Title: 'jsTree' Bindings for 'Shiny'
Description: Bindings to 'jsTree' <https://www.jstree.com>, a 'JavaScript'
library for interactive trees, to enable rich, editable trees in 'Shiny'
applications. Trees can be searched, checked, rearranged,
styled and remembered across visits, loaded lazily for very large
hierarchies, and built from data frames, 'data.tree' objects or
ontologies.
Author: Trestle Technology, LLC [aut],
Jeff Allen [aut],
Institut de Radioprotection et de Sûrete Nucleaire [cph],
Ivan Bozhanov [ctb, cph] ,
Orange Hill Development [ctb, cph] theme),
Accademia di Belle Arti di Urbino [cph] ,
Mike Schaffer [ctb],
Timm Dank [...truncated...]
Maintainer: Michael Bell <bell_michael_a@lilly.com>
Diff between shinyTree versions 0.3.1 dated 2023-08-07 and 1.0.0 dated 2026-10-28
shinyTree-0.3.1/shinyTree/NEWS |only shinyTree-0.3.1/shinyTree/inst/examples/21-options/app_setState_refresh.R |only shinyTree-0.3.1/shinyTree/inst/www/jsTree-3.3.7/libs |only shinyTree-0.3.1/shinyTree/tests/testthat/test_tree_interactive.R |only shinyTree-1.0.0/shinyTree/DESCRIPTION | 39 shinyTree-1.0.0/shinyTree/MD5 | 215 +- shinyTree-1.0.0/shinyTree/NAMESPACE | 13 shinyTree-1.0.0/shinyTree/NEWS.md |only shinyTree-1.0.0/shinyTree/R/data.tree-conversion.R | 102 - shinyTree-1.0.0/shinyTree/R/get-checked.R | 98 - shinyTree-1.0.0/shinyTree/R/get-selected.R | 171 +- shinyTree-1.0.0/shinyTree/R/init.R | 90 - shinyTree-1.0.0/shinyTree/R/ontology.R |only shinyTree-1.0.0/shinyTree/R/render-tree-lazy.R |only shinyTree-1.0.0/shinyTree/R/render-tree.R | 277 +++ shinyTree-1.0.0/shinyTree/R/render-tree_async.R | 136 - shinyTree-1.0.0/shinyTree/R/shiny-tree.R | 274 ++- shinyTree-1.0.0/shinyTree/R/tree_traversal.R | 6 shinyTree-1.0.0/shinyTree/R/update-tree.R | 354 +++- shinyTree-1.0.0/shinyTree/README.md | 199 +- shinyTree-1.0.0/shinyTree/inst/COPYRIGHTS |only shinyTree-1.0.0/shinyTree/inst/WORDLIST |only shinyTree-1.0.0/shinyTree/inst/examples/01-simple/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/02-attributes/server.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/02-attributes/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/03-checkbox/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/04-selected/server.R | 89 - shinyTree-1.0.0/shinyTree/inst/examples/04-selected/ui.R | 33 shinyTree-1.0.0/shinyTree/inst/examples/05-structure/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/06-search/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/07-drag-and-drop/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/08-class/server.R | 17 shinyTree-1.0.0/shinyTree/inst/examples/08-class/ui.R | 12 shinyTree-1.0.0/shinyTree/inst/examples/11-tree-update/server.R | 66 shinyTree-1.0.0/shinyTree/inst/examples/11-tree-update/ui.R | 54 shinyTree-1.0.0/shinyTree/inst/examples/12-types/ui.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/13-icons/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/14-files/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/14-files/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/15-data/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/15-data/ui.R | 4 shinyTree-1.0.0/shinyTree/inst/examples/16-async/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/17-contextmenu/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/18-modules/app.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/20-api/ui.R | 10 shinyTree-1.0.0/shinyTree/inst/examples/21-options/app.R |only shinyTree-1.0.0/shinyTree/inst/examples/22-dfToTree/server.R | 5 shinyTree-1.0.0/shinyTree/inst/examples/22-dfToTree/ui.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/23-file-icons/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/24-checkbox-options/server.R | 11 shinyTree-1.0.0/shinyTree/inst/examples/24-checkbox-options/ui.R | 11 shinyTree-1.0.0/shinyTree/inst/examples/25-duplicate-names |only shinyTree-1.0.0/shinyTree/inst/examples/26-state |only shinyTree-1.0.0/shinyTree/inst/examples/27-lazy |only shinyTree-1.0.0/shinyTree/inst/examples/28-ontology |only shinyTree-1.0.0/shinyTree/inst/www/shinyTree.css |only shinyTree-1.0.0/shinyTree/inst/www/shinyTree.js | 850 ++++++++-- shinyTree-1.0.0/shinyTree/man/depth.Rd | 1 shinyTree-1.0.0/shinyTree/man/dfToTree.Rd | 16 shinyTree-1.0.0/shinyTree/man/dfrapply.Rd | 1 shinyTree-1.0.0/shinyTree/man/expandTree.Rd |only shinyTree-1.0.0/shinyTree/man/get_checked.Rd | 32 shinyTree-1.0.0/shinyTree/man/get_selected.Rd | 37 shinyTree-1.0.0/shinyTree/man/ontologyToTree.Rd |only shinyTree-1.0.0/shinyTree/man/renderEmptyTree.Rd | 3 shinyTree-1.0.0/shinyTree/man/renderTree.Rd | 190 ++ shinyTree-1.0.0/shinyTree/man/renderTreeAsync.Rd | 46 shinyTree-1.0.0/shinyTree/man/set_node_attrs.Rd | 6 shinyTree-1.0.0/shinyTree/man/shinyTree.Rd | 177 +- shinyTree-1.0.0/shinyTree/man/treeToDf.Rd | 12 shinyTree-1.0.0/shinyTree/man/treeToJSON.Rd | 10 shinyTree-1.0.0/shinyTree/man/updateTree.Rd | 36 shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_attr_whitespace |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_bind_cache |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_bind_cache_modal |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_tied |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_untied |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_untied_cascade |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_contextmenu |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_css_class |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_dnd |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_duplicates |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_empty_tree |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_events_all |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_events_checkbox |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_expand_collapse |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_js_dotted_id |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_js_robust |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_lazy |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_modal_rerender |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_reject_change |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_rmarkdown |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_default |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_default_dark |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_proton |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_shared_id |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_shared_id_real |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_slow_render |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_state |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_tooltip |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_treetojson |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_types_nested |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_update_loop |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_update_loop_changing |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-app.R |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-examples.R |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-traversal.R |only shinyTree-1.0.0/shinyTree/tests/testthat/ontology |only shinyTree-1.0.0/shinyTree/tests/testthat/test_dfTreeConversion.R | 34 shinyTree-1.0.0/shinyTree/tests/testthat/test_duplicate_names.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_get_checked.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_init.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_large_tree.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_lazy.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_leaves_only.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_ontology.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_partial_state.