Title: JSS 'LaTeX'/'BibTeX' Style Checker
Description: Lints 'LaTeX'/'BibTeX' manuscripts against the Journal of Statistical
Software (JSS) style guide. Wraps the same 'Rust' rule engine used by the
standalone 'jsslint' binary, the browser/'WASM' build, and the 'Python'
binding, exposed to R via 'extendr'.
Author: Manuel Koller [aut, cre] ,
The authors of the vendored 'Rust' crates [cph]
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between jsslintr versions 1.1.0-2 dated 2026-07-29 and 1.2.0 dated 2026-09-10
DESCRIPTION | 6 MD5 | 82 +-- NAMESPACE | 1 R/extendr-wrappers.R | 8 R/jsslint.R | 27 + inst/doc/jsslintr.Rmd | 5 inst/doc/jsslintr.html | 39 - man/jss_files.Rd | 5 man/jsslint_version.Rd |only man/render.Rd | 2 src/rust/Cargo.lock | 6 src/rust/Cargo.toml | 2 src/rust/jsslint-core/Cargo.toml | 2 src/rust/jsslint-core/build.rs | 136 +++++ src/rust/jsslint-core/src/baseline.rs |only src/rust/jsslint-core/src/catalogue.rs | 70 +++ src/rust/jsslint-core/src/color.rs |only src/rust/jsslint-core/src/config.rs | 33 + src/rust/jsslint-core/src/coverage.rs |only src/rust/jsslint-core/src/engine.rs | 78 +++ src/rust/jsslint-core/src/explain.rs | 31 + src/rust/jsslint-core/src/fixer.rs | 66 ++ src/rust/jsslint-core/src/html_output.rs | 81 +++ src/rust/jsslint-core/src/json_output.rs | 102 ++++ src/rust/jsslint-core/src/lib.rs | 5 src/rust/jsslint-core/src/report.rs | 120 +++++ src/rust/jsslint-core/src/rules/capitalization.rs | 18 src/rust/jsslint-core/src/rules/citations.rs | 28 - src/rust/jsslint-core/src/rules/code_style.rs | 85 ++- src/rust/jsslint-core/src/rules/crossrefs.rs | 104 +++- src/rust/jsslint-core/src/rules/operators.rs | 22 src/rust/jsslint-core/src/rules/references.rs | 32 + src/rust/jsslint-core/src/rules/tex_common.rs | 78 +++ src/rust/jsslint-core/src/rules/typography.rs | 9 src/rust/jsslint-core/src/sarif.rs | 28 + src/rust/jsslint-core/src/suppress.rs |only src/rust/jsslint-core/src/terminal.rs | 440 +++++++++++++++---- src/rust/jsslint-core/src/version.rs |only src/rust/src/lib.rs | 25 + src/rust/vendor.tar.xz |binary src/specs/003-jss-rule-catalogue/catalogue.yaml | 26 + src/specs/003-jss-rule-catalogue/guide-coverage.yaml |only src/specs/003-jss-rule-catalogue/recall.json |only tests/testthat/test-jsslint.R | 17 tools/vendor-jsslint-core.sh | 8 vignettes/jsslintr.Rmd | 5 46 files changed, 1602 insertions(+), 230 deletions(-)
Title: Statistical Learning Methods for Optimizing Dynamic Treatment
Regimes
Description: We provide a comprehensive software to estimate general K-stage DTRs from SMARTs with Q-learning and a variety of outcome-weighted learning methods. Penalizations are allowed for variable selection and model regularization. With the outcome-weighted learning scheme, different loss functions - SVM hinge loss, SVM ramp loss, binomial deviance loss, and L2 loss - are adopted to solve the weighted classification problem at each stage; augmentation in the outcomes is allowed to improve efficiency. The estimated DTR can be easily applied to a new sample for individualized treatment recommendations or DTR evaluation.
Author: Yuan Chen [aut, cre],
Ying Liu [aut],
Tianchen Xu [ctb] ,
Donglin Zeng [ctb],
Yuanjia Wang [ctb]
Maintainer: Yuan Chen <irene.yuan.chen@gmail.com>
Diff between DTRlearn2 versions 1.1 dated 2020-04-22 and 2.1 dated 2026-09-10
DESCRIPTION | 25 + MD5 | 35 +- NAMESPACE | 23 - R/owl.R | 466 ++++++++++++++--------------- R/owl_aug.R | 218 ++++++------- R/owl_l2.R | 92 ++--- R/owl_logit.R | 88 ++--- R/owl_ramp.R | 350 ++++++++++----------- R/predict_all.R | 846 ++++++++++++++++++++++++++--------------------------- R/ql.R | 208 ++++++------- R/sim_Kstage.R | 94 ++--- R/wsvm_solve.R | 149 +++++---- README.md |only man/adhd.Rd | 102 +++--- man/owl.Rd | 286 +++++++++-------- man/predict.owl.Rd | 190 +++++------ man/predict.ql.Rd | 196 ++++++------ man/ql.Rd | 186 +++++------ man/sim_Kstage.Rd | 138 ++++---- 19 files changed, 1863 insertions(+), 1829 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.9.8.7 dated 2026-04-25 and 1.9.9.1 dated 2026-09-10
DESCRIPTION | 10 ++-- MD5 | 16 ++++--- inst/NEWS.Rd | 6 ++ inst/doc/haplostats.R | 14 +++--- inst/doc/haplostats.Rmd | 53 +++++++++++++----------- inst/doc/haplostats.html | 88 ++++++++++++++++++++--------------------- tests/testthat/cchladf.rds |only tests/testthat/cctestdf.rds |only tests/testthat/test.haplo.cc.R | 37 ++++++++++------- vignettes/haplostats.Rmd | 53 +++++++++++++----------- 10 files changed, 150 insertions(+), 127 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgleish [aut, cre] ,
Yonghong Wang [aut],
Jack Zhu [aut],
Paul Meltzer [aut, sad]
Maintainer: James Dalgleish <jamesdalg@gmail.com>
Diff between CNVScope versions 3.7.6 dated 2026-07-04 and 3.7.7 dated 2026-09-10
DESCRIPTION | 8 +++--- MD5 | 36 ++++++++++++++-------------- NEWS.md | 16 ++++++++++++ R/CNVScopeserver.R | 2 - R/calcCNVKernelProbDist.R | 2 - R/downsample_genomic_matrix.R | 11 +++----- R/formSampleMatrixFromRawGDCData.R | 5 +++ R/getBlockAverageMatrixFromBreakpoints.R | 2 - R/getInterchromosomalInteractivePlot.R | 2 - R/importBreakpointBed.R | 2 - R/rebinGenomicInteractions.R | 2 - man/CNVScopeserver.Rd | 3 ++ man/calcCNVKernelProbDist.Rd | 9 +++++++ man/downsample_genomic_matrix.Rd | 3 ++ man/formSampleMatrixFromRawGDCData.Rd | 22 +++++++++++++++++ man/getBlockAverageMatrixFromBreakpoints.Rd | 10 +++++++ man/getInterchromosomalInteractivePlot.Rd | 3 ++ man/importBreakpointBed.Rd | 3 ++ man/rebinGenomicInteractions.Rd | 11 ++++++++ 19 files changed, 116 insertions(+), 36 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matthew Heaton [ctb] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.13.0 dated 2026-06-10 and 0.14.0 dated 2026-09-10
spmodel-0.13.0/spmodel/R/AIC_deprecated.R |only spmodel-0.13.0/spmodel/R/AIC_glm_deprecated.R |only spmodel-0.13.0/spmodel/R/BIC_deprecated.R |only spmodel-0.13.0/spmodel/R/BIC_glm_deprecated.R |only spmodel-0.13.0/spmodel/R/get_optim_par.R |only spmodel-0.13.0/spmodel/R/get_optim_par_glm.R |only spmodel-0.14.0/spmodel/DESCRIPTION | 19 spmodel-0.14.0/spmodel/MD5 | 554 - spmodel-0.14.0/spmodel/NAMESPACE | 68 spmodel-0.14.0/spmodel/NEWS.md | 651 - spmodel-0.14.0/spmodel/R/AICc.R | 136 spmodel-0.14.0/spmodel/R/AICc_glm.R | 2 spmodel-0.14.0/spmodel/R/AUROC.R | 7 spmodel-0.14.0/spmodel/R/PseudoR2.R | 2 spmodel-0.14.0/spmodel/R/PseudoR2_glm.R | 2 spmodel-0.14.0/spmodel/R/anova.R | 137 spmodel-0.14.0/spmodel/R/anova_glm.R | 3 spmodel-0.14.0/spmodel/R/augment.R | 61 spmodel-0.14.0/spmodel/R/augment_glm.R | 75 spmodel-0.14.0/spmodel/R/check_optim_method.R | 4 spmodel-0.14.0/spmodel/R/checks_shared.R |only spmodel-0.14.0/spmodel/R/coef.R | 3 spmodel-0.14.0/spmodel/R/coef_glm.R | 2 spmodel-0.14.0/spmodel/R/conditional.R |only spmodel-0.14.0/spmodel/R/confint.R | 26 spmodel-0.14.0/spmodel/R/confint_glm.R | 2 spmodel-0.14.0/spmodel/R/cooks.distance.R | 5 spmodel-0.14.0/spmodel/R/cooks.distance_glm.R | 4 spmodel-0.14.0/spmodel/R/cov_betahat_adjust.R | 58 spmodel-0.14.0/spmodel/R/cov_estimate_cl.R | 18 spmodel-0.14.0/spmodel/R/cov_estimate_dispatch_helpers.R |only spmodel-0.14.0/spmodel/R/cov_estimate_gloglik.R | 164 spmodel-0.14.0/spmodel/R/cov_estimate_laploglik.R | 122 spmodel-0.14.0/spmodel/R/cov_estimate_sv.R | 14 spmodel-0.14.0/spmodel/R/cov_initial_search.R | 1691 +--- spmodel-0.14.0/spmodel/R/cov_initial_search_glm.R | 711 - spmodel-0.14.0/spmodel/R/cov_initial_search_helpers.R |only spmodel-0.14.0/spmodel/R/cov_matrix.R | 91 spmodel-0.14.0/spmodel/R/cov_vector.R | 7 spmodel-0.14.0/spmodel/R/covmatrix.R | 50 spmodel-0.14.0/spmodel/R/covmatrix_glm.R | 4 spmodel-0.14.0/spmodel/R/data.R | 16 spmodel-0.14.0/spmodel/R/decorrelate.R |only spmodel-0.14.0/spmodel/R/decorrelate_data.R |only spmodel-0.14.0/spmodel/R/decorrelate_grid.R |only spmodel-0.14.0/spmodel/R/decorrelate_initial_search.R |only spmodel-0.14.0/spmodel/R/decorrelate_newdata.R |only spmodel-0.14.0/spmodel/R/deviance.R | 3 spmodel-0.14.0/spmodel/R/deviance_glm.R | 2 spmodel-0.14.0/spmodel/R/dispersion_checks.R | 11 spmodel-0.14.0/spmodel/R/dispersion_initial.R | 5 spmodel-0.14.0/spmodel/R/dispersion_initial_NA.R | 14 spmodel-0.14.0/spmodel/R/dispersion_optim2orig.R | 15 spmodel-0.14.0/spmodel/R/dispersion_orig2optim.R | 13 spmodel-0.14.0/spmodel/R/dispersion_params.R | 3 spmodel-0.14.0/spmodel/R/eacf.R | 88 spmodel-0.14.0/spmodel/R/emmeans.R | 98 spmodel-0.14.0/spmodel/R/esv.R | 90 spmodel-0.14.0/spmodel/R/fill_optim_par.R | 3 spmodel-0.14.0/spmodel/R/fitted.R | 2 spmodel-0.14.0/spmodel/R/fitted_glm.R | 4 spmodel-0.14.0/spmodel/R/floor_estimated_ie.R |only spmodel-0.14.0/spmodel/R/formula.R | 2 spmodel-0.14.0/spmodel/R/formula_glm.R | 2 spmodel-0.14.0/spmodel/R/get_L_list.R | 62 spmodel-0.14.0/spmodel/R/get_anisotropy_corrected.R | 17 spmodel-0.14.0/spmodel/R/get_avg_dist.R |only spmodel-0.14.0/spmodel/R/get_bounding_box_dist.R |only spmodel-0.14.0/spmodel/R/get_cholprods.R | 15 spmodel-0.14.0/spmodel/R/get_cholprods_glm.R | 15 spmodel-0.14.0/spmodel/R/get_coefficients.R | 2 spmodel-0.14.0/spmodel/R/get_coefficients_glm.R | 15 spmodel-0.14.0/spmodel/R/get_conditional_covparams.R |only spmodel-0.14.0/spmodel/R/get_conditional_new_from_base.R |only spmodel-0.14.0/spmodel/R/get_conditional_vecchia.R |only spmodel-0.14.0/spmodel/R/get_conditional_vecchia_glm.R |only spmodel-0.14.0/spmodel/R/get_cooks_distance.R | 4 spmodel-0.14.0/spmodel/R/get_cooks_distance_glm.R | 11 spmodel-0.14.0/spmodel/R/get_cov_gradients_context.R |only spmodel-0.14.0/spmodel/R/get_cov_matrix_list.R | 16 spmodel-0.14.0/spmodel/R/get_dSig_dtheta.R |only spmodel-0.14.0/spmodel/R/get_data_object.R | 477 - spmodel-0.14.0/spmodel/R/get_data_object_glm.R | 489 - spmodel-0.14.0/spmodel/R/get_data_object_helpers.R |only spmodel-0.14.0/spmodel/R/get_delta_se.R |only spmodel-0.14.0/spmodel/R/get_deviance_glm.R | 28 spmodel-0.14.0/spmodel/R/get_eacf.R | 37 spmodel-0.14.0/spmodel/R/get_eacf_dotlist.R | 31 spmodel-0.14.0/spmodel/R/get_effective_range.R |only spmodel-0.14.0/spmodel/R/get_eigenprods.R | 28 spmodel-0.14.0/spmodel/R/get_eigenprods_glm.R | 22 spmodel-0.14.0/spmodel/R/get_esv.R | 56 spmodel-0.14.0/spmodel/R/get_esv_dotlist.R | 23 spmodel-0.14.0/spmodel/R/get_fitted.R | 45 spmodel-0.14.0/spmodel/R/get_fitted_glm.R | 106 spmodel-0.14.0/spmodel/R/get_glogclikloss.R | 9 spmodel-0.14.0/spmodel/R/get_grad_g.R |only spmodel-0.14.0/spmodel/R/get_group_labels.R |only spmodel-0.14.0/spmodel/R/get_hatvalues.R | 6 spmodel-0.14.0/spmodel/R/get_hatvalues_glm.R | 196 spmodel-0.14.0/spmodel/R/get_initial_extra.R | 3 spmodel-0.14.0/spmodel/R/get_initial_range.R | 8 spmodel-0.14.0/spmodel/R/get_kcv.R |only spmodel-0.14.0/spmodel/R/get_kcv_glm.R |only spmodel-0.14.0/spmodel/R/get_local_list.R | 687 + spmodel-0.14.0/spmodel/R/get_loocv.R | 25 spmodel-0.14.0/spmodel/R/get_loocv_glm.R | 28 spmodel-0.14.0/spmodel/R/get_minustwolaploglik.R | 18 spmodel-0.14.0/spmodel/R/get_minustwologlik.R | 6 spmodel-0.14.0/spmodel/R/get_model_stats.R | 74 spmodel-0.14.0/spmodel/R/get_model_stats_glm.R | 71 spmodel-0.14.0/spmodel/R/get_optim_dotlist.R | 15 spmodel-0.14.0/spmodel/R/get_prediction_object.R |only spmodel-0.14.0/spmodel/R/get_prediction_object_glm.R |only spmodel-0.14.0/spmodel/R/get_prof_sigma2.R | 4 spmodel-0.14.0/spmodel/R/get_randcov_list.R | 184 spmodel-0.14.0/spmodel/R/get_randcov_names.R | 49 spmodel-0.14.0/spmodel/R/get_residuals.R | 26 spmodel-0.14.0/spmodel/R/get_residuals_glm.R | 37 spmodel-0.14.0/spmodel/R/get_spcov_params.R | 4 spmodel-0.14.0/spmodel/R/get_sprnorm_vecchia.R |only spmodel-0.14.0/spmodel/R/get_svloss.R | 8 spmodel-0.14.0/spmodel/R/get_vcov.R | 4 spmodel-0.14.0/spmodel/R/get_vcov_glm.R | 14 spmodel-0.14.0/spmodel/R/get_wts_varw.R | 46 spmodel-0.14.0/spmodel/R/glance.R | 6 spmodel-0.14.0/spmodel/R/glances.R | 39 spmodel-0.14.0/spmodel/R/glances_glm.R | 3 spmodel-0.14.0/spmodel/R/glogclik.R | 9 spmodel-0.14.0/spmodel/R/gloglik.R | 30 spmodel-0.14.0/spmodel/R/gloglik_anis.R | 80 spmodel-0.14.0/spmodel/R/gloglik_products.R | 22 spmodel-0.14.0/spmodel/R/hatvalues.R | 2 spmodel-0.14.0/spmodel/R/hatvalues_glm.R | 2 spmodel-0.14.0/spmodel/R/hwInv.R | 11 spmodel-0.14.0/spmodel/R/influence.R | 8 spmodel-0.14.0/spmodel/R/influence_glm.R | 7 spmodel-0.14.0/spmodel/R/kcv.R |only spmodel-0.14.0/spmodel/R/kcv_glm.R |only spmodel-0.14.0/spmodel/R/labels.R | 2 spmodel-0.14.0/spmodel/R/labels_glm.R | 2 spmodel-0.14.0/spmodel/R/laploglik.R | 58 spmodel-0.14.0/spmodel/R/laploglik_anis.R | 112 spmodel-0.14.0/spmodel/R/laploglik_products.R | 1163 +-- spmodel-0.14.0/spmodel/R/logLik.R | 6 spmodel-0.14.0/spmodel/R/logLik_glm.R | 2 spmodel-0.14.0/spmodel/R/loocv.R | 422 - spmodel-0.14.0/spmodel/R/loocv_glm.R | 242 spmodel-0.14.0/spmodel/R/model.frame.R | 6 spmodel-0.14.0/spmodel/R/model.frame_glm.R | 4 spmodel-0.14.0/spmodel/R/model.matrix.R | 5 spmodel-0.14.0/spmodel/R/model.matrix_glm.R | 2 spmodel-0.14.0/spmodel/R/nobs.R |only spmodel-0.14.0/spmodel/R/nobs_glm.R |only spmodel-0.14.0/spmodel/R/partition_matrix.R | 38 spmodel-0.14.0/spmodel/R/partition_vector.R | 83 spmodel-0.14.0/spmodel/R/plot.R | 34 spmodel-0.14.0/spmodel/R/plot_glm.R | 4 spmodel-0.14.0/spmodel/R/predict.R | 1215 +-- spmodel-0.14.0/spmodel/R/predict_block.R | 321 spmodel-0.14.0/spmodel/R/predict_decorrelate.R |only spmodel-0.14.0/spmodel/R/predict_glm.R | 1021 +- spmodel-0.14.0/spmodel/R/predict_helpers.R |only spmodel-0.14.0/spmodel/R/predict_terms.R | 34 spmodel-0.14.0/spmodel/R/print.R | 154 spmodel-0.14.0/spmodel/R/print_glm.R | 92 spmodel-0.14.0/spmodel/R/print_helpers.R |only spmodel-0.14.0/spmodel/R/print_rf.R |only spmodel-0.14.0/spmodel/R/randcov_initial.R | 3 spmodel-0.14.0/spmodel/R/randcov_intial_NA.R | 4 spmodel-0.14.0/spmodel/R/randcov_matrix.R | 2 spmodel-0.14.0/spmodel/R/randcov_optim2orig.R | 20 spmodel-0.14.0/spmodel/R/randcov_orig2optim.R | 13 spmodel-0.14.0/spmodel/R/randcov_params.R | 6 spmodel-0.14.0/spmodel/R/randcov_vector.R | 190 spmodel-0.14.0/spmodel/R/recorrelate_newdata.R |only spmodel-0.14.0/spmodel/R/replace_data_object_dimcoords1.R | 16 spmodel-0.14.0/spmodel/R/residuals.R | 4 spmodel-0.14.0/spmodel/R/residuals_glm.R | 3 spmodel-0.14.0/spmodel/R/response_checks_glm.R | 29 spmodel-0.14.0/spmodel/R/satterthwaite.R |only spmodel-0.14.0/spmodel/R/satterthwaite_anova.R |only spmodel-0.14.0/spmodel/R/satterthwaite_helpers.R |only spmodel-0.14.0/spmodel/R/sf_to_df.R | 3 spmodel-0.14.0/spmodel/R/smwInv_rand.R | 13 spmodel-0.14.0/spmodel/R/spautor.R | 70 spmodel-0.14.0/spmodel/R/spautorRF.R | 29 spmodel-0.14.0/spmodel/R/spautor_checks.R | 20 spmodel-0.14.0/spmodel/R/spautor_matrixInv.R | 26 spmodel-0.14.0/spmodel/R/spcov_initial.R | 33 spmodel-0.14.0/spmodel/R/spcov_initial_NA.R | 9 spmodel-0.14.0/spmodel/R/spcov_initial_NA_glm.R | 28 spmodel-0.14.0/spmodel/R/spcov_matrix.R | 14 spmodel-0.14.0/spmodel/R/spcov_matrixInv_de.R | 14 spmodel-0.14.0/spmodel/R/spcov_optim2orig.R | 107 spmodel-0.14.0/spmodel/R/spcov_orig2optim.R | 328 spmodel-0.14.0/spmodel/R/spcov_params.R | 15 spmodel-0.14.0/spmodel/R/spcov_transform_helpers.R |only spmodel-0.14.0/spmodel/R/spcov_vector.R | 15 spmodel-0.14.0/spmodel/R/spdist.R | 3 spmodel-0.14.0/spmodel/R/spdist_vectors.R | 55 spmodel-0.14.0/spmodel/R/spgautor.R | 59 spmodel-0.14.0/spmodel/R/spgautor_checks.R | 27 spmodel-0.14.0/spmodel/R/spglm.R | 82 spmodel-0.14.0/spmodel/R/spglm_checks.R | 22 spmodel-0.14.0/spmodel/R/splm.R | 87 spmodel-0.14.0/spmodel/R/splmRF.R | 22 spmodel-0.14.0/spmodel/R/splm_checks.R | 10 spmodel-0.14.0/spmodel/R/spmodel-package.R | 8 spmodel-0.14.0/spmodel/R/sprbeta.R | 5 spmodel-0.14.0/spmodel/R/sprbinom.R | 3 spmodel-0.14.0/spmodel/R/sprgamma.R | 3 spmodel-0.14.0/spmodel/R/sprinvgauss.R | 5 spmodel-0.14.0/spmodel/R/sprnbinom.R | 6 spmodel-0.14.0/spmodel/R/sprnorm.R | 792 +- spmodel-0.14.0/spmodel/R/sprpois.R | 5 spmodel-0.14.0/spmodel/R/summary.R | 23 spmodel-0.14.0/spmodel/R/summary_glm.R | 5 spmodel-0.14.0/spmodel/R/summary_rf.R |only spmodel-0.14.0/spmodel/R/svloss.R | 10 spmodel-0.14.0/spmodel/R/tidy.R | 62 spmodel-0.14.0/spmodel/R/tidy_glm.R | 30 spmodel-0.14.0/spmodel/R/transform_anis.R | 80 spmodel-0.14.0/spmodel/R/use_glogclik.R | 27 spmodel-0.14.0/spmodel/R/use_glogclik_known.R | 12 spmodel-0.14.0/spmodel/R/use_gloglik.R | 80 spmodel-0.14.0/spmodel/R/use_gloglik_anis.R | 130 spmodel-0.14.0/spmodel/R/use_gloglik_iid.R | 20 spmodel-0.14.0/spmodel/R/use_gloglik_known.R | 16 spmodel-0.14.0/spmodel/R/use_gloglik_known_anis.R | 21 spmodel-0.14.0/spmodel/R/use_laploglik.R | 105 spmodel-0.14.0/spmodel/R/use_laploglik_anis.R | 153 spmodel-0.14.0/spmodel/R/use_laploglik_known.R | 26 spmodel-0.14.0/spmodel/R/use_laploglik_known_anis.R | 33 spmodel-0.14.0/spmodel/R/use_loglik_helpers.R |only spmodel-0.14.0/spmodel/R/use_svloss.R | 25 spmodel-0.14.0/spmodel/R/use_svloss_known.R | 4 spmodel-0.14.0/spmodel/R/utils.R | 72 spmodel-0.14.0/spmodel/R/varcomp.R | 37 spmodel-0.14.0/spmodel/R/varcomp_glm.R | 2 spmodel-0.14.0/spmodel/R/vcov.R | 27 spmodel-0.14.0/spmodel/R/vcov_glm.R | 4 spmodel-0.14.0/spmodel/R/warn_fitted_saturation.R |only spmodel-0.14.0/spmodel/R/warn_optim_convergence.R |only spmodel-0.14.0/spmodel/R/warn_spcov_boundary.R |only spmodel-0.14.0/spmodel/R/weights.R | 47 spmodel-0.14.0/spmodel/R/zzz.R | 20 spmodel-0.14.0/spmodel/README.md | 4 spmodel-0.14.0/spmodel/data/lake.rda |binary spmodel-0.14.0/spmodel/data/lake_preds.rda |binary spmodel-0.14.0/spmodel/data/moss.rda |binary spmodel-0.14.0/spmodel/data/seal.rda |binary spmodel-0.14.0/spmodel/data/texas.rda |binary spmodel-0.14.0/spmodel/inst/doc/introduction.Rmd | 29 spmodel-0.14.0/spmodel/inst/doc/introduction.html | 189 spmodel-0.14.0/spmodel/inst/references.bib | 529 - spmodel-0.14.0/spmodel/man/anova.spmodel.Rd | 25 spmodel-0.14.0/spmodel/man/augment.spmodel.Rd | 24 spmodel-0.14.0/spmodel/man/conditional.Rd |only spmodel-0.14.0/spmodel/man/confint.spmodel.Rd | 6 spmodel-0.14.0/spmodel/man/decorrelate.