R | 4 tests/testthat/test-filter.R | 58 + tests/testthat/test-filter_missing.R | 19 tests/testthat/test-format.R | 3 tests/testthat/test-formula.R | 13 tests/testthat/test-geodist.R | 229 ++++--- tests/testthat/test-grouped_df.R | 2 tests/testthat/test-harmonic.R | 214 ++---- tests/testthat/test-holiday.R | 78 ++ tests/testthat/test-hyperbolic.R | 3 tests/testthat/test-ica.R | 107 ++- tests/testthat/test-impute_bag.R | 56 + tests/testthat/test-impute_knn.R | 94 +-- tests/testthat/test-impute_linear.R | 31 - tests/testthat/test-impute_lower.R | 13 tests/testthat/test-impute_mean.R | 41 - tests/testthat/test-impute_median.R | 30 tests/testthat/test-impute_mode.R | 25 tests/testthat/test-impute_roll.R | 23 tests/testthat/test-indicate_na.R | 90 ++ tests/testthat/test-integer.R | 24 tests/testthat/test-interact.R | 121 ++- tests/testthat/test-intercept.R | 9 tests/testthat/test-inverse.R | 6 tests/testthat/test-invlogit.R | 2 tests/testthat/test-isomap.R | 75 +- tests/testthat/test-kpca.R | 27 tests/testthat/test-kpca_poly.R | 42 - tests/testthat/test-kpca_rbf.R | 37 - tests/testthat/test-lag.R | 25 tests/testthat/test-lincomb.R | 22 tests/testthat/test-list_cols.R | 2 tests/testthat/test-log.R | 2 tests/testthat/test-logit.R | 17 tests/testthat/test-matrix.R | 20 tests/testthat/test-misc.R | 20 tests/testthat/test-missing.R | 6 tests/testthat/test-multivariate.R | 6 tests/testthat/test-mutate.R | 58 - tests/testthat/test-mutate_at.R | 60 - tests/testthat/test-naomit.R | 19 tests/testthat/test-newvalues.R | 85 +- tests/testthat/test-nnmf_sparse.R | 21 tests/testthat/test-nomial_types.R | 77 +- tests/testthat/test-normalize.R | 36 - tests/testthat/test-novel.R | 10 tests/testthat/test-ns.R | 48 - tests/testthat/test-num2factor.R | 6 tests/testthat/test-nzv.R | 16 tests/testthat/test-ordinalscore.R | 43 - tests/testthat/test-other.R | 172 +++-- tests/testthat/test-pca.R | 139 +++- tests/testthat/test-percentile.R | 38 - tests/testthat/test-pls.R | 154 +++- tests/testthat/test-poly.R | 54 + tests/testthat/test-poly_bernstein.R | 41 - tests/testthat/test-profile.R | 42 - tests/testthat/test-ptype.R | 34 - tests/testthat/test-range.R | 144 +++- tests/testthat/test-range_check.R | 22 tests/testthat/test-ratio.R | 83 +- tests/testthat/test-regex.R | 105 ++- tests/testthat/test-relevel.R | 9 tests/testthat/test-relu.R | 16 tests/testthat/test-rename.R | 52 + tests/testthat/test-rename_at.R | 33 - tests/testthat/test-retraining.R | 3 tests/testthat/test-rm.R | 59 + tests/testthat/test-roles.R | 104 +-- tests/testthat/test-sample.R | 104 +-- tests/testthat/test-scale.R | 65 +- tests/testthat/test-select.R | 21 tests/testthat/test-selections.R | 280 +++++++-- tests/testthat/test-shuffle.R | 14 tests/testthat/test-skipping.R | 34 - tests/testthat/test-slice.R | 54 + tests/testthat/test-sparsevctrs.R | 9 tests/testthat/test-sparsity.R | 22 tests/testthat/test-spatialsign.R | 19 tests/testthat/test-spline_b.R | 44 - tests/testthat/test-spline_convex.R | 58 + tests/testthat/test-spline_monotone.R | 72 +- tests/testthat/test-spline_natural.R | 41 - tests/testthat/test-spline_nonnegative.R | 72 +- tests/testthat/test-sqrt.R | 14 tests/testthat/test-string2factor.R | 6 tests/testthat/test-stringsAsFactors.R | 17 tests/testthat/test-term_info.R | 802 ++++++++++++++++++++------ tests/testthat/test-tidy.R | 7 tests/testthat/test-time.R | 64 +- tests/testthat/test-tune_args.R | 17 tests/testthat/test-unknown.R | 16 tests/testthat/test-unorder.R | 13 tests/testthat/test-update.R | 49 + tests/testthat/test-window.R | 59 - tests/testthat/test-zv.R | 21 341 files changed, 9569 insertions(+), 5254 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.1 dated 2025-03-05 and 3.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ src/Makevars.in | 17 ++++++----------- src/Makevars.win | 8 +++----- src/osx/Makevars | 16 ++++++---------- 6 files changed, 26 insertions(+), 34 deletions(-)
Title: Minimal Examples of Using Rust Code in R
Description: Template R package with minimal setup to use Rust code in R without
hacks or frameworks. Includes basic examples of importing cargo dependencies,
spawning threads and passing numbers or strings from Rust to R. Cargo crates
are automatically 'vendored' in the R source package to support offline
installation. The GitHub repository for this package has more details and also
explains how to set up CI. This project was first presented at 'Erum2018' to
showcase R-Rust integration <https://jeroen.github.io/erum2018/>; for a real
world use-case, see the 'gifski' package on 'CRAN'.
Author: Jeroen Ooms [aut, cre] ,
Authors of the dependency Rust crates [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between hellorust versions 1.2.2 dated 2024-09-22 and 1.2.3 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ inst/AUTHORS | 4 ++-- src/Makevars | 6 +++--- src/Makevars.win | 9 +++------ src/myrustlib/vendor.tar.xz |binary 7 files changed, 20 insertions(+), 20 deletions(-)
Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL
<https://graphql.org> syntax and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut],
Barret Schloerke [ctb],
Scott Wolchok [ctb],
Facebook, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between graphql versions 1.5.2 dated 2024-10-04 and 1.5.3 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars | 8 +++----- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Tree-Guided Rare Feature Selection and Logic Aggregation
Description: Implementation of the tree-guided feature selection and logic aggregation approach introduced in Chen et al. (2024) <doi:10.1080/01621459.2024.2326621>. The method enables the selection and aggregation of large-scale rare binary features with a known hierarchical structure using a convex, linearly-constrained regularized regression framework. The package facilitates the application of this method to both linear regression and binary classification problems by solving the optimization problem via the smoothing proximal gradient descent algorithm (Chen et al. (2012) <doi:10.1214/11-AOAS514>).
Author: Jianmin Chen [aut, cre],
Kun Chen [aut]
Maintainer: Jianmin Chen <jianminc000@gmail.com>
Diff between TSLA versions 0.1.1 dated 2025-02-10 and 0.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/SPGlinear.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Sparse Vectors for Use in Data Frames
Description: Provides sparse vectors powered by ALTREP (Alternative
Representations for R Objects) that behave like regular vectors, and
can thus be used in data frames. Also provides tools to convert
between sparse matrices and data frames with sparse columns and
functions to interact with sparse vectors.
Author: Emil Hvitfeldt [aut, cre] ,
Davis Vaughan [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between sparsevctrs versions 0.3.0 dated 2025-03-10 and 0.3.1 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/sparse-arithmatic.c | 21 ++++++++++++++------- 4 files changed, 24 insertions(+), 13 deletions(-)
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] ,
Jeffrey Horner [ctb],
Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.12 dated 2021-09-28 and 0.13 dated 2025-03-17
DESCRIPTION | 13 MD5 | 17 R/mime.R | 94 -- R/mimeextra.R |only R/mimemap.R | 1965 +++++++++++++++++++++++++++++++++++++------------ R/parse.R | 6 README.md | 12 man/guess_type.Rd | 21 man/mimemap.Rd | 10 man/parse_multipart.Rd | 8 10 files changed, 1551 insertions(+), 595 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-0 dated 2025-03-01 and 0.9-1 dated 2025-03-17
DESCRIPTION | 8 MD5 | 58 NEWS.md | 23 R/blrm_exnex.R | 94 R/example_single_agent.R | 16 R/posterior.R | 2 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 14 inst/doc/introduction.html | 314 - inst/doc/map_approach.R |only inst/doc/map_approach.Rmd |only inst/doc/map_approach.html |only inst/sbc/calibration.md5 | 6 inst/sbc/sbc_example_models.R | 34 inst/sbc/sbc_report.html | 1488 ++++----- inst/stan/blrm_exnex.stan | 58 man/blrm_exnex.Rd | 10 man/example-single-agent.Rd | 34 man/hist_SA.Rd | 18 src/stanExports_blrm_exnex.h | 2963 +++++++++--------- tests/testthat/helper-sampling.R | 3 tests/testthat/test-blrm_exnex.R | 353 +- tests/testthat/test-blrm_trial.R | 6 tests/testthat/test-plot_toxicity_curve.R | 9 tests/testthat/test-plot_toxicity_intervals.R | 21 tests/testthat/test-plot_toxicity_intervals_stacked.R | 11 tests/testthat/test-posterior.R | 29 vignettes/map_approach.Rmd |only vignettes/settings-knitr.txt | 4 vignettes/settings-sampling.txt | 10 32 files changed, 2949 insertions(+), 2637 deletions(-)
Title: Gaussian Processes on Graphs and Lattices in 'Stan'
Description: Gaussian processes are flexible distributions to model functional data. Whilst
theoretically appealing, they are computationally cumbersome except for small datasets.
This package implements two methods for scaling Gaussian process inference in 'Stan'. First, a
sparse approximation of the likelihood that is generally applicable and, second, an exact method
for regularly spaced data modeled by stationary kernels using fast Fourier methods. Utility
functions are provided to compile and fit 'Stan' models using the 'cmdstanr' interface.
