Title: A Simple Package for Testing R Packages
Description: A minimal, dependency-free testing framework for R packages.
Write tests as simple R expressions that return TRUE, using assert() for
assertions (with informative error messages on failure), has_error() /
has_warning() / has_message() for testing conditions, and test_pkg() to
run all tests with full access to internal (non-exported) package
functions. Snapshot testing via Markdown files is also supported.
Author: Yihui Xie [aut, cre] ,
Tomas Kalibera [ctb],
Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 1.1.2 dated 2026-09-04 and 1.2 dated 2026-10-15
DESCRIPTION | 8 +- MD5 | 15 ++-- NAMESPACE | 1 R/testit.R | 154 +++++++++++++++++++++++++++++++++------------ R/utils.R | 4 - man/assert.Rd | 9 +- man/has_match.Rd |only man/test_pkg.Rd | 11 +-- tests/testit/test-testit.R | 129 ++++++++++++++++++++++++++++++------- 9 files changed, 244 insertions(+), 87 deletions(-)
Title: Custom Gov Style Inputs for Shiny
Description: Provides 'shiny' components styled using the GOV.UK Design System.
See <https://design-system.service.gov.uk/components/> for component guidance.
Author: Ross Wyatt [aut],
Cam Race [aut, cre],
Sarah Wong [aut],
Richard Bielby [ctb],
Charlotte Foster [ctb],
Jeni Martin [ctb],
Andrew Baker [ctb]
Maintainer: Cam Race <camrace8@gmail.com>
Diff between shinyGovstyle versions 0.2.0 dated 2026-04-13 and 0.3.0 dated 2026-10-15
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shinyGovstyle-0.3.0/shinyGovstyle/R/confirmation_panel.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/contents_links.R | 278 --- shinyGovstyle-0.3.0/shinyGovstyle/R/cookieBanner.R | 30 shinyGovstyle-0.3.0/shinyGovstyle/R/date_Input.R | 188 +- shinyGovstyle-0.3.0/shinyGovstyle/R/details.R | 13 shinyGovstyle-0.3.0/shinyGovstyle/R/download_button.R | 8 shinyGovstyle-0.3.0/shinyGovstyle/R/download_link.R | 10 shinyGovstyle-0.3.0/shinyGovstyle/R/download_radios.R | 2 shinyGovstyle-0.3.0/shinyGovstyle/R/error_off.R | 11 shinyGovstyle-0.3.0/shinyGovstyle/R/error_on.R | 18 shinyGovstyle-0.3.0/shinyGovstyle/R/error_sum_update.R | 7 shinyGovstyle-0.3.0/shinyGovstyle/R/error_summary.R | 7 shinyGovstyle-0.3.0/shinyGovstyle/R/external_link.R | 125 + shinyGovstyle-0.3.0/shinyGovstyle/R/file_Input.R | 27 shinyGovstyle-0.3.0/shinyGovstyle/R/font.R | 9 shinyGovstyle-0.3.0/shinyGovstyle/R/footer.R | 25 shinyGovstyle-0.3.0/shinyGovstyle/R/govLayouts.R | 36 shinyGovstyle-0.3.0/shinyGovstyle/R/govReactable.R | 150 +- shinyGovstyle-0.3.0/shinyGovstyle/R/govTable.R | 43 shinyGovstyle-0.3.0/shinyGovstyle/R/govTabs.R | 16 shinyGovstyle-0.3.0/shinyGovstyle/R/gov_layout.R | 89 - shinyGovstyle-0.3.0/shinyGovstyle/R/gov_list.R | 25 shinyGovstyle-0.3.0/shinyGovstyle/R/gov_page.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/gov_tag.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/gov_width_container.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/header.R | 215 +- shinyGovstyle-0.3.0/shinyGovstyle/R/heading_text.R | 9 shinyGovstyle-0.3.0/shinyGovstyle/R/input_field.R | 25 shinyGovstyle-0.3.0/shinyGovstyle/R/insert_text.R | 79 - shinyGovstyle-0.3.0/shinyGovstyle/R/inset_text.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/label_hint.R | 27 shinyGovstyle-0.3.0/shinyGovstyle/R/navigate_to.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/noti_banner.R | 10 shinyGovstyle-0.3.0/shinyGovstyle/R/panel_output.R | 67 shinyGovstyle-0.3.0/shinyGovstyle/R/params.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/phase_banner.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/radio_button_input.R | 202 ++ shinyGovstyle-0.3.0/shinyGovstyle/R/select_input.R | 13 shinyGovstyle-0.3.0/shinyGovstyle/R/service_navigation.R | 317 +++- shinyGovstyle-0.3.0/shinyGovstyle/R/skip_to_main.R | 4 shinyGovstyle-0.3.0/shinyGovstyle/R/summary.R | 14 shinyGovstyle-0.3.0/shinyGovstyle/R/tag.R | 80 - shinyGovstyle-0.3.0/shinyGovstyle/R/text_area_input.R | 116 + shinyGovstyle-0.3.0/shinyGovstyle/R/text_input.R | 43 shinyGovstyle-0.3.0/shinyGovstyle/R/update_page_title.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/utils.R |only shinyGovstyle-0.3.0/shinyGovstyle/R/value_box.R | 40 shinyGovstyle-0.3.0/shinyGovstyle/R/warning_text.R | 8 shinyGovstyle-0.3.0/shinyGovstyle/R/word_count.R | 47 shinyGovstyle-0.3.0/shinyGovstyle/README.md | 5 shinyGovstyle-0.3.0/shinyGovstyle/build/vignette.rds |binary shinyGovstyle-0.3.0/shinyGovstyle/inst/WORDLIST |only shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/cookies-and-analytics.R |only shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/cookies-and-analytics.Rmd |only shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/cookies-and-analytics.html |only shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/headings-and-text.R | 74 - shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/headings-and-text.Rmd | 152 +- shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/headings-and-text.html | 343 +++- shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/layout-options.R | 175 +- shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/layout-options.Rmd | 296 ++-- shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/layout-options.html | 720 ++++++---- shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/shinyGovstyle.R | 17 shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/shinyGovstyle.Rmd | 27 shinyGovstyle-0.3.0/shinyGovstyle/inst/doc/shinyGovstyle.html | 83 - shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/global.R | 5 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_action_types.R | 40 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_cookies.R | 131 + shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_feedback_types.R | 36 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_select_types.R | 6 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_tables_tabs.R | 17 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_text_types.R | 41 shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/modules/mod_width_toggle.R |only shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/server.R | 144 -- shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/tests/testthat/test-basic_load.R | 97 + shinyGovstyle-0.3.0/shinyGovstyle/inst/example_app/ui.R | 61 shinyGovstyle-0.3.0/shinyGovstyle/inst/govuk-brand.yml |only shinyGovstyle-0.3.0/shinyGovstyle/inst/logo |only shinyGovstyle-0.3.0/shinyGovstyle/inst/www/css/govuk-frontend-6.6.0.min.css |only shinyGovstyle-0.3.0/shinyGovstyle/inst/www/css/header-overrides.css | 45 shinyGovstyle-0.3.0/shinyGovstyle/inst/www/css/reactable-overrides.css |only shinyGovstyle-0.3.0/shinyGovstyle/inst/www/css/width-overrides.css |only shinyGovstyle-0.3.0/shinyGovstyle/inst/www/images/govuk-icon-180.png |binary shinyGovstyle-0.3.0/shinyGovstyle/inst/www/images/govuk-icon-192.png |binary shinyGovstyle-0.3.0/shinyGovstyle/inst/www/images/govuk-icon-512.png |binary shinyGovstyle-0.3.0/shinyGovstyle/inst/www/js/accordion.js | 139 - 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Title: Explore and Code Responses to Check-All-that-Apply Survey Items
Description: Analyzing responses to check-all-that-apply survey items often requires
data transformations and subjective decisions for combining categories. 'CATAcode'
contains tools for exploring response patterns, facilitating data transformations,
applying a set of decision rules for coding responses, and summarizing response frequencies.
Author: Kyle Nickodem [aut, cre] ,
Gabriel J. Merrin [aut]
Maintainer: Kyle Nickodem <kyle.nickodem@gmail.com>
Diff between CATAcode versions 1.0.0 dated 2025-08-26 and 1.0.1 dated 2026-10-15
CATAcode-1.0.0/CATAcode/man/figures/logo.PNG |only CATAcode-1.0.1/CATAcode/DESCRIPTION | 9 +++--- CATAcode-1.0.1/CATAcode/MD5 | 22 ++++++++-------- CATAcode-1.0.1/CATAcode/NEWS.md | 6 +++- CATAcode-1.0.1/CATAcode/R/cata_code.R | 16 +++++------ CATAcode-1.0.1/CATAcode/README.md | 6 +++- CATAcode-1.0.1/CATAcode/build/partial.rdb |binary CATAcode-1.0.1/CATAcode/build/vignette.rds |binary CATAcode-1.0.1/CATAcode/inst/doc/CATAcode-overview.R | 12 ++++---- CATAcode-1.0.1/CATAcode/inst/doc/CATAcode-overview.html | 22 +++------------- CATAcode-1.0.1/CATAcode/man/CATAcode.Rd | 1 CATAcode-1.0.1/CATAcode/man/cata_code.Rd | 16 +++++------ CATAcode-1.0.1/CATAcode/man/figures/logo.png |only 13 files changed, 54 insertions(+), 56 deletions(-)
Title: Load 'Overture' Datasets as 'dbplyr' and 'sf'-Ready Data Frames
Description: An integrated R interface to the 'Overture' API
(<https://docs.overturemaps.org/>). Allows R users to return 'Overture' data as
'dbplyr' data frames or materialized 'sf' spatial data frames.
Author: Arthur Gailes [aut, cre, cph]
Maintainer: Arthur Gailes <agailes1@gmail.com>
Diff between overtureR versions 0.3.1 dated 2026-10-08 and 0.3.2 dated 2026-10-15
DESCRIPTION | 6 MD5 | 6 NEWS.md | 4 tests/testthat/test-open_curtain.R | 942 ++++++++++++++++++------------------- 4 files changed, 481 insertions(+), 477 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 0.4.1 dated 2025-05-20 and 0.4.3 dated 2026-10-15
officedown-0.4.1/officedown/tests/testthat/rmd/long-text.Rmd |only officedown-0.4.1/officedown/tests/testthat/rmd/template-hdr-ftr.docx |only officedown-0.4.3/officedown/DESCRIPTION | 23 officedown-0.4.3/officedown/MD5 | 77 +- officedown-0.4.3/officedown/NAMESPACE | 84 +-- officedown-0.4.3/officedown/NEWS.md | 45 + officedown-0.4.3/officedown/R/hooks.R | 277 ++++++---- officedown-0.4.3/officedown/R/knit_print_dml.R | 92 ++- officedown-0.4.3/officedown/R/knit_print_table.R | 176 +++--- officedown-0.4.3/officedown/R/onAttach.R | 3 officedown-0.4.3/officedown/R/rdocx_document.R | 178 ++++-- officedown-0.4.3/officedown/R/rdocx_knit_print.R | 137 +++- officedown-0.4.3/officedown/R/rdocx_officer_bindings.R | 36 - officedown-0.4.3/officedown/R/rdocx_post_knit.R | 103 ++- officedown-0.4.3/officedown/R/rdocx_post_proc.R | 103 ++- officedown-0.4.3/officedown/R/rdocx_pre_proc.R | 46 + officedown-0.4.3/officedown/R/rpptx_document.R | 50 + officedown-0.4.3/officedown/R/utils.R | 98 ++- officedown-0.4.3/officedown/build/vignette.rds |binary officedown-0.4.3/officedown/inst/examples/bookdown/02-toc.Rmd | 7 officedown-0.4.3/officedown/inst/examples/bookdown/03-tables.Rmd | 2 officedown-0.4.3/officedown/inst/rmarkdown/templates/word/skeleton/skeleton.Rmd | 4 officedown-0.4.3/officedown/man/figures/README-bookdown.png |binary officedown-0.4.3/officedown/man/figures/README-minimal-rmd.png |binary officedown-0.4.3/officedown/man/figures/README-rstudio-new.png |binary officedown-0.4.3/officedown/man/hook_plot_officedown.Rd |only officedown-0.4.3/officedown/man/knit_print.dml.Rd |only officedown-0.4.3/officedown/man/knit_print_block.Rd | 4 officedown-0.4.3/officedown/man/knit_print_run.Rd | 4 officedown-0.4.3/officedown/man/rdocx/plots.Rmd | 7 officedown-0.4.3/officedown/man/rdocx/tables.Rmd | 7 officedown-0.4.3/officedown/man/rdocx_document.Rd | 18 officedown-0.4.3/officedown/man/rpptx_document.Rd | 2 officedown-0.4.3/officedown/tests/testthat/helper-utils.R | 25 officedown-0.4.3/officedown/tests/testthat/rmd/template-similar-list-styles.docx |only officedown-0.4.3/officedown/tests/testthat/test-knit-print.R |only officedown-0.4.3/officedown/tests/testthat/test-rdocx-lists.R | 101 ++- officedown-0.4.3/officedown/tests/testthat/test-rdocx-par-settings.R | 15 officedown-0.4.3/officedown/tests/testthat/test-rdocx-plots.R | 62 ++ officedown-0.4.3/officedown/tests/testthat/test-rdocx-references.R |only officedown-0.4.3/officedown/tests/testthat/test-rdocx-sections.R | 122 +++- officedown-0.4.3/officedown/tests/testthat/test-rdocx-tables.R | 9 officedown-0.4.3/officedown/tests/testthat/test-rpptx.R | 4 43 files changed, 1299 insertions(+), 622 deletions(-)
Title: Geoadditive Small Area Estimation for Area-Level Model
Description: Fits area-level geoadditive small area estimation (SAE)
models by extending the Fay-Herriot area-level model with linear,
nonlinear, and spatial effects. The Fay-Herriot model is described by
Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>.
Geoadditive models combine nonlinear covariate effects and spatial
variation as described by Kammann and Wand (2003)
<doi:10.1111/1467-9876.00385>, while their application to small area
estimation is discussed by Pusponegoro et al. (2019)
<doi:10.21108/JDSA.2019.2.15>. Nonlinear covariate effects are represented
using penalized splines, while spatial effects are represented using a
smooth function of geographic coordinates. Models are estimated using
restricted maximum likelihood (REML), and mean squared error (MSE) is
estimated using a parametric bootstrap. The package also provides
comparisons with the Fay-Herriot and spatial Fay-Herriot (SFH) models.
Author: Amalyah Rizky Khairunnisa Sutarto [aut, cre],
Novi Hidayat Pusponegoro [aut, ths]
Maintainer: Amalyah Rizky Khairunnisa Sutarto <222212489@stis.ac.id>
Diff between geoaddSAE2 versions 0.1.1 dated 2026-10-05 and 0.1.2 dated 2026-10-15
DESCRIPTION | 10 MD5 | 26 - NEWS.md | 4 R/data.R | 2 R/geoadditive.R | 116 +++--- build/vignette.rds |binary data/simulated_sae.rda |binary inst/doc/geoaddSAE2-intro.R | 105 +++++ inst/doc/geoaddSAE2-intro.Rmd | 296 ++++++++++++++- inst/doc/geoaddSAE2-intro.html | 776 +++++++++++++++++++++++++++++------------ man/geosae.Rd | 71 ++- man/simulated_sae.Rd | 2 tests/testthat/test-data.R | 94 ++-- vignettes/geoaddSAE2-intro.Rmd | 296 ++++++++++++++- 14 files changed, 1392 insertions(+), 406 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/documentation/ads-commerce/marketing-api>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.16.1 dated 2026-08-25 and 2.17.0 dated 2026-10-15
DESCRIPTION | 6 MD5 | 20 - NAMESPACE | 173 +++++------ NEWS.md | 751 +++++++++++++++++++++++++------------------------- R/authorization.R | 2 R/fbGetAdAccount.R |only R/fbSetters.R | 10 R/zzz.R | 235 +++++++-------- build/partial.rdb |binary man/fbAuth.Rd | 2 man/fbGetAdAccount.Rd |only man/fbGetToken.Rd | 2 12 files changed, 604 insertions(+), 597 deletions(-)
Title: Font Metrics and Font Management Utilities for R Graphics
Description: Compute text metrics (width, ascent, descent) using 'Cairo'
and 'FreeType', independently of the active graphic device. Font
lookup is delegated to 'systemfonts'. Additional utilities let users
register 'Google Fonts' or bundled 'Liberation' fonts, check font
availability, and assemble 'htmlDependency' objects so that fonts are
correctly embedded in 'Shiny' applications, 'R Markdown' documents,
and 'htmlwidgets' outputs such as 'ggiraph'.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.5.1 dated 2026-05-25 and 0.5.2 dated 2026-10-15
DESCRIPTION | 10 ++-- MD5 | 52 +++++++++++---------- NAMESPACE | 21 +++++--- NEWS.md | 15 +++++- R/font_family_exists.R | 42 ++++++++++++++++- R/fontconfig.R | 4 - R/gdtools.R | 1 R/str-metrics.R | 17 ++---- R/sysdata.rda |binary man/addGFontHtmlDependency.Rd | 3 - man/fonts_cache_dir.Rd | 3 - man/gfontHtmlDependency.Rd | 3 - man/install_gfont_script.Rd | 3 - man/installed_gfonts.Rd | 3 - man/liberationmonoHtmlDependency.Rd | 3 - man/liberationsansHtmlDependency.Rd | 3 - man/liberationserifHtmlDependency.Rd | 3 - man/m_str_extents.Rd | 17 +----- man/match_family.Rd | 4 - man/register_gfont.Rd | 3 - man/register_liberationmono.Rd | 3 - man/register_liberationsans.Rd | 3 - man/register_liberationserif.Rd | 3 - man/sys_fonts.Rd | 6 ++ man/sys_fonts_reset.Rd |only tests/testthat/test-font-set.R | 83 +++++++++++++++++++++++++++++++++- tests/testthat/test-str_metrics.R | 11 ++-- tests/testthat/test-sys-fonts-cache.R |only 28 files changed, 229 insertions(+), 90 deletions(-)
Title: US College Scorecard Data
Description: Provides a tidied subset of the US College Scorecard dataset,
containing institutional characteristics, enrollment, student aid,
costs, and student outcomes at institutions of higher education in the
United States.
Author: Garrick Aden-Buie [aut, cre, cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between collegeScorecard versions 0.2.0 dated 2025-02-13 and 0.3.0 dated 2026-10-15
DESCRIPTION | 12 +- MD5 | 20 ++-- NEWS.md | 4 R/collegeScorecard-package.R | 21 ++-- README.md | 164 ++++++++++++++++++------------------- data/school.rda |binary data/scorecard.rda |binary inst/scorecard-data-dictionary.rds |binary man/collegeScorecard-package.Rd | 7 + man/school.Rd | 2 man/scorecard.Rd | 2 11 files changed, 122 insertions(+), 110 deletions(-)
More information about collegeScorecard at CRAN
Permanent link
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between parameters versions 0.29.3 dated 2026-09-02 and 0.30.0 dated 2026-10-15
DESCRIPTION | 26 +-- MD5 | 88 ++++++----- NAMESPACE | 39 ++--- NEWS.md | 83 ++++++++++ R/1_model_parameters.R | 3 R/bootstrap_model.R | 23 ++ R/extract_parameters.R | 70 ++++---- R/format_parameters.R | 15 + R/methods_aov.R | 187 +++++++++++++----------- R/methods_brms.R | 10 + R/methods_coxme.R | 1 R/methods_gee.R | 46 ++--- R/methods_glmmTMB.R | 22 ++ R/methods_htest.R | 58 +++++++ R/methods_lavaan.R | 117 ++++++++++++++- R/methods_marginaleffects.R | 94 ++++++++++-- R/methods_merTools.R | 4 R/methods_metafor.R | 43 ++--- R/methods_panelr.R | 10 + R/parameters_type.R | 47 +++--- R/print.parameters_model.R | 16 +- R/utils.R | 29 +++ R/utils_model_parameters.R | 56 ++++++- man/bootstrap_model.Rd | 10 - man/model_parameters.Rd | 2 man/model_parameters.aov.Rd | 4 man/model_parameters.brmsfit.Rd | 10 + man/model_parameters.htest.Rd | 10 + tests/testthat/test-betareg.R | 2 tests/testthat/test-blavaan.R |only tests/testthat/test-bootstrap_parameters.R | 24 +++ tests/testthat/test-bracl.R | 2 tests/testthat/test-format_parameters.R | 20 ++ tests/testthat/test-gee.R | 35 ++-- tests/testthat/test-glmmTMB-ordinal.R |only tests/testthat/test-glmmTMB.R | 4 tests/testthat/test-lavaan.R | 19 ++ tests/testthat/test-marginaleffects.R | 155 +++++++++++++++++++ tests/testthat/test-merTools.R |only tests/testthat/test-model_parameters.Arima.R |only tests/testthat/test-model_parameters.TukeyHSD.R |only tests/testthat/test-model_parameters.htest.R | 18 ++ tests/testthat/test-model_parameters.metafor.R | 27 ++- tests/testthat/test-model_parameters.mixed.R | 14 + tests/testthat/test-model_parameters_ordinal.R | 127 ++++++++++++++-- tests/testthat/test-model_parameters_robust.R | 120 +++++++++++---- tests/testthat/test-print_caption.R |only tests/testthat/test-printing.R | 16 +- 48 files changed, 1328 insertions(+), 378 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre] ,
Pedro Miranda-Afonso [aut] ,
Grigorios Papageorgiou [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.6-0 dated 2026-01-28 and 0.6-5 dated 2026-10-15
DESCRIPTION | 11 MD5 | 44 - NAMESPACE | 3 NEWS.md | 5 R/basic_methods.R | 30 - R/help_functions.R | 52 ++ R/jm.R | 9 R/jm_fit.R | 7 R/optimal_model.R | 250 ++++++++++ R/predict_funs.R | 31 - README.md | 2 man/JMbayes2.Rd | 4 man/jm.Rd | 2 man/prothro.Rd | 9 src/JMbayes2_D.h | 183 +++++-- src/JMbayes2_FE.h | 462 +++++++++++-------- src/JMbayes2_Funs.h | 1177 ++++++++++++++++++++++++++++++++++++------------- src/JMbayes2_LogDens.h | 489 +++++++++++++++----- src/JMbayes2_RE.h | 283 ++++++----- src/JMbayes2_Surv.h | 409 ++++++++--------- src/JMbayes2_sigmas.h | 125 +++-- src/JMbayes2_tau.h | 3 src/mcmc_fit.cpp | 562 +++++++++++++++++------ 23 files changed, 2880 insertions(+), 1272 deletions(-)
Title: A Simplified and Scalable Urban Water Quality Model for
Simulation of Combined Sewer Overflows
Description: Provides a fast and parallelised calculator to estimate combined sewage water emissions. It supports the planning and design of urban drainage systems without extensive simulation tools. The methods are described in Torres-Matallana et al. (2018) <doi:10.3390/w10060782>.
Author: J.A. Torres-Matallana [aut, cre],
K. Klepiszewski [aut],
U. Leopold [ctb],
G. Schutz [ctb],
G.B.M. Heuvelink [ctb]
Maintainer: J.A. Torres-Matallana <jairo.torres@hereon.de>
This is a re-admission after prior archival of version 1.2.3.0 dated 2021-09-28
Diff between EmiStatR versions 1.2.3.0 dated 2021-09-28 and 1.2.6 dated 2026-10-15
DESCRIPTION | 37 +-- MD5 | 61 +++-- NEWS.md |only R/Agg.R | 7 R/CInp2TS.R | 33 +- R/Class-input.R | 5 R/EmiStatR.R | 539 ++++++++++++++++++++++-------------------------- build |only man/Agg.Rd | 2 man/CInp2TS.Rd | 29 +- man/Delay.Rd | 13 - man/E1.Rd | 6 man/E2.Rd | 6 man/E3.Rd | 6 man/EmiStatR-methods.Rd | 33 -- man/EmiStatR-package.Rd | 34 +-- man/Esch_Sure2010.Rd | 6 man/IsReg.Rd | 6 man/Level2Volume.Rd | 7 man/P1.Rd | 6 man/P1_20111216.Rd | 6 man/Volume2Level.Rd | 15 - man/inf.Rd | 6 man/input-class.Rd | 197 +++++++---------- man/pe_factor.Rd | 6 man/qs_factor.Rd | 6 man/qs_factor_ATV.Rd | 3 man/rw.Rd | 6 man/ww.Rd | 16 - tests |only 30 files changed, 474 insertions(+), 623 deletions(-)
Title: Predictive Approaches in Psychology
Description: Recent years have seen an increased interest in novel methods
for analyzing quantitative data from experimental psychology. Currently, however, they lack an
established and accessible software framework. Many existing implementations provide no guidelines,
consisting of small code snippets, or sets of packages. In addition, the use of existing packages
often requires advanced programming experience. 'PredPsych' is a user-friendly toolbox based on
machine learning predictive algorithms. It comprises of multiple functionalities for multivariate
analyses of quantitative behavioral data based on machine learning models.
Author: Atesh Koul [aut, cre]
Maintainer: Atesh Koul <atesh.koul@gmail.com>
Diff between PredPsych versions 0.5 dated 2025-10-31 and 0.6 dated 2026-10-15
DESCRIPTION | 11 ++++++----- MD5 | 10 ++++++---- R/DTModel.R | 18 +++++++++++++----- R/LinearDA.R | 22 ++++++++++++++-------- R/classifyFun.R | 18 +++++++++++++----- tests |only 6 files changed, 52 insertions(+), 27 deletions(-)
Title: Computation of the Double-Entry Intraclass Correlation
Description: The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Author: Christian Bloetner [aut, cre],
Michael Paul Grosz [aut]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between iccde versions 0.3.9 dated 2026-06-12 and 0.3.10 dated 2026-10-15
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/iccdeboot.R | 29 ++++++++++++++++++----------- R/iccdemat.R | 28 +++++++++++++++++----------- man/iccdeboot.Rd | 5 ++++- man/iccdemat.Rd | 7 ++++++- 6 files changed, 53 insertions(+), 32 deletions(-)
Title: VCG Sampling using Energy-Based Covariate Balancing
Description: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing. The package offers visualization tools to assess covariate balance and includes a permutation test to evaluate the statistical significance of observed deviations.
Author: Andreas Schulz [aut, cre] ,
Sanofi [cph, fnd]
Maintainer: Andreas Schulz <andreas.schulz2@sanofi.com>
Diff between eVCGsampler versions 1.1.2 dated 2026-07-22 and 1.2.0 dated 2026-10-15
eVCGsampler-1.1.2/eVCGsampler/inst/app/www/logo.png |only eVCGsampler-1.2.0/eVCGsampler/DESCRIPTION | 9 eVCGsampler-1.2.0/eVCGsampler/MD5 | 57 +- eVCGsampler-1.2.0/eVCGsampler/NEWS.md | 16 eVCGsampler-1.2.0/eVCGsampler/R/BestVCGsize.R | 28 - eVCGsampler-1.2.0/eVCGsampler/R/VCG_sampler.R | 22 eVCGsampler-1.2.0/eVCGsampler/R/launchApp.R | 49 + eVCGsampler-1.2.0/eVCGsampler/R/plot_var.R | 3 eVCGsampler-1.2.0/eVCGsampler/R/robust_scale.R | 5 eVCGsampler-1.2.0/eVCGsampler/inst/app/R |only eVCGsampler-1.2.0/eVCGsampler/inst/app/data |only eVCGsampler-1.2.0/eVCGsampler/inst/app/global.R |only eVCGsampler-1.2.0/eVCGsampler/inst/app/helpfiles |only eVCGsampler-1.2.0/eVCGsampler/inst/app/server.R | 264 ++-------- eVCGsampler-1.2.0/eVCGsampler/inst/app/ui.R | 196 +++++-- eVCGsampler-1.2.0/eVCGsampler/inst/app/www/css |only eVCGsampler-1.2.0/eVCGsampler/inst/app/www/img |only eVCGsampler-1.2.0/eVCGsampler/inst/app/www/js |only eVCGsampler-1.2.0/eVCGsampler/inst/app/www/rmd |only eVCGsampler-1.2.0/eVCGsampler/inst/app/www/sass |only eVCGsampler-1.2.0/eVCGsampler/man/launchApp.Rd | 16 eVCGsampler-1.2.0/eVCGsampler/tests/testthat/test-BestVCGsize.R | 15 eVCGsampler-1.2.0/eVCGsampler/tests/testthat/test-VCG_sampler.R | 29 + eVCGsampler-1.2.0/eVCGsampler/tests/testthat/test-plot_var.R | 8 eVCGsampler-1.2.0/eVCGsampler/tests/testthat/test-robust_scale.R | 10 25 files changed, 436 insertions(+), 291 deletions(-)
Title: Routines for Evaluating Forest Inventory Data
Description: Provides a collection of routines for evaluating data from
larger forest management units, typically sample inventories, but also
stand-wise inventories. The idea is to support modern forest planning
approaches and to be open by design to new data sources and evaluation
methods. For the methodological background of forest inventories see
Kangas and Maltamo (2006) "Forest Inventory: Methodology and Applications"
<doi:10.1007/1-4020-4381-3>.
Author: Peter Biber [aut, cre] ,
Astor Torano Caicoya [aut]
Maintainer: Peter Biber <peter.biber@lwf.bayern.de>
Diff between FeNEU versions 3.0.2 dated 2026-09-09 and 3.0.3 dated 2026-10-15
DESCRIPTION | 13 MD5 | 49 +-- NEWS.md | 80 ++++ R/convert_and_plausis.R | 14 R/import_functions_BaySF.R | 7 R/import_helpers_build.R | 10 R/import_sample_concentric_format1_raw_to_pre.R | 9 R/import_sample_concentric_format2_raw_to_pre.R | 4 R/inv_increment_fill_gaps_gnfi3.R | 26 + R/pdf_dependencies.R | 20 - R/plot_info_sheet_pdf.R | 226 +++++++++++++- README.md | 8 build/partial.rdb |binary inst/doc/data_formats.Rmd | 4 inst/doc/data_formats.html | 8 inst/rmd/plot_info_template_ger_fe_ccircle_spatial.Rmd | 188 +++++++++-- man/check_pdf_dependencies.Rd | 8 man/dot-plot_info_sheet_data.Rd |only man/dot-tree_id_order.Rd |only man/inv_inc_fill_gaps_gnfi3.Rd | 26 + man/pdf_dependencies.Rd | 3 man/plot_info_sheet_pdf.Rd | 57 +++ tests/testthat/helper-crs.R |only tests/testthat/test-fe_inventory.R | 15 tests/testthat/test-import_sample_concentric_raw_to_pre.R | 57 +++ tests/testthat/test-plot_info_sheet_pdf.R | 140 ++++++++ vignettes/data_formats.Rmd | 4 27 files changed, 840 insertions(+), 136 deletions(-)
Title: Power Analyses for SEM
Description: Provides a-priori, post-hoc, and compromise power-analyses
for structural equation models (SEM).
Author: Morten Moshagen [aut, cre] ,
Martina Bader [aut]
Maintainer: Morten Moshagen <morten.moshagen@uni-ulm.de>
Diff between semPower versions 2.1.3 dated 2025-08-22 and 2.2.0 dated 2026-10-15
DESCRIPTION | 8 MD5 | 76 ++-- NEWS | 26 + R/aPriori.R | 14 R/cf_arma.R | 32 + R/cf_autoreg.R | 56 ++- R/cf_bifactor.R | 17 - R/cf_cfa.R | 12 R/cf_clpm.R | 23 + R/cf_lav.R | 29 + R/cf_lgcm.R | 25 + R/cf_li.R | 496 +++++++++++++++++++++-------- R/cf_mediation.R | 5 R/cf_mi.R | 209 ++++++++---- R/cf_path.R | 14 R/cf_regression.R | 472 +++++++++++++++++++--------- R/cf_riclpm.R | 23 + R/compromise.R | 19 - R/effectSizes.R | 2 R/helperFunctions.R | 70 ++-- R/simulate.R | 83 +++- R/validator.R | 15 R/zUnitTests.R | 669 ++++++++++++++++++++++++++++------------ build/vignette.rds |binary man/doSim.Rd | 4 man/semPower.powerARMA.Rd | 5 man/semPower.powerAutoreg.Rd | 3 man/semPower.powerBifactor.Rd | 3 man/semPower.powerCFA.Rd | 3 man/semPower.powerCLPM.Rd | 3 man/semPower.powerLGCM.Rd | 5 man/semPower.powerLI.Rd | 230 ++++++++----- man/semPower.powerLav.Rd | 3 man/semPower.powerMI.Rd | 110 +++--- man/semPower.powerMediation.Rd | 3 man/semPower.powerPath.Rd | 3 man/semPower.powerRICLPM.Rd | 3 man/semPower.powerRegression.Rd | 310 ++++++++++++------ man/simulate.Rd | 3 39 files changed, 2115 insertions(+), 971 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for analyses of multiple social networks are provided with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' supports the
creation and analysis of multiplex, multimode, and multilevel network data in various formats.
It combines methods based on partially ordered semigroups, decomposition procedures, semiring
structures, and relational bundles for multivariate network analysis. It also provides an
algebraic approach to affiliation networks using Galois derivations, with visualization options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 4.0 dated 2026-07-30 and 4.2 dated 2026-10-15
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- R/mlvl.R | 52 +++++++++++++++++++++++-- R/reduc.R | 2 build/partial.rdb |binary inst/CHANGELOG | 77 ++++++++++++++++++++++++++++++++++++++ inst/doc/AffiliationNetworks.R | 6 +- inst/doc/AffiliationNetworks.Rnw | 21 ++++++---- inst/doc/AffiliationNetworks.pdf |binary man/multiplex-package.Rd | 4 - man/read.gml.Rd | 2 vignettes/AffiliationNetworks.Rnw | 21 ++++++---- 12 files changed, 173 insertions(+), 44 deletions(-)
Title: Client for the 'Toggl Track' API
Description: Read and write time entries, projects and clients of the
'Toggl Track' time tracker <https://toggl.com> from R, and download its
reports. Reads never return silently truncated or empty results: HTTP
errors are raised, the hourly quota and rate limits are respected, and
paginated reports are checked for completeness.
Author: Vincent Guyader [aut, cre],
ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between togglr versions 0.2.1 dated 2024-02-19 and 1.0.0 dated 2026-10-15
togglr-0.2.1/togglr/inst/dependencies.R |only togglr-0.2.1/togglr/man/correct_date.Rd |only togglr-0.2.1/togglr/man/get_detailled_report_paged.Rd |only togglr-1.0.0/togglr/DESCRIPTION | 28 togglr-1.0.0/togglr/MD5 | 172 ++- togglr-1.0.0/togglr/NAMESPACE | 114 +- togglr-1.0.0/togglr/NEWS.md | 231 +++++ togglr-1.0.0/togglr/R/Get_time_entries.R | 95 +- togglr-1.0.0/togglr/R/aaa_env.R |only togglr-1.0.0/togglr/R/client.R | 44 togglr-1.0.0/togglr/R/doc_package.R | 49 - togglr-1.0.0/togglr/R/get.R | 110 +- togglr-1.0.0/togglr/R/get_current_duration.R | 60 - togglr-1.0.0/togglr/R/get_dashboard.R | 488 +++++----- togglr-1.0.0/togglr/R/get_detailled_report.R | 588 ++++++++++--- togglr-1.0.0/togglr/R/get_project.R | 109 +- togglr-1.0.0/togglr/R/get_summary_report.R | 56 - togglr-1.0.0/togglr/R/get_weekly_report.R | 104 +- togglr-1.0.0/togglr/R/get_workspace.R | 68 - togglr-1.0.0/togglr/R/get_workspace_users.R | 8 togglr-1.0.0/togglr/R/globals.R | 9 togglr-1.0.0/togglr/R/http.R |only togglr-1.0.0/togglr/R/notification.R | 49 - togglr-1.0.0/togglr/R/open_toggl.R | 42 togglr-1.0.0/togglr/R/put.R | 95 +- togglr-1.0.0/togglr/R/put_project.R | 151 +-- togglr-1.0.0/togglr/R/put_update_time_entries.R | 41 togglr-1.0.0/togglr/R/reports_v3.R |only togglr-1.0.0/togglr/R/simplify.R | 21 togglr-1.0.0/togglr/R/tools.R | 116 ++ togglr-1.0.0/togglr/README.md | 195 ++-- togglr-1.0.0/togglr/build/vignette.rds |binary togglr-1.0.0/togglr/inst/doc/togglr.R | 49 - togglr-1.0.0/togglr/inst/doc/togglr.Rmd | 217 ++-- togglr-1.0.0/togglr/inst/doc/togglr.html | 15 togglr-1.0.0/togglr/inst/rstudio/addins.dcf | 20 togglr-1.0.0/togglr/man/ask_toggl_api_token.Rd | 31 togglr-1.0.0/togglr/man/clean_cache.Rd |only togglr-1.0.0/togglr/man/clean_memoise_cache.Rd |only togglr-1.0.0/togglr/man/client_id_to_name.Rd | 44 togglr-1.0.0/togglr/man/client_name_to_id.Rd | 44 togglr-1.0.0/togglr/man/create_client.Rd | 59 - togglr-1.0.0/togglr/man/delete_toggl_api_token.Rd | 25 togglr-1.0.0/togglr/man/get_all_client_info.Rd | 54 - togglr-1.0.0/togglr/man/get_all_client_names.Rd | 53 - togglr-1.0.0/togglr/man/get_all_project_names.Rd | 56 - togglr-1.0.0/togglr/man/get_client_project.Rd | 50 - togglr-1.0.0/togglr/man/get_context.Rd | 25 togglr-1.0.0/togglr/man/get_context_project.Rd | 25 togglr-1.0.0/togglr/man/get_current.Rd | 31 togglr-1.0.0/togglr/man/get_current_duration.Rd | 44 togglr-1.0.0/togglr/man/get_current_project_task_detail.Rd | 9 togglr-1.0.0/togglr/man/get_dashboard.Rd | 59 - togglr-1.0.0/togglr/man/get_detailled_report.Rd |only togglr-1.0.0/togglr/man/get_project_data.Rd |only togglr-1.0.0/togglr/man/get_project_id.Rd | 65 - togglr-1.0.0/togglr/man/get_project_id_and_name.Rd | 46 - togglr-1.0.0/togglr/man/get_project_total.Rd | 63 - togglr-1.0.0/togglr/man/get_summary_report.Rd | 73 - togglr-1.0.0/togglr/man/get_time_entries.Rd | 67 - togglr-1.0.0/togglr/man/get_toggl_api_token.Rd | 31 togglr-1.0.0/togglr/man/get_weekly_report.Rd | 69 - togglr-1.0.0/togglr/man/get_workspace_id.Rd | 35 togglr-1.0.0/togglr/man/get_workspace_users.Rd | 41 togglr-1.0.0/togglr/man/get_workspaces.Rd |only togglr-1.0.0/togglr/man/notification.Rd | 35 togglr-1.0.0/togglr/man/open_toggl_website_app.Rd | 25 togglr-1.0.0/togglr/man/open_toggl_website_profile.Rd | 25 togglr-1.0.0/togglr/man/set_toggl_api_token.Rd | 31 togglr-1.0.0/togglr/man/simplify.Rd | 36 togglr-1.0.0/togglr/man/to_humain.Rd | 31 togglr-1.0.0/togglr/man/toggl_create.Rd | 111 +- togglr-1.0.0/togglr/man/toggl_create_project.Rd | 82 - togglr-1.0.0/togglr/man/toggl_start.Rd | 83 - togglr-1.0.0/togglr/man/toggl_stop.Rd | 61 - togglr-1.0.0/togglr/man/toggl_update_entries.Rd | 11 togglr-1.0.0/togglr/man/togglr-package.Rd | 74 + togglr-1.0.0/togglr/man/update_toggl_api_token.Rd | 25 togglr-1.0.0/togglr/tests |only togglr-1.0.0/togglr/vignettes/togglr.Rmd | 217 ++-- 80 files changed, 3149 insertions(+), 2141 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb],
Miles McBain [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.12.0 dated 2026-07-23 and 0.13.0 dated 2026-10-15
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++--------------- NAMESPACE | 38 ++++++++++++++++++++---------------- NEWS.md | 9 ++++++++ R/get_credit.R | 1 R/get_tiles.R | 5 ++-- R/plot_tiles.R | 1 R/providers.R | 18 ++++++++--------- R/utils.R | 5 +++- README.md | 40 ++++++++++++++++++++++++-------------- inst/tinytest/test_maptiles.R | 13 +++++------- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/figures/README-front.png |binary man/get_credit.Rd | 3 ++ man/get_tiles.Rd | 5 ++-- man/plot_tiles.Rd | 3 ++ 17 files changed, 110 insertions(+), 71 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>.
Author: Lukas A. Widmer [aut, cre] ,
Craig Gower-Page [aut],
Isaac Gravestock [aut] ,
Alessandro Noci [aut],
Marcel Wolbers [aut] ,
Daniel Sabanes Bove [aut] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Lukas A. Widmer <lukas_andreas.widmer@novartis.com>
Diff between rbmi versions 1.6.1 dated 2026-07-22 and 1.7.0 dated 2026-10-15
DESCRIPTION | 9 MD5 | 68 +- NAMESPACE | 67 +- NEWS.md | 28 R/analyse.R | 25 R/ancova.R | 651 ++++++++++++++++++++-- R/pool.R | 206 ++++++ R/utilities.R | 133 ++++ inst/WORDLIST | 121 +--- inst/doc/advanced.html | 4 inst/doc/quickstart.html | 478 ++++++++-------- inst/doc/stat_specs.html | 14 man/analyse.Rd | 5 man/ancova.Rd | 98 ++- man/ancova_contrast_design.Rd |only man/ancova_contrast_name.Rd |only man/ancova_core.Rd |only man/ancova_group_labels.Rd |only man/ancova_linear_contrast.Rd |only man/ancova_resolve_contrasts.Rd |only man/ancova_single.Rd | 20 man/as_analysis.Rd | 13 man/formula_has_interaction.Rd |only man/frm_find_and_replace.Rd |only man/pool.Rd | 25 man/pool_internal.Rd | 18 man/resolve_contrast_weights.Rd |only man/rubin_df.Rd | 6 man/rubin_orig_df.Rd |only man/rubin_rules.Rd | 15 man/set_vars.Rd | 29 tests/testthat/helper-misc.R | 5 tests/testthat/test-ancova.R | 1179 ++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-pool.R | 110 +++ tests/testthat/test-utilities.R | 96 +++ vignettes/FAQ.Rmd | 62 ++ vignettes/FAQ.html | 48 + vignettes/quickstart.Rmd | 46 + vignettes/references.bib | 8 vignettes/stat_specs.Rmd | 13 40 files changed, 3138 insertions(+), 462 deletions(-)
Title: Vegetation Analysis and Forest Inventory
Description: Provides functions and example datasets for phytosociological
analysis, forest inventory, biomass and carbon estimation, and visualization
of vegetation data. Includes functions to compute structural parameters
[phytoparam(), summary.param(), stats()], estimate above-ground biomass
and carbon [AGB()], stratify wood volume by diameter at breast height (DBH)
classes [stratvol()], generate collector and rarefaction curves [collector.curve(),
rarefaction()], and visualize basal areas on quadrat maps [BAplot(), including
rectangular plots and individual coordinates]. Several example datasets are provided
to demonstrate the functionality of these tools. For more details see FAO
(1981, ISBN:92-5-101132-X) "Manual of forest inventory", IBGE (2012, ISBN:9788524042720)
"Manual técnico da vegetação brasileira" and Heringer et al. (2020) "Phytosociology in
R: A routine to estimate phytosociological parameters" <doi:10.22533/at.ed.3552009033>.
Author: Rodrigo Augusto Santinelo Pereira [aut, cre]
Maintainer: Rodrigo Augusto Santinelo Pereira <raspereira@usp.br>
This is a re-admission after prior archival of version 0.2.0 dated 2025-10-01
Diff between PhytoIn versions 0.2.0 dated 2025-10-01 and 0.2.1 dated 2026-10-15
DESCRIPTION | 10 MD5 | 38 - NAMESPACE | 2 NEWS.md | 78 ++- R/AGB.R | 531 ++++++++++++------------ R/BAplot.R | 400 +++++++++--------- R/PhytoIn-package.R | 40 - R/collector.curve.R | 472 ++++++++++----------- R/data.R | 248 +++++------ R/phytoparam.R | 1128 ++++++++++++++++++++++++++-------------------------- R/rarefaction.R | 458 ++++++++++----------- R/stats.R | 402 +++++++++--------- R/stratvol.R | 228 +++++----- R/zzz.R | 12 README.md | 364 ++++++++-------- inst/WORDLIST | 286 ++++++------- man/AGB.Rd | 24 - man/BAplot.Rd | 3 man/phytoparam.Rd | 336 +++++++-------- tests/spelling.R | 6 20 files changed, 2582 insertions(+), 2484 deletions(-)
Title: Single-Index Neural Network for Skewed Heavy-Tailed Data
Description: Provides a deep neural network model with a monotonic increasing single index function tailored for periodontal disease studies. The residuals are assumed to follow a skewed T distribution, a skewed normal distribution, or a normal distribution. More details can be found at Liu, Wang, Bai and Bandyopadhyay (2026) <doi:10.1093/biostatistics/kxag040>.
Author: Qingyang Liu [aut, cre] ,
Shijie Wang [aut],
Ray Bai [aut] ,
Dipankar Bandyopadhyay [aut]
Maintainer: Qingyang Liu <rh8liuqy@gmail.com>
Diff between DNNSIM versions 0.1.1 dated 2025-01-07 and 0.2.1 dated 2026-10-15
DESCRIPTION | 15 +- MD5 | 27 ++- NEWS.md | 6 R/DNNSIM-package.R | 22 +-- R/DNN_model.R | 74 +++++++++- R/data_simulation.R | 4 build/partial.rdb |binary inst/DNN_Model/DNN_Model.py | 307 ++++++++++++++++++++++++++++++++------------ inst/DNN_Model/__pycache__ |only inst/REFERENCES.bib | 26 +++ man/DNNSIM.Rd | 3 man/DNN_model.Rd | 25 +++ man/data_simulation.Rd | 4 13 files changed, 389 insertions(+), 124 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use
set of functions. With its progressive approach, we can construct
display tables with a cohesive set of table parts. Table values can be
formatted using any of the included formatting functions. Footnotes
and cell styles can be precisely added through a location targeting
system. The way in which 'gt' handles things for you means that you
don't often have to worry about the fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Shannon Haughton [aut],
Ellis Hughes [aut] ,
Alexandra Lauer [aut] ,
Romain Francois [aut],
JooYoung Seo [aut] ,
Ken Brevoort [aut] ,
Olivier Roy [aut],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Richard Iannone <rich@posit.co>
Diff between gt versions 1.3.0 dated 2026-01-22 and 1.4.0 dated 2026-10-15
gt-1.3.0/gt/tests/testthat/test-as_rtf.R |only gt-1.3.0/gt/tests/testthat/test-cols_nanoplot.R |only gt-1.3.0/gt/tests/testthat/test-multicolumn_stub_latex.R |only gt-1.3.0/gt/tests/testthat/test-multicolumn_stub_na_handling.R |only gt-1.3.0/gt/tests/testthat/test-rtf_table_parts.R |only gt-1.3.0/gt/tests/testthat/test-stub_helper_multicolumn.R |only gt-1.4.0/gt/DESCRIPTION | 23 gt-1.4.0/gt/MD5 | 156 +-- gt-1.4.0/gt/NAMESPACE | 9 gt-1.4.0/gt/NEWS.md | 62 + gt-1.4.0/gt/R/build_data.R | 5 gt-1.4.0/gt/R/dt_groups_rows.R | 7 gt-1.4.0/gt/R/dt_options.R | 1 gt-1.4.0/gt/R/dt_rows_hidden.R |only gt-1.4.0/gt/R/dt_stub_df.R | 29 gt-1.4.0/gt/R/dt_styles.R | 37 gt-1.4.0/gt/R/dt_transforms.R | 4 gt-1.4.0/gt/R/fmt.R | 24 gt-1.4.0/gt/R/fmt_date_time.R | 2 gt-1.4.0/gt/R/fmt_number.R | 26 gt-1.4.0/gt/R/format_data.R | 120 ++ gt-1.4.0/gt/R/format_vec.R | 18 gt-1.4.0/gt/R/gt-package.R | 5 gt-1.4.0/gt/R/gt.R | 2 gt-1.4.0/gt/R/gt_group.R | 39 gt-1.4.0/gt/R/gt_split.R | 4 gt-1.4.0/gt/R/gtsave.R | 141 ++ gt-1.4.0/gt/R/info_tables.R | 7 gt-1.4.0/gt/R/modify_rows.R | 2 gt-1.4.0/gt/R/ooxml2.R |only gt-1.4.0/gt/R/reexports.R | 2 gt-1.4.0/gt/R/resolver.R | 30 gt-1.4.0/gt/R/rows_hide.R |only gt-1.4.0/gt/R/substitution.R | 40 gt-1.4.0/gt/R/tab_options.R | 8 gt-1.4.0/gt/R/tab_style.R | 11 gt-1.4.0/gt/R/text_transform.R | 57 - gt-1.4.0/gt/R/utils.R | 71 + gt-1.4.0/gt/R/utils_examples.R | 2 gt-1.4.0/gt/R/utils_general_str_formatting.R | 8 gt-1.4.0/gt/R/utils_render_common.R | 62 - gt-1.4.0/gt/R/utils_render_grid.R | 63 - gt-1.4.0/gt/R/utils_render_html.R | 198 +++ gt-1.4.0/gt/R/utils_render_latex.R | 52 - gt-1.4.0/gt/R/utils_render_ooxml.R |only gt-1.4.0/gt/R/utils_render_rtf.R | 90 - gt-1.4.0/gt/R/utils_render_xml.R | 59 - gt-1.4.0/gt/R/z_utils_render_footnotes.R | 44 gt-1.4.0/gt/man/fmt_bytes.Rd | 10 gt-1.4.0/gt/man/fmt_currency.Rd | 10 gt-1.4.0/gt/man/fmt_datetime.Rd | 2 gt-1.4.0/gt/man/fmt_engineering.Rd | 10 gt-1.4.0/gt/man/fmt_number.Rd | 22 gt-1.4.0/gt/man/fmt_number_si.Rd | 11 gt-1.4.0/gt/man/fmt_partsper.Rd | 10 gt-1.4.0/gt/man/fmt_percent.Rd | 10 gt-1.4.0/gt/man/fmt_scientific.Rd | 10 gt-1.4.0/gt/man/grand_summary_rows.Rd | 2 gt-1.4.0/gt/man/gt_group.Rd | 8 gt-1.4.0/gt/man/info_tf_style.Rd | 2 gt-1.4.0/gt/man/row_group_order.Rd | 2 gt-1.4.0/gt/man/row_order.Rd | 4 gt-1.4.0/gt/man/rows_add.Rd | 2 gt-1.4.0/gt/man/rows_hide.Rd |only gt-1.4.0/gt/man/rows_unhide.Rd |only gt-1.4.0/gt/man/summary_columns.Rd | 2 gt-1.4.0/gt/man/summary_rows.Rd | 2 gt-1.4.0/gt/man/tab_options.Rd | 8 gt-1.4.0/gt/man/vec_fmt_bytes.Rd | 9 gt-1.4.0/gt/man/vec_fmt_currency.Rd | 9 gt-1.4.0/gt/man/vec_fmt_datetime.Rd | 2 gt-1.4.0/gt/man/vec_fmt_engineering.Rd | 9 gt-1.4.0/gt/man/vec_fmt_number.Rd | 9 gt-1.4.0/gt/man/vec_fmt_number_si.Rd | 9 gt-1.4.0/gt/man/vec_fmt_partsper.Rd | 9 gt-1.4.0/gt/man/vec_fmt_percent.Rd | 9 gt-1.4.0/gt/man/vec_fmt_scientific.Rd | 9 gt-1.4.0/gt/tests/testthat/Rplots.pdf |binary gt-1.4.0/gt/tests/testthat/_snaps/rows_hide.md |only gt-1.4.0/gt/tests/testthat/helper-gt_object.R | 12 gt-1.4.0/gt/tests/testthat/helper-ooxml.R |only gt-1.4.0/gt/tests/testthat/helper.R | 28 gt-1.4.0/gt/tests/testthat/test-fmt.R | 520 ++++++++++ gt-1.4.0/gt/tests/testthat/test-format_data_internals.R |only gt-1.4.0/gt/tests/testthat/test-l_cell_text_alignment.R | 34 gt-1.4.0/gt/tests/testthat/test-l_cols_width.R | 36 gt-1.4.0/gt/tests/testthat/test-rows_hide.R |only 87 files changed, 1985 insertions(+), 366 deletions(-)
Title: Evolutionary Computation in R
Description: Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.
Author: Jakob Bossek [aut, cre, cph],
Michael H. Buselli [ctb, cph],
Wessel Dankers [ctb, cph],
Carlos M. Fonseca [ctb, cph],
Manuel Lopez-Ibanez [ctb, cph],
Luis Paquete [ctb, cph],
Joshua Knowles [ctb, cph],
Eckart Zitzler [ctb, cph],
Olaf Mersmann [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between ecr versions 2.1.1 dated 2023-03-08 and 2.1.1.1 dated 2026-10-15
DESCRIPTION | 7 MD5 | 18 +- R/transformFitness.R | 2 build/vignette.rds |binary data/mcMST.rda |binary inst/doc/introduction.R | 4 inst/doc/introduction.html | 309 ++++++++++++++++++++---------------- inst/doc/multiobjective.R | 10 - inst/doc/multiobjective.html | 364 +++++++++++++++++++++++++------------------ man/transformFitness.Rd | 2 10 files changed, 413 insertions(+), 303 deletions(-)
Title: Conformal Prediction Methods for Multistep-Ahead Time Series
Forecasting
Description: Methods and tools for performing multistep-ahead time series
forecasting using conformal prediction methods including classical
conformal prediction, adaptive conformal prediction, conformal PID
(Proportional-Integral-Derivative) control, and autocorrelated
multistep-ahead conformal prediction.
The methods were described by Wang and Hyndman (2024) <doi:10.48550/arXiv.2410.13115>.
Author: Xiaoqian Wang [aut, cre, cph] ,
Rob Hyndman [aut] ,
Daniele Girolimetto [aut]
Maintainer: Xiaoqian Wang <Xiaoqian.Wang@amss.ac.cn>
Diff between conformalForecast versions 0.1.1 dated 2026-01-15 and 0.2.0 dated 2026-10-15
conformalForecast-0.1.1/conformalForecast/R/utils.R |only conformalForecast-0.2.0/conformalForecast/DESCRIPTION | 19 conformalForecast-0.2.0/conformalForecast/MD5 | 90 - conformalForecast-0.2.0/conformalForecast/NAMESPACE | 12 conformalForecast-0.2.0/conformalForecast/NEWS.md | 55 conformalForecast-0.2.0/conformalForecast/R/acmcp.R | 665 ++++++-- conformalForecast-0.2.0/conformalForecast/R/acp.R | 380 ++--- conformalForecast-0.2.0/conformalForecast/R/conformal.R | 52 conformalForecast-0.2.0/conformalForecast/R/conformalForecast-package.R | 3 conformalForecast-0.2.0/conformalForecast/R/coverage.R | 109 + conformalForecast-0.2.0/conformalForecast/R/cvforecast.R | 347 ++-- conformalForecast-0.2.0/conformalForecast/R/errors.R | 305 ++-- conformalForecast-0.2.0/conformalForecast/R/lagmatrix.R | 40 conformalForecast-0.2.0/conformalForecast/R/pid.R | 712 ++++++--- conformalForecast-0.2.0/conformalForecast/R/scp.R | 380 +++-- conformalForecast-0.2.0/conformalForecast/R/update.R | 226 +-- conformalForecast-0.2.0/conformalForecast/R/width.R | 140 + conformalForecast-0.2.0/conformalForecast/README.md | 94 + conformalForecast-0.2.0/conformalForecast/build/vignette.rds |binary conformalForecast-0.2.0/conformalForecast/inst/doc/conformalForecast.R | 82 - conformalForecast-0.2.0/conformalForecast/inst/doc/conformalForecast.Rmd | 189 ++ conformalForecast-0.2.0/conformalForecast/inst/doc/conformalForecast.html | 748 +++++++--- conformalForecast-0.2.0/conformalForecast/inst/doc/update.R |only conformalForecast-0.2.0/conformalForecast/inst/doc/update.Rmd |only conformalForecast-0.2.0/conformalForecast/inst/doc/update.html |only conformalForecast-0.2.0/conformalForecast/man/accuracy.cvforecast.Rd | 53 conformalForecast-0.2.0/conformalForecast/man/acmcp.Rd | 186 +- conformalForecast-0.2.0/conformalForecast/man/acp.Rd | 140 + conformalForecast-0.2.0/conformalForecast/man/conformal.Rd | 45 conformalForecast-0.2.0/conformalForecast/man/conformalForecast-package.Rd | 1 conformalForecast-0.2.0/conformalForecast/man/coverage.Rd | 58 conformalForecast-0.2.0/conformalForecast/man/cvforecast.Rd | 110 - conformalForecast-0.2.0/conformalForecast/man/figures |only conformalForecast-0.2.0/conformalForecast/man/interval_measures.Rd | 36 conformalForecast-0.2.0/conformalForecast/man/lagmatrix.Rd | 17 conformalForecast-0.2.0/conformalForecast/man/pid.Rd | 193 +- conformalForecast-0.2.0/conformalForecast/man/point_measures.Rd | 36 conformalForecast-0.2.0/conformalForecast/man/scp.Rd | 174 +- conformalForecast-0.2.0/conformalForecast/man/update.cpforecast.Rd | 50 conformalForecast-0.2.0/conformalForecast/man/width.Rd | 68 conformalForecast-0.2.0/conformalForecast/tests |only conformalForecast-0.2.0/conformalForecast/vignettes/conformalForecast.Rmd | 189 ++ conformalForecast-0.2.0/conformalForecast/vignettes/update.Rmd |only 43 files changed, 4112 insertions(+), 1892 deletions(-)
More information about conformalForecast at CRAN
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Title: Approximate and Exact Optimal Transport Methods
Description: R and C++ functions to perform exact and
approximate optimal transport. All C++ methods can be linked
to other R packages via their header files.
Author: Eric Dunipace [aut, cre] ,
Andrew Johnson [ctb] ,
Espen Bernton [ctb] ,
Mathieu Gerber [ctb] ,
Pierre Jacob [ctb] ,
Dominic Schuhmacher [ctb] ,
Nicolas Bonneel [ctb]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between approxOT versions 1.2 dated 2025-01-09 and 1.3 dated 2026-10-15
DESCRIPTION | 15 MD5 | 63 +- NAMESPACE | 7 NEWS.md | 28 + R/RcppExports.R | 8 R/sinkhorn.R | 121 ++-- R/threads.R |only R/transport_plan.R | 706 ++++++++++++++++----------- R/wasserstein_distance.R | 478 +++++++++++------- R/zzz.R |only README.md | 23 inst/WORDLIST |only inst/include/approxOT/round_feasible.h | 8 inst/include/approxOT/shortsimplex.h | 13 inst/include/approxOT/threads.h |only inst/include/approxOT/trans_approxOT.h | 18 inst/include/approxOT/trans_greenkhorn.h | 66 -- inst/include/approxOT/trans_sinkhorn.h | 171 ++++-- inst/include/approxOT/transport.h | 12 man/approxOT_threads.Rd |only man/as.matrix.transport.plan.Rd | 6 man/as.transport.plan.Rd | 6 man/is.transport.plan.Rd | 6 man/sinkhorn_pot.Rd | 2 man/transport_plan.Rd | 8 man/transport_plan_given_C.Rd | 6 man/wasserstein.Rd | 14 src/Makevars | 10 src/Makevars.win | 9 src/RcppExports.cpp | 23 src/threads.cpp |only src/trans_sinkhorn.cpp | 79 ++- tests/testthat/setup.R |only tests/testthat/test-sinkhorn_pot_.R | 390 +++++++++++---- tests/testthat/test-transport_plan.R | 162 +++--- tests/testthat/test-wasserstein.R | 805 ++++++++++++++++++++++--------- 36 files changed, 2166 insertions(+), 1097 deletions(-)
Title: Fast Survival Analysis and Simulation for Clinical Trials
Description: Provides fast alternatives to standard survival analysis functions
in the 'survival' package, together with tools for time-to-event trial
simulation and sequential analysis. The estimation and testing functions
cover a single-time-point Kaplan-Meier estimator (survfit_fast()), log-rank
tests including weighted and stratified variants (survdiff_fast()), a
closed-form hazard ratio estimator based on the Pike-Halley Estimator method
(coxph_fast()), restricted mean survival time (rmst_fast()), window mean
survival time (wmst_fast()), milestone survival comparison
(milestone_fast()), median survival time (medsurv_fast()), the max-combo
test (maxcombo_fast()), the robust modestly-weighted log-rank test
(rmw_fast()), the weighted Kaplan-Meier (Pepe-Fleming) test (wkm_fast()),
the average hazard with survival weight (ahsw_fast()), and the
Kalbfleisch-Prentice average hazard ratio (ahr_fast()). Besides vectors,
these functions accept a model formula with a data frame, and their
results can be r [...truncated...]
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between FastSurvival versions 1.1.0 dated 2026-10-08 and 1.2.0 dated 2026-10-14
DESCRIPTION | 18 - MD5 | 308 ++++++++++++----------- NAMESPACE | 7 NEWS.md | 259 +++++++++++++++++++ R/FastSurvival-package.R | 18 - R/RcppExports.R | 20 - R/ahr_fast.R | 41 ++- R/ahsw_fast.R | 36 ++ R/analysis_fast.R | 163 +++++++++--- R/as.data.frame.fastsurv.R |only R/as.data.frame.kmcurve_fast.R |only R/check_output_size.R | 3 R/check_time_event.R | 10 R/coef.fastsurv.R |only R/confint.fastsurv.R |only R/coxph_fast.R | 56 +++- R/cutoff_fast.R | 13 R/fastsurv_formula.R |only R/fastsurv_table.R |only R/formula_interface.R |only R/gen_scenario_fast.R | 18 + R/km_band_step.R |only R/km_risk_counts.R |only R/km_step_median.R | 6 R/kmcurve_fast.R | 42 ++- R/maxcombo_fast.R | 75 ++++- R/medsurv_fast.R | 47 +++ R/milestone_fast.R | 53 +++ R/plot.kmcurve_fast.R | 109 +++++++- R/plot.simsummary_fast.R |only R/print.ahr_fast.R | 7 R/print.ahsw_fast.R | 2 R/print.coxph_fast.R | 10 R/print.medsurv_fast.R | 5 R/print.milestone_fast.R | 18 + R/print.rmst_fast.R | 8 R/print.simsummary_fast.R | 77 +++++ R/print.wkm_fast.R | 5 R/print.wmst_fast.R | 5 R/rmst_fast.R | 35 ++ R/rmw_fast.R | 38 ++ R/simdata_fast.R | 130 +++++++-- R/simdata_fast_id_sub.R | 23 + R/simsummary_blocks.R |only R/simsummary_fast.R | 17 - R/spec_arg_label.R |only R/step_vertices.R |only R/survdiff_fast.R | 57 +++- R/survfit_fast.R | 29 ++ R/switch_fast.R | 12 R/wkm_fast.R | 55 +++- R/wmst_fast.R | 51 +++ README.md | 64 +++- inst/WORDLIST | 1 inst/doc/FastSurvival.R | 12 inst/doc/FastSurvival.Rmd | 32 ++ inst/doc/FastSurvival.html | 47 ++- inst/doc/compare-logrank-rmst.Rmd | 5 inst/doc/compare-logrank-rmst.html | 9 inst/doc/correlated-pfs-os-gsd.Rmd | 10 inst/doc/correlated-pfs-os-gsd.html | 66 ++-- inst/doc/external-data.Rmd | 4 inst/doc/external-data.html | 6 inst/doc/group-sequential-design.R | 3 inst/doc/group-sequential-design.Rmd | 25 + inst/doc/group-sequential-design.html | 191 +++++++------- inst/doc/investigate-freidlin-and-korn.Rmd | 24 - inst/doc/investigate-freidlin-and-korn.html | 29 +- inst/doc/mrct-regional-consistency.Rmd | 2 inst/doc/mrct-regional-consistency.html | 65 ++-- inst/doc/speed-comparison.Rmd | 18 - inst/doc/speed-comparison.html | 27 +- inst/doc/treatment-switching.Rmd | 4 inst/doc/treatment-switching.html | 6 inst/doc/validation.Rmd | 7 inst/doc/validation.html | 10 man/FastSurvival-package.Rd | 18 - man/ahr_fast.Rd | 22 + man/ahsw_fast.Rd | 26 + man/analysis_fast.Rd | 110 +++++--- man/as.data.frame.fastsurv.Rd |only man/as.data.frame.kmcurve_fast.Rd |only man/coxph_fast.Rd | 44 ++- man/cutoff_fast.Rd | 6 man/formula_interface.Rd |only man/gen_scenario_fast.Rd | 6 man/kmcurve_fast.Rd | 32 +- man/maxcombo_fast.Rd | 62 +++- man/medsurv_fast.Rd | 33 ++ man/milestone_fast.Rd | 38 ++ man/plot.kmcurve_fast.Rd | 33 ++ man/plot.simsummary_fast.Rd |only man/print.ahr_fast.Rd | 4 man/print.ahsw_fast.Rd | 2 man/print.coxph_fast.Rd | 7 man/print.medsurv_fast.Rd | 3 man/print.milestone_fast.Rd | 6 man/print.rmst_fast.Rd | 6 man/print.simsummary_fast.Rd | 22 + man/print.wkm_fast.Rd | 3 man/print.wmst_fast.Rd | 3 man/rmst_fast.Rd | 23 + man/rmw_core.Rd | 4 man/rmw_fast.Rd | 28 +- man/simdata_fast.Rd | 37 ++ man/simsummary_fast.Rd | 6 man/stratified_weighted_logrank_core.Rd | 13 man/survdiff_fast.Rd | 35 ++ man/survfit_fast.Rd | 21 + man/switch_fast.Rd | 10 man/weighted_logrank_core.Rd | 3 man/wkm_fast.Rd | 42 ++- man/wmst_fast.Rd | 31 +- src/ahr_core.cpp | 7 src/medsurv_core.cpp | 18 + src/rmw_core.cpp | 4 src/simdata_core_full.cpp | 8 src/simdata_core_id.cpp | 8 src/stratified_weighted_logrank_core.cpp | 21 - src/weighted_logrank_core.cpp | 10 src/wkm_core.cpp | 14 - tests/testthat/test-ahr_fast.R | 43 ++- tests/testthat/test-ahsw_fast.R | 26 + tests/testthat/test-analysis_fast.R | 192 ++++++++++++++ tests/testthat/test-as.data.frame.fastsurv.R |only tests/testthat/test-as.data.frame.kmcurve_fast.R |only tests/testthat/test-coef.fastsurv.R |only tests/testthat/test-confint.fastsurv.R |only tests/testthat/test-coxph_fast.R | 40 ++ tests/testthat/test-cutoff_fast.R | 12 tests/testthat/test-fastsurv_formula.R |only tests/testthat/test-gen_scenario_fast.R | 24 + tests/testthat/test-km_risk_counts.R |only tests/testthat/test-kmcurve_fast.R | 42 +++ tests/testthat/test-maxcombo_fast.R | 132 +++++++++ tests/testthat/test-medsurv_fast.R | 100 ++++++- tests/testthat/test-milestone_fast.R | 78 +++++ tests/testthat/test-plot.kmcurve_fast.R |only tests/testthat/test-plot.simsummary_fast.R |only tests/testthat/test-print.ahr_fast.R | 10 tests/testthat/test-print.coxph_fast.R |only tests/testthat/test-print.medsurv_fast.R | 10 tests/testthat/test-print.milestone_fast.R |only tests/testthat/test-print.rmst_fast.R | 10 tests/testthat/test-print.simsummary_fast.R |only tests/testthat/test-print.wkm_fast.R | 10 tests/testthat/test-print.wmst_fast.R | 11 tests/testthat/test-rmst_fast.R | 31 ++ tests/testthat/test-rmw_fast.R | 78 ++++- tests/testthat/test-simdata_fast.R | 73 +++++ tests/testthat/test-simdata_fast_id.R | 93 ++++++ tests/testthat/test-simdata_fast_karm.R | 17 + tests/testthat/test-simsummary_blocks.R |only tests/testthat/test-simsummary_fast.R | 15 - tests/testthat/test-step_vertices.R |only tests/testthat/test-survdiff_fast.R | 86 ++++++ tests/testthat/test-survfit_fast.R | 33 ++ tests/testthat/test-switch_fast.R | 13 tests/testthat/test-wkm_fast.R | 59 ++++ tests/testthat/test-wmst_fast.R | 61 ++++ vignettes/FastSurvival.Rmd | 32 ++ vignettes/compare-logrank-rmst.Rmd | 5 vignettes/correlated-pfs-os-gsd.Rmd | 10 vignettes/external-data.Rmd | 4 vignettes/group-sequential-design.Rmd | 25 + vignettes/investigate-freidlin-and-korn.Rmd | 24 - vignettes/mrct-regional-consistency.Rmd | 2 vignettes/speed-comparison.Rmd | 18 - vignettes/treatment-switching.Rmd | 4 vignettes/validation.Rmd | 7 170 files changed, 3854 insertions(+), 958 deletions(-)
Title: Age-Specific Bayesian Survival Trajectory Analysis from
Incomplete Census or Capture-Recapture/Recovery Data
Description: Estimates survival and mortality with covariates and random effects from census or capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots, as described in Colchero, Jones, and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and Colchero et al. (2021) <doi:10.1038/s41467-021-23894-3>.
