Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods for
operating on such matrices, often wrapping the 'BLAS', 'LAPACK',
and 'SuiteSparse' libraries.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] ,
pattern="License", full.names=TRUE, recursive=TRUE)),
George Karypis [ctb] ,
Jason Riedy [ctb] and onenormest, Copyright: Regents of the
University of C [...truncated...]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.7-5 dated 2026-03-21 and 1.7-6 dated 2026-07-24
DESCRIPTION | 12 ++++++------ MD5 | 42 +++++++++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 25 +++++++++++++++++++++++++ inst/doc/Comparisons.R | 2 -- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.R | 2 -- inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.R | 2 -- inst/doc/Intro2Matrix.Rnw | 2 +- inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.R | 2 -- inst/doc/Introduction.pdf |binary inst/doc/sparseModels.R | 2 -- inst/doc/sparseModels.pdf |binary inst/include/Matrix/version.h | 8 ++++---- src/dense.c | 6 ++++-- src/sparse.c | 6 ++++-- src/t_subassign.c | 6 +++--- src/version.h | 4 ++-- vignettes/Intro2Matrix.Rnw | 2 +- 22 files changed, 71 insertions(+), 52 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting.
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.3 dated 2026-07-11 and 0.3.4 dated 2026-07-24
surveyframe-0.3.3/surveyframe/demo |only surveyframe-0.3.4/surveyframe/DESCRIPTION | 12 surveyframe-0.3.4/surveyframe/LICENSE | 2 surveyframe-0.3.4/surveyframe/MD5 | 157 surveyframe-0.3.4/surveyframe/NAMESPACE | 33 surveyframe-0.3.4/surveyframe/NEWS.md | 141 surveyframe-0.3.4/surveyframe/R/analysis_plan.R | 333 +- surveyframe-0.3.4/surveyframe/R/bootstrap_ci.R |only surveyframe-0.3.4/surveyframe/R/model_layer.R | 42 surveyframe-0.3.4/surveyframe/R/plots.R | 1600 +++++++++- surveyframe-0.3.4/surveyframe/R/psychometrics.R | 8 surveyframe-0.3.4/surveyframe/R/quality_report.R | 5 surveyframe-0.3.4/surveyframe/R/read_write_sframe.R | 10 surveyframe-0.3.4/surveyframe/R/render_survey.R | 4 surveyframe-0.3.4/surveyframe/R/reporting.R | 488 ++- surveyframe-0.3.4/surveyframe/R/sf_item.R | 35 surveyframe-0.3.4/surveyframe/R/statistics_reports.R | 174 + surveyframe-0.3.4/surveyframe/R/survey_module.R | 4 surveyframe-0.3.4/surveyframe/R/surveyframe-package.R | 2 surveyframe-0.3.4/surveyframe/R/utils.R | 64 surveyframe-0.3.4/surveyframe/README.md | 22 surveyframe-0.3.4/surveyframe/inst/builder/survey_builder.html | 758 +++- surveyframe-0.3.4/surveyframe/inst/doc/analysing-survey-responses.R | 4 surveyframe-0.3.4/surveyframe/inst/doc/analysing-survey-responses.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/analysing-survey-responses.html | 37 surveyframe-0.3.4/surveyframe/inst/doc/building-survey-instrument.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/building-survey-instrument.html | 13 surveyframe-0.3.4/surveyframe/inst/doc/deploying-and-collecting.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/deploying-and-collecting.html | 13 surveyframe-0.3.4/surveyframe/inst/doc/efa-cfa-sem-pls-syntax.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/efa-cfa-sem-pls-syntax.html | 13 surveyframe-0.3.4/surveyframe/inst/doc/scale-reliability-validity.Rmd | 14 surveyframe-0.3.4/surveyframe/inst/doc/scale-reliability-validity.html | 12 surveyframe-0.3.4/surveyframe/inst/doc/surveybuilder-gui-overview.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/surveybuilder-gui-overview.html | 13 surveyframe-0.3.4/surveyframe/inst/doc/surveyframe.R | 4 surveyframe-0.3.4/surveyframe/inst/doc/surveyframe.Rmd | 18 surveyframe-0.3.4/surveyframe/inst/doc/surveyframe.html | 39 surveyframe-0.3.4/surveyframe/inst/shiny/app.R | 396 ++ surveyframe-0.3.4/surveyframe/inst/shiny/dashboard/app.R | 139 surveyframe-0.3.4/surveyframe/inst/static_survey/template.html | 53 surveyframe-0.3.4/surveyframe/inst/templates/report.qmd | 144 surveyframe-0.3.4/surveyframe/man/bootstrap_ci.Rd |only surveyframe-0.3.4/surveyframe/man/cohens_d_ci.Rd |only surveyframe-0.3.4/surveyframe/man/cramers_v_ci.Rd |only surveyframe-0.3.4/surveyframe/man/efa_solution.Rd | 7 surveyframe-0.3.4/surveyframe/man/eta_sq_ci.Rd |only surveyframe-0.3.4/surveyframe/man/plot.sframe_analysis_results.Rd |only surveyframe-0.3.4/surveyframe/man/render_report.Rd | 25 surveyframe-0.3.4/surveyframe/man/render_results.Rd | 12 surveyframe-0.3.4/surveyframe/man/run_analysis_plan.Rd | 14 surveyframe-0.3.4/surveyframe/man/sf_item.Rd | 8 surveyframe-0.3.4/surveyframe/man/sframe_codebook_items_display.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_draw_likert_diverging.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_draw_mosaic.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_likert_scale_groups.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_correlation_matrix.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_descriptives.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_efa_loadings.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_efa_scree.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_group_comparison.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_item_chart.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_likert_matrix.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_likert_scale.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_missingness.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_paired_comparison.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_quality.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_regression_diagnostics.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_reliability.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_scale_chart.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_validity.Rd |only surveyframe-0.3.4/surveyframe/man/sframe_plot_variable_distribution.Rd |only surveyframe-0.3.4/surveyframe/man/surveyframe-package.Rd | 1 surveyframe-0.3.4/surveyframe/man/theme_surveyframe.Rd | 21 surveyframe-0.3.4/surveyframe/man/validity_report.Rd | 15 surveyframe-0.3.4/surveyframe/tests/testthat/test-builder-analysis.R | 8 surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-date-bounds.R |only surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-effect-cis.R |only surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-family-plots.R |only surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-interpretations.R |only surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-plots.R | 11 surveyframe-0.3.4/surveyframe/tests/testthat/test-v034-stats-reporting.R |only surveyframe-0.3.4/surveyframe/vignettes/analysing-survey-responses.Rmd | 18 surveyframe-0.3.4/surveyframe/vignettes/building-survey-instrument.Rmd | 18 surveyframe-0.3.4/surveyframe/vignettes/deploying-and-collecting.Rmd | 18 surveyframe-0.3.4/surveyframe/vignettes/efa-cfa-sem-pls-syntax.Rmd | 18 surveyframe-0.3.4/surveyframe/vignettes/scale-reliability-validity.Rmd | 14 surveyframe-0.3.4/surveyframe/vignettes/surveybuilder-gui-overview.Rmd | 18 surveyframe-0.3.4/surveyframe/vignettes/surveyframe.Rmd | 18 89 files changed, 4568 insertions(+), 572 deletions(-)
Title: Certified Partial Eigenvalue and Singular Value Computation
Description: Computes the top-k singular triplets or eigenpairs of large
sparse and structured matrices: the computation behind principal component
analysis on big sparse data, spectral embeddings, and low-rank
approximation. Every result carries a numerical certificate with
residuals, a backward-error bound, orthogonality loss, and a pass/fail
flag, and bounds that can only be estimated are reported as such rather
than passed. Centered, scaled, and composed operators are solved through
native 'C++' kernels without forming dense matrices. Drop-in replacements
for the 'RSpectra' interface are included.
Author: Bradley Buchsbaum [aut, cre, cph]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between eigencore versions 1.0.0 dated 2026-07-23 and 1.0.1 dated 2026-07-24
eigencore-1.0.0/eigencore/inst/doc/sparse-pca.R |only eigencore-1.0.0/eigencore/inst/doc/sparse-pca.Rmd |only eigencore-1.0.0/eigencore/inst/doc/sparse-pca.html |only eigencore-1.0.0/eigencore/vignettes/articles |only eigencore-1.0.0/eigencore/vignettes/sparse-pca.Rmd |only eigencore-1.0.1/eigencore/DESCRIPTION | 6 eigencore-1.0.1/eigencore/MD5 | 59 - eigencore-1.0.1/eigencore/NEWS.md | 14 eigencore-1.0.1/eigencore/R/validation.R | 5 eigencore-1.0.1/eigencore/README.md | 14 eigencore-1.0.1/eigencore/build/vignette.rds |binary eigencore-1.0.1/eigencore/inst/benchmarks/_helpers.R | 8 eigencore-1.0.1/eigencore/inst/doc/benchmarks.R |only eigencore-1.0.1/eigencore/inst/doc/benchmarks.Rmd |only eigencore-1.0.1/eigencore/inst/doc/benchmarks.html |only eigencore-1.0.1/eigencore/inst/doc/certificates.R | 6 eigencore-1.0.1/eigencore/inst/doc/certificates.Rmd | 93 +- eigencore-1.0.1/eigencore/inst/doc/certificates.html | 125 +-- eigencore-1.0.1/eigencore/inst/doc/eigencore.R | 64 + eigencore-1.0.1/eigencore/inst/doc/eigencore.Rmd | 213 +++-- eigencore-1.0.1/eigencore/inst/doc/eigencore.html | 373 +++++----- eigencore-1.0.1/eigencore/inst/doc/generalized-eigenproblems.R | 45 - eigencore-1.0.1/eigencore/inst/doc/generalized-eigenproblems.Rmd | 79 -- eigencore-1.0.1/eigencore/inst/doc/generalized-eigenproblems.html | 54 - eigencore-1.0.1/eigencore/man/eigencore-package.Rd | 9 eigencore-1.0.1/eigencore/tests/testthat/test-bench-smoke.R | 58 - eigencore-1.0.1/eigencore/vignettes/benchmarks.Rmd |only eigencore-1.0.1/eigencore/vignettes/certificates.Rmd | 93 +- eigencore-1.0.1/eigencore/vignettes/eigencore.Rmd | 213 +++-- eigencore-1.0.1/eigencore/vignettes/generalized-eigenproblems.Rmd | 79 -- 30 files changed, 744 insertions(+), 866 deletions(-)
Title: Tool-Box of Chain Ladder Plus Models
Description: Implementation of the age-period-cohort models for the claim development presented in the manuscript 'Replicating and extending chain-ladder via an age-period-cohort structure on the claim development in a run-off triangle' <doi:10.1080/10920277.2025.2496725>.
Author: Gabriele Pittarello [aut, cre, cph] ,
Munir Hiabu [aut, cph] ,
Andres Villegas [aut, cph]
Maintainer: Gabriele Pittarello <gabriele.pittarello@sund.ku.dk>
Diff between clmplus versions 1.0.1 dated 2025-07-31 and 1.1.0 dated 2026-07-24
clmplus-1.0.1/clmplus/R/globalVariables.R |only clmplus-1.0.1/clmplus/R/properties.R |only clmplus-1.0.1/clmplus/data/amases.gtpl.R |only clmplus-1.0.1/clmplus/data/amases.gtpl.RDa |only clmplus-1.0.1/clmplus/data/amases.mod.R |only clmplus-1.0.1/clmplus/data/amases.mod.RDa |only clmplus-1.0.1/clmplus/data/amases.mtpl.R |only clmplus-1.0.1/clmplus/data/amases.mtpl.RDa |only clmplus-1.0.1/clmplus/data/amasesgtpl.RDa |only clmplus-1.0.1/clmplus/data/amasesmod.RDa |only clmplus-1.0.1/clmplus/data/amasesmtpl.RDa |only clmplus-1.0.1/clmplus/data/sifa.gtpl.R |only clmplus-1.0.1/clmplus/data/sifa.gtpl.RDa |only clmplus-1.0.1/clmplus/data/sifa.mod.R |only clmplus-1.0.1/clmplus/data/sifa.mod.RDa |only clmplus-1.0.1/clmplus/data/sifa.mtpl.R |only clmplus-1.0.1/clmplus/data/sifa.mtpl.RDa |only clmplus-1.0.1/clmplus/data/sifagtpl.RDa |only clmplus-1.0.1/clmplus/data/sifamod.RDa |only clmplus-1.0.1/clmplus/data/sifamtpl.RDa |only clmplus-1.0.1/clmplus/man/clmplus.AggregateDataPP.Rd |only clmplus-1.0.1/clmplus/man/clmplus.default.Rd |only clmplus-1.1.0/clmplus/DESCRIPTION | 18 clmplus-1.1.0/clmplus/MD5 | 105 - clmplus-1.1.0/clmplus/R/AggregateDataPP.R | 59 clmplus-1.1.0/clmplus/R/clmplusAggregateDataPP.R | 449 ++----- clmplus-1.1.0/clmplus/R/data.R | 30 clmplus-1.1.0/clmplus/R/fitted-effects.R |only clmplus-1.1.0/clmplus/R/forecasting.R |only clmplus-1.1.0/clmplus/R/model-definitions.R |only clmplus-1.1.0/clmplus/R/plotAggregateDataPP.R | 11 clmplus-1.1.0/clmplus/R/plotclmplusmodel.R | 60 clmplus-1.1.0/clmplus/R/plotclmpluspredictions.R | 47 clmplus-1.1.0/clmplus/R/predictclmplusmodel.R | 148 -- clmplus-1.1.0/clmplus/R/triangle-transformations.R |only clmplus-1.1.0/clmplus/R/validation.R |only clmplus-1.1.0/clmplus/README.md | 1 clmplus-1.1.0/clmplus/build/vignette.rds |binary clmplus-1.1.0/clmplus/data/amases.gtpl.rda |only clmplus-1.1.0/clmplus/data/amases.mod.rda |only clmplus-1.1.0/clmplus/data/amases.mtpl.rda |only clmplus-1.1.0/clmplus/data/sifa.gtpl.rda |only clmplus-1.1.0/clmplus/data/sifa.mod.rda |only clmplus-1.1.0/clmplus/data/sifa.mtpl.rda |only clmplus-1.1.0/clmplus/inst/doc/casestudy1.R | 38 clmplus-1.1.0/clmplus/inst/doc/casestudy1.Rmd | 632 +++++----- clmplus-1.1.0/clmplus/inst/doc/casestudy1.html | 197 +-- clmplus-1.1.0/clmplus/inst/doc/modelscomparison.R | 1004 ---------------- clmplus-1.1.0/clmplus/inst/doc/modelscomparison.Rmd | 1147 +------------------ clmplus-1.1.0/clmplus/inst/doc/modelscomparison.html | 815 +------------ clmplus-1.1.0/clmplus/inst/references.bib | 8 clmplus-1.1.0/clmplus/man/AggregateDataPP.Rd | 42 clmplus-1.1.0/clmplus/man/amases.gtpl.Rd | 5 clmplus-1.1.0/clmplus/man/amases.mod.Rd | 5 clmplus-1.1.0/clmplus/man/amases.mtpl.Rd | 5 clmplus-1.1.0/clmplus/man/clmplus.Rd | 159 +- clmplus-1.1.0/clmplus/man/plot.AggregateDataPP.Rd | 7 clmplus-1.1.0/clmplus/man/plot.clmplusmodel.Rd | 10 clmplus-1.1.0/clmplus/man/plot.clmpluspredictions.Rd | 11 clmplus-1.1.0/clmplus/man/predict.clmplusmodel.Rd | 3 clmplus-1.1.0/clmplus/man/sifa.gtpl.Rd | 5 clmplus-1.1.0/clmplus/man/sifa.mod.Rd | 5 clmplus-1.1.0/clmplus/man/sifa.mtpl.Rd | 5 clmplus-1.1.0/clmplus/tests |only clmplus-1.1.0/clmplus/vignettes/casestudy1.Rmd | 632 +++++----- clmplus-1.1.0/clmplus/vignettes/modelscomparison.Rmd | 1147 +------------------ 66 files changed, 1486 insertions(+), 5324 deletions(-)
Title: Methods for Cross-Cultural Psychology
Description: Combines multiple functions that automate and simplify methods
commonly employed in cross-cultural psychology, providing a unified
analysis approach for measurement invariance testing, effect sizes for
differential item functioning, factor congruence and multi-group
reliability. Methods follow Fischer and Karl (2019)
<doi:10.3389/fpsyg.2019.01507> and Gunn, Grimm and Edwards (2020)
<doi:10.1080/10705511.2019.1689507>.
Author: Johannes Karl [aut, cre]
Maintainer: Johannes Karl <johannes.a.karl@gmail.com>
Diff between ccpsyc versions 0.2.6 dated 2022-05-11 and 0.2.8 dated 2026-07-24
ccpsyc-0.2.6/ccpsyc/data/example.csv |only ccpsyc-0.2.6/ccpsyc/man/MNCI.Rd |only ccpsyc-0.2.6/ccpsyc/man/gamma_hat_scaled.Rd |only ccpsyc-0.2.8/ccpsyc/DESCRIPTION | 24 ccpsyc-0.2.8/ccpsyc/MD5 | 56 - ccpsyc-0.2.8/ccpsyc/NAMESPACE | 2 ccpsyc-0.2.8/ccpsyc/NEWS.md |only ccpsyc-0.2.8/ccpsyc/R/MNCI.R | 40 - ccpsyc-0.2.8/ccpsyc/R/Pooled.R | 6 ccpsyc-0.2.8/ccpsyc/R/bonferroni_chi.R | 153 ++-- ccpsyc-0.2.8/ccpsyc/R/boot_inv_eff.R | 96 +-- ccpsyc-0.2.8/ccpsyc/R/cfa_equivalence.R | 258 ++++---- ccpsyc-0.2.8/ccpsyc/R/dmacs.R | 209 +++--- ccpsyc-0.2.8/ccpsyc/R/dmacs_multi.R | 102 +-- ccpsyc-0.2.8/ccpsyc/R/example_data.R | 44 - ccpsyc-0.2.8/ccpsyc/R/fa_clean.R | 173 ++--- ccpsyc-0.2.8/ccpsyc/R/format_boot_inv.R | 64 +- ccpsyc-0.2.8/ccpsyc/R/gamma_hat.R | 37 - ccpsyc-0.2.8/ccpsyc/R/inv_effects.R | 432 +++++++------- ccpsyc-0.2.8/ccpsyc/R/invariance_eff_new.R |only ccpsyc-0.2.8/ccpsyc/R/lavaan_helper.R | 118 +-- ccpsyc-0.2.8/ccpsyc/R/mg_rel_table.R | 182 +++-- ccpsyc-0.2.8/ccpsyc/R/procrustes.R | 94 +-- ccpsyc-0.2.8/ccpsyc/R/scale_reliability.R |only ccpsyc-0.2.8/ccpsyc/R/split_group.R | 7 ccpsyc-0.2.8/ccpsyc/R/utils-pipe.R | 28 ccpsyc-0.2.8/ccpsyc/man/calculate_dif_indices.Rd |only ccpsyc-0.2.8/ccpsyc/man/dMACS.Rd | 7 ccpsyc-0.2.8/ccpsyc/man/mg_rel_table.Rd | 35 + ccpsyc-0.2.8/ccpsyc/tests/testthat/test-boot_inv_eff.R | 10 ccpsyc-0.2.8/ccpsyc/tests/testthat/test-cfa_equivalence.R | 10 ccpsyc-0.2.8/ccpsyc/tests/testthat/test-dmacs_multi.R | 10 ccpsyc-0.2.8/ccpsyc/tests/testthat/test-mg_rel_table.R |only 33 files changed, 1143 insertions(+), 1054 deletions(-)
Title: Robust Effect Size Index (RESI) Estimation
Description: Summarize model output using a robust effect size index. The index is introduced in Vandekar, Tao, & Blume (2020, <doi:10.1007/s11336-020-09698-2>). Software paper available at <doi:10.18637/jss.v112.i03>.