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_render_tree.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_render_tree_async.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_review_fixes.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_attr_whitespace.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_bind_cache.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_tied.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_untied.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_untied_cascade.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_contextmenu.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_css_class.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_dnd.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_duplicates.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example04.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example25.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example27.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example28.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_01_07.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_08_14.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_15_24.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_expand_collapse.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_rmarkdown.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_search.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_search_themes.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_shared_id.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_tooltip.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_treetojson.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_types_nested.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_update_loop.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_tree.R | 248 ++ shinyTree-1.0.0/shinyTree/tests/testthat/test_tree_traversal.R | 15 150 files changed, 3174 insertions(+), 863 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Author: Sounkou Mahamane Toure [aut, cre],
Ryan Ward [aut] ,
Nurture Bio [cph] ,
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
DuckHTS Contributors [cph] ),
RBCFTools Authors [cph [...truncated...]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 2.0.1.0.1.0 dated 2026-10-24 and 2.0.2.0.1.1 dated 2026-10-28
DESCRIPTION | 6 MD5 | 36 ++- NEWS.md | 21 ++ inst/duckhts_extension/hts_index_builder.c | 213 ++++++++++++++--------- inst/duckhts_extension/mosdepth_table.c | 41 +++- inst/duckhts_extension/samtools_idxstats_table.c | 52 +++-- inst/duckhts_extension/seq_reader.c | 80 +++++--- inst/extdata/geno_format_case.bcf.csi |only inst/extdata/geno_format_case.vcf.gz.tbi |only inst/function_catalog/functions.yaml | 16 + inst/function_catalog/reference.md | 24 ++ inst/tinytest/bcf_snapshot_query.R | 35 ++- inst/tinytest/test_ancestry.R | 3 inst/tinytest/test_bcf.R | 29 ++- inst/tinytest/test_count_error_fit.R | 3 inst/tinytest/test_depth_state_model.R | 3 inst/tinytest/test_mosdepth.R | 6 inst/tinytest/test_samtools_idxstats.R | 6 inst/tinytest/test_somalier_extraction.R | 7 tests/tinytest.R | 8 20 files changed, 409 insertions(+), 180 deletions(-)
Title: Likelihood Contribution Models for Heterogeneous Observation
Types
Description: Constructs likelihood models from heterogeneous observation types
by composing named contributions. Each observation type (exact, left-censored,
right-censored, interval-censored, or custom) contributes independently to the
total log-likelihood, which is summed under an i.i.d. assumption. Provides
contr_name() for standard R distributions and contr_fn() for user-defined
contributions, composed via likelihood_contr() into objects compatible with
the likelihood.model inference framework.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between likelihood.contr versions 0.1.1 dated 2026-04-01 and 0.2.0 dated 2026-10-28
DESCRIPTION | 8 ++++---- MD5 | 26 ++++++++++++++++++-------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/cache.R | 4 ++++ R/frequency.R |only R/likelihood.contr-package.R | 5 +++++ R/likelihood_contr.R | 5 ++++- build/vignette.rds |binary demo |only inst/doc/timeout-benchmarking.R |only inst/doc/timeout-benchmarking.Rmd |only inst/doc/timeout-benchmarking.html |only man/contr_freq.Rd |only man/loglik.Rd | 7 +++++++ tests/testthat/test-frequency.R |only tests/testthat/test-observation-schema.R |only vignettes/timeout-benchmarking.Rmd |only 18 files changed, 50 insertions(+), 13 deletions(-)
More information about likelihood.contr at CRAN
Permanent link
Title: General Transit Feed Specification (GTFS) Editing and Analysing
Tools
Description: Utility functions to read, manipulate, analyse and write
transit feeds in the General Transit Feed Specification (GTFS) data
format.
Author: Daniel Herszenhut [aut] ,
Rafael H. M. Pereira [aut, cre] ,
Pedro R. Andrade [aut] ,
Joao Bazzo [aut] ,
Mark Padgham [ctb],
Christopher Higgins [ctb],
Goncalo F. Matos [ctb],
Yigit Han Eroglu [ctb],
Arthur Bazolli [ctb],
Marcus Saraiva [ctb] ,
Ipea - [...truncated...]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between gtfstools versions 1.4.0 dated 2025-01-08 and 2.0.0 dated 2026-10-28
gtfstools-1.4.0/gtfstools/inst/doc/validating.R |only gtfstools-2.0.0/gtfstools/DESCRIPTION | 51 gtfstools-2.0.0/gtfstools/MD5 | 425 ++- gtfstools-2.0.0/gtfstools/NAMESPACE | 51 gtfstools-2.0.0/gtfstools/NEWS.md | 140 + gtfstools-2.0.0/gtfstools/R/build_graph.R |only gtfstools-2.0.0/gtfstools/R/calendar_helpers.R |only gtfstools-2.0.0/gtfstools/R/combine_nearby_stops.R |only gtfstools-2.0.0/gtfstools/R/convert_seconds_to_time.R |only gtfstools-2.0.0/gtfstools/R/convert_sf_to_shapes.R | 79 gtfstools-2.0.0/gtfstools/R/convert_shapes_to_sf.R | 125 - gtfstools-2.0.0/gtfstools/R/convert_stops_to_sf.R | 98 gtfstools-2.0.0/gtfstools/R/convert_stops_to_shapes.R |only gtfstools-2.0.0/gtfstools/R/convert_time_to_seconds.R | 11 gtfstools-2.0.0/gtfstools/R/cpp11.R | 24 gtfstools-2.0.0/gtfstools/R/crop_gtfs.R | 735 ++++++ gtfstools-2.0.0/gtfstools/R/download_validator.R | 408 ++- gtfstools-2.0.0/gtfstools/R/dt_gtfs.R | 10 gtfstools-2.0.0/gtfstools/R/dwell_time_helpers.R |only gtfstools-2.0.0/gtfstools/R/filter_by_agency_id.R | 27 gtfstools-2.0.0/gtfstools/R/filter_by_date.R |only gtfstools-2.0.0/gtfstools/R/filter_by_period.R |only gtfstools-2.0.0/gtfstools/R/filter_by_route_id.R | 57 gtfstools-2.0.0/gtfstools/R/filter_by_service_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_sf.R | 81 gtfstools-2.0.0/gtfstools/R/filter_by_shape_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_spatial_extent.R | 113 - gtfstools-2.0.0/gtfstools/R/filter_by_stop_id.R | 131 - gtfstools-2.0.0/gtfstools/R/filter_by_time_of_day.R | 328 +-- gtfstools-2.0.0/gtfstools/R/filter_by_trip_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_weekday.R | 29 gtfstools-2.0.0/gtfstools/R/filter_helpers.R | 427 ++-- gtfstools-2.0.0/gtfstools/R/fix_gtfs.R |only gtfstools-2.0.0/gtfstools/R/frequencies_to_stop_times.R | 492 ++-- gtfstools-2.0.0/gtfstools/R/get_active_services.R |only gtfstools-2.0.0/gtfstools/R/get_calendar_overlap.R |only gtfstools-2.0.0/gtfstools/R/get_children_stops.R | 57 gtfstools-2.0.0/gtfstools/R/get_dates.R |only gtfstools-2.0.0/gtfstools/R/get_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/get_parent_station.R | 15 gtfstools-2.0.0/gtfstools/R/get_route_frequency.R |only gtfstools-2.0.0/gtfstools/R/get_route_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_route_speed.R |only gtfstools-2.0.0/gtfstools/R/get_route_timetable.R |only gtfstools-2.0.0/gtfstools/R/get_shape_length.R |only gtfstools-2.0.0/gtfstools/R/get_shapes_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_start_and_end_times.R |only gtfstools-2.0.0/gtfstools/R/get_stop_distances.R |only gtfstools-2.0.0/gtfstools/R/get_stop_frequency.R |only gtfstools-2.0.0/gtfstools/R/get_stop_times_patterns.R | 163 - gtfstools-2.0.0/gtfstools/R/get_stop_timetable.R |only gtfstools-2.0.0/gtfstools/R/get_stops.R |only gtfstools-2.0.0/gtfstools/R/get_stops_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_summary.R |only gtfstools-2.0.0/gtfstools/R/get_trip_duration.R | 198 + gtfstools-2.0.0/gtfstools/R/get_trip_geometry.R | 363 +-- gtfstools-2.0.0/gtfstools/R/get_trip_length.R | 407 +-- gtfstools-2.0.0/gtfstools/R/get_trip_segment_duration.R | 334 +-- gtfstools-2.0.0/gtfstools/R/get_trip_speed.R | 325 +-- gtfstools-2.0.0/gtfstools/R/get_vkt.R |only gtfstools-2.0.0/gtfstools/R/get_vmt.R |only gtfstools-2.0.0/gtfstools/R/gtfstools.R | 308 +- gtfstools-2.0.0/gtfstools/R/interpolate_shape_dist_traveled.R |only gtfstools-2.0.0/gtfstools/R/interpolate_stop_times.R |only gtfstools-2.0.0/gtfstools/R/merge_gtfs.R | 270 ++ gtfstools-2.0.0/gtfstools/R/read_gtfs.R | 17 gtfstools-2.0.0/gtfstools/R/remove_duplicates.R | 7 gtfstools-2.0.0/gtfstools/R/remove_unused_ids.R |only gtfstools-2.0.0/gtfstools/R/set_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/set_max_speed.R |only gtfstools-2.0.0/gtfstools/R/set_min_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/set_route_frequency.R |only gtfstools-2.0.0/gtfstools/R/set_route_speed.R |only 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gtfstools-2.0.0/gtfstools/inst/doc/graphs.R |only gtfstools-2.0.0/gtfstools/inst/doc/graphs.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/graphs.html |only gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.R | 36 gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.Rmd | 48 gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.html | 458 ++-- gtfstools-2.0.0/gtfstools/inst/doc/mapping.R |only gtfstools-2.0.0/gtfstools/inst/doc/mapping.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/mapping.html |only gtfstools-2.0.0/gtfstools/inst/doc/querying.R |only gtfstools-2.0.0/gtfstools/inst/doc/querying.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/querying.html |only gtfstools-2.0.0/gtfstools/inst/doc/validating.Rmd | 59 gtfstools-2.0.0/gtfstools/inst/doc/validating.html | 81 gtfstools-2.0.0/gtfstools/man/as_dt_gtfs.Rd | 8 gtfstools-2.0.0/gtfstools/man/assert_shapes_fields.Rd |only gtfstools-2.0.0/gtfstools/man/assert_trip_stops_fields.Rd |only gtfstools-2.0.0/gtfstools/man/build_graph.Rd |only 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gtfstools-2.0.0/gtfstools/man/warn_times_not_interpolated.Rd |only gtfstools-2.0.0/gtfstools/man/warn_trips_without_shape.Rd |only gtfstools-2.0.0/gtfstools/man/write_gtfs.Rd | 12 gtfstools-2.0.0/gtfstools/man/write_summary_report.Rd |only gtfstools-2.0.0/gtfstools/src/Makevars |only gtfstools-2.0.0/gtfstools/src/Makevars.win |only gtfstools-2.0.0/gtfstools/src/convert-time.cpp | 64 gtfstools-2.0.0/gtfstools/src/convert-time.h | 1 gtfstools-2.0.0/gtfstools/src/cpp11.cpp | 52 gtfstools-2.0.0/gtfstools/src/distance_haversine.cpp |only gtfstools-2.0.0/gtfstools/src/sequence_pattern.cpp |only gtfstools-2.0.0/gtfstools/tests/testthat/_snaps/filter_by_sf.md | 15 gtfstools-2.0.0/gtfstools/tests/testthat/_snaps/filter_by_stop_id.md | 17 gtfstools-2.0.0/gtfstools/tests/testthat/test-as_dt_gtfs.R | 2 gtfstools-2.0.0/gtfstools/tests/testthat/test-build_graph.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-combine_nearby_stops.R |only 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gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_spatial_extent.R | 149 + gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_stop_id.R | 662 ++---- gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_time_of_day.R | 154 + gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_trip_id.R | 16 gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_helpers.R | 123 + gtfstools-2.0.0/gtfstools/tests/testthat/test-fix_gtfs.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-frequencies_to_stop_times.R | 281 ++ gtfstools-2.0.0/gtfstools/tests/testthat/test-get_active_services.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_calendar_overlap.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_dates.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_timetable.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_shape_length.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_shapes_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_start_and_end_times.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_distances.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_times_patterns.R | 169 + gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_timetable.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stops.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stops_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_summary.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_duration.R | 176 + gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_geometry.R | 690 ++++-- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_length.R | 904 ++++++-- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_segment_duration.R | 119 - gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_speed.R | 541 ++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_vkt.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_vmt.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-interpolate_shape_dist_traveled.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-interpolate_stop_times.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-merge_gtfs.R | 762 ++++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-read_gtfs.R | 4 gtfstools-2.0.0/gtfstools/tests/testthat/test-remove_duplicates.R | 22 gtfstools-2.0.0/gtfstools/tests/testthat/test-remove_unused_ids.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_max_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_min_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_route_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_route_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_trip_speed.R | 1063 +++++++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-stop_times_to_frequencies.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-utils.R | 188 + gtfstools-2.0.0/gtfstools/tests/testthat/test-write_gtfs.R | 16 gtfstools-2.0.0/gtfstools/vignettes/calendar_overlap.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/editing.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/filtering.Rmd | 89 gtfstools-2.0.0/gtfstools/vignettes/graphs.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/gtfstools.Rmd | 48 gtfstools-2.0.0/gtfstools/vignettes/mapping.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/querying.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/validating.Rmd | 59 311 files changed, 11464 insertions(+), 6015 deletions(-)
Title: 'shiny' Application for Population Structure and Ancestry
Assessments
Description: Provides a 'shiny' web application developed by the Breeding Insight team
to support pedigree validation and ancestry assessment of plant and animal
populations. The app integrates Mendelian error analysis, parentage assignment
and genetic composition/ancestry methods to help researchers evaluate genomic
relationships through an accessible, web-based interface without requiring
command-line tools. Pedigree validation, Mendelian error analysis and
parentage assignment build on the 'BIGpopA' package
(<https://CRAN.R-project.org/package=BIGpopA>) and support diploid and
polyploid data. Genotypes can be uploaded as dosage tables, VCF files,
or 'PLINK' .ped files. Ancestry estimation uses
the sparse non-negative matrix
factorization method of Frichot et al. (2014) <doi:10.1534/genetics.113.160572>
as implemented in the 'LEA' package by Frichot and Francois (2015)
<doi:10.1111/2041-210X.12382>. Line and breed composition are
estimated using the breed composition regression [...truncated...]