References: Hoffmann and Onnela (2025) <doi:10.18637/jss.v112.i02>.
Author: Till Hoffmann [aut, cre] ,
Jukka-Pekka Onnela [ctb]
Maintainer: Till Hoffmann <thoffmann@hsph.harvard.edu>
Diff between gptoolsStan versions 0.2.0 dated 2024-12-12 and 1.0.0 dated 2025-03-17
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- README.md | 2 +- inst/CITATION |only inst/doc/getting_started.html | 20 +++++++++++++++++--- 5 files changed, 26 insertions(+), 11 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Maria Jose Ginzo Villamayor [aut, com],
Manuel Antonio Novo Perez [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
Diff between FORTLS versions 1.4.0 dated 2024-01-21 and 1.5.0 dated 2025-03-17
FORTLS-1.4.0/FORTLS/R/PythonFunctions.R |only FORTLS-1.4.0/FORTLS/inst/python/my_python_script.py |only FORTLS-1.4.0/FORTLS/man/ncr_point_cloud_double.Rd |only FORTLS-1.4.0/FORTLS/man/ver_point_cloud_double.Rd |only FORTLS-1.4.0/FORTLS/src/simulations_1.5.cpp |only FORTLS-1.4.0/FORTLS/src/surface_variation_1.3.cpp |only FORTLS-1.5.0/FORTLS/DESCRIPTION | 33 FORTLS-1.5.0/FORTLS/MD5 | 103 + FORTLS-1.5.0/FORTLS/NAMESPACE | 1 FORTLS-1.5.0/FORTLS/R/RcppExports.R | 40 FORTLS-1.5.0/FORTLS/R/auxiliary.functions.R | 674 +++++-------- FORTLS-1.5.0/FORTLS/R/correlations.R | 3 FORTLS-1.5.0/FORTLS/R/geometric.features.R |only FORTLS-1.5.0/FORTLS/R/globals.R |only FORTLS-1.5.0/FORTLS/R/normalize.R | 153 ++ FORTLS-1.5.0/FORTLS/R/optimize.plot.design.R | 20 FORTLS-1.5.0/FORTLS/R/python.functions.R |only FORTLS-1.5.0/FORTLS/R/relative.bias.R | 8 FORTLS-1.5.0/FORTLS/R/section.functions.R | 73 - FORTLS-1.5.0/FORTLS/R/species.classification.R |only FORTLS-1.5.0/FORTLS/R/stem.analysis.R | 16 FORTLS-1.5.0/FORTLS/R/tree.detection.multi.scan.R | 419 +++++--- FORTLS-1.5.0/FORTLS/R/tree.detection.several.plots.R | 23 FORTLS-1.5.0/FORTLS/R/tree.detection.single.scan.R | 405 +++++-- FORTLS-1.5.0/FORTLS/build/partial.rdb |binary FORTLS-1.5.0/FORTLS/build/vignette.rds |binary FORTLS-1.5.0/FORTLS/inst/CITATION | 2 FORTLS-1.5.0/FORTLS/inst/doc/plot_design_optimization.R | 30 FORTLS-1.5.0/FORTLS/inst/doc/plot_design_optimization.html | 14 FORTLS-1.5.0/FORTLS/inst/doc/stand_level.R | 18 FORTLS-1.5.0/FORTLS/inst/doc/stand_level.html | 4 FORTLS-1.5.0/FORTLS/inst/doc/tree_level.R | 96 - FORTLS-1.5.0/FORTLS/inst/doc/tree_level.Rmd | 2 FORTLS-1.5.0/FORTLS/inst/doc/tree_level.html | 10 FORTLS-1.5.0/FORTLS/inst/python/random_forest_fit.py |only FORTLS-1.5.0/FORTLS/inst/python/random_forest_sp.py |only FORTLS-1.5.0/FORTLS/inst/python/voxel_grid_downsampling.py |only FORTLS-1.5.0/FORTLS/man/RANSAC_cpp.Rd |only FORTLS-1.5.0/FORTLS/man/VoxR_vox_update.Rd |only FORTLS-1.5.0/FORTLS/man/chunk_size_from_area.Rd |only FORTLS-1.5.0/FORTLS/man/correlations.Rd | 4 FORTLS-1.5.0/FORTLS/man/datatable_grid.Rd |only FORTLS-1.5.0/FORTLS/man/distance.sampling.Rd | 8 FORTLS-1.5.0/FORTLS/man/fit_circle_cpp_modified.Rd |only FORTLS-1.5.0/FORTLS/man/geometric.features.Rd |only FORTLS-1.5.0/FORTLS/man/geometric_features.Rd |only FORTLS-1.5.0/FORTLS/man/geometric_features_point.Rd |only FORTLS-1.5.0/FORTLS/man/internal_ransac.Rd |only FORTLS-1.5.0/FORTLS/man/is_one_row_all_na.Rd |only FORTLS-1.5.0/FORTLS/man/iterations_RANSAC.Rd |only FORTLS-1.5.0/FORTLS/man/normalize.Rd | 29 FORTLS-1.5.0/FORTLS/man/optimize.plot.design.Rd | 4 FORTLS-1.5.0/FORTLS/man/random.forest.fit.Rd |only FORTLS-1.5.0/FORTLS/man/random.forest.sp.Rd |only FORTLS-1.5.0/FORTLS/man/relative.bias.Rd | 4 FORTLS-1.5.0/FORTLS/man/sample_indices.Rd |only FORTLS-1.5.0/FORTLS/man/save_file_as_laz.Rd |only FORTLS-1.5.0/FORTLS/man/save_to_tiles.Rd |only FORTLS-1.5.0/FORTLS/man/simulations.Rd | 2 FORTLS-1.5.0/FORTLS/man/sort_sublists.Rd |only FORTLS-1.5.0/FORTLS/man/species.classification.Rd |only FORTLS-1.5.0/FORTLS/man/tree.detection.multi.scan.Rd | 11 FORTLS-1.5.0/FORTLS/man/tree.detection.several.plots.Rd | 16 FORTLS-1.5.0/FORTLS/man/tree.detection.single.scan.Rd | 16 FORTLS-1.5.0/FORTLS/man/voxel_grid_downsampling.Rd |only FORTLS-1.5.0/FORTLS/src/RcppExports.cpp | 167 ++- FORTLS-1.5.0/FORTLS/src/geometric.features.cpp |only FORTLS-1.5.0/FORTLS/src/ransac_and_util.cpp |only FORTLS-1.5.0/FORTLS/src/simulations.cpp |only FORTLS-1.5.0/FORTLS/vignettes/tree_level.Rmd | 2 70 files changed, 1446 insertions(+), 964 deletions(-)
Title: Get Basic Information from Chinese ID Number
Description: The Chinese ID number contains a lot of information,
this package helps you get the region, date of birth, age,
age based on year, gender, zodiac, constellation information from
the Chinese ID number.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between CNID versions 2.0.2 dated 2025-02-28 and 2.1.0 dated 2025-03-17
DESCRIPTION | 10 - MD5 | 46 ++--- NAMESPACE | 1 R/age.R | 56 +++--- R/age_by_year.R | 56 +++--- R/birth_date.R | 56 +++--- R/check_id.R | 56 +++--- R/cnid_info.R | 453 +++++++++++++++++++++++++++-------------------------- R/convert18.R |only R/cstl.R | 56 +++--- R/gender.R | 56 +++--- R/region.R | 56 +++--- R/sysdata.rda |binary R/zodiac.R | 56 +++--- README.md | 6 man/age.Rd | 12 - man/age_by_year.Rd | 12 - man/birth_date.Rd | 12 - man/check_id.Rd | 12 - man/cnid_info.Rd | 14 - man/convert18.Rd |only man/cstl.Rd | 12 - man/gender.Rd | 12 - man/region.Rd | 12 - man/zodiac.Rd | 12 - 25 files changed, 549 insertions(+), 525 deletions(-)
Title: Data Collection from the Central Bank of Brazil
Description: Provides tools to facilitate the access and processing of data
from the Central Bank of Brazil API. The package allows users
to retrieve economic and financial data, transforming them into usable
tabular formats for further analysis. The data is obtained from the
Central Bank of Brazil API: <https://api.bcb.gov.br/dados/serie/bcdata.sgs.{series_code}/dados?formato=json&dataInicial={start_date}&dataFinal={end_date}>.
