Title: Raw Data for 'pharmaversesdtm' Package
Description: A set of raw datasets used to create SDTM domains in
'pharmaversesdtm' package.
Author: Rammprasad Ganapathy [aut, cre],
Shiyu Chen [aut]
Maintainer: Rammprasad Ganapathy <ganapathy.rammprasad@gene.com>
Diff between pharmaverseraw versions 0.1.0 dated 2025-05-23 and 0.1.1 dated 2025-08-29
DESCRIPTION | 6 +++--- MD5 | 9 ++++++--- NEWS.md | 6 ++++++ R/vs_raw.R |only data/vs_raw.rda |only inst/WORDLIST | 1 + man/vs_raw.Rd |only 7 files changed, 16 insertions(+), 6 deletions(-)
More information about pharmaverseraw at CRAN
Permanent link
Title: Predict with 'tidymodels' Workflows in Databases
Description: Turn 'tidymodels' workflows into objects containing the
sufficient sequential equations to perform predictions. These smaller
objects allow for low dependency prediction locally or directly in
databases.
Author: Emil Hvitfeldt [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between orbital versions 0.3.0 dated 2024-12-21 and 0.3.1 dated 2025-08-29
DESCRIPTION | 13 - LICENSE | 2 MD5 | 292 ++++++++++++------------- NEWS.md | 10 R/aaa.R | 6 R/augment.R | 14 - R/dt.R | 10 R/inline.R | 6 R/json.R | 42 +-- R/last_fit.R | 4 R/model-glm.R | 64 ++--- R/model-partykit.R | 46 ++-- R/model-xgboost.R | 174 +++++++-------- R/orbital.R | 72 +++--- R/parsnip.R | 176 +++++++-------- R/predict.R | 16 - R/r_fun.R | 20 - R/recipes-utils.R | 114 ++++++--- R/recipes.R | 116 +++++----- R/sql.R | 4 R/step_adasyn.R | 6 R/step_bin2factor.R | 20 - R/step_boxcox.R | 22 - R/step_bsmote.R | 6 R/step_center.R | 18 - R/step_corr.R | 2 R/step_discretize.R | 80 +++---- R/step_downsample.R | 6 R/step_dummy.R | 24 +- R/step_filter_missing.R | 2 R/step_impute_mean.R | 20 - R/step_impute_median.R | 20 - R/step_impute_mode.R | 20 - R/step_indicate_na.R | 22 - R/step_intercept.R | 16 - R/step_inverse.R | 26 +- R/step_lag.R | 26 +- R/step_lencode_bayes.R | 4 R/step_lencode_glm.R | 4 R/step_lencode_mixed.R | 4 R/step_lincomb.R | 2 R/step_log.R | 34 +- R/step_mutate.R | 10 R/step_nearmiss.R | 6 R/step_normalize.R | 22 - R/step_novel.R | 32 +- R/step_nzv.R | 2 R/step_other.R | 38 +-- R/step_pca.R | 6 R/step_pca_sparse.R | 6 R/step_pca_sparse_bayes.R | 6 R/step_pca_truncated.R | 6 R/step_range.R | 40 +-- R/step_ratio.R | 22 - R/step_rename.R | 8 R/step_rm.R | 2 R/step_rose.R | 6 R/step_scale.R | 18 - R/step_select.R | 2 R/step_smote.R | 6 R/step_smotenc.R | 6 R/step_sqrt.R | 16 - R/step_tomek.R | 6 R/step_unknown.R | 16 - R/step_upsample.R | 6 R/step_zv.R | 2 R/utils.R | 10 R/workflows.R | 34 +- README.md | 14 - build/vignette.rds |binary inst/doc/supported-models.R | 6 inst/doc/supported-models.Rmd | 12 - inst/doc/supported-models.html | 114 +++++---- man/augment.orbital_class.Rd | 2 man/orbital.Rd | 6 man/orbital_dt.Rd | 2 man/orbital_inline.Rd | 4 man/orbital_json_read.Rd | 2 man/orbital_json_write.Rd | 2 man/orbital_r_fun.Rd | 2 man/orbital_sql.Rd | 2 man/predict.orbital_class.Rd | 2 tests/testthat/derby.log | 12 - tests/testthat/helper-context.R | 148 ++++++------ tests/testthat/helper-initialize.R | 320 ++++++++++++++-------------- tests/testthat/helper-reporter.R | 264 +++++++++++------------ tests/testthat/helper-utils.R | 14 - tests/testthat/test-augment.R | 138 ++++++------ tests/testthat/test-dt.R | 34 +- tests/testthat/test-inline.R | 30 +- tests/testthat/test-json.R | 68 ++--- tests/testthat/test-model-glm.R | 110 ++++----- tests/testthat/test-model-partykit.R | 122 +++++----- tests/testthat/test-model-xgboost.R | 254 +++++++++++----------- tests/testthat/test-orbital.R | 292 ++++++++++++------------- tests/testthat/test-parsnip.R | 162 +++++++------- tests/testthat/test-predict.R | 30 +- tests/testthat/test-recipes.R | 66 ++--- tests/testthat/test-sql.R | 34 +- tests/testthat/test-step_adasyn.R | 190 ++++++++-------- tests/testthat/test-step_bin2factor.R | 168 +++++++------- tests/testthat/test-step_boxcox.R | 164 +++++++------- tests/testthat/test-step_bsmote.R | 188 ++++++++-------- tests/testthat/test-step_center.R | 164 +++++++------- tests/testthat/test-step_corr.R | 48 ++-- tests/testthat/test-step_discretize.R | 252 +++++++++++----------- tests/testthat/test-step_downsample.R | 188 ++++++++-------- tests/testthat/test-step_dummy.R | 208 +++++++++--------- tests/testthat/test-step_filter_missing.R | 48 ++-- tests/testthat/test-step_impute_mean.R | 176 +++++++-------- tests/testthat/test-step_impute_median.R | 178 +++++++-------- tests/testthat/test-step_impute_mode.R | 208 +++++++++--------- tests/testthat/test-step_indicate_na.R | 176 +++++++-------- tests/testthat/test-step_intercept.R | 148 ++++++------ tests/testthat/test-step_inverse.R | 182 +++++++-------- tests/testthat/test-step_lag.R | 126 +++++------ tests/testthat/test-step_lencode_bayes.R | 258 +++++++++++----------- tests/testthat/test-step_lencode_glm.R | 228 +++++++++---------- tests/testthat/test-step_lencode_mixed.R | 268 +++++++++++------------ tests/testthat/test-step_lincomb.R | 48 ++-- tests/testthat/test-step_log.R | 182 +++++++-------- tests/testthat/test-step_mutate.R | 164 +++++++------- tests/testthat/test-step_nearmiss.R | 188 ++++++++-------- tests/testthat/test-step_normalize.R | 164 +++++++------- tests/testthat/test-step_novel.R | 228 +++++++++---------- tests/testthat/test-step_nzv.R | 48 ++-- tests/testthat/test-step_other.R | 262 +++++++++++----------- tests/testthat/test-step_pca.R | 250 +++++++++++++-------- tests/testthat/test-step_pca_sparse.R | 262 ++++++++++++---------- tests/testthat/test-step_pca_sparse_bayes.R | 266 +++++++++++------------ tests/testthat/test-step_pca_truncated.R | 238 ++++++++++---------- tests/testthat/test-step_range.R | 194 ++++++++-------- tests/testthat/test-step_ratio.R | 198 ++++++++--------- tests/testthat/test-step_rename.R | 164 +++++++------- tests/testthat/test-step_rm.R | 48 ++-- tests/testthat/test-step_rose.R | 188 ++++++++-------- tests/testthat/test-step_scale.R | 164 +++++++------- tests/testthat/test-step_select.R | 48 ++-- tests/testthat/test-step_smote.R | 188 ++++++++-------- tests/testthat/test-step_smotenc.R | 188 ++++++++-------- tests/testthat/test-step_sqrt.R | 164 +++++++------- tests/testthat/test-step_tomek.R | 188 ++++++++-------- tests/testthat/test-step_unknown.R | 216 +++++++++--------- tests/testthat/test-step_upsample.R | 188 ++++++++-------- tests/testthat/test-step_zv.R | 48 ++-- tests/testthat/test-workflows.R | 170 +++++++------- vignettes/supported-models.Rmd | 12 - 147 files changed, 6270 insertions(+), 6149 deletions(-)
Title: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
Description: Tables summarizing clinical trial results are often complex
and require detailed tailoring prior to submission to a health
authority. The 'crane' package supplements the functionality of the
'gtsummary' package for creating these often highly bespoke tables in
the pharmaceutical industry.
Author: Daniel D. Sjoberg [aut, cre] ,
Emily de la Rua [aut] ,
Davide Garolini [aut],
Abinaya Yogasekaram [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between crane versions 0.1.0 dated 2025-02-24 and 0.2.0 dated 2025-08-29
crane-0.1.0/crane/R/add_blank_row.R |only crane-0.1.0/crane/R/tbl_demographics.R |only crane-0.1.0/crane/man/add_blank_row.Rd |only crane-0.1.0/crane/man/roche_pvalue.Rd |only crane-0.1.0/crane/man/tbl_demographics.Rd |only crane-0.1.0/crane/tests/testthat/_snaps/add_blank_row.md |only crane-0.1.0/crane/tests/testthat/test-add_blank_row.R |only crane-0.1.0/crane/tests/testthat/test-tbl_demographics.R |only crane-0.2.0/crane/DESCRIPTION | 27 + crane-0.2.0/crane/MD5 | 97 +++++- crane-0.2.0/crane/NAMESPACE | 39 ++ crane-0.2.0/crane/NEWS.md | 58 +++- crane-0.2.0/crane/R/add_blank_rows.R |only crane-0.2.0/crane/R/add_hierarchical_count_row.R |only crane-0.2.0/crane/R/crane-package.R | 10 crane-0.2.0/crane/R/deprecated.R |only crane-0.2.0/crane/R/import-standalone-check_pkg_installed.R |only crane-0.2.0/crane/R/import-standalone-cli_call_env.R | 3 crane-0.2.0/crane/R/import-standalone-forcats.R |only crane-0.2.0/crane/R/import-standalone-stringr.R |only crane-0.2.0/crane/R/label_roche.R | 143 +++++++++- crane-0.2.0/crane/R/modify_header_rm_md.R |only crane-0.2.0/crane/R/modify_zero_recode.R |only crane-0.2.0/crane/R/reexport.R | 16 - crane-0.2.0/crane/R/tbl_baseline_chg.R |only crane-0.2.0/crane/R/tbl_hierarchical_rate_and_count.R |only crane-0.2.0/crane/R/tbl_hierarchical_rate_by_grade.R |only crane-0.2.0/crane/R/tbl_listing.R |only crane-0.2.0/crane/R/tbl_roche_summary.R |only crane-0.2.0/crane/R/tbl_shift.R |only crane-0.2.0/crane/R/tbl_survfit_quantiles.R |only crane-0.2.0/crane/R/tbl_survfit_times.R |only crane-0.2.0/crane/R/theme_gtsummary_roche.R | 101 +++++-- crane-0.2.0/crane/R/utils.R |only crane-0.2.0/crane/README.md | 21 + crane-0.2.0/crane/inst/WORDLIST | 19 + crane-0.2.0/crane/man/add_blank_rows.Rd |only crane-0.2.0/crane/man/add_hierarchical_count_row.Rd |only crane-0.2.0/crane/man/crane-package.Rd | 4 crane-0.2.0/crane/man/deprecated.Rd |only crane-0.2.0/crane/man/figures/README-tbl_print_simple-1.png |binary crane-0.2.0/crane/man/figures/logo.png |only crane-0.2.0/crane/man/label_roche.Rd |only crane-0.2.0/crane/man/modify_header_rm_md.Rd |only crane-0.2.0/crane/man/modify_zero_recode.Rd |only crane-0.2.0/crane/man/reexports.Rd | 8 crane-0.2.0/crane/man/tbl_baseline_chg.Rd |only crane-0.2.0/crane/man/tbl_hierarchical_rate_and_count.Rd |only crane-0.2.0/crane/man/tbl_hierarchical_rate_by_grade.Rd |only crane-0.2.0/crane/man/tbl_listing.Rd |only crane-0.2.0/crane/man/tbl_roche_summary.Rd |only crane-0.2.0/crane/man/tbl_shift.Rd |only crane-0.2.0/crane/man/tbl_survfit_quantiles.Rd |only crane-0.2.0/crane/man/tbl_survfit_times.Rd |only crane-0.2.0/crane/man/theme_gtsummary_roche.Rd | 37 +- crane-0.2.0/crane/tests/testthat/_snaps/add_blank_rows.md |only crane-0.2.0/crane/tests/testthat/_snaps/add_hierarchical_count_row.md |only crane-0.2.0/crane/tests/testthat/_snaps/modify_zero_recode.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_baseline_chg.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_hierarchical_rate_and_count.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_hierarchical_rate_by_grade.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_listing.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_roche_summary.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_shift.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_survfit_quantiles.md |only crane-0.2.0/crane/tests/testthat/_snaps/tbl_survfit_times.md |only crane-0.2.0/crane/tests/testthat/_snaps/theme_gtsummary_roche.md | 47 +++ crane-0.2.0/crane/tests/testthat/setup-theme.R |only crane-0.2.0/crane/tests/testthat/test-add_blank_rows.R |only crane-0.2.0/crane/tests/testthat/test-add_hierarchical_count_row.R |only crane-0.2.0/crane/tests/testthat/test-label_roche.R |only crane-0.2.0/crane/tests/testthat/test-modify_header_rm_md.R |only crane-0.2.0/crane/tests/testthat/test-modify_zero_recode.R |only crane-0.2.0/crane/tests/testthat/test-tbl_baseline_chg.R |only crane-0.2.0/crane/tests/testthat/test-tbl_hierarchical_rate_and_count.R |only crane-0.2.0/crane/tests/testthat/test-tbl_hierarchical_rate_by_grade.R |only crane-0.2.0/crane/tests/testthat/test-tbl_listing.R |only crane-0.2.0/crane/tests/testthat/test-tbl_roche_summary.R |only crane-0.2.0/crane/tests/testthat/test-tbl_shift.R |only crane-0.2.0/crane/tests/testthat/test-tbl_survfit_quantiles.R |only crane-0.2.0/crane/tests/testthat/test-tbl_survfit_times.R |only crane-0.2.0/crane/tests/testthat/test-theme_gtsummary_roche.R | 90 ++++++ 82 files changed, 625 insertions(+), 95 deletions(-)
Title: Behavior Insight Design: A Toolkit for Integrating Behavioral
Science in UI/UX Design
Description: Provides a framework and toolkit to guide 'shiny' developers in
implementing the Behavior Insight Design (BID) framework. The package offers
functions for documenting each of the five stages (Notice, Interpret,
Structure, Anticipate, and Validate), along with a comprehensive concept
dictionary.
Author: Jeremy Winget [aut, cre]
Maintainer: Jeremy Winget <contact@jrwinget.com>
Diff between bidux versions 0.1.0 dated 2025-06-13 and 0.3.0 dated 2025-08-29
bidux-0.1.0/bidux/R/bid_classes.R |only bidux-0.1.0/bidux/R/bid_concepts.R |only bidux-0.1.0/bidux/R/bid_mappings.R |only bidux-0.1.0/bidux/R/bid_suggest_components.R |only bidux-0.1.0/bidux/man/generate_notice_suggestions.Rd |only bidux-0.3.0/bidux/DESCRIPTION | 13 bidux-0.3.0/bidux/MD5 | 198 +- bidux-0.3.0/bidux/NAMESPACE | 16 bidux-0.3.0/bidux/NEWS.md |only bidux-0.3.0/bidux/R/bid-classes.R |only bidux-0.3.0/bidux/R/bid-concepts.R |only bidux-0.3.0/bidux/R/bid_anticipate.R | 308 +-- bidux-0.3.0/bidux/R/bid_interpret.R | 174 -- bidux-0.3.0/bidux/R/bid_notice.R | 277 --- bidux-0.3.0/bidux/R/bid_report.R | 634 +++---- bidux-0.3.0/bidux/R/bid_structure.R | 804 ---------- bidux-0.3.0/bidux/R/bid_validate.R | 274 ++- bidux-0.3.0/bidux/R/bidux-package.R | 13 bidux-0.3.0/bidux/R/globals.R | 79 bidux-0.3.0/bidux/R/mappings.R |only bidux-0.3.0/bidux/R/structure_rank.R |only bidux-0.3.0/bidux/R/structure_suggest.R |only bidux-0.3.0/bidux/R/suggest-components.R |only bidux-0.3.0/bidux/R/telemetry.R |only bidux-0.3.0/bidux/R/utils.R | 793 +++++++++ bidux-0.3.0/bidux/README.md | 507 +----- bidux-0.3.0/bidux/build/vignette.rds |binary bidux-0.3.0/bidux/inst/WORDLIST | 15 bidux-0.3.0/bidux/inst/doc/concepts-reference.R | 14 bidux-0.3.0/bidux/inst/doc/concepts-reference.Rmd | 75 bidux-0.3.0/bidux/inst/doc/concepts-reference.html | 247 +-- bidux-0.3.0/bidux/inst/doc/getting-started.R | 58 bidux-0.3.0/bidux/inst/doc/getting-started.Rmd | 104 - bidux-0.3.0/bidux/inst/doc/getting-started.html | 212 +- bidux-0.3.0/bidux/inst/doc/introduction-to-bid.Rmd | 10 bidux-0.3.0/bidux/inst/doc/introduction-to-bid.html | 21 bidux-0.3.0/bidux/inst/doc/telemetry-integration.R |only bidux-0.3.0/bidux/inst/doc/telemetry-integration.Rmd |only bidux-0.3.0/bidux/inst/doc/telemetry-integration.html |only bidux-0.3.0/bidux/man/adjust_suggestion_score.Rd |only bidux-0.3.0/bidux/man/as_tibble.bid_stage.Rd | 2 bidux-0.3.0/bidux/man/bid_anticipate.Rd | 19 bidux-0.3.0/bidux/man/bid_concept.Rd | 2 bidux-0.3.0/bidux/man/bid_concepts.Rd | 8 bidux-0.3.0/bidux/man/bid_ingest_telemetry.Rd |only bidux-0.3.0/bidux/man/bid_notice.Rd | 18 bidux-0.3.0/bidux/man/bid_report.Rd | 2 bidux-0.3.0/bidux/man/bid_result.Rd | 2 bidux-0.3.0/bidux/man/bid_stage.Rd | 2 bidux-0.3.0/bidux/man/bid_structure.Rd | 58 bidux-0.3.0/bidux/man/bid_suggest_components.Rd | 4 bidux-0.3.0/bidux/man/bid_validate.Rd | 33 bidux-0.3.0/bidux/man/bidux-package.Rd | 7 bidux-0.3.0/bidux/man/build_concept_group.Rd |only bidux-0.3.0/bidux/man/build_groups_with_suggestions.Rd |only bidux-0.3.0/bidux/man/create_confusion_notice.Rd |only bidux-0.3.0/bidux/man/create_delay_notice.Rd |only bidux-0.3.0/bidux/man/create_error_notice.Rd |only bidux-0.3.0/bidux/man/create_navigation_notice.Rd |only bidux-0.3.0/bidux/man/create_unused_input_notice.Rd |only bidux-0.3.0/bidux/man/detect_telemetry_format.Rd |only bidux-0.3.0/bidux/man/extract_stage.Rd | 2 bidux-0.3.0/bidux/man/extract_stage1_theory.Rd |only bidux-0.3.0/bidux/man/find_confusion_patterns.Rd |only bidux-0.3.0/bidux/man/find_delayed_sessions.Rd |only bidux-0.3.0/bidux/man/find_error_patterns.Rd |only bidux-0.3.0/bidux/man/find_navigation_dropoffs.Rd |only bidux-0.3.0/bidux/man/find_unused_inputs.Rd |only bidux-0.3.0/bidux/man/format_label.Rd |only bidux-0.3.0/bidux/man/get_accessibility_recommendations.Rd | 2 bidux-0.3.0/bidux/man/get_cognitive_load_suggestions.Rd |only bidux-0.3.0/bidux/man/get_concept_bias_mappings.Rd | 2 bidux-0.3.0/bidux/man/get_concepts_data.Rd | 2 bidux-0.3.0/bidux/man/get_default_concepts_data.Rd | 2 bidux-0.3.0/bidux/man/get_default_layout_mappings.Rd | 2 bidux-0.3.0/bidux/man/get_default_theory_mappings.Rd | 2 bidux-0.3.0/bidux/man/get_dual_processing_suggestions.Rd |only bidux-0.3.0/bidux/man/get_generic_suggestions.Rd |only bidux-0.3.0/bidux/man/get_information_scent_suggestions.Rd |only bidux-0.3.0/bidux/man/get_layout_concepts.Rd | 2 bidux-0.3.0/bidux/man/get_metadata.Rd | 2 bidux-0.3.0/bidux/man/get_onboarding_suggestions.Rd |only bidux-0.3.0/bidux/man/get_progressive_disclosure_suggestions.Rd |only bidux-0.3.0/bidux/man/get_proximity_suggestions.Rd |only bidux-0.3.0/bidux/man/get_stage.Rd | 2 bidux-0.3.0/bidux/man/get_visual_hierarchy_suggestions.Rd |only bidux-0.3.0/bidux/man/infer_concepts_from_story.Rd |only bidux-0.3.0/bidux/man/is_bid_stage.Rd | 2 bidux-0.3.0/bidux/man/is_complete.Rd | 2 bidux-0.3.0/bidux/man/layout_rationale.Rd |only bidux-0.3.0/bidux/man/load_accessibility_guidelines.Rd | 2 bidux-0.3.0/bidux/man/load_concept_bias_mappings.Rd | 2 bidux-0.3.0/bidux/man/load_layout_mappings.Rd | 2 bidux-0.3.0/bidux/man/load_theory_mappings.Rd | 2 bidux-0.3.0/bidux/man/new_bid_result.Rd | 2 bidux-0.3.0/bidux/man/new_bid_stage.Rd | 2 bidux-0.3.0/bidux/man/normalize_telemetry_columns.Rd |only bidux-0.3.0/bidux/man/print.bid_result.Rd | 2 bidux-0.3.0/bidux/man/print.bid_stage.Rd | 2 bidux-0.3.0/bidux/man/rank_and_sort_suggestions.Rd |only bidux-0.3.0/bidux/man/read_telemetry_data.Rd |only bidux-0.3.0/bidux/man/read_telemetry_json.Rd |only bidux-0.3.0/bidux/man/read_telemetry_sqlite.Rd |only bidux-0.3.0/bidux/man/safe_lower.Rd |only bidux-0.3.0/bidux/man/safe_stage_data_story_access.Rd |only bidux-0.3.0/bidux/man/structure_suggestions.Rd |only bidux-0.3.0/bidux/man/suggest_layout_from_previous.Rd |only bidux-0.3.0/bidux/man/suggest_theory_from_mappings.Rd | 2 bidux-0.3.0/bidux/man/summary.bid_result.Rd | 2 bidux-0.3.0/bidux/man/summary.bid_stage.Rd | 2 bidux-0.3.0/bidux/man/validate_bid_result.Rd | 2 bidux-0.3.0/bidux/man/validate_bid_stage.Rd | 2 bidux-0.3.0/bidux/tests/spelling.R | 10 bidux-0.3.0/bidux/tests/testthat/test-bid_anticipate.R | 99 - bidux-0.3.0/bidux/tests/testthat/test-bid_classes.R | 90 - bidux-0.3.0/bidux/tests/testthat/test-bid_ingest_telemetry.R |only bidux-0.3.0/bidux/tests/testthat/test-bid_interpret.R | 39 bidux-0.3.0/bidux/tests/testthat/test-bid_mappings.R | 263 +-- bidux-0.3.0/bidux/tests/testthat/test-bid_notice.R | 129 - bidux-0.3.0/bidux/tests/testthat/test-bid_report.R | 13 bidux-0.3.0/bidux/tests/testthat/test-bid_structure.R | 552 +++--- bidux-0.3.0/bidux/tests/testthat/test-bid_suggest_components.R | 63 bidux-0.3.0/bidux/tests/testthat/test-bid_validate.R | 260 +++ bidux-0.3.0/bidux/vignettes/concepts-reference.Rmd | 75 bidux-0.3.0/bidux/vignettes/getting-started.Rmd | 104 - bidux-0.3.0/bidux/vignettes/introduction-to-bid.Rmd | 10 bidux-0.3.0/bidux/vignettes/telemetry-integration.Rmd |only 127 files changed, 3448 insertions(+), 3312 deletions(-)
Title: Input/Output 'SomaScan' Data
Description: Load and export 'SomaScan' data via the
'Standard BioTools, Inc.' structured text file
called an ADAT ('*.adat'). For file format see
<https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>.