Author: Megan Jones [aut],
Kaidi Kang [aut],
Simon Vandekar [aut, cre],
Gina Yu [ctb],
Xinyu Zhang [ctb]
Maintainer: Simon Vandekar <simon.vandekar@vumc.org>
Diff between RESI versions 1.3.2 dated 2025-07-29 and 1.4.2 dated 2026-07-24
RESI-1.3.2/RESI/build |only RESI-1.3.2/RESI/inst/doc |only RESI-1.3.2/RESI/vignettes |only RESI-1.4.2/RESI/DESCRIPTION | 29 RESI-1.4.2/RESI/MD5 | 113 RESI-1.4.2/RESI/NAMESPACE | 224 - RESI-1.4.2/RESI/NEWS.md | 127 RESI-1.4.2/RESI/R/Anova.resi.R | 264 + RESI-1.4.2/RESI/R/Rsq2S.R | 56 RESI-1.4.2/RESI/R/S2Rsq.R | 52 RESI-1.4.2/RESI/R/S2chisq.R | 72 RESI-1.4.2/RESI/R/S2d.R | 80 RESI-1.4.2/RESI/R/S2fsq.R | 52 RESI-1.4.2/RESI/R/S2z.R | 94 RESI-1.4.2/RESI/R/chisq2S.R | 70 RESI-1.4.2/RESI/R/d2S.R | 62 RESI-1.4.2/RESI/R/data.R | 70 RESI-1.4.2/RESI/R/f2S.R | 74 RESI-1.4.2/RESI/R/fsq2S.R | 40 RESI-1.4.2/RESI/R/ggplot.R | 325 +- RESI-1.4.2/RESI/R/internal_functions.R | 194 - RESI-1.4.2/RESI/R/omnibus.R | 116 RESI-1.4.2/RESI/R/plot.R | 385 +- RESI-1.4.2/RESI/R/print.R | 150 RESI-1.4.2/RESI/R/resi.R | 1424 ++++----- RESI-1.4.2/RESI/R/resi_asymptotic.R |only RESI-1.4.2/RESI/R/resi_pe.R | 1874 ++++++----- RESI-1.4.2/RESI/R/simulations.R |only RESI-1.4.2/RESI/R/summary.resi.R | 148 RESI-1.4.2/RESI/R/t2S.R | 98 RESI-1.4.2/RESI/R/z2S.R | 92 RESI-1.4.2/RESI/README.md | 112 RESI-1.4.2/RESI/inst/CITATION | 34 RESI-1.4.2/RESI/man/Rsq2S.Rd | 56 RESI-1.4.2/RESI/man/S2Rsq.Rd | 74 RESI-1.4.2/RESI/man/S2d.Rd | 98 RESI-1.4.2/RESI/man/S2fsq.Rd | 74 RESI-1.4.2/RESI/man/anova.resi.Rd | 68 RESI-1.4.2/RESI/man/chisq2S.Rd | 88 RESI-1.4.2/RESI/man/d2S.Rd | 80 RESI-1.4.2/RESI/man/f2S.Rd | 90 RESI-1.4.2/RESI/man/fsq2S.Rd | 56 RESI-1.4.2/RESI/man/ggplot.resi.Rd | 72 RESI-1.4.2/RESI/man/insurance.Rd | 2 RESI-1.4.2/RESI/man/insurancePlasmodeSim.Rd |only RESI-1.4.2/RESI/man/omnibus.Rd | 68 RESI-1.4.2/RESI/man/plot.resi.Rd | 108 RESI-1.4.2/RESI/man/resi.Rd | 940 +++-- RESI-1.4.2/RESI/man/resi_pe.Rd | 651 ++-- RESI-1.4.2/RESI/man/resi_pe_asymptotic.Rd |only RESI-1.4.2/RESI/man/simCalibrationFigures.Rd |only RESI-1.4.2/RESI/man/simCalibrationSim.Rd |only RESI-1.4.2/RESI/man/simCompareMethodsFigures.Rd |only RESI-1.4.2/RESI/man/simEstimatorFigures.Rd |only RESI-1.4.2/RESI/man/simFigures.Rd |only RESI-1.4.2/RESI/man/simRecomputeSummary.Rd |only RESI-1.4.2/RESI/man/summary.resi.Rd | 68 RESI-1.4.2/RESI/man/t2S.Rd | 112 RESI-1.4.2/RESI/man/z2S.Rd | 108 RESI-1.4.2/RESI/tests/testthat/test-resi.R | 1082 +++--- RESI-1.4.2/RESI/tests/testthat/test-resi_asymptotic.R |only RESI-1.4.2/RESI/tests/testthat/testdata/depression.csv | 2042 ++++++------ RESI-1.4.2/RESI/tests/testthat/testdata/insurance.csv | 2678 ++++++++--------- 63 files changed, 7874 insertions(+), 7172 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
This is a re-admission after prior archival of version 2.1.1 dated 2026-05-13
Diff between LaMa versions 2.1.1 dated 2026-05-13 and 2.1.2 dated 2026-07-24
LaMa-2.1.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_f12d9a0927ff80dc12518220e5dc26b2.RData |only LaMa-2.1.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_f12d9a0927ff80dc12518220e5dc26b2.rdb |only LaMa-2.1.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_f12d9a0927ff80dc12518220e5dc26b2.rdx |only LaMa-2.1.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_315a5c90bf429aeaec847ee3b73d4a41.RData |only LaMa-2.1.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_315a5c90bf429aeaec847ee3b73d4a41.rdb |only LaMa-2.1.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_315a5c90bf429aeaec847ee3b73d4a41.rdx |only LaMa-2.1.1/LaMa/vignettes/State_space_models_cache/html/model_d966e404cd90247d0ce1b33c96833702.RData |only LaMa-2.1.1/LaMa/vignettes/State_space_models_cache/html/model_d966e404cd90247d0ce1b33c96833702.rdb |only LaMa-2.1.1/LaMa/vignettes/State_space_models_cache/html/model_d966e404cd90247d0ce1b33c96833702.rdx |only LaMa-2.1.2/LaMa/DESCRIPTION | 8 LaMa-2.1.2/LaMa/MD5 | 145 +- LaMa-2.1.2/LaMa/NEWS.md | 24 LaMa-2.1.2/LaMa/R/decoding_functions.R | 6 LaMa-2.1.2/LaMa/R/distribution_functions.R | 19 LaMa-2.1.2/LaMa/R/forward_algorithms.R | 22 LaMa-2.1.2/LaMa/R/mcreport.R | 8 LaMa-2.1.2/LaMa/R/qreml_functions.R | 54 LaMa-2.1.2/LaMa/R/residual_functions.R | 12 LaMa-2.1.2/LaMa/R/stationary_functions.R | 7 LaMa-2.1.2/LaMa/README.md | 24 LaMa-2.1.2/LaMa/build/vignette.rds |binary LaMa-2.1.2/LaMa/inst/doc/Continuous_time_HMMs.R | 248 ++-- LaMa-2.1.2/LaMa/inst/doc/Continuous_time_HMMs.Rmd | 339 +++-- LaMa-2.1.2/LaMa/inst/doc/Continuous_time_HMMs.html | 515 +++++--- LaMa-2.1.2/LaMa/inst/doc/Extensions.R | 35 LaMa-2.1.2/LaMa/inst/doc/Extensions.Rmd | 35 LaMa-2.1.2/LaMa/inst/doc/Extensions.html | 81 - LaMa-2.1.2/LaMa/inst/doc/HSMMs.R | 2 LaMa-2.1.2/LaMa/inst/doc/HSMMs.Rmd | 2 LaMa-2.1.2/LaMa/inst/doc/HSMMs.html | 4 LaMa-2.1.2/LaMa/inst/doc/Intro_to_LaMa.R | 2 LaMa-2.1.2/LaMa/inst/doc/Intro_to_LaMa.Rmd | 2 LaMa-2.1.2/LaMa/inst/doc/Intro_to_LaMa.html | 10 LaMa-2.1.2/LaMa/inst/doc/LaMa_and_RTMB.R | 4 LaMa-2.1.2/LaMa/inst/doc/LaMa_and_RTMB.Rmd | 6 LaMa-2.1.2/LaMa/inst/doc/LaMa_and_RTMB.html | 9 LaMa-2.1.2/LaMa/inst/doc/Longitudinal_data.R | 263 +++- LaMa-2.1.2/LaMa/inst/doc/Longitudinal_data.Rmd | 334 +++-- LaMa-2.1.2/LaMa/inst/doc/Longitudinal_data.html | 500 +++++--- LaMa-2.1.2/LaMa/inst/doc/MMMPPs.R | 290 ++-- LaMa-2.1.2/LaMa/inst/doc/MMMPPs.Rmd | 394 ++++-- LaMa-2.1.2/LaMa/inst/doc/MMMPPs.html | 593 +++++----- LaMa-2.1.2/LaMa/inst/doc/Penalised_splines.R | 69 - LaMa-2.1.2/LaMa/inst/doc/Penalised_splines.Rmd | 88 - LaMa-2.1.2/LaMa/inst/doc/Penalised_splines.html | 185 +-- LaMa-2.1.2/LaMa/inst/doc/State_space_models.R | 136 +- LaMa-2.1.2/LaMa/inst/doc/State_space_models.Rmd | 184 ++- LaMa-2.1.2/LaMa/inst/doc/State_space_models.html | 264 +++- LaMa-2.1.2/LaMa/man/MCreport.Rd | 8 LaMa-2.1.2/LaMa/man/ddwell.Rd | 6 LaMa-2.1.2/LaMa/man/forward.Rd | 9 LaMa-2.1.2/LaMa/man/forward_g.Rd | 9 LaMa-2.1.2/LaMa/man/penalty.Rd | 4 LaMa-2.1.2/LaMa/man/penalty2.Rd | 4 LaMa-2.1.2/LaMa/man/plot.LaMaResiduals.Rd | 6 LaMa-2.1.2/LaMa/man/pseudo_res.Rd | 6 LaMa-2.1.2/LaMa/man/qreml.Rd | 6 LaMa-2.1.2/LaMa/man/skewnorm.Rd | 8 LaMa-2.1.2/LaMa/man/stateprobs.Rd | 2 LaMa-2.1.2/LaMa/man/stateprobs_g.Rd | 2 LaMa-2.1.2/LaMa/man/stateprobs_p.Rd | 2 LaMa-2.1.2/LaMa/man/stationary_p.Rd | 6 LaMa-2.1.2/LaMa/vignettes/Continuous_time_HMMs.Rmd | 339 +++-- LaMa-2.1.2/LaMa/vignettes/Extensions.Rmd | 35 LaMa-2.1.2/LaMa/vignettes/HSMMs.Rmd | 2 LaMa-2.1.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_ecb54e6e7a46fa9dbc9b42b1ae94389f.RData |only LaMa-2.1.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_ecb54e6e7a46fa9dbc9b42b1ae94389f.rdb |only LaMa-2.1.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_ecb54e6e7a46fa9dbc9b42b1ae94389f.rdx |only LaMa-2.1.2/LaMa/vignettes/Intro_to_LaMa.Rmd | 2 LaMa-2.1.2/LaMa/vignettes/LaMa_and_RTMB.Rmd | 6 LaMa-2.1.2/LaMa/vignettes/Longitudinal_data.Rmd | 334 +++-- LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_49b8684dd756cc4b031ea799937c0f64.RData |only LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_49b8684dd756cc4b031ea799937c0f64.rdb |only LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_49b8684dd756cc4b031ea799937c0f64.rdx |only LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_re_ff9ca52db6513f7097251422e488f4e7.RData |only LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_re_ff9ca52db6513f7097251422e488f4e7.rdb |only LaMa-2.1.2/LaMa/vignettes/Longitudinal_data_cache/html/model_re_ff9ca52db6513f7097251422e488f4e7.rdx |only LaMa-2.1.2/LaMa/vignettes/MMMPPs.Rmd | 394 ++++-- LaMa-2.1.2/LaMa/vignettes/Penalised_splines.Rmd | 88 - LaMa-2.1.2/LaMa/vignettes/State_space_models.Rmd | 184 ++- LaMa-2.1.2/LaMa/vignettes/State_space_models_cache/html/__packages | 3 LaMa-2.1.2/LaMa/vignettes/State_space_models_cache/html/model_4f71a2d0074fb83858b7041cc6b8168f.RData |only LaMa-2.1.2/LaMa/vignettes/State_space_models_cache/html/model_4f71a2d0074fb83858b7041cc6b8168f.rdb |only LaMa-2.1.2/LaMa/vignettes/State_space_models_cache/html/model_4f71a2d0074fb83858b7041cc6b8168f.rdx |only 84 files changed, 4068 insertions(+), 2320 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download datasets of German elections
covering local, state, federal, mayoral, European Parliament, and county
(Kreistag) elections, with federal county-level coverage from 1953 and
other families extending through 2025. The package supplies turnout, vote
shares, and derived indicators at the municipal and county level, including
geographically harmonized datasets that account for changes in municipal
boundaries over time and incorporate mail-in voting districts. Bundled data
includes county-level INKAR covariates (1995-2022) and municipality-level
Zensus 2022 indicators. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.7.1 dated 2026-07-15 and 0.8.0 dated 2026-07-24
DESCRIPTION | 6 MD5 | 55 +-- NAMESPACE | 1 NEWS.md | 27 + R/gerda_catalog.R | 16 R/gerda_census.R | 77 ++++ R/gerda_covariates.R | 98 +++++ R/gerda_join.R |only R/load_gerda_web.R | 26 - R/sysdata.rda |binary README.md | 73 +++- build/vignette.rds |binary inst/doc/agent-workflow.R |only inst/doc/agent-workflow.Rmd |only inst/doc/agent-workflow.html |only inst/doc/gerda.R | 50 ++ inst/doc/gerda.Rmd | 125 +++++-- inst/doc/gerda.html | 472 +++++++++++++++++---------- man/add_gerda_census.Rd | 21 + man/add_gerda_covariates.Rd | 23 + man/gerda_census.Rd | 8 man/gerda_join_diagnostics.Rd |only tests/README.md | 94 +---- tests/testthat/test-gerda_catalog.R | 2 tests/testthat/test-gerda_census.R | 18 - tests/testthat/test-gerda_covariates.R | 2 tests/testthat/test-gerda_data_list.R | 6 tests/testthat/test-gerda_join.R |only tests/testthat/test-load_gerda_web-catalog.R | 3 tests/testthat/test-load_gerda_web-schema.R | 22 - vignettes/agent-workflow.Rmd |only vignettes/gerda.Rmd | 125 +++++-- 32 files changed, 961 insertions(+), 389 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines is now augmented with splines
of degree 1 to 4. Constraints for degrees 3 (monotone) and 4
(monotone and convex) use the Karlin-Studden SOCP characterization
for the sign of the polynomial, while other constraints applied
at the knots are added as linear problems. The method for cubic
splines is described in Abbes (2026) <doi:10.5281/zenodo.17427913>.
Other formulations are simple consequences of the other given
references. This R implementation is intended for demonstration
and prototyping. All B-spline and polynomial functions have been
rewritten for consistency. An equivalent Python package is available
at <https://pypi.org/project/BsplineQuantRegpy/>.
