Title: Publication-Ready Summary Tables and Forest Plots
Description: A comprehensive framework for descriptive statistics and regression
analysis that produces publication-ready tables and forest plots. Provides a
unified interface from descriptive statistics through multivariable modeling,
with support for linear models, generalized linear models, Cox proportional
hazards, and mixed-effects models. Also includes univariable screening,
multivariate regression, model comparison, and export to multiple formats
including PDF, DOCX, PPTX, 'LaTeX', HTML, and RTF. Built on 'data.table'
for computational efficiency.
Author: Paul Hsin-ti McClelland [aut, cre, cph]
Maintainer: Paul Hsin-ti McClelland <PaulHMcClelland@protonmail.com>
Diff between summata versions 0.12.0 dated 2026-08-21 and 0.13.0 dated 2026-10-18
summata-0.12.0/summata/man/get_event_variable.Rd |only summata-0.13.0/summata/DESCRIPTION | 14 summata-0.13.0/summata/MD5 | 260 ++- summata-0.13.0/summata/NEWS.md | 23 summata-0.13.0/summata/R/comp_utils.R | 95 - summata-0.13.0/summata/R/compfit.R | 32 summata-0.13.0/summata/R/coxforest.R | 292 +--- summata-0.13.0/summata/R/desc_utils.R | 450 +++++- summata-0.13.0/summata/R/desctable.R | 77 - summata-0.13.0/summata/R/fit.R | 44 summata-0.13.0/summata/R/fit_utils.R | 324 ++++ summata-0.13.0/summata/R/forest_utils.R | 375 +++++ summata-0.13.0/summata/R/fullfit.R | 22 summata-0.13.0/summata/R/glmforest.R | 230 +-- summata-0.13.0/summata/R/globals.R | 14 summata-0.13.0/summata/R/lmforest.R | 231 +-- summata-0.13.0/summata/R/m2dt.R | 243 ++- summata-0.13.0/summata/R/m2dt_utils.R | 671 ++++++++-- summata-0.13.0/summata/R/multifit.R | 390 ++++- summata-0.13.0/summata/R/multiforest.R | 56 summata-0.13.0/summata/R/number_utils.R | 32 summata-0.13.0/summata/R/surv_utils.R | 177 ++ summata-0.13.0/summata/R/survtable.R | 102 + summata-0.13.0/summata/R/table2_utils.R | 171 +- summata-0.13.0/summata/R/table2docx.R | 7 summata-0.13.0/summata/R/table2pptx.R | 7 summata-0.13.0/summata/R/table2rtf.R | 6 summata-0.13.0/summata/R/tablesave.R | 26 summata-0.13.0/summata/R/uniforest.R | 25 summata-0.13.0/summata/R/uniscreen.R | 85 - summata-0.13.0/summata/README.md | 26 summata-0.13.0/summata/build/vignette.rds |binary summata-0.13.0/summata/inst/CITATION | 2 summata-0.13.0/summata/inst/doc/advanced_workflows.html | 64 summata-0.13.0/summata/inst/doc/descriptive_tables.html | 2 summata-0.13.0/summata/inst/doc/installation_setup.R | 4 summata-0.13.0/summata/inst/doc/installation_setup.Rmd | 8 summata-0.13.0/summata/inst/doc/installation_setup.html | 16 summata-0.13.0/summata/inst/doc/model_comparison.html | 72 - summata-0.13.0/summata/inst/doc/multivariate_regression.html | 20 summata-0.13.0/summata/inst/doc/regression_modeling.html | 12 summata-0.13.0/summata/inst/doc/survival_tables.html | 10 summata-0.13.0/summata/man/add_event_column.Rd |only summata-0.13.0/summata/man/add_logical_levels.Rd |only summata-0.13.0/summata/man/aliased_coefficients.Rd |only summata-0.13.0/summata/man/average_ranks.Rd |only summata-0.13.0/summata/man/c_statistic.Rd |only summata-0.13.0/summata/man/capture_fit_error.Rd |only summata-0.13.0/summata/man/claimed_by_longer_term.Rd |only summata-0.13.0/summata/man/coef_confint.Rd |only summata-0.13.0/summata/man/compfit.Rd | 6 summata-0.13.0/summata/man/coxforest.Rd | 7 summata-0.13.0/summata/man/derive_group_index.Rd |only summata-0.13.0/summata/man/derive_group_levels.Rd |only summata-0.13.0/summata/man/desctable.Rd | 37 summata-0.13.0/summata/man/detect_plot_font.Rd | 2 summata-0.13.0/summata/man/determined_levels.Rd |only summata-0.13.0/summata/man/drop_aliased_rows.Rd |only summata-0.13.0/summata/man/drop_empty_levels.Rd |only summata-0.13.0/summata/man/effect_ci_columns.Rd |only summata-0.13.0/summata/man/effective_reference_level.Rd |only summata-0.13.0/summata/man/extract_predictor_effects.Rd | 8 summata-0.13.0/summata/man/factor_reference.Rd |only summata-0.13.0/summata/man/filter_test_args.Rd |only summata-0.13.0/summata/man/fisher_test_pvalue.Rd |only summata-0.13.0/summata/man/fit.Rd | 4 summata-0.13.0/summata/man/fixed_effect_classes.Rd |only summata-0.13.0/summata/man/format_categorical_stat.Rd | 4 summata-0.13.0/summata/man/format_interaction_term.Rd | 13 summata-0.13.0/summata/man/format_multifit_table.Rd | 16 summata-0.13.0/summata/man/format_num.Rd | 3 summata-0.13.0/summata/man/formula_names.Rd |only summata-0.13.0/summata/man/fullfit.Rd | 4 summata-0.13.0/summata/man/get_analysis_counts.Rd | 8 summata-0.13.0/summata/man/get_cached_confint.Rd | 11 summata-0.13.0/summata/man/get_event_indicator.Rd |only summata-0.13.0/summata/man/get_model_xlevels.Rd | 3 summata-0.13.0/summata/man/glmforest.Rd | 13 summata-0.13.0/summata/man/interval_quantile.Rd |only summata-0.13.0/summata/man/is_interaction_term.Rd |only summata-0.13.0/summata/man/is_significant_pvalue.Rd |only summata-0.13.0/summata/man/kruskal_wallis_pvalue.Rd |only summata-0.13.0/summata/man/level_terms.Rd |only summata-0.13.0/summata/man/lmforest.Rd | 13 summata-0.13.0/summata/man/m2dt.Rd | 17 summata-0.13.0/summata/man/main_effect_labels.Rd |only summata-0.13.0/summata/man/model_term_labels.Rd |only summata-0.13.0/summata/man/multifit.Rd | 5 summata-0.13.0/summata/man/multiforest.Rd | 7 summata-0.13.0/summata/man/parse_term.Rd | 10 summata-0.13.0/summata/man/perform_categorical_test.Rd | 15 summata-0.13.0/summata/man/perform_continuous_test.Rd | 12 summata-0.13.0/summata/man/perform_survival_test.Rd | 17 summata-0.13.0/summata/man/predictor_classes.Rd |only summata-0.13.0/summata/man/process_categorical.Rd | 3 summata-0.13.0/summata/man/process_continuous.Rd | 7 summata-0.13.0/summata/man/process_single_outcome.Rd | 3 summata-0.13.0/summata/man/process_survival.Rd | 10 summata-0.13.0/summata/man/process_variable.Rd | 9 summata-0.13.0/summata/man/rank_sum_pvalue.Rd |only summata-0.13.0/summata/man/resolve_core_count.Rd |only summata-0.13.0/summata/man/split_interaction_term.Rd |only summata-0.13.0/summata/man/stop_if_no_estimates.Rd |only summata-0.13.0/summata/man/stop_on_failed_fits.Rd |only summata-0.13.0/summata/man/surv_event_expression.Rd |only summata-0.13.0/summata/man/surv_event_indicator.Rd |only summata-0.13.0/summata/man/survtable.Rd | 34 summata-0.13.0/summata/man/table2docx.Rd | 7 summata-0.13.0/summata/man/table2pptx.Rd | 7 summata-0.13.0/summata/man/table2rtf.Rd | 6 summata-0.13.0/summata/man/tablesave.Rd | 26 summata-0.13.0/summata/man/test_arg_names.Rd |only summata-0.13.0/summata/man/uniforest.Rd | 8 summata-0.13.0/summata/man/uniscreen.Rd | 6 summata-0.13.0/summata/man/validate_predictors_exist.Rd | 4 summata-0.13.0/summata/man/weighted_logrank_test.Rd |only summata-0.13.0/summata/man/wilcox_digits_rank.Rd |only summata-0.13.0/summata/tests/testthat/helper-summata.R | 30 summata-0.13.0/summata/tests/testthat/test-c-statistic.R |only summata-0.13.0/summata/tests/testthat/test-colon-levels.R |only summata-0.13.0/summata/tests/testthat/test-compfit-intervals.R |only summata-0.13.0/summata/tests/testthat/test-compfit-scoring.R |only summata-0.13.0/summata/tests/testthat/test-compfit.R | 52 summata-0.13.0/summata/tests/testthat/test-cox-empty-levels.R |only summata-0.13.0/summata/tests/testthat/test-cox-events.R |only summata-0.13.0/summata/tests/testthat/test-coxforest-estimates.R |only summata-0.13.0/summata/tests/testthat/test-desctable-categorical.R |only summata-0.13.0/summata/tests/testthat/test-desctable-order.R |only summata-0.13.0/summata/tests/testthat/test-desctable-rank-tests.R |only summata-0.13.0/summata/tests/testthat/test-desctable-survival.R |only summata-0.13.0/summata/tests/testthat/test-desctable-test-args.R |only summata-0.13.0/summata/tests/testthat/test-desctable.R | 85 - summata-0.13.0/summata/tests/testthat/test-export-condense.R |only summata-0.13.0/summata/tests/testthat/test-export-indent.R |only summata-0.13.0/summata/tests/testthat/test-export-pvalues.R |only summata-0.13.0/summata/tests/testthat/test-fit.R | 124 - summata-0.13.0/summata/tests/testthat/test-forest-aliased.R |only summata-0.13.0/summata/tests/testthat/test-forest-font.R |only summata-0.13.0/summata/tests/testthat/test-forest-interactions.R |only summata-0.13.0/summata/tests/testthat/test-forest-intervals.R |only summata-0.13.0/summata/tests/testthat/test-forest.R | 106 - summata-0.13.0/summata/tests/testthat/test-forestsave.R | 21 summata-0.13.0/summata/tests/testthat/test-format-num.R |only summata-0.13.0/summata/tests/testthat/test-fullfit.R | 127 - summata-0.13.0/summata/tests/testthat/test-interaction-labels.R |only summata-0.13.0/summata/tests/testthat/test-logical-predictors.R |only summata-0.13.0/summata/tests/testthat/test-m2dt-order.R |only summata-0.13.0/summata/tests/testthat/test-m2dt.R | 88 - summata-0.13.0/summata/tests/testthat/test-model-counts.R |only summata-0.13.0/summata/tests/testthat/test-model-type-name.R |only summata-0.13.0/summata/tests/testthat/test-multifit-cox-counts.R |only summata-0.13.0/summata/tests/testthat/test-multifit-intervals.R |only summata-0.13.0/summata/tests/testthat/test-multifit-order.R |only summata-0.13.0/summata/tests/testthat/test-multifit-terms.R |only summata-0.13.0/summata/tests/testthat/test-multiforest-intervals.R |only summata-0.13.0/summata/tests/testthat/test-multivariate.R | 201 +- summata-0.13.0/summata/tests/testthat/test-nonsyntactic-names.R |only summata-0.13.0/summata/tests/testthat/test-number-format.R | 50 summata-0.13.0/summata/tests/testthat/test-parallel-fits.R |only summata-0.13.0/summata/tests/testthat/test-recdims.R | 26 summata-0.13.0/summata/tests/testthat/test-survtable-groups.R |only summata-0.13.0/summata/tests/testthat/test-survtable-pdigits.R |only summata-0.13.0/summata/tests/testthat/test-survtable-tests.R |only summata-0.13.0/summata/tests/testthat/test-survtable.R | 88 - summata-0.13.0/summata/tests/testthat/test-table2.R | 109 - summata-0.13.0/summata/tests/testthat/test-term-parsing.R | 210 +++ summata-0.13.0/summata/tests/testthat/test-uniforest-intervals.R |only summata-0.13.0/summata/vignettes/articles/development_roadmap.Rmd | 6 summata-0.13.0/summata/vignettes/installation_setup.Rmd | 8 169 files changed, 4333 insertions(+), 2080 deletions(-)
Title: Estimating Density after Logarithmic or Power Transformation of
Data
Description: Functions for computing: (1) the adaptive normal plug-in(PI) density estimate for data after the logarithmic transformation; (2) the adaptive log-normal PI density estimate for data after the power transformation with an exponent ranging from zero to one; (3) the single-bandwidth PI density estimate for data after the logarithmic transformation; (4) the single-bandwidth PI density estimate for data after the power transformation; (5) the data-driven bandwidth for the single-bandwidth PI estimator for data after the logarithmic transformation; (6) the rule-of-thumb bandwidth for the single-bandwidth PI estimator for data after the power transformation. For details, see the articles: (1) Savchuk, O. (2026) (submitted). Adaptive log-normal plug-in density estimator for power transformations. (2) Savchuk, O. (2026). Density estimation for log-transformed data. Computational Statistics, 41(98) <doi:10.1007/s00180-026-01766-y>. (3) Savchuk, O., Schick A. (2013). Density estimation for [...truncated...]