The package also exports auxiliary functions for
manipulating, wrangling, and extracting relevant
information from an ADAT object once in memory.
Author: Stu Field [aut] ,
Caleb Scheidel [cre],
Standard BioTools, Inc. [cph, fnd]
Maintainer: Caleb Scheidel <calebjscheidel@gmail.com>
Diff between SomaDataIO versions 6.3.0 dated 2025-05-06 and 6.4.0 dated 2025-08-29
DESCRIPTION | 6 +-- MD5 | 29 ++++++++++-------- NAMESPACE | 2 + NEWS.md | 30 ++++++++++++++++++ R/SeqId.R | 9 +++++ R/preProcessAdat.R | 13 ++++++-- R/read-annotations.R | 29 +++++++++--------- R/updateColMeta.R |only README.md | 20 ++++++------ build/vignette.rds |binary man/SeqId.Rd | 7 ++++ man/updateColMeta.Rd |only tests/testthat/_snaps/preProcessAdat.md | 51 ++++++++++++++++++++++++++++++++ tests/testthat/test-SeqId.R | 14 ++++++++ tests/testthat/test-preProcessAdat.R | 7 ++++ tests/testthat/test-read-annotations.R | 6 +-- tests/testthat/test-updateColMeta.R |only 17 files changed, 177 insertions(+), 46 deletions(-)
Title: R Interface to MPI for HPC Clusters (Programming with Big Data
Project)
Description: A simplified, efficient, interface to MPI for HPC clusters. It is
a derivation and rethinking of the Rmpi package. pbdMPI embraces the
prevalent parallel programming style on HPC clusters. Beyond the
interface, a collection of functions for global work with
distributed data and resource-independent RNG reproducibility is
included. It is based on S4 classes and methods.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] ,
Brian Ripley [ctb] ,
R Core team [ctb] ,
Sebastien Lamy de la Chapelle [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.5-3 dated 2025-04-13 and 0.5-4 dated 2025-08-29
ChangeLog | 8 DESCRIPTION | 8 MD5 | 36 +- R/comm_allcommon.r | 13 R/comm_chunk.R | 11 R/comm_seed.r | 2 R/spmd_gatherv.r | 2 R/spmd_scatterv_obj.r | 2 R/spmd_tool.r | 172 +++++----- R/zzz.r.in | 46 -- README.md | 1 configure | 815 ++++++++++++++++++++++++++---------------------- configure.ac | 9 demo/00Index | 4 demo/alltoall_col.r |only demo/split_comm_col.r |only man/cc_comm.chunk.Rd | 31 + man/vv_print_cat.Rd | 16 man/zz_spmd_internal.Rd | 1 src/spmd.c | 10 20 files changed, 650 insertions(+), 537 deletions(-)
Title: Converts 'Monolix' Models to 'rxode2'
Description: 'Monolix' is a tool for running mixed effects model using
'saem'. This tool allows you to convert 'Monolix' models to 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the
form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>).
If available, the 'rxode2' model will
read in the 'Monolix' data and compare the simulation for the
population model individual model and residual
model to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rxode2' model. This is complementary to the
'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can
convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not
required, you c [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Justin Wilkins [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between monolix2rx versions 0.0.5 dated 2025-07-15 and 0.0.6 dated 2025-08-29
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/buildParser.R | 24 ++++++++++++++++++++++++ R/rxUiGet.R | 2 ++ R/rxUiGetGen.R |only R/zzz.R | 2 +- 7 files changed, 40 insertions(+), 9 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 6.5.0 dated 2025-05-01 and 6.5.1 dated 2025-08-29
DESCRIPTION | 8 +-- MD5 | 38 +++++++-------- NEWS.md | 9 +++ R/RcppExports.R | 8 +-- R/matrixcreation.R | 117 ++++++++++--------------------------------------- build/vignette.rds |binary inst/doc/Chapter1.html | 8 +-- inst/doc/Chapter2.html | 2 inst/doc/Chapter5.html | 4 - inst/doc/Chapter6.html | 2 inst/doc/Chapter8.html | 2 man/aflefko2.Rd | 19 +------ man/arlefko2.Rd | 19 +------ man/f_projection3.Rd | 4 - man/flefko2.Rd | 19 +------ man/flefko3.Rd | 21 +------- man/projection3.Rd | 4 - man/rlefko2.Rd | 19 +------ man/rlefko3.Rd | 20 +------- src/MatsNProj.cpp | 10 ++-- 20 files changed, 102 insertions(+), 231 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.11 dated 2025-07-10 and 2.8.12 dated 2025-08-29
DESCRIPTION | 6 +- MD5 | 60 ++++++++++++--------- NEWS.md | 19 ++++++ R/ISSR800.R | 2 R/OSDquery.R | 17 +++--- R/SDA-spatial.R | 97 +++++++++++++++++++++++++++------- R/SSURGO_spatial_query.R | 2 R/createSSURGO.R | 100 +++++++++++++++++++++++++++--------- R/fetchKSSL.R | 17 +++--- R/fetchNASIS_pedons.R | 11 ++- R/fetchOSD.R | 21 +++++-- R/fetchRaCA.R | 14 ++--- R/get_NASIS_table_name_by_purpose.R | 1 R/get_SDA_coecoclass.R | 63 ++++++++++++++++------ R/get_component_from_SDA.R | 2 R/get_extended_data_from_NASIS_db.R | 14 ++--- R/get_vegplot_data_from_NASIS_db.R | 6 +- R/mukey-WCS.R | 2 R/soilColorWCS.R | 2 build/vignette.rds |binary inst/CITATION | 15 +++-- inst/doc/dominant-es.R |only inst/doc/dominant-es.Rmd |only inst/doc/dominant-es.html |only inst/doc/local-ssurgo.R |only inst/doc/local-ssurgo.Rmd |only inst/doc/local-ssurgo.html |only man/OSDquery.Rd | 6 +- man/SDA_spatialQuery.Rd | 5 + man/createSSURGO.Rd | 6 +- man/fetchKSSL.Rd | 11 ++- man/fetchNASISWebReport.Rd | 2 man/get_SDA_coecoclass.Rd | 55 +++++++++++++++---- vignettes/dominant-es.Rmd |only vignettes/local-ssurgo.Rmd |only 35 files changed, 391 insertions(+), 165 deletions(-)
Title: Converts 'NONMEM' Models to 'rxode2'
Description: 'NONMEM' has been a tool for running nonlinear mixed
effects models since the 80s and is still used today (Bauer 2019
<doi:10.1002/psp4.12404>). This tool allows you to convert
'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016)
<doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax
(Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2'
syntax requires the residual specification to be included and it
is not always translated. If available, the 'rxode2' model will
read in the 'NONMEM' data and compare the simulation for the
population model ('PRED') individual model ('IPRED') and residual
model ('IWRES') to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rx [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Philip Delff [ctb],
Gabriel Staples [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nonmem2rx versions 0.1.7 dated 2025-07-15 and 0.1.8 dated 2025-08-29
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 6 R/buildParser.R | 18 + R/readInNonmemInput.R | 4 R/rxUiGetGen.R | 12 inst/doc/import-nonmem.html | 574 ++++++++++++++++++++++---------------------- src/abbrev.c | 11 8 files changed, 351 insertions(+), 294 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.0.2 dated 2025-07-24 and 4.1.0 dated 2025-08-29
DESCRIPTION | 12 MD5 | 96 ++++--- NAMESPACE | 27 ++ NEWS.md | 42 +++ R/agq.R |only R/agqGen.R |only R/build.R |only R/complete.R | 29 ++ R/fo.R |only R/foce.R |only R/focei.R | 182 ++++---------- R/foceiControl.R | 41 ++- R/foi.R |only R/iov.R |only R/laplace.R |only R/nlm.R | 11 R/nlmShared.R | 11 R/nlmeRxUiGet.R | 13 - R/nlmixr2.R | 7 R/nlmixr2Est.R | 1 R/nlmixr2_md5.R | 2 R/nlmixr2output.R | 3 R/nls.R | 22 + R/nmObjGet.R | 90 ++++++- R/nmObjHandle.R | 15 - R/optim.R | 2 R/posthoc.R |only R/preProcessCovariatesPresent.R | 3 R/resid.R | 23 + R/rstudio.R |only R/saem.R | 7 R/saemRxUiGet.R | 41 +++ R/saemRxUiGetModel.R | 15 + R/sharedControl.R | 23 - R/uninformativeEtas.R | 5 R/utils.R | 8 man/agqControl.Rd |only man/dot-agq.Rd |only man/dot-collectWarn.Rd |only man/dot-nlmAdjustCov.Rd |only man/dot-nlmixr2FitUpdateParams.Rd |only man/foControl.Rd |only man/foceControl.Rd |only man/foceiControl.Rd | 26 +- man/foiControl.Rd |only man/getValidNlmixrControl.Rd | 39 +-- man/laplaceControl.Rd |only man/nlmixr2Est.Rd | 33 +- man/nmGetDistributionSaemLines.Rd | 6 man/nmObjGetControl.Rd | 38 +-- man/nmObjGetFoceiControl.Rd | 17 + man/nmObjHandleControlObject.Rd | 26 +- man/posthocControl.Rd |only src/inner.cpp | 422 ++++++++++++++++++++++----------- tests/testthat/helper-quiet.R | 1 tests/testthat/test-broom.R | 4 tests/testthat/test-control-infer.R |only tests/testthat/test-focei-wang2007.R | 441 +++++++++++++++++++++++++---------- tests/testthat/test-iov.R |only tests/testthat/test-ui-est-change.R | 3 60 files changed, 1223 insertions(+), 564 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Anne Keunecke [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Richard Hooijmaijers [ctb],
Michael Wayne Ke [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 4.0.0 dated 2025-07-17 and 4.0.1 dated 2025-08-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 8 ++++++++ R/verse.R | 1 + 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Probabilistic Record Linkage Using Pretrained Text Embeddings
Description: Links datasets through fuzzy string matching using pretrained text embeddings. Produces more accurate record linkage when lexical string distance metrics are a poor guide to match quality (e.g., "Patricia" is more lexically similar to "Patrick" than it is to "Trish"). Capable of performing multilingual record linkage. Methods are described in Ornstein (2025) <doi:10.1017/pan.2025.10016>.
Author: Joe Ornstein [aut, cre, cph]
Maintainer: Joe Ornstein <jornstein@uga.edu>
Diff between fuzzylink versions 0.2.4 dated 2025-08-18 and 0.2.5 dated 2025-08-29
DESCRIPTION | 8 - MD5 | 6 - NEWS.md | 4 README.md | 259 +++--------------------------------------------------------- 4 files changed, 26 insertions(+), 251 deletions(-)
Title: Interactive Text Annotation Tool with 'shiny' GUI
Description: A lightweight and focused text annotation tool built with 'shiny'. Provides an
interactive graphical user interface for coding text documents,
managing code hierarchies, creating memos, and analyzing coding patterns.
Features include code co-occurrence analysis, visualization of coding patterns,
comparison of multiple coding sets, and export capabilities. Supports
collaborative qualitative research through standardized annotation formats
and analysis tools.
Author: Chao Liu [aut, cre, cph]
Maintainer: Chao Liu <chaoliu@cedarville.edu>
Diff between textAnnotatoR versions 0.1.4 dated 2024-11-12 and 1.0.1 dated 2025-08-29
textAnnotatoR-0.1.4/textAnnotatoR/README.md |only textAnnotatoR-0.1.4/textAnnotatoR/build |only textAnnotatoR-0.1.4/textAnnotatoR/inst/doc |only textAnnotatoR-0.1.4/textAnnotatoR/man/figures |only textAnnotatoR-0.1.4/textAnnotatoR/vignettes |only textAnnotatoR-1.0.1/textAnnotatoR/DESCRIPTION | 21 textAnnotatoR-1.0.1/textAnnotatoR/MD5 | 104 textAnnotatoR-1.0.1/textAnnotatoR/NAMESPACE | 6 textAnnotatoR-1.0.1/textAnnotatoR/NEWS.md | 2 textAnnotatoR-1.0.1/textAnnotatoR/R/annotate_gui.R |14481 +++++----- textAnnotatoR-1.0.1/textAnnotatoR/R/directory_management.R | 834 textAnnotatoR-1.0.1/textAnnotatoR/R/package.R | 11 textAnnotatoR-1.0.1/textAnnotatoR/R/project.R | 718 textAnnotatoR-1.0.1/textAnnotatoR/R/utils.R | 328 textAnnotatoR-1.0.1/textAnnotatoR/inst/extdata |only textAnnotatoR-1.0.1/textAnnotatoR/man/analyze_code_combinations.Rd | 66 textAnnotatoR-1.0.1/textAnnotatoR/man/analyze_code_distribution.Rd | 54 textAnnotatoR-1.0.1/textAnnotatoR/man/analyze_coding_density.Rd | 68 textAnnotatoR-1.0.1/textAnnotatoR/man/analyze_overlap_characteristics.Rd | 64 textAnnotatoR-1.0.1/textAnnotatoR/man/apply_action.Rd | 11 textAnnotatoR-1.0.1/textAnnotatoR/man/calculate_hierarchy_stats.Rd | 8 textAnnotatoR-1.0.1/textAnnotatoR/man/code_exists_in_hierarchy.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/create_new_project.Rd | 9 textAnnotatoR-1.0.1/textAnnotatoR/man/create_plain_text_annotations.Rd | 10 textAnnotatoR-1.0.1/textAnnotatoR/man/find_node_by_name.Rd | 60 textAnnotatoR-1.0.1/textAnnotatoR/man/generate_code_co_occurrence_analysis.Rd | 10 textAnnotatoR-1.0.1/textAnnotatoR/man/generate_heatmap_visualization.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/generate_network_visualization.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/generate_readable_color.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/getVolumes.Rd | 34 textAnnotatoR-1.0.1/textAnnotatoR/man/get_calendar_icon.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/get_closed_folder_icon.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/get_file_icon.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/get_folder_icon.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/get_next_palette_color.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/get_project_dir.Rd | 30 textAnnotatoR-1.0.1/textAnnotatoR/man/handle_dir_confirmation.Rd | 38 textAnnotatoR-1.0.1/textAnnotatoR/man/handle_load_project_confirmation.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/handle_save_project_confirmation.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/handle_storage_confirmation.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/hsl_to_rgb.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/init_data_dir.Rd | 15 textAnnotatoR-1.0.1/textAnnotatoR/man/is_color_readable.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/load_project_from_path.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/load_project_interactive.Rd | 13 textAnnotatoR-1.0.1/textAnnotatoR/man/load_selected_project.Rd | 13 textAnnotatoR-1.0.1/textAnnotatoR/man/remove_annotation.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/save_annotated_text_interactive.Rd | 50 textAnnotatoR-1.0.1/textAnnotatoR/man/save_as_html.Rd | 2 textAnnotatoR-1.0.1/textAnnotatoR/man/save_project_interactive.Rd | 19 textAnnotatoR-1.0.1/textAnnotatoR/man/save_records_interactive.Rd | 50 textAnnotatoR-1.0.1/textAnnotatoR/man/sync_codes_with_hierarchy.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/textAnnotatoR-package.Rd | 2 textAnnotatoR-1.0.1/textAnnotatoR/man/update_dark_colors.Rd |only textAnnotatoR-1.0.1/textAnnotatoR/man/update_text_display.Rd | 4 textAnnotatoR-1.0.1/textAnnotatoR/man/visualize_hierarchy.Rd | 14 textAnnotatoR-1.0.1/textAnnotatoR/tests/testthat/helper.R | 196 textAnnotatoR-1.0.1/textAnnotatoR/tests/testthat/test-annotate_gui.R | 268 textAnnotatoR-1.0.1/textAnnotatoR/tests/testthat/test-directory_management.R | 486 textAnnotatoR-1.0.1/textAnnotatoR/tests/testthat/test-project.R | 491 textAnnotatoR-1.0.1/textAnnotatoR/tests/testthat/test-utils.R | 489 textAnnotatoR-1.0.1/textAnnotatoR/tools |only 62 files changed, 11077 insertions(+), 8002 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.0.3 dated 2025-07-24 and 4.1.0 dated 2025-08-29
DESCRIPTION | 11 +- MD5 | 103 ++++++++++++---------- NAMESPACE | 9 + NEWS.md | 31 ++++++ R/assert.R | 29 ++++++ R/dfIni.R | 173 ++++++++++++++++++------------------- R/err-foceiBase.R | 1 R/err-sim.R | 9 + R/err.R | 14 ++ R/mix.R |only R/mlogit.R |only R/mu.R | 29 +++++- R/piping-model.R | 1 R/rstudio.R |only R/rudfui.R | 1 R/rxUiBlessed.R | 12 +- R/rxUiGet.R | 140 +++++++++++++++++++++++++++-- R/rxode2_md5.R | 2 R/symengine.R | 17 +++ R/ui.R | 2 R/utils.R | 78 +++++++++++++++- inst/doc/rxode2-syntax.html | 26 ++--- inst/include/rxode2_model_shared.c | 34 +++++++ inst/include/rxode2_model_shared.h | 7 + inst/include/rxode2parseStruct.h | 10 +- inst/include/rxode2parseVer.h | 4 inst/include/rxode2parse_control.h | 1 inst/include/rxode2ptr.h | 25 +++++ man/assertRxUi.Rd | 8 + man/dot-rstudioComplete.Rd |only man/mexpit.Rd |only man/mix.Rd |only man/mlogit.Rd |only man/rxUiDevelop.Rd |only man/rxUiGet.Rd | 3 man/rxUnloadAll.Rd | 4 src/codegen2.h | 30 ++++++ src/genModelVars.h | 6 - src/init.c | 37 +++++++ src/mlogit.c |only src/mlogit.h |only src/par_solve.h | 9 + src/parseAllowAssign.h | 2 src/parseFuns.h | 25 ++++- src/parseVars.h | 3 src/print_node.c | 5 - src/print_node.h | 28 +++++ src/rx2api.c | 23 ++++ src/rx2api.h | 12 ++ src/rxData.cpp | 11 +- src/rxthreefry.cpp | 5 + src/tran.c | 2 src/tran.h | 1 tests/testthat/test-assert.R | 69 ++++++++++++++ tests/testthat/test-mix.R |only tests/testthat/test-mlogit.R |only tests/testthat/test-probit.R |only tests/testthat/test-ui.R | 57 ++++++++++++ tests/testthat/test-zzzzz.R | 2 59 files changed, 908 insertions(+), 203 deletions(-)
Title: Fitting Combined Action with the BRAID Response Surface Model
Description: Contains functions for evaluating, analyzing, and fitting combined
action dose response surfaces with the Bivariate Response to Additive
Interacting Doses (BRAID) model of combined action, along with tools for
implementing other combination analysis methods, including Bliss independence,
combination index, and additional response surface methods.
Author: Anang Shelat [aut],
Nathaniel R. Twarog [aut, cre]
Maintainer: Nathaniel R. Twarog <nathaniel.twarog@stjude.org>
Diff between braidrm versions 1.0.3 dated 2024-09-26 and 1.0.6 dated 2025-08-29
DESCRIPTION | 8 MD5 | 32 R/bestBraidModel.R | 474 +++++++------- R/boundedOpt.R | 634 +++++++++---------- R/braidModel.R | 860 +++++++++++++------------- R/braidScenarios.R | 54 - R/estimateIAE.R | 458 +++++++------- R/musycModel.R | 12 R/ursaModel.R | 456 ++++++------- R/volumeMetrics.R | 1206 ++++++++++++++++++------------------- README.md | 16 build/vignette.rds |binary inst/doc/alternateMethods.html | 2 inst/doc/basicBraid.html | 2 inst/doc/bayesianKappa.html | 2 inst/doc/confidenceIntervals.html | 2 inst/doc/modelsAndConstraints.html | 2 17 files changed, 2115 insertions(+), 2105 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [c [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.53 dated 2025-04-10 and 0.3.57 dated 2025-08-29
DESCRIPTION | 15 +- MD5 | 54 +++++----- NEWS | 10 + R/chips.R | 57 +++++++++- R/dlso.R | 24 ++-- R/enumerate.partitions.R | 4 R/enumerate.permutations.R | 14 +- R/internal.R | 66 +++++++++--- R/iris.clusterings-data.R | 2 R/minimize.by.enumeration.R | 23 ++-- R/partition.loss.R | 94 ++++++++++------- R/partition.loss.dendrogram.R | 48 ++++----- R/plot.salso.summary.R | 205 +++++++++++++++++++++++++++++---------- R/psm.R | 14 +- R/roxido.R | 2 R/salso.R | 178 ++++++++++++++++++++++++--------- R/summary.salso.estimate.R | 105 +++++++++++++------ src/Makevars.win | 6 + src/rust/Cargo.lock | 90 +++++++---------- src/rust/Cargo.toml | 2 src/rust/rbindings/src/lib.rs | 1 src/rust/roxido/Cargo.lock | 8 - src/rust/roxido/src/lib.rs | 38 ++++++- src/rust/roxido_macro/Cargo.lock | 8 - src/rust/roxido_macro/src/lib.rs | 13 +- src/rust/src/lib.rs | 11 +- src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 14 ++ 28 files changed, 755 insertions(+), 351 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized maximum likelihood estimators for precision
matrices and supporting functions to employ these estimators in a graphical
modeling setting. For details, see Peeters, Bilgrau, & van Wieringen (2022)
<doi:10.18637/jss.v102.i04> and associated publications.