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.2.0 dated 2026-07-21 and 0.2.1 dated 2026-07-24
BsplineQuantReg-0.2.0/BsplineQuantReg/R/test_bsqr.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/test_karlin_simple.Rd |only BsplineQuantReg-0.2.1/BsplineQuantReg/DESCRIPTION | 10 BsplineQuantReg-0.2.1/BsplineQuantReg/MD5 | 49 +- BsplineQuantReg-0.2.1/BsplineQuantReg/NAMESPACE | 2 BsplineQuantReg-0.2.1/BsplineQuantReg/NEWS | 21 BsplineQuantReg-0.2.1/BsplineQuantReg/R/bspline-eval.R | 212 ++++++---- BsplineQuantReg-0.2.1/BsplineQuantReg/R/cubic-regression.R | 140 ++++-- BsplineQuantReg-0.2.1/BsplineQuantReg/R/deriv-coeffs.R | 19 BsplineQuantReg-0.2.1/BsplineQuantReg/R/linear-regression.R | 37 - BsplineQuantReg-0.2.1/BsplineQuantReg/R/quadratic-regression.R | 46 +- BsplineQuantReg-0.2.1/BsplineQuantReg/R/quantile-regression.R | 5 BsplineQuantReg-0.2.1/BsplineQuantReg/R/quartic-regression.R | 35 - BsplineQuantReg-0.2.1/BsplineQuantReg/demo/comprehensive.R | 15 BsplineQuantReg-0.2.1/BsplineQuantReg/man/SplineConstQuantRegBs1.Rd | 2 BsplineQuantReg-0.2.1/BsplineQuantReg/man/SplineConstQuantRegBs2.Rd | 10 BsplineQuantReg-0.2.1/BsplineQuantReg/man/SplineLinearQuant.Rd | 2 BsplineQuantReg-0.2.1/BsplineQuantReg/man/SplineQuadraticQuant.Rd | 10 BsplineQuantReg-0.2.1/BsplineQuantReg/man/SplineQuarticQuant.Rd | 2 BsplineQuantReg-0.2.1/BsplineQuantReg/man/bs_direct.Rd | 4 BsplineQuantReg-0.2.1/BsplineQuantReg/man/bspline_to_deriv_coeffs_cubic.Rd | 7 BsplineQuantReg-0.2.1/BsplineQuantReg/man/bspline_to_deriv_coeffs_lin.Rd | 5 BsplineQuantReg-0.2.1/BsplineQuantReg/man/evalpp.Rd | 4 BsplineQuantReg-0.2.1/BsplineQuantReg/man/get_parameters.Rd |only BsplineQuantReg-0.2.1/BsplineQuantReg/man/make_spline.Rd | 21 BsplineQuantReg-0.2.1/BsplineQuantReg/man/quantile_spline.Rd | 4 BsplineQuantReg-0.2.1/BsplineQuantReg/man/spline_eval.Rd | 5 27 files changed, 439 insertions(+), 228 deletions(-)
More information about BsplineQuantReg at CRAN
Permanent link
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre] ,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between baRulho versions 2.1.6 dated 2025-10-24 and 2.1.7 dated 2026-07-24
DESCRIPTION | 8 MD5 | 124 +- NEWS.md | 9 R/add_noise.R | 26 R/align_test_files.R | 23 R/attenuation.R | 22 R/auto_realign.R | 24 R/blur_ratio.R | 26 R/detection_distance.R | 32 R/envelope_correlation.R | 24 R/excess_attenuation.R | 23 R/find_markers.R | 24 R/internal_functions.R | 33 R/manual_realign.R | 36 R/master_sound_file.R | 490 +++++----- R/noise_profile.R | 43 R/plot_aligned_sounds.R | 39 R/plot_blur_ratio.R | 35 R/plot_degradation.R | 31 R/set_reference_sounds.R | 22 R/signal_to_noise_ratio.R | 30 R/spcc.R | 24 R/spectrum_blur_ratio.R | 31 R/spectrum_correlation.R | 28 R/spot_ambient_noise.R | 25 R/synth_sounds.R | 30 R/tail_to_signal_ratio.R | 25 README.md | 7 build/vignette.rds |binary data/master_est.rda |binary data/test_sounds_est.rda |binary inst/doc/align_test_sounds.R | 3 inst/doc/align_test_sounds.Rmd | 6 inst/doc/align_test_sounds.html | 109 +- inst/doc/quantify_degradation.R | 4 inst/doc/quantify_degradation.Rmd | 7 inst/doc/quantify_degradation.html | 1787 ++++++++++++++++++------------------- man/add_noise.Rd | 6 man/align_test_files.Rd | 10 man/attenuation.Rd | 6 man/auto_realign.Rd | 10 man/blur_ratio.Rd | 22 man/detection_distance.Rd | 22 man/envelope_correlation.Rd | 22 man/find_markers.Rd | 12 man/manual_realign.Rd | 10 man/master_est.Rd | 2 man/master_sound_file.Rd | 6 man/noise_profile.Rd | 6 man/plot_aligned_sounds.Rd | 10 man/plot_blur_ratio.Rd | 22 man/plot_degradation.Rd | 22 man/set_reference_sounds.Rd | 22 man/signal_to_noise_ratio.Rd | 22 man/spcc.Rd | 22 man/spectrum_blur_ratio.Rd | 27 man/spectrum_correlation.Rd | 22 man/spot_ambient_noise.Rd | 6 man/synth_sounds.Rd | 6 man/tail_to_signal_ratio.Rd | 22 man/test_sounds_est.Rd | 2 vignettes/align_test_sounds.Rmd | 6 vignettes/quantify_degradation.Rmd | 7 63 files changed, 1872 insertions(+), 1690 deletions(-)
Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a
correlation matrix using 'ggplot2'. It provides a solution for
reordering the correlation matrix and displays the significance level
on the plot. It also includes a function for computing a matrix of
correlation p-values.
Author: Alboukadel Kassambara [aut, cre],
Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggcorrplot versions 0.2.0 dated 2026-07-08 and 0.3.0 dated 2026-07-24
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Title: Spatiotemporal Mixture Risk Assessment
Description: Connecting spatiotemporal exposure to individual and
population-level risk via source-to-outcome continuum modeling. The
package, methods, and case-studies are described in Messier, Reif, and
Marvel (2025) <doi:10.1186/s40246-024-00711-8> and Eccles et al.
(2023) <doi:10.1016/j.scitotenv.2022.158905>.
Author: Skylar Marvel [aut, cre] ,
David Reif [aut] ,
Kyle Messier [aut] ,
Spatiotemporal Exposures and Toxicology Group [cph]
Maintainer: Skylar Marvel <skylar.marvel@nih.gov>
Diff between GeoTox versions 1.0.0 dated 2026-05-19 and 1.0.1 dated 2026-07-24
DESCRIPTION | 6 ++-- MD5 | 43 ++++++++++++++--------------- NEWS.md | 9 ++++++ R/GeoTox.R | 9 ++---- README.md | 4 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/package_data.html | 2 - man/GeoTox.Rd | 4 +- man/calc_sensitivity.Rd | 1 man/get_risk_values.Rd | 1 man/sensitivity_analysis.Rd | 1 tests/testthat/setup.R |only tests/testthat/test-GeoTox-package.R | 2 - tests/testthat/test-calc_sensitivity.R | 4 +- tests/testthat/test-sample_simulated_css.R | 4 +- tests/testthat/test-sensitivity_analysis.R | 2 - tests/testthat/test-set_sample.R | 2 - tests/testthat/test-set_simulated_css.R | 4 +- tests/testthat/test-simulate_age.R | 4 +- tests/testthat/test-simulate_exposure.R | 14 ++++----- tests/testthat/test-simulate_obesity.R | 4 +- tests/testthat/test-simulate_population.R | 4 +- 23 files changed, 70 insertions(+), 54 deletions(-)
Title: Flexible Time-to-Event Figures
Description: Ease the creation of time-to-event (i.e. survival) endpoint
figures. The modular functions create figures ready for publication.
Each of the functions that add to or modify the figure are written as
proper 'ggplot2' geoms or stat methods, allowing the functions from
this package to be combined with any function or customization from
'ggplot2' and other 'ggplot2' extension packages.
Author: Daniel D. Sjoberg [aut, cre, cph] ,
Shreya Sreeram [aut],
Mark Baillie [aut],
Charlotta Fruechtenicht [aut] ,
Steven Haesendonckx [aut] ,
Tim Treis [aut]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between ggsurvfit versions 1.2.0 dated 2025-09-13 and 1.2.1 dated 2026-07-24
DESCRIPTION | 12 LICENSE | 4 MD5 | 432 +-- NAMESPACE | 114 NEWS.md | 8 R/Surv_CNSR.R | 165 - R/add_censor_mark.R | 160 - R/add_confidence_interval.R | 188 - R/add_legend_title.R | 146 - R/add_pvalue.R | 21 R/add_quantile.R | 533 ++- R/add_risktable.R | 338 +- R/add_risktable_strata_symbol.R | 216 - R/data.R | 156 - R/format_p.R | 140 - R/ggcuminc.R | 176 - R/ggsurvfit-package.R | 34 R/ggsurvfit.R | 516 +-- R/ggsurvfit_align_plots.R | 220 - R/ggsurvfit_build.R | 148 - R/ggsurvfit_options.R | 60 R/grid.draw_ggsurvfit.R | 68 R/print.R | 52 R/reexport.R | 46 R/scale_ggsurvfit.R | 198 - R/stat_stepribbon.R | 166 - R/survfit2.R | 266 - R/survfit2_p.R | 130 R/theme_ggsurvfit.R | 84 R/theme_risktable.R | 132 R/tidy_cuminc.R | 80 R/tidy_survfit.R | 764 ++--- R/utils-add_risktable.R | 594 ++-- R/utils.R | 80 R/zzz.R | 24 README.md | 284 +- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 92 inst/doc/themes.R | 100 inst/doc/themes.Rmd | 196 - inst/doc/themes.html | 879 +++--- man/Surv_CNSR.Rd | 128 man/add_censor_mark.Rd | 58 man/add_confidence_interval.Rd | 76 man/add_legend_title.Rd | 52 man/add_pvalue.Rd | 119 man/add_quantile.Rd | 80 man/add_risktable.Rd | 290 +- man/add_risktable_strata_symbol.Rd | 92 man/adtte.Rd | 146 - 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tests/testthat/test-add_censor_mark.R | 176 - tests/testthat/test-add_confidence_interval.R | 194 - tests/testthat/test-add_legend_title.R | 310 +- tests/testthat/test-add_pvalue.R | 261 + tests/testthat/test-add_quantile.R | 416 +- tests/testthat/test-add_risktable.R | 704 ++--- tests/testthat/test-add_risktable_strata_symbol.R | 626 ++-- tests/testthat/test-format_p.R | 42 tests/testthat/test-ggcuminc.R | 244 - tests/testthat/test-ggsurvfit.R | 426 +-- tests/testthat/test-ggsurvfit_build.R | 26 tests/testthat/test-ggsurvfit_options.R | 98 tests/testthat/test-grid.draw_ggsurvfit.R | 52 tests/testthat/test-scale_ggsurvfit.R | 80 tests/testthat/test-stat_stepribbon.R | 58 tests/testthat/test-survfit2.R | 120 tests/testthat/test-survfit2_p.R | 116 tests/testthat/test-theme_risktable.R | 88 tests/testthat/test-tidy_cuminc.R | 180 - tests/testthat/test-tidy_survfit.R | 602 ++-- vignettes/themes.Rmd | 196 - 217 files changed, 37112 insertions(+), 36946 deletions(-)
Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut] ,
Samuel Bosch [aut] ,
Ward Appeltans [ctb] ,
Stephen Formel [ctb] ,
OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Diff between robis versions 2.11.3 dated 2022-09-24 and 2.12.0 dated 2026-07-24
robis-2.11.3/robis/R/robis.R |only robis-2.12.0/robis/DESCRIPTION | 34 ++-- robis-2.12.0/robis/MD5 | 42 +++-- robis-2.12.0/robis/NAMESPACE | 2 robis-2.12.0/robis/NEWS.md | 7 robis-2.12.0/robis/R/checklist.R | 11 + robis-2.12.0/robis/R/dataset.R | 105 ++++++++++---- robis-2.12.0/robis/R/occurrence.R | 21 ++ robis-2.12.0/robis/R/robis-imports.R |only robis-2.12.0/robis/R/robis-package.R |only robis-2.12.0/robis/R/taxon.R | 2 robis-2.12.0/robis/R/util.R | 37 ++++ robis-2.12.0/robis/R/zzz.R |only robis-2.12.0/robis/README.md | 76 +++++++++- robis-2.12.0/robis/build/vignette.rds |binary robis-2.12.0/robis/inst/WORDLIST | 15 +- robis-2.12.0/robis/inst/doc/getting-started.R | 2 robis-2.12.0/robis/inst/doc/getting-started.html | 172 +++++++++++------------ robis-2.12.0/robis/man/checklist.Rd | 10 - robis-2.12.0/robis/man/dataset.Rd | 33 +++- robis-2.12.0/robis/man/figures/map.png |only robis-2.12.0/robis/man/occurrence.Rd | 16 +- robis-2.12.0/robis/man/robis.Rd | 35 +++- robis-2.12.0/robis/man/unnest_extension.Rd | 2 robis-2.12.0/robis/tests/testthat/test_dataset.R |only 25 files changed, 439 insertions(+), 183 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: One interface to many large language model providers: a single
configuration object and a single calling function serve chat and embedding
models alike, so research code does not change when the provider does. The
same calls scale to multi-model and multi-condition studies.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.8.10 dated 2026-07-10 and 0.8.11 dated 2026-07-24
LLMR-0.8.10/LLMR/man/bind_tools.Rd |only LLMR-0.8.10/LLMR/man/cache_llm_call.Rd |only LLMR-0.8.10/LLMR/man/expand_llm_config.Rd |only LLMR-0.8.10/LLMR/man/llm_add_request_hash.Rd |only LLMR-0.8.10/LLMR/man/llm_cross_design.Rd |only LLMR-0.8.10/LLMR/man/llm_parse_rowpack_tags.Rd |only LLMR-0.8.10/LLMR/man/llm_persona_dictionary.Rd |only LLMR-0.8.10/LLMR/man/llm_uuid.Rd |only LLMR-0.8.10/LLMR/man/log_llm_error.Rd |only LLMR-0.8.11/LLMR/DESCRIPTION | 14 LLMR-0.8.11/LLMR/MD5 | 211 +++----- LLMR-0.8.11/LLMR/NAMESPACE | 13 LLMR-0.8.11/LLMR/NEWS.md | 33 + LLMR-0.8.11/LLMR/R/LLMR.R | 135 ++--- LLMR-0.8.11/LLMR/R/LLMR_response.R | 3 LLMR-0.8.11/LLMR/R/LLMR_tidy.R | 10 LLMR-0.8.11/LLMR/R/LLM_chat_session.R | 8 LLMR-0.8.11/LLMR/R/LLM_parallel_utils.R | 82 ++- LLMR-0.8.11/LLMR/R/LLM_param_translate.R | 2 LLMR-0.8.11/LLMR/R/LLM_robust_utils.R | 66 -- LLMR-0.8.11/LLMR/R/audit_log.R | 28 - LLMR-0.8.11/LLMR/R/batch_api.R | 20 LLMR-0.8.11/LLMR/R/batch_mode.R | 39 - LLMR-0.8.11/LLMR/R/data.R | 2 LLMR-0.8.11/LLMR/R/generics.R | 31 - LLMR-0.8.11/LLMR/R/hash.R | 38 - LLMR-0.8.11/LLMR/R/json_mode.R | 23 LLMR-0.8.11/LLMR/R/log_messages.R | 119 ++++ LLMR-0.8.11/LLMR/R/log_read.R | 4 LLMR-0.8.11/LLMR/R/personas.R | 14 LLMR-0.8.11/LLMR/R/render_messages.R | 2 LLMR-0.8.11/LLMR/R/replicate.R | 83 ++- LLMR-0.8.11/LLMR/R/request_hash.R | 15 LLMR-0.8.11/LLMR/R/stream.R | 2 LLMR-0.8.11/LLMR/R/tools.R | 32 - LLMR-0.8.11/LLMR/R/usage.R | 69 +- LLMR-0.8.11/LLMR/README.md | 260 +++++++--- LLMR-0.8.11/LLMR/inst/ai/LLMR.md | 65 +- LLMR-0.8.11/LLMR/inst/doc/about-schema.Rmd | 8 LLMR-0.8.11/LLMR/inst/doc/about-schema.html | 10 LLMR-0.8.11/LLMR/inst/doc/chat-basics.Rmd | 16 LLMR-0.8.11/LLMR/inst/doc/chat-basics.html | 15 LLMR-0.8.11/LLMR/inst/doc/experiments.Rmd | 21 LLMR-0.8.11/LLMR/inst/doc/experiments.html | 25 LLMR-0.8.11/LLMR/inst/doc/interactive-calls.R | 4 LLMR-0.8.11/LLMR/inst/doc/interactive-calls.Rmd | 14 LLMR-0.8.11/LLMR/inst/doc/interactive-calls.html | 41 - LLMR-0.8.11/LLMR/inst/doc/presidential_embeddings.Rmd | 9 LLMR-0.8.11/LLMR/inst/doc/presidential_embeddings.html | 13 LLMR-0.8.11/LLMR/inst/doc/reproducibility-and-cost.R | 2 LLMR-0.8.11/LLMR/inst/doc/reproducibility-and-cost.Rmd | 16 LLMR-0.8.11/LLMR/inst/doc/reproducibility-and-cost.html | 27 - LLMR-0.8.11/LLMR/inst/doc/tidy-and-structured.Rmd | 11 LLMR-0.8.11/LLMR/inst/doc/tidy-and-structured.html | 13 LLMR-0.8.11/LLMR/inst/doc/trolley-dilemma-experiment.Rmd | 2 LLMR-0.8.11/LLMR/inst/doc/trolley-dilemma-experiment.html | 4 LLMR-0.8.11/LLMR/inst/examples/JSON-Scheme.R | 2 LLMR-0.8.11/LLMR/inst/examples/LLM_experiment.R | 4 LLMR-0.8.11/LLMR/inst/examples/demo.qmd | 30 - LLMR-0.8.11/LLMR/man/LLMR-package.Rd | 6 LLMR-0.8.11/LLMR/man/anes_2024_personas.Rd | 2 LLMR-0.8.11/LLMR/man/call_llm.Rd | 4 LLMR-0.8.11/LLMR/man/call_llm_broadcast.Rd | 2 LLMR-0.8.11/LLMR/man/call_llm_compare.Rd | 2 LLMR-0.8.11/LLMR/man/call_llm_par.Rd | 8 LLMR-0.8.11/LLMR/man/call_llm_robust.Rd | 1 LLMR-0.8.11/LLMR/man/call_llm_sweep.Rd | 2 LLMR-0.8.11/LLMR/man/call_llm_tools.Rd | 14 LLMR-0.8.11/LLMR/man/diagnostics.Rd | 2 LLMR-0.8.11/LLMR/man/enable_structured_output.Rd | 18 LLMR-0.8.11/LLMR/man/get_batched_embeddings.Rd | 8 LLMR-0.8.11/LLMR/man/llm_agreement.Rd | 16 LLMR-0.8.11/LLMR/man/llm_batch_submit.Rd | 10 LLMR-0.8.11/LLMR/man/llm_chat_session.Rd | 4 LLMR-0.8.11/LLMR/man/llm_config.Rd | 6 LLMR-0.8.11/LLMR/man/llm_fn.Rd | 4 LLMR-0.8.11/LLMR/man/llm_fn_structured.Rd | 2 LLMR-0.8.11/LLMR/man/llm_fn_tags.Rd | 2 LLMR-0.8.11/LLMR/man/llm_hash.Rd | 10 LLMR-0.8.11/LLMR/man/llm_log_enable.Rd | 18 LLMR-0.8.11/LLMR/man/llm_methods_text.Rd | 30 - LLMR-0.8.11/LLMR/man/llm_mutate.Rd | 6 LLMR-0.8.11/LLMR/man/llm_mutate_structured.Rd | 2 LLMR-0.8.11/LLMR/man/llm_mutate_tags.Rd | 2 LLMR-0.8.11/LLMR/man/llm_request_hash.Rd | 15 LLMR-0.8.11/LLMR/man/llmr_response.Rd | 3 LLMR-0.8.11/LLMR/man/report.Rd | 27 - LLMR-0.8.11/LLMR/tests/testthat/test-000-experiment-reporting.R |only LLMR-0.8.11/LLMR/tests/testthat/test-083-core.R | 29 - LLMR-0.8.11/LLMR/tests/testthat/test-083-features.R | 43 + LLMR-0.8.11/LLMR/tests/testthat/test-audit-fixes.R | 31 - LLMR-0.8.11/LLMR/tests/testthat/test-batch-state.R |only LLMR-0.8.11/LLMR/tests/testthat/test-batch_mode.R | 9 LLMR-0.8.11/LLMR/tests/testthat/test-bugfixes.R | 7 LLMR-0.8.11/LLMR/tests/testthat/test-canonical-hash.R | 33 - LLMR-0.8.11/LLMR/tests/testthat/test-enrichment.R | 60 +- LLMR-0.8.11/LLMR/tests/testthat/test-fast-follow-0811.R |only LLMR-0.8.11/LLMR/tests/testthat/test-live-cheap.R | 22 LLMR-0.8.11/LLMR/tests/testthat/test-log-read.R | 6 LLMR-0.8.11/LLMR/tests/testthat/test-personas.R | 8 LLMR-0.8.11/LLMR/tests/testthat/test-preview.R | 4 LLMR-0.8.11/LLMR/tests/testthat/test-request-hash.R | 52 +- LLMR-0.8.11/LLMR/tests/testthat/test-response-record.R | 2 LLMR-0.8.11/LLMR/tests/testthat/test-tool-provenance-fields.R |only LLMR-0.8.11/LLMR/tests/testthat/test-usage.R | 2 LLMR-0.8.11/LLMR/vignettes/about-schema.Rmd | 8 LLMR-0.8.11/LLMR/vignettes/chat-basics.Rmd | 16 LLMR-0.8.11/LLMR/vignettes/experiments.Rmd | 21 LLMR-0.8.11/LLMR/vignettes/interactive-calls.Rmd | 14 LLMR-0.8.11/LLMR/vignettes/presidential_embeddings.Rmd | 9 LLMR-0.8.11/LLMR/vignettes/reproducibility-and-cost.Rmd | 16 LLMR-0.8.11/LLMR/vignettes/tidy-and-structured.Rmd | 11 LLMR-0.8.11/LLMR/vignettes/trolley-dilemma-experiment.Rmd | 2 113 files changed, 1313 insertions(+), 1028 deletions(-)
Title: Sequence Clustering with Discrete-Output HMMs
Description: Provides an implementation of a mixture of hidden Markov models
(HMMs) for discrete sequence data in the Discrete Bayesian HMM Clustering
(DBHC) algorithm. The DBHC algorithm is an HMM Clustering
algorithm that finds a mixture of discrete-output HMMs while using
heuristics based on Bayesian Information Criterion (BIC) to search for the
optimal number of HMM states and the optimal number of clusters.
