Title: Graphical User Interface for 'r5r' Router
Description: Interactively build and explore public transit routes with
'r5r' package via a graphical user interface in a 'shiny' app. The
underlying routing methods are described in Pereira et al. (2021)
<doi:10.32866/001c.21262>.
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between r5rgui versions 0.1.0 dated 2025-11-25 and 0.2.0 dated 2026-02-11
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 17 R/r5r_gui.R | 73 +++ R/r5r_gui_demo.R | 10 README.md | 50 ++ inst/CITATION | 1 inst/schemaorg.json | 9 inst/shiny_app/server.R | 747 ++++++++++++++++++++++++++++++++-------- inst/shiny_app/ui.R | 506 ++++++++++++++++++++++++--- man/r5r_gui.Rd | 25 + man/r5r_gui_demo.Rd | 8 tests/testthat/test-launchers.R | 8 13 files changed, 1250 insertions(+), 234 deletions(-)
Title: Conditional Manifold Learning
Description: Finds a low-dimensional embedding of high-dimensional data, conditioning on available manifold information.
Author: Anh Tuan Bui [aut, cre]
Maintainer: Anh Tuan Bui <atbui@u.northwestern.edu>
Diff between cml versions 0.2.2 dated 2023-04-24 and 0.3.1 dated 2026-02-11
DESCRIPTION | 19 +++- MD5 | 32 ++++---- NAMESPACE | 1 R/condDist.R | 10 +- R/condDist2.R | 8 +- R/condIsomap.R | 8 +- R/condMDS.R | 10 ++ R/condMDSeigen.R | 10 +- R/condSmacof.R | 196 +++++++++++++++++++++++++++++--------------------- R/condSmacof_mer.R |only inst/CITATION | 36 ++------- man/cml-package.Rd | 42 ++++------ man/condDist.Rd | 10 +- man/condIsomap.Rd | 24 ++++-- man/condMDS.Rd | 23 +++-- man/condSmacof.Rd | 27 +++--- man/condSmacof_mer.Rd |only man/cz.Rd | 2 18 files changed, 251 insertions(+), 207 deletions(-)
Title: Extra Functions for 'gtsummary' Table Styling
Description: Provides additional convenience functions for 'gtsummary'
(Sjoberg et al. (2021) <doi:10.32614/RJ-2021-053>) & 'gt' tables,
including automatic variable labeling from dictionaries, standardized
missing value display, and consistent formatting helpers for streamlined
table styling workflows.
Author: Kyle Grealis [aut, cre] ,
Raymond Balise [ctb] ,
Daniel Maya [ctb]
Maintainer: Kyle Grealis <kyleGrealis@proton.me>
Diff between sumExtras versions 0.3.0 dated 2026-01-22 and 1.0.0 dated 2026-02-11
sumExtras-0.3.0/sumExtras/R/zzz.R |only sumExtras-0.3.0/sumExtras/man/apply_labels_from_dictionary.Rd |only sumExtras-0.3.0/sumExtras/man/figures/table-a.png |only sumExtras-0.3.0/sumExtras/man/figures/table-b.png |only sumExtras-0.3.0/sumExtras/man/figures/table-basic.png |only sumExtras-0.3.0/sumExtras/man/figures/table-styled.png |only sumExtras-0.3.0/sumExtras/man/figures/tables-side-by-side.png |only sumExtras-1.0.0/sumExtras/DESCRIPTION | 15 sumExtras-1.0.0/sumExtras/LICENSE | 2 sumExtras-1.0.0/sumExtras/MD5 | 101 sumExtras-1.0.0/sumExtras/NAMESPACE | 7 sumExtras-1.0.0/sumExtras/NEWS.md | 129 sumExtras-1.0.0/sumExtras/R/clean_table.R | 178 sumExtras-1.0.0/sumExtras/R/extras.R | 322 sumExtras-1.0.0/sumExtras/R/labels.R | 408 sumExtras-1.0.0/sumExtras/R/styling.R | 306 sumExtras-1.0.0/sumExtras/R/sumExtras-package.R | 51 sumExtras-1.0.0/sumExtras/R/use_jama_theme.R | 58 sumExtras-1.0.0/sumExtras/R/utils.R | 4 sumExtras-1.0.0/sumExtras/README.md | 270 sumExtras-1.0.0/sumExtras/build/vignette.rds |binary sumExtras-1.0.0/sumExtras/inst/CITATION | 29 sumExtras-1.0.0/sumExtras/inst/doc/labeling.R | 256 sumExtras-1.0.0/sumExtras/inst/doc/labeling.Rmd | 478 sumExtras-1.0.0/sumExtras/inst/doc/labeling.html | 5450 ------ sumExtras-1.0.0/sumExtras/inst/doc/options.R |only sumExtras-1.0.0/sumExtras/inst/doc/options.Rmd |only sumExtras-1.0.0/sumExtras/inst/doc/options.html |only sumExtras-1.0.0/sumExtras/inst/doc/styling.R | 475 sumExtras-1.0.0/sumExtras/inst/doc/styling.Rmd | 774 sumExtras-1.0.0/sumExtras/inst/doc/styling.html | 8424 ---------- sumExtras-1.0.0/sumExtras/inst/doc/sumExtras-intro.R | 138 sumExtras-1.0.0/sumExtras/inst/doc/sumExtras-intro.Rmd | 272 sumExtras-1.0.0/sumExtras/inst/doc/sumExtras-intro.html | 3050 --- sumExtras-1.0.0/sumExtras/inst/doc/themes.R |only sumExtras-1.0.0/sumExtras/inst/doc/themes.Rmd |only sumExtras-1.0.0/sumExtras/inst/doc/themes.html |only sumExtras-1.0.0/sumExtras/man/add_auto_labels.Rd | 136 sumExtras-1.0.0/sumExtras/man/add_group_colors.Rd | 48 sumExtras-1.0.0/sumExtras/man/add_group_styling.Rd | 53 sumExtras-1.0.0/sumExtras/man/clean_table.Rd | 94 sumExtras-1.0.0/sumExtras/man/extras.Rd | 127 sumExtras-1.0.0/sumExtras/man/figures/readme-example.png |only sumExtras-1.0.0/sumExtras/man/get_group_rows.Rd | 19 sumExtras-1.0.0/sumExtras/man/sumExtras-package.Rd | 45 sumExtras-1.0.0/sumExtras/man/theme_gt_compact.Rd | 28 sumExtras-1.0.0/sumExtras/man/use_jama_theme.Rd | 48 sumExtras-1.0.0/sumExtras/tests/testthat/helper-utils.R |only sumExtras-1.0.0/sumExtras/tests/testthat/test-clean_table-regex.R | 129 sumExtras-1.0.0/sumExtras/tests/testthat/test-clean_table.R | 105 sumExtras-1.0.0/sumExtras/tests/testthat/test-extras-warnings.R | 319 sumExtras-1.0.0/sumExtras/tests/testthat/test-extras.R | 240 sumExtras-1.0.0/sumExtras/tests/testthat/test-labels.R | 718 sumExtras-1.0.0/sumExtras/tests/testthat/test-styling.R | 118 sumExtras-1.0.0/sumExtras/tests/testthat/test-use_jama_theme.R | 37 sumExtras-1.0.0/sumExtras/vignettes/labeling.Rmd | 478 sumExtras-1.0.0/sumExtras/vignettes/options.Rmd |only sumExtras-1.0.0/sumExtras/vignettes/styling.Rmd | 774 sumExtras-1.0.0/sumExtras/vignettes/sumExtras-intro.Rmd | 272 sumExtras-1.0.0/sumExtras/vignettes/themes.Rmd |only 60 files changed, 4625 insertions(+), 20360 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) exporter for both tables and listings, 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 0.1.3 dated 2026-01-15 and 0.1.4 dated 2026-02-11
junco-0.1.3/junco/man/assert_rbmi.Rd |only junco-0.1.3/junco/tests/testthat/_snaps/docx_exporter_functions.md |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part1of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part1of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part2of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part2of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part3of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part3of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part4of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part4of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part5of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part5of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part6of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part6of7.rtf |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part7of7.csv |only junco-0.1.3/junco/tests/testthat/_snaps/tt_to_tblfile/test2part7of7.rtf |only junco-0.1.4/junco/DESCRIPTION | 20 junco-0.1.4/junco/MD5 | 80 junco-0.1.4/junco/NEWS.md | 12 junco-0.1.4/junco/R/ancova_rbmi.R | 11 junco-0.1.4/junco/R/docx_exporter_functions.R | 18 junco-0.1.4/junco/R/mmrm_rbmi.R | 1 junco-0.1.4/junco/R/pool_rbmi.R | 1 junco-0.1.4/junco/R/rbmi.R | 96 junco-0.1.4/junco/R/tt_to_tblfile.R | 6 junco-0.1.4/junco/R/utils.R | 15 junco-0.1.4/junco/README.md | 17 junco-0.1.4/junco/inst/WORDLIST | 2 junco-0.1.4/junco/inst/doc/table_and_listing_customizations.R | 263 junco-0.1.4/junco/inst/doc/table_and_listing_customizations.html | 2660 ++++------ junco-0.1.4/junco/inst/doc/table_and_listing_customizations.rmd | 80 junco-0.1.4/junco/man/rbmi_analyse.Rd | 92 junco-0.1.4/junco/man/rbmi_ancova_single.Rd | 9 junco-0.1.4/junco/tests/testthat/_snaps/summarize_mmrm.md | 148 junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part1of3.csv |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part1of3.rtf |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part2of3.csv |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part2of3.rtf |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part3of3.csv |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test2part3of3.rtf |only junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/test3allparts.rtf | 2190 +------- junco-0.1.4/junco/tests/testthat/_snaps/tt_to_tblfile/testemptylisting.rtf | 50 junco-0.1.4/junco/tests/testthat/test-a_summarize_aval_chg_diff.R | 2 junco-0.1.4/junco/tests/testthat/test-ancova_rbmi.R | 13 junco-0.1.4/junco/tests/testthat/test-docx_exporter_functions.R | 11 junco-0.1.4/junco/tests/testthat/test-mmrm_rbmi.R | 6 junco-0.1.4/junco/tests/testthat/test-pool_rbmi.R | 12 junco-0.1.4/junco/tests/testthat/test-rbmi.R | 92 junco-0.1.4/junco/tests/testthat/test-summarize_mmrm.R | 20 junco-0.1.4/junco/tests/testthat/test-tabulate_rbmi.R | 11 junco-0.1.4/junco/tests/testthat/test-tt_to_tblfile.R | 45 junco-0.1.4/junco/vignettes/table_and_listing_customizations.rmd | 80 52 files changed, 2317 insertions(+), 3746 deletions(-)
Title: Just a Rather Bayesian Evidence Synthesis
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between jarbes versions 2.4.0 dated 2025-08-29 and 2.4.2 dated 2026-02-11
ChangeLog | 48 +++ DESCRIPTION | 10 MD5 | 57 ++- NAMESPACE | 7 R/bcbnp.R | 725 +++++++++++++++++++++++------------------------ R/bcbnp_0.R |only R/bcmeta.R | 385 ++++++++++++------------ R/bcmixmeta.R | 543 ++++------------------------------- R/data-documentation.R | 182 +++++++++++ R/dpmeta.R | 13 R/plot.bcbnp_0.R |only R/plot.bcmeta.R | 199 +++++++----- R/plot.bcmixmeta.R | 42 +- R/plot_data.R | 68 +++- R/summary.bcbnp_0.R |only R/summary.bcmeta.R | 81 ++--- R/summary.bcmixmeta.R |only data/ai_distress.rda |only data/macula_rwe.rda |binary data/personality.rda |only data/preterm.rda |only man/ai_distress.Rd |only man/bcbnp.Rd | 2 man/bcbnp_0.Rd |only man/bcmeta.Rd | 20 - man/bcmixmeta.Rd | 22 - man/macula_rwe.Rd | 15 man/personality.Rd |only man/plot.bcbnp_0.Rd |only man/plot.bcmeta.Rd | 64 +++- man/plot.bcmixmeta.Rd | 6 man/plot_data.Rd | 10 man/preterm.Rd |only man/print.bcbnp_0.Rd |only man/summary.bcbnp_0.Rd |only man/summary.bcmeta.Rd | 4 man/summary.bcmixmeta.Rd |only 37 files changed, 1243 insertions(+), 1260 deletions(-)
Title: Geospatial Regression Equation for European Nutrient Losses
(GREEN)
Description: Tools and methods to apply the model Geospatial Regression Equation
for European Nutrient losses (GREEN);
Grizzetti et al. (2005) <doi:10.1016/j.jhydrol.2004.07.036>;
Grizzetti et al. (2008);
Grizzetti et al. (2012) <doi:10.1111/j.1365-2486.2011.02576.x>;
Grizzetti et al. (2021) <doi:10.1016/j.gloenvcha.2021.102281>.