Author: Olga Savchuk [aut, cre, cph]
Maintainer: Olga Savchuk <olga.y.savchuk@gmail.com>
Diff between DENSaftertransform versions 0.1 dated 2026-06-02 and 1.0 dated 2026-10-18
DESCRIPTION | 16 +-- MD5 | 18 ++- NAMESPACE | 18 ++- NEWS.md |only R/DENSaftertransform.R | 183 +++++++++++++++++++++++++++++++++----- build |only man/KDE_PI_adapt_lognorm_power.Rd |only man/KDE_PI_adapt_norm.Rd | 6 - man/KDE_ln_PI.Rd | 6 - man/KDE_power_PI.Rd | 14 ++ man/h_ln_PI.Rd | 10 +- man/h_pi_datadriven_power.Rd |only 12 files changed, 214 insertions(+), 57 deletions(-)
More information about DENSaftertransform at CRAN
Permanent link
Title: Stochastic Quasi-Gradient Differential Evolution Optimization
Description: An optim-style implementation of the Stochastic Quasi-Gradient Differential Evolution (SQG-DE) optimization algorithm first published by Sala, Baldanzini, and Pierini (2018; <doi:10.1007/978-3-319-72926-8_27>). This optimization algorithm fuses the robustness of the population-based global optimization algorithm "Differential Evolution" with the efficiency of gradient-based optimization. The derivative-free algorithm uses population members to build stochastic gradient estimates, without any additional objective function evaluations. Sala, Baldanzini, and Pierini argue this algorithm is useful for 'difficult optimization problems under a tight function evaluation budget.' This package can run SQG-DE in parallel and sequentially.
Author: Brendan Matthew Galdo [aut, cre]
Maintainer: Brendan Matthew Galdo <Brendan.m.galdo@gmail.com>
Diff between graDiEnt versions 1.0.1 dated 2022-05-10 and 1.1.0 dated 2026-10-18
graDiEnt-1.0.1/graDiEnt/R/SQG_DE_bin_1_best.R |only graDiEnt-1.0.1/graDiEnt/R/SQG_DE_bin_1_curr.R |only graDiEnt-1.0.1/graDiEnt/R/SQG_DE_bin_1_rand.R |only graDiEnt-1.1.0/graDiEnt/DESCRIPTION | 17 +- graDiEnt-1.1.0/graDiEnt/MD5 | 28 +++- graDiEnt-1.1.0/graDiEnt/NEWS.md | 21 +++ graDiEnt-1.1.0/graDiEnt/R/GetAlgoParams.R | 139 ++++++++++++++++++---- graDiEnt-1.1.0/graDiEnt/R/SQG_DE_bin_1.R |only graDiEnt-1.1.0/graDiEnt/R/apply_bounds.R |only graDiEnt-1.1.0/graDiEnt/R/optim_SQGDE.R | 162 +++++++++++++++++--------- graDiEnt-1.1.0/graDiEnt/man/GetAlgoParams.Rd | 29 ++++ graDiEnt-1.1.0/graDiEnt/man/optim_SQGDE.Rd | 4 graDiEnt-1.1.0/graDiEnt/tests |only 13 files changed, 305 insertions(+), 95 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.8 dated 2024-01-24 and 1.0.9 dated 2026-10-18
HistDAWass-1.0.8/HistDAWass/man/WH.SSQ-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.SSQ2-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.bind.col-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.bind.row-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.correlation-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.correlation2-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.var.covar2-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/WH.vec.sum-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/get.MatH.ncols-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/get.MatH.nrows-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/get.MatH.rownames-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/get.MatH.varnames-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/is.registeredMH-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/minus.Rd |only HistDAWass-1.0.8/HistDAWass/man/plus-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/set.cell.MatH-methods.Rd |only HistDAWass-1.0.8/HistDAWass/man/times-methods.Rd |only HistDAWass-1.0.9/HistDAWass/DESCRIPTION | 21 HistDAWass-1.0.9/HistDAWass/MD5 | 212 HistDAWass-1.0.9/HistDAWass/NAMESPACE | 55 HistDAWass-1.0.9/HistDAWass/NEWS.md |only HistDAWass-1.0.9/HistDAWass/R/All_classes.R | 841 +-- HistDAWass-1.0.9/HistDAWass/R/Fuzzy_cmeans.R | 1464 ++--- HistDAWass-1.0.9/HistDAWass/R/H_time_series.R | 270 - HistDAWass-1.0.9/HistDAWass/R/HistDAWass-package.R | 453 - HistDAWass-1.0.9/HistDAWass/R/Kohonen_maps.R | 1097 ++-- HistDAWass-1.0.9/HistDAWass/R/Met_HTS.R | 229 HistDAWass-1.0.9/HistDAWass/R/Met_MatH.R | 2568 ++++------ HistDAWass-1.0.9/HistDAWass/R/Met_distributionH.R | 1941 +++---- HistDAWass-1.0.9/HistDAWass/R/Plotting_with_ggplot.R | 1179 +--- HistDAWass-1.0.9/HistDAWass/R/RcppExports.R | 358 - HistDAWass-1.0.9/HistDAWass/R/Utility.R | 1529 +++-- HistDAWass-1.0.9/HistDAWass/R/principal_components.R | 1828 +++---- HistDAWass-1.0.9/HistDAWass/R/regression.R | 593 +- HistDAWass-1.0.9/HistDAWass/R/unsuperv_classification.R | 1085 ++-- HistDAWass-1.0.9/HistDAWass/README.md | 188 HistDAWass-1.0.9/HistDAWass/build/partial.rdb |binary HistDAWass-1.0.9/HistDAWass/data/HData.RData |binary HistDAWass-1.0.9/HistDAWass/man/Age_Pyramids_2014.Rd | 20 HistDAWass-1.0.9/HistDAWass/man/Agronomique.Rd | 20 HistDAWass-1.0.9/HistDAWass/man/Arith-distributionH.Rd |only HistDAWass-1.0.9/HistDAWass/man/BLOOD.Rd | 18 HistDAWass-1.0.9/HistDAWass/man/BloodBRITO.Rd | 17 HistDAWass-1.0.9/HistDAWass/man/Center.cell.MatH-methods.Rd | 13 HistDAWass-1.0.9/HistDAWass/man/China_Month.Rd | 31 HistDAWass-1.0.9/HistDAWass/man/China_Seas.Rd | 33 HistDAWass-1.0.9/HistDAWass/man/DouglasPeucker.Rd | 19 HistDAWass-1.0.9/HistDAWass/man/HTS-class.Rd | 33 HistDAWass-1.0.9/HistDAWass/man/HTS.exponential.smoothing.Rd | 27 HistDAWass-1.0.9/HistDAWass/man/HTS.moving.averages.Rd | 32 HistDAWass-1.0.9/HistDAWass/man/HTS.predict.knn.Rd | 33 HistDAWass-1.0.9/HistDAWass/man/HistDAWass-package.Rd | 122 HistDAWass-1.0.9/HistDAWass/man/MatH-class.Rd | 101 HistDAWass-1.0.9/HistDAWass/man/OzoneFull.Rd | 18 HistDAWass-1.0.9/HistDAWass/man/OzoneH.Rd | 18 HistDAWass-1.0.9/HistDAWass/man/RetHTS.Rd | 12 HistDAWass-1.0.9/HistDAWass/man/ShortestDistance.Rd | 16 HistDAWass-1.0.9/HistDAWass/man/TMatH-class.Rd | 36 HistDAWass-1.0.9/HistDAWass/man/TdistributionH-class.Rd | 52 HistDAWass-1.0.9/HistDAWass/man/WH.1d.PCA.Rd | 64 HistDAWass-1.0.9/HistDAWass/man/WH.MultiplePCA.Rd | 40 HistDAWass-1.0.9/HistDAWass/man/WH.bind-methods.Rd | 42 HistDAWass-1.0.9/HistDAWass/man/WH.mat.prod-methods.Rd | 28 HistDAWass-1.0.9/HistDAWass/man/WH.mat.sum-methods.Rd | 21 HistDAWass-1.0.9/HistDAWass/man/WH.plot_multiple_Spanish.funs.Rd | 37 HistDAWass-1.0.9/HistDAWass/man/WH.plot_multiple_indivs.Rd | 61 HistDAWass-1.0.9/HistDAWass/man/WH.regression.GOF.Rd | 33 HistDAWass-1.0.9/HistDAWass/man/WH.regression.two.components.Rd | 51 HistDAWass-1.0.9/HistDAWass/man/WH.regression.two.components.predict.Rd | 29 HistDAWass-1.0.9/HistDAWass/man/WH.var.covar-methods.Rd | 59 HistDAWass-1.0.9/HistDAWass/man/WH.vec.mean-methods.Rd | 31 HistDAWass-1.0.9/HistDAWass/man/WH_2d_Adaptive_Kohonen_maps.Rd | 133 HistDAWass-1.0.9/HistDAWass/man/WH_2d_Kohonen_maps.Rd | 102 HistDAWass-1.0.9/HistDAWass/man/WH_MAT_DIST.Rd | 31 HistDAWass-1.0.9/HistDAWass/man/WH_adaptive.kmeans.Rd | 87 HistDAWass-1.0.9/HistDAWass/man/WH_adaptive_fcmeans.Rd | 64 HistDAWass-1.0.9/HistDAWass/man/WH_fcmeans.Rd | 60 HistDAWass-1.0.9/HistDAWass/man/WH_hclust.Rd | 45 HistDAWass-1.0.9/HistDAWass/man/WH_kmeans.Rd | 68 HistDAWass-1.0.9/HistDAWass/man/WassSqDistH-methods.Rd | 43 HistDAWass-1.0.9/HistDAWass/man/checkEmptyBins-methods.Rd | 35 HistDAWass-1.0.9/HistDAWass/man/compP-methods.Rd | 23 HistDAWass-1.0.9/HistDAWass/man/compQ-methods.Rd | 31 HistDAWass-1.0.9/HistDAWass/man/crwtransform-methods.Rd | 29 HistDAWass-1.0.9/HistDAWass/man/data2hist.Rd | 45 HistDAWass-1.0.9/HistDAWass/man/distributionH-class.Rd | 110 HistDAWass-1.0.9/HistDAWass/man/dotpW-methods.Rd | 50 HistDAWass-1.0.9/HistDAWass/man/extract-methods.Rd | 25 HistDAWass-1.0.9/HistDAWass/man/get.MatH.main.info-methods.Rd | 49 HistDAWass-1.0.9/HistDAWass/man/get.MatH.stats-methods.Rd | 56 HistDAWass-1.0.9/HistDAWass/man/get.cell.MatH-methods.Rd | 22 HistDAWass-1.0.9/HistDAWass/man/get.distr-methods.Rd | 17 HistDAWass-1.0.9/HistDAWass/man/get.histo-methods.Rd | 17 HistDAWass-1.0.9/HistDAWass/man/get.m-methods.Rd | 16 HistDAWass-1.0.9/HistDAWass/man/get.s-methods.Rd | 17 HistDAWass-1.0.9/HistDAWass/man/kurtH-methods.Rd | 22 HistDAWass-1.0.9/HistDAWass/man/meanH-methods.Rd | 20 HistDAWass-1.0.9/HistDAWass/man/plot-HTS.Rd | 33 HistDAWass-1.0.9/HistDAWass/man/plot-MatH.Rd | 34 HistDAWass-1.0.9/HistDAWass/man/plot-TdistributionH.Rd | 28 HistDAWass-1.0.9/HistDAWass/man/plot-distributionH.Rd | 41 HistDAWass-1.0.9/HistDAWass/man/plotPredVsObs.Rd | 31 HistDAWass-1.0.9/HistDAWass/man/plot_errors.Rd | 30 HistDAWass-1.0.9/HistDAWass/man/rQQ-methods.Rd | 30 HistDAWass-1.0.9/HistDAWass/man/register-methods.Rd | 48 HistDAWass-1.0.9/HistDAWass/man/registerMH-methods.Rd | 73 HistDAWass-1.0.9/HistDAWass/man/show-MatH-methods.Rd | 14 HistDAWass-1.0.9/HistDAWass/man/show-distributionH-methods.Rd | 18 HistDAWass-1.0.9/HistDAWass/man/skewH-methods.Rd | 21 HistDAWass-1.0.9/HistDAWass/man/stations_coordinates.Rd | 20 HistDAWass-1.0.9/HistDAWass/man/stdH-methods.Rd | 22 HistDAWass-1.0.9/HistDAWass/man/subsetHTS-methods.Rd | 14 HistDAWass-1.0.9/HistDAWass/man/summaryHTS.Rd | 9 HistDAWass-1.0.9/HistDAWass/src/Utility_fun.cpp | 281 - HistDAWass-1.0.9/HistDAWass/tests |only 115 files changed, 9389 insertions(+), 9653 deletions(-)
Title: Access CDC Behavioral Risk Factor Surveillance System Data
Description: Download, cache, and analyze annual microdata from the United States Centers for Disease Control and Prevention Behavioral Risk Factor Surveillance System (BRFSS) <https://www.cdc.gov/brfss/>. Each requested survey year is downloaded once as a compact file hosted on public releases, verified against a published checksum, and cached locally; queries then run through 'DuckDB' (via the 'duckdb' package), so column selection and repeat analyses never re-transfer data. Survey-design helpers construct 'srvyr' design objects with year-appropriate weights, strata, and primary sampling units, including explicit handling of the 2011 weighting methodology change and of the codes CDC uses for missing-type answers.