Author: Gabriel Budel [aut, cre],
Flavius Frasincar [aut]
Maintainer: Gabriel Budel <gabysp_budel@hotmail.com>
Diff between DBHC versions 0.0.3 dated 2022-12-22 and 0.0.4 dated 2026-07-24
DESCRIPTION | 37 - MD5 | 43 - NAMESPACE | 43 - NEWS.md | 55 + R/DBHC.R | 15 R/hmmclustering.R | 1416 ++++++++++++++++++++++---------------------- R/plotfunctions.R | 182 ++--- README.md | 128 +-- man/assign.clusters.Rd | 64 - man/cluster.bic.Rd | 46 - man/count.parameters.Rd | 48 - man/emission.heatmap.Rd | 42 - man/hmm.clust.Rd | 324 ++++------ man/model.ll.Rd | 50 - man/partition.bic.Rd | 50 - man/select.seeds.Rd | 96 +- man/seq2hmm.ll.Rd | 52 - man/size.search.Rd | 65 +- man/smooth.hmm.Rd | 52 - man/smooth.probabilities.Rd | 50 - man/transition.heatmap.Rd | 46 - tests/testthat/Rplots.pdf |only tests/testthat/test-DBHC.R | 92 ++ 23 files changed, 1581 insertions(+), 1415 deletions(-)
Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: Claudia Beleites [aut, cre]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.eu>
Diff between arrayhelpers versions 1.1-1 dated 2026-07-05 and 1.1-2 dated 2026-07-24
DESCRIPTION | 10 ++++------ MD5 | 21 +++++++++++---------- R/array2df.R | 16 ++++++++-------- R/arrayhelpers.R | 9 ++++++++- R/colSums.R | 8 ++++---- R/ensuredim.R | 12 ++++++------ R/groupsum.R | 6 +++--- R/restoredim.R | 6 +++--- man/arrayhelpers-package.Rd | 12 +++++++++--- tests/tests.R |only tests/testthat.R | 13 +------------ tests/testthat/tests.R | 4 +--- 12 files changed, 58 insertions(+), 59 deletions(-)
Title: Feature Importance Methods for Global Explanations
Description: Provides a consistent interface for common feature importance
methods as described in Ewald et al. (2024)
<doi:10.1007/978-3-031-63797-1_22>, including permutation feature
importance (PFI), conditional and relative feature importance (CFI,
RFI), leave one covariate out (LOCO), and Shapley additive global
importance (SAGE), as well as feature sampling mechanisms to support
conditional importance methods.
Author: Lukas Burk [aut, cre, cph]
Maintainer: Lukas Burk <cran@lukasburk.de>
Diff between xplainfi versions 1.1.0 dated 2026-02-26 and 1.2.0 dated 2026-07-24
xplainfi-1.1.0/xplainfi/tests/testthat/_problems |only xplainfi-1.2.0/xplainfi/DESCRIPTION | 9 xplainfi-1.2.0/xplainfi/MD5 | 200 - xplainfi-1.2.0/xplainfi/NEWS.md | 42 xplainfi-1.2.0/xplainfi/R/ConditionalARFSampler.R | 497 ++-- xplainfi-1.2.0/xplainfi/R/ConditionalCtreeSampler.R | 367 +-- xplainfi-1.2.0/xplainfi/R/ConditionalGaussianSampler.R | 198 - xplainfi-1.2.0/xplainfi/R/ConditionalKNNSampler.R | 302 +- xplainfi-1.2.0/xplainfi/R/ConditionalSampler.R | 229 + xplainfi-1.2.0/xplainfi/R/FeatureImportanceMethod.R | 1081 ++++----- xplainfi-1.2.0/xplainfi/R/FeatureSampler.R | 221 - xplainfi-1.2.0/xplainfi/R/KnockoffSampler.R | 312 +- xplainfi-1.2.0/xplainfi/R/MarginalPermutationSampler.R | 63 xplainfi-1.2.0/xplainfi/R/MarginalReferenceSampler.R | 93 xplainfi-1.2.0/xplainfi/R/MarginalSampler.R | 79 xplainfi-1.2.0/xplainfi/R/PerturbationImportance.R | 1160 +++++----- xplainfi-1.2.0/xplainfi/R/SAGE-conditional.R | 229 - xplainfi-1.2.0/xplainfi/R/SAGE-marginal.R | 172 - xplainfi-1.2.0/xplainfi/R/SAGE.R | 1152 ++++----- xplainfi-1.2.0/xplainfi/R/WVIM.R | 843 +++---- xplainfi-1.2.0/xplainfi/R/bibentries.R | 602 ++--- xplainfi-1.2.0/xplainfi/R/check_groups.R | 66 xplainfi-1.2.0/xplainfi/R/data-sim.R | 298 +- xplainfi-1.2.0/xplainfi/R/op-null-default.R | 2 xplainfi-1.2.0/xplainfi/R/predict-batched.R | 226 - xplainfi-1.2.0/xplainfi/R/sage-internals.R | 229 + xplainfi-1.2.0/xplainfi/R/utils-importance.R | 691 +++-- xplainfi-1.2.0/xplainfi/R/utils-mlr3.R | 154 - xplainfi-1.2.0/xplainfi/R/utils-opt.R | 159 - xplainfi-1.2.0/xplainfi/R/utils-parallel.R | 176 - xplainfi-1.2.0/xplainfi/R/utils-pkg.R | 24 xplainfi-1.2.0/xplainfi/R/utils-sampler.R |only xplainfi-1.2.0/xplainfi/R/utils-test.R | 56 xplainfi-1.2.0/xplainfi/R/wvim-design-matrix.R | 74 xplainfi-1.2.0/xplainfi/build/partial.rdb |binary xplainfi-1.2.0/xplainfi/build/vignette.rds |binary xplainfi-1.2.0/xplainfi/inst/doc/feature-samplers.html | 163 - xplainfi-1.2.0/xplainfi/inst/doc/simulation-settings.html | 5 xplainfi-1.2.0/xplainfi/inst/doc/xplainfi.R | 11 xplainfi-1.2.0/xplainfi/inst/doc/xplainfi.Rmd | 13 xplainfi-1.2.0/xplainfi/inst/doc/xplainfi.html | 304 +- xplainfi-1.2.0/xplainfi/man/CFI.Rd | 125 - xplainfi-1.2.0/xplainfi/man/ConditionalARFSampler.Rd | 240 -- xplainfi-1.2.0/xplainfi/man/ConditionalCtreeSampler.Rd | 109 xplainfi-1.2.0/xplainfi/man/ConditionalGaussianSampler.Rd | 95 xplainfi-1.2.0/xplainfi/man/ConditionalKNNSampler.Rd | 188 - xplainfi-1.2.0/xplainfi/man/ConditionalSAGE.Rd | 101 xplainfi-1.2.0/xplainfi/man/ConditionalSampler.Rd | 173 - xplainfi-1.2.0/xplainfi/man/FeatureImportanceMethod.Rd | 315 +- xplainfi-1.2.0/xplainfi/man/FeatureSampler.Rd | 183 - xplainfi-1.2.0/xplainfi/man/KnockoffGaussianSampler.Rd | 95 xplainfi-1.2.0/xplainfi/man/KnockoffSampler.Rd | 135 - xplainfi-1.2.0/xplainfi/man/LOCO.Rd | 140 - xplainfi-1.2.0/xplainfi/man/MarginalPermutationSampler.Rd | 78 xplainfi-1.2.0/xplainfi/man/MarginalReferenceSampler.Rd | 93 xplainfi-1.2.0/xplainfi/man/MarginalSAGE.Rd | 94 xplainfi-1.2.0/xplainfi/man/MarginalSampler.Rd | 122 - xplainfi-1.2.0/xplainfi/man/PFI.Rd | 122 - xplainfi-1.2.0/xplainfi/man/PerturbationImportance.Rd | 170 - xplainfi-1.2.0/xplainfi/man/RFI.Rd | 133 - xplainfi-1.2.0/xplainfi/man/SAGE.Rd | 204 - xplainfi-1.2.0/xplainfi/man/WVIM.Rd | 222 - xplainfi-1.2.0/xplainfi/man/sim_dgp_ewald.Rd | 5 xplainfi-1.2.0/xplainfi/man/sim_dgp_scenarios.Rd | 19 xplainfi-1.2.0/xplainfi/man/xplainfi-package.Rd | 5 xplainfi-1.2.0/xplainfi/tests/testthat.R | 4 xplainfi-1.2.0/xplainfi/tests/testthat/helper-feature-importance.R | 464 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/helper-importance.R | 64 xplainfi-1.2.0/xplainfi/tests/testthat/helper-samplers.R | 542 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/setup.R | 23 xplainfi-1.2.0/xplainfi/tests/testthat/test-CFI.R | 606 ++--- xplainfi-1.2.0/xplainfi/tests/testthat/test-ConditionalARFSampler.R | 292 +- xplainfi-1.2.0/xplainfi/tests/testthat/test-ConditionalCtreeSampler.R | 312 +- xplainfi-1.2.0/xplainfi/tests/testthat/test-ConditionalGaussianSampler.R | 179 - xplainfi-1.2.0/xplainfi/tests/testthat/test-ConditionalKNNSampler.R | 331 +- xplainfi-1.2.0/xplainfi/tests/testthat/test-ConditionalSAGE.R | 473 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/test-FeatureImportanceMethod.R |only xplainfi-1.2.0/xplainfi/tests/testthat/test-KnockoffSampler.R | 540 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/test-MarginalPermutationSampler.R | 146 - xplainfi-1.2.0/xplainfi/tests/testthat/test-MarginalReferenceSampler.R | 256 +- xplainfi-1.2.0/xplainfi/tests/testthat/test-MarginalSAGE.R | 488 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/test-PFI.R | 196 - xplainfi-1.2.0/xplainfi/tests/testthat/test-RFI.R | 426 +-- xplainfi-1.2.0/xplainfi/tests/testthat/test-WVIM.R | 691 +++-- xplainfi-1.2.0/xplainfi/tests/testthat/test-bibentries.R | 16 xplainfi-1.2.0/xplainfi/tests/testthat/test-data-sim.R | 540 ++-- xplainfi-1.2.0/xplainfi/tests/testthat/test-has_obs_loss.R | 58 xplainfi-1.2.0/xplainfi/tests/testthat/test-pretrained.R | 456 +-- xplainfi-1.2.0/xplainfi/tests/testthat/test-require_package.R | 14 xplainfi-1.2.0/xplainfi/tests/testthat/test-utils-sage.R | 381 +-- xplainfi-1.2.0/xplainfi/tests/testthat/test-utils-sampler.R |only xplainfi-1.2.0/xplainfi/tests/testthat/test-variance-estimation.R | 722 +++--- xplainfi-1.2.0/xplainfi/tests/testthat/test-xplain_options.R | 128 - xplainfi-1.2.0/xplainfi/vignettes/xplainfi.Rmd | 13 94 files changed, 11493 insertions(+), 10536 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://ametris.com/> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Samuel T Afolabi [ctb] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerra [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.3-6 dated 2026-04-21 and 3.3-8 dated 2026-07-24
DESCRIPTION | 15 +- MD5 | 64 +++++---- NAMESPACE | 3 NEWS.md | 221 ++++++++++++++------------------ R/DFA.R | 95 +++++++------ R/GGIR.R | 8 + R/SSP.R | 42 +++++- R/check_log.R | 6 R/check_params.R | 3 R/g.analyse.perday.R | 3 R/g.calibrate.R | 9 + R/g.impute.R | 8 - R/g.part6.R | 15 +- R/load_params.R | 3 R/visualReport.R | 1 R/write_parquet.R |only inst/CITATION | 3 inst/doc/GGIRParameters.Rmd | 1 inst/doc/GGIRParameters.html | 29 +++- inst/doc/GGIRoutput.Rmd | 5 inst/doc/GGIRoutput.html | 27 +++ man/DFA.Rd | 5 man/GGIR-package.Rd | 4 man/GGIR.Rd | 14 ++ man/SSP.Rd | 30 +++- man/build_epoch_table.Rd |only man/write_dashboard_parquet.Rd |only man/write_epoch_parquet.Rd |only tests/testthat/test_StudyDatesFile.R | 56 +++----- tests/testthat/test_check_log.R |only tests/testthat/test_dfa.R | 20 +- tests/testthat/test_load_check_params.R | 2 tests/testthat/test_write_parquet.R |only vignettes/GGIRParameters.Rmd | 1 vignettes/GGIRoutput.Rmd | 5 vignettes/LLR_Tutorial_Banner.png |only vignettes/doubleplot.png |only 37 files changed, 416 insertions(+), 282 deletions(-)
Title: An R Package for Mining Global Plant Diversity and Distribution
Data
Description: Produces diversity estimates and species lists with associated global distribution for any vascular plant family and genus from Plants of the World Online database, by interacting with the source code of each plant taxon page. It also creates global maps of species richness, graphics of species discoveries and name changes over time. For more details: 'Zuanny, D.C., B.Vilela, P.W.Moonlight, T.E.Särkinen, and D.Cardoso. 2024. expowo: An R package for mining global plant diversity and distribution data. Applications in Plant Sciences 12: e11609'.
Author: Debora Zuanny [aut, cre, cph] ,
Domingos Cardoso [aut, ths, cph]
Maintainer: Debora Zuanny <deborazuanny@gmail.com>
Diff between expowo versions 3.0 dated 2026-02-24 and 3.1 dated 2026-07-24
DESCRIPTION | 8 MD5 | 88 +- R/getInfo.R | 1026 +++++++++++++-------------- R/megaGen.R | 226 ++--- R/powoFam.R | 2 R/powoGenera.R | 9 R/powoSpDist.R | 2 R/powoSpecies.R | 10 R/topGen.R | 2 README.md | 8 inst/doc/data_package.Rmd | 2 inst/doc/data_package.html | 2 inst/doc/mapping_distribution.Rmd | 2 inst/doc/mapping_distribution.html | 2 inst/doc/mining_accepted_genera.R | 42 - inst/doc/mining_accepted_genera.Rmd | 48 - inst/doc/mining_accepted_genera.html | 141 --- inst/doc/mining_family_species_number.R | 5 inst/doc/mining_family_species_number.Rmd | 9 inst/doc/mining_family_species_number.html | 20 inst/doc/mining_species.Rmd | 6 inst/doc/mining_species.html | 8 inst/doc/mining_species_distribution.Rmd | 4 inst/doc/mining_species_distribution.html | 6 inst/doc/mining_toprichest_genera.Rmd | 4 inst/doc/mining_toprichest_genera.html | 6 inst/doc/plotting_discoveries.Rmd | 15 inst/doc/plotting_discoveries.html | 16 inst/doc/plotting_nomenclatural_changes.Rmd | 2 inst/doc/plotting_nomenclatural_changes.html | 4 man/megaGen.Rd | 6 man/powoFam.Rd | 2 man/powoGenera.Rd | 2 man/powoSpDist.Rd | 2 man/powoSpecies.Rd | 3 man/topGen.Rd | 2 vignettes/data_package.Rmd | 2 vignettes/mapping_distribution.Rmd | 2 vignettes/mining_accepted_genera.Rmd | 48 - vignettes/mining_family_species_number.Rmd | 9 vignettes/mining_species.Rmd | 6 vignettes/mining_species_distribution.Rmd | 4 vignettes/mining_toprichest_genera.Rmd | 4 vignettes/plotting_discoveries.Rmd | 15 vignettes/plotting_nomenclatural_changes.Rmd | 2 45 files changed, 865 insertions(+), 969 deletions(-)
Title: Bounded Time Series Regression
Description: Simulate, estimate and forecast a wide range of regression
based dynamic models for bounded time series, covering the most
commonly applied models in the literature. The main calculations are
done in FORTRAN, which translates into very fast algorithms.