Author: A. Udias [aut],
B. Grizzetti [aut],
O. Vigiak [aut],
J. Gomez [aut],
C. Alfaro [aut, cre],
A. Aloe [aut]
Maintainer: C. Alfaro <c.alfarog@gmail.com>
Diff between GREENeR versions 1.0.0 dated 2024-02-01 and 1.0.1 dated 2026-02-11
DESCRIPTION | 17 +-- MD5 | 32 +++--- NAMESPACE | 207 ++++++++++++++++++++++----------------------- NEWS.md | 12 +- R/GREENeR-package.R | 14 --- R/optimization_metrics.R | 12 ++ R/rgreen_plots.R | 61 +++++++------ README.md |only inst/doc/GREENeR.Rmd | 44 ++++----- inst/doc/GREENeR.html | 186 +++++++++++++++++++++++++--------------- man/GREENeR-package.Rd | 105 +++++++++++++--------- man/create_lits_of_maps.Rd | 4 man/evolution_plot_area.Rd | 5 - man/gof.Rd |only man/gr_density_plot.Rd | 6 + man/nutrient_maps.Rd | 114 ++++++++++++------------ man/simobs_annual_plot.Rd | 6 + vignettes/GREENeR.Rmd | 44 ++++----- 18 files changed, 484 insertions(+), 385 deletions(-)
Title: Multiple Time Series Scanner
Description: Generate interactive html reports that enable quick visual review of multiple related time series stored in a data frame. For static datasets, this can help to identify any temporal artefacts that may affect the validity of subsequent analyses. For live data feeds, regularly scheduled reports can help to pro-actively identify data feed problems or unexpected trends that may require action. The reports are self-contained and shareable without a web server.
Author: T. Phuong Quan [aut, cre] ,
University of Oxford [cph],
National Institute for Health Research [fnd],
Rodrigo Pires [rev],
Margaret Siple [rev]
Maintainer: T. Phuong Quan <phuongquan567@outlook.com>
Diff between mantis versions 1.0.1 dated 2026-01-13 and 1.0.2 dated 2026-02-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/prepare.R | 12 +++++++----- tests/testthat/test-plots-interactive.R | 26 ++++++++++++++++---------- tests/testthat/test-prepare.R | 3 ++- 6 files changed, 39 insertions(+), 24 deletions(-)
Title: Read the Swiss Register of Plant Protection Products
Description: Generate data objects from XML versions of the Swiss
Register of Plant Protection Products. An online version of the
register can be accessed at <https://www.psm.admin.ch/de/produkte>. There is no
guarantee of correspondence of the data read in using this package with that
online version, or with the original registration documents. Also, the
Federal Food Safety and Veterinary Office, coordinating the authorisation of
plant protection products in Switzerland, does not answer requests regarding
this package.
Author: Daniel Baumgartner [ctb] ,
Marcel Mathis [rev, ctb],
Romualdus Kasteel [rev] ,
Elisabeth Lutz [ctb],
Johannes Ranke [aut, cre] ,
Agroscope [cph]
Maintainer: Johannes Ranke <johannes.ranke@agroscope.admin.ch>
Diff between srppp versions 2.0.0 dated 2025-12-11 and 2.0.2 dated 2026-02-11
srppp-2.0.0/srppp/inst/testdata/PublicationData_2025_12_01.xml.xz |only srppp-2.0.2/srppp/DESCRIPTION | 8 srppp-2.0.2/srppp/MD5 | 22 srppp-2.0.2/srppp/NEWS.md | 9 srppp-2.0.2/srppp/R/resolve_cultures.R | 6 srppp-2.0.2/srppp/R/srppp-xml.R | 7 srppp-2.0.2/srppp/inst/doc/srppp.html | 3849 +++++----- srppp-2.0.2/srppp/inst/doc/srppp_products_with_MO.html | 156 srppp-2.0.2/srppp/inst/testdata/PublicationData_2026_02_03.xml.xz |only srppp-2.0.2/srppp/tests/testthat/setup.R | 4 srppp-2.0.2/srppp/tests/testthat/test-alternative_products.R | 12 srppp-2.0.2/srppp/tests/testthat/test-resolve_cultures.R | 50 srppp-2.0.2/srppp/tests/testthat/test-srppp_xml.R | 31 13 files changed, 2118 insertions(+), 2036 deletions(-)
More information about likelihood.model at CRAN
Permanent link
Title: EcoCleanR: Enhancing Data Quality of Biogeographic Ranges with
Application for Marine Invertebrates
Description: Provides step-by-step automation for integrating biodiversity data from multiple online aggregators, merging and cleaning datasets while addressing challenges such as taxonomic inconsistencies, georeferencing issues, and spatial or environmental outliers. Includes functions to extract environmental data and to define the biogeographic ranges in which species are most likely to occur.
Author: Priyanka Soni [aut, cre] ,
Austin Hendy [ctb] ,
David Bottjer [ctb] ,
Vijay Barve [ctb]
Maintainer: Priyanka Soni <sonip@usc.edu>
This is a re-admission after prior archival of version 1.0.1 dated 2025-11-19
Diff between EcoCleanR versions 1.0.1 dated 2025-11-19 and 1.0.2 dated 2026-02-11
DESCRIPTION | 39 +- LICENSE | 2 MD5 | 67 ++-- NEWS.md |only R/ec_extract_env_layers.R | 97 ++--- R/ec_flag_non_east_atlantic.R | 2 R/ec_flag_non_east_pacific.R | 2 R/ec_flag_non_region.R | 2 R/ec_flag_non_west_atlantic.R | 2 R/ec_flag_non_west_pacific.R | 2 R/ec_geographic_map.R | 5 R/ec_geographic_map_w_flag.R | 5 R/ec_worms_synonym.R | 107 +++--- README.md | 36 +- build/vignette.rds |binary inst/CITATION | 14 inst/WORDLIST |only inst/doc/data_cleaning.R | 130 +++---- inst/doc/data_cleaning.Rmd | 594 ++++++++++++++++++------------------ inst/doc/data_cleaning.html | 89 +---- inst/doc/data_merging.R | 200 ++++++------ inst/doc/data_merging.Rmd | 4 inst/doc/data_merging.html | 66 +--- man/ec_extract_env_layers.Rd | 3 man/ec_flag_non_east_atlantic.Rd | 2 man/ec_flag_non_east_pacific.Rd | 2 man/ec_flag_non_region.Rd | 2 man/ec_flag_non_west_atlantic.Rd | 2 man/ec_flag_non_west_pacific.Rd | 2 man/ec_geographic_map.Rd | 3 man/ec_geographic_map_w_flag.Rd | 3 man/ec_worms_synonym.Rd | 3 man/figures/logo.png |only tests/testthat/test-data_cleaning.R | 31 + vignettes/data_cleaning.Rmd | 594 ++++++++++++++++++------------------ vignettes/data_merging.Rmd | 4 36 files changed, 1051 insertions(+), 1065 deletions(-)
Title: 'shiny' App Companion to the 'tfrmt' Package
Description: Provides an interactive interface to the 'tfrmt' package. Users
can import, modify, and export tables and templates with little to no code.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
Karima Ahmad [aut] ,
Ellis Hughes [aut] ,
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmtbuilder versions 0.1.0 dated 2024-10-11 and 0.1.1 dated 2026-02-11
DESCRIPTION | 22 ++-- MD5 | 66 ++++++------ NAMESPACE | 33 ------ NEWS.md | 5 R/mod_big_n.R | 2 R/mod_big_n_edit.R | 4 R/mod_body_plan.R | 6 - R/mod_body_plan_edit.R | 2 R/mod_body_plan_edit_frmts.R | 6 - R/mod_col_plan_simple.R | 6 - R/mod_col_style_plan.R | 6 - R/mod_col_style_plan_edit.R | 6 - R/mod_datamapping.R | 10 - R/mod_datamapping_inputs.R | 18 +-- R/mod_export_table.R | 8 - R/mod_filters.R | 26 ++-- R/mod_footnote_plan.R | 6 - R/mod_load.R | 22 ++-- R/mod_page_plan.R | 12 -- R/mod_row_grp_plan.R | 6 - R/mod_row_grp_plan_edit.R | 4 R/mod_table_inner.R | 16 +- R/tfrmtbuilder_server.R | 4 R/tfrmtbuilder_ui.R | 20 ++- R/utils_app.R | 46 ++++---- R/utils_tfrmt.R | 20 +-- R/zzz.R | 18 --- tests/testthat/module_examples/mod_body_plan/app.R | 6 - tests/testthat/module_examples/mod_datamapping/app.R | 6 - tests/testthat/module_examples/mod_datamapping_inputs/app.R | 6 - tests/testthat/test-mod_body_plan-shinytest2.R | 24 ++-- tests/testthat/test-mod_datamapping-shinytest2.R | 29 ++--- tests/testthat/test-mod_datamapping_inputs-shinytest2.R | 14 +- tests/testthat/test-mod_load.R | 4 34 files changed, 230 insertions(+), 259 deletions(-)
Title: Path Diagrams and Visual Analysis of Various SEM Packages'
Output
Description: Path diagrams and visual analysis of various SEM packages' output.