Author: Muntasir Masum [aut, cre, cph]
Maintainer: Muntasir Masum <muntasir.1124@gmail.com>
Diff between brfssdata versions 0.1.0 dated 2026-08-21 and 0.1.1 dated 2026-10-18
DESCRIPTION | 6 MD5 | 50 ++-- NEWS.md | 44 +++ R/brfss_crosswalk.R | 4 R/brfss_year_info.R | 10 R/cache.R | 4 README.md | 67 ++++- inst/CITATION | 3 inst/WORDLIST | 6 inst/doc/brfssdata.Rmd | 10 inst/doc/brfssdata.html | 45 ++- inst/extdata/brfss_crosswalk.parquet |binary inst/extdata/brfss_labels.parquet |binary inst/extdata/brfss_variables.parquet |binary inst/extdata/manifest.json | 391 +++++++++++++++++++++++++++++----- man/brfss_cache_dir.Rd | 4 man/brfss_crosswalk.Rd | 4 man/brfss_year_info.Rd | 10 man/figures/logo-static.svg | 2 man/figures/logo.png |binary man/figures/logo.svg | 2 tests/testthat/helper-fixtures.R | 4 tests/testthat/test-brfss_year_info.R | 7 tests/testthat/test-constants.R | 3 tests/testthat/test-manifest.R | 35 +++ vignettes/brfssdata.Rmd | 10 26 files changed, 577 insertions(+), 144 deletions(-)
Title: Command Line Tools to Produce Accessible Documents using 'R
Markdown'
Description: Provides functions to produce accessible 'HTML' slides, 'HTML',
'Word' and 'PDF' documents from input 'R markdown' files. Accessible 'PDF'
files are produced only on a 'Windows' Operating System. One aspect of
accessibility is providing a headings structure that is recognised by a
screen reader, providing a navigational tool for a blind or
partially-sighted person. A key aim is to produce documents of different
formats easily from each of a collection of 'R markdown' source files.
Input 'R markdown' files are rendered using the render() function from the
'rmarkdown' package <https://cran.r-project.org/package=rmarkdown>. A 'zip'
file containing multiple output files can be produced from one function
call. A user-supplied template 'Word' document can be used to determine the
formatting of an output 'Word' document. Accessible 'PDF' files are
produced from 'Word' documents using 'OfficeToPDF'
<https://github.com/cognidox/OfficeToPDF>. A convenience function,
install_otp() is [...truncated...]
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between accessr versions 1.1.3 dated 2025-03-30 and 1.1.4 dated 2026-10-18
accessr-1.1.3/accessr/R/word_figures.R |only accessr-1.1.3/accessr/inst/examples/example.pptx |only accessr-1.1.3/accessr/inst/examples/template.pptx |only accessr-1.1.3/accessr/man/ext_img.Rd |only accessr-1.1.4/accessr/DESCRIPTION | 16 accessr-1.1.4/accessr/MD5 | 61 accessr-1.1.4/accessr/NAMESPACE | 1 accessr-1.1.4/accessr/NEWS.md | 11 accessr-1.1.4/accessr/R/accessr-package.R | 4 accessr-1.1.4/accessr/R/rmd2html.R | 39 accessr-1.1.4/accessr/R/rmd2word.R | 6 accessr-1.1.4/accessr/README.md | 8 accessr-1.1.4/accessr/inst/ioslides/default.html | 426 +- accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/fonts/fonts.css | 60 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/hammer.js | 1170 +++---- accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/modernizr.custom.45394.js | 6 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/order.js | 16 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/polyfills/classList.min.js | 2 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/polyfills/dataset.min.js | 2 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/prettify/lang-r.js | 114 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/prettify/lang-tex.js | 2 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/prettify/lang-yaml.js | 4 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/prettify/prettify.js | 56 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/require-1.0.8.min.js | 66 accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/slide-controller.js | 244 - accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/js/slide-deck.js | 1624 +++++----- accessr-1.1.4/accessr/inst/ioslides/ioslides-13.5.1/theme/css/phone.css | 12 accessr-1.1.4/accessr/man/accessr-package.Rd | 169 - accessr-1.1.4/accessr/man/figures |only accessr-1.1.4/accessr/man/rmd2html.Rd | 26 accessr-1.1.4/accessr/man/rmd2ioslides.Rd | 2 accessr-1.1.4/accessr/man/rmd2many.Rd | 266 - accessr-1.1.4/accessr/man/rmd2slidy.Rd | 2 accessr-1.1.4/accessr/tests/testthat.R | 24 34 files changed, 2235 insertions(+), 2204 deletions(-)
Title: Regularized Linear Models
Description: Algorithms compute robust estimators for loss functions in the concave convex (CC) family by the iteratively reweighted convex optimization (IRCO), an extension of the iteratively reweighted least squares (IRLS). The IRCO reduces the weight of the observation that leads to a large loss; it also provides weights to help identify outliers. Applications include robust (penalized) generalized linear models and robust support vector machines. The package also contains penalized Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial regression models and robust models with non-convex loss functions. Wang et al. (2014) <doi:10.1002/sim.6314>,
Wang et al. (2015) <doi:10.1002/bimj.201400143>,
Wang et al. (2016) <doi:10.1177/0962280214530608>,
Wang (2021) <doi:10.1007/s11749-021-00770-2>,
Wang (2024) <doi:10.1111/anzs.12409>.
Author: Zhu Wang [aut, cre],
Achim Zeileis [aut],
Simon Jackman [aut],
Brian Ripley [aut],
Patrick Breheny [aut]
Maintainer: Zhu Wang <zwang145@uthsc.edu>
Diff between mpath versions 0.4-2.27 dated 2026-07-12 and 0.4-2.28 dated 2026-10-18
DESCRIPTION | 11 ++-- MD5 | 51 +++++++++---------- NEWS | 7 ++ R/cv.glmreg.R | 79 +++++++++++++++++------------- R/cv.glmregNegbin.R | 102 +++++++++++++++++++++++---------------- R/cv.irglmreg.R | 70 +++++++++++++++++--------- R/cv.irsvm.R | 85 +++++++++++++++++++++----------- R/cv.nclreg.R | 70 +++++++++++++++++--------- R/cv.zipath.R | 64 ++++++++++++++++-------- R/glmreg.R | 1 R/glmregNB.R | 41 ++++++++++++--- R/globals.R |only R/irglmreg.R | 75 ++++++++++++++++++---------- inst/doc/brcancer.pdf |binary inst/doc/kkt.pdf |binary inst/doc/static_brcancer.pdf |binary inst/doc/static_german.pdf |binary inst/doc/static_irglmExample.pdf |binary inst/doc/static_irsvmExample.pdf |binary man/cv.glmregNB.Rd | 2 man/cv.glmreg_fit.Rd | 4 - man/cv.irglmreg_fit.Rd | 2 man/cv.irsvm_fit.Rd | 2 man/cv.nclreg_fit.Rd | 2 man/cv.zipath_fit.Rd | 2 man/glmregNB.Rd | 4 - man/irglmreg_fit.Rd | 2 27 files changed, 429 insertions(+), 247 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- lapply(files, FUN = process) |> futurize::futurize()'.
Author: Henrik Bengtsson [aut, cre, cph] ,
Michel Lang [ctb, cph] ,
Bernd Bischl [ctb, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.22.0 dated 2026-04-24 and 0.30.0 dated 2026-10-18
DESCRIPTION | 29 ++++-- MD5 | 90 ++++++++++--------- NAMESPACE | 135 ++++++++++++++++------------- NEWS.md | 52 +++++++++-- R/BatchtoolsFutureBackend-class.R | 10 +- R/batchtools_custom.R | 1 R/batchtools_interactive.R | 2 R/batchtools_local.R | 2 R/batchtools_multicore.R | 4 R/batchtools_sge.R | 4 R/batchtools_slurm.R | 16 +-- R/batchtools_ssh.R | 4 R/find_template_file.R | 13 ++ R/makeClusterFutureSlurm2.R | 5 + R/options.R | 21 ++-- R/render_template.R |only R/runOSCommand.R | 4 R/utils-debug.R | 3 R/waitForWorker.R | 2 build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/future.batchtools.html | 21 ++-- inst/doc/future.batchtools.md.rsp | 3 inst/templates/bash.tmpl | 4 inst/templates/lsf.tmpl | 2 inst/templates/openlava.tmpl | 2 inst/templates/sge.tmpl | 2 inst/templates/slurm.tmpl | 2 inst/templates/torque.tmpl | 2 inst/testme/test-BatchtoolsFutureBackend.R | 42 ++++++++- inst/testme/test-batchtools_hpc.R | 24 ++++- man/BatchtoolsFutureBackend.Rd | 7 - man/BatchtoolsFutureError.Rd | 2 man/BatchtoolsMulticoreFutureBackend.Rd | 1 man/batchtools_bash.Rd | 4 man/batchtools_interactive.Rd | 2 man/batchtools_local.Rd | 2 man/batchtools_lsf.Rd | 2 man/batchtools_openlava.Rd | 2 man/batchtools_sge.Rd | 4 man/batchtools_slurm.Rd | 18 ++- man/batchtools_torque.Rd | 2 man/find_template_file.Rd |only man/future.batchtools.Rd | 11 ++ man/makeClusterFunctionsSlurm2.Rd | 2 man/render_template.Rd |only man/zzz-future.batchtools.options.Rd | 2 vignettes/future.batchtools.md.rsp | 3 48 files changed, 363 insertions(+), 202 deletions(-)
More information about future.batchtools at CRAN
Permanent link
Title: Download, Edit and Include Wind and Sea Currents Data in
Ecological and Evolutionary Analysis
Description: Downloads and processes surface wind data from the Global Forecast System
<https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast>
and sea-current data from Ocean Surface Current Analyses Real-time (OSCAR).
Converts flow speed and direction into spatial rasters and directed
movement costs and conductances for connectivity and least-cost path analyses.