Author: Josue Chinchilla-Vargas [aut, cre],
Alexander M. Sandercock [aut],
Breeding Insight Team [aut]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Diff between Familia versions 2.0.0 dated 2026-08-24 and 2.2.0 dated 2026-10-28
Familia-2.0.0/Familia/inst/app/www/BIG_R_logo.png |only Familia-2.0.0/Familia/inst/app/www/BreedingInsight_Primary_RGBColor_400px.png |only Familia-2.0.0/Familia/inst/app/www/BreedingInsight_Secondary_RGBColor_400px.png |only Familia-2.0.0/Familia/tests/testthat/test-convert_to_dosage.R |only Familia-2.2.0/Familia/DESCRIPTION | 16 Familia-2.2.0/Familia/MD5 | 71 +- Familia-2.2.0/Familia/NAMESPACE | 24 Familia-2.2.0/Familia/NEWS.md | 74 ++ Familia-2.2.0/Familia/R/app_server.R | 48 + Familia-2.2.0/Familia/R/app_ui.R | 6 Familia-2.2.0/Familia/R/globals.R | 6 Familia-2.2.0/Familia/R/help_SNMF.R | 77 ++- Familia-2.2.0/Familia/R/help_find_parentage.R | 81 ++- Familia-2.2.0/Familia/R/help_ped_cleaner.R | 3 Familia-2.2.0/Familia/R/help_polybreedtools.R | 91 +++ Familia-2.2.0/Familia/R/help_validate_ped.R | 49 + Familia-2.2.0/Familia/R/mod_Home.R | 15 Familia-2.2.0/Familia/R/mod_SNMF.R | 184 ++++--- Familia-2.2.0/Familia/R/mod_find_parentage.R | 139 ++++- Familia-2.2.0/Familia/R/mod_ped_cleaner.R | 10 Familia-2.2.0/Familia/R/mod_polybreedtools.R | 234 ++++++--- Familia-2.2.0/Familia/R/mod_validate_ped.R | 85 +-- Familia-2.2.0/Familia/R/utils.R | 249 +++++++++- Familia-2.2.0/Familia/README.md | 37 + Familia-2.2.0/Familia/build |only Familia-2.2.0/Familia/inst/CITATION | 2 Familia-2.2.0/Familia/inst/WORDLIST | 21 Familia-2.2.0/Familia/inst/app/www/custom.css | 11 Familia-2.2.0/Familia/inst/app/www/custom.js | 8 Familia-2.2.0/Familia/inst/doc |only Familia-2.2.0/Familia/inst/extdata |only Familia-2.2.0/Familia/tests/testthat/test-example_files.R |only Familia-2.2.0/Familia/tests/testthat/test-read_genotype_upload.R |only Familia-2.2.0/Familia/vignettes |only 34 files changed, 1125 insertions(+), 416 deletions(-)
Title: Sparse Geometry Rasterization with Exact Coverage Fractions
Description: Rasterize polygon, line, and point geometry without
materializing any pixel values. For polygons it computes exact coverage
fractions for polygon-grid intersections, returning sparse tables:
run-length encoded interior cells and individually weighted boundary
cells. The scanline algorithm is O(perimeter) in both time and memory,
using the scan line fill attributed to Wylie et al. (1967)
<doi:10.1145/1465611.1465619>. Exact coverage fractions use the
exactextract algorithm by Daniel Baston, vendored from the
'exactextractr' package <doi:10.32614/CRAN.package.exactextractr>.
Derived from the 'fasterize' package by Noam Ross.
Author: Michael Sumner [aut, cre] ,
Noam Ross [aut] ,
EcoHealth Alliance [cph] ,
Jim Hester [ctb] ,
Daniel Baston [cph] ),
ISciences, LLC [cph] )
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between controlledburn versions 0.3.1 dated 2026-10-24 and 0.3.2 dated 2026-10-28
DESCRIPTION | 12 +-- MD5 | 29 ++++--- NAMESPACE | 4 + NEWS.md | 12 +++ R/plot.R |only R/summary.R |only README.md | 19 ++++- inst/doc/algorithms.Rmd | 10 ++ inst/doc/algorithms.html | 30 ++++---- man/controlledburn-package.Rd | 3 man/overview_burn.Rd |only man/plot.controlledburn.Rd |only man/summary.controlledburn.Rd |only src/analytical_coverage.h | 8 +- src/core_scanline.cpp | 135 +++++++++++++++++++++++++++++-------- tests/testthat/test-holes.R |only tests/testthat/test-lattice-snap.R | 34 +++++++++ tests/testthat/test-summary-plot.R |only vignettes/algorithms.Rmd | 10 ++ 19 files changed, 243 insertions(+), 63 deletions(-)
More information about controlledburn at CRAN
Permanent link
Title: Isolate Functions for Remote Execution
Description: Sending functions to remote processes can be wasteful of
resources because they carry their environments with them. With the
carrier package, it is easy to create functions that are isolated from
their environment. These isolated functions, also called crates, print
at the console with their total size and can be easily tested locally
before being sent to a remote.
Author: Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between carrier versions 0.3.0.4 dated 2025-09-11 and 0.4.0 dated 2026-10-28
DESCRIPTION | 11 ++-- MD5 | 16 ++--- NEWS.md | 25 ++++++++- R/crate.R | 111 +++++++++++++++++++++++++++++++---------- README.md | 14 ++--- man/carrier-package.Rd | 5 + man/crate.Rd | 59 ++++++++++++++------- tests/testthat/_snaps/crate.md | 33 +++++++++++- tests/testthat/test-crate.R | 88 +++++++++++++++++++++++++++++++- 9 files changed, 289 insertions(+), 73 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre] ,
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb],
Stephen Roecker [aut, ctb],
David Rossiter [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.3.2 dated 2026-04-30 and 2.3.3 dated 2026-10-28
DESCRIPTION | 8 MD5 | 56 NAMESPACE | 224 ++- NEWS.md | 6 R/SoilProfileCollection-coercion.R | 27 R/SoilProfileCollection-methods.R | 2 R/allocate.R | 2 R/aqp-label-placement-solvers.R | 72 - R/colorChart.R | 2 R/colorQuantiles.R | 2 R/plotSPC.R | 22 R/slab.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 129 +- inst/doc/Munsell-color-conversion.html | 9 inst/doc/NCSP.html | 13 inst/doc/label-placement.R | 71 - inst/doc/label-placement.Rmd | 87 + inst/doc/label-placement.html | 675 ++++++------ man/SoilProfileCollection-plotting-methods.Rd | 2 man/allocate.Rd | 2 man/coercion-methods.Rd | 35 man/fixOverlap.Rd | 48 man/overlapMetrics.Rd | 14 man/slab.Rd | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-genhz.R | 6 vignettes/label-placement.Rmd | 87 + 29 files changed, 955 insertions(+), 668 deletions(-)
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH)
Data
Description: A toolkit to set up an R data package in a consistent
structure. Automates tasks like tidy data export, data dictionary
documentation, README and website creation, and citation management.