Author: Sacha Epskamp [aut, cre],
Simon Stuber [ctb],
Jason Nak [ctb],
Myrthe Veenman [ctb],
Terrence D. Jorgensen [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between semPlot versions 1.1.7 dated 2025-09-01 and 1.1.8 dated 2026-02-11
DESCRIPTION | 7 MD5 | 18 NAMESPACE | 124 +++--- NEWS | 8 R/OpenMx.R | 5 R/glm.R | 12 R/lavaan.R | 21 - R/semPaths.R | 28 - R/semspec.R | 190 ++++----- man/semPaths.Rd | 1138 ++++++++++++++++++++++++++++---------------------------- 10 files changed, 790 insertions(+), 761 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Author: Cody L Marquart [aut, cre] ,
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.3.0 dated 2025-09-29 and 0.3.1 dated 2026-02-11
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS.md | 14 +++- R/ena.rotate.by.generalized.R | 6 - R/ena.rotate.by.mean.R | 31 +++++++-- R/piped.R | 65 +++++++++++------- inst/include/rENA_RcppExports.h | 32 ++++----- man/ena.rotate.by.mean.Rd | 4 - src/RcppExports.cpp | 68 +++++++++---------- src/ena.cpp | 137 +++++++++++++++++++--------------------- tests/testthat/test-piping.R | 15 ++++ 11 files changed, 229 insertions(+), 171 deletions(-)
Title: Interface to 'LibBi'
Description: Provides a complete interface to 'LibBi', a library for Bayesian
inference (see <https://libbi.org> and Murray, 2015
<doi:10.18637/jss.v067.i10> for more information). This includes functions
for manipulating 'LibBi' models, for reading and writing 'LibBi'
input/output files, for converting 'LibBi' output to provide traces for use
with the coda package, and for running 'LibBi' to conduct inference.
Author: Pierre E. Jacob [aut],
Anthony Lee [ctb],
Lawrence M. Murray [ctb],
Sebastian Funk [aut, cre],
Sam Abbott [ctb]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi versions 1.0.0 dated 2023-08-15 and 1.0.1 dated 2026-02-11
DESCRIPTION | 8 - MD5 | 32 ++-- NAMESPACE | 1 NEWS.md | 5 R/bi_read.R | 16 +- R/bi_write.R | 86 +++++++++++-- R/libbi.R | 62 +++++---- README.md | 2 build/vignette.rds |binary inst/doc/idd_models.html | 1 inst/doc/rbi.R | 285 ++++++++++++++++++++++---------------------- inst/doc/rbi.Rmd | 3 inst/doc/rbi.html | 3 man/factorise.Rd |only man/get_char_levels.Rd |only tests/testthat/test-io.r | 28 ++++ tests/testthat/test-libbi.r | 4 vignettes/rbi.Rmd | 3 18 files changed, 333 insertions(+), 206 deletions(-)
Title: Euclidean and Mutual Reachability Minimum Spanning Trees
Description: Functions to compute Euclidean minimum spanning trees using single-,
sesqui-, and dual-tree Boruvka algorithms. Thanks to K-d trees, they are
fast in spaces of low intrinsic dimensionality. Mutual reachability
distances (used in the definition of the 'HDBSCAN*' algorithm)
are supported too. The package also includes relatively fast fallback
minimum spanning tree and nearest-neighbours algorithms for spaces of
higher dimensionality. The 'Python' version of 'quitefastmst' is available
via 'PyPI'.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between quitefastmst versions 0.9.0 dated 2025-07-23 and 0.9.1 dated 2026-02-11
quitefastmst-0.9.0/quitefastmst/src/Makevars.win |only quitefastmst-0.9.1/quitefastmst/DESCRIPTION | 14 quitefastmst-0.9.1/quitefastmst/MD5 | 39 - quitefastmst-0.9.1/quitefastmst/NEWS | 33 + quitefastmst-0.9.1/quitefastmst/R/RcppExports.R | 121 ++--- quitefastmst-0.9.1/quitefastmst/R/quitefastmst-package.R | 2 quitefastmst-0.9.1/quitefastmst/man/knn_euclid.Rd | 20 quitefastmst-0.9.1/quitefastmst/man/mst_euclid.Rd | 104 ++-- quitefastmst-0.9.1/quitefastmst/man/omp.Rd | 2 quitefastmst-0.9.1/quitefastmst/src/RcppExports.cpp | 11 quitefastmst-0.9.1/quitefastmst/src/RcppFastmst.cpp | 182 ++++---- quitefastmst-0.9.1/quitefastmst/src/c_common.h | 2 quitefastmst-0.9.1/quitefastmst/src/c_disjoint_sets.h | 2 quitefastmst-0.9.1/quitefastmst/src/c_fastmst.h | 38 + quitefastmst-0.9.1/quitefastmst/src/c_kdtree.h | 2 quitefastmst-0.9.1/quitefastmst/src/c_kdtree_boruvka.h | 195 +++++---- quitefastmst-0.9.1/quitefastmst/src/c_mst_triple.h | 2 quitefastmst-0.9.1/quitefastmst/src/knn_euclid_brute.cpp | 18 quitefastmst-0.9.1/quitefastmst/src/knn_euclid_kdtree.cpp | 8 quitefastmst-0.9.1/quitefastmst/src/mst_euclid_brute.cpp | 300 +++++++++----- quitefastmst-0.9.1/quitefastmst/src/mst_euclid_kdtree.cpp | 78 +-- 21 files changed, 668 insertions(+), 505 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.7-5 dated 2025-10-21 and 0.7-6 dated 2026-02-11
DESCRIPTION | 8 - MD5 | 16 +-- NEWS.md | 10 ++ R/nplmodel.R | 147 +++++++++++++++----------------- inst/doc/toolbox-simulation.Rnw | 8 - inst/doc/toolbox-simulation.pdf |binary man/YouthGratitude.Rd | 2 tests/Examples/psychotools-Ex.Rout.save | 79 ++++------------- vignettes/toolbox-simulation.Rnw | 8 - 9 files changed, 122 insertions(+), 156 deletions(-)
Title: Optimal Design and Statistical Power for Experimental Studies
Investigating Main, Mediation, and Moderation Effects
Description: Calculate the optimal sample size allocation that
uses the minimum resources to achieve targeted statistical
power in experiments.
Perform power analyses with and without accommodating
costs and budget. The designs cover single-level
and multilevel experiments detecting main, mediation,
and moderation effects (and some combinations).
The references for the proposed methods include:
(1) Shen, Z., & Kelcey, B. (2020).
Optimal sample allocation under unequal costs in
cluster-randomized trials.
Journal of Educational and Behavioral Statistics, 45(4): 446-474.
<doi:10.3102/1076998620912418>.
(2) Shen, Z., & Kelcey, B. (2022b). Optimal sample allocation for
three-level multisite cluster-randomized trials.
Journal of Research on Educational Effectiveness, 15 (1), 130-150.
<doi:10.1080/19345747.2021.1953200>.
(3) Shen, Z., & Kelcey, B. (2022a). Optimal sample allocation in
multisite randomized trials. The Journal of Experimental Education,
90(3), 693-711. <doi:10.108 [...truncated...]
Author: Zuchao Shen [aut, cre] ,
Benjamin Kelcey [aut]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between odr versions 1.7.3 dated 2025-10-31 and 1.8.3 dated 2026-02-11
odr-1.7.3/odr/R/od.2.221m.R |only odr-1.7.3/odr/R/od.2m.111m.R |only odr-1.7.3/odr/R/power.2m.111m.R |only odr-1.7.3/odr/man/od.2.221m.Rd |only odr-1.7.3/odr/man/od.2m.111m.Rd |only odr-1.7.3/odr/man/power.2m.111m.Rd |only odr-1.8.3/odr/DESCRIPTION | 10 - odr-1.8.3/odr/MD5 | 44 ++-- odr-1.8.3/odr/NAMESPACE | 5 odr-1.8.3/odr/R/od.2.mod.R |only odr-1.8.3/odr/R/od.2m.R | 12 - odr-1.8.3/odr/R/od.2m.mod.R | 7 odr-1.8.3/odr/R/od.2m.only.mod.R | 8 odr-1.8.3/odr/R/od.3m.R | 20 +- odr-1.8.3/odr/R/plot.power.R | 66 ++++--- odr-1.8.3/odr/R/power.2.mod.R |only odr-1.8.3/odr/R/power.2m.mod.R | 10 - odr-1.8.3/odr/build/vignette.rds |binary odr-1.8.3/odr/inst/doc/odr.R | 4 odr-1.8.3/odr/inst/doc/odr.Rmd | 19 +- odr-1.8.3/odr/inst/doc/odr.html | 30 +-- odr-1.8.3/odr/man/od.2.mod.Rd |only odr-1.8.3/odr/man/od.2m.mod.Rd | 336 ++++++++++++++++++------------------- odr-1.8.3/odr/man/od.3m.Rd | 8 odr-1.8.3/odr/man/plot.power.Rd | 34 ++- odr-1.8.3/odr/man/power.2.mod.Rd |only odr-1.8.3/odr/man/power.2m.mod.Rd | 310 +++++++++++++++++----------------- odr-1.8.3/odr/vignettes/odr.Rmd | 19 +- 28 files changed, 495 insertions(+), 447 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut] ,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 4.2.1 dated 2026-01-30 and 4.2.3 dated 2026-02-11
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 9 +++++++++ README.md | 8 ++++---- build/vignette.rds |binary data/nleach_table.rda |binary inst/doc/description-of-the-columns.html | 4 ++-- inst/doc/obic_introduction.html | 12 ++++++------ inst/doc/obic_score_aggregation.html | 6 +++--- inst/doc/obic_water_functions.html | 4 ++-- inst/doc/obic_workability.html | 4 ++-- tests/testthat/test-nitrogen_efficiency.R | 4 ++-- tests/testthat/test-nretention.R | 4 ++-- tests/testthat/test-obic_field_dt.R | 8 ++++---- 14 files changed, 54 insertions(+), 45 deletions(-)
Title: Computing a New Informative Distribution Set of Asset Returns
Description: Estimation of the most-left informative set of gross returns
(i.e., the informative set).
The procedure to compute the informative set adjusts the method
proposed by
Mariani et al. (2022a) <doi:10.1007/s11205-020-02440-6>
and
Mariani et al. (2022b) <doi:10.1007/s10287-022-00422-2>
to gross returns of financial assets.
This is accomplished through an adaptive algorithm
that identifies sub-groups of gross returns in
each iteration by approximating their distribution with a
sequence of two-component log-normal mixtures.
These sub-groups emerge when a significant change
in the distribution occurs below the median of the
financial returns, with their boundary termed as
the “change point" of the mixture.
The process concludes when no further change points are detected.
The outcome encompasses parameters of the leftmost mixture
distributions and change points of the
analyzed financial time series.
The functionalities of the INFOSET package include: (i) modelling asset distribution [...truncated...]
Author: Gloria Polinesi [aut, cre],
Francesca Mariani [aut],
Maria Cristina Recchioni [aut]
Maintainer: Gloria Polinesi <g.polinesi@staff.univpm.it>
Diff between INFOSET versions 4.1 dated 2024-11-23 and 4.1.1 dated 2026-02-11
DESCRIPTION | 8 +++--- MD5 | 17 ++++++++------ NAMESPACE | 48 ++++++++++++++++++++++++----------------- R/utils_imports.R |only build/vignette.rds |binary inst/doc/INFOSET_vignette.pdf |only inst/doc/my-vignette.Rmd | 4 +-- inst/doc/my-vignette.html | 5 ++-- tests/testthat/Rplots.pdf |binary vignettes/.install_extras |only vignettes/INFOSET_vignette.pdf |only vignettes/my-vignette.Rmd | 4 +-- 12 files changed, 50 insertions(+), 36 deletions(-)
Title: Marine Benthic Ecosystem Analysis
Description: Preprocessing tools and biodiversity measures
(species abundance, species richness, population heterogeneity and
sensitivity) for analysing marine benthic data. See Van Loon et al.
(2015) <doi:10.1016/j.seares.2015.05.002> for an application of
these tools.