Author: Javier Fernandez-Lopez [aut, cre],
Klaus Schliep [aut],
Yurena Arjona [aut]
Maintainer: Javier Fernandez-Lopez <jflopez.bio@gmail.com>
This is a re-admission after prior archival of version 1.1.7 dated 2021-10-19
Diff between rWind versions 1.1.7 dated 2021-10-19 and 1.2.0 dated 2026-10-18
DESCRIPTION | 23 MD5 | 61 +- NAMESPACE | 7 NEWS | 34 + R/rWind-package.R | 21 R/wind_functions2.R | 1187 ++++++++++++++++++++++++++----------------- README.md | 70 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 10 inst/doc/Shortest_paths.R | 127 ++-- inst/doc/Shortest_paths.Rmd | 239 +++++--- inst/doc/Shortest_paths.html | 586 ++++++++++++++++----- man/arrowDir.Rd | 12 man/cost.active.Rd |only man/flow.dispersion.Rd | 85 ++- man/flow.dispersion_int.Rd | 60 +- man/rWind-package.Rd | 19 man/seaOscar.dl.Rd | 34 - man/tidy.rWind_series.Rd | 22 man/uv2ds.Rd | 8 man/wind.data.Rd | 4 man/wind.dl.Rd | 26 man/wind.dl_2.Rd | 58 +- man/wind.fit_int.Rd | 2 man/wind.mean.Rd | 7 man/wind.series.Rd | 4 man/wind2raster.Rd | 25 man/wind2raster_int.Rd | 19 tests/testthat/fixtures |only tests/testthat/test_rWind.R | 167 +++++- vignettes/Shortest_paths.Rmd | 239 +++++--- vignettes/rWind.bib | 62 -- 33 files changed, 2137 insertions(+), 1081 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 1.0.0 dated 2026-07-03 and 1.1.0 dated 2026-10-18
progressr-1.0.0/progressr/R/uuid.R |only progressr-1.0.0/progressr/man/_cache/handler_cli-default_92c35eba24162ac33c8a7f91e2ac7dd3.RData |only progressr-1.0.0/progressr/man/_cache/handler_cli-default_92c35eba24162ac33c8a7f91e2ac7dd3.rdb |only progressr-1.0.0/progressr/man/_cache/handler_cli-default_92c35eba24162ac33c8a7f91e2ac7dd3.rdx |only progressr-1.0.0/progressr/man/_cache/handler_cli-format-1_ecd5856580d0fb4252a98415c73cf506.RData |only progressr-1.0.0/progressr/man/_cache/handler_cli-format-1_ecd5856580d0fb4252a98415c73cf506.rdb |only progressr-1.0.0/progressr/man/_cache/handler_cli-format-1_ecd5856580d0fb4252a98415c73cf506.rdx |only progressr-1.0.0/progressr/man/_cache/handler_cli-type-percent_ed5d0a15a99bc442075f19f49aec46bb.RData |only progressr-1.0.0/progressr/man/_cache/handler_cli-type-percent_ed5d0a15a99bc442075f19f49aec46bb.rdb |only progressr-1.0.0/progressr/man/_cache/handler_cli-type-percent_ed5d0a15a99bc442075f19f49aec46bb.rdx |only 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Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.17.0 dated 2026-08-28 and 0.18.0 dated 2026-10-18
DESCRIPTION | 32 MD5 | 90 - NEWS.md | 195 +++ R/checks.R |only R/data.R | 33 R/estimate_contrasts.R | 21 R/estimate_means.R | 34 R/estimate_predicted.R | 19 R/estimate_slopes.R | 25 R/format.R | 235 +++- R/get_emcontrasts.R | 75 + R/get_emmeans.R | 281 ++++- R/get_emtrends.R | 107 + R/get_inequalitycontrasts.R | 30 R/get_marginalcontrasts.R | 66 - R/get_marginaleffects_type.R | 14 R/get_marginalmeans.R | 296 ++--- R/get_marginaltrends.R | 27 R/p_adjust.R | 52 R/print.R | 10 R/print_html.R | 31 R/table_footer.R | 49 R/utils.R | 72 - R/visualisation_recipe_internal.R | 44 data/stigma.rda |only inst/doc/overview_of_vignettes.Rmd | 32 inst/doc/overview_of_vignettes.html | 59 - man/estimate_contrasts.Rd | 41 man/estimate_means.Rd | 28 man/estimate_slopes.Rd | 27 man/get_emmeans.Rd | 29 man/puppy_love.Rd | 64 - man/stigma.Rd |only tests/testthat/test-attributes_estimatefun.R | 2 tests/testthat/test-brms.R | 125 ++ tests/testthat/test-discovr_bookexamples.R | 2 tests/testthat/test-estimate_contrasts-average.R | 113 +- tests/testthat/test-estimate_contrasts.R | 75 + tests/testthat/test-estimate_slopes.R | 172 +++ tests/testthat/test-focal-name-clashes.R |only tests/testthat/test-keep_iterations.R | 4 tests/testthat/test-offset.R | 68 + tests/testthat/test-ordinal.R | 1289 +++++++++++++++++++++++ tests/testthat/test-print.R | 196 +++ tests/testthat/test-table_footer.R | 149 ++ tests/testthat/test-visualisation_recipe.R | 342 ++++++ vignettes/bibliography.bib | 120 +- vignettes/overview_of_vignettes.Rmd | 32 48 files changed, 4180 insertions(+), 627 deletions(-)
Title: L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
Description: Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs),
distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate
Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and
maximum product spacings estimation are available. Right-tail and left-tail LM censoring
by threshold or indicator variable are available. LMs of residual (resid) and reversed
(rev) residual life are implemented along with 13 quantile operators for reliability analyses.
Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available.
Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added
(+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L],
Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp
Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L],
Gen Pareto [L+RC, TL], Govindara [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between lmomco versions 2.5.7 dated 2026-07-03 and 2.5.8 dated 2026-10-18
DESCRIPTION | 8 ++-- MD5 | 40 +++++++++++------------ NEWS | 15 ++++++++ R/Lcomoment.correlation.R | 2 - R/add.lmomco.axis.R | 51 +++++++++++++++++++++++------- R/lcomoms2.R | 12 +++---- R/plotlmrdia.R | 64 ++++++++++++++++++++++++++------------ R/plotlmrdia46.R | 49 ++++++++++++++++++++--------- man/add.lmomco.axis.Rd | 73 +++++++++++++++++++++++++++++++------------ man/add.log.axis.Rd | 36 ++++++++++----------- man/dat2bernqua.Rd | 6 +-- man/grv2prob.Rd | 2 - man/lrv2prob.Rd | 2 - man/parglo.Rd | 18 +++++----- man/plmomco.Rd | 2 - man/plotlmrdia.Rd | 72 +++++++++++++++++++++++-------------------- man/plotlmrdia46.Rd | 77 ++++++++++++++++++++++++---------------------- man/prob2grv.Rd | 7 ++-- man/prob2lrv.Rd | 4 +- man/qlmomco.Rd | 2 - man/slmomco.Rd | 2 - 21 files changed, 338 insertions(+), 206 deletions(-)
Title: Distance Metrics for High-Dimensional Clustering
Description: We provide three distance metrics for measuring the separation between two clusters in high-dimensional spaces. The first metric is the centroid distance, which calculates the Euclidean distance between the centers of the two groups. The second is a ridge Mahalanobis distance, which incorporates a ridge correction constant, alpha, to ensure that the covariance matrix is invertible. The third metric is the maximal data piling distance, which computes the orthogonal distance between the affine spaces spanned by each class. These three distances are asymptotically interconnected and are applicable in tasks such as discrimination, clustering, and outlier detection in high-dimensional settings. The package also provides a distance-based outlier detection procedure for high-dimensional, low-sample-size data, as described in Ahn, Lee and Lee (2018).
Author: Jung Ae Lee [aut, cre],
Jeongyoun Ahn [aut]
Maintainer: Jung Ae Lee <jungaeleeb@gmail.com>
Diff between distanceHD versions 1.2 dated 2025-01-31 and 1.4 dated 2026-10-18
DESCRIPTION | 32 ++++---- MD5 | 13 ++- NAMESPACE | 4 - R/distanceHD.R | 165 ++++++++++++++++++++++++++++++++++++++++++++-- data/leukemia.RData |binary data/simdata.RData |only man/HDout.Rd |only man/distanceHD-package.Rd | 2 man/simdata.Rd |only 9 files changed, 186 insertions(+), 30 deletions(-)
Title: Biodiversity Assessment Using Hill-Number Functional Tools
Description: Tools for biodiversity assessment through Hill-number diversity
profiles treated as functions of the order q. The package computes the
profiles of Hill (1973) <doi:10.2307/1934352>, their analytical first and
second derivatives, curvature, radius of curvature, arc length, cumulative
integral functions, profile areas, area-based rankings and relative changes
over time, together with static and interactive three-dimensional
biodiversity surfaces. The functional approach follows Di Battista, Fortuna
and Maturo (2017) <doi:10.1016/j.ecolind.2016.10.032>, Maturo and
Di Battista (2018) <doi:10.1016/j.ecolind.2017.08.016> and Maturo (2018)
<doi:10.1016/j.ecolind.2018.03.013>.
Author: Fabrizio Maturo [aut, cre],
Francesca Fortuna [aut],
Tonio Di Battista [aut]
Maintainer: Fabrizio Maturo <fabrizio.maturo@unimercatorum.it>
This is a re-admission after prior archival of version 1.2-0 dated 2016-09-26
Diff between BioFTF versions 1.2-0 dated 2016-09-26 and 3.0.0 dated 2026-10-18
BioFTF-1.2-0/BioFTF/R/alltools.R |only BioFTF-1.2-0/BioFTF/R/arc.R |only BioFTF-1.2-0/BioFTF/R/area.R |only BioFTF-1.2-0/BioFTF/R/beta.R |only BioFTF-1.2-0/BioFTF/R/beta_plot.R |only BioFTF-1.2-0/BioFTF/R/betaprime.R |only BioFTF-1.2-0/BioFTF/R/betaprime_plot.R |only BioFTF-1.2-0/BioFTF/R/betasecond.R |only BioFTF-1.2-0/BioFTF/R/betasecond_plot.R |only BioFTF-1.2-0/BioFTF/R/curvature.R |only BioFTF-1.2-0/BioFTF/R/curvature_plot.R |only BioFTF-1.2-0/BioFTF/R/datirel.R |only BioFTF-1.2-0/BioFTF/R/export_plots.R |only BioFTF-1.2-0/BioFTF/R/radius.R |only BioFTF-1.2-0/BioFTF/R/radius_plot.R |only BioFTF-1.2-0/BioFTF/R/ranking.R |only BioFTF-1.2-0/BioFTF/R/summary_species.R |only BioFTF-1.2-0/BioFTF/man/alltools.Rd |only BioFTF-1.2-0/BioFTF/man/arc.Rd |only BioFTF-1.2-0/BioFTF/man/area.Rd |only BioFTF-1.2-0/BioFTF/man/beta.Rd |only BioFTF-1.2-0/BioFTF/man/beta_plot.Rd |only BioFTF-1.2-0/BioFTF/man/betaprime.Rd |only BioFTF-1.2-0/BioFTF/man/betaprime_plot.Rd |only BioFTF-1.2-0/BioFTF/man/betasecond.Rd |only BioFTF-1.2-0/BioFTF/man/betasecond_plot.Rd |only BioFTF-1.2-0/BioFTF/man/curvature.Rd |only BioFTF-1.2-0/BioFTF/man/curvature_plot.Rd |only BioFTF-1.2-0/BioFTF/man/datirel.Rd |only BioFTF-1.2-0/BioFTF/man/export_plots.Rd |only BioFTF-1.2-0/BioFTF/man/radius.Rd |only BioFTF-1.2-0/BioFTF/man/radius_plot.Rd |only BioFTF-1.2-0/BioFTF/man/ranking.Rd |only BioFTF-1.2-0/BioFTF/man/summary_species.Rd |only BioFTF-3.0.0/BioFTF/DESCRIPTION | 48 +++++++++++++------ BioFTF-3.0.0/BioFTF/MD5 | 56 ++++++++--------------- BioFTF-3.0.0/BioFTF/NAMESPACE | 48 ++++++++++++++++--- BioFTF-3.0.0/BioFTF/NEWS.md |only BioFTF-3.0.0/BioFTF/R/bioftf.R |only BioFTF-3.0.0/BioFTF/README.md |only BioFTF-3.0.0/BioFTF/build |only BioFTF-3.0.0/BioFTF/inst |only BioFTF-3.0.0/BioFTF/man/BioFTF-deprecated.Rd |only BioFTF-3.0.0/BioFTF/man/BioFTF-package.Rd |only BioFTF-3.0.0/BioFTF/man/hill_functional_tools.Rd |only BioFTF-3.0.0/BioFTF/man/hill_profile.Rd |only BioFTF-3.0.0/BioFTF/man/hill_surfaces.Rd |only BioFTF-3.0.0/BioFTF/man/summary_tools.Rd |only BioFTF-3.0.0/BioFTF/tests |only BioFTF-3.0.0/BioFTF/vignettes |only 50 files changed, 93 insertions(+), 59 deletions(-)
Title: Augmented Modelling of Relational Events
Description: An integrated workflow for relational event models, in which
timestamped interactions among actors arrive in continuous time and the
event rate depends on the history of the network itself. Event streams are
simulated by an exact Gillespie kernel or an approximate tau-leap kernel;
non-events are drawn by case-control sampling in the manner of Lerner and
Lomi (2020) <doi:10.1017/nws.2019.57>, or from a time-shifted copy of the
process so that covariates shared by all dyads at a given time remain
estimable (Lembo et al. 2025, <doi:10.1093/jrsssc/qlaf058>); the
timing- and closure-based
endogenous statistics of Juozaitiene and Wit (2024)
<doi:10.1093/jrsssa/qnae132> are computed from that history; and one
front-end fits the resulting case-control data by conditional-logistic
partial likelihood, by penalised regression on its degenerate
one-control binomial form (which admits smooth, time-varying and actor
random effects), or by stochastic gradient descent, including the
[...truncated...]