Author: Fernando Colchero [aut, cre],
Owen Jones [ctb]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Diff between BaSTA versions 2.0.2 dated 2025-06-13 and 2.0.3 dated 2026-10-14
DESCRIPTION | 16 MD5 | 24 - NAMESPACE | 5 R/basta.R | 1049 ++++++++++++++++++++++++++++++++------------- data/bastaCMRdat.RData |binary data/bastaCMRout.RData |binary data/bastaCensDat.RData |binary data/bastaCensOut.RData |binary inst/doc/BaSTAoverview.pdf |binary man/BaSTA-package.Rd | 6 man/basta.Rd | 28 - man/multibasta.Rd | 10 man/summary.multibasta.Rd | 4 13 files changed, 806 insertions(+), 336 deletions(-)
Title: Optimal Stratification of Univariate Populations
Description: Determines Optimum Strata Boundaries (OSB) and Optimum Sample
Sizes (OSS) for univariate stratified sampling designs under Neyman
allocation. The stratification variable is described by a best-fitting
parametric distribution, selected automatically by AIC from a set of
continuous families (normal, log-normal, gamma, Weibull, exponential,
Cauchy, uniform, Pareto, triangular and right-triangular), and the
optimum boundaries are obtained by minimising the Neyman objective.
Version 2.0 keeps the Dynamic Programming (DP) solver of Reddy and Khan
(2020), which is globally optimal for the fitted distribution, as the
default. It adds two fast derivative-free solvers, a multi-start
'COBYLA' solver and a two-phase global solver that couples 'DIRECT-L'
with 'BOBYQA' refinement, and an exact solver that runs dynamic
programming on the sorted data and returns the partition with the
smallest empirical Neyman cost. It also provides cost-constrained
allocation with unequal per-stratum costs, a desi [...truncated...]
Author: Karuna G. Reddy [aut, cre] ,
M. G. M. Khan [aut]
Maintainer: Karuna G. Reddy <karuna.reddy@auckland.ac.nz>
Diff between stratifyR versions 2.0-1 dated 2026-09-10 and 2.0-2 dated 2026-10-14
DESCRIPTION | 28 MD5 | 44 NEWS.md | 116 ++ R/app.R | 6 R/cobyla.optim.R | 113 +- R/data.alloc.R | 13 R/distr.alloc.R | 4 R/exact.optim.R |only R/fit_distribution.R | 5 R/get.dist.R | 8 R/realloc.R | 29 R/strata.data.R | 40 R/strata.distr.R | 4 R/summary.strata.R | 2 inst/app/app.R | 101 -- inst/app/www |only inst/doc/stratifyR-vignette.R | 178 ++- inst/doc/stratifyR-vignette.Rmd | 366 ++++--- inst/doc/stratifyR-vignette.html | 1956 +++++++++++++++------------------------ man/figures/logo.png |only man/strata.data.Rd | 29 man/stratifyRApp.Rd | 4 tests |only vignettes/stratifyR-vignette.Rmd | 366 ++++--- 24 files changed, 1714 insertions(+), 1698 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.5-1 dated 2023-10-24 and 1.6-0 dated 2026-10-14
DESCRIPTION | 9 ++++----- MD5 | 9 ++++++--- NAMESPACE | 4 +++- R/count_tests.R |only inst/NEWS.Rd | 9 +++++++++ man/count_tests.Rd |only tests/count_tests-tests.R |only 7 files changed, 22 insertions(+), 9 deletions(-)
Title: Datasets and Utilities for Essentials of Statistics for the
Behavioral Sciences
Description: Provides instructional datasets and simple wrapper functions
for selected analyses used in 'Essentials of Statistics for the
Behavioral Sciences' (Gravetter et al., 2026).
The package is intended to support textbook examples by distributing
data in a form that is easy for students and instructors to access
within R. Current functionality includes packaged datasets and
convenience wrappers for functions from 'ez', 'pwr', and 'WebPower'
for analysis of variance and statistical power calculations.
Author: James Witnauer [aut, cre]
Maintainer: James Witnauer <jwitnaue@brockport.edu>
Diff between essentialstools versions 0.1.7 dated 2026-06-04 and 0.1.8 dated 2026-10-14
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++++++++++- NEWS.md |only R/data-exercise-hummingbird.R |only R/data-imported-2026.R |only data/balance_duration.rda |only data/blick.rda |only data/exercise.rda |only data/hummingbird.rda |only data/illusion.rda |only data/intuition.rda |only data/rapport.rda |only man/balance_duration.Rd |only man/blick.Rd |only man/exercise.Rd |only man/hummingbird.Rd |only man/illusion.Rd |only man/intuition.Rd |only man/rapport.Rd |only 19 files changed, 21 insertions(+), 4 deletions(-)
More information about essentialstools at CRAN
Permanent link
Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre]
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetDictionaries versions 0.2.1 dated 2025-05-08 and 0.3.0 dated 2026-10-14
SemNetDictionaries-0.2.1/SemNetDictionaries/R/ShinyWoRdle.R |only SemNetDictionaries-0.2.1/SemNetDictionaries/R/hot.moinker.R |only SemNetDictionaries-0.2.1/SemNetDictionaries/inst/ShinyWoRdle |only SemNetDictionaries-0.2.1/SemNetDictionaries/man/ShinyWoRdle.Rd |only SemNetDictionaries-0.3.0/SemNetDictionaries/DESCRIPTION | 16 SemNetDictionaries-0.3.0/SemNetDictionaries/MD5 | 176 ++-- SemNetDictionaries-0.3.0/SemNetDictionaries/NAMESPACE | 9 SemNetDictionaries-0.3.0/SemNetDictionaries/NEWS | 281 ++++-- SemNetDictionaries-0.3.0/SemNetDictionaries/R/SemNetDictionaries.R | 29 SemNetDictionaries-0.3.0/SemNetDictionaries/R/animals.dictionary.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/animals.moniker.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/append.dictionary.R | 326 ++++--- SemNetDictionaries-0.3.0/SemNetDictionaries/R/brit2us.R | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/R/coca.dictionary.R | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/R/coca.moniker.R | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/R/cocaspell.dictionary.R | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/R/cocaspell.moniker.R | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/R/dictionaries.R | 92 +- SemNetDictionaries-0.3.0/SemNetDictionaries/R/find.dictionaries.R | 409 ++-------- SemNetDictionaries-0.3.0/SemNetDictionaries/R/fruits.dictionary.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/fruits.moniker.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/general.dictionary.R | 46 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/good.dictionary.R | 40 SemNetDictionaries-0.3.0/SemNetDictionaries/R/good.moniker.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/hot.dictionary.R | 40 SemNetDictionaries-0.3.0/SemNetDictionaries/R/hot.moniker.R |only SemNetDictionaries-0.3.0/SemNetDictionaries/R/hunspell.dictionary.R | 21 SemNetDictionaries-0.3.0/SemNetDictionaries/R/jobs.dictionary.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/jobs.moniker.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/load.dictionaries.R | 406 +++++---- SemNetDictionaries-0.3.0/SemNetDictionaries/R/load.monikers.R | 165 ++-- SemNetDictionaries-0.3.0/SemNetDictionaries/R/most_common.dictionary.R | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/R/stop_words.dictionary.R | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/R/utils-SemNetDictionaries.R | 73 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/utils-data.R |only SemNetDictionaries-0.3.0/SemNetDictionaries/R/utils-words.R |only SemNetDictionaries-0.3.0/SemNetDictionaries/R/vegetables.dictionary.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/vegetables.moniker.R | 42 - SemNetDictionaries-0.3.0/SemNetDictionaries/R/zzz.R | 22 SemNetDictionaries-0.3.0/SemNetDictionaries/build/stage23.rdb |only SemNetDictionaries-0.3.0/SemNetDictionaries/build/vignette.rds |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/animals.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/animals.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/brit2us.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/coca.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/coca.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/cocaspell.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/cocaspell.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/fruits.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/fruits.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/general.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/good.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/good.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/hot.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/hot.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/hunspell.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/jobs.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/jobs.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/most_common.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/stop_words.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/vegetables.dictionary.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/data/vegetables.moniker.RData |binary SemNetDictionaries-0.3.0/SemNetDictionaries/inst/doc/Appendix_Dictionaries.R | 32 SemNetDictionaries-0.3.0/SemNetDictionaries/inst/doc/Appendix_Dictionaries.Rmd | 198 ++-- SemNetDictionaries-0.3.0/SemNetDictionaries/inst/doc/Appendix_Dictionaries.html | 76 + SemNetDictionaries-0.3.0/SemNetDictionaries/man/animals.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/animals.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/append.dictionary.Rd | 20 SemNetDictionaries-0.3.0/SemNetDictionaries/man/brit2us.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/coca.dictionary.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/coca.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/cocaspell.dictionary.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/cocaspell.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/dictionaries.Rd | 3 SemNetDictionaries-0.3.0/SemNetDictionaries/man/find.dictionaries.Rd | 40 SemNetDictionaries-0.3.0/SemNetDictionaries/man/fruits.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/fruits.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/general.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/good.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/good.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/hot.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/hot.moniker.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/hunspell.dictionary.Rd | 5 SemNetDictionaries-0.3.0/SemNetDictionaries/man/jobs.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/jobs.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/load.dictionaries.Rd | 37 SemNetDictionaries-0.3.0/SemNetDictionaries/man/load.monikers.Rd | 27 SemNetDictionaries-0.3.0/SemNetDictionaries/man/most_common.dictionary.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/man/stop_words.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/vegetables.dictionary.Rd | 4 SemNetDictionaries-0.3.0/SemNetDictionaries/man/vegetables.moniker.Rd | 2 SemNetDictionaries-0.3.0/SemNetDictionaries/vignettes/Appendix_Dictionaries.Rmd | 198 ++-- 92 files changed, 1605 insertions(+), 1638 deletions(-)
More information about SemNetDictionaries at CRAN
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Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 7.2.0 dated 2026-10-13 and 7.2.1 dated 2026-10-14
DESCRIPTION | 6 +-- MD5 | 14 ++++----- NEWS.md | 16 ++++++++++ R/nlmixr2_md5.R | 2 - src/inner.cpp | 15 ++++++--- tests/testthat/test-focei-outer-trust.R | 5 +-- tests/testthat/test-nlmixrGrad.R | 31 +++++++++++++++++--- tests/testthat/test-tolFactor.R | 49 ++++++++++++++++++++++++-------- 8 files changed, 104 insertions(+), 34 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut],
Alex David [aut, cre]
Maintainer: Alex David <alex@synthesize.bio>
Diff between rsynthbio versions 4.2.1 dated 2026-10-13 and 4.2.2 dated 2026-10-14
DESCRIPTION | 20 ++++++++++++-------- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/baseline.html | 3 +-- inst/doc/getting-started.html | 3 +-- inst/doc/metadata-prediction.html | 3 +-- inst/doc/reference-conditioning.html | 3 +-- inst/doc/self-hosted.html | 3 +-- 9 files changed, 30 insertions(+), 26 deletions(-)
Title: Person Parameter Estimation
Description: Estimation of person parameters (abilities) for the 1, 2, 3
and 4 parameter logistic model, the (generalized) partial credit model
and tests that mix dichotomous and polytomous items, under the
assumption that the item parameters are known and fixed: maximum
likelihood, weighted likelihood (Warm, 1989 <doi:10.1007/BF02294627>),
maximum and expected a posteriori and robust estimation (Schuster and
Yuan, 2011 <doi:10.3102/1076998610396890>). Further features are
jackknife estimates (Wainer and Wright, 1980 <doi:10.1007/BF02293910>),
plausible values, the person fit statistics lz, lz* (Snijders, 2001
<doi:10.1007/BF02294437>), infit and outfit, and the simulation of
response data. Models fitted with the 'eRm' package can be passed on
directly. The package is useful, e.g., when items of an item bank are
given to a new sample of persons.
Author: Manuel Reif [cre, aut],
Jan Steinfeld [aut]
Maintainer: Manuel Reif <manuel.reif@gmail.com>
Diff between PP versions 0.6.4-1 dated 2026-04-21 and 1.0.0 dated 2026-10-14
PP-0.6.4-1/PP/R/Infit.R |only PP-0.6.4-1/PP/R/Infitpoly.R |only PP-0.6.4-1/PP/R/JKpp.R |only PP-0.6.4-1/PP/R/Outfit.R |only PP-0.6.4-1/PP/R/Outfitpoly.R |only PP-0.6.4-1/PP/R/PP.R |only PP-0.6.4-1/PP/R/PP_4pl.R |only PP-0.6.4-1/PP/R/PP_gpcm.R |only PP-0.6.4-1/PP/R/PPall.R |only PP-0.6.4-1/PP/R/PPass.R |only PP-0.6.4-1/PP/R/PV.R |only PP-0.6.4-1/PP/R/Pfit.R |only PP-0.6.4-1/PP/R/checkINP.R |only PP-0.6.4-1/PP/R/eap.R |only PP-0.6.4-1/PP/R/findmodel.R |only PP-0.6.4-1/PP/R/jackknife.R |only PP-0.6.4-1/PP/R/lz.R |only PP-0.6.4-1/PP/R/lzstar.R |only PP-0.6.4-1/PP/R/lzstar_mixed.R |only PP-0.6.4-1/PP/R/make_dup.R |only PP-0.6.4-1/PP/R/pkg_start.R |only PP-0.6.4-1/PP/R/prints.R |only PP-0.6.4-1/PP/R/quadIT.R |only PP-0.6.4-1/PP/R/sim_gpcm.R |only PP-0.6.4-1/PP/R/stdrdize_hist.R |only PP-0.6.4-1/PP/inst/doc/ppass_par_and_fit.R |only PP-0.6.4-1/PP/inst/doc/ppass_par_and_fit.Rmd |only PP-0.6.4-1/PP/inst/doc/ppass_par_and_fit.html |only PP-0.6.4-1/PP/man/Pfit_lzstarmix.Rd |only PP-0.6.4-1/PP/man/lzstar_mixed.Rd |only PP-0.6.4-1/PP/man/print_personfit_summary.Rd |only PP-0.6.4-1/PP/src/GPCM4PL_stuff.cpp |only PP-0.6.4-1/PP/src/helper_func.cpp |only PP-0.6.4-1/PP/vignettes/literatur.bib |only PP-0.6.4-1/PP/vignettes/ppass_par_and_fit.Rmd |only PP-1.0.0/PP/DESCRIPTION | 72 - PP-1.0.0/PP/MD5 | 141 +-- PP-1.0.0/PP/NAMESPACE | 86 +- PP-1.0.0/PP/NEWS.md |only PP-1.0.0/PP/R/PP-package.R |only PP-1.0.0/PP/R/RcppExports.R | 149 +-- PP-1.0.0/PP/R/dataRd.R | 96 +- PP-1.0.0/PP/R/estimate.R |only PP-1.0.0/PP/R/jk.R |only PP-1.0.0/PP/R/methods.R |only PP-1.0.0/PP/R/pfit.R |only PP-1.0.0/PP/R/plot.R |only PP-1.0.0/PP/R/ppass.R |only PP-1.0.0/PP/R/prepare.R |only PP-1.0.0/PP/R/pv.R |only PP-1.0.0/PP/R/sim.R |only PP-1.0.0/PP/build/vignette.rds |binary PP-1.0.0/PP/inst/CITATION | 39 PP-1.0.0/PP/inst/doc/intro_pfit.R | 218 +---- PP-1.0.0/PP/inst/doc/intro_pfit.Rmd | 349 ++------ PP-1.0.0/PP/inst/doc/intro_pfit.html | 901 +++++++++++---------- PP-1.0.0/PP/inst/doc/intro_pp.R | 134 +-- PP-1.0.0/PP/inst/doc/intro_pp.Rmd | 338 +++---- PP-1.0.0/PP/inst/doc/intro_pp.html | 1015 +++++++++++++----------- PP-1.0.0/PP/inst/doc/ppass_erm.R |only PP-1.0.0/PP/inst/doc/ppass_erm.Rmd |only PP-1.0.0/PP/inst/doc/ppass_erm.html |only PP-1.0.0/PP/man/Jkpp.Rd | 332 ++----- PP-1.0.0/PP/man/PP-package.Rd | 129 +-- PP-1.0.0/PP/man/PP_4pl.Rd | 400 +++------ PP-1.0.0/PP/man/PP_gpcm.Rd | 278 +++--- PP-1.0.0/PP/man/PPall.Rd | 302 +++---- PP-1.0.0/PP/man/PPass.Rd | 260 +++--- PP-1.0.0/PP/man/PV.Rd | 300 ++----- PP-1.0.0/PP/man/findmodel.Rd | 117 -- PP-1.0.0/PP/man/fourpl_df.Rd | 40 PP-1.0.0/PP/man/pfit.Rd | 330 +++---- PP-1.0.0/PP/man/pp-plots.Rd |only PP-1.0.0/PP/man/pp_amt.Rd | 86 +- PP-1.0.0/PP/man/ppeo-methods.Rd |only PP-1.0.0/PP/man/sim_4pl.Rd | 126 +- PP-1.0.0/PP/man/sim_gpcm.Rd | 96 -- PP-1.0.0/PP/man/sim_mixed.Rd |only PP-1.0.0/PP/src/RcppExports.cpp | 383 ++------- PP-1.0.0/PP/src/core.cpp |only PP-1.0.0/PP/src/fit_sim.cpp |only PP-1.0.0/PP/src/items.h |only PP-1.0.0/PP/tests/testthat.R | 6 PP-1.0.0/PP/tests/testthat/helper-1-expect.R |only PP-1.0.0/PP/tests/testthat/helper-2-reference.R |only PP-1.0.0/PP/tests/testthat/helper-3-data.R |only PP-1.0.0/PP/tests/testthat/test-core.R |only PP-1.0.0/PP/tests/testthat/test-eap.R |only PP-1.0.0/PP/tests/testthat/test-erm.R |only PP-1.0.0/PP/tests/testthat/test-estimate.R |only PP-1.0.0/PP/tests/testthat/test-input.R |only PP-1.0.0/PP/tests/testthat/test-jackknife.R |only PP-1.0.0/PP/tests/testthat/test-kernel.R |only PP-1.0.0/PP/tests/testthat/test-object.R |only PP-1.0.0/PP/tests/testthat/test-pfit.R |only PP-1.0.0/PP/tests/testthat/test-plot.R |only PP-1.0.0/PP/tests/testthat/test-posterior.R |only PP-1.0.0/PP/tests/testthat/test-ppass.R |only PP-1.0.0/PP/tests/testthat/test-prepare.R |only PP-1.0.0/PP/tests/testthat/test-pv.R |only PP-1.0.0/PP/tests/testthat/test-reference.R |only PP-1.0.0/PP/tests/testthat/test-sim.R |only PP-1.0.0/PP/tests/testthat/tests4pl.R | 192 +--- PP-1.0.0/PP/tests/testthat/testsgpcm.R | 57 - PP-1.0.0/PP/tests/testthat/testsgpcm4pl.R | 104 +- PP-1.0.0/PP/tests/testthat/testsjk.R | 102 +- PP-1.0.0/PP/vignettes/intro_pfit.Rmd | 349 ++------ PP-1.0.0/PP/vignettes/intro_pp.Rmd | 338 +++---- PP-1.0.0/PP/vignettes/ppass_erm.Rmd |only 109 files changed, 3438 insertions(+), 4427 deletions(-)
Title: Linear Model Functions
Description: Functions to access and test results from a linear model.
Author: Jared Studyvin [aut, cre]
Maintainer: Jared Studyvin <studyvinstat@gmail.com>
Diff between linearModel versions 1.0.2 dated 2022-01-04 and 1.1.1 dated 2026-10-14
linearModel-1.0.2/linearModel/R/contrastTest.R |only linearModel-1.0.2/linearModel/man/contrastTest.Rd |only linearModel-1.1.1/linearModel/DESCRIPTION | 12 ++++++------ linearModel-1.1.1/linearModel/LICENSE | 4 ++-- linearModel-1.1.1/linearModel/MD5 | 19 ++++++++++++------- linearModel-1.1.1/linearModel/NAMESPACE | 6 +++++- linearModel-1.1.1/linearModel/R/anovaTable.R | 5 +++-- linearModel-1.1.1/linearModel/R/cellMeans.R |only linearModel-1.1.1/linearModel/R/contrast.R |only linearModel-1.1.1/linearModel/R/testContrast.R |only linearModel-1.1.1/linearModel/man/anovaTable.Rd | 2 +- linearModel-1.1.1/linearModel/man/cellMeans.Rd |only linearModel-1.1.1/linearModel/man/contrast.Rd |only linearModel-1.1.1/linearModel/man/print.cellMeans.Rd |only linearModel-1.1.1/linearModel/man/testContrast.Rd |only 15 files changed, 29 insertions(+), 19 deletions(-)
Title: Tracking Communities in Changing Temporal Networks
Description: Tools for temporal networks that change over time, where nodes enter and leave, groups form, split, merge and dissolve, and periods differ in size. The temporal fitters track nodes and communities across periods. A community keeps one identifier while it persists, and a newly formed group receives a new one. Two-stage fitters run Louvain or Leiden community detection in each period and link communities in linked periods by Jaccard similarity, the overlap coefficient or node-strength weighted variants. The 'layer_links' argument sets which periods are directly linked, adjacent periods only by default. By default all periods are fitted jointly, so later periods can change earlier labels, and tracking = 'filtered' prevents this. Multislice modularity (Mucha et al. 2010) <doi:10.1126/science.1184819> and Hungarian matching are included as comparison methods, and a bootstrap stability score helps choose between the two-stage and multislice approaches.
Author: Jared Edgerton [aut, cre]
Maintainer: Jared Edgerton <jared.edgerton@gmail.com>
Diff between dynamicmultiplex versions 1.3.1 dated 2026-09-24 and 1.4.0 dated 2026-10-14
dynamicmultiplex-1.3.1/dynamicmultiplex/R/co_assignment_ci.R |only dynamicmultiplex-1.3.1/dynamicmultiplex/inst |only dynamicmultiplex-1.3.1/dynamicmultiplex/man/co_assignment_ci.Rd |only dynamicmultiplex-1.3.1/dynamicmultiplex/man/community_est.Rd |only dynamicmultiplex-1.4.0/dynamicmultiplex/DESCRIPTION | 12 dynamicmultiplex-1.4.0/dynamicmultiplex/MD5 | 79 - dynamicmultiplex-1.4.0/dynamicmultiplex/NAMESPACE | 5 dynamicmultiplex-1.4.0/dynamicmultiplex/NEWS.md | 153 ++ dynamicmultiplex-1.4.0/dynamicmultiplex/R/bootstrap_multilayer.R | 203 +-- dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_hungarian.R | 75 + dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_identity_ties.R | 43 dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_jaccard.R | 70 - dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_overlap.R | 70 - dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_weighted_jaccard.R | 70 - dynamicmultiplex-1.4.0/dynamicmultiplex/R/fit_multilayer_weighted_overlap.R | 70 - dynamicmultiplex-1.4.0/dynamicmultiplex/R/layers_from_membership.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/R/multilayer_utils.R | 542 +++++++++- dynamicmultiplex-1.4.0/dynamicmultiplex/R/partition_stability.R | 134 -- dynamicmultiplex-1.4.0/dynamicmultiplex/R/plot_multilayer_visualizations.R | 66 - dynamicmultiplex-1.4.0/dynamicmultiplex/R/simulate_and_fit_multilayer.R | 7 dynamicmultiplex-1.4.0/dynamicmultiplex/README.md | 42 dynamicmultiplex-1.4.0/dynamicmultiplex/man/animate_multilayer_gif.Rd | 5 dynamicmultiplex-1.4.0/dynamicmultiplex/man/bootstrap_multilayer.Rd | 37 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_hungarian.Rd | 24 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_identity_ties.Rd | 40 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_jaccard.Rd | 36 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_overlap.Rd | 36 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_weighted_jaccard.Rd | 36 dynamicmultiplex-1.4.0/dynamicmultiplex/man/fit_multilayer_weighted_overlap.Rd | 36 dynamicmultiplex-1.4.0/dynamicmultiplex/man/layers_from_membership.Rd |only dynamicmultiplex-1.4.0/dynamicmultiplex/man/partition_stability.Rd | 77 - dynamicmultiplex-1.4.0/dynamicmultiplex/man/plot_multilayer_alluvial.Rd | 5 dynamicmultiplex-1.4.0/dynamicmultiplex/man/plot_multilayer_series.Rd | 5 dynamicmultiplex-1.4.0/dynamicmultiplex/man/simulate_and_fit_multilayer.Rd | 7 dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/fixtures |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/helper-140.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-140-bootstrap-s.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-140-nodes.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-140-tracking.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-140-twomode.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-bootstrap.R | 107 - dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-input-policy-and-alignment.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-multislice-directed.R |only dynamicmultiplex-1.4.0/dynamicmultiplex/tests/testthat/test-multislice-restart.R |only 44 files changed, 1387 insertions(+), 705 deletions(-)
More information about dynamicmultiplex at CRAN
Permanent link
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft
PowerPoint' documents from R. The package focuses on tabular and
graphical reporting from R; it also provides two functions that let
users get document content into data objects. A set of functions lets
add and remove images, tables and paragraphs of text in new or
existing documents. The package does not require any installation of
Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Stefan Moog [aut],
Mark Heckmann [aut] ,
ArData [cph],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Gr [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.7.6 dated 2026-07-16 and 0.7.7 dated 2026-10-14
DESCRIPTION | 10 - MD5 | 52 +++++----- NAMESPACE | 154 ++++++++++++++++-------------- NEWS.md | 31 ++++++ R/docx_add.R | 24 ++++ R/docx_section.R | 102 +++++++++++-------- R/docx_settings.R | 6 - R/docx_write.R | 26 +++-- R/fortify_docx.R | 9 + R/post-proc.R | 40 +++++++ man/body_add_gg.Rd | 4 man/body_add_img.Rd | 13 ++ man/body_end_block_section.Rd | 17 +++ man/body_end_section_columns.Rd | 17 +++ man/body_end_section_columns_landscape.Rd | 17 +++ man/body_end_section_continuous.Rd | 17 +++ man/body_end_section_landscape.Rd | 17 +++ man/body_end_section_portrait.Rd | 17 +++ man/docx_summary.Rd | 3 man/print.rdocx.Rd | 8 - tests/testthat/test-block_list.R | 154 ++++++++++++++++++++++++++++++ tests/testthat/test-doc-summary.R | 19 +++ tests/testthat/test-docx_settings.R | 15 ++ tests/testthat/test-images.R | 84 ++++++++++++++++ tests/testthat/test-pptx-add.R | 18 ++- tests/testthat/test-pptx-info.R | 7 + tests/testthat/test-sections.R | 91 +++++++++++++++++ 27 files changed, 803 insertions(+), 169 deletions(-)
Title: Spatial Data Operations for Database-Backed Geometries
Description: Provides database-backed spatial geometry classes and methods for
working with vector spatial data in 'DuckDB'. The package supports loading,
converting, querying, joining, and measuring spatial geometries through
familiar 'sf'-style interfaces while keeping geometry columns lazy inside
the database. It integrates with 'dbProject' to preserve database paths,
live connections, and spatial table metadata across interactive sessions.
The package follows the Simple Features framework described by Pebesma
(2018) <doi:10.32614/RJ-2018-009> and uses DuckDB's spatial extension
<https://duckdb.org/docs/stable/core_extensions/spatial/overview.html>.
Author: Edward C. Ruiz [aut, cre] ,
Jiaji George Chen [aut],
Ruben Dries [aut, rev]
Maintainer: Edward C. Ruiz <ecr7407@gmail.com>
Diff between dbSpatial versions 0.1.2 dated 2026-06-23 and 0.1.3 dated 2026-10-14
DESCRIPTION | 6 GPL-3 | 1348 ++++++++++++++++---------------- LICENSE | 4 MD5 | 170 ++-- NAMESPACE | 136 +-- NEWS.md | 677 ++++++++-------- R/accessors.R | 58 - R/as_dbSpatial.R | 194 ++-- R/classes.R | 18 R/coerce.R | 82 - R/constructors.R | 34 R/dbSpatial.R | 476 +++++------ R/extract.R | 112 +- R/generics.R | 937 +++++++++++----------- R/geometry_ops.R | 140 +-- R/global.R | 24 R/imports.R | 66 - R/input_validation.R | 112 +- R/loadSpatial.R | 12 R/measurements.R | 46 - R/show.R | 110 +- R/sim_dbSpatial.R | 120 +- R/sql_gen.R | 146 +-- R/st_as_sf.R | 114 +- R/st_bbox.R | 100 +- R/st_geometry_type.R | 24 R/st_geometrytype.R | 92 +- R/st_is_valid.R | 24 R/st_join.R | 188 ++-- R/st_read.R | 166 +-- R/st_spatial_join.R | 186 ++-- R/st_translate.R | 50 - R/st_xmax.R | 46 - R/st_ymax.R | 46 - R/utils.R | 74 - R/vect.R | 86 +- README.md | 150 +-- inst/doc/class_structure.R | 40 inst/doc/class_structure.Rmd | 106 +- inst/doc/class_structure.html | 47 - inst/doc/getting_started.R | 86 +- inst/doc/getting_started.Rmd | 152 +-- inst/doc/getting_started.html | 74 + inst/doc/spatial_operations.R | 64 - inst/doc/spatial_operations.Rmd | 152 +-- inst/doc/spatial_operations.html | 112 ++ man/as_dbSpatial.Rd | 128 +-- man/cash-dbSpatial-method.Rd | 38 man/dbSpatial.Rd | 186 ++-- man/dbSpatial_options.Rd | 62 - man/dot-sim_dbSpatial.Rd | 48 - man/dot-st_read.Rd | 98 +- man/dot-st_spatial_join.Rd | 102 +- man/head.Rd | 52 - man/loadSpatial.Rd | 70 - man/show.Rd | 44 - man/st_area.Rd | 90 +- man/st_as_geojson.Rd | 90 +- man/st_as_sf.dbSpatial.Rd | 80 - man/st_as_text.Rd | 72 - man/st_bbox.Rd | 52 - man/st_buffer.Rd | 94 +- man/st_centroid.Rd | 91 +- man/st_geometrytype.Rd | 60 - man/st_join.dbSpatial.Rd | 116 +- man/st_length.Rd | 86 +- man/st_npoints.Rd | 98 +- man/st_perimeter.Rd | 90 +- man/st_simplify.Rd | 95 +- man/st_translate.Rd | 120 +- man/st_x.Rd | 92 +- man/st_xmax.Rd | 122 +- man/st_y.Rd | 92 +- man/st_ymax.Rd | 120 +- man/tail.Rd | 52 - man/vect-dbSpatial-method.Rd | 90 +- tests/testthat.R | 8 tests/testthat/test-extract.R | 32 tests/testthat/test-spatial-functions.R | 304 +++---- vignettes/class_structure.Rmd | 106 +- vignettes/class_structure.md | 30 vignettes/getting_started.Rmd | 152 +-- vignettes/getting_started.md | 236 ++--- vignettes/spatial_operations.Rmd | 152 +-- vignettes/spatial_operations.md | 412 ++++----- vignettes/test_data.csv | 22 86 files changed, 5760 insertions(+), 5531 deletions(-)
Title: Various Methods for the Goodness-of-Fit Problem in D>1
Dimensions
Description: Provides multivariate goodness-of-fit testing with a common
interface for several test statistics. Null models may be simple or include
parameter estimation, with p-values obtained by parametric bootstrap
simulation. The function gof_test_adjusted_pvalue() combines several tests
and computes a p-value adjusted for simultaneous inference. The function
gof_power() estimates test power. The functions hybrid_test() and
hybrid_power() use Monte Carlo samples under the null together with
two-sample procedures. The function run.studies() supports systematic power
comparisons of user-supplied and included methods across case studies. See
the included vignettes for method details and references.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MDgof versions 1.2.0 dated 2026-09-18 and 1.2.1 dated 2026-10-14
DESCRIPTION | 6 MD5 | 8 NEWS.md | 3 R/gof_test_adjusted_pvalue.R | 605 +++++++++++++++++++-------------------- inst/doc/MDgof-Case-Studies.html | 54 +-- 5 files changed, 341 insertions(+), 335 deletions(-)
Title: Various Methods for the Two Sample Problem in D>1 Dimensions
Description: The routine twosample_test() in this package runs the
two-sample test using various test statistic for multivariate data.
The user can also run several tests and then find a p value adjusted for simultaneous inference.
The p values are found via permutation or via the parametric bootstrap.
The routine twosample_power() allows the estimation of the power of the tests.
The routine run.studies() allows a user to quickly study the power of a new method and
how it compares to those included in the package.
For details of the methods and references see the included vignettes.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MD2sample versions 1.4.0 dated 2026-09-15 and 1.4.1 dated 2026-10-14
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 3 R/power_pvals.R | 229 ++++++++++++++++++++++++---------------------- R/twosample_power.R | 15 ++- inst/doc/CaseStudies.html | 68 ++++++------- inst/doc/MD2sample.html | 6 - src/TS_cont.cpp | 2 8 files changed, 181 insertions(+), 162 deletions(-)
Title: Content Analysis in R: Integrated Qualitative (LLMs) and
Quantitative Pipeline
Description: Provides an integrated pipeline for content analysis
combining qualitative coding assisted by large language models (LLMs)
with classical quantitative text analysis. Includes modules for
pre-processing (tokenization, stopwords for Brazilian Portuguese),
descriptive statistics, keyness, co-occurrence networks, word clouds
(including comparative and X-ray variants), sentiment analysis via
OpLexicon, Latent Dirichlet Allocation (LDA), inter-coder
reliability metrics (Krippendorff, Gwet), and modern visualizations
based on ggplot2. Special focus on Brazilian corpora and
political-institutional codebooks. Inspired by Maerz and Benoit (2025)
<https://quallmer.github.io/quallmer/>.
Author: Anderson Henrique [aut, cre]
Maintainer: Anderson Henrique <anderson.henrique@usp.br>
Diff between acR versions 0.3.4 dated 2026-09-09 and 0.4.0 dated 2026-10-14
DESCRIPTION | 12 LICENSE | 4 MD5 | 375 +- NAMESPACE | 145 - NEWS.md | 855 +++-- R/acR-package.R | 74 R/ac_chat_local.R |only R/ac_clean.R | 846 ++--- R/ac_cluster.R | 484 +-- R/ac_cooccurrence.R | 422 +- R/ac_corpus.R | 738 ++--- R/ac_count.R | 334 +- R/ac_ellmer_chat.R | 126 R/ac_estimate_tokens.R |only R/ac_export.R | 474 +-- R/ac_fetch_camara.R | 994 +++--- R/ac_fetch_senado.R | 1042 +++---- R/ac_import.R | 430 +- R/ac_keyness.R | 480 +-- R/ac_lda.R | 846 ++--- R/ac_plot_cluster.R | 428 +- R/ac_plot_cooccurrence.R | 246 - R/ac_plot_keyness.R | 308 +- R/ac_plot_tf_idf.R | 350 +- R/ac_plot_top_terms.R | 328 +- R/ac_plot_wordcloud_comparative.R | 748 ++--- R/ac_qual_code.R | 1382 +++++---- R/ac_qual_codebook.R | 2494 ++++++++--------- R/ac_qual_irr.R | 686 ++-- R/ac_qual_live.R | 353 +- R/ac_qual_models.R | 1156 +++---- R/ac_qual_reliability.R | 1387 +++++---- R/ac_qual_report.R | 1558 +++++----- R/ac_qual_search_literature.R | 932 +++--- R/ac_sentiment.R | 620 ++-- R/ac_tf_idf.R | 290 +- R/ac_theme.R | 208 - R/ac_tokenize.R | 426 +- R/ac_top_terms.R | 224 - R/ac_wordcloud.R | 348 +- R/globals.R | 64 R/is_ac_corpus.R | 50 R/stopwords_pt_br.R | 250 - R/utils.R | 10 R/zzz.R | 26 README.md | 978 +++--- build/vignette.rds |binary inst/CITATION | 154 - inst/WORDLIST | 2894 ++++++++++---------- inst/doc/analise-proposicoes.R | 482 +-- inst/doc/analise-proposicoes.Rmd | 888 +++--- inst/doc/analise-proposicoes.html | 1466 +++++----- inst/doc/cluster.R | 318 +- inst/doc/cluster.Rmd | 740 ++--- inst/doc/cluster.html | 1572 +++++----- inst/doc/introducao-acR.R | 224 - inst/doc/introducao-acR.Rmd | 446 +-- inst/doc/introducao-acR.html | 1486 +++++----- inst/doc/lda.R | 348 +- inst/doc/lda.Rmd | 694 ++-- inst/doc/lda.html | 1630 +++++------ inst/doc/llm-local-em-escala.R |only inst/doc/llm-local-em-escala.Rmd |only inst/doc/llm-local-em-escala.html |only inst/doc/qualitativo-llm.R | 420 +- inst/doc/qualitativo-llm.Rmd | 1250 ++++---- inst/doc/qualitativo-llm.html | 2174 +++++++-------- inst/doc/quantitativo.R | 294 +- inst/doc/quantitativo.Rmd | 670 ++-- inst/doc/quantitativo.html | 1601 +++++------ inst/doc/quickstart.R | 88 inst/doc/quickstart.Rmd | 174 - inst/doc/quickstart.html | 966 +++--- inst/doc/replicabilidade.R | 330 +- inst/doc/replicabilidade.Rmd | 630 ++-- inst/doc/replicabilidade.html | 1918 ++++++------- inst/doc/sentimento.R | 316 +- inst/doc/sentimento.Rmd | 552 +-- inst/doc/sentimento.html | 1416 ++++----- inst/docs/adr/0001-decisoes-iniciais-acR.md | 538 +-- inst/docs/dependencies-todo.md | 44 man/acR-package.Rd | 115 man/ac_calibrate_tokens.Rd |only man/ac_chat_local.Rd |only man/ac_clean.Rd | 310 +- man/ac_clean_stopwords.Rd | 98 man/ac_cluster_documents.Rd | 162 - man/ac_cooccurrence.Rd | 164 - man/ac_corpus.Rd | 166 - man/ac_count.Rd | 164 - man/ac_estimate_tokens.Rd |only man/ac_export.Rd | 264 - man/ac_fetch_camara.Rd | 234 - man/ac_fetch_senado.Rd | 300 +- man/ac_import.Rd | 196 - man/ac_keyness.Rd | 218 - man/ac_lda.Rd | 142 man/ac_lda_tune.Rd | 128 man/ac_palette.Rd | 74 man/ac_plot_cluster.Rd | 116 man/ac_plot_cooccurrence.Rd | 138 man/ac_plot_keyness.Rd | 140 man/ac_plot_lda_topics.Rd | 110 man/ac_plot_lda_tune.Rd | 106 man/ac_plot_sentiment.Rd | 116 man/ac_plot_tf_idf.Rd | 146 - man/ac_plot_top_terms.Rd | 140 man/ac_plot_wordcloud_comparative.Rd | 152 - man/ac_plot_xray.Rd | 112 man/ac_qual_code.Rd | 387 +- man/ac_qual_codebook.Rd | 276 - man/ac_qual_codebook_add.Rd | 96 man/ac_qual_codebook_history.Rd | 80 man/ac_qual_codebook_hybrid.Rd | 134 man/ac_qual_codebook_merge.Rd | 116 man/ac_qual_codebook_remove.Rd | 82 man/ac_qual_codebook_translate.Rd | 112 man/ac_qual_export_for_review.Rd | 96 man/ac_qual_import_human.Rd | 100 man/ac_qual_irr.Rd | 262 - man/ac_qual_list_models.Rd | 146 - man/ac_qual_load_codebook.Rd | 80 man/ac_qual_recommend_model.Rd | 170 - man/ac_qual_reliability.Rd | 229 - man/ac_qual_report.Rd | 180 - man/ac_qual_report_full.Rd | 212 - man/ac_qual_sample.Rd | 150 - man/ac_qual_save_codebook.Rd | 88 man/ac_qual_search_literature.Rd | 174 - man/ac_sentiment.Rd | 174 - man/ac_tf_idf.Rd | 176 - man/ac_tokenize.Rd | 184 - man/ac_top_terms.Rd | 132 man/ac_wordcloud.Rd | 174 - man/as_prompt.Rd | 108 man/figures/pipeline.svg | 316 +- man/is_ac_corpus.Rd | 60 man/print.ac_cluster.Rd | 40 man/print.ac_irr.Rd | 42 man/theme_ac.Rd | 76 tests/spelling.R | 14 tests/testthat.R | 14 tests/testthat/helper-corpus.R | 34 tests/testthat/test-ac_chat_local.R |only tests/testthat/test-ac_clean.R | 968 +++--- tests/testthat/test-ac_cluster.R | 412 +- tests/testthat/test-ac_cooccurrence.R | 372 +- tests/testthat/test-ac_corpus.R | 570 +-- tests/testthat/test-ac_count.R | 364 +- tests/testthat/test-ac_ellmer_chat.R | 102 tests/testthat/test-ac_estimate_tokens.R |only tests/testthat/test-ac_export.R | 144 tests/testthat/test-ac_fetch_camara.R | 340 +- tests/testthat/test-ac_fetch_senado.R | 80 tests/testthat/test-ac_import.R | 320 +- tests/testthat/test-ac_keyness.R | 94 tests/testthat/test-ac_lda.R | 236 - tests/testthat/test-ac_plot_cooccurrence.R | 292 +- tests/testthat/test-ac_plot_keyness.R | 110 tests/testthat/test-ac_plot_tf_idf.R | 120 tests/testthat/test-ac_plot_top_terms.R | 112 tests/testthat/test-ac_plot_wordcloud_comparative.R | 552 +-- tests/testthat/test-ac_qual_code-live.R | 68 tests/testthat/test-ac_qual_code.R | 1176 +++++--- tests/testthat/test-ac_qual_codebook.R | 1108 +++---- tests/testthat/test-ac_qual_irr.R | 166 - tests/testthat/test-ac_qual_irr_export.R | 490 +-- tests/testthat/test-ac_qual_live.R | 144 tests/testthat/test-ac_qual_models.R | 340 +- tests/testthat/test-ac_qual_reliability.R | 813 +++-- tests/testthat/test-ac_qual_report.R | 382 +- tests/testthat/test-ac_qual_search_literature.R | 470 +-- tests/testthat/test-ac_sentiment.R | 496 +-- tests/testthat/test-ac_tf_idf.R | 88 tests/testthat/test-ac_theme.R | 56 tests/testthat/test-ac_tokenize.R | 442 +-- tests/testthat/test-ac_top_terms.R | 162 - tests/testthat/test-ac_wordcloud.R | 130 tests/testthat/test-is_ac_corpus.R | 28 tests/testthat/test-package.R | 12 tests/testthat/test-plots-snapshot.R | 222 - vignettes/analise-proposicoes.Rmd | 888 +++--- vignettes/cluster.Rmd | 740 ++--- vignettes/introducao-acR.Rmd | 446 +-- vignettes/lda.Rmd | 694 ++-- vignettes/llm-local-em-escala.Rmd |only vignettes/qualitativo-llm.Rmd | 1250 ++++---- vignettes/quantitativo.Rmd | 670 ++-- vignettes/quickstart.Rmd | 174 - vignettes/replicabilidade.Rmd | 630 ++-- vignettes/sentimento.Rmd | 552 +-- vignettes/sentimento.csv | 18 vignettes/sentimento_resumo.csv | 18 vignettes/sentimento_resumo.tex | 36 194 files changed, 39760 insertions(+), 38316 deletions(-)
Title: Automated Soil Profile Classification per WRB 2022, 'SiBCS' 5
and USDA Soil Taxonomy 13
Description: Implements deterministic classification keys for the World
Reference Base for Soil Resources 2022 (4th edition) and the Brazilian
System of Soil Classification ('SiBCS', 5th edition). Provides a unified
profile representation with explicit per-attribute provenance, multimodal
extraction from field reports and photos via vision-language models,
spatial priors from 'SoilGrids' and national soil maps, and gap-filling of
soil attributes from Vis-NIR or MIR spectra via the Open Soil Spectral
Library ('OSSL'). The taxonomic key itself is never delegated to a language
model; LLMs are restricted to schema-validated extraction. Each
classification result reports a key trace, a provenance-aware evidence
grade, and ambiguities that further measurement would resolve.
Author: Hugo Rodrigues [aut, cre, cph]
Maintainer: Hugo Rodrigues <rodrigues.machado.hugo@gmail.com>
Diff between soilKey versions 0.9.184 dated 2026-07-07 and 0.9.259 dated 2026-10-14
soilKey-0.9.184/soilKey/inst/benchmarks/reports |only soilKey-0.9.184/soilKey/inst/extdata/canonical/ST_criteria_13th.rda |only soilKey-0.9.184/soilKey/inst/extdata/canonical/ST_features.rda |only soilKey-0.9.184/soilKey/inst/extdata/canonical/WRB_4th_2022.rda |only soilKey-0.9.184/soilKey/inst/extdata/wosis_sa_sample.rds |only soilKey-0.9.184/soilKey/inst/rules/usda/canonical |only soilKey-0.9.184/soilKey/tests/testthat/_problems |only soilKey-0.9.184/soilKey/tests/testthat/testthat-problems.rds |only soilKey-0.9.259/soilKey/DESCRIPTION | 23 soilKey-0.9.259/soilKey/MD5 | 791 +- soilKey-0.9.259/soilKey/NAMESPACE | 8 soilKey-0.9.259/soilKey/NEWS.md | 3729 +++++++++- soilKey-0.9.259/soilKey/R/afsp.R | 38 soilKey-0.9.259/soilKey/R/audit-argic-films.R | 41 soilKey-0.9.259/soilKey/R/bdsolos.R | 429 + soilKey-0.9.259/soilKey/R/benchmark-bdsolos.R | 90 soilKey-0.9.259/soilKey/R/benchmark-febr-loader.R | 296 soilKey-0.9.259/soilKey/R/benchmark-kssl-nasis.R | 11 soilKey-0.9.259/soilKey/R/benchmark-suite.R | 31 soilKey-0.9.259/soilKey/R/benchmark-unified.R | 12 soilKey-0.9.259/soilKey/R/canonical-kst13.R | 99 soilKey-0.9.259/soilKey/R/canonical-references.R | 117 soilKey-0.9.259/soilKey/R/class-ClassificationResult.R | 9 soilKey-0.9.259/soilKey/R/class-PedonRecord.R | 22 soilKey-0.9.259/soilKey/R/classify-from-documents.R | 2 soilKey-0.9.259/soilKey/R/classify-smartsolos.R | 36 soilKey-0.9.259/soilKey/R/coverage.R | 120 soilKey-0.9.259/soilKey/R/designation-inference.R |only soilKey-0.9.259/soilKey/R/diagnostics-atributos-sibcs.R | 311 soilKey-0.9.259/soilKey/R/diagnostics-horizons-sibcs.R | 1242 ++- soilKey-0.9.259/soilKey/R/diagnostics-horizons-usda.R | 10 soilKey-0.9.259/soilKey/R/diagnostics-horizons-wrb-v033.R | 88 soilKey-0.9.259/soilKey/R/diagnostics-horizons-wrb-v09186.R |only soilKey-0.9.259/soilKey/R/diagnostics-horizons-wrb.R | 444 - soilKey-0.9.259/soilKey/R/diagnostics-materials-wrb-v033.R | 35 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soilKey-0.9.259/soilKey/tests/testthat/test-usda-oxisols-v087.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-usda-spodosols-v085.R | 5 soilKey-0.9.259/soilKey/tests/testthat/test-usda-ultisols-v0810.R | 3 soilKey-0.9.259/soilKey/tests/testthat/test-usda-vertisols-v088.R | 5 soilKey-0.9.259/soilKey/tests/testthat/test-v09101-shiny-map.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v09104-usda-family.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v09106-benchmark-suite.R | 7 soilKey-0.9.259/soilKey/tests/testthat/test-v09107-sibcs-accuracy.R | 18 soilKey-0.9.259/soilKey/tests/testthat/test-v09108-app-polish.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v09129-wrb-base-status.R | 48 soilKey-0.9.259/soilKey/tests/testthat/test-v09132-wrb-qual-audit.R | 16 soilKey-0.9.259/soilKey/tests/testthat/test-v09133-schema-blocked-quals.R | 22 soilKey-0.9.259/soilKey/tests/testthat/test-v09137-sibcs-subsurface-b-audit.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v09138-sibcs-relacao-textural.R | 22 soilKey-0.9.259/soilKey/tests/testthat/test-v09142-calcic-morphology-raptic-urbic.R | 5 soilKey-0.9.259/soilKey/tests/testthat/test-v09147-usda-subgroup-coverage.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v09149-usda-humic-colour.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v09174-shiny-map-unified.R | 27 soilKey-0.9.259/soilKey/tests/testthat/test-v09175-app-reactivity.R | 11 soilKey-0.9.259/soilKey/tests/testthat/test-v09178-map-fixes.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v09180-uncertainty-group.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v09185-neutral-chroma-exact-zero.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09190-artefacts-weighted.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09191-spectra-backend-label.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09192-horizon-name-recognition.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09193-vlm-reasoning-parse.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09194-munsell-schema-budget.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09195-missing-coverage.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09196-photo-horizon-matching.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09197-munsellname-adoption.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09200-pedon-source-options.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09202-wosis-live-picker.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09203-munsell-raw-chroma.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09204-no-third-party-data.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09206-wosis-layers.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09207-assistant-grounding.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09207-groq-models.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09208-empty-profile.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09209-async-app.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09210-visitor-fixes.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09211-per-session-settings.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09212-strict-limits.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09213-no-properties-grade.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09215-static-deps.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09216-wrb2022-qualifier-names.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09217-wrb2022-ch4-names.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09218-app-theme.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09218-widget-jquery.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09221-fe-loaders.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09222-bdsolos-reader.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09223-afsp-suite-row.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09224-widget-deps.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09225-sibcs-label-gate.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09226-sibcs-old-names.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09227-b-nitico-terms.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09228-designation-prefix.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09229-sibcs-stated-order.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09230-b-latossolico-many.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09231-b-nitico-grade-ranges.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09232-bdsolos-friction-gravel-hue.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09233-b-planico-colour.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09234-sibcs-morph-v-pl.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09235-sibcs-variegated-colours.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09236-report-grade-badge.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09237-redape-structure-codes.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09238-b-planico-structure-colours.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09239-horizonte-glei.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09240-sibcs-old-notation-b-incipiente.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09241-sibcs-b-textural-b-latossolico.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09242-bdsolos-sampling-type.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09243-sibcs-b-latossolico-ki.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09244-sibcs-mudanca-abrupta-b-planico.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09245-sibcs-horizonte-vertico.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09246-sibcs-thickness-adjoining.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09247-sibcs-b-espodico-ir.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09248-sibcs-plintico-p1.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09249-sibcs-b-latossolico-camadas.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09250-sibcs-notacao-antiga-a2-b3.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09251-bdsolos-cerosidade-texto.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09252-sibcs-neossolos-vertico-abaixo-do-a.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09253-sibcs-horizonte-histico.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09254-sibcs-histico-camadas-para-cima.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09255-sibcs-b-espodico-item-a.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09256-sibcs-notacao-antiga-marcas.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v09257-sibcs-atividade-saturacao-maior-parte.R |only soilKey-0.9.259/soilKey/tests/testthat/test-v0928-classify-all.R | 5 soilKey-0.9.259/soilKey/tests/testthat/test-v0928-designation-proxy.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v0929-neossolo-litolico-heuristic.R | 3 soilKey-0.9.259/soilKey/tests/testthat/test-v0930-wosis-sample.R | 68 soilKey-0.9.259/soilKey/tests/testthat/test-v0933-wrb-qualifier-closure.R | 37 soilKey-0.9.259/soilKey/tests/testthat/test-v0935-quartzarenico-units.R | 3 soilKey-0.9.259/soilKey/tests/testthat/test-v0943-json-schema.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v0945-color-undetermined.R | 6 soilKey-0.9.259/soilKey/tests/testthat/test-v0946-pls-training.R | 8 soilKey-0.9.259/soilKey/tests/testthat/test-v0952-vignette-pt.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v0953-performance.R | 5 soilKey-0.9.259/soilKey/tests/testthat/test-v0954-smartsolos-api.R | 33 soilKey-0.9.259/soilKey/tests/testthat/test-v0955-bdsolos.R | 32 soilKey-0.9.259/soilKey/tests/testthat/test-v0961-diagnostic-fixes.R | 15 soilKey-0.9.259/soilKey/tests/testthat/test-v0962-aqp-interop.R | 8 soilKey-0.9.259/soilKey/tests/testthat/test-v0963-qualifiers.R | 133 soilKey-0.9.259/soilKey/tests/testthat/test-v0964-qualifiers.R | 127 soilKey-0.9.259/soilKey/tests/testthat/test-v0965-engine-and-tier3.R | 38 soilKey-0.9.259/soilKey/tests/testthat/test-v0968-b-latossolico-engine.R | 6 soilKey-0.9.259/soilKey/tests/testthat/test-v0970-ferralic-texture-morph.R | 13 soilKey-0.9.259/soilKey/tests/testthat/test-v0971-redape.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v0979-mollic-vertic-priority.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v0981-sibcs-subordem.R | 20 soilKey-0.9.259/soilKey/tests/testthat/test-v0983-argic-films-audit.R | 65 soilKey-0.9.259/soilKey/tests/testthat/test-v0985-andisol-buried-extend.R | 3 soilKey-0.9.259/soilKey/tests/testthat/test-v0986-ferralic-engine-aqp-fallback.R | 11 soilKey-0.9.259/soilKey/tests/testthat/test-v0989-texture-engine-fallback.R | 3 soilKey-0.9.259/soilKey/tests/testthat/test-v0990-argic-designation-inference.R | 21 soilKey-0.9.259/soilKey/tests/testthat/test-v0994-lazy-fetch.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-v0997-shiny-pro-app.R | 2 soilKey-0.9.259/soilKey/tests/testthat/test-v0998-tier3-strict.R | 4 soilKey-0.9.259/soilKey/tests/testthat/test-validate-rules.R | 1 soilKey-0.9.259/soilKey/tests/testthat/test-wrb-decomp-qualifiers.R | 13 soilKey-0.9.259/soilKey/tests/testthat/test-wrb-diagnostics-completeness-v09186.R |only soilKey-0.9.259/soilKey/vignettes/v02_classify_wrb_end_to_end.Rmd | 78 soilKey-0.9.259/soilKey/vignettes/v04_vlm_extraction.Rmd | 2 soilKey-0.9.259/soilKey/vignettes/v07_end_to_end_pipeline.Rmd | 2 400 files changed, 19762 insertions(+), 7641 deletions(-)
Title: Function and Pipeline Development
Description: Set of functions that perform checks according to the safer-r project recommendations for R function development (see <https://github.com/safer-r>). This includes checking argument values, ensuring correct specification of all mandatory arguments for embedded functions, as well as their explicit package namespace qualification, among other things.
Author: Haiding Wang [ctb],
Yushi Han [ctb],
Mia Legras [ctb],
Gael Millot [cre, aut, ctb]
Maintainer: Gael Millot <gael.millot@pasteur.fr>
Diff between saferDev versions 1.0.0 dated 2026-06-08 and 2.0.0 dated 2026-10-14
DESCRIPTION | 11 MD5 | 61 +-- NEWS.md | 7 R/all_args_here.R | 68 +++- R/arg_check.R | 209 +++++++------ R/colons_check.R | 52 ++- R/env_check.R | 53 ++- R/get_message.R | 64 +++ R/intern_.all_args_here_fill.R | 72 +++- R/intern_.base_op_check.R | 37 ++ R/intern_.colons_check_message.R | 68 +++- R/intern_.extract_all_fun_names.R | 57 ++- R/intern_.fun_args_pos.R | 56 ++- R/intern_.functions_detect.R | 52 ++- R/intern_.has_odd_number_of_quotes.R | 50 ++- R/intern_.in_parenthesis_replacement.R | 66 +++- R/intern_.in_quotes_replacement.R | 62 +++ R/intern_.noclean_functions.R | 60 +++ R/intern_.pack_and_function_check.R | 52 ++- R/is_function_here.R | 54 ++- R/is_package_here.R | 54 ++- R/report.R | 66 +++- build/vignette.rds |binary inst/doc/saferDev.Rmd | 4 inst/doc/saferDev.html | 12 man/arg_check.Rd | 57 ++- tests/testthat/Rplots.pdf |only tests/testthat/check_pos_fun_args_pos_internal_error_1.txt |only tests/testthat/test-.base_op_check.R | 1 tests/testthat/test-arg_check.R | 133 ++++++-- tests/testthat/test-get_message.R | 32 - tests/testthat/test-mandatory_args.R |only vignettes/saferDev.Rmd | 4 33 files changed, 1184 insertions(+), 390 deletions(-)
Title: 'Creates Color Palettes Inspired by Dune'
Description: Enables the use of color palettes inspired by the 'Dune' movies. These palettes are compatible with 'ggplot2'. See Wickham (2016) <doi:10.1007/978-3-319-24277-4> for more details on 'ggplot2'.
Author: Nicholas Vietto [aut, cre, cph]
Maintainer: Nicholas Vietto <nicholasvietto@gmail.com>
Diff between Rdune versions 1.1.1 dated 2024-07-29 and 1.1.2 dated 2026-10-14
Rdune-1.1.1/Rdune/man/figures/logo.jpg |only Rdune-1.1.2/Rdune/DESCRIPTION | 8 +- Rdune-1.1.2/Rdune/MD5 | 26 ++++---- Rdune-1.1.2/Rdune/NEWS.md | 4 + Rdune-1.1.2/Rdune/README.md | 29 ++++++++- Rdune-1.1.2/Rdune/build/partial.rdb |binary Rdune-1.1.2/Rdune/build/vignette.rds |binary Rdune-1.1.2/Rdune/inst/doc/my-vignette.R | 10 +-- Rdune-1.1.2/Rdune/inst/doc/my-vignette.Rmd | 19 ++---- Rdune-1.1.2/Rdune/inst/doc/my-vignette.html | 41 ++++++------- Rdune-1.1.2/Rdune/man/figures/README-example1-1.png |binary Rdune-1.1.2/Rdune/man/figures/README-example2-1.png |binary Rdune-1.1.2/Rdune/man/figures/README-unnamed-chunk-2-1.png |binary Rdune-1.1.2/Rdune/man/figures/logo.png |only Rdune-1.1.2/Rdune/vignettes/my-vignette.Rmd | 19 ++---- 15 files changed, 90 insertions(+), 66 deletions(-)
Title: Luck-Corrected Peer Performance Analysis in R
Description: Provides functions to perform the peer performance analysis of
funds' returns as described in Ardia and Boudt (2018)
<doi:10.1016/j.jbankfin.2017.10.014>. For each fund, the package estimates
the proportion of peers it outperforms, is equalled by, and is outperformed
by, correcting for luck with the false discovery approach of Storey (2002)
<doi:10.1111/1467-9868.00346>. Screenings can be based on factor-model
alphas, Sharpe ratios, or modified Sharpe ratios, the latter using the
equality test of Ardia and Boudt (2015) <doi:10.1016/j.frl.2015.02.008>.
Funds can be screened within a universe or against a separate peer group,
over rolling windows, and results come with peer-bootstrap
intervals, summary, plot, and tidy data frame methods.
Author: David Ardia [aut, cre, cph, fnd] ,
Nabil Bouamara [ctb],
Kris Boudt [aut] ,
Sebastien Legros [ctb],
Murilo Andre Peres Pereira [ctb] ,
Benjamin Seguin [ctb]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between PeerPerformance versions 2.4.0 dated 2026-08-02 and 2.4.1 dated 2026-10-14
DESCRIPTION | 10 +- MD5 | 57 +++++++------- NEWS.md | 60 +++++++++++++++ R/alphaScreening.R | 47 +++++------- R/alphaTesting.R | 39 +++++----- R/computePi.R | 25 +++--- R/functions.R | 40 +++++++++- R/methods.R | 25 ++++-- R/msharpeScreening.R | 40 +++++----- R/msharpeTesting.R | 18 ++-- R/screeningXY.R | 35 +++++--- R/sharpeScreening.R | 40 +++++----- R/sharpeTesting.R | 20 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 - inst/doc/PeerPerformance.Rmd | 23 +++-- inst/doc/PeerPerformance.html | 42 +++++----- inst/scripts/validation-extended.R |only inst/scripts/validation.R | 12 +-- man/alphaScreening.Rd | 13 +-- man/confint.SCREENING.Rd | 18 ++-- man/exposureHeterogeneity.Rd | 4 - man/msharpeScreening.Rd | 19 ++-- man/msharpeTesting.Rd | 5 - man/sharpeScreening.Rd | 20 ++--- man/sharpeTesting.Rd | 7 + tests/testthat/test_numerical.R | 144 +++++++++++++++++++++++++++++++++++++ tests/testthat/test_screening.R | 19 ++++ vignettes/PeerPerformance.Rmd | 23 +++-- 30 files changed, 563 insertions(+), 246 deletions(-)
More information about PeerPerformance at CRAN
Permanent link
Title: Search and Explore BOLD Data Packages Efficiently
Description: Provides efficient tools for exploring and transforming
the Barcode of Life Data Systems (BOLD) data packages on local
machines. It enables fast local querying of the data packages without
relying on live API calls. Results can be easily converted into formats
compatible with widely used R packages and third party tools.
Author: Sameer Padhye [aut, cre],
Spencer K. Monckton [aut],
Dirk Steinke [ctb],
Jireh Agda [ctb],
Teresita M. Porter [ctb]
Maintainer: Sameer Padhye <spadhye@uoguelph.ca>
Diff between BOLDNODE versions 1.0.0 dated 2026-09-09 and 1.0.1 dated 2026-10-14
DESCRIPTION | 13 ++--- MD5 | 18 +++---- NAMESPACE | 99 +++++++++++++++++++++++------------------ R/external.bcdm_to_occmatrix.R | 2 R/external.get_bin_consensus.R | 17 ++++--- R/helper.functions.R | 2 inst/doc/Using_BOLDNODE.R | 8 +-- inst/doc/Using_BOLDNODE.Rmd | 8 +-- inst/doc/Using_BOLDNODE.html | 70 ++++++++++++++-------------- vignettes/Using_BOLDNODE.Rmd | 8 +-- 10 files changed, 132 insertions(+), 113 deletions(-)
Title: A Package for BInary Longitudinal Data
Description: Performs logistic regression for binary longitudinal
data, allowing for serial dependence among observations from a given
individual and a random intercept term. Estimation is via maximization
of the exact likelihood of a suitably defined model. Missing values and
unbalanced data are allowed, with some restrictions.