Author: Dennis Walvoort [aut, cre, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between benthos versions 1.3-9 dated 2025-07-04 and 2.0-0 dated 2026-02-11
DESCRIPTION | 14 MD5 | 98 +- NAMESPACE | 39 R/bc.R | 35 R/benthos.R | 12 R/data_northsea.R | 6 R/data_oosterschelde.R | 12 R/indicators.R | 1180 ++++++++++---------------- R/io.R | 1516 ++++++++++++++++------------------ R/utils.R | 976 ++++++++++------------ build/vignette.rds |binary inst/NEWS.Rd | 9 inst/doc/benthos.R | 439 ++++----- inst/doc/benthos.Rmd | 1671 ++++++++++++++++++-------------------- inst/doc/benthos.html | 938 +++++++++------------ man/abundance.Rd | 23 man/ambi.Rd | 39 man/as_accepted.Rd | 6 man/benthos-package.Rd | 11 man/eqr.Rd | 4 man/genus_to_species.Rd | 10 man/get_ambi.Rd | 8 man/get_iti.Rd | 10 man/harmonize.Rd | 2 man/hill.Rd | 68 - man/hpie.Rd | 40 man/hurlbert.Rd | 24 man/is_azoic.Rd | 4 man/is_binomen.Rd | 10 man/iti.Rd | 40 man/margalef.Rd | 21 man/oosterschelde.Rd | 4 man/pool.Rd | 12 man/read_ambi.Rd | 17 man/read_beqi2.Rd | 12 man/read_iti.Rd | 16 man/read_ref.Rd | 17 man/read_taxa.Rd | 7 man/read_twn.Rd | 9 man/rygg.Rd | 31 man/shannon.Rd | 18 man/simpson.Rd | 36 man/species_richness.Rd | 22 man/to_worms.Rd | 22 man/total_abundance.Rd | 24 tests/testthat/test-bray_curtis.R | 29 tests/testthat/test-indicators.R | 886 +++++++++----------- tests/testthat/test-poole.R | 226 ++--- tests/testthat/test-utils.R | 275 +++--- vignettes/benthos.Rmd | 1671 ++++++++++++++++++-------------------- 50 files changed, 4952 insertions(+), 5647 deletions(-)
Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with
with various kinds of text matrices. Focusing on
the text matrix as the primary object - represented
either as a base R dense matrix or a 'Matrix' package sparse
matrix - allows for a consistent and intuitive interface
that stays close to the underlying mathematical foundation
of computational text analysis. In particular, the package
includes functions for working with word embeddings,
text networks, and document-term matrices. Methods developed in
Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>,
Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>,
Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and
Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] ,
Marshall Taylor [aut]
Maintainer: Dustin Stoltz <dss219@lehigh.edu>
Diff between text2map versions 0.2.0 dated 2024-04-11 and 0.2.3 dated 2026-02-11
DESCRIPTION | 21 +- MD5 | 41 ++-- NAMESPACE | 11 + NEWS.md | 10 + R/CMDist.R | 10 - R/CoCA.R | 52 +++--- R/data.R | 4 R/utils-embedding-relco.R |only R/utils-embedding-vectors.R | 215 ++++++++++++++++---------- R/utils.R | 17 ++ README.md | 6 data/anchor_lists.rda |binary inst/REFERENCES.bib | 25 +++ man/CoCA.Rd | 18 +- man/anchor_lists.Rd | 4 man/get_direction.Rd | 6 man/get_regions.Rd | 2 man/test_anchors.Rd | 89 +++++++++- man/text2map-package.Rd | 2 tests/testthat/helper-data.R | 9 - tests/testthat/test-utils-embedding-vectors.R | 65 +++++++ tests/testthat/test-y-nocran-CoCA.R | 33 +-- 22 files changed, 457 insertions(+), 183 deletions(-)
Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: Provides a collection of tools for
detecting influential cases in generalized mixed effects
models. It analyses models that were estimated using 'lme4'. The
basic rationale behind identifying influential data is that
when single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice, such as Cook's Distance.
In addition, we provide a measure of percentage change of the fixed point
estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis [aut, cre] ,
Ben Pelzer [aut],
Manfred Te Grotenhuis [aut]
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Diff between influence.ME versions 0.9-9 dated 2017-06-07 and 0.9-10 dated 2026-02-11
DESCRIPTION | 25 ++++++++++++++++++++----- MD5 | 6 +++--- inst/CITATION | 28 ++++++++++------------------ man/school23.Rd | 4 ++-- 4 files changed, 35 insertions(+), 28 deletions(-)
Title: Generate Samples from Multivariate Truncated Normal
Distributions
Description: Efficient sampling from high-dimensional truncated Gaussian
distributions, or multivariate truncated normal (MTN). Techniques include
zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and
Marc A. Suchard (2024) <doi:10.1080/01621459.2024.2395587>, and harmonic Monte Carlo in Ari Pakman
and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.
Author: Zhenyu Zhang [aut, cre],
Andrew Chin [aut],
Akihiko Nishimura [aut],
Marc A. Suchard [aut],
John W. Ratcliff et al. [cph, ctb]
Maintainer: Zhenyu Zhang <zhangzhenyusa@gmail.com>
Diff between hdtg versions 0.3.3 dated 2026-01-25 and 0.3.4 dated 2026-02-11
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/RcppExports.R | 10 ++++------ R/zigzagHMC.R | 4 ---- R/zigzagMarkovian.R | 3 --- man/createEngine.Rd | 5 +---- man/createNutsEngine.Rd | 5 +---- man/markovianZigzag.Rd | 3 --- man/zigzagHMC.Rd | 3 --- src/RcppExports.cpp | 18 ++++++++---------- src/RcppZigZag.cpp | 12 ++++-------- 11 files changed, 31 insertions(+), 58 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.5 dated 2026-01-08 and 1.6.6 dated 2026-02-11
DESCRIPTION | 8 MD5 | 83 R/GPModel.R | 212 + R/gpb.Booster.R | 26 R/gpb.cv.R | 1 R/gpboost.R | 11 README.md | 32 configure.ac | 2 demo/GPBoost_algorithm.R | 80 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 5 man/GPModel.Rd | 36 man/GPModel_shared_params.Rd | 40 man/fit.GPModel.Rd | 8 man/fit.Rd | 8 man/fitGPModel.Rd | 40 man/gpb.cv.Rd | 11 man/gpb.grid.search.tune.parameters.Rd | 11 man/gpb.save.Rd | 6 man/gpb_shared_params.Rd | 11 man/predict.gpb.Booster.Rd | 9 man/set_optim_params.GPModel.Rd | 8 man/set_optim_params.Rd | 8 man/summary.GPModel.Rd | 6 src/GP_utils.cpp | 168 + src/Vecchia_utils.cpp | 690 +++- src/c_api.cpp | 2 src/cuda_kernel.cu |only src/gpboost_R.cpp | 4 src/gpboost_R.h | 2 src/include/GPBoost/CG_utils.h | 2 src/include/GPBoost/GP_utils.h | 42 src/include/GPBoost/Vecchia_utils.h | 120 src/include/GPBoost/cov_fcts.h | 922 ++++-- src/include/GPBoost/likelihoods.h | 1488 ++++++++-- src/include/GPBoost/re_comp.h | 100 src/include/GPBoost/re_model.h | 2 src/include/GPBoost/re_model_template.h | 1412 +++++---- src/include/GPBoost/utils.h | 20 src/include/LightGBM/c_api.h | 2 src/re_model.cpp | 7 tests/testthat/test_GPModel_gaussian_process.R | 88 tests/testthat/test_GPModel_non_Gaussian_data.R | 1235 +++++++- tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 61 43 files changed, 5341 insertions(+), 1688 deletions(-)
Title: The Research Data Warehouse of Miguel de Carvalho
Description: Pulls together a collection of datasets from Miguel de Carvalho research articles and books. Including, for example:
- de Carvalho (2012) <doi:10.1016/j.jspi.2011.08.016>;
- de Carvalho et al (2012) <doi:10.1080/03610926.2012.709905>;
- de Carvalho et al (2012) <doi:10.1016/j.econlet.2011.09.007>);
- de Carvalho and Davison (2014) <doi:10.1080/01621459.2013.872651>;
- de Carvalho and Rua (2017) <doi:10.1016/j.ijforecast.2015.09.004>;
- de Carvalho et al (2023) <doi:10.1002/sta4.560>;
- de Carvalho et al (2022) <doi:10.1007/s13253-021-00469-9>;
- Palacios et al (2025) <doi:10.1214/24-BA1420>.
Author: Miguel de Carvalho [aut, cre]
Maintainer: Miguel de Carvalho <Miguel.deCarvalho@ed.ac.uk>
Diff between DATAstudio versions 1.2.2 dated 2026-02-06 and 1.2.3 dated 2026-02-11
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++++++---- data/cyclone_sst.RData |only data/earthquake_tsunami.RData |only man/DATAstudio.Rd | 5 ++++- man/alps.Rd | 2 +- man/california.Rd | 6 ++++-- man/cyclone_sst.Rd |only man/danube.Rd |only man/earthquake_tsunami.Rd |only man/epilepsy.Rd |only man/flights.Rd |only man/landslide.Rd |only man/loss.Rd |only 14 files changed, 26 insertions(+), 12 deletions(-)
Title: Datasets and Basic Statistics for Symbolic Data Analysis
Description: Collects a diverse range of symbolic data and offers a comprehensive set of functions that facilitate the conversion of traditional data into the symbolic data format.
Author: Po-Wei Chen [aut],
Chun-houh Chen [aut],
Han-Ming Wu [cre]
Maintainer: Han-Ming Wu <wuhm@g.nccu.edu.tw>
Diff between dataSDA versions 0.1.2 dated 2025-06-07 and 0.1.8 dated 2026-02-11
dataSDA-0.1.2/dataSDA/R/MM_to_iGAP.R |only dataSDA-0.1.2/dataSDA/R/RSDA_to_MM.R |only dataSDA-0.1.2/dataSDA/R/RSDA_to_iGAP.R |only dataSDA-0.1.2/dataSDA/R/SODAS_to_MM.R |only dataSDA-0.1.2/dataSDA/R/SODAS_to_iGAP.R |only dataSDA-0.1.2/dataSDA/R/clean_colnames.R |only dataSDA-0.1.2/dataSDA/R/iGAP_to_MM.R |only dataSDA-0.1.2/dataSDA/R/rsda_format.R |only dataSDA-0.1.2/dataSDA/R/set_variable_format.R |only dataSDA-0.1.2/dataSDA/R/write_csv_table.R |only dataSDA-0.1.2/dataSDA/data/Abalone.iGAP.rda |only dataSDA-0.1.2/dataSDA/data/Abalone.rda |only dataSDA-0.1.2/dataSDA/data/Cars.int.rda |only dataSDA-0.1.2/dataSDA/data/ChinaTemp.int.rda |only dataSDA-0.1.2/dataSDA/data/Face.iGAP.rda |only dataSDA-0.1.2/dataSDA/data/LoansbyPurpose.int.rda |only dataSDA-0.1.2/dataSDA/data/airline_flights.rda |only dataSDA-0.1.2/dataSDA/data/bird.int.rda |only dataSDA-0.1.2/dataSDA/data/health_insurance.rda |only dataSDA-0.1.2/dataSDA/data/soccer.bivar.int.rda |only dataSDA-0.1.2/dataSDA/inst/doc/dataSDA_v3.R |only dataSDA-0.1.2/dataSDA/inst/doc/dataSDA_v3.Rmd |only dataSDA-0.1.2/dataSDA/inst/doc/dataSDA_v3.html |only dataSDA-0.1.2/dataSDA/man/Abalone.Rd |only dataSDA-0.1.2/dataSDA/man/Abalone.iGAP.Rd |only dataSDA-0.1.2/dataSDA/man/Cars.int.Rd |only dataSDA-0.1.2/dataSDA/man/ChinaTemp.int.Rd |only dataSDA-0.1.2/dataSDA/man/Face.iGAP.Rd |only dataSDA-0.1.2/dataSDA/man/LoansbyPurpose.int.Rd |only dataSDA-0.1.2/dataSDA/man/airline_flights.Rd |only dataSDA-0.1.2/dataSDA/man/bird.int.Rd |only dataSDA-0.1.2/dataSDA/man/health_insurance.Rd |only dataSDA-0.1.2/dataSDA/man/soccer.bivar.int.Rd |only dataSDA-0.1.2/dataSDA/vignettes/dataSDA_v3.Rmd |only dataSDA-0.1.8/dataSDA/DESCRIPTION | 10 dataSDA-0.1.8/dataSDA/MD5 | 210 +- dataSDA-0.1.8/dataSDA/NAMESPACE | 50 dataSDA-0.1.8/dataSDA/NEWS.md |only dataSDA-0.1.8/dataSDA/R/data.R | 1515 ++++++++++----- dataSDA-0.1.8/dataSDA/R/histogram_stats.R | 430 ---- dataSDA-0.1.8/dataSDA/R/histogram_utils.R |only dataSDA-0.1.8/dataSDA/R/interval_dist.R |only 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insertions(+), 1411 deletions(-)
Title: Automatic Replication Tools for Meta-Analysis
Description: Provides a unified and straightforward interface for
performing a variety of meta-analysis methods directly from user data.