Author: Paulo Icaro [aut],
Lissandro Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Sousa <lisandrosousa54@gmail.com>
Diff between BacenAPI versions 0.1.0 dated 2025-03-07 and 0.1.1 dated 2025-03-17
DESCRIPTION | 14 +++++-- MD5 | 16 ++++---- R/bacen_api.R | 103 +++++++++++++++++++++------------------------------- R/bacen_series.R | 6 ++- R/bacen_url.R | 4 +- README.md | 53 ++++++++++---------------- man/bacen_api.Rd | 4 -- man/bacen_series.Rd | 6 ++- man/bacen_url.Rd | 4 +- 9 files changed, 98 insertions(+), 112 deletions(-)
Title: Fast Tidy Tools for Date and Date-Time Manipulation
Description: A set of fast tidy functions for wrangling, completing and
summarising date and date-time data. It combines 'tidyverse' syntax
with the efficiency of 'data.table' and speed of 'collapse'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between timeplyr versions 1.0.0 dated 2025-02-03 and 1.1.0 dated 2025-03-17
timeplyr-1.0.0/timeplyr/R/GRP_utils.R |only timeplyr-1.0.0/timeplyr/R/utils.R |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-12-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-14-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-15-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-15-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-16-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-17-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-2-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-22-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-22-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-23-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-23-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-25-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-26-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-26-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-27-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-27-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-28-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-28-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-29-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-3-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-30-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-30-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-31-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-31-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-34-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-34-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-35-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-35-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-4-1.png |only timeplyr-1.0.0/timeplyr/src/utils.cpp |only timeplyr-1.1.0/timeplyr/DESCRIPTION | 14 timeplyr-1.1.0/timeplyr/MD5 | 220 +-- timeplyr-1.1.0/timeplyr/NAMESPACE | 18 timeplyr-1.1.0/timeplyr/NEWS.md | 22 timeplyr-1.1.0/timeplyr/R/abc.R |only timeplyr-1.1.0/timeplyr/R/age_years.R | 66 timeplyr-1.1.0/timeplyr/R/calendar.R | 2 timeplyr-1.1.0/timeplyr/R/collapse_utils.R |only timeplyr-1.1.0/timeplyr/R/cpp11.R | 20 timeplyr-1.1.0/timeplyr/R/df_utils.R | 4 timeplyr-1.1.0/timeplyr/R/get_time_delay.R | 2 timeplyr-1.1.0/timeplyr/R/growth.R | 2 timeplyr-1.1.0/timeplyr/R/growth_rate.R | 2 timeplyr-1.1.0/timeplyr/R/is_whole_number.R | 15 timeplyr-1.1.0/timeplyr/R/iso_week.R | 2 timeplyr-1.1.0/timeplyr/R/legacy_time_utils.R | 2 timeplyr-1.1.0/timeplyr/R/reset.R | 4 timeplyr-1.1.0/timeplyr/R/resolution.R | 27 timeplyr-1.1.0/timeplyr/R/roll.R | 2 timeplyr-1.1.0/timeplyr/R/roll_apply.R | 2 timeplyr-1.1.0/timeplyr/R/roll_lag.R | 2 timeplyr-1.1.0/timeplyr/R/roll_na_fill.R | 3 timeplyr-1.1.0/timeplyr/R/scales.R | 22 timeplyr-1.1.0/timeplyr/R/time_arithmetic.R |only timeplyr-1.1.0/timeplyr/R/time_core.R | 5 timeplyr-1.1.0/timeplyr/R/time_cut.R | 30 timeplyr-1.1.0/timeplyr/R/time_diff.R | 24 timeplyr-1.1.0/timeplyr/R/time_elapsed.R | 2 timeplyr-1.1.0/timeplyr/R/time_episodes.R | 2 timeplyr-1.1.0/timeplyr/R/time_expand.R | 132 - timeplyr-1.1.0/timeplyr/R/time_ggplot.R | 2 timeplyr-1.1.0/timeplyr/R/time_id.R | 3 timeplyr-1.1.0/timeplyr/R/time_interval.R | 28 timeplyr-1.1.0/timeplyr/R/time_is_regular.R | 2 timeplyr-1.1.0/timeplyr/R/time_roll.R | 4 timeplyr-1.1.0/timeplyr/R/time_seq.R | 220 +-- timeplyr-1.1.0/timeplyr/R/time_seq_fill.R | 28 timeplyr-1.1.0/timeplyr/R/time_seq_id.R | 4 timeplyr-1.1.0/timeplyr/R/time_utils.R | 207 +-- timeplyr-1.1.0/timeplyr/R/timeplyr-package.R | 32 timeplyr-1.1.0/timeplyr/R/timespan.R | 25 timeplyr-1.1.0/timeplyr/R/ts_as_tbl.R | 2 timeplyr-1.1.0/timeplyr/R/utils-pipe.R |only timeplyr-1.1.0/timeplyr/R/year_month.R | 8 timeplyr-1.1.0/timeplyr/R/zzz.R | 4 timeplyr-1.1.0/timeplyr/README.md | 530 ++++++- timeplyr-1.1.0/timeplyr/man/calendar.Rd | 2 timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-21-1.png |only timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-29-1.png |binary timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-44-1.png |only timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-44-2.png |only timeplyr-1.1.0/timeplyr/man/get_time_delay.Rd | 2 timeplyr-1.1.0/timeplyr/man/growth.Rd | 2 timeplyr-1.1.0/timeplyr/man/growth_rate.Rd | 2 timeplyr-1.1.0/timeplyr/man/is_whole_number.Rd | 11 timeplyr-1.1.0/timeplyr/man/iso_week.Rd | 2 timeplyr-1.1.0/timeplyr/man/pipe.Rd |only timeplyr-1.1.0/timeplyr/man/roll_lag.Rd | 2 timeplyr-1.1.0/timeplyr/man/roll_sum.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_add.Rd |only timeplyr-1.1.0/timeplyr/man/time_cut.Rd | 21 timeplyr-1.1.0/timeplyr/man/time_elapsed.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_episodes.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_expand.Rd | 7 timeplyr-1.1.0/timeplyr/man/time_ggplot.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_is_regular.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_roll.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_seq.Rd | 22 timeplyr-1.1.0/timeplyr/man/time_seq_id.Rd | 2 timeplyr-1.1.0/timeplyr/man/timeplyr-package.Rd | 23 timeplyr-1.1.0/timeplyr/man/ts_as_tbl.Rd | 2 timeplyr-1.1.0/timeplyr/src/cpp11.cpp | 44 timeplyr-1.1.0/timeplyr/src/diff.cpp | 11 timeplyr-1.1.0/timeplyr/src/is_whole_num.cpp | 85 - timeplyr-1.1.0/timeplyr/src/roll.cpp | 107 + timeplyr-1.1.0/timeplyr/src/time_arithmetic.cpp |only timeplyr-1.1.0/timeplyr/src/timeplyr.h | 15 timeplyr-1.1.0/timeplyr/tests/testthat/test-age_years.R | 11 timeplyr-1.1.0/timeplyr/tests/testthat/test-calendar.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-get_time_delay.R | 90 - timeplyr-1.1.0/timeplyr/tests/testthat/test-growth.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-growth_rate.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-is_whole_number.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-iso_week.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_lag.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_mean.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_na_fill.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_by.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_core.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_cut.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_diff.R | 171 ++ timeplyr-1.1.0/timeplyr/tests/testthat/test-time_elapsed.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_episodes.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_expand.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_gaps.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_is_regular.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_roll.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_seq.R | 666 ++++------ timeplyr-1.1.0/timeplyr/tests/testthat/test-time_seq_id.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-ts_as_tbl.R | 2 132 files changed, 1737 insertions(+), 1376 deletions(-)
Title: Measure Memory and CPU Usage for Parallel R Code
Description: Measures memory and CPU usage of R code by regularly taking
snapshots of calls to the system command 'ps'. The package provides an entry
point (albeit coarse) to profile usage of system resources by R code run
in parallel.
Author: Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between syrup versions 0.1.1 dated 2024-07-18 and 0.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/syrup.R | 3 +-- R/utils.R | 14 ++++++++++++++ 5 files changed, 26 insertions(+), 9 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Centofanti et al. (2022) <doi:10.48550/arXiv.2205.06256>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.6.0 dated 2024-12-11 and 1.7.0 dated 2025-03-17
DESCRIPTION | 6 ++-- MD5 | 55 ++++++++++++++++++++++++-------------------- NAMESPACE | 4 +++ NEWS.md | 30 +++++++++++++++++------- R/02_fof_pc.R | 2 - R/03_phaseI_training.R | 2 - R/04_phaseII.R | 2 - R/AMFCC.R |only R/FRTM.R | 2 - R/amfewma.R | 10 ++++---- R/funcharts-package.R | 11 ++++---- R/rmfcc.R | 14 +++++------ R/simulate.R | 4 +-- man/AMFCC_PhaseI.Rd |only man/AMFCC_PhaseII.Rd |only man/AMFEWMA_PhaseI.Rd | 5 ++-- man/AMFEWMA_PhaseII.Rd | 5 ++-- man/RoMFCC_PhaseI.Rd | 2 - man/RoMFCC_PhaseII.Rd | 2 - man/RoMFDI.Rd | 2 - man/funcharts-package.Rd | 13 +++++----- man/functional_filter.Rd | 6 ++-- man/mFPCA.Rd | 2 - man/plot.AMFCC_PhaseI.Rd |only man/predict_fof_pc.Rd | 2 - man/regr_cc_fof.Rd | 2 - man/rpca_mfd.Rd | 2 - man/sim_funcharts.Rd | 2 - man/simulate_mfd.Rd | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/test_AMFCC.R |only 31 files changed, 109 insertions(+), 80 deletions(-)
Title: Bayesian State-Space Modeling of Mouse-Tracking Experiments via
Stan
Description: Estimates previously compiled state-space modeling for mouse-tracking experiments using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.
Author: Antonio Calcagnì [aut, cre],
Massimiliano Pastore [ctb]
Maintainer: Antonio Calcagnì <ant.calcagni@gmail.com>
Diff between ssMousetrack versions 1.1.6 dated 2023-04-05 and 1.1.7 dated 2025-03-17
ssMousetrack-1.1.6/ssMousetrack/src/Makevars.win |only ssMousetrack-1.1.7/ssMousetrack/DESCRIPTION | 15 ssMousetrack-1.1.7/ssMousetrack/MD5 | 51 ssMousetrack-1.1.7/ssMousetrack/NEWS | 17 ssMousetrack-1.1.7/ssMousetrack/R/ssMousetrack-package.R | 2 ssMousetrack-1.1.7/ssMousetrack/R/stanmodels.R | 2 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model_gomp.stan | 24 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model_log.stan | 24 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data_gomp.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data_log.stan | 16 ssMousetrack-1.1.7/ssMousetrack/man/ssMousetrack-package.Rd | 10 ssMousetrack-1.1.7/ssMousetrack/src/Makevars | 5 ssMousetrack-1.1.7/ssMousetrack/src/RcppExports.cpp | 5 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model.h | 2896 ++++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_gomp.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_gomp.h | 3727 +++++----- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_log.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_log.h | 3365 +++++---- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data.h | 2347 +++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_gomp.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_gomp.h | 2729 ++++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_log.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_log.h | 2362 +++--- 27 files changed, 10204 insertions(+), 7453 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification <https://github.github.com/gfm/> defines
a rationalized version of markdown syntax. This package uses the 'cmark'
reference implementation for converting markdown text into various formats
including html, latex and groff man. In addition it exposes the markdown
parse tree in xml format. Also includes opt-in support for GFM extensions
including tables, autolinks, and strikethrough text.