M. Helena Goncalves et al. (2012) <DOI: 10.18637/jss.v046.i09>.
Author: M. Helena Goncalves [aut, cre] ,
M. Salome Cabral [aut],
Adelchi Azzalini [aut],
R. Piessens [ctb] ,
E. de Doncker [ctb]
Maintainer: M. Helena Goncalves <mhgoncal@ualg.pt>
Diff between bild versions 1.2-1 dated 2023-11-03 and 1.3-0 dated 2026-10-14
bild-1.2-1/bild/R/anova_bild.R |only bild-1.2-1/bild/R/bild.R |only bild-1.2-1/bild/R/bildControl.R |only bild-1.2-1/bild/R/bildIntegrate.R |only bild-1.2-1/bild/R/fitted_bild.R |only bild-1.2-1/bild/R/fixeff_bild.R |only bild-1.2-1/bild/R/getAIC_bild.R |only bild-1.2-1/bild/R/getLogLik_bild.R |only bild-1.2-1/bild/R/getcoef_bild.R |only bild-1.2-1/bild/R/getvcov_bild.R |only bild-1.2-1/bild/R/modelmatrix_bild.R |only bild-1.2-1/bild/R/randeff_bild.R |only bild-1.2-1/bild/R/show_bild.R |only bild-1.2-1/bild/R/show_summary.bild.R |only bild-1.2-1/bild/R/summary_bild.R |only bild-1.2-1/bild/R/vareff_bild.R |only bild-1.2-1/bild/man/airpollution.rd |only bild-1.2-1/bild/man/anova-methods.Rd |only bild-1.2-1/bild/man/bild-internal.Rd |only bild-1.2-1/bild/man/fitted-methods.Rd |only bild-1.2-1/bild/man/fixeff-methods.Rd |only bild-1.2-1/bild/man/getAIC-methods.Rd |only bild-1.2-1/bild/man/getLogLik-methods.Rd |only bild-1.2-1/bild/man/getcoef-methods.Rd |only bild-1.2-1/bild/man/getvcov-methods.Rd |only bild-1.2-1/bild/man/locust.rd |only bild-1.2-1/bild/man/modelmatrix-methods.Rd |only bild-1.2-1/bild/man/modelmatrix.Rd |only bild-1.2-1/bild/man/muscatine.rd |only bild-1.2-1/bild/man/plot-methods.Rd |only bild-1.2-1/bild/man/randeff-methods.Rd |only bild-1.2-1/bild/man/show-methods.Rd |only bild-1.2-1/bild/man/summary-methods.Rd |only bild-1.2-1/bild/man/vareff-methods.Rd |only bild-1.3-0/bild/DESCRIPTION | 68 +- bild-1.3-0/bild/MD5 | 91 +-- bild-1.3-0/bild/NAMESPACE | 78 ++ bild-1.3-0/bild/NEWS | 8 bild-1.3-0/bild/R/autoplot.bild.R |only bild-1.3-0/bild/R/bild_main.R |only bild-1.3-0/bild/R/classes_and_generics.R |only bild-1.3-0/bild/R/data.R |only bild-1.3-0/bild/R/methods_complex.R |only bild-1.3-0/bild/R/methods_getters.R |only bild-1.3-0/bild/R/plot_bild_missing.R | 833 ++++++++++++++--------------- bild-1.3-0/bild/R/predict.bild.R |only bild-1.3-0/bild/R/zzz.R |only bild-1.3-0/bild/build |only bild-1.3-0/bild/man/airpollution.Rd |only bild-1.3-0/bild/man/anova-bild-method.Rd |only bild-1.3-0/bild/man/autoplot.bild.Rd |only bild-1.3-0/bild/man/bild-class.Rd | 120 ++-- bild-1.3-0/bild/man/bild-package.Rd | 56 - bild-1.3-0/bild/man/bild.Rd | 231 ++------ bild-1.3-0/bild/man/bildControl.Rd | 48 - bild-1.3-0/bild/man/bildIntegrate.Rd | 143 ++-- bild-1.3-0/bild/man/fitted.bild.Rd |only bild-1.3-0/bild/man/fixeff.Rd | 30 - bild-1.3-0/bild/man/getAIC.Rd | 32 - bild-1.3-0/bild/man/getLogLik.Rd | 33 - bild-1.3-0/bild/man/getVariance.Rd |only bild-1.3-0/bild/man/getcoef.Rd | 30 - bild-1.3-0/bild/man/getvcov.Rd | 31 - bild-1.3-0/bild/man/glance-bild.Rd |only bild-1.3-0/bild/man/locust.Rd |only bild-1.3-0/bild/man/model.mat.Rd |only bild-1.3-0/bild/man/muscatine.Rd |only bild-1.3-0/bild/man/plot-bild-method.Rd |only bild-1.3-0/bild/man/predict.bild.Rd |only bild-1.3-0/bild/man/randeff.Rd | 31 - bild-1.3-0/bild/man/show-bild-method.Rd |only bild-1.3-0/bild/man/summary-bild-method.Rd |only bild-1.3-0/bild/man/summary.bild-class.Rd | 70 +- bild-1.3-0/bild/man/tidy-bild.Rd |only bild-1.3-0/bild/man/vareff.Rd | 31 - 75 files changed, 1016 insertions(+), 948 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020) <doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.6.0 dated 2026-05-29 and 1.0.0 dated 2026-10-14
DESCRIPTION | 21 - MD5 | 91 ++++-- NEWS.md | 86 ++++++ R/compute.ci.R | 72 +++++ R/fwb.R | 398 ++++++++++++++++++++---------- R/fwb.array.R | 79 ++++- R/fwb.ci.R | 52 ++- R/plot.fwb.R | 4 R/set_fwb_wtype.R | 2 R/simultaneous.R | 102 ++++--- R/summary.fwb.R | 18 - R/utils.R | 209 ++++++++++----- R/vcovFWB.R | 267 +++++++++++++++----- R/weighted-statistics.R | 22 - README.md | 134 ++++++---- build/stage23.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/fwb-rep.R |only inst/doc/fwb-rep.Rmd | 115 ++++---- inst/doc/fwb-rep.html | 375 +++++++++++++++------------- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/figures/logo.png |only man/fwb-package.Rd | 2 man/fwb.Rd | 37 +- man/fwb.array.Rd | 4 man/fwb.ci.Rd | 19 + man/plot.fwb.Rd | 2 man/set_fwb_wtype.Rd | 2 man/summary.fwb.Rd | 8 man/vcovFWB.Rd | 28 +- man/w_mean.Rd | 8 tests/testthat/helpers.R | 388 ++++++++++++++++++++++++++++- tests/testthat/setup.R |only tests/testthat/test-boot.R | 2 tests/testthat/test-futurize.R |only tests/testthat/test-fwb-array.R |only tests/testthat/test-fwb-ci.R |only tests/testthat/test-fwb.R | 103 ++++--- tests/testthat/test-input-guards.R |only tests/testthat/test-p-values.R | 18 - tests/testthat/test-plot.R |only tests/testthat/test-progressify.R |only tests/testthat/test-replicability.R |only tests/testthat/test-strata.R |only tests/testthat/test-summary.R |only tests/testthat/test-vcovFWB-internals.R |only tests/testthat/test-vcovFWB.R | 35 -- tests/testthat/test-w_mean.R | 4 tests/testthat/test-weighted-statistics.R |only tests/testthat/test-wtypes.R |only vignettes/fwb-rep.Rmd | 115 ++++---- vignettes/references.bib |only 55 files changed, 1974 insertions(+), 848 deletions(-)
Title: Density Estimation with Semidefinite Programming
Description: The models of probability density functions are Gaussian or
exponential distributions with polynomial correction terms.
Using a maximum likelihood method, 'dsdp' computes parameters of Gaussian
or exponential distributions together with degrees of polynomials by
a grid search, and coefficient of polynomials by a variant of semidefinite
programming. It adopts Akaike Information Criterion for model selection.
See a vignette for a tutorial and more on our 'Github' repository
<https://github.com/tsuchiya-lab/dsdp/>.
Author: Satoshi Kakihara [aut, cre],
Takashi Tsuchiya [aut]
Maintainer: Satoshi Kakihara <skakihara@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2026-08-21
Diff between dsdp versions 0.1.2 dated 2026-08-21 and 0.1.3 dated 2026-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/Tutorial.pdf |binary src/slatec/dgamit.f | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joseph Zemme [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.26 dated 2026-09-10 and 2.7.27 dated 2026-10-14
dataRetrieval-2.7.26/dataRetrieval/man/readNWISuse.Rd |only dataRetrieval-2.7.27/dataRetrieval/DESCRIPTION | 8 dataRetrieval-2.7.27/dataRetrieval/MD5 | 87 +- dataRetrieval-2.7.27/dataRetrieval/NAMESPACE | 1 dataRetrieval-2.7.27/dataRetrieval/NEWS.md | 7 dataRetrieval-2.7.27/dataRetrieval/R/constructNWISURL.R | 8 dataRetrieval-2.7.27/dataRetrieval/R/readNWISdata.R | 191 ++--- dataRetrieval-2.7.27/dataRetrieval/R/readNWISdv.R | 65 - dataRetrieval-2.7.27/dataRetrieval/R/readNWISpCode.R | 194 ++--- dataRetrieval-2.7.27/dataRetrieval/R/readNWISsite.R | 76 +- dataRetrieval-2.7.27/dataRetrieval/R/readNWISunit.R | 380 +++++----- dataRetrieval-2.7.27/dataRetrieval/R/readWQPdata.R | 2 dataRetrieval-2.7.27/dataRetrieval/R/read_waterdata_continuous.R | 2 dataRetrieval-2.7.27/dataRetrieval/R/read_waterdata_field_measurements.R | 2 dataRetrieval-2.7.27/dataRetrieval/R/read_waterdata_field_meta.R | 3 dataRetrieval-2.7.27/dataRetrieval/R/renameColumns.R | 13 dataRetrieval-2.7.27/dataRetrieval/R/whatNWISdata.R | 203 ++--- dataRetrieval-2.7.27/dataRetrieval/R/whatNWISsites.R | 171 ++-- dataRetrieval-2.7.27/dataRetrieval/inst/CITATION | 6 dataRetrieval-2.7.27/dataRetrieval/inst/doc/dataRetrieval.html | 8 dataRetrieval-2.7.27/dataRetrieval/man/get_monitoring_location_arguments.Rd | 32 dataRetrieval-2.7.27/dataRetrieval/man/readNWISdata.Rd | 13 dataRetrieval-2.7.27/dataRetrieval/man/readNWISdv.Rd | 25 dataRetrieval-2.7.27/dataRetrieval/man/readNWISpCode.Rd | 7 dataRetrieval-2.7.27/dataRetrieval/man/readNWISpeak.Rd | 8 dataRetrieval-2.7.27/dataRetrieval/man/readNWISrating.Rd | 12 dataRetrieval-2.7.27/dataRetrieval/man/readNWISsite.Rd | 7 dataRetrieval-2.7.27/dataRetrieval/man/readNWISstat.Rd | 8 dataRetrieval-2.7.27/dataRetrieval/man/readNWISuv.Rd | 14 dataRetrieval-2.7.27/dataRetrieval/man/readWQPdata.Rd | 2 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_combined_meta.Rd | 32 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_continuous.Rd | 7 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_daily.Rd | 4 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_field_measurements.Rd | 9 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_field_meta.Rd | 13 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_latest_continuous.Rd | 2 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_latest_daily.Rd | 4 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_latest_field_measurements.Rd | 4 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_monitoring_location.Rd | 28 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_peaks.Rd | 2 dataRetrieval-2.7.27/dataRetrieval/man/read_waterdata_ts_meta.Rd | 6 dataRetrieval-2.7.27/dataRetrieval/man/renameNWISColumns.Rd | 14 dataRetrieval-2.7.27/dataRetrieval/man/whatNWISdata.Rd | 24 dataRetrieval-2.7.27/dataRetrieval/man/whatNWISsites.Rd | 7 dataRetrieval-2.7.27/dataRetrieval/tests/testthat/tests_general.R | 15 45 files changed, 873 insertions(+), 853 deletions(-)
Title: 'AV1' Video Encoding for Biological Microscopy Data
Description: Converts microscopy video and image data (H.264/H.265,
AVI/MJPEG, TIFF stacks) to the 'AV1' codec for compact storage, and
archives 16-bit image stacks and videos losslessly in the 'FFV1'
format. Encoding runs on the GPU via 'Vulkan' or 'VAAPI' when
available and falls back to the CPU through 'FFmpeg' and 'SVT-AV1'.
Whole experiment folders can be converted at once.
Author: Yuri Baramykov [aut, cre] ,
The Khronos Group Inc. [cph],
FFmpeg developers [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between AV1R versions 0.1.4 dated 2026-10-12 and 0.1.4.1 dated 2026-10-14
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ src/av1r_commands.cpp | 1 + src/av1r_device.cpp | 1 + src/av1r_encode_vulkan.cpp | 1 + src/av1r_ffv1_encoder.h | 1 + src/av1r_ffv1_gpu.cpp | 1 + src/av1r_ffv1_gpu_encoder.cpp | 1 + src/av1r_ffv1_rangecoder.h | 1 + src/av1r_memory.cpp | 1 + src/av1r_mkv_writer.h | 1 + 12 files changed, 29 insertions(+), 14 deletions(-)
Title: Shared Utilities to Extend the 'teal' Modules
Description: Provides decorators, transformators, and utility functions
to extend the 'teal' framework for interactive data analysis
applications. Implements methods for data visualization enhancement,
statistical data transformations, and workflow integration tools.
Designed to support clinical and pharmaceutical research workflows
within the 'teal' ecosystem through modular and reusable components.
Author: Nadia Abraham [aut],
Chanchal Bhalla [aut],
Peyman Eshghi [aut, cre],
Pranith Gourisetty [aut],
Sohan Lal [aut],
Przemyslaw Posiadala [aut],
Alina Tselinina [aut],
Konrad Pagacz [aut],
PHUSE [cph]
Maintainer: Peyman Eshghi <peymaan.es@gmail.com>
Diff between uteals versions 0.0.5 dated 2026-07-09 and 0.0.6 dated 2026-10-14
DESCRIPTION | 10 +++++----- MD5 | 9 ++++++--- NAMESPACE | 1 + NEWS.md | 4 ++++ R/freeze_tables.R |only man/use_freeze_tables.Rd |only tests/testthat/test-freeze_tables.R |only 7 files changed, 16 insertions(+), 8 deletions(-)
Title: Presidential Election Data of "Sri Lanka" from 1982 to 2019
Description: Provides Sri Lankan presidential election results for
1982, 1988, 1994, 1999, 2005, 2010, 2015, and 2019. The datasets
contain candidate vote counts, reported percentages, and summary
statistics for polling divisions and district results, including
postal and displaced votes where available. Results were extracted
from PDF documents and prepared in a consistent tabular format.
Author: Amalan Mahendran [aut, cre]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between SLPresElection versions 1.0.0 dated 2023-01-17 and 1.1.0 dated 2026-10-14
DESCRIPTION | 32 MD5 | 70 + NAMESPACE | 1 R/Data.R | 390 +++++++---- R/zzz.R |only build |only data/Election1982.rda |binary data/Election1988.rda |binary data/Election1994.rda |binary data/Election1999.rda |binary data/Election2005.rda |binary data/Election2010.rda |binary data/Election2015.rda |binary data/Election2019.rda |only inst/WORDLIST | 107 ++- inst/doc |only man/Election1982.Rd | 44 - man/Election1988.Rd | 46 - man/Election1994.Rd | 45 - man/Election1999.Rd | 45 - man/Election2005.Rd | 51 - man/Election2010.Rd | 44 - man/Election2015.Rd | 45 - man/Election2019.Rd |only man/figures/Registered_and_Polled_Votes-1.png |binary man/figures/Registered_and_Polled_Votes_over_the_years-1.png |binary man/figures/Rejected_Votes_over_the_years-1.png |binary vignettes |only 28 files changed, 645 insertions(+), 275 deletions(-)
More information about SLPresElection at CRAN
Permanent link
Title: Interface to the Biological Magnetic Resonance Data Bank
('BMRB')
Description: A comprehensive interface to the Biological Magnetic Resonance
Data Bank ('BMRB') <https://bmrb.io>, mirroring all functionality of the
'PyBMRB' 'Python' package (v3.0). Provides four modules: (1) 'ChemicalShift'
for fetching per-entry chemical shift data from the 'BMRB' 'REST' 'API'
or local 'NMR-STAR' files; (2) 'ChemicalShiftStatistics' for database-wide
statistical queries; (3) Spectra for simulating '1H-15N' 'HSQC', '1H-13C'
'HSQC', '1H-1H' 'TOCSY', and generic 2D 'NMR' spectra as interactive plots;
and (4) Histogram for chemical shift distribution visualizations with
optional filtering by pH, temperature, and ambiguity code.
All interactive plots are rendered via 'plotly'.
Uses the 'BMRB' REST API v2 <https://api.bmrb.io/v2/>.
Author: Kumaran Baskaran [aut, cre]
Maintainer: Kumaran Baskaran <baskaran@uchc.edu>
This is a re-admission after prior archival of version 2.1.7 dated 2021-07-11
Diff between RBMRB versions 2.1.7 dated 2021-07-11 and 3.0.0 dated 2026-10-14
RBMRB-2.1.7/RBMRB/R/RBMRB.R |only RBMRB-2.1.7/RBMRB/man/HSQC_13C.Rd |only RBMRB-2.1.7/RBMRB/man/HSQC_15N.Rd |only RBMRB-2.1.7/RBMRB/man/TOCSY.Rd |only RBMRB-2.1.7/RBMRB/man/atom_chem_shift_corr.Rd |only RBMRB-2.1.7/RBMRB/man/chem_shift_corr.Rd |only RBMRB-2.1.7/RBMRB/man/chemical_shift_hist.Rd |only RBMRB-2.1.7/RBMRB/man/chemical_shift_hist_res.Rd |only RBMRB-2.1.7/RBMRB/man/chemical_shift_hists.Rd |only RBMRB-2.1.7/RBMRB/man/convert_cs_to_c13hsqc.Rd |only RBMRB-2.1.7/RBMRB/man/convert_cs_to_n15hsqc.Rd |only RBMRB-2.1.7/RBMRB/man/convert_cs_to_tocsy.Rd |only RBMRB-2.1.7/RBMRB/man/export_star_data.Rd |only RBMRB-2.1.7/RBMRB/man/fetch_atom_chemical_shifts.Rd |only RBMRB-2.1.7/RBMRB/man/fetch_entry_chemical_shifts.Rd |only RBMRB-2.1.7/RBMRB/man/fetch_entry_cs.Rd |only RBMRB-2.1.7/RBMRB/man/fetch_res_chemical_shifts.Rd |only RBMRB-2.1.7/RBMRB/man/filter_outlier.Rd |only RBMRB-2.1.7/RBMRB/man/filter_residue.Rd |only RBMRB-2.1.7/RBMRB/man/makeRandomString.Rd |only RBMRB-3.0.0/RBMRB/DESCRIPTION | 60 ++++++++----- RBMRB-3.0.0/RBMRB/MD5 | 83 +++++++++++++------ RBMRB-3.0.0/RBMRB/NAMESPACE | 56 ++++++++---- RBMRB-3.0.0/RBMRB/NEWS.md |only RBMRB-3.0.0/RBMRB/R/api_utils.R |only RBMRB-3.0.0/RBMRB/R/chemical_shift.R |only RBMRB-3.0.0/RBMRB/R/chemical_shift_statistics.R |only RBMRB-3.0.0/RBMRB/R/colors.R |only RBMRB-3.0.0/RBMRB/R/histogram.R |only RBMRB-3.0.0/RBMRB/R/nmrstar_parser.R |only RBMRB-3.0.0/RBMRB/R/spectra.R |only RBMRB-3.0.0/RBMRB/R/utils.R |only RBMRB-3.0.0/RBMRB/R/zzz.R |only RBMRB-3.0.0/RBMRB/README.md |only RBMRB-3.0.0/RBMRB/build |only RBMRB-3.0.0/RBMRB/inst |only RBMRB-3.0.0/RBMRB/man/RBMRB-package.Rd |only RBMRB-3.0.0/RBMRB/man/RBMRB_version.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_citation.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_debug_entry.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_fetch_entry.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_from_pdb.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_list_entries.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_pdb_ids.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_search.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_status.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_test.Rd |only RBMRB-3.0.0/RBMRB/man/bmrb_upload_entry.Rd |only RBMRB-3.0.0/RBMRB/man/c13hsqc.Rd |only RBMRB-3.0.0/RBMRB/man/conditional_cs_hist.Rd |only RBMRB-3.0.0/RBMRB/man/create_2d_peaklist.Rd |only RBMRB-3.0.0/RBMRB/man/create_c13hsqc_peaklist.Rd |only RBMRB-3.0.0/RBMRB/man/create_n15hsqc_peaklist.Rd |only RBMRB-3.0.0/RBMRB/man/create_tocsy_peaklist.Rd |only RBMRB-3.0.0/RBMRB/man/cs_from_bmrb.Rd |only RBMRB-3.0.0/RBMRB/man/cs_from_file.Rd |only RBMRB-3.0.0/RBMRB/man/cs_hist.Rd |only RBMRB-3.0.0/RBMRB/man/cs_hist2d.Rd |only RBMRB-3.0.0/RBMRB/man/cs_peek.Rd |only RBMRB-3.0.0/RBMRB/man/cs_stats.Rd |only RBMRB-3.0.0/RBMRB/man/cs_summary.Rd |only RBMRB-3.0.0/RBMRB/man/cs_table.Rd |only RBMRB-3.0.0/RBMRB/man/cs_to_df.Rd |only RBMRB-3.0.0/RBMRB/man/export_peak_list.Rd |only RBMRB-3.0.0/RBMRB/man/filter_cs_outliers.Rd |only RBMRB-3.0.0/RBMRB/man/generic_2d.Rd |only RBMRB-3.0.0/RBMRB/man/get_2d_cs_data.Rd |only RBMRB-3.0.0/RBMRB/man/get_cs_data.Rd |only RBMRB-3.0.0/RBMRB/man/get_cs_from_bmrb_db.Rd |only RBMRB-3.0.0/RBMRB/man/n15hsqc.Rd |only RBMRB-3.0.0/RBMRB/man/standard_amino_acids.Rd |only RBMRB-3.0.0/RBMRB/man/standard_nucleic_acids.Rd |only RBMRB-3.0.0/RBMRB/man/tocsy.Rd |only RBMRB-3.0.0/RBMRB/tests |only RBMRB-3.0.0/RBMRB/vignettes |only 75 files changed, 135 insertions(+), 64 deletions(-)
Title: Gaussian Kernel Robust Regression (GKRReg)
Description: Implements the Gaussian Kernel Robust Regression (GKRReg / GKRR)
method proposed by De Carvalho, Lima Neto and Ferreira (2017)
<doi:10.1016/j.neucom.2016.12.035>. The method re-weights observations
iteratively using the Gaussian kernel so that poorly-fitted observations
(outliers, leverage points) receive small weights, yielding resistance to
Y-space outliers, X-space outliers and leverage points. Convergence is
guaranteed by Propositions 4.1 and 4.2 of the original paper. Four
estimators for the kernel width hyper-parameter are provided (S1: Caputo,
S2: pairwise median, S3: residual variance, S4: corrected Akaike
bandwidth), together with a data-driven selection rule. Inference is
provided by a sandwich variance estimator with a family of
heteroskedasticity-consistent finite-sample corrections adapted to the
weighted leverage of the method, or by a pairs bootstrap that re-estimates
the kernel width on each replicate (percentile, normal and bias-corrected
accelerated intervals wi [...truncated...]
Author: Eufrasio de Andrade Lima Neto [aut],
Marcelo Rodrigo Portela Ferreira [aut, cre]
Maintainer: Marcelo Rodrigo Portela Ferreira <marcelo@de.ufpb.br>
Diff between gkrreg versions 0.4.0 dated 2026-06-17 and 0.5.0 dated 2026-10-14
gkrreg-0.4.0/gkrreg/inst/doc/introduction.R |only gkrreg-0.4.0/gkrreg/inst/doc/introduction.Rmd |only gkrreg-0.4.0/gkrreg/inst/doc/introduction.html |only gkrreg-0.4.0/gkrreg/vignettes/introduction.Rmd |only gkrreg-0.5.0/gkrreg/DESCRIPTION | 25 +++++---- gkrreg-0.5.0/gkrreg/MD5 | 55 +++++++++++--------- gkrreg-0.5.0/gkrreg/NAMESPACE | 4 + gkrreg-0.5.0/gkrreg/NEWS.md | 47 +++++++++++++++++ gkrreg-0.5.0/gkrreg/R/data.R | 12 ++-- gkrreg-0.5.0/gkrreg/R/gkrr.R | 48 ++++++++++++++--- gkrreg-0.5.0/gkrreg/R/gkrr_boot.R | 12 +++- gkrreg-0.5.0/gkrreg/R/gkrr_vcov.R |only gkrreg-0.5.0/gkrreg/R/gkrreg-package.R | 3 - gkrreg-0.5.0/gkrreg/build/partial.rdb |binary gkrreg-0.5.0/gkrreg/build/vignette.rds |binary gkrreg-0.5.0/gkrreg/inst/doc/gkrreg.R |only gkrreg-0.5.0/gkrreg/inst/doc/gkrreg.Rmd |only gkrreg-0.5.0/gkrreg/inst/doc/gkrreg.html |only gkrreg-0.5.0/gkrreg/man/belgium_calls.Rd | 2 gkrreg-0.5.0/gkrreg/man/cloud_point.Rd | 2 gkrreg-0.5.0/gkrreg/man/delivery.Rd | 2 gkrreg-0.5.0/gkrreg/man/gkrr.Rd | 9 ++- gkrreg-0.5.0/gkrreg/man/gkrr_jackknife.Rd |only gkrreg-0.5.0/gkrreg/man/gkrr_vcov.Rd |only gkrreg-0.5.0/gkrreg/man/gkrr_vcov_all.Rd |only gkrreg-0.5.0/gkrreg/man/gkrreg-package.Rd | 3 - gkrreg-0.5.0/gkrreg/man/kootenay.Rd | 2 gkrreg-0.5.0/gkrreg/man/mammals.Rd | 2 gkrreg-0.5.0/gkrreg/man/sigma2_estimators.Rd | 6 +- gkrreg-0.5.0/gkrreg/man/stars_cyg.Rd | 2 gkrreg-0.5.0/gkrreg/man/vcov.gkrr.Rd |only gkrreg-0.5.0/gkrreg/tests/testthat.R |only gkrreg-0.5.0/gkrreg/tests/testthat/test-gkrr-vcov.R |only gkrreg-0.5.0/gkrreg/tests/testthat/test-gkrr.R | 5 - gkrreg-0.5.0/gkrreg/vignettes/gkrreg.Rmd |only gkrreg-0.5.0/gkrreg/vignettes/references.bib | 42 +++++++++++++++ 36 files changed, 215 insertions(+), 68 deletions(-)
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation, and a function to compute global network measures. Significance tests, including permutation testing, and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre] ,
Yoed N. Kenett [aut, ctb]
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 2.0.0 dated 2026-09-12 and 2.1.0 dated 2026-10-14
SemNeT-2.0.0/SemNeT/NEWS.md |only SemNeT-2.0.0/SemNeT/man/responses_to_binary.Rd |only SemNeT-2.0.0/SemNeT/tests |only SemNeT-2.1.0/SemNeT/DESCRIPTION | 12 SemNeT-2.1.0/SemNeT/MD5 | 171 - SemNeT-2.1.0/SemNeT/NAMESPACE | 11 SemNeT-2.1.0/SemNeT/NEWS |only SemNeT-2.1.0/SemNeT/R/SemNeT-package.R | 6 SemNeT-2.1.0/SemNeT/R/SemNeTShiny.R | 13 SemNeT-2.1.0/SemNeT/R/aspl.R | 146 - SemNeT-2.1.0/SemNeT/R/bootstrap_SemNeT.R | 751 +++-- SemNeT-2.1.0/SemNeT/R/bootstrap_test_SemNeT.R | 1737 ++++++++++-- SemNeT-2.1.0/SemNeT/R/cc.R | 112 SemNeT-2.1.0/SemNeT/R/cn.R | 300 +- SemNeT-2.1.0/SemNeT/R/compare_networks.R | 165 - SemNeT-2.1.0/SemNeT/R/convert2cytoscape.R | 31 SemNeT-2.1.0/SemNeT/R/convert2igraph.R | 31 SemNeT-2.1.0/SemNeT/R/equate.R | 88 SemNeT-2.1.0/SemNeT/R/finalize.R | 53 SemNeT-2.1.0/SemNeT/R/forward_flow.R | 226 + SemNeT-2.1.0/SemNeT/R/helpers.R | 928 ++++-- SemNeT-2.1.0/SemNeT/R/legacy.R | 301 +- SemNeT-2.1.0/SemNeT/R/nrw.R | 130 SemNeT-2.1.0/SemNeT/R/permutation_SemNeT.R | 1008 +++++- SemNeT-2.1.0/SemNeT/R/pf.R | 345 +- SemNeT-2.1.0/SemNeT/R/plot.bootstrap_SemNeT.R | 192 - SemNeT-2.1.0/SemNeT/R/q.R | 114 SemNeT-2.1.0/SemNeT/R/random_network_test.R | 272 + SemNeT-2.1.0/SemNeT/R/random_walk.R | 338 +- SemNeT-2.1.0/SemNeT/R/response_analysis.R | 218 + SemNeT-2.1.0/SemNeT/R/semantic_network_measures.R | 118 SemNeT-2.1.0/SemNeT/R/shiny_helpers.R | 120 SemNeT-2.1.0/SemNeT/R/similarity.R | 134 SemNeT-2.1.0/SemNeT/R/simulate_fluency.R | 72 SemNeT-2.1.0/SemNeT/R/tmfg.R | 207 + SemNeT-2.1.0/SemNeT/R/zzz.R | 56 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_bootstrap.R | 251 + SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_export.R | 94 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_load_data.R | 206 + SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_network_estimation.R | 104 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_permutation.R | 145 - SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_random_network.R | 76 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_random_walk.R | 97 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_shared.R | 144 SemNeT-2.1.0/SemNeT/inst/Shiny/R/mod_spreading_activation.R | 107 SemNeT-2.1.0/SemNeT/inst/Shiny/global.R | 43 SemNeT-2.1.0/SemNeT/inst/Shiny/server.R | 67 SemNeT-2.1.0/SemNeT/inst/Shiny/ui.R | 34 SemNeT-2.1.0/SemNeT/man/aspl.Rd | 46 SemNeT-2.1.0/SemNeT/man/binary2responses.Rd |only SemNeT-2.1.0/SemNeT/man/bootstrap_SemNeT.Rd | 144 SemNeT-2.1.0/SemNeT/man/bootstrap_test_SemNeT.Rd | 256 + SemNeT-2.1.0/SemNeT/man/cc.Rd | 19 SemNeT-2.1.0/SemNeT/man/cn.Rd | 22 SemNeT-2.1.0/SemNeT/man/compare_networks.Rd | 4 SemNeT-2.1.0/SemNeT/man/find_textcleaner_objects.Rd |only SemNeT-2.1.0/SemNeT/man/forward_flow.Rd | 7 SemNeT-2.1.0/SemNeT/man/nrw.Rd | 13 SemNeT-2.1.0/SemNeT/man/permutation_SemNeT.Rd | 236 + SemNeT-2.1.0/SemNeT/man/pf.Rd | 47 SemNeT-2.1.0/SemNeT/man/plot.bootstrap_SemNeT.Rd | 19 SemNeT-2.1.0/SemNeT/man/q.Rd | 18 SemNeT-2.1.0/SemNeT/man/randnet.test.Rd | 7 SemNeT-2.1.0/SemNeT/man/random_network_test.Rd | 60 SemNeT-2.1.0/SemNeT/man/random_walk.Rd | 44 SemNeT-2.1.0/SemNeT/man/randwalk.Rd | 6 SemNeT-2.1.0/SemNeT/man/response_analysis.Rd | 40 SemNeT-2.1.0/SemNeT/man/responses2binary.Rd |only SemNeT-2.1.0/SemNeT/man/semantic_network_measures.Rd | 35 SemNeT-2.1.0/SemNeT/man/similarity.Rd | 22 SemNeT-2.1.0/SemNeT/man/simulate_fluency.Rd | 9 SemNeT-2.1.0/SemNeT/man/test.bootSemNeT.Rd | 18 SemNeT-2.1.0/SemNeT/man/tmfg.Rd | 20 SemNeT-2.1.0/SemNeT/src/init.c | 18 SemNeT-2.1.0/SemNeT/src/louvain.c | 5 SemNeT-2.1.0/SemNeT/src/modularity.c | 10 SemNeT-2.1.0/SemNeT/src/xoshiro.c | 6 77 files changed, 8472 insertions(+), 2433 deletions(-)
Title: Lightweight Hardware and GPU Compute Detection
Description: Detects central processing unit topology, process-available cores,
host and container memory, graphics processing unit hardware, and reports
the apparent availability of 'CUDA', 'Metal', 'ROCm',
and 'OpenCL' compute backends, with a read-only shared-library inventory for
the 'CUDA' runtime, 'cuBLAS', 'cuFFT', 'cuSOLVER', 'cuRAND', and optional
'NCCL' libraries. Detection uses operating-system information,
documented platform interfaces, and optional command-line utilities,
without requiring a GPU framework, 'Python', or a vendor software
development kit. Backend interpretation follows the official 'CUDA'
<https://docs.nvidia.com/cuda/cuda-driver-api/>, 'Metal'
<https://developer.apple.com/documentation/metal>, 'ROCm'
<https://rocm.docs.amd.com/>, and 'OpenCL'
<https://registry.khronos.org/OpenCL/> documentation. 'NCCL' version
inspection follows its documented API
<https://docs.nvidia.com/deeplearning/nccl/user-guide/docs/api/comms.html>.
Process-level GPU [...truncated...]
Author: Stefano Cacciatore [aut, cre]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between gpuinfo versions 0.1.0 dated 2026-09-26 and 0.2.0 dated 2026-10-14
DESCRIPTION | 21 + MD5 | 82 ++++-- NAMESPACE | 14 + NEWS.md |only R/accelerator.R | 8 R/cuda-build.R |only R/cuda-libraries.R |only R/cuda-preflight.R |only R/cuda.R | 447 +++++++++++++++++++++++++--------- R/environment.R | 7 R/gpu.R | 165 +++++++++--- R/gpuinfo-package.R | 15 - R/manifest.R |only R/memory-sampler.R |only R/native.R | 77 ++++- R/nccl.R |only R/sitrep.R | 70 ++++- R/system.R | 376 +++++++++++++++++++++++++--- R/utils.R | 29 ++ README.md | 137 +++++++++- inst/VALIDATION.md | 13 inst/doc/hardware-validation.R | 19 + inst/doc/hardware-validation.Rmd | 96 ++++++- inst/doc/hardware-validation.html | 159 +++++++++--- inst/extdata/validation.csv | 5 man/cpu_info.Rd |only man/cuda_build_info.Rd |only man/cuda_info.Rd |only man/cuda_libraries.Rd |only man/cuda_preflight.Rd |only man/gpu_devices.Rd |only man/gpu_memory_info.Rd |only man/gpu_memory_peak.Rd |only man/gpu_memory_sample.Rd |only man/gpu_sitrep.Rd | 4 man/gpuinfo-package.Rd | 15 - man/hardware_info.Rd | 31 +- man/hardware_manifest.Rd |only man/has_cuda.Rd | 22 - man/nccl_info.Rd |only man/system_memory_info.Rd |only src/gpuinfo.c | 299 ++++++++++++++++++++-- src/init.c | 6 tests/testthat/test-api.R | 8 tests/testthat/test-capabilities.R | 2 tests/testthat/test-cuda-build.R |only tests/testthat/test-cuda-components.R |only tests/testthat/test-cuda-libraries.R |only tests/testthat/test-info.R | 59 ++++ tests/testthat/test-memory-sampler.R |only tests/testthat/test-nccl.R |only tests/testthat/test-system.R |only tools/validate-cuda-hardware.R |only tools/validate-hardware.R | 17 + vignettes/hardware-validation.Rmd | 96 ++++++- 55 files changed, 1892 insertions(+), 407 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 1.3.1 dated 2026-09-15 and 1.4.0 dated 2026-10-14
DESCRIPTION | 8 +-- MD5 | 44 ++++++++++------ NAMESPACE | 2 NEWS.md | 8 +++ R/MaestroPipeline.R | 51 +++++++++++++++++++ R/MaestroPipelineList.R | 11 ++++ R/MaestroSchedule.R | 29 ++++++++--- R/metrics.R |only build/vignette.rds |binary inst/doc/maestro-1-quick-start.html | 4 - inst/doc/maestro-3-advanced-scheduling.html | 6 +- inst/doc/maestro-4-directed-acyclic-graphs.html | 20 +++---- inst/doc/maestro-4b-directed-acyclic-graphs.html | 44 ++++++++-------- inst/doc/maestro-5-logging.html | 60 +++++++++++------------ inst/doc/maestro-8-conditionals.html | 36 ++++++------- inst/doc/maestro-9-metrics.R |only inst/doc/maestro-9-metrics.html |only inst/doc/maestro-9-metrics.qmd |only man/MaestroPipeline.Rd | 47 ++++++++++++++++++ man/MaestroPipelineList.Rd | 16 ++++++ man/MaestroSchedule.Rd | 16 ++++++ man/get_metrics.Rd |only man/update_metric.Rd |only tests/testthat/test-metrics.R |only tests/testthat/test-multicore.R | 31 +++++++++++ tests/testthat/test_pipelines_run_metrics |only tests/testthat/test_pipelines_run_rng_warning |only vignettes/maestro-9-metrics.qmd |only 28 files changed, 319 insertions(+), 114 deletions(-)
Title: Use Images in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system. Images can be drawn at data points, used as the
background of a plot, or embedded as a sub-plot, and can be read from local
files or downloaded from remote services such as 'Pokemon', 'PhyloPic', and
emoji and icon collections. An interactive geom is provided for 'HTML'
output.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [ctb] ,
Yonghe Xia [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.3.6 dated 2026-09-27 and 0.3.7 dated 2026-10-14
ggimage-0.3.6/ggimage/R/color_image.R |only ggimage-0.3.6/ggimage/R/geom_twitchemote.R |only ggimage-0.3.7/ggimage/DESCRIPTION | 23 ggimage-0.3.7/ggimage/MD5 | 90 ++- ggimage-0.3.7/ggimage/NAMESPACE | 11 ggimage-0.3.7/ggimage/R/draw_key.R | 39 + ggimage-0.3.7/ggimage/R/geom_bgimage.R | 121 ++++- ggimage-0.3.7/ggimage/R/geom_emoji.R | 6 ggimage-0.3.7/ggimage/R/geom_flag.R | 85 +-- ggimage-0.3.7/ggimage/R/geom_icon.R | 5 ggimage-0.3.7/ggimage/R/geom_image.R | 184 ++++++- ggimage-0.3.7/ggimage/R/geom_image_repel.R | 135 ++++- ggimage-0.3.7/ggimage/R/geom_interactive.R | 4 ggimage-0.3.7/ggimage/R/geom_phylopic.R | 176 ++++++- ggimage-0.3.7/ggimage/R/geom_subview.R | 157 ++++++ ggimage-0.3.7/ggimage/R/ggbackground.R | 74 ++- ggimage-0.3.7/ggimage/R/ggpreview.R | 7 ggimage-0.3.7/ggimage/R/image_read2.R | 62 +- ggimage-0.3.7/ggimage/R/theme.R | 5 ggimage-0.3.7/ggimage/R/utilities.R | 59 ++ ggimage-0.3.7/ggimage/build |only ggimage-0.3.7/ggimage/inst/doc |only ggimage-0.3.7/ggimage/man/clear_image_cache.Rd |only ggimage-0.3.7/ggimage/man/draw_key.Rd | 6 ggimage-0.3.7/ggimage/man/geom_bgimage.Rd | 48 + ggimage-0.3.7/ggimage/man/geom_image.Rd | 27 + ggimage-0.3.7/ggimage/man/geom_image_repel.Rd | 43 + ggimage-0.3.7/ggimage/man/geom_subview.Rd | 27 + ggimage-0.3.7/ggimage/man/ggbackground.Rd | 5 ggimage-0.3.7/ggimage/man/ggimage-package.Rd | 4 ggimage-0.3.7/ggimage/tests/testthat/helper-docs.R |only ggimage-0.3.7/ggimage/tests/testthat/helper-grobs.R |only ggimage-0.3.7/ggimage/tests/testthat/test-draw-key.R | 127 +++++ ggimage-0.3.7/ggimage/tests/testthat/test-geom-bgimage.R | 241 +++++++++- ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-aesthetics.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-alpha.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-by-height.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-cache.R | 143 +++++ ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-failures.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-list-column.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-repel-cleanup.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-repel-example.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-repel-hjust.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-image-repel.R | 111 ++++ ggimage-0.3.7/ggimage/tests/testthat/test-geom-interactive.R |only ggimage-0.3.7/ggimage/tests/testthat/test-geom-phylopic.R | 213 ++++++++ ggimage-0.3.7/ggimage/tests/testthat/test-geom-subview-compat.R |only ggimage-0.3.7/ggimage/tests/testthat/test-get-github-files.R |only ggimage-0.3.7/ggimage/tests/testthat/test-ggbackground.R | 99 ++++ ggimage-0.3.7/ggimage/tests/testthat/test-ggpreview.R |only ggimage-0.3.7/ggimage/tests/testthat/test-image-file-readers.R |only ggimage-0.3.7/ggimage/tests/testthat/test-image-read2.R | 132 +++++ ggimage-0.3.7/ggimage/tests/testthat/test-repel-broadphase.R | 59 ++ ggimage-0.3.7/ggimage/tests/testthat/test-theme.R |only ggimage-0.3.7/ggimage/tests/testthat/test-url-validation.R | 188 +++++++ ggimage-0.3.7/ggimage/vignettes |only 56 files changed, 2458 insertions(+), 258 deletions(-)
Title: Effect Stars
Description: Provides functions for the method of effect stars as proposed by Tutz and Schauberger (2013) <doi:10.1080/10618600.2012.701379>. Effect stars can be used to visualize estimates of parameters corresponding to different groups, for example in multinomial logit models. Beside the main function 'effectstars' there exist methods for special objects, for example for 'vglm' objects from the 'VGAM' package.
Author: Gunther Schauberger [aut, cre]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between EffectStars2 versions 0.1-3 dated 2019-10-22 and 0.1-4 dated 2026-10-14
DESCRIPTION | 16 ++++++++++------ MD5 | 16 ++++++++-------- R/effect.stars.vglm.R | 4 +++- man/effectstars.default.Rd | 16 ++++++++++++---- man/effectstars.vglm.Rd | 3 +-- man/election.Rd | 6 ++++-- man/insolvency.Rd | 6 ++++-- man/plebiscite.Rd | 6 ++++-- man/star.ctrl.Rd | 20 +++++++++++++++----- 9 files changed, 61 insertions(+), 32 deletions(-)
Title: Visualization of Categorical Response Models
Description: Notice: The package EffectStars2 provides a more up-to-date implementation of effect stars! EffectStars provides functions to visualize regression models with categorical response as proposed by Tutz and Schauberger (2013) <doi:10.1080/10618600.2012.701379>. The effects of the variables are plotted with star plots in order to allow for an optical impression of the fitted model.
Author: Gunther Schauberger [aut, cre]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between EffectStars versions 1.9-1 dated 2019-10-22 and 1.9-2 dated 2026-10-14
DESCRIPTION | 14 +++++++++----- MD5 | 4 ++-- man/alligator.Rd | 2 +- 3 files changed, 12 insertions(+), 8 deletions(-)
Title: The Scaled von Mises-Fisher Distribution
Description: Functions to perform maximum likelihood estimation of and random value simulation from the scaled von Mises-Fisher distribution. The distribution is elliptical symmetric and can be applied to spherical and hyper-spherical data. The reference paper is Scealy J.L. and Wood A.T.A. (2019), <doi:10.1080/01621459.2019.1585249>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between svmf versions 1.0 dated 2026-06-18 and 1.1 dated 2026-10-14
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/dsvmf.R |only R/svmf.mle.R | 94 ++++++---------------------------------------------- man/dsvmf.Rd |only man/svmf-package.Rd | 4 +- 6 files changed, 23 insertions(+), 91 deletions(-)
Title: Access the 'IBGE' Aggregate Data API from 'R'
Description: 'Tidyverse'-friendly interface to the Brazilian Institute of Geography and Statistics ('IBGE') aggregate data 'API'
<https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Query aggregates, variables, localities, periods, and metadata
from surveys and censuses conducted by 'IBGE'.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Allan Quadros [rev] ,
Diana Garcia-Cortes [rev]
Maintainer: Andre Leite <leite@castlab.org>
Diff between ibger versions 0.2.0 dated 2026-07-08 and 0.2.1 dated 2026-10-14
ibger-0.2.0/ibger/inst/doc/api-concepts.R |only ibger-0.2.0/ibger/inst/doc/getting-started.R |only ibger-0.2.0/ibger/inst/doc/ipca-example.R |only ibger-0.2.0/ibger/inst/doc/tutorial.R |only ibger-0.2.1/ibger/DESCRIPTION | 59 ibger-0.2.1/ibger/MD5 | 129 - ibger-0.2.1/ibger/NAMESPACE | 1 ibger-0.2.1/ibger/NEWS.md | 118 + ibger-0.2.1/ibger/R/agregados.R | 129 - ibger-0.2.1/ibger/R/chunking.R | 69 ibger-0.2.1/ibger/R/ibger-package.R | 5 ibger-0.2.1/ibger/R/localidades.R | 55 ibger-0.2.1/ibger/R/metadados.R | 244 +- ibger-0.2.1/ibger/R/periodos.R | 6 ibger-0.2.1/ibger/R/shiny.R | 38 ibger-0.2.1/ibger/R/sidra_url.R | 676 +++--- ibger-0.2.1/ibger/R/subjects.R | 40 ibger-0.2.1/ibger/R/surveys.R | 285 +- ibger-0.2.1/ibger/R/utils.R | 54 ibger-0.2.1/ibger/R/validacao.R | 246 +- ibger-0.2.1/ibger/R/variaveis.R | 24 ibger-0.2.1/ibger/README.md | 131 - ibger-0.2.1/ibger/build/vignette.rds |binary ibger-0.2.1/ibger/inst/doc/api-concepts.Rmd | 567 ++++- ibger-0.2.1/ibger/inst/doc/api-concepts.html | 642 ++++- ibger-0.2.1/ibger/inst/doc/getting-started.Rmd | 991 +++++++- ibger-0.2.1/ibger/inst/doc/getting-started.html | 1114 +++++++--- ibger-0.2.1/ibger/inst/doc/ipca-example.Rmd | 199 + ibger-0.2.1/ibger/inst/doc/ipca-example.html | 222 + ibger-0.2.1/ibger/inst/doc/tutorial.Rmd | 254 +- ibger-0.2.1/ibger/inst/doc/tutorial.html | 191 + ibger-0.2.1/ibger/inst/httptest2 |only ibger-0.2.1/ibger/inst/shiny/explorer/app.R | 83 ibger-0.2.1/ibger/man/fetch_sidra_url.Rd | 10 ibger-0.2.1/ibger/man/ibge_aggregates.Rd | 38 ibger-0.2.1/ibger/man/ibge_clear_cache.Rd | 4 ibger-0.2.1/ibger/man/ibge_explorer.Rd | 12 ibger-0.2.1/ibger/man/ibge_localities.Rd | 13 ibger-0.2.1/ibger/man/ibge_metadata.Rd | 5 ibger-0.2.1/ibger/man/ibge_periods.Rd | 5 ibger-0.2.1/ibger/man/ibge_survey_metadata.Rd | 9 ibger-0.2.1/ibger/man/ibge_survey_periods.Rd | 7 ibger-0.2.1/ibger/man/ibge_surveys.Rd | 8 ibger-0.2.1/ibger/man/ibge_variables.Rd | 14 ibger-0.2.1/ibger/man/ibger-package.Rd | 24 ibger-0.2.1/ibger/man/parse_ibge_value.Rd | 5 ibger-0.2.1/ibger/man/parse_sidra_url.Rd | 10 ibger-0.2.1/ibger/tests/testthat/api |only ibger-0.2.1/ibger/tests/testthat/helper-meta.R |only ibger-0.2.1/ibger/tests/testthat/test-aggregates.R |only ibger-0.2.1/ibger/tests/testthat/test-api.R |only ibger-0.2.1/ibger/tests/testthat/test-chunking.R | 89 ibger-0.2.1/ibger/tests/testthat/test-localities.R |only ibger-0.2.1/ibger/tests/testthat/test-parse-variables.R |only ibger-0.2.1/ibger/tests/testthat/test-sidra-url.R |only ibger-0.2.1/ibger/tests/testthat/test-subjects.R |only ibger-0.2.1/ibger/tests/testthat/test-utils.R |only ibger-0.2.1/ibger/tests/testthat/test-validacao.R |only ibger-0.2.1/ibger/vignettes/api-concepts.Rmd | 567 ++++- ibger-0.2.1/ibger/vignettes/getting-started.Rmd | 991 +++++++- ibger-0.2.1/ibger/vignettes/ipca-example-unnamed-chunk-11-1.png |only ibger-0.2.1/ibger/vignettes/ipca-example-unnamed-chunk-6-1.png |only ibger-0.2.1/ibger/vignettes/ipca-example-unnamed-chunk-7-1.png |only ibger-0.2.1/ibger/vignettes/ipca-example-unnamed-chunk-9-1.png |only ibger-0.2.1/ibger/vignettes/ipca-example.Rmd | 199 + ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-12-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-15-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-17-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-19-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-22-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-25-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-28-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-30-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-32-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-6-1.png |only ibger-0.2.1/ibger/vignettes/tutorial-unnamed-chunk-9-1.png |only ibger-0.2.1/ibger/vignettes/tutorial.Rmd | 254 +- 77 files changed, 6725 insertions(+), 2111 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'Typst', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint', R 'Grid Graphics' and
'patchwork'. 'R Markdown', 'Quarto' and the package 'officer' can be
used to produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.10.1 dated 2026-09-10 and 0.10.3 dated 2026-10-14
DESCRIPTION | 6 +- MD5 | 30 +++++----- NEWS.md | 20 ++++++ R/as_flextable_rtables.R | 18 ++---- R/as_flextable_tabulator.R | 6 +- R/flextable.R | 2 R/flextable_sizes.R | 97 +++++++++++++++++++++++++++++++-- inst/examples/rmd/captions_example.Rmd | 28 ++++----- inst/examples/rmd/demo.Rmd | 26 ++++---- man/as_flextable.TableTree.Rd | 18 +++--- man/set_caption.Rd | 2 man/tabulator.Rd | 6 +- tests/testthat/rmd/captions.Rmd | 4 - tests/testthat/test-captions-rmd.R | 14 +++- tests/testthat/test-df_printer.R | 2 tests/testthat/test-fit_columns.R | 59 ++++++++++++++++++++ 16 files changed, 255 insertions(+), 83 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully
configurable HTTP/FTP requests where responses can be processed in memory, on
disk, or streaming via the callback or connection interfaces. Some knowledge
of 'libcurl' is recommended; for a more-user-friendly web client see the
'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 8.0.0 dated 2026-08-25 and 8.1.0 dated 2026-10-14
DESCRIPTION | 6 +- MD5 | 24 +++++----- NEWS | 5 ++ R/parser.R | 6 -- R/utilities.R | 8 +-- inst/doc/intro.html | 96 +++++++++++++++++++++---------------------- inst/doc/windows.html | 2 src/findport.c | 2 src/form.c | 3 + src/utils.c | 22 ++++++++- tests/testthat/test-parser.R | 5 ++ tests/testthat/test-post.R | 7 ++- tools/winlibs.R | 6 +- 13 files changed, 110 insertions(+), 82 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 1.0.4 dated 2026-05-13 and 2.0.0 dated 2026-10-14
BayesSIM-1.0.4/BayesSIM/R/utils.R |only BayesSIM-2.0.0/BayesSIM/DESCRIPTION | 15 BayesSIM-2.0.0/BayesSIM/MD5 | 111 BayesSIM-2.0.0/BayesSIM/NAMESPACE | 81 BayesSIM-2.0.0/BayesSIM/NEWS.md |only BayesSIM-2.0.0/BayesSIM/R/bayesSIM.R | 72 BayesSIM-2.0.0/BayesSIM/R/bsFisher-functions.R | 676 +- BayesSIM-2.0.0/BayesSIM/R/bsFisher-sampler.R | 190 BayesSIM-2.0.0/BayesSIM/R/bsFisher.R | 1149 +-- BayesSIM-2.0.0/BayesSIM/R/bsPolar.R | 727 +- BayesSIM-2.0.0/BayesSIM/R/bsSphere-functions.R | 1124 +-- BayesSIM-2.0.0/BayesSIM/R/bsSphere-sampler.R | 924 +-- BayesSIM-2.0.0/BayesSIM/R/bsSphere.R | 820 +- BayesSIM-2.0.0/BayesSIM/R/bsSpike.R | 803 +- BayesSIM-2.0.0/BayesSIM/R/generics.R | 5009 +++++++++-------- BayesSIM-2.0.0/BayesSIM/R/gpFisher.R | 679 +- BayesSIM-2.0.0/BayesSIM/R/gpPolar-sampler.R | 4 BayesSIM-2.0.0/BayesSIM/R/gpPolar.R | 636 +- BayesSIM-2.0.0/BayesSIM/R/gpPolarTemp.R | 611 +- BayesSIM-2.0.0/BayesSIM/R/gpSphere-functions.R | 8 BayesSIM-2.0.0/BayesSIM/R/gpSphere-sampler.R | 245 BayesSIM-2.0.0/BayesSIM/R/gpSphere-united.R | 997 +-- BayesSIM-2.0.0/BayesSIM/R/gpspike-functions.R | 2 BayesSIM-2.0.0/BayesSIM/R/gpspike-sampler.R | 552 - BayesSIM-2.0.0/BayesSIM/R/gpspike.R | 753 +- BayesSIM-2.0.0/BayesSIM/R/prior-params.R | 9 BayesSIM-2.0.0/BayesSIM/R/utils2.R |only BayesSIM-2.0.0/BayesSIM/README.md |only BayesSIM-2.0.0/BayesSIM/build/partial.rdb |binary BayesSIM-2.0.0/BayesSIM/man/BayesSIM-package.Rd | 8 BayesSIM-2.0.0/BayesSIM/man/BayesSIM.Rd | 24 BayesSIM-2.0.0/BayesSIM/man/GOF.bsim.Rd | 12 BayesSIM-2.0.0/BayesSIM/man/as.data.frame.bsimPred.Rd | 4 BayesSIM-2.0.0/BayesSIM/man/as_bsim.bsimSetup.Rd | 12 BayesSIM-2.0.0/BayesSIM/man/bsFisher.Rd | 36 BayesSIM-2.0.0/BayesSIM/man/bsPolar.Rd | 38 BayesSIM-2.0.0/BayesSIM/man/bsSphere.Rd | 27 BayesSIM-2.0.0/BayesSIM/man/bsSpike.Rd | 30 BayesSIM-2.0.0/BayesSIM/man/coef.bsim.Rd | 24 BayesSIM-2.0.0/BayesSIM/man/compileModelAndMCMC.Rd | 10 BayesSIM-2.0.0/BayesSIM/man/fitted.bsim.Rd | 12 BayesSIM-2.0.0/BayesSIM/man/getFunction.Rd | 30 BayesSIM-2.0.0/BayesSIM/man/getInit.Rd | 8 BayesSIM-2.0.0/BayesSIM/man/getModelDef.Rd | 2 BayesSIM-2.0.0/BayesSIM/man/getVarMonitor.Rd | 2 BayesSIM-2.0.0/BayesSIM/man/getWAIC.Rd |only BayesSIM-2.0.0/BayesSIM/man/gpFisher.Rd | 24 BayesSIM-2.0.0/BayesSIM/man/gpPolar.Rd | 31 BayesSIM-2.0.0/BayesSIM/man/gpSphere.Rd | 29 BayesSIM-2.0.0/BayesSIM/man/gpSpike.Rd | 28 BayesSIM-2.0.0/BayesSIM/man/nimTraceplot.Rd | 16 BayesSIM-2.0.0/BayesSIM/man/plot.bsim.Rd | 18 BayesSIM-2.0.0/BayesSIM/man/predict.bsim.Rd | 34 BayesSIM-2.0.0/BayesSIM/man/residuals.bsim.Rd | 13 BayesSIM-2.0.0/BayesSIM/man/summary.bsim.Rd | 18 BayesSIM-2.0.0/BayesSIM/man/summary.bsimPred.Rd | 4 BayesSIM-2.0.0/BayesSIM/man/summary.bsimSetup.Rd | 8 BayesSIM-2.0.0/BayesSIM/tests/testthat/test-BayesSIM.R | 178 BayesSIM-2.0.0/BayesSIM/tests/testthat/test-generic.R | 89 59 files changed, 9073 insertions(+), 7893 deletions(-)
Title: Genetic Study of Plant Mixtures
Description: Fit linear mixed models dedicated to the genetic study of plant mixtures, such as those based on general and specific mixing abilities (GMA-SMA) as well as direct and social breeding values (DBV-SBV), also known as direct and indirect genetic effects (DGE-IGE). More details in Forst et al (2019, <doi:10.1016/j.fcr.2019.107571>) for GMA-SMA models, and Salomon et al (2026, <doi:10.1093/genetics/iyag177>) for DBV-SBV models. The package also provides functions to optimize experimental designs, simulate data sets and compute interaction indices.
Author: Timothee Flutre [aut, ctb, cre] ,
INRAE [cph, fnd],
Jerome Enjalbert [ctb] ,
Emma Forst [ctb] ,
Maxence Remerand [ctb] ,
Jemay Salomon [ctb]
Maintainer: Timothee Flutre <timothee.flutre@inrae.fr>
Diff between plantmix versions 1.0.3 dated 2026-06-20 and 1.0.4 dated 2026-10-14
DESCRIPTION | 8 MD5 | 77 ++++--- NAMESPACE | 2 NEWS.md | 17 + R/DBV_SBV_crop_mix_simul.R | 165 ++++++++++++++-- R/indices.R | 228 ++++++++++++++++------- R/mixing_ability.R | 6 R/optim_designs_common.R | 151 +++++++++++++++ R/optim_designs_crop_mix.R | 19 + R/optim_designs_var_mix.R | 30 ++- R/plantmix-package.R | 4 R/uncertainty_RY.R | 113 ++++++----- R/uncertainty_RYM.R | 120 ++++++++---- R/utils_linear_algebra.R | 2 R/utils_stat.R | 31 +-- inst/doc/vig1_intro-GMA-SMA.html | 22 +- inst/doc/vig2_GMA-SMA_simul-infer.html | 144 +++++++------- inst/doc/vig3_DBV-SBV_crop-mix_testers.Rmd | 3 inst/doc/vig3_DBV-SBV_crop-mix_testers.html | 264 +++++++++++++-------------- man/LER.Rd | 8 man/RY.Rd | 14 - man/RYM.Rd | 6 man/RYP.Rd | 76 ++++++- man/RYT.Rd | 10 - man/estimRYMRep.Rd | 13 - man/estimRYRep.Rd | 2 man/getDesignBinaryCropMix.Rd | 6 man/getDesignBinaryVarMix.Rd | 11 + man/invvecMixes.Rd | 2 man/plotDesignCropMix.Rd | 3 man/plotDesignVarMix.Rd | 3 man/plotDiallel.Rd | 22 ++ src/TMB/DBV_SBV_crop_mix.hpp | 16 - src/TMB/include/helper.hpp | 2 tests/testthat/test_incomp-balanced-design.R |only tests/testthat/test_indices.R | 89 ++++++++- tests/testthat/test_mixing_ability.R | 16 + tests/testthat/test_uncertainty_RY.R |only tests/testthat/test_uncertainty_RYM.R |only tests/testthat/test_utils_stat.R | 29 ++ vignettes/vig3_DBV-SBV_crop-mix_testers.Rmd | 3 41 files changed, 1215 insertions(+), 522 deletions(-)
Title: Calculate High Resolution Water Balance of Starch Potatoes
Description: Calculates the water balance of starch potatoes from Normalized Distance Vegetation Index (NDVI) images, German Weather Service (DWD) reference evapotranspiration, German Weather Service RADOLAN precipitation data and irrigation information. For more details see Piernicke et al. (2025) <doi:10.3390/rs17183227>.
Author: Thomas Piernicke [aut, cre]
Maintainer: Thomas Piernicke <thomasp@gfz.de>
Diff between WaterBalanceR versions 0.1.21 dated 2026-03-13 and 0.1.22 dated 2026-10-14
DESCRIPTION | 12 MD5 | 18 NEWS.md | 13 R/DownloadET0fromDWD.R | 33 R/DownloadSentinel2.R | 251 +++--- R/calcWB.R | 31 R/calcWBplots.R | 1338 +++++++++++++++++++++++--------- inst/doc/WaterBalanceR_DataSources.html | 10 inst/doc/WaterBalanceR_Workflow.html | 16 man/DownloadSentinel2.Rd | 5 10 files changed, 1243 insertions(+), 484 deletions(-)
Title: Multiscale Systematic Conservation Planning Across Nested H3
Grids
Description: Provides tools for multiscale systematic conservation planning
using the H3 hierarchical hexagonal grid system (Uber Technologies (2024)
<https://h3geo.org>) and the 'prioritizr' package (Hanson et al. (2025)
<doi:10.1111/cobi.14376>). Supports the definition and solution of
conservation problems across nested H3 resolutions with resolution-specific
features, costs, and management attributes, including cross-scale
connectivity penalties derived from parent-child relationships. Includes
a multiscale minimum-set objective that allows planning units at different
resolutions to contribute toward feature representation targets while
accounting for overlapping costs and feature amounts across nested planning
units. Also includes utilities to evaluate solutions using
multiscale-aware diagnostics and to post-process optimization outputs
into alternative area-targeted conservation scenarios.
Author: Pablo Merlo [aut, cre] ,
Oisin Callery [aut] ,
Carlos Tighe [ctb],
Anthony Grehan [ctb]
Maintainer: Pablo Merlo <pablo.merlo@universityofgalway.ie>
Diff between MultiscaleSCP versions 0.1.1 dated 2026-03-30 and 0.2.0 dated 2026-10-14
DESCRIPTION | 30 MD5 | 78 - NAMESPACE | 11 NEWS.md | 20 R/RcppExports.R |only R/add-multiscale-min-set-objective.R |only R/add-multiscale-min-set.R |only R/add-multiscale-relative-targets.R |only R/build-multiscale-atoms.R |only R/build-multiscale-objective-data.R |only R/deduplicate_retune.R | 292 ++-- R/eval-multiscale-atom-solution.R |only R/evaluation.R | 1524 +++++++++++------------ R/globals.R | 10 R/h3_hierarchy.R | 421 +++--- R/load-multiscale-feature.R |only R/multiscale-atom-internal.R |only R/multiscale-backend.R |only R/multiscale_connect_matrix.R | 160 +- R/multiscale_connectivity.R | 490 +++---- R/scoring.R | 920 ++++++------- R/selection_stratified.R | 1129 ++++++++--------- R/utils.R | 58 build/vignette.rds |binary inst/doc/MultiscaleSCP_workflow_vignette.R | 388 +++-- inst/doc/MultiscaleSCP_workflow_vignette.Rmd | 713 ++++++---- inst/doc/MultiscaleSCP_workflow_vignette.html | 1714 ++++++++++++++------------ man/add_multiscale_connectivity_penalties.Rd | 35 man/add_multiscale_min_set.Rd |only man/add_multiscale_min_set_objective.Rd |only man/add_multiscale_relative_targets.Rd |only man/build_crossscale_index.Rd | 11 man/build_h3_maps.Rd | 29 man/build_multiscale_atoms.Rd |only man/build_multiscale_connectivity_matrix.Rd | 14 man/build_multiscale_feature_atoms.Rd |only man/build_multiscale_objective_data.Rd |only man/deduplicate_h3_selections.Rd | 2 man/eval_exact_raster_coverage.Rd | 9 man/eval_geom_feature_coverage.Rd | 9 man/eval_multiscale_atom_solution.Rd |only man/load_multiscale_feature.Rd |only man/multiscale_feature_cols.Rd |only src |only tests |only vignettes/MultiscaleSCP_workflow_vignette.Rmd | 713 ++++++---- 46 files changed, 4696 insertions(+), 4084 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data handling (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and resid [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.8.3 dated 2026-08-02 and 0.8.4 dated 2026-10-14
DESCRIPTION | 8 MD5 | 494 +++---- NAMESPACE | 20 NEWS.md | 301 ++-- R/aov.b.R | 160 +- R/aov.w.R | 288 ++-- R/blimp.R | 18 R/blimp.bayes.R | 16 R/blimp.plot.R | 24 R/blimp.print.R | 28 R/blimp.run.R | 6 R/blimp.update.R | 18 R/boot.bs.R | 16 R/center.R | 129 - R/check.collin.R | 26 R/check.outlier.R | 306 +++- R/check.resid.R | 676 ++------- R/chr.color.R | 10 R/chr.grep.R | 14 R/chr.gsub.R | 10 R/chr.omit.R | 10 R/chr.trim.R | 12 R/chr.trunc.R | 21 R/ci.cor.R | 534 +++---- R/ci.mean.R | 629 ++++----- R/ci.mean.diff.R | 617 ++++---- R/ci.mean.w.R | 57 R/ci.prop.R | 442 +++--- R/ci.prop.diff.R | 432 +++--- R/ci.var.R | 575 ++++---- R/cluster.rwg.R | 46 R/cluster.scores.R | 57 R/coding.R | 51 R/coeff.robust.R | 14 R/coeff.std.R | 12 R/cohens.d.R | 459 +++--- R/cor.matrix.R | 153 +- R/crosstab.R | 47 R/descript.R | 95 - R/df.check.R | 21 R/df.duplicated.R | 25 R/df.head.R | 32 R/df.long.R | 24 R/df.merge.R | 10 R/df.move.R | 10 R/df.rbind.R | 2 R/df.rename.R | 19 R/df.sort.R | 10 R/df.subset.R | 8 R/difftest.chibarsq.R | 17 R/dominance.R | 22 R/dominance.manual.R | 21 R/effsize.R | 52 R/freq.R | 37 R/indirect.R | 29 R/item.alpha.R | 36 R/item.cfa.R | 78 - R/item.dfi.R | 24 R/item.distract.R | 41 R/item.invar.R | 121 - R/item.noninvar.R | 26 R/item.omega.R | 37 R/item.reverse.R | 51 R/item.scores.R | 30 R/item.stats.R | 80 - R/lagged.R | 37 R/libraries.R | 8 R/modcomp.R | 14 R/mplus.R | 34 R/mplus.bayes.R | 16 R/mplus.lca.R | 59 R/mplus.lca.summa.R | 16 R/mplus.plot.R | 56 R/mplus.print.R | 230 +-- R/mplus.run.R | 8 R/mplus.update.R | 20 R/multilevel.alpha.R | 48 R/multilevel.cfa.R | 80 - R/multilevel.cor.R | 162 +- R/multilevel.descript.R | 88 - R/multilevel.fit.R | 28 R/multilevel.icc.R | 48 R/multilevel.indirect.R | 14 R/multilevel.invar.R | 99 - R/multilevel.omega.R | 44 R/multilevel.r2.R | 62 R/multilevel.r2.manual.R | 55 R/na.as.R | 48 R/na.auxiliary.R | 35 R/na.coverage.R | 42 R/na.descript.R | 51 R/na.indicator.R | 30 R/na.pattern.R | 148 -- R/na.prop.R | 28 R/na.satcor.R | 15 R/na.test.R | 41 R/plot.misty.object.R | 3048 ++++++++++++++++++++++++++++++-------------- R/print.misty.object.R | 1977 ++++++++++++++++++++-------- R/read.data.R | 10 R/read.dta.R | 10 R/read.mplus.R | 16 R/read.sav.R | 10 R/read.xlsx.R | 10 R/rec.R | 53 R/restart.R | 4 R/robust.lmer.R | 16 R/script.copy.R | 6 R/script.new.R | 6 R/script.open.R | 22 R/setsource.R | 6 R/sim.lavaan.R | 10 R/size.mean.R | 54 R/skewness.R | 62 R/summa.R | 20 R/test.bm.R |only R/test.homo.R |only R/test.levene.R | 134 + R/test.linear.R |only R/test.norm.R |only R/test.t.R | 551 ++++--- R/test.welch.R | 264 ++- R/test.z.R | 516 ++++--- R/uniq.R | 52 R/utils.R | 1431 ++++++++++++++++++-- R/write.result.R | 622 ++++++-- man/aov.b.Rd | 69 man/aov.w.Rd | 88 - man/blimp.Rd | 2 man/blimp.bayes.Rd | 6 man/blimp.plot.Rd | 2 man/blimp.print.Rd | 2 man/blimp.run.Rd | 6 man/blimp.update.Rd | 2 man/boot.bs.Rd | 4 man/center.Rd | 68 man/check.collin.Rd | 4 man/check.outlier.Rd | 180 ++ man/check.resid.Rd | 221 +-- man/chr.color.Rd | 2 man/chr.grep.Rd | 2 man/chr.gsub.Rd | 4 man/chr.omit.Rd | 4 man/chr.trim.Rd | 4 man/chr.trunc.Rd | 2 man/ci.cor.Rd | 114 - man/ci.mean.Rd | 126 - man/ci.mean.diff.Rd | 127 - man/ci.mean.w.Rd | 6 man/ci.prop.Rd | 120 - man/ci.prop.diff.Rd | 85 - man/ci.var.Rd | 115 - man/clear.Rd | 2 man/cluster.rwg.Rd | 4 man/cluster.scores.Rd | 6 man/coding.Rd | 6 man/coeff.robust.Rd | 8 man/coeff.std.Rd | 4 man/cohens.d.Rd | 182 +- man/cor.matrix.Rd | 82 - man/crosstab.Rd | 6 man/data.items.Rd | 2 man/descript.Rd | 42 man/df.check.Rd | 4 man/df.duplicated.Rd | 4 man/df.head.Rd | 2 man/df.long.Rd | 2 man/df.merge.Rd | 4 man/df.move.Rd | 4 man/df.rbind.Rd | 4 man/df.rename.Rd | 8 man/df.sort.Rd | 4 man/df.subset.Rd | 4 man/difftest.chibarsq.Rd | 8 man/dominance.Rd | 6 man/dominance.manual.Rd | 6 man/effsize.Rd | 15 man/freq.Rd | 4 man/indirect.Rd | 6 man/item.alpha.Rd | 6 man/item.cfa.Rd | 14 man/item.dfi.Rd | 8 man/item.distract.Rd | 9 man/item.invar.Rd | 14 man/item.noninvar.Rd | 6 man/item.omega.Rd | 4 man/item.reverse.Rd | 6 man/item.scores.Rd | 4 man/item.stats.Rd | 8 man/lagged.Rd | 8 man/libraries.Rd | 4 man/modcomp.Rd | 2 man/mplus.Rd | 2 man/mplus.bayes.Rd | 2 man/mplus.lca.Rd | 8 man/mplus.lca.summa.Rd | 4 man/mplus.plot.Rd | 2 man/mplus.print.Rd | 11 man/mplus.run.Rd | 4 man/mplus.update.Rd | 2 man/multilevel.alpha.Rd | 6 man/multilevel.cfa.Rd | 16 man/multilevel.cor.Rd | 83 + man/multilevel.descript.Rd | 8 man/multilevel.fit.Rd | 6 man/multilevel.icc.Rd | 6 man/multilevel.indirect.Rd | 4 man/multilevel.invar.Rd | 14 man/multilevel.omega.Rd | 6 man/multilevel.r2.Rd | 42 man/multilevel.r2.manual.Rd | 34 man/na.as.Rd | 4 man/na.auxiliary.Rd | 4 man/na.coverage.Rd | 6 man/na.descript.Rd | 6 man/na.indicator.Rd | 4 man/na.pattern.Rd | 83 - man/na.prop.Rd | 4 man/na.satcor.Rd | 2 man/na.test.Rd | 8 man/plot.misty.object.Rd | 1050 +++++++++------ man/print.misty.object.Rd | 37 man/read.data.Rd | 2 man/read.dta.Rd | 4 man/read.mplus.Rd | 4 man/read.sav.Rd | 4 man/read.xlsx.Rd | 4 man/rec.Rd | 6 man/restart.Rd | 4 man/robust.lmer.Rd | 4 man/script.copy.Rd | 4 man/script.new.Rd | 4 man/script.open.Rd | 4 man/setsource.Rd | 4 man/sim.lavaan.Rd | 2 man/size.mean.Rd | 4 man/skewness.Rd | 10 man/summa.Rd | 2 man/test.bm.Rd |only man/test.homo.Rd |only man/test.levene.Rd | 37 man/test.linear.Rd |only man/test.norm.Rd |only man/test.t.Rd | 155 +- man/test.welch.Rd | 71 - man/test.z.Rd | 116 - man/uniq.Rd | 4 man/write.data.Rd | 2 man/write.dta.Rd | 4 man/write.mplus.Rd | 4 man/write.result.Rd | 53 man/write.sav.Rd | 4 man/write.xlsx.Rd | 4 252 files changed, 12664 insertions(+), 9479 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Maelle Salmon [aut] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.4.1 dated 2026-08-19 and 2.5.0 dated 2026-10-14
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ configure | 10 ++++++++-- inst/doc/gert.html | 29 +++++++++++++++-------------- man/gert-package.Rd | 1 + src/clone.c | 16 ++++++++++------ src/utils.c | 22 ++++++++++++++++++++++ src/utils.h | 1 + src/version.c | 12 ++++++++++-- 10 files changed, 84 insertions(+), 36 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models. There is also a function for partial and semipartial
correlations and a function for conducting Cohen's
set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.3.1 dated 2026-01-21 and 0.3.4 dated 2026-10-14
DESCRIPTION | 8 +- MD5 | 18 +++--- R/COUNT_REGRESSION.R | 7 +- R/LOGISTIC_REGRESSION.R | 7 +- R/MODERATED_REGRESSION.R | 5 + R/OLS_REGRESSION.R | 7 +- R/utilities_boc.R | 134 +++++++++++++++++++++------------------------ man/COUNT_REGRESSION.Rd | 15 +---- man/LOGISTIC_REGRESSION.Rd | 15 +---- man/OLS_REGRESSION.Rd | 6 +- 10 files changed, 104 insertions(+), 118 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: Download Insee French Institute of Statistics Open Data
Description: A wrapper for the French Institute of Statistics (Insee) API
Melodi <https://catalogue-donnees.insee.fr>. Download, search, filter data
and metadata from open data statistical public datasets,
in french or in english.