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_data.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_grid.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_newdata.Rd |only spmodel-0.14.0/spmodel/man/eacf.Rd | 6 spmodel-0.14.0/spmodel/man/esv.Rd | 6 spmodel-0.14.0/spmodel/man/kcv.Rd |only spmodel-0.14.0/spmodel/man/lake.Rd | 3 spmodel-0.14.0/spmodel/man/loocv.Rd | 51 spmodel-0.14.0/spmodel/man/moss.Rd | 4 spmodel-0.14.0/spmodel/man/plot.spmodel.Rd | 2 spmodel-0.14.0/spmodel/man/predict.spmodel.Rd | 103 spmodel-0.14.0/spmodel/man/print.spmodel.Rd | 40 spmodel-0.14.0/spmodel/man/recorrelate_newdata.Rd |only spmodel-0.14.0/spmodel/man/satterthwaite.Rd |only spmodel-0.14.0/spmodel/man/seal.Rd | 3 spmodel-0.14.0/spmodel/man/spautor.Rd | 12 spmodel-0.14.0/spmodel/man/spautorRF.Rd | 3 spmodel-0.14.0/spmodel/man/spcov_initial.Rd | 2 spmodel-0.14.0/spmodel/man/spglm.Rd | 2 spmodel-0.14.0/spmodel/man/splm.Rd | 14 spmodel-0.14.0/spmodel/man/splmRF.Rd | 6 spmodel-0.14.0/spmodel/man/spmodel-package.Rd | 7 spmodel-0.14.0/spmodel/man/sprnorm.Rd | 8 spmodel-0.14.0/spmodel/man/summary.spmodel.Rd | 18 spmodel-0.14.0/spmodel/man/texas.Rd | 3 spmodel-0.14.0/spmodel/man/varcomp.Rd | 30 spmodel-0.14.0/spmodel/man/vcov.spmodel.Rd | 16 spmodel-0.14.0/spmodel/tests/testthat/_snaps |only spmodel-0.14.0/spmodel/tests/testthat/setup.R |only spmodel-0.14.0/spmodel/tests/testthat/test-conditional.R |only spmodel-0.14.0/spmodel/tests/testthat/test-cov-initial-search.R |only spmodel-0.14.0/spmodel/tests/testthat/test-decorrelate.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-block-predict.R |only 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spmodel-0.14.0/spmodel/tests/testthat/test-spgautor.R | 23 spmodel-0.14.0/spmodel/tests/testthat/test-spglm.R | 34 spmodel-0.14.0/spmodel/tests/testthat/test-splm.R | 78 spmodel-0.14.0/spmodel/tests/testthat/test-utils.R | 22 spmodel-0.14.0/spmodel/vignettes/introduction.Rmd | 29 314 files changed, 14783 insertions(+), 12274 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.3.0 dated 2026-01-23 and 0.3.1 dated 2026-09-10
ragnar-0.3.0/ragnar/inst/python/_ragnartools/__pycache__ |only ragnar-0.3.1/ragnar/DESCRIPTION | 21 - ragnar-0.3.1/ragnar/MD5 | 75 ++-- ragnar-0.3.1/ragnar/NAMESPACE | 250 ++++++++------- ragnar-0.3.1/ragnar/NEWS.md | 23 + ragnar-0.3.1/ragnar/R/aaa-utils.R | 7 ragnar-0.3.1/ragnar/R/embed-vertex.R | 2 ragnar-0.3.1/ragnar/R/embed.R | 4 ragnar-0.3.1/ragnar/R/ingest.R | 7 ragnar-0.3.1/ragnar/R/legacy.R | 2 ragnar-0.3.1/ragnar/R/markdown-chunk.R | 2 ragnar-0.3.1/ragnar/R/markdown-document.R | 2 ragnar-0.3.1/ragnar/R/markdown-segment.R | 2 ragnar-0.3.1/ragnar/R/ragnar-package.R | 20 - ragnar-0.3.1/ragnar/R/retrieve.R | 10 ragnar-0.3.1/ragnar/R/store.R | 35 +- ragnar-0.3.1/ragnar/build/partial.rdb |binary ragnar-0.3.1/ragnar/build/vignette.rds |binary ragnar-0.3.1/ragnar/inst/python/_ragnartools/atlas.py | 29 - ragnar-0.3.1/ragnar/man/MarkdownDocument.Rd | 3 ragnar-0.3.1/ragnar/man/MarkdownDocumentChunks.Rd | 3 ragnar-0.3.1/ragnar/man/embed_ollama.Rd | 2 ragnar-0.3.1/ragnar/man/mcp_serve_store.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar-package.Rd | 1 ragnar-0.3.1/ragnar/man/ragnar_chunk.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar_find_links.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar_retrieve.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_bm25.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_vss.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_vss_and_bm25.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_store_atlas.Rd | 23 + ragnar-0.3.1/ragnar/tests/testthat/test-embed-gemini.R | 27 - ragnar-0.3.1/ragnar/tests/testthat/test-frame.R | 2 ragnar-0.3.1/ragnar/tests/testthat/test-ragnar-package.R |only ragnar-0.3.1/ragnar/tests/testthat/test-retrieve.R | 27 + ragnar-0.3.1/ragnar/tests/testthat/test-store-atlas.R |only ragnar-0.3.1/ragnar/tools/configure_deps.R | 16 37 files changed, 362 insertions(+), 271 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut] ,
Rafael H. M. Pereira [aut, cre] ,
Gabriel Garcia de Almeida [aut] ,
Lucas Mation [aut]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between enderecobr versions 0.5.0 dated 2026-01-10 and 0.6.0 dated 2026-09-10
DESCRIPTION | 38 LICENSE | 4 MD5 | 170 - NAMESPACE | 40 NEWS.md | 231 +- R/codigos.R | 78 R/correspondencia_campos.R | 168 - R/correspondencia_logradouro.R | 118 - R/enderecobr.R | 56 R/erro.R | 32 R/extendr-wrappers.R | 118 - R/mensagem.R | 16 R/padronizar_bairros.R | 66 R/padronizar_ceps.R | 284 +- R/padronizar_complementos.R | 65 R/padronizar_enderecos.R | 540 ++-- R/padronizar_estados.R | 100 R/padronizar_logradouros.R | 68 R/padronizar_logradouros_completos.R | 602 ++--- R/padronizar_municipios.R | 96 R/padronizar_numeros.R | 218 - R/padronizar_tipos_de_logradouro.R | 66 R/warning.R | 22 README.md | 324 +- build/vignette.rds |binary cleanup |only cleanup.win |only configure | 4 configure.win | 4 inst/doc/enderecobr.R | 388 +-- inst/doc/enderecobr.Rmd | 842 +++---- inst/doc/enderecobr.html | 1614 +++++++------- man/codigos_estados.Rd | 58 man/codigos_municipios.Rd | 58 man/correspondencia_campos.Rd | 114 man/correspondencia_logradouro.Rd | 86 man/enderecobr.Rd | 67 man/figures/logo.svg | 304 +- man/padronizar_bairros.Rd | 78 man/padronizar_ceps.Rd | 76 man/padronizar_complementos.Rd | 78 man/padronizar_enderecos.Rd | 210 - man/padronizar_estados.Rd | 98 man/padronizar_logradouros.Rd | 80 man/padronizar_logradouros_completos.Rd | 162 - man/padronizar_municipios.Rd | 102 man/padronizar_numeros.Rd | 90 man/padronizar_tipos_de_logradouro.Rd | 78 src/Makevars.in | 14 src/Makevars.win.in | 93 src/enderecobr-win.def | 4 src/entrypoint.c | 2 src/rust/Cargo.lock | 74 src/rust/Cargo.toml | 41 src/rust/README.md |only src/rust/document.c |only src/rust/document.rs |only src/rust/src/lib.rs | 589 ++--- src/rust/vendor.tar.xz |binary tests/testes_nao_automaticos/rust-bench.R | 130 - tests/testes_nao_automaticos/test-grandes_bases.R | 112 tests/testthat.R | 24 tests/testthat/_snaps/correspondencia_campos.md | 16 tests/testthat/_snaps/correspondencia_logradouro.md | 16 tests/testthat/_snaps/erro.md | 18 tests/testthat/_snaps/padronizar_ceps.md | 126 - tests/testthat/_snaps/padronizar_enderecos.md | 404 +-- tests/testthat/_snaps/padronizar_logradouros_completos.md | 166 - tests/testthat/_snaps/padronizar_numeros.md | 16 tests/testthat/_snaps/warning.md | 18 tests/testthat/helper-mensagens.R |only tests/testthat/test-correspondencia_campos.R | 104 tests/testthat/test-correspondencia_logradouro.R | 86 tests/testthat/test-erro.R | 24 tests/testthat/test-mensagem.R | 36 tests/testthat/test-padronizar_bairros.R | 38 tests/testthat/test-padronizar_ceps.R | 128 - tests/testthat/test-padronizar_complementos.R | 34 tests/testthat/test-padronizar_enderecos.R | 842 +++---- tests/testthat/test-padronizar_estados.R | 126 - tests/testthat/test-padronizar_logradouros.R | 34 tests/testthat/test-padronizar_logradouros_completos.R | 420 +-- tests/testthat/test-padronizar_municipios.R | 58 tests/testthat/test-padronizar_numeros.R | 280 +- tests/testthat/test-padronizar_tipos_de_logradouro.R | 610 ++--- tests/testthat/test-warning.R | 24 tools/config.R | 244 +- tools/msrv.R | 232 +- vignettes/enderecobr.Rmd | 842 +++---- 89 files changed, 7168 insertions(+), 6968 deletions(-)
Title: Assessment of Cluster Stability by Randomized Maps
Description: The reliability of clusters is estimated using random projections.
A set of stability measures is provided to assess the reliability of the clusters
discovered by a generic clustering algorithm.
The stability measures are taylored to high dimensional data (e.g. DNA microarray data)
(Valentini, G (2005), <doi:10.1093/bioinformatics/bti817>.
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between clusterv versions 1.1.1 dated 2025-05-14 and 1.1.2 dated 2026-09-10
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- build/vignette.rds |binary 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Surface Fire Spread Model
Description: Implements the surface fire spread model of Rothermel (1972)
<doi:10.2737/INT-RP-115> in R. Additional utilities support uncertainty
propagation, selection among standard fuel models, optimization of fuel
model parameters by genetic algorithms, and example datasets.
Author: Giorgio Vacchiano [aut, cre] ,
Davide Ascoli [ctb]
Maintainer: Giorgio Vacchiano <gvacchiano@gmail.com>
This is a re-admission after prior archival of version 1.2 dated 2014-11-10
Diff between Rothermel versions 1.2 dated 2014-11-10 and 1.4.1 dated 2026-09-10
DESCRIPTION | 35 +++++++++++++++++++++++++---------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 7 ++++--- R/bestFM.R | 6 ++++-- R/gaRoth.R | 13 ++++++++----- R/ros.R | 5 +++-- R/rosunc.R | 28 +++++++++++++++------------- build |only inst/CITATION | 29 +++++++++++++++-------------- man/Rothermel-package.Rd | 17 +++++++---------- man/firexp.Rd | 4 ++-- man/gaRoth.Rd | 12 ++++++------ man/ros.Rd | 8 ++++++-- man/scenarios.Rd | 2 +- tests |only 15 files changed, 110 insertions(+), 82 deletions(-)
Title: Robust Marginal Bayesian Variable Selection for Gene-Environment
Interactions
Description: Recently, multiple marginal variable selection methods have been developed and shown to be effective in Gene-Environment interactions studies. We propose a novel marginal Bayesian variable selection method for Gene-Environment interactions studies. In particular, our marginal Bayesian method is robust to data contamination and outliers in the outcome variables. With the incorporation of spike-and-slab priors, we have implemented the Gibbs sampler based on Markov Chain Monte Carlo. The core algorithms of the package have been developed in 'C++'.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu0521@gmail.com>
Diff between marble versions 0.0.3 dated 2024-04-04 and 0.0.4 dated 2026-09-10
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector'
objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://web.archive.org/web/20250719184025/https://www.wim.uni-mannheim.de/schlather/publications/software> and <https://github.com/cran/RandomFields>.
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 2.0.10 dated 2026-02-26 and 2.2.0 dated 2026-09-10
geostatsp-2.0.10/geostatsp/R/grfConditional.R |only geostatsp-2.2.0/geostatsp/DESCRIPTION | 20 geostatsp-2.2.0/geostatsp/MD5 | 97 + geostatsp-2.2.0/geostatsp/NAMESPACE | 7 geostatsp-2.2.0/geostatsp/NEWS |only geostatsp-2.2.0/geostatsp/R/0gm.R | 51 - geostatsp-2.2.0/geostatsp/R/RFsimulate.R | 2 geostatsp-2.2.0/geostatsp/R/forInla.R | 20 geostatsp-2.2.0/geostatsp/R/glgm.R | 22 geostatsp-2.2.0/geostatsp/R/krige.R | 10 geostatsp-2.2.0/geostatsp/R/lgm.R | 5 geostatsp-2.2.0/geostatsp/R/lgm.Raster.R | 2 geostatsp-2.2.0/geostatsp/R/maternGmrfPrec.R | 1119 +++++++++++------------ geostatsp-2.2.0/geostatsp/R/onload.R | 1 geostatsp-2.2.0/geostatsp/R/profLlgm.R | 316 +++--- geostatsp-2.2.0/geostatsp/build/stage23.rdb |binary geostatsp-2.2.0/geostatsp/build/vignette.rds |binary geostatsp-2.2.0/geostatsp/inst/doc/glgm.R | 8 geostatsp-2.2.0/geostatsp/inst/doc/glgm.Rnw | 8 geostatsp-2.2.0/geostatsp/inst/doc/glgm.pdf |binary geostatsp-2.2.0/geostatsp/inst/doc/lgcp.R | 6 geostatsp-2.2.0/geostatsp/inst/doc/lgcp.Rnw | 6 geostatsp-2.2.0/geostatsp/inst/doc/lgcp.pdf |binary geostatsp-2.2.0/geostatsp/inst/extR/loaloaData.R | 4 geostatsp-2.2.0/geostatsp/man/RFsimulate.Rd | 14 geostatsp-2.2.0/geostatsp/man/excProb.Rd | 6 geostatsp-2.2.0/geostatsp/man/geostatData.Rd |only geostatsp-2.2.0/geostatsp/man/glgm.Rd | 16 geostatsp-2.2.0/geostatsp/man/inlaAvailable.Rd |only geostatsp-2.2.0/geostatsp/man/krige.Rd | 7 geostatsp-2.2.0/geostatsp/man/murder.Rd | 2 geostatsp-2.2.0/geostatsp/man/postExp.Rd | 6 geostatsp-2.2.0/geostatsp/man/simLgcp.Rd | 4 geostatsp-2.2.0/geostatsp/man/stackRasterList.Rd | 4 geostatsp-2.2.0/geostatsp/man/swissRainR.Rd | 2 geostatsp-2.2.0/geostatsp/src/geostatsp.h | 24 geostatsp-2.2.0/geostatsp/src/matern.c | 236 ---- geostatsp-2.2.0/geostatsp/src/maternPoint.c |only geostatsp-2.2.0/geostatsp/tests/RFsimulate.R | 14 geostatsp-2.2.0/geostatsp/tests/geostatData.R |only geostatsp-2.2.0/geostatsp/tests/krige.R | 4 geostatsp-2.2.0/geostatsp/tests/lgcp.R | 12 geostatsp-2.2.0/geostatsp/tests/lgm.R | 2 geostatsp-2.2.0/geostatsp/tests/lgmRaster.R | 2 geostatsp-2.2.0/geostatsp/tests/likfitLgm.R | 2 geostatsp-2.2.0/geostatsp/tests/matern.R | 2 geostatsp-2.2.0/geostatsp/tests/maternGmrfPrec.R | 10 geostatsp-2.2.0/geostatsp/tests/maternPoint.R |only geostatsp-2.2.0/geostatsp/tests/profLlgm.R | 14 geostatsp-2.2.0/geostatsp/tests/simLgcp.R | 18 geostatsp-2.2.0/geostatsp/vignettes/Makefile | 4 geostatsp-2.2.0/geostatsp/vignettes/glgm.Rnw | 8 geostatsp-2.2.0/geostatsp/vignettes/lgcp.Rnw | 6 53 files changed, 1036 insertions(+), 1087 deletions(-)
Title: Robust Bayesian Elastic Net
Description: As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in 'C++' and R.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu0521@gmail.com>
Diff between Bayenet versions 0.3 dated 2025-03-19 and 0.4 dated 2026-09-10
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Latent Dirichlet Allocation Using 'tidyverse' Conventions
Description: Implements an algorithm for Latent Dirichlet
Allocation (LDA), Blei et al. (2003) <https://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf>,
using style conventions from the 'tidyverse',
Wickham et al. (2019)<doi:10.21105/joss.01686>,
and 'tidymodels', Kuhn et al.<https://tidymodels.github.io/model-implementation-principles/>.
Fitting is done via 'warpLDA', a Metropolis-Hastings sampler,
Chen et al. (2016) <doi:10.48550/arXiv.1510.08628>.
Also implements several novel features for LDA such as guided models and
transfer learning.
Author: Tommy Jones [aut, cre] ,
Brendan Knapp [ctb] ,
Barum Park [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between tidylda versions 0.1.0 dated 2026-08-28 and 0.1.1 dated 2026-09-10
tidylda-0.1.0/tidylda/src/Makevars |only tidylda-0.1.1/tidylda/DESCRIPTION | 6 ++-- tidylda-0.1.1/tidylda/MD5 | 16 ++++++------ tidylda-0.1.1/tidylda/NEWS.md | 11 ++++++++ tidylda-0.1.1/tidylda/cleanup |only tidylda-0.1.1/tidylda/configure |only tidylda-0.1.1/tidylda/inst/WORDLIST | 7 +++++ tidylda-0.1.1/tidylda/inst/doc/probabilistic-coherence.html | 4 +-- tidylda-0.1.1/tidylda/inst/doc/tLDA.html | 4 +-- tidylda-0.1.1/tidylda/inst/doc/tidylda-intro.html | 4 +-- tidylda-0.1.1/tidylda/src/Makevars.in |only 11 files changed, 36 insertions(+), 16 deletions(-)
Title: Prepare 'WEXTOR' Data
Description: Facilitate data preparation for data collected on 'WEXTOR' <https://wextor.eu>, created by Reips and Neuhaus (2002) <doi:10.3758/bf03195449>. Perform plausibility and other checks and make use of cool color palettes and themes for data visualization.