Author: Mian Zhong [aut] ,
Margaux Goetschmann [aut] ,
Colin Walder [aut] ,
Lars Schoebitz [aut, cre] ,
Global Health Engineering, ETH Zurich [cph]
Maintainer: Lars Schoebitz <lschoebitz@ethz.ch>
Diff between washr versions 1.1.0 dated 2026-09-02 and 1.2.0 dated 2026-10-28
DESCRIPTION | 14 - MD5 | 99 +++++---- NAMESPACE | 6 NEWS.md | 180 +++++++++++++++++ R/check_publication_readiness.R |only R/config.R |only R/generate_jsonld.R | 56 +++-- R/setup_ci.R | 27 +- R/setup_dictionary.R | 40 ++- R/setup_rawdata.R | 34 +-- R/setup_readme.R | 75 +++++-- R/setup_roxygen.R | 52 +++- R/setup_website.R | 47 +++- R/source_article.R |only R/ui.R |only R/update_citation.R | 121 +++++++++-- R/update_description.R | 99 ++++++++- R/update_dictionary.R |only R/update_metadata.R | 44 ++-- R/use_brand.R | 230 ++++++++++++++++++---- R/utils.R | 29 ++ R/washr-package.R | 10 R/zenodo_json.R |only README.md | 31 ++ inst/doc/washr.R | 15 + inst/doc/washr.Rmd | 69 +++++- inst/doc/washr.html | 194 +++++++++++++++--- inst/templates/README.Rmd | 42 +++- inst/templates/_pkgdown.yml | 19 + man/check_publication_readiness.Rd |only man/setup_ci.Rd | 3 man/setup_dictionary.Rd | 8 man/setup_rawdata.Rd | 6 man/setup_readme.Rd | 14 + man/setup_roxygen.Rd | 9 man/setup_website.Rd | 13 - man/update_citation.Rd | 44 +++- man/update_description.Rd | 43 +++- man/update_dictionary.Rd |only man/update_metadata.Rd | 7 man/update_zenodo_json.Rd |only man/use_brand.Rd | 37 ++- man/washr-package.Rd | 12 + tests/testthat/_snaps/update_citation.md | 2 tests/testthat/_snaps/update_description.md | 7 tests/testthat/test_check_publication_readiness.R |only tests/testthat/test_config.R |only tests/testthat/test_edge_cases.R |only tests/testthat/test_setup_ci.R | 19 + tests/testthat/test_setup_readme.R | 52 ++++ tests/testthat/test_ui.R |only tests/testthat/test_update_citation.R | 113 ++++++++++ tests/testthat/test_update_description.R | 8 tests/testthat/test_update_dictionary.R |only tests/testthat/test_update_metadata.R | 12 + tests/testthat/test_update_zenodo_json.R |only tests/testthat/test_use_brand.R | 196 ++++++++++++++++++ vignettes/washr.Rmd | 69 +++++- 58 files changed, 1845 insertions(+), 362 deletions(-)
Title: Reliable Utilities for Reusable Research Workflows
Description: Provides reusable building blocks for research packages across
matrix representation, numerical computation, neighborhood evaluation,
controlled execution, and runtime interoperability. Core tools preserve
declared sparse semantics, expose dense-memory and output boundaries,
standardize neighborhood and classification results, and align serial and
parallel result and error behavior. Additional helpers support structured
messages, optional dependency checks, and common statistical workflows.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.5.0 dated 2026-08-21 and 0.5.3 dated 2026-10-28
thisutils-0.5.0/thisutils/inst/python |only thisutils-0.5.3/thisutils/DESCRIPTION | 15 thisutils-0.5.3/thisutils/MD5 | 85 - thisutils-0.5.3/thisutils/NAMESPACE | 8 thisutils-0.5.3/thisutils/NEWS.md | 91 + thisutils-0.5.3/thisutils/R/RcppExports.R | 12 thisutils-0.5.3/thisutils/R/add_pkg_file.R | 76 - thisutils-0.5.3/thisutils/R/as_matrix.R | 13 thisutils-0.5.3/thisutils/R/computation.R | 80 - thisutils-0.5.3/thisutils/R/figlet.R | 63 - thisutils-0.5.3/thisutils/R/fit_trends.R |only thisutils-0.5.3/thisutils/R/log_message.R | 62 - thisutils-0.5.3/thisutils/R/package_management.R | 36 thisutils-0.5.3/thisutils/R/parallelize_fun.R | 599 ++++++---- thisutils-0.5.3/thisutils/R/sparse_cor.R | 23 thisutils-0.5.3/thisutils/R/sparse_matrix_tools.R | 289 ++++ thisutils-0.5.3/thisutils/R/thisutils-package.R | 3 thisutils-0.5.3/thisutils/R/utils.R | 139 +- thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.R | 6 thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.Rmd | 6 thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.html | 40 thisutils-0.5.3/thisutils/inst/include/thisutils/log_message.h | 19 thisutils-0.5.3/thisutils/inst/scripts |only thisutils-0.5.3/thisutils/man/aggregate_matrix.Rd |only thisutils-0.5.3/thisutils/man/col_maxs.Rd |only thisutils-0.5.3/thisutils/man/detect_cores.Rd |only thisutils-0.5.3/thisutils/man/fast_aggregate.Rd |only thisutils-0.5.3/thisutils/man/fit_trends.Rd |only thisutils-0.5.3/thisutils/man/get_verbose.Rd | 4 thisutils-0.5.3/thisutils/man/grapes-or-or-or-grapes.Rd |only thisutils-0.5.3/thisutils/man/invoke_fun.Rd | 8 thisutils-0.5.3/thisutils/man/local_verbose.Rd |only thisutils-0.5.3/thisutils/man/row_maxs.Rd |only thisutils-0.5.3/thisutils/src/ClassificationMetrics.cpp | 24 thisutils-0.5.3/thisutils/src/RcppExports.cpp | 55 thisutils-0.5.3/thisutils/src/curve_summary.cpp |only thisutils-0.5.3/thisutils/src/lisi.cpp | 165 -- thisutils-0.5.3/thisutils/src/matrix_to_table.cpp | 3 thisutils-0.5.3/thisutils/src/table_to_matrix.cpp | 6 thisutils-0.5.3/thisutils/tests/testthat/test-fit-trends.R |only thisutils-0.5.3/thisutils/tests/testthat/test-invoke-fun.R |only thisutils-0.5.3/thisutils/tests/testthat/test-lisi.R | 46 thisutils-0.5.3/thisutils/tests/testthat/test-log_message.R | 12 thisutils-0.5.3/thisutils/tests/testthat/test-package-github-metadata.R |only thisutils-0.5.3/thisutils/tests/testthat/test-package-management.R | 2 thisutils-0.5.3/thisutils/tests/testthat/test-parallelize_fun.R | 533 +++++++- thisutils-0.5.3/thisutils/tests/testthat/test-sparse_matrix_tools.R | 125 ++ thisutils-0.5.3/thisutils/tests/testthat/test-utils.R | 23 thisutils-0.5.3/thisutils/vignettes/reliable-sparse-workflows.Rmd | 6 49 files changed, 1804 insertions(+), 873 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 1.0.5 dated 2025-10-17 and 1.0.6 dated 2026-10-28
DESCRIPTION | 12 +- MD5 | 36 +++--- NAMESPACE | 1 NEWS.md | 11 + R/index_scale.R | 88 +++++++++++---- R/ppi_noise_grid.R |only R/sample_size_effect.R | 114 +++++++++++++------ R/utils_tourr.R | 4 build/vignette.rds |binary inst/doc/more_descriptives.R | 8 + inst/doc/more_descriptives.html | 230 ++++++++++++++++++++++++++++++++-------- inst/doc/more_descriptives.qmd | 8 + inst/doc/ppi_diagnostics.html | 178 +++++++++++++++++++++++++++--- inst/doc/spinebil.html | 146 ++++++++++++++++++++++++- man/geodesic_info.Rd | 4 man/ppi_noise_grid.Rd |only man/ppi_samplesize_effect.Rd | 47 +++++++- man/ppi_scale.Rd | 38 +++++- man/spinebil-package.Rd | 1 vignettes/more_descriptives.qmd | 8 + 20 files changed, 773 insertions(+), 161 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see <doi:10.18637/jss.v033.i01> and <doi:10.18637/jss.v039.i05>. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (<doi:10.18637/jss.v106.i01>). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers cited.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Kenneth Tay [aut],
Noah Simon [aut],
Junyang Qian [ctb],
James Yang [aut],
Jonathan Taylor [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 5.1 dated 2026-09-24 and 5.2 dated 2026-10-28
DESCRIPTION | 10 MD5 | 65 NAMESPACE | 74 NEWS.md | 25 R/buildPredmat.coxnetlist.R | 6 R/coxgrad.R | 9 R/cv.glmnet.R | 6 R/cv.glmnet.raw.R | 21 R/cv.relaxed.raw.R | 22 R/getOptcv.relaxed.R | 3 R/getcoef.R | 3 R/glmnet-package.R | 18 R/glmnet.control.R | 36 R/predict.glmnet.R | 4 R/predict.multnet.R | 2 R/predict.relaxed.R | 13 README.md | 72 inst/doc/Coxnet.pdf |binary inst/doc/coxdev.html | 828 +++++---- inst/doc/glmnet-history.pdf |binary inst/doc/glmnet.pdf |binary inst/doc/glmnetFamily.pdf |binary inst/doc/relax.pdf |binary man/coxgrad.Rd | 9 man/glmnet.control.Rd | 4 man/predict.glmnet.Rd | 6 src/glmnet_control.cpp | 6 src/glmnetpp/coxdev/cpp/include/coxdev.h | 150 + src/glmnetpp/coxdev/cpp/src/coxdev.cpp | 908 +++++++++- src/glmnetpp/coxdev/cpp/tests |only src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_base.hpp | 11 tests/testthat/helper-functions.R | 45 tests/testthat/test_predict_relaxed.R |only tests/testthat/test_smoke_families.R | 14 34 files changed, 1866 insertions(+), 504 deletions(-)
Title: Implementation of the DISCO Metric for Internal Clustering
Evaluation
Description: Implementation of the DISCO (Density-based Internal Score for
Clusterings with nOise) metric, a cluster validity index for evaluating
density-based clustering results without ground truth labels. DISCO is the
first index to explicitly assess the quality of noise point assignments in
addition to cluster quality. It uses density-connectivity distance derived
from a minimum spanning tree of the mutual-reachability graph, providing
interpretable, bounded scores in [-1, 1]. Higher scores indicate better
clustering. Based on Beer et al. (2025)
<doi:10.48550/arXiv.2503.00127>.