Author: Taiane Schaedler Prass [aut, cre, com] ,
Guilherme Pumi [ctb, aut] ,
Fabio Mariano Bayer [ctb] ,
Jack Joseph Dongarra [ctb] ),
Cleve Moler [ctb] ),
Gilbert Wright Stewart [ctb] ),
Ciyou Zhu [ctb] ,
Richard H. Byrd [ctb] ,
Jorge Nocedal [ctb] ,
Jose L [...truncated...]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between BTSR versions 1.0.2 dated 2026-02-03 and 1.1.0 dated 2026-07-24
DESCRIPTION | 11 MD5 | 87 ++--- NAMESPACE | 11 R/barc.R | 8 R/btsr.R | 4 R/btsr_generic.R | 17 - R/btsr_internal.R | 15 R/btsr_parent_models.R | 64 +++- R/defaults.R | 355 ++++++++++++++++------- R/dlTest.R |only R/functions_check.R | 371 ++++++++++++++++-------- R/functions_convert.R | 382 +++++++++++++++++-------- R/functions_get.R | 373 +++++++++++++++++++----- R/functions_messages.R | 86 ++++- R/functions_misc.R | 365 +++++++++++++++++------ R/help.R | 83 ++++- R/zzz.R | 7 build/partial.rdb |binary inst/NEWS.md | 5 inst/REFERENCES.bib | 44 ++ man/BARC.functions.Rd | 7 man/BTSR.models.Rd | 2 man/BTSR.parent.models.Rd | 36 +- man/arguments.Rd | 86 +++-- man/arguments.coefs.Rd | 37 +- man/arguments.configs.Rd | 4 man/arguments.link.Rd | 6 man/arguments.loglik.Rd | 4 man/arguments.map.Rd | 3 man/arguments.model.Rd | 54 ++- man/arguments.order.Rd | 14 man/arguments.regressors.Rd | 4 man/arguments.series.Rd | 5 man/btsr-package.Rd | 12 man/coefs.start.Rd | 22 + man/dl.test.Rd |only man/dot-onAttach.Rd |only man/print.btsr.Rd | 52 +-- src/01_distrib.f90 | 2 src/02_main.f90 | 17 - src/03_alloc.f90 | 110 ++++--- src/04_base.f90 | 672 ++++++++++++++++++++++++-------------------- src/05_barc.f90 | 51 +-- src/05_generic.f90 | 86 +++-- src/BTSR_init.c | 16 - src/DLtest.f90 | 6 46 files changed, 2426 insertions(+), 1170 deletions(-)
Title: Many Ways to Measure and Classify Membership for Networks,
Nodes, and Ties
Description: Many tools for calculating network, node, or tie
marks, measures, motifs and memberships of many different types of networks.
Marks identify structural positions, measures quantify network properties,
memberships classify nodes into groups, and motifs tabulate substructure participation.
All functions operate with all classes of network data covered in 'manynet',
and on directed, undirected, multiplex, multimodal, signed, and other networks.
Author: James Hollway [cre, aut, ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between netrics versions 0.3.1 dated 2026-06-23 and 0.4.0 dated 2026-07-24
netrics-0.3.1/netrics/inst/tutorials/tutorial3 |only netrics-0.3.1/netrics/inst/tutorials/tutorial4 |only netrics-0.3.1/netrics/inst/tutorials/tutorial5 |only netrics-0.3.1/netrics/inst/tutorials/tutorial6 |only netrics-0.4.0/netrics/DESCRIPTION | 9 netrics-0.4.0/netrics/MD5 | 104 ++++---- netrics-0.4.0/netrics/NAMESPACE | 6 netrics-0.4.0/netrics/NEWS.md | 25 ++ netrics-0.4.0/netrics/R/class_metrics.R | 7 netrics-0.4.0/netrics/R/measure_centrality_between.R | 60 ++++- netrics-0.4.0/netrics/R/measure_centrality_closeness.R | 72 ++++-- netrics-0.4.0/netrics/R/measure_centrality_degree.R | 120 +++++++--- netrics-0.4.0/netrics/R/measure_centrality_eigen.R | 71 ++++- netrics-0.4.0/netrics/inst/tutorials/netrics1 |only netrics-0.4.0/netrics/inst/tutorials/netrics2 |only netrics-0.4.0/netrics/inst/tutorials/netrics3 |only netrics-0.4.0/netrics/inst/tutorials/netrics4 |only netrics-0.4.0/netrics/man/measure_assort_net.Rd | 4 netrics-0.4.0/netrics/man/measure_assort_node.Rd | 4 netrics-0.4.0/netrics/man/measure_breadth.Rd | 4 netrics-0.4.0/netrics/man/measure_broker_node.Rd | 4 netrics-0.4.0/netrics/man/measure_broker_tie.Rd | 4 netrics-0.4.0/netrics/man/measure_brokerage.Rd | 4 netrics-0.4.0/netrics/man/measure_central_between.Rd | 4 netrics-0.4.0/netrics/man/measure_central_close.Rd | 4 netrics-0.4.0/netrics/man/measure_central_degree.Rd | 4 netrics-0.4.0/netrics/man/measure_central_eigen.Rd | 16 - netrics-0.4.0/netrics/man/measure_centralisation_between.Rd | 64 ++--- netrics-0.4.0/netrics/man/measure_centralisation_close.Rd | 58 +--- netrics-0.4.0/netrics/man/measure_centralisation_degree.Rd | 72 ++---- netrics-0.4.0/netrics/man/measure_centralisation_eigen.Rd | 61 ++--- netrics-0.4.0/netrics/man/measure_centralities_between.Rd | 4 netrics-0.4.0/netrics/man/measure_centralities_close.Rd | 4 netrics-0.4.0/netrics/man/measure_centralities_degree.Rd | 4 netrics-0.4.0/netrics/man/measure_centralities_eigen.Rd | 4 netrics-0.4.0/netrics/man/measure_closure.Rd | 4 netrics-0.4.0/netrics/man/measure_closure_node.Rd | 4 netrics-0.4.0/netrics/man/measure_cohesion.Rd | 4 netrics-0.4.0/netrics/man/measure_core.Rd | 4 netrics-0.4.0/netrics/man/measure_diffusion_infection.Rd | 4 netrics-0.4.0/netrics/man/measure_diffusion_net.Rd | 4 netrics-0.4.0/netrics/man/measure_diffusion_node.Rd | 4 netrics-0.4.0/netrics/man/measure_diverse_net.Rd | 4 netrics-0.4.0/netrics/man/measure_diverse_node.Rd | 4 netrics-0.4.0/netrics/man/measure_features.Rd | 4 netrics-0.4.0/netrics/man/measure_fragmentation.Rd | 4 netrics-0.4.0/netrics/man/measure_hierarchy.Rd | 4 netrics-0.4.0/netrics/man/measure_periods.Rd | 4 netrics-0.4.0/netrics/tests/testthat/Rplots.pdf |only netrics-0.4.0/netrics/tests/testthat/helper-netrics.R | 103 ++++++++ netrics-0.4.0/netrics/tests/testthat/test-measure_centrality.R | 37 ++- netrics-0.4.0/netrics/tests/testthat/test-tutorials_netrics.R |only 52 files changed, 593 insertions(+), 396 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.2.1 dated 2026-07-02 and 1.3.0 dated 2026-07-24
DESCRIPTION | 6 MD5 | 85 NEWS.md | 10 R/addIntersect.R | 20 R/documentationHelpers.R | 150 + R/generateAtcCohortSet.R | 8 R/generateDrugUtilisationCohortSet.R | 9 R/generateIngredientCohortSet.R | 4 R/plots.R | 4 R/summariseDiscontinuationAsSurvival.R | 35 R/summariseDrugRestart.R | 29 R/summariseDrugUtilisation.R | 4 R/summariseIntersect.R | 53 R/summariseProportionOfPatientsCovered.R | 216 - R/tables.R | 4 inst/doc/create_cohorts.html | 199 - inst/doc/drug_utilisation.html | 1766 ++++++------- man/addDrugRestart.Rd | 15 man/addIndication.Rd | 16 man/addTreatment.Rd | 13 man/drugRestartFollowUpDaysDoc.Rd |only man/generateAtcCohortSet.Rd | 5 man/generateDrugUtilisationCohortSet.Rd | 2 man/generateIngredientCohortSet.Rd | 2 man/inObservationDoc.Rd |only man/incidentDoc.Rd |only man/indicationCohortIdDoc.Rd |only man/indicationCohortNameDoc.Rd |only man/indicationWindowDoc.Rd |only man/mutuallyExclusiveDoc.Rd |only man/restrictToFirstDiscontinuationDoc.Rd |only man/ribbonDoc.Rd |only man/subsetCohortDoc.Rd |only man/subsetCohortIdDoc.Rd |only man/summariseDiscontinuationAsSurvival.Rd | 12 man/summariseDrugRestart.Rd | 15 man/summariseIndication.Rd | 20 man/summariseTreatment.Rd | 24 man/switchCohortIdDoc.Rd |only man/switchCohortTableDoc.Rd |only man/tableIndication.Rd | 3 man/tableTreatment.Rd | 2 man/treatmentCohortIdDoc.Rd |only man/treatmentCohortNameDoc.Rd |only man/unknownIndicationTableDoc.Rd |only man/windowDoc.Rd |only tests/testthat/test-generateDrugUtilisationCohortSet.R | 10 tests/testthat/test-indication.R | 72 tests/testthat/test-summariseDiscontinuation.R | 8 tests/testthat/test-summariseProportionOfPatientsCovered.R | 31 tests/testthat/test-summariseTreatment.R | 37 tests/testthat/test-tables.R | 2 52 files changed, 1571 insertions(+), 1320 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Algorithms for Bundling Edges in Networks and Visualizing Flow
and Metro Maps
Description: Implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.
Author: David Schoch [aut, cre] ,
Jose Luis Blanco-Claraco [cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between edgebundle versions 0.4.2 dated 2023-12-16 and 1.0.0 dated 2026-07-24
edgebundle-0.4.2/edgebundle/man/install_bundle_py.Rd |only edgebundle-0.4.2/edgebundle/tests/testthat/test-bundle_test.R |only edgebundle-1.0.0/edgebundle/DESCRIPTION | 27 edgebundle-1.0.0/edgebundle/MD5 | 72 + edgebundle-1.0.0/edgebundle/NAMESPACE | 4 edgebundle-1.0.0/edgebundle/NEWS.md | 15 edgebundle-1.0.0/edgebundle/R/RcppExports.R | 16 edgebundle-1.0.0/edgebundle/R/bundle_divided.R |only edgebundle-1.0.0/edgebundle/R/bundle_force.R | 39 edgebundle-1.0.0/edgebundle/R/bundle_hammer.R | 93 -- edgebundle-1.0.0/edgebundle/R/bundle_mingle.R |only edgebundle-1.0.0/edgebundle/R/bundle_path.R | 46 - edgebundle-1.0.0/edgebundle/R/bundle_stub.R | 105 -- edgebundle-1.0.0/edgebundle/R/edge_bundle.R |only edgebundle-1.0.0/edgebundle/R/edgebundle-package.R | 5 edgebundle-1.0.0/edgebundle/R/flow_spiral.R |only edgebundle-1.0.0/edgebundle/R/flow_tnss.R | 78 - edgebundle-1.0.0/edgebundle/R/metro_multicriteria.R | 11 edgebundle-1.0.0/edgebundle/R/utils-bundle.R |only edgebundle-1.0.0/edgebundle/README.md | 408 +++++----- edgebundle-1.0.0/edgebundle/inst/COPYRIGHTS |only edgebundle-1.0.0/edgebundle/man/edge_bundle.Rd |only edgebundle-1.0.0/edgebundle/man/edge_bundle_force.Rd | 14 edgebundle-1.0.0/edgebundle/man/edge_bundle_hammer.Rd | 50 + edgebundle-1.0.0/edgebundle/man/edge_bundle_mingle.Rd |only edgebundle-1.0.0/edgebundle/man/edge_bundle_path.Rd | 14 edgebundle-1.0.0/edgebundle/man/edge_bundle_stub.Rd | 2 edgebundle-1.0.0/edgebundle/man/edgebundle-package.Rd | 15 edgebundle-1.0.0/edgebundle/man/flow_tree.Rd |only edgebundle-1.0.0/edgebundle/man/metro_multicriteria.Rd | 6 edgebundle-1.0.0/edgebundle/man/tnss_tree.Rd | 5 edgebundle-1.0.0/edgebundle/src/RcppExports.cpp | 67 + edgebundle-1.0.0/edgebundle/src/bundle_geom.h |only edgebundle-1.0.0/edgebundle/src/divided.cpp |only edgebundle-1.0.0/edgebundle/src/forceBundle.cpp | 400 +-------- edgebundle-1.0.0/edgebundle/src/kdeeb.cpp |only edgebundle-1.0.0/edgebundle/src/mingle.cpp |only edgebundle-1.0.0/edgebundle/src/nanoflann.h |only edgebundle-1.0.0/edgebundle/tests/testthat/helper-graphs.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-bugs.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-convert_edges.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-divided.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-edge_bundle.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-flow_spiral.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-force.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-hammer.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-metro.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-mingle.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-no-deprecation.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-path.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-stub.R |only edgebundle-1.0.0/edgebundle/tests/testthat/test-tnss.R |only 52 files changed, 698 insertions(+), 794 deletions(-)
Title: Tesselation Visualization Plots for 2D Data
Description: Creates visualization plots for 2D data including ellipse plots, Voronoi tesselation plots, and combined ellipse-Voronoi plots. Designed to visualize class separation in 2D data, raw of from projection techniques like principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) or others. For more details see Lotsch and Kringel (2026) and Lotsch, J., and Kringel, D. (2026) <doi:10.1371/journal.pone.0333653>.
Author: Jorn Lotsch [aut, cre]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between VoronoiBiomedPlot versions 0.3.2 dated 2026-04-25 and 0.4 dated 2026-07-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/create_tesselation_plots.R | 3 ++- R/create_voronoi_plot.R | 3 ++- build/partial.rdb |binary 5 files changed, 11 insertions(+), 9 deletions(-)
More information about VoronoiBiomedPlot at CRAN
Permanent link
Title: PCA on the Torus via Density Ridges
Description: Implementation of a Principal Component Analysis (PCA) in the
torus via density ridge estimation. The main function, ridge_pca(), obtains
the relevant density ridge for bivariate sine von Mises and bivariate
wrapped Cauchy distribution models and provides the associated scores and
variance decomposition. Auxiliary functions for evaluating, fitting, and
sampling these models are also provided. The package provides replicability
to GarcÃa-Portugués and Prieto-Tirado (2023)
<doi:10.1007/s11222-023-10273-9>.
Author: Eduardo Garcia-Portugues [aut, cre] ,
Arturo Prieto-Tirado [aut]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between ridgetorus versions 1.0.3 dated 2025-07-27 and 1.1.0 dated 2026-07-24
DESCRIPTION | 12 +++--- MD5 | 76 ++++++++++++++++++++++---------------------- NEWS.md | 9 +++++ R/BWC.R | 20 +++++++---- R/BWN.R | 33 +++++++++---------- R/BvM.R | 21 +++++++----- R/Frechet.R | 7 +++- R/data.R | 9 +++-- R/lrt.R | 5 ++ R/plots.R | 6 ++- R/ridge-curve.R | 7 ++-- R/ridge-fourier.R | 16 +++++---- R/ridge-pca.R | 6 ++- R/ridge-scores.R | 8 ++-- R/ridges-distr.R | 65 +++++++++++++++++-------------------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/ridgetorus.html | 48 +++++++++++++-------------- man/biv_lrt.Rd | 7 +++- man/bvm.Rd | 23 ++++++++----- man/bwc.Rd | 15 +++++--- man/bwn.Rd | 7 +++- man/earthquakes.Rd | 3 + man/figures |only man/frechet.Rd | 5 ++ man/ridge_curve.Rd | 9 ++++- man/ridge_distr.Rd | 5 ++ man/ridge_fourier_fit.Rd | 5 ++ man/ridge_pca.Rd | 6 +++ man/ridge_scores.Rd | 9 ++++- man/santabarbara.Rd | 5 ++ man/show_ridge_pca.Rd | 4 ++ man/torus_dist.Rd | 6 ++- man/torus_pairs.Rd | 6 ++- man/wind.Rd | 7 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test_BWC.R | 12 +++--- tests/testthat/test_BWN.R | 21 ++++++++++++ tests/testthat/test_plots.R |only 40 files changed, 321 insertions(+), 183 deletions(-)
Title: MRI Tissue Classification
Description: Implements various methods for tissue classification in magnetic
resonance (MR) images of the brain, including normal mixture models
and hidden Markov normal mixture models, as outlined in Feng &
Tierney (2011) <doi:10.18637/jss.v044.i07>. These methods allow a
structural MR image to be classified into gray matter, white matter
and cerebrospinal fluid tissue types.