Author: Jeroen Ooms [aut, cre] ,
John MacFarlane [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between commonmark versions 1.9.4 dated 2025-03-17 and 1.9.5 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.5 dated 2024-11-08 and 1.0.6 dated 2025-03-17
DESCRIPTION | 6 MD5 | 45 +++- NAMESPACE | 13 + NEWS.md | 5 R/FitCoupledGrowth_class.R |only R/data.R | 346 ++++++++++++++++++---------------- R/fit_coupled_growth.R |only R/initial_guesses.R | 14 - R/top_fit.R | 2 build/vignette.rds |binary data/example_coupled_onestep.rda |only data/example_coupled_twosteps.rda |only inst/doc/v01_growth_predictions.html | 2 inst/doc/v02_growth_fitting.html | 12 - inst/doc/v03_growth_uncertainty.html | 14 - inst/doc/v04_model_comparison.html | 6 inst/doc/v06_coupledmodels.R |only inst/doc/v06_coupledmodels.Rmd |only inst/doc/v06_coupledmodels.html |only inst/doc/v24_publication_figures.html | 6 inst/doc/v99_deprecated.html | 14 - man/FitCoupledGrowth.Rd |only man/cost_coupled_onestep.Rd |only man/cost_coupled_twosteps.Rd |only man/example_coupled_onestep.Rd |only man/example_coupled_twosteps.Rd |only man/fit_coupled_growth.Rd |only man/pred_coupled_baranyi.Rd |only man/pred_lambda.Rd |only man/pred_sqmu.Rd |only man/residuals_lambda.Rd |only man/residuals_sqmu.Rd |only vignettes/v06_coupledmodels.Rmd |only 33 files changed, 273 insertions(+), 212 deletions(-)
Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>,
including storage, database, and compute services, such as 'Simple
Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda'
functions-as-a-service.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws versions 0.8.0 dated 2025-02-10 and 0.9.0 dated 2025-03-17
paws-0.8.0/paws/man/elasticinference.Rd |only paws-0.9.0/paws/DESCRIPTION | 22 paws-0.9.0/paws/MD5 | 44 paws-0.9.0/paws/NAMESPACE | 2 paws-0.9.0/paws/R/paws.R | 5167 +++++++++++--------------------- paws-0.9.0/paws/man/accessanalyzer.Rd | 1 paws-0.9.0/paws/man/cloudformation.Rd | 5 paws-0.9.0/paws/man/cloudtrail.Rd | 1 paws-0.9.0/paws/man/connect.Rd | 3 paws-0.9.0/paws/man/connectcases.Rd | 12 paws-0.9.0/paws/man/ec2.Rd | 10 paws-0.9.0/paws/man/ecr.Rd | 2 paws-0.9.0/paws/man/iam.Rd | 2 paws-0.9.0/paws/man/lightsail.Rd | 4 paws-0.9.0/paws/man/networkfirewall.Rd | 7 paws-0.9.0/paws/man/opsworks.Rd | 2 paws-0.9.0/paws/man/rds.Rd | 2 paws-0.9.0/paws/man/s3tables.Rd |only paws-0.9.0/paws/man/sesv2.Rd | 1 paws-0.9.0/paws/man/ssm.Rd | 18 paws-0.9.0/paws/man/ssooidc.Rd | 7 paws-0.9.0/paws/man/storagegateway.Rd | 7 paws-0.9.0/paws/man/swf.Rd | 2 paws-0.9.0/paws/man/wafv2.Rd | 31 24 files changed, 2018 insertions(+), 3334 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detail data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored an shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.1.11 dated 2024-07-03 and 1.1.12 dated 2025-03-17
DESCRIPTION | 6 +- MD5 | 26 ++++----- NAMESPACE | 6 +- R/chMDB.R | 22 +++++++ R/fileMDB.R | 22 +++++++ R/namespace.R | 3 - build/vignette.rds |binary inst/doc/TKCat-KMR-POK.R | 4 - inst/doc/TKCat-KMR-POK.html | 6 +- inst/doc/TKCat.R | 112 +++++++++++++++++++-------------------- inst/doc/TKCat.html | 125 +++++++++++++++++++++++--------------------- inst/pkgdown.yml | 7 +- man/chMDB.Rd | 10 ++- man/fileMDB.Rd | 10 ++- 14 files changed, 215 insertions(+), 144 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 1.0.7 dated 2022-12-22 and 1.1.1 dated 2025-03-17
DESCRIPTION | 15 - MD5 | 37 +- NEWS.md | 16 + R/EasyData.R | 2 R/PTwrap.R | 12 R/ProtectTable.R | 40 +- R/ProtectTable1.R | 14 - build/vignette.rds |binary inst/doc/easySdcTableVignette.R | 10 inst/doc/easySdcTableVignette.Rmd | 12 inst/doc/easySdcTableVignette.html | 506 +++++++++++++++++++++++++++---------- inst/doc/singletonsAndZeros.Rmd | 10 inst/doc/singletonsAndZeros.html | 433 +++++++++++++++++++++++++------ man/EasyData.Rd | 2 man/PTwrap.Rd | 10 man/ProtectTable.Rd | 40 +- man/ProtectTable1.Rd | 14 - man/figures |only vignettes/easySdcTableVignette.Rmd | 12 vignettes/singletonsAndZeros.Rmd | 10 20 files changed, 882 insertions(+), 313 deletions(-)
Title: Connect to the 'nettskjema.no' API of the University of Oslo
Description: Enables users to retrieve data, meta-data, and codebooks from
<https://nettskjema.no/>. The data from the API is richer than from
the online data portal. Mowinckel (2021) <doi:10.5281/zenodo.4745481>.
Author: Athanasia Mo Mowinckel [aut, cre]
,
Trym Nohr Fjoertoft [ctb]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between nettskjemar versions 0.1.4 dated 2021-05-20 and 1.0.0 dated 2025-03-17
nettskjemar-0.1.4/nettskjemar/R/api-funcs.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-codebook.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-data_sorters.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-elements.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-meta.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_auth.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_get_form.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_write.R |only nettskjemar-0.1.4/nettskjemar/inst/background_docs |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.R |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.Rmd |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.html |only nettskjemar-0.1.4/nettskjemar/inst/doc/nettskjemar.R |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_codebook.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_data.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_extra.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_meta.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_renviron_edit.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_token2renviron.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_token_expiry.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_user_create.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_write_codebook.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_write_meta.Rd |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-data_sorters.R |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-nettskjema_auth.R |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-nettskjema_get.R |only nettskjemar-0.1.4/nettskjemar/vignettes/auth_setup.Rmd |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_create.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_create2.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_user.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_create_token.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_create_token2.png |only nettskjemar-1.0.0/nettskjemar/DESCRIPTION | 45 nettskjemar-1.0.0/nettskjemar/MD5 | 156 +- nettskjemar-1.0.0/nettskjemar/NAMESPACE | 89 - nettskjemar-1.0.0/nettskjemar/NEWS.md | 22 nettskjemar-1.0.0/nettskjemar/R/nettskjemar-package.R |only nettskjemar-1.0.0/nettskjemar/R/ns-attachment.R |only nettskjemar-1.0.0/nettskjemar/R/ns-auth.R |only nettskjemar-1.0.0/nettskjemar/R/ns-browser.R |only nettskjemar-1.0.0/nettskjemar/R/ns-checkbox.R |only nettskjemar-1.0.0/nettskjemar/R/ns-codebook.R |only nettskjemar-1.0.0/nettskjemar/R/ns-data.R |only nettskjemar-1.0.0/nettskjemar/R/ns-data_labels.R |only nettskjemar-1.0.0/nettskjemar/R/ns-form.R |only nettskjemar-1.0.0/nettskjemar/R/ns-me.R |only nettskjemar-1.0.0/nettskjemar/R/ns-meta.R |only nettskjemar-1.0.0/nettskjemar/R/ns-submission.R |only nettskjemar-1.0.0/nettskjemar/R/utils.R | 94 - nettskjemar-1.0.0/nettskjemar/README.md | 65 - nettskjemar-1.0.0/nettskjemar/build/partial.rdb |only nettskjemar-1.0.0/nettskjemar/build/vignette.rds |binary nettskjemar-1.0.0/nettskjemar/inst/WORDLIST | 47 nettskjemar-1.0.0/nettskjemar/inst/doc/attachments.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/attachments.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/authentication.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/authentication.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/forms.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/forms.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/labelled_data.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/labelled_data.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/metadata.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/metadata.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/nettskjemar.Rmd | 297 ++++ nettskjemar-1.0.0/nettskjemar/inst/doc/nettskjemar.html | 607 ++++++++-- nettskjemar-1.0.0/nettskjemar/inst/doc/submissions.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/submissions.html |only nettskjemar-1.0.0/nettskjemar/man/codebook.Rd | 10 nettskjemar-1.0.0/nettskjemar/man/get_raw_codebook.Rd | 12 nettskjemar-1.0.0/nettskjemar/man/has_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/nettskjemar-package.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_add_labels.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_alter_checkbox.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_api_docs.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_auth_token.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_create_client.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_attachment.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_data.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_form_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_form_reports.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_forms.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_me.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_meta.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission_pdf.