Author: Cedric Bobinec [aut, cre],
Christophe Goudeau [aut],
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Cedric Bobinec <cedric.bobinec@insee.fr>
Diff between melodi versions 1.1.2 dated 2026-08-28 and 1.2.0 dated 2026-10-14
DESCRIPTION | 6 - MD5 | 29 ++++----- NEWS.md | 6 + R/get_all_data.R | 9 +- R/get_catalog.R | 7 +- R/get_data.R | 18 ++++- R/get_file.R | 48 +++++++++++++-- R/get_metadata.R | 6 + R/get_range.R | 6 + R/get_range_geo.R | 6 + README.md | 3 man/get_file.Rd | 6 + tests/testthat/_vcr/get_file_deces_preserve_filename.yml |only tests/testthat/test-get_catalog.R | 18 ++++- tests/testthat/test-get_data.R | 13 ++-- tests/testthat/test-get_file.R | 25 +++++++ 16 files changed, 159 insertions(+), 47 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Idris A. Eckley [aut],
Paul Fearnhead [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.10 dated 2026-09-16 and 0.1.11 dated 2026-10-14
DESCRIPTION | 11 MD5 | 48 +- NAMESPACE | 10 R/RcppExports.R | 103 +--- R/detector.R |only R/methods.R | 219 +++++++++- inst/COPYRIGHTS/MODIFIED.txt | 20 man/detector_candidates.Rd | 19 man/detector_cands_len.Rd | 19 man/detector_create.Rd | 8 man/detector_info_n.Rd | 19 man/detector_info_sn.Rd | 20 man/focus-methods.Rd | 83 +++- man/focus-package.Rd | 113 +++-- man/focus_offline.Rd | 3 man/generate_projection_indexes.Rd | 23 - src/ARpInfo.h | 39 - src/CostsArp.h | 2 src/RcppExports.cpp | 2 src/focus_ARp.cpp | 766 +++++++++---------------------------- src/focus_rcpp_module.cpp | 116 +---- src/libqhull_r/poly_r.c | 2 src/libqhull_r/qset_r.c | 32 - src/libqhull_r/qset_r.h | 53 +- tests/testthat/test-generic.R | 118 +++-- tests/testthat/test-methods.R |only 26 files changed, 899 insertions(+), 949 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'OpenAI', 'Gemini', 'Mistral', and local models via 'Ollama' into R workflows. The package supports text, image, audio, video, and document interactions; a unified media interface for attaching inline files or uploading to provider file stores; batch request APIs for cost-efficient large-scale processing; and a pipeline-oriented interface for seamless integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.7.0 dated 2026-10-05 and 0.7.1 dated 2026-10-14
DESCRIPTION | 13 - MD5 | 53 ++-- NAMESPACE | 4 NEWS.md | 107 ++++++++ R/APIProvider.R | 2 R/api_claude.R | 8 R/api_claude_cli.R | 346 ++-------------------------- R/api_codex_cli.R |only R/api_ellmer.R | 2 R/api_gemini.R | 55 +++- R/api_mistral.R | 68 +++-- R/api_vibe_cli.R |only R/cli_process.R |only R/llm_verbs.R | 6 R/parallel_chat.R | 5 R/perform_api_requests.R | 22 + R/utilites.R | 43 +++ README.md | 27 +- inst/doc/tidyllm.Rmd | 12 inst/doc/tidyllm.html | 50 ++-- man/claude_cli_chat.Rd | 22 - man/codex_cli.Rd |only man/codex_cli_chat.Rd |only man/gemini_chat.Rd | 15 - man/mistral_chat.Rd | 2 man/send_gemini_batch.Rd | 10 man/send_mistral_batch.Rd | 3 man/vibe_cli.Rd |only man/vibe_cli_chat.Rd |only tests/testthat/test_provider_capabilities.R | 12 vignettes/tidyllm.Rmd | 12 31 files changed, 454 insertions(+), 445 deletions(-)
Title: ADaM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Analysis Data Model (ADaM) datasets constructed
using the Study Data Tabulation Model (SDTM) datasets contained in the
'pharmaversesdtm' package and the template scripts from the 'admiral'
family of packages. ADaM dataset specifications are described in the
CDISC ADaM implementation guide, accessible by creating a free account
on <https://www.cdisc.org/>.
Author: Fanny Gautier [aut, cre] ,
Stefan Bundfuss [aut] ,
Edoardo Mancini [aut] ,
Lina Patil [aut],
Gerardo Jose Rodriguez [aut] ,
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [cph, fnd]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between pharmaverseadam versions 1.3.0 dated 2026-02-20 and 1.4.0 dated 2026-10-14
DESCRIPTION | 14 MD5 | 101 +++--- NEWS.md | 30 + R/adlb_neuro.R |only R/adrs_onco.R | 3 R/adsl.R | 4 R/adsl_vaccine.R | 4 R/adtr_onco.R | 3 R/advfq_ophtha.R | 100 +++++ data/adab.rda |binary data/adae.rda |binary data/adapet_neuro.rda |binary data/adbcva_ophtha.rda |binary data/adce_vaccine.rda |binary data/adcm.rda |binary data/adcoeq_metabolic.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adface_vaccine.rda |binary data/adis_vaccine.rda |binary data/adlb.rda |binary data/adlb_metabolic.rda |binary data/adlb_neuro.rda |only data/adlbhy.rda |binary data/admh.rda |binary data/adnv_neuro.rda |binary data/adoe_ophtha.rda |binary data/adpc.rda |binary data/adpp.rda |binary data/adppk.rda |binary data/adrs_onco.rda |binary data/adsl.rda |binary data/adsl_vaccine.rda |binary data/adtpet_neuro.rda |binary data/adtr_onco.rda |binary data/adtte_onco.rda |binary data/advfq_ophtha.rda |binary data/advs.rda |binary data/advs_metabolic.rda |binary data/advs_peds.rda |binary inst/WORDLIST | 43 ++ inst/extdata/adams-specs.json | 684 +++++++++++++++++++++++++++++++++++++---- inst/extdata/adams-specs.xlsx |binary man/adlb_neuro.Rd |only man/adrs_onco.Rd | 3 man/adsl.Rd | 4 man/adsl_vaccine.Rd | 4 man/adtr_onco.Rd | 3 man/advfq_ophtha.Rd | 100 +++++ man/figures/gsk_logo.png |binary man/figures/logo.png |binary man/figures/roche_logo.png |binary man/pharmaverseadam-package.Rd | 1 53 files changed, 942 insertions(+), 159 deletions(-)
More information about pharmaverseadam at CRAN
Permanent link
Title: Converts 'NONMEM' Models to 'rxode2'
Description: 'NONMEM' has been a tool for running nonlinear mixed
effects models since the 80s and is still used today (Bauer 2019
<doi:10.1002/psp4.12404>). This tool allows you to convert
'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016)
<doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax
(Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2'
syntax requires the residual specification to be included and it
is not always translated. If available, the 'rxode2' model will
read in the 'NONMEM' data and compare the simulation for the
population model ('PRED') individual model ('IPRED') and residual
model ('IWRES') to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rx [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Philip Delff [ctb],
Gabriel Staples [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nonmem2rx versions 0.1.11 dated 2026-09-22 and 0.1.12 dated 2026-10-14
DESCRIPTION | 12 MD5 | 145 NEWS.md | 138 R/abbrev.R | 36 R/buildParser.R | 23 R/ext.R | 3 R/grd.R | 3 R/linCmt.R | 13 R/lst.R | 21 R/nminfo.R | 12 R/nmtab.R | 45 R/nonmem2rx.R | 40 R/omega.R | 70 R/readCov.R | 11 R/rxSolve.R | 59 R/solveNonmem.R |only R/validate.R | 588 + R/xml.R | 31 inst/abbrec.g | 2 inst/abbrev.g | 15 inst/data.g | 2 inst/doc/import-nonmem.html | 1067 +- inst/input.g | 2 inst/model.g | 2 inst/mods/multest |only inst/omega.g | 2 inst/stress |only inst/sub.g | 2 inst/tab.g | 12 inst/theta.g | 2 src/abbrec.c | 21 src/abbrec.g.d_parser.h | 1257 +-- src/abbrev.c | 9 src/abbrev.g.d_parser.h |10699 +++++++++++++++--------------- src/data.g.d_parser.h | 1122 +-- src/input.g.d_parser.h | 293 src/lst.c | 2 src/model.g.d_parser.h | 378 - src/omega.c | 2 src/omega.g.d_parser.h | 1285 +-- src/sub.g.d_parser.h | 101 src/tab.c | 10 src/tab.g.d_parser.h | 4795 ++++++++----- src/theta.g.d_parser.h | 1186 +-- tests/testthat.R | 10 tests/testthat/test-abbrev.R | 26 tests/testthat/test-advan5.R | 30 tests/testthat/test-dv-modeled-dur.R |only tests/testthat/test-linCmt.R | 68 tests/testthat/test-multiple-est.R |only tests/testthat/test-omega.R | 31 tests/testthat/test-rxsolve.R | 10 tests/testthat/test-solveNonmem.R |only tests/testthat/test-stress.R |only tests/testthat/test-tab.R | 218 tests/testthat/test-theta.R | 4 tests/testthat/test-undefined-theta-eta.R |only tests/testthat/test-validate-align.R |only 58 files changed, 12958 insertions(+), 10957 deletions(-)
Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
Description: Many tools for making, manipulating, and modifying many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Tomas Diviak [ctb],
Henrique Sposito [ctb] ,
Christian Steglich [ctb],
Alvaro Uzaheta [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 2.3.4 dated 2026-09-10 and 2.4.0 dated 2026-10-14
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Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson [aut, cre] ,
Julie Josse [aut],
Sebastien Le [aut],
Jeremy Mazet [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.17 dated 2026-09-08 and 2.18 dated 2026-10-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/HCPC.R | 5 ++--- R/MCA.R | 3 +-- build/vignette.rds |binary inst/doc/clustering.html | 18 +++++++++++------- vignettes/FactoMineR.html | 18 +++++++++++------- 7 files changed, 34 insertions(+), 28 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 1.3.0 dated 2026-07-02 and 1.3.1 dated 2026-10-14
DESCRIPTION | 18 +++++----- MD5 | 48 ++++++++++++++------------- NAMESPACE | 34 ++++++++++++------- NEWS.md | 9 +++++ R/convert_time.R | 16 +++++---- R/convert_units.R | 16 +++++---- R/fipscounty.R | 16 +++++---- R/global_search.R | 2 - R/grid.R | 35 ++++++++++++-------- R/info.R | 10 ++--- R/keywords.R | 16 +++++---- R/servers.R | 16 +++++---- R/table.R | 36 ++++++++++++-------- R/version.R | 16 +++++---- R/zzz.r | 19 +++++----- inst/agentic-skills |only inst/doc/Using_rerddap.R | 22 ++++++------ inst/doc/Using_rerddap.Rmd | 26 ++++++++------ inst/doc/Using_rerddap.html | 77 ++++++++++++++++++++++---------------------- man/disk.Rd | 4 +- man/eurl.Rd | 4 +- man/global_search.Rd | 2 - man/griddap.Rd | 12 +++--- vignettes/Using_rerddap.Rmd | 26 ++++++++------ vignettes/maxslp.png |binary vignettes/mean_density.png |only 26 files changed, 266 insertions(+), 214 deletions(-)
Title: Statistical Power, Sample Size, and Detectable Effect
Calculations
Description: Flexible and comprehensive functions for statistical power, minimum required
sample size, and minimum detectable effect calculations across a wide range of
commonly used hypothesis tests in psychological, biomedical, and social sciences.
Author: Metin Bulus [aut, cre, cph] ,
Sebastian Jentschke [aut, cph]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between pwrss versions 1.3.1 dated 2026-09-29 and 1.3.3 dated 2026-10-14
pwrss-1.3.1/pwrss/man/figures/README-unnamed-chunk-13-1.png |only pwrss-1.3.1/pwrss/man/figures/README-unnamed-chunk-14-1.png |only pwrss-1.3.1/pwrss/man/figures/README-unnamed-chunk-15-1.png |only pwrss-1.3.1/pwrss/man/figures/README-unnamed-chunk-18-1.png |only pwrss-1.3.1/pwrss/man/figures/README-unnamed-chunk-9-1.png |only pwrss-1.3.3/pwrss/DESCRIPTION | 8 pwrss-1.3.3/pwrss/MD5 | 39 +-- pwrss-1.3.3/pwrss/NEWS.md | 128 ++++++------ pwrss-1.3.3/pwrss/R/generic.lp.test.R | 8 pwrss-1.3.3/pwrss/R/helper.R | 19 - pwrss-1.3.3/pwrss/R/lambdap.R | 87 +++----- pwrss-1.3.3/pwrss/inst/CITATION | 21 - pwrss-1.3.3/pwrss/inst/doc/examples.R | 5 pwrss-1.3.3/pwrss/inst/doc/examples.Rmd | 21 + pwrss-1.3.3/pwrss/inst/doc/examples.html | 58 ++++- pwrss-1.3.3/pwrss/man/lambdap.Rd | 19 + pwrss-1.3.3/pwrss/man/power.lp.test.Rd | 8 pwrss-1.3.3/pwrss/tests/lambdap_CI.rds |only pwrss-1.3.3/pwrss/tests/testthat/test-generic.lp.test.R | 2 pwrss-1.3.3/pwrss/tests/testthat/test-helper.R | 16 - pwrss-1.3.3/pwrss/tests/testthat/test-lambdap.R | 70 ++++++ pwrss-1.3.3/pwrss/tests/testthat/test-plots.R | 22 +- pwrss-1.3.3/pwrss/vignettes/examples.Rmd | 21 + pwrss-1.3.3/pwrss/vignettes/otherrefs.bib |only 24 files changed, 347 insertions(+), 205 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://help.openalex.org/>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 3.1.1 dated 2026-10-09 and 3.1.2 dated 2026-10-14
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 10 ++++++++ R/oa2df.R | 16 +++++++++++--- README.md | 39 +++++++++++++++++++--------------- data/concept_abbrev.rda |binary data/countrycode.rda |binary data/oa2df_coverage.rda |binary tests/testthat/test-oa2df.R | 50 ++++++++++++++++++++++++++++++++++++-------- 9 files changed, 98 insertions(+), 39 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Description: Provides nonparametric procedures for the analysis of longitudinal data in factorial experiments. The package implements hypothesis tests on marginal distribution functions and unweighted relative marginal effects. It supports arbitrary crossed factorial designs with longitudinal or repeated-measures factors, missing observations, dependent replicates, rank- and pseudo-rank-based inference, Wald-type and ANOVA-type statistics, multiple contrast tests, and simultaneous confidence intervals.
Author: Frank Konietschke [aut, cre],
Kimihiro Noguchi [ctb] ,
Mahbub Latif [ctb] ,
Karthinathan Thangavelu [ctb] ,
Yulia R. Gel [ctb] ,
Marek Sztuka [ctb] ,
Edgar Brunner [ctb]
Maintainer: Frank Konietschke <frank.konietschke@charite.de>
Diff between nparLD versions 2.3.1 dated 2026-08-28 and 2.3.3 dated 2026-10-14
DESCRIPTION | 15 MD5 | 79 +-- NAMESPACE | 67 +- NEWS.md | 19 R/PairedData.R | 7 R/Utility.R | 336 ++++++++----- R/accessors.R |only R/data.R | 78 +-- R/nparLD-package.R | 2 R/nparLD.R | 18 README.md | 4 inst/WORDLIST | 4 inst/doc/nparLD.R | 44 + inst/doc/nparLD.Rmd | 120 ++-- inst/doc/nparLD.html | 1033 ++++++++++++++++------------------------ man/ATS.Rd |only man/MCTP.Rd |only man/WTS.Rd |only man/amylase.Rd | 4 man/brdu.Rd | 2 man/contrastMatrix.Rd |only man/covariance.Rd |only man/dental.Rd | 8 man/edema.Rd | 8 man/effects.nparld_fit.Rd |only man/factorInfo.Rd |only man/nparLD-package.Rd | 11 man/nparLD.Rd | 18 man/panic.Rd | 8 man/panic2.Rd | 8 man/permTest.Rd |only man/plasma.Rd | 8 man/plot.nparld_fit.Rd | 12 man/plot.nparld_mctp.Rd | 2 man/print.nparld_fit.Rd | 29 - man/print.nparld_mctp.Rd | 6 man/print.nparld_permtest.Rd |only man/print.nparld_test_table.Rd |only man/print.summary.nparld_fit.Rd | 25 man/rat.Rd | 8 man/respiration.Rd | 8 man/shoulder.Rd | 8 man/summary.nparld_fit.Rd | 29 - man/tree.Rd | 8 tests/testthat/test-examples.R | 121 ++++ vignettes/nparLD.Rmd | 120 ++-- 46 files changed, 1216 insertions(+), 1061 deletions(-)
Title: Linear Latent Non-Gaussian Models with Flexible Distributions
Description: Fits and analyzes linear latent non-Gaussian models for
temporal, spatial, and space-time data. The package provides model
components for autoregressive and Ornstein-Uhlenbeck processes, random
walks, Matern fields based on stochastic partial differential equations,
separable and non-separable space-time models, graph-based Matern models,
bivariate type-G fields, and user-defined sparse operators. Latent fields
and observation models can use Gaussian and non-Gaussian noise
distributions, including normal inverse Gaussian, generalized asymmetric
Laplace, and skew-t distributions. Functions are included for simulation,
likelihood-based estimation, prediction, cross-validation, convergence
diagnostics, stochastic gradient optimization, batch-means confidence
intervals, and posterior-like sampling. The modeling framework is described
in Bolin, Jin, Simas and Wallin (2026) "A Unified and Computationally
Efficient Non-Gaussian Statistical Modeling Framework"
<doi:10.48550/arXiv.2602.23987 [...truncated...]
Author: David Bolin [aut, cph],
Xiaotian Jin [aut, cre],
Alexandre Simas [aut],
Jonas Wallin [aut],
Andrea V. Rocha [ctb] ,
Timothy A. Davis [ctb, cph] ,
Patrick R. Amestoy [ctb, cph] ,
Iain S. Duff [ctb, cph] ,
John K. Reid [ctb, cph] ,
Yanqing Chen [ctb, c [...truncated...]
Maintainer: Xiaotian Jin <xiaotian.jin@kaust.edu.sa>
This is a re-admission after prior archival of version 1.0.0 dated 2026-09-27
Diff between ngme2 versions 1.0.0 dated 2026-09-27 and 1.0.1 dated 2026-10-14
ngme2-1.0.0/ngme2/src/SuiteSparse/CHOLMOD/Cholesky/cholmod_solve-faf9ff52.o.tmp |only ngme2-1.0.0/ngme2/tests/testthat/Rplots.pdf |only ngme2-1.0.1/ngme2/DESCRIPTION | 8 +- ngme2-1.0.1/ngme2/MD5 | 33 ++++------ ngme2-1.0.1/ngme2/NEWS.md | 10 +++ ngme2-1.0.1/ngme2/build/partial.rdb |binary ngme2-1.0.1/ngme2/build/vignette.rds |binary ngme2-1.0.1/ngme2/inst/include/Eigen/CholmodSupport |only ngme2-1.0.1/ngme2/src/block.cpp | 2 ngme2-1.0.1/ngme2/tests/testthat.R | 2 ngme2-1.0.1/ngme2/tests/testthat/test-compose-bv.R | 9 +- ngme2-1.0.1/ngme2/tests/testthat/test-core-feff-precond.R | 1 ngme2-1.0.1/ngme2/tests/testthat/test-core-generic-ns.R | 8 +- ngme2-1.0.1/ngme2/tests/testthat/test-core-generic.R | 5 + ngme2-1.0.1/ngme2/tests/testthat/test-core-noise.R | 12 ++- ngme2-1.0.1/ngme2/tests/testthat/test-predict-chain-average.R | 3 ngme2-1.0.1/ngme2/tests/testthat/test-regression-bv-c-param.R | 3 ngme2-1.0.1/ngme2/tests/testthat/test-regression-mesh-per-replicate.R | 6 + ngme2-1.0.1/ngme2/tests/testthat/test-regression-robust.R | 1 19 files changed, 67 insertions(+), 36 deletions(-)
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Catapult Sports [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@catapultsports.com>
Diff between impectR versions 2.5.6 dated 2026-06-25 and 2.6.0 dated 2026-10-14
DESCRIPTION | 18 ++--- MD5 | 42 +++++++---- NAMESPACE | 5 + NEWS.md | 16 ++++ R/getData.R |only R/getEvents.R | 3 R/getIterations.R | 40 +++++++++++ R/getMatchPredictions.R |only R/getMatches.R | 45 ++++++++---- R/getPlayerIterationAverages.R | 5 + R/getPlayerIterationScores.R | 5 + R/getPlayerMatchScores.R | 8 +- R/getPlayerMatchsums.R | 11 ++- R/getPlayerProfileScores.R | 7 + R/getSetPieces.R | 11 ++- R/getSquadIterationStyleOfPlay.R |only R/getSquadMatchStyleOfPlay.R |only R/getStartingPositions.R | 27 ++++++- R/getVideoClips.R |only R/utils.R | 129 +++++++++++++++++++++++++++++------- README.md | 42 ++++++++++- man/getData.Rd |only man/getMatchPredictions.Rd |only man/getSquadIterationStyleOfPlay.Rd |only man/getSquadMatchStyleOfPlay.Rd |only man/getStartingPositions.Rd | 12 ++- man/getVideoClips.Rd |only 27 files changed, 349 insertions(+), 77 deletions(-)
Title: AI Screening Tools in R for Systematic Reviewing
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://developers.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2025) <DOI:10.1037/met0000769>.
Author: Mikkel H. Vembye [aut, cre] ,
Thomas Olsen [aut]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Diff between AIscreenR versions 0.4.0 dated 2026-07-01 and 0.5.0 dated 2026-10-14
DESCRIPTION | 9 MD5 | 80 ++++--- NAMESPACE | 2 NEWS.md | 8 R/approximate_price.R | 2 R/data.R | 4 R/misc.func.hidden.solve_or_guess.R |only R/misc.helpers.R | 3 R/ollama_engine.r | 13 + R/rank_one_diagnostic.R |only R/rate_limits.R | 4 R/report_errors.r | 34 +++ R/sample_references.R | 186 +++++++++++++++--- R/save_functions.r | 94 ++++++++- R/screen_analyzer.R | 2 R/solve_or_guess.R |only R/tabscreen_gpt.R | 6 R/tabscreen_gpt.original.R | 4 R/tabscreen_gpt.tools.R | 4 R/tabscreen_groq.r | 2 R/tabscreen_ollama.r | 2 build/partial.rdb |binary build/vignette.rds |binary data/claude_model_prizes.rda |binary data/gemini_model_prizes.rda |binary data/groq_model_prizes.rda |binary data/mistral_model_prizes.rda |binary data/model_prizes.rda |binary inst/doc/Using-GPT-API-Models-For-Screening.html | 15 - man/approximate_price_gpt.Rd | 2 man/model_prizes.Rd | 4 man/rank_one_diagnostic.Rd |only man/rate_limits_per_minute.Rd | 4 man/read_ris_to_dataframe.Rd | 3 man/report.Rd | 2 man/sample_references.Rd | 92 +++++++- man/screen_analyzer.Rd | 2 man/solve_or_guess.Rd |only man/tabscreen_gpt.original.Rd | 4 man/tabscreen_gpt.tools.Rd | 4 man/tabscreen_gpt.tools_responses.Rd | 6 tests/testthat/test-misc.func.hidden.solve_or_guess.R |only tests/testthat/test-rank_one_diagnostic.R |only tests/testthat/test-solve_or_guess.R |only tests/testthat/test-tabscreen_gpt.R | 4 45 files changed, 477 insertions(+), 124 deletions(-)
Title: Matrix Profile for R
Description: This is the core functions needed by the 'tsmp' package. The
low level and carefully checked mathematical functions are here.
These are implementations of the Matrix Profile concept that was
created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] ,
Michael Yeh [res, ccp, ctb] ,
Diego Silva [res, ccp, ctb] ,
Yan Zhu [res, ccp, ctb] ,
Hoang Dau [res, ccp, ctb] ,
Michele Linardi [res, ccp, ctb]
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between matrixprofiler versions 0.1.10 dated 2025-12-01 and 0.1.12 dated 2026-10-14
matrixprofiler-0.1.10/matrixprofiler/data/datalist |only matrixprofiler-0.1.10/matrixprofiler/inst/API |only matrixprofiler-0.1.10/matrixprofiler/src/rcpp_parallel_fix.h |only matrixprofiler-0.1.10/matrixprofiler/tests/testthat/_snaps/stomp.md |only matrixprofiler-0.1.12/matrixprofiler/DESCRIPTION | 19 matrixprofiler-0.1.12/matrixprofiler/MD5 | 153 matrixprofiler-0.1.12/matrixprofiler/NAMESPACE | 9 matrixprofiler-0.1.12/matrixprofiler/NEWS | 350 + matrixprofiler-0.1.12/matrixprofiler/NEWS.md | 302 + matrixprofiler-0.1.12/matrixprofiler/R/RcppExports.R | 192 matrixprofiler-0.1.12/matrixprofiler/R/contrast.R | 57 matrixprofiler-0.1.12/matrixprofiler/R/mass.R | 158 matrixprofiler-0.1.12/matrixprofiler/R/matrixprofiler-package.R | 30 matrixprofiler-0.1.12/matrixprofiler/R/mpdist.R |only matrixprofiler-0.1.12/matrixprofiler/R/mpx.R | 331 + matrixprofiler-0.1.12/matrixprofiler/R/mstomp.R |only matrixprofiler-0.1.12/matrixprofiler/R/rfcp.R |only matrixprofiler-0.1.12/matrixprofiler/R/rfcp_top_k.R |only matrixprofiler-0.1.12/matrixprofiler/R/scrimp.R | 155 matrixprofiler-0.1.12/matrixprofiler/R/stamp.R | 153 matrixprofiler-0.1.12/matrixprofiler/R/stomp.R | 140 matrixprofiler-0.1.12/matrixprofiler/R/windowfunc.R | 342 - matrixprofiler-0.1.12/matrixprofiler/R/zzz.R | 2 matrixprofiler-0.1.12/matrixprofiler/README.md | 165 matrixprofiler-0.1.12/matrixprofiler/inst/API-v0.1.0 |only matrixprofiler-0.1.12/matrixprofiler/inst/API-v0.1.12 |only matrixprofiler-0.1.12/matrixprofiler/inst/WORDLIST | 82 matrixprofiler-0.1.12/matrixprofiler/inst/cuda |only matrixprofiler-0.1.12/matrixprofiler/inst/schemaorg.json | 4 matrixprofiler-0.1.12/matrixprofiler/man/contrast.Rd | 4 matrixprofiler-0.1.12/matrixprofiler/man/figures/dependency_plot-1.png |binary matrixprofiler-0.1.12/matrixprofiler/man/figures/logo.png |only matrixprofiler-0.1.12/matrixprofiler/man/has_cuda.Rd |only matrixprofiler-0.1.12/matrixprofiler/man/mass.Rd | 4 matrixprofiler-0.1.12/matrixprofiler/man/matrixprofiler.Rd | 30 matrixprofiler-0.1.12/matrixprofiler/man/mp_algos.Rd | 121 matrixprofiler-0.1.12/matrixprofiler/man/mpdist.Rd |only matrixprofiler-0.1.12/matrixprofiler/man/mstomp.Rd |only matrixprofiler-0.1.12/matrixprofiler/man/rfcp.Rd |only matrixprofiler-0.1.12/matrixprofiler/man/rfcp_top_k.Rd |only matrixprofiler-0.1.12/matrixprofiler/man/windowfunc.Rd | 69 matrixprofiler-0.1.12/matrixprofiler/src/Makevars | 9 matrixprofiler-0.1.12/matrixprofiler/src/Makevars.win | 4 matrixprofiler-0.1.12/matrixprofiler/src/RcppExports.cpp | 567 ++ matrixprofiler-0.1.12/matrixprofiler/src/contrast.cpp | 5 matrixprofiler-0.1.12/matrixprofiler/src/contrast.h | 4 matrixprofiler-0.1.12/matrixprofiler/src/fft.cpp | 12 matrixprofiler-0.1.12/matrixprofiler/src/mass.cpp | 450 + matrixprofiler-0.1.12/matrixprofiler/src/mass.h | 58 matrixprofiler-0.1.12/matrixprofiler/src/mathtools.cpp | 10 matrixprofiler-0.1.12/matrixprofiler/src/mpdist.cpp |only matrixprofiler-0.1.12/matrixprofiler/src/mpdist.h |only matrixprofiler-0.1.12/matrixprofiler/src/mpx.cpp | 599 +- matrixprofiler-0.1.12/matrixprofiler/src/mpx.h | 8 matrixprofiler-0.1.12/matrixprofiler/src/mpx_gpu.cpp |only matrixprofiler-0.1.12/matrixprofiler/src/mpx_gpu.h |only matrixprofiler-0.1.12/matrixprofiler/src/mpx_parallel.cpp | 2335 +++++++++- matrixprofiler-0.1.12/matrixprofiler/src/mpx_parallel.h | 18 matrixprofiler-0.1.12/matrixprofiler/src/mstomp.cpp |only matrixprofiler-0.1.12/matrixprofiler/src/mstomp.h |only matrixprofiler-0.1.12/matrixprofiler/src/progress_bar.h |only matrixprofiler-0.1.12/matrixprofiler/src/rfcp.cpp |only matrixprofiler-0.1.12/matrixprofiler/src/rfcp.h |only matrixprofiler-0.1.12/matrixprofiler/src/rfcp_gpu.cpp |only matrixprofiler-0.1.12/matrixprofiler/src/rfcp_gpu.h |only matrixprofiler-0.1.12/matrixprofiler/src/scrimp.cpp | 705 --- matrixprofiler-0.1.12/matrixprofiler/src/scrimp.h | 6 matrixprofiler-0.1.12/matrixprofiler/src/stamp.cpp | 451 - matrixprofiler-0.1.12/matrixprofiler/src/stamp.h | 2 matrixprofiler-0.1.12/matrixprofiler/src/stomp.cpp | 383 - matrixprofiler-0.1.12/matrixprofiler/src/stomp.h | 4 matrixprofiler-0.1.12/matrixprofiler/src/windowfunc.cpp | 982 +++- matrixprofiler-0.1.12/matrixprofiler/src/windowfunc.h | 25 matrixprofiler-0.1.12/matrixprofiler/tests/testthat.R | 25 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-algorithms.R | 51 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-contrast.R | 22 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mass.R | 30 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-math.R | 39 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mpdist.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mpx-branches.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mpx-na.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mpx-stream.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mpx.R | 212 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-mstomp.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-rfcp-branches.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-rfcp-top-k-checkpoint.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-rfcp-top-k.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-rfcp.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-scrimp.R | 71 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-stamp.R | 48 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-stomp.R | 198 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-windowfunc-branches.R |only matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-windowfunc.R | 57 matrixprofiler-0.1.12/matrixprofiler/tests/testthat/test-zero-crossing.R |only 94 files changed, 7352 insertions(+), 2910 deletions(-)
More information about matrixprofiler at CRAN
Permanent link
Title: Parametric and Non-Parametric Demographic Functions and
Applications
Description: Calculate parametric mortality and Fertility models, following packages 'BaSTA' in Colchero, Jones and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and 'BaFTA' <https://github.com/fercol/BaFTA>, summary statistics (e.g. ageing rates, life expectancy, lifespan equality, etc.), life table and product limit estimators from census data.
Author: Fernando Colchero [aut, cre]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Diff between paramDemo versions 1.0.2 dated 2025-01-16 and 1.0.3 dated 2026-10-13
DESCRIPTION | 12 ++-- MD5 | 10 +-- R/paramDemo.R | 126 +++++++++++++++++++++++++++++++++++++++++------ man/CalcLifeHist.Rd | 6 -- man/CalcMort.Rd | 9 +++ man/paramDemo-package.Rd | 4 - 6 files changed, 135 insertions(+), 32 deletions(-)
Title: Extra CRAN Submission Checks
Description: Provides automated checks for common Comprehensive R Archive
Network (CRAN) submission issues that are not caught by standard
'R CMD check'. Consolidates ad-hoc requirements that CRAN reviewers
enforce but standard checks do not surface, helping R package
maintainers identify and fix issues before submission to reduce
rejection rates. Covers code-pattern issues, DESCRIPTION-field
formatting, documentation problems, and general package structure
concerns.
Author: James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <james.balamuta@gmail.com>
Diff between checktor versions 0.1.0 dated 2026-07-02 and 0.2.0 dated 2026-10-13
checktor-0.1.0/checktor/man/diagnose_cran_comments_file.Rd |only checktor-0.1.0/checktor/man/diagnose_example_structure.Rd |only checktor-0.1.0/checktor/man/diagnose_missing_examples.Rd |only checktor-0.1.0/checktor/man/diagnose_news_file.Rd |only checktor-0.1.0/checktor/man/diagnose_package_size.Rd |only checktor-0.1.0/checktor/man/diagnose_print_cat_usage.Rd |only checktor-0.1.0/checktor/man/diagnose_readme_relative_links.Rd |only checktor-0.1.0/checktor/man/diagnose_roxygen_usage.Rd |only checktor-0.1.0/checktor/man/diagnose_seed_setting.Rd |only checktor-0.1.0/checktor/man/diagnose_suggested_in_examples.Rd |only checktor-0.1.0/checktor/man/diagnose_tf_usage.Rd |only checktor-0.1.0/checktor/man/diagnose_urls.Rd |only checktor-0.1.0/checktor/man/diagnose_value_tags.Rd |only checktor-0.1.0/checktor/tests/testthat/test-diagnostics-new.R |only checktor-0.2.0/checktor/.aspell |only checktor-0.2.0/checktor/DESCRIPTION | 12 checktor-0.2.0/checktor/MD5 | 385 +++- checktor-0.2.0/checktor/NAMESPACE | 97 + checktor-0.2.0/checktor/NEWS.md | 659 +++++++ checktor-0.2.0/checktor/R/accessors.R | 345 +++- checktor-0.2.0/checktor/R/ast-guards.R |only checktor-0.2.0/checktor/R/ast-output.R |only checktor-0.2.0/checktor/R/ast-writes.R |only checktor-0.2.0/checktor/R/ast.R | 616 ++++++- checktor-0.2.0/checktor/R/cache.R |only checktor-0.2.0/checktor/R/checktor-classes.R | 112 - checktor-0.2.0/checktor/R/checktor.R | 353 +++- checktor-0.2.0/checktor/R/ci-report.R |only checktor-0.2.0/checktor/R/config.R |only checktor-0.2.0/checktor/R/dependencies.R |only checktor-0.2.0/checktor/R/diagnostics-bibliography.R |only checktor-0.2.0/checktor/R/diagnostics-code-cores.R |only checktor-0.2.0/checktor/R/diagnostics-code-files.R |only checktor-0.2.0/checktor/R/diagnostics-code-output.R |only checktor-0.2.0/checktor/R/diagnostics-code-packages.R |only checktor-0.2.0/checktor/R/diagnostics-code-state.R |only checktor-0.2.0/checktor/R/diagnostics-code.R | 664 ++----- 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Title: Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Description: Calculates power for assessment of intermediate biomarker responses as correlates of risk in the active treatment group in clinical efficacy trials, as described in Gilbert, Janes, and Huang, Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials (2016, Statistics in Medicine). The methods differ from past approaches by accounting for the level of clinical treatment efficacy overall and in biomarker response subgroups, which enables the correlates of risk results to be interpreted in terms of potential correlates of efficacy/protection. The methods also account for inter-individual variability of the observed biomarker response that is not biologically relevant (e.g., due to technical measurement error of the laboratory assay used to measure the biomarker response), which is important because power to detect a specified correlate of risk effect size is heavily affected by the biomarker's measurement error. The methods can be used for a general binar [...truncated...]
Author: Stephanie Wu [aut],
Michal Juraska [aut, cre],
Peter Gilbert [aut],
Yunda Huang [aut],
Sebastien Haneuse [ctb, cph] code from
the osDesign package),
Takumi Saegusa [ctb, cph] code from the
osDesign package),
Nilanjan Chatterjee [ctb, cph] code fro [...truncated...]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between CoRpower versions 1.0.4 dated 2020-11-17 and 1.0.5 dated 2026-10-13
DESCRIPTION | 27 MD5 | 38 NAMESPACE | 7 NEWS.md |only R/computePower.R | 3686 ++++++++++---------- R/plotPowerCont.R | 396 +- R/plotPowerTri.R | 498 +- R/plotROCcurveTri.R | 336 - R/plotRRgradVE.R | 346 - R/tps.R |only build/vignette.rds |binary inst/doc/CoRpowerIntroduction.R | 588 +-- inst/doc/CoRpowerIntroduction.Rmd | 4 inst/doc/CoRpowerIntroduction.html | 2313 ++++++------ inst/doc/placeboAndBIPdataSimulationAlgorithms.html | 1005 ++--- man/computePower.Rd | 820 ++-- man/plotPowerCont.Rd | 202 - man/plotPowerTri.Rd | 182 man/plotROCcurveTri.Rd | 74 man/plotRRgradVE.Rd | 192 - vignettes/CoRpowerIntroduction.Rmd | 4 21 files changed, 5541 insertions(+), 5177 deletions(-)
Title: Building and Estimating Structural Equation Models
Description: A powerful, easy to use syntax for specifying and estimating complex
Structural Equation Models. Models can be estimated using Partial
Least Squares Path Modeling or Covariance-Based Structural Equation
Modeling or covariance based Confirmatory Factor Analysis (Ray, Danks, and Valdez 2021 <doi:10.2139/ssrn.3900621>).
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
Andre Calero Valdez [aut],
Juan Manuel Velasquez Estrada [ctb],
James Uanhoro [ctb],
Johannes Nakayama [ctb],
Lilian Koyan [ctb],
Laura Burbach [ctb],
Arturo Heynar Cano Bejar [ctb],
Susanne A [...truncated...]
Maintainer: Nicholas Patrick Danks <seminrgroup@gmail.com>
Diff between seminr versions 2.5.0 dated 2026-05-25 and 2.6.0 dated 2026-10-13
DESCRIPTION | 12 MD5 | 94 - NAMESPACE | 1 NEWS.md | 171 +++ R/compute_safe.R | 15 R/estimate_bootstrap.R | 86 + R/estimate_pls.R | 17 R/estimate_pls_mga.R | 7 R/estimate_simplePLS.R | 17 R/evaluate_effects.R | 6 R/evaluate_reliability.R | 2 R/evaluate_validity.R | 49 R/feature_cbsempredict.R |only R/feature_consistent.R | 151 ++ R/feature_plscpredict.R |only R/feature_plspredict.R | 558 ++++++---- R/helpers-mmMatrix.R | 5 R/helpers-model.R | 19 R/helpers-smMatrix.R | 13 R/library.R | 15 R/library_parallel.R | 50 R/plot_results.R | 18 R/report_summary.R | 7 inst/doc/SEMinR.R | 4 inst/doc/SEMinR.Rmd | 17 inst/doc/SEMinR.html | 51 man/PLSc.Rd | 11 man/bootstrap_model.Rd | 10 man/plot.reliability_table.Rd | 11 man/predict.cbsem_model.Rd |only man/predict.seminr_model.Rd | 23 man/predict_pls.Rd | 12 man/seminr-package.Rd | 2 tests/fixtures/V_3_6_0/composite_indicator_weights_p_values.csv | 10 tests/fixtures/V_3_6_0/composite_indicator_weights_t_values.csv | 10 tests/fixtures/V_3_6_0/factor_discriminant_validity_p_values.csv | 6 tests/fixtures/V_3_6_0/factor_discriminant_validity_t_values.csv | 6 tests/testthat/_snaps/plot-dot-snapshots.md | 24 tests/testthat/fixtures |only tests/testthat/test-accessors-mmMatrix.R | 34 tests/testthat/test-cbsempredict.R |only tests/testthat/test-consistent-interactions.R | 12 tests/testthat/test-consistent.R | 119 ++ tests/testthat/test-cran-core-limit.R |only tests/testthat/test-parallel-setup.R | 15 tests/testthat/test-plot-reliability.R |only tests/testthat/test-plsc-hoc.R |only tests/testthat/test-plscpredict.R |only tests/testthat/test-plspredict.R | 76 + tests/testthat/test-structure.r | 45 vignettes/SEMinR.Rmd | 17 51 files changed, 1462 insertions(+), 366 deletions(-)
Title: Flexible and Efficient Evaluation of Principal
Surrogates/Treatment Effect Modifiers
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB (2020), Inference on treatment effect modification by biomarker response in a three-phase sampling design, Biostatistics, 21(3): 545-560 <doi:10.1093/biostatistics/kxy074>. The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response ( [...truncated...]
Author: Michal Juraska [aut, cre],
Sebastien Haneuse [ctb, cph] code from
the osDesign package),
Takumi Saegusa [ctb, cph] code from the
osDesign package),
Nilanjan Chatterjee [ctb, cph] code from
the osDesign package),
Norman Breslow [ctb, cph] code fro [...truncated...]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between pssmooth versions 1.0.3 dated 2020-11-18 and 1.0.4 dated 2026-10-13
DESCRIPTION | 25 ++++++++++++++++--------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 - NEWS |binary R/pssmooth.R | 20 +++++++++++--------- R/tps.R |only build |only inst/CITATION | 19 +++++++------------ man/bootRiskCurve.Rd | 2 +- man/riskCurve.Rd | 6 +++--- man/summary.riskCurve.Rd | 2 +- man/testConstancy.Rd | 2 +- man/testEquality.Rd | 2 +- 13 files changed, 53 insertions(+), 48 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and its API borrows heavily from
the 'PyTorch' vision package.
Author: Tomasz Kalinowski [ctb, cre],
Daniel Falbel [aut, cph],
Christophe Regouby [ctb],
Akanksha Koshti [ctb],
Derrick Richard [ctb],
ANAMASGARD [ctb],
Chandraveer Singh [ctb],
Srishti Dutta [ctb],
Sebastian Fischer [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between torchvision versions 0.9.0 dated 2026-04-22 and 0.10.0 dated 2026-10-13
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Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
Author: Michael Hahsler [aut, cre, cph] ,
John Forrest [aut, cph],
Matthew Bolanos [ctb],
Matthias Carnein [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.3-1 dated 2024-04-20 and 1.4.0 dated 2026-10-13
streamMOA-1.3-1/streamMOA/R/DSClassifier_MOA.R |only streamMOA-1.3-1/streamMOA/R/DSRegressor_MOA.R |only streamMOA-1.3-1/streamMOA/inst/doc/streamMOA.Rnw |only streamMOA-1.3-1/streamMOA/inst/doc/streamMOA.pdf |only streamMOA-1.3-1/streamMOA/man/DSClassifier_MOA.Rd |only streamMOA-1.3-1/streamMOA/man/DSRegressor_MOA.Rd |only streamMOA-1.3-1/streamMOA/vignettes/streamMOA.Rnw |only streamMOA-1.4.0/streamMOA/DESCRIPTION | 22 - streamMOA-1.4.0/streamMOA/MD5 | 87 ++--- streamMOA-1.4.0/streamMOA/NAMESPACE | 20 - streamMOA-1.4.0/streamMOA/NEWS.md | 8 streamMOA-1.4.0/streamMOA/R/DSC_BICO_MOA.R | 17 - streamMOA-1.4.0/streamMOA/R/DSC_CluStream.R | 15 streamMOA-1.4.0/streamMOA/R/DSC_ClusTree.R | 18 - streamMOA-1.4.0/streamMOA/R/DSC_DStream_MOA.R | 18 - streamMOA-1.4.0/streamMOA/R/DSC_DenStream.R | 47 +- streamMOA-1.4.0/streamMOA/R/DSC_MOA.R | 28 + streamMOA-1.4.0/streamMOA/R/DSC_streamkm.R | 41 +- streamMOA-1.4.0/streamMOA/R/DSD_MOA.R | 19 - streamMOA-1.4.0/streamMOA/R/DSD_RandomRBFGeneratorEvents.R | 50 +-- streamMOA-1.4.0/streamMOA/R/DSOutlier_MCOD.R | 55 --- streamMOA-1.4.0/streamMOA/R/ellipse.R | 2 streamMOA-1.4.0/streamMOA/README.md | 27 - streamMOA-1.4.0/streamMOA/build/partial.rdb |binary streamMOA-1.4.0/streamMOA/build/vignette.rds |binary streamMOA-1.4.0/streamMOA/inst/README_files/plot-1.png |binary streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.R | 164 +--------- streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.Rmd |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.html |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.R |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.Rnw |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.pdf |only streamMOA-1.4.0/streamMOA/java/README | 3 streamMOA-1.4.0/streamMOA/java/StreamMOA.java | 2 streamMOA-1.4.0/streamMOA/man/DSC_BICO_MOA.Rd | 36 +- streamMOA-1.4.0/streamMOA/man/DSC_CluStream.Rd | 31 - streamMOA-1.4.0/streamMOA/man/DSC_ClusTree.Rd | 34 +- streamMOA-1.4.0/streamMOA/man/DSC_DStream_MOA.Rd | 34 +- streamMOA-1.4.0/streamMOA/man/DSC_DenStream.Rd | 63 +-- streamMOA-1.4.0/streamMOA/man/DSC_MCOD.Rd | 47 +- streamMOA-1.4.0/streamMOA/man/DSC_MOA.Rd | 18 - streamMOA-1.4.0/streamMOA/man/DSC_StreamKM.Rd | 39 +- streamMOA-1.4.0/streamMOA/man/DSD_MOA.Rd | 23 - streamMOA-1.4.0/streamMOA/man/DSD_RandomRBFGeneratorEvents.Rd | 56 +-- streamMOA-1.4.0/streamMOA/man/figures/README-plot-1.png |only streamMOA-1.4.0/streamMOA/man/streamMOA-package.Rd | 7 streamMOA-1.4.0/streamMOA/tests |only streamMOA-1.4.0/streamMOA/vignettes/head.tex | 10 streamMOA-1.4.0/streamMOA/vignettes/streamMOA.Rmd |only streamMOA-1.4.0/streamMOA/vignettes/streamMOA_vignette.Rnw |only 50 files changed, 474 insertions(+), 567 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of the
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. It also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Author: Michael Hahsler [aut, cre, cph] ,
Margaret H. Dunham [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.2.1 dated 2024-04-21 and 1.2.3 dated 2026-10-13
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Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.1.3 dated 2026-07-21 and 0.1.4 dated 2026-10-13
ChangeLog | 78 +++++++ DESCRIPTION | 8 MD5 | 83 ++++---- R/RcppExports.R | 4 R/calendars.R | 8 R/dates.R | 2 README.md | 6 build/partial.rdb |binary configure | 2 inst/NEWS.Rd | 13 + man/advanceUnits.Rd | 2 man/getCalendar.Rd | 2 man/getName.Rd | 2 src/Makevars.in | 2 src/Makevars.win.in | 2 src/calendars.cpp | 65 ++++-- src/ql/optional.hpp | 34 +-- src/ql/patterns/observable.cpp | 53 +++-- src/ql/settings.cpp | 19 + src/ql/settings.hpp | 25 -- src/ql/time/calendars/all.hpp | 2 src/ql/time/calendars/argentina.hpp | 2 src/ql/time/calendars/bespokecalendar.hpp | 2 src/ql/time/calendars/hongkong.cpp | 15 + src/ql/time/calendars/indonesia.cpp | 311 +++++++++++++++++++++++++++++- src/ql/time/calendars/italy.cpp | 4 src/ql/time/calendars/italy.hpp | 27 -- src/ql/time/calendars/malaysia.cpp |only src/ql/time/calendars/malaysia.hpp |only src/ql/time/calendars/philippines.cpp |only src/ql/time/calendars/philippines.hpp |only src/ql/time/calendars/saudiarabia.cpp | 161 ++++++++------- src/ql/time/calendars/saudiarabia.hpp | 12 - src/ql/time/calendars/singapore.cpp | 16 + src/ql/time/calendars/singapore.hpp | 2 src/ql/time/calendars/southafrica.cpp | 11 - src/ql/time/calendars/sweden.hpp | 2 src/ql/time/calendars/thailand.cpp | 6 src/ql/time/calendars/thailand.hpp | 4 src/ql/time/calendars/turkey.cpp | 2 src/ql/time/date.cpp | 38 +++ src/ql/time/period.cpp | 7 src/ql/utilities/null.hpp | 44 +--- src/ql/utilities/null_deleter.hpp |only src/xptr.cpp | 4 45 files changed, 804 insertions(+), 278 deletions(-)
Title: Regularized Point Processes and Stochastic Marginalization for
Extremes
Description: Implements a non-stationary extreme value analysis framework
by coupling a covariate-driven non-homogeneous Poisson process (NHPP)
with (adaptive) elastic-net regularization and analytical gradients.
Provides methods for estimating conditional return levels and
unconditional (marginalized) return levels via parametric stochastic
integration over stable vector autoregressive VAR(p) covariate
trajectories, or non-parametric annual-block resampling. Supports
block-specific penalty controls, BIC selection along a regularization
path, Karush-Kuhn-Tucker convergence checks, time-rescaling residual
diagnostics, conditional parametric bootstrap inference, and
walk-forward assessment.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between margEVT versions 0.3.0 dated 2026-09-23 and 0.4.0 dated 2026-10-13
margEVT-0.3.0/margEVT/man/dot-select_lambda_bic.Rd |only margEVT-0.4.0/margEVT/DESCRIPTION | 27 margEVT-0.4.0/margEVT/MD5 | 100 - margEVT-0.4.0/margEVT/NAMESPACE | 8 margEVT-0.4.0/margEVT/NEWS.md | 78 margEVT-0.4.0/margEVT/R/backtest.R | 179 +- margEVT-0.4.0/margEVT/R/bootstrap.R | 729 ++++---- margEVT-0.4.0/margEVT/R/covariate.R | 459 +++-- margEVT-0.4.0/margEVT/R/design.R | 8 margEVT-0.4.0/margEVT/R/fit.R | 1104 +++++++------ margEVT-0.4.0/margEVT/R/generator.R | 492 +++-- margEVT-0.4.0/margEVT/R/likelihood.R | 521 +++--- margEVT-0.4.0/margEVT/R/marginalize.R | 764 +++++--- margEVT-0.4.0/margEVT/R/methods.R |only margEVT-0.4.0/margEVT/R/params.R | 8 margEVT-0.4.0/margEVT/R/select.R | 438 ++--- margEVT-0.4.0/margEVT/R/utils.R | 531 ++---- margEVT-0.4.0/margEVT/build |only margEVT-0.4.0/margEVT/inst/CITATION | 44 margEVT-0.4.0/margEVT/inst/doc |only margEVT-0.4.0/margEVT/man/active_covariates.Rd | 14 margEVT-0.4.0/margEVT/man/backtest.Rd | 42 margEVT-0.4.0/margEVT/man/bic_nhpp.Rd | 13 margEVT-0.4.0/margEVT/man/bootstrap_coef.Rd | 39 margEVT-0.4.0/margEVT/man/bootstrap_rl.Rd | 41 margEVT-0.4.0/margEVT/man/build_cov_annual.Rd | 21 margEVT-0.4.0/margEVT/man/build_design_matrices.Rd | 9 margEVT-0.4.0/margEVT/man/coef.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/fit_nhpp.Rd | 92 - margEVT-0.4.0/margEVT/man/fit_var_generator.Rd | 92 - margEVT-0.4.0/margEVT/man/is_nhpp_fit.Rd | 3 margEVT-0.4.0/margEVT/man/marginalize.Rd | 61 margEVT-0.4.0/margEVT/man/n_exceedances.Rd | 10 margEVT-0.4.0/margEVT/man/nhpp_fit-methods.Rd |only margEVT-0.4.0/margEVT/man/plot.nhpp_fit.Rd | 38 margEVT-0.4.0/margEVT/man/plot.nhpp_rl.Rd |only margEVT-0.4.0/margEVT/man/pp_grad.Rd | 20 margEVT-0.4.0/margEVT/man/pp_nllh.Rd | 29 margEVT-0.4.0/margEVT/man/predict_params.Rd | 9 margEVT-0.4.0/margEVT/man/print.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/print.summary.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/residuals.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/rl_table.Rd | 9 margEVT-0.4.0/margEVT/man/seasonal_harmonics.Rd |only margEVT-0.4.0/margEVT/man/simulate_covariates.Rd | 33 margEVT-0.4.0/margEVT/man/summary.nhpp_fit.Rd | 21 margEVT-0.4.0/margEVT/tests/testthat/test-bootstrap-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-bootstrap.R | 4 margEVT-0.4.0/margEVT/tests/testthat/test-covariate.R | 15 margEVT-0.4.0/margEVT/tests/testthat/test-estimation-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-fit.R | 8 margEVT-0.4.0/margEVT/tests/testthat/test-generator-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-generator.R | 43 margEVT-0.4.0/margEVT/tests/testthat/test-marginalize.R | 81 margEVT-0.4.0/margEVT/tests/testthat/test-methods.R |only margEVT-0.4.0/margEVT/tests/testthat/test-select.R | 56 margEVT-0.4.0/margEVT/tests/testthat/test-utils.R | 14 margEVT-0.4.0/margEVT/vignettes |only 58 files changed, 3872 insertions(+), 2435 deletions(-)
Title: Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq
Data
Description: A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>).
Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any
type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),
TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends
standard NR-seq standard NR-seq mutational modeling to support multi-label analyses
(e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better
account for transcript-to-transcript variance in metabolic label incorporation.
'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses
of premature mRNA processing and flow between subcellular compartments. Finally,
'EZbakR' implements flexible and well-powered comparative analyses of all
estimated parameters via design matrix-specified generalized linear modeling.
Author: Isaac Vock [aut, cre, cph]
Maintainer: Isaac Vock <isaac.vock@gmail.com>
Diff between EZbakR versions 0.1.0 dated 2025-12-10 and 0.2.2 dated 2026-10-13
DESCRIPTION | 9 LICENSE | 4 MD5 | 151 NEWS.md | 28 R/Comparisons.R | 2915 +++++++++--------- R/Dropout.R | 1932 ++++++------ R/EZbakRArrowData.R | 856 ++--- R/EZbakRData.R | 814 ++--- R/EZbakRFractions.R | 905 ++--- R/EZbakRKinetics.R | 775 ++-- R/Fractions.R | 5524 +++++++++++++++++----------------- R/Helpers.R | 2740 ++++++++--------- R/Isoforms.R | 2396 +++++++-------- R/Kinetics.R | 1988 ++++++------ R/ODEs.R | 3577 +++++++++++----------- R/QC.R | 2748 ++++++++--------- R/Simulations.R | 6166 +++++++++++++++++++-------------------- R/Visualizations.R | 1902 ++++++------ R/data.R | 204 - R/simple-functions.R | 482 +-- README.md | 148 build/partial.rdb |only build/vignette.rds |binary inst/doc/EZDynamics.R | 53 inst/doc/EZDynamics.Rmd | 1695 +++++----- inst/doc/EZDynamics.html | 628 ++- inst/doc/EZQC.Rmd | 274 - inst/doc/EZQC.html | 176 - inst/doc/EZget.html | 65 inst/doc/EstimateFractions.Rmd | 1260 +++---- inst/doc/EstimateFractions.html | 30 inst/doc/EstimateKinetics.Rmd | 4 inst/doc/EstimateKinetics.html | 15 inst/doc/Linear-modeling.Rmd | 1094 +++--- inst/doc/Linear-modeling.html | 13 inst/doc/Quickstart.html | 15 man/CompareParameters.Rd | 3 man/CorrectDropout.Rd | 8 man/DeconvolveFractions.Rd | 296 - man/EZDynamics.Rd | 5 man/EZQC.EZbakRArrowData.Rd | 86 man/EZQC.Rd | 2 man/EZSimulate.Rd | 9 man/EZbakRArrowData.Rd | 270 - man/EZbakRData.Rd | 238 - man/EZbakRFractions.Rd | 3 man/EZbakRKinetics.Rd | 3 man/EZpcaPlot.Rd | 186 - man/EstimateFractions.Rd | 2 man/EstimateIsoformFractions.Rd | 2 man/EstimateMutRates.Rd | 210 - man/ImportIsoformQuant.Rd | 166 - man/NormalizeForDropout.Rd | 238 - man/SimpleSim.Rd | 92 man/SimulateIsoforms.Rd | 192 - man/SimulateMultiCondition.Rd | 398 +- man/SimulateOneRep.Rd | 254 - man/create_fraction_design.Rd | 98 man/example_cB.Rd | 68 man/example_metadf.Rd | 56 man/new_EZbakRArrowData.Rd | 38 man/new_EZbakRData.Rd | 38 man/print.EZbakRArrowData.Rd | 68 man/print.EZbakRData.Rd | 68 man/standard_fraction_design.Rd | 52 man/tilac_fraction_design.Rd | 66 man/validate_EZbakRArrowData.Rd | 30 man/validate_EZbakRData.Rd | 30 man/validate_EZbakRFractions.Rd | 30 tests/testthat.R | 24 tests/testthat/test-EZbakRData.R | 282 - tests/testthat/test-SimpleSim.R | 10 vignettes/EZDynamics.Rmd | 1695 +++++----- vignettes/EZQC.Rmd | 274 - vignettes/EstimateFractions.Rmd | 1260 +++---- vignettes/EstimateKinetics.Rmd | 4 vignettes/Linear-modeling.Rmd | 1094 +++--- 77 files changed, 24975 insertions(+), 24559 deletions(-)
Title: Bias and Uncertainty Corrected Sample Size
Description: Implements sample size planning for a future study from the summary
statistics of a prior study, correcting the prior effect for publication bias
and uncertainty so the planned study attains its target statistical power more
reliably than methods that take a sample effect size at face value. Planners
cover the one-sample, paired, independent, and Welch t tests; between-subjects
analysis of variance and covariance; within-subjects and split-plot analysis
of variance; a regression coefficient, the squared multiple correlation, and a
subset of predictors; the Pearson correlation; a two-group multivariate
comparison; and the chi square difference between nested models. The
regression planners can treat the predictors as fixed or as sampled, the
within-subjects and split-plot planners accept a sphericity correction, and
each plan reports the effect size it is built on. A simulation function
audits how often a plan attains its target power. The method is described in
Anderson, Kelley, and Ma [...truncated...]
Author: Ken Kelley [aut, cre] ,
Samantha F. Anderson [aut] ,
Scott E. Maxwell [aut]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between BUCSS versions 1.2.1 dated 2020-08-25 and 2.0.0 dated 2026-10-13
BUCSS-1.2.1/BUCSS/R/ss.power.ba.R |only BUCSS-1.2.1/BUCSS/R/ss.power.ba.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.dt.r |only BUCSS-1.2.1/BUCSS/R/ss.power.it.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg.all.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg.joint.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg1.R |only BUCSS-1.2.1/BUCSS/R/ss.power.spa.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.spa.r |only BUCSS-1.2.1/BUCSS/R/ss.power.wa.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.wa.r |only BUCSS-1.2.1/BUCSS/man/ss.power.ba.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.ba.general.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.dt.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.it.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg.all.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg.joint.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg1.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.spa.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.spa.general.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.wa.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.wa.general.Rd |only BUCSS-2.0.0/BUCSS/DESCRIPTION | 55 +- BUCSS-2.0.0/BUCSS/MD5 | 137 ++++- BUCSS-2.0.0/BUCSS/NAMESPACE | 69 ++- BUCSS-2.0.0/BUCSS/NEWS.md |only BUCSS-2.0.0/BUCSS/R/BUCSS.R | 178 +++++++ BUCSS-2.0.0/BUCSS/R/bucss-broom.R |only BUCSS-2.0.0/BUCSS/R/bucss-design-registry.R |only BUCSS-2.0.0/BUCSS/R/bucss-internal.R |only BUCSS-2.0.0/BUCSS/R/bucss-output-helpers.R |only BUCSS-2.0.0/BUCSS/R/bucss-plot.R |only BUCSS-2.0.0/BUCSS/R/bucss-sensitivity.R |only BUCSS-2.0.0/BUCSS/R/legacy.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_R2.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_ancova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_chisq_diff.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_correlation.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_factorial_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_factorial_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_independent_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_manova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_mixed_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_mixed_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_one_sample_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_one_way_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_paired_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_reg_coef.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_reg_joint.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_rm_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_rm_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_welch_t.R |only BUCSS-2.0.0/BUCSS/README.md | 367 +++++++++++++++- BUCSS-2.0.0/BUCSS/build |only BUCSS-2.0.0/BUCSS/inst |only BUCSS-2.0.0/BUCSS/man/BUCSS-package.Rd | 164 ++++++- BUCSS-2.0.0/BUCSS/man/bucss-deprecated.Rd |only BUCSS-2.0.0/BUCSS/man/bucss_tidiers.Rd |only BUCSS-2.0.0/BUCSS/man/figures |only BUCSS-2.0.0/BUCSS/man/planning_sentence.Rd |only BUCSS-2.0.0/BUCSS/man/plot.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/print.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/print.bucss_sensitivity.Rd |only BUCSS-2.0.0/BUCSS/man/reexports.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_R2.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_ancova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_chisq_diff.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_correlation.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_factorial_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_factorial_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_independent_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_manova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_mixed_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_mixed_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_one_sample_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_one_way_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_paired_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_reg_coef.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_reg_joint.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_rm_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_rm_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_sensitivity.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_welch_t.Rd |only BUCSS-2.0.0/BUCSS/man/sub-.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/sub-sub-.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/tests |only BUCSS-2.0.0/BUCSS/vignettes |only 87 files changed, 905 insertions(+), 65 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut, cre]
Maintainer: Synthesize Bio <candace@synthesize.bio>
Diff between rsynthbio versions 4.2.0 dated 2026-06-12 and 4.2.1 dated 2026-10-13
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++------- NEWS.md | 7 ++++ R/call_model_api.R | 45 +++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/baseline.R | 2 - inst/doc/baseline.Rmd | 2 - inst/doc/getting-started.R | 2 - inst/doc/getting-started.Rmd | 2 - tests/testthat/fixtures |only tests/testthat/test-validation-errors.R |only vignettes/baseline.Rmd | 2 - vignettes/getting-started.Rmd | 2 - 13 files changed, 69 insertions(+), 23 deletions(-)
Title: 'rmarkdown' Extension for Formatted 'RJDemetra' Outputs
Description: Functions to have nice 'rmarkdown' outputs of the
seasonal and trading day adjustment models made with 'RJDemetra'.