Author: Dai Feng [aut],
Luke Tierney [aut],
Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between mritc versions 0.5-3 dated 2023-01-27 and 0.6.0 dated 2026-07-24
mritc-0.5-3/mritc/ChangeLog |only mritc-0.5-3/mritc/R/sub.R |only mritc-0.5-3/mritc/TODO |only mritc-0.6.0/mritc/DESCRIPTION | 16 +++----- mritc-0.6.0/mritc/MD5 | 49 +++++++++++++++----------- mritc-0.6.0/mritc/NAMESPACE | 2 - mritc-0.6.0/mritc/NEWS.md |only mritc-0.6.0/mritc/R/measureMRI.R | 8 ++-- mritc-0.6.0/mritc/R/mriio.R | 2 - mritc-0.6.0/mritc/R/mritc.R | 24 ++++++------ mritc-0.6.0/mritc/R/mritc.pvhmrfem.R | 3 + mritc-0.6.0/mritc/R/plot.mritc.R | 14 +++++-- mritc-0.6.0/mritc/R/print.mritc.R | 8 ++-- mritc-0.6.0/mritc/R/summary.mritc.R | 2 - mritc-0.6.0/mritc/README.md |only mritc-0.6.0/mritc/inst/CITATION | 6 +-- mritc-0.6.0/mritc/inst/extdata/mask.rawb.gz |binary mritc-0.6.0/mritc/inst/tinytest |only mritc-0.6.0/mritc/man/mritc.Rd | 4 +- mritc-0.6.0/mritc/man/plot.mritc.Rd | 20 +++++++--- mritc-0.6.0/mritc/man/print.mritc.Rd | 4 +- mritc-0.6.0/mritc/man/rnormmix.Rd | 5 -- mritc-0.6.0/mritc/src/registerDynamicSymbol.c | 24 +++++++++++- mritc-0.6.0/mritc/tests |only mritc-0.6.0/mritc/tools |only 25 files changed, 118 insertions(+), 73 deletions(-)
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.2-0-1 dated 2026-07-05 and 1.2-0-2 dated 2026-07-24
DESCRIPTION | 6 +- MD5 | 64 +++++++++++++++---------------- build/partial.rdb |binary inst/doc/clifford.pdf |binary inst/doc/complex_clifford.R | 1 inst/doc/complex_clifford.Rmd | 3 - inst/doc/complex_clifford.html | 11 +---- inst/doc/conformal_algebra_clifford.html | 3 - inst/doc/cramer_clifford.R | 4 - inst/doc/cramer_clifford.Rmd | 4 - inst/doc/cramer_clifford.html | 7 +-- inst/doc/determinants_clifford.html | 3 - inst/doc/dual_quaternion_clifford.Rmd | 2 inst/doc/dual_quaternion_clifford.html | 5 -- inst/doc/getcoeffs.Rmd | 2 inst/doc/getcoeffs.html | 5 -- inst/doc/lorentz_clifford.html | 3 - inst/doc/pauli_clifford.html | 3 - inst/doc/pseudoscalar.html | 3 - inst/doc/quaternion_clifford.html | 3 - inst/doc/signature.html | 3 - man/Ops.clifford.Rd | 4 - man/allcliff.Rd | 2 man/dot.Rd | 16 +++---- man/grade.Rd | 2 man/signature.Rd | 8 +-- man/term.Rd | 11 ----- tests/testthat/test_aaf.R | 10 ++-- vignettes/clifford.bib | 11 +++++ vignettes/complex_clifford.Rmd | 3 - vignettes/cramer_clifford.Rmd | 4 - vignettes/dual_quaternion_clifford.Rmd | 2 vignettes/getcoeffs.Rmd | 2 33 files changed, 98 insertions(+), 112 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 1.2.0 dated 2026-07-13 and 1.2.1 dated 2026-07-24
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/Rush.R | 36 ++++++++++++++++++++++++------------ README.md | 1 + inst/CITATION |only tests/testthat/test-Rush.R | 40 ++++++++++++++++++++++++++++++++++++++++ 7 files changed, 78 insertions(+), 20 deletions(-)
Title: Vertical Weighted Strips
Description: A reference implementation of the Vertical Weighted Strips method
explored by Raim, Livsey, and Irimata (2025) <doi:10.48550/arXiv.2401.09696>
for rejection sampling.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between vws versions 0.3.0 dated 2025-11-11 and 0.4.0 dated 2026-07-24
vws-0.3.0/vws/inst/doc/examples/bessel/LinearVWSRegion.h |only vws-0.3.0/vws/inst/doc/examples/ln-norm |only vws-0.3.0/vws/inst/doc/examples/vmf/LinearVWSRegion.h |only vws-0.3.0/vws/inst/include/FMMProposal.h |only vws-0.3.0/vws/inst/include/IntConstRegion.h |only vws-0.3.0/vws/inst/include/RealConstRegion-defaults.h |only vws-0.3.0/vws/inst/include/RealConstRegion.h |only vws-0.3.0/vws/inst/include/Region.h |only vws-0.3.0/vws/inst/include/UnivariateHelper.h |only vws-0.3.0/vws/inst/include/timestamp.h |only vws-0.3.0/vws/vignettes/examples/bessel/LinearVWSRegion.h |only vws-0.3.0/vws/vignettes/examples/ln-norm |only vws-0.3.0/vws/vignettes/examples/vmf/LinearVWSRegion.h |only vws-0.4.0/vws/DESCRIPTION | 8 vws-0.4.0/vws/MD5 | 137 - vws-0.4.0/vws/NEWS.md |only vws-0.4.0/vws/build/vignette.rds |binary vws-0.4.0/vws/inst/doc/examples/bessel/bessel-v1.cpp | 10 vws-0.4.0/vws/inst/doc/examples/bessel/bessel-v2.cpp | 10 vws-0.4.0/vws/inst/doc/examples/bessel/bessel-v3.cpp | 10 vws-0.4.0/vws/inst/doc/examples/bessel/functions.h | 2 vws-0.4.0/vws/inst/doc/examples/bessel/linear-vws-region.h |only vws-0.4.0/vws/inst/doc/examples/privacy |only vws-0.4.0/vws/inst/doc/examples/privacy-gibbs |only vws-0.4.0/vws/inst/doc/examples/vmf/driver.R | 29 vws-0.4.0/vws/inst/doc/examples/vmf/linear-vws-region.h |only vws-0.4.0/vws/inst/doc/examples/vmf/vmf-v1-module.cpp |only vws-0.4.0/vws/inst/doc/examples/vmf/vmf-v1-xptr.cpp |only vws-0.4.0/vws/inst/doc/examples/vmf/vmf-v1.cpp | 6 vws-0.4.0/vws/inst/doc/examples/vmf/vmf-v2.cpp | 6 vws-0.4.0/vws/inst/doc/examples/vmf/vmf-v3.cpp | 6 vws-0.4.0/vws/inst/doc/vws.R | 477 +++- vws-0.4.0/vws/inst/doc/vws.pdf |binary vws-0.4.0/vws/inst/doc/vws.qmd | 1209 ++++++++---- vws-0.4.0/vws/inst/include/fmm-proposal.h |only vws-0.4.0/vws/inst/include/int-const-region.h |only vws-0.4.0/vws/inst/include/optimize-hybrid.h | 2 vws-0.4.0/vws/inst/include/real-const-region-defaults.h |only vws-0.4.0/vws/inst/include/real-const-region.h |only vws-0.4.0/vws/inst/include/region.h |only vws-0.4.0/vws/inst/include/rejection-args.h | 24 vws-0.4.0/vws/inst/include/rejection-tune.h |only vws-0.4.0/vws/inst/include/rejection.h | 34 vws-0.4.0/vws/inst/include/result.h | 18 vws-0.4.0/vws/inst/include/univariate-helper.h |only vws-0.4.0/vws/inst/include/vws.h | 30 vws-0.4.0/vws/man/vws-package.Rd | 5 vws-0.4.0/vws/vignettes/common.sty | 6 vws-0.4.0/vws/vignettes/examples/bessel/bessel-v1.cpp | 10 vws-0.4.0/vws/vignettes/examples/bessel/bessel-v2.cpp | 10 vws-0.4.0/vws/vignettes/examples/bessel/bessel-v3.cpp | 10 vws-0.4.0/vws/vignettes/examples/bessel/functions.h | 2 vws-0.4.0/vws/vignettes/examples/bessel/linear-vws-region.h |only vws-0.4.0/vws/vignettes/examples/privacy |only vws-0.4.0/vws/vignettes/examples/privacy-gibbs |only vws-0.4.0/vws/vignettes/examples/vmf/driver.R | 29 vws-0.4.0/vws/vignettes/examples/vmf/linear-vws-region.h |only vws-0.4.0/vws/vignettes/examples/vmf/vmf-v1-module.cpp |only vws-0.4.0/vws/vignettes/examples/vmf/vmf-v1-xptr.cpp |only vws-0.4.0/vws/vignettes/examples/vmf/vmf-v1.cpp | 6 vws-0.4.0/vws/vignettes/examples/vmf/vmf-v2.cpp | 6 vws-0.4.0/vws/vignettes/examples/vmf/vmf-v3.cpp | 6 vws-0.4.0/vws/vignettes/references.bib | 115 - vws-0.4.0/vws/vignettes/software-design.pdf |binary vws-0.4.0/vws/vignettes/vws.qmd | 1209 ++++++++---- 65 files changed, 2519 insertions(+), 913 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.15 dated 2026-07-17 and 2.0.16 dated 2026-07-24
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 12 insertions(+), 7 deletions(-)
Title: Retrieval, Analysis and Visualization of Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation
data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows
retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala [aut, cre] ,
Daniel Ayala [aut] ,
David Ruiz [aut] ,
Aleix Selles [aut],
Pablo Hernandez [aut] ,
Lara Selles Vidal [aut]
Maintainer: Rafael Ayala <rafaelayalahernandez@gmail.com>
Diff between openSkies versions 1.3.0 dated 2026-01-20 and 1.3.1 dated 2026-07-24
DESCRIPTION | 12 +- MD5 | 18 ++-- NAMESPACE | 2 NEWS | 7 + R/openSkies_getStateVectorsFunctions.R | 5 - R/openSkies_otherSupportFunctions.R | 138 ++++++++++++++++++++++++++++----- inst/doc/openSkies.html | 2 inst/unitTests/test_all.R | 51 ++++++++++++ man/getIntervalStateVectors.Rd | 2 tests/runTests.R | 8 + 10 files changed, 203 insertions(+), 42 deletions(-)
Title: Optimal Transport Based Testing in Factorial Designs
Description: Perform optimal transport based tests in factorial designs as introduced in Groppe et al. (2025) <doi:10.48550/arXiv.2509.13970> via the FDOTT() function. These tests are inspired by ANOVA and its nonparametric counterparts. They allow for testing linear relationships in factorial designs between finitely supported probability measures on a metric space. Such relationships include equality of all measures (no treatment effect), interaction effects between a number of factors, as well as main and simple factor effects.
Author: Michel Groppe [aut, cre],
Linus Niemoeller [aut]
Maintainer: Michel Groppe <michel.groppe@uni-goettingen.de>
Diff between FDOTT versions 0.1.0 dated 2025-10-01 and 0.2.0 dated 2026-07-24
FDOTT-0.1.0/FDOTT/man/sim_barycenter.Rd |only FDOTT-0.1.0/FDOTT/man/sim_fac.Rd |only FDOTT-0.2.0/FDOTT/DESCRIPTION | 12 FDOTT-0.2.0/FDOTT/MD5 | 39 +- FDOTT-0.2.0/FDOTT/NAMESPACE | 1 FDOTT-0.2.0/FDOTT/NEWS.md |only FDOTT-0.2.0/FDOTT/R/FDOTT-package.R | 10 FDOTT-0.2.0/FDOTT/R/barycenter_simulation.R | 37 +- FDOTT-0.2.0/FDOTT/R/barycenter_test.R | 2 FDOTT-0.2.0/FDOTT/R/contrast_formula.R |only FDOTT-0.2.0/FDOTT/R/contrast_mat.R | 71 ++-- FDOTT-0.2.0/FDOTT/R/fd_hsd.R | 50 +-- FDOTT-0.2.0/FDOTT/R/fd_simulation.R | 39 +- FDOTT-0.2.0/FDOTT/R/fd_test.R | 88 ++++- FDOTT-0.2.0/FDOTT/R/had_deriv_ot_barycenter.R | 3 FDOTT-0.2.0/FDOTT/R/ot.R | 31 + FDOTT-0.2.0/FDOTT/R/sampling.R | 18 - FDOTT-0.2.0/FDOTT/R/utils.R | 10 FDOTT-0.2.0/FDOTT/build/partial.rdb |binary FDOTT-0.2.0/FDOTT/man/FDOTT-deprecated.Rd |only FDOTT-0.2.0/FDOTT/man/FDOTT-package.Rd | 3 FDOTT-0.2.0/FDOTT/man/FDOTT.Rd | 159 ++++------ FDOTT-0.2.0/FDOTT/man/simulate_limit_FDOTT-deprecated.Rd |only FDOTT-0.2.0/FDOTT/man/simulate_limit_ot_barycenter_test-deprecated.Rd |only 24 files changed, 355 insertions(+), 218 deletions(-)
More information about SteadyStateBVAR at CRAN
Permanent link
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.8.0 dated 2026-07-23 and 1.8.1 dated 2026-07-24
DESCRIPTION | 6 +-- MD5 | 18 ++++----- NEWS.md | 2 - inst/doc/DIF_vignette.html | 4 +- inst/doc/Equating.html | 8 ++-- inst/doc/Plausible_Values.html | 16 ++++---- inst/doc/Test_Individual_differences.html | 14 +++---- inst/doc/dexter.html | 56 +++++++++++++++--------------- inst/doc/profile-plots.html | 4 +- tests/testthat/test_plausible_values.R | 5 ++ 10 files changed, 68 insertions(+), 65 deletions(-)
Title: Visual Diagnostics for Multiple Imputation
Description: A comprehensive suite of static and interactive visual diagnostics for assessing the quality of multiply-imputed data obtained from packages such as 'mixgb' and 'mice'. The package supports inspection of distributional characteristics, diagnostics based on masking observed values and comparing them with re-imputed values, and convergence diagnostics.
Author: Yongshi Deng [aut, cre] ,
Thomas Lumley [ths]
Maintainer: Yongshi Deng <agnes.yongshideng@gmail.com>
Diff between vismi versions 0.9.5 dated 2026-02-03 and 1.0.0 dated 2026-07-24
DESCRIPTION | 11 ++-- MD5 | 65 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 5 ++ R/aesthetic_vismi.R | 95 ++++++++++++++++++++++---------------- R/aesthetic_vsimi_overimp.R | 12 +++- R/ggplot1d.R | 13 ++--- R/ggplot2d.R | 22 +++----- R/ggplot3d.R | 24 ++++----- R/overimp.R | 39 +++++++++++---- R/overimp1D.R | 105 ++++++++++++++++++++++-------------------- R/overimp2D.R | 18 +++---- R/overimp_mice.R |only R/overimp_mixgb.R | 9 ++- R/overimp_postprocess.R | 35 ++++++++++++++ R/plotly1d.R | 8 +-- R/plotly2d.R | 12 ++-- R/plotly3d.R | 16 +++--- R/trellis_vismi_converge.R | 14 ++++- R/trellis_vismi_overimp.R | 8 ++- R/validate.R | 2 R/vismi-package.R | 3 - R/vismi.R | 96 +++++++++++++++++++++++++++++++++++++- R/vismi_converge.R | 14 ++++- R/vismi_overimp.R | 90 ++++++++++++++++++++++++++++++------ README.md | 7 ++ inst/CITATION | 8 ++- man/overimp.Rd | 11 +++- man/trellis_vismi_converge.Rd | 14 ++++- man/trellis_vismi_overimp.Rd | 8 ++- man/vismi-package.Rd | 2 man/vismi.Rd | 87 ++++++++++++++++++++++++++++++++++ man/vismi_converge.Rd | 14 ++++- man/vismi_overimp.Rd | 48 ++++++++++++++++++- 34 files changed, 669 insertions(+), 248 deletions(-)
Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: Provides geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling makes it possible to estimate net rainfall from streamflow
measurements following Boudhraâ et al. (2018)
<doi:10.1080/02626667.2018.1425801>. The resulting net rainfall is then
interpolated to ungauged catchments to simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 1.1.12 dated 2026-07-20 and 1.1.18 dated 2026-07-24
DESCRIPTION | 18 - MD5 | 94 ++++----- R/as_transfr.R | 53 +++-- R/convolution.R | 24 +- R/hdist.R | 32 ++- R/inversion.R | 127 ++++++++----- R/lagtime.R | 13 - R/mixr.R | 56 +++-- R/plot.R | 4 R/quick_transfr.R | 24 +- R/rapriori.R | 25 +- R/rsimilarity.R | 15 + R/rsimilarity_model.R | 34 +-- R/uh.R | 12 - R/velocity.R | 7 R/weightr.R | 16 - README.md | 13 - build/partial.rdb |binary inst/doc/V01_get_started.Rmd | 24 +- inst/doc/V01_get_started.html | 149 +++++++-------- inst/doc/V02_inputs_preparation_stars.R | 16 - inst/doc/V02_inputs_preparation_stars.Rmd | 32 +-- inst/doc/V02_inputs_preparation_stars.html | 71 +++---- inst/doc/V03_inputs_preparation_whitebox.R | 148 +++++++-------- inst/doc/V03_inputs_preparation_whitebox.Rmd | 64 +++--- inst/doc/V03_inputs_preparation_whitebox.html | 250 +++++++++++++------------- man/Blavet.Rd | 8 man/Oudon.Rd | 6 man/as_transfr.Rd | 19 + man/convolution.Rd | 18 - man/hdist.Rd | 10 - man/inversion.Rd | 55 +++-- man/lagtime.Rd | 8 man/mixr.Rd | 26 +- man/plot.Rd | 2 man/quick_transfr.Rd | 22 +- man/rapriori.Rd | 18 - man/rsimilarity.Rd | 6 man/rsimilarity_model.Rd | 24 +- man/transfR.Rd | 14 - man/uh.Rd | 8 man/velocity.Rd | 6 man/weightr.Rd | 16 - src/gdist.f90 | 10 - src/similarity_module.f90 | 6 vignettes/V01_get_started.Rmd | 24 +- vignettes/V02_inputs_preparation_stars.Rmd | 32 +-- vignettes/V03_inputs_preparation_whitebox.Rmd | 64 +++--- 48 files changed, 900 insertions(+), 823 deletions(-)
Title: Statistical Pattern Recognition and daTing using Archaeological
Artefacts assemblageS
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages.