Author: Annika Tave Overlander [aut, cre] ,
Ulf-Dietrich Reips [ths, cph]
Maintainer: Annika Tave Overlander <annika-tave.overlander@uni.kn>
Diff between rextor versions 1.1.0 dated 2026-05-21 and 1.2.0 dated 2026-09-10
DESCRIPTION | 15 +++++++++------ MD5 | 25 ++++++++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 13 ++++++++++++- R/BiFiX_data_raw.R | 2 +- R/fake_wextor_log.R |only R/read_WEXTOR.R | 18 ++++++++++++++++++ R/read_WEXTOR_log.R |only R/scale_rextor.R | 24 ++++++++++++++---------- R/tidy_WEXTOR_log.R |only README.md | 2 +- inst/extdata/fake_wextor_log.txt |only man/BiFiX_data_raw.Rd | 2 +- man/fake_wextor_log.Rd |only man/read_WEXTOR_log.Rd |only man/scale_rextor.Rd | 6 +++++- man/tidy_WEXTOR_log.Rd |only 17 files changed, 79 insertions(+), 30 deletions(-)
Title: Alocă Pe Ore Lecțiile Zilei
Description: Lecțiile prof/cls trebuie completate cu un câmp "ora", astfel ca
oricare două lecții prof/cls/ora să nu se suprapună într-o aceeași oră.
The prof/cls lessons must be completed with a "hour" field ('ora), so that
any two prof/cls/ora lessons do not overlap in the same hour.
<https://vlad.bazon.net/>.
Author: Vlad Bazon [aut, cre]
Maintainer: Vlad Bazon <vlad.bazon@gmail.com>
Diff between hours2lessons versions 0.1.5 dated 2026-09-05 and 1.0.0 dated 2026-09-10
hours2lessons-0.1.5/hours2lessons/R/on_tuples.R |only hours2lessons-0.1.5/hours2lessons/data/LSS.rda |only hours2lessons-0.1.5/hours2lessons/data/Tuplaje.rda |only hours2lessons-0.1.5/hours2lessons/man/LSS.Rd |only hours2lessons-0.1.5/hours2lessons/man/Tuplaje.Rd |only hours2lessons-0.1.5/hours2lessons/man/on_tuples.Rd |only hours2lessons-1.0.0/hours2lessons/DESCRIPTION | 8 hours2lessons-1.0.0/hours2lessons/MD5 | 41 +- hours2lessons-1.0.0/hours2lessons/NAMESPACE | 30 +- hours2lessons-1.0.0/hours2lessons/NEWS.md | 9 hours2lessons-1.0.0/hours2lessons/R/data.R | 28 + hours2lessons-1.0.0/hours2lessons/R/globals.R |only hours2lessons-1.0.0/hours2lessons/R/hlp.R | 4 hours2lessons-1.0.0/hours2lessons/R/long2matrix.R | 4 hours2lessons-1.0.0/hours2lessons/R/mount_hours.R | 82 ++--- hours2lessons-1.0.0/hours2lessons/build/vignette.rds |binary hours2lessons-1.0.0/hours2lessons/data/dayLessons.rda |only hours2lessons-1.0.0/hours2lessons/data/dayTuples.rda |only hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.R | 8 hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.Rmd | 36 +- hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.html | 141 +++++----- hours2lessons-1.0.0/hours2lessons/man/dayLessons.Rd |only hours2lessons-1.0.0/hours2lessons/man/dayTuples.Rd |only hours2lessons-1.0.0/hours2lessons/man/hours2lessons-package.Rd | 5 hours2lessons-1.0.0/hours2lessons/man/long2matrix.Rd | 2 hours2lessons-1.0.0/hours2lessons/man/mount_hours.Rd | 19 - hours2lessons-1.0.0/hours2lessons/vignettes/orarul-zilei.Rmd | 36 +- 27 files changed, 242 insertions(+), 211 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.7.0 dated 2026-08-29 and 1.7.1 dated 2026-09-10
DESCRIPTION | 8 ++-- MD5 | 35 +++++++++++++------ NAMESPACE | 2 + NEWS.md | 6 +++ R/gtdd_get_yield_curve.R | 38 ++++++++++++++++++--- R/td_get.R | 17 +++++++++ R/td_get2.R |only R/td_get_current.R | 6 +-- README.md | 54 ++++++++++++++---------------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-retired.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/td_get.Rd | 7 +++ man/td_get2.Rd |only man/td_get_current.Rd | 2 - tests/testthat/test-importing-data.R | 27 +++++++++++++-- tests/testthat/test-td-get2.R |only 25 files changed, 149 insertions(+), 53 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546>, Doc2vec (Le & Mikolov, 2014) <doi:10.48550/arXiv.1405.4053> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.6.3 dated 2026-07-28 and 0.6.4 dated 2026-09-10
DESCRIPTION | 6 ++-- MD5 | 35 +++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 7 ++++ R/as.doc2vec.R | 10 +++--- R/as.word2vec.R |only R/utils.R | 40 +++++++++++++++++++++----- R/word2vec.R | 2 - man/as.textmodel_doc2vec.Rd | 6 ++-- man/as.textmodel_word2vec.Rd |only man/perplexity.Rd | 4 -- man/probability.Rd | 31 +++----------------- man/probability.textmodel_wordvector.Rd |only man/similarity.Rd | 29 +++---------------- man/similarity.textmodel_wordvector.Rd |only man/textmodel_word2vec.Rd | 2 - tests/testthat/test-as.doc2vec.R | 24 ++++++++++++++-- tests/testthat/test-as.word2vec.R |only tests/testthat/test-doc2vec.R | 2 - tests/testthat/test-utils.R | 48 ++++++++++++++++++++++++++------ tests/testthat/test-word2vec.R | 2 - 21 files changed, 149 insertions(+), 103 deletions(-)
Title: Optimal Stratification of Univariate Populations
Description: Determines Optimum Strata Boundaries (OSB) and Optimum Sample
Sizes (OSS) for univariate stratified sampling designs under Neyman
allocation. The stratification variable is described by a best-fitting
parametric distribution, selected automatically by AIC from a set of
continuous families (normal, log-normal, gamma, Weibull, exponential,
Cauchy, uniform, Pareto, triangular and right-triangular), and the
optimum boundaries are obtained by minimising the Neyman objective.
Version 2.0 keeps the original globally optimal Dynamic Programming (DP)
solver of Reddy and Khan (2020) as the default and adds two faster
derivative-free alternatives for interactive and large-scale use: a
multi-start 'COBYLA' solver and a two-phase 'global' solver that couples
'DIRECT-L' with 'COBYLA' refinement. It also provides cost-constrained
allocation with unequal per-stratum costs, a design-efficiency comparison
(compare_designs), two- and three-dimensional and interactive
visualisations, solution-quality di [...truncated...]
Author: Karuna G. Reddy [aut, cre],
M. G. M. Khan [aut]
Maintainer: Karuna G. Reddy <karuna.reddy@auckland.ac.nz>
Diff between stratifyR versions 1.0-5 dated 2026-06-23 and 2.0-1 dated 2026-09-10
stratifyR-1.0-5/stratifyR/R/mode.val.r |only stratifyR-1.0-5/stratifyR/README.md |only stratifyR-2.0-1/stratifyR/DESCRIPTION | 61 stratifyR-2.0-1/stratifyR/MD5 | 60 stratifyR-2.0-1/stratifyR/NAMESPACE | 53 stratifyR-2.0-1/stratifyR/NEWS.md | 71 stratifyR-2.0-1/stratifyR/R/app.R |only stratifyR-2.0-1/stratifyR/R/cobyla.optim.R |only stratifyR-2.0-1/stratifyR/R/compare_designs.R |only stratifyR-2.0-1/stratifyR/R/create.mat.R | 2 stratifyR-2.0-1/stratifyR/R/data.alloc.R | 25 stratifyR-2.0-1/stratifyR/R/data.optim.R | 23 stratifyR-2.0-1/stratifyR/R/data.root.R | 45 stratifyR-2.0-1/stratifyR/R/distr.alloc.R | 37 stratifyR-2.0-1/stratifyR/R/distr.optim.R | 23 stratifyR-2.0-1/stratifyR/R/distr.root.R | 28 stratifyR-2.0-1/stratifyR/R/fit_distribution.R |only stratifyR-2.0-1/stratifyR/R/mode.val.R |only stratifyR-2.0-1/stratifyR/R/plot.strata.R |only stratifyR-2.0-1/stratifyR/R/print.strata.R |only stratifyR-2.0-1/stratifyR/R/realloc.R | 10 stratifyR-2.0-1/stratifyR/R/strata.data.R | 699 +++- stratifyR-2.0-1/stratifyR/R/strata.distr.R | 519 ++- stratifyR-2.0-1/stratifyR/R/summary.strata.R | 14 stratifyR-2.0-1/stratifyR/build/vignette.rds |binary stratifyR-2.0-1/stratifyR/inst/app |only stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.R | 129 stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.Rmd | 325 ++ stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.html | 1857 +++++++++++-- stratifyR-2.0-1/stratifyR/man/compare_designs.Rd |only stratifyR-2.0-1/stratifyR/man/plot.strata.Rd |only stratifyR-2.0-1/stratifyR/man/print.strata.Rd |only stratifyR-2.0-1/stratifyR/man/strata.data.Rd | 29 stratifyR-2.0-1/stratifyR/man/strata.distr.Rd | 31 stratifyR-2.0-1/stratifyR/man/stratifyRApp.Rd |only stratifyR-2.0-1/stratifyR/man/summary.strata.Rd | 11 stratifyR-2.0-1/stratifyR/vignettes/library.bib | 19 stratifyR-2.0-1/stratifyR/vignettes/stratifyR-vignette.Rmd | 325 ++ 38 files changed, 3422 insertions(+), 974 deletions(-)
Title: Covariate Selection Based on VIMP Permutation-Like Testing
Description: A statistical method for reducing the number of covariates in
an analysis by evaluating Variable Importance Measures (VIMPs) derived
from the Random Forest algorithm. It performs statistical tests on the
VIMPs and outputs whether the covariate is significant along with the
p-values.
Author: Tim Mueller [aut, cre],
Oktawia Miluch [aut],
Staburo GmbH [cph, fnd]
Maintainer: Tim Mueller <mueller@staburo.de>
Diff between shadowVIMP versions 1.0.2 dated 2025-06-19 and 1.0.3 dated 2026-09-10
shadowVIMP-1.0.2/shadowVIMP/vignettes/figure-html |only shadowVIMP-1.0.3/shadowVIMP/DESCRIPTION | 22 shadowVIMP-1.0.3/shadowVIMP/MD5 | 52 shadowVIMP-1.0.3/shadowVIMP/NEWS.md | 22 shadowVIMP-1.0.3/shadowVIMP/R/plot_vimps.R | 894 +++++----- shadowVIMP-1.0.3/shadowVIMP/R/print.shadow_vimp.R | 220 +- shadowVIMP-1.0.3/shadowVIMP/R/shadow_vimp.R | 776 ++++---- shadowVIMP-1.0.3/shadowVIMP/R/vim_perm_sim.R | 340 +-- shadowVIMP-1.0.3/shadowVIMP/README.md | 24 shadowVIMP-1.0.3/shadowVIMP/build/vignette.rds |binary shadowVIMP-1.0.3/shadowVIMP/inst/doc/shadowVIMP-vignette.Rmd | 754 ++++---- shadowVIMP-1.0.3/shadowVIMP/inst/doc/shadowVIMP-vignette.html | 85 shadowVIMP-1.0.3/shadowVIMP/man/figures/README-example_cont-1.png |binary shadowVIMP-1.0.3/shadowVIMP/man/print.shadow_vimp.Rd | 46 shadowVIMP-1.0.3/shadowVIMP/man/shadowVIMP-package.Rd | 66 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/helper.R | 74 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-add_test_results.R | 74 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-plot_vimps.R | 298 +-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-print.shadow_vimp.R | 340 +-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-shadow_vimp.R | 390 ++-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-vim_perm_sim.R | 80 shadowVIMP-1.0.3/shadowVIMP/vignettes/shadowVIMP-vignette.Rmd | 754 ++++---- 22 files changed, 2643 insertions(+), 2668 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chenghua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 1.0.0 dated 2026-08-21 and 1.0.1 dated 2026-09-10
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/timeSeries.R | 11 ++++++----- man/sentopics_sentiment.Rd | 8 ++++---- tests/testthat/test-rJST-sentiment.R |only 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Model Order Selection for Clustering
Description: Stability based methods for model order selection in clustering problems
(Valentini, G (2007), <doi:10.1093/bioinformatics/btl600>).
Using multiple perturbations of the data the stability of clustering solutions is assessed. Different
perturbations may be used: resampling techniques, random projections and noise injection. Stability measures
for the estimate of clustering solutions and statistical tests to assess their significance are provided.
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between mosclust versions 1.0.2 dated 2025-05-27 and 1.0.3 dated 2026-09-10
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Calculation of Comorbidity and Frailty Scores
Description: Computes comorbidity indices and combined frailty scores for multiple ICD coding systems, including ICD-10-CA, ICD-10-CM, and ICD-11. The package provides tools to preprocess episode data, map diagnosis codes to chronic categories, propagate conditions across episodes, and generate comorbidity and frailty measures. The methods implemented are original to this package and were developed by the authors for research applications; a manuscript describing the methodology is currently in preparation.
Author: Azadeh Bayani [aut, cre] ,
Jean Noel Nikiema [ctb],
Michele Bally [ctb]
Maintainer: Azadeh Bayani <azadeh.bayani@umontreal.ca>
Diff between LABTNSCPSS versions 1.0.3 dated 2026-09-05 and 1.0.4 dated 2026-09-10
DESCRIPTION | 9 +++++---- MD5 | 11 +++++++---- R/setup_package.R |only README.md | 43 +++++++++++++++++++++++++++++++------------ build |only inst/CITATION |only man/LABTNSCPSS-package.Rd | 1 + man/LABTNSCPSS.Rd | 2 ++ 8 files changed, 46 insertions(+), 20 deletions(-)
Title: Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov
Models
Description: Inference, goodness-of-fit tests, and predictions for continuous and discrete univariate Hidden Markov Models (HMM), including zero-inflated distributions. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Nasri et al (2020) <doi:10.1029/2019WR025122>.
Author: Bouchra R. Nasri [aut, cre, cph],
Mamadou Yamar Thioub [aut, cph],
Bruno N. Remillard [aut, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GenHMM1d versions 0.2.6 dated 2025-09-07 and 0.2.8 dated 2026-09-10
DESCRIPTION | 10 +-- MD5 | 26 ++++---- R/CDF.R | 39 ++++++------- R/CDF_est.R | 31 ++++++---- R/EstHMMGen.R | 161 +++++++++++++++++++++++++++++++------------------------ R/GofHMMGen.R | 4 + R/PDF.R | 29 ++++++--- R/PDF_unc.R | 43 +++++++++----- R/QUANTILE.R | 22 +++---- R/SimHMMGen.R | 37 +++++++----- R/alpha2theta.R | 46 +++++++++------ R/theta2alpha.R | 49 ++++++++++------ man/GofHMMGen.Rd | 4 + man/SimHMMGen.Rd | 5 - 14 files changed, 291 insertions(+), 215 deletions(-)
Title: A Genetic Algorithm for Learning Directed Acyclic Graphs
Description: Learns sparse large Directed Acyclic Graphs with a combination of a convex program and a tailored genetic algorithm.
Author: Magali Champion [aut, cre],
Victor Picheny [aut],
Matthieu Vignes [aut]
Maintainer: Magali Champion <magali.champion@u-paris.fr>
Diff between GADAG versions 0.99.0 dated 2017-04-11 and 0.99.1 dated 2026-09-10
GADAG-0.99.0/GADAG/src/registerDynamicSymbol.c |only GADAG-0.99.1/GADAG/DESCRIPTION | 27 GADAG-0.99.1/GADAG/MD5 | 48 - GADAG-0.99.1/GADAG/NAMESPACE | 42 - GADAG-0.99.1/GADAG/R/GADAG_Analyze.R | 609 +++++++++++----------- GADAG-0.99.1/GADAG/R/GADAG_CV.R |only GADAG-0.99.1/GADAG/R/GADAG_Run.R | 680 +++++++++++-------------- GADAG-0.99.1/GADAG/R/RcppExports.R | 14 GADAG-0.99.1/GADAG/R/chrom.R | 72 +- GADAG-0.99.1/GADAG/R/create.population.R | 70 +- GADAG-0.99.1/GADAG/R/crossover.R | 145 ++--- GADAG-0.99.1/GADAG/R/evaluation.R | 234 ++++---- GADAG-0.99.1/GADAG/R/fitness.R | 114 ++-- GADAG-0.99.1/GADAG/R/generateToyData.R | 256 ++++----- GADAG-0.99.1/GADAG/R/mutation.R | 115 ++-- GADAG-0.99.1/GADAG/R/selection.R | 111 ++-- GADAG-0.99.1/GADAG/R/toy_data.R |only GADAG-0.99.1/GADAG/build/partial.rdb |binary GADAG-0.99.1/GADAG/man/GADAG-package.Rd | 174 +++--- GADAG-0.99.1/GADAG/man/GADAG_Analyze.Rd | 203 +++---- GADAG-0.99.1/GADAG/man/GADAG_CV.Rd |only GADAG-0.99.1/GADAG/man/GADAG_Run.Rd | 265 +++++---- GADAG-0.99.1/GADAG/man/evaluation.Rd | 174 +++--- GADAG-0.99.1/GADAG/man/fitness.Rd | 120 ++-- GADAG-0.99.1/GADAG/man/generateToyData.Rd | 135 ++-- GADAG-0.99.1/GADAG/man/toy_data.Rd | 34 - GADAG-0.99.1/GADAG/src/RcppExports.cpp | 17 27 files changed, 1868 insertions(+), 1791 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'Typst', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint', R 'Grid Graphics' and
'patchwork'. 'R Markdown', 'Quarto' and the package 'officer' can be
used to produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.10.0 dated 2026-07-07 and 0.10.1 dated 2026-09-10
DESCRIPTION | 8 MD5 | 31 +- NAMESPACE | 367 +++++++++++++++++--------------- NEWS.md | 23 ++ R/docx_str.R | 15 - R/html_str.R | 16 + R/pptx_str.R | 9 R/read_structure.R | 101 +++++++- R/rtf_str.R | 6 R/runs_as_functions.R | 15 - R/typst_str.R | 29 ++ R/xtable_to_flextable.R | 2 tests/testthat/test-cell_content.R | 6 tests/testthat/test-deterministic-css.R |only tests/testthat/test-footers.R | 2 tests/testthat/test-headers.R | 4 tests/testthat/test-typst.R | 43 +++ 17 files changed, 427 insertions(+), 250 deletions(-)
Title: Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver", symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Jeroen van Raak [aut] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.29 dated 2026-05-04 and 1.30 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 10 - NEWS.md | 4 R/partition.R | 259 ++++++++++++++++++++++++++++++++++++++------ inst/doc/liver-example.html | 14 +- man/partition.Rd | 31 +++-- 6 files changed, 268 insertions(+), 56 deletions(-)
Title: Machine Learning Immunogenicity and Vaccine Response Analysis
Description: Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Author: Ivan Tomic [aut, cre, cph] ,
Adriana Tomic [aut, ctb, cph, fnd] ,
Stephanie Hao [aut]
Maintainer: Ivan Tomic <info@ivantomic.com>
Diff between immunaut versions 1.0.2 dated 2025-04-09 and 1.0.3 dated 2026-09-10
DESCRIPTION | 24 +- MD5 | 27 +- NAMESPACE | 2 NEWS.md | 23 ++ R/functions.R | 465 ++++++++++++++++++++++++--------------------- R/immunaut.R | 119 +++++++---- R/utils.R | 308 +++++++++++++++++++---------- README.md | 416 ++++++++++++++++++++-------------------- man/auto_simon_ml.Rd | 98 ++++----- man/immunaut.Rd | 8 man/plot_clustered_tsne.Rd | 2 man/preProcessData.Rd | 34 ++- man/preProcessResample.Rd | 27 +- tests |only 14 files changed, 883 insertions(+), 670 deletions(-)
Title: Multivariate Random Forest with Compositional Responses
Description: Multivariate random forests with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, or the alpha-transformation of Tsagris, Preston and Wood (2011), <doi:10.48550/arXiv.1106.1451>, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalRF versions 1.6 dated 2026-02-28 and 1.7 dated 2026-09-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/alfa.comp.rf.R | 21 +++++++++++++++------ R/cv.alfacomprf.R | 6 +++--- man/CompositionalRF-package.Rd | 4 ++-- 5 files changed, 28 insertions(+), 19 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library code is included.