Author: Francisco Richter [aut, cre],
Martina Boschi [aut],
Ernst C. Wit [aut],
Melania Lembo [aut]
Maintainer: Francisco Richter <richtf@usi.ch>
Diff between amorem versions 1.1.0 dated 2026-10-17 and 1.2.0 dated 2026-10-18
amorem-1.1.0/amorem/man/figures/amorem.png |only amorem-1.1.0/amorem/man/figures/logo-github-dark.png |only amorem-1.1.0/amorem/man/figures/logo-github-light.png |only amorem-1.1.0/amorem/man/figures/logo-github-white.png |only amorem-1.1.0/amorem/man/figures/logo-hexagon.png |only amorem-1.1.0/amorem/man/figures/logo-square.png |only amorem-1.2.0/amorem/DESCRIPTION | 10 amorem-1.2.0/amorem/LICENSE | 2 amorem-1.2.0/amorem/MD5 | 88 ++- amorem-1.2.0/amorem/NAMESPACE | 3 amorem-1.2.0/amorem/NEWS.md | 82 +++ amorem-1.2.0/amorem/R/data.R | 253 +++++++++- amorem-1.2.0/amorem/R/gof_rem.R |only amorem-1.2.0/amorem/R/preprocess.R | 5 amorem-1.2.0/amorem/R/rem.R | 10 amorem-1.2.0/amorem/R/rem_nn.R | 38 + amorem-1.2.0/amorem/R/rem_nn_uncertainty.R | 18 amorem-1.2.0/amorem/R/simulate_events.R | 9 amorem-1.2.0/amorem/README.md | 25 amorem-1.2.0/amorem/data/alien_invasions.rda |only amorem-1.2.0/amorem/data/alien_mammals.rda |only amorem-1.2.0/amorem/data/congress_bills_118.rda |only amorem-1.2.0/amorem/data/congress_members_118.rda |only amorem-1.2.0/amorem/data/copenhagen_actors.rda |only amorem-1.2.0/amorem/data/copenhagen_calls.rda |only amorem-1.2.0/amorem/data/copenhagen_sms.rda |only amorem-1.2.0/amorem/data/daily_weather.rda |only amorem-1.2.0/amorem/data/football_results.rda |only amorem-1.2.0/amorem/data/oni.rda |only amorem-1.2.0/amorem/data/public_holidays.rda |only amorem-1.2.0/amorem/data/radoslaw_email.rda |binary amorem-1.2.0/amorem/data/radoslaw_hierarchy.rda |only amorem-1.2.0/amorem/data/ucdp_dyads.rda |only amorem-1.2.0/amorem/data/us_leader_visits.rda |only amorem-1.2.0/amorem/inst/doc/species-invasion.Rmd | 8 amorem-1.2.0/amorem/inst/doc/species-invasion.html | 14 amorem-1.2.0/amorem/man/alien_invasions.Rd |only amorem-1.2.0/amorem/man/alien_mammals.Rd |only amorem-1.2.0/amorem/man/amorem-package.Rd | 4 amorem-1.2.0/amorem/man/congress_bills_118.Rd |only amorem-1.2.0/amorem/man/congress_members_118.Rd |only amorem-1.2.0/amorem/man/copenhagen.Rd |only amorem-1.2.0/amorem/man/daily_weather.Rd |only amorem-1.2.0/amorem/man/figures/logo.png |binary amorem-1.2.0/amorem/man/football_results.Rd |only amorem-1.2.0/amorem/man/gof_rem.Rd |only amorem-1.2.0/amorem/man/nn_uncertainty.Rd | 3 amorem-1.2.0/amorem/man/oni.Rd |only amorem-1.2.0/amorem/man/public_holidays.Rd |only amorem-1.2.0/amorem/man/radoslaw_email.Rd | 33 - amorem-1.2.0/amorem/man/radoslaw_hierarchy.Rd |only amorem-1.2.0/amorem/man/sample_non_events.Rd | 3 amorem-1.2.0/amorem/man/social_evolution_actors.Rd | 2 amorem-1.2.0/amorem/man/social_evolution_calls.Rd | 8 amorem-1.2.0/amorem/man/social_evolution_friendship.Rd | 2 amorem-1.2.0/amorem/man/ucdp_dyads.Rd |only amorem-1.2.0/amorem/man/us_leader_visits.Rd |only amorem-1.2.0/amorem/tests/testthat/test-gof-rem.R |only amorem-1.2.0/amorem/tests/testthat/test-open-datasets.R |only amorem-1.2.0/amorem/tests/testthat/test-rem-nn.R | 30 + amorem-1.2.0/amorem/tests/testthat/test-sample-non-events-issue102.R | 19 amorem-1.2.0/amorem/tests/testthat/test-tau-leap.R | 11 amorem-1.2.0/amorem/vignettes/species-invasion.Rmd | 8 63 files changed, 565 insertions(+), 123 deletions(-)
Title: 'COIN-OR' 'Clp' Plugin for the 'R' Optimization Infrastructure
Description: Registers the 'COIN-OR' 'Clp' linear programming solver with
'ROI', the 'R' Optimization Infrastructure, through the 'coinclp'
package. Linear programs with continuous variables are then solved by
'ROI' with the 'coinclp' solver, keeping sparse constraint matrices
sparse all the way to the solver, and returning dual values, reduced
costs and row activities alongside the primal solution.
Author: Sam Lovick [aut, cre]
Maintainer: Sam Lovick <sam@lovickconsulting.com>
Diff between ROI.plugin.coinclp versions 0.1.0 dated 2026-09-28 and 0.1.1 dated 2026-10-18
DESCRIPTION | 18 +++++++++--------- MD5 | 12 ++++++------ NEWS.md | 20 ++++++++++++++++++++ R/ROI.plugin.coinclp-package.R | 3 ++- R/plugin.R | 4 ++-- README.md | 13 +++++++++---- man/ROI.plugin.coinclp-package.Rd | 3 ++- 7 files changed, 50 insertions(+), 23 deletions(-)
More information about ROI.plugin.coinclp at CRAN
Permanent link
Title: Draw from Sequence of 'My Man' Posts by Kevin Kruse
Description: Starting on the afternoon of July 17, 2026, Kevin Kruse fired off an astonishing
array of 'BlueSky' replies to an initial post of his featuring a certain government figure:
<https://bsky.app/profile/did:plc:cnpe7qvcyjrhm6w7w7e4atur/post/3mqum4mxsuk2g>. This lasted a
week and generated nearly seven hundred posts. Over the next few weeks, several more waves
followed, each taking aim at a different prominent figure. All of the by now over two thousand
posts from these series start with 'My man ...' and make for excellent input to a 'fortunes'-like
function. So this small package obliges and offers a random draw each time its myman() function
is called. The overall package structure follows package 'fortunes', and 'atrrr' was used to
(bulk-)retrieve posts. Neither package is required to run this package to display random
selections.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between myman versions 0.10.0 dated 2026-10-08 and 0.12.0 dated 2026-10-18
ChangeLog | 64 ++++++++++++++++ DESCRIPTION | 31 +++---- MD5 | 14 +-- R/myman.R | 14 ++- README.md | 17 ++-- inst/NEWS.Rd | 9 ++ inst/myman/myman.csv | 200 +++++++++++++++++++++++++++++++++++++++++++++++++++ man/myman.Rd | 9 +- 8 files changed, 316 insertions(+), 42 deletions(-)
Title: Context-Aware AI Assistant for 'RStudio'
Description: A context-aware AI assistant for 'RStudio' that works directly in
the source editor without switching context or opening a separate chat
window. Reads the cursor position and selection to automatically choose the
right action - generate, complete, continue, edit, or comment. Results are
presented as ghost text or an in-place diff suggestion. Supports
configuration of multiple large language model providers and can be invoked
via the keyboard shortcut or Addins menu.
Author: S.A. van der Wulp [aut, cre, cph]
Maintainer: S.A. van der Wulp <vdwulp@gmail.com>
Diff between codriver versions 1.0.0 dated 2026-08-08 and 1.1.0 dated 2026-10-18
DESCRIPTION | 15 + MD5 | 76 +++++----- NAMESPACE | 55 ++++--- NEWS.md | 34 ++++ R/build_prompt.R | 61 ++++---- R/build_prompt_workspace.R | 66 ++++++-- R/check_rstudio.R | 3 R/codriver.R | 26 +-- R/configure.R | 6 R/info.R |only R/last_request.R |only R/resolve_action.R | 55 ++++--- R/send_prompt.R | 12 + R/show_result.R | 17 +- R/zzz.R | 12 + README.md | 51 +++++- build/vignette.rds |binary inst/WORDLIST |only inst/doc/free-api-access.R |only inst/doc/free-api-access.Rmd |only inst/doc/free-api-access.html |only inst/doc/getting-started-with-codriver.R | 3 inst/doc/getting-started-with-codriver.Rmd | 157 +++++++++++++++----- inst/doc/getting-started-with-codriver.html | 204 ++++++++++++++++++--------- inst/doc/start-using-codriver.R | 1 inst/doc/start-using-codriver.Rmd | 18 -- inst/doc/start-using-codriver.html | 22 +- man/codriver_configure.Rd | 6 man/codriver_info.Rd |only man/codriver_last_request.Rd |only tests/spelling.R |only tests/testthat.R | 8 - tests/testthat/test-build_prompt.R | 99 +++++++++---- tests/testthat/test-build_prompt_workspace.R | 13 + tests/testthat/test-check_rstudio.R | 8 - tests/testthat/test-codriver.R | 4 tests/testthat/test-configure.R | 125 ++++++++++++---- tests/testthat/test-info.R |only tests/testthat/test-last_request.R |only tests/testthat/test-resolve_action.R | 147 +++++++++++++------ tests/testthat/test-send_prompt.R | 120 ++++++++++++--- tests/testthat/test-show_result.R | 112 ++++++++++---- vignettes/free-api-access.Rmd |only vignettes/getting-started-with-codriver.Rmd | 157 +++++++++++++++----- vignettes/start-using-codriver.Rmd | 18 -- 45 files changed, 1168 insertions(+), 543 deletions(-)
Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in
'Tidy Eval' code that calculates the predictions. It works with
several databases back-ends because it leverages 'dplyr' and 'dbplyr'
for the final 'SQL' translation of the algorithm. Dozens of model
classes are supported; see the "Supported models" article at
<https://tidypredict.tidymodels.org/articles/models.html> for the
current list.
Author: Emil Hvitfeldt [aut, cre] ,
Edgar Ruiz [aut],
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidypredict versions 1.2.1 dated 2026-09-09 and 1.2.2 dated 2026-10-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/h2o.html | 10 +++++----- inst/doc/lm.R | 2 +- inst/doc/lm.Rmd | 2 +- inst/doc/lm.html | 2 +- vignettes/lm.Rmd | 2 +- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Spectral Majorization for Statistical Estimation
Description: Fits generalized linear, asymmetric and robust regression models
using spectral majorization and iterative quadratic subproblem solvers.