Package of statistical tools for archaeology.
hclustcompro()/perioclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021, ISBN:978-3-030-60103-4).
mapclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>.
seriograph(): Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>.
cerardat(): Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Author: Arthur Coulon [aut, cre],
Lise Bellanger [aut],
Philippe Husi [aut],
Bruno Desachy [ctb],
Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>
This is a re-admission after prior archival of version 1.2.6 dated 2026-07-02
Diff between SPARTAAS versions 1.2.6 dated 2026-07-02 and 1.2.7 dated 2026-07-24
DESCRIPTION | 10 +- MD5 | 18 ++-- R/cerardat.R | 150 +++++++++++++++++++++++++---------- R/mapclust.R | 4 R/zzz.R | 2 build/partial.rdb |binary inst/shiny-examples/map.app/server.R | 4 man/arrangePlot.Rd | 7 + man/cerardat.Rd | 5 - man/plot.cerardat_obj.Rd | 12 ++ 10 files changed, 150 insertions(+), 62 deletions(-)
Title: Inference Tool for Antibody Haplotype
Description: Infers V-D-J (Variable-Diversity-Joining) haplotypes and gene
deletions from AIRR-seq (Adaptive Immune Receptor Repertoire sequencing)
data for Ig (Immunoglobulin) and TR (T cell Receptor) chains, based on J
(Joining), D (Diversity), or V (Variable) genes as anchor, by adapting a
Bayesian framework.
It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene.
Citation:
Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>.
Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.
Author: Ayelet Peres [aut, cre],
Moriah Gidoni [aut],
Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <ayelet.peres@yale.edu>
This is a re-admission after prior archival of version 0.2.5 dated 2023-02-06
Diff between rabhit versions 0.2.5 dated 2023-02-06 and 0.4.0 dated 2026-07-24
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More information about heatmapbehavior at CRAN
Permanent link
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Brent Pedersen [cph] ,
Giulio Genovese [cph] ,
Nicola Asuni [cph] ,
Devon Ryan [cph] ,
Duc [...truncated...]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 1.4.0-0.1.0 dated 2026-07-10 and 1.5.0-0.1.0 dated 2026-07-24
DESCRIPTION | 12 MD5 | 333 + NAMESPACE | 4 NEWS.md | 247 + R/bootstrap.R | 125 R/duckhts.R | 206 + configure | 52 configure.win | 47 inst/COPYRIGHT | 6 inst/duckhts_extension/bam_bin_counts.c | 6 inst/duckhts_extension/bcf_reader.c | 476 +- inst/duckhts_extension/bcftools_norm_udf.c | 23 inst/duckhts_extension/bigwig_reader.c |only inst/duckhts_extension/duckhts.c | 109 inst/duckhts_extension/duckvep |only inst/duckhts_extension/fastq_qc.c |only inst/duckhts_extension/htslib/LICENSE | 4 inst/duckhts_extension/htslib/Makefile | 108 inst/duckhts_extension/htslib/NEWS | 141 inst/duckhts_extension/htslib/VERSION | 2 inst/duckhts_extension/htslib/annot-tsv.1 | 2 inst/duckhts_extension/htslib/annot-tsv.c | 11 inst/duckhts_extension/htslib/bcf_sr_sort.c | 200 - inst/duckhts_extension/htslib/bgzf.c | 39 inst/duckhts_extension/htslib/bgzf_internal.h | 6 inst/duckhts_extension/htslib/bgzip.1 | 2 inst/duckhts_extension/htslib/bgzip.c | 14 inst/duckhts_extension/htslib/config.guess | 27 inst/duckhts_extension/htslib/config.h.in | 6 inst/duckhts_extension/htslib/config.mk.in | 2 inst/duckhts_extension/htslib/config.sub | 768 +++- inst/duckhts_extension/htslib/configure | 1902 +++++----- inst/duckhts_extension/htslib/configure.ac | 33 inst/duckhts_extension/htslib/cram/cram_codecs.c | 1848 --------- inst/duckhts_extension/htslib/cram/cram_codecs.h | 67 inst/duckhts_extension/htslib/cram/cram_decode.c | 314 - inst/duckhts_extension/htslib/cram/cram_decode.h | 4 inst/duckhts_extension/htslib/cram/cram_encode.c | 408 -- inst/duckhts_extension/htslib/cram/cram_external.c | 9 inst/duckhts_extension/htslib/cram/cram_index.c | 47 inst/duckhts_extension/htslib/cram/cram_io.c | 416 -- inst/duckhts_extension/htslib/cram/cram_stats.c | 25 inst/duckhts_extension/htslib/cram/cram_structs.h | 56 inst/duckhts_extension/htslib/cram/pooled_alloc.c | 5 inst/duckhts_extension/htslib/cram/string_alloc.c | 18 inst/duckhts_extension/htslib/faidx.c | 79 inst/duckhts_extension/htslib/header.c | 50 inst/duckhts_extension/htslib/hfile.c | 15 inst/duckhts_extension/htslib/hfile_libcurl.c | 214 + inst/duckhts_extension/htslib/hfile_s3.c | 181 inst/duckhts_extension/htslib/hts.c | 55 inst/duckhts_extension/htslib/hts_expr.c | 7 inst/duckhts_extension/htslib/htscodecs/NEWS.md | 13 inst/duckhts_extension/htslib/htscodecs/htscodecs/htscodecs.h | 2 inst/duckhts_extension/htslib/htscodecs/htscodecs/tokenise_name3.c | 6 inst/duckhts_extension/htslib/htscodecs/htscodecs/version.h | 2 inst/duckhts_extension/htslib/htsfile.1 | 2 inst/duckhts_extension/htslib/htsfile.c | 2 inst/duckhts_extension/htslib/htslib-s3-plugin.7 | 2 inst/duckhts_extension/htslib/htslib.map | 10 inst/duckhts_extension/htslib/htslib/bgzf.h | 13 inst/duckhts_extension/htslib/htslib/faidx.h | 4 inst/duckhts_extension/htslib/htslib/hfile.h | 15 inst/duckhts_extension/htslib/htslib/hts.h | 2 inst/duckhts_extension/htslib/htslib/hts_alloc.h |only inst/duckhts_extension/htslib/htslib/hts_defs.h | 15 inst/duckhts_extension/htslib/htslib/kbitset.h | 5 inst/duckhts_extension/htslib/htslib/ksort.h | 6 inst/duckhts_extension/htslib/htslib/kstring.h | 4 inst/duckhts_extension/htslib/htslib/sam.h | 3 inst/duckhts_extension/htslib/htslib/synced_bcf_reader.h | 232 - inst/duckhts_extension/htslib/htslib/tbx.h | 13 inst/duckhts_extension/htslib/htslib/vcf.h | 50 inst/duckhts_extension/htslib/htslib_vars.mk | 5 inst/duckhts_extension/htslib/kstring.c | 20 inst/duckhts_extension/htslib/m4/hts_prog_cc_warnings.m4 | 46 inst/duckhts_extension/htslib/probaln.c | 5 inst/duckhts_extension/htslib/realn.c | 24 inst/duckhts_extension/htslib/ref_cache/listener.c | 5 inst/duckhts_extension/htslib/ref_cache/log_files.c | 3 inst/duckhts_extension/htslib/ref_cache/main.c | 10 inst/duckhts_extension/htslib/ref_cache/poll_wrap_poll.c | 17 inst/duckhts_extension/htslib/ref_cache/ref-cache.1 | 2 inst/duckhts_extension/htslib/regidx.c | 9 inst/duckhts_extension/htslib/sam.c | 80 inst/duckhts_extension/htslib/sam_internal.h | 2 inst/duckhts_extension/htslib/synced_bcf_reader.c | 475 +- inst/duckhts_extension/htslib/tabix.1 | 45 inst/duckhts_extension/htslib/tabix.c | 77 inst/duckhts_extension/htslib/tbx.c | 79 inst/duckhts_extension/htslib/thread_pool.c | 5 inst/duckhts_extension/htslib/vcf.c | 115 inst/duckhts_extension/htslib/vcfutils.c | 8 inst/duckhts_extension/htslib/version.sh | 2 inst/duckhts_extension/include/duckhts_simd.h | 37 inst/duckhts_extension/include/duckhts_simd_internal.h | 19 inst/duckhts_extension/include/duckhts_simd_kernels.def | 1 inst/duckhts_extension/include/duckvep_sql.h |only inst/duckhts_extension/include/hts_io_tuning.h | 46 inst/duckhts_extension/libBigWig |only inst/duckhts_extension/libbigwig_hfile_io.c |only inst/duckhts_extension/seq_reader.c | 508 ++ inst/duckhts_extension/simd/duckhts_simd_avx2.c | 151 inst/duckhts_extension/simd/duckhts_simd_dispatch.c | 43 inst/duckhts_extension/simd/duckhts_simd_neon.c | 260 + inst/duckhts_extension/simd/duckhts_simd_scalar.c | 56 inst/duckhts_extension/simd/duckhts_simd_wasm_simd128.c | 265 + inst/duckhts_extension/tabix_reader.c | 32 inst/duckhts_extension/variantkey_udf.c | 79 inst/duckhts_extension/vep_parser.c | 21 inst/extdata/duckvep |only inst/extdata/duckvep_clinvar_terminal_partial.fa |only inst/extdata/duckvep_clinvar_terminal_partial.fa.fai |only inst/extdata/duckvep_terminal_partial.fa |only inst/extdata/duckvep_terminal_partial.fa.fai |only inst/extdata/ensembl_release_consequences.vcf |only inst/extdata/fastq_long_qname.fq |only inst/extdata/fastq_multiline.fq |only inst/extdata/fastq_truncated.fq |only inst/extdata/libbigwig_test.bw |only inst/extdata/parallel_empty_contigs.bcf |only inst/extdata/parallel_empty_contigs.bcf.csi |only inst/extdata/parallel_empty_contigs.vcf | 248 + inst/function_catalog/functions.md | 37 inst/function_catalog/functions.tsv | 27 inst/function_catalog/functions.yaml | 196 - inst/htslib_config.R.in | 158 inst/tinytest/test_basic.R | 27 inst/tinytest/test_bcf.R | 71 inst/tinytest/test_bigwig.R |only inst/tinytest/test_duckvep.R |only inst/tinytest/test_fastq_qc.R |only inst/tinytest/test_htslib_contract.R |only inst/tinytest/test_integration.R | 30 inst/tinytest/test_parallel_empty_contigs.R | 44 inst/tinytest/test_seq_ops.R | 73 inst/tinytest/test_variantkey_regionkey.R | 15 man/rduckhts_bigwig.Rd |only man/rduckhts_htslib_config.Rd |only man/rduckhts_htslib_info.Rd |only man/rduckhts_htslib_version.Rd |only man/setup_hts_env.Rd | 3 142 files changed, 7769 insertions(+), 4844 deletions(-)
Title: Generating Cluster Masks for Single-Cell Dimensional Reduction
Plots
Description: Implements a procedure to automatically generate 2D masks
for clusters on dimensional reduction plots from methods like
t-SNE (t-distributed stochastic neighbor embedding) or
UMAP (uniform manifold approximation and projection),
with a focus on single-cell RNA-sequencing data.
Author: Alexey Sergushichev [aut, cre]
Maintainer: Alexey Sergushichev <alsergbox@gmail.com>
Diff between mascarade versions 0.4.1 dated 2026-07-21 and 0.4.2 dated 2026-07-24
DESCRIPTION | 10 - MD5 | 25 +- NAMESPACE | 4 R/ggforce_mark_label.R | 32 ++- R/mascarade-package.R | 7 data/exampleMaskTable.rda |only inst/doc/mascarade-gallery.html | 2 inst/doc/mascarade-tutorial.html | 24 +- man/exampleMaskTable.Rd |only tests/testthat/fixtures/golden_scores.rds |binary tests/testthat/fixtures/make-placement-fixtures.R |only tests/testthat/fixtures/placement_geom.rds |only tests/testthat/helper-fixtures.R |only tests/testthat/helper-score.R | 155 ++++++++++++----- tests/testthat/test-fancyMask.R | 54 ++---- tests/testthat/test-placement.R | 197 +++++++++++----------- 16 files changed, 307 insertions(+), 203 deletions(-)
Title: Extract and Visualize the Results of Multivariate Data Analyses
Description: Provides easy-to-use functions to extract and visualize the output
of multivariate data analyses, including 'PCA' (Principal Component Analysis),
'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis),
'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis),
and 'HMFA' (Hierarchical Multiple Factor Analysis) from different R packages.
It standardizes coordinates, squared cosines, contributions, and eigenvalues
from several analysis backends and produces 'ggplot2'-based factor maps,
scree plots, contribution plots, clustering diagnostics, dendrograms, and
silhouette plots. It also visualizes two-dimensional 'UMAP' and t-SNE
embeddings and adapts precomputed or 'tidymodels' principal-component
results for the same plotting interface.
Author: Alboukadel Kassambara [aut, cre] ,
Fabian Mundt [aut],
Laszlo Erdey [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between factoextra versions 2.1.0 dated 2026-06-26 and 2.2.0 dated 2026-07-24
factoextra-2.1.0/factoextra/tests/testthat/Rplots.pdf |only factoextra-2.1.0/factoextra/tools |only factoextra-2.2.0/factoextra/DESCRIPTION | 33 factoextra-2.2.0/factoextra/MD5 | 206 +-- factoextra-2.2.0/factoextra/NAMESPACE | 7 factoextra-2.2.0/factoextra/NEWS.md | 246 +++ factoextra-2.2.0/factoextra/R/as_factoextra.R | 380 +++++ factoextra-2.2.0/factoextra/R/dist.R | 8 factoextra-2.2.0/factoextra/R/eclust.R | 22 factoextra-2.2.0/factoextra/R/eigenvalue.R | 385 ++++- factoextra-2.2.0/factoextra/R/facto_summarize.R | 104 + factoextra-2.2.0/factoextra/R/fviz.R | 242 +++ factoextra-2.2.0/factoextra/R/fviz_add.R | 6 factoextra-2.2.0/factoextra/R/fviz_ca.R | 44 factoextra-2.2.0/factoextra/R/fviz_cluster.R | 157 +- factoextra-2.2.0/factoextra/R/fviz_contrib.R | 30 factoextra-2.2.0/factoextra/R/fviz_cos2.R | 40 factoextra-2.2.0/factoextra/R/fviz_dend.R | 133 +- factoextra-2.2.0/factoextra/R/fviz_famd.R | 29 factoextra-2.2.0/factoextra/R/fviz_hmfa.R | 40 factoextra-2.2.0/factoextra/R/fviz_mca.R | 110 + factoextra-2.2.0/factoextra/R/fviz_mclust.R | 10 factoextra-2.2.0/factoextra/R/fviz_mfa.R | 36 factoextra-2.2.0/factoextra/R/fviz_nbclust.R | 184 ++ factoextra-2.2.0/factoextra/R/fviz_pca.R | 144 +- factoextra-2.2.0/factoextra/R/fviz_silhouette.R | 34 factoextra-2.2.0/factoextra/R/fviz_umap.R |only factoextra-2.2.0/factoextra/R/get_ca.R | 10 factoextra-2.2.0/factoextra/R/get_clust_tendency.R | 173 +- factoextra-2.2.0/factoextra/R/get_famd.R | 7 factoextra-2.2.0/factoextra/R/get_hmfa.R | 11 factoextra-2.2.0/factoextra/R/get_mca.R | 9 factoextra-2.2.0/factoextra/R/get_mfa.R | 11 factoextra-2.2.0/factoextra/R/get_pca.R | 186 +- factoextra-2.2.0/factoextra/R/hcut.R | 8 factoextra-2.2.0/factoextra/R/hkmeans.R | 6 factoextra-2.2.0/factoextra/R/print.factoextra.R | 25 factoextra-2.2.0/factoextra/R/theme_palette.R |only factoextra-2.2.0/factoextra/R/utilities.R | 182 ++ factoextra-2.2.0/factoextra/R/zzz.R | 24 factoextra-2.2.0/factoextra/README.md | 187 +- factoextra-2.2.0/factoextra/build/partial.rdb |only factoextra-2.2.0/factoextra/inst/doc/extending-factoextra.R | 169 -- factoextra-2.2.0/factoextra/inst/doc/extending-factoextra.Rmd | 104 - factoextra-2.2.0/factoextra/inst/doc/extending-factoextra.html | 652 ++++------ factoextra-2.2.0/factoextra/man/as_factoextra.Rd | 101 + factoextra-2.2.0/factoextra/man/clean_lock_files.Rd | 22 factoextra-2.2.0/factoextra/man/dist.Rd | 8 factoextra-2.2.0/factoextra/man/eclust.Rd | 20 factoextra-2.2.0/factoextra/man/eigenvalue.Rd | 53 factoextra-2.2.0/factoextra/man/facto_summarize.Rd | 16 factoextra-2.2.0/factoextra/man/factoextra_palette.Rd |only factoextra-2.2.0/factoextra/man/figures |only factoextra-2.2.0/factoextra/man/fviz.Rd | 52 factoextra-2.2.0/factoextra/man/fviz_add.Rd | 6 factoextra-2.2.0/factoextra/man/fviz_ca.Rd | 44 factoextra-2.2.0/factoextra/man/fviz_cluster.Rd | 58 factoextra-2.2.0/factoextra/man/fviz_contrib.Rd | 30 factoextra-2.2.0/factoextra/man/fviz_cos2.Rd | 28 factoextra-2.2.0/factoextra/man/fviz_dend.Rd | 77 - factoextra-2.2.0/factoextra/man/fviz_ellipses.Rd | 6 factoextra-2.2.0/factoextra/man/fviz_famd.Rd | 31 factoextra-2.2.0/factoextra/man/fviz_hmfa.Rd | 28 factoextra-2.2.0/factoextra/man/fviz_mca.Rd | 87 - 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93 files changed, 4844 insertions(+), 1670 deletions(-)
Title: Generate Density Rasters from Polygon and Census Data
Description: Creates continuous density raster surfaces by joining vector spatial
layers with tabular data frameworks, normalizing values by ellipsoidal
polygon area calculations. Reconciles discrete boundary-constrained census or
survey counts with uniform grids. Accepts spatial objects in-memory or via
file paths. Methods are based on spatial rasterization workflows implemented
in the 'terra' package Hijmans (2025) <https://rspatial.github.io/terra/>.