Author: Dirk Eddelbuettel [aut, cre] ,
Robert G Brown [aut],
David Bauer [aut],
DieHarder Contributors [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.7 dated 2025-03-26 and 0.2.8 dated 2026-09-10
ChangeLog | 32 ++++++++++++++++++++++++++++++++ DESCRIPTION | 11 ++++++----- MD5 | 22 +++++++++++----------- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/RDieHarder.R | 3 +-- inst/doc/RDieHarder.Rnw | 18 +++++++++--------- inst/doc/RDieHarder.pdf |binary man/dieharder.Rd | 4 ++-- vignettes/RDieHarder.Rnw | 18 +++++++++--------- vignettes/RDieHarder.bib | 31 ++++++++++++++++++------------- 12 files changed, 98 insertions(+), 61 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Elin Waring [ctb],
Thomas J. Faulkenberry [rev],
Robert Garrett [rev [...truncated...]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 1.3.1 dated 2026-04-26 and 1.4.0 dated 2026-09-10
DESCRIPTION | 26 MD5 | 266 +-- NAMESPACE | 10 NEWS.md | 26 R/assign_labels.R | 362 ++-- R/center.R | 708 ++++---- R/contrs.R | 201 +- R/convert_na_to.R | 434 ++--- R/data.R | 42 R/data_addprefix.R | 148 - R/data_arrange.R | 308 +-- R/data_codebook.R | 1144 +++++++------- R/data_duplicated.R | 210 +- R/data_extract.R | 310 +-- R/data_group.R | 158 - R/data_partition.R | 326 ++-- R/data_peek.R | 304 +-- R/data_read.R | 10 R/data_relocate.R | 354 ++-- R/data_rescale.R | 718 ++++----- R/data_restoretype.R | 100 - R/data_reverse.R | 624 +++---- R/data_rotate.R | 206 +- R/data_seek.R | 380 ++-- R/data_select.R | 88 - R/data_separate.R | 876 +++++------ R/data_tabulate.R | 94 + R/data_to_long.R | 764 ++++----- R/data_to_wide.R | 946 +++++------ R/data_unique.R | 308 +-- R/data_unite.R | 238 +- R/data_xtabulate.R | 9 R/datawizard-package.R | 42 R/demean.R | 4 R/describe_distribution.R | 1640 ++++++++++---------- R/descriptives.R | 426 ++--- R/extract_column_names.R | 360 ++-- R/format.R | 214 +- R/labels_to_levels.R | 216 +- R/makepredictcall.R | 166 +- R/mean_sd.R | 192 +- R/means_by_group.R | 19 R/ranktransform.R | 404 ++--- R/remove_empty.R | 254 +-- R/replace_nan_inf.R | 126 - R/rescale_weights.R | 950 +++++------ R/row_count.R | 266 +-- R/row_means.R | 428 ++--- R/select_nse.R | 1516 +++++++++---------- R/slide.R | 210 +- R/smoothness.R | 270 +-- R/standardize.R | 874 +++++----- R/to_factor.R | 284 +-- R/to_numeric.R | 674 ++++---- R/unnormalize.R | 332 ++-- R/unstandardize.R | 686 ++++---- R/utils-cols.R | 188 +- R/utils_standardize_center.R | 1056 ++++++------- R/visualisation_recipe.R | 184 +- R/weighted_mean_median_sd_mad.R | 328 ++-- R/winsorize.R | 298 +-- build/partial.rdb |binary build/vignette.rds |binary man/assign_labels.Rd | 296 +-- man/categorize.Rd | 528 +++--- man/center.Rd | 400 ++--- man/coef_var.Rd | 186 +- man/coerce_to_numeric.Rd | 44 man/colnames.Rd | 100 - man/contr.deviation.Rd | 22 man/convert_na_to.Rd | 344 ++-- man/convert_to_na.Rd | 252 +-- man/data_arrange.Rd | 70 man/data_duplicated.Rd | 218 +- man/data_extract.Rd | 294 +-- man/data_merge.Rd | 412 ++--- man/data_partition.Rd | 168 +- man/data_peek.Rd | 210 +- man/data_prefix_suffix.Rd | 214 +- man/data_read.Rd | 6 man/data_relocate.Rd | 310 +-- man/data_replicate.Rd | 200 +- man/data_restoretype.Rd | 70 man/data_rotate.Rd | 136 - man/data_seek.Rd | 136 - man/data_separate.Rd | 454 ++--- man/data_tabulate.Rd | 10 man/data_unique.Rd | 214 +- man/data_unite.Rd | 232 +- man/datawizard-package.Rd | 103 - man/distribution_mode.Rd | 68 man/efc.Rd | 24 man/extract_column_names.Rd | 398 ++--- man/labels_to_levels.Rd | 240 +-- man/makepredictcall.dw_transformer.Rd | 106 - man/mean_sd.Rd | 98 - man/means_by_group.Rd | 4 man/nhanes_sample.Rd | 28 man/normalize.Rd | 10 man/ranktransform.Rd | 288 +-- man/recode_into.Rd | 252 +-- man/reexports.Rd | 2 man/replace_nan_inf.Rd | 64 man/rescale.Rd | 390 ++-- man/reverse.Rd | 300 +-- man/row_count.Rd | 274 +-- man/row_means.Rd | 336 ++-- man/rownames.Rd | 110 - man/skewness.Rd | 296 +-- man/slide.Rd | 288 +-- man/smoothness.Rd | 74 man/standardize.Rd | 584 +++---- man/standardize.default.Rd | 200 +- man/text_format.Rd | 162 +- man/to_factor.Rd | 268 +-- man/to_numeric.Rd | 290 +-- man/visualisation_recipe.Rd | 60 man/weighted_mean.Rd | 112 - man/winsorize.Rd | 196 +- tests/testthat/_snaps/data_read.md | 240 +-- tests/testthat/_snaps/data_summary.md | 134 - tests/testthat/_snaps/data_tabulate.md | 1990 ++++++++++++------------- tests/testthat/_snaps/data_to_factor.md | 168 +- tests/testthat/_snaps/describe_distribution.md | 276 +-- tests/testthat/_snaps/discovr.md |only tests/testthat/test-convert_to_na.R | 4 tests/testthat/test-data_match.R | 3 tests/testthat/test-data_modify.R | 4 tests/testthat/test-data_read.R | 8 tests/testthat/test-data_recode.R | 20 tests/testthat/test-data_tabulate.R | 208 ++ tests/testthat/test-data_to_factor.R | 2 tests/testthat/test-describe_distribution.R | 29 tests/testthat/test-discovr.R |only tests/testthat/test-standardize_models.R | 910 +++++------ 135 files changed, 19451 insertions(+), 19001 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.4.0 dated 2026-06-02 and 2.4.1 dated 2026-09-10
DESCRIPTION | 15 MD5 | 585 +- NAMESPACE | 1036 +-- NEWS.md | 24 R/AddTip.R | 550 +- R/ArtificialExtinction.R | 1 R/Cherries.R | 68 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/Consensus.R | 38 R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/DropTip.R | 4 R/EdgeRatio.R | 70 R/ImposeConstraint.R | 278 - R/Information.R | 1 R/KeptPaths.R | 94 R/KeptVerts.R | 2 R/LongBranchScore.R | 150 R/MatchNodes.R | 216 R/MatchStrings.R | 66 R/PathLengths.R | 96 R/PhyToString.R | 284 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 7 R/RcppExports.R | 4 R/ReadMrBayes.R | 190 R/ReadTntTree.R | 580 +- R/Reweight.R | 220 R/RoguePlot.R | 9 R/SplitFunctions.R | 912 +-- R/Splits.R | 1336 ++-- R/Stemwardness.R | 218 R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TotalCopheneticIndex.R | 1 R/TreeNumber.R | 1166 ++-- R/TreeTools-package.R | 3 R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/fastmatch.R |only R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/parse_files.R | 17 R/phylo.R | 3 R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_display.R | 292 - R/tree_generation.R | 1006 +-- R/tree_information.R | 206 R/tree_numbering.R | 62 R/tree_properties.R | 1 R/tree_rearrangement.R | 2 R/tree_shape.R | 572 +- R/tree_write.R | 262 R/zzz.R | 16 build/partial.rdb |binary build/vignette.rds |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 35 inst/REFERENCES.bib | 778 +- inst/WORDLIST | 204 inst/apa-old-doi-prefix.csl | 4546 ++++++++--------- inst/doc/filesystem-navigation.Rmd | 104 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 - inst/doc/load-data.html | 4 inst/doc/load-trees.Rmd | 250 inst/doc/load-trees.html | 4 inst/extdata/input/dataset.nex | 44 inst/extdata/input/notes.nex | 54 inst/extdata/output/named.tre | 6 inst/extdata/output/numbered.tre | 8 inst/extdata/tests/ape-tree.nex | 10 inst/extdata/tests/continuous.nex | 44 inst/extdata/tests/encoding.nex | 48 inst/extdata/tests/parse-nexus.nexus | 510 - inst/extdata/tests/statelabels-semicolon.nex |only inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-amp-continuation.tnt | 20 inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-cp1252-taxa.tnt | 12 inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-midline-xread.tnt | 12 inst/extdata/tests/tnt-multiline-comment.tnt | 26 inst/extdata/tests/tnt-multiline-taxa.tnt | 26 inst/extdata/tests/tnt-multitaxon-line.tnt | 10 inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-smartquote-taxa.tnt | 24 inst/extdata/tests/tnt-taxon-taxonomy.tnt | 14 inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/extdata/tests/tnt-xgroup.tnt | 32 inst/include/TreeTools/root_tree.h | 24 man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 108 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 108 man/CladeSizes.Rd | 98 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 152 man/ConsensusWithout.Rd | 212 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 168 man/DescendantEdges.Rd | 164 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 126 man/EdgeDistances.Rd | 106 man/EdgeRatio.Rd | 92 man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 202 man/Hamming.Rd | 156 man/ImposeConstraint.Rd | 148 man/J1Index.Rd | 190 man/KeptPaths.Rd | 132 man/KeptVerts.Rd | 138 man/LabelSplits.Rd | 172 man/LeafLabelInterchange.Rd | 118 man/ListAncestors.Rd | 192 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 130 man/MRCA.Rd | 136 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 140 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 158 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 100 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 172 man/NTip.Rd | 140 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NexusTokensToInteger.Rd | 128 man/NodeDepth.Rd | 128 man/NodeNumbers.Rd | 116 man/NodeOrder.Rd | 110 man/PaintTree.Rd | 196 man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 118 man/PhyToString.Rd | 214 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 314 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 550 +- man/Reweight.Rd | 158 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 106 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 180 man/SplitInformation.Rd | 256 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 162 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 252 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 86 man/TreeNumber.Rd | 432 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 93 man/Treeness.Rd | 114 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 126 man/Unquote.Rd | 64 man/UnrootedTreesMatchingSplit.Rd | 96 man/UnshiftTree.Rd | 116 man/WriteTntCharacters.Rd | 140 man/as.Newick.Rd | 96 man/as.multiPhylo.Rd | 106 man/brewer.Rd | 66 man/dot-RandomParent.Rd | 54 man/doubleFactorials.Rd | 52 man/edge_to_splits.Rd | 98 man/is.TreeNumber.Rd | 64 man/logDoubleFactorials.Rd | 46 man/match.Splits.Rd | 136 man/match.multiPhylo.Rd | 144 man/nRootedShapes.Rd | 56 man/print.TreeNumber.Rd | 44 man/root_on_node.Rd | 62 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports.cpp | 13 src/consensus.cpp | 123 src/renumber_tips.cpp | 98 tests/figs/rogueplot.svg | 68 tests/spelling.R | 8 tests/testthat.R | 8 tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg | 82 tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg | 94 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/_snaps/Support/labelsplits.svg | 148 tests/testthat/_snaps/mst/mst-plotting.svg | 142 tests/testthat/_snaps/tree_display/sorted-tree.svg | 270 - tests/testthat/test-AddTip.R | 2 tests/testthat/test-ArtificialExtinction.R | 94 tests/testthat/test-Cherries.R | 24 tests/testthat/test-ClusterTable.R | 284 - tests/testthat/test-Decompose.R | 152 tests/testthat/test-DropTip.R | 6 tests/testthat/test-EdgeRatio.R | 18 tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-ImposeConstraint.R | 4 tests/testthat/test-KeptPaths.R | 40 tests/testthat/test-KeptVerts.R | 172 tests/testthat/test-LongBranchScore.R | 36 tests/testthat/test-MatchNodes.R | 148 tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PathLengths.R | 70 tests/testthat/test-PhyToString.R | 150 tests/testthat/test-RUtreebalance.R | 128 tests/testthat/test-ReadMrBayes.R | 8 tests/testthat/test-ReadTntTree.R | 4 tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 15 tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Splits.R | 16 tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TotalCopheneticIndex.R | 2 tests/testthat/test-TreeNumber.R | 360 - tests/testthat/test-Treeness.R | 38 tests/testthat/test-as.matrix.R | 14 tests/testthat/test-as.multiPhylo.R | 70 tests/testthat/test-combinatorics.R | 178 tests/testthat/test-consensus.R | 419 + tests/testthat/test-fastmatch.R |only tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 84 tests/testthat/test-int_to_tree.cpp.R | 130 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-parsers.R | 42 tests/testthat/test-phylo.R | 2 tests/testthat/test-root_tree.h.R | 34 tests/testthat/test-sort.R | 44 tests/testthat/test-split_analysis.R | 22 tests/testthat/test-splits.cpp.R | 74 tests/testthat/test-tree_ancestors.R | 40 tests/testthat/test-tree_comparison.R | 48 tests/testthat/test-tree_descendants.R | 168 tests/testthat/test-tree_display.R | 128 tests/testthat/test-tree_generation-random.R | 90 tests/testthat/test-tree_information.R | 38 tests/testthat/test-tree_numbering.R | 40 tests/testthat/test-tree_properties.R | 2 tests/testthat/test-tree_rearrange.R | 22 tests/testthat/test-tree_shape.R | 2 tests/testthat/test-tree_write.R | 2 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 295 files changed, 23198 insertions(+), 22655 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Most synthesising methods available in the package synthesise from conditional distributions where variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Methods that are not sequential, but synthesise all variables at once, are 'sample', 'ipf', and 'catall'. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb],
Timon Huijser [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.9-2 dated 2025-07-12 and 1.9-3 dated 2026-09-10
synthpop-1.9-2/synthpop/man/syn.pmm.Rd |only synthpop-1.9-3/synthpop/DESCRIPTION | 20 synthpop-1.9-3/synthpop/MD5 | 83 - synthpop-1.9-3/synthpop/NAMESPACE | 1 synthpop-1.9-3/synthpop/NEWS | 1147 +++++++++++------------ synthpop-1.9-3/synthpop/R/IO.r | 4 synthpop-1.9-3/synthpop/R/disclosure.R | 959 +++++++++---------- synthpop-1.9-3/synthpop/R/functions.syn.r | 81 - synthpop-1.9-3/synthpop/R/methods.syn.r | 9 synthpop-1.9-3/synthpop/R/syn.r | 5 synthpop-1.9-3/synthpop/R/syn.strata.r | 43 synthpop-1.9-3/synthpop/R/zzz.r | 2 synthpop-1.9-3/synthpop/build/partial.rdb |binary synthpop-1.9-3/synthpop/build/vignette.rds |binary synthpop-1.9-3/synthpop/inst/doc/disclosure.R | 8 synthpop-1.9-3/synthpop/inst/doc/disclosure.Rnw | 990 ++++++++++--------- synthpop-1.9-3/synthpop/inst/doc/disclosure.pdf |binary synthpop-1.9-3/synthpop/inst/doc/inference.R | 2 synthpop-1.9-3/synthpop/inst/doc/inference.pdf |binary synthpop-1.9-3/synthpop/inst/doc/synthpop.R | 2 synthpop-1.9-3/synthpop/inst/doc/synthpop.Rnw | 6 synthpop-1.9-3/synthpop/inst/doc/synthpop.pdf |binary synthpop-1.9-3/synthpop/inst/doc/utility.R | 2 synthpop-1.9-3/synthpop/inst/doc/utility.Rnw | 4 synthpop-1.9-3/synthpop/inst/doc/utility.pdf |binary synthpop-1.9-3/synthpop/man/SD2011.Rd | 2 synthpop-1.9-3/synthpop/man/disclosure.Rd | 403 ++++---- synthpop-1.9-3/synthpop/man/multi.disclosure.Rd | 397 +++---- synthpop-1.9-3/synthpop/man/syn.Rd | 8 synthpop-1.9-3/synthpop/man/syn.smooth.Rd | 2 synthpop-1.9-3/synthpop/man/synthpop-package.Rd | 116 +- synthpop-1.9-3/synthpop/man/utility.gen.Rd | 500 +++++----- synthpop-1.9-3/synthpop/man/utility.tab.Rd | 444 ++++---- synthpop-1.9-3/synthpop/man/utility.tables.Rd | 448 ++++---- synthpop-1.9-3/synthpop/vignettes/disclosure.Rnw | 990 ++++++++++--------- synthpop-1.9-3/synthpop/vignettes/disclosure.bib | 727 +++++++------- synthpop-1.9-3/synthpop/vignettes/fig2dis.png |binary synthpop-1.9-3/synthpop/vignettes/fig3dis.png |binary synthpop-1.9-3/synthpop/vignettes/inference.bib | 2 synthpop-1.9-3/synthpop/vignettes/synthpop.Rnw | 6 synthpop-1.9-3/synthpop/vignettes/synthpop.bib | 729 +++++++------- synthpop-1.9-3/synthpop/vignettes/utility.Rnw | 4 synthpop-1.9-3/synthpop/vignettes/utility.bib | 240 ++-- 43 files changed, 4329 insertions(+), 4057 deletions(-)
Title: Univariate Kernel Density Estimation
Description: Provides an efficient implementation of univariate local polynomial
kernel density estimators that can handle bounded, discrete, and zero-inflated
data. See Geenens and Wang (2018) <doi:10.48550/arXiv.1602.04862>,
Geenens (2014) <doi:10.48550/arXiv.1303.4121>,
Nagler (2018a) <doi:10.48550/arXiv.1704.07457>,
Nagler (2018b) <doi:10.48550/arXiv.1705.05431>.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kde1d versions 1.1.1 dated 2025-06-12 and 1.2.0 dated 2026-09-10
.Rinstignore |only DESCRIPTION | 14 MD5 | 62 +- NEWS.md | 52 + R/RcppExports.R | 16 R/jitter.R | 2 R/kde1d-methods.R | 2 R/kde1d.R | 55 +- inst/include/kde1d-cpp |only inst/include/kde1d-wrappers.hpp | 53 - inst/include/kde1d.hpp | 2 inst/include/kde1d/dpik.hpp | 176 ------ inst/include/kde1d/interpolation.hpp | 279 ---------- inst/include/kde1d/kde1d.hpp | 928 ----------------------------------- inst/include/kde1d/kdefft.hpp | 98 --- inst/include/kde1d/stats.hpp | 229 -------- inst/include/kde1d/tools.hpp | 128 ---- inst/include/kde1d/version.hpp | 26 man/dkde1d.Rd | 4 man/equi_jitter.Rd | 2 man/kde1d-package.Rd | 1 man/kde1d.Rd | 55 +- src/Makevars | 2 src/Makevars.win | 3 src/RcppExports.cpp | 9 src/kde1d-interface.cpp | 19 tests/testthat/Rplots.pdf |binary tests/testthat/cpp |only tests/testthat/test_cpp_headers.R |only tests/testthat/test_kde1d.R | 100 +++ 30 files changed, 323 insertions(+), 1994 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports cross-sectional network models for ordinal, binary, continuous, and mixed data,
fitted using the packages 'bgms' (default), 'BDgraph', and 'BGGM',
as well as network comparison tests fitted using the packages 'bgms' and 'BGGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.4.0 dated 2026-04-02 and 0.5.0 dated 2026-09-10
DESCRIPTION | 26 - MD5 | 59 +- NEWS.md |only R/AuxiliaryFunctions.R | 506 +++++++++++++++++++--- R/bgm_plot_class.R | 48 +- R/easybgm.R | 597 +++++++++++++++++++------- R/easybgm_compare.R | 376 +++++++++++----- R/functions.bdgraph.R | 4 R/functions.bggm.R | 6 R/functions.bgms.R | 208 +++++++-- R/functions.bgmscompare.R | 415 ++++++------------ R/plottingfunctions.bgmCompare.R | 140 +----- R/plottingfunctions.bgms.R | 86 +-- R/plottingfunctions.easybgm.R | 59 +- R/summary.easybgm.R | 90 +++ R/summary.easybgm_compare.R | 9 README.md | 6 man/HDI.Rd | 4 man/centrality.Rd | 6 man/clusterBayesfactor.Rd | 46 +- man/complexity_probs.Rd | 6 man/easybgm.Rd | 396 ++++++++++++----- man/easybgm_compare.Rd | 213 ++++++--- man/edgeevidence.Rd | 6 man/network.Rd | 11 man/prior_sensitivity.Rd | 4 man/structure.Rd | 4 man/structure_probs.Rd | 6 tests/testthat.R | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-easybgm.R | 887 ++++++++++++++++++++++++++------------- 31 files changed, 2817 insertions(+), 1408 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 0.3.0 dated 2026-08-20 and 0.4.0 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 78 ++++++------- NEWS.md | 21 +++ R/MCMC_Fit.R | 51 ++++++++ R/NUTS.R | 54 ++++++++- R/RTMB_Model.R | 28 +++- R/RTMB_Model_impl_classic.R | 168 ++++++++++++++++++++++++++++- R/RTMB_Model_impl_optimize.R | 4 R/RTMB_Model_impl_sampling.R | 73 +++++++++++- R/mcmc_continue.R |only R/plot.R | 13 +- R/posterior_predict.R | 16 ++ R/upgrade_fit.R | 7 - R/wrapper_corr.R | 45 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/analysis_reference.html | 1 inst/doc/introduction.html | 1 inst/doc/ja-analysis_reference.html | 156 +++++++++++--------------- inst/doc/ja-introduction.html | 33 ++--- inst/doc/ja-quick_start.html | 45 +++---- inst/doc/ja-rtmb_glmer.html | 1 inst/doc/ja-rtmb_internals.html | 1 inst/doc/ja-wrapper_functions.R | 22 +-- inst/doc/ja-wrapper_functions.Rmd | 22 +-- inst/doc/ja-wrapper_functions.html | 45 +++---- inst/doc/ja-writing_models.html | 38 +++--- inst/doc/quick_start.html | 11 + inst/doc/rtmb_glmer.html | 1 inst/doc/rtmb_internals.html | 1 inst/doc/wrapper_functions.html | 3 inst/doc/writing_models.html | 1 man/MCMC_Fit.Rd | 66 +++++++++++ man/RTMB_Model-class.Rd | 6 - man/plot_mdu.Rd | 6 - tests/testthat/test-fixed-jacobian.R | 31 +++++ tests/testthat/test-mcmc-continuation.R |only tests/testthat/test-optimize-marginal-df.R | 70 ++++++++++++ tests/testthat/test-plot.R | 20 +++ tests/testthat/test-posterior-predict.R | 10 + vignettes/ja-wrapper_functions.Rmd | 22 +-- 41 files changed, 887 insertions(+), 290 deletions(-)
Title: Bayesian Prediction of Complex Computer Codes
Description: Performs Bayesian prediction of complex computer codes when fast approximations are available. It uses a hierarchical version of the Gaussian process, originally proposed by Kennedy and O'Hagan (2000), Biometrika 87(1):1.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between approximator versions 1.2-8 dated 2023-08-24 and 1.3-0 dated 2026-09-10
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 3 ++- R/approximator.R | 47 +++++++++++++++++++++-------------------------- build/vignette.rds |binary data/genie.rda |binary data/toyapps.rda |binary inst/apprex_1d.R | 4 ---- inst/doc/apprex.R | 2 -- inst/doc/apprex.pdf |binary inst/hpafun_1d.R | 1 - man/H.fun.Rd | 2 +- man/is.consistent.Rd | 2 +- man/mdash.fun.Rd | 6 +++--- man/tee.fun.Rd | 2 +- 15 files changed, 59 insertions(+), 61 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 0.18.1 dated 2026-09-01 and 0.18.2 dated 2026-09-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 12 ++++++++++++ R/check_heteroscedasticity.R | 2 +- R/check_singularity.R | 2 +- tests/testthat/test-check_heteroskedasticity.R | 21 +++++++++++++++++++++ tests/testthat/test-check_outliers.R | 3 ++- 7 files changed, 47 insertions(+), 13 deletions(-)
Title: Bayesian Analysis of Non-Stationary Gaussian Process Models
Description: Enables off-the-shelf functionality for fully Bayesian, nonstationary Gaussian process modeling. The approach to nonstationary modeling involves a closed-form, convolution-based covariance function with spatially-varying parameters; these parameter processes can be specified either deterministically (using covariates or basis functions) or stochastically (using approximate Gaussian processes). Stationary Gaussian processes are a special case of our methodology, and we furthermore implement approximate Gaussian process inference to account for very large spatial data sets (Finley, et al (2017) <doi:10.48550/arXiv.1702.00434>). Bayesian inference is carried out using Markov chain Monte Carlo methods via the "nimble" package, and posterior prediction for the Gaussian process at unobserved locations is provided as a post-processing step. Also provided are nearest-neighbor Gaussian process components for use directly in user-written model code, where the spatial process is retained as [...truncated...]