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_list_form_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_list_submission_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_req.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_write_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_write_meta.Rd |only nettskjemar-1.0.0/nettskjemar/tests/fixtures |only nettskjemar-1.0.0/nettskjemar/tests/spelling.R | 9 nettskjemar-1.0.0/nettskjemar/tests/testthat.R | 6 nettskjemar-1.0.0/nettskjemar/tests/testthat/helper-vcr.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/helpers.R | 8 nettskjemar-1.0.0/nettskjemar/tests/testthat/test-data_labels.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-attachment.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-auth.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-codebook.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-form.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-me.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-meta.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-submission.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns_checkbox.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-utils.R | 85 - nettskjemar-1.0.0/nettskjemar/vignettes/attachments.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/attachments.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/authentication.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/authentication.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/forms.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/forms.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/labelled_data.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/labelled_data.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/metadata.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/metadata.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/nettskjemar.Rmd | 297 ++++ nettskjemar-1.0.0/nettskjemar/vignettes/nettskjemar.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/static/lab-overview-1.png |only nettskjemar-1.0.0/nettskjemar/vignettes/static/ns_vidat-1.png |only nettskjemar-1.0.0/nettskjemar/vignettes/submissions.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/submissions.Rmd.orig |only 123 files changed, 1462 insertions(+), 387 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.18 dated 2024-12-14 and 2.19.1 dated 2025-03-17
DESCRIPTION | 22 - MD5 | 108 +++-- NAMESPACE | 11 NEWS.md | 17 R/Design.R | 23 + R/PBA.R | 69 ++- R/SimCheck.R | 8 R/SimCollect.R | 8 R/SimDesign.R | 2 R/SimFunctions.R | 8 R/SimSolve.R | 16 R/analysis.R | 35 + R/functions.R | 30 + R/notifications.R |only R/reSummarise.R | 24 + R/runArraySimulation.R | 16 R/runSimulation.R | 135 ++++--- R/summary_functions.R | 6 R/util.R | 62 +-- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Catch_errors.R | 14 inst/doc/Catch_errors.html | 342 +++++++++++------- inst/doc/Fixed_obj_fun.R | 14 inst/doc/Fixed_obj_fun.html | 241 +++++++----- inst/doc/HPC-computing.R | 225 ++++++----- inst/doc/HPC-computing.Rmd | 15 inst/doc/HPC-computing.html | 733 ++++++++++++++++++++++++++++----------- inst/doc/MultipleAnalyses.R | 194 +++++----- inst/doc/MultipleAnalyses.html | 318 ++++++++++------ inst/doc/Parallel-computing.R | 74 +-- inst/doc/Parallel-computing.html | 315 ++++++++++------ inst/doc/Saving-results.R | 18 inst/doc/Saving-results.html | 311 ++++++++++------ inst/doc/SimDesign-intro.R | 4 inst/doc/SimDesign-intro.html | 453 ++++++++++++++++-------- man/PBA.Rd | 8 man/SimCheck.Rd | 3 man/SimCollect.Rd | 8 man/SimFunctions.Rd | 8 man/SimSolve.Rd | 9 man/bias.Rd | 2 man/clusterSetRNGSubStream.Rd | 2 man/createDesign.Rd | 13 man/listAvailableNotifiers.Rd |only man/new_PushbulletNotifier.Rd |only man/new_TelegramNotifier.Rd |only man/notify.PushbulletNotifier.Rd |only man/notify.Rd |only man/notify.TelegramNotifier.Rd |only man/reSummarise.Rd | 8 man/runSimulation.Rd | 79 ++-- man/timeFormater.Rd | 14 tests/tests/archive |only tests/tests/test-01-core.R | 11 tests/tests/test-02-aggregate.R | 2 tests/tests/test-03-array.R | 16 vignettes/HPC-computing.Rmd | 15 59 files changed, 2575 insertions(+), 1498 deletions(-)
Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. The site <https://gallery.rcpp.org> regroups a large
number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.9 dated 2019-08-24 and 0.1.10 dated 2025-03-17
ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++- DESCRIPTION | 24 +++++++---- MD5 | 26 ++++++------ NAMESPACE | 6 +- R/RcppExports.R | 26 ++++++++++++ README.md | 15 ++++--- inst/NEWS.Rd | 19 +++++++- man/RcppExamples-package.Rd | 2 man/RcppRNGsExample.Rd | 8 +-- man/factor2char.Rd |only src/DateExample.cpp | 23 ---------- src/FactorExample.cpp |only src/Makevars | 7 +-- src/Makevars.win | 8 +-- src/RcppExports.cpp | 29 +++++++++++++ 15 files changed, 217 insertions(+), 70 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 1.0.1 dated 2023-09-18 and 1.0.2 dated 2025-03-17
DESCRIPTION | 11 +- MD5 | 80 +++++++++--------- NEWS.md | 41 +++++++++ R/assign_to_R_env.R | 2 R/check_digit.R |only R/check_if_unique_rows.R | 2 R/clean_path_name.R | 2 R/clear.R | 2 R/close_all_connections.R | 2 R/dot_helper.R | 2 R/dt_row_to_string.R | 2 R/equals2.R | 2 R/feedback.R | 2 R/file_lines_to_list.R | 4 R/firstup.R | 2 R/format_POSIXct.R | 2 R/get_config.R | 2 R/get_current_timestamp.R | 2 R/is.empty.R | 4 R/is_date_format.R | 2 R/notin.R | 2 R/number_to_position.R | 2 R/paste2.R | 2 R/paste_pct_sum.R | 2 R/pretty_timestamp.R | 2 R/rep2.R | 2 R/robust_round.R | 2 R/setdiff_all.R | 2 R/setenv2.R | 2 R/setenv_file.R | 2 R/string_replacements.R | 2 R/time_diff_print.R | 6 - R/trim.space.R | 16 +-- R/vgsub.R | 2 R/zzz.R | 2 README.md | 167 ++++++++++++++++++++------------------ man/dt_row_to_string.Rd | 3 man/paste2.Rd | 11 +- man/time_diff_print.Rd | 4 tests/testthat/test-check_digit.R |only tests/testthat/test-feedback.R | 2 tests/testthat/test-lints.R | 2 42 files changed, 229 insertions(+), 176 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification <https://github.github.com/gfm/> defines
a rationalized version of markdown syntax. This package uses the 'cmark'
reference implementation for converting markdown text into various formats
including html, latex and groff man. In addition it exposes the markdown
parse tree in xml format. Also includes opt-in support for GFM extensions
including tables, autolinks, and strikethrough text.
Author: Jeroen Ooms [aut, cre] ,
John MacFarlane [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between commonmark versions 1.9.2 dated 2024-10-04 and 1.9.4 dated 2025-03-17
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NEWS | 4 ++++ R/extensions.R | 2 +- man/extensions.Rd | 2 +- src/Makevars | 6 +++--- src/cmark/node.c | 4 ++++ src/cmark/xml.c | 19 +++++++++++++++++++ src/patches |only src/wrapper.c | 1 + tests/testthat/test-extensions.R | 18 +++++++++--------- 11 files changed, 57 insertions(+), 27 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.15.5 dated 2025-03-01 and 0.15.7 dated 2025-03-17
DESCRIPTION | 6 MD5 | 75 ++++---- NEWS.md | 14 + R/nix_build.R | 62 +++---- R/rix.R | 19 ++ R/rix_helpers.R | 102 ++++++++++-- README.md | 21 ++ inst/doc/d1-installing-r-packages-in-a-nix-environment.R | 11 + inst/doc/d1-installing-r-packages-in-a-nix-environment.Rmd | 25 ++ inst/doc/d1-installing-r-packages-in-a-nix-environment.html | 68 +++++--- inst/extdata/available_df.csv | 2 inst/extdata/default.nix | 30 +-- man/nix_build.Rd | 35 ++-- man/renv2nix.Rd | 4 man/rix.Rd | 6 tests/testthat/_snaps/renv_helpers/default_datathin.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v1-0-7.nix | 20 +- tests/testthat/_snaps/rix-python |only tests/testthat/_snaps/rix/bioc-devel_default.nix | 20 +- tests/testthat/_snaps/rix/bleeding-edge_default.nix | 20 +- tests/testthat/_snaps/rix/code_default.nix | 20 +- tests/testthat/_snaps/rix/codium_default.nix | 20 +- tests/testthat/_snaps/rix/date_default.nix | 20 +- tests/testthat/_snaps/rix/frozen-edge_default.nix | 20 +- tests/testthat/_snaps/rix/no_quarto_default.nix | 20 +- tests/testthat/_snaps/rix/one_git_default.nix | 20 +- tests/testthat/_snaps/rix/other_default.nix | 20 +- tests/testthat/_snaps/rix/positron_default.nix | 20 +- tests/testthat/_snaps/rix/r-devel-bioc-devel_default.nix | 20 +- tests/testthat/_snaps/rix/r-devel_default.nix | 20 +- tests/testthat/_snaps/rix/rstudio_default.nix | 20 +- tests/testthat/_snaps/rix/yes_quarto_default.nix | 20 +- tests/testthat/test-rix-python.R |only tests/testthat/testdata/remote-pkgs/gen_envs.R |only tests/testthat/testdata/remote-pkgs/mlr3_default.nix | 20 +- tests/testthat/testdata/remote-pkgs/mlr3_dups_default.nix | 20 +- vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd | 25 ++ 40 files changed, 588 insertions(+), 337 deletions(-)
Title: Single Tree Simulator
Description: Framework to build an individual tree simulator.
Author: Clara Anton Fernandez [aut] ,
Ignacio Sevillano [cre]
Maintainer: Ignacio Sevillano <ignacio.sevillano@nibio.no>
Diff between sitree versions 0.1-14 dated 2024-02-07 and 0.1-15 dated 2025-03-17
DESCRIPTION | 22 ++++++++----- MD5 | 8 ++-- build/vignette.rds |binary inst/doc/SiTree.html | 72 ++++++++++++++++++++++---------------------- inst/doc/TestEquations.html | 6 +-- 5 files changed, 57 insertions(+), 51 deletions(-)
Title: Power Analysis for Research Experiments
Description: Provides tools for calculating statistical power for experiments
analyzed using linear mixed models. It supports standard designs, including
randomized block, split-plot, and Latin Square designs, while offering flexibility
to accommodate a variety of other complex study designs.