Author: Amin Entezari [aut, cre] ,
Davide Chicco [ctb] ,
Anna Beer [aut] ),
Lena Krieger [aut] ),
Pascal Weber [aut] )
Maintainer: Amin Entezari <amin_entezari@outlook.com>
Diff between discoCVI versions 0.2.0 dated 2026-10-27 and 0.2.1 dated 2026-10-28
DESCRIPTION | 9 +++++---- MD5 | 9 +++++++-- NEWS.md | 7 +++++++ build |only inst/doc |only vignettes |only 6 files changed, 19 insertions(+), 6 deletions(-)
Title: Within-Subject Mediation Analysis Using Structural Equation
Modeling
Description: Within-subject mediation analysis using structural equation modeling.
Examine how changes in an outcome variable between two conditions are mediated
through one or more variables. Supports within-subject mediation analysis using
the 'lavaan' package by Rosseel (2012) <doi:10.18637/jss.v048.i02>,
and extends Monte Carlo confidence interval estimation to missing data scenarios
using the 'semmcci' package by Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between wsMed versions 1.1.0 dated 2026-09-18 and 1.2.0 dated 2026-10-28
wsMed-1.1.0/wsMed/man/print.wsMed.Rd |only wsMed-1.2.0/wsMed/DESCRIPTION | 14 wsMed-1.2.0/wsMed/MD5 | 438 +- wsMed-1.2.0/wsMed/NAMESPACE | 43 wsMed-1.2.0/wsMed/NEWS.md | 163 wsMed-1.2.0/wsMed/R/ARIVwrapper.R | 2 wsMed-1.2.0/wsMed/R/GenerateModelCN.R | 32 wsMed-1.2.0/wsMed/R/GenerateModelCP.R | 22 wsMed-1.2.0/wsMed/R/GenerateModelCustom.R | 11 wsMed-1.2.0/wsMed/R/GenerateModelP.R | 19 wsMed-1.2.0/wsMed/R/GenerateModelPC.R | 22 wsMed-1.2.0/wsMed/R/ImputeData.R | 28 wsMed-1.2.0/wsMed/R/Locationwrapper.R | 2 wsMed-1.2.0/wsMed/R/MCDefWrapper.R | 2 wsMed-1.2.0/wsMed/R/MCLav_Lav2RAM2.R | 2 wsMed-1.2.0/wsMed/R/MCMI2.R | 84 wsMed-1.2.0/wsMed/R/MC_apply_standardization.R | 2 wsMed-1.2.0/wsMed/R/MC_bootstrap_sd_list.R | 2 wsMed-1.2.0/wsMed/R/MC_build_definitions.R | 2 wsMed-1.2.0/wsMed/R/MC_build_std_map.R | 4 wsMed-1.2.0/wsMed/R/MC_evaluate_definitions.R | 4 wsMed-1.2.0/wsMed/R/MC_extract_all_parameters.R | 2 wsMed-1.2.0/wsMed/R/MC_generate_mc_samples.R | 2 wsMed-1.2.0/wsMed/R/MC_get_sd_target_variables.R | 10 wsMed-1.2.0/wsMed/R/MC_resolve_all_dependencies.R | 2 wsMed-1.2.0/wsMed/R/MC_run_mc_mediation.R | 4 wsMed-1.2.0/wsMed/R/MC_summarize_mc_ci.R | 2 wsMed-1.2.0/wsMed/R/MClav_MCStd2.R | 2 wsMed-1.2.0/wsMed/R/MClav_RAM2Lav2.R | 4 wsMed-1.2.0/wsMed/R/MClav_StdLav2.R | 9 wsMed-1.2.0/wsMed/R/MClav_StdRAM2.R | 11 wsMed-1.2.0/wsMed/R/MClav_ThetaHat2.R | 2 wsMed-1.2.0/wsMed/R/MICombineWrapper.R | 2 wsMed-1.2.0/wsMed/R/PrepareData.R | 20 wsMed-1.2.0/wsMed/R/PrepareMissingData.R | 4 wsMed-1.2.0/wsMed/R/RandomGaussianCholwrapper.R | 3 wsMed-1.2.0/wsMed/R/RandomGaussianEigenwrapper.R | 20 wsMed-1.2.0/wsMed/R/RandomGaussianSVDwrapper.R | 3 wsMed-1.2.0/wsMed/R/RandomGaussianZwrapper.R | 2 wsMed-1.2.0/wsMed/R/RunMCMIAnalysis.R | 8 wsMed-1.2.0/wsMed/R/TestPositiveDefinitewrapper.R | 2 wsMed-1.2.0/wsMed/R/ThetaHatStarWrapper.R | 13 wsMed-1.2.0/wsMed/R/ThetaHatWrapper.R | 2 wsMed-1.2.0/wsMed/R/TransformMidsWithPrepareData.R | 10 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Title: Utility Functions for Plotting
Description: Provides utility functions for plotting. Includes functions for color manipulation, plot customization, panel size control, data optimization for plots, and layout adjustments.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisplot versions 0.4.3 dated 2026-08-01 and 0.4.6 dated 2026-10-28
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Title: Spatial Regression Models with Compositional Data
Description: Spatial and non-spatial regression models with compositional responses (and compositional predictors) using the alpha--transformation. Relevant papers include: Tsagris M. and Pantazis Y. (2026), <doi:10.48550/arXiv.2510.12663>, Tsagris M. (2015), <https://soche.cl/chjs/volumes/06/02/Tsagris(2015).pdf>, Tsagris M.T., Preston S. and Wood A.T.A. (2011), <doi:10.48550/arXiv.1106.1451>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalSR versions 1.4 dated 2026-04-14 and 1.5 dated 2026-10-28
DESCRIPTION | 8 +++--- MD5 | 28 +++++++++++---------- NAMESPACE | 2 - R/alfa.betest.R |only R/alfa.esf.R | 53 ++++++++++++++++++++++++++++++++++------- R/alfa.reg.R | 2 - R/alfa.reg2.R | 2 - R/alfa.sar.R | 2 - R/alfa.slx.R | 2 - R/alfa.slx2.R | 2 - R/areg.R | 18 ++++++++----- R/rob.alfareg.R | 2 - man/CompositionalSR-package.Rd | 4 +-- man/alfa.betest.Rd |only man/alfa.esf.Rd | 17 +++++++++---- man/cv.alfaesf.Rd | 3 -- 16 files changed, 97 insertions(+), 48 deletions(-)
More information about CompositionalSR at CRAN
Permanent link
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2020) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures. Moreover, as of version 4.0, it is the only method of its kind that provides measures for model evaluation and selection that are custom-made for the problem of INUS-discovery.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 4.0.3 dated 2025-06-02 and 4.1.0 dated 2026-10-28