Author: Daniel Turek [aut, cre],
Mark Risser [aut],
Fabian Ketwaroo [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between BayesNSGP versions 0.3.0 dated 2026-08-19 and 0.3.1 dated 2026-09-10
DESCRIPTION | 13 ++++++++----- MD5 | 15 ++++++++++----- R/v03_NNGP_density.R | 13 ++++++++++--- R/v03_NNGP_neighbors.R | 14 ++++++++------ build/partial.rdb |binary man/NNGP.pred.Rd | 13 ++++++++++--- tests |only 7 files changed, 46 insertions(+), 22 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using Stan
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.2 dated 2026-08-31 and 1.0.3 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 50 ++++---- NEWS.md | 7 + R/bayes_factor.R | 6 - R/extract_param.R | 26 ++-- R/helpers.R | 152 +++++++++++++++++++++++--- R/set_priors.R | 7 - R/sim_bvarnet.R | 14 +- R/to_stan_data.R | 2 inst/doc/MCMC-Diagnostics.Rmd | 2 inst/doc/MCMC-Diagnostics.html | 2 man/bvarnet-package.Rd | 2 man/extract_draws.Rd | 39 +++++- man/prior.Rd | 3 man/set_priors.Rd | 3 man/sim_var.Rd | 6 - src/stan/model_ordinal.stan | 7 - tests/testthat/helper-fixtures.R | 54 +++++++-- tests/testthat/helper-oracles.R |only tests/testthat/test-extract_param.R | 189 ++++++++++++++++++++++++++++++++- tests/testthat/test-helpers.R | 2 tests/testthat/test-input-validation.R | 11 + tests/testthat/test-prior-scaling.R | 2 tests/testthat/test-sim_bvarnet.R | 6 - tests/testthat/test-stan-likelihood.R |only vignettes/MCMC-Diagnostics.Rmd | 2 vignettes/MCMC-Diagnostics.Rmd.orig | 2 27 files changed, 491 insertions(+), 111 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 'log' or a 'logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph] ,
Robert Rigby [aut] ,
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb] ,
Fernanda De Bastiani [ctb] ,
Raydonal Ospina [ctb] ,
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [...truncated...]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss.dist versions 6.1-1 dated 2023-08-23 and 6.1-11 dated 2026-09-10
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gamlss.dist-6.1-11/gamlss.dist/R/rqres.R |only gamlss.dist-6.1-11/gamlss.dist/README.md |only gamlss.dist-6.1-11/gamlss.dist/build/partial.rdb |binary gamlss.dist-6.1-11/gamlss.dist/inst/CITATION |only gamlss.dist-6.1-11/gamlss.dist/man/BB.Rd | 18 gamlss.dist-6.1-11/gamlss.dist/man/DPO.Rd | 4 gamlss.dist-6.1-11/gamlss.dist/man/GEOM.Rd | 12 gamlss.dist-6.1-11/gamlss.dist/man/GG.Rd | 7 gamlss.dist-6.1-11/gamlss.dist/man/GPO.Rd | 4 gamlss.dist-6.1-11/gamlss.dist/man/GU.rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/IG.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/LG.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/LOGITNO.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/LQNO.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/Multinomial.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/NBI.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/NBII.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/PARETO2.Rd | 5 gamlss.dist-6.1-11/gamlss.dist/man/PIG.Rd | 21 gamlss.dist-6.1-11/gamlss.dist/man/SHASH.Rd | 23 gamlss.dist-6.1-11/gamlss.dist/man/SI.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/SICHEL.Rd | 6 gamlss.dist-6.1-11/gamlss.dist/man/WARING.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/ZIP.Rd | 2 gamlss.dist-6.1-11/gamlss.dist/man/count_1_31.Rd | 22 146 files changed, 6970 insertions(+), 4425 deletions(-)
Title: Data Envelopment Analysis
Description: Nonparametric efficiency measurement by data envelopment analysis.
Provides radial (Charnes-Cooper-Rhodes and Banker-Charnes-Cooper) technical
efficiency under constant, variable, non-increasing and non-decreasing
returns to scale, the slacks-based measure of Tone (2001), the additive
model of Charnes and others (1985), and the directional distance function
of Chambers, Chung and Fare (1996), all through one interface and one
result object. Efficiency estimates are accompanied by peers, slacks,
returns-to-scale classification, scale efficiency and the optimal
multipliers, and by bias-corrected estimates and confidence intervals from
the smoothed homogeneous bootstrap of Simar and Wilson (1998). Where
prices are known, cost, revenue and Nerlovian profit efficiency separate
the technical component from the allocative one; where they are not,
cross-efficiency with the secondary goals of Doyle and Green (1994) ranks
units that a self-appraisal leaves tied. This package succeeds the
arch [...truncated...]
Author: David Bernstein [aut, cre] ,
Zuleyka Diaz-Martinez [aut],
Jose Fernandez-Menendez [aut]
Maintainer: David Bernstein <davebernstein1@gmail.com>
This is a re-admission after prior archival of version 0.1-2 dated 2008-02-19
Diff between DEA versions 0.1-2 dated 2008-02-19 and 1.0.0 dated 2026-09-10
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Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
Description: Many tools for making, manipulating, and modifying many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Tomas Diviak [ctb],
Henrique Sposito [ctb] ,
Christian Steglich [ctb],
Alvaro Uzaheta [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 2.3.1 dated 2026-08-28 and 2.3.4 dated 2026-09-10
DESCRIPTION | 6 MD5 | 123 +++++++++-------- NAMESPACE | 26 +++ NEWS.md | 126 ++++++++++++++++++ R/class_describe.R | 12 + R/class_interface.R | 99 ++++++++++---- R/class_marks.R | 17 +- R/class_measures.R | 27 --- R/class_members.R | 39 +++++ R/class_missing.R | 13 - R/class_validate.R | 15 +- R/coerce_graph.R | 63 +++++++-- R/data_ison.R | 9 + R/make_generate.R | 173 +++++++++++++++++++++++-- R/manip_changes.R | 21 ++- R/manip_globals.R | 117 ++++++++++++++++- R/manip_info.R | 52 +++++++ R/manip_nodes.R | 52 +++++++ R/mark_format.R | 42 ++++-- R/measure_properties.R | 98 +++++++++++++- R/modif_labels.R | 6 R/modif_motifs.R | 4 R/modif_project.R | 46 ++++++ R/modif_scope.R | 24 +++ R/modif_weight.R | 111 +++++++++++----- data/ison_southern_women.rda |binary inst/tutorials/manynet1/making.Rmd | 8 - inst/tutorials/manynet1/making.html | 100 +++++++------- inst/tutorials/manynet2/manipulating.html | 206 +++++++++++++++--------------- man/interface.Rd | 48 +++++- man/ison_southern_women.Rd | 55 ++++---- man/make_stochastic.Rd | 30 +++- man/manip_globals.Rd | 31 ++++ man/manip_nodes_num.Rd | 2 man/mark_format_tie.Rd | 23 ++- man/measure_dims.Rd | 4 man/member_names.Rd | 20 ++ man/modif_project.Rd | 4 man/modif_weight.Rd | 22 ++- man/progress.Rd | 5 tests/testthat/helper-functional.R | 12 + tests/testthat/helper-manynet.R | 8 + tests/testthat/test-class_interface.R |only tests/testthat/test-coercion.R | 59 ++++++++ tests/testthat/test-functional_from.R | 15 +- tests/testthat/test-functional_impute.R | 4 tests/testthat/test-functional_lists.R | 2 tests/testthat/test-functional_manips.R | 87 ++++++++++++ tests/testthat/test-functional_marks.R | 11 - tests/testthat/test-functional_prints.R | 67 ++++++++- tests/testthat/test-functional_to.R | 5 tests/testthat/test-make_collect.R | 4 tests/testthat/test-make_generate.R | 51 +++++++ tests/testthat/test-manip_add.R | 29 ++++ tests/testthat/test-manip_format.R | 97 +++++++++++++- tests/testthat/test-manip_layers.R | 26 +++ tests/testthat/test-manip_miss.R | 8 - tests/testthat/test-manip_nodes.R | 52 ++++++- tests/testthat/test-manip_transform.R | 73 ++++++---- tests/testthat/test-manynet-data.R | 16 +- tests/testthat/test-mark_is.R | 43 ++++++ tests/testthat/test-modif_proximity.R | 18 +- tests/testthat/test-to_motifs.R | 4 63 files changed, 2036 insertions(+), 534 deletions(-)
Title: Haplotype-Based Tracking of Admixed Population for Breed
Composition Estimation
Description: Simulate populations and track haplotypes over generations to evaluate population admixture. The 'HAPTRACE' supports customisable population parameters, including size, number of markers, mutation rates and recombination.
Author: Shweta Sahoo [aut, cre] ,
Sara de las Heras-Saldana [aut] ,
Julius H. J. van der Werf [aut] ,
Mohammad H. Ferdosi [aut]
Maintainer: Shweta Sahoo <queryhap01@gmail.com>
Diff between HAPTRACE versions 0.1.1 dated 2026-07-30 and 0.1.2 dated 2026-09-10
DESCRIPTION | 8 +-- MD5 | 19 ++++---- NAMESPACE | 54 +++++++++++++--------- R/Core_Simulation_function.R | 2 R/Extract_Phenotype.R | 2 R/Simulation_Data_function.R | 2 README.md |only inst/doc/Introduction_HAPTRACE.R | 9 ++- inst/doc/Introduction_HAPTRACE.Rmd | 9 ++- inst/doc/Introduction_HAPTRACE.html | 85 ++++++++++++++++++------------------ vignettes/Introduction_HAPTRACE.Rmd | 9 ++- 11 files changed, 106 insertions(+), 93 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths] ,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.6 dated 2025-10-21 and 2.1.7 dated 2026-09-10
GerminaR-2.1.6/GerminaR/inst/doc/GerminaQuant.Rmd |only GerminaR-2.1.6/GerminaR/inst/doc/GerminaR.Rmd |only GerminaR-2.1.6/GerminaR/inst/doc/introduction.Rmd |only GerminaR-2.1.6/GerminaR/vignettes/GerminaQuant.Rmd |only GerminaR-2.1.6/GerminaR/vignettes/GerminaR.Rmd |only GerminaR-2.1.6/GerminaR/vignettes/introduction.Rmd |only GerminaR-2.1.7/GerminaR/DESCRIPTION | 13 GerminaR-2.1.7/GerminaR/MD5 | 98 GerminaR-2.1.7/GerminaR/NAMESPACE | 50 GerminaR-2.1.7/GerminaR/NEWS.md | 249 GerminaR-2.1.7/GerminaR/R/GerminaQuant.R | 2 GerminaR-2.1.7/GerminaR/R/ger_summary.R | 16 GerminaR-2.1.7/GerminaR/README.md | 12 GerminaR-2.1.7/GerminaR/build/vignette.rds |binary GerminaR-2.1.7/GerminaR/inst/CITATION | 2 GerminaR-2.1.7/GerminaR/inst/GerminaQuant/msgs.R | 2 GerminaR-2.1.7/GerminaR/inst/GerminaQuant/pkgs.R | 2 GerminaR-2.1.7/GerminaR/inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 4 GerminaR-2.1.7/GerminaR/inst/GerminaQuant/server.R | 2 GerminaR-2.1.7/GerminaR/inst/GerminaQuant/ui.R | 6 GerminaR-2.1.7/GerminaR/inst/doc/GerminaQuant.R | 7 GerminaR-2.1.7/GerminaR/inst/doc/GerminaQuant.html | 359 - GerminaR-2.1.7/GerminaR/inst/doc/GerminaQuant.qmd |only GerminaR-2.1.7/GerminaR/inst/doc/GerminaR.R | 8 GerminaR-2.1.7/GerminaR/inst/doc/GerminaR.html | 2908 ++++------ GerminaR-2.1.7/GerminaR/inst/doc/GerminaR.qmd |only GerminaR-2.1.7/GerminaR/inst/doc/introduction.R | 3 GerminaR-2.1.7/GerminaR/inst/doc/introduction.html | 287 GerminaR-2.1.7/GerminaR/inst/doc/introduction.qmd |only GerminaR-2.1.7/GerminaR/man/GerminaQuant.Rd | 50 GerminaR-2.1.7/GerminaR/man/fplot.Rd | 216 GerminaR-2.1.7/GerminaR/man/ger_ASG.Rd | 54 GerminaR-2.1.7/GerminaR/man/ger_CVG.Rd | 50 GerminaR-2.1.7/GerminaR/man/ger_GRP.Rd | 72 GerminaR-2.1.7/GerminaR/man/ger_GRS.Rd | 52 GerminaR-2.1.7/GerminaR/man/ger_GSP.Rd | 50 GerminaR-2.1.7/GerminaR/man/ger_MGR.Rd | 64 GerminaR-2.1.7/GerminaR/man/ger_MGT.Rd | 70 GerminaR-2.1.7/GerminaR/man/ger_SDG.Rd | 50 GerminaR-2.1.7/GerminaR/man/ger_SYN.Rd | 72 GerminaR-2.1.7/GerminaR/man/ger_UNC.Rd | 70 GerminaR-2.1.7/GerminaR/man/ger_VGT.Rd | 50 GerminaR-2.1.7/GerminaR/man/ger_boxp.Rd | 146 GerminaR-2.1.7/GerminaR/man/ger_intime.Rd | 104 GerminaR-2.1.7/GerminaR/man/ger_summary.Rd | 74 GerminaR-2.1.7/GerminaR/man/ger_testcomp.Rd | 86 GerminaR-2.1.7/GerminaR/man/gquant_analysis.Rd | 122 GerminaR-2.1.7/GerminaR/man/osmp.Rd | 54 GerminaR-2.1.7/GerminaR/man/prosopis.Rd | 56 GerminaR-2.1.7/GerminaR/man/reexports.Rd | 32 GerminaR-2.1.7/GerminaR/man/rep_row.Rd | 38 GerminaR-2.1.7/GerminaR/man/textcolor.Rd | 68 GerminaR-2.1.7/GerminaR/man/webTable.Rd | 68 GerminaR-2.1.7/GerminaR/vignettes/GerminaQuant.qmd |only GerminaR-2.1.7/GerminaR/vignettes/GerminaR.qmd |only GerminaR-2.1.7/GerminaR/vignettes/introduction.qmd |only 56 files changed, 2755 insertions(+), 3043 deletions(-)
Title: Automatic Short Form Creation
Description: Performs automatic creation of short forms of scales with an
ant colony optimization algorithm and a Tabu search. As implemented in the
package, the ant colony algorithm randomly selects items to build a model of
a specified length, then updates the probability of item selection according
to the fit of the best model within each set of searches. The algorithm
continues until the same items are selected by multiple ants a given number
of times in a row. On the other hand, the Tabu search changes one parameter at
a time to be either free, constrained, or fixed while keeping track of the
changes made and putting changes that result in worse fit in a "tabu" list
so that the algorithm does not revisit them for some number of searches.
See Leite, Huang, & Marcoulides (2008) <doi:10.1080/00273170802285743> for
an applied example of the ant colony algorithm, and Marcoulides & Falk (2018)
<doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
Author: Anthony Raborn [aut, cre] ,
Walter Leite [aut]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between ShortForm versions 0.5.8 dated 2026-05-06 and 1.0.0 dated 2026-09-09
ShortForm-0.5.8/ShortForm/R/ACO_lavaan.R |only ShortForm-0.5.8/ShortForm/R/tabu_sem_shortform.R |only ShortForm-0.5.8/ShortForm/man/antcolony.lavaan.Rd |only ShortForm-0.5.8/ShortForm/man/tabuShortForm.Rd |only ShortForm-0.5.8/ShortForm/tests/testthat/test-aco-internals |only ShortForm-0.5.8/ShortForm/tests/testthat/test-tabu-internals |only ShortForm-1.0.0/ShortForm/DESCRIPTION | 9 ShortForm-1.0.0/ShortForm/MD5 | 84 + ShortForm-1.0.0/ShortForm/NAMESPACE | 5 ShortForm-1.0.0/ShortForm/NEWS | 379 +++++-- ShortForm-1.0.0/ShortForm/NEWS.md | 193 +++ ShortForm-1.0.0/ShortForm/R/ACO.R | 27 ShortForm-1.0.0/ShortForm/R/ACO_MPlus.R | 2 ShortForm-1.0.0/ShortForm/R/ACO_internals.R | 6 ShortForm-1.0.0/ShortForm/R/SA.R | 95 + ShortForm-1.0.0/ShortForm/R/TS.R | 186 +-- ShortForm-1.0.0/ShortForm/R/Tabu_sem.R | 63 - ShortForm-1.0.0/ShortForm/R/antColony.R |only ShortForm-1.0.0/ShortForm/R/call_helpers.R |only ShortForm-1.0.0/ShortForm/R/data.R | 8 ShortForm-1.0.0/ShortForm/R/lavaan_syntax_helpers.R |only ShortForm-1.0.0/ShortForm/R/parallel_helpers.R |only ShortForm-1.0.0/ShortForm/R/simulated_annealing.R | 250 ++-- ShortForm-1.0.0/ShortForm/R/simulated_annealing_internals.R | 334 +++--- ShortForm-1.0.0/ShortForm/R/tabu_search.R |only ShortForm-1.0.0/ShortForm/build/partial.rdb |binary ShortForm-1.0.0/ShortForm/build/vignette.rds |only ShortForm-1.0.0/ShortForm/inst |only ShortForm-1.0.0/ShortForm/man/TS-class.Rd | 8 ShortForm-1.0.0/ShortForm/man/antColony.Rd |only ShortForm-1.0.0/ShortForm/man/antcolony.mplus.Rd | 4 ShortForm-1.0.0/ShortForm/man/exampleAntModel.Rd | 4 ShortForm-1.0.0/ShortForm/man/plot-SA-ANY-method.Rd | 17 ShortForm-1.0.0/ShortForm/man/plot-TS-ANY-method.Rd | 5 ShortForm-1.0.0/ShortForm/man/shortExampleAntModel.Rd | 4 ShortForm-1.0.0/ShortForm/man/simulatedAnnealing.Rd | 57 - ShortForm-1.0.0/ShortForm/man/tabu.sem.Rd | 28 ShortForm-1.0.0/ShortForm/man/tabuSearch.Rd |only ShortForm-1.0.0/ShortForm/tests/testthat/test-SA-plot.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-TS-plot.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-aco-internals.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-criterion-summary-line.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-lavaan_syntax_helpers.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-parallel-helpers.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-simulated_annealing_internals.R | 509 +++++++--- ShortForm-1.0.0/ShortForm/tests/testthat/test-tabu-internals.R |only ShortForm-1.0.0/ShortForm/tests/testthat/test-top-level-algorithms.R |only ShortForm-1.0.0/ShortForm/vignettes |only 48 files changed, 1565 insertions(+), 712 deletions(-)
Title: Cumulative Standardized Binomial EWMA for Multiple Stream
Processes
Description: Implements the Cumulative Standardized Binomial Exponentially Weighted Moving Average (CSB-EWMA) control chart for monitoring multiple independent streams with binomial outcomes. Provides exact variance calculations, adaptive control limits, post-hoc identification with multiple testing corrections (Bonferroni, Holm, Benjamini-Hochberg), and visualization tools. The method is described in Muritala et al. (2026) <doi:10.48550/arXiv.2601.09968>.
Author: Faruk Muritala [aut, cre],
Austin Brown [aut],
Dhrubajyoti Ghosh [aut],
Sherry Ni [aut]
Maintainer: Faruk Muritala <fmurital@students.kennesaw.edu>
Diff between csbewma versions 1.0.1 dated 2026-06-05 and 1.1.0 dated 2026-09-09
csbewma |only 1 file changed
Title: Content Analysis in R: Integrated Qualitative (LLMs) and
Quantitative Pipeline
Description: Provides an integrated pipeline for content analysis
combining qualitative coding assisted by large language models (LLMs)
with classical quantitative text analysis. Includes modules for
pre-processing (tokenization, stopwords for Brazilian Portuguese),
descriptive statistics, keyness, co-occurrence networks, word clouds
(including comparative and X-ray variants), sentiment analysis via
OpLexicon, Latent Dirichlet Allocation (LDA), inter-coder
reliability metrics (Krippendorff, Gwet), and modern visualizations
based on ggplot2. Special focus on Brazilian corpora and
political-institutional codebooks. Inspired by Maerz and Benoit (2025)
<https://quallmer.github.io/quallmer/>.