Author: Kai Wang [aut, cre, cph] ,
Mutian Niu [aut, cph]
Maintainer: Kai Wang <kai.wang@usys.ethz.ch>
Diff between pwr4exp versions 0.1.0 dated 2024-10-11 and 1.0.0 dated 2025-03-17
pwr4exp-0.1.0/pwr4exp/LICENSE |only pwr4exp-0.1.0/pwr4exp/R/data.R |only pwr4exp-0.1.0/pwr4exp/R/design-generating.R |only pwr4exp-0.1.0/pwr4exp/R/power-calculation.R |only pwr4exp-0.1.0/pwr4exp/R/sample-size.R |only pwr4exp-0.1.0/pwr4exp/R/utils_df.R |only pwr4exp-0.1.0/pwr4exp/man/calc.theta.Rd |only pwr4exp-0.1.0/pwr4exp/man/customLmerMod-class.Rd |only pwr4exp-0.1.0/pwr4exp/man/find_sample_size.Rd |only pwr4exp-0.1.0/pwr4exp/man/fit.pseu.model.Rd |only pwr4exp-0.1.0/pwr4exp/man/theta.names.Rd |only pwr4exp-1.0.0/pwr4exp/DESCRIPTION | 36 pwr4exp-1.0.0/pwr4exp/MD5 | 66 pwr4exp-1.0.0/pwr4exp/NAMESPACE | 28 pwr4exp-1.0.0/pwr4exp/NEWS.md | 2 pwr4exp-1.0.0/pwr4exp/R/data_documentation.R |only pwr4exp-1.0.0/pwr4exp/R/df_utils.R |only pwr4exp-1.0.0/pwr4exp/R/mkdesign.R |only pwr4exp-1.0.0/pwr4exp/R/power_calculation.R |only pwr4exp-1.0.0/pwr4exp/R/standard_designs.R |only pwr4exp-1.0.0/pwr4exp/R/utils.R | 1737 ++++++++++++++++++++-- pwr4exp-1.0.0/pwr4exp/README.md | 147 + pwr4exp-1.0.0/pwr4exp/build/vignette.rds |binary pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.R | 189 +- pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.Rmd | 1288 ++++++++-------- pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.html | 1756 +++++++++++++---------- pwr4exp-1.0.0/pwr4exp/man/contrast1D.Rd |only pwr4exp-1.0.0/pwr4exp/man/contrastMD.Rd |only pwr4exp-1.0.0/pwr4exp/man/create_designs.Rd | 260 +-- pwr4exp-1.0.0/pwr4exp/man/df.cod.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.crd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.lsd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.rcbd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.spd.Rd | 22 pwr4exp-1.0.0/pwr4exp/man/expandDoubleVerts.Rd |only pwr4exp-1.0.0/pwr4exp/man/factorize.Rd |only pwr4exp-1.0.0/pwr4exp/man/findbars.Rd |only pwr4exp-1.0.0/pwr4exp/man/milk.Rd | 2 pwr4exp-1.0.0/pwr4exp/man/mkRTrms.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkReTrms.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkStruct.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkdesign.Rd |only pwr4exp-1.0.0/pwr4exp/man/nobars.Rd |only pwr4exp-1.0.0/pwr4exp/man/pwr.anova.Rd | 42 pwr4exp-1.0.0/pwr4exp/man/pwr.contrast.Rd | 75 pwr4exp-1.0.0/pwr4exp/man/pwr.summary.Rd |only pwr4exp-1.0.0/pwr4exp/man/subbars.Rd |only pwr4exp-1.0.0/pwr4exp/vignettes/pwr4exp.Rmd | 1288 ++++++++-------- 48 files changed, 4500 insertions(+), 2578 deletions(-)
Title: Periodically Correlated and Periodically Integrated Time Series
Description: Classes and methods for modelling and simulation of
periodically correlated (PC) and periodically integrated time
series. Compute theoretical periodic autocovariances and related
properties of PC autoregressive moving average models. Some original
methods including Boshnakov & Iqelan (2009)
<doi:10.1111/j.1467-9892.2009.00617.x>, Boshnakov (1996)
<doi:10.1111/j.1467-9892.1996.tb00281.x>.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between pcts versions 0.15.7 dated 2023-11-25 and 0.15.8 dated 2025-03-17
pcts-0.15.7/pcts/data/ex1f.rda |only pcts-0.15.8/pcts/DESCRIPTION | 10 pcts-0.15.8/pcts/MD5 | 62 pcts-0.15.8/pcts/NAMESPACE | 838 +-- pcts-0.15.8/pcts/NEWS.md | 880 ++-- pcts-0.15.8/pcts/R/classCycle.R | 2138 +++++----- pcts-0.15.8/pcts/build/partial.rdb |binary pcts-0.15.8/pcts/build/vignette.rds |binary pcts-0.15.8/pcts/data/ex1f.R |only pcts-0.15.8/pcts/inst/REFERENCES.bib | 1 pcts-0.15.8/pcts/inst/auto/REFERENCES.el | 52 pcts-0.15.8/pcts/inst/doc/pcts_data.R | 128 pcts-0.15.8/pcts/inst/doc/pcts_data.html | 1014 ++-- pcts-0.15.8/pcts/man/FittedPeriodicArmaModel-class.Rd | 6 pcts-0.15.8/pcts/man/PartialPeriodicAutocorrelations-class.Rd | 4 pcts-0.15.8/pcts/man/Pctime.Rd | 326 - pcts-0.15.8/pcts/man/PeriodicArmaFilter-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicAutocorrelations-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicAutocovariances-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicBJFilter-class.Rd | 6 pcts-0.15.8/pcts/man/PeriodicInterceptSpec-class.Rd | 8 pcts-0.15.8/pcts/man/PeriodicMTS-class.Rd | 2 pcts-0.15.8/pcts/man/PeriodicSPFilter-class.Rd | 6 pcts-0.15.8/pcts/man/PeriodicTS-class.Rd | 8 pcts-0.15.8/pcts/man/PeriodicVector-class.Rd | 8 pcts-0.15.8/pcts/man/SamplePeriodicAutocorrelations-class.Rd | 6 pcts-0.15.8/pcts/man/SamplePeriodicAutocovariances-class.Rd | 6 pcts-0.15.8/pcts/man/fit_trigPAR_optim.Rd | 170 pcts-0.15.8/pcts/man/partialAutocovariances-methods.Rd | 1 pcts-0.15.8/pcts/man/pcTest-methods.Rd | 210 pcts-0.15.8/pcts/man/pcacfMat.Rd | 4 pcts-0.15.8/pcts/man/pcarma_solve.Rd | 514 +- pcts-0.15.8/pcts/man/sim_parCoef.Rd | 4 33 files changed, 3220 insertions(+), 3204 deletions(-)
Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a
pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4
class system. This package allows the user to read/write a
pharmacometric model from/to files and adapt it further on the fly in
the R environment. For this purpose, this package provides an
intuitive API to add, modify or delete equations, ordinary
differential equations (ODE's), model parameters or compartment
properties (like infusion duration or rate, bioavailability and
initial values). Finally, this package also provides a useful export
of the model for use with simulation packages 'rxode2' and 'mrgsolve'.
This package is designed and intended to be used with package
'campsis', a PK/PD simulation platform built on top of 'rxode2' and
'mrgsolve'.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsismod versions 1.2.0 dated 2025-02-07 and 1.2.1 dated 2025-03-17
campsismod-1.2.0/campsismod/man/extractModelParametersFromNames.Rd |only campsismod-1.2.1/campsismod/DESCRIPTION | 10 campsismod-1.2.1/campsismod/MD5 | 31 +- campsismod-1.2.1/campsismod/NAMESPACE | 10 campsismod-1.2.1/campsismod/NEWS.md | 6 campsismod-1.2.1/campsismod/R/campsis_model.R | 8 campsismod-1.2.1/campsismod/R/omega_block.R | 9 campsismod-1.2.1/campsismod/R/parameter_uncertainty_utils.R | 76 +++-- campsismod-1.2.1/campsismod/R/replicated_campsis_model.R | 131 +++++++--- campsismod-1.2.1/campsismod/R/replication_settings.R | 19 - campsismod-1.2.1/campsismod/R/rxode_conversion.R | 65 +--- campsismod-1.2.1/campsismod/man/AutoReplicationSettings.Rd | 6 campsismod-1.2.1/campsismod/man/add.Rd | 3 campsismod-1.2.1/campsismod/man/auto_replication_settings-class.Rd | 6 campsismod-1.2.1/campsismod/man/sampleFromInverseWishartCore.Rd | 4 campsismod-1.2.1/campsismod/tests/testthat/testMiscellaneous.R | 48 +++ campsismod-1.2.1/campsismod/tests/testthat/testReplicatedCampsisModel.R | 92 ++++--- 17 files changed, 345 insertions(+), 179 deletions(-)
Title: Generate and Simulate Deterministic Discrete-Time Compartmental
Models
Description: R package to build and simulate deterministic discrete-time compartmental models that can be non-Markov. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).