Author: Carel F.W. Peeters [aut, cre, cph] ,
Anders Ellern Bilgrau [aut, cph] ,
Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
Diff between rags2ridges versions 2.2.7 dated 2023-10-14 and 2.2.8 dated 2025-08-29
DESCRIPTION | 17 ++++++----- MD5 | 24 ++++++++-------- NEWS.md | 6 ++++ R/rags2ridges.R | 38 ++++++++++++++------------ README.md | 4 +- inst/doc/rags2ridges.Rmd | 2 - inst/doc/rags2ridges.html | 66 +++++++++++++++++++++++----------------------- man/Communities.Rd | 8 ++--- man/DiffGraph.Rd | 8 ++--- man/GGMpathStats.Rd | 10 +++--- man/Ugraph.Rd | 8 ++--- src/rags2ridges.cpp | 2 - vignettes/rags2ridges.Rmd | 2 - 13 files changed, 103 insertions(+), 92 deletions(-)
Title: Methods in Structural Reliability
Description: Various reliability analysis methods for rare event inference (computing failure probability and quantile from model/function outputs).
Author: Bertrand Iooss [aut, cre],
Clement Walter [aut],
Gilles defaux [aut],
Vincent Moutoussamy [aut]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between mistral versions 2.2.3 dated 2025-07-16 and 2.2.4 dated 2025-08-29
DESCRIPTION | 6 MD5 | 8 NAMESPACE | 1 NEWS | 5 inst/doc/mistral-vignette.html | 2324 ++--------------------------------------- 5 files changed, 151 insertions(+), 2193 deletions(-)
Title: Group Sequential Design for Historical Control Trial with
Survival Outcome
Description: It provides functions to design historical controlled trials with survival outcome by group sequential method. The options for interim look boundaries are efficacy only, efficacy & futility or futility only. It also provides the function to monitor the trial for any unplanned look. The package is based on Jianrong Wu, Xiaoping Xiong (2016) <doi:10.1002/pst.1756> and Jianrong Wu, Yimei Li (2020) <doi:10.1080/10543406.2019.1684305>.
Author: Tushar Patni [aut, cre],
Yimei Li [aut],
Jianrong Wu [aut]
Maintainer: Tushar Patni <tushar.patni006@gmail.com>
Diff between HCTDesign versions 0.7.2 dated 2022-11-17 and 0.7.3 dated 2025-08-29
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Bayesian Graph Structure Learning using Spike-and-Slab Priors
Description: Bayesian estimation for undirected graphical models using spike-and-slab priors. The package handles continuous, discrete, and mixed data.
Author: Reza Mohammadi [aut, cre]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between ssgraph versions 1.15 dated 2022-12-24 and 1.16 dated 2025-08-29
DESCRIPTION | 9 - MD5 | 26 +- build/vignette.rds |binary inst/CITATION | 7 inst/doc/ssgraph-example.R | 4 inst/doc/ssgraph-example.html | 376 ++++++++++++++++++++++++++++++++---------- man/plot.ssgraph.Rd | 10 - man/predict.ssgraph.Rd | 8 man/print.ssgraph.Rd | 8 man/ssgraph-package.Rd | 14 - man/ssgraph.Rd | 32 +-- man/summary.ssgraph.Rd | 8 src/Makevars | 4 src/Makevars.win | 2 14 files changed, 353 insertions(+), 155 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block
diagonal matrices (often used for covariance matrices). This is based
on the domain specific language implemented in 'nlmixr2' but expanded
to create matrices in R generally instead of specifying parts of
matrices to estimate. It has expanded to include some matrix manipulation
functions that are generally useful for 'rxode2' and 'nlmixr2'.
Author: Matthew L. Fidler [aut, cre] ,
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 1.0.1 dated 2025-07-18 and 1.0.2 dated 2025-08-29
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/lotri.R | 15 ++++++++++++--- inst/doc/lotri-motivation.html | 12 ++++++------ tests/testthat/test-iov.R |only 6 files changed, 30 insertions(+), 16 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 2.3.0 dated 2025-06-27 and 2.4.0 dated 2025-08-29
jarbes-2.3.0/jarbes/R/caterplot_compare.R |only jarbes-2.3.0/jarbes/man/caterplot_compare.Rd |only jarbes-2.4.0/jarbes/ChangeLog | 39 +++++ jarbes-2.4.0/jarbes/DESCRIPTION | 10 - jarbes-2.4.0/jarbes/MD5 | 56 +++++--- jarbes-2.4.0/jarbes/NAMESPACE | 17 ++ jarbes-2.4.0/jarbes/R/bcbnp.R |only jarbes-2.4.0/jarbes/R/bcmixmeta.R | 30 +++- jarbes-2.4.0/jarbes/R/cocluster_plot.R |only jarbes-2.4.0/jarbes/R/diagnostic.bcmixmeta.R | 68 +++++---- jarbes-2.4.0/jarbes/R/dpmeta.R | 4 jarbes-2.4.0/jarbes/R/dpmetareg.R | 37 ++++- jarbes-2.4.0/jarbes/R/effect.hmr.R | 4 jarbes-2.4.0/jarbes/R/forestplot_compare.R |only jarbes-2.4.0/jarbes/R/jarbes-package.R | 4 jarbes-2.4.0/jarbes/R/plot.bcbnp.R |only jarbes-2.4.0/jarbes/R/plot.bcmixmeta.R |only jarbes-2.4.0/jarbes/R/plot.bmeta.R | 165 ++++++++++++++++++------ jarbes-2.4.0/jarbes/R/plot.dpmeta.R | 120 +++++++++++------ jarbes-2.4.0/jarbes/R/plot.dpmmeta.R | 2 jarbes-2.4.0/jarbes/R/plot_data.R |only jarbes-2.4.0/jarbes/R/plotdata_reg.bcbnp.R |only jarbes-2.4.0/jarbes/R/summary.bcbnp.R |only jarbes-2.4.0/jarbes/R/summary.bcmeta.R | 111 ++++++++-------- jarbes-2.4.0/jarbes/R/summary.bmeta.R | 17 +- jarbes-2.4.0/jarbes/man/bcbnp.Rd |only jarbes-2.4.0/jarbes/man/cocluster_plot.Rd |only jarbes-2.4.0/jarbes/man/diagnostic.bcmixmeta.Rd | 7 - jarbes-2.4.0/jarbes/man/forestplot_compare.Rd |only jarbes-2.4.0/jarbes/man/plot.bcbnp.Rd |only jarbes-2.4.0/jarbes/man/plot.bcmixmeta.Rd |only jarbes-2.4.0/jarbes/man/plot.bmeta.Rd | 64 ++++++++- jarbes-2.4.0/jarbes/man/plot.dpmeta.Rd | 65 +++++++-- jarbes-2.4.0/jarbes/man/plot.dpmmeta.Rd | 6 jarbes-2.4.0/jarbes/man/plot_data.Rd |only jarbes-2.4.0/jarbes/man/plotdata_reg.bcbnp.Rd |only jarbes-2.4.0/jarbes/man/summary.bcbnp.Rd |only jarbes-2.4.0/jarbes/man/summary.bmeta.Rd | 4 38 files changed, 587 insertions(+), 243 deletions(-)
Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Author: Paulo Justiniano Ribeiro Jr [aut, cre],
Peter Diggle [aut],
Ole Christensen [ctb],
Martin Schlather [ctb],
Roger Bivand [ctb],
Brian Ripley [ctb]
Maintainer: Paulo Justiniano Ribeiro Jr <paulojus@ufpr.br>
Diff between geoR versions 1.9-5 dated 2025-04-25 and 1.9-6 dated 2025-08-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/kriging.R | 4 ++-- inst/doc/CHANGES | 15 +++++++++++++++ 4 files changed, 24 insertions(+), 9 deletions(-)
Title: Build a Package from Rmarkdown Files
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut] ,
Vincent Guyader [aut, cre] ,
Yohann Mansiaux [aut],
ThinkR [cph]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between fusen versions 0.7.1 dated 2025-01-26 and 0.7.2 dated 2025-08-29
DESCRIPTION | 13 MD5 | 46 NEWS.md | 6 build/vignette.rds |binary inst/doc/How-to-use-fusen.R | 138 inst/doc/How-to-use-fusen.html | 1050 +++--- inst/doc/Maintain-packages-with-fusen.R | 210 - inst/doc/Maintain-packages-with-fusen.html | 1266 +++---- inst/doc/deal-with-a-fusen-flat-file.R | 80 inst/doc/deal-with-a-fusen-flat-file.html | 868 ++--- inst/doc/draw-a-tree-of-your-package-files-and-functions.R | 128 inst/doc/draw-a-tree-of-your-package-files-and-functions.html | 984 +++--- inst/doc/inflate-all-your-flat-files.R | 144 inst/doc/inflate-all-your-flat-files.html | 1000 +++--- inst/doc/register-files-in-config.R | 180 - inst/doc/register-files-in-config.html | 1206 +++---- inst/doc/share-on-a-github-website.R | 74 inst/doc/share-on-a-github-website.html | 934 ++--- inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.R | 230 - inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.html | 976 +++--- inst/doc/tips-and-tricks.R | 50 inst/doc/tips-and-tricks.html | 1602 +++++----- tests/testthat/config_fusen_register.yaml | 80 tests/testthat/test-create_fusen_rsproject.R | 1 24 files changed, 5638 insertions(+), 5628 deletions(-)
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Alexander Tedeschi [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael N [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.10.0 dated 2025-06-16 and 0.11.0 dated 2025-08-29
bioRad-0.10.0/bioRad/man/skip_if_no_aws.s3.Rd |only bioRad-0.11.0/bioRad/DESCRIPTION | 20 bioRad-0.11.0/bioRad/MD5 | 55 bioRad-0.11.0/bioRad/NEWS.md | 17 bioRad-0.11.0/bioRad/R/apply_mistnet.R | 2 bioRad-0.11.0/bioRad/R/bioRad-package.R | 3 bioRad-0.11.0/bioRad/R/download_pvolfiles.R | 57 bioRad-0.11.0/bioRad/R/download_vpfiles.R | 3 bioRad-0.11.0/bioRad/R/list_vpts_aloft.R | 19 bioRad-0.11.0/bioRad/R/nexrad_odim.R | 2 bioRad-0.11.0/bioRad/R/s3.R |only bioRad-0.11.0/bioRad/R/scan_convert.R | 10 bioRad-0.11.0/bioRad/R/utils.R | 13 bioRad-0.11.0/bioRad/README.md | 30 bioRad-0.11.0/bioRad/build/partial.rdb |binary bioRad-0.11.0/bioRad/build/vignette.rds |binary bioRad-0.11.0/bioRad/inst/doc/bioRad.html | 5 bioRad-0.11.0/bioRad/inst/doc/rad_aero_22.R | 868 +++++----- bioRad-0.11.0/bioRad/inst/doc/rad_aero_22.html | 3 bioRad-0.11.0/bioRad/inst/doc/range_correction.html | 39 bioRad-0.11.0/bioRad/man/apply_mistnet.Rd | 2 bioRad-0.11.0/bioRad/man/bioRad-package.Rd | 3 bioRad-0.11.0/bioRad/man/download_pvolfiles.Rd | 15 bioRad-0.11.0/bioRad/man/download_vpfiles.Rd | 3 bioRad-0.11.0/bioRad/man/list_vpts_aloft.Rd | 5 bioRad-0.11.0/bioRad/man/nexrad_to_odim.Rd | 2 bioRad-0.11.0/bioRad/tests/testthat/test-download_pvolfiles.R | 5 bioRad-0.11.0/bioRad/tests/testthat/test-list_vpts_aloft.R | 11 bioRad-0.11.0/bioRad/tests/testthat/test-read_vpts.R | 16 bioRad-0.11.0/bioRad/tests/testthat/test-s3.R |only 30 files changed, 588 insertions(+), 620 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.16.1 dated 2025-07-01 and 0.17.0 dated 2025-08-29
DESCRIPTION | 12 - MD5 | 46 ++++--- NAMESPACE | 17 ++ NEWS.md | 18 ++ R/append_datagrid.R |only R/display.R |only R/distribution.R | 18 -- R/is_baysian_grid.R |only R/p_rope.R | 11 + R/print.R | 1 R/print.rope.R | 11 + R/print_html.R | 9 - R/print_md.R | 1 R/reexports.R | 4 R/rope.R | 159 ++++++++++++++++++------- R/utils.R | 161 ++++---------------------- README.md | 68 ++++------- inst/WORDLIST | 1 man/display.describe_posterior.Rd |only man/distribution.Rd | 12 - man/p_rope.Rd | 2 man/reexports.Rd | 3 man/rope.Rd | 89 +++++++++----- tests/testthat/test-describe_posterior.R | 2 tests/testthat/test-marginaleffects.R | 70 ++++++----- tests/testthat/test-rope.R | 191 ++++++++++++++++++++++++------- 26 files changed, 528 insertions(+), 378 deletions(-)
Title: Measuring Association with Recursive Binning
Description: An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2025) <doi:10.48550/arXiv.2311.08561>.
Author: Chris Salahub [aut, cre]
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Diff between AssocBin versions 1.1-0 dated 2025-03-26 and 1.1-1 dated 2025-08-29
AssocBin-1.1-0/AssocBin/man/inDep.Rd |only AssocBin-1.1-1/AssocBin/DESCRIPTION | 15 AssocBin-1.1-1/AssocBin/MD5 | 56 - AssocBin-1.1-1/AssocBin/NAMESPACE | 12 AssocBin-1.1-1/AssocBin/R/binner.R | 66 +- AssocBin-1.1-1/AssocBin/R/departureDisplays.R |only AssocBin-1.1-1/AssocBin/R/dispatch.R | 178 +++-- AssocBin-1.1-1/AssocBin/R/plotBinning.R | 52 - AssocBin-1.1-1/AssocBin/R/scoring.R | 12 AssocBin-1.1-1/AssocBin/R/splitters.R | 139 ++-- AssocBin-1.1-1/AssocBin/build/vignette.rds |binary AssocBin-1.1-1/AssocBin/data/heart.rda |binary AssocBin-1.1-1/AssocBin/data/sp500pseudo.rda |binary AssocBin-1.1-1/AssocBin/inst/doc/AssocBin.R | 174 +++-- AssocBin-1.1-1/AssocBin/inst/doc/AssocBin.Rmd | 348 ++++++++-- AssocBin-1.1-1/AssocBin/inst/doc/AssocBin.html | 772 ++++++++++++++++++------ AssocBin-1.1-1/AssocBin/inst/doc/complex.R | 12 AssocBin-1.1-1/AssocBin/inst/doc/complex.Rmd | 18 AssocBin-1.1-1/AssocBin/inst/doc/complex.html | 96 ++ AssocBin-1.1-1/AssocBin/man/DepSearch.Rd |only AssocBin-1.1-1/AssocBin/man/depDisplay.Rd |only AssocBin-1.1-1/AssocBin/man/methods.Rd | 34 - AssocBin-1.1-1/AssocBin/man/plotBinning.Rd | 12 AssocBin-1.1-1/AssocBin/man/rIntSplit.Rd | 2 AssocBin-1.1-1/AssocBin/man/scorings.Rd | 12 AssocBin-1.1-1/AssocBin/man/shadings.Rd | 13 AssocBin-1.1-1/AssocBin/man/uniBinner.Rd | 14 AssocBin-1.1-1/AssocBin/man/uniMaxScoreSplit.Rd | 4 AssocBin-1.1-1/AssocBin/man/uniRIntSplit.Rd | 4 AssocBin-1.1-1/AssocBin/vignettes/AssocBin.Rmd | 348 ++++++++-- AssocBin-1.1-1/AssocBin/vignettes/complex.Rmd | 18 31 files changed, 1767 insertions(+), 644 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.60 dated 2025-07-22 and 0.62 dated 2025-08-29
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NAMESPACE | 7 ------- R/2_1_1_topicsModel_Pred.R | 22 +++++++++++++++++++++- R/2_1_2_inferencer.R | 1 + README.md | 13 ++++++++++--- inst/CITATION | 24 +++++++++++++++++------- 7 files changed, 63 insertions(+), 31 deletions(-)
Title: Scales, Geometries, and Extensions of 'ggplot2' for Election
Mapping
Description: Provides 'ggplot2' extensions for political map making. Implements
new geometries for groups of simple feature geometries. Adds palettes and scales
for red to blue color mapping and for discrete maps. Implements tools for easy
label generation and placement, automatic map coloring, and themes.
Author: Cory McCartan [aut],
Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between ggredist versions 0.0.2 dated 2022-11-23 and 0.0.3 dated 2025-08-29
DESCRIPTION | 20 - MD5 | 60 ++-- NAMESPACE | 29 +- NEWS.md | 12 R/538.R | 81 +++--- R/alaska.R |only R/colors.R | 90 +++++-- R/dra.R | 70 ++--- R/florida.R |only R/geom_city_road.R | 372 ++++++++++++++--------------- R/geom_district.R | 2 R/geom_district_text.R | 500 +++++++++++++++++++-------------------- R/geom_place.R | 2 R/ggredist-package.R | 1 R/nature.R | 118 ++++----- R/party.R | 310 ++++++++++++------------ R/penn82.R | 68 ++--- R/polimap.R | 120 ++++----- R/texas.R |only R/theme.R | 52 ++-- R/utils.R | 28 -- R/washington.R |only R/wiki.R |only README.md | 113 ++++---- man/StatCityRoad.Rd | 2 man/StatDistrict.Rd | 2 man/StatDistrictCoordinates.Rd | 2 man/StatPlaces.Rd | 146 +++++------ man/figures/README-example-1.png |binary man/ggredist.Rd | 28 ++ man/scale_538.Rd | 9 man/scale_alaska.Rd |only man/scale_florida.Rd |only man/scale_texas.Rd |only man/scale_washington.Rd |only man/scale_wiki.Rd |only 36 files changed, 1175 insertions(+), 1062 deletions(-)
Title: Clinical Trial Registry History
Description: Retrieves historical versions of clinical trial registry
entries from <https://ClinicalTrials.gov>. Package functionality
and implementation for v 1.0.0 is documented in Carlisle (2022)
<DOI:10.1371/journal.pone.0270909>.
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Diff between cthist versions 2.1.11 dated 2024-07-17 and 2.1.12 dated 2025-08-29
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NEWS.md | 6 ++ build/partial.rdb |binary tests/testthat/test-clinicaltrials_gov_version_criteria.R | 2 tests/testthat/test-overall_status_lengths.R | 32 +++++++------- 6 files changed, 34 insertions(+), 26 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Advanced statistical tools for Bayesian structure learning in undirected graphical models, accommodating continuous, ordinal, discrete, count, and mixed data. It integrates recent advancements in Bayesian graphical models as presented in the literature, including the works of Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2021) <doi:10.1080/01621459.2021.1996377>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, and Mohammadi et al. (2023) <doi:10.48550/arXiv.2307.00127>.
Author: Reza Mohammadi [aut, cre] ,
Ernst Wit [aut] ,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.73 dated 2024-08-23 and 2.74 dated 2025-08-29
DESCRIPTION | 14 ++- MD5 | 136 ++++++++++++++++++------------------- R/bdgraph.R | 32 ++++---- R/bdgraph.sim.R | 11 +- README.md | 6 - data/geneExpression.RData |binary data/reinis.RData |binary data/surveyData.RData |binary inst/CITATION | 23 +++--- inst/doc/BDgraph-Examples.R | 42 +++++------ inst/doc/BDgraph-Examples.Rmd | 46 ++++++------ inst/doc/BDgraph-Examples.html | 48 ++++++------- inst/doc/Introduction-BDgraph.R | 76 ++++++++++---------- inst/doc/Introduction-BDgraph.Rmd | 92 ++++++++++++------------- inst/doc/Introduction-BDgraph.html | 104 ++++++++++++++-------------- man/BDgraph-package.Rd | 34 ++++----- man/adj2link.Rd | 6 - man/auc.Rd | 10 +- man/bdgraph.Rd | 44 +++++------ man/bdgraph.dw.Rd | 32 ++++---- man/bdgraph.mpl.Rd | 22 ++--- man/bdgraph.npn.Rd | 12 +-- man/bdgraph.sim.Rd | 30 ++++---- man/bdw.reg.Rd | 90 ++++++++++++------------ man/bf.Rd | 12 +-- man/compare.Rd | 14 +-- man/conf.mat.Rd | 12 +-- man/conf.mat.plot.Rd | 12 +-- man/covariance.Rd | 10 +- man/ddweibull.Rd | 24 +++--- man/geneExpression.Rd | 8 +- man/gnorm.Rd | 10 +- man/graph.sim.Rd | 8 +- man/link2adj.Rd | 8 +- man/mse.Rd | 10 +- man/pgraph.Rd | 10 +- man/plinks.Rd | 8 +- man/plot.bdgraph.Rd | 18 ++-- man/plot.graph.Rd | 8 +- man/plot.sim.Rd | 8 +- man/plotcoda.Rd | 10 +- man/plotroc.Rd | 16 ++-- man/posterior.predict.Rd | 12 +-- man/precision.Rd | 10 +- man/predict.bdgraph.Rd | 12 +-- man/print.bdgraph.Rd | 8 +- man/print.sim.Rd | 6 - man/reinis.Rd | 6 - man/rgwish.Rd | 12 +-- man/rmvnorm.Rd | 20 ++--- man/roc.Rd | 16 ++-- man/rwish.Rd | 6 - man/select.Rd | 14 +-- man/sparsity.Rd | 6 - man/summary.bdgraph.Rd | 14 +-- man/surveyData.Rd | 6 - man/traceplot.Rd | 10 +- man/trensfer.Rd | 8 +- src/gcgm_DMH.cpp | 36 ++++----- src/gcgm_bd.cpp | 24 +++--- src/gcgm_dw_bd.cpp | 22 ++--- src/ggm_DMH.cpp | 24 +++--- src/ggm_bd.cpp | 30 ++++---- src/ggm_mpl_bd.cpp | 40 +++++----- src/gm_mpl_bd_dis.cpp | 94 ++++++++++++------------- src/gm_rj.cpp | 24 +++--- src/tgm_bd.cpp | 19 ++--- vignettes/BDgraph-Examples.Rmd | 46 ++++++------ vignettes/Introduction-BDgraph.Rmd | 92 ++++++++++++------------- 69 files changed, 870 insertions(+), 863 deletions(-)
Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided.