Users can input a data frame, specify key parameters, and effortlessly
execute and compare multiple common meta-analytic models. Designed for
immediate usability, the package facilitates transparent, reproducible
research without manual implementation of each analytical method.
Ideal for researchers aiming for efficiency and reproducibility, it
streamlines workflows from data preparation to results interpretation.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between artma versions 0.2.1 dated 2025-04-25 and 0.3.3 dated 2026-02-11
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artma-0.3.3/artma/man/options.remove.Rd |only artma-0.3.3/artma/man/options.validate.Rd | 7 artma-0.3.3/artma/man/print.artma_box_plot.Rd |only artma-0.3.3/artma/man/print.artma_funnel_plot.Rd |only artma-0.3.3/artma/man/print.artma_t_stat_histogram.Rd |only artma-0.3.3/artma/man/read_last_export_dir.Rd |only artma-0.3.3/artma/man/results.dir.Rd |only artma-0.3.3/artma/man/results.open.Rd |only artma-0.3.3/artma/man/viz.get.Rd |only artma-0.3.3/artma/man/viz.set.Rd |only artma-0.3.3/artma/man/viz.themes.Rd |only artma-0.3.3/artma/src |only artma-0.3.3/artma/tests/E2E/test-installation.R | 9 artma-0.3.3/artma/tests/testthat.R | 4 artma-0.3.3/artma/tests/testthat/test-autonomy.R |only artma-0.3.3/artma/tests/testthat/test-bma-auto-select.R |only artma-0.3.3/artma/tests/testthat/test-bma-collinearity.R |only artma-0.3.3/artma/tests/testthat/test-bma.R |only artma-0.3.3/artma/tests/testthat/test-box-plot-study-label.R |only artma-0.3.3/artma/tests/testthat/test-data-auto-detection-confirmation.R |only artma-0.3.3/artma/tests/testthat/test-data-column-recognition.R |only artma-0.3.3/artma/tests/testthat/test-data-column-resolution.R |only artma-0.3.3/artma/tests/testthat/test-data-compute.R |only artma-0.3.3/artma/tests/testthat/test-data-config-defaults.R |only artma-0.3.3/artma/tests/testthat/test-data-config-resolve.R |only artma-0.3.3/artma/tests/testthat/test-data-index.R |only artma-0.3.3/artma/tests/testthat/test-data-interactive-mapping.R |only artma-0.3.3/artma/tests/testthat/test-data-preprocess.R |only artma-0.3.3/artma/tests/testthat/test-data-preview.R |only artma-0.3.3/artma/tests/testthat/test-data-smart-detection.R |only artma-0.3.3/artma/tests/testthat/test-data-utils.R | 31 artma-0.3.3/artma/tests/testthat/test-dir_create_linter.R | 2 artma-0.3.3/artma/tests/testthat/test-effect-summary-stats-integration.R |only artma-0.3.3/artma/tests/testthat/test-effect-summary-stats-interactive.R |only artma-0.3.3/artma/tests/testthat/test-effect-summary-stats.R |only artma-0.3.3/artma/tests/testthat/test-elliott-simulate-cdfs.R |only artma-0.3.3/artma/tests/testthat/test-fma.R |only artma-0.3.3/artma/tests/testthat/test-funnel-plot.R |only artma-0.3.3/artma/tests/testthat/test-indentation_guard_clause_linter.R |only artma-0.3.3/artma/tests/testthat/test-libs-cache.R |only artma-0.3.3/artma/tests/testthat/test-libs-editor.R |only artma-0.3.3/artma/tests/testthat/test-linear-tests.R |only artma-0.3.3/artma/tests/testthat/test-modules-path.R |only artma-0.3.3/artma/tests/testthat/test-nonlinear-tests.R |only artma-0.3.3/artma/tests/testthat/test-options-column-preprocessing.R |only artma-0.3.3/artma/tests/testthat/test-options-significance-marks.R |only artma-0.3.3/artma/tests/testthat/test-options.R |only artma-0.3.3/artma/tests/testthat/test-polyfills.R |only artma-0.3.3/artma/tests/testthat/test-result-formatters.R |only artma-0.3.3/artma/tests/testthat/test-run.R |only artma-0.3.3/artma/tests/testthat/test-runtime-methods.R |only artma-0.3.3/artma/tests/testthat/test-t-stat-histogram.R |only artma-0.3.3/artma/tests/testthat/test-variable-suggestion.R |only artma-0.3.3/artma/vignettes/getting-started.Rmd |only artma-0.3.3/artma/vignettes/options-files.Rmd |only 175 files changed, 3766 insertions(+), 825 deletions(-)
Title: Native and Extensible R Driver for 'Zarr'
Description: The 'Zarr' specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native 'Zarr' implementation in R with support for all required features of 'Zarr' version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between zarr versions 0.1.1 dated 2025-12-06 and 0.2.0 dated 2026-02-11
DESCRIPTION | 13 +++--- LICENSE | 2 MD5 | 51 +++++++++++++----------- NAMESPACE | 1 NEWS.md | 11 +++-- R/api.R | 28 ++++++++----- R/array.R | 28 +++++++++++-- R/array_builder.R | 49 ++++++++++++++++------- R/chunking_regular.R | 67 ++++++++++++++++++++++++-------- R/codec.R | 95 ++++++++++++++++++++++++++++++++++++++++++---- R/group.R | 8 ++- R/node.R | 2 R/store.R | 76 +++++++++++++++++++++++++++++++++++- R/store_http.R |only R/store_local.R | 78 +++++++++++++++++++++++++++---------- R/utils.R | 9 ++++ R/zarr.R | 4 - README.md | 9 ++-- man/array_builder.Rd | 11 +++++ man/chunk_grid_regular.Rd | 4 - man/create_zarr.Rd | 6 +- man/open_zarr.Rd | 12 +++-- man/zarr-package.Rd | 1 man/zarr_codec_zstd.Rd |only man/zarr_httpstore.Rd |only man/zarr_localstore.Rd | 9 ++-- man/zarr_node.Rd | 2 man/zarr_store.Rd | 2 28 files changed, 442 insertions(+), 136 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-21 0.3-4
2025-03-18 0.3-3
Title: Simulate Typing Script
Description: Simulates typing of R script files for presentations and demonstrations.
Provides character-by-character animation with optional live code execution.
Supports R scripts (.R), R Markdown (.Rmd), and Quarto (.qmd) documents.
Author: Federica Gazzelloni [aut, cre]
Maintainer: Federica Gazzelloni <fede.gazzelloni@gmail.com>
Diff between typeR versions 0.2.0 dated 2026-02-04 and 0.2.1 dated 2026-02-11
DESCRIPTION | 6 MD5 | 25 +- NEWS.md | 14 + R/utils-typerun.R | 6 README.md | 14 - inst/WORDLIST | 8 inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 2 inst/doc/typerun-demo.R | 12 + inst/doc/typerun-demo.Rmd | 49 ++++ inst/doc/typerun-demo.html | 402 +++++++++++++++++++++----------------- vignettes/getting-started.Rmd | 2 vignettes/images/typeRun_demo.gif |only vignettes/typerun-demo.Rmd | 49 ++++ 14 files changed, 382 insertions(+), 209 deletions(-)
Title: R-Based Visualization Techniques for Task-Based Applications
Description: Performance analysis workflow that combines the power of the R
language (and the tidyverse realm) and many auxiliary tools to
provide a consistent, flexible, extensible, fast, and versatile
framework for the performance analysis of task-based applications
that run on top of the StarPU runtime (with its MPI (Message
Passing Interface) layer for multi-node support). Its goal is to
provide a fruitful prototypical environment to conduct performance
analysis hypothesis-checking for task-based applications that run
on heterogeneous (multi-GPU, multi-core) multi-node HPC
(High-performance computing) platforms.
Author: Lucas Mello Schnorr [aut, ths] ,
Vinicius Garcia Pinto [aut, cre] ,
Lucas Leandro Nesi [aut] ,
Marcelo Cogo Miletto [aut] ,
Guilherme Alles [ctb],
Arnaud Legrand [ctb],
Luka Stanisic [ctb],
Remy Drouilhet [ctb]
Maintainer: Vinicius Garcia Pinto <vinicius.pinto@furg.br>
This is a re-admission after prior archival of version 0.8.3 dated 2025-06-18
Diff between starvz versions 0.8.3 dated 2025-06-18 and 0.8.4 dated 2026-02-11
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/RcppExports.R | 11 ++++++----- R/phase1.R | 2 +- R/phase2_aggregation.R | 33 ++++++++++++++++++++++++++++----- R/phase2_memory.R | 10 +++++----- R/phase2_metrics.R | 6 +++--- R/phase2_pmtool.R | 4 ++-- man/panel_st_raw.Rd | 2 +- man/starvz_phase1.Rd | 2 +- 10 files changed, 61 insertions(+), 37 deletions(-)
Title: Surrogate Functional False Discovery Rates for Genome-Wide
Association Studies
Description: Pleiotropy-informed significance analysis of genome-wide association studies with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and $q$-value, and uses these estimates to derive a functional $p$-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization).