cna-4.0.3/cna/R/condition.r |only cna-4.0.3/cna/man/condition.Rd |only cna-4.1.0/cna/DESCRIPTION | 8 cna-4.1.0/cna/MD5 | 143 +++++----- cna-4.1.0/cna/NAMESPACE | 6 cna-4.1.0/cna/R/RcppExports.R | 8 cna-4.1.0/cna/R/auxConfigTable.R | 4 cna-4.1.0/cna/R/cna.r | 26 + cna-4.1.0/cna/R/cnaControl.R | 10 cna-4.1.0/cna/R/cna_aux.r | 43 +++ cna-4.1.0/cna/R/coherence.r | 5 cna-4.1.0/cna/R/condList.r |only cna-4.1.0/cna/R/condTbl.r | 21 - cna-4.1.0/cna/R/condition_aux.R | 2 cna-4.1.0/cna/R/configTable.R | 15 - cna-4.1.0/cna/R/csf.R | 74 ++++- cna-4.1.0/cna/R/ctiList.R | 117 +++++++- cna-4.1.0/cna/R/cyclic.R | 9 cna-4.1.0/cna/R/detailMeasures.R | 144 +++++++--- cna-4.1.0/cna/R/full.ct.R | 7 cna-4.1.0/cna/R/func_minim.R |only cna-4.1.0/cna/R/getCondtype.R | 3 cna-4.1.0/cna/R/is.inus.R | 33 +- cna-4.1.0/cna/R/is.submodel.R | 4 cna-4.1.0/cna/R/measures_definitions.R | 4 cna-4.1.0/cna/R/minimalizeCsf.R | 8 cna-4.1.0/cna/R/print.cna.r | 27 -- cna-4.1.0/cna/R/qcond.R | 12 cna-4.1.0/cna/R/randomConds.R | 8 cna-4.1.0/cna/build/partial.rdb |binary cna-4.1.0/cna/build/vignette.rds |binary cna-4.1.0/cna/inst/NEWS | 10 cna-4.1.0/cna/inst/doc/cna.R | 66 +++-- cna-4.1.0/cna/inst/doc/cna.Rnw | 279 +++++++++++++-------- cna-4.1.0/cna/inst/doc/cna.pdf |binary cna-4.1.0/cna/man/cna-internals.Rd | 4 cna-4.1.0/cna/man/cna-package.Rd | 54 ++-- cna-4.1.0/cna/man/cna-solutions.Rd | 370 ++++++++++++++-------------- cna-4.1.0/cna/man/cna.Rd | 149 ++++++----- cna-4.1.0/cna/man/cnaControl.Rd | 382 +++++++++++++++-------------- cna-4.1.0/cna/man/coherence.Rd | 96 +++---- cna-4.1.0/cna/man/condList-methods.Rd | 2 cna-4.1.0/cna/man/condList.Rd |only cna-4.1.0/cna/man/condTbl.Rd | 229 ++++++++--------- cna-4.1.0/cna/man/configTable.Rd | 2 cna-4.1.0/cna/man/ct2df.Rd | 2 cna-4.1.0/cna/man/cyclic.Rd | 4 cna-4.1.0/cna/man/d.autonomy.Rd | 4 cna-4.1.0/cna/man/d.educate.Rd | 6 cna-4.1.0/cna/man/d.irrigate.Rd | 4 cna-4.1.0/cna/man/d.jobsecurity.Rd | 6 cna-4.1.0/cna/man/d.minaret.Rd | 78 ++--- cna-4.1.0/cna/man/d.pacts.Rd | 74 ++--- cna-4.1.0/cna/man/d.pban.Rd | 68 ++--- cna-4.1.0/cna/man/d.performance.Rd | 4 cna-4.1.0/cna/man/d.volatile.Rd | 4 cna-4.1.0/cna/man/d.women.Rd | 4 cna-4.1.0/cna/man/detailMeasures.Rd | 174 +++++++------ cna-4.1.0/cna/man/fs2cs.Rd | 2 cna-4.1.0/cna/man/full.ct.Rd | 18 - cna-4.1.0/cna/man/func_minim.Rd |only cna-4.1.0/cna/man/is.inus.Rd | 434 +++++++++++++++++---------------- cna-4.1.0/cna/man/is.submodel.Rd | 174 ++++++------- cna-4.1.0/cna/man/minimalize.Rd | 8 cna-4.1.0/cna/man/print.cna.Rd | 169 ++++++------ cna-4.1.0/cna/man/randomConds.Rd | 404 +++++++++++++++--------------- cna-4.1.0/cna/man/selectCases.Rd | 178 ++++++------- cna-4.1.0/cna/man/showMeasures.Rd | 115 +++----- cna-4.1.0/cna/man/some.Rd | 2 cna-4.1.0/cna/src/RcppExports.cpp | 14 - cna-4.1.0/cna/src/cna_init.c | 8 cna-4.1.0/cna/src/headers.h | 3 cna-4.1.0/cna/src/minimal_submodel.cpp | 2 cna-4.1.0/cna/src/utils.cpp | 20 - cna-4.1.0/cna/vignettes/cna.Rnw | 279 +++++++++++++-------- cna-4.1.0/cna/vignettes/stfloats.sty |only 76 files changed, 2579 insertions(+), 2067 deletions(-)
Title: Likelihood-Based Statistical Inference in the Fisherian
Tradition
Description: Facilitates building likelihood models in the Fisherian tradition
following Richard Royall (1997, ISBN:978-0412044113) "Statistical Evidence: A
Likelihood Paradigm". Defines generic methods for working with likelihoods
(loglik(), score(), hess_loglik(), fim()) and provides functions for pure
likelihood-based inference (support(), relative_likelihood(),
likelihood_interval(), profile_loglik()).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between likelihood.model versions 1.0.1 dated 2026-05-24 and 1.0.2 dated 2026-10-28
DESCRIPTION | 6 +- MD5 | 15 ++--- NEWS.md | 10 +++ R/core-fisherian.R | 111 +++++++++++++++++++++++++------------ inst/doc/exponential-lifetime.html | 2 inst/doc/getting-started.html | 2 man/likelihood_interval.Rd | 7 ++ man/profile_loglik.Rd | 6 ++ tests/regression-profile-domain.R |only 9 files changed, 113 insertions(+), 46 deletions(-)
More information about likelihood.model at CRAN
Permanent link
Title: Dynamic Failure Rate Distributions for Survival Analysis
Description: Flexible framework for specifying survival distributions through
their hazard (failure rate) functions. Define arbitrary time-varying
hazard functions to model complex failure patterns including bathtub
curves, proportional hazards with covariates, and other non-standard
hazard behaviors. Provides automatic computation of survival, CDF, PDF,
quantiles, and sampling. Implements the likelihood model interface for
maximum likelihood estimation with right-censored and left-censored
survival data.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between flexhaz versions 0.5.2 dated 2026-05-23 and 0.5.3 dated 2026-10-28
DESCRIPTION | 6 +-- MD5 | 21 ++++++------ NEWS.md | 8 ++++ R/dfr_dist.R | 17 +++++++--- R/utils.R | 25 ++++++++++++++- README.md | 44 ++++++++++++--------------- inst/doc/custom_distributions.html | 6 +-- inst/doc/failure_rate.html | 4 +- inst/doc/flexhaz-package.html | 4 +- man/dfr_dist.Rd | 8 +++- tests/testthat/Rplots.pdf |binary tests/testthat/test-observation-validation.R |only 12 files changed, 92 insertions(+), 51 deletions(-)
Title: Compositional Maximum Likelihood Estimation
Description: Provides composable optimization strategies for maximum likelihood
estimation (MLE). Solvers are first-class functions that combine via
sequential chaining, parallel racing, and random restarts. Implements
gradient ascent, Newton-Raphson, quasi-Newton (BFGS), and derivative-free
methods with support for constrained optimization and tracing. Returns
'mle' objects compatible with 'algebraic.mle' for downstream analysis.