The first, Alternating Conditional Expectations (ACE),
is an algorithm to find the fixed point of maximal
correlation, i.e. it finds a set of transformed response variables that maximizes R^2
using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations
for Multiple Regression and Correlation". Journal of the American Statistical Association.
80:580-598. <doi:10.1080/01621459.1985.10478157>].
Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R. 1986. "Estimating Transformations for Regression via Additivity
and Variance Stabilization". Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two methods is in chapter 16 of
Frank Harrell's "Regression Modeling Strategies" in the Springer Serie [...truncated...]
Author: Phil Spector [aut],
Jerome Friedman [aut],
Robert Tibshirani [aut],
Thomas Lumley [aut],
Shawn Garbett [cre, aut] ,
Jonathan Baron [aut],
Bernhard Klar [aut],
Scott Chasalow [aut]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between acepack versions 1.6.1 dated 2025-02-13 and 1.6.3 dated 2025-08-29
DESCRIPTION | 9 +++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS.md | 11 ++++++++++- R/ace.R | 17 ++++++++++++----- R/acetest.R | 2 +- R/avas.R | 2 +- R/set_control.R | 2 +- src/acedata.f90 | 2 +- src/acemod.f90 | 2 +- src/bakfit.f90 | 2 +- src/calcmu.f90 | 2 +- src/ctsub.f90 | 2 +- src/favas.f90 | 2 +- src/mace.f90 | 2 +- src/model.f90 | 2 +- src/montne.f90 | 2 +- src/rlsmo.f90 | 2 +- src/scail.f90 | 2 +- src/smooth.f90 | 2 +- src/smothr.f90 | 2 +- src/sort.f90 | 2 +- src/supersmoother.f90 | 2 +- src/supsmu.f90 | 2 +- tests/testthat/test_ace.R | 9 +++++++-- 24 files changed, 76 insertions(+), 54 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between worldbank versions 0.6.0 dated 2025-05-29 and 0.6.1 dated 2025-08-29
DESCRIPTION | 6 - MD5 | 50 ++++++++-------- NEWS.md | 4 + R/assertions.R | 43 ++++++-------- R/fone.R | 19 +++--- R/indicators.R | 108 +++++++++++++++++------------------ R/pip.R | 110 ++++++++++++++++++------------------ R/utils.R | 2 README.md | 22 +++---- man/figures/README-plotting-1.png |binary man/fone.Rd | 15 +++- man/pip_aux.Rd | 17 ++--- man/pip_citation.Rd | 11 +-- man/pip_data.Rd | 44 +++++++------- man/pip_group.Rd | 48 ++++++++------- man/pip_valid_params.Rd | 15 ++-- man/wb_country.Rd | 7 +- man/wb_country_indicator.Rd | 18 +++-- man/wb_income_level.Rd | 7 +- man/wb_indicator.Rd | 7 +- man/wb_lending_type.Rd | 7 +- man/wb_region.Rd | 7 +- man/wb_source.Rd | 7 +- man/wb_topic.Rd | 7 +- tests/testthat/_snaps/indicators.md | 6 - tests/testthat/test-utils.R | 36 +++++------ 26 files changed, 330 insertions(+), 293 deletions(-)
Title: Optimal Confidence Intervals for Visual Testing
Description: Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.
Author: Dave Armstrong [aut, cre] ,
William Poirier [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between VizTest versions 0.4 dated 2025-06-28 and 0.5 dated 2025-08-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/viztest_intro.R | 12 ++++++++++-- inst/doc/viztest_intro.Rmd | 12 ++++++++++-- inst/doc/viztest_intro.html | 38 +++++++++++++++++++++++--------------- vignettes/viztest_intro.Rmd | 12 ++++++++++-- 6 files changed, 61 insertions(+), 29 deletions(-)
Title: Computation of Volatility Impulse Response Function of
Multivariate Time Series
Description: Computation of volatility impulse response function for multivariate time series model using algorithm by Jin, Lin and Tamvakis (2012) <doi:10.1016/j.eneco.2012.03.003>.
Author: Dr. Ranjit Kumar Paul [aut, cre],
Dr. Md Yeasin [aut],
Mr. Ankit Tanwar [aut]
Maintainer: Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2019-05-01
Diff between VIRF versions 0.1.0 dated 2019-05-01 and 0.1.1 dated 2025-08-29
DESCRIPTION | 16 ++++++++++------ MD5 | 2 +- 2 files changed, 11 insertions(+), 7 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 1.0.0 dated 2025-07-08 and 1.0.1 dated 2025-08-29
DESCRIPTION | 25 +++++++----- MD5 | 22 +++++------ NEWS.md | 10 +++++ R/RcppExports.R | 33 ++++++++++------- build/partial.rdb |binary man/PreviousDate.Rd | 13 ++++-- man/PreviousResult.Rd | 15 +++++-- man/Transitions.Rd | 11 +++-- man/uniques.Rd | 4 +- src/RcppExports.cpp | 18 +++++---- src/transition.cpp | 97 +++++++++++++++++++++++++++++++++++--------------- src/transition.h | 4 +- 12 files changed, 163 insertions(+), 89 deletions(-)
Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based
spatial relative risk functions that are estimated using the 'sparr' package.
Details about the 'sparr' package methods can be found in the tutorial: Davies
et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation
can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More
information about relative risk functions using kernel density estimation can
be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Derek W. Brown [aut, cph] ,
Mitchell J. Machiela [ctb] ,
Timothy A. Myers [ctb],
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between sparrpowR versions 0.2.8 dated 2024-01-23 and 0.2.9 dated 2025-08-29
sparrpowR-0.2.8/sparrpowR/R/package.R |only sparrpowR-0.2.9/sparrpowR/DESCRIPTION | 19 sparrpowR-0.2.9/sparrpowR/MD5 | 28 - sparrpowR-0.2.9/sparrpowR/NEWS.md | 5 sparrpowR-0.2.9/sparrpowR/R/sparrpowR-package.R |only sparrpowR-0.2.9/sparrpowR/R/spatial_data.R | 2 sparrpowR-0.2.9/sparrpowR/R/spatial_power.R | 2 sparrpowR-0.2.9/sparrpowR/README.md | 10 sparrpowR-0.2.9/sparrpowR/build/partial.rdb |binary sparrpowR-0.2.9/sparrpowR/build/vignette.rds |binary sparrpowR-0.2.9/sparrpowR/inst/CITATION | 23 + sparrpowR-0.2.9/sparrpowR/inst/doc/vignette.html | 421 +++++++++++---------- sparrpowR-0.2.9/sparrpowR/man/sparrpowR-package.Rd | 14 sparrpowR-0.2.9/sparrpowR/man/spatial_data.Rd | 2 sparrpowR-0.2.9/sparrpowR/man/spatial_power.Rd | 2 sparrpowR-0.2.9/sparrpowR/vignettes/vignette.Rmd | 222 ++++++----- 16 files changed, 416 insertions(+), 334 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to make it
easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between rvest versions 1.0.4 dated 2024-02-12 and 1.0.5 dated 2025-08-29
rvest-1.0.4/rvest/tests/spelling.R |only rvest-1.0.5/rvest/DESCRIPTION | 22 ++-- rvest-1.0.5/rvest/MD5 | 96 ++++++++++--------- rvest-1.0.5/rvest/NEWS.md | 6 + rvest-1.0.5/rvest/R/encoding.R | 6 - rvest-1.0.5/rvest/R/form.R | 4 rvest-1.0.5/rvest/R/html.R | 14 +- rvest-1.0.5/rvest/R/import-standalone-purrr.R |only rvest-1.0.5/rvest/R/live.R | 49 +++++---- rvest-1.0.5/rvest/R/rvest-package.R | 12 +- rvest-1.0.5/rvest/R/selectors.R | 18 +-- rvest-1.0.5/rvest/R/session.R | 16 +-- rvest-1.0.5/rvest/R/table.R | 12 +- rvest-1.0.5/rvest/R/text.R | 8 - rvest-1.0.5/rvest/R/utils.R | 7 - rvest-1.0.5/rvest/README.md | 18 +-- rvest-1.0.5/rvest/build/vignette.rds |binary rvest-1.0.5/rvest/demo/tripadvisor.R | 34 +++--- rvest-1.0.5/rvest/demo/united.R | 16 +-- rvest-1.0.5/rvest/demo/zillow.R | 26 ++--- rvest-1.0.5/rvest/inst/WORDLIST | 5 rvest-1.0.5/rvest/inst/doc/rvest.R | 70 ++++++------- rvest-1.0.5/rvest/inst/doc/rvest.Rmd | 70 ++++++------- rvest-1.0.5/rvest/inst/doc/rvest.html | 73 +++++++------- rvest-1.0.5/rvest/inst/doc/starwars-dynamic.R |only rvest-1.0.5/rvest/inst/doc/starwars-dynamic.Rmd |only rvest-1.0.5/rvest/inst/doc/starwars-dynamic.html |only rvest-1.0.5/rvest/inst/doc/starwars.R | 9 - rvest-1.0.5/rvest/inst/doc/starwars.Rmd | 13 +- rvest-1.0.5/rvest/inst/doc/starwars.html | 4 rvest-1.0.5/rvest/man/LiveHTML.Rd | 16 +-- rvest-1.0.5/rvest/man/html_attr.Rd | 8 - rvest-1.0.5/rvest/man/html_element.Rd | 18 +-- rvest-1.0.5/rvest/man/html_encoding_guess.Rd | 6 - rvest-1.0.5/rvest/man/html_form.Rd | 4 rvest-1.0.5/rvest/man/html_name.Rd | 6 - rvest-1.0.5/rvest/man/html_table.Rd | 12 +- rvest-1.0.5/rvest/man/html_text.Rd | 8 - rvest-1.0.5/rvest/man/read_html.Rd | 21 ++-- rvest-1.0.5/rvest/man/read_html_live.Rd | 17 ++- rvest-1.0.5/rvest/man/rvest-package.Rd | 2 rvest-1.0.5/rvest/man/session.Rd | 16 +-- rvest-1.0.5/rvest/tests/testthat/_snaps/session.md | 4 rvest-1.0.5/rvest/tests/testthat/helper.R | 3 rvest-1.0.5/rvest/tests/testthat/html/navigate1.html |only rvest-1.0.5/rvest/tests/testthat/html/navigate2.html |only rvest-1.0.5/rvest/tests/testthat/test-form.R | 14 +- rvest-1.0.5/rvest/tests/testthat/test-live.R | 17 ++- rvest-1.0.5/rvest/tests/testthat/test-selectors.R | 13 +- rvest-1.0.5/rvest/tests/testthat/test-session.R | 3 rvest-1.0.5/rvest/vignettes/rvest.Rmd | 70 ++++++------- rvest-1.0.5/rvest/vignettes/starwars-dynamic.Rmd |only rvest-1.0.5/rvest/vignettes/starwars.Rmd | 13 +- 53 files changed, 455 insertions(+), 424 deletions(-)
Title: OpenTelemetry R API
Description: High-quality, ubiquitous, and portable telemetry to enable
effective observability. OpenTelemetry is a collection of tools,
APIs, and SDKs used to instrument, generate, collect, and export
telemetry data (metrics, logs, and traces) for analysis in order to
understand your software's performance and behavior.
This package implements the OpenTelemetry API:
<https://opentelemetry.io/docs/specs/otel/>.
Use this package as a dependency if you want to instrument your R
package for OpenTelemetry.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between otel versions 0.1.0 dated 2025-07-31 and 0.2.0 dated 2025-08-29
.aspell |only DESCRIPTION | 24 +-- MD5 | 63 +++++---- NAMESPACE | 1 NEWS.md | 7 + R/api-dev.R | 26 +-- R/api.R | 54 +++++-- R/as-attributes.R | 3 R/docs.R | 180 +++++++------------------- R/logger-provider-noop.R | 10 - R/onload.R | 11 - R/rtrace.R | 33 ++-- R/tracer-name.R | 9 + R/tracer-provider-noop.R | 19 ++ R/utils.R | 13 + inst/air.toml | 2 inst/dox/ev-exporters.Rmd |only inst/dox/ev-others.Rmd |only inst/dox/ev-suppress.Rmd |only inst/dox/ev-zci.Rmd |only man/as_attributes.Rd | 4 man/default_tracer_name.Rd | 5 man/environmentvariables.Rd | 95 +++++-------- man/get_active_span.Rd |only man/log.Rd | 20 +- man/otel_logger.Rd | 3 man/zci.Rd | 1 tests/testthat/_snaps/api.md | 23 +++ tests/testthat/_snaps/cov |only tests/testthat/_snaps/nocov |only tests/testthat/_snaps/rtrace.md | 68 ++++++--- tests/testthat/_snaps/tracer-provider-noop.md |only tests/testthat/fixtures |only tests/testthat/test-api.R | 32 ++++ tests/testthat/test-logger-provider-noop.R |only tests/testthat/test-meter-provider-noop.R |only tests/testthat/test-rtrace.R | 66 +++++++++ tests/testthat/test-tracer-provider-noop.R |only 38 files changed, 447 insertions(+), 325 deletions(-)
Title: Environmental Interpolation using Spatial Kernel Density
Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel
density-based estimation methods. For a single species with presence and absence data,
the 'envi' package uses the spatial relative risk function that is estimated using the
'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
relative risk functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Lance A. Waller [ctb, ths] ,
Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between envi versions 1.0.0 dated 2024-11-06 and 1.0.1 dated 2025-08-29
DESCRIPTION | 14 - MD5 | 26 +- NEWS.md | 7 R/envi-package.R | 4 R/lrren.R | 2 R/utils.R | 49 ---- README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 8 inst/doc/vignette.html | 581 +++++++++++++++++++++++++++---------------------- man/envi-package.Rd | 4 man/lrren.Rd | 2 vignettes/vignette.Rmd | 326 ++++++++++++++++----------- 14 files changed, 571 insertions(+), 458 deletions(-)
Title: Semiparametric Least Squares Inference for Causal Effects
Description: Several causal effects are measured using least squares regressions and basis function approximations. Backward and forward selection methods based on different criteria are used to select the basis functions.
Author: Pierre Chausse Developer [aut, cre],
Mihai Giurcanu Developer [aut]
Maintainer: Pierre Chausse Developer <pchausse@uwaterloo.ca>
Diff between causalSLSE versions 0.4 dated 2025-08-26 and 0.4-1 dated 2025-08-29
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- inst/doc/causalSLSE.pdf |binary src/causal.f | 14 -------------- src/rsum.f90 |only 5 files changed, 8 insertions(+), 21 deletions(-)
Title: Build Species Distribution Modeling using 'caret'
Description: Use machine learning algorithms and advanced geographic information system tools to
build Species Distribution Modeling in a extensible and modern fashion.
Author: Dayani Bailly [aut] ,
Edivando Couto [aut] ,
Jose Hilario Delconte Ferreira [aut] ,
Marcos R. Lima [aut] ,
Reginaldo Re [aut] ,
Valeria Batista [aut] ,
Luiz Fernando Esser [aut, cre, cph]
Maintainer: Luiz Fernando Esser <luizesser@gmail.com>
Diff between caretSDM versions 1.1.0.1 dated 2025-07-10 and 1.1.4 dated 2025-08-29
caretSDM-1.1.0.1/caretSDM/R/globals.R |only caretSDM-1.1.0.1/caretSDM/tests/testthat/_snaps/pca_predictors.md |only caretSDM-1.1.4/caretSDM/DESCRIPTION | 11 caretSDM-1.1.4/caretSDM/MD5 | 135 caretSDM-1.1.4/caretSDM/NAMESPACE | 20 caretSDM-1.1.4/caretSDM/NEWS.md | 19 caretSDM-1.1.4/caretSDM/R/add_predictors.R | 24 caretSDM-1.1.4/caretSDM/R/add_scenarios.R | 102 caretSDM-1.1.4/caretSDM/R/checkmate.R | 12 caretSDM-1.1.4/caretSDM/R/data_clean.R | 9 caretSDM-1.1.4/caretSDM/R/generated-globals.R |only caretSDM-1.1.4/caretSDM/R/input_sdm.R | 27 caretSDM-1.1.4/caretSDM/R/is.R | 12 caretSDM-1.1.4/caretSDM/R/names.R | 5 caretSDM-1.1.4/caretSDM/R/occurrences_sdm.R | 48 caretSDM-1.1.4/caretSDM/R/pdp_sdm.R | 26 caretSDM-1.1.4/caretSDM/R/plot.R | 189 + caretSDM-1.1.4/caretSDM/R/predict_sdm.R | 24 caretSDM-1.1.4/caretSDM/R/pseudoabsences.R | 114 caretSDM-1.1.4/caretSDM/R/scen_rs.R |only caretSDM-1.1.4/caretSDM/R/sdm_area.R | 107 caretSDM-1.1.4/caretSDM/R/sdm_as.R | 48 caretSDM-1.1.4/caretSDM/R/summary_sdm.R | 89 caretSDM-1.1.4/caretSDM/R/tidyverse.R | 16 caretSDM-1.1.4/caretSDM/R/train_sdm.R | 146 - caretSDM-1.1.4/caretSDM/R/tsne_sdm.R | 16 caretSDM-1.1.4/caretSDM/R/use_esm.R |only caretSDM-1.1.4/caretSDM/R/varImp_sdm.R | 4 caretSDM-1.1.4/caretSDM/R/vif_predictors.R | 3 caretSDM-1.1.4/caretSDM/R/write.R | 56 caretSDM-1.1.4/caretSDM/README.md | 15 caretSDM-1.1.4/caretSDM/data/scen_rs.rda |only caretSDM-1.1.4/caretSDM/man/add_scenarios.Rd | 4 caretSDM-1.1.4/caretSDM/man/caretSDM-package.Rd | 1 caretSDM-1.1.4/caretSDM/man/input_sdm.Rd | 7 caretSDM-1.1.4/caretSDM/man/is_input_sdm.Rd | 6 caretSDM-1.1.4/caretSDM/man/pdp_sdm.Rd | 2 caretSDM-1.1.4/caretSDM/man/plot_occurrences.Rd | 28 caretSDM-1.1.4/caretSDM/man/predict_sdm.Rd | 7 caretSDM-1.1.4/caretSDM/man/pseudoabsences.Rd | 2 caretSDM-1.1.4/caretSDM/man/scen_rs.Rd |only caretSDM-1.1.4/caretSDM/man/sdm_area.Rd | 19 caretSDM-1.1.4/caretSDM/man/sdm_as_stars.Rd | 6 caretSDM-1.1.4/caretSDM/man/summary_sdm.Rd | 14 caretSDM-1.1.4/caretSDM/man/train_sdm.Rd | 11 caretSDM-1.1.4/caretSDM/man/use_esm.Rd |only caretSDM-1.1.4/caretSDM/man/varImp_sdm.Rd | 4 caretSDM-1.1.4/caretSDM/tests/testthat/_snaps/gcms_ensembles.md |only caretSDM-1.1.4/caretSDM/tests/testthat/_snaps/predict_sdm.md | 392 ++ caretSDM-1.1.4/caretSDM/tests/testthat/_snaps/sdm_area.md | 6 caretSDM-1.1.4/caretSDM/tests/testthat/_snaps/train_sdm.md | 1456 +++++++++- caretSDM-1.1.4/caretSDM/tests/testthat/_snaps/vif_predictors.md |only caretSDM-1.1.4/caretSDM/tests/testthat/test-GBIF_data.R |only caretSDM-1.1.4/caretSDM/tests/testthat/test-WorldClim_data.R |only caretSDM-1.1.4/caretSDM/tests/testthat/test-add_predictors.R | 39 caretSDM-1.1.4/caretSDM/tests/testthat/test-add_scenarios.R | 125 caretSDM-1.1.4/caretSDM/tests/testthat/test-buffer_sdm.R | 10 caretSDM-1.1.4/caretSDM/tests/testthat/test-data_clean.R | 59 caretSDM-1.1.4/caretSDM/tests/testthat/test-gcms_ensembles.R |only caretSDM-1.1.4/caretSDM/tests/testthat/test-join_area.R |only caretSDM-1.1.4/caretSDM/tests/testthat/test-names.R | 10 caretSDM-1.1.4/caretSDM/tests/testthat/test-occurrences_sdm.R | 60 caretSDM-1.1.4/caretSDM/tests/testthat/test-pca_predictors.R | 37 caretSDM-1.1.4/caretSDM/tests/testthat/test-pdp_sdm.R | 21 caretSDM-1.1.4/caretSDM/tests/testthat/test-plot.R | 45 caretSDM-1.1.4/caretSDM/tests/testthat/test-predict_sdm.R | 99 caretSDM-1.1.4/caretSDM/tests/testthat/test-pseudoabsences.R | 29 caretSDM-1.1.4/caretSDM/tests/testthat/test-sdm_area.R | 71 caretSDM-1.1.4/caretSDM/tests/testthat/test-sdm_as.R | 35 caretSDM-1.1.4/caretSDM/tests/testthat/test-tidyverse.R | 93 caretSDM-1.1.4/caretSDM/tests/testthat/test-train_sdm.R | 238 + caretSDM-1.1.4/caretSDM/tests/testthat/test-tsne_sdm.R | 43 caretSDM-1.1.4/caretSDM/tests/testthat/test-use_esm.R |only caretSDM-1.1.4/caretSDM/tests/testthat/test-varImp_sdm.R | 4 caretSDM-1.1.4/caretSDM/tests/testthat/test-vif_predictors.R | 31 caretSDM-1.1.4/caretSDM/tests/testthat/test-write.R | 151 - 76 files changed, 3802 insertions(+), 640 deletions(-)
Title: A Tool Kit for Working with Time Series
Description: Easy visualization, wrangling, and feature engineering of time series data for
forecasting and machine learning prediction. Consolidates and extends time series functionality
from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timetk versions 2.9.0 dated 2023-10-31 and 2.9.1 dated 2025-08-29
DESCRIPTION | 8 - MD5 | 94 +++++------ NAMESPACE | 14 + R/data-m4_daily.R | 2 R/data-m4_hourly.R | 2 R/data-m4_monthly.R | 2 R/data-m4_quarterly.R | 2 R/data-m4_weekly.R | 2 R/data-m4_yearly.R | 2 R/lubridate-date_parsers.R | 4 R/make-tk_make_timeseries_future.R | 15 + R/recipes-step_box_cox.R | 14 - R/recipes-step_diff.R | 10 - R/recipes-step_fourier.R | 12 - R/recipes-step_holiday_signature.R | 12 - R/recipes-step_log_interval.R | 14 - R/recipes-step_slidify.R | 10 - R/recipes-step_slidify_augment.R | 9 - R/recipes-step_smooth.R | 12 - R/recipes-step_timeseries_signature.R | 10 - R/recipes-step_ts_clean.R | 6 R/recipes-step_ts_impute.R | 10 - R/recipes-step_ts_pad.R | 10 - R/utils-parse-time.R | 32 ++++ README.md | 78 +++++---- inst/doc/TK04_Plotting_Time_Series.html | 20 +- man/m4_daily.Rd | 2 man/m4_hourly.Rd | 2 man/m4_monthly.Rd | 2 man/m4_quarterly.Rd | 2 man/m4_weekly.Rd | 2 man/m4_yearly.Rd | 2 man/parse_date2.Rd | 4 man/slidify.Rd | 14 - man/step_box_cox.Rd | 14 - man/step_diff.Rd | 10 - man/step_fourier.Rd | 12 - man/step_holiday_signature.Rd | 12 - man/step_log_interval.Rd | 14 - man/step_slidify.Rd | 10 - man/step_slidify_augment.Rd | 9 - man/step_smooth.Rd | 12 - man/step_timeseries_signature.Rd | 10 - man/step_ts_clean.Rd | 10 - man/step_ts_impute.Rd | 12 - man/step_ts_pad.Rd | 10 - tests/testthat/test-tk_tbl.R | 4 vignettes/temp_archive/TK08_Automatic_Anomaly_Detection.Rmd | 95 ++++++++++-- 48 files changed, 393 insertions(+), 277 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Elena Hsieh [ctb] ,
Debashis Ghosh [ctb] ,
Lance A. Waller [ctb] ,
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between gateR versions 0.1.15 dated 2024-01-23 and 0.1.16 dated 2025-08-29
gateR-0.1.15/gateR/R/package.R |only gateR-0.1.16/gateR/DESCRIPTION | 19 gateR-0.1.16/gateR/MD5 | 20 gateR-0.1.16/gateR/NEWS.md | 5 gateR-0.1.16/gateR/R/gateR-package.R |only gateR-0.1.16/gateR/README.md | 10 gateR-0.1.16/gateR/build/partial.rdb |binary gateR-0.1.16/gateR/build/vignette.rds |binary gateR-0.1.16/gateR/inst/CITATION | 30 - gateR-0.1.16/gateR/inst/doc/vignette.html | 693 ++++++++++++++++-------------- gateR-0.1.16/gateR/man/gateR-package.Rd | 16 gateR-0.1.16/gateR/vignettes/vignette.Rmd | 545 +++++++++++++---------- 12 files changed, 735 insertions(+), 603 deletions(-)
Title: Bootstrap Functions
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Application" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut] ,
Brian Ripley [aut, trl] ,
Alessandra R. Brazzale [ctb, cre]
Maintainer: Alessandra R. Brazzale <brazzale@stat.unipd.it>
Diff between boot versions 1.3-31 dated 2024-08-28 and 1.3-32 dated 2025-08-29
ChangeLog | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/CITATION | 34 +++++++--------------------------- 4 files changed, 20 insertions(+), 36 deletions(-)
Title: Epilepsy Ontologies' Similarities
Description: Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.