Author: Andrew Bass [aut, cre],
Chris Wallace [aut]
Maintainer: Andrew Bass <ab3105@cam.ac.uk>
Diff between sffdr versions 1.0.0 dated 2024-12-02 and 1.1.0 dated 2026-02-11
sffdr-1.0.0/sffdr/R/RcppExports.R |only sffdr-1.0.0/sffdr/R/finemapping.R |only sffdr-1.0.0/sffdr/R/lfdr.R |only sffdr-1.0.0/sffdr/man/ffinemap.Rd |only sffdr-1.0.0/sffdr/src |only sffdr-1.1.0/sffdr/DESCRIPTION | 19 sffdr-1.1.0/sffdr/MD5 | 64 +- sffdr-1.1.0/sffdr/NAMESPACE | 41 - sffdr-1.1.0/sffdr/NEWS.md | 22 sffdr-1.1.0/sffdr/R/bmi.R | 66 -- sffdr-1.1.0/sffdr/R/fpi0est.R | 677 ++++++++++++++++++------ sffdr-1.1.0/sffdr/R/fpvalues.R | 120 ++-- sffdr-1.1.0/sffdr/R/kernelEstimator.R | 518 +++++++++++++++--- sffdr-1.1.0/sffdr/R/pi0_model.R | 329 +++++++++-- sffdr-1.1.0/sffdr/R/plot.R | 130 ++-- sffdr-1.1.0/sffdr/R/sffdr-package.R |only sffdr-1.1.0/sffdr/R/sffdr.R | 331 +++++++---- sffdr-1.1.0/sffdr/README.md | 194 +++--- sffdr-1.1.0/sffdr/build/vignette.rds |binary sffdr-1.1.0/sffdr/inst/doc/sffdr.R | 85 +-- sffdr-1.1.0/sffdr/inst/doc/sffdr.Rmd | 126 ++-- sffdr-1.1.0/sffdr/inst/doc/sffdr.html | 316 +++++++---- sffdr-1.1.0/sffdr/inst/figures/sffdr.png |binary sffdr-1.1.0/sffdr/man/bmi.Rd | 64 -- sffdr-1.1.0/sffdr/man/fit_bivariate_density.Rd |only sffdr-1.1.0/sffdr/man/fit_strategy_final.Rd |only sffdr-1.1.0/sffdr/man/fit_univariate_density.Rd |only sffdr-1.1.0/sffdr/man/fpi0est.Rd | 111 ++- sffdr-1.1.0/sffdr/man/fpvalues.Rd | 8 sffdr-1.1.0/sffdr/man/kernelEstimator.Rd | 144 +++-- sffdr-1.1.0/sffdr/man/pi0_model.Rd | 65 +- sffdr-1.1.0/sffdr/man/plot.sffdr.Rd | 20 sffdr-1.1.0/sffdr/man/sffdr-package.Rd |only sffdr-1.1.0/sffdr/man/sffdr.Rd | 108 ++- sffdr-1.1.0/sffdr/tests |only sffdr-1.1.0/sffdr/vignettes/sffdr.Rmd | 126 ++-- 36 files changed, 2426 insertions(+), 1258 deletions(-)
Title: 'Open Scoring' API Client
Description: Creativity research involves the need to score open-ended problems.
Usually done by humans, automatic scoring using AI becomes more
and more accurate. This package provides a simple interface to
the 'Open Scoring' API <https://openscoring.du.edu/docs>, leading creativity scoring technology by
Organiscak et al. (2023) <doi:10.1016/j.tsc.2023.101356>. With it,
you can score your own data directly from an R script.
Author: Jakub Jedrusiak [aut, cre, cph] ,
Peter Organisciak [ctb] ,
Selcuk Acar [ctb] ,
Denis Dumas [ctb] ,
Pier-Luc de Chantal [ctb] ,
Kelly Berthiaume [ctb]
Maintainer: Jakub Jedrusiak <jakub.jedrusiak2@uwr.edu.pl>
Diff between openscoring versions 1.0.4 dated 2024-08-24 and 1.0.6 dated 2026-02-11
openscoring-1.0.4/openscoring/R/oscai.R |only openscoring-1.0.4/openscoring/man/oscai.Rd |only openscoring-1.0.4/openscoring/tests/testthat/test-oscai.R |only openscoring-1.0.6/openscoring/DESCRIPTION | 42 +++++----- openscoring-1.0.6/openscoring/MD5 | 20 ++-- openscoring-1.0.6/openscoring/NAMESPACE | 2 openscoring-1.0.6/openscoring/NEWS.md | 20 +++- openscoring-1.0.6/openscoring/R/ocsai.R |only openscoring-1.0.6/openscoring/README.md | 9 +- openscoring-1.0.6/openscoring/build/partial.rdb |binary openscoring-1.0.6/openscoring/inst |only openscoring-1.0.6/openscoring/man/ocsai.Rd |only openscoring-1.0.6/openscoring/man/openscoring-package.Rd | 2 openscoring-1.0.6/openscoring/tests/testthat/autosplit_data.RDS |only openscoring-1.0.6/openscoring/tests/testthat/test-ocsai.R |only 15 files changed, 57 insertions(+), 38 deletions(-)
Title: Interactive Command-Line Menus
Description: Provides interactive command-line menu functionality with
single and multiple selection menus, keyboard navigation (arrow keys or
vi-style j/k), preselection, and graceful fallback for non-interactive
environments. Inspired by tools such as 'inquirer.js'
<https://github.com/SBoudrias/Inquirer.js>, 'pick'
<https://github.com/aisk/pick>, and 'survey'
<https://github.com/AlecAivazis/survey>. Designed to be lightweight and
easy to integrate into 'R' packages and scripts.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between climenu versions 0.1.3 dated 2026-02-06 and 0.1.4 dated 2026-02-11
DESCRIPTION | 6 MD5 | 18 +- R/checkbox.R | 9 - R/menu.R | 13 -- R/select.R | 3 R/utils.R | 6 inst/doc/climenu.R | 15 +- inst/doc/climenu.Rmd | 35 ++++- inst/doc/climenu.html | 312 ++++++++++++++++++++++++++------------------------ vignettes/climenu.Rmd | 35 ++++- 10 files changed, 263 insertions(+), 189 deletions(-)
Title: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data
Description: Prevents and detects information leakage in biomedical machine learning.
Provides leakage-resistant split policies (subject-grouped, batch-blocked, study leave-out, time-ordered),
guarded preprocessing (train-only imputation, normalization, filtering, feature selection),
cross-validated fitting with common learners, permutation-gap auditing, batch and fold association tests,
and duplicate detection.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between bioLeak versions 0.1.0 dated 2026-02-06 and 0.2.0 dated 2026-02-11
DESCRIPTION | 10 MD5 | 49 NEWS.md |only R/audit.R | 7 R/audit_report.R | 18 R/fit_resample.R | 126 + R/make_split_plan.R | 58 R/summary.R | 29 R/tidymodels.R | 22 R/tune_resample.R | 434 ++++ README.md | 2 build/vignette.rds |binary inst/doc/bioLeak-intro.R | 126 - inst/doc/bioLeak-intro.Rmd | 208 +- inst/doc/bioLeak-intro.html | 2273 +++++++++++++------------- inst/reports/audit_report.Rmd | 215 -- man/fit_resample.Rd | 11 man/make_split_plan.Rd | 14 man/tune_resample.Rd | 24 tests/testthat/test-audit-leakage-edge.R | 191 -- tests/testthat/test-audit-report.R | 6 tests/testthat/test-fit-resample-edge.R | 63 tests/testthat/test-make-split-plan-compact.R | 21 tests/testthat/test-make-split-plan-edge.R | 25 tests/testthat/test-tune-resample.R | 303 +++ vignettes/bioLeak-intro.Rmd | 208 +- 26 files changed, 2660 insertions(+), 1783 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.0.0 dated 2025-09-23 and 2.1.0 dated 2026-02-11
DESCRIPTION | 18 MD5 | 84 NAMESPACE | 2 NEWS.md | 16 R/Decompose.R | 2 R/Information.R | 2 R/RUtreebalance.R | 7 R/RcppExports.R | 8 R/Splits.R | 12 R/TreeNumber.R | 2 R/data.R | 2 R/match.R | 28 R/parse_files.R | 8 R/tree_numbering.R | 27 build/partial.rdb |binary inst/apa-old-doi-prefix.csl | 3164 ++++++++++++++++++------------- inst/doc/filesystem-navigation.html | 9 inst/doc/load-data.html | 19 inst/doc/load-trees.html | 15 inst/include/TreeTools/ClusterTable.h | 314 +-- inst/include/TreeTools/SplitList.h | 159 - inst/include/TreeTools/types.h | 5 man/Decompose.Rd | 2 man/J1Index.Rd | 8 man/MatrixToPhyDat.Rd | 5 man/PolarizeSplits.Rd | 4 man/RenumberTips.Rd | 8 man/SplitInformation.Rd | 2 man/TreeNumber.Rd | 2 man/TreeShape.Rd | 2 man/TreeTools-package.Rd | 4 man/match.Splits.Rd | 13 src/RcppExports.cpp | 34 src/consensus.cpp | 124 - src/first_matching_split.cpp |only src/int_to_tree.cpp | 171 - src/splits.cpp | 2 src/splits_to_tree.cpp | 69 tests/testthat/test-ClusterTable.R | 9 tests/testthat/test-FirstMatchingSplit.R |only tests/testthat/test-Splits.R | 15 tests/testthat/test-consensus.R | 12 tests/testthat/test-parsers.R | 8 tests/testthat/test-tree_numbering.R | 45 44 files changed, 2701 insertions(+), 1741 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed outputs from commonly used statistical and psychometric functions into compact, single-row tables and simple graphs, with utilities to export results to CSV, Word, and Excel formats. The package does not implement new statistical methods or estimation procedures; instead, it organises and presents results obtained from existing functions such as psych::describe(), psych::alpha(), stats::t.test(), and gtsummary::tbl_summary() to streamline reporting workflows in clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.1.3 dated 2026-02-08 and 0.2.0 dated 2026-02-11
DESCRIPTION | 16 ++-- LICENSE | 4 - MD5 | 24 ++++--- NAMESPACE | 3 R/make_alpha_table.R | 2 R/make_chisq_test_table.R |only R/make_dataframe_to_output.R | 117 ++++++++++++++++++++++++----------- R/make_independent_t_test_table.R |only R/make_scale_description_table.R | 91 +++++++++++++++------------ inst/CITATION | 6 - man/make_alpha_table.Rd | 4 - man/make_chisq_test_table.Rd |only man/make_dataframe_to_output.Rd | 56 ++++++++++++---- man/make_independent_t_test_table.Rd |only man/make_scale_description_table.Rd | 21 +++--- 15 files changed, 221 insertions(+), 123 deletions(-)
Title: Read Paradox Database Files into R
Description: Provides a simple and efficient way to read data from Paradox
database files (.db) directly into R as modern 'tibble' data frames.
It uses the underlying 'pxlib' C library, to handle the low-level file format
details and provides a clean, user-friendly R interface.
Author: Daniil Popov [aut, cre]
Maintainer: Daniil Popov <popov.daniil@gmail.com>
Diff between Rparadox versions 0.2.0 dated 2026-02-05 and 0.2.1 dated 2026-02-11
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 14 +++++++ README.md | 6 +++ src/interface.c | 105 ++++++++++++++++++++++++++++++++++++-------------------- 5 files changed, 96 insertions(+), 43 deletions(-)
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgstats versions 0.2.1 dated 2025-12-09 and 0.2.2 dated 2026-02-11
DESCRIPTION | 6 - MD5 | 36 +++++------ NEWS.md | 9 ++ R/cran-data-archive.R | 58 +++++++++--------- R/cran-data-update.R | 24 +++++-- R/ctags-test.R | 5 + R/extra-stats.R | 2 R/extract-tarball.R | 13 ++-- R/pkgstats-function.R | 9 ++ R/tag-data-ctags.R | 20 +++++- R/tag-data-gtags.R | 4 + R/tag-data.R | 122 +++++++++++++++++++++++++++----------- inst/doc/installation.html | 4 - inst/doc/pkgstats.html | 8 +- man/ctags_install.Rd | 2 man/extract_tarball.Rd | 4 - tests/testthat/test-cran-update.R | 2 tests/testthat/test-pkgstats.R | 2 vignettes/installation.md |only vignettes/pkgstats.md |only 20 files changed, 226 insertions(+), 104 deletions(-)
Title: Characterise Transitions in Test Result Status in Longitudinal
Studies
Description: Analyse data from longitudinal studies to characterise changes in values of
semi-quantitative outcome variables within individual subjects, using high performance C++
code to enable rapid processing of large datasets. A flexible methodology is available for
codifying these state transitions.