Author: Alain Quartier-la-Tente [aut, cre, cph]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjdmarkdown versions 0.2.2 dated 2023-10-04 and 0.2.3 dated 2026-10-13
DESCRIPTION | 17 ++--- MD5 | 20 +++--- NAMESPACE | 20 ++++-- NEWS.md | 5 + R/print_preprocessing.R | 2 README.md | 10 +-- build/vignette.rds |binary inst/doc/rjdmarkdown-html.R | 114 ++++++++++++++++++------------------- inst/doc/rjdmarkdown-html.html | 7 +- inst/doc/rjdmarkdown-pdf.R | 126 ++++++++++++++++++++--------------------- inst/doc/rjdmarkdown-pdf.pdf |binary 11 files changed, 167 insertions(+), 154 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet,
NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Author: Eduard Szoecs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmueller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
Joao Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Ethan Bass [ctb],
Tamas Stirling [ctb, cre [...truncated...]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.3.1 dated 2025-07-16 and 2.0.0 dated 2026-10-13
DESCRIPTION | 27 MD5 | 134 ++-- NAMESPACE | 77 +- NEWS.md | 27 R/bcpc.R | 31 - R/chebi.R | 21 R/chembl.R | 1045 ++++++++++++++++++++++++++++++++-- R/chembl_offline.R |only R/chemspider.R | 27 R/cir.R | 12 R/cts.R | 4 R/etox.R | 24 R/eup.R |only R/foodb.R |only R/onLoad.R |only R/pubchem.R | 553 +++++------------ R/pubchem_pugview.R |only R/utils.R | 83 ++ R/zzz.R | 4 build/vignette.rds |binary inst/doc/pubchem-pages.Rmd |only inst/doc/pubchem-pages.html |only inst/doc/webchem-offline.Rmd |only inst/doc/webchem-offline.html |only inst/doc/webchem.html | 5 man/bcpc_query.Rd | 2 man/chebi_comp_entity.Rd | 7 man/chembl_atc_classes.Rd | 4 man/chembl_check_db_version.Rd |only man/chembl_img.Rd |only man/chembl_query.Rd | 150 ++++ man/chembl_status.Rd |only man/cir_img.Rd | 3 man/cir_query.Rd | 9 man/cs_check_key.Rd | 6 man/cs_compinfo.Rd | 5 man/cs_convert.Rd | 5 man/cs_datasources.Rd | 5 man/cs_extcompinfo.Rd | 8 man/cts_from.Rd | 2 man/cts_to.Rd | 2 man/db_connect.Rd |only man/db_download_chembl.Rd |only man/db_download_eup.Rd |only man/db_download_foodb.Rd |only man/etox_basic.Rd | 5 man/etox_targets.Rd | 5 man/etox_tests.Rd | 5 man/eup_convert.Rd |only man/eup_list_entries.Rd |only man/eup_query.Rd |only man/foodb_convert.Rd |only man/foodb_list_compounds.Rd |only man/foodb_query.Rd |only man/get_chebiid.Rd | 9 man/get_cid.Rd | 8 man/get_csid.Rd | 5 man/get_etoxid.Rd | 5 man/pc_sect.Rd | 6 man/webchem-package.Rd | 3 tests/testthat/test-bcpc.R | 13 tests/testthat/test-chebi.R | 7 tests/testthat/test-chembl.R | 262 +++++++- tests/testthat/test-chembl_offline.R |only tests/testthat/test-cir.R | 7 tests/testthat/test-cts.R | 15 tests/testthat/test-etox.R | 380 ++++++------ tests/testthat/test-eup.R |only tests/testthat/test-extractors.R | 34 - tests/testthat/test-flavornet.R | 8 tests/testthat/test-foodb.R |only tests/testthat/test-integration.R | 12 tests/testthat/test-nist.R | 34 + tests/testthat/test-opsin.R | 4 tests/testthat/test-pubchem-pugview.R |only tests/testthat/test-pubchem.R | 45 - tests/testthat/test-srs.R | 3 tests/testthat/test-utils.R | 26 tests/testthat/test-wikidata.R | 7 vignettes/precompile.R | 2 vignettes/pubchem-pages.Rmd |only vignettes/webchem-offline.Rmd |only 82 files changed, 2280 insertions(+), 912 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.4-6 dated 2026-10-01 and 1.4-7 dated 2026-10-13
DESCRIPTION | 12 ++--- MD5 | 25 ++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/NAMI.R | 101 ++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/NAMI.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++++-- inst/doc/NAMI.pdf |binary inst/doc/mtram.pdf |binary inst/doc/survtram.pdf |binary inst/doc/tram.pdf |binary tests/Polr-Ex.Rout.save |only tests/bugfixes.R | 15 ++++--- vignettes/NAMI.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++++-- 14 files changed, 330 insertions(+), 33 deletions(-)
Title: Modeling Data with Functional Programming
Description: A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Author: Brian Lee Yung Rowe [aut, cre]
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between lambda.r versions 1.2.4 dated 2019-09-18 and 1.2.6 dated 2026-10-13
DESCRIPTION | 16 +++++++++++----- MD5 | 4 ++-- man/lambda.r-package.Rd | 7 ++++--- 3 files changed, 17 insertions(+), 10 deletions(-)
Title: Cluster Origin-Destination Flow Data
Description: Provides functionality for clustering
origin-destination (OD) pairs, representing desire lines (or flows).
This includes creating distance matrices between OD pairs and passing
distance matrices to a clustering algorithm. See the academic paper
Tao and Thill (2016) <doi:10.1111/gean.12100>
for more details on spatial clustering of flows.
See the paper on delineating demand-responsive operating areas
by Mahfouz et al. (2025) <doi:10.1016/j.urbmob.2025.100135>
for an example of how this package can be used to cluster flows for
applied transportation research.
Author: Hussein Mahfouz [aut, cre] ,
Robin Lovelace [aut]
Maintainer: Hussein Mahfouz <husseinmahfouz93@gmail.com>
Diff between flowcluster versions 0.2.1 dated 2025-08-21 and 0.2.2 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/testthat/test-clustering.R | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get star [...truncated...]
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
Rider Johnson [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 17.3 dated 2026-05-05 and 18.0 dated 2026-10-13
fields-17.3/fields/R/BD.R |only fields-17.3/fields/R/ChicagoO3.R |only fields-17.3/fields/R/RMprecip.R |only fields-17.3/fields/R/flame.R |only fields-17.3/fields/R/imagePlotOLD.R |only fields-17.3/fields/R/minitri.R |only fields-17.3/fields/R/panelPlotExample.R |only fields-17.3/fields/R/rat.diet.R |only fields-17.3/fields/R/setupLegend.R |only fields-17.3/fields/tests/cmdfile |only fields-18.0/fields/DESCRIPTION | 8 fields-18.0/fields/LICENSE.note | 2 fields-18.0/fields/MD5 | 711 +++++++------- fields-18.0/fields/NAMESPACE | 5 fields-18.0/fields/R/Exponential.R | 4 fields-18.0/fields/R/ExponentialUpper.R | 4 fields-18.0/fields/R/Krig.R | 34 fields-18.0/fields/R/Krig.family.R | 52 - fields-18.0/fields/R/KrigFindLambda.R | 14 fields-18.0/fields/R/Matern.R | 2 fields-18.0/fields/R/Matern.parameters.R | 4 fields-18.0/fields/R/Paciorek.cov.R | 2 fields-18.0/fields/R/QSreg.R | 6 fields-18.0/fields/R/QTps.R | 6 fields-18.0/fields/R/RadialBasis.R | 2 fields-18.0/fields/R/RdistEarth.R | 2 fields-18.0/fields/R/SUBSCRIPTINGSpatialDesign.R | 2 fields-18.0/fields/R/Tps.R | 2 fields-18.0/fields/R/Tps.cov.R | 27 fields-18.0/fields/R/US.R | 2 fields-18.0/fields/R/add.image.R | 4 fields-18.0/fields/R/addColorBar.R |only fields-18.0/fields/R/addColorBarTriangle.R | 2 fields-18.0/fields/R/addLegend.R | 36 fields-18.0/fields/R/addTitleBox.R |only fields-18.0/fields/R/approximateCovariance2D.R | 17 fields-18.0/fields/R/arrow.plot.R | 3 fields-18.0/fields/R/as.image.R | 2 fields-18.0/fields/R/as.surface.R | 2 fields-18.0/fields/R/augmentPredictionGrid.R | 21 fields-18.0/fields/R/bisection.search.R | 2 fields-18.0/fields/R/bplot.family.R | 35 fields-18.0/fields/R/bubblePlot.R | 95 + fields-18.0/fields/R/cat.matrix.R | 2 fields-18.0/fields/R/cat.to.list.R | 2 fields-18.0/fields/R/ceiling2.R | 2 fields-18.0/fields/R/circulantEmbedding.R | 4 fields-18.0/fields/R/circulantEmbeddingSetup.R | 2 fields-18.0/fields/R/coef.Krig.R | 2 fields-18.0/fields/R/color.scale.R | 4 fields-18.0/fields/R/colorBar.R | 4 fields-18.0/fields/R/colorbar.plot.R | 6 fields-18.0/fields/R/compactToMat.R | 6 fields-18.0/fields/R/confidenceIntervalMLE.R | 2 fields-18.0/fields/R/cover.design.R | 8 fields-18.0/fields/R/cubic.cov.R | 4 fields-18.0/fields/R/describe.R | 2 fields-18.0/fields/R/discretize.image.R | 2 fields-18.0/fields/R/divMap.R | 21 fields-18.0/fields/R/double.exp.R | 2 fields-18.0/fields/R/drape.color.R | 6 fields-18.0/fields/R/drape.plot.R | 2 fields-18.0/fields/R/dyadic.2check.R | 2 fields-18.0/fields/R/dyadic.check.R | 2 fields-18.0/fields/R/ensembleEnvelope.R |only fields-18.0/fields/R/envelopePlot.R | 15 fields-18.0/fields/R/evlpoly.R | 2 fields-18.0/fields/R/evlpoly2.R | 2 fields-18.0/fields/R/exp.cov.R | 4 fields-18.0/fields/R/exp.earth.cov.R | 4 fields-18.0/fields/R/exp.image.cov.R | 2 fields-18.0/fields/R/exp.simple.cov.R | 8 fields-18.0/fields/R/fast.1way.R | 2 fields-18.0/fields/R/fastTps.R | 4 fields-18.0/fields/R/fields.color.picker.R | 2 fields-18.0/fields/R/fields.convert.grid.R | 2 fields-18.0/fields/R/fields.derivative.poly.R | 2 fields-18.0/fields/R/fields.duplicated.matrix.R | 2 fields-18.0/fields/R/fields.mkpoly.R | 4 fields-18.0/fields/R/fields.rdist.near.R | 2 fields-18.0/fields/R/fields.style.R | 2 fields-18.0/fields/R/fields.x.to.grid.R | 4 fields-18.0/fields/R/fillGrid.R | 21 fields-18.0/fields/R/find.upcross.R | 2 fields-18.0/fields/R/findGridBox.R | 2 fields-18.0/fields/R/fitted.Krig.R | 2 fields-18.0/fields/R/gauss.cov.R | 2 fields-18.0/fields/R/gcv.sreg.R | 8 fields-18.0/fields/R/golden.section.search.R | 4 fields-18.0/fields/R/image.family.R | 6 fields-18.0/fields/R/image.plot.R | 4 fields-18.0/fields/R/image.smooth.R | 12 fields-18.0/fields/R/imagePlot.R | 15 fields-18.0/fields/R/in.poly.R | 2 fields-18.0/fields/R/interp.surface.FFT.R | 21 fields-18.0/fields/R/interp.surface.R | 6 fields-18.0/fields/R/interp.surface.grid.R | 2 fields-18.0/fields/R/larry.colors.R | 2 fields-18.0/fields/R/mKrig.R | 40 fields-18.0/fields/R/mKrigCheckXY.R | 12 fields-18.0/fields/R/mKrigFastPredict.R | 12 fields-18.0/fields/R/mKrigFastPredictSetup.R | 2 fields-18.0/fields/R/mKrigMLEGrid.R | 2 fields-18.0/fields/R/mKrigMLEJoint.R | 10 fields-18.0/fields/R/mKrigMisc.R | 8 fields-18.0/fields/R/make.surface.grid.R | 2 fields-18.0/fields/R/makeMultiIndex.R | 4 fields-18.0/fields/R/matern.image.cov.R | 4 fields-18.0/fields/R/minimax.crit.R | 2 fields-18.0/fields/R/multWendlandGrid.R | 2 fields-18.0/fields/R/naturalSplineBasis.R |only fields-18.0/fields/R/offGridWeights.R | 4 fields-18.0/fields/R/offGridWeights1D.R | 10 fields-18.0/fields/R/offGridWeights2D.R | 12 fields-18.0/fields/R/panelPlotCommonAxesNew.R |only fields-18.0/fields/R/parse.grid.list.R | 2 fields-18.0/fields/R/plot.Krig.R | 2 fields-18.0/fields/R/plot.spatialDesign.R | 2 fields-18.0/fields/R/plot.spatialProcess.R | 4 fields-18.0/fields/R/plot.sreg.R | 2 fields-18.0/fields/R/plot.surface.R | 4 fields-18.0/fields/R/plot.vgram.matrix.R | 2 fields-18.0/fields/R/plotMatrix.R | 21 fields-18.0/fields/R/poly.image.R | 4 fields-18.0/fields/R/predict.Krig.R | 4 fields-18.0/fields/R/predict.fastTps.R | 4 fields-18.0/fields/R/predict.interp.surface.R | 2 fields-18.0/fields/R/predict.mKrig.R | 6 fields-18.0/fields/R/predict.sreg.R | 2 fields-18.0/fields/R/predictDerivative.Krig.R | 8 fields-18.0/fields/R/predictSE.Krig.R | 4 fields-18.0/fields/R/predictSE.R | 2 fields-18.0/fields/R/predictSE.mKrig.R | 4 fields-18.0/fields/R/predictSEUsingKrigA.R | 4 fields-18.0/fields/R/predictSurface.Krig.R | 4 fields-18.0/fields/R/predictSurface.family.R | 2 fields-18.0/fields/R/predictSurface.fastTps.R | 2 fields-18.0/fields/R/predictSurface.mKrig.R | 6 fields-18.0/fields/R/predictSurfaceSE.R | 6 fields-18.0/fields/R/print.Krig.R | 2 fields-18.0/fields/R/print.mKrig.R | 2 fields-18.0/fields/R/print.mKrig.summary.R | 2 fields-18.0/fields/R/print.spatial.design.R | 2 fields-18.0/fields/R/print.spatialProcess.R | 2 fields-18.0/fields/R/print.spatialProcessSummary.R | 2 fields-18.0/fields/R/print.sreg.R | 2 fields-18.0/fields/R/print.summary.Krig.R | 2 fields-18.0/fields/R/print.summary.sreg.R | 2 fields-18.0/fields/R/print.summarySpatialDesign.R | 2 fields-18.0/fields/R/printGCVWarnings.R | 2 fields-18.0/fields/R/profile.R | 2 fields-18.0/fields/R/profileCI.R | 2 fields-18.0/fields/R/profileMLE.R | 6 fields-18.0/fields/R/qr.q2ty.R | 2 fields-18.0/fields/R/qr.yq2.R | 2 fields-18.0/fields/R/qsreg.family.R | 6 fields-18.0/fields/R/quantilePlot.R |only fields-18.0/fields/R/quickPrint.R | 2 fields-18.0/fields/R/quilt.plot.R | 2 fields-18.0/fields/R/rad.cov.R | 4 fields-18.0/fields/R/rad.image.cov.R | 2 fields-18.0/fields/R/rad.simple.cov.R | 2 fields-18.0/fields/R/radbas.constant.R | 2 fields-18.0/fields/R/rdist.R | 2 fields-18.0/fields/R/rdist.earth.R | 2 fields-18.0/fields/R/rdist.earth.vec.R | 2 fields-18.0/fields/R/rdist.vec.R | 2 fields-18.0/fields/R/residuals.Krig.R | 2 fields-18.0/fields/R/ribbon.plot.R | 2 fields-18.0/fields/R/set.panel.R | 2 fields-18.0/fields/R/setup.image.smooth.R | 4 fields-18.0/fields/R/sim.Krig.R | 4 fields-18.0/fields/R/sim.rf.R | 2 fields-18.0/fields/R/sim.spatialProcess.R | 6 fields-18.0/fields/R/simLocal.spatialProcess.R | 4 fields-18.0/fields/R/simSpatialData.R | 6 fields-18.0/fields/R/smooth.2d.R | 2 fields-18.0/fields/R/snow.colors.R | 2 fields-18.0/fields/R/spam_2lz.R | 4 fields-18.0/fields/R/spatialProcess.R | 22 fields-18.0/fields/R/spatialProcessSetDefaults.R | 44 fields-18.0/fields/R/splint.R | 4 fields-18.0/fields/R/sreg.family.R | 2 fields-18.0/fields/R/stationary.cov.R | 10 fields-18.0/fields/R/stationary.image.cov.R | 6 fields-18.0/fields/R/stationary.taper.cov.R | 6 fields-18.0/fields/R/stationaryImageCov.R | 2 fields-18.0/fields/R/stats.R | 2 fields-18.0/fields/R/stats.bin.R | 2 fields-18.0/fields/R/summary.Krig.R | 2 fields-18.0/fields/R/summary.mKrig.R | 2 fields-18.0/fields/R/summary.ncdf.R | 2 fields-18.0/fields/R/summary.spatialDesign.R | 2 fields-18.0/fields/R/summary.spatialProcess.R | 4 fields-18.0/fields/R/summary.sreg.R | 2 fields-18.0/fields/R/summaryGCV.Krig.R | 2 fields-18.0/fields/R/summaryGCV.sreg.R | 2 fields-18.0/fields/R/supportsArg.R | 2 fields-18.0/fields/R/surface.family.R | 4 fields-18.0/fields/R/test.for.zero.R | 2 fields-18.0/fields/R/tim.colors.R | 4 fields-18.0/fields/R/transformx.R | 2 fields-18.0/fields/R/unrollZGrid.R | 2 fields-18.0/fields/R/unscale.R | 2 fields-18.0/fields/R/vgram.family.R | 2 fields-18.0/fields/R/vgram.matrix.R | 6 fields-18.0/fields/R/wendland.family.R | 32 fields-18.0/fields/R/wendland.image.cov.R | 6 fields-18.0/fields/R/which.max.matrix.R | 2 fields-18.0/fields/R/world.R | 2 fields-18.0/fields/R/xline.R | 2 fields-18.0/fields/R/yline.R | 2 fields-18.0/fields/data/AudiA4.rda |only fields-18.0/fields/data/BD.rda |only fields-18.0/fields/data/ChicagoO3.rda |only fields-18.0/fields/data/RMprecip.rda |only fields-18.0/fields/data/datalist | 18 fields-18.0/fields/data/flame.rda |only fields-18.0/fields/data/minitri.rda |only fields-18.0/fields/man/AudiA4.Rd |only fields-18.0/fields/man/BD.Rd | 53 - fields-18.0/fields/man/CO.Rd | 169 --- fields-18.0/fields/man/CO2.Rd | 40 fields-18.0/fields/man/CovarianceUpper.Rd | 20 fields-18.0/fields/man/Exponential.Rd | 66 - fields-18.0/fields/man/FORTRAN.internal.Rd | 20 fields-18.0/fields/man/Krig.Amatrix.Rd | 86 - fields-18.0/fields/man/Krig.Rd | 464 ++++----- fields-18.0/fields/man/Krig.engine.default.Rd | 144 +- fields-18.0/fields/man/Krig.null.function.Rd | 18 fields-18.0/fields/man/Krig.replicates.Rd | 38 fields-18.0/fields/man/KrigFindLambda.Rd | 81 - fields-18.0/fields/man/LENSExample.Rd | 56 - fields-18.0/fields/man/NorthAmericanRainfall.Rd | 44 fields-18.0/fields/man/QTps.Rd | 144 +- fields-18.0/fields/man/RCMexample.Rd | 34 fields-18.0/fields/man/RMprecip.Rd | 54 - fields-18.0/fields/man/Tps.Rd | 123 +- fields-18.0/fields/man/US.Rd | 8 fields-18.0/fields/man/US.dat.Rd | 8 fields-18.0/fields/man/Wendland.Rd | 34 fields-18.0/fields/man/WorldBank.Rd | 34 fields-18.0/fields/man/add.image.Rd | 10 fields-18.0/fields/man/arrow.plot.Rd | 34 fields-18.0/fields/man/as.image.Rd | 37 fields-18.0/fields/man/as.surface.Rd | 30 fields-18.0/fields/man/bplot.Rd | 34 fields-18.0/fields/man/bplot.xy.Rd | 18 fields-18.0/fields/man/colorbar.plot.Rd | 38 fields-18.0/fields/man/compactToMat.Rd | 6 fields-18.0/fields/man/cover.design.Rd | 75 - fields-18.0/fields/man/drape.plot.Rd | 60 - fields-18.0/fields/man/envelopePlot.Rd | 8 fields-18.0/fields/man/exp.cov.Rd | 197 ++- fields-18.0/fields/man/fields-internal.Rd | 7 fields-18.0/fields/man/fields-stuff.Rd | 48 fields-18.0/fields/man/fields.Rd | 130 +- fields-18.0/fields/man/fields.grid.Rd | 13 fields-18.0/fields/man/fields.hints.Rd | 8 fields-18.0/fields/man/fields.tests.Rd | 30 fields-18.0/fields/man/flame.Rd | 26 fields-18.0/fields/man/glacier.Rd | 28 fields-18.0/fields/man/grid.list.Rd | 82 - fields-18.0/fields/man/image.cov.Rd | 70 - fields-18.0/fields/man/image.plot.Rd | 347 ++---- fields-18.0/fields/man/image.smooth.Rd | 29 fields-18.0/fields/man/image2lz.Rd | 50 fields-18.0/fields/man/imagePlot.Rd | 482 ++++----- fields-18.0/fields/man/interp.surface.Rd | 44 fields-18.0/fields/man/lennon.Rd | 4 fields-18.0/fields/man/mKrig.Rd | 176 +-- fields-18.0/fields/man/mKrigMLE.Rd | 104 +- fields-18.0/fields/man/minitri.Rd | 29 fields-18.0/fields/man/naturalSplineBasis.Rd |only fields-18.0/fields/man/offGridWeights.Rd | 104 +- fields-18.0/fields/man/ozone.Rd | 21 fields-18.0/fields/man/ozone2.Rd | 32 fields-18.0/fields/man/panelPlot.Rd | 572 +++++++++-- fields-18.0/fields/man/plot.Krig.Rd | 25 fields-18.0/fields/man/plot.surface.Rd | 33 fields-18.0/fields/man/poly.image.Rd | 42 fields-18.0/fields/man/predict.Krig.Rd | 53 - fields-18.0/fields/man/predictSE.Krig.Rd | 48 fields-18.0/fields/man/predictSurface.Rd | 108 +- fields-18.0/fields/man/print.Krig.Rd | 7 fields-18.0/fields/man/pushpin.Rd | 12 fields-18.0/fields/man/qsreg.Rd | 55 - fields-18.0/fields/man/quantilePlot.Rd |only fields-18.0/fields/man/quilt.plot.Rd | 167 +-- fields-18.0/fields/man/rat.diet.Rd | 25 fields-18.0/fields/man/rdist.Rd | 38 fields-18.0/fields/man/rdist.earth.Rd | 32 fields-18.0/fields/man/registeredC.Rd | 28 fields-18.0/fields/man/ribbon.plot.Rd | 10 fields-18.0/fields/man/set.panel.Rd | 16 fields-18.0/fields/man/sim.Krig.Rd | 179 ++- fields-18.0/fields/man/sim.rf.Rd | 82 - fields-18.0/fields/man/smooth.2d.Rd | 76 - fields-18.0/fields/man/spam2lz.Rd | 29 fields-18.0/fields/man/spatialProcess.Rd | 212 ++-- fields-18.0/fields/man/splint.Rd | 35 fields-18.0/fields/man/sreg.Rd | 88 - fields-18.0/fields/man/stats.Rd | 8 fields-18.0/fields/man/stats.bin.Rd | 14 fields-18.0/fields/man/summary.Krig.Rd | 9 fields-18.0/fields/man/summary.ncdf.Rd | 14 fields-18.0/fields/man/supportsArg.Rd | 10 fields-18.0/fields/man/surface.Krig.Rd | 26 fields-18.0/fields/man/tim.colors.Rd | 71 - fields-18.0/fields/man/transformx.Rd | 19 fields-18.0/fields/man/vgram.Rd | 38 fields-18.0/fields/man/vgram.matrix.Rd | 26 fields-18.0/fields/man/world.Rd | 8 fields-18.0/fields/man/xline.Rd | 8 fields-18.0/fields/man/yline.Rd | 11 fields-18.0/fields/tests/Krig.Z.test.R | 24 fields-18.0/fields/tests/Krig.Z.test.Rout.save | 8 fields-18.0/fields/tests/Krig.se.W.R | 8 fields-18.0/fields/tests/Krig.se.W.Rout.save | 8 fields-18.0/fields/tests/Krig.se.grid.test.R | 14 fields-18.0/fields/tests/Krig.se.grid.test.Rout.save | 8 fields-18.0/fields/tests/Krig.se.test.R | 32 fields-18.0/fields/tests/Krig.se.test.Rout.save | 40 fields-18.0/fields/tests/Krig.test.R | 17 fields-18.0/fields/tests/Krig.test.Rout.save | 8 fields-18.0/fields/tests/Krig.test.W.R | 14 fields-18.0/fields/tests/Krig.test.W.Rout.save | 8 fields-18.0/fields/tests/KrigGCVREML.test.R | 6 fields-18.0/fields/tests/KrigGCVREML.test.Rout.save | 8 fields-18.0/fields/tests/Likelihood.test.R | 2 fields-18.0/fields/tests/Likelihood.test.Rout.save | 8 fields-18.0/fields/tests/SEFixedParameters.R | 3 fields-18.0/fields/tests/SEFixedParameters.Rout.save | 8 fields-18.0/fields/tests/Tps.test.R | 4 fields-18.0/fields/tests/Tps.test.Rout.save | 8 fields-18.0/fields/tests/Wend.test.R | 20 fields-18.0/fields/tests/Wend.test.Rout.save | 8 fields-18.0/fields/tests/cov.test.R | 12 fields-18.0/fields/tests/cov.test.Rout.save | 8 fields-18.0/fields/tests/cov.test2.R | 12 fields-18.0/fields/tests/cov.test2.Rout.save | 8 fields-18.0/fields/tests/derivative.test.R | 54 - fields-18.0/fields/tests/derivative.test.Rout.save | 8 fields-18.0/fields/tests/diag.multiply.test.Rout.save | 8 fields-18.0/fields/tests/evlpoly.test.R | 10 fields-18.0/fields/tests/evlpoly.test.Rout.save | 8 fields-18.0/fields/tests/fastTpsPredict.test.Rout.save | 8 fields-18.0/fields/tests/mKrig.Z.Rout.save | 8 fields-18.0/fields/tests/mKrig.parameters.test.R | 8 fields-18.0/fields/tests/mKrig.parameters.test.Rout.save | 16 fields-18.0/fields/tests/mKrig.se.test.R | 14 fields-18.0/fields/tests/mKrig.se.test.Rout.save | 8 fields-18.0/fields/tests/mKrig.test.R | 76 - fields-18.0/fields/tests/mKrig.test.Rout.save | 8 fields-18.0/fields/tests/mKrigMLETest.Rout.save | 8 fields-18.0/fields/tests/mKrigREMLTest.Rout.save | 8 fields-18.0/fields/tests/misc.test.Rout.save | 8 fields-18.0/fields/tests/offGridWeights.test.Rout.save | 8 fields-18.0/fields/tests/offGridWeightsNEW.test.Rout.save | 8 fields-18.0/fields/tests/spam.test.R | 34 fields-18.0/fields/tests/spam.test.Rout.save | 8 fields-18.0/fields/tests/sreg.test.R | 23 fields-18.0/fields/tests/sreg.test.Rout.save | 8 fields-18.0/fields/tests/testO3LocalExample.Rout.save | 8 fields-18.0/fields/tests/testZCommon.Rout.save | 8 fields-18.0/fields/tests/vgram.test.R | 16 fields-18.0/fields/tests/vgram.test.Rout.save | 8 fields-18.0/fields/tests/vgram2.test.R | 16 fields-18.0/fields/tests/vgram2.test.Rout.save | 8 369 files changed, 4842 insertions(+), 4168 deletions(-)
Title: Tidy Epidemiological Rates
Description: Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, using internal statistical calculations.
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Diff between tidyrates versions 0.0.1 dated 2024-03-19 and 0.0.2 dated 2026-10-13
DESCRIPTION | 16 ++++++++------- MD5 | 29 +++++++++++++++------------- NEWS.md | 33 ++++++++++++++++++++++++++++++++ R/adjustment.R |only R/rate_adj_direct.R | 4 +-- R/rate_adj_indirect.R | 12 +++++------ README.md | 17 ++++++++++------ build/vignette.rds |binary inst/doc/quickstart.R | 2 - inst/doc/quickstart.Rmd | 6 ++--- inst/doc/quickstart.html | 23 ++++++++++++---------- man/rate_adj_direct.Rd | 2 - man/rate_adj_indirect.Rd | 6 ++--- tests/testthat/helper-legacy-rates.R |only tests/testthat/test-adjustment.R |only tests/testthat/test-rate_adj_indirect.R | 12 +++++++++++ vignettes/quickstart.Rmd | 6 ++--- 17 files changed, 113 insertions(+), 55 deletions(-)
Title: Access your Coletum's Data from API
Description: Get your data (forms, structures, answers) from Coletum
<https://coletum.com> to handle and analyse.
Author: Andre Smaniotto [aut, cre],
Marcelo Magnani [aut],
Rodrigo Sant'Ana [aut],
GeoSapiens [cph, fnd]
Maintainer: Andre Smaniotto <smaniotto@geosapiens.com.br>
Diff between RColetum versions 1.1.0 dated 2026-08-21 and 1.2.0 dated 2026-10-13
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NEWS.md | 11 +++++++++++ R/GetForm.R | 5 ++++- R/utils.R | 13 ++++++++++++- man/GetForm.Rd | 5 ++++- tests/testthat/test-SeparatorComponents.R |only tests/testthat/test-UserAgent.R |only 8 files changed, 42 insertions(+), 12 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 7.1.0 dated 2026-09-20 and 7.2.0 dated 2026-10-13
nlmixr2est-7.1.0/nlmixr2est/R/pkpars.R |only nlmixr2est-7.1.0/nlmixr2est/R/sourceCppFunction.R |only nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixrNlsFun.Rd |only nlmixr2est-7.1.0/nlmixr2est/src/merge3.c |only nlmixr2est-7.1.0/nlmixr2est/src/resid.cpp |only nlmixr2est-7.1.0/nlmixr2est/src/slice.cpp |only nlmixr2est-7.2.0/nlmixr2est/DESCRIPTION | 20 nlmixr2est-7.2.0/nlmixr2est/MD5 | 499 nlmixr2est-7.2.0/nlmixr2est/NAMESPACE | 21 nlmixr2est-7.2.0/nlmixr2est/NEWS.md | 1406 ++ nlmixr2est-7.2.0/nlmixr2est/R/RcppExports.R | 202 nlmixr2est-7.2.0/nlmixr2est/R/addCwres.R | 12 nlmixr2est-7.2.0/nlmixr2est/R/agq.R | 76 nlmixr2est-7.2.0/nlmixr2est/R/augPred.R | 67 nlmixr2est-7.2.0/nlmixr2est/R/bobyqa.R | 113 nlmixr2est-7.2.0/nlmixr2est/R/broom.R | 2 nlmixr2est-7.2.0/nlmixr2est/R/complete.R | 1 nlmixr2est-7.2.0/nlmixr2est/R/cov.R | 721 - nlmixr2est-7.2.0/nlmixr2est/R/covControl.R | 138 nlmixr2est-7.2.0/nlmixr2est/R/covPrecursor.R |only nlmixr2est-7.2.0/nlmixr2est/R/covRecompute.R | 194 nlmixr2est-7.2.0/nlmixr2est/R/covSelect.R |only nlmixr2est-7.2.0/nlmixr2est/R/covStore.R |only nlmixr2est-7.2.0/nlmixr2est/R/deparse.R | 181 nlmixr2est-7.2.0/nlmixr2est/R/emviControl.R | 50 nlmixr2est-7.2.0/nlmixr2est/R/fo.R | 76 nlmixr2est-7.2.0/nlmixr2est/R/foce.R | 74 nlmixr2est-7.2.0/nlmixr2est/R/focei.R | 836 + nlmixr2est-7.2.0/nlmixr2est/R/foceiControl.R | 505 nlmixr2est-7.2.0/nlmixr2est/R/foceiCov.R | 28 nlmixr2est-7.2.0/nlmixr2est/R/foceiCovAnalytic.R | 956 - nlmixr2est-7.2.0/nlmixr2est/R/foceiCovFdFull.R | 161 nlmixr2est-7.2.0/nlmixr2est/R/foceiGradAnalytic.R | 1171 -- nlmixr2est-7.2.0/nlmixr2est/R/foceiLagOde.R |only nlmixr2est-7.2.0/nlmixr2est/R/foceiLagSens.R |only nlmixr2est-7.2.0/nlmixr2est/R/foceiLik.R | 165 nlmixr2est-7.2.0/nlmixr2est/R/foceiLinCmtAlagSens.R | 7 nlmixr2est-7.2.0/nlmixr2est/R/foceiLinCmtCarryEligible.R | 7 nlmixr2est-7.2.0/nlmixr2est/R/foceiLinCmtCarryPredCall.R | 7 nlmixr2est-7.2.0/nlmixr2est/R/focep.R | 74 nlmixr2est-7.2.0/nlmixr2est/R/foi.R | 79 nlmixr2est-7.2.0/nlmixr2est/R/hook.R | 14 nlmixr2est-7.2.0/nlmixr2est/R/iagq.R | 6 nlmixr2est-7.2.0/nlmixr2est/R/ifoce.R | 5 nlmixr2est-7.2.0/nlmixr2est/R/ifocei.R | 5 nlmixr2est-7.2.0/nlmixr2est/R/ifocep.R | 65 nlmixr2est-7.2.0/nlmixr2est/R/ilaplace.R | 6 nlmixr2est-7.2.0/nlmixr2est/R/impmap.R | 323 nlmixr2est-7.2.0/nlmixr2est/R/impmapThetaSens.R | 21 nlmixr2est-7.2.0/nlmixr2est/R/iov.R | 11 nlmixr2est-7.2.0/nlmixr2est/R/iterPrintControl.R | 5 nlmixr2est-7.2.0/nlmixr2est/R/laplace.R | 77 nlmixr2est-7.2.0/nlmixr2est/R/lbfgsb3c.R | 173 nlmixr2est-7.2.0/nlmixr2est/R/magq.R | 6 nlmixr2est-7.2.0/nlmixr2est/R/mfoce.R | 5 nlmixr2est-7.2.0/nlmixr2est/R/mfocei.R | 5 nlmixr2est-7.2.0/nlmixr2est/R/mfocep.R | 65 nlmixr2est-7.2.0/nlmixr2est/R/mix.R | 242 nlmixr2est-7.2.0/nlmixr2est/R/mlaplace.R | 6 nlmixr2est-7.2.0/nlmixr2est/R/muRefControl.R | 505 nlmixr2est-7.2.0/nlmixr2est/R/n1qn1.R | 126 nlmixr2est-7.2.0/nlmixr2est/R/newuoa.R | 113 nlmixr2est-7.2.0/nlmixr2est/R/nlm.R | 750 - nlmixr2est-7.2.0/nlmixr2est/R/nlmShared.R | 366 nlmixr2est-7.2.0/nlmixr2est/R/nlme.R | 150 nlmixr2est-7.2.0/nlmixr2est/R/nlmeRxUiGet.R | 64 nlmixr2est-7.2.0/nlmixr2est/R/nlminb.R | 159 nlmixr2est-7.2.0/nlmixr2est/R/nlmixr2.R | 12 nlmixr2est-7.2.0/nlmixr2est/R/nlmixr2Est.R | 163 nlmixr2est-7.2.0/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-7.2.0/nlmixr2est/R/nlmixr2global.R | 1 nlmixr2est-7.2.0/nlmixr2est/R/nlmixr2output.R | 161 nlmixr2est-7.2.0/nlmixr2est/R/nlmixrAddObjectiveFunction.R | 35 nlmixr2est-7.2.0/nlmixr2est/R/nlmixrGrad.R | 37 nlmixr2est-7.2.0/nlmixr2est/R/nlmixrUpdateObject.R | 9 nlmixr2est-7.2.0/nlmixr2est/R/nls.R | 539 nlmixr2est-7.2.0/nlmixr2est/R/nmObjGet.R | 2 nlmixr2est-7.2.0/nlmixr2est/R/nmObjGetEtaMat.R | 73 nlmixr2est-7.2.0/nlmixr2est/R/nmObjHandle.R | 66 nlmixr2est-7.2.0/nlmixr2est/R/npCommon.R | 24 nlmixr2est-7.2.0/nlmixr2est/R/npInner.R | 56 nlmixr2est-7.2.0/nlmixr2est/R/npde.R | 8 nlmixr2est-7.2.0/nlmixr2est/R/odeSwapVerify.R | 15 nlmixr2est-7.2.0/nlmixr2est/R/ofv.R | 111 nlmixr2est-7.2.0/nlmixr2est/R/optim.R | 135 nlmixr2est-7.2.0/nlmixr2est/R/posthoc.R | 66 nlmixr2est-7.2.0/nlmixr2est/R/preProcessBoundedTransform.R | 15 nlmixr2est-7.2.0/nlmixr2est/R/preProcessLinCmtOde.R | 107 nlmixr2est-7.2.0/nlmixr2est/R/print.R | 8 nlmixr2est-7.2.0/nlmixr2est/R/priors.R | 13 nlmixr2est-7.2.0/nlmixr2est/R/resid.R | 186 nlmixr2est-7.2.0/nlmixr2est/R/rxEvents.R |only nlmixr2est-7.2.0/nlmixr2est/R/saem.R | 1048 + nlmixr2est-7.2.0/nlmixr2est/R/saemControl.R | 118 nlmixr2est-7.2.0/nlmixr2est/R/saemIov.R | 10 nlmixr2est-7.2.0/nlmixr2est/R/saemRxUiGet.R | 82 nlmixr2est-7.2.0/nlmixr2est/R/saem_fit.R | 113 nlmixr2est-7.2.0/nlmixr2est/R/saem_fit_aux.R | 167 nlmixr2est-7.2.0/nlmixr2est/R/sharedControl.R | 146 nlmixr2est-7.2.0/nlmixr2est/R/simulate.R | 48 nlmixr2est-7.2.0/nlmixr2est/R/timing.R | 39 nlmixr2est-7.2.0/nlmixr2est/R/trust.R | 138 nlmixr2est-7.2.0/nlmixr2est/R/uninformativeEtas.R | 71 nlmixr2est-7.2.0/nlmixr2est/R/uobyqa.R | 113 nlmixr2est-7.2.0/nlmixr2est/R/vae.R | 51 nlmixr2est-7.2.0/nlmixr2est/R/vaeData.R | 61 nlmixr2est-7.2.0/nlmixr2est/R/vaeFit.R | 61 nlmixr2est-7.2.0/nlmixr2est/R/vaeInner.R | 64 nlmixr2est-7.2.0/nlmixr2est/R/vaeOutput.R | 99 nlmixr2est-7.2.0/nlmixr2est/R/vi.R | 246 nlmixr2est-7.2.0/nlmixr2est/R/vpc.R | 24 nlmixr2est-7.2.0/nlmixr2est/R/zzz.R | 1 nlmixr2est-7.2.0/nlmixr2est/build/vignette.rds |binary nlmixr2est-7.2.0/nlmixr2est/inst/doc/events.R |only nlmixr2est-7.2.0/nlmixr2est/inst/doc/events.Rmd |only nlmixr2est-7.2.0/nlmixr2est/inst/doc/events.html |only nlmixr2est-7.2.0/nlmixr2est/man/dot-nlmFamilyFitGeneric.Rd | 15 nlmixr2est-7.2.0/nlmixr2est/man/dot-nlmixrNlsFunValGrad.Rd |only nlmixr2est-7.2.0/nlmixr2est/man/emviControl.Rd | 66 nlmixr2est-7.2.0/nlmixr2est/man/foceiControl.Rd | 183 nlmixr2est-7.2.0/nlmixr2est/man/impCovControl.Rd | 7 nlmixr2est-7.2.0/nlmixr2est/man/impmapControl.Rd | 18 nlmixr2est-7.2.0/nlmixr2est/man/lbfgsb3cControl.Rd | 11 nlmixr2est-7.2.0/nlmixr2est/man/n1qn1Control.Rd | 4 nlmixr2est-7.2.0/nlmixr2est/man/nlmControl.Rd | 6 nlmixr2est-7.2.0/nlmixr2est/man/nlminbControl.Rd | 10 nlmixr2est-7.2.0/nlmixr2est/man/nlmixr2AugPredSolve.Rd | 26 nlmixr2est-7.2.0/nlmixr2est/man/nlmixr2CreateOutputFromUi.Rd | 4 nlmixr2est-7.2.0/nlmixr2est/man/nlmixr2Gill83.Rd | 4 nlmixr2est-7.2.0/nlmixr2est/man/nlmixr2Hess.Rd | 4 nlmixr2est-7.2.0/nlmixr2est/man/nlmixrUpdateObject.Rd | 3 nlmixr2est-7.2.0/nlmixr2est/man/nmObjGetFoceiControl.Rd | 11 nlmixr2est-7.2.0/nlmixr2est/man/optimControl.Rd | 5 nlmixr2est-7.2.0/nlmixr2est/man/rsControl.Rd | 30 nlmixr2est-7.2.0/nlmixr2est/man/saControl.Rd | 24 nlmixr2est-7.2.0/nlmixr2est/man/saemControl.Rd | 31 nlmixr2est-7.2.0/nlmixr2est/man/setCov.Rd | 21 nlmixr2est-7.2.0/nlmixr2est/man/sqrtm.Rd | 3 nlmixr2est-7.2.0/nlmixr2est/man/trustControl.Rd | 11 nlmixr2est-7.2.0/nlmixr2est/man/vaeControl.Rd | 4 nlmixr2est-7.2.0/nlmixr2est/src/Makevars.in | 7 nlmixr2est-7.2.0/nlmixr2est/src/RcppExports.cpp | 651 - nlmixr2est-7.2.0/nlmixr2est/src/armahead.h | 2 nlmixr2est-7.2.0/nlmixr2est/src/cholse.cpp | 66 nlmixr2est-7.2.0/nlmixr2est/src/covShortcut.cpp |only nlmixr2est-7.2.0/nlmixr2est/src/covShortcut.h |only nlmixr2est-7.2.0/nlmixr2est/src/cwres.cpp | 20 nlmixr2est-7.2.0/nlmixr2est/src/fdHess.h |only nlmixr2est-7.2.0/nlmixr2est/src/foceiGrad.cpp | 440 nlmixr2est-7.2.0/nlmixr2est/src/imp.cpp | 198 nlmixr2est-7.2.0/nlmixr2est/src/imp.h | 26 nlmixr2est-7.2.0/nlmixr2est/src/init.c | 89 nlmixr2est-7.2.0/nlmixr2est/src/inner.cpp | 5425 +++++----- nlmixr2est-7.2.0/nlmixr2est/src/ires.cpp | 15 nlmixr2est-7.2.0/nlmixr2est/src/lbfgsbTask.h |only nlmixr2est-7.2.0/nlmixr2est/src/nearPD.cpp | 8 nlmixr2est-7.2.0/nlmixr2est/src/nearPD.h | 31 nlmixr2est-7.2.0/nlmixr2est/src/nlm.cpp | 577 - nlmixr2est-7.2.0/nlmixr2est/src/nmProgress.h |only nlmixr2est-7.2.0/nlmixr2est/src/np.h | 8 nlmixr2est-7.2.0/nlmixr2est/src/npag.cpp | 21 nlmixr2est-7.2.0/nlmixr2est/src/npb.cpp | 8 nlmixr2est-7.2.0/nlmixr2est/src/npde.cpp | 5 nlmixr2est-7.2.0/nlmixr2est/src/odeSwap.cpp | 18 nlmixr2est-7.2.0/nlmixr2est/src/odeSwap.h | 34 nlmixr2est-7.2.0/nlmixr2est/src/res.cpp | 70 nlmixr2est-7.2.0/nlmixr2est/src/res.h | 5 nlmixr2est-7.2.0/nlmixr2est/src/saem.cpp | 241 nlmixr2est-7.2.0/nlmixr2est/src/scale.h | 497 nlmixr2est-7.2.0/nlmixr2est/src/shi21.cpp | 199 nlmixr2est-7.2.0/nlmixr2est/src/shi21.h | 32 nlmixr2est-7.2.0/nlmixr2est/src/trustHessianUpdate.h | 47 nlmixr2est-7.2.0/nlmixr2est/src/utilc.c | 110 nlmixr2est-7.2.0/nlmixr2est/src/utilc.h | 5 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/baselines/gradref-focei-combined-prop-first.rds |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/helper-omega-block.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-ar-est.R | 4 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-bounded-transform.R | 59 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-control.R | 28 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov-analytic.R | 103 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov-decouple-saimp.R | 70 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov-fdfull-install.R | 56 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov-focei.R | 624 + nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov-setcov-generic.R | 53 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-cov.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covControl.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covPrecursor.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covSelect.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covShortcut.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covStore.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-covs-interpolation-1137.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-etaMat.R | 109 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-event-hooks.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-bobyqa-stationary-1196.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-family-control.R | 44 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-fast-ar.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-fast-grad.R | 68 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-hessian-method.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-inner-conditional.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-inner.R | 249 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-lag.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-lbfgsb3c-inner.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-eligible-gates.R | 20 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-lincmt-detect-1103.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-ll-fast-grad-fit.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-ll-fast-grad.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-mix-cov.R | 77 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-mix-grad.R | 69 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-norm-scale-1114.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-outer-fd-fallback.R | 43 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-outer-trust.R | 115 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-pooled-solve-args.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-prior.R | 24 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-scalec.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-syminvchol.R | 17 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-theta-reset-bounds.R | 51 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-theta-reset.R | 107 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-trust-inner.R | 35 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-trust-polish-1152.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-variance-floor.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-focei-zero-init-scale.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-foceiCovAnalytic.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-foceiCovFdFull.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-gc-protect.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-hook.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-imp-auto.R | 35 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-imp-cov.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-impmap.R | 32 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-iov-mifocei-1083.R | 52 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-issue-515.R | 41 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-lag-multi-endpoint-ipred-1182.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-lincmt-ode.R | 237 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-lint-superassign.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-manual-back-transform.R | 159 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-mix.R | 192 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-mtime.R | 25 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-mu-family.R | 47 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-n1qn1.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nearPd.R | 15 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlm-cens.R | 45 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlm-lag.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlm-lbfgsb3c.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlm.R | 92 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlmShared.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlme.R | 291 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlminb.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlmixr2Est.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlmixr2output.R | 94 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nlmixrGrad.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nls.R | 245 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nonmem-pktime-1167.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npInner.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-error-models.R | 8 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-fixed.R | 18 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-general-lik.R | 93 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-ofv.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-omega-block.R | 41 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-optim.R | 35 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-progress-bar-1171.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-resid-ode-fallback.R | 56 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-resid.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-rxuideparse.R | 271 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-cov-analytic.R | 67 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-cov-sa.R | 241 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-degraded-fit.R | 81 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-iov-twolevel-fit.R | 32 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-mix-ofv.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-mix.R | 74 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-nearpd.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-scale-normtype.R | 162 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21-hessian.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21-ratio.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shierr-positive.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-simModelLag.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-sqrtm.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-tolFactor.R | 52 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-trust.R | 91 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vae-errmodel.R | 3 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vae-residopt.R | 41 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vi-control.R | 14 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vi.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/testthat-problems.rds |binary nlmixr2est-7.2.0/nlmixr2est/vignettes/events.Rmd |only 285 files changed, 17285 insertions(+), 12758 deletions(-)
Title: Builds the 'TinyCC' Command-Line Interface and Library for 'C'
Scripting in 'R'
Description: Builds the 'TinyCC' (Tiny 'C' Compiler) command-line interface
and library for package use in 'R'. The package compiles 'TinyCC' from source and
provides R functions to interact with the compiler. 'TinyCC' can be
used for header preprocessing, just-in-time compilation of 'C' code in
'R', and lightweight 'C' scripting workflows.
Author: Sounkou Mahamane Toure [aut, cre],
Mike Cheng [cph] ,
Adam Dunkels [ctb] ,
Swedish Institute of Computer Science [cph] ,
Fabrice Bellard and TinyCC authors [cph] ,
Brian Lee Yung Rowe [ctb, cph]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rtinycc versions 0.1.15 dated 2026-07-25 and 0.1.16 dated 2026-10-13
Rtinycc-0.1.15/Rtinycc/src/tinycc-199f07b.tar.gz |only Rtinycc-0.1.16/Rtinycc/DESCRIPTION | 20 +++-- Rtinycc-0.1.16/Rtinycc/MD5 | 32 +++++---- Rtinycc-0.1.16/Rtinycc/NAMESPACE | 2 Rtinycc-0.1.16/Rtinycc/NEWS.md | 6 + Rtinycc-0.1.16/Rtinycc/R/aaa.R | 1 Rtinycc-0.1.16/Rtinycc/R/aaa_ffi_codegen_dispatch.R |only Rtinycc-0.1.16/Rtinycc/R/aaa_ffi_codegen_rules.R | 8 +- Rtinycc-0.1.16/Rtinycc/configure.win | 16 ++++ Rtinycc-0.1.16/Rtinycc/inst/LICENSE.note | 23 +++++- Rtinycc-0.1.16/Rtinycc/inst/doc/compilation-and-call-overhead.html | 20 ++--- Rtinycc-0.1.16/Rtinycc/inst/doc/ffi-helpers.html | 8 +- Rtinycc-0.1.16/Rtinycc/inst/doc/getting-started.html | 12 +-- Rtinycc-0.1.16/Rtinycc/inst/doc/internals.Rmd | 27 +++---- Rtinycc-0.1.16/Rtinycc/inst/doc/internals.html | 34 ++++------ Rtinycc-0.1.16/Rtinycc/inst/tinytest/test_codegen_dispatch.R |only Rtinycc-0.1.16/Rtinycc/src/tinycc-1bed0f3.tar.gz |only Rtinycc-0.1.16/Rtinycc/tools/vendortinycc.R | 6 - Rtinycc-0.1.16/Rtinycc/vignettes/internals.Rmd | 27 +++---- 19 files changed, 133 insertions(+), 109 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel [aut, cre] ,
Khanh Nguyen [aut] ,
Terry Leitch [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.28 dated 2026-07-10 and 0.4.29 dated 2026-10-13
ChangeLog | 92 ++++++++++++++++++++++++ DESCRIPTION | 8 +- MD5 | 72 +++++++++---------- R/affine.R | 8 +- R/arrays.R | 2 R/bermudan.R | 2 R/bond.R | 148 ++++++++++++++++++++------------------- R/calendars.R | 19 ++++- R/datasets.R | 2 R/discount.R | 2 R/implied.R | 1 README.md | 6 - configure | 25 +++--- configure.ac | 18 +++- inst/NEWS.Rd | 27 ++++++- man/AffineSwaption.Rd | 8 +- man/AsianOption.Rd | 2 man/BermudanSwaption.Rd | 4 - man/Bond.Rd | 2 man/CallableBond.Rd | 6 - man/ConvertibleBond.Rd | 8 +- man/DiscountCurve.Rd | 4 - man/FittedBondCurve.Rd | 2 man/FixedRateBond.Rd | 4 - man/FloatingRateBond.Rd | 8 +- man/ImpliedVolatility.Rd | 2 man/Option.Rd | 2 man/SabrSwaption.Rd | 20 ++--- man/Schedule.Rd | 2 man/ZeroCouponBond.Rd | 57 +++++++-------- man/tsQuotes.Rd | 2 src/Makevars.in | 5 - src/Makevars.win | 11 +- src/calendars.cpp | 174 +++++++++++++++++++++++++++++++++++------------ src/sabr.cpp | 20 +++++ src/utils.cpp | 10 +- tests/tinytest.R | 12 --- 37 files changed, 521 insertions(+), 276 deletions(-)
Title: Missing Cost Effectiveness Models
Description: Performs Bayesian cost-effectiveness analysis with missing outcome data. Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models. The package allows to assess model convergence and summarise the statistical and economic results using different types of measures and graphs. The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Author: Andrea Gabrio [aut, cre, cph]
Maintainer: Andrea Gabrio <a.gabrio@maastrichtuniversity.nl>
Diff between missingHE versions 1.6.1 dated 2026-06-01 and 1.6.2 dated 2026-10-13
missingHE-1.6.1/missingHE/README.md |only missingHE-1.6.2/missingHE/DESCRIPTION | 27 - missingHE-1.6.2/missingHE/MD5 | 173 +++--- missingHE-1.6.2/missingHE/NAMESPACE | 108 ++-- missingHE-1.6.2/missingHE/R/anyBars.R | 2 missingHE-1.6.2/missingHE/R/coef.missingHE.R | 39 - missingHE-1.6.2/missingHE/R/data_read_hurdle.R | 2 missingHE-1.6.2/missingHE/R/data_read_lmdm.R | 2 missingHE-1.6.2/missingHE/R/data_read_pattern.R | 2 missingHE-1.6.2/missingHE/R/data_read_selection.R | 2 missingHE-1.6.2/missingHE/R/diagnostic.R | 2 missingHE-1.6.2/missingHE/R/fb.R | 2 missingHE-1.6.2/missingHE/R/hurdle.R | 54 +- missingHE-1.6.2/missingHE/R/isAnyArgBar.R | 2 missingHE-1.6.2/missingHE/R/isBar.R | 2 missingHE-1.6.2/missingHE/R/jagsresults.R | 4 missingHE-1.6.2/missingHE/R/lmdm.R | 61 ++ missingHE-1.6.2/missingHE/R/nobars_.R | 2 missingHE-1.6.2/missingHE/R/pattern.R | 35 + missingHE-1.6.2/missingHE/R/postsum.R |only missingHE-1.6.2/missingHE/R/ppc.R | 87 ++- missingHE-1.6.2/missingHE/R/print.missingHE.R | 117 +--- missingHE-1.6.2/missingHE/R/prior_hurdle.R | 2 missingHE-1.6.2/missingHE/R/prior_lmdm.R | 2 missingHE-1.6.2/missingHE/R/prior_pattern.R | 2 missingHE-1.6.2/missingHE/R/prior_selection.R | 2 missingHE-1.6.2/missingHE/R/run_hurdle.R | 12 missingHE-1.6.2/missingHE/R/run_lmdm.R | 18 missingHE-1.6.2/missingHE/R/run_pattern.R | 14 missingHE-1.6.2/missingHE/R/run_selection.R | 12 missingHE-1.6.2/missingHE/R/selection.R | 30 + missingHE-1.6.2/missingHE/R/summary.missingHE.R | 2 missingHE-1.6.2/missingHE/R/write_hurdle.R | 2 missingHE-1.6.2/missingHE/R/write_lmdm.R | 2 missingHE-1.6.2/missingHE/R/write_pattern.R | 2 missingHE-1.6.2/missingHE/R/write_selection.R | 2 missingHE-1.6.2/missingHE/build/vignette.rds |binary missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.R | 140 ++--- missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.Rmd | 212 ++++---- missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.html | 162 +++--- missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.R | 33 - missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.Rmd | 199 ++++--- missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.html | 169 +++--- missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.R | 16 missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.Rmd | 118 ++-- missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.html | 250 ++++------ missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.R | 68 +- missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.Rmd | 160 +++--- missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.html | 226 ++++----- missingHE-1.6.2/missingHE/man/MenSS.Rd | 61 +- missingHE-1.6.2/missingHE/man/PBS.Rd | 92 +-- missingHE-1.6.2/missingHE/man/anyBars.Rd | 4 missingHE-1.6.2/missingHE/man/coef.missingHE.Rd | 2 missingHE-1.6.2/missingHE/man/data_read_hurdle.Rd | 23 missingHE-1.6.2/missingHE/man/data_read_lmdm.Rd | 15 missingHE-1.6.2/missingHE/man/data_read_pattern.Rd | 7 missingHE-1.6.2/missingHE/man/data_read_selection.Rd | 15 missingHE-1.6.2/missingHE/man/diagnostic.Rd | 14 missingHE-1.6.2/missingHE/man/fb.Rd | 4 missingHE-1.6.2/missingHE/man/hurdle.Rd | 72 +- missingHE-1.6.2/missingHE/man/isAnyArgBar.Rd | 4 missingHE-1.6.2/missingHE/man/isBar.Rd | 4 missingHE-1.6.2/missingHE/man/jagsresults.Rd | 26 - missingHE-1.6.2/missingHE/man/lmdm.Rd | 52 +- missingHE-1.6.2/missingHE/man/nobars_.Rd | 4 missingHE-1.6.2/missingHE/man/pattern.Rd | 58 +- missingHE-1.6.2/missingHE/man/pic.Rd | 62 +- missingHE-1.6.2/missingHE/man/plot.missingHE.Rd | 8 missingHE-1.6.2/missingHE/man/postsum.Rd |only missingHE-1.6.2/missingHE/man/ppc.Rd | 12 missingHE-1.6.2/missingHE/man/print.missingHE.Rd | 36 - missingHE-1.6.2/missingHE/man/prior_hurdle.Rd | 9 missingHE-1.6.2/missingHE/man/prior_lmdm.Rd | 11 missingHE-1.6.2/missingHE/man/prior_pattern.Rd | 10 missingHE-1.6.2/missingHE/man/prior_selection.Rd | 9 missingHE-1.6.2/missingHE/man/run_hurdle.Rd | 5 missingHE-1.6.2/missingHE/man/run_lmdm.Rd | 7 missingHE-1.6.2/missingHE/man/run_pattern.Rd | 6 missingHE-1.6.2/missingHE/man/run_selection.Rd | 5 missingHE-1.6.2/missingHE/man/selection.Rd | 50 +- missingHE-1.6.2/missingHE/man/summary.missingHE.Rd | 2 missingHE-1.6.2/missingHE/man/write_hurdle.Rd | 8 missingHE-1.6.2/missingHE/man/write_lmdm.Rd | 10 missingHE-1.6.2/missingHE/man/write_pattern.Rd | 9 missingHE-1.6.2/missingHE/man/write_selection.Rd | 8 missingHE-1.6.2/missingHE/vignettes/Fitting_MNAR_models_in_missingHE.Rmd | 212 ++++---- missingHE-1.6.2/missingHE/vignettes/Introduction_to_missingHE.Rmd | 199 ++++--- missingHE-1.6.2/missingHE/vignettes/Longitudinal_models_in_missingHE.Rmd | 118 ++-- missingHE-1.6.2/missingHE/vignettes/Model_customisation_in_missingHE.Rmd | 160 +++--- 89 files changed, 1990 insertions(+), 2005 deletions(-)
Title: Create Common Tables and Listings Used in Clinical Trials
Description: Structure and formatting requirements for clinical trial table and listing outputs
vary between pharmaceutical companies. 'junco' provides additional tooling for use alongside
the 'rtables', 'rlistings' and 'tern' packages when creating table and listing outputs. While
motivated by the specifics of Johnson and Johnson Clinical and Statistical Programming's
table and listing shells, 'junco' provides functionality that is general and reusable.
Major features include a) alternative and extended statistical analyses beyond what 'tern'
supports for use in standard safety and efficacy tables, b) a robust production-grade
Rich Text Format (RTF) and DOCX exporter for tables, listings and graphs, c) structural support
for spanning column headers and risk difference columns in tables, and d) robust
font-aware automatic column width algorithms for both listings and tables.
Author: Gabriel Becker [cre, aut] ,
Ilse Augustyns [aut],
Paul Jenkins [aut],
Daniel Hofstaedter [aut],
Joseph Kovach [aut],
David Munoz Tord [aut],
Daniel Sabanes Bove [aut],
Ezequiel Anokian [ctb],
Renfei Mao [ctb],
Mrinal Das [ctb],
Wojciech Wojciak [ctb] [...truncated...]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between junco versions 0.1.6 dated 2026-05-10 and 0.1.7 dated 2026-10-13
junco-0.1.6/junco/R/a_summary.r |only junco-0.1.6/junco/R/a_summary_diff_mvars.r |only junco-0.1.6/junco/R/count_denom_fraction.R |only junco-0.1.6/junco/R/coxph_hr.R |only junco-0.1.6/junco/R/filter_df_prior_afun.r |only junco-0.1.6/junco/R/kaplan_meier.R |only junco-0.1.6/junco/R/rbmi.R |only junco-0.1.6/junco/R/s_diff_mean_ci.r |only junco-0.1.6/junco/R/s_summary_diff.r |only junco-0.1.6/junco/R/safe_t_test.r |only junco-0.1.6/junco/man/a_summary_diff_mvars.Rd |only junco-0.1.6/junco/man/c_summary_subset_label.Rd |only junco-0.1.6/junco/man/coxph_hr.Rd |only junco-0.1.6/junco/man/filter_df_prior_afun.Rd |only junco-0.1.6/junco/man/h_get_trtvar_refpath.Rd |only junco-0.1.6/junco/man/kaplan_meier.Rd |only junco-0.1.6/junco/man/postfun_eq5d.Rd |only junco-0.1.6/junco/man/s_diff_mean_ci.Rd |only junco-0.1.6/junco/man/safe_t_test.Rd |only junco-0.1.6/junco/tests/testthat/_snaps/coxph_hr.md |only junco-0.1.6/junco/tests/testthat/_snaps/kaplan_meier.md |only junco-0.1.6/junco/tests/testthat/_snaps/summarize_ancova.new.md |only junco-0.1.6/junco/tests/testthat/test-coxph_hr.R |only junco-0.1.6/junco/tests/testthat/test-kaplan_meier.R |only junco-0.1.7/junco/DESCRIPTION | 23 junco-0.1.7/junco/MD5 | 413 ++++-- junco-0.1.7/junco/NAMESPACE | 59 junco-0.1.7/junco/NEWS.md | 102 + junco-0.1.7/junco/R/a_combo_prop_diff_pval_mf.R |only junco-0.1.7/junco/R/a_diff_means.R |only junco-0.1.7/junco/R/a_eair_diff.R |only junco-0.1.7/junco/R/a_eair_j.R | 593 ++++++--- junco-0.1.7/junco/R/a_eair_strat_j.R |only junco-0.1.7/junco/R/a_freq_combos_j.R | 58 junco-0.1.7/junco/R/a_freq_j.R | 285 +++- junco-0.1.7/junco/R/a_freq_resp_var_j.R | 85 - junco-0.1.7/junco/R/a_freq_subcol_j.R | 51 junco-0.1.7/junco/R/a_maxlev.R | 3 junco-0.1.7/junco/R/a_sum_ratio_j.R |only junco-0.1.7/junco/R/a_summarize_aval_chg_diff.R | 167 -- junco-0.1.7/junco/R/a_summarize_ex_j.R | 80 - junco-0.1.7/junco/R/a_summary_j.R |only junco-0.1.7/junco/R/a_summary_subset.R |only junco-0.1.7/junco/R/a_two_tier.R | 206 +++ junco-0.1.7/junco/R/ancova.R | 11 junco-0.1.7/junco/R/blank_line.R | 114 + junco-0.1.7/junco/R/column_stats.R | 290 +++- junco-0.1.7/junco/R/colwidths.R | 62 - junco-0.1.7/junco/R/cond_proportion_diff.R |only junco-0.1.7/junco/R/cond_proportion_j.R |only junco-0.1.7/junco/R/coxreg_multivar.R | 21 junco-0.1.7/junco/R/cur_col_split_path_utils.R |only junco-0.1.7/junco/R/deprecate.R |only junco-0.1.7/junco/R/docx_exporter_functions.R | 79 - junco-0.1.7/junco/R/estimate_proportion_diff.R | 94 - junco-0.1.7/junco/R/event_free.R | 15 junco-0.1.7/junco/R/get_ref_info.R | 125 +- junco-0.1.7/junco/R/h_eair_funs.R | 76 + junco-0.1.7/junco/R/h_freq_funs.R | 151 +- junco-0.1.7/junco/R/jjcsformats.R | 253 ++++ junco-0.1.7/junco/R/jjcsformats_d.R |only junco-0.1.7/junco/R/junco-package.R | 2 junco-0.1.7/junco/R/junco_utils_default_stats_formats_labels.R | 176 ++ junco-0.1.7/junco/R/odds_ratio.R | 41 junco-0.1.7/junco/R/pool_funs.R |only junco-0.1.7/junco/R/pool_rbmi.R | 16 junco-0.1.7/junco/R/proportions.R | 11 junco-0.1.7/junco/R/pruning_functions.R | 28 junco-0.1.7/junco/R/pval_cat.R |only junco-0.1.7/junco/R/relative_risk.R | 36 junco-0.1.7/junco/R/resp_imputation.R |only junco-0.1.7/junco/R/response_by_var.R |only junco-0.1.7/junco/R/risk_diff_col_struct.R | 449 ++++++- junco-0.1.7/junco/R/s_summary_diff.R |only junco-0.1.7/junco/R/safe_t_test.R |only junco-0.1.7/junco/R/sorting_functions.R | 12 junco-0.1.7/junco/R/span_var_map.R | 28 junco-0.1.7/junco/R/split_functions.R | 7 junco-0.1.7/junco/R/summarize_ancova.R | 163 +- junco-0.1.7/junco/R/summarize_mmrm.R | 63 - junco-0.1.7/junco/R/tabulate_rbmi.R | 17 junco-0.1.7/junco/R/tern_utils_default_stats_formats_labels.R | 79 + junco-0.1.7/junco/R/tt_to_tblfile.R | 4 junco-0.1.7/junco/R/utils.R | 597 +++++++++- junco-0.1.7/junco/R/zz_format_utils.R |only junco-0.1.7/junco/R/zzz_format_d_setup.R |only junco-0.1.7/junco/README.md | 3 junco-0.1.7/junco/build/partial.rdb 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Title: Assurance Methods for Clinical Trials with a Delayed Treatment
Effect
Description: Provides functions for planning clinical trials subject to a delayed
treatment effect using assurance-based methods. Includes two 'shiny'
applications for interactive exploration, simulation, and visualisation of
trial designs and outcomes. The methodology is described in:
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Assurance methods for designing a clinical trial with a delayed treatment
effect" <doi:10.1002/sim.10136>,
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Adaptive clinical trial design with delayed treatment effects using
elicited prior distributions" <doi:10.48550/arXiv.2509.07602>.