A shared C++ computational core supports dense and sparse designs, automatic
intercepts, optional Wald inference and detailed iteration diagnostics.
Native code is compiled automatically during package installation.
Author: Xun-Jian Li [aut, cre]
Maintainer: Xun-Jian Li <xunjianli@ucla.edu>
Diff between SpectralMM versions 0.1.0 dated 2026-10-15 and 0.2.0 dated 2026-10-18
SpectralMM-0.1.0/SpectralMM/tests/smoke.R |only SpectralMM-0.2.0/SpectralMM/DESCRIPTION | 8 SpectralMM-0.2.0/SpectralMM/MD5 | 28 +-- SpectralMM-0.2.0/SpectralMM/R/families.R | 4 SpectralMM-0.2.0/SpectralMM/R/model.R | 82 +++++++-- SpectralMM-0.2.0/SpectralMM/R/spectralmm.R | 41 ++-- SpectralMM-0.2.0/SpectralMM/README.md | 29 +-- SpectralMM-0.2.0/SpectralMM/man/spectralmm_fit.Rd | 2 SpectralMM-0.2.0/SpectralMM/man/spectralmm_methods.Rd | 4 SpectralMM-0.2.0/SpectralMM/src/native/c_api.cpp | 52 +++++ SpectralMM-0.2.0/SpectralMM/src/native/core.cpp | 88 +++++++++- SpectralMM-0.2.0/SpectralMM/src/native/include/spectralmm/c_api.h | 15 + SpectralMM-0.2.0/SpectralMM/src/native/include/spectralmm/core.hpp | 3 SpectralMM-0.2.0/SpectralMM/src/r_bridge.cpp | 11 - SpectralMM-0.2.0/SpectralMM/tests/model-api.R | 2 SpectralMM-0.2.0/SpectralMM/tests/output-prediction.R |only 16 files changed, 290 insertions(+), 79 deletions(-)
Title: Sampling Hi-C Contact Matrices for Aparametric Normalization
Description: Generate expected Hi-C (genome-wide chromosome conformation
capture) data maintaining marginal coverage, and the decay in contact probability
with increasing genomic distance. Expected Hi-C data is used for normalization
and graphical presentation of statistical significance of observed Hi-C contact
enrichments. The method is described in Mendelson Cohen et al. (2017)
<doi:10.1101/187203>.
Author: Amos Tanay [aut],
Netta Mendelson Cohen [aut],
Aviezer Lifshitz [aut, cre],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between shaman versions 2.1.0 dated 2026-10-16 and 2.1.1 dated 2026-10-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/import.html | 4 ++-- src/ContactShuffler.cpp | 11 +++++++---- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Grammar of Graphics on 'base' Graphics
Description: Implements a grammar of graphics on top of the 'base' graphics
system. A 'bbplot' object is built incrementally with a '+' operator from
data, aesthetic mappings and layers, then rendered with base graphics, so
plotbb layers can be mixed with ordinary base plotting calls. The package
provides layers for points, lines, bars, histograms, densities, boxplots,
violins, ribbons, smooths, error bars and tiles, together with colour and
other aesthetic scales, automatic legends, faceting, themes, coordinate
flipping and significance annotations.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between plotbb versions 0.1.2 dated 2026-05-21 and 1.0.0 dated 2026-10-18
plotbb-0.1.2/plotbb/man/reexports.Rd |only plotbb-1.0.0/plotbb/DESCRIPTION | 36 plotbb-1.0.0/plotbb/MD5 | 121 plotbb-1.0.0/plotbb/NAMESPACE | 182 - plotbb-1.0.0/plotbb/NEWS.md | 215 + plotbb-1.0.0/plotbb/R/add-layer.R | 237 - plotbb-1.0.0/plotbb/R/aes.R | 32 plotbb-1.0.0/plotbb/R/auto-legend.R |only plotbb-1.0.0/plotbb/R/bb-bar-horizontal.R |only plotbb-1.0.0/plotbb/R/bb-bar.R | 129 plotbb-1.0.0/plotbb/R/bb-boxplot.R | 230 - plotbb-1.0.0/plotbb/R/bb-build.R |only plotbb-1.0.0/plotbb/R/bb-density.R | 145 plotbb-1.0.0/plotbb/R/bb-errorbar.R | 185 - plotbb-1.0.0/plotbb/R/bb-hist.R | 307 + plotbb-1.0.0/plotbb/R/bb-layer.R |only plotbb-1.0.0/plotbb/R/bb-line.R | 49 plotbb-1.0.0/plotbb/R/bb-lm.R | 392 +- plotbb-1.0.0/plotbb/R/bb-point.R | 114 plotbb-1.0.0/plotbb/R/bb-reference.R |only plotbb-1.0.0/plotbb/R/bb-ribbon.R |only plotbb-1.0.0/plotbb/R/bb-save.R |only plotbb-1.0.0/plotbb/R/bb-segment.R | 54 plotbb-1.0.0/plotbb/R/bb-signif.R | 90 plotbb-1.0.0/plotbb/R/bb-smooth.R |only plotbb-1.0.0/plotbb/R/bb-text.R | 80 plotbb-1.0.0/plotbb/R/bb-tile.R | 77 plotbb-1.0.0/plotbb/R/bb-violin.R |only plotbb-1.0.0/plotbb/R/bbplot.R | 36 plotbb-1.0.0/plotbb/R/coord-flip.R |only plotbb-1.0.0/plotbb/R/facet-grid.R |only plotbb-1.0.0/plotbb/R/grid.R | 88 plotbb-1.0.0/plotbb/R/labs.R | 120 plotbb-1.0.0/plotbb/R/position-scale.R |only plotbb-1.0.0/plotbb/R/print.R | 537 ++- plotbb-1.0.0/plotbb/R/scale.R | 1321 +++++--- plotbb-1.0.0/plotbb/R/state.R |only plotbb-1.0.0/plotbb/R/theme.R | 305 + plotbb-1.0.0/plotbb/R/utilities.R | 1348 +++++--- plotbb-1.0.0/plotbb/R/validate.R |only plotbb-1.0.0/plotbb/R/zzz.R | 20 plotbb-1.0.0/plotbb/build/vignette.rds |binary plotbb-1.0.0/plotbb/inst/WORDLIST |only plotbb-1.0.0/plotbb/inst/doc/plotbb.R | 772 +++- plotbb-1.0.0/plotbb/inst/doc/plotbb.html | 2169 +++++++++----- plotbb-1.0.0/plotbb/inst/doc/plotbb.qmd | 1467 +++++++-- plotbb-1.0.0/plotbb/man/bb-scale-aes.Rd | 21 plotbb-1.0.0/plotbb/man/bb-scale-fill.Rd |only plotbb-1.0.0/plotbb/man/bb-scale.Rd | 52 plotbb-1.0.0/plotbb/man/bb_build.Rd |only plotbb-1.0.0/plotbb/man/bb_coord_flip.Rd |only plotbb-1.0.0/plotbb/man/bb_facet_grid.Rd |only plotbb-1.0.0/plotbb/man/bb_facet_wrap.Rd | 31 plotbb-1.0.0/plotbb/man/bb_group_values.Rd |only plotbb-1.0.0/plotbb/man/bb_layer.Rd |only plotbb-1.0.0/plotbb/man/bb_legend.Rd | 22 plotbb-1.0.0/plotbb/man/bb_position.Rd |only plotbb-1.0.0/plotbb/man/bb_save.Rd |only plotbb-1.0.0/plotbb/man/bb_scale_x_continuous.Rd |only plotbb-1.0.0/plotbb/man/bbplot.Rd | 20 plotbb-1.0.0/plotbb/man/bbplot_add.Rd | 35 plotbb-1.0.0/plotbb/man/layer.Rd | 248 + plotbb-1.0.0/plotbb/man/set_bb_theme.Rd | 6 plotbb-1.0.0/plotbb/man/unset_bb_theme.Rd | 4 plotbb-1.0.0/plotbb/man/with_bb_theme.Rd |only plotbb-1.0.0/plotbb/tests/testthat.R | 8 plotbb-1.0.0/plotbb/tests/testthat/helper-device.R |only plotbb-1.0.0/plotbb/tests/testthat/test-auto-legend-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-build-save.R |only plotbb-1.0.0/plotbb/tests/testthat/test-coord-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-facets-0.6.R |only plotbb-1.0.0/plotbb/tests/testthat/test-grammar.R |only plotbb-1.0.0/plotbb/tests/testthat/test-inputs.R |only plotbb-1.0.0/plotbb/tests/testthat/test-layers-0.4.R |only plotbb-1.0.0/plotbb/tests/testthat/test-layers-0.7.R |only plotbb-1.0.0/plotbb/tests/testthat/test-legends-0.8.R |only plotbb-1.0.0/plotbb/tests/testthat/test-orientation-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-position-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-registry-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-scales.R |only plotbb-1.0.0/plotbb/tests/testthat/test-state.R |only plotbb-1.0.0/plotbb/vignettes/plotbb.qmd | 1467 +++++++-- 82 files changed, 9160 insertions(+), 3612 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.18.2 dated 2026-09-10 and 0.19.0 dated 2026-10-18
DESCRIPTION | 40 MD5 | 91 +- NAMESPACE | 5 NEWS.md | 256 +++++ R/check_collinearity.R | 668 +++++++++++++-- R/check_model.R | 430 +++++++++ R/check_model_diagnostics.R | 288 ++++++ R/check_outliers.R | 808 +++++++++++++++++- R/check_overdispersion.R | 158 +++ R/check_predictions.R | 76 + R/check_singularity.R | 9 R/compare_performance.R | 13 R/format.R | 21 R/helpers.R | 46 + R/icc.R | 5 R/model_performance.lavaan.R | 192 ++-- R/r2_efron.R | 8 R/r2_mckelvey.R | 8 R/r2_nakagawa.R | 7 R/r2_somers.R | 7 R/r2_tjur.R | 8 R/test_performance.R | 102 ++ R/test_vuong.R | 8 R/test_wald.R | 8 inst/WORDLIST | 3 man/check_collinearity.Rd | 41 man/check_model.Rd | 36 man/check_outliers.Rd | 50 + man/check_overdispersion.Rd | 15 man/check_predictions.Rd | 6 man/icc.Rd | 5 man/model_performance.lavaan.Rd | 26 man/r2_nakagawa.Rd | 7 tests/testthat/test-check_collinearity.R | 1104 ++++++++++++++++++++++++- tests/testthat/test-check_group_variation.R | 5 tests/testthat/test-check_model.R | 372 ++++++++ tests/testthat/test-check_model_glmmTMB.R |only tests/testthat/test-check_outliers.R | 55 + tests/testthat/test-check_outliers_cook.R |only tests/testthat/test-check_outliers_glmmTMB.R |only tests/testthat/test-check_outliers_group.R |only tests/testthat/test-check_overdispersion.R | 460 ++++++++++ tests/testthat/test-check_predictions.R | 173 +++ tests/testthat/test-check_singularity.R | 20 tests/testthat/test-compare_performance.R | 36 tests/testthat/test-model_performance.lavaan.R | 252 +++++ tests/testthat/test-r2_binomial_aggregated.R |only tests/testthat/test-r2_nakagawa.R | 42 tests/testthat/test-test_performance.R | 64 + 49 files changed, 5670 insertions(+), 364 deletions(-)
Title: Exponential Multivariate Hawkes Model
Description: Simulate and fit multivariate Hawkes models with exponential
kernels, introduced by Hawkes (1971) <doi:10.2307/2334319>.
Includes marked, state-dependent, and multi-kernel specifications.