Author: Mark Eisler [aut, cre, cph] ,
Ana Rabaza [aut]
Maintainer: Mark Eisler <mark.eisler@bristol.ac.uk>
Diff between Transition versions 1.0.1 dated 2025-08-29 and 1.0.2 dated 2026-02-11
DESCRIPTION | 10 ++++---- MD5 | 21 +++++++++++------- NEWS.md | 10 ++++++++ R/RcppExports.R | 55 +++++------------------------------------------ build/partial.rdb |binary build/vignette.rds |only inst |only man/PreviousDate.Rd | 50 ++----------------------------------------- man/PreviousResult.Rd | 2 - man/Transitions.Rd | 3 +- src/transition.cpp | 58 ++++++-------------------------------------------- vignettes |only 12 files changed, 47 insertions(+), 162 deletions(-)
Title: Synthesise and Correlate Likert Scale and Rating-Scale Data
Based on Summary Statistics
Description: Generate and correlate synthetic Likert and rating-scale data
with predefined means, standard deviations, Cronbach's Alpha, Factor
Loading table, coefficients, and other summary statistics.
Worked examples and documentation are available in the package
articles, accessible via the package website,
<https://winzarh.github.io/LikertMakeR/>.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 1.3.0 dated 2025-11-25 and 1.4.0 dated 2026-02-11
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Title: Cognitive Diagnostic Computerized Adaptive Testing
Description: Provides a set of functions for conducting cognitive diagnostic computerized adaptive testing applications (Chen, 2009) <DOI:10.1007/s11336-009-9123-2>). It includes different item selection rules such us the global discrimination index (Kaplan, de la Torre, and Barrada (2015) <DOI:10.1177/0146621614554650>) and the nonparametric selection method (Chang, Chiu, and Tsai (2019) <DOI:10.1177/0146621618813113>), as well as several stopping rules. Functions for generating item banks and responses are also provided. To guide item bank calibration, model comparison at the item level can be conducted using the two-step likelihood ratio test statistic by Sorrel, de la Torre, Abad and Olea (2017) <DOI:10.1027/1614-2241/a000131>.
Author: Miguel A. Sorrel [aut, cre, cph],
Pablo Najera [aut, cph],
Francisco J. Abad [aut, cph]
Maintainer: Miguel A. Sorrel <miguel.sorrel@uam.es>
Diff between cdcatR versions 1.0.6 dated 2022-05-25 and 1.0.7 dated 2026-02-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 42 +++++++++++++++++++++++------------------- R/helper.R | 4 ++-- 4 files changed, 33 insertions(+), 29 deletions(-)
Title: Trust Region Optimization
Description: Does local optimization using two derivatives and trust regions.
Guaranteed to converge to local minimum of objective function.
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between trust versions 0.1-8 dated 2020-01-10 and 0.1-9 dated 2026-02-11
ChangeLog | 2 ++ DESCRIPTION | 18 +++++++++++------- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/doc/trust.pdf |binary tests/bar.R | 2 ++ tests/bar.Rout.save | 11 ++++++++--- tests/baz.R | 2 ++ tests/baz.Rout.save | 11 ++++++++--- 9 files changed, 41 insertions(+), 21 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
is a field survey and analytical method that estimates density and
abundance of survey targets (e.g., animals) when
detection probability declines with observation distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects. Analysis involves fitting smooth (parametric) curves to
histograms of observation distances and using those functions to
adjust density estimates for missed targets. Routines included here
fit curves to observation distance histograms, estimate effective
sampling area, density of targets in surveyed areas, and the abundance
of targets in a surrounding study area. Confidence interval estimation
uses built-in bootstrap resampling. Help files are extensive and have been
vetted by multiple authors. Many tutorials are available on the package's
website (URL below).
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.3.0 dated 2026-01-09 and 4.3.1 dated 2026-02-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 11 +++++++++++ R/ESW.r | 3 +++ R/parseModel.R | 2 +- man/parseModel.Rd | 2 +- 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.2.0 dated 2026-01-13 and 1.2.1 dated 2026-02-11
qol-1.2.0/qol/inst/extdata/qol_example_data.csv |only qol-1.2.0/qol/inst/extdata/qol_example_data.xlsx |only qol-1.2.1/qol/DESCRIPTION | 8 qol-1.2.1/qol/MD5 | 122 ++-- qol-1.2.1/qol/NAMESPACE | 14 qol-1.2.1/qol/NEWS.md | 81 ++- qol-1.2.1/qol/R/any_table.R | 478 ++++++++++++++---- qol-1.2.1/qol/R/apply_format.R | 13 qol-1.2.1/qol/R/build_master.R | 4 qol-1.2.1/qol/R/content_report.R | 2 qol-1.2.1/qol/R/conversion.R | 28 - qol-1.2.1/qol/R/create_format.R | 158 +++++ qol-1.2.1/qol/R/crosstabs.R | 101 ++- qol-1.2.1/qol/R/excel_helpers.R | 232 +++++--- qol-1.2.1/qol/R/export_with_style.R | 8 qol-1.2.1/qol/R/free_memory.R |only qol-1.2.1/qol/R/frequencies.R | 343 ++++++++---- qol-1.2.1/qol/R/globals.R | 7 qol-1.2.1/qol/R/if_else.R | 101 +++ qol-1.2.1/qol/R/import_export.R | 188 ++++++- qol-1.2.1/qol/R/internal.R | 20 qol-1.2.1/qol/R/keep_drop.R | 448 ++++++++-------- qol-1.2.1/qol/R/macro.R |only qol-1.2.1/qol/R/options.R | 112 +++- qol-1.2.1/qol/R/qol.R | 13 qol-1.2.1/qol/R/recode.R | 63 +- qol-1.2.1/qol/R/renaming.R | 26 qol-1.2.1/qol/R/retain.R | 185 +++--- qol-1.2.1/qol/R/small_helpers.R | 57 ++ qol-1.2.1/qol/R/sort_plus.R | 21 qol-1.2.1/qol/R/strings.R |only qol-1.2.1/qol/R/summarise_plus.R | 194 ++++++- qol-1.2.1/qol/R/transpose_plus.R | 5 qol-1.2.1/qol/README.md | 6 qol-1.2.1/qol/inst/extdata/qol_example_data_csv.csv |only qol-1.2.1/qol/inst/extdata/qol_example_data_xlsx.xlsx |only qol-1.2.1/qol/man/any_table.Rd | 35 - qol-1.2.1/qol/man/combine_into_workbook.Rd | 53 - qol-1.2.1/qol/man/concat.Rd |only qol-1.2.1/qol/man/crosstabs.Rd | 7 qol-1.2.1/qol/man/duplicates.Rd |only qol-1.2.1/qol/man/excel_output_style.Rd | 34 + qol-1.2.1/qol/man/expand_formats.Rd |only qol-1.2.1/qol/man/free_memory.Rd |only qol-1.2.1/qol/man/frequencies.Rd | 9 qol-1.2.1/qol/man/import_export.Rd | 63 ++ qol-1.2.1/qol/man/keep_dropp.Rd | 2 qol-1.2.1/qol/man/macro.Rd |only qol-1.2.1/qol/man/qol-package.Rd | 13 qol-1.2.1/qol/man/qol_options.Rd | 22 qol-1.2.1/qol/man/recode.Rd | 18 qol-1.2.1/qol/man/remove_blanks.Rd |only qol-1.2.1/qol/man/retain.Rd | 68 +- qol-1.2.1/qol/man/style_options.Rd | 5 qol-1.2.1/qol/man/sub_string.Rd |only qol-1.2.1/qol/man/summarise_plus.Rd | 5 qol-1.2.1/qol/man/where..Rd |only qol-1.2.1/qol/tests/testthat/test-any_table.R | 133 +++-- qol-1.2.1/qol/tests/testthat/test-create_format.R | 99 +++ qol-1.2.1/qol/tests/testthat/test-free_memory.R |only qol-1.2.1/qol/tests/testthat/test-frequencies.R | 57 +- qol-1.2.1/qol/tests/testthat/test-if_else.R | 12 qol-1.2.1/qol/tests/testthat/test-import_export.R | 94 ++- qol-1.2.1/qol/tests/testthat/test-loading.R | 2 qol-1.2.1/qol/tests/testthat/test-macro.R |only qol-1.2.1/qol/tests/testthat/test-options.R | 51 + qol-1.2.1/qol/tests/testthat/test-recode.R | 421 +++++++-------- qol-1.2.1/qol/tests/testthat/test-retain.R | 164 +++--- qol-1.2.1/qol/tests/testthat/test-small_helpers.R | 15 qol-1.2.1/qol/tests/testthat/test-strings.R |only qol-1.2.1/qol/tests/testthat/test-summarise_plus.R | 155 ++++- 71 files changed, 3257 insertions(+), 1318 deletions(-)
Title: Evolutionary Diversity Metrics for Raster Data
Description: Phylogenetic Diversity (PD, Faith 1992), Evolutionary
Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE,
Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE,
Laffan et al. 2016) for presence-absence raster. Faith, D. P. (1992)
<doi:10.1016/0006-3207(92)91201-3> Isaac, N. J. et al. (2007)
<doi:10.1371/journal.pone.0000296> Laffan, S. W. et al. (2016)
<doi:10.1111/2041-210X.12513> Rosauer, D. et al. (2009)
<doi:10.1111/j.1365-294X.2009.04311.x>.