Author: Thinh Ong [aut, cph] ,
Anh Phan [aut, cre] ,
Marc Choisy [aut] ,
Niels Lohman [ctb],
Bjoern Hoehrmann [ctb],
Florian Loitsch [ctb],
Ingo Berg [ctb]
Maintainer: Anh Phan <anhptq@oucru.org>
Diff between denim versions 1.0.0 dated 2024-06-05 and 1.0.1 dated 2025-03-17
denim-1.0.0/denim/inst/doc/denim_vs_deSolve.R |only denim-1.0.0/denim/inst/doc/denim_vs_deSolve.Rmd |only denim-1.0.0/denim/inst/doc/denim_vs_deSolve.html |only denim-1.0.0/denim/man/figures/logo.png |only denim-1.0.0/denim/vignettes/denim_vs_deSolve.Rmd |only denim-1.0.1/denim/DESCRIPTION | 17 denim-1.0.1/denim/MD5 | 35 denim-1.0.1/denim/NEWS.md | 2 denim-1.0.1/denim/R/simulators.R | 9 denim-1.0.1/denim/README.md | 2 denim-1.0.1/denim/build/vignette.rds |binary denim-1.0.1/denim/inst/doc/deSolve_to_denim.R |only denim-1.0.1/denim/inst/doc/deSolve_to_denim.Rmd |only denim-1.0.1/denim/inst/doc/deSolve_to_denim.html |only denim-1.0.1/denim/inst/doc/denim.R | 26 denim-1.0.1/denim/inst/doc/denim.Rmd | 29 denim-1.0.1/denim/inst/doc/denim.html | 1263 ++++++++++++++++++++--- denim-1.0.1/denim/man/figures/logo.svg |only denim-1.0.1/denim/src/ModelJSON.cpp | 3 denim-1.0.1/denim/src/json.h | 4 denim-1.0.1/denim/tests/testthat/test-result.R | 2 denim-1.0.1/denim/vignettes/deSolve_to_denim.Rmd |only denim-1.0.1/denim/vignettes/denim.Rmd | 29 denim-1.0.1/denim/vignettes/references.bib |only 24 files changed, 1260 insertions(+), 161 deletions(-)
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
Author: Zheng Ren [aut, cre, cph] ,
Andrew Chen [aut, cph] ,
Elizabeth Horwath [ctb]
Maintainer: Zheng Ren <zren1422@gmail.com>
Diff between ComBatFamQC versions 1.0.4 dated 2025-01-25 and 1.0.5 dated 2025-03-17
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 4 tests/testthat/test-age_shiny.R | 79 ++------------ tests/testthat/test-comfam_shiny.R | 206 +++++++++++-------------------------- 5 files changed, 88 insertions(+), 217 deletions(-)
Title: Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies
Description: DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the met [...truncated...]
Author: Sara Castillo Vicente [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Diff between MethEvolSIM versions 0.1.7 dated 2024-09-22 and 0.2 dated 2025-03-17
DESCRIPTION | 8 MD5 | 94 NAMESPACE | 26 R/multiRegion_SIM.R | 1090 ++++++++--- R/summaryStatistics.R |only R/user_functions.R | 73 build/vignette.rds |binary inst/doc/CFTP_method-vignette.R |only inst/doc/CFTP_method-vignette.Rmd |only inst/doc/CFTP_method-vignette.html |only inst/doc/intro-vignette.R | 16 inst/doc/intro-vignette.Rmd | 4 inst/doc/intro-vignette.html | 250 +- inst/doc/sumstats-vignette.R |only inst/doc/sumstats-vignette.Rmd |only inst/doc/sumstats-vignette.html |only man/MeanSiteFChange_cherry.Rd |only man/categorize_islandGlbSt.Rd |only man/categorize_siteMethSt.Rd |only man/cftpStepGenerator.Rd |only man/combiStructureGenerator.Rd | 196 + man/compare_CherryFreqs.Rd |only man/computeFitch_islandGlbSt.Rd |only man/compute_fitch.Rd |only man/compute_meanCor_i.Rd |only man/compute_meanCor_ni.Rd |only man/countSites_cherryMethDiff.Rd |only man/count_upm.Rd |only man/freqSites_cherryMethDiff.Rd |only man/get_cherryDist.Rd |only man/get_islandMeanFreqM.Rd |only man/get_islandMeanFreqP.Rd |only man/get_islandSDFreqM.Rd |only man/get_islandSDFreqP.Rd |only man/get_meanMeth_islands.Rd |only man/get_nonislandMeanFreqM.Rd |only man/get_nonislandMeanFreqP.Rd |only man/get_nonislandSDFreqM.Rd |only man/get_nonislandSDFreqP.Rd |only man/get_siteFChange_cherry.Rd |only man/mean_CherryFreqsChange_i.Rd |only man/mean_TreeFreqsChange_i.Rd |only man/pValue_CherryFreqsChange_i.Rd |only man/simulate_evolData.Rd | 9 man/simulate_initialData.Rd | 14 man/singleStructureGenerator.Rd | 188 + man/treeMultiRegionSimulator.Rd | 13 man/validate_dataAcrossTips.Rd |only man/validate_data_cherryDist.Rd |only man/validate_structureIndices.Rd |only man/validate_tree.Rd |only tests/testthat/test-multiRegion_SIM.R | 3144 +++++++++++++++++++++++++------- tests/testthat/test-summaryStatistics.R |only tests/testthat/test-user_functions.R | 94 vignettes/CFTP_method-vignette.Rmd |only vignettes/Figures |only vignettes/intro-vignette.Rmd | 4 vignettes/references.bib | 170 + vignettes/sumstats-vignette.Rmd |only 59 files changed, 4318 insertions(+), 1075 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 1.1.1 dated 2025-02-26 and 1.1.2 dated 2025-03-17
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 6 +++++ R/args_validation.R | 12 +++++++++- R/ctable.R | 50 +++++++++++++++++++++++++++++++++++++-------- R/helpers.R | 5 ++++ inst/doc/introduction.html | 14 ++++++------ inst/doc/rmarkdown.html | 42 ++++++++++++++++++------------------- man/ctable.Rd | 32 ++++++++++++++++++++++++---- 9 files changed, 130 insertions(+), 53 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 3.1-4 dated 2024-11-15 and 3.1-6 dated 2025-03-17
DESCRIPTION | 16 +++-- MD5 | 138 ++++++++++++++++++++++----------------------- NEWS | 23 +++++++ 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 |only 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 | 2 inst/info/packagesizes.txt | 3 man/macros/defns.Rd | 4 - man/meningitis.Rd |only man/paracou.Rd | 2 man/shelling.Rd | 4 + man/spruces.Rd | 2 71 files changed, 116 insertions(+), 78 deletions(-)
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Author: Abigail G. Keller [aut, cre],
Ryan P. Kelly [ctb],
Chitra M. Saraswati [rev],
Saras M. Windecker [rev]
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Diff between eDNAjoint versions 0.3.1 dated 2025-01-25 and 0.3.2 dated 2025-03-17
DESCRIPTION | 6 - MD5 | 20 ++--- R/goby_data.R | 2 inst/stan/functions/calc_loglik.stan | 118 +++++++++++++++++----------------- inst/stan/functions/calc_mu.stan | 8 +- inst/stan/functions/calc_p11.stan | 2 inst/stan/joint_continuous.stan | 4 - inst/stan/joint_count.stan | 6 - inst/stan/traditional_continuous.stan | 4 - inst/stan/traditional_count.stan | 6 - man/goby_data.Rd | 2 11 files changed, 89 insertions(+), 89 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more
information on the available algorithms. Building from included sources
requires 'CMake'. On Linux and 'macOS', if a suitable system build of
NLopt (2.7.0 or later) is found, it is used; otherwise, it is built
from included sources via 'CMake'. On Windows, NLopt is obtained through
'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for
'R >= 4.2.0'.
Author: Jelmer Ypma [aut],
Steven G. Johnson [aut] ,
Aymeric Stamm [ctb, cre] ,
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] ,
Kurt Hornik [ctb] ,
Julien Chiquet [ctb],
Avraham Adler [ctb] ,
Xiongtao Dai [ctb],
Jeroen Ooms [ctb],
Tomas [...truncated...]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between nloptr versions 2.2.0 dated 2025-03-12 and 2.2.1 dated 2025-03-16
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- NEWS.md | 12 ++++++++++- R/nloptr.R | 4 +++ README.md | 2 - inst/doc/nloptr.html | 43 +++++++++++++++++++++++++----------------- inst/tinytest/test-nloptr.R | 9 ++++++++ src/nlopt-src.tar.gz |binary src/nloptr.c | 9 +++++--- src/scripts/nlopt_download.sh | 2 - 10 files changed, 70 insertions(+), 35 deletions(-)
Title: Clustering and PCA with Weights, and Data Nuggets Clustering
Description: K-means clustering, hierarchical clustering, and PCA with observational
weights and/or variable weights. It also includes the corresponding functions
for data nuggets which serve as representative samples of large datasets.
Cherasia et al., (2022) <doi:10.1007/978-3-031-22687-8_20>.
Amaratunga et al., (2009) <doi:10.1002/9780470317129>.
Author: Rituparna Dey [aut, cre],
Yajie Duan [aut],
Javier Cabrera [aut],
Ge Cheng [aut]
Maintainer: Rituparna Dey <rituparnadey525@gmail.com>
Diff between WCluster versions 1.2.0 dated 2023-11-17 and 1.3.0 dated 2025-03-16
DESCRIPTION | 16 ++- MD5 | 38 ++++----- NAMESPACE | 1 R/DN.Wkmeans.R | 6 - R/DN.Wpca.R | 2 R/DNcluster.predict.R | 7 - R/Whclust.R | 7 - R/Wkmeans.R | 198 ++++++++++++++++++++++++++++--------------------- R/Wpca.R | 37 +++++---- R/cluster.predict.R | 39 ++++++--- R/distw.R | 26 ++---- R/wmean.R | 17 ++-- R/wss.R | 12 +- R/wwcss.R | 10 +- man/DN.Whclust.Rd | 2 man/DN.Wkmeans.Rd | 8 - man/Whclust.Rd | 12 +- man/Wkmeans.Rd | 16 +-- man/Wpca.Rd | 4 man/cluster.predict.Rd | 2 20 files changed, 256 insertions(+), 204 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.3.0 dated 2025-03-04 and 0.3.1 dated 2025-03-16
DESCRIPTION | 8 MD5 | 22 NEWS.md | 7 R/summariseClinicalRecords.R | 1 R/summariseMissingData.R | 2 R/tableClinicalRecords.R | 9 R/tableConceptIdCounts.R | 31 inst/doc/characterisation.html | 5751 ++++++++---------------- inst/doc/summarise_clinical_tables_records.html | 305 - inst/doc/summarise_concept_set_counts.html | 14 inst/doc/summarise_observation_period.html | 230 tests/testthat/test-summariseMissingData.R | 3 12 files changed, 2368 insertions(+), 4015 deletions(-)
Title: Implementation of Learning Gamma CUSUM (Cumulative Sum) Control
Charts
Description: Implements Cumulative Sum (CUSUM) control charts specifically
designed for monitoring processes following a Gamma distribution. Provides
functions to estimate distribution parameters, simulate control limits, and
apply cautious learning schemes for adaptive thresholding. It supports
upward and downward monitoring with guaranteed performance evaluated via
Monte Carlo simulations. It is useful for quality control applications in
industries where data follows a Gamma distribution. Methods are based on
Madrid-Alvarez et al. (2024) <doi:10.1002/qre.3464> and Madrid-Alvarez et
al. (2024) <doi:10.1080/08982112.2024.2440368>.