Author: Anderson Henrique [aut, cre]
Maintainer: Anderson Henrique <anderson.henrique@usp.br>
Diff between acR versions 0.3.3 dated 2026-08-20 and 0.3.4 dated 2026-09-09
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NEWS.md | 14 +++++++++++++ R/ac_qual_code.R | 12 ++++++++++- inst/doc/qualitativo-llm.html | 2 - inst/doc/replicabilidade.html | 14 ++++++------- tests/testthat/test-ac_qual_code.R | 39 +++++++++++++++++++++++++++++++++++++ 7 files changed, 81 insertions(+), 18 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: Provides a self-contained, static build of the 'HDF5'
(Hierarchical Data Format 5) 'C' library (release 2.2.0) for R
package developers. Designed for use in the 'LinkingTo' field,
it enables zero-dependency integration by building the library
entirely from source during installation. Additionally, it compiles
and internally links a comprehensive suite of advanced compression
filters and their 'HDF5' plugins (Zstd, LZ4, Blosc/Blosc2, Snappy,
ZFP, Bzip2, LZF, Bitshuffle, szip, and gzip). These plugins are
integrated out-of-the-box, allowing downstream packages to utilize
high-performance compression directly through the standard 'HDF5'
API while keeping the underlying third-party headers fully
encapsulated. 'HDF5' is developed by The HDF Group
<https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd],
The HDF Group [ctb, cph] ,
The Board of Trustees of the University of Illinois [cph] ,
Jean-loup Gailly [ctb, cph] ,
Mark Adler [ctb, cph] ,
Kiyoshi Masui [...truncated...]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.1.1.2 dated 2026-07-21 and 2.2.0.0 dated 2026-09-09
hdf5lib-2.1.1.2/hdf5lib/src/filters/c-blosc2-2.23.1.tar.gz |only hdf5lib-2.1.1.2/hdf5lib/src/filters/libaec-1.1.6.tar.gz |only hdf5lib-2.1.1.2/hdf5lib/src/hdf5-2.1.1.tar.gz |only hdf5lib-2.2.0.0/hdf5lib/DESCRIPTION | 8 - hdf5lib-2.2.0.0/hdf5lib/MD5 | 39 ++++- hdf5lib-2.2.0.0/hdf5lib/NEWS.md | 7 hdf5lib-2.2.0.0/hdf5lib/README.md | 55 +++---- hdf5lib-2.2.0.0/hdf5lib/configure | 9 - hdf5lib-2.2.0.0/hdf5lib/src/filters/c-blosc2-3.3.3.tar.gz |only hdf5lib-2.2.0.0/hdf5lib/src/filters/libaec-1.1.7.tar.gz |only hdf5lib-2.2.0.0/hdf5lib/src/hdf5-2.2.0.tar.gz |only hdf5lib-2.2.0.0/hdf5lib/src/lib/H5pubconf.h | 6 hdf5lib-2.2.0.0/hdf5lib/src/patches/c-blosc2-3.3.3 |only hdf5lib-2.2.0.0/hdf5lib/src/patches/hdf5-2.2.0 |only hdf5lib-2.2.0.0/hdf5lib/src/patches/libaec-1.1.7 |only hdf5lib-2.2.0.0/hdf5lib/src/plugins/blosc2_plugin.c | 90 ++++++++++-- hdf5lib-2.2.0.0/hdf5lib/tests/smoke_test.c | 93 +++++++++++-- 17 files changed, 231 insertions(+), 76 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph] ,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.6.65 dated 2026-04-06 and 4.7.0 dated 2026-09-09
spaMM-4.6.65/spaMM/R/HLfit_body_NOT_loopenv.R |only spaMM-4.6.65/spaMM/tests/testthat/test-negbin1.R |only spaMM-4.7.0/spaMM/DESCRIPTION | 22 spaMM-4.7.0/spaMM/MD5 | 316 +-- spaMM-4.7.0/spaMM/NAMESPACE | 8 spaMM-4.7.0/spaMM/R/Beta.R | 2 spaMM-4.7.0/spaMM/R/COMPoisson.R | 37 spaMM-4.7.0/spaMM/R/GLM.fit.R | 47 spaMM-4.7.0/spaMM/R/HLCor_body.R | 4 spaMM-4.7.0/spaMM/R/HLFactorList.R | 124 - spaMM-4.7.0/spaMM/R/HLfit.R | 27 spaMM-4.7.0/spaMM/R/HLfit_Internals.R | 812 +++++--- spaMM-4.7.0/spaMM/R/HLfit_b_internals.R | 76 spaMM-4.7.0/spaMM/R/HLfit_body.R | 47 spaMM-4.7.0/spaMM/R/HLfit_body_augZXy.R | 8 spaMM-4.7.0/spaMM/R/HLfit_loop.R | 52 spaMM-4.7.0/spaMM/R/HLframes.R | 108 - spaMM-4.7.0/spaMM/R/IRLS_internals.R | 4 spaMM-4.7.0/spaMM/R/LLM.R | 23 spaMM-4.7.0/spaMM/R/LR.R | 46 spaMM-4.7.0/spaMM/R/LevM_internals.R | 3 spaMM-4.7.0/spaMM/R/LevM_v_h.R | 16 spaMM-4.7.0/spaMM/R/LevM_v_h_spprec.R | 15 spaMM-4.7.0/spaMM/R/MakeCovEst.R | 9 spaMM-4.7.0/spaMM/R/Matern_family.R | 6 spaMM-4.7.0/spaMM/R/ZAL_class.R | 14 spaMM-4.7.0/spaMM/R/antisym.R | 7 spaMM-4.7.0/spaMM/R/augZXy_obj.R | 5 spaMM-4.7.0/spaMM/R/betabin.R | 46 spaMM-4.7.0/spaMM/R/betaresp.R | 27 spaMM-4.7.0/spaMM/R/calc_logdisp_cov.R | 13 spaMM-4.7.0/spaMM/R/combinepar.R | 2 spaMM-4.7.0/spaMM/R/confint.R | 416 ++++ spaMM-4.7.0/spaMM/R/constructors_IMRFs.R | 2 spaMM-4.7.0/spaMM/R/corrFamilies.R | 8 spaMM-4.7.0/spaMM/R/corrHLfit-internals.R | 65 spaMM-4.7.0/spaMM/R/corrMM.LRT.R | 23 spaMM-4.7.0/spaMM/R/corrPars.R | 7 spaMM-4.7.0/spaMM/R/correlationFns.R | 73 spaMM-4.7.0/spaMM/R/cov_new_fix.R | 117 - spaMM-4.7.0/spaMM/R/dispGammaGLM.R | 14 spaMM-4.7.0/spaMM/R/dofuture.R | 2 spaMM-4.7.0/spaMM/R/drop1.R | 147 - spaMM-4.7.0/spaMM/R/extractors.R | 168 + spaMM-4.7.0/spaMM/R/fit_as_ZX.R | 69 spaMM-4.7.0/spaMM/R/fit_as_sparsePrecision.R | 35 spaMM-4.7.0/spaMM/R/fitme.R | 3 spaMM-4.7.0/spaMM/R/fitme_body.R | 29 spaMM-4.7.0/spaMM/R/fitme_fitmv_internals.R | 19 spaMM-4.7.0/spaMM/R/fitmecorrHLfit_body_internals.R | 248 +- spaMM-4.7.0/spaMM/R/fitmv.R | 55 spaMM-4.7.0/spaMM/R/fitmv_body.R | 63 spaMM-4.7.0/spaMM/R/fitmv_internals.R | 5 spaMM-4.7.0/spaMM/R/geo_info.R | 13 spaMM-4.7.0/spaMM/R/get_inits_by_glm.R | 26 spaMM-4.7.0/spaMM/R/glm.nodev.fit.R | 15 spaMM-4.7.0/spaMM/R/goftest.R | 9 spaMM-4.7.0/spaMM/R/hatvalues.R | 59 spaMM-4.7.0/spaMM/R/llm.fit.R | 37 spaMM-4.7.0/spaMM/R/locoptim.R | 2 spaMM-4.7.0/spaMM/R/makeLowerUpper.R | 74 spaMM-4.7.0/spaMM/R/multiFRK.R | 31 spaMM-4.7.0/spaMM/R/negbin1.R | 30 spaMM-4.7.0/spaMM/R/negbin2.R | 60 spaMM-4.7.0/spaMM/R/numInfo.R | 108 - spaMM-4.7.0/spaMM/R/plot.HLfit.R | 2 spaMM-4.7.0/spaMM/R/plot_effects.R | 30 spaMM-4.7.0/spaMM/R/pois4mlogit.R | 945 +++++++--- spaMM-4.7.0/spaMM/R/poisson.R | 5 spaMM-4.7.0/spaMM/R/postfit_internals.R | 43 spaMM-4.7.0/spaMM/R/predict.R | 162 - spaMM-4.7.0/spaMM/R/predict_marg.R | 1 spaMM-4.7.0/spaMM/R/predict_mv.R | 178 + spaMM-4.7.0/spaMM/R/preprocess.R | 312 ++- spaMM-4.7.0/spaMM/R/preprocess_MV.R | 243 +- spaMM-4.7.0/spaMM/R/preprocess_internals.R | 68 spaMM-4.7.0/spaMM/R/profile.R | 8 spaMM-4.7.0/spaMM/R/sXaug_EigenDense_QRP_Chol_scaled.R | 15 spaMM-4.7.0/spaMM/R/sXaug_Matrix_CHM_Hess.R | 62 spaMM-4.7.0/spaMM/R/sXaug_Matrix_QRP_CHM.R | 150 + spaMM-4.7.0/spaMM/R/sXaug_sparsePrecisions.R | 141 - spaMM-4.7.0/spaMM/R/safe_opt.R | 33 spaMM-4.7.0/spaMM/R/simulate.HL.R | 564 ++++- spaMM-4.7.0/spaMM/R/spaMM.data.R | 9 spaMM-4.7.0/spaMM/R/spaMM_boot.R | 452 ++-- spaMM-4.7.0/spaMM/R/spaMM_error.R | 78 spaMM-4.7.0/spaMM/R/summary.HL.R | 151 + spaMM-4.7.0/spaMM/R/tweedie.R |only spaMM-4.7.0/spaMM/R/update.HL.R | 59 spaMM-4.7.0/spaMM/R/utils.R | 71 spaMM-4.7.0/spaMM/build/partial.rdb |binary spaMM-4.7.0/spaMM/build/vignette.rds |only spaMM-4.7.0/spaMM/inst/NEWS.Rd | 77 spaMM-4.7.0/spaMM/inst/doc |only spaMM-4.7.0/spaMM/man/COMPoisson.Rd | 12 spaMM-4.7.0/spaMM/man/HLCor.Rd | 3 spaMM-4.7.0/spaMM/man/HLfit.Rd | 7 spaMM-4.7.0/spaMM/man/LRT.Rd | 7 spaMM-4.7.0/spaMM/man/algebra.Rd | 5 spaMM-4.7.0/spaMM/man/aliases.Rd | 3 spaMM-4.7.0/spaMM/man/autoregressive.Rd | 7 spaMM-4.7.0/spaMM/man/beta_resp.Rd | 14 spaMM-4.7.0/spaMM/man/betabin.Rd | 21 spaMM-4.7.0/spaMM/man/confint.Rd | 11 spaMM-4.7.0/spaMM/man/control.HLfit.Rd | 43 spaMM-4.7.0/spaMM/man/convergence.Rd | 4 spaMM-4.7.0/spaMM/man/corrHLfit.Rd | 4 spaMM-4.7.0/spaMM/man/corrMatrix.Rd | 5 spaMM-4.7.0/spaMM/man/covStruct.Rd | 30 spaMM-4.7.0/spaMM/man/diallel.Rd | 5 spaMM-4.7.0/spaMM/man/div_info.Rd | 2 spaMM-4.7.0/spaMM/man/dopar.Rd | 2 spaMM-4.7.0/spaMM/man/extractors.Rd | 36 spaMM-4.7.0/spaMM/man/fitme.Rd | 43 spaMM-4.7.0/spaMM/man/fitmv.Rd | 2 spaMM-4.7.0/spaMM/man/genX2X.Rd | 13 spaMM-4.7.0/spaMM/man/get_fittedPars.Rd | 2 spaMM-4.7.0/spaMM/man/get_inits_from_fit.Rd | 2 spaMM-4.7.0/spaMM/man/get_matrix.Rd | 7 spaMM-4.7.0/spaMM/man/hatvalues.HLfit.Rd | 29 spaMM-4.7.0/spaMM/man/how.Rd | 3 spaMM-4.7.0/spaMM/man/inits.Rd | 4 spaMM-4.7.0/spaMM/man/inner-vs-outer.Rd |only spaMM-4.7.0/spaMM/man/llm.fit.Rd | 6 spaMM-4.7.0/spaMM/man/make.scaled.dist.Rd | 7 spaMM-4.7.0/spaMM/man/mapMM.Rd | 2 spaMM-4.7.0/spaMM/man/method.Rd | 19 spaMM-4.7.0/spaMM/man/multinomial.Rd | 6 spaMM-4.7.0/spaMM/man/negbin.Rd | 19 spaMM-4.7.0/spaMM/man/negbin1.Rd | 32 spaMM-4.7.0/spaMM/man/numInfo.Rd | 23 spaMM-4.7.0/spaMM/man/phi-resid.model.Rd | 2 spaMM-4.7.0/spaMM/man/pois4mlogit.Rd | 104 - spaMM-4.7.0/spaMM/man/poisson.Rd | 2 spaMM-4.7.0/spaMM/man/predict.Rd | 13 spaMM-4.7.0/spaMM/man/remove_fixef.Rd |only spaMM-4.7.0/spaMM/man/residVar.Rd | 8 spaMM-4.7.0/spaMM/man/residuals.HLfit.Rd | 33 spaMM-4.7.0/spaMM/man/simulate.Rd | 30 spaMM-4.7.0/spaMM/man/spaMM-S3.Rd | 1 spaMM-4.7.0/spaMM/man/spaMM-internal.Rd | 1 spaMM-4.7.0/spaMM/man/spaMM.Rd | 14 spaMM-4.7.0/spaMM/man/summary.HL.Rd | 12 spaMM-4.7.0/spaMM/man/tweedie.Rd |only spaMM-4.7.0/spaMM/man/vcov.Rd | 4 spaMM-4.7.0/spaMM/man/verbose.Rd | 23 spaMM-4.7.0/spaMM/src/internals.cpp | 4 spaMM-4.7.0/spaMM/tests/test-all.R | 21 spaMM-4.7.0/spaMM/tests/testthat/extralong/test-composite-extra.R | 4 spaMM-4.7.0/spaMM/tests/testthat/extralong/test-mv-extra.R | 107 - spaMM-4.7.0/spaMM/tests/testthat/test-GxE_variance_stability.R | 2 spaMM-4.7.0/spaMM/tests/testthat/test-LLM.R | 24 spaMM-4.7.0/spaMM/tests/testthat/test-Rasch.R | 2 spaMM-4.7.0/spaMM/tests/testthat/test-augZXy.R | 15 spaMM-4.7.0/spaMM/tests/testthat/test-confint.R | 10 spaMM-4.7.0/spaMM/tests/testthat/test-corrFamilies.R | 2 spaMM-4.7.0/spaMM/tests/testthat/test-negbin1.by.negbin2.R |only spaMM-4.7.0/spaMM/tests/testthat/test-numInfo.R | 7 spaMM-4.7.0/spaMM/tests/testthat/test-pois4mlogit.R | 131 - spaMM-4.7.0/spaMM/tests/testthat/test-predVar.R | 8 spaMM-4.7.0/spaMM/tests/testthat/test-simulate.R | 213 +- spaMM-4.7.0/spaMM/tests/testthat/test-tweedie.R |only spaMM-4.7.0/spaMM/vignettes |only 163 files changed, 5980 insertions(+), 3074 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.2 dated 2025-08-27 and 1.3.3 dated 2026-09-09
DESCRIPTION | 8 MD5 | 296 ++++++++-------- NAMESPACE | 27 + NEWS.md | 43 ++ R/antpath.R | 29 + R/arrowhead.R | 22 - R/buildings.R | 9 R/clusterCharts.R | 29 - R/contextmenu.R | 1 R/easyprint.R | 98 ++++- R/geosearch.R | 26 + R/heightgraph.R | 34 - R/hexbin.R | 26 - R/layergroupcollision.R | 7 R/leafletsync.R | 7 R/mapkeyIcon.R | 67 +-- R/movingmarker.R | 17 R/openweather.R | 7 R/playback.R | 31 - R/sidebar.R | 2 R/spin.R | 87 ++++ R/timeslider.R | 27 - R/vectorgrid.R |only R/velocity.R | 3 R/wms.R | 83 ++++ inst/examples/easyprint.R |only inst/examples/easyprint_app.R | 19 - inst/examples/spin_app.R | 53 +- inst/examples/vectorgrid_app.R |only inst/examples/vectorgrid_pbf_app.R |only inst/examples/wms_app.R | 7 inst/examples/wms_geoserver_app.R |only inst/examples/wms_time_app.R |only inst/htmlwidgets/lfx-easyprint/lfx-easyprint_full.js | 282 ++++++++++++--- inst/htmlwidgets/lfx-sidebar/leaflet-sidebar-binding.js | 128 +++++- inst/htmlwidgets/lfx-sidebar/leaflet-sidebar.css | 15 inst/htmlwidgets/lfx-sidebar/leaflet-sidebar.js | 4 inst/htmlwidgets/lfx-spin/leaflet.spin-binding.js | 19 - inst/htmlwidgets/lfx-vectorgrid |only inst/htmlwidgets/lfx-wms/leaflet.wms-bindings.js | 77 +++- inst/htmlwidgets/lfx-wms/leaflet.wms.js | 263 +++++++++++--- man/addAntpath.Rd | 38 +- man/addArrowhead.Rd | 36 + man/addBuildings.Rd | 8 man/addClusterCharts.Rd | 16 man/addContextmenu.Rd | 32 - man/addDivicon.Rd | 12 man/addEasyprint.Rd | 22 - man/addGIBS.Rd | 12 man/addGeosearch.Rd | 31 + man/addHeightgraph.Rd | 14 man/addHexbin.Rd | 18 man/addHistory.Rd | 12 man/addItemContextmenu.Rd | 32 - man/addLayerGroupConditional.Rd | 6 man/addLeafletsync.Rd | 10 man/addLeafletsyncDependency.Rd | 10 man/addMapkeyMarkers.Rd | 22 - man/addMovingMarker.Rd | 16 man/addOpenweatherCurrent.Rd | 14 man/addOpenweatherTiles.Rd | 14 man/addPlayback.Rd | 10 man/addProtobuf.Rd |only man/addReachability.Rd | 6 man/addSidebar.Rd | 12 man/addSidebyside.Rd | 4 man/addSpinner.Rd | 42 ++ man/addTangram.Rd | 6 man/addTimeslider.Rd | 20 - man/addVectorgrid.Rd |only man/addVelocity.Rd | 14 man/addWMS.Rd | 30 + man/antpathOptions.Rd | 22 - man/arrowheadOptions.Rd | 8 man/clearAntpath.Rd | 12 man/clearArrowhead.Rd | 8 man/clearConditionalLayers.Rd | 6 man/clearFuture.Rd | 12 man/clearHexbin.Rd | 12 man/clearHistory.Rd | 12 man/clearVectorgrid.Rd |only man/closeSidebar.Rd | 12 man/clusterchartOptions.Rd | 4 man/context_mapmenuItems.Rd | 32 - man/context_markermenuItems.Rd | 32 - man/context_menuItem.Rd | 32 - man/disableContextmenu.Rd | 32 - man/easyprintMap.Rd | 8 man/easyprintOptions.Rd | 33 + man/enableContextmenu.Rd | 32 - man/geosearchOptions.Rd | 8 man/goBackHistory.Rd | 12 man/goForwardHistory.Rd | 12 man/heightgraphOptions.Rd | 4 man/hexbinOptions.Rd | 12 man/hideContextmenu.Rd | 32 - man/hideHexbin.Rd | 12 man/historyOptions.Rd | 12 man/insertItemContextmenu.Rd | 32 - man/isSynced.Rd | 10 man/leaflet.extras2-package.Rd | 5 man/leafletsyncOptions.Rd | 10 man/makeMapkeyIcon.Rd | 10 man/mapkeyIconList.Rd | 10 man/mapkeyIcons.Rd | 10 man/mapmenuItems.Rd | 32 - man/markermenuItems.Rd | 32 - man/menuItem.Rd | 32 - man/movingMarkerOptions.Rd | 6 man/openSidebar.Rd | 12 man/openweatherCurrentOptions.Rd | 8 man/openweatherOptions.Rd | 8 man/playbackOptions.Rd | 6 man/reachabilityOptions.Rd | 6 man/removeAntpath.Rd | 12 man/removeArrowhead.Rd | 8 man/removeConditionalLayer.Rd | 6 man/removeEasyprint.Rd | 8 man/removeGeosearch.Rd | 6 man/removeItemContextmenu.Rd | 32 - man/removePlayback.Rd | 6 man/removeReachability.Rd | 6 man/removeSidebar.Rd | 12 man/removeSidebyside.Rd | 4 man/removeTimeslider.Rd | 6 man/removeVectorgrid.Rd |only man/removeVelocity.Rd | 8 man/removeallItemsContextmenu.Rd | 32 - man/setBuildingData.Rd | 8 man/setBuildingStyle.Rd | 8 man/setDate.Rd | 8 man/setDisabledContextmenu.Rd | 32 - man/setOptionsVelocity.Rd | 8 man/setTransparent.Rd | 8 man/setWMSParams.Rd |only man/showContextmenu.Rd | 34 - man/showHexbin.Rd | 12 man/sidebar_pane.Rd | 12 man/sidebar_tabs.Rd | 12 man/spinWhile.Rd |only man/startMoving.Rd | 6 man/sub-.leaflet_mapkey_icon_set.Rd | 10 man/timesliderOptions.Rd | 6 man/unsync.Rd | 10 man/updateBuildingTime.Rd | 8 man/updateHexbin.Rd | 14 man/vectorStyling.Rd |only man/velocityOptions.Rd | 8 tests/testthat/test-contextmenu.R | 1 tests/testthat/test-easyprint.R | 169 ++++++++- tests/testthat/test-mapkeyicon.R | 2 tests/testthat/test-playback.R | 3 tests/testthat/test-sidebar.R | 19 + tests/testthat/test-spin.R | 169 +++++++++ tests/testthat/test-vectorgrid.R |only tests/testthat/test-wms.R | 108 +++++ 156 files changed, 2645 insertions(+), 1190 deletions(-)
More information about leaflet.extras2 at CRAN
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Title: Fast Multivariate Analyses of Big Genomic Data
Description: Fast computation of multivariate analyses of small (10s to 100s markers) to big (1000s to 100000s) genotype data. Runs Principal Component Analysis allowing for centering, z-score standardization and scaling for genetic drift, projection of ancient samples to modern genetic space and multivariate tests for differences in group location (Permutation-Based Multivariate Analysis of Variance) and dispersion (Permutation-Based Multivariate Analysis of Dispersion).
Author: Salvador Herrando-Perez [aut] ,
Ray Tobler [ctb] ,
Christian Huber [ctb, cre]
Maintainer: Christian Huber <christian.domitian.huber@gmail.com>
Diff between smartsnp versions 1.2.0 dated 2025-06-09 and 1.2.1 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++----------- NEWS.md | 6 ++++++ R/smart_mva.R | 14 +++++++------- R/smart_pca.R | 14 +++++++------- R/smart_permanova.R | 8 ++++---- R/smart_permdisp.R | 8 ++++---- build/vignette.rds |binary man/smart_mva.Rd | 12 +++++++++++- man/smart_pca.Rd | 10 ++++++++-- man/smart_permanova.Rd | 9 ++++++++- man/smart_permdisp.Rd | 10 +++++++++- tests |only 13 files changed, 79 insertions(+), 41 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut],
Zachary Deane-Mayer [aut],
David Chudzicki [aut],
Dallin Akagi [aut],
Sergey Yurgenson [aut],
Thakur Raj Anand [aut],
Peter Hurford [aut],
Chester Ismay [aut],
AJ Alon [aut, cre],
Andrew Watson [aut],
Gregory Williams [aut],
Anasta [...truncated...]