Methods based on Nocedal J, Wright SJ (2006) "Numerical Optimization"
<doi:10.1007/978-0-387-40065-5>.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between compositional.mle versions 2.0.0 dated 2026-03-19 and 2.0.1 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/compose.R | 8 ++++---- inst/doc/case-studies.html | 4 ++-- inst/doc/getting-started.html | 4 ++-- inst/doc/mle-ecosystem.html | 4 ++-- inst/doc/strategy-design.html | 4 ++-- inst/doc/theory-and-intuition.html | 4 ++-- tests/testthat/test-meta-solvers.R | 37 +++++++++++++++++++++++++++++++++++++ 10 files changed, 70 insertions(+), 26 deletions(-)
More information about compositional.mle at CRAN
Permanent link
Title: Algebraic Maximum Likelihood Estimators
Description: The maximum likelihood estimator (MLE) is a technology: under
regularity conditions, any MLE is asymptotically normal with variance given
by the inverse Fisher information. This package exploits that structure by
defining an algebra over MLEs. Compose independent estimators into joint
MLEs via block-diagonal covariance ('joint'), optimally combine repeated
estimates via inverse-variance weighting ('combine'), propagate
transformations via the delta method ('rmap'), and bridge to distribution
algebra via conversion to normal or multivariate normal objects ('as_dist').
Supports asymptotic ('mle', 'mle_numerical') and bootstrap ('mle_boot')
estimators with a unified interface for inference: confidence intervals,
standard errors, AIC, Fisher information, and predictive intervals.
For background on maximum likelihood estimation, see Casella and Berger
(2002, ISBN:978-0534243128). For the delta method and variance estimation,
see Lehmann and Casella (1998, ISBN:978-0387985022).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between algebraic.mle versions 2.0.2 dated 2026-03-19 and 2.0.3 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/combine.R | 37 +++++++++++++++++++++++++++++++++---- R/mle_rmap.R | 2 +- man/combine.Rd | 5 +++++ tests/testthat/test-combine.R | 35 +++++++++++++++++++++++++++++++++++ tests/testthat/test-mle_rmap.R | 13 +++++++++++++ 8 files changed, 108 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-26 1.0.1
2024-01-19 1.0.0
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.12 dated 2025-09-02 and 1.0.13 dated 2026-10-28
dynutils-1.0.12/dynutils/man/dynutils.Rd |only dynutils-1.0.13/dynutils/DESCRIPTION | 10 dynutils-1.0.13/dynutils/MD5 | 52 ++-- dynutils-1.0.13/dynutils/NAMESPACE | 129 +++++----- dynutils-1.0.13/dynutils/NEWS.md | 6 dynutils-1.0.13/dynutils/R/calculate_distance.R | 43 +-- dynutils-1.0.13/dynutils/R/package.R | 5 dynutils-1.0.13/dynutils/R/spearman_rank_sparse.R | 1 dynutils-1.0.13/dynutils/build/vignette.rds |binary dynutils-1.0.13/dynutils/inst/doc/functionality.html | 82 +++--- dynutils-1.0.13/dynutils/man/dynutils-package.Rd |only dynutils-1.0.13/dynutils/tests/testthat/test-add_class.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-assertions.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-calculate_distance.R | 79 +++++- dynutils-1.0.13/dynutils/tests/testthat/test-calculate_mean.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-check_packages.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-expand_matrix.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-extend_with.R | 10 dynutils-1.0.13/dynutils/tests/testthat/test-h5.R | 65 ++--- dynutils-1.0.13/dynutils/tests/testthat/test-inherit_default_params.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-mapdf.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-news.R | 4 dynutils-1.0.13/dynutils/tests/testthat/test-project_to_segments.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-random_time_string.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-safe_tempdir.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-scaling.R | 34 +- dynutils-1.0.13/dynutils/tests/testthat/test-spearman_rank_sparse.R | 20 + dynutils-1.0.13/dynutils/tests/testthat/test-tibble.R | 2 28 files changed, 331 insertions(+), 231 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
design-aware GSEA on RNA-seq counts with per-sample gene set scoring, Weighted Enrichment
Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA), multi-layer
network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.6 dated 2026-10-06 and 0.2.7 dated 2026-10-28
DESCRIPTION | 21 +- MD5 | 51 +++-- NAMESPACE | 10 NEWS.md | 336 +++++++++++++++++++-------------- R/bayes_enrich.R | 41 +++- R/deseq2.R |only R/dsea_pathway.R |only R/gsea.R | 104 +++++++++- R/nsea.R | 38 ++- R/ora_gson.R | 57 ++++- R/utilities.R | 94 ++++++++- README.md | 15 + man/as_genes.Rd |only man/as_ranked.Rd |only man/bayes_enrich.Rd | 9 man/dsea.Rd |only man/enrichit-package.Rd | 2 man/ssgsea_scores.Rd |only src/enrichit.cpp | 30 ++ src/gsea_multilevel.cpp | 20 + tests/testthat/test-accessors.R | 34 +++ tests/testthat/test-bayes-enrich.R | 71 ++++++ tests/testthat/test-converters.R | 25 +- tests/testthat/test-deseq2.R |only tests/testthat/test-dsea-pathway.R |only tests/testthat/test-filter-gene-sets.R |only tests/testthat/test-gsea-edge-guards.R |only tests/testthat/test-gsea.R | 88 +++++--- tests/testthat/test-gson-helpers.R | 5 tests/testthat/test-nsea.R | 60 +++++ tests/testthat/test-ora.R | 176 +++++++++++++++++ tests/testthat/test-qvalue-cutoff.R |only 32 files changed, 1028 insertions(+), 259 deletions(-)