Author: Sahal Paladan [aut, cre]
Maintainer: Sahal Paladan <sahalpaladan@gmail.com>
Diff between GeoDensityR versions 0.1.2 dated 2026-06-05 and 0.2.0 dated 2026-07-24
DESCRIPTION | 21 +-- MD5 | 7 - NEWS.md |only R/generate_density_raster.R | 223 +++++++++++++++-------------------------- man/generate_density_raster.Rd | 53 ++++----- 5 files changed, 124 insertions(+), 180 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package development
infrastructure inside the data integration centers ('DIZ') to
standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
Helene Koester [ctb],
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.1.3 dated 2024-11-26 and 0.1.4 dated 2026-07-24
DESCRIPTION | 21 MD5 | 42 - NAMESPACE | 20 R/check_if_table_exists.R | 126 ++--- R/close_connection.R | 90 ++-- R/combine_stats.R | 316 +++++++------- R/db_connection.R | 740 +++++++++++++++++------------------ R/get_config_env.R | 406 +++++++++---------- R/get_db_systems.R | 66 +-- R/query_database.R | 204 ++++----- README.md | 6 man/check_if_table_exists.Rd | 54 +- man/close_connection.Rd | 64 +-- man/combine_stats.Rd | 62 +- man/db_connection.Rd | 156 +++---- man/get_config_env.Rd | 116 ++--- man/get_db_systems.Rd | 44 +- man/get_default_config_elements.Rd | 30 - man/query_database.Rd | 118 ++--- man/xml_2_json.Rd | 34 - tests/testthat/test-get_config_env.R | 506 +++++++++++------------ tests/testthat/test-lints.R | 66 +-- 22 files changed, 1642 insertions(+), 1645 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.2.3 dated 2026-07-13 and 0.2.4 dated 2026-07-24
DESCRIPTION | 6 MD5 | 104 +++--- NEWS.md | 20 + R/RTMB_Model.R | 4 R/distributions.R | 76 ++-- R/wrapper_fa.R | 20 - R/wrapper_glmer.R | 289 ++++++++++++++--- R/wrapper_irt.R | 8 R/wrapper_lm_glm_lmer.R | 27 + R/wrapper_lrt.R | 31 + R/wrapper_mixture.R | 55 +++ R/wrapper_ttest.R | 17 - R/wrappers_prior.R | 56 +++ build/vignette.rds |binary inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 4 inst/doc/ja-introduction.Rmd | 4 inst/doc/ja-introduction.html | 4 inst/doc/ja-quick_start.Rmd | 6 inst/doc/ja-quick_start.html | 6 inst/doc/ja-rtmb_glmer.R | 11 inst/doc/ja-rtmb_glmer.Rmd | 24 + inst/doc/ja-rtmb_glmer.html | 363 +++++++++++----------- inst/doc/ja-wrapper_functions.Rmd | 27 + inst/doc/ja-wrapper_functions.html | 33 +- inst/doc/quick_start.Rmd | 4 inst/doc/quick_start.html | 6 inst/doc/rtmb_glmer.R | 11 inst/doc/rtmb_glmer.Rmd | 26 + inst/doc/rtmb_glmer.html | 267 ++++++++-------- inst/doc/wrapper_functions.R | 4 inst/doc/wrapper_functions.Rmd | 23 - inst/doc/wrapper_functions.html | 23 - man/prior_normal.Rd | 12 man/rtmb_fa.Rd | 8 man/rtmb_glm.Rd | 6 man/rtmb_glmer.Rd | 6 man/rtmb_irt.Rd | 4 man/rtmb_lm.Rd | 6 man/rtmb_lmer.Rd | 6 man/rtmb_lrt.Rd | 7 man/rtmb_mixture.Rd | 7 man/rtmb_ttest.Rd | 7 tests/testthat/test-formula-data-environment.R |only tests/testthat/test-multivariate-normal-density.R |only tests/testthat/test-wrappers.R | 180 ++++++++++ vignettes/introduction.Rmd | 4 vignettes/ja-introduction.Rmd | 4 vignettes/ja-quick_start.Rmd | 6 vignettes/ja-rtmb_glmer.Rmd | 24 + vignettes/ja-wrapper_functions.Rmd | 27 + vignettes/quick_start.Rmd | 4 vignettes/rtmb_glmer.Rmd | 26 + vignettes/wrapper_functions.Rmd | 23 - 54 files changed, 1345 insertions(+), 585 deletions(-)
Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>
Diff between basemaps versions 0.0.8 dated 2024-11-01 and 0.1.1 dated 2026-07-24
basemaps-0.0.8/basemaps/R/get_maptypes.R |only basemaps-0.0.8/basemaps/man/get_maptypes.Rd |only basemaps-0.0.8/basemaps/tests/testthat/test-get_maptypes.R |only basemaps-0.1.1/basemaps/DESCRIPTION | 21 basemaps-0.1.1/basemaps/MD5 | 34 - basemaps-0.1.1/basemaps/NAMESPACE | 15 basemaps-0.1.1/basemaps/NEWS.md | 38 + basemaps-0.1.1/basemaps/R/basemap.R | 45 + basemaps-0.1.1/basemaps/R/defaults.R | 182 +++++++ basemaps-0.1.1/basemaps/R/internal.R | 324 ++++++------- basemaps-0.1.1/basemaps/R/plot.R | 9 basemaps-0.1.1/basemaps/README.md | 37 + basemaps-0.1.1/basemaps/man/basemap.Rd | 32 - basemaps-0.1.1/basemaps/man/defaults.Rd | 2 basemaps-0.1.1/basemaps/man/maptypes.Rd |only basemaps-0.1.1/basemaps/man/plot.Rd | 9 basemaps-0.1.1/basemaps/tests/testthat/test-basemap.R | 1 basemaps-0.1.1/basemaps/tests/testthat/test-defaults.R | 55 ++ basemaps-0.1.1/basemaps/tests/testthat/test-internal.R | 2 basemaps-0.1.1/basemaps/tests/testthat/test-plot.R | 2 20 files changed, 562 insertions(+), 246 deletions(-)
Title: Fast Fuzzy String Joins for Data Frames
Description: Perform fuzzy joins on data frames using approximate string
matching. Implements inner, left, right, full, semi, and anti joins with
string distance metrics from the 'stringdist' package, including Optimal
String Alignment, Levenshtein, Damerau-Levenshtein, Jaro-Winkler, q-gram,
cosine, Jaccard, and Soundex. Uses a 'data.table' backend plus compiled
'C++' result assembly to reduce overhead in large joins, while adaptive
candidate planning avoids unnecessary distance evaluations in single-column
string joins. Suitable for reconciling misspellings, inconsistent labels,
and other near-match identifiers while optionally returning the computed
distance for each match. Bibliographic references include the 'stringdist'
package documentation (2014) <https://CRAN.R-project.org/package=stringdist>
and Robinson, D. (2015) <https://github.com/dgrtwo/fuzzyjoin>.
Author: Paul E. Santos Andrade [aut, cre, cph] ,
David Robinson [ctb]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between fuzzystring versions 0.0.5 dated 2026-03-28 and 0.0.6 dated 2026-07-24
DESCRIPTION | 16 LICENSE | 2 MD5 | 52 - NEWS.md | 8 R/RcppExports.R | 14 R/dt_fuzzy_join_cpp.R | 392 +++++--- R/dt_stringdist_join.R | 297 ++++-- R/fuzzystring-package.R | 2 R/globals.R | 23 R/misspellings.R | 2 R/utils.R | 104 ++ README.md | 4 build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/benchmark_fuzzyjoin_comparison.R | 4 inst/doc/benchmark_fuzzyjoin_comparison.Rmd | 4 inst/doc/benchmark_fuzzyjoin_comparison.html | 290 ++++++ inst/doc/getting_started.html | 4 inst/extdata/rbase_string_benchmark.csv | 1200 +++++++++++++------------- man/fuzzystring.Rd | 9 man/fuzzystring_join.Rd | 5 man/misspellings.Rd | 2 src/bind_by_rowid_cpp_matches.cpp | 114 +- tests/testthat.R | 4 tests/testthat/_snaps |only tests/testthat/test-dt_stringdist_join.R | 212 +++- tests/testthat/test-exact-join.R |only tests/testthat/test-validation-and-distance.R |only vignettes/benchmark_fuzzyjoin_comparison.Rmd | 4 29 files changed, 1829 insertions(+), 939 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Diff between castor versions 1.8.5 dated 2026-01-21 and 1.8.6 dated 2026-07-24
DESCRIPTION | 8 MD5 | 48 ++--- NAMESPACE | 5 R/RcppExports.R | 16 + R/auxiliary_routines.R | 157 +++++++++++++++--- R/consensus_taxonomies.R | 16 + R/correlate_discrete_traits.R |only R/fit_mk.R | 27 +-- R/get_all_distances_to_root.R | 2 R/get_stationary_distribution.R | 2 R/inherit_taxonomies.R |only R/place_tips_taxonomically.R | 27 ++- R/plot_tree_radial.R | 33 ++- R/read_tree.R | 4 R/simulate_mk_model.R | 2 R/write_tree.R | 2 man/collapse_tree_at_resolution.Rd | 6 man/consensus_taxonomies.Rd | 8 man/correlate_discrete_traits.Rd |only man/fit_mk.Rd | 19 +- man/inherit_taxonomies.Rd |only man/place_tips_taxonomically.Rd | 14 + man/plot_tree_radial.Rd | 4 man/read_tree.Rd | 2 man/write_tree.Rd | 2 src/RcppExports.cpp | 72 ++++++-- src/phylogenetics_cpp_routines.cpp | 321 +++++++++++++++++++++++++++++-------- 27 files changed, 611 insertions(+), 186 deletions(-)
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from
R. Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane
support, quality of life functions to make 'Databricks' simpler to
use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.13 dated 2026-05-20 and 0.2.14 dated 2026-07-24
DESCRIPTION | 10 MD5 | 142 ++--- NEWS.md | 18 R/clusters.R | 5 R/connection-pane.R | 14 R/data-structures.R | 6 R/databricks-dbi.R | 178 ++++-- R/databricks-dbplyr.R | 40 - R/dbfs.R | 4 R/experiments.R | 3 R/package-auth.R | 282 +++++++--- R/query-history.R | 2 R/request-helpers.R | 85 +-- R/sql-query-execution.R | 24 R/uc-catalogs.R | 21 R/uc-schemas.R | 20 R/uc-tables.R | 7 R/uc-volumes.R | 11 R/vector-search.R | 6 R/volume-fs.R | 5 R/warehouses.R | 2 R/workspaces.R | 2 README.md | 14 inst/doc/cluster-management.html | 5 inst/doc/managing-jobs.html | 5 inst/doc/remote-repl.html | 5 inst/doc/setup-auth.R | 25 inst/doc/setup-auth.Rmd | 97 ++- inst/doc/setup-auth.html | 128 +++- inst/doc/sql-backend.R | 5 inst/doc/sql-backend.Rmd | 7 inst/doc/sql-backend.html | 12 inst/doc/working-with-volumes.Rmd | 2 inst/doc/working-with-volumes.html | 7 man/dbConnect-DatabricksDriver-method.Rd | 4 man/dbFetch-DatabricksResult-method.Rd | 5 man/dbGetQuery-DatabricksConnection-character-method.Rd | 5 man/dbWriteTable-DatabricksConnection-AsIs-data.frame-method.Rd | 5 man/dbWriteTable-DatabricksConnection-Id-data.frame-method.Rd | 5 man/dbWriteTable-DatabricksConnection-character-data.frame-method.Rd | 5 man/db_assert_show_progress.Rd |only man/db_collect.DatabricksConnection.Rd | 12 man/db_oauth_client.Rd | 3 man/db_sql_query_history.Rd | 2 man/db_uc_catalogs_list.Rd | 3 man/db_uc_schemas_list.Rd | 3 man/db_uc_tables_list.Rd | 3 man/db_uc_volumes_list.Rd | 3 man/db_vs_indexes_query.Rd | 3 man/db_write_table_standard.Rd | 3 man/default_config_profile.Rd | 4 man/read_env_var.Rd | 4 tests/testthat/test-auth-offline-helpers.R |only tests/testthat/test-auth.R | 101 +-- tests/testthat/test-connection-pane-offline.R | 58 +- tests/testthat/test-data-structures.R | 12 tests/testthat/test-databricks-dbi-offline-helpers.R | 207 +++++++ tests/testthat/test-databricks-dbplyr-offline-helpers.R | 20 tests/testthat/test-experiments.R | 42 + tests/testthat/test-request-helpers.R | 124 +++- tests/testthat/test-uc-catalogs.R | 34 + tests/testthat/test-uc-schemas.R | 29 - tests/testthat/test-uc-tables.R | 31 + tests/testthat/test-uc-volumes.R | 35 + tests/testthat/test-unity-catalog.R | 4 tests/testthat/test-vector-search.R | 2 tests/testthat/test-volumes-fs-offline-helpers.R | 46 + tests/testthat/test-volumes-fs.R | 28 tests/testthat/test-warehouses.R | 12 vignettes/rmarkdown-databricks-notebook.R |only vignettes/rmarkdown-databricks-notebook.html |only vignettes/setup-auth.Rmd | 97 ++- vignettes/sql-backend.Rmd | 7 vignettes/working-with-volumes.Rmd | 2 74 files changed, 1618 insertions(+), 544 deletions(-)
Title: Machine Learning Benchmark Problems
Description: A collection of artificial and real-world machine learning
benchmark problems, including, e.g., several
data sets from the UCI repository.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [aut],
Kurt Hornik [cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between mlbench versions 2.1-9 dated 2026-07-13 and 2.1-10 dated 2026-07-24
mlbench-2.1-10/mlbench/DESCRIPTION | 6 +++--- mlbench-2.1-10/mlbench/MD5 | 9 +++------ mlbench-2.1-10/mlbench/NEWS | 6 ++++++ mlbench-2.1-10/mlbench/build/partial.rdb |binary mlbench-2.1-9/mlbench/data/PimaIndiansDiabetes.rda |only mlbench-2.1-9/mlbench/data/PimaIndiansDiabetes2.rda |only mlbench-2.1-9/mlbench/man/PimaIndiansDiabetes.Rd |only 7 files changed, 12 insertions(+), 9 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.8-1 dated 2026-05-23 and 3.8-2 dated 2026-07-24
DESCRIPTION | 12 ++-- MD5 | 32 +++++----- NAMESPACE | 9 +++ NEWS | 46 +++++++++++++++ R/distbdry.R | 126 +++++++++++++++++++----------------------- R/morphology.R | 33 +++++++---- R/pp3.R | 26 +++++++- R/randombasic.R | 100 ++++++++++++++++++++++++++++++++- R/unique.ppp.R | 41 +++++++++---- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/distbdry.Rd |only man/duplicated.ppp.Rd | 9 --- man/macros/defns.Rd | 30 +++++++--- man/rjitter.Rd | 2 man/rjitter.pp3.Rd |only man/spatstat.geom-internal.Rd | 4 + tests/testsM.R | 24 +++++++- 18 files changed, 365 insertions(+), 131 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo, as described
in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>.
The approximation uses Pareto smoothed importance sampling (PSIS), a
new procedure for regularizing importance weights. As a byproduct of
the calculations, we also obtain approximate standard errors for
estimated predictive errors and for the comparison of predictive
errors between models. The package also provides methods for using
stacking and other model weighting techniques to average Bayesian
predictive distributions.
Author: Aki Vehtari [aut],
Jonah Gabry [cre, aut],
Mans Magnusson [aut],
Yuling Yao [aut],
Paul-Christian Buerkner [aut],
Topi Paananen [aut],
Andrew Gelman [aut],
Ben Goodrich [ctb],
Juho Piironen [ctb],
Bruno Nicenboim [ctb],
Leevi Lindgren [ctb],
Visruth S [...truncated...]
Maintainer: Jonah Gabry <jgabry@gmail.com>
Diff between loo versions 2.10.0 dated 2026-06-26 and 2.10.1 dated 2026-07-24
DESCRIPTION | 8 ++-- MD5 | 42 ++++++++++++------------- NEWS.md | 8 ++++ R/loo_compare.R | 47 ++++++++++++++++++++-------- R/psis.R | 3 + inst/doc/loo2-elpd.html | 4 +- inst/doc/loo2-example.html | 4 +- inst/doc/loo2-large-data.html | 4 +- inst/doc/loo2-lfo.html | 16 ++++----- inst/doc/loo2-mixis.html | 4 +- inst/doc/loo2-moment-matching.html | 6 +-- inst/doc/loo2-non-factorized.html | 4 +- inst/doc/loo2-weights.html | 4 +- inst/doc/loo2-with-rstan.html | 4 +- man/loo_compare.Rd | 9 ++++- tests/testthat/_snaps/compare.md | 45 ++++++++++++++++++++++++++ tests/testthat/test_E_loo.R | 4 +- tests/testthat/test_compare.R | 12 ++++++- tests/testthat/test_loo_and_waic.R | 9 +++++ tests/testthat/test_loo_moment_matching.R | 3 + tests/testthat/test_loo_predictive_metric.R | 4 +- tests/testthat/test_psis.R | 8 +--- 22 files changed, 181 insertions(+), 71 deletions(-)
Title: Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Description: Tools for the identification of unique multilocus genotypes when
both genotyping error and missing data may be present. Includes a data
pre-screening utility to analyze pairwise locus overlap and protect against
underlying mathematical sorting constraints. Targeted for use with large
datasets and databases containing multiple samples of each individual (a common
situation in conservation genetics, particularly in non-invasive wildlife
sampling applications). Functions explicitly incorporate missing data and can
tolerate allele mismatches created by genotyping error. If you use this package,
please cite the original publication in Molecular Ecology Resources (Galpern
et al., 2012), the details for which can be generated using
citation('allelematch'). The complete user manual and analytical tutorials
are included locally as an R vignette and can be accessed within an active R
session using vignette('allelematch').
Author: Paul Galpern [aut],
Micheline Manseau [aut],
Pete Hettinga [aut],
Karen Smith [aut],
Paul Wilson [aut],
Todd Cross [cre]
Maintainer: Todd Cross <todd.cross@gmail.com>
Diff between allelematch versions 2.6.0 dated 2026-07-05 and 3.0.0 dated 2026-07-24
DESCRIPTION | 8 +- MD5 | 12 ++-- NAMESPACE | 2 R/allelematch.r | 121 +++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/allelematch.html | 4 - man/allelematch-package.Rd | 4 - 7 files changed, 95 insertions(+), 56 deletions(-)