Maintainer: AJ Alon <api-maintainer@datarobot.com>
Diff between datarobot versions 2.18.8 dated 2026-05-26 and 2.18.9 dated 2026-09-09
datarobot-2.18.8/datarobot/inst/doc/ComparingSubsets.R |only datarobot-2.18.8/datarobot/inst/doc/ComparingSubsets.Rmd |only datarobot-2.18.8/datarobot/inst/doc/ComparingSubsets.html |only datarobot-2.18.8/datarobot/vignettes/ComparingSubsets.Rmd |only datarobot-2.18.9/datarobot/DESCRIPTION | 6 datarobot-2.18.9/datarobot/MD5 | 63 +++--- datarobot-2.18.9/datarobot/NEWS.md | 14 + datarobot-2.18.9/datarobot/R/ConnectToDataRobot.R | 98 +++++++++- datarobot-2.18.9/datarobot/R/DataRobotRequests.R | 11 + datarobot-2.18.9/datarobot/build/vignette.rds |binary datarobot-2.18.9/datarobot/inst/doc/AdvancedTuning.html | 4 datarobot-2.18.9/datarobot/inst/doc/AdvancedVignette.html | 6 datarobot-2.18.9/datarobot/inst/doc/Calendars.html | 4 datarobot-2.18.9/datarobot/inst/doc/ComplianceDocumentation.html | 4 datarobot-2.18.9/datarobot/inst/doc/CustomCABundle.R |only datarobot-2.18.9/datarobot/inst/doc/CustomCABundle.Rmd |only datarobot-2.18.9/datarobot/inst/doc/CustomCABundle.html |only datarobot-2.18.9/datarobot/inst/doc/DatetimePartitionedProjects.html | 4 datarobot-2.18.9/datarobot/inst/doc/Deployment.html | 4 datarobot-2.18.9/datarobot/inst/doc/IntroductionToDataRobot.R | 8 datarobot-2.18.9/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 15 + datarobot-2.18.9/datarobot/inst/doc/IntroductionToDataRobot.html | 59 +++--- datarobot-2.18.9/datarobot/inst/doc/Multiclass.html | 4 datarobot-2.18.9/datarobot/inst/doc/PartialDependence.html | 4 datarobot-2.18.9/datarobot/inst/doc/PredictionExplanations.html | 4 datarobot-2.18.9/datarobot/inst/doc/RatingTables.html | 4 datarobot-2.18.9/datarobot/inst/doc/TimeSeries.html | 4 datarobot-2.18.9/datarobot/inst/doc/TrainingPredictions.html | 4 datarobot-2.18.9/datarobot/inst/doc/VariableImportance.html | 4 datarobot-2.18.9/datarobot/man/CABundle.Rd |only datarobot-2.18.9/datarobot/man/ConnectToDataRobot.Rd | 31 ++- datarobot-2.18.9/datarobot/man/GetAnomalyAssessmentExplanations.Rd | 4 datarobot-2.18.9/datarobot/man/GetDeploymentAssociationId.Rd | 4 datarobot-2.18.9/datarobot/man/SaveCABundlePreference.Rd |only datarobot-2.18.9/datarobot/man/SetSSLVerification.Rd |only datarobot-2.18.9/datarobot/man/datarobot-package.Rd | 27 ++ datarobot-2.18.9/datarobot/vignettes/CustomCABundle.Rmd |only datarobot-2.18.9/datarobot/vignettes/IntroductionToDataRobot.Rmd | 15 + 38 files changed, 317 insertions(+), 92 deletions(-)
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted, optional
persistence of the look, named wallpaper scenes, and helpers to
match 'ggplot2', 'plotly', and 'gt' output to the glass pack.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-09-09
DESCRIPTION | 15 - MD5 | 71 +++--- NAMESPACE | 9 NEWS.md | 42 +++ R/glass-accent.R |only R/glass-intensity.R | 31 +- R/glass-page.R |only R/glass-plots.R |only R/glass-theme.R | 119 +++++++++- R/shinyglass-package.R | 18 - README.md | 124 +++-------- build/vignette.rds |binary inst/WORDLIST | 10 inst/doc/compatibility.Rmd | 4 inst/doc/compatibility.html | 12 - inst/doc/playground.R |only inst/doc/playground.Rmd |only inst/doc/playground.html |only inst/doc/theming.R | 18 + inst/doc/theming.Rmd | 69 +++++- inst/doc/theming.html | 82 ++++++- inst/examples/bslib-dashboard.R | 55 +--- inst/examples/demo-app.R | 41 +-- inst/examples/inputs-gallery.R | 13 - inst/examples/playground.R |only inst/examples/plotly-gt-demo.R | 95 +++----- inst/js/shiny-glass.js | 426 ++++++++++++++++++++++++++++++-------- inst/scss/glass.scss | 359 ++++++++++++++++++++++++-------- man/glass_accent_input.Rd |only man/glass_intensity_slider.Rd | 8 man/glass_page.Rd |only man/glass_plot_colors.Rd |only man/glass_system_colors.Rd |only man/glass_theme.Rd | 17 + man/gt_theme_glass.Rd |only man/observe_glass.Rd |only man/observe_glass_accent.Rd |only man/plotly_glass.Rd |only man/shinyglass-package.Rd | 17 - man/theme_glass.Rd |only man/update_glass_theme.Rd | 11 tests/testthat/test-glass-theme.R | 123 ++++++++++ vignettes/compatibility.Rmd | 4 vignettes/playground.Rmd |only vignettes/theming.Rmd | 69 +++++- 45 files changed, 1359 insertions(+), 503 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 4.0.1 dated 2026-07-02 and 4.0.2 dated 2026-09-09
DESCRIPTION | 8 - MD5 | 40 ++++--- NEWS.md | 20 +++ R/alignSpCols.R |only R/byFileAOP.R | 133 ++++++++++------------- R/byTileAOP.R | 137 ++++++++++-------------- R/checkUrlExp.R |only R/checkVarFields.R | 4 R/datasetQuery.R | 12 +- R/downloadNEONFile.R |only R/loadByProduct.R | 7 - R/stackByTable.R | 6 - R/stackDataFilesArrow.R | 254 +++++++++++++++++++++++---------------------- R/stackDataFilesDuck.R | 22 ++- R/zipsByProduct.R | 111 +++++++------------ README.md | 12 +- man/alignSpCols.Rd |only man/checkUrlExp.Rd |only man/datasetQuery.Rd | 5 man/downloadNEONFile.Rd |only man/loadByProduct.Rd | 5 man/stackByTable.Rd | 5 man/stackDataFilesArrow.Rd | 10 + man/stackDataFilesDuck.Rd | 4 24 files changed, 409 insertions(+), 386 deletions(-)
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Description: Estimate haplotypic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.
Author: David Gerard [aut, cre]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between ldsep versions 2.1.6 dated 2025-09-18 and 2.1.7 dated 2026-09-09
DESCRIPTION | 10 +++---- MD5 | 20 +++++++------- NAMESPACE | 1 NEWS.md | 4 ++ R/fast.R | 64 +++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fast.html | 6 ++-- inst/doc/vcf.html | 16 +++++------ man/hsm.Rd |only man/ldsep-package.Rd | 5 +++ tests/testthat/test-hsm.R |only 12 files changed, 100 insertions(+), 26 deletions(-)
Title: Behavioral Contracts and Generative Laws for 'S7'
Description: Contract helpers built with 'S7' for expressing runtime protocols
around ordinary 'S7' dispatch. Structural interfaces describe small sets of
required 'S7' generics, while explicit traits record registered
implementations with optional default methods and associated metadata.
Optional runtime checks can validate argument and return specifications in
contract-scoped evaluation. Generative laws combine generators,
deterministic shrinking, and one-result 'tinytest' expectations.
Author: Sounkou Mahamane Toure [aut, cre]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between s7contract versions 0.1.0 dated 2026-05-07 and 0.2.3 dated 2026-09-09
DESCRIPTION | 13 MD5 | 98 +++- NAMESPACE | 25 + NEWS.md | 57 ++ R/aaa-classes.R | 9 R/aaa-property-classes.R |only R/coverage.R |only R/generator-double.R |only R/generator-sample.R |only R/generator.R |only R/interface.R | 36 - R/law.R |only R/package.R | 25 - R/progressive.R | 219 ++++----- R/state-law.R |only R/trait.R | 104 ++-- R/utils.R | 41 - build/vignette.rds |binary inst/doc/bioinformatics-interfaces.Rmd | 10 inst/doc/bioinformatics-interfaces.html | 17 inst/doc/calendar-intervals.R |only inst/doc/calendar-intervals.Rmd |only inst/doc/calendar-intervals.html |only inst/doc/monad-dictionaries.R |only inst/doc/monad-dictionaries.Rmd |only inst/doc/monad-dictionaries.html |only inst/doc/property-laws.R |only inst/doc/property-laws.Rmd |only inst/doc/property-laws.html |only inst/doc/protocol-laws.R |only inst/doc/protocol-laws.Rmd |only inst/doc/protocol-laws.html |only inst/doc/s7-interfaces-and-traits.R | 305 +------------ inst/doc/s7-interfaces-and-traits.Rmd | 553 +++--------------------- inst/doc/s7-interfaces-and-traits.html | 661 +++++++---------------------- inst/doc/stateful-protocols.R |only inst/doc/stateful-protocols.Rmd |only inst/doc/stateful-protocols.html |only inst/examples/calendar-laws.R |only inst/examples/maybe-laws.R |only inst/examples/store-laws.R |only inst/examples/vector-laws.R |only inst/tinytest/test-calendar-laws.R |only inst/tinytest/test-contract-semantics.R |only inst/tinytest/test-coverage.R |only inst/tinytest/test-generator-composition.R |only inst/tinytest/test-generator-double.R |only inst/tinytest/test-generator-sample.R |only inst/tinytest/test-law-integration.R |only inst/tinytest/test-law.R |only inst/tinytest/test-maybe-laws.R |only inst/tinytest/test-protocol-laws.R |only inst/tinytest/test-state-law.R |only inst/tinytest/test-state-protocol.R |only man/gen_bind.Rd |only man/gen_commands.Rd |only man/gen_constant.Rd |only man/gen_double.Rd |only man/gen_element.Rd |only man/gen_example.Rd |only man/gen_sample.Rd |only man/grapes-colon-colon-grapes.Rd | 10 man/new_command.Rd |only man/new_generator.Rd |only man/new_interface.Rd | 12 man/new_law.Rd |only man/new_state_law.Rd |only man/new_trait.Rd | 5 man/s7contract.Rd | 15 man/trait_methods.Rd | 3 vignettes/bioinformatics-interfaces.Rmd | 10 vignettes/calendar-intervals.Rmd |only vignettes/monad-dictionaries.Rmd |only vignettes/property-laws.Rmd |only vignettes/protocol-laws.Rmd |only vignettes/s7-interfaces-and-traits.Rmd | 553 +++--------------------- vignettes/stateful-protocols.Rmd |only 77 files changed, 748 insertions(+), 2033 deletions(-)
Title: A Lasso for Hierarchical Interactions
Description: Fits sparse interaction models for continuous and binary responses subject to the strong (or weak) hierarchy restriction that an interaction between two variables only be included if both (or at least one of) the variables is included as a main effect. For more details, see Bien, J., Taylor, J., Tibshirani, R., (2013) "A Lasso for Hierarchical Interactions." Annals of Statistics. 41(3). 1111-1141.
Author: Jacob Bien [aut, cre],
Rob Tibshirani [aut]
Maintainer: Jacob Bien <jbien@usc.edu>
Diff between hierNet versions 1.9 dated 2020-02-05 and 1.10.1 dated 2026-09-09
DESCRIPTION | 16 - MD5 | 24 - NAMESPACE | 1 R/funcs.R | 505 ++++++++++++++++++++++++++++++++++++++++ man/hierNet.Rd | 155 ++++++++---- man/hierNet.cv.Rd | 61 +++- man/hierNet.logistic.Rd | 160 ++++++++---- man/hierNet.logistic.path.Rd | 141 +++++++---- man/hierNet.path.Rd | 143 +++++++---- man/hierNet.varimp.Rd | 36 +- man/predict.hierNet.Rd | 52 ++-- man/predict.hierNet.logistic.Rd | 51 ++-- man/predict.hierNet.path.Rd | 52 ++-- 13 files changed, 1087 insertions(+), 310 deletions(-)
Title: Causal Graph Interface
Description: Create, query, and modify causal graphs. 'caugi' (Causal Graph
Interface) is a causality-first, high performance graph package that
provides a simple interface to build, structure, and examine causal
relationships.
Author: Frederik Fabricius-Bjerre [aut, cre, cph] ,
Johan Larsson [aut] ,
Michael Sachs [aut] ,
Bjarke Hautop Kristensen [aut],
Leonard Henckel [ctb, cph] ; see LICENSE.note),
Theo Wuertzen [ctb, cph] ,
Sebastian Weichwald [ctb, cph] ,
Authors of the bundled [...truncated...]
Maintainer: Frederik Fabricius-Bjerre <frederik@fabriciusbjerre.dk>
Diff between caugi versions 1.2.0 dated 2026-05-05 and 1.3.0 dated 2026-09-09
caugi-1.2.0/caugi/man/all.equal.caugi-colon-colon-caugi.Rd |only caugi-1.2.0/caugi/man/compare_proxy.caugi-colon-colon-caugi.Rd |only caugi-1.2.0/caugi/man/length.Rd |only caugi-1.2.0/caugi/man/plot.Rd |only caugi-1.2.0/caugi/man/print.Rd |only caugi-1.2.0/caugi/src/rust/src/reactive |only caugi-1.3.0/caugi/DESCRIPTION | 55 caugi-1.3.0/caugi/LICENSE.note |only caugi-1.3.0/caugi/MD5 | 346 ++-- caugi-1.3.0/caugi/NAMESPACE | 14 caugi-1.3.0/caugi/NEWS.md | 94 + caugi-1.3.0/caugi/R/adjustment.R | 9 caugi-1.3.0/caugi/R/all-classes.R | 11 caugi-1.3.0/caugi/R/as_caugi.R | 130 + caugi-1.3.0/caugi/R/caugi.R | 18 caugi-1.3.0/caugi/R/caugi_to.R | 2 caugi-1.3.0/caugi/R/extendr-wrappers.R | 4 caugi-1.3.0/caugi/R/format-dot.R | 24 caugi-1.3.0/caugi/R/format-graphml.R | 2 caugi-1.3.0/caugi/R/format-mermaid.R | 15 caugi-1.3.0/caugi/R/methods.R | 52 caugi-1.3.0/caugi/R/metrics.R | 9 caugi-1.3.0/caugi/R/operations.R | 125 + caugi-1.3.0/caugi/R/options.R | 9 caugi-1.3.0/caugi/R/plot-core.R | 40 caugi-1.3.0/caugi/R/plot-grobs.R | 136 + caugi-1.3.0/caugi/R/plot-routing.R |only caugi-1.3.0/caugi/R/queries.R | 17 caugi-1.3.0/caugi/R/simulation.R | 7 caugi-1.3.0/caugi/R/zzz.R | 14 caugi-1.3.0/caugi/README.md | 23 caugi-1.3.0/caugi/build/partial.rdb |binary caugi-1.3.0/caugi/build/vignette.rds |binary caugi-1.3.0/caugi/inst/doc/caugi.html | 8 caugi-1.3.0/caugi/inst/doc/comparisons.Rmd |only caugi-1.3.0/caugi/inst/doc/comparisons.html |only caugi-1.3.0/caugi/inst/doc/package_use.html | 4 caugi-1.3.0/caugi/inst/doc/performance.R |only caugi-1.3.0/caugi/inst/doc/performance.Rmd |only caugi-1.3.0/caugi/inst/doc/performance.html |only caugi-1.3.0/caugi/inst/doc/visualization.R | 15 caugi-1.3.0/caugi/inst/doc/visualization.Rmd | 44 caugi-1.3.0/caugi/inst/doc/visualization.html | 836 +++++----- caugi-1.3.0/caugi/man/add-caugi_plot-caugi_plot.Rd | 27 caugi-1.3.0/caugi/man/adjustment_set.Rd | 23 caugi-1.3.0/caugi/man/aid.Rd | 15 caugi-1.3.0/caugi/man/all.equal.caugi-caugi.Rd |only 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| 60 caugi-1.3.0/caugi/man/to_dot.Rd | 37 caugi-1.3.0/caugi/man/to_graphml.Rd | 32 caugi-1.3.0/caugi/man/to_mermaid.Rd | 36 caugi-1.3.0/caugi/man/topological_sort.Rd | 60 caugi-1.3.0/caugi/man/write_caugi.Rd | 32 caugi-1.3.0/caugi/man/write_dot.Rd | 32 caugi-1.3.0/caugi/man/write_graphml.Rd | 32 caugi-1.3.0/caugi/man/write_mermaid.Rd | 32 caugi-1.3.0/caugi/src/rust/Cargo.lock | 257 --- caugi-1.3.0/caugi/src/rust/Cargo.toml | 20 caugi-1.3.0/caugi/src/rust/src/graph/admg/mod.rs | 17 caugi-1.3.0/caugi/src/rust/src/graph/ag/mod.rs | 57 caugi-1.3.0/caugi/src/rust/src/graph/aid.rs |only caugi-1.3.0/caugi/src/rust/src/graph/alg.rs | 1 caugi-1.3.0/caugi/src/rust/src/graph/alg/adjustment.rs |only caugi-1.3.0/caugi/src/rust/src/graph/cpdag |only caugi-1.3.0/caugi/src/rust/src/graph/dag/adjustment.rs | 149 + caugi-1.3.0/caugi/src/rust/src/graph/dag/mod.rs | 18 caugi-1.3.0/caugi/src/rust/src/graph/dag/transforms.rs | 14 caugi-1.3.0/caugi/src/rust/src/graph/graphml.rs | 18 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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 1.2.0 dated 2026-09-04 and 1.2.1 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/h2o.R | 8 ++++++++ inst/doc/h2o.Rmd | 9 +++++++++ inst/doc/h2o.html | 10 +++++----- vignettes/h2o.Rmd | 9 +++++++++ 7 files changed, 44 insertions(+), 14 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <terry.therneau@proton.me>
Diff between survival versions 3.8-11 dated 2026-08-21 and 3.8-12 dated 2026-09-09
survival-3.8-11/survival/vignettes/test |only survival-3.8-12/survival/DESCRIPTION | 8 survival-3.8-12/survival/MD5 | 104 +- survival-3.8-12/survival/R/Surv.R | 13 survival-3.8-12/survival/R/Surv2.R | 47 - survival-3.8-12/survival/R/fromtimeline.R | 26 survival-3.8-12/survival/R/parsecovar.R | 4 survival-3.8-12/survival/R/survcheck.R | 11 survival-3.8-12/survival/R/survfit.R | 2 survival-3.8-12/survival/R/survfitAJ.R | 11 survival-3.8-12/survival/R/survfitKM.R | 37 survival-3.8-12/survival/R/survpenal.fit.R | 16 survival-3.8-12/survival/R/yates.R | 21 survival-3.8-12/survival/inst/NEWS.Rd | 23 survival-3.8-12/survival/inst/doc/adjcurve.pdf |binary survival-3.8-12/survival/inst/doc/approximate.pdf |binary survival-3.8-12/survival/inst/doc/compete.pdf |binary survival-3.8-12/survival/inst/doc/concordance.pdf |binary survival-3.8-12/survival/inst/doc/matrix.pdf |binary survival-3.8-12/survival/inst/doc/methods.pdf |binary survival-3.8-12/survival/inst/doc/modelframe.pdf |binary survival-3.8-12/survival/inst/doc/multi.pdf |binary survival-3.8-12/survival/inst/doc/other.pdf |binary survival-3.8-12/survival/inst/doc/population.pdf |binary survival-3.8-12/survival/inst/doc/redistribute.pdf |binary survival-3.8-12/survival/inst/doc/splines.pdf |binary survival-3.8-12/survival/inst/doc/survival.pdf |binary survival-3.8-12/survival/inst/doc/tiedtimes.pdf |binary survival-3.8-12/survival/inst/doc/timeline.pdf |binary survival-3.8-12/survival/inst/doc/validate.pdf |binary survival-3.8-12/survival/man/Surv.Rd | 53 - survival-3.8-12/survival/man/Surv2.Rd | 2 survival-3.8-12/survival/man/survcheck.Rd | 22 survival-3.8-12/survival/man/survfit.formula.Rd | 13 survival-3.8-12/survival/man/yates.Rd | 2 survival-3.8-12/survival/noweb/code.nw | 438 ---------- survival-3.8-12/survival/noweb/parse.Rnw | 4 survival-3.8-12/survival/noweb/yates2.Rnw | 21 survival-3.8-12/survival/src/init.c | 2 survival-3.8-12/survival/src/survfitkm.c | 98 -- survival-3.8-12/survival/src/survproto.h | 2 survival-3.8-12/survival/tests/Examples/survival-Ex.Rout.save | 14 survival-3.8-12/survival/tests/checkSurv2.R | 7 survival-3.8-12/survival/tests/checkSurv2.Rout.save | 11 survival-3.8-12/survival/tests/coxsurv6.Rout.save | 28 survival-3.8-12/survival/tests/mstrata.Rout.save | 14 survival-3.8-12/survival/tests/multi3.Rout.save | 20 survival-3.8-12/survival/tests/survcheck.R | 4 survival-3.8-12/survival/tests/survcheck.Rout.save | 10 survival-3.8-12/survival/tests/survfit3.R |only survival-3.8-12/survival/tests/survfit3.Rout.save |only survival-3.8-12/survival/tests/yates.R |only survival-3.8-12/survival/tests/yates2.R | 37 survival-3.8-12/survival/tests/yates2.Rout.save |only 54 files changed, 402 insertions(+), 723 deletions(-)
Title: Clinical Trial Simulation
Description: Provides some basic routines for simulating a
clinical trial. The primary intent is to provide some tools to
generate trial simulations for trials with time to event outcomes.
Piecewise exponential failure rates and piecewise constant
enrollment rates are the underlying mechanism used to simulate
a broad range of scenarios such as those presented in
Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>.