Parameter estimation uses maximum likelihood, following Ozaki (1979)
<doi:10.1007/BF02480272>, through the optional 'maxLik' package or
the optimization functions supplied with R.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>
Diff between emhawkes versions 1.0.0 dated 2026-10-17 and 1.0.1 dated 2026-10-18
DESCRIPTION | 6 +- MD5 | 60 +++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 26 ++++++++++++ R/harrival.R | 78 +++++++++++++++++++++++++++++++------- R/hengine.R | 1 R/hfitted.R | 8 +++ R/hgfit.R | 6 +- R/himpact.R | 6 +- R/hinterface.R | 4 + R/hllf.R | 12 +++++ R/hmoment.R | 18 +++++++- R/hoptimizer.R | 26 ++++++++++++ R/tzexp.R | 23 ++++++++--- R/zzz.R | 2 inst/doc/example.html | 4 - man/fitted_hspec.Rd | 8 +++ man/logLik.Rd | 4 + src/hawkes_simulate.cpp | 7 --- src/hawkes_simulate_callbacks.cpp | 7 --- src/hawkes_simulate_equal.cpp | 7 --- src/simulation_state.h | 15 +++++++ tests/callback-history-context.R |only tests/computation-regressions.R | 8 +++ tests/expected-wait.R | 26 ++++++++++++ tests/fit-rds-session.R | 32 ++++++++++----- tests/s4-minimal-session.R | 26 ++++++++---- tests/simulation-subnormal.R |only tests/state-replay.R | 4 - tests/stats-isolated-session.R | 39 ++++++++++++------- tests/tzexp-distribution.R | 8 +++ tests/volatility.R | 10 ++++ 32 files changed, 370 insertions(+), 112 deletions(-)
Title: Census of India Data, 1901-2011, with Boundaries and Projections
Description: Tables from every decennial Census of India from 1901 to 2011:
population time series, Primary Census Abstracts at state, district and
sub-district level, mother tongue tables, Scheduled Caste and
Scheduled Tribe populations, and the 1931 caste tables by religion,
together with Ministry of Health and Family Welfare population
projections to 2036. Historical series are drawn
from Jolad and Singh (2026) <doi:10.7910/DVN/ON8CP8>. Census variables
can be returned with state or district boundaries of the matching
census year attached for mapping. Boundary files and the largest
village-level tables are downloaded on first use and cached locally.
Author: Saket Choudhary [aut, cre, cph]
Maintainer: Saket Choudhary <saketc@iitb.ac.in>
Diff between censusindia versions 0.2.0 dated 2026-10-15 and 0.2.1 dated 2026-10-18
DESCRIPTION | 18 ++-- MD5 | 65 +++++++++------- NAMESPACE | 2 NEWS.md | 43 ++++++---- R/data.R | 108 +++++++++++++++++++++++---- R/download.R | 13 +-- R/geometry.R | 6 - R/get_census.R | 45 ++++++++--- R/population.R | 54 +++++++++++-- R/serve.R |only R/variables.R | 2 README.md | 1 data/census_1931_castes.rda |only data/census_1931_exterior_castes.rda |only data/census_1971.rda |binary data/census_1981.rda |binary data/census_subdistricts_2011.rda |binary data/population_projections_district_lgd.rda |binary data/population_projections_state.rda |binary inst/COPYRIGHTS | 6 + inst/manifest.csv | 4 - inst/plumber |only man/census_1931_castes.Rd |only man/census_1931_exterior_castes.Rd |only man/census_subdistricts_2011.Rd | 9 ++ man/censusindia-package.Rd | 4 - man/figures/logo.png |binary man/get_census.Rd | 3 man/get_population.Rd | 26 +++++- man/population_projections_district_age.Rd | 9 +- man/population_projections_district_lgd.Rd | 6 - man/population_projections_state.Rd | 39 +++++++-- man/serve.Rd |only tests/testthat/test-castes-1931.R |only tests/testthat/test-get-census.R | 19 ++-- tests/testthat/test-na-fixes.R |only tests/testthat/test-population-estimate.R | 36 +++++++++ tests/testthat/test-reconciliation.R |only tests/testthat/test-serve.R |only 39 files changed, 384 insertions(+), 134 deletions(-)
Title: Prospective Trial Planning for Average Hazard Estimands
Description: Provides a simulation-based prospective planning workflow for
average hazard estimands in two-arm time-to-event trials. Supports
calibration and freezing of design-specific information-support rules,
assessment of clinically preferred truncation horizons, conditional
selection of clinically acceptable alternative horizons, and reverse
design over sample size and additional follow-up. Separates information
support from statistical power and supports auditable planning reports.
Author: Xinyue Zhao [aut, cre],
Haitao Pan [aut]
Maintainer: Xinyue Zhao <xinyuezhao27@gwu.edu>
Diff between AHTauDesign versions 0.1.0 dated 2026-09-10 and 1.0 dated 2026-10-18
AHTauDesign-0.1.0/AHTauDesign/R/assess_tau.R |only AHTauDesign-0.1.0/AHTauDesign/R/optimize_tau.R |only AHTauDesign-0.1.0/AHTauDesign/R/twostage_tau.R |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.R |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.Rmd |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.html |only AHTauDesign-0.1.0/AHTauDesign/man/assess_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/default_fail_thresholds.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/default_feasibility_thresholds.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/optimize_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/twostage_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/vignettes/AHTauDesign.Rmd |only AHTauDesign-0.1.0/AHTauDesign/vignettes/precomputed_results.rds |only AHTauDesign-1.0/AHTauDesign/DESCRIPTION | 41 +++---- AHTauDesign-1.0/AHTauDesign/MD5 | 58 +++++++--- AHTauDesign-1.0/AHTauDesign/NAMESPACE | 21 +-- AHTauDesign-1.0/AHTauDesign/NEWS.md |only AHTauDesign-1.0/AHTauDesign/R/calib_reliability_functions.R |only AHTauDesign-1.0/AHTauDesign/R/calibration.R |only AHTauDesign-1.0/AHTauDesign/R/calibration_simulation.R |only AHTauDesign-1.0/AHTauDesign/R/part2_design.R |only AHTauDesign-1.0/AHTauDesign/R/planning_report.R |only AHTauDesign-1.0/AHTauDesign/R/simulate_design.R |only AHTauDesign-1.0/AHTauDesign/R/stage1_audit.R |only AHTauDesign-1.0/AHTauDesign/R/stage2_select.R |only AHTauDesign-1.0/AHTauDesign/R/support_rule.R |only AHTauDesign-1.0/AHTauDesign/README.md |only AHTauDesign-1.0/AHTauDesign/build/vignette.rds |binary AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.R |only AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.Rmd |only AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.html |only AHTauDesign-1.0/AHTauDesign/inst/extdata |only AHTauDesign-1.0/AHTauDesign/man/classify_calib_reliability.Rd |only AHTauDesign-1.0/AHTauDesign/man/count_calib_reliability.Rd |only AHTauDesign-1.0/AHTauDesign/man/evaluate_calib_rules.Rd |only AHTauDesign-1.0/AHTauDesign/man/find_n_req.Rd |only AHTauDesign-1.0/AHTauDesign/man/freeze_support_rule.Rd |only AHTauDesign-1.0/AHTauDesign/man/planning_report.Rd |only AHTauDesign-1.0/AHTauDesign/man/print.ahtau_planning_report.Rd |only AHTauDesign-1.0/AHTauDesign/man/simulate_calibration_null.Rd |only AHTauDesign-1.0/AHTauDesign/man/simulate_design.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage1_audit.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage2_evaluate.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage2_select.Rd |only AHTauDesign-1.0/AHTauDesign/man/summarize_calibration_support.Rd |only AHTauDesign-1.0/AHTauDesign/tests |only AHTauDesign-1.0/AHTauDesign/vignettes/getting-started.Rmd |only 47 files changed, 71 insertions(+), 49 deletions(-)
Title: Health Geography Toolbox for Model-Based Analysis of Infections
Panel Data
Description: Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. Cluster and hotspot analyses can be conducted using neighborhood matrices. See Wieland (2020) <doi:10.18335/region.v7i2.324> for an application of some of the mentioned analysis methods. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the [...truncated...]
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 3.0.1 dated 2026-10-11 and 3.0.2 dated 2026-10-18
DESCRIPTION | 8 +- MD5 | 66 ++++++++++---------- NEWS.md |only R/config.R | 6 - R/growthmodels.R | 47 ++++++++++---- R/helper.R | 119 +++++++++++++++++++++++++++++++++++-- R/infpan.R | 43 +++++++++++-- R/stathelp.R | 53 +++++++++++----- R/swash.R | 84 ++++++++++++++++++-------- inst |only man/C19dNUTSdata.Rd | 4 - man/COVID19Cases_geoRegion.Rd | 2 man/K4kant20260101gf_ch2007Poly.Rd | 6 - man/RKI_Corona_counties.Rd | 4 - man/add_geodata.Rd | 2 man/as_balanced.Rd | 11 ++- man/binary_metrics.Rd | 4 - man/binary_metrics_glm.Rd | 4 - man/breaks_growth.Rd | 7 +- man/calculate_incidence-method.Rd | 2 man/calculate_incidence.Rd | 2 man/countries-class.Rd | 6 - man/growth-methods.Rd | 2 man/growth_hawkes.Rd | 2 man/growth_initial.Rd | 2 man/growthmodels-class.Rd | 7 +- man/hawkes_growth.Rd | 6 - man/infpan-class.Rd | 6 - man/is_balanced.Rd | 18 ++++- man/nbstat.Rd | 2 man/plot-methods.Rd | 2 man/plot_map.Rd | 2 man/sbm-class.Rd | 2 man/sbm_ci-class.Rd | 2 man/swash-package.Rd | 8 +- 35 files changed, 386 insertions(+), 155 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre, art, cph]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.5.0 dated 2026-08-21 and 2.0.0 dated 2026-10-18
IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_issues.R |only IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_labels.R |only IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_milestones.R |only IssueTrackeR-1.5.0/IssueTrackeR/inst/data_issues/closed_issues.yaml |only IssueTrackeR-1.5.0/IssueTrackeR/inst/data_issues/open_issues.yaml |only IssueTrackeR-1.5.0/IssueTrackeR/man/figures/README-pressure-1.png |only IssueTrackeR-1.5.0/IssueTrackeR/man/reset_options.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/data/closed_issues.yaml |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/data/open_issues.yaml |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-add_n_years.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-bin_count.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-count_issues.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-finding.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-format_timestamp.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-isDark.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-null_to_default.R |only IssueTrackeR-2.0.0/IssueTrackeR/DESCRIPTION | 15 IssueTrackeR-2.0.0/IssueTrackeR/MD5 | 151 +- IssueTrackeR-2.0.0/IssueTrackeR/NAMESPACE | 56 IssueTrackeR-2.0.0/IssueTrackeR/NEWS.md | 50 IssueTrackeR-2.0.0/IssueTrackeR/R/IssueTrackeR-package.R | 2 IssueTrackeR-2.0.0/IssueTrackeR/R/check.R | 96 - IssueTrackeR-2.0.0/IssueTrackeR/R/contributor.R | 94 + IssueTrackeR-2.0.0/IssueTrackeR/R/finding-objects.R | 225 ++- IssueTrackeR-2.0.0/IssueTrackeR/R/format.R | 627 ++++++++-- IssueTrackeR-2.0.0/IssueTrackeR/R/get.R |only IssueTrackeR-2.0.0/IssueTrackeR/R/options.R | 106 + IssueTrackeR-2.0.0/IssueTrackeR/R/plot.R | 355 +++-- IssueTrackeR-2.0.0/IssueTrackeR/R/print.R | 171 ++ IssueTrackeR-2.0.0/IssueTrackeR/R/selector.R |only IssueTrackeR-2.0.0/IssueTrackeR/R/summary.R | 89 - IssueTrackeR-2.0.0/IssueTrackeR/R/update_database.R | 88 - IssueTrackeR-2.0.0/IssueTrackeR/R/utils.R | 118 + IssueTrackeR-2.0.0/IssueTrackeR/R/wrangling_issues.R | 539 ++++---- IssueTrackeR-2.0.0/IssueTrackeR/R/wrangling_repo.R | 74 - IssueTrackeR-2.0.0/IssueTrackeR/R/write.R | 286 ++-- IssueTrackeR-2.0.0/IssueTrackeR/R/zzz.R | 18 IssueTrackeR-2.0.0/IssueTrackeR/README.md | 156 +- IssueTrackeR-2.0.0/IssueTrackeR/build |only IssueTrackeR-2.0.0/IssueTrackeR/inst/WORDLIST | 5 IssueTrackeR-2.0.0/IssueTrackeR/inst/data_issues/generate-files.R | 12 IssueTrackeR-2.0.0/IssueTrackeR/inst/data_issues/list_issues.yaml |only IssueTrackeR-2.0.0/IssueTrackeR/inst/data_issues/list_labels.yaml | 26 IssueTrackeR-2.0.0/IssueTrackeR/inst/data_issues/list_milestones.yaml | 18 IssueTrackeR-2.0.0/IssueTrackeR/inst/doc |only IssueTrackeR-2.0.0/IssueTrackeR/man/IssueTrackeR-options.