Author: James Salsbury [aut, cre]
Maintainer: James Salsbury <jsalsbury1@sheffield.ac.uk>
Diff between DTEAssurance versions 1.1.0 dated 2025-12-02 and 1.3.0 dated 2026-10-13
DTEAssurance-1.1.0/DTEAssurance/man/BPP_func.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_threshold.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_timing.Rd |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-BPP_func.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_threshold.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_timing.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-make_rpact_design_from_GSD_model.R |only DTEAssurance-1.3.0/DTEAssurance/DESCRIPTION | 16 DTEAssurance-1.3.0/DTEAssurance/LICENSE | 4 DTEAssurance-1.3.0/DTEAssurance/MD5 | 96 DTEAssurance-1.3.0/DTEAssurance/NAMESPACE | 52 DTEAssurance-1.3.0/DTEAssurance/NEWS.md | 198 DTEAssurance-1.3.0/DTEAssurance/R/deprecated.R |only DTEAssurance-1.3.0/DTEAssurance/R/helpers.R |only DTEAssurance-1.3.0/DTEAssurance/R/main.R | 1446 ++-- DTEAssurance-1.3.0/DTEAssurance/R/paired.R |only DTEAssurance-1.3.0/DTEAssurance/R/shiny_apps.R | 42 DTEAssurance-1.3.0/DTEAssurance/R/utils.R | 1090 ++- DTEAssurance-1.3.0/DTEAssurance/README.md | 471 - DTEAssurance-1.3.0/DTEAssurance/inst/shiny/adaptive_app/app.R | 362 - DTEAssurance-1.3.0/DTEAssurance/inst/shiny/adaptive_app/rsconnect |only DTEAssurance-1.3.0/DTEAssurance/inst/shiny/assurance_app/app.R | 3301 ++++------ DTEAssurance-1.3.0/DTEAssurance/inst/shiny/assurance_app/rsconnect |only DTEAssurance-1.3.0/DTEAssurance/man/DTEAssurance-deprecated.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/PP_func.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/apply_GSD_to_trial.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/apply_design_rule.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/assurance_adaptive_shiny_app.Rd | 46 DTEAssurance-1.3.0/DTEAssurance/man/calc_dte_assurance.Rd | 202 DTEAssurance-1.3.0/DTEAssurance/man/calc_dte_assurance_adaptive.Rd | 253 DTEAssurance-1.3.0/DTEAssurance/man/calibrate_PP_threshold.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/calibrate_PP_timing.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/calibrate_matched_futility_boundary.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/cens_data.Rd | 106 DTEAssurance-1.3.0/DTEAssurance/man/compute_relative_floors.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/figures/README-unnamed-chunk-8-1.png |binary DTEAssurance-1.3.0/DTEAssurance/man/figures/README-unnamed-chunk-9-1.png |binary DTEAssurance-1.3.0/DTEAssurance/man/make_gsd_design.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/run_calibration_grid.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/run_paired_scenario.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/select_kappa_star.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/sim_dte.Rd | 94 DTEAssurance-1.3.0/DTEAssurance/man/single_matched_futility_rep.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/single_paired_rep.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/summarize_grid_by_kappa.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/survival_test.Rd | 129 DTEAssurance-1.3.0/DTEAssurance/man/update_priors.Rd | 227 DTEAssurance-1.3.0/DTEAssurance/tests/testthat.R | 4 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/fixtures |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/helper-paired.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func_equivalence.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func_exp_weibull.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-apply_GSD_to_trial.R | 117 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-assurance_shiny_app.R | 26 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calc_dte_assurance_adaptive.R | 18 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calibrate_PP_threshold.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calibrate_PP_timing.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-deprecated.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-design_rules.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-event_cuts.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-futility_types.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-kappa_selection.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-make_gsd_design.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-paired.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-refactor_equivalence.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-simulate_trial_with_recruitment.R | 8 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-single_calibration_rep.R | 8 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-survival_test.R | 77 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-update_priors_seed.R |only 70 files changed, 4925 insertions(+), 3468 deletions(-)
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplementary tools for evaluating and validating partial least
squares structural equation models estimated with 'seminr'. Provides methods
for predictive model assessment, importance-performance analysis with
necessary condition testing, overfitting diagnostics, measurement model
verification, mediator contribution analysis, unobserved heterogeneity
detection via latent class and prediction-oriented segmentation, and
congruence coefficient testing. All functions accept estimated 'seminr'
model objects and return results with print, summary, and plot methods.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre]
Maintainer: Nicholas Patrick Danks <seminrgroup@gmail.com>
Diff between seminrExtras versions 1.0.3 dated 2026-08-19 and 1.0.4 dated 2026-10-13
DESCRIPTION | 9 MD5 | 57 ++-- NAMESPACE | 4 NEWS.md | 123 ++++++++ R/feature_congruence.R | 356 +++++++++++++++++++++----- R/feature_cta.R | 2 R/feature_cvpat.R | 83 ++---- R/helpers.R | 52 +++ README.md | 37 +- demo/00Index | 2 demo/seminr-help-debugging.R | 34 +- demo/seminr-pls-congruence.R | 36 +- demo/seminr-primer-v2-chap2.R | 4 demo/seminr-primer-v2-chap3.R | 10 demo/seminr-primer-v2-chap4.R | 5 demo/seminr-primer-v2-chap8.R | 8 inst/doc/SEMinRExtras.R | 6 inst/doc/SEMinRExtras.Rmd | 18 - inst/doc/SEMinRExtras.html | 62 ++-- man/assess_cta.Rd | 2 man/assess_cvpat.Rd | 5 man/assess_cvpat_compare.Rd | 5 man/congruence.Rd |only tests/testthat/helper-textbook.R |only tests/testthat/test-congruence-coefficients.R |only tests/testthat/test-congruence.R | 51 +++ tests/testthat/test-cvpat-reps.R |only tests/testthat/test-textbook-defaults.R |only tests/testthat/test-textbook-golden.R |only tests/testthat/test-textbook-seed-audit.R |only tests/testthat/textbook |only vignettes/SEMinRExtras.Rmd | 18 - 32 files changed, 737 insertions(+), 252 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.5.4 dated 2026-09-05 and 1.6.0 dated 2026-10-13
DESCRIPTION | 50 - MD5 | 148 ++--- NAMESPACE | 10 NEWS.md | 354 ++++++++++++ R/clean_parameters.R | 146 ++++- R/compute_variances.R | 93 ++- R/export_table.R | 416 +++++++++++++- R/find_auxiliary.R | 76 ++ R/find_formula.R | 40 + R/find_parameters.R | 52 - R/find_parameters_bayesian.R | 4 R/find_parameters_brms.R | 21 R/find_parameters_mixed.R | 7 R/find_predictors.R | 50 + R/find_random_slopes.R | 43 + R/format_table.R | 9 R/get_data.R | 242 +++++++- R/get_mixed_info.R | 51 + R/get_modelmatrix.R | 84 ++ R/get_nested_lme_varcorr.R | 46 + R/get_parameters.R | 89 ++- R/get_parameters_bayesian.R | 8 R/get_parameters_mixed.R | 7 R/get_predicted.R | 84 ++ R/get_predicted_args.R | 10 R/get_predicted_ci.R | 6 R/get_predicted_ci_zeroinflated.R | 7 R/get_predicted_mixed.R | 235 +++++++- R/get_predicted_zeroinfl.R | 19 R/get_residuals.R | 48 + R/get_sigma.R | 44 + R/get_statistic.R | 19 R/get_varcov.R | 60 +- R/get_variances.R | 14 R/is_converged.R | 655 ++++++++++++++++++++++- R/n_obs.R | 62 ++ R/null_model.R | 46 + R/utils_get_data.R | 20 R/utils_glmmtmb_ordinal.R |only inst/WORDLIST | 7 inst/doc/display.html | 370 ++++++------- man/export_table.Rd | 23 man/find_auxiliary.Rd | 4 man/find_parameters.BGGM.Rd | 4 man/get_data.Rd | 7 man/get_parameters.BGGM.Rd | 2 man/get_parameters.Rd | 1 man/get_parameters.blavaan.Rd |only man/get_predicted.Rd | 5 man/get_predicted_ci.Rd | 5 man/get_response.Rd | 7 man/get_varcov.Rd | 5 man/insight-package.Rd | 1 man/is_converged.Rd | 131 ++++ man/n_obs.Rd | 4 tests/testthat/test-blavaan.R |only tests/testthat/test-brms.R | 14 tests/testthat/test-brms_autocor.R |only tests/testthat/test-brms_dpars.R |only tests/testthat/test-brms_nonlinear.R |only tests/testthat/test-coxph.R | 15 tests/testthat/test-export_table.R | 791 +++++++++++++++++++++++++++- tests/testthat/test-find_random_slopes.R |only tests/testthat/test-format_table.R | 44 + tests/testthat/test-gamlss.R | 71 ++ tests/testthat/test-get_data-changed_data.R |only tests/testthat/test-get_modelmatrix.R | 384 +++++++++++++ tests/testthat/test-get_predicted-coxph.R |only tests/testthat/test-get_predicted-newdata.R |only tests/testthat/test-get_predicted.R | 3 tests/testthat/test-get_varcov.R | 54 + tests/testthat/test-get_variance.R | 119 ++++ tests/testthat/test-glmmTMB-ordinal.R |only tests/testthat/test-is_converged_cmdstanr.R |only tests/testthat/test-is_converged_coxph.R |only tests/testthat/test-is_converged_stan.R |only tests/testthat/test-iv_robust.R | 3 tests/testthat/test-lavaan.R | 50 + tests/testthat/test-lme.R | 669 +++++++++++++++++++++++ tests/testthat/test-merModList.R |only tests/testthat/test-mmrm.R | 2 tests/testthat/test-n_obs_brms.R |only tests/testthat/test-null_model.R | 59 ++ 83 files changed, 5636 insertions(+), 593 deletions(-)
Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between contfrac versions 1.1-12 dated 2018-05-17 and 1.1-13 dated 2026-10-13
contfrac-1.1-12/contfrac/tests/aaa.R |only contfrac-1.1-13/contfrac/DESCRIPTION | 20 +++++++++++---- contfrac-1.1-13/contfrac/MD5 | 23 +++++++++++++---- contfrac-1.1-13/contfrac/R/contfrac.R | 30 +++++++++++++++++++---- contfrac-1.1-13/contfrac/README.md |only contfrac-1.1-13/contfrac/build |only contfrac-1.1-13/contfrac/inst |only contfrac-1.1-13/contfrac/man/CF.Rd | 8 +++--- contfrac-1.1-13/contfrac/man/contfrac-package.Rd |only contfrac-1.1-13/contfrac/man/convergents.Rd | 16 ++++++++++-- contfrac-1.1-13/contfrac/man/figures |only contfrac-1.1-13/contfrac/src/contfrac.c | 20 +++++++-------- contfrac-1.1-13/contfrac/tests/testthat |only contfrac-1.1-13/contfrac/tests/testthat.R |only contfrac-1.1-13/contfrac/vignettes |only 15 files changed, 85 insertions(+), 32 deletions(-)
Title: Direction-Aware Sufficient Condition Analysis
Description: Tests whether a high or low level of a condition is enough to
guarantee a high or low level of an outcome. Such a claim predicts that one
corner of the condition-outcome scatter plot is empty of observations. The
package estimates the boundary of that empty corner, its size as a share of
the scope (the effect size), a permutation test against random pairing, and
a threshold table giving the condition level that guarantees each outcome
level, in actual units, percentages, percentiles or standard deviations.
Each of the four directions (high or low condition, high or low outcome) is
stated as a claim and mapped to its empty corner. Because a condition can
rule out low outcomes while barely moving the average, results can be set
beside ordinary least-squares and median regression slopes, showing whether
the data hold an average effect, a sufficiency effect or both. Also
provides plots, influential-case diagnostics, scope-sensitivity and
resampling checks, random-data generation and power [...truncated...]
Author: Young Chan [aut, cre]
Maintainer: Young Chan <youngchanresearcher@gmail.com>
Diff between SCAtools versions 0.4.3 dated 2026-09-18 and 0.5.1 dated 2026-10-13
SCAtools-0.4.3/SCAtools/man/sca_corners.Rd |only SCAtools-0.4.3/SCAtools/man/sca_diagnostics.Rd |only SCAtools-0.4.3/SCAtools/man/sca_plots.Rd |only SCAtools-0.4.3/SCAtools/man/sca_results.Rd |only SCAtools-0.5.1/SCAtools/DESCRIPTION | 44 SCAtools-0.5.1/SCAtools/MD5 | 94 SCAtools-0.5.1/SCAtools/NAMESPACE | 23 SCAtools-0.5.1/SCAtools/NEWS.md | 1046 +++++++++ SCAtools-0.5.1/SCAtools/R/SCAtools-package.R |only SCAtools-0.5.1/SCAtools/R/analysis.R | 977 ++++++++ SCAtools-0.5.1/SCAtools/R/compare.R |only SCAtools-0.5.1/SCAtools/R/corners.R | 223 +- SCAtools-0.5.1/SCAtools/R/data.R |only SCAtools-0.5.1/SCAtools/R/diagnostics.R | 230 +- SCAtools-0.5.1/SCAtools/R/magnitude.R |only SCAtools-0.5.1/SCAtools/R/plots.R | 204 + SCAtools-0.5.1/SCAtools/R/resample.R |only SCAtools-0.5.1/SCAtools/R/results.R | 1110 +++++++++- SCAtools-0.5.1/SCAtools/R/scales.R | 52 SCAtools-0.5.1/SCAtools/R/simulation.R | 91 SCAtools-0.5.1/SCAtools/README.md | 291 +- SCAtools-0.5.1/SCAtools/build |only SCAtools-0.5.1/SCAtools/data |only SCAtools-0.5.1/SCAtools/inst/CITATION | 24 SCAtools-0.5.1/SCAtools/inst/NOTICE | 2 SCAtools-0.5.1/SCAtools/inst/docs/README_zh-TW.md | 253 -- SCAtools-0.5.1/SCAtools/inst/docs/sufficiency-logic.md | 7 SCAtools-0.5.1/SCAtools/inst/extdata |only SCAtools-0.5.1/SCAtools/man/SCAtools-package.Rd | 128 + SCAtools-0.5.1/SCAtools/man/sca.Rd |only SCAtools-0.5.1/SCAtools/man/sca_analysis.Rd | 212 + SCAtools-0.5.1/SCAtools/man/sca_boundary_type.Rd |only SCAtools-0.5.1/SCAtools/man/sca_check_direction.Rd |only SCAtools-0.5.1/SCAtools/man/sca_compare.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner_location.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner_map.Rd |only SCAtools-0.5.1/SCAtools/man/sca_direction.Rd |only SCAtools-0.5.1/SCAtools/man/sca_empty_space.Rd |only SCAtools-0.5.1/SCAtools/man/sca_extract.Rd |only SCAtools-0.5.1/SCAtools/man/sca_four_configurations.Rd |only SCAtools-0.5.1/SCAtools/man/sca_legacy_names.Rd |only SCAtools-0.5.1/SCAtools/man/sca_locationshift.Rd |only SCAtools-0.5.1/SCAtools/man/sca_magnitude.Rd |only SCAtools-0.5.1/SCAtools/man/sca_normalize.Rd |only SCAtools-0.5.1/SCAtools/man/sca_outliers.Rd |only SCAtools-0.5.1/SCAtools/man/sca_output.Rd |only SCAtools-0.5.1/SCAtools/man/sca_plot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_power.Rd | 100 SCAtools-0.5.1/SCAtools/man/sca_powerplot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_random.Rd | 50 SCAtools-0.5.1/SCAtools/man/sca_reference.Rd | 86 SCAtools-0.5.1/SCAtools/man/sca_relationship.Rd |only SCAtools-0.5.1/SCAtools/man/sca_resample.Rd |only SCAtools-0.5.1/SCAtools/man/sca_rescale.Rd |only SCAtools-0.5.1/SCAtools/man/sca_scales.Rd | 72 SCAtools-0.5.1/SCAtools/man/sca_scope.Rd |only SCAtools-0.5.1/SCAtools/man/sca_scope_sensitivity.Rd |only SCAtools-0.5.1/SCAtools/man/sca_table.Rd |only SCAtools-0.5.1/SCAtools/man/sca_terms.Rd |only SCAtools-0.5.1/SCAtools/man/sca_test_plot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_thresholds.Rd |only SCAtools-0.5.1/SCAtools/tests/testthat/test-adjust-resample.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-analysis.R | 54 SCAtools-0.5.1/SCAtools/tests/testthat/test-api-0-5-0.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-configurations.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-magnitude.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-refusals.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-scope.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-settings.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-simulation.R | 40 SCAtools-0.5.1/SCAtools/tests/testthat/test-symmetry.R |only 72 files changed, 4455 insertions(+), 958 deletions(-)
Title: Fast Interactive Data Analysis Pipelines
Description: A lightweight and intuitive framework for building interactive data
analysis pipelines. You add R functions one by one, and 'pipeflow'
wires them into a pipeline that stays consistent as you go. Modify,
remove, or insert steps at any stage, manage all parameters in one
place, fast execution (C++-powered DAG) for interactive use and Shiny
backends.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between pipeflow versions 0.4.0 dated 2026-09-27 and 0.5.0 dated 2026-10-13
DESCRIPTION | 10 LICENSE | 4 MD5 | 126 + NAMESPACE | 4 NEWS.md | 76 + R/RcppExports.R | 8 R/generic.pipeflow.R | 52 R/log.R | 38 R/pipeflow-package.R | 11 R/pipeflow.R | 1114 +++++++++++++---- R/print.pipeflow.R | 71 + R/utils.R | 51 build/vignette.rds |binary inst/doc/v01-get-started.R | 26 inst/doc/v01-get-started.Rmd | 54 inst/doc/v01-get-started.html | 177 +- inst/doc/v02-modify-pipeline.html | 34 inst/doc/v03a-combine-pipelines.R | 19 inst/doc/v03a-combine-pipelines.Rmd | 42 inst/doc/v03a-combine-pipelines.html | 124 + inst/doc/v03b-pipeline-views.R | 46 inst/doc/v03b-pipeline-views.Rmd | 73 - inst/doc/v03b-pipeline-views.html | 206 ++- inst/doc/v04-collect-output.R | 8 inst/doc/v04-collect-output.Rmd | 8 inst/doc/v04-collect-output.html | 27 inst/doc/v05a-split-map-reduce.html | 85 - inst/doc/v05b-nested-pipeline.R | 2 inst/doc/v05b-nested-pipeline.Rmd | 28 inst/doc/v05b-nested-pipeline.html | 145 +- inst/doc/v05c-error-handling.R |only inst/doc/v05c-error-handling.Rmd |only inst/doc/v05c-error-handling.html |only inst/doc/v05d-param-value.R |only inst/doc/v05d-param-value.Rmd |only inst/doc/v05d-param-value.html |only inst/doc/v06-self-modify-pipeline.Rmd | 8 inst/doc/v06-self-modify-pipeline.html | 121 + man/Extract.pipeflow.Rd | 18 man/pip_add.Rd | 27 man/pip_new.Rd | 20 man/pip_param_value.Rd |only man/pip_remove.Rd | 21 man/pip_replace.Rd | 52 man/pip_run.Rd | 117 + man/pip_run_state.Rd |only man/pip_set_params.Rd | 51 man/pip_view.Rd | 11 man/pipeflow_lgr.Rd |only man/print.Rd | 8 src/RcppExports.cpp | 27 src/dag.cpp | 161 ++ tests/testthat/helper_dag.R | 25 tests/testthat/helper_general.R | 10 tests/testthat/test_RcppExports.R | 124 + tests/testthat/test_generic.pipeflow.R | 240 +++ tests/testthat/test_log.R | 92 + tests/testthat/test_pipeflow.R | 2107 ++++++++++++++++++++++++++++++++- tests/testthat/test_print.pipeflow.R | 176 ++ tests/testthat/test_utils.R | 31 vignettes/articles/v07-vs-targets.Rmd | 996 +++++++++++---- vignettes/articles/v07-vs-targets.html |only vignettes/v01-get-started.Rmd | 54 vignettes/v03a-combine-pipelines.Rmd | 42 vignettes/v03b-pipeline-views.Rmd | 73 - vignettes/v04-collect-output.Rmd | 8 vignettes/v05b-nested-pipeline.Rmd | 28 vignettes/v05c-error-handling.Rmd |only vignettes/v05d-param-value.Rmd |only vignettes/v06-self-modify-pipeline.Rmd | 8 70 files changed, 6086 insertions(+), 1239 deletions(-)
Title: Modelling Reproduction and Survival Data in Ecotoxicology
Description: Advanced methods for a valuable quantitative environmental risk
assessment using Bayesian inference of survival and reproduction Data. Among
others, it facilitates Bayesian inference of the general unified
threshold model of survival (GUTS). See our companion paper
Baudrot and Charles (2021) <doi:10.21105/joss.03200>,
as well as complementary details in Baudrot et al. (2018)
<doi:10.1021/acs.est.7b05464> and Delignette-Muller et al.
(2017) <doi:10.1021/acs.est.6b05326>.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Nils Kehrein [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [ctb],
Alexander Singer [ [...truncated...]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between morse versions 3.3.5 dated 2026-01-14 and 3.6.0 dated 2026-10-13
DESCRIPTION | 16 +++--- MD5 | 46 ++++++++++--------- NAMESPACE | 2 NEWS | 6 ++ R/morse-internal.R | 19 ++++++++ R/morse.R | 2 R/plot.reproFitTT.R | 1 R/plotDoseResponse.reproData.R | 9 +-- R/plot_prior_post.R | 2 R/predict_Nsurv_check.R | 2 R/priors_distribution.R | 2 R/summary.survFit.R | 2 build/partial.rdb |only inst/doc/MinimalWorkingExample.html | 3 - inst/doc/modelling.html | 2 inst/doc/tutorial.html | 84 +++++++++++++++++------------------- man/morse-package.Rd | 2 man/plotDoseResponse.reproData.Rd | 7 --- man/plot_prior_post.survFit.Rd | 2 man/predict_check.Rd | 2 man/priors_distribution.survFit.Rd | 2 man/summary.survFit.Rd | 2 tests/testthat/test-LCx.R | 4 - tests/testthat/test-surv.R | 74 +++++++++++++++++++++++++++++++ tests/testthat/test-survFit.R |only 25 files changed, 188 insertions(+), 105 deletions(-)
Title: Statistical Matching Using Latent Class Models
Description: Provides a revised framework (1.2->2.0) for statistical matching of categorical data based on latent class models, including multiple imputation, predictive modeling, nearest-neighbour hot-deck matching, and probabilistic assignment of categorical target variables. It allows researchers to perform data integration when no unique identifiers are available by modeling the joint distribution of variables through latent categorical structures. The package supports estimation of latent class models, probabilistic matching between donor and recipient data sets, and generation of synthetic linked data under uncertainty. It is particularly useful in survey research and data fusion applications where combining information from multiple sources is required while preserving statistical properties and accounting for measurement error and missing data mechanisms.
Author: Alicja Wolny-Dominiak [aut, cre],
Israa Lewaaelhamd [aut],
Mohammed Ali Ismail [aut]
Maintainer: Alicja Wolny-Dominiak <woali@ue.katowice.pl>
Diff between statMatchLCM versions 1.2 dated 2026-05-15 and 2.0 dated 2026-10-13
DESCRIPTION | 8 MD5 | 40 NAMESPACE | 2 R/statMatchLCM.R | 2185 +++++++++++++++++++++++++++++----------------------- R/zzz.R |only data/datA.rda |binary data/datB.rda |binary data/datC.rda |only man/datA.Rd | 4 man/datABC_to_SM.Rd |only man/datAB_to_SM.Rd | 10 man/datB.Rd | 6 man/datC.Rd |only man/num_to_fact.Rd | 14 man/sm_quality.Rd | 8 man/sma1_step2.Rd | 14 man/sma2_step2.Rd | 22 man/sma3_step2.Rd | 23 man/sma_step1.Rd | 32 man/smc1_step2.Rd | 6 man/smc2_step2.Rd | 10 man/smc3_step2.Rd | 9 man/smc_step1.Rd | 20 23 files changed, 1339 insertions(+), 1074 deletions(-)
Title: Package Checks for 'rOpenSci'
Description: Check whether a package is ready for submission to the 'rOpenSci'
peer review system ('rOpenSci' authors (2026) <doi:10.5281/zenodo.2553043>
"'rOpenSci' Packages: Development, Maintenance, and Peer Review").
Incorporates the 'goodpractice' package and many additional checks,
including aspects related to maintenance of online public code
repositories.
Author: Mark Padgham [aut, cre] ,
Maelle Salmon [aut],
Jacob Wujciak-Jens [aut] ,
Kelli F. Johnson [ctb] ,
Eunseop Kim [aut] ,
Katrina Brock [ctb] ,
Andy Teucher [aut] ,
Eric R. Scott [aut]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgcheck versions 0.3.3 dated 2026-10-06 and 0.3.4 dated 2026-10-13
DESCRIPTION | 6 - MD5 | 60 +++++++++-------- NEWS.md | 10 ++ R/info-ci.R | 3 R/info-git.R | 3 R/info-github.R | 4 - R/pkgcheck-info.R | 3 R/stats-checks.R | 65 +++++++++++-------- R/utils.R | 16 ++++ inst/doc/autotest-pkgcheck-gp.html | 6 - inst/doc/environment.html | 6 - inst/doc/extending-checks.html | 6 - inst/doc/list-checks.html | 6 - tests/testthat/_snaps/extra-checks/checks-extra.html | 50 +++++++------- tests/testthat/_snaps/extra-checks/checks-extra.md | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks0.html | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks0.md | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks1.html | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks1.md | 50 +++++++------- tests/testthat/helper-check-data.R | 17 +++- tests/testthat/test-cache.R | 5 + tests/testthat/test-check-ci.R | 8 +- tests/testthat/test-check-left-assign.R | 2 tests/testthat/test-check-scrap.R | 8 ++ tests/testthat/test-extra-checks.R | 11 +-- tests/testthat/test-extra-env-check.R | 4 - tests/testthat/test-goodpractice.R | 2 tests/testthat/test-pkgcheck.R | 5 - tests/testthat/test-pkgcheck_bg.R | 4 - vignettes/autotest-pkgcheck-gp.md |only vignettes/environment.md |only vignettes/extending-checks.md |only vignettes/list-checks.md |only 33 files changed, 312 insertions(+), 248 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests for independent groups designs under homoscedasticity and heteroscedasticity. The tests described by Dag et al. (2018) <doi:10.32614/RJ-2018-022> include one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second-order test, and Kruskal-Wallis test. Additional tests described by Kasikci et al. (2026) <doi:10.32614/RJ-2026-014> include Scott-Smith test, Box F test, Johansen F test, generalized tests equivalent to parametric bootstrap and fiducial tests, Alvandi's F test, Alvandi's generalized p-value, approximate F test, B square test, Cochran test, Weerahandi's generalized F test, modified Brown-Forsythe test, adjusted Welch's heteroscedastic F test, Welch-Aspin test, and permutation F test. The package also provides pairwise comparisons and graphical methods, as well as Student's t test, Welch's t test, and M [...truncated...]
Author: Osman Dag [aut, cre],
Merve Kasikci [aut],
Anil Dolgun [aut],
N. Meric Konar [aut],
Sam Weerahandi [aut],
Malwane Ananda [aut],
H. Erkin Sulekli [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 3.1 dated 2025-07-22 and 3.2 dated 2026-10-13
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- inst/citation | 50 ++++++++++++++++++++++++++++++++++---------------- 3 files changed, 43 insertions(+), 25 deletions(-)
Title: Technology Appraisal Toolbox for Health Economic Evaluations in
the Netherlands
Description: Functions to support economic modelling in R based on the methods of the
Dutch guideline for economic evaluations in healthcare <https://www.zorginstituutnederland.nl/documenten/2024/01/16/richtlijn-voor-het-uitvoeren-van-economische-evaluaties-in-de-gezondheidszorg>,
CBS data <https://www.cbs.nl/>, and OECD data <https://www.oecd.org/en.html>.
Author: Stijn Peeters [aut, cre] ,
Eline Krijkamp [aut] ,
Frederick Thielen [aut]
Maintainer: Stijn Peeters <s.b.peeters@eshpm.eur.nl>
Diff between tatooheene versions 1.0.0 dated 2025-12-15 and 1.0.1 dated 2026-10-13
DESCRIPTION | 8 - MD5 | 44 ++++--- R/apply_discounting.R | 2 R/globals.R | 43 +++---- R/nl_ppp.R | 72 ++++++------ R/nl_price_index.R | 185 ++++++++++++++++--------------- R/nl_ref_prices.R | 34 ++++- build/vignette.rds |binary data/df_cpi_combined.rda |binary data/df_fp.rda |binary data/df_ppp.rda |binary data/df_ref_prices.rda |binary inst/doc/apply-discounting.html | 142 +++++++++++------------- inst/doc/depreciation-interest.R | 2 inst/doc/depreciation-interest.html | 10 + inst/doc/friction-period.html | 11 + inst/doc/getting-started.R | 44 +++---- inst/doc/getting-started.html | 3 inst/doc/nl-ref-prices.html | 188 +++++++++++++++++++++++++++++--- man/nl_price_index.Rd | 1 tests/testthat/test-apply_discounting.R |only tests/testthat/test-nl_ppp.R |only tests/testthat/test-nl_price_index.R | 7 + tests/testthat/test-nl_ref_prices.R |only tests/testthat/test-pretty_price.R |only 25 files changed, 505 insertions(+), 291 deletions(-)
Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>. The software itself
is introduced in Feng, Y., Gries, T., Letmathe, S., and Schulz, D. (2022)
<doi:10.32614/RJ-2022-017>.
Author: Yuanhua Feng [aut] ,
Sebastian Letmathe [aut] ,
Dominik Schulz [aut, cre] ,
Thomas Gries [ctb] ,
Marlon Fritz [ctb]
Maintainer: Dominik Schulz <dominik.schulz.r@gmail.com>
Diff between smoots versions 1.1.4 dated 2023-09-11 and 1.1.5 dated 2026-10-13
smoots-1.1.4/smoots/man/smoots.Rd |only smoots-1.1.5/smoots/DESCRIPTION | 30 +-- smoots-1.1.5/smoots/MD5 | 101 ++++++------- smoots-1.1.5/smoots/NAMESPACE | 52 ++++-- smoots-1.1.5/smoots/NEWS.md | 14 + smoots-1.1.5/smoots/R/Welcome.R | 2 smoots-1.1.5/smoots/R/algorithms.R | 5 smoots-1.1.5/smoots/R/bootCast.R | 25 +-- smoots-1.1.5/smoots/R/cf0.LW.est.R | 42 +++-- smoots-1.1.5/smoots/R/confBounds.R | 13 - smoots-1.1.5/smoots/R/critMatrix.R | 2 smoots-1.1.5/smoots/R/dsmooth.R | 13 - smoots-1.1.5/smoots/R/fitted.R | 2 smoots-1.1.5/smoots/R/gsmooth.R | 3 smoots-1.1.5/smoots/R/knsmooth.R | 3 smoots-1.1.5/smoots/R/modelCast.R | 17 +- smoots-1.1.5/smoots/R/msmooth.R | 31 ++- smoots-1.1.5/smoots/R/msmoothCalc.R | 6 smoots-1.1.5/smoots/R/normCast.R | 12 - smoots-1.1.5/smoots/R/optOrd.R | 2 smoots-1.1.5/smoots/R/plot.smoots.R | 2 smoots-1.1.5/smoots/R/print.smoots.R | 2 smoots-1.1.5/smoots/R/rescale.R | 2 smoots-1.1.5/smoots/R/residuals.R | 2 smoots-1.1.5/smoots/R/rollCast.R | 7 smoots-1.1.5/smoots/R/smoots.R | 14 - smoots-1.1.5/smoots/R/trendCast.R | 3 smoots-1.1.5/smoots/R/tsmooth.R | 34 +++- smoots-1.1.5/smoots/R/tsmoothCalc.R | 27 ++- smoots-1.1.5/smoots/README.md | 59 ++++--- smoots-1.1.5/smoots/inst |only smoots-1.1.5/smoots/man/bootCast.Rd | 16 +- smoots-1.1.5/smoots/man/confBounds.Rd | 13 - smoots-1.1.5/smoots/man/critMatrix.Rd | 2 smoots-1.1.5/smoots/man/dsmooth.Rd | 13 - smoots-1.1.5/smoots/man/figures/logo_smoots.png |only smoots-1.1.5/smoots/man/fitted.smoots.Rd | 2 smoots-1.1.5/smoots/man/gsmooth.Rd | 3 smoots-1.1.5/smoots/man/knsmooth.Rd | 3 smoots-1.1.5/smoots/man/modelCast.Rd | 17 +- smoots-1.1.5/smoots/man/msmooth.Rd | 30 ++- smoots-1.1.5/smoots/man/normCast.Rd | 12 - smoots-1.1.5/smoots/man/optOrd.Rd | 2 smoots-1.1.5/smoots/man/plot.smoots.Rd | 2 smoots-1.1.5/smoots/man/print.smoots.Rd | 2 smoots-1.1.5/smoots/man/rescale.Rd | 2 smoots-1.1.5/smoots/man/residuals.smoots.Rd | 2 smoots-1.1.5/smoots/man/rollCast.Rd | 7 smoots-1.1.5/smoots/man/smoots-package.Rd |only smoots-1.1.5/smoots/man/trendCast.Rd | 3 smoots-1.1.5/smoots/man/tsmooth.Rd | 30 ++- smoots-1.1.5/smoots/src/gsmoothCpp.cpp | 8 - smoots-1.1.5/smoots/tests/testthat/test_cores_number.R |only smoots-1.1.5/smoots/tests/testthat/test_smoots_algorithm.R | 2 54 files changed, 401 insertions(+), 297 deletions(-)
Title: Parameter Space Partitioning MCMC for Global Model Evaluation
Description: Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.
Author: Lenard Dome [aut, cre],
Andy Wills [aut]
Maintainer: Lenard Dome <lenarddome@gmail.com>
Diff between psp versions 1.0.5 dated 2026-01-15 and 1.0.6 dated 2026-10-13
DESCRIPTION | 11 MD5 | 15 - NEWS.md |only build/partial.rdb |binary man/figures |only man/pspGlobal.Rd | 2 src/pspGlobal.cpp | 417 +++++++++++++++----------------- tests/testthat/helper-models.R |only tests/testthat/test_psp_cpp.R | 4 tests/testthat/test_psp_cpp_callbacks.R |only tests/testthat/test_psp_cpp_sampler.R |only 11 files changed, 223 insertions(+), 226 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut] ,
Nicolas Lambert [aut] ,
Timothee Giraud [aut, cre]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.6.0 dated 2023-10-31 and 0.7.0 dated 2026-10-13
MTA-0.6.0/MTA/NEWS |only MTA-0.7.0/MTA/DESCRIPTION | 20 MTA-0.7.0/MTA/MD5 | 44 MTA-0.7.0/MTA/NAMESPACE | 18 MTA-0.7.0/MTA/NEWS.md |only MTA-0.7.0/MTA/R/gdev.R | 2 MTA-0.7.0/MTA/R/package.R | 16 MTA-0.7.0/MTA/R/tdev.R | 2 MTA-0.7.0/MTA/README.md | 22 MTA-0.7.0/MTA/build/vignette.rds |binary MTA-0.7.0/MTA/inst/doc/MTA.Rmd | 6 MTA-0.7.0/MTA/inst/doc/MTA.html | 172 +-- MTA-0.7.0/MTA/inst/doc/MTA_Scenario.R | 56 - MTA-0.7.0/MTA/inst/doc/MTA_Scenario.Rmd | 72 - MTA-0.7.0/MTA/inst/doc/MTA_Scenario.html | 1429 +++++++++++++++---------------- MTA-0.7.0/MTA/man/MTA.Rd | 12 MTA-0.7.0/MTA/man/cardist.Rd | 4 MTA-0.7.0/MTA/man/com.Rd | 4 MTA-0.7.0/MTA/man/ept.Rd | 4 MTA-0.7.0/MTA/man/gdev.Rd | 2 MTA-0.7.0/MTA/man/tdev.Rd | 2 MTA-0.7.0/MTA/vignettes/MTA.Rmd | 6 MTA-0.7.0/MTA/vignettes/MTA_Scenario.Rmd | 72 - MTA-0.7.0/MTA/vignettes/mta.bib | 31 24 files changed, 1027 insertions(+), 969 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 1.8-3 dated 2026-10-06 and 1.8-4 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/dpq_etc.R | 4 ++-- R/mmlt.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++++++++ tests/bugfixes.R | 6 ++++++ tests/bugfixes.Rout.save | 12 ++++++++++-- 8 files changed, 39 insertions(+), 15 deletions(-)
Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between cpop versions 1.0.9 dated 2026-05-29 and 1.0.10 dated 2026-10-13
DESCRIPTION | 16 +- MD5 | 36 ++-- NAMESPACE | 13 + NEWS.md | 7 R/cpop.R | 14 + R/cpop.crops.R | 284 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/stage23.rdb |binary man/changepoints-methods.Rd | 3 man/cost-methods.Rd | 3 man/cpop.crops-methods.Rd | 2 man/cpop.crops.models-methods.Rd | 2 man/estimate-methods.Rd | 3 man/plot-methods.Rd | 23 ++- man/print-methods.Rd |only man/segmentations-methods.Rd |only man/show-methods.Rd | 3 man/subset-methods.Rd |only man/summary-methods.Rd | 14 + man/unique-methods.Rd |only src/prune.impl.cpp | 2 21 files changed, 385 insertions(+), 40 deletions(-)
Title: Predict and Map Oyster Growth Suitability from Environmental
Data
Description: Predicts spatial suitability for oyster growth from environmental
survey data using rank-reciprocal weighted scoring.
Users supply sensor data from Acoustic Doppler Current Profilers (ADCP),
Conductivity-Temperature-Depth (CTD) sensors, bathymetric sonar, and
sidescan sonar, specify a target species, and receive per-location
suitability scores, a five-band 'GeoTIFF' heatmap for 'QGIS', contour
lines, and a formatted PDF or HTML report. Supports seventeen species across
global aquaculture regions, including Ostrea edulis, Magallana gigas,
Crassostrea virginica, Crassostrea hongkongensis, and thirteen further
species; see list_species(). Includes ocean acidification scoring via
in-house aragonite saturation state (Omega_arag) calculation using
Lueker et al. (2000) <doi:10.1016/S0304-4203(00)00022-0> and Mucci (1983)
<doi:10.1357/002224083788520153> equilibrium constants (no external
dependencies), variable impact diagnostics (variable_impact()), fine-scale
habitat area analys [...truncated...]
Author: T Tucker [aut, cre]
Maintainer: T Tucker <tristantucker48@gmail.com>
Diff between oystermapR versions 1.5.0 dated 2026-08-31 and 1.6.0 dated 2026-10-13
DESCRIPTION | 20 +- MD5 | 88 ++++++---- NAMESPACE | 20 ++ NEWS.md | 173 +++++++++++++++++++ R/area_summary.R | 31 ++- R/bayesian_update.R | 207 +++++++++++++++-------- R/evidence_weights.R |only R/exclusion_check.R | 43 ++-- R/export_geotiff.R | 107 +++++++++++- R/help.R | 144 +++++++++++++++- R/layer_reproducibility.R |only R/lineage_tolerances.R |only R/oystermapR-package.R | 2 R/predict_oyster.R | 244 +++++++++++++++++++++++++++- R/species_tolerances.R | 2 R/summary_pdf.R | 64 +++++-- R/validate.R | 4 R/variable_importance.R | 2 README.md | 67 +++++++ inst/REFERENCES.md | 4 inst/doc/example-bay-survey.R | 47 +++++ inst/doc/example-bay-survey.Rmd | 172 ++++++++++++++++++- inst/doc/example-bay-survey.html | 170 ++++++++++++++++++- inst/rmd/oystermapR_report.Rmd | 2 man/area_summary.Rd | 15 + man/as_lineage_distances.Rd |only man/confidence_score.Rd |only man/dot-apply_evidence_weighting.Rd |only man/dot-evidence_row_support.Rd |only man/dot-fit_suitability.Rd |only man/dot-params_at.Rd |only man/evidence_coverage.Rd |only man/evidence_suitability.Rd |only man/evidence_weights.Rd |only man/export_contours.Rd | 3 man/export_geotiff.Rd | 19 +- man/export_qml_style.Rd | 10 + man/fit_lineages.Rd |only man/layer_reproducibility.Rd |only man/lineage_fits_as_list.Rd |only man/lineage_occurrence.Rd |only man/lineage_signal.Rd |only man/oystermapR-package.Rd | 2 man/oystermapR_help.Rd | 5 man/predict_oyster.Rd | 88 +++++++++- man/rank_source_populations.Rd |only man/reliability_from_perturbation.Rd |only man/reliability_from_replicates.Rd |only man/update_species_tolerances.Rd | 24 ++ man/validate_against_records.Rd | 2 man/weight_table_md.Rd |only tests/testthat/test-bayesian.R | 84 +++++++++ tests/testthat/test-core.R | 65 +++++++ tests/testthat/test-evidence-weights.R |only tests/testthat/test-layer-reproducibility.R |only tests/testthat/test-lineage-tolerances.R |only vignettes/example-bay-survey.Rmd | 172 ++++++++++++++++++- 57 files changed, 1874 insertions(+), 228 deletions(-)
Title: Fitting the Metastatistical Extreme Value Distribution MEVD
Description: Extreme value analysis with the metastatistical extreme value distribution MEVD (Marani and Ignaccolo, 2015, <doi:10.1016/j.advwatres.2015.03.001>) and some of its variants. In particular, analysis can be performed with the simplified metastatistical extreme value distribution SMEV (Marra et al., 2019, <doi:10.1016/j.advwatres.2019.04.002>) and the temporal metastatistical extreme value distribution TMEV (Falkensteiner et al., 2023, <doi:10.1016/j.wace.2023.100601>). Parameters can be estimated with probability weighted moments, maximum likelihood and least squares. The data can also be left-censored prior to a fit. Density, distribution function, quantile function and random generation for the MEVD, SMEV and TMEV are included. In addition, functions for the calculation of return levels including confidence intervals are provided. For a description of use cases please see the provided references.
Author: Harald Schellander [aut, cre] ,
Alexander Lieb [ctb] ,
Marc-Andre Falkensteiner [ctb]
Maintainer: Harald Schellander <harald.schellander@geosphere.at>
Diff between mevr versions 1.1.1 dated 2024-06-30 and 1.3.3 dated 2026-10-13
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 88 - NEWS | 84 - R/mevr.R | 2651 ++++++++++++++++++++++---------- R/weibull_tail_test.R | 263 +-- README.md | 10 build |only man/censored_weibull_fit.Rd | 15 man/dailyrainfall.Rd | 20 man/dmev.Rd | 22 man/dtmev.Rd | 19 man/event_separation.Rd |only man/fmev.Rd | 170 +- man/fsmev.Rd | 209 +- man/ftmev.Rd | 207 +- man/ordinary_events.Rd |only man/plot.mevr.Rd | 24 man/pp.weibull.Rd | 9 man/predict.mevr.Rd | 40 man/return.levels.mev.Rd | 29 man/weibull_tail_test.Rd | 70 tests/testthat/test-dtmev.R | 44 tests/testthat/test-event_separation.R |only tests/testthat/test-fmev.R | 183 +- tests/testthat/test-fsmev.R | 344 ++-- tests/testthat/test-ftmev.R | 147 + tests/testthat/test-left-censoring.R |only tests/testthat/test-ordinary_events.R |only tests/testthat/test-pp-weibull.R | 12 tests/testthat/test-predict-mevr.R | 85 - tests/testthat/test-print-mevr.R | 150 + tests/testthat/test-qtmev.R | 8 tests/testthat/test-return-levels-mev.R | 173 +- tests/testthat/test-return-levels.R | 222 +- tests/testthat/test-weibull-tail-test.R | 119 - 36 files changed, 3618 insertions(+), 1881 deletions(-)
Title: Chinese Text Segmentation, POS Tagging, and Keyword Extraction
Description: Provides fast Chinese text segmentation, keyword extraction
via 'TF-IDF' and 'TextRank', and part-of-speech tagging, powered by a
'Rust' backend ('jieba-rs'). Supports custom dictionaries, user words,
stop words, IDF files, and HMM models, with parallel batch processing
of multiple strings. Serves as a modern, maintained replacement for
the 'jiebaR' package.
Author: Hao Cheng [aut, cre, cph]
Maintainer: Hao Cheng <Yousa-Mirage@foxmail.com>
Diff between jiebaRS versions 0.3.0 dated 2026-08-26 and 0.3.1 dated 2026-10-13
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 5 + README.md | 10 +-- inst/WORDLIST | 2 src/rust/Cargo.lock | 147 +------------------------------------------------ src/rust/Cargo.toml | 2 src/rust/vendor.tar.xz |binary 8 files changed, 25 insertions(+), 161 deletions(-)
Title: Geometric Features and Footprint Comparison for 'sf' Objects
Description: Extracts reproducible geometric and urban-morphology descriptors from
polygon and multipart polygon building footprints stored as 'sf' objects,
including area, perimeter, compactness, shape, topology, convexity, orientation,
and optional building-height and floor-area metrics. Compares polygon footprints
across periods using the intersection-over-union (Jaccard) index (Jaccard,
1912) <doi:10.1111/j.1469-8137.1912.tb05611.x> to identify new constructions,
potential demolitions, and footprint changes. Supports vector file formats
readable by 'sf', including Shapefiles and GeoPackage (GPKG) vector files with
named layers, optional boundary clipping, and reprojection to a common coordinate
reference system. Returned 'sf' objects preserve source attributes and geometry
for spatial analysis and downstream workflows, with optional parallel processing
using 'future' for larger feature-extraction jobs.
Author: Jonathan Cohen [aut, cre]
Maintainer: Jonathan Cohen <cohen.jota@gmail.com>
Diff between geomorphR versions 0.1.0 dated 2026-10-04 and 0.2.0 dated 2026-10-13
DESCRIPTION | 21 ++- MD5 | 27 ++++ NAMESPACE | 1 NEWS.md |only R/compare_footprints.R |only README.md | 130 +++++++++++++++++++++-- inst/examples |only inst/extdata/footprint_comparison |only man/compare_footprints.Rd |only tests/testthat/test_compare_footprints.R |only tests/testthat/test_extract_geometric_features.R | 1 11 files changed, 162 insertions(+), 18 deletions(-)
Title: Genotyping Triploids/Tetraploids (or Diploids) from Luminescence
Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids and tetraploids.
Three main functions: Create_Dataset_from_file() to build dataset ; Clustering_parallele_from_dir() that regroups individuals with a same genotype based on proximity and
Genotyping_parallele_from_dir() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between GenoTriplo versions 2.2.1 dated 2026-07-28 and 2.2.2 dated 2026-10-13
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- R/App_GenoTriploShiny.R | 37 +++++++++++++++++++++-------------- R/function_create_dataset.R | 2 - R/function_run_clustering.R | 8 +++++-- R/function_run_genotyping.R | 4 +-- man/Clustering_from_dir.Rd | 8 +++---- man/Create_Dataset_from_file.Rd | 2 - man/Genotyping_from_file.Rd | 2 - man/Genotyping_parallele_from_dir.Rd | 2 - 10 files changed, 51 insertions(+), 38 deletions(-)
Title: Continuous Epidemiological Week Indexing for Time-Series
Analysis
Description: Provides a simple algorithm to generate a continuous epidemiological week index from date variables in a data frame. Weeks are computed as sequential 7-day intervals aligned to Mondays, starting from the earliest observed date or from a user-supplied start date. They do not reset at calendar year boundaries and are not ISO 8601 nor MMWR calendar weeks. Missing or non-convertible dates are returned as NA instead of stopping the computation. The approach is intended for epidemiological modeling and time-series analysis where temporal continuity is required.
Author: Daniel Degina [aut, cre],
Joel Mbuyi [ctb]
Maintainer: Daniel Degina <deginadan@gmail.com>
Diff between cepiweek versions 0.1.2 dated 2026-02-19 and 0.2.0 dated 2026-10-13
DESCRIPTION | 14 +-- LICENSE | 4 MD5 | 16 +-- NAMESPACE | 6 - R/cepiweek.R | 165 +++++++++++++++++++++++++++-------------- README.md | 124 +++++++++++++++--------------- man/cepiweek.Rd | 141 +++++++++++++++++++---------------- tests/testthat.R | 107 +++++++++++++++++++++++--- tests/testthat/test-cepiweek.R | 118 +++++++++++++++++++++-------- 9 files changed, 456 insertions(+), 239 deletions(-)
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Francisco
Martinez et al. (2022) <doi:10.1016/j.neucom.2021.12.028>. When the forecasting
horizon is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.5 dated 2024-02-15 and 1.0.6 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/tsfgrnn.html | 48 +++++++++++++++++++++++++++++------------------- src/code.cpp | 6 +++--- 6 files changed, 46 insertions(+), 32 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Brian Ripley [ctb],
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.7.1 dated 2026-09-29 and 5.1.8 dated 2026-10-13
rxode2-5.1.7.1/rxode2/src/linCmt.cpp |only rxode2-5.1.7.1/rxode2/src/linCmt.h |only rxode2-5.1.7.1/rxode2/src/linCmtDualN.h |only rxode2-5.1.7.1/rxode2/src/macros2micros.cpp |only rxode2-5.1.7.1/rxode2/src/macros2micros.h |only rxode2-5.1.7.1/rxode2/src/rxDerived.cpp |only rxode2-5.1.7.1/rxode2/src/rxode2_sundials_stan_compat.h |only rxode2-5.1.7.1/rxode2/src/solComp.cpp |only rxode2-5.1.7.1/rxode2/src/solComp.h |only rxode2-5.1.7.1/rxode2/tests/testthat/test-lincmt-modeldouble-senstype.R |only rxode2-5.1.8/rxode2/DESCRIPTION | 38 rxode2-5.1.8/rxode2/MD5 | 1156 rxode2-5.1.8/rxode2/NAMESPACE | 49 rxode2-5.1.8/rxode2/NEWS.md | 729 rxode2-5.1.8/rxode2/R/000.R | 6 rxode2-5.1.8/rxode2/R/CTS.R | 21 rxode2-5.1.8/rxode2/R/RcppExports.R | 89 rxode2-5.1.8/rxode2/R/adjoint.R | 995 rxode2-5.1.8/rxode2/R/adjointDiscrete.R | 536 rxode2-5.1.8/rxode2/R/asFunction.R | 16 rxode2-5.1.8/rxode2/R/asIni.R | 21 rxode2-5.1.8/rxode2/R/asModel.R | 33 rxode2-5.1.8/rxode2/R/asRxui.R | 18 rxode2-5.1.8/rxode2/R/assert.R | 697 rxode2-5.1.8/rxode2/R/build.R | 269 rxode2-5.1.8/rxode2/R/collectWarnings.R | 9 rxode2-5.1.8/rxode2/R/confint.R | 46 rxode2-5.1.8/rxode2/R/confintSummary.R | 89 rxode2-5.1.8/rxode2/R/d.R | 614 rxode2-5.1.8/rxode2/R/dde.R | 1166 rxode2-5.1.8/rxode2/R/dfIni.R | 222 rxode2-5.1.8/rxode2/R/dfWishart.R | 42 rxode2-5.1.8/rxode2/R/dsl.R | 317 rxode2-5.1.8/rxode2/R/elu.R | 48 rxode2-5.1.8/rxode2/R/err-foceiBase.R | 405 rxode2-5.1.8/rxode2/R/err-sim.R | 486 rxode2-5.1.8/rxode2/R/err.R | 1506 rxode2-5.1.8/rxode2/R/et-helpers.R | 475 rxode2-5.1.8/rxode2/R/et-methods.R | 263 rxode2-5.1.8/rxode2/R/et.R | 972 rxode2-5.1.8/rxode2/R/etNew.R | 499 rxode2-5.1.8/rxode2/R/etTran.R | 164 rxode2-5.1.8/rxode2/R/etVctrs.R | 37 rxode2-5.1.8/rxode2/R/etaDist.R |only rxode2-5.1.8/rxode2/R/eventSens.R | 633 rxode2-5.1.8/rxode2/R/evidPush.R | 89 rxode2-5.1.8/rxode2/R/fixef.R | 8 rxode2-5.1.8/rxode2/R/forder.R | 40 rxode2-5.1.8/rxode2/R/format.R | 18 rxode2-5.1.8/rxode2/R/gelu.R | 11 rxode2-5.1.8/rxode2/R/genShinyApp.template.R | 61 rxode2-5.1.8/rxode2/R/geom-amt.R | 17 rxode2-5.1.8/rxode2/R/geom-cens.R | 49 rxode2-5.1.8/rxode2/R/getBaseSim.R | 45 rxode2-5.1.8/rxode2/R/indLin.R | 146 rxode2-5.1.8/rxode2/R/intern.R | 47 rxode2-5.1.8/rxode2/R/linCmt.R | 160 rxode2-5.1.8/rxode2/R/linMod.R | 215 rxode2-5.1.8/rxode2/R/llik.R | 222 rxode2-5.1.8/rxode2/R/lotriCompat.R | 22 rxode2-5.1.8/rxode2/R/lrelu.R | 4 rxode2-5.1.8/rxode2/R/mix.R | 136 rxode2-5.1.8/rxode2/R/mlogit.R | 82 rxode2-5.1.8/rxode2/R/modelExtract.R | 198 rxode2-5.1.8/rxode2/R/modlib.R | 147 rxode2-5.1.8/rxode2/R/mu-cov-downgrade.R | 97 rxode2-5.1.8/rxode2/R/mu.R | 1011 rxode2-5.1.8/rxode2/R/normui.R |only rxode2-5.1.8/rxode2/R/odeToLin.R | 546 rxode2-5.1.8/rxode2/R/parseFuns.R | 64 rxode2-5.1.8/rxode2/R/piping-ini.R | 687 rxode2-5.1.8/rxode2/R/piping-model.R | 600 rxode2-5.1.8/rxode2/R/piping-update.R | 12 rxode2-5.1.8/rxode2/R/piping.R | 327 rxode2-5.1.8/rxode2/R/plogis.R | 12 rxode2-5.1.8/rxode2/R/plot.R | 201 rxode2-5.1.8/rxode2/R/prelu.R | 32 rxode2-5.1.8/rxode2/R/print.R | 234 rxode2-5.1.8/rxode2/R/prior-density-families.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels-cdf.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels.R |only rxode2-5.1.8/rxode2/R/prior-sim.R | 509 rxode2-5.1.8/rxode2/R/priorDensity.R | 447 rxode2-5.1.8/rxode2/R/progress.R | 2 rxode2-5.1.8/rxode2/R/rbind.R | 46 rxode2-5.1.8/rxode2/R/reexport.R | 1 rxode2-5.1.8/rxode2/R/relu.R | 4 rxode2-5.1.8/rxode2/R/rstudio.R | 12 rxode2-5.1.8/rxode2/R/rudf.R | 557 rxode2-5.1.8/rxode2/R/rudfModelC.R |only rxode2-5.1.8/rxode2/R/rudfModelFind.R |only rxode2-5.1.8/rxode2/R/rudfModelLookup.R |only rxode2-5.1.8/rxode2/R/rudfModelReg.R |only rxode2-5.1.8/rxode2/R/rudfModelScope.R |only rxode2-5.1.8/rxode2/R/rudfui.R | 455 rxode2-5.1.8/rxode2/R/rxEvent.R |only rxode2-5.1.8/rxode2/R/rxEventEmit.R |only rxode2-5.1.8/rxode2/R/rxFormat.R | 22 rxode2-5.1.8/rxode2/R/rxIndLin.R | 21 rxode2-5.1.8/rxode2/R/rxJacobian.R | 164 rxode2-5.1.8/rxode2/R/rxLinCmt.R | 407 rxode2-5.1.8/rxode2/R/rxMemoryEstimate.R | 450 rxode2-5.1.8/rxode2/R/rxOom.R | 627 rxode2-5.1.8/rxode2/R/rxOptExpr.R | 428 rxode2-5.1.8/rxode2/R/rxParams.R | 166 rxode2-5.1.8/rxode2/R/rxPrune.R | 175 rxode2-5.1.8/rxode2/R/rxRaw.R | 102 rxode2-5.1.8/rxode2/R/rxReq.R | 5 rxode2-5.1.8/rxode2/R/rxResidualError.R | 3 rxode2-5.1.8/rxode2/R/rxSerialize.R | 20 rxode2-5.1.8/rxode2/R/rxShiny.R | 57 rxode2-5.1.8/rxode2/R/rxStack.R | 113 rxode2-5.1.8/rxode2/R/rxSymInv.R | 250 rxode2-5.1.8/rxode2/R/rxSyntaxFunctions.R | 2 rxode2-5.1.8/rxode2/R/rxUiGet.R | 443 rxode2-5.1.8/rxode2/R/rxValidate.R | 19 rxode2-5.1.8/rxode2/R/rxode-options.R | 89 rxode2-5.1.8/rxode2/R/rxode2.R | 1001 rxode2-5.1.8/rxode2/R/rxode2_md5.R | 3 rxode2-5.1.8/rxode2/R/rxrandom.R | 148 rxode2-5.1.8/rxode2/R/rxsolve.R | 4008 +- rxode2-5.1.8/rxode2/R/selu.R | 4 rxode2-5.1.8/rxode2/R/softplus.R | 10 rxode2-5.1.8/rxode2/R/splitBolus.R | 143 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rxode2-5.1.8/rxode2/src/init.c | 125 rxode2-5.1.8/rxode2/src/install.libs.R | 8 rxode2-5.1.8/rxode2/src/invCdfMemo.h |only rxode2-5.1.8/rxode2/src/linCmtSensType.h | 2 rxode2-5.1.8/rxode2/src/par_solve.cpp | 496 rxode2-5.1.8/rxode2/src/par_solve.h | 19 rxode2-5.1.8/rxode2/src/parseAssignStr.h | 5 rxode2-5.1.8/rxode2/src/parseDdt.h | 8 rxode2-5.1.8/rxode2/src/parseDfdy.h | 11 rxode2-5.1.8/rxode2/src/parseFuns.h | 216 rxode2-5.1.8/rxode2/src/parseFunsDiff.h | 39 rxode2-5.1.8/rxode2/src/parseFunsRandom.h | 57 rxode2-5.1.8/rxode2/src/parseLogical.h | 36 rxode2-5.1.8/rxode2/src/parseSyntaxErrors.h | 1 rxode2-5.1.8/rxode2/src/parseVars.h | 43 rxode2-5.1.8/rxode2/src/pkTime.h |only rxode2-5.1.8/rxode2/src/print_node.c | 90 rxode2-5.1.8/rxode2/src/print_node.h | 18 rxode2-5.1.8/rxode2/src/priorDensity.cpp | 276 rxode2-5.1.8/rxode2/src/rk4s.cpp | 5 rxode2-5.1.8/rxode2/src/ros4.cpp | 7 rxode2-5.1.8/rxode2/src/rxCse.cpp | 5 rxode2-5.1.8/rxode2/src/rxCseRun.h | 10 rxode2-5.1.8/rxode2/src/rxCseSel.h | 22 rxode2-5.1.8/rxode2/src/rxData.cpp | 122 rxode2-5.1.8/rxode2/src/rxGlobals.h | 2 rxode2-5.1.8/rxode2/src/rxMemoryComponents.cpp | 8 rxode2-5.1.8/rxode2/src/rxSerialize.cpp | 73 rxode2-5.1.8/rxode2/src/rxode2_df.cpp | 77 rxode2-5.1.8/rxode2/src/rxode2lincmtLink.cpp |only rxode2-5.1.8/rxode2/src/rxode2lincmtLink.h |only rxode2-5.1.8/rxode2/src/rxomp.h | 14 rxode2-5.1.8/rxode2/src/rxthreefry.cpp | 201 rxode2-5.1.8/rxode2/src/rxthreefry.h | 1 rxode2-5.1.8/rxode2/src/seBatch.h | 11 rxode2-5.1.8/rxode2/src/seed.cpp | 8 rxode2-5.1.8/rxode2/src/tran.c | 62 rxode2-5.1.8/rxode2/src/tran.g.d_parser.h |19138 ++++++---- rxode2-5.1.8/rxode2/src/tran.h | 16 rxode2-5.1.8/rxode2/src/utilc.cpp | 111 rxode2-5.1.8/rxode2/tests/testthat.R | 4 rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-corpus.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-grid.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden.R | 335 rxode2-5.1.8/rxode2/tests/testthat/helper-etaDistDirect.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etaDistLotri.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-lincmt-grad.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-lincmt-origin.R | 27 rxode2-5.1.8/rxode2/tests/testthat/helper-lotri.R | 3 rxode2-5.1.8/rxode2/tests/testthat/helper-methods.R | 130 rxode2-5.1.8/rxode2/tests/testthat/helper-symengine-fixture.R |only rxode2-5.1.8/rxode2/tests/testthat/nmtest-pktime.rds |only rxode2-5.1.8/rxode2/tests/testthat/test-000-modelVars.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-001-sum.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-abi-subject-stride.R | 95 rxode2-5.1.8/rxode2/tests/testthat/test-activation.R | 306 rxode2-5.1.8/rxode2/tests/testthat/test-adaptive-dosing-arg-vars.R | 128 rxode2-5.1.8/rxode2/tests/testthat/test-adjoint-discrete.R | 1740 rxode2-5.1.8/rxode2/tests/testthat/test-adjoint-sens.R | 583 rxode2-5.1.8/rxode2/tests/testthat/test-alag-first-record-cov.R 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rxode2-5.1.8/rxode2/tests/testthat/test-lhs-ifelse.R | 104 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-lag-symengine.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lhs-lag.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-param.R | 29 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-str.R | 284 rxode2-5.1.8/rxode2/tests/testthat/test-linCmtMicro.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-alag-batch.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-carry-live.R | 81 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-cmt-ref.R | 10 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-delta-memo.R | 135 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-dose-time-sens.R | 98 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-dual.R | 129 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-link.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-modelvars.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-neg-depot-1275.R | 56 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-origin-limits.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-origin-sens.R | 83 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-partial-mask-ss.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-phi-analytic.R | 115 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-phi-engage.R | 80 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sens-adr-threads.R | 58 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sens-auto.R | 86 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sensH-1276.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-seq-tail.R | 114 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-solve-sens.R | 43 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-solve.R | 335 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-state-read.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-value-memo.R | 149 rxode2-5.1.8/rxode2/tests/testthat/test-llik.R | 256 rxode2-5.1.8/rxode2/tests/testthat/test-locally-constant-se.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-lock.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-logical.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-logit.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-meanProb.R | 111 rxode2-5.1.8/rxode2/tests/testthat/test-memory-growth.R | 57 rxode2-5.1.8/rxode2/tests/testthat/test-mexp-nonmem.R | 735 rxode2-5.1.8/rxode2/tests/testthat/test-missing-evid.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-mix.R | 151 rxode2-5.1.8/rxode2/tests/testthat/test-mlogit.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-model-fun-types.R |only rxode2-5.1.8/rxode2/tests/testthat/test-model-rate.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-modelargs.R | 7 rxode2-5.1.8/rxode2/tests/testthat/test-mtime.R | 61 rxode2-5.1.8/rxode2/tests/testthat/test-mu.R | 824 rxode2-5.1.8/rxode2/tests/testthat/test-mu2.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-multi.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-multisim-shared-event-oob.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-nearpd.R | 61 rxode2-5.1.8/rxode2/tests/testthat/test-nested-sim-iov-cor.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-nesting.R | 49 rxode2-5.1.8/rxode2/tests/testthat/test-nmtest.R | 356 rxode2-5.1.8/rxode2/tests/testthat/test-nodup-keep.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-nonmem-pk-time.R |only rxode2-5.1.8/rxode2/tests/testthat/test-nopred-ui.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-nsim-ind-alloc-412.R | 58 rxode2-5.1.8/rxode2/tests/testthat/test-null-assign.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-occ.R | 485 rxode2-5.1.8/rxode2/tests/testthat/test-odeToLin.R | 278 rxode2-5.1.8/rxode2/tests/testthat/test-omega-chol.R | 68 rxode2-5.1.8/rxode2/tests/testthat/test-omega-varcov.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-omegaCubeConvert.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-omegaRse.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-omp-num-threads.R | 77 rxode2-5.1.8/rxode2/tests/testthat/test-oom.R | 468 rxode2-5.1.8/rxode2/tests/testthat/test-opt-expr.R | 424 rxode2-5.1.8/rxode2/tests/testthat/test-optexpr-cse-c.R | 141 rxode2-5.1.8/rxode2/tests/testthat/test-optexpr-fixture.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-par-dop853.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-par-loader.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-par-solve.R | 189 rxode2-5.1.8/rxode2/tests/testthat/test-param-order.R | 160 rxode2-5.1.8/rxode2/tests/testthat/test-param-statements.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parse-double-sign.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parse-empty-statement.R | 117 rxode2-5.1.8/rxode2/tests/testthat/test-parse-translation-gc.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parsefuns-compile.R | 72 rxode2-5.1.8/rxode2/tests/testthat/test-parsing.R | 251 rxode2-5.1.8/rxode2/tests/testthat/test-pheno.R | 23 rxode2-5.1.8/rxode2/tests/testthat/test-pipeline.R | 49 rxode2-5.1.8/rxode2/tests/testthat/test-piping-equivalence.R |only rxode2-5.1.8/rxode2/tests/testthat/test-piping-ini.R | 181 rxode2-5.1.8/rxode2/tests/testthat/test-piping-reserved-vars.R | 84 rxode2-5.1.8/rxode2/tests/testthat/test-pkg-exported-funs.R | 618 rxode2-5.1.8/rxode2/tests/testthat/test-plogis.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-plot.R | 56 rxode2-5.1.8/rxode2/tests/testthat/test-print.R | 538 rxode2-5.1.8/rxode2/tests/testthat/test-prior-density.R | 691 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-nested.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-nwpri.R | 50 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-spec.R | 66 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-tnpri-general.R | 318 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-tnpri.R | 75 rxode2-5.1.8/rxode2/tests/testthat/test-progress.R |only rxode2-5.1.8/rxode2/tests/testthat/test-random.R | 161 rxode2-5.1.8/rxode2/tests/testthat/test-raw.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rbind.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-recompile-model.R | 8 rxode2-5.1.8/rxode2/tests/testthat/test-resample-time-varying.R |only rxode2-5.1.8/rxode2/tests/testthat/test-resample.R | 264 rxode2-5.1.8/rxode2/tests/testthat/test-reserved-names.R |only rxode2-5.1.8/rxode2/tests/testthat/test-reset.R | 16 rxode2-5.1.8/rxode2/tests/testthat/test-rhs.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-rk-decay.R | 120 rxode2-5.1.8/rxode2/tests/testthat/test-rk-order.R | 152 rxode2-5.1.8/rxode2/tests/testthat/test-rk4.R | 25 rxode2-5.1.8/rxode2/tests/testthat/test-rx2api-parallel-error.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rxFix.R | 130 rxode2-5.1.8/rxode2/tests/testthat/test-rxMemoryEstimate.R | 256 rxode2-5.1.8/rxode2/tests/testthat/test-rxRmvn.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-rxStack-factor.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-rxState.R |only rxode2-5.1.8/rxode2/tests/testthat/test-rxSumProd.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-rxUiDeparse.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-rxflag.R | 10 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-007.R | 116 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-050.R | 24 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-054.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-056.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-067.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-1211.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-1229.R | 26 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-160.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-163.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-169.R | 29 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-178.R | 8 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-213.R | 88 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-299.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-349.R | 42 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-375.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-393.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-410.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-430.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-431.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-445.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-449.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-450.R | 127 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-468.R | 134 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-982.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-rxpre-cache-key.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-rxs-function-cache.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-rxs.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-rxsolve-ui-dispatch.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-rxui-ctl.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-s3-delayed-register.R | 37 rxode2-5.1.8/rxode2/tests/testthat/test-safeZero.R | 118 rxode2-5.1.8/rxode2/tests/testthat/test-scale.R | 136 rxode2-5.1.8/rxode2/tests/testthat/test-seed-threads.R |only rxode2-5.1.8/rxode2/tests/testthat/test-sens3.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-seq.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-serialize.R | 168 rxode2-5.1.8/rxode2/tests/testthat/test-sigdig-tol.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-sigma-hom-et-1341.R | 38 rxode2-5.1.8/rxode2/tests/testthat/test-sigma-one-obs-1364.R |only rxode2-5.1.8/rxode2/tests/testthat/test-sim-err-670.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-sim-zeros.R | 67 rxode2-5.1.8/rxode2/tests/testthat/test-solComp.R | 4225 +- rxode2-5.1.8/rxode2/tests/testthat/test-solve-warn-id.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-solver-basic.R | 57 rxode2-5.1.8/rxode2/tests/testthat/test-sortids-throttle.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-ss-extra-dose-duration.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-dur.R | 115 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-f.R | 100 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-lag.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-rate.R | 117 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-sort.R | 9 rxode2-5.1.8/rxode2/tests/testthat/test-statePropDf.R | 169 rxode2-5.1.8/rxode2/tests/testthat/test-steady-state.R | 89 rxode2-5.1.8/rxode2/tests/testthat/test-sticky-vars.R | 32 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-constants-downstream.R | 87 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-constants.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-rxq-string.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-second-derivative.R |only rxode2-5.1.8/rxode2/tests/testthat/test-symengine-simplify.R | 33 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-translate-fixture-toSE.R |only rxode2-5.1.8/rxode2/tests/testthat/test-symengine-translate-fixture.R | 141 rxode2-5.1.8/rxode2/tests/testthat/test-symmetric.R | 43 rxode2-5.1.8/rxode2/tests/testthat/test-symplectic-solvers.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-tad-infusion-after-bolus.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-tad.R | 1637 rxode2-5.1.8/rxode2/tests/testthat/test-theta-eta.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-tied-modeled-rate-dur.R | 45 rxode2-5.1.8/rxode2/tests/testthat/test-tlast-rxS.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-tolFactor.R | 21 rxode2-5.1.8/rxode2/tests/testthat/test-transit.R | 13 rxode2-5.1.8/rxode2/tests/testthat/test-tvcov-modeled-dur.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model-c.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model-scope.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-search-list.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf.R | 545 rxode2-5.1.8/rxode2/tests/testthat/test-ui-assembled.R | 189 rxode2-5.1.8/rxode2/tests/testthat/test-ui-assert.R | 337 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rxode2-5.1.8/rxode2/tests/testthat/test-ui-model.R | 50 rxode2-5.1.8/rxode2/tests/testthat/test-ui-modelExtract.R | 94 rxode2-5.1.8/rxode2/tests/testthat/test-ui-modelName.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-ui-multiple-endpoint.R | 81 rxode2-5.1.8/rxode2/tests/testthat/test-ui-mv.R | 53 rxode2-5.1.8/rxode2/tests/testthat/test-ui-piping-single-endpoint.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-piping.R | 1550 rxode2-5.1.8/rxode2/tests/testthat/test-ui-pred-err.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-promote.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-props.R | 128 rxode2-5.1.8/rxode2/tests/testthat/test-ui-rename.R | 67 rxode2-5.1.8/rxode2/tests/testthat/test-ui-simulation.R | 233 rxode2-5.1.8/rxode2/tests/testthat/test-ui-single-theta.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-solve.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-ui.R | 595 rxode2-5.1.8/rxode2/tests/testthat/test-unload.R |only rxode2-5.1.8/rxode2/tests/testthat/test-yeojohnson-derivative.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-zzzz-plot.R | 33 rxode2-5.1.8/rxode2/tests/testthat/test-zzzz-rxUse.R | 10 629 files changed, 65681 insertions(+), 36415 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level". Messages are signalled as classed R conditions, so that calling code can decide how serious a situation is, rather than the function which detects it having to be told in advance.