Author: Harold Manuel Madrid-Alvarez [aut, cre],
Victor Gustavo Tercero-Gomez [aut],
Juan Carlos Garcia-Diaz [aut]
Maintainer: Harold Manuel Madrid-Alvarez <harold.madrid@unisimon.edu.co>
Diff between LGCU versions 0.1.4 dated 2025-03-11 and 0.1.5 dated 2025-03-16
DESCRIPTION | 14 +++++++++----- MD5 | 4 ++-- NEWS.md | 24 ++++++++---------------- 3 files changed, 19 insertions(+), 23 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.1.0 dated 2025-02-25 and 1.1.1 dated 2025-03-16
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 1 NEWS.md | 6 R/classAchillesTable.R | 2 R/classCodelist.R | 8 R/classCohortTable.R | 133 ++-- R/classOmopTable.R | 2 R/classSummarisedResult.R | 9 R/exportSummarisedResult.R | 9 R/importSummarisedResult.R | 151 ++--- R/methodSuppress.R | 4 R/pivot.R | 4 R/unite.R | 13 R/validate.R | 6 inst/doc/summarised_result.html | 882 ++++++++++++++++----------------- man/importSummarisedResult.Rd | 4 man/validateCohortArgument.Rd | 4 tests/testthat/test-classCodelist.R | 2 tests/testthat/test-classCohortTable.R | 14 20 files changed, 663 insertions(+), 637 deletions(-)
Title: Weighted and Unweighted Spatial Centers
Description: Generate mean and median weighted or unweighted spatial centers.
Functions are analogous to their identically named counterparts within
'ArcGIS Pro'. Median center methodology based off of Kuhn and Kuenne
(1962) <doi:10.1111/j.1467-9787.1962.tb00902.x>.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between centr versions 0.2.2 dated 2025-02-07 and 0.2.3 dated 2025-03-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 +++++- tests/testthat/test-median_center.R | 29 +++++++++++++++++++++++------ 4 files changed, 35 insertions(+), 14 deletions(-)
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.1 dated 2025-02-03 and 4.4.2 dated 2025-03-16
DESCRIPTION | 10 MD5 | 58 ++-- NAMESPACE | 3 NEWS.md | 64 ++++ R/BarChart.R | 43 +-- R/PieChart.R | 42 +- R/Plot.R | 395 +++++++++++++--------------- R/Read.R | 161 +++++++---- R/Write.R | 226 ++++++++-------- R/bc.main.R | 32 +- R/dpmat.main.R | 16 - R/pc.main.R | 16 - R/plt.bubble.R | 4 R/plt.by.legend.R | 10 R/plt.colors.R | 6 R/plt.lattice.R | 7 R/plt.legend.R | 3 R/plt.main.R | 673 +++++++++++++++++++++++------------------------- R/plt.txt.R | 114 -------- R/zzz.R | 13 data/dataEmployee.rda |binary data/dataStockPrice.rda |binary inst/doc/intro.html | 318 ++++++++++------------ man/BarChart.Rd | 39 +- man/Histogram.Rd | 6 man/PieChart.Rd | 35 +- man/Plot.Rd | 48 +-- man/Read.Rd | 29 +- man/Write.Rd | 51 ++- man/pivot.Rd | 3 30 files changed, 1224 insertions(+), 1201 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.8 dated 2025-01-21 and 0.1.0 dated 2025-03-16
DESCRIPTION | 10 ++--- MD5 | 31 ++++++++------- NEWS.md | 8 ++++ R/expect_snapshot_plot.R | 6 ++- R/expect_snapshot_print.R | 42 +++++++++++++-------- build/partial.rdb |binary inst/tinytest/_tinysnapshot/png-base.png |binary inst/tinytest/_tinysnapshot/print-sub_label_fn.txt |only inst/tinytest/helpers.R | 7 ++- inst/tinytest/test-png.R | 32 ++++++++-------- inst/tinytest/test-print.R | 14 ++++++- inst/tinytest/test-ragg.R | 13 ++++-- inst/tinytest/test-svg.R | 13 ++++-- inst/tinytest/test-svglite.R | 13 ++++-- man/expect_equivalent_images.Rd | 3 + man/expect_snapshot_plot.Rd | 3 + man/expect_snapshot_print.Rd | 6 +++ 17 files changed, 130 insertions(+), 71 deletions(-)
Title: Various Methods for the Two Sample Problem
Description: The routine twosample_test() in this package runs the
two sample test using various test statistic. The p values are
found via permutation or large sample theory. The routine twosample_power() allows the
calculation of the power in various cases, and plot_power() draws the corresponding power graphs.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between R2sample versions 3.1.0 dated 2025-03-09 and 3.1.1 dated 2025-03-16
DESCRIPTION | 6 ++--- MD5 | 29 ++++++++++++++---------- NEWS.md | 7 +++++- R/RcppExports.R | 39 +++++++++++++++++++++++++++++++++ R/power_cont_R.R | 7 ++++-- R/twosample_power.R | 24 ++++++++------------ R/twosample_test.R | 4 ++- inst/doc/R2sample.html | 8 +++--- man/calcTS.Rd |only man/ts_C.Rd |only man/ts_D.Rd |only src/RcppExports.cpp | 57 ++++++++++++++++++++++++++++++++++++++++++++++--- src/perm_test_cont.cpp | 33 ++++++++++++++++++---------- src/perm_test_disc.cpp | 33 +++++++++++----------------- src/power_cont.cpp | 46 ++++++++++++++++++--------------------- src/power_disc.cpp | 31 +++++--------------------- src/teststatistics.cpp |only src/teststatistics.h |only 18 files changed, 203 insertions(+), 121 deletions(-)
Title: Utilities for the Open Geospatial Consortium 'GeoPackage' Format
Description: Build Open Geospatial Consortium 'GeoPackage' files (<https://www.geopackage.org/>). 'GDAL' utilities for reading and writing spatial data are provided by the 'terra' package. Additional 'GeoPackage' and 'SQLite' features for attributes and tabular data are implemented with the 'RSQLite' package.
Author: Andrew Brown [aut, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between gpkg versions 0.0.8 dated 2024-02-19 and 0.0.12 dated 2025-03-16
DESCRIPTION | 12 - MD5 | 91 ++++--- NAMESPACE | 29 ++ NEWS.md | 43 +++ R/gpkg-2d-gridded-ancillary.R |only R/gpkg-attributes.R | 32 ++ R/gpkg-class.R | 57 ++++ R/gpkg-connection.R | 45 +++ R/gpkg-contents.R | 119 ++++++---- R/gpkg-datasets.R | 4 R/gpkg-dummy.R | 65 +---- R/gpkg-execute.R | 3 R/gpkg-extensions.R | 48 ++++ R/gpkg-features.R |only R/gpkg-geometry-columns.R |only R/gpkg-grid.R |only R/gpkg-io.R | 217 ++++++++++++------ R/gpkg-metadata.R |only R/gpkg-query.R | 26 +- R/gpkg-sqlite.R | 38 ++- R/gpkg-srs.R |only R/gpkg-table.R | 133 +++++++---- R/gpkg-util.R | 73 ++++-- R/gpkg-validate.R | 34 ++ R/gpkg_bbox.R | 19 - README.md | 166 ++++++++------ build/vignette.rds |binary inst/doc/intro.R | 22 + inst/doc/intro.Rmd | 45 ++- inst/doc/intro.html | 398 ++++++++++++++++++---------------- inst/tinytest/test_gpkg.R | 197 ++++++++-------- man/geopackage-class.Rd | 14 + man/gpkg-connection.Rd | 14 + man/gpkg-contents.Rd | 13 - man/gpkg-features.Rd |only man/gpkg-geometry-columns.Rd |only man/gpkg-package.Rd | 1 man/gpkg-srs.Rd |only man/gpkg_2d_gridded_tile_ancillary.Rd |only man/gpkg_bbox.Rd | 11 man/gpkg_create_dummy_features.Rd | 6 man/gpkg_create_empty_grid.Rd |only man/gpkg_creation_options.Rd | 2 man/gpkg_extensions.Rd |only man/gpkg_query.Rd | 20 + man/gpkg_read.Rd | 10 man/gpkg_sqlite_tables.Rd | 2 man/gpkg_table.Rd | 57 +++- man/gpkg_tables.Rd | 6 man/gpkg_validate.Rd | 14 - man/gpkg_write.Rd | 37 ++- man/gridded-ancillary.Rd |only vignettes/intro.Rmd | 45 ++- 53 files changed, 1409 insertions(+), 759 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.37 dated 2024-12-16 and 1.5.38 dated 2025-03-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + R/Effectsize.R | 43 +++++++++++++++++++++++++++++++++++++++++-- 4 files changed, 50 insertions(+), 10 deletions(-)