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/append.Rd | 17 IssueTrackeR-2.0.0/IssueTrackeR/man/author_last_comment.Rd | 16 IssueTrackeR-2.0.0/IssueTrackeR/man/check_github_connection.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/compute_contribution.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/count_issues.Rd | 12 IssueTrackeR-2.0.0/IssueTrackeR/man/extract_nth.Rd | 37 IssueTrackeR-2.0.0/IssueTrackeR/man/extraction-issues.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/figures/README-plot-1.png |only IssueTrackeR-2.0.0/IssueTrackeR/man/figures/README-plot-2.png |only IssueTrackeR-2.0.0/IssueTrackeR/man/figures/README-plot-3.png |only IssueTrackeR-2.0.0/IssueTrackeR/man/get.Rd | 112 - IssueTrackeR-2.0.0/IssueTrackeR/man/get_all_repos.Rd | 10 IssueTrackeR-2.0.0/IssueTrackeR/man/get_nbr_comments.Rd | 13 IssueTrackeR-2.0.0/IssueTrackeR/man/init_selector.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/merge_selector.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/new_issue.Rd | 33 IssueTrackeR-2.0.0/IssueTrackeR/man/new_issues.Rd | 41 IssueTrackeR-2.0.0/IssueTrackeR/man/plot-issues.Rd | 50 IssueTrackeR-2.0.0/IssueTrackeR/man/print-issues.Rd | 41 IssueTrackeR-2.0.0/IssueTrackeR/man/rbind-issues.Rd | 27 IssueTrackeR-2.0.0/IssueTrackeR/man/remove_nth.Rd |only IssueTrackeR-2.0.0/IssueTrackeR/man/sample-issues.Rd | 12 IssueTrackeR-2.0.0/IssueTrackeR/man/subset.Rd | 12 IssueTrackeR-2.0.0/IssueTrackeR/man/summary.Rd | 13 IssueTrackeR-2.0.0/IssueTrackeR/man/unique-issues.Rd | 14 IssueTrackeR-2.0.0/IssueTrackeR/man/update_database.Rd | 61 IssueTrackeR-2.0.0/IssueTrackeR/man/with_comments.Rd | 13 IssueTrackeR-2.0.0/IssueTrackeR/man/with_labels.Rd | 50 IssueTrackeR-2.0.0/IssueTrackeR/man/with_text.Rd | 50 IssueTrackeR-2.0.0/IssueTrackeR/man/write.Rd | 91 - IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/data/list_issues.yaml |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/helper.R | 71 - IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-IssueTrackeR-package.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-comments.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-contributor.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-extract.R | 64 - IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-finding-objects.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-format.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-get.R | 123 + IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-options.R | 31 IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-plot.R | 72 - IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-print.R | 24 IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-selector.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-summary.R | 10 IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-update_database.R | 22 IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-utils.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-wrangling_issues.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-wrangling_repo.R |only IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-write.R | 16 IssueTrackeR-2.0.0/IssueTrackeR/tests/testthat/test-zzz.R |only IssueTrackeR-2.0.0/IssueTrackeR/vignettes |only 97 files changed, 2960 insertions(+), 1575 deletions(-)
Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Description: Imputes missing species trait data for comparative analyses
by combining three sources of information: phylogenetic similarity
(closely related species share similar traits), cross-trait
correlations (observed traits inform missing ones), and optional
environmental covariates (climate, habitat, geography). Handles
continuous measurements, counts, binary variables, ordered categories,
unordered categories, bounded proportions, zero-inflated counts, and
compositional multi-proportion data in a single call. The default
method is a phylogenetic baseline calibrated on held-out data; an
optional graph neural network correction, which is needed to use
covariates, is blended in through a per-trait gate that retains a
baseline fallback. Provides conformal
prediction intervals for continuous, count, ordinal, and proportion
traits and an experimental analysis-aware multiple-imputation workflow
for one missing continuous covariate in Gaussian linear, binomial-logit,
and Gaussian random-intercept m [...truncated...]
Author: Shinichi Nakagawa [aut, cre, cph]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between pigauto versions 0.10.0 dated 2026-07-30 and 0.11.0 dated 2026-10-18
DESCRIPTION | 31 MD5 | 271 +- NAMESPACE | 6 NEWS.md | 1003 ++++++++- R/active_impute.R | 20 R/bm_internal.R | 104 R/build_phylo_graph.R | 10 R/check_pigauto.R |only R/cross_validate.R | 10 R/data.R | 75 R/draws_conditional.R |only R/evaluate.R | 57 R/exact_conditional.R |only R/fit_baseline.R | 1210 ++++++++++ R/fit_helpers.R | 886 ++++++-- R/fit_pigauto.R | 1321 +++++++++--- R/henderson_s_inv.R | 49 R/impute.R | 386 +++ R/joint_mvn_baseline.R | 85 R/joint_mvn_solver.R | 850 +++++++ R/joint_threshold_baseline.R | 175 + R/mask_missing.R | 12 R/mi_posterior.R |only R/multi_impute.R | 617 +++++ R/multi_impute_analysis.R | 5 R/multi_impute_trees.R | 278 +- R/ovr_categorical.R | 78 R/pagel_lambda.R | 197 + R/phylo_signal.R | 37 R/plot.R | 53 R/plot_pigauto.R | 14 R/pool_mi.R | 211 + R/predict_pigauto.R | 809 +++++-- R/preprocess_traits.R | 241 ++ R/read_traits.R | 13 R/read_tree.R | 34 R/report.R | 183 + R/result_accessors.R |only R/save_load.R | 8 R/simulate_benchmark.R | 9 R/utils.R | 36 R/utils_torch.R | 11 R/with_imputations.R | 132 - README.md | 405 +-- build/partial.rdb |only build/vignette.rds |binary inst/NOTICE | 30 inst/doc/common-pitfalls.R | 6 inst/doc/common-pitfalls.Rmd | 81 inst/doc/common-pitfalls.html | 117 - inst/doc/getting-started.R | 79 inst/doc/getting-started.Rmd | 328 +- inst/doc/getting-started.html | 647 +++-- inst/doc/gnn-architecture.Rmd | 138 - inst/doc/gnn-architecture.html | 184 - inst/doc/mixed-types.R | 3 inst/doc/mixed-types.Rmd | 27 inst/doc/mixed-types.html | 202 - inst/doc/multiple-imputation.R |only inst/doc/multiple-imputation.Rmd |only inst/doc/multiple-imputation.html |only inst/doc/tree-uncertainty.R | 10 inst/doc/tree-uncertainty.Rmd | 56 inst/doc/tree-uncertainty.html | 95 inst/examples |only inst/extdata/novice_traits.csv |only inst/extdata/novice_tree.nwk |only man/build_phylo_graph.Rd | 7 man/calibration_df.Rd | 5 man/check_pigauto.Rd |only man/compare_methods.Rd | 26 man/completed_data.Rd |only man/cross_validate.Rd | 12 man/evaluate.Rd | 2 man/fit_baseline.Rd | 265 ++ man/fit_pigauto.Rd | 320 ++ man/impute.Rd | 254 +- man/multi_impute.Rd | 315 ++ man/multi_impute_analysis.Rd | 4 man/multi_impute_trees.Rd | 110 man/pigauto_report.Rd | 29 man/plot.pigauto_fit.Rd | 13 man/plot.pigauto_result.Rd |only man/plot_comparison.Rd | 13 man/plot_uncertainty.Rd | 3 man/pool_mi.Rd | 43 man/predict.pigauto_fit.Rd | 76 man/preprocess_traits.Rd | 14 man/print.pigauto_check.Rd |only man/print.summary_pigauto_result.Rd |only man/read_traits.Rd | 13 man/read_tree.Rd | 39 man/save_pigauto.Rd | 3 man/simulate_benchmark.Rd | 8 man/suggest_next_observation.Rd | 16 man/summary.pigauto_result.Rd |only man/tree300.Rd | 27 man/tree_full.Rd | 26 man/trees300.Rd | 32 man/with_imputations.Rd | 49 tests/testthat/fixtures/cran-audit-exported-formals.tsv |only tests/testthat/fixtures/lambda_fixed1_reference_ab02e31.rds |only tests/testthat/test-bm-internal.R | 29 tests/testthat/test-calibration-df.R |only tests/testthat/test-check-pigauto.R |only tests/testthat/test-clamp-outliers.R | 24 tests/testthat/test-community-surface.R |only tests/testthat/test-covariate-alignment.R |only tests/testthat/test-cran-audit-defaults.R |only tests/testthat/test-discrete-lambda.R |only tests/testthat/test-docs-phytools-warning.R |only tests/testthat/test-draws-auto.R |only tests/testthat/test-draws-conditional.R |only tests/testthat/test-evaluate-null.R |only tests/testthat/test-exact-centring.R |only tests/testthat/test-exact-conditional.R |only tests/testthat/test-exact-default.R |only tests/testthat/test-fit-predict.R | 36 tests/testthat/test-gbif-centroids.R | 2 tests/testthat/test-gnn-off.R |only tests/testthat/test-gnn-train-cal-symmetry.R |only tests/testthat/test-honesty-warnings.R |only tests/testthat/test-input-checks-206-207.R |only tests/testthat/test-input-checks-210-214.R |only tests/testthat/test-joint-baseline.R | 82 tests/testthat/test-joint-lambda.R |only tests/testthat/test-joint-refine-iter.R |only tests/testthat/test-joint-solver.R |only tests/testthat/test-joint-threshold-baseline.R | 75 tests/testthat/test-lambda-covariates.R |only tests/testthat/test-lambda-default.R |only tests/testthat/test-lambda-dispatch.R |only tests/testthat/test-lambda-per-type.R |only tests/testthat/test-mi-posterior.R |only tests/testthat/test-mi-provenance.R |only tests/testthat/test-mondrian-conformal.R |only tests/testthat/test-mondrian-mi-draws.R |only tests/testthat/test-monomorphic-discrete.R |only tests/testthat/test-multi-impute-posterior.R |only tests/testthat/test-multi-impute-trees.R |only tests/testthat/test-multi-impute.R | 352 --- tests/testthat/test-new-features.R | 22 tests/testthat/test-pagel-eigendecomp.R | 11 tests/testthat/test-pagel-lambda.R | 77 tests/testthat/test-phase9-integration.R | 4 tests/testthat/test-phylo-signal-gate.R | 13 tests/testthat/test-phylo-signal-multiobs.R |only tests/testthat/test-plot-comparison-methods.R |only tests/testthat/test-pmm.R | 14 tests/testthat/test-pool-mi-adapter-fixtures.R |only tests/testthat/test-pool-mi-backends.R |only tests/testthat/test-read-tree-multiphlo.R |only tests/testthat/test-report-213.R |only tests/testthat/test-result-contract.R |only tests/testthat/test-result-save-209.R |only tests/testthat/test-route-choice.R |only tests/testthat/test-safety-floor.R | 105 tests/testthat/test-shipping-coverage.R | 17 tests/testthat/test-sigma-fisher-ml.R |only tests/testthat/test-small-tree-k-eigen.R |only tests/testthat/test-species-mismatch-205.R |only tests/testthat/test-type-detection.R |only tests/testthat/test-zi-count-conformal-intervals.R |only tests/testthat/test-zi-count-conformal-mi.R |only tests/testthat/test-zi-count-splits.R |only vignettes/common-pitfalls.Rmd | 81 vignettes/getting-started.Rmd | 328 +- vignettes/gnn-architecture.Rmd | 138 - vignettes/mixed-types.Rmd | 27 vignettes/multiple-imputation.Rmd |only vignettes/tree-uncertainty.Rmd | 56 171 files changed, 11621 insertions(+), 3531 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-23 1.2.6
2026-07-08 1.2.5
2026-04-23 1.2.4
2026-04-10 1.2.3
2026-03-30 1.2.2
2026-03-18 1.2.1
2026-03-15 1.2
2025-11-28 1.1
2025-11-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-09 0.7.0
2025-12-10 0.6.0
2025-11-16 0.5.0
2025-07-08 0.4.0
2025-04-15 0.3.0
2024-11-27 0.2.0