Author: Jon Clayden [aut, cre]
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.3.1 dated 2025-03-29 and 2.0.0 dated 2026-10-13
reportr-1.3.1/reportr/R/reportr.R |only reportr-1.3.1/reportr/man/reportr.Rd |only reportr-2.0.0/reportr/DESCRIPTION | 17 reportr-2.0.0/reportr/MD5 | 32 + reportr-2.0.0/reportr/NAMESPACE | 10 reportr-2.0.0/reportr/NEWS | 95 ++++ reportr-2.0.0/reportr/R/00_constants.R | 10 reportr-2.0.0/reportr/R/conditions.R |only reportr-2.0.0/reportr/R/fallback.R |only reportr-2.0.0/reportr/R/handlers.R |only reportr-2.0.0/reportr/R/render.R |only reportr-2.0.0/reportr/R/report.R |only reportr-2.0.0/reportr/R/reportr-package.R |only reportr-2.0.0/reportr/README.md | 316 +++++++++++---- reportr-2.0.0/reportr/inst/tinytest/test-10-ask.R | 45 +- reportr-2.0.0/reportr/inst/tinytest/test-20-conditions.R |only reportr-2.0.0/reportr/inst/tinytest/test-25-fallback.R |only reportr-2.0.0/reportr/inst/tinytest/test-30-reportAs.R |only reportr-2.0.0/reportr/inst/tinytest/test-35-handlers.R |only reportr-2.0.0/reportr/inst/tinytest/test-40-targets.R |only reportr-2.0.0/reportr/man/fallback.Rd |only reportr-2.0.0/reportr/man/handlers.Rd |only reportr-2.0.0/reportr/man/report.Rd |only reportr-2.0.0/reportr/man/reportr-package.Rd |only reportr-2.0.0/reportr/man/reportrCondition.Rd |only reportr-2.0.0/reportr/man/setOutputLevel.Rd |only reportr-2.0.0/reportr/man/targets.Rd |only 27 files changed, 429 insertions(+), 96 deletions(-)
Title: Data Envelopment Analysis for Pollution-Generating Technologies
Description: Nonparametric efficiency analysis for pollution-generating
technologies under the materials-balance principle. Implements the
weak-G-disposability technology of Hampf and Rodseth (2015)
<doi:10.1016/j.eneco.2015.04.001>, scored by the minimal-emission
programme of Rodseth (2025) <doi:10.1007/s11123-025-00768-0> with
its directional representation and five-component decomposition,
the by-production intersection
technology of Murty, Russell and Levkoff (2012)
<doi:10.1016/j.jeem.2012.02.005>, the materials-balance cost model of
Coelli, Lauwers and Van Huylenbroeck (2007)
<doi:10.1007/s11123-007-0052-8> and a weak-disposability reference
model, with a pre-estimation audit of every materials-balance
account, metafrontier decompositions, bad-output shadow prices,
marginal abatement cost curves, a cross-axiom comparison harness, a
global Malmquist-Luenberger productivity index and subsampling
sensitivity intervals. Estimators are solved with 'lpSolveAPI'.
Author: Erik Enstad [aut, cre]
Maintainer: Erik Enstad <erik.enstad@nhh.no>
Diff between pgt versions 0.7.0 dated 2026-09-22 and 0.7.1 dated 2026-10-13
DESCRIPTION | 16 +- MD5 | 84 +++++----- NEWS.md | 155 +++++++++++++++++++ R/boot.R | 29 ++- R/compare_models.R | 31 +++ R/data.R | 17 +- R/decompose.R | 24 ++- R/lp_solvers.R | 251 +++++++++++++++++++++++++------ R/ml_index.R | 52 ++++-- R/pgt.R | 121 ++++++++++----- README.md | 14 + inst/doc/comparing-axioms.Rmd | 16 +- inst/doc/comparing-axioms.html | 26 +-- inst/doc/introduction.Rmd | 19 +- inst/doc/introduction.html | 63 ++++--- inst/doc/models.Rmd | 83 +++++++--- inst/doc/models.html | 100 +++++++++--- inst/doc/productivity.R | 13 + inst/doc/productivity.Rmd | 87 +++++++---- inst/doc/productivity.html | 142 ++++++++++++------ inst/doc/replication.R | 35 ++-- inst/doc/replication.Rmd | 108 +++++++------ inst/doc/replication.html | 268 ++++++++++++++++++---------------- inst/simulations/coverage-reps.csv |only inst/simulations/coverage-results.csv | 16 +- inst/simulations/coverage.R | 156 ++++++++++++++----- man/boot_pgt.Rd | 29 ++- man/compare_models.Rd | 9 + man/pgt.Rd | 112 +++++++++----- man/pgt_decompose.Rd | 24 ++- man/pgt_ml.Rd | 45 +++-- man/pigfarms.Rd | 13 + man/uscoal.Rd | 4 tests/testthat/test-byprod.R | 6 tests/testthat/test-compare.R | 17 ++ tests/testthat/test-fdmo.R | 46 +++++ tests/testthat/test-pigfarms.R | 59 +++++-- tests/testthat/test-scaling.R |only tests/testthat/test-wgd.R | 15 + vignettes/comparing-axioms.Rmd | 16 +- vignettes/introduction.Rmd | 19 +- vignettes/models.Rmd | 83 +++++++--- vignettes/productivity.Rmd | 87 +++++++---- vignettes/replication.Rmd | 108 +++++++------ 44 files changed, 1823 insertions(+), 795 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.2 dated 2026-08-31 and 1.1.0 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- src/algebra.cpp | 3 +++ src/identification.cpp | 16 ++++++++++++---- src/identification.h | 2 ++ src/random.cpp | 16 +++++++++++++--- src/random.h | 1 + tests/testthat/test-one-option.R | 2 +- 8 files changed, 42 insertions(+), 18 deletions(-)
Title: Inequality Measures for Weighted Data
Description: Computes inequality measures of a given variable taking into account weights. Suitable for ratio, interval and ordered scale. Includes measures developed by Gini, Theil, Leti, Palma ratio, 20:20 ratio, Allison and Foster, Jenkins, Cowell and Flechaire, Abul Naga and Yalcin, Apouey, Blair and Lacy. Bootstrap provides distribution of inequality measures enabling significance tests.
Author: Sebastian Wojcik [aut, cre] ,
Agnieszka Giemza [aut],
Jaroslaw Napora [aut]
Maintainer: Sebastian Wojcik <S.Wojcik@stat.gov.pl>
Diff between wINEQ versions 1.2.2 dated 2026-04-23 and 1.2.3 dated 2026-10-13
DESCRIPTION | 10 MD5 | 47 +-- NAMESPACE | 7 NEWS.md | 237 ++++++++------- R/inequalityMeasure.R | 660 ++++++++++++++++++++++++++++++++++---------- R/inequalityMeasureBoot.R | 574 ++++++++++++++++++++------------------ data/Tourism.rda |binary man/Abul_Naga_and_Yalcin.Rd | 17 - man/Allison_and_Foster.Rd | 21 - man/Apouey.Rd | 13 man/Atkinson.Rd | 8 man/Blair_Lacy.Rd | 17 - man/Bonferroni.Rd |only man/Gini.Rd | 6 man/Hoover.Rd | 1 man/Jenkins.Rd | 1 man/Kakwani.Rd |only man/Leti.Rd | 14 man/LowerSum.Rd | 1 man/Rosenbluth.Rd |only man/SST.Rd |only man/Theil_T.Rd | 2 man/Wolfson.Rd |only man/Zenga.Rd |only man/figures |only man/ineq_weighted.Rd | 20 + man/ineq_weighted_boot.Rd | 18 + man/medianf.Rd | 2 28 files changed, 1067 insertions(+), 609 deletions(-)
Title: Time Series Forecasting Using Nearest Neighbors
Description: Allows forecasting time series using nearest neighbors regression
Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
Rivera (2019) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is univariate and autoregressive, that is, it is only based
on the observations of the time series. The nearest neighbors used in a
prediction can be consulted and plotted.
Author: Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfknn versions 0.6.0 dated 2023-12-20 and 0.7.1 dated 2026-10-13
DESCRIPTION | 14 ++++++------ MD5 | 28 ++++++++++++------------- NEWS.md | 5 +++- R/forecasting.R | 37 +++++++++++++++++----------------- R/knn.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tsfknn.html | 26 +++++++++++------------ man/knn_examples.Rd | 17 +++++++-------- man/knn_forecasting.Rd | 2 - man/n_training_examples.Rd | 4 +-- man/nearest_neighbors.Rd | 4 +-- man/tsfknn-package.Rd | 7 +++++- src/code.cpp | 6 ++--- tests/testthat/test_knn_forecasting.R | 14 ++++++++++++ 15 files changed, 93 insertions(+), 72 deletions(-)
Title: Estimating Trend, Velocity, and Acceleration from Sea Level
Records
Description: Provides tools for analysing annual average ocean water level time series,
estimating mean sea level trends, velocities, and accelerations using Singular
Spectrum Analysis (SSA). The detailed methodology for resolving mean sea level
with improved temporal resolution follows Watson (2018)
"Improved Techniques to Estimate Mean Sea Level, Velocity and Acceleration from
Long Ocean Water Level Time Series to Augment Sea Level (and Climate Change)
Research" <https://unsworks.unsw.edu.au/entities/publication/5e835c87-aa0a-4457-807e-29d354e91d45>.
Additional methodological developments and applications are described in Watson (2020)
"Status of Mean Sea Level Rise around the USA" <doi:10.3390/geohazards2020005>
and Watson and Lim (2020) "An Update on the Status of Mean Sea Level Rise around
the Korean Peninsula" <doi:10.3390/atmos11111153>. Includes multiple gap-filling
methods for incomplete records, diagnostic tools for inspecting SSA components,
and plotting functions for g [...truncated...]
Author: Phil Watson [aut, cre]
Maintainer: Phil Watson <philwatson.slr@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2019-08-07
Diff between TrendSLR versions 1.0 dated 2019-08-07 and 2.0.0 dated 2026-10-13
DESCRIPTION | 55 +++++++++++++---------- MD5 | 40 ++++++++--------- NAMESPACE | 1 R/balt-data.R | 4 - R/check.decomp.R | 42 +++++++++-------- R/custom.trend.R | 34 ++++++-------- R/msl-name.R | 4 + R/msl.fileplot.R | 29 ++++++------ R/msl.screenplot.R | 16 ++++-- R/msltrend.R | 40 ++++++++--------- man/Balt.Rd | 10 ++-- man/TrendSLR.Rd | 104 +++++++++++++++++++++++--------------------- man/check.decomp.Rd | 93 ++++++++++++++++++++++----------------- man/custom.trend.Rd | 115 ++++++++++++++++++++++++++----------------------- man/gap.fillview.Rd | 37 +++++++-------- man/msl.fileplot.Rd | 35 +++++++++----- man/msl.screenplot.Rd | 23 +++++---- man/msl.trend.Rd | 117 ++++++++++++++++++++++++++------------------------ man/s.Rd | 4 + man/summary.Rd | 5 ++ man/t.Rd | 4 + 21 files changed, 445 insertions(+), 367 deletions(-)
Title: ROC-Based Methods for Comparing Survival Distributions with
Right, Left, and Doubly Censored Data
Description: Implements nonparametric and semiparametric methods for comparing two survival distributions under non-proportional hazards (non-PH) with right, left, or doubly censored data. The methods are based on the Receiver Operating Characteristic (ROC) curve length and its kernel-based estimate (Bantis et al. (2021) <doi:10.1002/sim.8869>) and the overlap coefficient (OVL) and its kernel-based estimate (Schmid and Schmidt (2006) <doi:10.1016/j.csda.2005.01.014>), as well as a new joint inference approach involving both the kernel-based ROC length and the kernel-based OVL. These methods do not require prior knowledge of the underlying non-PH pattern. The methods also accommodate the "last is censored" phenomenon for right-censored data by using flexible parametric approaches only for the portion of the tail of the distribution that corresponds to time values beyond the last observed event (see also Bantis et al. (2017) <doi:10.1002/sim.7394>). The analogous "first is censored" [...truncated...]
Author: Mohammod Mahmudur Rahman [aut, cre],
Leonidas Bantis [aut]
Maintainer: Mohammod Mahmudur Rahman <mahmudur.asif13@gmail.com>
Diff between ROCsurvcomp versions 0.1.2 dated 2026-05-11 and 0.1.3 dated 2026-10-13
DESCRIPTION | 12 ++--- MD5 | 12 ++--- NAMESPACE | 50 ++++++++++++---------- NEWS.md | 6 ++ inst/doc/ROCsurvcomp.Rmd | 2 inst/doc/ROCsurvcomp.html | 101 ++++++++++++++++++++++------------------------ vignettes/ROCsurvcomp.Rmd | 2 7 files changed, 97 insertions(+), 88 deletions(-)
Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>).
ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information
about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys.
More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>.
The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] ,
Luana Francesconi [aut],
Alice Musina [aut],
Luca Di Nuzzo [aut],
Gabriele Gheza [aut],
Chiara Pistocchi [aut],
Juri Nascimbene [aut],
Pier Luigi Nimis [aut],
Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Diff between ritalic versions 0.13.0 dated 2026-10-12 and 0.13.1 dated 2026-10-13
DESCRIPTION | 6 +-- MD5 | 4 +- tests/testthat/test_api_utils.R | 66 ++++++++++++++++++++++++---------------- 3 files changed, 45 insertions(+), 31 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.5 dated 2026-10-13 and 1.0.6 dated 2026-10-13
DESCRIPTION | 6 ++-- MD5 | 6 ++-- R/drw.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++------- man/drw.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++----- 4 files changed, 127 insertions(+), 21 deletions(-)
Title: Restricted Bridge Estimation
Description: Implements bridge regression with linear coefficient restrictions
using the local quadratic approximation described by Yuzbasi, Arashi and
Akdeniz (2021) <doi:10.1007/s00500-021-05763-9>. Provides coefficient paths,
cross-validation, prediction and coefficient extraction for restricted and
unrestricted linear models.
Author: Bahadir Yuzbasi [aut, cre],
Mohammad Arashi [aut],
Fikri Akdeniz [aut],
Jerome Friedman [ctb] ,
Trevor Hastie [ctb] ,
Robert Tibshirani [ctb]
Maintainer: Bahadir Yuzbasi <b.yzb@hotmail.com>
Diff between rbridge versions 1.0.3 dated 2026-10-11 and 1.0.4 dated 2026-10-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 11 ++++++++++- README.md | 18 ++++++++++++------ inst/doc/getting-started.html | 2 +- src/Main_functions.cpp | 1 - src/Makevars | 2 ++ src/Makevars.win | 2 ++ 8 files changed, 38 insertions(+), 20 deletions(-)
Title: Multilevel Unanchored Meta-Regression for Indirect Treatment
Comparisons
Description: Bayesian multilevel unanchored meta-regression (ML-UMR) for
indirect treatment comparisons using individual patient data (IPD) and
aggregate data (AgD). Implements shared prognostic factor assumption
(SPFA) and relaxed SPFA models for binary, continuous, count, and
time-to-event (survival) outcomes via 'Stan', including parametric and
flexible M-spline survival baselines. Also provides a one-arm simulated
treatment comparison (STC) via comparator-population G-computation and
naive unadjusted benchmarks. ML-UMR is an adaptation of the ML-NMR
methodology (Phillippo et al. 2020,
<doi:10.1111/rssa.12579>) implemented in the 'multinma' package
(GPL-3) to the unanchored two-trial case. The public API uses familiar
names for data setup, integration and effect summaries, but ML-NMR and
ML-UMR specifications and fitted objects are not interchangeable because
their evidence structures and models differ.
Author: Ahmad Sofi-Mahmudi [aut, cre] ,
Conor Chandler [aut]
Maintainer: Ahmad Sofi-Mahmudi <a.sofimahmudi@gmail.com>
Diff between mlumr versions 0.1.0 dated 2026-05-20 and 0.2.0 dated 2026-10-13
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mlumr-0.1.0/mlumr/man/dot-bound_unit_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-bounded_wald_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-check_required_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstan_available.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_cache_root.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_compile_dir.Rd |only mlumr-0.1.0/mlumr/man/dot-comparison_names.Rd |only mlumr-0.1.0/mlumr/man/dot-compute_mean_lp.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_effect_choices.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_eta.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_profiles.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_count.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_value.Rd |only mlumr-0.1.0/mlumr/man/dot-drop_missing_rows.Rd |only mlumr-0.1.0/mlumr/man/dot-ensure_positive_definite_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-finite_numeric_values.Rd |only mlumr-0.1.0/mlumr/man/dot-generate_copula_uniforms.Rd 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mlumr-0.1.0/mlumr/man/dot-require_draw_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-rescale_prior_beta.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_integration_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_mlumr_engine.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_broadcast_label.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_family_label.Rd |only mlumr-0.1.0/mlumr/man/dot-safe_positive_ratio.Rd |only mlumr-0.1.0/mlumr/man/dot-sqrt_variance.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_agd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_ipd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_agd_mean_newdata.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_comparator_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_index_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_comparator_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_formula.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_glm_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_model_matrix.Rd 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mlumr-0.2.0/mlumr/vignettes/data-preparation.Rmd | 440 - mlumr-0.2.0/mlumr/vignettes/fitting-and-diagnostics.html.asis |only mlumr-0.2.0/mlumr/vignettes/introduction.Rmd | 231 - mlumr-0.2.0/mlumr/vignettes/subgroup-identification.html.asis |only mlumr-0.2.0/mlumr/vignettes/survival-outcomes.html.asis |only 361 files changed, 19714 insertions(+), 8372 deletions(-)
Title: Hierarchical Risk Clustering Portfolio Allocation Strategies
Description: Machine learning hierarchical risk clustering portfolio allocation strategies.
The implemented methods are:
Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
Hierarchical clustering-based asset allocation (Raffinot, 2017)
<DOI: 10.3905/jpm.2018.44.2.089>.
Hierarchical equal risk contribution portfolio (Raffinot, 2018)
<DOI: 10.2139/ssrn.3237540>.
A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
<https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Hierarchical Risk Budgeting (Koumou, 2024) <DOI: 10.3905/jfds.2024.1.156>.
Author: Carlos Trucios [aut, cre] ,
Moon Jun Kwon [aut],
Sao Paulo Research Foundation , grants 2022/09122-0,
2025/06131-7 and 2025/08502-2 [fnd],
Programa de Incentivo a Novos Docentes da UNICAMP , grant 2525/23
[fnd]
Maintainer: Carlos Trucios <ctrucios@unicamp.br>
Diff between HierPortfolios versions 1.0.2 dated 2025-09-12 and 1.1.0 dated 2026-10-13
DESCRIPTION | 16 +++++++++------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + R/DHRP_Portfolio.R | 4 ++-- R/HCAA_Portfolio.R | 4 ++-- R/HERC_Portfolio.R | 18 +++++++----------- R/HRB_Portfolio.R |only R/HRP_Portfolio.R | 4 ++-- man/DHRP_Portfolio.Rd | 4 ++-- man/HCAA_Portfolio.Rd | 4 ++-- man/HERC_Portfolio.Rd | 4 ++-- man/HRB_Portfolio.Rd |only man/HRP_Portfolio.Rd | 4 ++-- 13 files changed, 43 insertions(+), 42 deletions(-)
More information about HierPortfolios at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue (202 [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.5 dated 2026-09-25 and 1.5.6 dated 2026-10-13
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS | 4 ++++ R/scraping_games_acb.R | 2 +- inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- inst/doc/BAwiR_sc.html | 4 ++-- 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.9 dated 2026-08-28 and 0.5.0 dated 2026-10-13
DESCRIPTION | 11 MD5 | 34 - NAMESPACE | 10 NEWS.md | 390 ++++++------ R/cms_download_native.R | 9 R/cms_download_subset.r | 983 +++++++++++++++---------------- R/import.r | 2 README.md | 6 build/vignette.rds |binary inst/doc/blosc.html | 5 inst/doc/glossary.html | 4 inst/doc/product-info.html | 7 inst/doc/proxy.html | 11 inst/doc/translate.html | 7 man/cms_native_s3.Rd | 1 man/figures/README-download-subset-1.png |binary tests/testthat/test_login.r | 2 tests/testthat/test_subset.r | 442 +++++++------ 18 files changed, 981 insertions(+), 943 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Citations are:
* Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
* Luis F.S. Castro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and Timothy Charles Bates (2026). umx version 4.5: Extending Twin and Path-Based SEM in R with CLPM, MR-DoC, Definition Variables, Onyx Integration, and Censored Distributions. Twin Research and Human Genetics, 1-6. <doi:10.1017/thg.2026.10056>.
Author: Timothy C. Bates [aut, cre] ,
Luis De Araujo [ctb],
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.80.0 dated 2026-10-11 and 4.80.1 dated 2026-10-13
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Title: Post-Linkage Data Analysis
Description: Provides a suite of statistical tools for post-linkage data analysis (PLDA), designed to account for record linkage errors in downstream modeling. The package implements a familiar, formula-based regression interface that adjusts for linkage uncertainty, accommodating workflows where direct access to unlinked primary files is restricted. It consolidates diverse adjustment methodologies, all of which support generalized linear models (linear, logistic, Poisson, and Gamma). These methodologies include weighting approaches (Chambers (2009) <https://hdl.handle.net/10779/uow.27788247>; Chambers et al. (2023) <doi:10.1002/wics.1596>), mixture modeling (Slawski et al. (2025) <doi:10.1093/jrsssa/qnae083>), and Bayesian mixture modeling (Gutman et al. (2016) <doi:10.1002/sim.6586>). For time-to-event data, both the weighting (Vo et al. (2024) <doi:10.1002/sim.9960>) and mixture modeling approaches accommodate Cox proportional hazards models, while the Bayesian appr [...truncated...]
Author: Priyanjali Bukke [aut, cre],
Gauri Kamat [aut],
Jiahao Cui [aut],
Roee Gutman [aut],
Martin Slawski [aut],
Zhenbang Wang [ctb],
Brady T. West [ctb],
Emanuel Ben-David [ctb],
Guoqing Diao [ctb]
Maintainer: Priyanjali Bukke <postlink.group@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2026-09-04
Diff between postlink versions 0.1.1 dated 2026-09-04 and 0.1.2 dated 2026-10-13
DESCRIPTION | 12 - MD5 | 110 ++++++------ NEWS.md | 13 + R/mixture_coxph.R | 33 ++- R/mixture_glm.R | 120 ++++++------- README.md | 16 + configure.win | 3 inst/stan/glmMixBayes_binomial.stan | 4 inst/stan/glmMixBayes_gamma.stan | 2 inst/stan/glmMixBayes_gaussian.stan | 2 inst/stan/glmMixBayes_poisson.stan | 4 inst/stan/survMixBayes_gamma.stan | 4 inst/stan/survMixBayes_weibull.stan | 4 man/adjELE.Rd | 180 ++++++++++---------- man/adjMixture.Rd | 182 ++++++++++---------- man/brfss.Rd | 106 +++++------ man/confint.coxphELE.Rd | 124 ++++++------- man/confint.coxphMixture.Rd | 142 +++++++-------- man/confint.glmELE.Rd | 82 ++++----- man/confint.glmMixture.Rd | 110 ++++++------ man/coxphELE.Rd | 192 ++++++++++----------- man/coxphMixture.Rd | 242 +++++++++++++------------- man/ctableMixture.Rd | 204 +++++++++++----------- man/glmELE.Rd | 166 +++++++++--------- man/glmMixture.Rd | 186 ++++++++++---------- man/predict.coxphELE.Rd | 140 +++++++-------- man/predict.coxphMixture.Rd | 208 +++++++++++------------ man/predict.glmELE.Rd | 132 +++++++------- man/predict.glmMixture.Rd | 160 ++++++++--------- man/print.adjELE.Rd | 78 ++++---- man/print.adjMixture.Rd | 88 ++++----- man/print.coxphELE.Rd | 116 ++++++------ man/print.coxphMixture.Rd | 122 ++++++------- man/print.glmELE.Rd | 74 ++++---- man/print.glmMixture.Rd | 92 +++++----- man/summary.coxphELE.Rd | 132 +++++++------- man/summary.coxphMixture.Rd | 148 ++++++++-------- man/summary.glmELE.Rd | 80 ++++---- man/summary.glmMixture.Rd | 108 ++++++------ man/vcov.coxphELE.Rd | 114 ++++++------ man/vcov.coxphMixture.Rd | 142 +++++++-------- man/vcov.glmELE.Rd | 74 ++++---- man/vcov.glmMixture.Rd | 94 +++++----- src/Makevars.win | 2 src/stanExports_glmMixBayes_binomial.cc | 34 +-- src/stanExports_glmMixBayes_binomial.h | 181 ++++++++++++++------ src/stanExports_glmMixBayes_gamma.cc | 34 +-- src/stanExports_glmMixBayes_gamma.h | 233 ++++++++++++++++++------- src/stanExports_glmMixBayes_gaussian.cc | 34 +-- src/stanExports_glmMixBayes_gaussian.h | 220 +++++++++++++++++------- src/stanExports_glmMixBayes_poisson.cc | 34 +-- src/stanExports_glmMixBayes_poisson.h | 181 ++++++++++++++------ src/stanExports_survMixBayes_gamma.cc | 34 +-- src/stanExports_survMixBayes_gamma.h | 273 +++++++++++++++++++++--------- src/stanExports_survMixBayes_weibull.cc | 34 +-- src/stanExports_survMixBayes_weibull.h | 287 +++++++++++++++++++++++--------- 56 files changed, 3283 insertions(+), 2643 deletions(-)
Title: One-Way Statistical Analyses
Description: Performs one-way tests of assumptions (normality and homoscedasticity),
analysis of variance, robust and nonparametric alternatives, multiple comparison
procedures, effect size estimators, confidence intervals, and descriptive summaries.
Functions are designed with a consistent interface to support reproducible and
user-friendly statistical workflows. For more details see
Howell (2010, ISBN:978-0-495-59784-1),
Zar (2014, ISBN:978-0-13-100846-5),
Hollander et al. (2014, ISBN:978-0-470-38737-5),
Montgomery (2017, ISBN:978-1-119-11347-8),
Lakens (2013) <doi:10.3389/fpsyg.2013.00863>, and
Piepho (2004) <doi:10.1198/1061860043515>.
Author: Joon-Keat Lai [aut, cre, cph]
Maintainer: Joon-Keat Lai <p10911004@gmail.com>
Diff between oneway versions 0.0.2 dated 2026-09-15 and 0.0.3 dated 2026-10-13
DESCRIPTION | 26 +++++++++--------- MD5 | 53 +++++++++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 16 +++++++++-- R/Dunn_test.R | 2 - R/Games_Howell_test.R | 4 +- R/REGWQ_test.R | 20 ++++++------- R/Scheffe_test.R |only R/Tukey_HSD_test.R | 16 ++++------- R/Tukey_Kramer_test.R | 4 +- R/anova.R | 34 +++++++++++------------ R/compact_letter_display.R | 2 - R/pairwise_comparison.R | 4 +- R/utils.R | 2 - README.md | 10 ++++++ build |only data/O_O_O.rda |binary inst |only man/Kruskal_Wallis_test.Rd | 8 ++++- man/REGWQ_test.Rd | 16 ++++------- man/Scheffe_test.Rd |only man/Tukey_HSD_test.Rd | 12 +++----- man/oneway_anova.Rd | 2 - man/oneway_art.Rd | 2 - man/pairwise_comparison.Rd | 2 - man/pairwise_contrasts.Rd |only man/simulated_data.Rd | 2 - tests/testthat/test-REGWQ_test.R | 9 ++++-- tests/testthat/test-Scheffe_test.R |only vignettes |only 30 files changed, 143 insertions(+), 105 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.2-6 dated 2026-03-06 and 1.2-7 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Bernstein.R | 40 ++++++++++++++++++++-------------------- R/formula.R | 6 +++--- R/legendre.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ tests/bugfixes.R | 12 ++++++++++++ 9 files changed, 56 insertions(+), 38 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.4 dated 2026-08-20 and 1.0.5 dated 2026-10-13
DESCRIPTION | 8 - MD5 | 6 R/drw.R | 369 ++++++++++++++++++++++++++++++++++++++++++++++-------------- man/drw.Rd | 36 +++-- 4 files changed, 313 insertions(+), 106 deletions(-)
Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.17.4. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
awPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot [aut],
Paul Brooks [aut, cre],
Andrea Visentin [aut],
Young Woong Park [aut],
and Yi-Hui Zhou [aut]
Maintainer: Paul Brooks <jpbrooks@ou.edu>
Diff between pcaL1 versions 1.5.9 dated 2025-05-03 and 1.5.10 dated 2026-10-13
ChangeLog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS | 14 ++++++++++++++ configure | 18 +++++++++--------- configure.ac | 2 +- man/pcaL1-package.Rd | 8 ++++---- src/sparsel1pca.c | 2 +- 8 files changed, 48 insertions(+), 29 deletions(-)
Title: Multipurpose Aids for R Kit
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.3 dated 2025-04-22 and 0.9.0 dated 2026-10-13
mark-0.8.3/mark/R/fct_expand_seq.R |only mark-0.8.3/mark/R/namespace.R |only mark-0.8.3/mark/tests/testthat/test-array.R |only mark-0.8.3/mark/tests/testthat/test-namespace.R |only mark-0.8.3/mark/tests/testthat/test-time-report.R |only mark-0.9.0/mark/DESCRIPTION | 52 +- mark-0.9.0/mark/MD5 | 391 +++++++++--------- mark-0.9.0/mark/NAMESPACE | 77 ++- mark-0.9.0/mark/NEWS.md | 45 ++ mark-0.9.0/mark/R/aaa.R | 48 +- mark-0.9.0/mark/R/append.R | 13 mark-0.9.0/mark/R/apply.R | 58 -- mark-0.9.0/mark/R/array.R | 21 mark-0.9.0/mark/R/base-conversion.R | 133 ++---- mark-0.9.0/mark/R/bib.R | 62 -- mark-0.9.0/mark/R/blank.R | 24 - mark-0.9.0/mark/R/boolean.R | 93 +++- mark-0.9.0/mark/R/char2fact.R | 19 mark-0.9.0/mark/R/clipboard.R | 154 +++---- mark-0.9.0/mark/R/counts.R | 36 + mark-0.9.0/mark/R/dataframes.R | 185 +++----- mark-0.9.0/mark/R/dates.R | 30 - mark-0.9.0/mark/R/depth.R | 11 mark-0.9.0/mark/R/description.R | 97 ++-- mark-0.9.0/mark/R/detail.R | 34 - mark-0.9.0/mark/R/diff-time.R | 133 +++--- mark-0.9.0/mark/R/directory.R | 178 ++++---- mark-0.9.0/mark/R/environments.R | 55 +- mark-0.9.0/mark/R/expand.R | 98 ++-- mark-0.9.0/mark/R/fact.R | 71 +-- mark-0.9.0/mark/R/fct-expand-seq.R |only mark-0.9.0/mark/R/file.R | 30 - 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Title: Implement Fleming-Viot-Dependent Dirichlet Processes
Description: A Bayesian Nonparametric model for the study of time-evolving frequencies, which has become renowned in the study of population genetics.
The model consists of a Hidden Markov Model (HMM) in which the latent signal is a distribution-valued stochastic process that takes the form of a finite mixture of Dirichlet Processes, indexed by vectors that count how many times each value is observed in the population.
The package implements methodologies presented in Ascolani, Lijoi and Ruggiero (2021) <doi:10.1214/20-BA1206> and Ascolani, Lijoi and Ruggiero (2023) <doi:10.3150/22-BEJ1504> that make it possible to study the process at the time of data collection or to predict its evolution in future or in the past.
The package itself is described in Ascolani, Damato and Ruggiero (2024) <doi:10.1089/cmb.2024.0600>.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between FVDDPpkg versions 0.1.2 dated 2024-07-09 and 0.1.3 dated 2026-10-13
DESCRIPTION | 11 - MD5 | 13 - README.md | 58 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/FVDDPpkg.html | 489 +++++++++++++++++++++++++------------------------ src/C++FVDDP.cpp | 2 8 files changed, 290 insertions(+), 283 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.5 dated 2020-07-17 and 0.3.6 dated 2026-10-13
ChangeLog | 4 DESCRIPTION | 11 LICENSE | 2 MD5 | 54 - NAMESPACE | 6 NEWS.md | 4 R/configr.R | 1 R/configtype.R | 8 R/parse.R | 16 R/read.R | 14 R/utils.R | 2 README.md | 69 -- build/vignette.rds |binary inst/doc/configr.R | 22 inst/doc/configr.Rmd | 2 inst/doc/configr.html | 1567 ++++++++++++++++++++++++------------------------ inst/doc/filetypes.R | 2 inst/doc/filetypes.Rmd | 2 inst/doc/filetypes.html | 572 +++++++++-------- man/configr.Rd | 1 man/is.ini.file.Rd | 4 man/is.json.file.Rd | 4 man/is.toml.file.Rd | 4 man/is.yaml.file.Rd | 4 man/parse.extra.Rd | 16 man/read.config.Rd | 14 vignettes/configr.Rmd | 2 vignettes/filetypes.Rmd | 2 28 files changed, 1228 insertions(+), 1181 deletions(-)
Title: Mixed Temporal Vectors and Operations
Description: Flexible time classes for time series analysis and forecasting with
mixed temporal granularities. Supports linear and cyclical time
representations in discrete and continuous forms, with timezone support,
across multiple calendar systems including Gregorian and ISO week date
calendars. Time points are stored numerically relative to a chronon; an
atomic time granule defined by time units of a calendar. Calendrical
arithmetic enables conversion between time granules (e.g. days to months)
and calendar systems. Multi-unit arithmetic allows for temporal analysis
with other granules of common calendars (e.g. fortnights are 2-week units).
Time vectors of different granularities (e.g. monthly and quarterly) can be
combined in a single vector, making 'mixtime' ideal for data that changes
observation frequency over time or requires temporal reconciliation across
scales. The package is extensible, allowing users to define custom calendars
that build upon civil and astronomical time systems.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Cynthia Huang [ctb] ,
Rob Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between mixtime versions 0.3.0 dated 2026-08-24 and 0.4.0 dated 2026-10-12
mixtime-0.3.0/mixtime/man/chronon_common.Rd |only mixtime-0.4.0/mixtime/DESCRIPTION | 20 mixtime-0.4.0/mixtime/MD5 | 151 +- mixtime-0.4.0/mixtime/NAMESPACE | 17 mixtime-0.4.0/mixtime/NEWS.md | 151 ++ mixtime-0.4.0/mixtime/R/00_classes.R | 2 mixtime-0.4.0/mixtime/R/00_utils.R | 4 mixtime-0.4.0/mixtime/R/01_calendar.R | 2 mixtime-0.4.0/mixtime/R/01_chronon_cardinality.R | 50 mixtime-0.4.0/mixtime/R/01_chronon_divmod.R | 3 mixtime-0.4.0/mixtime/R/01_chronon_format.R | 16 mixtime-0.4.0/mixtime/R/01_labels.R | 4 mixtime-0.4.0/mixtime/R/arithmetic.R | 315 ++++- mixtime-0.4.0/mixtime/R/cal0_time_civil.R | 97 + mixtime-0.4.0/mixtime/R/cal0_time_lunar.R | 6 mixtime-0.4.0/mixtime/R/cal0_time_solar.R | 8 mixtime-0.4.0/mixtime/R/cal_gregorian.R | 28 mixtime-0.4.0/mixtime/R/cal_isoweek.R | 27 mixtime-0.4.0/mixtime/R/cal_sym454.R | 32 mixtime-0.4.0/mixtime/R/chronon_common.R | 134 +- mixtime-0.4.0/mixtime/R/chronon_context.R |only mixtime-0.4.0/mixtime/R/chronon_convert.R | 140 +- mixtime-0.4.0/mixtime/R/clamp.R | 108 +- mixtime-0.4.0/mixtime/R/coerce.R | 13 mixtime-0.4.0/mixtime/R/compare.R | 533 ++++++++-- mixtime-0.4.0/mixtime/R/components.R | 6 mixtime-0.4.0/mixtime/R/compose.R | 14 mixtime-0.4.0/mixtime/R/duration.R | 14 mixtime-0.4.0/mixtime/R/format.R | 17 mixtime-0.4.0/mixtime/R/graph_dispatch.R | 113 +- mixtime-0.4.0/mixtime/R/mixtime-package.R | 7 mixtime-0.4.0/mixtime/R/mixtime.R | 52 mixtime-0.4.0/mixtime/R/parse.R | 20 mixtime-0.4.0/mixtime/R/predicates.R | 16 mixtime-0.4.0/mixtime/R/round.R | 29 mixtime-0.4.0/mixtime/R/sequence.R | 336 +++--- mixtime-0.4.0/mixtime/R/time.R | 110 -- mixtime-0.4.0/mixtime/R/time_chronon.R | 85 + mixtime-0.4.0/mixtime/R/time_granule.R | 36 mixtime-0.4.0/mixtime/R/time_parts.R | 34 mixtime-0.4.0/mixtime/R/timezone.R | 334 +++++- mixtime-0.4.0/mixtime/R/tsbl-compat.R | 18 mixtime-0.4.0/mixtime/R/vctrs.R | 17 mixtime-0.4.0/mixtime/README.md | 4 mixtime-0.4.0/mixtime/build/vignette.rds |binary mixtime-0.4.0/mixtime/inst/doc/invalid-time-points.R |only mixtime-0.4.0/mixtime/inst/doc/invalid-time-points.Rmd |only mixtime-0.4.0/mixtime/inst/doc/invalid-time-points.html |only mixtime-0.4.0/mixtime/inst/doc/time-format-strings.html | 22 mixtime-0.4.0/mixtime/man/allen-interval-algebra.Rd |only mixtime-0.4.0/mixtime/man/calendar_time_lunar.Rd | 5 mixtime-0.4.0/mixtime/man/chronon_cardinality_fixed.Rd | 18 mixtime-0.4.0/mixtime/man/chronon_glb.Rd |only mixtime-0.4.0/mixtime/man/class_mixtime.Rd | 2 mixtime-0.4.0/mixtime/man/duration.Rd | 4 mixtime-0.4.0/mixtime/man/mixtime-package.Rd | 17 mixtime-0.4.0/mixtime/man/mt_cyclical-compare.Rd | 6 mixtime-0.4.0/mixtime/man/mt_linear-compare.Rd | 21 mixtime-0.4.0/mixtime/man/new_mixtime.Rd | 2 mixtime-0.4.0/mixtime/man/new_time.Rd | 53 mixtime-0.4.0/mixtime/man/seq.mixtime.Rd | 53 mixtime-0.4.0/mixtime/man/time_chronon.Rd | 17 mixtime-0.4.0/mixtime/man/time_shift.Rd |only mixtime-0.4.0/mixtime/src/timezone-info.cpp | 185 +++ mixtime-0.4.0/mixtime/src/timezone-utils.h | 7 mixtime-0.4.0/mixtime/tests/testthat/test-allen.R |only mixtime-0.4.0/mixtime/tests/testthat/test-arithmetic.R | 415 +++++++ mixtime-0.4.0/mixtime/tests/testthat/test-chronon-cardinality-fixed.R | 25 mixtime-0.4.0/mixtime/tests/testthat/test-chronon-glb.R |only mixtime-0.4.0/mixtime/tests/testthat/test-compare-span-instant.R |only mixtime-0.4.0/mixtime/tests/testthat/test-divmod.R | 35 mixtime-0.4.0/mixtime/tests/testthat/test-duration.R | 57 + mixtime-0.4.0/mixtime/tests/testthat/test-format.R | 44 mixtime-0.4.0/mixtime/tests/testthat/test-graph_dispatch.R |only mixtime-0.4.0/mixtime/tests/testthat/test-math.R | 18 mixtime-0.4.0/mixtime/tests/testthat/test-mixtime.R | 90 + mixtime-0.4.0/mixtime/tests/testthat/test-nesting.R | 22 mixtime-0.4.0/mixtime/tests/testthat/test-parse.R | 113 ++ mixtime-0.4.0/mixtime/tests/testthat/test-seq.R | 312 +++++ mixtime-0.4.0/mixtime/tests/testthat/test-time-solar.R | 44 mixtime-0.4.0/mixtime/tests/testthat/test-timezones.R | 459 ++++++++ mixtime-0.4.0/mixtime/tests/testthat/test-tsibble.R | 13 mixtime-0.4.0/mixtime/vignettes/invalid-time-points.Rmd |only 83 files changed, 4246 insertions(+), 936 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Ian Kopacka [ctb],
Klemens Fuchs [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.99 dated 2026-10-01 and 3.0.0 dated 2026-10-12
epiR-2.0.99/epiR/inst/doc/epiR_descriptive_epi.R |only epiR-2.0.99/epiR/inst/doc/epiR_descriptive_epi.Rmd |only epiR-2.0.99/epiR/inst/doc/epiR_descriptive_epi.html |only epiR-2.0.99/epiR/inst/doc/epiR_diagnostic_tests.R |only epiR-2.0.99/epiR/inst/doc/epiR_diagnostic_tests.Rmd |only epiR-2.0.99/epiR/inst/doc/epiR_diagnostic_tests.html |only epiR-2.0.99/epiR/inst/doc/epiR_measures_of_assoc.R |only epiR-2.0.99/epiR/inst/doc/epiR_measures_of_assoc.Rmd |only epiR-2.0.99/epiR/inst/doc/epiR_measures_of_assoc.html |only epiR-2.0.99/epiR/inst/doc/epiR_sample_size.R |only epiR-2.0.99/epiR/inst/doc/epiR_sample_size.Rmd |only epiR-2.0.99/epiR/inst/doc/epiR_sample_size.html |only epiR-2.0.99/epiR/inst/doc/epiR_surveillance.R |only epiR-2.0.99/epiR/inst/doc/epiR_surveillance.Rmd |only epiR-2.0.99/epiR/inst/doc/epiR_surveillance.html |only epiR-2.0.99/epiR/vignettes/epiR_descriptive_epi.Rmd |only epiR-2.0.99/epiR/vignettes/epiR_descriptive_epi.bib |only epiR-2.0.99/epiR/vignettes/epiR_diagnostic_tests.Rmd |only epiR-2.0.99/epiR/vignettes/epiR_diagnostic_tests.bib |only epiR-2.0.99/epiR/vignettes/epiR_measures_of_assoc.Rmd |only epiR-2.0.99/epiR/vignettes/epiR_measures_of_assoc.bib |only epiR-2.0.99/epiR/vignettes/epiR_sample_size.Rmd |only epiR-2.0.99/epiR/vignettes/epiR_sample_size.bib |only epiR-2.0.99/epiR/vignettes/epiR_surveillance.Rmd |only epiR-2.0.99/epiR/vignettes/epiR_surveillance.bib |only epiR-3.0.0/epiR/DESCRIPTION | 8 - epiR-3.0.0/epiR/MD5 | 80 +++++++++------ epiR-3.0.0/epiR/NEWS | 16 +++ epiR-3.0.0/epiR/R/epi.sscc.R | 7 - epiR-3.0.0/epiR/build/vignette.rds |binary epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-html.R |only epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-html.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-html.html |only epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-pdf.R |only epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-pdf.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_descriptive_epi-pdf.pdf |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-html.R |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-html.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-html.html |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-pdf.R |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-pdf.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_diagnostic_tests-pdf.pdf |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-html.R |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-html.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-html.html |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-pdf.R |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-pdf.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_sample_size-pdf.pdf |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-html.R |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-html.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-html.html |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-pdf.R |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-pdf.Rmd |only epiR-3.0.0/epiR/inst/doc/epiR_surveillance-pdf.pdf |only epiR-3.0.0/epiR/man/epi.iref.Rd | 8 - epiR-3.0.0/epiR/man/epi.sscc.Rd | 18 ++- epiR-3.0.0/epiR/vignettes/content |only epiR-3.0.0/epiR/vignettes/epiR_descriptive_epi-html.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_descriptive_epi-pdf.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_diagnostic_tests-html.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_diagnostic_tests-pdf.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_sample_size-html.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_sample_size-pdf.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_surveillance-html.Rmd |only epiR-3.0.0/epiR/vignettes/epiR_surveillance-pdf.Rmd |only epiR-3.0.0/epiR/vignettes/preamble.tex |only 66 files changed, 88 insertions(+), 49 deletions(-)
Title: 'Rcpp' Integration for 'CGAL'
Description: Creates a header only package to link to the 'CGAL'
(Computational Geometry Algorithms Library)
header files in 'Rcpp'. There are a variety of potential uses for
the software such as Hilbert sorting, K-D Tree nearest neighbors,
and convex hull algorithms. For more information about how to use the header files,
see the 'CGAL' documentation at <https://www.cgal.org>. Currently
downloads version 6.2.1 of the 'CGAL' header files.
Author: Eric Dunipace [aut, cre] ,
Tyler Morgan-Wall [ctb],
Michael Chirico [ctb],
The CGAL Project [cph]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between RcppCGAL versions 6.2.1 dated 2026-09-05 and 6.2.1.1 dated 2026-10-12
RcppCGAL-6.2.1.1/RcppCGAL/DESCRIPTION | 15 RcppCGAL-6.2.1.1/RcppCGAL/MD5 | 57 - RcppCGAL-6.2.1.1/RcppCGAL/NAMESPACE | 3 RcppCGAL-6.2.1.1/RcppCGAL/NEWS.md | 11 RcppCGAL-6.2.1.1/RcppCGAL/R/RcppCGAL-package.R | 6 RcppCGAL-6.2.1.1/RcppCGAL/R/cgal_check.R | 37 RcppCGAL-6.2.1.1/RcppCGAL/R/cgal_header_info.R |only RcppCGAL-6.2.1.1/RcppCGAL/R/downloader.R | 50 - RcppCGAL-6.2.1.1/RcppCGAL/R/pkg_state.R.in | 4 RcppCGAL-6.2.1.1/RcppCGAL/README.md | 8 RcppCGAL-6.2.1.1/RcppCGAL/inst/AUTHORS | 1 RcppCGAL-6.2.1.1/RcppCGAL/inst/WORDLIST | 2 RcppCGAL-6.2.1.1/RcppCGAL/inst/doc/Installation.Rmd | 4 RcppCGAL-6.2.1.1/RcppCGAL/inst/doc/Installation.html | 12 RcppCGAL-6.2.1.1/RcppCGAL/inst/include/CGAL_zip.tar.xz |binary RcppCGAL-6.2.1.1/RcppCGAL/inst/include/RcppCGAL |only RcppCGAL-6.2.1.1/RcppCGAL/man/RcppCGAL-package.Rd | 3 RcppCGAL-6.2.1.1/RcppCGAL/man/cgal_bundled_version.Rd |only RcppCGAL-6.2.1.1/RcppCGAL/man/cgal_header_info.Rd |only RcppCGAL-6.2.1.1/RcppCGAL/man/cgal_is_installed.Rd | 2 RcppCGAL-6.2.1.1/RcppCGAL/man/cgal_version.Rd | 11 RcppCGAL-6.2.1.1/RcppCGAL/man/figures |only RcppCGAL-6.2.1.1/RcppCGAL/man/set_cgal.Rd | 5 RcppCGAL-6.2.1.1/RcppCGAL/man/unset_cgal.Rd | 3 RcppCGAL-6.2.1.1/RcppCGAL/tools/config/configure.R | 26 RcppCGAL-6.2.1.1/RcppCGAL/tools/config/downloader_functions.R | 372 +++++----- RcppCGAL-6.2.1.1/RcppCGAL/tools/config/semantic_patches.R |only RcppCGAL-6.2.1.1/RcppCGAL/tools/cran-probe |only RcppCGAL-6.2.1.1/RcppCGAL/tools/patch_cgal_semantics.R |only RcppCGAL-6.2.1.1/RcppCGAL/vignettes/Installation.Rmd | 4 RcppCGAL-6.2.1/RcppCGAL/R/cgal_version.R |only 31 files changed, 375 insertions(+), 261 deletions(-)
Title: CAGED Microdata Download and Storage in 'DuckDB'
Description: Tools to download, parse, and store Brazilian CAGED
(Cadastro Geral de Empregados e Desempregados) microdata using 'DuckDB'.
Supports both legacy CAGED (pre-2020), Novo CAGED (2020+), and adjustment files,
enabling efficient local storage and analysis workflows.
Data is sourced from the HuggingFace repository
<https://huggingface.co/datasets/alexsandroprado/caged>.
Author: Alexsandro Prado [aut, cre]
Maintainer: Alexsandro Prado <alexsandro.prado@ufersa.edu.br>
Diff between datacaged versions 0.2.1 dated 2026-09-09 and 0.2.3 dated 2026-10-12
DESCRIPTION | 12 MD5 | 109 - NAMESPACE | 12 NEWS.md | 114 + R/adjustments.R | 52 R/availability.R | 24 R/database.R | 428 ++++--- R/datacaged.R | 64 - R/download.R | 38 R/layouts.R | 299 +---- R/parse.R | 59 - R/status.R | 48 R/utils.R | 20 build/vignette.rds |binary inst/CITATION | 4 inst/doc/casos_de_uso.R | 1086 +++++++++--------- inst/doc/casos_de_uso.html | 1826 +++++++++++++++---------------- inst/doc/introducao.R | 336 ++--- inst/doc/introducao.Rmd | 26 inst/doc/introducao.html | 1470 ++++++++++++------------ inst/doc/introduction.R | 336 ++--- inst/doc/introduction.Rmd | 26 inst/doc/introduction.html | 1468 ++++++++++++------------ inst/doc/pipeline-en.R | 590 +++++----- inst/doc/pipeline-en.Rmd | 34 inst/doc/pipeline-en.html | 1384 +++++++++++------------ inst/doc/pipeline.R | 590 +++++----- inst/doc/pipeline.Rmd | 33 inst/doc/pipeline.html | 1380 +++++++++++------------ inst/doc/use-cases.R | 1086 +++++++++--------- inst/doc/use-cases.html | 1818 +++++++++++++++--------------- inst/po/en@quot |only inst/po/pt_BR/LC_MESSAGES/R-datacaged.mo |binary man/caged_adjustments_load.Rd | 4 man/caged_download_layouts.Rd | 14 man/caged_to_duckdb.Rd | 14 man/caged_to_parquet.Rd | 24 man/caged_update.Rd | 10 man/datacaged-package.Rd | 19 po/R-datacaged.pot | 651 ++++++----- po/R-pt_BR.po | 513 ++++---- tests/testthat/setup.R |only tests/testthat/test-adjustments.R | 32 tests/testthat/test-availability.R | 7 tests/testthat/test-database.R | 45 tests/testthat/test-download.R | 36 tests/testthat/test-extdata.R | 2 tests/testthat/test-i18n.R |only tests/testthat/test-parse.R | 8 tests/testthat/test-pipelines.R | 81 + tests/testthat/test-status.R | 2 tests/testthat/test-update-parquet.R | 206 +++ tests/testthat/test-utils.R | 31 vignettes/introducao.Rmd | 26 vignettes/introduction.Rmd | 26 vignettes/pipeline-en.Rmd | 34 vignettes/pipeline.Rmd | 33 57 files changed, 8722 insertions(+), 7868 deletions(-)
Title: An Alternative Advanced Normalization Tools ('ANTs')
Description: Provides portable access from 'R' to biomedical image processing toolbox
'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless
integration with the 'Python' implementation 'ANTsPy'. Allows biomedical
images to be processed in 'Python' and analyzed in 'R', and vice versa
via shared memory. See 'citation("rpyANTs")' for more reference information.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between rpyANTs versions 0.0.6 dated 2026-01-11 and 0.0.7 dated 2026-10-12
DESCRIPTION | 10 - MD5 | 58 +++---- NEWS.md | 7 R/aaa.R | 22 +- R/ants-plot.R | 127 +++++++++------- R/brain_extraction.R | 14 - R/generics-ANTsImage.R | 34 ++-- R/generics-ANTsTransform.R | 48 +++--- R/generics-ants.R | 4 R/motion_correction.R | 14 - R/preprocess_brain_image.R | 10 - R/registration.R | 106 +++++++------ R/resample.R | 12 - R/segmentation.R | 4 R/templates.R | 35 ++-- R/utils.R | 56 +++---- R/zzz.R | 44 ++--- README.md | 6 inst/rpyants/rpyants/registration/normalization.py | 164 +++++++++++++++++---- inst/rpyants/rpyants/registration/yael.py | 72 +++++++-- inst/rpyants/rpyants/utils/cache.py | 12 + man/ants_resample_image.Rd | 2 man/figures/README-load-image-into-r-1.png |binary man/py.Rd | 2 man/reexports.Rd | 4 tests/testthat.R | 4 tests/testthat/helper-toy.R |only tests/testthat/test-normalization.R |only tests/testthat/test-sanity.R | 4 tests/testthat/test-transform.R | 101 +++++++----- tests/testthat/test-yael-template-mapping.R |only tests/testthat/test-yael.R |only 32 files changed, 601 insertions(+), 375 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre] ,
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlag [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.3.2 dated 2026-09-04 and 0.4.0 dated 2026-10-12
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 5 NEWS.md | 17 R/RcppExports.R | 48 ++ R/imaging-ants-io.R | 9 R/imaging-intensity-n4.R |only R/imaging-registration-native.R | 128 ++++++- R/imaging-segment-gmm.R |only R/imaging-transform-apply.R |only R/vcg.R | 154 +++++++- inst/CITATION | 19 + inst/doc/mesh-geometry.html | 10 man/apply_transform3d.Rd | 10 man/apply_transform3d_volume.Rd |only man/bias_correction_n4.Rd |only man/register_volume3d.Rd | 68 +++ man/segment_volume_tissue_gmm.Rd |only man/vcg_decimate.Rd |only man/vcg_smooth.Rd | 50 ++ src/RcppExports.cpp | 204 ++++++++++- src/imaging_intensity_n4.cpp |only src/imaging_segment_gmm.cpp |only src/reg_apply.cpp |only src/reg_apply.h |only src/reg_syn.cpp | 47 +- src/vcgCommon.cpp | 615 ++++++++++++++++++++++++++++++---- src/vcgDecimate.cpp |only tests/testthat/test-intensity-n4.R |only tests/testthat/test-segment-gmm.R |only tests/testthat/test-transform-apply.R |only tests/testthat/test-vcg-decimate.R |only tests/testthat/test-vcg-mesh-io.R | 190 ++++++++++ 33 files changed, 1473 insertions(+), 155 deletions(-)
Title: Pedigree Validation Genetic Composition of Diploids & Polyploids
Description: Tools for pedigree quality control and genomic breed/line
composition estimation in diploid and polyploid breeding populations.
'BIGpopA' provides functions to check and correct common pedigree
errors, assign parentage from SNP genotype data using Mendelian error
rates, validate parent-offspring trios, and estimate genome-wide
breed or line composition using quadratic programming. Pedigree
validation and parentage assignment support any ploidy, using a
polysomic Mendelian test for even ploidy and a homozygosity-based
check for odd ploidy. Genotypes can be supplied as dosage tables, VCF
files, or 'PLINK' .ped files. For more details about the included
'breedTools' functions, see Funkhouser et al. (2017)
<doi:10.2527/tas2016.0003>.
Author: Josue Chinchilla-Vargas [cre, aut],
Alexander Sandercock [aut],
University of Florida [cph]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Diff between BIGpopA versions 2.1.0 dated 2026-10-05 and 2.2.0 dated 2026-10-12
DESCRIPTION | 6 MD5 | 45 + NAMESPACE | 1 NEWS.md | 15 R/allele_freq_poly.R | 2 R/assign_composition_line.R |only R/find_parentage.R | 442 ++++++++++++----- R/ped_to_dosage.R | 102 +-- R/utils.R | 148 ++++- R/validate_pedigree.R | 314 ++++++------ R/vcf_to_dosage.R | 146 ++--- README.md | 5 inst/doc/BIGpopA.R | 29 - inst/doc/BIGpopA.Rmd | 70 ++ inst/doc/BIGpopA.html | 311 +++++++---- man/assign_composition_line.Rd |only man/find_parentage.Rd | 49 + man/ped_to_dosage.Rd | 2 man/validate_pedigree.Rd | 55 +- tests/testthat/test-assign_composition_line.R |only tests/testthat/test-find_parentage.R | 148 +++++ tests/testthat/test-founders_input.R |only tests/testthat/test-hard.R |only tests/testthat/test-validate_pedigree.R | 88 ++- tests/testthat/test-validate_pedigree_marker_summary.R |only tests/testthat/test-validate_pedigree_marker_trio.R |only vignettes/BIGpopA.Rmd | 70 ++ 27 files changed, 1365 insertions(+), 683 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.8 dated 2026-09-03 and 1.1.9 dated 2026-10-12
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/itam.R | 10 ++++++---- inst/NEWS.Rd | 8 ++++++++ inst/doc/trend.pdf |binary 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Transparent and Assisted Linear Modeling Engine
Description: Unified estimation, diagnostics, and reporting for ordinary least
squares (OLS) regression, ANOVA/t-tests, logistic regression, panel data
(fixed/random effects with Hausman test), instrumental variables (2SLS with
weak instrument diagnostics), and difference-in-differences. Designed for
applied researchers in social sciences with integrated "Methodological Customs"
that audit assumptions and provide literature references. All methods
implemented in pure base R without external dependencies beyond stats and
graphics packages.
Author: Manuel Soto-Perez [aut, cre]
Maintainer: Manuel Soto-Perez <msoto@up.edu.mx>
Diff between OLSengine versions 1.2.0 dated 2026-09-18 and 1.2.1 dated 2026-10-12
DESCRIPTION | 6 - MD5 | 20 ++-- NAMESPACE | 2 NEWS.md | 58 +++++++++++++ R/OLS_engine.R | 176 ++++++++++++++++++++++++++++++---------- README.md | 13 +- inst/doc/vignette_tutorial.R | 5 - inst/doc/vignette_tutorial.Rmd | 9 +- inst/doc/vignette_tutorial.html | 53 +++++++----- man/paper_engine.Rd | 38 ++++++-- vignettes/vignette_tutorial.Rmd | 9 +- 11 files changed, 284 insertions(+), 105 deletions(-)
Title: Interactive 3D Visualization of Large Cayley Graphs via Vulkan
Description: Provides interactive 3D visualization for large-scale Cayley graphs.
Specifically designed for analyzing state spaces of the 'TopSpin' puzzle.
Leverages the 'Datoviz' library and Vulkan-based GPU rendering for smooth
real-time exploration of large graphs and complex state transitions.
Implements efficient coordinate mapping for high-dimensional permutation
groups, allowing users to visualize the connectivity and structural
properties of the puzzle's state space. The rendering engine provides
high-performance visuals and interactive camera controls, making it suitable
for mathematical analysis of group-theoretic puzzles within the R
environment.
Author: Yuri Baramykov [aut, cre] ,
Cyrille Rossant [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between cgvR versions 0.1.2 dated 2026-05-11 and 0.1.3 dated 2026-10-12
DESCRIPTION | 6 +- MD5 | 27 ++++++---- NAMESPACE | 1 NEWS.md | 4 + R/graph_render.R | 18 +++++++ configure.win | 10 +++ inst/examples/demo_cube3_sheets.R |only inst/examples/demo_cube3_solutions.R |only inst/examples/demo_path_coords.R |only inst/examples/demo_path_in_graph.R |only man/cgv_set_edge_colors.Rd |only src/cgvR.h | 1 src/cgv_graph.c | 30 +++++++++++ src/cgv_stub.c | 88 +++++++++++++++++++---------------- src/datoviz/renderer.cpp | 1 src/datoviz/scene/atlas.cpp | 1 src/init.c | 1 17 files changed, 134 insertions(+), 54 deletions(-)
Title: Visualization 2D of Binary Classification Models
Description: Visual contour and 2D point and contour plots for binary classification modeling under algorithms such as 'glm', 'rf', 'gbm', 'nnet' and 'svm', presented over two dimensions generated by 'famd' and 'mca' methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses under the 'XAI' paradigm.
Author: Javier Portela [aut, cre]
Maintainer: Javier Portela <javipgm@gmail.com>
Diff between visualpred versions 0.1.2 dated 2025-10-19 and 0.1.3 dated 2026-10-12
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 5 +++-- NEWS.md | 6 +++++- R/famdcontour.R | 2 +- R/mcacontour.R | 2 +- R/mcacontourjitter.R | 2 +- R/mcamodelo.R | 18 +++++++++++++++--- inst/doc/Basic_example.html | 2 +- man/mcamodelobis.Rd | 2 +- 10 files changed, 41 insertions(+), 24 deletions(-)
Title: Spatial Environmental Risk Assessment Through Food Webs
Description: A workflow for spatially explicit environmental risk assessment
of contaminated sites: habitat, food web, dispersal, exposure and risk.
Starting from a raster of soil contamination, the package builds habitat
layers for a set of species, organises them in a directed acyclic graph
representing a food web, and propagates the flow of elements (e.g., food,
energy, contaminants) along its links. It also provides soil interpolation
by kriging, dispersal by kernel convolution or by circuit theory (through
the optional 'Julia' package 'Omniscape'), land cover retrieval for France
('OCS-GE') and Europe ('EUNIS'), and Bayesian calibration of transfer
models with 'Stan'.
Author: Virgile Baudrot [aut, cre, cph],
Lea Bariod [ctb],
Clementine Fritsch [ctb, cph],
Renaud Scheifler [ctb]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between spacemodR versions 0.1.3 dated 2026-02-20 and 0.3.5 dated 2026-10-12
spacemodR-0.1.3/spacemodR/R/intakes.R |only spacemodR-0.1.3/spacemodR/inst/extdata/ground_concentration_pb_compressed.tif |only spacemodR-0.1.3/spacemodR/inst/extdata/ground_concentration_zn_compressed.tif |only spacemodR-0.1.3/spacemodR/man/intake.Rd |only spacemodR-0.3.5/spacemodR/DESCRIPTION | 54 spacemodR-0.3.5/spacemodR/LICENSE | 2 spacemodR-0.3.5/spacemodR/MD5 | 144 + spacemodR-0.3.5/spacemodR/NAMESPACE | 44 spacemodR-0.3.5/spacemodR/NEWS.md |only spacemodR-0.3.5/spacemodR/R/data.R | 430 +++++ spacemodR-0.3.5/spacemodR/R/data_eunis.R |only spacemodR-0.3.5/spacemodR/R/data_gbif.R |only spacemodR-0.3.5/spacemodR/R/data_ocsge.R | 471 +++++ spacemodR-0.3.5/spacemodR/R/data_soil.R |only spacemodR-0.3.5/spacemodR/R/departements.R | 11 spacemodR-0.3.5/spacemodR/R/dispersal.R | 120 - spacemodR-0.3.5/spacemodR/R/flux.R |only spacemodR-0.3.5/spacemodR/R/habitat.R | 324 +++ spacemodR-0.3.5/spacemodR/R/kriging.R |only spacemodR-0.3.5/spacemodR/R/soil_interpolation.R |only spacemodR-0.3.5/spacemodR/R/spacemodR-internal.R | 22 spacemodR-0.3.5/spacemodR/R/stan.R |only spacemodR-0.3.5/spacemodR/R/stanmodels.R |only spacemodR-0.3.5/spacemodR/R/transfer.R | 32 spacemodR-0.3.5/spacemodR/R/trophic.R | 96 - spacemodR-0.3.5/spacemodR/README.md | 216 ++ spacemodR-0.3.5/spacemodR/build/vignette.rds |binary spacemodR-0.3.5/spacemodR/configure |only spacemodR-0.3.5/spacemodR/configure.win |only spacemodR-0.3.5/spacemodR/data/DBFunc_BirdFuncDat.rda |only spacemodR-0.3.5/spacemodR/data/DBFunc_MamFuncDat.rda |only spacemodR-0.3.5/spacemodR/data/FmrBT.rda |only spacemodR-0.3.5/spacemodR/data/SSD_ecoSSL_all.rda |only spacemodR-0.3.5/spacemodR/data/bappet_cd.rda |only spacemodR-0.3.5/spacemodR/data/earthworm_cd.rda |only spacemodR-0.3.5/spacemodR/data/eunis_species_dict.rda |only spacemodR-0.3.5/spacemodR/data/ocsge_species_dict.rda |binary spacemodR-0.3.5/spacemodR/data/ocsge_us_metaleurop.rda |only spacemodR-0.3.5/spacemodR/data/ref_eunis.rda |only spacemodR-0.3.5/spacemodR/data/ref_ocsge_eunis.rda |only spacemodR-0.3.5/spacemodR/data/soil_metaleurop.rda |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_EN.R |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_EN.Rmd |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_EN.html |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_FR.R |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_FR.Rmd |only spacemodR-0.3.5/spacemodR/inst/doc/Getting_Started_FR.html |only spacemodR-0.3.5/spacemodR/inst/doc/Tutorial.R | 186 -- spacemodR-0.3.5/spacemodR/inst/doc/Tutorial.Rmd | 450 ++--- spacemodR-0.3.5/spacemodR/inst/doc/Tutorial.html | 836 ++++------ spacemodR-0.3.5/spacemodR/inst/include |only spacemodR-0.3.5/spacemodR/inst/stan |only spacemodR-0.3.5/spacemodR/man/DBFunc_BirdFuncDat.Rd |only spacemodR-0.3.5/spacemodR/man/DBFunc_MamFuncDat.Rd |only spacemodR-0.3.5/spacemodR/man/FmrBT.Rd |only spacemodR-0.3.5/spacemodR/man/SSD_ecoSSL_all.Rd |only spacemodR-0.3.5/spacemodR/man/add_flux.Rd |only spacemodR-0.3.5/spacemodR/man/add_habitat.Rd | 51 spacemodR-0.3.5/spacemodR/man/add_nohabitat.Rd | 15 spacemodR-0.3.5/spacemodR/man/apply_flux.Rd |only spacemodR-0.3.5/spacemodR/man/bappet_cd.Rd |only spacemodR-0.3.5/spacemodR/man/calibrate_direct.Rd |only spacemodR-0.3.5/spacemodR/man/calibrate_simple.Rd |only spacemodR-0.3.5/spacemodR/man/calibrate_trophic.Rd |only spacemodR-0.3.5/spacemodR/man/cv_soil.Rd |only spacemodR-0.3.5/spacemodR/man/earthworm_cd.Rd |only spacemodR-0.3.5/spacemodR/man/eunis_species_dict.Rd |only spacemodR-0.3.5/spacemodR/man/fit_soil_variogram.Rd |only spacemodR-0.3.5/spacemodR/man/flux.Rd | 30 spacemodR-0.3.5/spacemodR/man/get_departements_for_roi.Rd | 2 spacemodR-0.3.5/spacemodR/man/get_eunis_data.Rd |only spacemodR-0.3.5/spacemodR/man/get_gbif_data.Rd |only spacemodR-0.3.5/spacemodR/man/get_ocsge.Rd |only spacemodR-0.3.5/spacemodR/man/get_ocsge_data_fgb.Rd | 3 spacemodR-0.3.5/spacemodR/man/get_ocsge_data_ign.Rd |only spacemodR-0.3.5/spacemodR/man/habitat.Rd | 21 spacemodR-0.3.5/spacemodR/man/habitat_raster.Rd | 79 spacemodR-0.3.5/spacemodR/man/join_ocsge_species.Rd |only spacemodR-0.3.5/spacemodR/man/kernel_smooth_soil.Rd |only spacemodR-0.3.5/spacemodR/man/krige_soil.Rd |only spacemodR-0.3.5/spacemodR/man/ocsge_species_dict.Rd | 82 spacemodR-0.3.5/spacemodR/man/ocsge_us_metaleurop.Rd |only spacemodR-0.3.5/spacemodR/man/plot.habitat.Rd |only spacemodR-0.3.5/spacemodR/man/plot.soil_vgm.Rd |only spacemodR-0.3.5/spacemodR/man/plot.trophic_tbl.Rd | 22 spacemodR-0.3.5/spacemodR/man/plot_species_habitat.Rd |only spacemodR-0.3.5/spacemodR/man/ref_eunis.Rd |only spacemodR-0.3.5/spacemodR/man/ref_ocsge_eunis.Rd |only spacemodR-0.3.5/spacemodR/man/soil_grid.Rd |only spacemodR-0.3.5/spacemodR/man/soil_metaleurop.Rd |only spacemodR-0.3.5/spacemodR/man/soil_variogram.Rd |only spacemodR-0.3.5/spacemodR/man/soil_vgm.Rd |only spacemodR-0.3.5/spacemodR/man/source_covariates.Rd |only spacemodR-0.3.5/spacemodR/man/spacemodR-package.Rd |only spacemodR-0.3.5/spacemodR/man/summary.soil_cv.Rd |only spacemodR-0.3.5/spacemodR/man/transfer.Rd | 10 spacemodR-0.3.5/spacemodR/src |only spacemodR-0.3.5/spacemodR/tests/testthat/test-eunis.R |only spacemodR-0.3.5/spacemodR/tests/testthat/test-gbif.R |only spacemodR-0.3.5/spacemodR/tests/testthat/test-habitat.R | 253 +++ spacemodR-0.3.5/spacemodR/tests/testthat/test-kriging.R |only spacemodR-0.3.5/spacemodR/tests/testthat/test-ocsge.R | 111 + spacemodR-0.3.5/spacemodR/vignettes/Getting_Started_EN.Rmd |only spacemodR-0.3.5/spacemodR/vignettes/Getting_Started_FR.Rmd |only spacemodR-0.3.5/spacemodR/vignettes/Tutorial.Rmd | 450 ++--- 105 files changed, 3269 insertions(+), 1298 deletions(-)
Title: Tools to Evaluate Disclosure Risk
Description: Functions and tools for calculating disclosure risk measures. This includes
record-level measures primarily using exhaustive tabulation, as well as
file-level measures using a loglinear model.