Author: Bernd Mueller [aut, cre]
Maintainer: Bernd Mueller <bernd.mueller@zbmed.de>
Diff between epos versions 1.1 dated 2024-03-15 and 1.2 dated 2025-08-29
DESCRIPTION | 16 +++++++++++----- MD5 | 8 ++++---- R/writeNeuroTable.R | 6 +++--- man/sortTableByRefMatches.Rd | 6 +++--- tests/testthat/test_createTanimotoBaseline.R | 2 +- 5 files changed, 22 insertions(+), 16 deletions(-)
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
This is a re-admission after prior archival of version 2.1.3 dated 2025-01-13
Diff between PointedSDMs versions 2.1.3 dated 2025-01-13 and 2.1.4 dated 2025-08-29
DESCRIPTION | 8 MD5 | 84 ++-- NAMESPACE | 2 NEWS.md | 9 R/assignCovariate.R |only R/blockedCV.R | 14 R/bruSDM_outputs.R | 3 R/bruSDM_predict.R | 11 R/dataOrganize.R | 60 ++- R/fitISDM.R | 25 + R/intModel.R | 2 R/makeFormulaComps.R | 25 - R/makeLhoods.R | 6 R/modISDM_predict.R | 40 +- R/modMarks_predict.R | 9 R/modSpecies_predict.R | 117 +++--- R/modelOutputs.R | 92 +++-- R/specifyISDM.R | 181 +++++---- R/specifyMarks.R | 12 R/specifySpecies.R | 287 +++++---------- R/startISDM.R | 9 R/startMarks.R | 7 R/startSpecies.R | 22 - inst/doc/Marked_Point_Process.R | 246 ++++++------- inst/doc/Marked_Point_Process.html | 4 inst/doc/Setophaga.R | 532 ++++++++++++++--------------- inst/doc/Setophaga.html | 4 inst/doc/Solitary_tinamou.R | 246 ++++++------- inst/doc/Spatiotemporal_example.R | 250 ++++++------- inst/doc/Spatiotemporal_example.html | 4 man/dataOrganize.Rd | 1 man/intModel.Rd | 20 - man/specifyISDM.Rd | 22 - man/specifyMarks.Rd | 2 man/specifySpecies.Rd | 27 - man/startISDM.Rd | 2 man/startSpecies.Rd | 4 tests/testthat/testthat_assignCovariate.R |only tests/testthat/testthat_dataOrganize.R | 213 +++++++---- tests/testthat/testthat_fitISDM.R | 8 tests/testthat/testthat_makeFormulaComps.R | 26 - tests/testthat/testthat_makeLhoods.R | 2 tests/testthat/testthat_specifyISDM.R | 28 + tests/testthat/testthat_specifySpecies.R | 54 ++ 44 files changed, 1484 insertions(+), 1236 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.4.0 dated 2025-08-18 and 1.4.1 dated 2025-08-29
insight-1.4.0/insight/man/dot-colour_detect.Rd |only insight-1.4.1/insight/DESCRIPTION | 30 insight-1.4.1/insight/MD5 | 80 +- insight-1.4.1/insight/NEWS.md | 25 insight-1.4.1/insight/R/color_if.R | 16 insight-1.4.1/insight/R/colour_tools.R | 274 ++----- insight-1.4.1/insight/R/display.R | 13 insight-1.4.1/insight/R/export_table.R | 38 - insight-1.4.1/insight/R/find_formula.R | 8 insight-1.4.1/insight/R/find_predictors.R | 2 insight-1.4.1/insight/R/format_message.R | 8 insight-1.4.1/insight/R/format_table.R | 222 +++-- insight-1.4.1/insight/R/get_datagrid.R | 28 insight-1.4.1/insight/R/get_varcov.R | 71 + insight-1.4.1/insight/R/get_varcov_sandwich.R | 5 insight-1.4.1/insight/R/helper_functions.R | 3 insight-1.4.1/insight/R/is_mixed_model.R | 4 insight-1.4.1/insight/R/link_inverse.R | 3 insight-1.4.1/insight/R/model_info.R | 3 insight-1.4.1/insight/R/n_obs.R | 10 insight-1.4.1/insight/R/print_color.R | 36 insight-1.4.1/insight/R/standardize_column_order.R | 2 insight-1.4.1/insight/inst/WORDLIST | 1 insight-1.4.1/insight/inst/doc/display.html | 380 +++++----- insight-1.4.1/insight/man/display.Rd | 9 insight-1.4.1/insight/man/get_datagrid.Rd | 6 insight-1.4.1/insight/man/get_datagrid.emmGrid.Rd | 2 insight-1.4.1/insight/man/get_predicted.Rd | 10 insight-1.4.1/insight/man/get_predicted_ci.Rd | 10 insight-1.4.1/insight/man/get_varcov.Rd | 14 insight-1.4.1/insight/man/print_color.Rd | 26 insight-1.4.1/insight/tests/testthat/test-check_if_installed.R | 2 insight-1.4.1/insight/tests/testthat/test-export_table.R | 4 insight-1.4.1/insight/tests/testthat/test-fixest.R | 2 insight-1.4.1/insight/tests/testthat/test-format_table.R | 35 insight-1.4.1/insight/tests/testthat/test-get_datagrid.R | 86 ++ insight-1.4.1/insight/tests/testthat/test-get_predicted.R | 2 insight-1.4.1/insight/tests/testthat/test-get_varcov.R | 100 ++ insight-1.4.1/insight/tests/testthat/test-lavaan.R | 2 insight-1.4.1/insight/tests/testthat/test-marginaleffects.R | 14 insight-1.4.1/insight/tests/testthat/test-mhurdle.R |only insight-1.4.1/insight/tests/testthat/test-selection.R | 2 42 files changed, 942 insertions(+), 646 deletions(-)
Title: Clustering and Model Selection with the Integrated
Classification Likelihood
Description: An ensemble of algorithms that enable the clustering of networks and data matrices (such as counts, categorical or continuous) with different type of generative models. Model selection and clustering is performed in combination by optimizing the Integrated Classification Likelihood (which is equivalent to minimizing the description length). Several models are available such as: Stochastic Block Model, degree corrected Stochastic Block Model, Mixtures of Multinomial, Latent Block Model. The optimization is performed thanks to a combination of greedy local search and a genetic algorithm (see <arXiv:2002:11577> for more details).
Author: Etienne Come [aut, cre],
Nicolas Jouvin [aut]
Maintainer: Etienne Come <etienne.come@univ-eiffel.fr>
Diff between greed versions 0.6.1 dated 2022-10-03 and 0.6.2 dated 2025-08-29
DESCRIPTION | 14 - MD5 | 106 +++++++------- NEWS.md | 8 + R/alg_classes.R | 2 R/model_combinedmodels.R | 2 R/model_dclbm.R | 4 R/model_dcsbm.R | 2 R/model_diaggmm.R | 2 R/model_gmm.R | 2 R/model_lca.R | 4 R/model_mom.R | 2 R/model_multsbm.R | 2 R/model_sbm.R | 2 R/tools_ploting.R | 4 README.md | 2 build/vignette.rds |binary inst/CITATION | 8 - inst/doc/greed.R | 18 +- inst/doc/greed.Rmd | 2 inst/doc/greed.html | 248 +++++++++++++++++----------------- man/Genetic-class.Rd | 4 man/Hybrid-class.Rd | 4 man/ICL.Rd | 4 man/K.Rd | 4 man/Multistarts-class.Rd | 4 man/Seed-class.Rd | 4 man/clustering.Rd | 4 man/extractSubModel.Rd | 4 man/gmmpairs.Rd | 2 man/greed.Rd | 18 ++ man/plot-DcLbmFit-missing-method.Rd | 2 man/plot-DcLbmPath-missing-method.Rd | 2 man/plot-DcSbmFit-missing-method.Rd | 2 man/plot-DiagGmmFit-missing-method.Rd | 2 man/plot-GmmFit-missing-method.Rd | 2 man/plot-IclPath-missing-method.Rd | 2 man/plot-LcaFit-missing-method.Rd | 2 man/plot-MoMFit-missing-method.Rd | 2 man/plot-MultSbmFit-missing-method.Rd | 2 man/plot-SbmFit-missing-method.Rd | 2 man/prior.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_combinedmodels.R | 187 +++++++++++-------------- tests/testthat/test_dclbm.R | 20 +- tests/testthat/test_dcsbm.R | 40 ++--- tests/testthat/test_diaggmm.R | 20 +- tests/testthat/test_gmm.R | 20 +- tests/testthat/test_lca.R | 8 - tests/testthat/test_mom.R | 16 +- tests/testthat/test_mor.R | 12 - tests/testthat/test_multsbm.R | 60 ++------ tests/testthat/test_sbm.R | 60 ++++---- vignettes/greed.Rmd | 2 54 files changed, 467 insertions(+), 492 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit()' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reducing adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bi [...truncated...]
Author: Ioannis Kosmidis [aut, cre] ,
Euloge Clovis Kenne Pagui [aut] ,
Federico Boiocchi [ctb],
Philipp Sterzinger [ctb] ,
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.9.2 dated 2023-10-11 and 1.0.0 dated 2025-08-29
DESCRIPTION | 30 +- MD5 | 98 +++++--- NAMESPACE | 20 + NEWS.md | 24 ++ R/add1.R |only R/brglm2-package.R | 9 R/brglmFit.R | 38 +-- R/brnb.R | 150 ++++++------- R/data.R | 61 +++++ R/drop1.R |only R/mdyplFit.R |only R/plrtest.R |only R/se.R |only R/solve_se.R |only R/utils.R | 20 + R/zzz_conventions.R | 11 README.md | 337 ++++++++++++++++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary data/MultipleFeatures.rda |only inst/CITATION | 10 inst/WORDLIST | 52 ++++ inst/doc/adjacent.html | 3 inst/doc/expo.html | 3 inst/doc/iteration.Rmd | 2 inst/doc/iteration.html | 2 inst/doc/multinomial.R | 2 inst/doc/multinomial.html | 5 inst/doc/negativeBinomial.html | 3 inst/tinytest/test-binomial.R | 18 - inst/tinytest/test-bracl.R | 19 - inst/tinytest/test-brnp.R | 19 + inst/tinytest/test-jeffreys.R | 12 - inst/tinytest/test-mdyplFit.R |only inst/tinytest/test-median-binomial.R | 16 - inst/tinytest/test-median-poisson.R | 6 inst/tinytest/test-multinom-binom.R | 10 inst/tinytest/test-multinom.R | 31 +- inst/tinytest/test-print.R | 2 inst/tinytest/test-se.R |only inst/tinytest/test-summary_mdyplFit.R |only man/MultipleFeatures.Rd |only man/aids.Rd | 2 man/brglmFit.Rd | 7 man/brnb.Rd | 8 man/confint.mdyplFit.Rd |only man/enzymes.Rd | 2 man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/mdyplControl.Rd |only man/mdyplFit.Rd |only man/plrtest.mdyplFit.Rd |only man/se0.Rd |only man/se1.Rd |only man/simulate.brnb.Rd | 2 man/sloe.Rd |only man/solve_se.Rd |only man/stemcell.Rd | 2 man/summary.brglmFit.Rd | 4 man/summary.mdyplFit.Rd |only vignettes/iteration.Rmd | 2 61 files changed, 757 insertions(+), 285 deletions(-)
Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or
point-related data. There are multiple models implemented for two bark
beetle species. The models can be customized and their submodels (onset of
infestation, beetle development, diapause initiation, mortality) can be
combined. The following models are available in the package:
PHENIPS-Clim (first-time release in this package),
PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>,
RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>,
CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>,
BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>,
Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>,
Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>.
The package may be expanded by models for other bark beetle species in the
future.
Author: Jakob Jentschke [aut, cre],
FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>
Diff between barrks versions 1.1.1 dated 2025-03-27 and 1.1.2 dated 2025-08-29
DESCRIPTION | 7 MD5 | 24 NEWS.md | 107 + R/model-phenips-clim.R | 1204 +++++++++++----------- R/model-phenips.R | 1054 +++++++++---------- R/plot-development-diagram.R | 815 +++++++------- R/utils-model-functions.R | 4 R/utils.R | 350 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/tinytest/data/test-data-phenips-clim.rda |binary inst/tinytest/data/test-data-spring-mortality.rda |binary man/model.phenips_clim.customize.Rd | 2 13 files changed, 1794 insertions(+), 1773 deletions(-)
Title: Interpretable Machine Learning and Statistical Inference with
Accumulated Local Effects (ALE)
Description: Accumulated Local Effects (ALE) were initially developed as a model-agnostic approach for global explanations of the results of black-box machine learning algorithms. ALE has a key advantage over other approaches like partial dependency plots (PDP) and SHapley Additive exPlanations (SHAP): its values represent a clean functional decomposition of the model. As such, ALE values are not affected by the presence or absence of interactions among variables in a mode. Moreover, its computation is relatively rapid. This package reimplements the algorithms for calculating ALE data and develops highly interpretable visualizations for plotting these ALE values. It also extends the original ALE concept to add bootstrap-based confidence intervals and ALE-based statistics that can be used for statistical inference. For more details, see Okoli, Chitu. 2023. “Statistical Inference Using Machine Learning and Classical Techniques Based on Accumulated Local Effects (ALE).” arXiv. <doi:10.48550/arXiv.2 [...truncated...]
Author: Chitu Okoli [aut, cre]
Maintainer: Chitu Okoli <Chitu.Okoli@skema.edu>
This is a re-admission after prior archival of version 0.5.0 dated 2025-04-09
Diff between ale versions 0.5.0 dated 2025-04-09 and 0.5.2 dated 2025-08-29
ale-0.5.0/ale/R/aaa.R |only ale-0.5.0/ale/R/ale.R |only ale-0.5.0/ale/R/generics.R |only ale-0.5.0/ale/R/methods.R |only ale-0.5.0/ale/man/ALE.Rd |only ale-0.5.0/ale/tests/testthat/test-ALEPlot-gold-standard.R |only ale-0.5.2/ale/DESCRIPTION | 12 ale-0.5.2/ale/MD5 | 120 ale-0.5.2/ale/NAMESPACE | 2 ale-0.5.2/ale/NEWS.md | 18 ale-0.5.2/ale/R/000-startup.R |only ale-0.5.2/ale/R/ALE.R |only ale-0.5.2/ale/R/ALEPlots.R | 522 ale-0.5.2/ale/R/ALEPlots_methods.R |only ale-0.5.2/ale/R/ALE_methods.R |only ale-0.5.2/ale/R/ALEpDist.R | 200 ale-0.5.2/ale/R/ModelBoot.R | 73 ale-0.5.2/ale/R/ModelBoot_methods.R |only ale-0.5.2/ale/R/array.R | 6 ale-0.5.2/ale/R/utils.R | 402 ale-0.5.2/ale/R/validation.R | 15 ale-0.5.2/ale/README.md | 106 ale-0.5.2/ale/build/vignette.rds |binary ale-0.5.2/ale/inst/doc/ale-intro.R | 54 ale-0.5.2/ale/inst/doc/ale-intro.Rmd | 67 ale-0.5.2/ale/inst/doc/ale-intro.html | 171 ale-0.5.2/ale/inst/doc/ale-small-datasets.R | 86 ale-0.5.2/ale/inst/doc/ale-small-datasets.Rmd | 88 ale-0.5.2/ale/inst/doc/ale-small-datasets.html | 205 ale-0.5.2/ale/inst/doc/ale-statistics.R | 4 ale-0.5.2/ale/inst/doc/ale-statistics.Rmd | 4 ale-0.5.2/ale/inst/doc/ale-statistics.html | 42 ale-0.5.2/ale/inst/doc/ale-x-datatypes.R | 45 ale-0.5.2/ale/inst/doc/ale-x-datatypes.Rmd | 55 ale-0.5.2/ale/inst/doc/ale-x-datatypes.html | 93 ale-0.5.2/ale/man/ALEPlots.Rd | 2 ale-0.5.2/ale/man/ALEpDist.Rd | 106 ale-0.5.2/ale/man/ModelBoot.Rd | 48 ale-0.5.2/ale/man/ale.Rd |only ale-0.5.2/ale/man/customize.Rd |only ale-0.5.2/ale/man/figures/README-2D-plot-1.png |binary ale-0.5.2/ale/man/figures/README-ale-p-and-1D-plot-1.png |binary ale-0.5.2/ale/man/figures/README-simple-ale-1.png |binary ale-0.5.2/ale/man/get.ALE.Rd | 2 ale-0.5.2/ale/man/get.ALEPlots.Rd | 2 ale-0.5.2/ale/man/get.ModelBoot.Rd | 2 ale-0.5.2/ale/man/get.Rd | 2 ale-0.5.2/ale/man/invert_probs.Rd |only ale-0.5.2/ale/man/plot.ALE.Rd | 2 ale-0.5.2/ale/man/plot.ALEPlots.Rd | 2 ale-0.5.2/ale/man/plot.ModelBoot.Rd | 2 ale-0.5.2/ale/man/print.ALE.Rd | 2 ale-0.5.2/ale/man/print.ALEPlots.Rd | 2 ale-0.5.2/ale/man/print.ModelBoot.Rd | 2 ale-0.5.2/ale/man/subset.ALEPlots.Rd | 2 ale-0.5.2/ale/man/summary.ALEPlots.Rd | 2 ale-0.5.2/ale/tests/testthat/Rplots.pdf |binary ale-0.5.2/ale/tests/testthat/_snaps/ALE-binary.md |20744 +- ale-0.5.2/ale/tests/testthat/_snaps/ALE-categorical.md |123088 +++++++------- ale-0.5.2/ale/tests/testthat/_snaps/ALE-numerical.md |14528 - ale-0.5.2/ale/tests/testthat/_snaps/ALEpDist.md | 1754 ale-0.5.2/ale/tests/testthat/_snaps/ModelBoot.md | 7698 ale-0.5.2/ale/tests/testthat/_snaps/array.md | 76 ale-0.5.2/ale/tests/testthat/_snaps/stats.md | 50 ale-0.5.2/ale/vignettes/ale-intro.Rmd | 67 ale-0.5.2/ale/vignettes/ale-small-datasets.Rmd | 88 ale-0.5.2/ale/vignettes/ale-statistics.Rmd | 4 ale-0.5.2/ale/vignettes/ale-x-datatypes.Rmd | 55 68 files changed, 85605 insertions(+), 85117 deletions(-)
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Description: Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and
PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically
access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types.
Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between PubChemR versions 2.1.4 dated 2025-03-07 and 2.1.5 dated 2025-08-29
DESCRIPTION | 16 MD5 | 10 R/get_substances.R | 101 inst/doc/Enhancing_Chemical_Data_Access_with_PubChemR.html | 1035 +- inst/doc/Exploring_Chemical_Data_with_PubChemR.html | 5017 ++++++------ inst/doc/Working_with_PubChemR_to_Access_Chemical_Data.html | 1858 ++-- 6 files changed, 4344 insertions(+), 3693 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Kimberly Truong [aut] ,
Colin Thomson [aut] ,
Meredith Scherer [aut] [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.7.1 dated 2025-08-21 and 2.7.2 dated 2025-08-29
httk-2.7.1/httk/tests/1comp_test.R |only httk-2.7.1/httk/tests/1comp_test.Rout.save |only httk-2.7.1/httk/tests/adddata_test.R |only httk-2.7.1/httk/tests/adddata_test.Rout.save |only httk-2.7.2/httk/DESCRIPTION | 8 - httk-2.7.2/httk/MD5 | 100 ++++++++++----------- httk-2.7.2/httk/NEWS.md | 4 httk-2.7.2/httk/R/add_chemtable.R | 47 +++++++++ httk-2.7.2/httk/R/armitage.R | 2 httk-2.7.2/httk/R/calc_clearance_frac.R | 2 httk-2.7.2/httk/R/calc_css.R | 2 httk-2.7.2/httk/R/calc_hep_clearance.R | 6 - httk-2.7.2/httk/R/calc_volume_of_distribution.R | 3 httk-2.7.2/httk/R/data.R | 5 - httk-2.7.2/httk/R/parameterize_dermal_pbtk.R | 2 httk-2.7.2/httk/R/parameterize_steadystate.R | 4 httk-2.7.2/httk/R/rmed0non0u95.R | 2 httk-2.7.2/httk/R/solve_dermal_pbtk.R | 15 ++- httk-2.7.2/httk/R/solve_fetal_pbtk.R | 2 httk-2.7.2/httk/R/solve_full_pregnancy.R | 8 - httk-2.7.2/httk/R/solve_gas_pbtk.R | 2 httk-2.7.2/httk/R/solve_model.R | 1 httk-2.7.2/httk/build/partial.rdb |binary httk-2.7.2/httk/inst/doc/V1_IntroToHTTK.html | 10 +- httk-2.7.2/httk/inst/doc/V2_IntrotoIVIVE.Rmd | 2 httk-2.7.2/httk/inst/doc/V2_IntrotoIVIVE.html | 2 httk-2.7.2/httk/inst/doc/Va_Pearce2017.html | 22 ++-- httk-2.7.2/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.7.2/httk/inst/doc/Ve_Truong2025.html | 4 httk-2.7.2/httk/inst/doc/Vf_WambaughSubmitted.html | 4 httk-2.7.2/httk/inst/doc/Vg_MeadeSubmitted.html | 8 - httk-2.7.2/httk/inst/doc/Vh_SchererSubmitted.html | 4 httk-2.7.2/httk/man/add_chemtable.Rd | 47 +++++++++ httk-2.7.2/httk/man/armitage_eval.Rd | 2 httk-2.7.2/httk/man/calc_clearance_frac.Rd | 2 httk-2.7.2/httk/man/calc_css.Rd | 2 httk-2.7.2/httk/man/calc_hep_clearance.Rd | 3 httk-2.7.2/httk/man/calc_hepatic_clearance.Rd | 3 httk-2.7.2/httk/man/calc_vdist.Rd | 3 httk-2.7.2/httk/man/parameterize_dermal_pbtk.Rd | 2 httk-2.7.2/httk/man/physiology.data.Rd | 2 httk-2.7.2/httk/man/rmed0non0u95.Rd | 2 httk-2.7.2/httk/man/solve_dermal_pbtk.Rd | 15 ++- httk-2.7.2/httk/man/solve_fetal_pbtk.Rd | 2 httk-2.7.2/httk/man/solve_full_pregnancy.Rd | 6 - httk-2.7.2/httk/man/solve_gas_pbtk.Rd | 2 httk-2.7.2/httk/man/tissue.data.Rd | 3 httk-2.7.2/httk/src/dermal.c | 4 httk-2.7.2/httk/src/dermal_1subcomp.c | 80 ++++++++++------ httk-2.7.2/httk/src/model3comp2.c | 2 httk-2.7.2/httk/tests/solve_dermal_test.R | 4 httk-2.7.2/httk/tests/solve_dermal_test.Rout.save | 76 --------------- httk-2.7.2/httk/vignettes/V2_IntrotoIVIVE.Rmd | 2 53 files changed, 308 insertions(+), 231 deletions(-)
Title: Calculates the Density-Based Clustering Validation (DBCV) Index
Description: A metric called 'Density-Based Clustering Validation index' (DBCV) index to evaluate clustering results, following the <https://github.com/pajaskowiak/clusterConfusion/blob/main/R/dbcv.R> 'R' implementation by Pablo Andretta Jaskowiak. Original 'DBCV' index article: Moulavi, D., Jaskowiak, P. A., Campello, R. J., Zimek, A., and Sander, J. (April 2014), "Density-based clustering validation", Proceedings of SDM 2014 -- the 2014 SIAM International Conference on Data Mining (pp. 839-847), <doi:10.1137/1.9781611973440.96>. A more recent article on the 'DBCV' index: Chicco, D., Sabino, G.; Oneto, L.; Jurman, G. (August 2025), "The DBCV index is more informative than DCSI, CDbw, and VIASCKDE indices for unsupervised clustering internal assessment of concave-shaped and density-based clusters", PeerJ Computer Science 11:e3095 (pp. 1-), <doi:10.7717/peerj-cs.3095>.
Author: Davide Chicco [cre] ,
Pablo Andretta Jaskowiak [aut]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between DBCVindex versions 1.4 dated 2025-02-19 and 1.5 dated 2025-08-29
DESCRIPTION | 14 +- MD5 | 12 + R/DBCV_function.r | 29 ++++ build/vignette.rds |binary inst/CITATION |only inst/doc/DBCVindex.html | 311 ++++++++++++++++++++++++++++++++++++++---------- man/dbcv_index.Rd | 4 man/norm_dbcv_index.Rd |only 8 files changed, 295 insertions(+), 75 deletions(-)
Title: US Maps Including Alaska and Hawaii
Description: Obtain United States map data frames of varying region types (e.g. county,
state). The map data frames include Alaska and Hawaii conveniently placed to the
bottom left, as they appear in most maps of the US. Convenience functions for plotting
choropleths, visualizing spatial data, and working with FIPS codes are also provided.
Author: Paolo Di Lorenzo [aut, cph, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.org>
Diff between usmap versions 0.8.0 dated 2025-05-28 and 1.0.0 dated 2025-08-29
DESCRIPTION | 10 MD5 | 93 - NEWS.md | 23 R/fips.R | 4 R/join-data.R | 21 R/plot-map.R | 54 R/transform.R | 10 R/us-map.R | 38 R/usmap-package.R | 8 README.md | 90 - data/citypop.rda |binary data/countypop.rda |binary data/countypov.rda |binary data/earthquakes.rda |binary data/statepop.rda |binary data/statepov.rda |binary data/usrivers.rda |binary inst/WORDLIST | 2 inst/doc/usmap1.Rmd | 4 inst/doc/usmap1.html | 26 inst/doc/usmap2.R | 4 inst/doc/usmap2.Rmd | 4 inst/doc/usmap2.html | 204 +-- inst/doc/usmap3.Rmd | 2 inst/doc/usmap3.html | 20 man/map_with_data.Rd | 20 man/plot_usmap.Rd | 27 man/us_map.Rd | 26 man/usmap.Rd | 6 tests/testthat/_snaps/data/countypop.svg | 552 ++++----- tests/testthat/_snaps/data/countypov.svg | 558 +++++----- tests/testthat/_snaps/data/statepop.svg | 82 - tests/testthat/_snaps/data/statepov.svg | 82 - tests/testthat/_snaps/plot/arizona-county-map-with-labels-and-fill.svg | 74 - tests/testthat/_snaps/plot/example-data-state-map-with-custom-linewidth.svg | 304 ++--- tests/testthat/_snaps/plot/new-england-state-map-with-labels-excluding-maine.svg | 40 tests/testthat/_snaps/plot/pr-county-map-with-labels-and-excludes.svg |only tests/testthat/_snaps/plot/southeastern-states-map-with-labels.svg | 32 tests/testthat/_snaps/plot/state-map-with-labels.svg | 377 +++--- tests/testthat/_snaps/plot/state-map-with-major-rivers.svg | 420 +++---- tests/testthat/_snaps/plot/state-population-map-with-blue-outlines.svg | 298 ++--- tests/testthat/test-data.R | 2 tests/testthat/test-fips.R | 8 tests/testthat/test-plot.R | 51 tests/testthat/test-usmap.R | 4 vignettes/usmap1.Rmd | 4 vignettes/usmap2.Rmd | 4 vignettes/usmap3.Rmd | 2 48 files changed, 1815 insertions(+), 1775 deletions(-)
Title: Nondetects and Data Analysis for Environmental Data
Description: Contains methods described by Dennis Helsel in
his book "Nondetects And Data Analysis: Statistics
for Censored Environmental Data".
Author: Lopaka Lee [aut, cre]
Maintainer: Lopaka Lee <rclee@usgs.gov>
This is a re-admission after prior archival of version 1.6-1.1 dated 2020-03-22
Diff between NADA versions 1.6-1.1 dated 2020-03-22 and 1.6-1.2 dated 2025-08-29
DESCRIPTION | 12 ++++++++---- MD5 | 18 +++++++++--------- man/cendiff.Rd | 4 ++-- man/cenfit.Rd | 2 +- man/cenmle-class.Rd | 2 +- man/cenmle-gaussian-class.Rd | 2 +- man/cenmle-lognormal-class.Rd | 2 +- man/cenreg-class.Rd | 2 +- man/cenreg-gaussian-class.Rd | 2 +- man/cenreg-lognormal-class.Rd | 2 +- 10 files changed, 26 insertions(+), 22 deletions(-)
Title: Assessing Proximal and Distal Causal Excursion Effects for
Micro-Randomized Trials
Description: Estimates marginal causal excursion effects and moderated causal excursion effects for micro-randomized trial (MRT). Applicable to MRT with binary treatment options and continuous or binary outcomes. The method for MRT with continuous outcomes is the weighted centered least squares (WCLS) by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274>. The method for MRT with binary outcomes is the estimator for marginal excursion effect (EMEE) by Qian et al. (2021) <doi:10.1093/biomet/asaa070>.
Estimates marginal and moderated causal excursion effects for micro-randomized trials (MRTs) with binary treatment options. Supports continuous and binary proximal outcomes as well as distal outcomes. Methods include weighted and centered least squares (WCLS) for continuous proximal outcomes by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274>, the estimator for marginal excursion effect (EMEE) for binary proximal outcomes by Qian et al. (2021) <doi:10.1093/biomet/asaa [...truncated...]
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.1.2 dated 2023-07-01 and 0.2.0 dated 2025-08-29
MRTAnalysis-0.1.2/MRTAnalysis/inst/doc/mrt-analysis.R |only MRTAnalysis-0.1.2/MRTAnalysis/inst/doc/mrt-analysis.Rmd |only MRTAnalysis-0.1.2/MRTAnalysis/inst/doc/mrt-analysis.html |only MRTAnalysis-0.1.2/MRTAnalysis/vignettes/mrt-analysis.Rmd |only MRTAnalysis-0.2.0/MRTAnalysis/DESCRIPTION | 22 ++- MRTAnalysis-0.2.0/MRTAnalysis/MD5 | 56 ++++++--- MRTAnalysis-0.2.0/MRTAnalysis/NAMESPACE | 4 MRTAnalysis-0.2.0/MRTAnalysis/NEWS.md | 21 ++- MRTAnalysis-0.2.0/MRTAnalysis/R/data_binary.R | 45 ++++--- MRTAnalysis-0.2.0/MRTAnalysis/R/data_distal_continuous.R |only MRTAnalysis-0.2.0/MRTAnalysis/R/data_mimicHeartSteps.R | 2 MRTAnalysis-0.2.0/MRTAnalysis/R/dcee.R |only MRTAnalysis-0.2.0/MRTAnalysis/R/dcee_helper.R |only MRTAnalysis-0.2.0/MRTAnalysis/R/preprocess_input.R | 22 ++- MRTAnalysis-0.2.0/MRTAnalysis/R/summary.dcee.R |only MRTAnalysis-0.2.0/MRTAnalysis/R/wcls.R | 46 ++++--- MRTAnalysis-0.2.0/MRTAnalysis/README.md | 59 ++++++++-- MRTAnalysis-0.2.0/MRTAnalysis/build/vignette.rds |binary MRTAnalysis-0.2.0/MRTAnalysis/data/data_distal_continuous.rda |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-distal-causal-effect.R |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-distal-causal-effect.Rmd |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-distal-causal-effect.html |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-proximal-causal-effect.R |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-proximal-causal-effect.Rmd |only MRTAnalysis-0.2.0/MRTAnalysis/inst/doc/mrt-proximal-causal-effect.html |only MRTAnalysis-0.2.0/MRTAnalysis/man/data_binary.Rd | 44 ++++--- MRTAnalysis-0.2.0/MRTAnalysis/man/data_distal_continuous.Rd |only MRTAnalysis-0.2.0/MRTAnalysis/man/data_mimicHeartSteps.Rd | 4 MRTAnalysis-0.2.0/MRTAnalysis/man/dcee.Rd |only MRTAnalysis-0.2.0/MRTAnalysis/man/summary.dcee_fit.Rd |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-basic.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-crossfit.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-errors.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-gam.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-numeric-golden-crossfit.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-numeric-golden-lm.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-numeric-golden-other-learners.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-summary.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-superlearner.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-dcee-weighting-and-availability.R |only MRTAnalysis-0.2.0/MRTAnalysis/tests/testthat/test-emee2.R | 8 - MRTAnalysis-0.2.0/MRTAnalysis/vignettes/mhealth-ref.bib | 18 +++ MRTAnalysis-0.2.0/MRTAnalysis/vignettes/mrt-distal-causal-effect.Rmd |only MRTAnalysis-0.2.0/MRTAnalysis/vignettes/mrt-proximal-causal-effect.Rmd |only 44 files changed, 243 insertions(+), 108 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model as described in Zinn (2014) <doi:10.34196/IJM.00105>.
Author: Sabine Zinn [aut, cre],
Felix von Heusinger [ctb],
Camila Weber [ctb],
Claudio Bosco [ctb],
Maurizio Teobaldell [ctb]
Maintainer: Sabine Zinn <szinn@diw.de>
Diff between MicSim versions 2.0.1 dated 2024-01-23 and 3.0.0 dated 2025-08-29
MicSim-2.0.1/MicSim/inst/doc/MicSim_vignette.R |only MicSim-2.0.1/MicSim/inst/doc/MicSim_vignette.Rmd |only MicSim-2.0.1/MicSim/inst/doc/MicSim_vignette.html |only MicSim-2.0.1/MicSim/vignettes/MicSim_vignette.Rmd |only MicSim-3.0.0/MicSim/DESCRIPTION | 37 MicSim-3.0.0/MicSim/MD5 | 43 MicSim-3.0.0/MicSim/NAMESPACE | 43 MicSim-3.0.0/MicSim/R/MicSim-package.r |only MicSim-3.0.0/MicSim/R/auxFcTDates.r |only MicSim-3.0.0/MicSim/R/auxFctMicSim.r | 225 - MicSim-3.0.0/MicSim/R/buildTransitionMatrix.r |only MicSim-3.0.0/MicSim/R/convertToLong.r | 176 - MicSim-3.0.0/MicSim/R/convertToWide.r | 51 MicSim-3.0.0/MicSim/R/data.r |only MicSim-3.0.0/MicSim/R/micSim.r | 1467 +++++++---- MicSim-3.0.0/MicSim/R/micSimParallel.r |only MicSim-3.0.0/MicSim/build/vignette.rds |binary MicSim-3.0.0/MicSim/data/rates_mdd.rda |only MicSim-3.0.0/MicSim/inst/LICENSE.md |only MicSim-3.0.0/MicSim/inst/NEWS.Rd | 10 MicSim-3.0.0/MicSim/inst/doc/Simulating_Migration_Flows.R |only MicSim-3.0.0/MicSim/inst/doc/Simulating_Migration_Flows.Rmd |only MicSim-3.0.0/MicSim/inst/doc/Simulating_Migration_Flows.html |only MicSim-3.0.0/MicSim/inst/doc/simulation_mdd.R |only MicSim-3.0.0/MicSim/inst/doc/simulation_mdd.Rmd |only MicSim-3.0.0/MicSim/inst/doc/simulation_mdd.html |only MicSim-3.0.0/MicSim/man/MicSim-package.Rd | 4 MicSim-3.0.0/MicSim/man/micSim.Rd | 373 +- MicSim-3.0.0/MicSim/man/micSimParallel.Rd | 266 - MicSim-3.0.0/MicSim/man/rates_mdd.Rd |only MicSim-3.0.0/MicSim/vignettes/Simulating_Migration_Flows.Rmd |only MicSim-3.0.0/MicSim/vignettes/references.bib |only MicSim-3.0.0/MicSim/vignettes/simulation_mdd.Rmd |only 33 files changed, 1606 insertions(+), 1089 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from the Manifesto
Corpus and to the Manifesto Project's Main Dataset and routines to analyse this
data. The Manifesto Project <https://manifesto-project.wzb.eu> collects and
analyses election programmes across time and space to measure the political
preferences of parties. The Manifesto Corpus contains the collected and
annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut],
Nicolas Merz [aut],
Sven Regel [aut],
Pola Lehmann [cre, ctb],
Paul Muscat [ctb]
Maintainer: Pola Lehmann <pola.lehmann@wzb.eu>
Diff between manifestoR versions 1.6.0 dated 2024-05-16 and 1.6.1 dated 2025-08-29
DESCRIPTION | 48 +++++++++++++++++++-------------------- MD5 | 30 +++++++++++++----------- NAMESPACE | 27 ++++++++++++++------- NEWS | 6 ++++ R/codebook.R | 15 ++++++++---- R/dataset.R | 8 +++++- R/db_api.R | 16 +++++++++---- R/manifestoR-package.r | 6 +--- R/reexport-NLP.R |only R/reexport-tibble.R |only R/reexport-tm.R |only R/scaling_functions.R | 6 ++++ inst/doc/manifestoRworkflow.pdf |binary man/manifestoR-package.Rd | 8 ++---- man/mp_interpolate.Rd | 2 - man/mpdb_api_request.Rd | 5 +++- man/reexports.Rd |only vignettes/manifestoRworkflow.Rmd | 11 +++++--- 18 files changed, 117 insertions(+), 71 deletions(-)
Title: Bindings to 'GDAL'
Description: API bindings to the Geospatial Data Abstraction Library ('GDAL',
<https://gdal.org>). Implements the 'GDAL' Raster and Vector Data Models.
Bindings are implemented with 'Rcpp' modules. Exposed C++ classes and
stand-alone functions wrap much of the 'GDAL' API and provide additional
functionality. Calling signatures resemble the native C, C++ and Python APIs
provided by the 'GDAL' project. Class 'GDALRaster' encapsulates a
'GDALDataset' and its raster band objects. Class 'GDALVector' encapsulates
an 'OGRLayer' and the 'GDALDataset' that contains it. Initial bindings are
provided to the unified 'gdal' command line interface added in 'GDAL' 3.11.
C++ stand-alone functions provide bindings to most 'GDAL' "traditional"
raster and vector utilities, including 'OGR' facilities for vector
geoprocessing, several algorithms, as well as the Geometry API ('GEOS' via
'GDAL' headers), the Spatial Reference Systems API, and methods for
coordinate transformation. Bindings to the Virtual Systems In [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [ctb],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <jctoney@gmail.com>
Diff between gdalraster versions 2.2.0 dated 2025-08-22 and 2.2.1 dated 2025-08-29
DESCRIPTION | 6 MD5 | 88 +++---- NEWS.md | 17 + R/RcppExports.R | 23 + R/cmb_table.R | 4 R/display.R | 8 R/gdal_cli.R | 146 ++++++----- R/gdalalg.R | 50 +--- R/gdalraster.R | 8 R/gdalvector.R | 4 R/running_stats.R | 4 R/vsifile.R | 4 README.md | 10 configure | 18 - configure.ac | 2 inst/doc/gdal-config-quick-ref.html | 3 inst/doc/raster-api-tutorial.html | 7 inst/doc/raster-attribute-tables.html | 117 ++++----- man/CmbTable-class.Rd | 6 man/GDALAlg-class.Rd | 96 +++---- man/GDALRaster-class.Rd | 10 man/GDALVector-class.Rd | 6 man/RunningStats-class.Rd | 6 man/VSIFile-class.Rd | 6 man/gdal_cli.Rd | 112 +++++---- man/gdal_version.Rd | 10 man/gdalraster-package.Rd | 8 man/push_error_handler.Rd | 6 src/RcppExports.cpp | 11 src/gdal_exp.cpp | 21 - src/gdalalg.cpp | 410 ++++++++++++++++++--------------- src/gdalalg.h | 2 src/gdalraster.cpp | 73 +++++ src/gdalraster.h | 7 src/gdalvector.cpp | 47 --- src/rcpp_util.cpp | 7 src/rcpp_util.h | 2 src/srs_api.cpp | 3 tests/testthat/test-GDALAlg-class.R | 16 - tests/testthat/test-GDALVector-class.R | 35 +- tests/testthat/test-gdal_cli.R | 6 tests/testthat/test-gdal_exp.R | 9 tests/testthat/test-gdalraster_proc.R | 28 +- tests/testthat/test-ogr_reproject.R | 12 tests/testthat/test-s3_methods.R | 21 + 45 files changed, 830 insertions(+), 665 deletions(-)
Title: Flood Frequency Analysis Framework
Description: Tools to support systematic and reproducible workflows for both
stationary and nonstationary flood frequency analysis, with applications
extending to other hydroclimate extremes, such as precipitation frequency
analysis. This package implements the FFA framework proposed by Vidrio-
Sahagún et al. (2024) <doi:10.1016/j.envsoft.2024.105940>, originally
developed in 'MATLAB', now adapted for the 'R' environment. This work was
funded by the Flood Hazard Identification and Mapping Program of Environment
and Climate Change Canada, as well as the Canada Research Chair (Tier 1)
awarded to Dr. Pietroniro.