Author: Gabriela Alves-Ferreira [aut, cre, cph] ,
Flavio M. M. Mota [aut] ,
Neander Marcel Heming [aut]
Maintainer: Gabriela Alves-Ferreira <gabriela-alves77@hotmail.com>
This is a re-admission after prior archival of version 2.2.0 dated 2025-02-28
Diff between phyloraster versions 2.2.0 dated 2025-02-28 and 2.3.0 dated 2026-02-11
DESCRIPTION | 18 - MD5 | 32 +-- NEWS.md | 12 - R/arg.check.R | 89 ++++---- R/geo.phylo.R | 2 R/rast.ed.ses.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/phyloraster-vignette.R | 4 inst/doc/phyloraster-vignette.html | 54 ++--- man/shp2rast.Rd | 4 tests/testthat/test-delta-grid.R | 168 +++++++--------- tests/testthat/test-geo.phylo.R | 388 ++++++++++++++++++------------------- tests/testthat/test-rast-ed-ses.R | 244 +++++++++++------------ tests/testthat/test-rast.pd.ses.R | 242 +++++++++++------------ tests/testthat/test-rast.pe.ses.R | 206 +++++++++---------- tests/testthat/test-shp2rast.R | 208 +++++++++---------- 17 files changed, 834 insertions(+), 841 deletions(-)
Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility
('GBIF', <https://www.gbif.org>) sources data from an international network
of data providers, known as 'nodes'. Several of these nodes - the "living
atlases" (<https://living-atlases.gbif.org>) - maintain their own web
services using software originally developed by the Atlas of Living
Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community
to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre],
Dax Kellie [aut],
Shandiya Balasubramaniam [ctb],
Matilda Stevenson [ctb]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 2.1.2 dated 2025-06-12 and 2.2.0 dated 2026-02-11
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Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Cristiane Gea [aut],
Diego Carvalho [ctb],
Diogo Santos [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Fernando Alexandrino [aut],
Rebecca Salles [aut],
Vitoria Birindiba [aut],
CEFET/RJ [cp [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 1.2.747 dated 2025-10-27 and 1.2.767 dated 2026-02-11
DESCRIPTION | 6 +-- MD5 | 70 ++++++++++++++++++++++++++++++++++--------- NAMESPACE | 2 + R/data.R | 20 ------------ R/ts_arima.R | 2 + R/ts_elm.R | 2 + R/ts_knn.R | 2 + R/ts_mlp.R | 1 R/ts_reg.R | 1 R/ts_regsw.R | 3 + R/ts_rf.R | 2 + R/ts_svm.R | 2 + R/tspredbench.R |only R/tspredbench_loadfulldata.R |only README.md | 14 +++----- build |only data/CATS.RData |only data/EUNITE.Loads.RData |only data/EUNITE.Reg.RData |only data/EUNITE.Temp.RData |only data/NN3.RData |only data/NN5.RData |only data/SantaFe.A.RData |only data/SantaFe.D.RData |only data/bioenergy.RData |only data/climate.RData |only data/emissions.RData |only data/fertilizers.RData |binary data/gdp.RData |only data/ipeadata.d.RData |only data/ipeadata.m.RData |only data/m1.RData |only data/m3.RData |only data/m4.RData |only data/pesticides.RData |only data/stocks.RData |only man/CATS.Rd |only man/EUNITE.Loads.Rd |only man/EUNITE.Reg.Rd |only man/EUNITE.Temp.Rd |only man/NN3.Rd |only man/NN5.Rd |only man/SantaFe.A.Rd |only man/SantaFe.D.Rd |only man/bioenergy.Rd |only man/climate.Rd |only man/emissions.Rd |only man/fertilizers.Rd | 27 +++++++--------- man/gdp.Rd |only man/ipeadata.d.Rd |only man/ipeadata.m.Rd |only man/loadfulldata.Rd |only man/m1.Rd |only man/m3.Rd |only man/m4.Rd |only man/pesticides.Rd |only man/stocks.Rd |only 57 files changed, 94 insertions(+), 60 deletions(-)
Title: Utility Functions for Data Analysis and Visualization
Description: A comprehensive collection of utility functions for data analysis
and visualization in R. The package provides 60+ functions for data
manipulation, file handling, color palette management, bioinformatics
workflows, statistical analysis, plotting, and package management. Features include void value
handling, custom infix operators, flexible file I/O, and publication-ready
visualizations with sensible defaults. Implementation follows tidyverse
principles (Wickham et al. (2019) <doi:10.21105/joss.01686>) and incorporates
best practices from the R community.
Author: Evan Zhou [aut, cre]
Maintainer: Evan Zhou <evanzhou.bio@gmail.com>
Diff between evanverse versions 0.3.7 dated 2025-10-21 and 0.4.0 dated 2026-02-11
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Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.15.2 dated 2025-12-21 and 0.16.0 dated 2026-02-11
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tinytable-0.16.0/tinytable/inst/tinytest/_tinysnapshot/typst-tblr.typ | 4 tinytable-0.16.0/tinytable/inst/tinytest/helpers.R | 3 tinytable-0.16.0/tinytable/inst/tinytest/test-latex.R | 11 tinytable-0.16.0/tinytable/inst/tinytest/test-misc.R | 1 tinytable-0.16.0/tinytable/inst/tinytest/test-theme.R | 13 tinytable-0.16.0/tinytable/man/format_tt.Rd | 3 tinytable-0.16.0/tinytable/man/pkgdown_print.tinytable.Rd |only tinytable-0.16.0/tinytable/man/style_tt.Rd | 2 tinytable-0.16.0/tinytable/man/theme_default.Rd | 5 tinytable-0.16.0/tinytable/man/theme_rotate.Rd | 4 tinytable-0.16.0/tinytable/man/theme_tinytable.Rd |only 175 files changed, 854 insertions(+), 755 deletions(-)
Title: Functions and Datasets Required for ST370 Class
Description: Provides functions and datasets required for the ST 370 course at North Carolina State University.
Author: Dennis D. Boos [aut],
Douglas Nychka [aut],
Dennis Boos [cre]
Maintainer: Dennis Boos <boos@ncsu.edu>
Diff between Rlab versions 4.0 dated 2022-05-04 and 4.5.1 dated 2026-02-11
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 8 ++++---- man/Exponential.Rd | 2 +- man/Gamma.Rd | 2 +- man/college.Rd | 4 ++-- 5 files changed, 25 insertions(+), 13 deletions(-)
Title: Polytomous Variable Latent Class Analysis
Description: Latent class analysis and latent class regression models
for polytomous outcome variables. Also known as latent structure analysis.
Author: Drew Linzer [aut, cre],
Jeffrey Lewis [aut]
Maintainer: Drew Linzer <drew@votamatic.org>
Diff between poLCA versions 1.6.0.1 dated 2022-04-25 and 1.6.0.2 dated 2026-02-11
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 12 ++++++------ README.md | 4 ++-- inst/CITATION | 10 ++++++---- man/carcinoma.Rd | 2 +- man/poLCA.Rd | 4 ++-- src/poLCA.c | 2 +- 7 files changed, 33 insertions(+), 25 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre] ,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 6.7.1 dated 2026-01-31 and 6.7.2 dated 2026-02-11
DESCRIPTION | 8 +- MD5 | 28 ++++----- NEWS.md | 14 ++++ R/RcppExports.R | 28 ++++++++- R/matrixcreation.R | 30 +++++++--- man/arlefko2.Rd | 5 + man/bootstrap3.Rd | 8 ++ man/mpm_create.Rd | 6 ++ man/rlefko2.Rd | 5 + man/rlefko3.Rd | 5 + man/rleslie.Rd | 5 + src/DataManagement.cpp | 17 +++++ src/MatsNProj.cpp | 144 ++++++++++++++++++++++++++++++++++++------------- src/PopChar.cpp | 4 - src/RcppExports.cpp | 18 +++--- 15 files changed, 245 insertions(+), 80 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd],
sungho Choi [aut],
Mingu Jee [aut],
Wonbin Hahn [aut],
Taehong Kim [aut],
Sangho Oh [aut],
Sewon Lee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.6.0 dated 2026-01-27 and 0.6.1 dated 2026-02-11
DESCRIPTION | 18 +++++++++++------- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/jskm.R | 6 +++--- R/svyjskm.R | 12 ++++++------ README.md | 16 ++++++++-------- inst/doc/jskm.html | 36 ++++++++++++++++++------------------ 7 files changed, 57 insertions(+), 48 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung [aut],
Mike Danilov [aut],
Victor Yohai [aut],
Ruben Zamar [aut],
Claudio Agostinelli [cre]
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between GSE versions 4.2-3 dated 2025-10-10 and 4.2-4 dated 2026-02-11
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- src/Makevars | 2 +- src/Makevars.win | 2 +- src/cov-em.cpp | 2 ++ src/cov-em.h | 4 ++-- src/emve.cpp | 11 ++++++----- src/emve.h | 4 ++-- src/gse-rocke.cpp | 22 +++++++++++----------- src/gse.cpp | 16 ++++++++-------- 10 files changed, 46 insertions(+), 43 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],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.89 dated 2025-12-15 and 2.0.90 dated 2026-02-11
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 4 +++- NEWS | 7 +++++++ R/epi.evalue.R |only build/vignette.rds |binary inst/doc/epiR_descriptive_epi.html | 18 +++++++++--------- inst/doc/epiR_diagnostic_tests.html | 20 ++++++++++---------- inst/doc/epiR_measures_of_assoc.html | 12 ++++++------ inst/doc/epiR_sample_size.html | 4 ++-- inst/doc/epiR_surveillance.html | 14 +++++++------- man/epi.evalue.Rd |only 12 files changed, 60 insertions(+), 49 deletions(-)
Title: Data Table Back-End for 'dplyr'
Description: Provides a data.table backend for 'dplyr'. The goal of
'dtplyr' is to allow you to write 'dplyr' code that is automatically
translated to the equivalent, but usually much faster, data.table
code.
Author: Hadley Wickham [cre, aut],
Maximilian Girlich [aut],
Mark Fairbanks [aut],
Ryan Dickerson [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between dtplyr versions 1.3.2 dated 2025-09-10 and 1.3.3 dated 2026-02-11
dtplyr-1.3.2/dtplyr/tests/testthat/_snaps/step-group.md |only dtplyr-1.3.3/dtplyr/DESCRIPTION | 8 +-- dtplyr-1.3.3/dtplyr/MD5 | 33 +++++++------- dtplyr-1.3.3/dtplyr/NEWS.md | 4 + dtplyr-1.3.3/dtplyr/README.md | 4 - dtplyr-1.3.3/dtplyr/build/vignette.rds |binary dtplyr-1.3.3/dtplyr/inst/doc/translation.Rmd | 2 dtplyr-1.3.3/dtplyr/inst/doc/translation.html | 8 +-- dtplyr-1.3.3/dtplyr/man/expand.dtplyr_step.Rd | 18 +------- dtplyr-1.3.3/dtplyr/man/filter.dtplyr_step.Rd | 13 ++--- dtplyr-1.3.3/dtplyr/man/group_by.dtplyr_step.Rd | 8 +-- dtplyr-1.3.3/dtplyr/man/mutate.dtplyr_step.Rd | 4 - dtplyr-1.3.3/dtplyr/man/pivot_longer.dtplyr_step.Rd | 2 dtplyr-1.3.3/dtplyr/man/reframe.dtplyr_step.Rd | 4 - dtplyr-1.3.3/dtplyr/man/slice.dtplyr_step.Rd | 4 - dtplyr-1.3.3/dtplyr/man/summarise.dtplyr_step.Rd | 36 +++++----------- dtplyr-1.3.3/dtplyr/tests/testthat/test-step-group.R | 4 - dtplyr-1.3.3/dtplyr/vignettes/translation.Rmd | 2 18 files changed, 61 insertions(+), 93 deletions(-)
Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format
for describing software metadata, as detailed at
<https://codemeta.github.io>. This package provides utilities to
generate, parse, and modify 'codemeta.json' files automatically for R
packages, as well as tools and examples for working with
'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph] ,
Anna Krystalli [rev, ctb] ,
Toph Allen [rev] ,
Maelle Salmon [ctb, aut] ,
rOpenSci [fnd] ,
Katrin Leinweber [ctb] ,
Noam Ross [ctb] ,
Arfon Smith [ctb],
Jeroen Ooms [ctb] ,
Sebastian Meyer [ctb] ,
Michael Rustler [ctb [...truncated...]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between codemetar versions 0.3.6 dated 2025-07-28 and 0.3.7 dated 2026-02-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 +++- build/vignette.rds |binary inst/doc/codemetar.html | 4 ++-- tests/testthat/test-give_opinions.R | 29 +++++++++++++++++++++-------- 6 files changed, 34 insertions(+), 19 deletions(-)