Author: John Riddles [aut, cre],
Westat [cph]
Maintainer: John Riddles <JohnRiddles@westat.com>
This is a re-admission after prior archival of version 1.0.1 dated 2020-12-17
Diff between SDCNway versions 1.0.1 dated 2020-12-17 and 1.1.1 dated 2026-10-12
SDCNway-1.0.1/SDCNway/build/vignette.rds |only SDCNway-1.0.1/SDCNway/inst/doc |only SDCNway-1.0.1/SDCNway/vignettes |only SDCNway-1.1.1/SDCNway/DESCRIPTION | 39 - SDCNway-1.1.1/SDCNway/MD5 | 23 SDCNway-1.1.1/SDCNway/NAMESPACE | 3 SDCNway-1.1.1/SDCNway/R/loglinear.R | 649 +++++++++++++++++++++--- SDCNway-1.1.1/SDCNway/R/risk_measures.R | 2 SDCNway-1.1.1/SDCNway/R/sdc_extabs.R | 35 - SDCNway-1.1.1/SDCNway/build/partial.rdb |binary SDCNway-1.1.1/SDCNway/inst/REFERENCES.bib | 7 SDCNway-1.1.1/SDCNway/man/sdc_extabs.Rd | 2 SDCNway-1.1.1/SDCNway/man/sdc_loglinear.Rd | 4 SDCNway-1.1.1/SDCNway/man/sdc_loglinear_iter.Rd |only 14 files changed, 626 insertions(+), 138 deletions(-)
Title: Regularised and Information-Theoretic Sufficient Dimension
Reduction
Description: Implements covariance-stabilised sufficient dimension reduction
for continuous responses, with an additional sparse engine for continuous,
categorical, and right-censored survival responses and information-theoretic
structural dimension
selection. Supported methods include sliced inverse regression, sliced
average variance estimation, directional regression, and principal Hessian
directions. Sample, ridge, Oracle Approximating Shrinkage, Ledoit-Wolf, and
Maximum Entropy Covariance (MEC) estimators are provided alongside
prediction, resampling, simulation, and diagnostic utilities. The
sufficient dimension reduction
methods build on Li (1991) <doi:10.1080/01621459.1991.10475035>, Li (1992)
<doi:10.1080/01621459.1992.10476258>, and Li and Wang (2007)
<doi:10.1198/016214507000000536>. Covariance shrinkage follows Olorede and
Yahya (2019) <doi:10.48550/arXiv.1909.13017>, Ledoit and
Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4> and Chen et al. (2010)
<doi: [...truncated...]
Author: Kabir Olorede [aut, cre]
Maintainer: Kabir Olorede <kabirolorede@gmail.com>
Diff between risdr versions 0.3.1 dated 2026-07-28 and 0.4.0 dated 2026-10-12
DESCRIPTION | 18 ++-- MD5 | 52 +++++++++++-- NAMESPACE | 21 +++++ NEWS.md | 26 ++++++ R/risdr-package.R | 9 +- R/thesis_engine.R |only R/thesis_prediction.R |only README.md | 74 +++++++++++++++---- build/vignette.rds |binary inst/CITATION | 11 ++ inst/WORDLIST | 29 +++---- inst/doc/sparse-survival.R |only inst/doc/sparse-survival.Rmd |only inst/doc/sparse-survival.html |only man/C1F.Rd |only man/compute_ic.Rd |only man/compute_ic_values.Rd |only man/compute_penalty_weights.Rd |only man/dual_pca_scores.Rd |only man/fit_risdr_dual.Rd |only man/fit_risdr_sparse.Rd |only man/fit_risdr_sparse_realdata.Rd |only man/fit_sparse_grid.Rd |only man/predict.risdr_sparse.Rd |only man/print.risdr_dual.Rd |only man/print.risdr_sparse.Rd |only man/print.risdr_sparse_realdata.Rd |only man/print.summary.risdr_sparse.Rd |only man/risdr-package.Rd | 9 +- man/slice_response.Rd |only man/summarise_sparsity.Rd |only man/summary.risdr_dual.Rd |only man/summary.risdr_sparse.Rd |only man/weighted_soft_threshold.Rd |only man/weighted_sparsify_directions.Rd |only tests/testthat/helper-thesis-coverage.R |only tests/testthat/test-thesis-covariance-criteria.R |only tests/testthat/test-thesis-dual-selected-d-ranking.R |only tests/testthat/test-thesis-interface-contracts.R |only tests/testthat/test-thesis-prediction-contracts.R |only tests/testthat/test-thesis-prediction.R |only tests/testthat/test-thesis-realdata-wrapper.R |only tests/testthat/test-thesis-survival-unified-core.R |only vignettes/sparse-survival.Rmd |only 44 files changed, 194 insertions(+), 55 deletions(-)
Title: Faithful and Scalable MARCXML Parsing
Description: Parses Machine-Readable Cataloging ('MARC 21') XML
<https://www.loc.gov/standards/marcxml/> into a canonical tidy long
representation while preserving leaders, control fields, data fields,
indicators, repeated fields, repeated subfields, and source order.
Provides in-memory reading, bounded-memory conversion to 'Parquet',
and reconstruction of MARCXML from canonical data.
Supports structural diagnostics for in-memory and 'Arrow'-backed
representations, optional recovery from malformed MARC records,
and local parallel processing.
Author: Lorenzo Isella [aut, cre]
Maintainer: Lorenzo Isella <lorenzo.isella@gmail.com>
Diff between marcxmlr versions 0.3.1 dated 2026-09-28 and 0.4.0 dated 2026-10-12
DESCRIPTION | 21 MD5 | 35 NEWS.md | 16 R/arrow-writer.R | 175 +-- R/canonical-diagnostics.R | 189 +++ R/marc-recovery.R |only R/marcxml-to-parquet.R | 346 +++++- R/native-parser.R | 125 ++ R/read-marcxml.R | 47 README.md | 1265 ++++++++-------------- build |only inst/doc |only inst/extdata/orwell-marcxml.xml |only man/diagnose_canonical.Rd | 23 man/marcxml_to_parquet.Rd | 23 man/read_marcxml.Rd | 28 src/marcxml-native.c | 1018 +++++++++++++++++ tests/testthat/test-canonical-diagnostics-arrow.R |only tests/testthat/test-marc-recovery.R |only tests/testthat/test-parquet.R | 22 vignettes |only 21 files changed, 2425 insertions(+), 908 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.1.2 dated 2026-09-03 and 0.1.3 dated 2026-10-12
DESCRIPTION | 6 - MD5 | 13 +-- NEWS.md | 6 + R/aaa-generics-streamlines.R | 2 R/utils-vol2surf.R | 134 ++++++++++++++++++++++++++------ man/volume_to_surface.Rd | 35 +++++++- tests/testthat/test-volume-to-surface.R |only tests/testthat/test-vtk-polys.R | 3 8 files changed, 166 insertions(+), 33 deletions(-)
Title: Standard Dataset Manager for Observational Medical Outcomes
Partnership Common Data Model Sample Datasets
Description: Facilitates access to sample datasets from the 'EunomiaDatasets' repository (<https://github.com/ohdsi/EunomiaDatasets>).
Author: Anthony Sena [aut, cre],
Frank DeFalco [aut],
Martijn Schuemie [aut],
Natthawut Adulyanukosol [aut],
Star Liu [aut],
Adam Black [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between Eunomia versions 2.1.0 dated 2025-09-15 and 2.2.0 dated 2026-10-12
DESCRIPTION | 24 ++++---- MD5 | 32 +++++------ NAMESPACE | 12 ++-- NEWS.md | 11 +++ R/Cohorts.R | 2 R/Connection.R | 14 ++-- R/Eunomia.R | 2 R/EunomiaData.R | 21 +++++-- README.md | 2 man/Eunomia-package.Rd | 6 +- man/downloadEunomiaData.Rd | 4 - man/extractLoadData.Rd | 4 - man/getDatabaseFile.Rd | 16 ++--- man/getEunomiaConnectionDetails.Rd | 6 +- man/loadDataFiles.Rd | 4 - tests/testthat/test-EunomiaData.R | 107 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-basic.R | 12 ++-- 17 files changed, 206 insertions(+), 73 deletions(-)
Title: Probability Distributions with Certain or Uncertain Parameters
Description: Represents probability distributions with fixed or potentially
uncertain parameters, with tools to discretise, convolve, sample from and
summarise them.
Author: Sebastian Funk [aut, cre] ,
James M. Azam [aut] ,
Sam Abbott [aut]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between distspec versions 0.2.0 dated 2026-09-01 and 0.3.0 dated 2026-10-12
DESCRIPTION | 6 MD5 | 47 ++-- NAMESPACE | 22 ++ NEWS.md | 14 + R/beta.R | 4 R/discretise.R | 14 - R/dist_spec.R | 358 ++++++++++++++++++++++++++++++++++++- R/distribution.R | 48 ++++ R/exp.R | 7 R/gamma.R | 7 R/lognormal.R | 7 R/normal.R | 7 R/weibull.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/distspec.html | 13 - man/bound_dist.Rd | 14 - man/cdf.Rd |only man/cdf_bounded.Rd |only man/dist_cdf.Rd |only man/dist_quantile.Rd |only man/draw_components.Rd |only man/log_upper_bound.Rd |only man/quantile.dist_spec.Rd |only man/quantile_bounded.Rd |only man/sample_bounded.Rd |only man/sample_dist.Rd | 19 + tests/testthat/test-distribution.R |only tests/testthat/test-quantile.R |only tests/testthat/test-sample_dist.R | 155 ++++++++++++++++ 30 files changed, 681 insertions(+), 68 deletions(-)
Title: Geometric Analysis of Configurations in High-Dimensional Spaces
Description: Computes Average Membership Degree (AMD) from soft-membership
matrices and constructs AMD curves across candidate configuration counts.
The current curve backend uses repeated fuzzy c-means fits while keeping
the AMD definition, membership estimation, curve construction, and final
assignment as separate operations. Fitted memberships, convergence
diagnostics, preprocessing transformations, seeds, row maps, and
process-level reproducibility links are retained. The package reports
numerical curve features but leaves their scientific interpretation to an
explicitly justified analysis. The method was introduced by Mendoza and
Araújo (2022) <doi:10.1111/ecog.06289>.
Author: Manuel Mendoza [aut, cre]
Maintainer: Manuel Mendoza <mmendoza@mncn.csic.es>
Diff between AMDconfigurations versions 0.1.0 dated 2026-03-17 and 0.2.1 dated 2026-10-12
AMDconfigurations-0.1.0/AMDconfigurations/R/estimate_sigma_equivalent.R |only AMDconfigurations-0.1.0/AMDconfigurations/R/plot_amd_sigma.R |only AMDconfigurations-0.1.0/AMDconfigurations/R/print_amd_sigma.R |only AMDconfigurations-0.1.0/AMDconfigurations/R/summary_amd_sigma.R |only AMDconfigurations-0.1.0/AMDconfigurations/R/summary_sigma_equivalent.R |only AMDconfigurations-0.1.0/AMDconfigurations/man/estimate_sigma_equivalent.Rd |only AMDconfigurations-0.1.0/AMDconfigurations/man/plot.amd_sigma.Rd |only AMDconfigurations-0.1.0/AMDconfigurations/man/print.amd_sigma.Rd |only AMDconfigurations-0.1.0/AMDconfigurations/man/summary.amd_sigma.Rd |only AMDconfigurations-0.1.0/AMDconfigurations/man/summary.sigma_equivalent.Rd |only AMDconfigurations-0.1.0/AMDconfigurations/tests/testthat/test_estimate_sigma_equivalent.R |only AMDconfigurations-0.2.1/AMDconfigurations/DESCRIPTION | 36 AMDconfigurations-0.2.1/AMDconfigurations/MD5 | 113 - AMDconfigurations-0.2.1/AMDconfigurations/NAMESPACE | 39 AMDconfigurations-0.2.1/AMDconfigurations/NEWS.md |only AMDconfigurations-0.2.1/AMDconfigurations/R/AMDconfigurations-package.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/Fulldata.R | 27 AMDconfigurations-0.2.1/AMDconfigurations/R/Transcdata_small.R | 24 AMDconfigurations-0.2.1/AMDconfigurations/R/amd_curve_schema.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor_advanced_features.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor_candidate_features.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor_curve_features.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor_data_features.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_predictor_partition_features.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_reproducibility_manifest.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/amd_score.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/assign_configurations.R | 374 ++- AMDconfigurations-0.2.1/AMDconfigurations/R/compute_amd_curve.R | 426 +++- AMDconfigurations-0.2.1/AMDconfigurations/R/diagnose_amd.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/imports.R | 8 AMDconfigurations-0.2.1/AMDconfigurations/R/plot_AMD().R | 151 - AMDconfigurations-0.2.1/AMDconfigurations/R/print.amd_curve().R | 50 AMDconfigurations-0.2.1/AMDconfigurations/R/summary.amd_curve().R | 72 AMDconfigurations-0.2.1/AMDconfigurations/R/utils_rng.R |only AMDconfigurations-0.2.1/AMDconfigurations/R/zzz_globals.R | 4 AMDconfigurations-0.2.1/AMDconfigurations/README.md | 311 +- AMDconfigurations-0.2.1/AMDconfigurations/build/partial.rdb |only AMDconfigurations-0.2.1/AMDconfigurations/build/vignette.rds |binary AMDconfigurations-0.2.1/AMDconfigurations/inst/CITATION |only AMDconfigurations-0.2.1/AMDconfigurations/inst/COPYRIGHTS |only AMDconfigurations-0.2.1/AMDconfigurations/inst/MIGRATION.md |only AMDconfigurations-0.2.1/AMDconfigurations/inst/doc/AMDconfigurations.R | 82 AMDconfigurations-0.2.1/AMDconfigurations/inst/doc/AMDconfigurations.Rmd | 293 +- AMDconfigurations-0.2.1/AMDconfigurations/inst/doc/AMDconfigurations.html | 1050 +++++----- AMDconfigurations-0.2.1/AMDconfigurations/inst/examples/example_ecology.R | 208 - AMDconfigurations-0.2.1/AMDconfigurations/inst/examples/example_transcriptomics.R | 338 --- AMDconfigurations-0.2.1/AMDconfigurations/man/AMDconfigurations-package.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/Fulldata.Rd | 51 AMDconfigurations-0.2.1/AMDconfigurations/man/Transcdata_small.Rd | 52 AMDconfigurations-0.2.1/AMDconfigurations/man/amd_reproducibility_manifest.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/amd_score.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/assign_configurations.Rd | 171 + AMDconfigurations-0.2.1/AMDconfigurations/man/compute_amd_curve.Rd | 197 + AMDconfigurations-0.2.1/AMDconfigurations/man/diagnose_amd.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/load_amd_predictor.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/plot.amd_curve.Rd | 49 AMDconfigurations-0.2.1/AMDconfigurations/man/plot.amd_prediction.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/plot_AMD.Rd | 79 AMDconfigurations-0.2.1/AMDconfigurations/man/predict_amd.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/print.amd_curve.Rd | 40 AMDconfigurations-0.2.1/AMDconfigurations/man/print.amd_diagnostics.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/print.amd_prediction.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/man/summary.amd_curve.Rd | 40 AMDconfigurations-0.2.1/AMDconfigurations/man/summary.amd_prediction.Rd |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat.R | 8 AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/fixtures |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/helper-curve-profile.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/helper-legacy-curve.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/helper-mixed-convergence.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_amd_predictor.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_amd_reproducibility_manifest.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_amd_score.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_assign_configurations.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_compute_amd_curve.R | 502 ++++ AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_corrected_reader.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_data_contracts.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_diagnose_amd.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_e1071_contract.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_plot_methods.R | 64 AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_predict_amd_integration.R |only AMDconfigurations-0.2.1/AMDconfigurations/tests/testthat/test_print_summary_methods.R | 60 AMDconfigurations-0.2.1/AMDconfigurations/vignettes/AMDconfigurations.Rmd | 293 +- 83 files changed, 3238 insertions(+), 1974 deletions(-)
More information about AMDconfigurations at CRAN
Permanent link
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012)
<doi:10.1890/11-1183.1>.
Author: Stephane Dray [aut] ,
David Bauman [ctb],
Guillaume Blanchet [ctb],
Daniel Borcard [ctb],
Sylvie Clappe [ctb],
Guillaume Guenard [ctb] ,
Thibaut Jombart [ctb],
Guillaume Larocque [ctb],
Pierre Legendre [ctb] ,
Naima Madi [ctb],
Helene H Wagner [ctb], [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adespatial versions 0.3-29 dated 2026-03-20 and 0.3-30 dated 2026-10-12
DESCRIPTION | 11 MD5 | 30 +- NAMESPACE | 211 +++++++++-------- R/aem.weight.time.R | 2 R/envspace.test.R | 580 ++++++++++++++++++++++++++++++------------------ R/globloc.rtests.R | 4 R/plot.constr.hclust.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tutorial.Rmd | 2 inst/doc/tutorial.html | 440 +++++++++++++++++------------------- man/aem.weight.edges.Rd | 5 man/envspace.test.Rd | 201 ++++++++++------ man/global.rtest.Rd | 2 tests |only vignettes/tutorial.Rmd | 2 16 files changed, 860 insertions(+), 631 deletions(-)
Title: Skewed Generalized T Distribution Tree
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis [aut, cre]
Maintainer: Carter Davis <cdavis40@chicagobooth.edu>
Diff between sgt versions 2.0 dated 2015-09-03 and 2.0-2 dated 2026-10-12
DESCRIPTION | 18 +++++++++++------- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/sgt.pdf |binary man/sgt.Rd | 2 +- man/sgtmle.Rd | 4 ++-- man/summarysgtest.Rd | 2 +- 7 files changed, 21 insertions(+), 17 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre, cph] ,
Adrian Chong [aut]
Maintainer: Hongyuan Jia <hongyuanjia@cqust.edu.cn>
Diff between eplusr versions 0.17.0 dated 2026-06-20 and 0.18.0 dated 2026-10-12
DESCRIPTION | 17 MD5 | 212 - NAMESPACE | 9 NEWS.md | 73 R/assert.R | 374 +- R/constants.R | 35 R/diagram.R | 122 R/epw.R | 140 R/err.R | 6 R/format.R | 2459 ++++++++-------- R/group.R | 85 R/idd.R | 12 R/iddobj.R | 3966 ++++++++++++------------- R/idf.R | 200 + R/idfobj-sch.R | 1160 +++---- R/idfobj.R | 150 R/impl-epw.R | 53 R/impl-geom.R | 3674 ++++++++++++----------- R/impl-idd.R | 4 R/impl-iddobj.R | 228 - R/impl-idf.R | 487 ++- R/impl-idfobj-sch.R | 2010 ++++++------- R/impl-idfobj.R | 38 R/impl-sql.R | 1572 +++++----- R/impl-viewer.R | 135 R/impl.R | 39 R/install.R | 34 R/param.R | 11 R/rdd.R | 814 ++--- R/reload.R | 1 R/sql.R | 1309 ++++---- R/sysdata.rda |binary R/transition.R | 44 R/utils.R | 69 R/validate.R | 49 R/viewer.R | 1809 +++++------ README.md | 12 inst/CITATION | 32 inst/extdata/epw.idd | 1816 +++++------ man/EplusSql.Rd | 1600 +++++----- man/Idd.Rd | 12 man/IddObject.Rd | 5217 +++++++++++++++++----------------- man/Idf.Rd | 173 + man/IdfObject.Rd | 155 - man/IdfSchedule.Rd | 1162 +++---- man/IdfViewer.Rd | 1797 +++++------ man/as.character.IddObject.Rd | 13 man/as.character.Idf.Rd | 4 man/as.character.IdfObject.Rd | 93 man/as_EpwDate.Rd | 64 man/assertion.Rd | 182 - man/clean_wd.Rd | 86 man/custom_validate.Rd | 3 man/eplusr-package.Rd | 116 man/expand_idf_regex.Rd | 82 man/format.Idf.Rd | 4 man/format.IdfObject.Rd | 93 man/get_idd_relation.Rd | 126 man/get_idf_table.Rd | 3 man/idd_object.Rd | 60 man/init_idf_value.Rd | 126 man/install_duckdb_sqlite.Rd |only man/path_eplus.Rd | 136 man/rdd.Rd | 144 man/read_epw.Rd | 100 man/transition.Rd | 128 man/version_updater.Rd | 118 man/with_option.Rd | 96 tests/testthat.R | 10 tests/testthat/helper-cnd.R | 12 tests/testthat/helper-copy.R | 72 tests/testthat/helper-eplus.R | 14 tests/testthat/helper-latest-output.R |only tests/testthat/helper-text.R | 222 - tests/testthat/helper-transition.R | 28 tests/testthat/test-assert.R | 146 tests/testthat/test-diagram.R | 32 tests/testthat/test-epw.R | 40 tests/testthat/test-format.R | 1049 +++--- tests/testthat/test-group.R | 125 tests/testthat/test-idd.R | 120 tests/testthat/test-iddobj.R | 9 tests/testthat/test-idf.R | 240 + tests/testthat/test-idfobj-sch.R | 684 ++-- tests/testthat/test-idfobj.R | 78 tests/testthat/test-impl-epw.R | 1017 +++--- tests/testthat/test-impl-geom.R | 637 ++-- tests/testthat/test-impl-idd.R | 5 tests/testthat/test-impl-iddobj.R | 262 - tests/testthat/test-impl-idf.R | 137 tests/testthat/test-impl-idfobj-sch.R | 636 ++-- tests/testthat/test-impl-idfobj.R | 40 tests/testthat/test-impl-viewer.R | 200 + tests/testthat/test-impl.R | 46 tests/testthat/test-install.R | 86 tests/testthat/test-job-json.R | 20 tests/testthat/test-job.R | 255 - tests/testthat/test-options.R | 64 tests/testthat/test-param.R | 17 tests/testthat/test-parse.R | 1174 +++---- tests/testthat/test-rdd.R | 126 tests/testthat/test-reload.R | 9 tests/testthat/test-run.R | 1687 +++++----- tests/testthat/test-sql.R | 179 - tests/testthat/test-transition.R | 239 + tests/testthat/test-utils.R | 261 - tests/testthat/test-validate.R | 30 tests/testthat/test-viewer.R | 15 108 files changed, 24114 insertions(+), 21062 deletions(-)
Title: 'MUI X Tree View' for 'shiny' Apps and 'Quarto'
Description: Wraps the 'MUI X Tree View' React components <https://mui.com/x/react-tree-view/>
for use in 'shiny' applications and 'quarto' documents, letting users navigate
hierarchical data with nested levels that can be expanded and collapsed. Bundles
the MIT-licensed community edition of the '@mui/x-tree-view' JavaScript library
(the commercial 'Pro' tier is not included).
Author: Felix Luginbuhl [aut, cre, cph] ,
MUI [cph] JavaScript libraries; see LICENSE.note),
Meta Platforms, Inc. and affiliates [cph] ,
React Community [cph] ,
Luke Edwards [cph] ,
Reselect contributors [cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between muiTreeView versions 0.1.1 dated 2026-01-26 and 0.2.0 dated 2026-10-12
DESCRIPTION | 59 ++++++-- LICENSE.note |only MD5 | 83 +++++++++-- NAMESPACE | 13 + NEWS.md | 11 + R/browser.R |only R/components.R | 103 ++++++++++---- R/documentation.R | 168 ++++++++++++++++++++++++ R/muiTreeDependency.R | 40 +++-- R/zzz.R |only README.md | 134 +++++++++---------- inst/components.txt |only inst/examples |only inst/www/muiTreeView/x-tree-view.js | 64 ++++----- inst/www/muiTreeView/x-tree-view.js.LICENSE.txt | 26 --- man/RichTreeViewRoot.Rd |only man/SimpleTreeViewRoot.Rd |only man/TreeItemCheckbox.Rd |only man/TreeItemContent.Rd |only man/TreeItemGroupTransition.Rd |only man/TreeItemIconContainer.Rd |only man/TreeItemLabel.Rd |only man/TreeItemLabelInput.Rd |only man/TreeItemProvider.Rd |only man/TreeItemRoot.Rd |only man/TreeViewCollapseIcon.Rd |only man/TreeViewExpandIcon.Rd |only man/muiTreeViewDependency.Rd | 12 + man/print.muiTreeView.Rd |only tests/testthat/test-RichTreeView.R | 26 +-- tests/testthat/test-RichTreeViewRoot.R |only tests/testthat/test-SimpleTreeView.R | 26 +-- tests/testthat/test-SimpleTreeViewRoot.R |only tests/testthat/test-TreeItem.R | 26 +-- tests/testthat/test-TreeItemCheckbox.R |only tests/testthat/test-TreeItemContent.R |only tests/testthat/test-TreeItemGroupTransition.R |only tests/testthat/test-TreeItemIcon.R | 26 +-- tests/testthat/test-TreeItemIconContainer.R |only tests/testthat/test-TreeItemLabel.R |only tests/testthat/test-TreeItemLabelInput.R |only tests/testthat/test-TreeItemProvider.R |only tests/testthat/test-TreeItemRoot.R |only tests/testthat/test-TreeViewCollapseIcon.R |only tests/testthat/test-TreeViewExpandIcon.R |only tests/testthat/test-js-exports.R |only tests/testthat/test-muiTreeViewDependency.R |only 47 files changed, 571 insertions(+), 246 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.6.3 dated 2026-09-30 and 0.6.4 dated 2026-10-12
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 12 ++++++++++++ R/html_getTables.R | 3 +-- R/timeStamp.R | 27 ++++++++++++++++++++++++--- README.md | 14 +++++++------- inst/doc/date-parsing.Rmd | 4 ++-- inst/doc/date-parsing.html | 4 ++-- inst/doc/logging.html | 32 ++++++++++++++++---------------- man/timeStamp.Rd | 13 +++++++++++-- tests/testthat/test-html_getTables.R | 24 ++++++++++++++++++++++++ tests/testthat/test-setIfNull.R | 2 ++ tests/testthat/test-timeStamp.R | 35 +++++++++++++++++++++++++++++++++++ vignettes/date-parsing.Rmd | 4 ++-- 14 files changed, 156 insertions(+), 53 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>).
ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information
about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys.
More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>.
The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] ,
Luana Francesconi [aut],
Alice Musina [aut],
Luca Di Nuzzo [aut],
Gabriele Gheza [aut],
Chiara Pistocchi [aut],
Juri Nascimbene [aut],
Pier Luigi Nimis [aut],
Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Diff between ritalic versions 0.12.0 dated 2026-03-16 and 0.13.0 dated 2026-10-12
DESCRIPTION | 11 +++-- MD5 | 23 ++++++++--- NAMESPACE | 34 ++++++++++------- R/api_utils.R | 76 +++++++++++++++++++++------------------ R/italic_search.R |only R/italic_taxon_data.R | 24 ++++++++---- R/mcp.R |only README.md | 74 +++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/italic_mcp_server.Rd |only man/italic_mcp_tools.Rd |only man/italic_search.Rd |only man/italic_search_filters.Rd |only man/italic_taxon_data.Rd | 11 +++++ tests/testthat/test_api_utils.R |only tests/testthat/test_mcp.R |only tests/testthat/test_taxon_data.R |only 17 files changed, 185 insertions(+), 68 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.3.0 dated 2026-06-22 and 2.3.1 dated 2026-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Cluster.R | 37 ++++++++++++++++++++++++++++++++----- R/DA.R | 2 +- R/IM.R | 12 ++++++++---- man/MVar.pt-package.Rd | 4 ++-- 6 files changed, 52 insertions(+), 21 deletions(-)
Title: Multivariate Analysis
Description: Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.3.0 dated 2026-06-21 and 2.3.1 dated 2026-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Cluster_English.R | 35 +++++++++++++++++++++++++++++++---- R/DA_English.R | 2 +- R/IM_English.R | 15 +++++++++------ man/MVar-package.Rd | 4 ++-- 6 files changed, 52 insertions(+), 22 deletions(-)
Title: Mobility Network Analysis
Description: Implements the method to analyse weighted mobility networks or distribution networks as outlined in:
Block, P., Stadtfeld, C., & Robins, G. (2022) <doi:10.1016/j.socnet.2021.08.003>.
The purpose of the model is to analyse the structure of mobility,
incorporating exogenous predictors pertaining to individuals and locations
known from classical mobility analyses, as well as modelling emergent mobility
patterns akin to structural patterns known from the statistical analysis of social networks.
Version 2 runs the simulations in 'C++' (using 'Rcpp') and, besides stochastic
approximation (Robbins-Monro), can estimate parameters with Geyer-Thompson MCMC
maximum likelihood estimation.
Author: Per Block [cre, aut, cph] ,
Christoph Stadtfeld [aut] ,
Nico Keiser [aut] ,
Marion Hoffman [aut] ,
Jingying Wang [aut]
Maintainer: Per Block <block@soziologie.uzh.ch>
Diff between MoNAn versions 2.0.0 dated 2026-10-11 and 2.1.1 dated 2026-10-12
DESCRIPTION | 10 MD5 | 72 ++-- NAMESPACE | 13 NEWS.md | 75 ++++ R/1_hiddenFunctions.R | 359 +++++++++++----------- R/1b_cppSampler.R | 19 + R/2c_effectFunctions_concentration.R | 376 +++++++++++++----------- R/3_coreFunctions.R | 38 +- R/4_auxiliaryFunctions.R | 222 ++++++++++---- R/5_gofParamFunctions.R | 37 +- R/RcppExports.R | 4 README.md | 78 +++- data/myResDN.rda |binary man/concentration_basic_squared.Rd |only man/concentration_norm.Rd |only man/concentration_norm_squared.Rd |only man/concentration_prop_orig_cov.Rd |only man/concentration_rankGW.Rd |only man/estimateMobilityNetwork.Rd | 13 man/extractTraces.Rd | 5 man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-17-2.png |binary man/figures/README-unnamed-chunk-17-3.png |binary man/figures/README-unnamed-chunk-17-4.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-19-2.png |binary man/getIndegree.Rd | 8 man/getTieWeights.Rd | 7 man/gofMobilityNetwork.Rd | 22 + man/scoreTest.Rd | 59 ++- src/RcppExports.cpp | 20 + src/effects.cpp | 164 ++++++++++ src/sampler.cpp | 92 +++++ tests/testthat/helper-cpp.R | 18 - tests/testthat/test-cpp-effects-concentration.R | 19 + tests/testthat/test-effects-change-target.R | 6 tests/testthat/test-geyer-thompson.R | 56 +++ tests/testthat/test-gof.R |only tests/testthat/test-parallel.R |only tests/testthat/test-sampler-cpp.R | 4 tests/testthat/test-score-test.R |only 41 files changed, 1270 insertions(+), 526 deletions(-)
Title: Machine Learning
Description: Machine learning, containing several algorithms for supervised and unsupervised classification, in addition to a function that plots the Receiver Operating Characteristic (ROC) and Precision-Recall (PRC) curve graphs, and also a function that returns several metrics used for model evaluation, the latter can be used in ranking results from other packs.
Author: Paulo Cesar Ossani [aut, cre]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between Kira versions 1.0.8 dated 2026-04-13 and 1.0.9 dated 2026-10-12
DESCRIPTION | 8 ++++---- MD5 | 32 +++++++++++++++++--------------- NAMESPACE | 7 ++++--- R/IM.R |only R/brute.force.R | 8 ++++---- R/elbow.R | 9 +++++++-- R/hierarchical.R | 17 +++++++++++------ R/kmeans.R | 7 ++++++- R/knn.R | 6 ++++++ R/lda.R | 4 ++-- R/qda.R | 2 +- R/regression.R | 13 ++++++++++--- R/silhouette.R | 9 +++++++-- R/transf.data.R |only man/Kira-package.Rd | 4 ++-- man/elbow.Rd | 6 +++--- man/hierarchical.Rd | 4 ++-- man/silhouette.Rd | 8 ++++---- 18 files changed, 90 insertions(+), 54 deletions(-)
Title: Quantifying and Monetizing Health Impacts Attributable to
Exposure
Description: This R package has been developed with a focus on air pollution and noise but can be applied to other exposures. The initial development has been funded by the European Union project BEST-COST. Disclaimer: It is work in progress and the developers are not liable for any calculation errors or inaccuracies resulting from the use of this package.
Selection of relevant references (in chronological order):
WHO (2003) <https://www.who.int/publications/i/item/9241546204>,
Murray et al. (2003) <doi:10.1186/1478-7954-1-1>,
Miller & Hurley (2003) <doi:10.1136/jech.57.3.200>,
Steenland & Armstrong (2006) <doi:10.1097/01.ede.0000229155.05644.43>,
WHO (2011) <https://iris.who.int/items/723ab97c-5c33-4e3b-8df1-744aa5bc1c27>,
GBD 2019 Risk Factors Collaborators (2020) <doi:10.1016/S0140-6736(20)30752-2>.
Author: Alberto Castro [cre, aut] ,
Axel Luyten [aut] ,
Arno Pauwels [ctb] ,
Liliana Vazquez Fernandez [ctb] ,
Gianni Ardielli [ctb] ,
Iracy Pimenta [ctb] ,
Susanne Breitner [ctb] ,
Carl Baravelli [ctb] ,
Vanessa Gorasso [ctb] ,
Maria Lepnurm [ctb] ,
Andreia [...truncated...]
Maintainer: Alberto Castro <alberto.castrofernandez@swisstph.ch>
Diff between healthiar versions 0.2.6 dated 2026-09-11 and 0.2.7 dated 2026-10-12
DESCRIPTION | 8 MD5 | 68 NEWS.md | 41 R/attribute_lifetable.R | 9 R/attribute_master.R | 2 R/compare.R | 66 R/compile_input.R | 5 R/get_impact_with_lifetable.R | 59 R/get_output.R | 34 R/get_risk_and_pop_fraction.R | 31 R/prepare_lifetable.R | 731 + R/socialize.R | 6 R/summarize_uncertainty.R | 154 R/validate_input_attribute.R | 82 R/zzz_global_variables.R | 114 README.md | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro_to_healthiar.R | 20 inst/doc/intro_to_healthiar.Rmd | 5697 +++++++-------- inst/doc/intro_to_healthiar.html | 179 man/attribute_health.Rd | 2 man/attribute_lifetable.Rd | 11 man/attribute_master.Rd | 2 man/attribute_mod.Rd | 2 man/healthiar-package.Rd | 1 man/prepare_lifetable.Rd | 8 tests/testthat/test-attribute_health.R |10348 ++++++++++++++-------------- tests/testthat/test-attribute_lifetable.R | 2521 +++--- tests/testthat/test-compare.R | 24 tests/testthat/test-multiexpose.R | 70 tests/testthat/test-prepare_lifetable.R | 24 tests/testthat/test-socialize.R | 45 tests/testthat/test-summarize_uncertainty.R | 2157 ++--- vignettes/intro_to_healthiar.Rmd | 5697 +++++++-------- 35 files changed, 14491 insertions(+), 13736 deletions(-)
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, every
node-level test statistic is divided by the number of imputations M,
the node-level p-values are recomputed from the chi-squared reference
distribution 'ctree' uses (including its multiplicity adjustment across
candidate splitting variables), and the tree is compressed bottom-up
(the Stack/M correction). Degrees of freedom are derived for each node
and each candidate variable, so univariate, bivariate and
higher-dimensional outcomes are all handled, as are unordered factor
predictors, whose degrees of freedom depend on how many levels remain
in a node. The result is a single interpretable tree [...truncated...]
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 1.1.0 dated 2026-09-18 and 1.2.0 dated 2026-10-12
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 33 ++ R/confirm.R | 523 +++++++++++++++++++++++++++++++----------- R/ctree_stacked.R | 2 man/confirm_ctreeMI.Rd | 57 ++++ man/ctree_stacked.Rd | 2 man/discover_confirm.Rd | 14 + man/split_holdout.Rd | 28 +- tests/testthat/test-confirm.R | 162 +++++++++++++ 10 files changed, 695 insertions(+), 152 deletions(-)
Title: Ballot-Level Microdata and Summaries for Ecological Inference
(Florida 2000)
Description: Provides access to ballot-level electoral microdata from the Florida 2000
general election and tools for computing summaries suitable for ecological inference.
Includes functions to load data by county or race (election), compute marginal distributions
at the precinct level, and build joint contingency arrays across multiple races for
use with ecological inference packages. Data files are stored in a remote repository
and downloaded on demand; local copies are supported via the 'data_dir' option.
Acknowledgements:
We thank Jaime Ventura (ANES, University of Michigan) and Dan Keating (The Washington Post) for providing the raw data that serve as the starting point for the construction of this package. We also acknowledge funding from the Conselleria de Educación, Cultura y Universidades (grant CIACIO/2023/031).
Author: Cristina Aybar [aut] ,
Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between eiballots versions 0.1.0-1 dated 2026-09-26 and 0.2.0-1 dated 2026-10-12
DESCRIPTION | 6 MD5 | 77 ++--- NEWS.md |only R/county.R | 3 R/county_docs.R | 646 ++++++++++++++++++++++------------------------ R/data-objects.R | 25 - R/data_access.R | 22 + R/ei_summary.R | 5 R/ei_summary_random.R | 15 - R/utils.R | 87 +++--- README.md | 417 +++++++++++++++++++++++------ data/Broward.rda |binary data/Highlands.rda |binary data/Hillsborough.rda |binary data/Lee.rda |binary data/Marion.rda |binary data/Miami_Dade.rda |binary data/Palm_Beach.rda |binary data/Pasco.rda |binary data/Pinellas.rda |binary data/Sarasota.rda |binary data/county_catalog.rda |binary data/election_catalog.rda |binary man/Broward.Rd | 55 +-- man/Highlands.Rd | 35 +- man/Hillsborough.Rd | 135 ++++----- man/Lee.Rd | 35 +- man/Marion.Rd | 81 ++--- man/Miami_Dade.Rd | 79 ++--- man/Palm_Beach.Rd | 121 ++++---- man/Pasco.Rd | 25 - man/Pinellas.Rd | 39 +- man/Sarasota.Rd | 31 +- man/ei_summary.Rd | 4 man/ei_summary_random.Rd | 14 man/election_catalog.Rd | 20 - man/example_ballots.Rd | 4 man/get_county_data.Rd | 12 man/get_election_data.Rd | 2 man/list_elections.Rd | 4 40 files changed, 1154 insertions(+), 845 deletions(-)
Title: Taxonomic Hierarchy Distances and Lineage Analysis
Description: Computes distances between taxonomic hierarchy nodes using lineage
data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For
distinct nodes, distance is defined as the reciprocal of the depth of their
most recent common ancestor; identical nodes have distance zero. This
definition yields an ultrametric within each connected hierarchy. Functions
are provided for auditable name resolution, online or user-supplied lineage
analysis, clade membership, pairwise, matrix, and cross-set distance
calculation, classification trees with named clades, hierarchical
clustering, principal coordinates analysis, portable and comparable JSON
analysis bundles, and cache management. Distance matrices are returned as
base R 'dist' objects. The distances represent classification depth rather
than evolutionary time or phylogenetic branch length.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between taxodist versions 0.8.0 dated 2026-09-24 and 0.9.0 dated 2026-10-12
DESCRIPTION | 18 MD5 | 86 - NAMESPACE | 9 NEWS.md | 102 + R/bundle.R | 187 ++ R/distance.R | 1274 ++++++++++--------- R/fetch.R | 2040 ++++++++++++++++--------------- R/taxodist-package.R | 11 R/tree.R |only R/utils.R | 23 inst/CITATION | 2 inst/WORDLIST | 58 inst/doc/introduction.R | 52 inst/doc/introduction.Rmd | 117 + inst/doc/introduction.html | 361 +++-- inst/doc/statistical-applications.R | 4 inst/doc/statistical-applications.Rmd | 10 inst/doc/statistical-applications.html | 375 ++--- man/cache_info.Rd | 5 man/check_coverage.Rd | 6 man/compare_bundles.Rd |only man/cross_distances.Rd |only man/distance_matrix.Rd | 11 man/focal_distances.Rd | 3 man/get_lineage.Rd | 5 man/get_lineage_by_id.Rd | 11 man/get_taxonomicon_id.Rd | 19 man/load_cache.Rd | 6 man/print.taxodist_bundle_comparison.Rd |only man/save_cache.Rd | 8 man/taxo_bundle.Rd | 11 man/taxo_cluster.Rd | 3 man/taxo_heatmap.Rd | 14 man/taxo_ordinate.Rd | 2 man/taxo_resolve.Rd | 17 man/taxo_search.Rd | 2 man/taxo_tree.Rd |only man/taxodist-package.Rd | 12 tests/testthat/test-analysis.R |only tests/testthat/test-bundle-compare.R |only tests/testthat/test-bundle.R |only tests/testthat/test-cache.R |only tests/testthat/test-data.R |only tests/testthat/test-distance.R | 2098 -------------------------------- tests/testthat/test-fetch.R |only tests/testthat/test-matrix.R |only tests/testthat/test-network.R |only tests/testthat/test-path.R |only tests/testthat/test-resolution.R |only tests/testthat/test-tree.R |only vignettes/introduction.Rmd | 117 + vignettes/statistical-applications.Rmd | 10 52 files changed, 3028 insertions(+), 4061 deletions(-)
Title: Interface to 'TA-Lib' for Technical Analysis and Candlestick
Patterns
Description: Interface to the 'TA-Lib' (Technical Analysis Library) 'C'
library, providing access to 150+ indicators (e.g. Average Directional
Movement Index (ADX), Moving Average Convergence Divergence (MACD),
Relative Strength Index (RSI), Stochastic Oscillator, Bollinger Bands),
candlestick pattern recognition, and rolling-window utilities. Core
computations are implemented in 'C' for fast Open-High-Low-Close-Volume
(OHLCV) time-series feature engineering and rule-based signal
generation, with optional interactive visualization via 'plotly'.
Author: Serkan Korkmaz [cre, aut, cph] ,
Mario Fortier [cph] )
Maintainer: Serkan Korkmaz <serkor1@duck.com>
Diff between talib versions 0.9-4 dated 2026-10-05 and 0.9-5 dated 2026-10-12
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 4 ++ README.md | 2 - inst/doc/candlestick.html | 8 ++-- inst/doc/charting.html | 92 +++++++++++++++++++++++----------------------- inst/doc/talib.html | 4 +- src/shift.c | 34 ++++++++++------- 8 files changed, 87 insertions(+), 77 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Tom Palmer [aut] ,
Paul Madley-Dowd [aut] ,
Alejandro Szmulewicz [aut] ,
Miguel A. Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.4.4 dated 2026-08-28 and 1.4.5 dated 2026-10-12
SEQTaRget-1.4.4/SEQTaRget/man/bake_followup_spline.Rd |only SEQTaRget-1.4.5/SEQTaRget/DESCRIPTION | 13 SEQTaRget-1.4.5/SEQTaRget/MD5 | 93 ++--- SEQTaRget-1.4.5/SEQTaRget/NAMESPACE | 3 SEQTaRget-1.4.5/SEQTaRget/NEWS.md | 25 + SEQTaRget-1.4.5/SEQTaRget/R/SEQestimate.R | 2 SEQTaRget-1.4.5/SEQTaRget/R/SEQexpand.R | 21 - SEQTaRget-1.4.5/SEQTaRget/R/SEQopts.R | 35 + SEQTaRget-1.4.5/SEQTaRget/R/SEQuential.R | 71 ++- SEQTaRget-1.4.5/SEQTaRget/R/class_definitions.R | 4 SEQTaRget-1.4.5/SEQTaRget/R/class_setters.R | 2 SEQTaRget-1.4.5/SEQTaRget/R/internal_analysis.R | 10 SEQTaRget-1.4.5/SEQTaRget/R/internal_covariates.R | 26 + SEQTaRget-1.4.5/SEQTaRget/R/internal_endoffup.R | 63 +-- SEQTaRget-1.4.5/SEQTaRget/R/internal_glmHelpers.R | 32 + SEQTaRget-1.4.5/SEQTaRget/R/internal_hazard.R | 23 - SEQTaRget-1.4.5/SEQTaRget/R/internal_misc.R | 138 ++++--- SEQTaRget-1.4.5/SEQTaRget/R/internal_models.R | 2 SEQTaRget-1.4.5/SEQTaRget/R/internal_multinomial.R | 7 SEQTaRget-1.4.5/SEQTaRget/R/internal_survival.R | 21 - SEQTaRget-1.4.5/SEQTaRget/R/internal_weights.R | 34 + SEQTaRget-1.4.5/SEQTaRget/inst/doc/SEQuential.html | 42 +- SEQTaRget-1.4.5/SEQTaRget/inst/doc/censoring.R | 47 ++ SEQTaRget-1.4.5/SEQTaRget/inst/doc/censoring.Rmd | 68 +++ SEQTaRget-1.4.5/SEQTaRget/inst/doc/censoring.html | 200 +++++++---- SEQTaRget-1.4.5/SEQTaRget/inst/doc/endoffollowup.Rmd | 2 SEQTaRget-1.4.5/SEQTaRget/inst/doc/endoffollowup.html | 4 SEQTaRget-1.4.5/SEQTaRget/inst/doc/seqopts.Rmd | 4 SEQTaRget-1.4.5/SEQTaRget/inst/doc/seqopts.html | 18 SEQTaRget-1.4.5/SEQTaRget/man/SEQopts.Rd | 12 SEQTaRget-1.4.5/SEQTaRget/man/SEQuential.Rd | 2 SEQTaRget-1.4.5/SEQTaRget/man/bake_spline_knots.Rd |only SEQTaRget-1.4.5/SEQTaRget/man/bake_spline_knots_one.Rd |only SEQTaRget-1.4.5/SEQTaRget/man/check_design.Rd |only SEQTaRget-1.4.5/SEQTaRget/man/design_matrix.Rd |only SEQTaRget-1.4.5/SEQTaRget/man/endoffup.periods.Rd |only SEQTaRget-1.4.5/SEQTaRget/man/internal.hazard.Rd | 2 SEQTaRget-1.4.5/SEQTaRget/man/internal.survival.Rd | 2 SEQTaRget-1.4.5/SEQTaRget/man/subgroup_rows.Rd |only SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_coefficients.R | 51 +- SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_covariates.R | 106 +++++ SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_deviation.R | 28 + SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_end_of_fup.R | 12 SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_errors.R | 32 + SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_misc.R | 148 ++++++++ SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_multinomial.R | 65 ++- SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_parallel.R | 13 SEQTaRget-1.4.5/SEQTaRget/tests/testthat/test_splines.R | 165 ++++++++- SEQTaRget-1.4.5/SEQTaRget/vignettes/censoring.Rmd | 68 +++ SEQTaRget-1.4.5/SEQTaRget/vignettes/endoffollowup.Rmd | 2 SEQTaRget-1.4.5/SEQTaRget/vignettes/seqopts.Rmd | 4 51 files changed, 1346 insertions(+), 376 deletions(-)
Title: Donor-Adjusted Post-Shock Forecasting
Description: Implements donor-adjusted methods for forecasting conditional
means and variances after structural shocks. Historical donor episodes
are weighted using covariates observed before each shock, and their
estimated post-shock effects are combined with forecasts from a
target-series model. The methods build on Lin and Eck (2021)
<doi:10.1016/j.ijforecast.2021.03.010>. The package supports donor
balancing weights, structured donor pools, autoregressive integrated
moving average models, and generalized autoregressive conditional
heteroscedasticity models with external regressors.
Author: Qiyang Wang [aut, cre] ,
Daniel J. Eck [aut]
Maintainer: Qiyang Wang <wangqiyang497@gmail.com>
Diff between postshock versions 0.2.0 dated 2026-07-27 and 0.2.1 dated 2026-10-12
DESCRIPTION | 6 MD5 | 47 +++++-- NEWS.md |only R/SynthPrediction.R | 169 +++++++++++++++++++++++---- R/SynthPredictionMultiPool.R | 13 +- R/SynthVolForecast.R | 10 - R/auto-garchx.R | 68 +++++++--- R/data_aapl_s1_input.R |only R/dbw.R | 40 +++++- R/validate-donor-arimax.R |only data/aapl_s1_input.rda |only inst/doc/postshock-workflow.R | 10 - inst/doc/postshock-workflow.Rmd | 28 ++-- inst/doc/postshock-workflow.html | 45 ++++--- inst/replication |only man/SynthPrediction.Rd | 79 ++++++++++-- man/SynthPredictionMultiPool.Rd | 14 +- man/SynthVolForecast.Rd | 12 + man/aapl_s1_input.Rd |only man/auto_garchx.Rd | 17 ++ man/dbw.Rd | 22 +++ tests/testthat/helper-maintenance.R |only tests/testthat/test-maintenance-apple-data.R |only tests/testthat/test-maintenance-arimax.R |only tests/testthat/test-maintenance-garch.R |only tests/testthat/test-maintenance-multipool.R |only tests/testthat/test-maintenance-seasonal.R |only tests/testthat/test-pca-stage.R |only tests/testthat/test-runtime-fingerprint.R |only vignettes/postshock-workflow.Rmd | 28 ++-- 30 files changed, 466 insertions(+), 142 deletions(-)
Title: Goodness-of-Fit Tests for Skew-Normal and Skew-t Models
Description: Provides precomputed-quantile goodness-of-fit tests for
skew-normal distributions, parametric-bootstrap tests for skew-normal and
skew-t distributions, robust fitting, and graphical diagnostics.
Package methods and documentation are described by Li, Xu, and Khang
(2026) <https://github.com/Divo-Lee/PBGoF>.
Author: Hongxiang Li [aut, cre],
Chenglin Xu [aut],
Tsung Fei Khang [aut]
Maintainer: Hongxiang Li <hxli@ynnu.edu.cn>
Diff between PBGoF versions 0.1.0 dated 2026-10-02 and 0.2.0 dated 2026-10-12
PBGoF-0.1.0/PBGoF/R/PBGoF.precomputed.tests.R |only PBGoF-0.1.0/PBGoF/man/PBGoF-precomputed-tests.Rd |only PBGoF-0.2.0/PBGoF/DESCRIPTION | 27 PBGoF-0.2.0/PBGoF/MD5 | 36 - PBGoF-0.2.0/PBGoF/NAMESPACE | 7 PBGoF-0.2.0/PBGoF/R/PBGoF.precomputed.test.R |only PBGoF-0.2.0/PBGoF/R/QQ.plot.R |only PBGoF-0.2.0/PBGoF/R/cdf.plot.check.R |only PBGoF-0.2.0/PBGoF/R/para.bootstrap.test.R |only PBGoF-0.2.0/PBGoF/R/sn.plot.check.R | 12 PBGoF-0.2.0/PBGoF/R/st.fit.robust.R |only PBGoF-0.2.0/PBGoF/R/st.para.bootstrap.gof.R |only PBGoF-0.2.0/PBGoF/R/st.plot.check.R |only PBGoF-0.2.0/PBGoF/README.md | 101 ++- PBGoF-0.2.0/PBGoF/inst/CITATION | 7 PBGoF-0.2.0/PBGoF/inst/doc/Introduction.Rmd | 604 +++++++++++----------- PBGoF-0.2.0/PBGoF/inst/doc/Introduction.html | 149 +++-- PBGoF-0.2.0/PBGoF/inst/documents/Introduction.pdf |binary PBGoF-0.2.0/PBGoF/man/PBGoF-precomputed-test.Rd |only PBGoF-0.2.0/PBGoF/man/QQ.plot.Rd |only PBGoF-0.2.0/PBGoF/man/cdf.plot.check.Rd |only PBGoF-0.2.0/PBGoF/man/para.bootstrap.test.Rd |only PBGoF-0.2.0/PBGoF/man/sn.plot.check.Rd | 5 PBGoF-0.2.0/PBGoF/man/st-parametric-bootstrap.Rd |only PBGoF-0.2.0/PBGoF/man/st.fit.robust.Rd |only PBGoF-0.2.0/PBGoF/man/st.plot.check.Rd |only PBGoF-0.2.0/PBGoF/vignettes/Introduction.Rmd | 604 +++++++++++----------- 27 files changed, 850 insertions(+), 702 deletions(-)
Title: Multi-Action, Multi-Objective Spatial Planning
Description: Provides a modular framework for exact multi-objective spatial
planning using mixed-integer programming. The package supports the
definition of planning problems through planning units, features,
management actions, action effects, spatial relations, targets,
constraints, and objective functions. It enables the optimisation of
spatial planning portfolios under considerations such as boundary
structure, connectivity, and fragmentation. Supported multi-objective
methods include weighted-sum aggregation, epsilon-constraint, and the
augmented epsilon-constraint method. Problems can be solved with several
commercial and open-source optimisation solvers. Optional solver backends
include the 'gurobi' R package, which is distributed with the Gurobi Optimizer
installation <https://docs.gurobi.com/projects/optimizer/en/13.0/reference/r/setup.html>,
and the 'rcbc' R package, available from GitHub at
<https://github.com/dirkschumacher/rcbc>. For background on multi-objective
optimisati [...truncated...]
Author: Jose Salgado-Rojas [aut, cre] ,
Matias Moreno-Faguett [aut] ,
Victoria Madrid-Ayala [aut] ,
Sara Pineda-Zapata [aut] ,
Nuria Aquilue [aut]
Maintainer: Jose Salgado-Rojas <jose.salgroj@gmail.com>
Diff between multiscape versions 1.0.7 dated 2026-04-30 and 1.4.2 dated 2026-10-12
multiscape-1.0.7/multiscape/R/add_constraint_locked_pu.R |only multiscape-1.0.7/multiscape/R/get_solution.R |only multiscape-1.0.7/multiscape/man/figures/overview_multiscape.png |only multiscape-1.0.7/multiscape/man/get_solution_vector.Rd |only multiscape-1.0.7/multiscape/man/plot_spatial.Rd |only multiscape-1.0.7/multiscape/man/solution-class.Rd |only multiscape-1.0.7/multiscape/src/functions.cpp |only multiscape-1.0.7/multiscape/src/functions.h |only multiscape-1.0.7/multiscape/src/rcpp_fix_z_ineligible_by_positive_delta.cpp |only multiscape-1.4.2/multiscape/DESCRIPTION | 50 multiscape-1.4.2/multiscape/MD5 | 476 +- multiscape-1.4.2/multiscape/NAMESPACE | 43 multiscape-1.4.2/multiscape/NEWS.md | 345 + multiscape-1.4.2/multiscape/R/RcppExports.R | 20 multiscape-1.4.2/multiscape/R/add_action_sets.R |only multiscape-1.4.2/multiscape/R/add_actions.R | 1136 ++++- multiscape-1.4.2/multiscape/R/add_constraint_action_cardinality.R |only multiscape-1.4.2/multiscape/R/add_constraint_action_relations.R |only multiscape-1.4.2/multiscape/R/add_constraint_area.R | 171 multiscape-1.4.2/multiscape/R/add_constraint_budget.R | 53 multiscape-1.4.2/multiscape/R/add_constraint_locked_actions.R | 89 multiscape-1.4.2/multiscape/R/add_constraint_locked_planning_units.R |only multiscape-1.4.2/multiscape/R/add_constraint_targets.R | 100 multiscape-1.4.2/multiscape/R/add_effects.R | 1520 ++++-- multiscape-1.4.2/multiscape/R/add_objectives.R | 1137 ++--- multiscape-1.4.2/multiscape/R/add_profit.R | 379 + multiscape-1.4.2/multiscape/R/add_spatial_relations.R | 250 - multiscape-1.4.2/multiscape/R/analysis_frontier.R |only multiscape-1.4.2/multiscape/R/analysis_get.R |only multiscape-1.4.2/multiscape/R/analysis_linkage.R |only multiscape-1.4.2/multiscape/R/analysis_selection.R |only multiscape-1.4.2/multiscape/R/analysis_solution.R |only multiscape-1.4.2/multiscape/R/build_model.R | 389 + multiscape-1.4.2/multiscape/R/compile_model.R | 23 multiscape-1.4.2/multiscape/R/create_problem.R | 74 multiscape-1.4.2/multiscape/R/data-sim.R | 41 multiscape-1.4.2/multiscape/R/internal.R | 2172 +++++++--- multiscape-1.4.2/multiscape/R/internalMO.R | 2166 +++++++-- multiscape-1.4.2/multiscape/R/joint_effects.R |only multiscape-1.4.2/multiscape/R/load_sim.R | 151 multiscape-1.4.2/multiscape/R/plot.R | 901 ++-- multiscape-1.4.2/multiscape/R/print.R | 84 multiscape-1.4.2/multiscape/R/problem-class.R | 94 multiscape-1.4.2/multiscape/R/set_method_augmecon.R | 644 +- multiscape-1.4.2/multiscape/R/set_method_epsilon_constraint.R | 636 +- multiscape-1.4.2/multiscape/R/set_method_weighted_sum.R | 673 +-- multiscape-1.4.2/multiscape/R/set_run_design.R |only multiscape-1.4.2/multiscape/R/set_solver.R | 595 +- multiscape-1.4.2/multiscape/R/solution-class.R | 179 multiscape-1.4.2/multiscape/R/solutionset-class.R | 585 +- multiscape-1.4.2/multiscape/R/solve.R | 238 - multiscape-1.4.2/multiscape/README.md | 1380 ++++-- multiscape-1.4.2/multiscape/build |only multiscape-1.4.2/multiscape/data/sim_multiaction.rda |only multiscape-1.4.2/multiscape/inst/doc |only multiscape-1.4.2/multiscape/inst/extdata/meseta_iberica_inputs.rds |only multiscape-1.4.2/multiscape/man/add_action_sets.Rd |only multiscape-1.4.2/multiscape/man/add_actions.Rd | 119 multiscape-1.4.2/multiscape/man/add_benefits.Rd | 64 multiscape-1.4.2/multiscape/man/add_constraint_action_cardinality.Rd |only multiscape-1.4.2/multiscape/man/add_constraint_action_excludes.Rd |only multiscape-1.4.2/multiscape/man/add_constraint_action_requires.Rd |only multiscape-1.4.2/multiscape/man/add_constraint_action_together.Rd |only multiscape-1.4.2/multiscape/man/add_constraint_area.Rd | 169 multiscape-1.4.2/multiscape/man/add_constraint_budget.Rd | 51 multiscape-1.4.2/multiscape/man/add_constraint_locked_actions.Rd | 81 multiscape-1.4.2/multiscape/man/add_constraint_locked_planning_units.Rd |only multiscape-1.4.2/multiscape/man/add_constraint_locked_pu.Rd 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multiscape-1.4.2/multiscape/man/add_objective_min_loss.Rd | 117 multiscape-1.4.2/multiscape/man/add_profit.Rd | 292 - multiscape-1.4.2/multiscape/man/add_spatial_boundary.Rd | 30 multiscape-1.4.2/multiscape/man/add_spatial_distance.Rd | 25 multiscape-1.4.2/multiscape/man/add_spatial_knn.Rd | 25 multiscape-1.4.2/multiscape/man/add_spatial_queen.Rd | 15 multiscape-1.4.2/multiscape/man/add_spatial_relations.Rd | 49 multiscape-1.4.2/multiscape/man/add_spatial_rook.Rd | 15 multiscape-1.4.2/multiscape/man/compile_model.Rd | 23 multiscape-1.4.2/multiscape/man/create_problem.Rd | 48 multiscape-1.4.2/multiscape/man/figures/README-example-features-1.png |only multiscape-1.4.2/multiscape/man/figures/README-example-maps-1.png |only multiscape-1.4.2/multiscape/man/figures/README-example-tradeoff-1.png |only multiscape-1.4.2/multiscape/man/figures/README-meseta-alternative-action-maps-1.png |only multiscape-1.4.2/multiscape/man/figures/README-meseta-cost-map-1.png |only 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| 1 multiscape-1.4.2/multiscape/src/rcpp_add_objective_max_net_profit.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_add_objective_max_profit.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_add_objective_min_fragmentation.cpp | 113 multiscape-1.4.2/multiscape/src/rcpp_add_objective_min_fragmentation_actions.cpp | 167 multiscape-1.4.2/multiscape/src/rcpp_add_objective_min_intervention_impact.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_add_pu_locks.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_add_target_recovery.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_effect_aggregation.cpp |only multiscape-1.4.2/multiscape/src/rcpp_objective_runtime.cpp | 53 multiscape-1.4.2/multiscape/src/rcpp_prepare_objective_max_net_profit.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_prepare_objective_max_profit.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_prepare_objective_min_cost.cpp | 1 multiscape-1.4.2/multiscape/src/rcpp_prepare_objective_min_intervention_impact.cpp | 1 multiscape-1.4.2/multiscape/tests/testthat/helper-coverage.R |only multiscape-1.4.2/multiscape/tests/testthat/helper-effects-reference.R |only multiscape-1.4.2/multiscape/tests/testthat/helper-legacy-objectives.R |only multiscape-1.4.2/multiscape/tests/testthat/helper-mock-solutionset.R |only multiscape-1.4.2/multiscape/tests/testthat/helper-new-api.R |only multiscape-1.4.2/multiscape/tests/testthat/helper-toy-problems.R | 4 multiscape-1.4.2/multiscape/tests/testthat/test-accessors-handmade-solutionset.R |only multiscape-1.4.2/multiscape/tests/testthat/test-action-cardinality.R |only multiscape-1.4.2/multiscape/tests/testthat/test-action-locks.R |only multiscape-1.4.2/multiscape/tests/testthat/test-action-max-per-pu.R |only multiscape-1.4.2/multiscape/tests/testthat/test-action-relations.R |only multiscape-1.4.2/multiscape/tests/testthat/test-action-sets.R |only multiscape-1.4.2/multiscape/tests/testthat/test-actions-effects.R |only 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multiscape-1.4.2/multiscape/tests/testthat/test-equivalence-prioritizr-cost.R | 5 multiscape-1.4.2/multiscape/tests/testthat/test-equivalence-prioritizr-frag.R | 14 multiscape-1.4.2/multiscape/tests/testthat/test-frontier-extra-no-solver.R |only multiscape-1.4.2/multiscape/tests/testthat/test-frontier-selection.R |only multiscape-1.4.2/multiscape/tests/testthat/test-get_actions.R | 17 multiscape-1.4.2/multiscape/tests/testthat/test-get_features.R | 30 multiscape-1.4.2/multiscape/tests/testthat/test-get_pu.R | 17 multiscape-1.4.2/multiscape/tests/testthat/test-internal-helpers-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-intervention-impact-deprecation.R |only multiscape-1.4.2/multiscape/tests/testthat/test-joint-effects.R |only multiscape-1.4.2/multiscape/tests/testthat/test-linkage-analysis.R |only multiscape-1.4.2/multiscape/tests/testthat/test-load-sim-data.R |only multiscape-1.4.2/multiscape/tests/testthat/test-locked-actions-and-effects-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-locked.R | 11 multiscape-1.4.2/multiscape/tests/testthat/test-max_one_action.R | 9 multiscape-1.4.2/multiscape/tests/testthat/test-method-contracts.R | 205 multiscape-1.4.2/multiscape/tests/testthat/test-methods-validation-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-mo-numerical-regressions.R |only multiscape-1.4.2/multiscape/tests/testthat/test-net-benefit-and-final-loss.R |only multiscape-1.4.2/multiscape/tests/testthat/test-new-accessors.R |only multiscape-1.4.2/multiscape/tests/testthat/test-plot-internal-validation.R |only multiscape-1.4.2/multiscape/tests/testthat/test-plot-spatial.R |only multiscape-1.4.2/multiscape/tests/testthat/test-plot-tradeoff-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-plot.R |only multiscape-1.4.2/multiscape/tests/testthat/test-print-show-solution-classes.R |only multiscape-1.4.2/multiscape/tests/testthat/test-print-structure.R | 13 multiscape-1.4.2/multiscape/tests/testthat/test-problem-build.R |only multiscape-1.4.2/multiscape/tests/testthat/test-problem-class-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-problem-class.R |only multiscape-1.4.2/multiscape/tests/testthat/test-proto-creation-memory.R |only multiscape-1.4.2/multiscape/tests/testthat/test-repeated-calls-contract.R |only multiscape-1.4.2/multiscape/tests/testthat/test-restoration_needed.R | 9 multiscape-1.4.2/multiscape/tests/testthat/test-run-design-and-solver-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-run-design-control.R |only multiscape-1.4.2/multiscape/tests/testthat/test-selection-frequency-counts.R |only multiscape-1.4.2/multiscape/tests/testthat/test-selection-objective-evaluation.R |only multiscape-1.4.2/multiscape/tests/testthat/test-set-solver-solve.R |only multiscape-1.4.2/multiscape/tests/testthat/test-set-solver.R |only multiscape-1.4.2/multiscape/tests/testthat/test-solution-management-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-solution-management.R |only multiscape-1.4.2/multiscape/tests/testthat/test-solution-structure.R | 27 multiscape-1.4.2/multiscape/tests/testthat/test-solve-method-errors.R | 2 multiscape-1.4.2/multiscape/tests/testthat/test-solve-multiobjective.R | 11 multiscape-1.4.2/multiscape/tests/testthat/test-solve-single.R | 9 multiscape-1.4.2/multiscape/tests/testthat/test-solve_requires_method.R | 4 multiscape-1.4.2/multiscape/tests/testthat/test-solver-effects.R |only multiscape-1.4.2/multiscape/tests/testthat/test-solver-parameters.R |only multiscape-1.4.2/multiscape/tests/testthat/test-spatial-plot-more.R |only multiscape-1.4.2/multiscape/tests/testthat/test-spatial-relations-extra.R |only multiscape-1.4.2/multiscape/tests/testthat/test-spatial-relations.R |only multiscape-1.4.2/multiscape/tests/testthat/toy_multiaction_semantics.R |only multiscape-1.4.2/multiscape/vignettes |only 305 files changed, 15040 insertions(+), 9191 deletions(-)