Author: Riley Wheadon [aut, cre],
Cuauhtemoc Vidrio-Sahagun [aut],
Alain Pietroniro [aut, fnd],
Jianxun He [aut],
Environment and Climate Change Canada [fnd]
Maintainer: Riley Wheadon <rileywheadon@gmail.com>
Diff between ffaframework versions 0.1.0 dated 2025-08-25 and 0.1.1 dated 2025-08-29
ffaframework-0.1.0/ffaframework/inst/templates/data_summary.Rmd |only ffaframework-0.1.1/ffaframework/DESCRIPTION | 8 ffaframework-0.1.1/ffaframework/MD5 | 103 +++++----- ffaframework-0.1.1/ffaframework/NEWS.md |only ffaframework-0.1.1/ffaframework/R/eda-kpss-test.R | 2 ffaframework-0.1.1/ffaframework/R/eda-pp-test.R | 2 ffaframework-0.1.1/ffaframework/R/ffaframework-package.R | 2 ffaframework-0.1.1/ffaframework/R/ffaframework-parameters.R | 2 ffaframework-0.1.1/ffaframework/R/fit-lmoments-kappa.R | 2 ffaframework-0.1.1/ffaframework/R/framework-eda.R | 7 ffaframework-0.1.1/ffaframework/R/framework-ffa.R | 7 ffaframework-0.1.1/ffaframework/R/framework-full.R | 11 - ffaframework-0.1.1/ffaframework/R/framework-helpers.R | 15 - ffaframework-0.1.1/ffaframework/R/internal-fit.R | 2 ffaframework-0.1.1/ffaframework/R/plot-mks-test.R | 2 ffaframework-0.1.1/ffaframework/R/plot-nsffa-estimates.R | 5 ffaframework-0.1.1/ffaframework/R/plot-pettitt-test.R | 2 ffaframework-0.1.1/ffaframework/R/plot-sffa-estimates.R | 5 ffaframework-0.1.1/ffaframework/README.md |only ffaframework-0.1.1/ffaframework/build/vignette.rds |binary ffaframework-0.1.1/ffaframework/inst/WORDLIST | 4 ffaframework-0.1.1/ffaframework/inst/doc/trend-mean.Rmd | 4 ffaframework-0.1.1/ffaframework/inst/doc/trend-mean.html | 4 ffaframework-0.1.1/ffaframework/inst/doc/trend-variability.Rmd | 4 ffaframework-0.1.1/ffaframework/inst/doc/trend-variability.html | 5 ffaframework-0.1.1/ffaframework/inst/templates/_master.Rmd | 32 +++ ffaframework-0.1.1/ffaframework/inst/templates/assessment_report.Rmd | 6 ffaframework-0.1.1/ffaframework/inst/templates/bbmk_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/estimation_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/mks_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/pettitt_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/runs_mean_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/runs_variance_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/selection_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/sens_mean_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/sens_variance_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/spearman_report.Rmd | 3 ffaframework-0.1.1/ffaframework/inst/templates/uncertainty_report.Rmd | 5 ffaframework-0.1.1/ffaframework/man/eda_kpss_test.Rd | 2 ffaframework-0.1.1/ffaframework/man/eda_pp_test.Rd | 2 ffaframework-0.1.1/ffaframework/man/ffaframework-package.Rd | 2 ffaframework-0.1.1/ffaframework/man/fit_lmoments_kappa.Rd | 2 ffaframework-0.1.1/ffaframework/man/framework_eda.Rd | 10 ffaframework-0.1.1/ffaframework/man/framework_ffa.Rd | 10 ffaframework-0.1.1/ffaframework/man/framework_full.Rd | 10 ffaframework-0.1.1/ffaframework/man/param-ns-splits.Rd | 2 ffaframework-0.1.1/ffaframework/man/plot_mks_test.Rd | 2 ffaframework-0.1.1/ffaframework/man/plot_pettitt_test.Rd | 2 ffaframework-0.1.1/ffaframework/tests/testthat/test-framework-eda.R | 15 + ffaframework-0.1.1/ffaframework/tests/testthat/test-framework-ffa.R | 16 + ffaframework-0.1.1/ffaframework/tests/testthat/test-framework-full.R | 17 + ffaframework-0.1.1/ffaframework/tests/testthat/test-plots.R | 24 ++ ffaframework-0.1.1/ffaframework/vignettes/trend-mean.Rmd | 4 ffaframework-0.1.1/ffaframework/vignettes/trend-variability.Rmd | 4 54 files changed, 269 insertions(+), 126 deletions(-)
Title: R Client for the 'Civis Platform API'
Description: A convenient interface for making
requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform>.
Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.
Author: Dustin Leatherman [cre],
Peter Cooman [ctb],
Patrick Miller [aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Stephen Hoover [ctb],
Danning Chen [ctb],
Elizabeth Sander [ctb],
Madison Hobb [...truncated...]
Maintainer: Dustin Leatherman <dleatherman@civisanalytics.com>
This is a re-admission after prior archival of version 3.1.2 dated 2023-03-31
Diff between civis versions 3.1.2 dated 2023-03-31 and 3.1.3 dated 2025-08-29
civis-3.1.2/civis/man/notebooks_post_git_checkout.Rd |only civis-3.1.2/civis/man/notebooks_post_git_checkout_latest.Rd |only civis-3.1.2/civis/man/reports_post_git_checkout.Rd |only civis-3.1.2/civis/man/reports_post_git_checkout_latest.Rd |only civis-3.1.2/civis/man/saml_service_providers_delete_shares_groups.Rd |only civis-3.1.2/civis/man/saml_service_providers_delete_shares_users.Rd |only civis-3.1.2/civis/man/saml_service_providers_list_shares.Rd |only civis-3.1.2/civis/man/saml_service_providers_put_shares_groups.Rd |only civis-3.1.2/civis/man/saml_service_providers_put_shares_users.Rd |only civis-3.1.2/civis/man/scripts_patch.Rd |only civis-3.1.2/civis/man/users_delete_me_superadmin.Rd |only civis-3.1.2/civis/man/users_get_me_themes.Rd |only civis-3.1.2/civis/man/users_list_me_themes.Rd |only civis-3.1.2/civis/man/users_post_me_superadmin.Rd |only civis-3.1.2/civis/man/workflows_post_git_checkout.Rd |only civis-3.1.3/civis/DESCRIPTION | 18 civis-3.1.3/civis/MD5 | 821 - civis-3.1.3/civis/NAMESPACE | 105 civis-3.1.3/civis/NEWS.md |only civis-3.1.3/civis/R/client_base.R | 8 civis-3.1.3/civis/R/generate_client.R | 6 civis-3.1.3/civis/R/generated_client.R | 7151 ++++++++-- civis-3.1.3/civis/R/io.R | 29 civis-3.1.3/civis/R/reports.R | 10 civis-3.1.3/civis/README.md | 4 civis-3.1.3/civis/build/vignette.rds |binary civis-3.1.3/civis/inst/doc/civis_ml.R | 38 civis-3.1.3/civis/inst/doc/civis_ml.Rmd | 2 civis-3.1.3/civis/inst/doc/civis_ml.html | 10 civis-3.1.3/civis/inst/doc/civis_scripts.R | 26 civis-3.1.3/civis/inst/doc/civis_scripts.html | 8 civis-3.1.3/civis/inst/doc/concurrency.R | 8 civis-3.1.3/civis/inst/doc/concurrency.html | 4 civis-3.1.3/civis/inst/doc/data_import_and_export.R | 18 civis-3.1.3/civis/inst/doc/data_import_and_export.html | 4 civis-3.1.3/civis/inst/doc/quick_start.R | 6 civis-3.1.3/civis/inst/doc/quick_start.html | 4 civis-3.1.3/civis/man/CivisFuture.Rd | 6 civis-3.1.3/civis/man/admin_list_organizations.Rd | 2 civis-3.1.3/civis/man/aliases_get.Rd | 2 civis-3.1.3/civis/man/aliases_get_object_type.Rd | 4 civis-3.1.3/civis/man/aliases_list.Rd | 4 civis-3.1.3/civis/man/aliases_list_dependencies.Rd | 3 civis-3.1.3/civis/man/aliases_patch.Rd | 4 civis-3.1.3/civis/man/aliases_post.Rd | 4 civis-3.1.3/civis/man/aliases_put.Rd | 4 civis-3.1.3/civis/man/aliases_put_transfer.Rd | 3 civis-3.1.3/civis/man/civis_platform.Rd | 2 civis-3.1.3/civis/man/clusters_get_kubernetes_instance_configs.Rd | 2 civis-3.1.3/civis/man/clusters_get_kubernetes_partitions.Rd | 2 civis-3.1.3/civis/man/clusters_list_kubernetes_compute_hours.Rd |only civis-3.1.3/civis/man/clusters_list_kubernetes_deployments.Rd | 6 civis-3.1.3/civis/man/clusters_list_kubernetes_instance_configs_historical_metrics.Rd |only civis-3.1.3/civis/man/clusters_list_kubernetes_partitions.Rd | 2 civis-3.1.3/civis/man/clusters_patch_kubernetes_partitions.Rd | 4 civis-3.1.3/civis/man/clusters_post_kubernetes_partitions.Rd | 4 civis-3.1.3/civis/man/credentials_get.Rd | 1 civis-3.1.3/civis/man/credentials_list.Rd | 1 civis-3.1.3/civis/man/credentials_list_dependencies.Rd | 3 civis-3.1.3/civis/man/credentials_patch.Rd | 6 civis-3.1.3/civis/man/credentials_post.Rd | 6 civis-3.1.3/civis/man/credentials_post_authenticate.Rd | 1 civis-3.1.3/civis/man/credentials_put.Rd | 6 civis-3.1.3/civis/man/credentials_put_transfer.Rd | 3 civis-3.1.3/civis/man/databases_delete_schemas_tables_projects.Rd |only civis-3.1.3/civis/man/databases_get.Rd | 7 civis-3.1.3/civis/man/databases_get_schema_privileges.Rd | 4 civis-3.1.3/civis/man/databases_get_schemas_tables.Rd |only civis-3.1.3/civis/man/databases_get_status_graphs_timeframe.Rd |only civis-3.1.3/civis/man/databases_get_table_privilegesschema_name.Rd | 9 civis-3.1.3/civis/man/databases_list.Rd | 7 civis-3.1.3/civis/man/databases_list_schemas.Rd | 2 civis-3.1.3/civis/man/databases_list_schemas_tables.Rd |only civis-3.1.3/civis/man/databases_list_schemas_tables_projects.Rd |only civis-3.1.3/civis/man/databases_list_users.Rd | 2 civis-3.1.3/civis/man/databases_patch_schemas_tables.Rd |only civis-3.1.3/civis/man/databases_put_schemas_tables_projects.Rd |only civis-3.1.3/civis/man/download_civis.Rd | 6 civis-3.1.3/civis/man/enhancements_delete_cass_ncoa_runs.Rd | 2 civis-3.1.3/civis/man/enhancements_delete_civis_data_match_runs.Rd | 2 civis-3.1.3/civis/man/enhancements_delete_geocode_runs.Rd | 2 civis-3.1.3/civis/man/enhancements_delete_identity_resolution_projects.Rd |only civis-3.1.3/civis/man/enhancements_delete_identity_resolution_runs.Rd |only civis-3.1.3/civis/man/enhancements_delete_identity_resolution_shares_groups.Rd |only civis-3.1.3/civis/man/enhancements_delete_identity_resolution_shares_users.Rd |only civis-3.1.3/civis/man/enhancements_get_cass_ncoa.Rd | 6 civis-3.1.3/civis/man/enhancements_get_cass_ncoa_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_get_civis_data_match.Rd | 8 civis-3.1.3/civis/man/enhancements_get_civis_data_match_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_get_geocode.Rd | 8 civis-3.1.3/civis/man/enhancements_get_geocode_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_get_identity_resolution.Rd |only civis-3.1.3/civis/man/enhancements_get_identity_resolution_runs.Rd |only civis-3.1.3/civis/man/enhancements_list_cass_ncoa_dependencies.Rd | 3 civis-3.1.3/civis/man/enhancements_list_cass_ncoa_runs.Rd | 8 civis-3.1.3/civis/man/enhancements_list_cass_ncoa_runs_logs.Rd | 2 civis-3.1.3/civis/man/enhancements_list_civis_data_match_dependencies.Rd | 3 civis-3.1.3/civis/man/enhancements_list_civis_data_match_runs.Rd | 8 civis-3.1.3/civis/man/enhancements_list_civis_data_match_runs_logs.Rd | 2 civis-3.1.3/civis/man/enhancements_list_geocode_dependencies.Rd | 3 civis-3.1.3/civis/man/enhancements_list_geocode_runs.Rd | 8 civis-3.1.3/civis/man/enhancements_list_geocode_runs_logs.Rd | 2 civis-3.1.3/civis/man/enhancements_list_identity_resolution.Rd |only civis-3.1.3/civis/man/enhancements_list_identity_resolution_dependencies.Rd |only civis-3.1.3/civis/man/enhancements_list_identity_resolution_projects.Rd |only civis-3.1.3/civis/man/enhancements_list_identity_resolution_runs.Rd |only civis-3.1.3/civis/man/enhancements_list_identity_resolution_runs_logs.Rd |only civis-3.1.3/civis/man/enhancements_list_identity_resolution_shares.Rd |only civis-3.1.3/civis/man/enhancements_patch_cass_ncoa.Rd | 18 civis-3.1.3/civis/man/enhancements_patch_civis_data_match.Rd | 22 civis-3.1.3/civis/man/enhancements_patch_geocode.Rd | 22 civis-3.1.3/civis/man/enhancements_patch_identity_resolution.Rd |only civis-3.1.3/civis/man/enhancements_post_cass_ncoa.Rd | 18 civis-3.1.3/civis/man/enhancements_post_cass_ncoa_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_post_civis_data_match.Rd | 22 civis-3.1.3/civis/man/enhancements_post_civis_data_match_clone.Rd | 8 civis-3.1.3/civis/man/enhancements_post_civis_data_match_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_post_geocode.Rd | 22 civis-3.1.3/civis/man/enhancements_post_geocode_runs.Rd | 4 civis-3.1.3/civis/man/enhancements_post_identity_resolution.Rd |only civis-3.1.3/civis/man/enhancements_post_identity_resolution_cancel.Rd |only civis-3.1.3/civis/man/enhancements_post_identity_resolution_clone.Rd |only civis-3.1.3/civis/man/enhancements_post_identity_resolution_runs.Rd |only civis-3.1.3/civis/man/enhancements_put_cass_ncoa.Rd | 18 civis-3.1.3/civis/man/enhancements_put_cass_ncoa_archive.Rd | 6 civis-3.1.3/civis/man/enhancements_put_cass_ncoa_transfer.Rd | 3 civis-3.1.3/civis/man/enhancements_put_civis_data_match.Rd | 22 civis-3.1.3/civis/man/enhancements_put_civis_data_match_archive.Rd | 8 civis-3.1.3/civis/man/enhancements_put_civis_data_match_transfer.Rd | 3 civis-3.1.3/civis/man/enhancements_put_geocode.Rd | 22 civis-3.1.3/civis/man/enhancements_put_geocode_archive.Rd | 8 civis-3.1.3/civis/man/enhancements_put_geocode_transfer.Rd | 3 civis-3.1.3/civis/man/enhancements_put_identity_resolution.Rd |only civis-3.1.3/civis/man/enhancements_put_identity_resolution_archive.Rd |only civis-3.1.3/civis/man/enhancements_put_identity_resolution_projects.Rd |only civis-3.1.3/civis/man/enhancements_put_identity_resolution_shares_groups.Rd |only civis-3.1.3/civis/man/enhancements_put_identity_resolution_shares_users.Rd |only civis-3.1.3/civis/man/enhancements_put_identity_resolution_transfer.Rd |only civis-3.1.3/civis/man/exports_delete_files_csv_runs.Rd | 2 civis-3.1.3/civis/man/exports_get_files_csv_runs.Rd | 2 civis-3.1.3/civis/man/exports_list_files_csv_runs.Rd | 6 civis-3.1.3/civis/man/exports_list_files_csv_runs_logs.Rd | 2 civis-3.1.3/civis/man/exports_post_files_csv_runs.Rd | 2 civis-3.1.3/civis/man/files_get.Rd | 1 civis-3.1.3/civis/man/files_list_dependencies.Rd | 3 civis-3.1.3/civis/man/files_patch.Rd | 5 civis-3.1.3/civis/man/files_post.Rd | 5 civis-3.1.3/civis/man/files_post_multipart.Rd | 5 civis-3.1.3/civis/man/files_put.Rd | 5 civis-3.1.3/civis/man/files_put_transfer.Rd | 3 civis-3.1.3/civis/man/imports_delete_files_csv_runs.Rd | 2 civis-3.1.3/civis/man/imports_delete_files_runs.Rd | 2 civis-3.1.3/civis/man/imports_get.Rd | 10 civis-3.1.3/civis/man/imports_get_files_csv_runs.Rd | 4 civis-3.1.3/civis/man/imports_get_files_runs.Rd | 4 civis-3.1.3/civis/man/imports_list.Rd | 10 civis-3.1.3/civis/man/imports_list_dependencies.Rd | 3 civis-3.1.3/civis/man/imports_list_files_csv_runs.Rd | 8 civis-3.1.3/civis/man/imports_list_files_csv_runs_logs.Rd | 2 civis-3.1.3/civis/man/imports_list_files_runs.Rd | 8 civis-3.1.3/civis/man/imports_list_files_runs_logs.Rd | 2 civis-3.1.3/civis/man/imports_list_runs_logs.Rd | 2 civis-3.1.3/civis/man/imports_post.Rd | 20 civis-3.1.3/civis/man/imports_post_files_csv_runs.Rd | 4 civis-3.1.3/civis/man/imports_post_files_runs.Rd | 4 civis-3.1.3/civis/man/imports_post_syncs.Rd | 96 civis-3.1.3/civis/man/imports_put.Rd | 20 civis-3.1.3/civis/man/imports_put_archive.Rd | 10 civis-3.1.3/civis/man/imports_put_syncs.Rd | 96 civis-3.1.3/civis/man/imports_put_syncs_archive.Rd | 48 civis-3.1.3/civis/man/imports_put_transfer.Rd | 3 civis-3.1.3/civis/man/jobs_list_dependencies.Rd | 3 civis-3.1.3/civis/man/jobs_list_runs_logs.Rd | 2 civis-3.1.3/civis/man/jobs_put_transfer.Rd | 3 civis-3.1.3/civis/man/json_values_list_dependencies.Rd | 3 civis-3.1.3/civis/man/json_values_put_transfer.Rd | 3 civis-3.1.3/civis/man/media_delete_optimizations_runs.Rd | 2 civis-3.1.3/civis/man/media_get_optimizations_runs.Rd | 4 civis-3.1.3/civis/man/media_list_optimizations_runs.Rd | 8 civis-3.1.3/civis/man/media_list_optimizations_runs_logs.Rd | 2 civis-3.1.3/civis/man/media_post_optimizations_runs.Rd | 4 civis-3.1.3/civis/man/models_delete_builds.Rd | 2 civis-3.1.3/civis/man/models_get.Rd | 6 civis-3.1.3/civis/man/models_get_builds.Rd | 2 civis-3.1.3/civis/man/models_list.Rd | 2 civis-3.1.3/civis/man/models_list_builds.Rd | 6 civis-3.1.3/civis/man/models_list_builds_logs.Rd | 2 civis-3.1.3/civis/man/models_list_dependencies.Rd | 3 civis-3.1.3/civis/man/models_put_archive.Rd | 6 civis-3.1.3/civis/man/models_put_transfer.Rd | 3 civis-3.1.3/civis/man/notebooks_get.Rd | 6 civis-3.1.3/civis/man/notebooks_get_deployments.Rd | 2 civis-3.1.3/civis/man/notebooks_get_git_commits.Rd | 2 civis-3.1.3/civis/man/notebooks_list.Rd | 4 civis-3.1.3/civis/man/notebooks_list_dependencies.Rd | 3 civis-3.1.3/civis/man/notebooks_list_deployments.Rd | 2 civis-3.1.3/civis/man/notebooks_list_git.Rd | 2 civis-3.1.3/civis/man/notebooks_list_git_commits.Rd | 2 civis-3.1.3/civis/man/notebooks_patch.Rd | 10 civis-3.1.3/civis/man/notebooks_patch_git.Rd | 4 civis-3.1.3/civis/man/notebooks_post.Rd | 10 civis-3.1.3/civis/man/notebooks_post_clone.Rd | 6 civis-3.1.3/civis/man/notebooks_post_deployments.Rd | 2 civis-3.1.3/civis/man/notebooks_post_git_commits.Rd | 2 civis-3.1.3/civis/man/notebooks_put.Rd | 10 civis-3.1.3/civis/man/notebooks_put_archive.Rd | 6 civis-3.1.3/civis/man/notebooks_put_git.Rd | 4 civis-3.1.3/civis/man/notebooks_put_transfer.Rd | 3 civis-3.1.3/civis/man/organizations_delete_favorites.Rd |only civis-3.1.3/civis/man/organizations_list_favorites.Rd |only civis-3.1.3/civis/man/organizations_post_favorites.Rd |only civis-3.1.3/civis/man/permission_sets_list_dependencies.Rd | 3 civis-3.1.3/civis/man/permission_sets_put_transfer.Rd | 3 civis-3.1.3/civis/man/projects_list_dependencies.Rd | 3 civis-3.1.3/civis/man/projects_put_transfer.Rd | 3 civis-3.1.3/civis/man/queries_delete.Rd | 8 civis-3.1.3/civis/man/queries_delete_runs.Rd | 2 civis-3.1.3/civis/man/queries_get.Rd | 8 civis-3.1.3/civis/man/queries_get_runs.Rd | 4 civis-3.1.3/civis/man/queries_list.Rd | 10 civis-3.1.3/civis/man/queries_list_runs.Rd | 8 civis-3.1.3/civis/man/queries_list_runs_logs.Rd | 2 civis-3.1.3/civis/man/queries_post.Rd | 12 civis-3.1.3/civis/man/queries_post_runs.Rd | 4 civis-3.1.3/civis/man/queries_put_scripts.Rd | 8 civis-3.1.3/civis/man/query_civis.Rd | 4 civis-3.1.3/civis/man/query_civis_file.Rd | 4 civis-3.1.3/civis/man/read_civis.Rd | 6 civis-3.1.3/civis/man/reports_delete_sql_projects.Rd |only civis-3.1.3/civis/man/reports_delete_sql_shares_groups.Rd |only civis-3.1.3/civis/man/reports_delete_sql_shares_users.Rd |only civis-3.1.3/civis/man/reports_get.Rd | 19 civis-3.1.3/civis/man/reports_get_git_commits.Rd | 2 civis-3.1.3/civis/man/reports_get_services.Rd | 12 civis-3.1.3/civis/man/reports_get_sql.Rd |only civis-3.1.3/civis/man/reports_list.Rd | 10 civis-3.1.3/civis/man/reports_list_dependencies.Rd | 3 civis-3.1.3/civis/man/reports_list_git.Rd | 2 civis-3.1.3/civis/man/reports_list_git_commits.Rd | 2 civis-3.1.3/civis/man/reports_list_services_dependencies.Rd | 3 civis-3.1.3/civis/man/reports_list_sql_dependencies.Rd |only civis-3.1.3/civis/man/reports_list_sql_projects.Rd |only civis-3.1.3/civis/man/reports_list_sql_shares.Rd |only civis-3.1.3/civis/man/reports_patch.Rd | 20 civis-3.1.3/civis/man/reports_patch_git.Rd | 4 civis-3.1.3/civis/man/reports_patch_services.Rd | 8 civis-3.1.3/civis/man/reports_patch_sql.Rd |only civis-3.1.3/civis/man/reports_post.Rd | 22 civis-3.1.3/civis/man/reports_post_git_commits.Rd | 2 civis-3.1.3/civis/man/reports_post_grants.Rd | 15 civis-3.1.3/civis/man/reports_post_services.Rd | 8 civis-3.1.3/civis/man/reports_post_sql.Rd |only civis-3.1.3/civis/man/reports_post_sql_refresh.Rd |only civis-3.1.3/civis/man/reports_put_archive.Rd | 15 civis-3.1.3/civis/man/reports_put_git.Rd | 4 civis-3.1.3/civis/man/reports_put_services_archive.Rd | 8 civis-3.1.3/civis/man/reports_put_services_transfer.Rd | 3 civis-3.1.3/civis/man/reports_put_sql_archive.Rd |only civis-3.1.3/civis/man/reports_put_sql_projects.Rd |only civis-3.1.3/civis/man/reports_put_sql_shares_groups.Rd |only civis-3.1.3/civis/man/reports_put_sql_shares_users.Rd |only civis-3.1.3/civis/man/reports_put_sql_transfer.Rd |only civis-3.1.3/civis/man/reports_put_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_delete_containers_runs.Rd | 2 civis-3.1.3/civis/man/scripts_delete_custom_runs.Rd | 2 civis-3.1.3/civis/man/scripts_delete_dbt.Rd |only civis-3.1.3/civis/man/scripts_delete_dbt_projects.Rd |only civis-3.1.3/civis/man/scripts_delete_dbt_runs.Rd |only civis-3.1.3/civis/man/scripts_delete_dbt_shares_groups.Rd |only civis-3.1.3/civis/man/scripts_delete_dbt_shares_users.Rd |only civis-3.1.3/civis/man/scripts_delete_javascript_runs.Rd | 2 civis-3.1.3/civis/man/scripts_delete_python3_runs.Rd | 2 civis-3.1.3/civis/man/scripts_delete_r_runs.Rd | 2 civis-3.1.3/civis/man/scripts_delete_sql.Rd | 4 civis-3.1.3/civis/man/scripts_delete_sql_projects.Rd | 6 civis-3.1.3/civis/man/scripts_delete_sql_runs.Rd | 2 civis-3.1.3/civis/man/scripts_get.Rd | 10 civis-3.1.3/civis/man/scripts_get_containers.Rd | 6 civis-3.1.3/civis/man/scripts_get_containers_runs.Rd | 4 civis-3.1.3/civis/man/scripts_get_custom.Rd | 6 civis-3.1.3/civis/man/scripts_get_custom_runs.Rd | 4 civis-3.1.3/civis/man/scripts_get_dbt.Rd |only civis-3.1.3/civis/man/scripts_get_dbt_runs.Rd |only civis-3.1.3/civis/man/scripts_get_javascript.Rd | 8 civis-3.1.3/civis/man/scripts_get_javascript_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_get_javascript_runs.Rd | 4 civis-3.1.3/civis/man/scripts_get_python3.Rd | 10 civis-3.1.3/civis/man/scripts_get_python3_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_get_python3_runs.Rd | 4 civis-3.1.3/civis/man/scripts_get_r.Rd | 10 civis-3.1.3/civis/man/scripts_get_r_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_get_r_runs.Rd | 4 civis-3.1.3/civis/man/scripts_get_sql.Rd | 12 civis-3.1.3/civis/man/scripts_get_sql_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_get_sql_runs.Rd | 4 civis-3.1.3/civis/man/scripts_list.Rd | 4 civis-3.1.3/civis/man/scripts_list_containers_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_containers_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_containers_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_list_custom_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_custom_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_custom_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_list_dbt_dependencies.Rd |only civis-3.1.3/civis/man/scripts_list_dbt_projects.Rd |only civis-3.1.3/civis/man/scripts_list_dbt_runs.Rd |only civis-3.1.3/civis/man/scripts_list_dbt_runs_logs.Rd |only civis-3.1.3/civis/man/scripts_list_dbt_runs_outputs.Rd |only civis-3.1.3/civis/man/scripts_list_dbt_shares.Rd |only civis-3.1.3/civis/man/scripts_list_javascript_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_javascript_git.Rd | 2 civis-3.1.3/civis/man/scripts_list_javascript_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_list_javascript_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_javascript_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_list_python3_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_python3_git.Rd | 2 civis-3.1.3/civis/man/scripts_list_python3_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_list_python3_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_python3_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_list_r_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_r_git.Rd | 2 civis-3.1.3/civis/man/scripts_list_r_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_list_r_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_r_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_list_sql_dependencies.Rd | 3 civis-3.1.3/civis/man/scripts_list_sql_git.Rd | 2 civis-3.1.3/civis/man/scripts_list_sql_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_list_sql_projects.Rd | 6 civis-3.1.3/civis/man/scripts_list_sql_runs.Rd | 8 civis-3.1.3/civis/man/scripts_list_sql_runs_logs.Rd | 2 civis-3.1.3/civis/man/scripts_patch_containers.Rd | 12 civis-3.1.3/civis/man/scripts_patch_custom.Rd | 10 civis-3.1.3/civis/man/scripts_patch_dbt.Rd |only civis-3.1.3/civis/man/scripts_patch_dbt_runs.Rd |only civis-3.1.3/civis/man/scripts_patch_javascript.Rd | 14 civis-3.1.3/civis/man/scripts_patch_javascript_git.Rd | 4 civis-3.1.3/civis/man/scripts_patch_python3.Rd | 24 civis-3.1.3/civis/man/scripts_patch_python3_git.Rd | 4 civis-3.1.3/civis/man/scripts_patch_r.Rd | 24 civis-3.1.3/civis/man/scripts_patch_r_git.Rd | 4 civis-3.1.3/civis/man/scripts_patch_sql.Rd | 18 civis-3.1.3/civis/man/scripts_patch_sql_git.Rd | 4 civis-3.1.3/civis/man/scripts_post.Rd | 18 civis-3.1.3/civis/man/scripts_post_containers.Rd | 18 civis-3.1.3/civis/man/scripts_post_containers_clone.Rd | 6 civis-3.1.3/civis/man/scripts_post_containers_runs.Rd | 4 civis-3.1.3/civis/man/scripts_post_custom.Rd | 10 civis-3.1.3/civis/man/scripts_post_custom_clone.Rd | 6 civis-3.1.3/civis/man/scripts_post_custom_runs.Rd | 4 civis-3.1.3/civis/man/scripts_post_dbt.Rd |only civis-3.1.3/civis/man/scripts_post_dbt_clone.Rd |only civis-3.1.3/civis/man/scripts_post_dbt_runs.Rd |only civis-3.1.3/civis/man/scripts_post_dbt_runs_outputs.Rd |only civis-3.1.3/civis/man/scripts_post_javascript.Rd | 14 civis-3.1.3/civis/man/scripts_post_javascript_clone.Rd | 8 civis-3.1.3/civis/man/scripts_post_javascript_git_checkout.Rd | 2 civis-3.1.3/civis/man/scripts_post_javascript_git_checkout_latest.Rd | 2 civis-3.1.3/civis/man/scripts_post_javascript_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_post_javascript_runs.Rd | 4 civis-3.1.3/civis/man/scripts_post_python3.Rd | 16 civis-3.1.3/civis/man/scripts_post_python3_clone.Rd | 10 civis-3.1.3/civis/man/scripts_post_python3_git_checkout.Rd | 2 civis-3.1.3/civis/man/scripts_post_python3_git_checkout_latest.Rd | 2 civis-3.1.3/civis/man/scripts_post_python3_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_post_python3_runs.Rd | 4 civis-3.1.3/civis/man/scripts_post_r.Rd | 16 civis-3.1.3/civis/man/scripts_post_r_clone.Rd | 10 civis-3.1.3/civis/man/scripts_post_r_git_checkout.Rd | 2 civis-3.1.3/civis/man/scripts_post_r_git_checkout_latest.Rd | 2 civis-3.1.3/civis/man/scripts_post_r_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_post_r_runs.Rd | 4 civis-3.1.3/civis/man/scripts_post_run.Rd | 4 civis-3.1.3/civis/man/scripts_post_sql.Rd | 18 civis-3.1.3/civis/man/scripts_post_sql_clone.Rd | 12 civis-3.1.3/civis/man/scripts_post_sql_git_checkout.Rd | 2 civis-3.1.3/civis/man/scripts_post_sql_git_checkout_latest.Rd | 2 civis-3.1.3/civis/man/scripts_post_sql_git_commits.Rd | 2 civis-3.1.3/civis/man/scripts_post_sql_runs.Rd | 4 civis-3.1.3/civis/man/scripts_put_containers.Rd | 18 civis-3.1.3/civis/man/scripts_put_containers_archive.Rd | 6 civis-3.1.3/civis/man/scripts_put_containers_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_put_custom.Rd | 10 civis-3.1.3/civis/man/scripts_put_custom_archive.Rd | 6 civis-3.1.3/civis/man/scripts_put_custom_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_put_dbt.Rd |only civis-3.1.3/civis/man/scripts_put_dbt_archive.Rd |only civis-3.1.3/civis/man/scripts_put_dbt_projects.Rd |only civis-3.1.3/civis/man/scripts_put_dbt_shares_groups.Rd |only civis-3.1.3/civis/man/scripts_put_dbt_shares_users.Rd |only civis-3.1.3/civis/man/scripts_put_dbt_transfer.Rd |only civis-3.1.3/civis/man/scripts_put_javascript.Rd | 14 civis-3.1.3/civis/man/scripts_put_javascript_archive.Rd | 8 civis-3.1.3/civis/man/scripts_put_javascript_git.Rd | 4 civis-3.1.3/civis/man/scripts_put_javascript_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_put_python3.Rd | 16 civis-3.1.3/civis/man/scripts_put_python3_archive.Rd | 10 civis-3.1.3/civis/man/scripts_put_python3_git.Rd | 4 civis-3.1.3/civis/man/scripts_put_python3_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_put_r.Rd | 16 civis-3.1.3/civis/man/scripts_put_r_archive.Rd | 10 civis-3.1.3/civis/man/scripts_put_r_git.Rd | 4 civis-3.1.3/civis/man/scripts_put_r_transfer.Rd | 3 civis-3.1.3/civis/man/scripts_put_sql.Rd | 18 civis-3.1.3/civis/man/scripts_put_sql_archive.Rd | 8 civis-3.1.3/civis/man/scripts_put_sql_git.Rd | 4 civis-3.1.3/civis/man/scripts_put_sql_projects.Rd | 6 civis-3.1.3/civis/man/scripts_put_sql_transfer.Rd | 3 civis-3.1.3/civis/man/services_list_dependencies.Rd | 3 civis-3.1.3/civis/man/services_put_transfer.Rd | 3 civis-3.1.3/civis/man/storage_hosts_list_dependencies.Rd | 3 civis-3.1.3/civis/man/storage_hosts_put_transfer.Rd | 3 civis-3.1.3/civis/man/templates_get_scripts.Rd | 2 civis-3.1.3/civis/man/templates_list_reports_dependencies.Rd | 3 civis-3.1.3/civis/man/templates_list_scripts_dependencies.Rd | 3 civis-3.1.3/civis/man/templates_patch_scripts.Rd | 2 civis-3.1.3/civis/man/templates_post_scripts.Rd | 2 civis-3.1.3/civis/man/templates_put_reports_transfer.Rd | 3 civis-3.1.3/civis/man/templates_put_scripts.Rd | 2 civis-3.1.3/civis/man/templates_put_scripts_transfer.Rd | 3 civis-3.1.3/civis/man/usage_get_llm.Rd |only civis-3.1.3/civis/man/usage_limits_get_llm.Rd |only civis-3.1.3/civis/man/usage_limits_get_matching.Rd |only civis-3.1.3/civis/man/usage_limits_list_llm.Rd |only civis-3.1.3/civis/man/usage_limits_list_matching.Rd |only civis-3.1.3/civis/man/usage_list_llm.Rd |only civis-3.1.3/civis/man/usage_list_llm_organization_summary.Rd |only civis-3.1.3/civis/man/usage_list_matching.Rd |only civis-3.1.3/civis/man/users_list_me.Rd | 2 civis-3.1.3/civis/man/users_list_me_activity.Rd |only civis-3.1.3/civis/man/users_list_me_favorites.Rd | 9 civis-3.1.3/civis/man/users_list_me_organization_admins.Rd |only civis-3.1.3/civis/man/users_patch_me.Rd | 5 civis-3.1.3/civis/man/users_patch_me_favorites_ranking_bottom.Rd |only civis-3.1.3/civis/man/users_patch_me_favorites_ranking_higher.Rd |only civis-3.1.3/civis/man/users_patch_me_favorites_ranking_lower.Rd |only civis-3.1.3/civis/man/users_patch_me_favorites_ranking_top.Rd |only civis-3.1.3/civis/man/users_post.Rd | 2 civis-3.1.3/civis/man/users_post_access_email.Rd |only civis-3.1.3/civis/man/users_post_me_favorites.Rd | 4 civis-3.1.3/civis/man/workflows_get_git_commits.Rd | 2 civis-3.1.3/civis/man/workflows_list.Rd | 2 civis-3.1.3/civis/man/workflows_list_dependencies.Rd | 3 civis-3.1.3/civis/man/workflows_list_git.Rd | 2 civis-3.1.3/civis/man/workflows_list_git_commits.Rd | 2 civis-3.1.3/civis/man/workflows_patch_git.Rd | 4 civis-3.1.3/civis/man/workflows_post_git_checkout_latest.Rd | 2 civis-3.1.3/civis/man/workflows_post_git_commits.Rd | 2 civis-3.1.3/civis/man/workflows_put_git.Rd | 4 civis-3.1.3/civis/man/workflows_put_transfer.Rd | 3 civis-3.1.3/civis/man/write_civis.Rd | 2 civis-3.1.3/civis/man/write_civis_file.Rd | 4 civis-3.1.3/civis/tests/testthat/test_civis_future.R | 70 civis-3.1.3/civis/tests/testthat/test_civis_ml.R | 662 civis-3.1.3/civis/tests/testthat/test_civis_ml_utils.R | 63 civis-3.1.3/civis/tests/testthat/test_civis_ml_workflows.R | 162 civis-3.1.3/civis/tests/testthat/test_client_base.R | 126 civis-3.1.3/civis/tests/testthat/test_io.R | 439 civis-3.1.3/civis/tests/testthat/test_logs.R | 30 civis-3.1.3/civis/tests/testthat/test_reports.R | 74 civis-3.1.3/civis/tests/testthat/test_rstudio.R | 44 civis-3.1.3/civis/tests/testthat/test_scripts.R | 108 civis-3.1.3/civis/tests/testthat/test_tables.R | 46 civis-3.1.3/civis/tests/testthat/test_utils.R | 34 civis-3.1.3/civis/tests/testthat/utils.R | 15 civis-3.1.3/civis/tools/install-and-run-tests.R |only civis-3.1.3/civis/vignettes/civis_ml.Rmd | 2 465 files changed, 8398 insertions(+), 3815 deletions(-)
Title: Access to Canadian Election Study Data
Description: Provides tools to easily access and analyze Canadian Election Study data.
The package simplifies the process of downloading, cleaning, and using 'CES' datasets
for political science research and analysis. The Canadian Election Study ('CES')
has been conducted during federal elections since 1965, surveying Canadians
on their political preferences, engagement, and demographics. Data is accessed
from multiple sources including the 'Borealis' Data repository
<https://borealisdata.ca/> and the official 'Canadian Election Study' website
<https://ces-eec.arts.ubc.ca/>. This package is not officially affiliated
with the Canadian Election Study, 'Borealis' Data, or the University of British
Columbia, and users should cite the original data sources in their work.
Author: Laurence-Olivier M. Foisy [aut, cre]
Maintainer: Laurence-Olivier M. Foisy <mail@mfoisy.com>
Diff between ces versions 1.0.1 dated 2025-07-25 and 1.0.2 dated 2025-08-29
DESCRIPTION | 6 +- MD5 | 8 +- NEWS.md | 8 ++ R/create_codebook.R | 11 +++ tests/testthat/test-codebook.R | 117 +++++++++++++++++++++++++++++++++++++++++ 5 files changed, 142 insertions(+), 8 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.20 dated 2025-07-30 and 0.2.21 dated 2025-08-29
BayesTools-0.2.20/BayesTools/man/contr.independent.Rd |only BayesTools-0.2.20/BayesTools/man/contr.meandif.Rd |only BayesTools-0.2.20/BayesTools/man/contr.orthonormal.Rd |only BayesTools-0.2.21/BayesTools/DESCRIPTION | 6 BayesTools-0.2.21/BayesTools/MD5 | 20 +- BayesTools-0.2.21/BayesTools/NEWS.md | 5 BayesTools-0.2.21/BayesTools/R/JAGS-fit.R | 8 BayesTools-0.2.21/BayesTools/R/JAGS-formula.R | 144 ++++++++++------ BayesTools-0.2.21/BayesTools/build/partial.rdb |binary BayesTools-0.2.21/BayesTools/inst/doc/ComparisonR.html | 4 BayesTools-0.2.21/BayesTools/inst/doc/SpikeAndSlab.html | 4 BayesTools-0.2.21/BayesTools/man/JAGS_formula.Rd | 28 ++- BayesTools-0.2.21/BayesTools/man/contr.BayesTools.Rd |only 13 files changed, 142 insertions(+), 77 deletions(-)
Title: Gliding Box Lacunarity and Other Metrics for 2D Random Closed
Sets
Description: Functions for estimating the gliding box lacunarity (GBL),
covariance, and pair-correlation of a random closed set (RACS) in 2D
from a binary coverage map (e.g. presence-absence land cover maps).
Contains a number of newly-developed covariance-based estimators of
GBL (Hingee et al., 2019) <doi:10.1007/s13253-019-00351-9> and
balanced estimators, proposed by Picka (2000)
<http://www.jstor.org/stable/1428408>, for covariance, centred
covariance, and pair-correlation. Also contains methods for
estimating contagion-like properties of RACS and simulating 2D Boolean
models. Binary coverage maps are usually represented as raster images
with pixel values of TRUE, FALSE or NA, with NA representing
unobserved pixels. A demo for extracting such a binary map from a
geospatial data format is provided. Binary maps may also be
represented using polygonal sets as the foreground, however for most
computations such maps are converted into raster images. The package
is based on research [...truncated...]
Author: Kassel Liam Hingee [aut, cre]
Maintainer: Kassel Liam Hingee <kassel.hingee@gmail.com>
Diff between lacunaritycovariance versions 1.1-7 dated 2023-11-02 and 1.1-9 dated 2025-08-29
DESCRIPTION | 16 ++++++++++------ MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/contagdiscstate.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/estimate_RACS_properties.pdf |binary man/contagdiscstate.Rd | 2 +- man/lacunaritycovariance-package.Rd | 4 ++++ tests/testthat/test-rbpto.R | 5 ++--- 10 files changed, 35 insertions(+), 20 deletions(-)
More information about lacunaritycovariance at CRAN
Permanent link
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
Description: A collection of functions allowing to derive the posterior distribution of the model parameters in random-effects meta-analysis or meta-regression, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.; For more details, see also Roever C (2020) <doi:10.18637/jss.v093.i06>, or Roever C and Friede T (2022) <doi:10.1016/j.cmpb.2022.107303>.
Author: Christian Roever [aut, cre] ,
Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 3.4 dated 2024-02-15 and 3.5 dated 2025-08-29
DESCRIPTION | 13 MD5 | 30 R/bayesmeta.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Roever2020-bayesmeta.pdf |binary inst/doc/RoeverFriede2023-UsingBayesmetaForMetaRegression.pdf |binary inst/doc/bayesmeta.R | 2 inst/doc/bayesmeta.Rmd | 2 inst/doc/bayesmeta.html | 823 ++++++---- man/BucherEtAl1997.Rd | 1 man/bayesmeta-package.Rd | 4 man/bayesmeta.Rd | 15 man/convolve.Rd | 10 man/traceplot.bayesmeta.Rd | 4 vignettes/bayesmeta.Rmd | 2 16 files changed, 599 insertions(+), 309 deletions(-)
Title: Infrastructure for Running, Cycling and Swimming Data from
GPS-Enabled Tracking Devices
Description: Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Author: Ioannis Kosmidis [aut, cre] ,
Hannah Frick [aut] ,
Robin Hornak [aut]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between trackeR versions 1.6.0 dated 2024-01-11 and 1.6.1 dated 2025-08-29
DESCRIPTION | 15 ++++---- MD5 | 38 ++++++++++----------- NAMESPACE | 1 NEWS.md | 12 ++++++ R/Wprime.R | 2 - R/reading.R | 2 - R/trackeR.R | 4 +- R/trackeRdata_plot.R | 24 ++----------- R/trackeRdata_smoother.R | 2 - R/trackeRdata_zones.R | 2 - build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/TourDetrackeR.R | 2 - inst/doc/TourDetrackeR.html | 65 +++++++++++++++++++++++------------- inst/doc/trackeR.pdf |binary man/Wprime.Rd | 2 - man/read_directory.Rd | 2 - man/smoother_control.trackeRdata.Rd | 2 - man/trackeR.Rd | 19 ++++++++++ man/zones.Rd | 2 - 20 files changed, 117 insertions(+), 82 deletions(-)
Title: Factor Modeling for Radiomics Data
Description: Functions that support stable prediction and classification with radiomics data through factor-analytic modeling. For details, see Peeters et al. (2019) <doi:10.48550/arXiv.1903.11696>.
Author: Carel F.W. Peeters [cre, aut],
Caroline Ubelhor [ctb],
Kevin Kunzmann [ctb]
Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
Diff between FMradio versions 1.1.1 dated 2019-12-16 and 1.1.2 dated 2025-08-29
DESCRIPTION | 24 ++++++--- MD5 | 39 +++++++------- R/FMradio.R | 128 ++++++++++++++++++++++++------------------------- README.md | 10 +-- inst/NEWS.Rd |only man/FAsim.Rd | 2 man/FMradio-package.Rd | 2 man/RF.Rd | 2 man/SA.Rd | 2 man/SMC.Rd | 2 man/autoFMradio.Rd | 4 - man/dimGB.Rd | 2 man/dimIC.Rd | 2 man/dimLRT.Rd | 2 man/dimVAR.Rd | 2 man/facSMC.Rd | 2 man/facScore.Rd | 2 man/mlFA.Rd | 3 - man/radioHeat.Rd | 4 - man/regcor.Rd | 2 man/subSet.Rd | 2 21 files changed, 127 insertions(+), 111 deletions(-)
Title: Produce Descriptive and Comparative Tables Easily
Description: Easily create descriptive and comparative tables.
It makes use and integrates directly with the tidyverse family of packages, and pipes.
Tables are produced as (nested) dataframes for easy manipulation.
Author: Maxime Wack [aut, cre],
Adrien Boukobza [aut],
Yihui Xie [ctb]
Maintainer: Maxime Wack <maximewack@free.fr>
Diff between desctable versions 0.3.0 dated 2022-03-25 and 0.3.1 dated 2025-08-29
DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 4 R/convenience_functions.R | 8 R/deprecated.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/desctable.R | 2 inst/doc/desctable.html | 883 +++++++++++--------------------- inst/doc/desctable_deprecated.R | 8 inst/doc/desctable_deprecated.html | 979 ++++++++++++----------------------- inst/doc/tips.R | 98 +-- inst/doc/tips.html | 1009 +++++++++++++------------------------ man/chisq.test.Rd | 2 man/datatable.Rd | 16 man/fisher.test.Rd | 12 man/pander.desctable.Rd | 2 17 files changed, 1121 insertions(+), 1956 deletions(-)