However, the basic generation of data is done using pipes to allow
maximum flexibility for users to meet different needs.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
John Blischak [aut],
Nan Xiao [ctb],
Yilong Zhang [aut],
Jianxiao Yang [ctb],
Lili Ling [ctb],
Xintong Li [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Yalin Zhu [ctb],
Heng Zhou [ctb],
Amin Sh [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between simtrial versions 1.0.2 dated 2025-11-20 and 1.1.0 dated 2026-09-09
DESCRIPTION | 15 MD5 | 93 NAMESPACE | 61 NEWS.md | 14 R/as_gt.R | 29 R/lt.R |only R/pvalue_maxcombo.R | 4 R/sim_fixed_n.R | 14 build/partial.rdb |binary build/vignette.rds |binary inst/doc/arbitrary-hazard.html | 10 inst/doc/discrepancy-between-simtrial-and-survival.R | 5 inst/doc/discrepancy-between-simtrial-and-survival.Rmd | 5 inst/doc/discrepancy-between-simtrial-and-survival.html | 941 ++++ inst/doc/maxcombo.R | 18 inst/doc/maxcombo.Rmd | 18 inst/doc/maxcombo.html | 2975 +++------------ inst/doc/modest-wlrt.html | 4 inst/doc/parallel.html | 22 inst/doc/rmst.R | 7 inst/doc/rmst.Rmd | 7 inst/doc/rmst.html | 6 inst/doc/routines.R | 21 inst/doc/routines.Rmd | 21 inst/doc/routines.html | 2637 +++---------- inst/doc/sim_fixed_design_custom.R | 14 inst/doc/sim_fixed_design_custom.Rmd | 14 inst/doc/sim_fixed_design_custom.html | 3094 ++++------------ inst/doc/sim_fixed_design_simple.R | 20 inst/doc/sim_fixed_design_simple.Rmd | 20 inst/doc/sim_fixed_design_simple.html | 2161 +++-------- inst/doc/sim_gs_design_simple.R | 14 inst/doc/sim_gs_design_simple.Rmd | 14 inst/doc/sim_gs_design_simple.html | 1658 +++----- inst/doc/workflow.html | 2 man/as_gt.Rd | 13 man/lt-methods.Rd |only man/reexports.Rd |only man/sim_fixed_n.Rd | 13 man/simtrial-package.Rd | 1 tests/testthat/test-unvalidated-sim_gs_n.R | 26 tests/testthat/test-unvalidated-summary.R | 18 vignettes/discrepancy-between-simtrial-and-survival.Rmd | 5 vignettes/maxcombo.Rmd | 18 vignettes/rmst.Rmd | 7 vignettes/routines.Rmd | 21 vignettes/sim_fixed_design_custom.Rmd | 14 vignettes/sim_fixed_design_simple.Rmd | 20 vignettes/sim_gs_design_simple.Rmd | 14 49 files changed, 5000 insertions(+), 9108 deletions(-)
Title: Chat UI Component for 'shiny'
Description: Provides a scrolling chat interface with multiline input,
suitable for creating chatbot apps based on Large Language Models
(LLMs). Designed to work particularly well with the 'ellmer' R package
for calling LLMs.
Author: Joe Cheng [aut],
Carson Sievert [aut],
Garrick Aden-Buie [aut, cre] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between shinychat versions 0.4.0 dated 2026-06-01 and 0.5.0 dated 2026-09-09
shinychat-0.4.0/shinychat/inst/lib/shiny/shinychat.css.map |only shinychat-0.4.0/shinychat/inst/lib/shiny/shinychat.js.map |only shinychat-0.5.0/shinychat/DESCRIPTION | 20 shinychat-0.5.0/shinychat/MD5 | 185 - shinychat-0.5.0/shinychat/NAMESPACE | 44 shinychat-0.5.0/shinychat/NEWS.md | 78 shinychat-0.5.0/shinychat/R/attachments.R |only shinychat-0.5.0/shinychat/R/chat.R | 1352 +++++++- shinychat-0.5.0/shinychat/R/chat_app.R | 1036 +++++- shinychat-0.5.0/shinychat/R/chat_drawer.R |only shinychat-0.5.0/shinychat/R/chat_history.R |only shinychat-0.5.0/shinychat/R/chat_history_client.R |only shinychat-0.5.0/shinychat/R/chat_history_store.R |only shinychat-0.5.0/shinychat/R/chat_history_title.R |only shinychat-0.5.0/shinychat/R/chat_history_types.R |only shinychat-0.5.0/shinychat/R/chat_restore.R | 77 shinychat-0.5.0/shinychat/R/client_state.R | 5 shinychat-0.5.0/shinychat/R/content-slash-command.R |only shinychat-0.5.0/shinychat/R/contents_shinychat.R | 981 +++++- 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|only shinychat-0.5.0/shinychat/tests/testthat/apps/icon/app.R | 2 shinychat-0.5.0/shinychat/tests/testthat/apps/page-chat-drawer |only shinychat-0.5.0/shinychat/tests/testthat/apps/page-chat-nav-visibility |only shinychat-0.5.0/shinychat/tests/testthat/apps/slash-command-async-stream |only shinychat-0.5.0/shinychat/tests/testthat/apps/tool-basic/app.R | 6 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-map/app.R | 4 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-01-simple.R | 4 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-02-annotations.R | 4 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-03-tool-result-simple.R | 14 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-04-tool-result-table.R | 17 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-05-tool-custom-result-class.R | 18 shinychat-0.5.0/shinychat/tests/testthat/apps/tool-weather/app-06-tool-custom-output.R | 14 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shinychat-0.5.0/shinychat/tests/testthat/test-chat_history_store.R |only shinychat-0.5.0/shinychat/tests/testthat/test-chat_history_title.R |only shinychat-0.5.0/shinychat/tests/testthat/test-chat_history_types.R |only shinychat-0.5.0/shinychat/tests/testthat/test-contents_shinychat.R | 1041 ++++++ shinychat-0.5.0/shinychat/tests/testthat/test-conversation-id.R |only shinychat-0.5.0/shinychat/tests/testthat/test-greeting.R | 399 ++ shinychat-0.5.0/shinychat/tests/testthat/test-history-shinytest2.R |only shinychat-0.5.0/shinychat/tests/testthat/test-html_islands.R | 267 + shinychat-0.5.0/shinychat/tests/testthat/test-markdown-stream.R | 541 +++ shinychat-0.5.0/shinychat/tests/testthat/test-page-chat-examples.R |only shinychat-0.5.0/shinychat/tests/testthat/test-page-chat-shinytest2.R |only shinychat-0.5.0/shinychat/tests/testthat/test-page-chat.R |only shinychat-0.5.0/shinychat/tests/testthat/test-slash-command-async-shinytest2.R |only 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Title: Random Forest-Based Multistate Survival Analysis
Description: Fits transition-specific cause-specific random survival forests
on a clock-reset duration scale for acyclic, non-recurrent multistate
processes. Entry-conditioned state-occupation probabilities are assembled
from predicted cumulative hazards by semi-Markov entry-mass and sojourn
convolution on a validated regular grid. The one-row-per-subject interface
supports one common initial state, one recorded entry per state, baseline
time-fixed covariates, competing exits, and independent right censoring.
Left truncation, recurrent visits, directed cycles, time-dependent
covariates, and ongoing-sojourn dynamic prediction are not supported.
The package also provides calendar-time Aalen-Johansen point estimates as
a covariate-free descriptive baseline, transition-specific permutation
importance, genuine ranger edge OOB concordance, and patient-level
cross-validated IPCW state-probability scoring. Methods are described in
Ishwaran et al. (2008) <doi:10.1214/08-AOAS169> for random survival
fo [...truncated...]
Author: Yiqing Chen [aut, cre]
Maintainer: Yiqing Chen <y.chen@tamu.edu>
Diff between RFmstate versions 0.1.2 dated 2026-03-11 and 0.1.9 dated 2026-09-09
RFmstate-0.1.2/RFmstate/inst/doc/introduction.md |only RFmstate-0.1.9/RFmstate/DESCRIPTION | 42 RFmstate-0.1.9/RFmstate/MD5 | 96 - RFmstate-0.1.9/RFmstate/NAMESPACE | 73 - RFmstate-0.1.9/RFmstate/R/RFmstate-package.R | 34 RFmstate-0.1.9/RFmstate/R/aalen_johansen.R | 85 - RFmstate-0.1.9/RFmstate/R/define_states.R | 166 ++ RFmstate-0.1.9/RFmstate/R/diagnose.R | 706 ++++++--- RFmstate-0.1.9/RFmstate/R/fit_rfmstate.R | 707 +++++++--- RFmstate-0.1.9/RFmstate/R/importance.R | 30 RFmstate-0.1.9/RFmstate/R/plot.R | 422 +++-- RFmstate-0.1.9/RFmstate/R/predict.R | 463 +++--- RFmstate-0.1.9/RFmstate/R/prepare_data.R | 638 ++++++--- RFmstate-0.1.9/RFmstate/R/public_methods.R |only RFmstate-0.1.9/RFmstate/R/sim_data.R | 100 - RFmstate-0.1.9/RFmstate/R/summary.R | 75 - RFmstate-0.1.9/RFmstate/R/transition_probability.R | 645 +++++++-- RFmstate-0.1.9/RFmstate/build/vignette.rds |binary RFmstate-0.1.9/RFmstate/inst/demo_custom_data.Rmd | 104 - RFmstate-0.1.9/RFmstate/inst/demo_custom_data.html | 375 ++--- RFmstate-0.1.9/RFmstate/inst/doc/introduction.R | 56 RFmstate-0.1.9/RFmstate/inst/doc/introduction.Rmd | 231 ++- RFmstate-0.1.9/RFmstate/inst/doc/introduction.html | 701 ++++++--- RFmstate-0.1.9/RFmstate/man/RFmstate-package.Rd | 47 RFmstate-0.1.9/RFmstate/man/aalen_johansen.Rd | 37 RFmstate-0.1.9/RFmstate/man/clinical_states.Rd | 7 RFmstate-0.1.9/RFmstate/man/compute_trans_prob.Rd | 110 + RFmstate-0.1.9/RFmstate/man/define_multistate.Rd | 12 RFmstate-0.1.9/RFmstate/man/diagnose.Rd | 115 - RFmstate-0.1.9/RFmstate/man/head.msdata.Rd |only RFmstate-0.1.9/RFmstate/man/importance.Rd | 30 RFmstate-0.1.9/RFmstate/man/plot.aj_estimate.Rd | 49 RFmstate-0.1.9/RFmstate/man/plot.rfmstate_diag.Rd | 30 RFmstate-0.1.9/RFmstate/man/plot.rfmstate_importance.Rd | 36 RFmstate-0.1.9/RFmstate/man/plot.rfmstate_pred.Rd | 35 RFmstate-0.1.9/RFmstate/man/plot_transition_diagram.Rd | 15 RFmstate-0.1.9/RFmstate/man/predict.rfmstate.Rd | 122 + RFmstate-0.1.9/RFmstate/man/prepare_data.Rd | 74 - RFmstate-0.1.9/RFmstate/man/print.msdata.Rd |only RFmstate-0.1.9/RFmstate/man/print.mstate_structure.Rd |only RFmstate-0.1.9/RFmstate/man/print_rfmstate_objects.Rd |only RFmstate-0.1.9/RFmstate/man/rfmstate.Rd | 144 +- RFmstate-0.1.9/RFmstate/man/sim_clinical_data.Rd | 24 RFmstate-0.1.9/RFmstate/man/summary.rfmstate.Rd | 24 RFmstate-0.1.9/RFmstate/tests/testthat/test-aalen_johansen.R | 20 RFmstate-0.1.9/RFmstate/tests/testthat/test-core-validation.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-fit-contract-diagnostics.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-fit_predict.R | 42 RFmstate-0.1.9/RFmstate/tests/testthat/test-plot-core.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-post-step05-contracts.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-post-step05-statistical-validation.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-prepare_data.R | 15 RFmstate-0.1.9/RFmstate/tests/testthat/test-semi-markov-probabilities.R |only RFmstate-0.1.9/RFmstate/tests/testthat/test-sim_data.R | 47 RFmstate-0.1.9/RFmstate/vignettes/introduction.Rmd | 231 ++- 55 files changed, 4858 insertions(+), 2157 deletions(-)
Title: Many Marks, Measures, Memberships, and Motifs for Networks
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 1.0.1 dated 2026-08-31 and 1.0.3 dated 2026-09-09
DESCRIPTION | 8 - MD5 | 95 ++++++++-------- NEWS.md | 67 +++++++++++ R/mark_nodes.R | 16 ++ R/mark_ties.R | 32 +++++ R/measure_centrality_between.R | 27 ++++ R/measure_centrality_closeness.R | 27 ++++ R/measure_centrality_degree.R | 2 R/measure_centrality_eigen.R | 37 +++++- R/measure_change.R | 6 - R/measure_cohesion.R | 43 ++++++- R/measure_features.R | 27 ++++ R/measure_heterogeneity.R | 165 ++++++++++++++++++++-------- R/measure_hierarchy.R | 8 + R/measure_holes.R | 12 +- R/member_community.R | 150 ++++++++++++++++++++----- R/method_coreness.R | 24 +++- R/motif_census.R | 7 + R/netrics-utils.R | 61 +++++----- man/mark_nodes.Rd | 15 ++ man/mark_select_tie.Rd | 3 man/mark_triangles.Rd | 8 + man/measure_assort_net.Rd | 35 ++++- man/measure_assort_node.Rd | 4 man/measure_broker_node.Rd | 9 + man/measure_central_between.Rd | 9 + man/measure_central_close.Rd | 9 + man/measure_central_eigen.Rd | 17 ++ man/measure_central_tie_between.Rd | 10 + man/measure_centralisation_between.Rd | 9 + man/measure_centralisation_close.Rd | 9 + man/measure_diverse_net.Rd | 14 ++ man/measure_fit.Rd | 16 ++ man/measure_fragmentation.Rd | 28 +++- man/measure_hierarchy.Rd | 9 + man/member_community.Rd | 10 + man/member_community_non.Rd | 40 +++++- man/method_coreness.Rd | 9 + man/motif_path.Rd | 8 + tests/testthat/Rplots.pdf |binary tests/testthat/helper-netrics.R | 59 ++++++++++ tests/testthat/test-mark_ties.R | 19 +++ tests/testthat/test-measure_cohesion.R | 9 + tests/testthat/test-measure_heterogeneity.R | 88 ++++++++++++++ tests/testthat/test-measure_net.R | 8 + tests/testthat/test-measure_nodes.R | 15 ++ tests/testthat/test-member_community.R | 85 ++++++++++++-- tests/testthat/test-member_equivalence.R | 3 tests/testthat/test-shapes.R |only 49 files changed, 1161 insertions(+), 210 deletions(-)
Title: Reference Values for CT-Assessed Body Composition
Description: Get z-scores, percentiles, absolute values, and percent of predicted of a reference cohort.
Functionality requires installing the data packages 'adiposerefdata' and 'musclerefdata' from p-mq.github.io/drat.
For more information on the underlying research, please visit our website which also includes a graphical interface.
The models and underlying data are described in
Marquardt J. Peter et al (2025),
"Subcutaneous and Visceral adipose tissue Reference Values from Framingham Heart Study Thoracic and Abdominal CT",
*Investigative Radiology*
<doi:10.1097/RLI.0000000000001104>
and
Tonnesen PE et al. (2023),
"Muscle Reference Values from Thoracic and Abdominal CT for Sarcopenia Assessment [column] The Framingham Heart Study",
*Investigative Radiology*,
<doi:10.1097/RLI.0000000000001012>.
Author: Dr. Peter Amin Marquardt [aut, cre]
Maintainer: Dr. Peter Amin Marquardt <peter@kmarquardt.de>
Diff between bodycompref versions 2.0.1 dated 2024-07-21 and 2.0.2 dated 2026-09-09
bodycompref-2.0.1/bodycompref/tests/testthat/_snaps |only bodycompref-2.0.2/bodycompref/DESCRIPTION | 22 ++- bodycompref-2.0.2/bodycompref/MD5 | 31 ++--- bodycompref-2.0.2/bodycompref/NAMESPACE | 1 bodycompref-2.0.2/bodycompref/R/reference_values.R | 56 +++++----- bodycompref-2.0.2/bodycompref/R/sysdata.rda |binary bodycompref-2.0.2/bodycompref/build/vignette.rds |binary bodycompref-2.0.2/bodycompref/inst/doc/getting_started.R | 14 +- bodycompref-2.0.2/bodycompref/inst/doc/getting_started.Rmd | 4 bodycompref-2.0.2/bodycompref/inst/doc/getting_started.html | 13 +- bodycompref-2.0.2/bodycompref/man/bodycomp_reference.Rd | 2 bodycompref-2.0.2/bodycompref/man/percent_predicted.Rd | 2 bodycompref-2.0.2/bodycompref/man/reference_percentiles.Rd | 2 bodycompref-2.0.2/bodycompref/man/reference_values.Rd | 2 bodycompref-2.0.2/bodycompref/man/reference_z_scores.Rd | 2 bodycompref-2.0.2/bodycompref/tests/testthat/test-ref_values.R | 52 ++++++++- bodycompref-2.0.2/bodycompref/vignettes/getting_started.Rmd | 4 17 files changed, 134 insertions(+), 73 deletions(-)
Title: Spatial Empirical Dynamic Modeling
Description: Inferring causation from spatial cross-sectional data through empirical dynamic modeling (EDM), with methodological extensions including geographical convergent cross mapping from Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>, geographical cross mapping cardinality as introduced by Lyu et al. (2026) <doi:10.1080/13658816.2026.2687121>, as well as the spatial causality test following the approach of Herrera et al. (2016) <doi:10.1111/pirs.12144>, together with geographical pattern causality proposed in Zhang & Wang (2025) <doi:10.1080/13658816.2025.2581207>.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.12 dated 2026-04-05 and 1.13 dated 2026-09-09
spEDM-1.12/spEDM/man/figures/scpcm/fig3-1.png |only spEDM-1.13/spEDM/DESCRIPTION | 11 spEDM-1.13/spEDM/MD5 | 188 ++--- spEDM-1.13/spEDM/NAMESPACE | 56 - spEDM-1.13/spEDM/NEWS.md | 586 +++++++++--------- spEDM-1.13/spEDM/R/Agenerics.R | 26 spEDM-1.13/spEDM/R/RcppExports.R | 60 - spEDM-1.13/spEDM/R/detectThreads.R | 22 spEDM-1.13/spEDM/R/embedded.R | 108 +-- spEDM-1.13/spEDM/R/fnn.R | 98 +-- spEDM-1.13/spEDM/R/formatoutput.R | 502 +++++++-------- spEDM-1.13/spEDM/R/gccm.R | 207 +++--- spEDM-1.13/spEDM/R/gcmc.R | 223 +++--- spEDM-1.13/spEDM/R/globals.R | 10 spEDM-1.13/spEDM/R/gpc.R | 126 +-- spEDM-1.13/spEDM/R/ic.R | 96 +- spEDM-1.13/spEDM/R/internal_utility.R | 580 ++++++++--------- spEDM-1.13/spEDM/R/multiview.R | 98 +-- spEDM-1.13/spEDM/R/pc.R | 106 +-- spEDM-1.13/spEDM/R/scpcm.R | 202 +++--- spEDM-1.13/spEDM/R/sctest.R | 114 +-- spEDM-1.13/spEDM/R/simplex.R | 110 +-- spEDM-1.13/spEDM/R/slm.R | 124 +-- spEDM-1.13/spEDM/R/smap.R | 100 +-- spEDM-1.13/spEDM/R/zzz.R | 5 spEDM-1.13/spEDM/README.md | 145 ++-- spEDM-1.13/spEDM/inst/CITATION | 26 spEDM-1.13/spEDM/inst/doc/main1_pkgintro.Rmd | 404 ++++++------ spEDM-1.13/spEDM/inst/doc/main1_pkgintro.html | 77 +- spEDM-1.13/spEDM/inst/doc/main2_ssr.Rmd | 282 ++++---- spEDM-1.13/spEDM/inst/doc/main2_ssr.html | 38 - spEDM-1.13/spEDM/inst/doc/main3_gccm.Rmd | 46 - spEDM-1.13/spEDM/inst/doc/main3_gccm.html | 48 - spEDM-1.13/spEDM/inst/doc/main4_gpc.Rmd | 20 spEDM-1.13/spEDM/inst/doc/main4_gpc.html | 20 spEDM-1.13/spEDM/inst/doc/main5_gcmc.Rmd | 58 - spEDM-1.13/spEDM/inst/doc/main5_gcmc.html | 67 +- spEDM-1.13/spEDM/inst/doc/main6_scpcm.Rmd | 191 ++--- spEDM-1.13/spEDM/inst/doc/main6_scpcm.html | 226 +++--- spEDM-1.13/spEDM/inst/doc/si1_slm.Rmd | 378 +++++------ spEDM-1.13/spEDM/inst/doc/si1_slm.html | 64 - spEDM-1.13/spEDM/inst/doc/si2_sct.Rmd | 2 spEDM-1.13/spEDM/inst/doc/si2_sct.html | 2 spEDM-1.13/spEDM/man/detectThreads.Rd | 36 - spEDM-1.13/spEDM/man/embedded.Rd | 136 ++-- spEDM-1.13/spEDM/man/figures/gccm/fig1-1.png |binary spEDM-1.13/spEDM/man/figures/gcmc/fig1-1.png |binary spEDM-1.13/spEDM/man/figures/scpcm/fig2-1.png |binary spEDM-1.13/spEDM/man/figures/slm/sim_trispecies-1.png |binary spEDM-1.13/spEDM/man/figures/slm/slm1-1.png |binary spEDM-1.13/spEDM/man/figures/slm/slm2-1.png |binary spEDM-1.13/spEDM/man/figures/ssr/fig1-1.png |binary spEDM-1.13/spEDM/man/fnn.Rd | 182 ++--- spEDM-1.13/spEDM/man/gccm.Rd | 258 +++---- spEDM-1.13/spEDM/man/gcmc.Rd | 214 +++--- spEDM-1.13/spEDM/man/gpc.Rd | 275 ++++---- spEDM-1.13/spEDM/man/ic.Rd | 181 ++--- spEDM-1.13/spEDM/man/multiview.Rd | 207 +++--- spEDM-1.13/spEDM/man/pc.Rd | 215 +++--- spEDM-1.13/spEDM/man/sc.test.Rd | 195 +++-- spEDM-1.13/spEDM/man/scpcm.Rd | 270 ++++---- spEDM-1.13/spEDM/man/simplex.Rd | 200 +++--- spEDM-1.13/spEDM/man/slm.Rd | 234 +++---- spEDM-1.13/spEDM/man/smap.Rd | 212 +++--- spEDM-1.13/spEDM/src/CppGridUtils.cpp | 327 ++++++---- spEDM-1.13/spEDM/src/CppGridUtils.h | 48 + spEDM-1.13/spEDM/src/DelayedMI.cpp |only spEDM-1.13/spEDM/src/Forecast4Grid.cpp | 46 - spEDM-1.13/spEDM/src/Forecast4Grid.h | 26 spEDM-1.13/spEDM/src/GCCM4Grid.cpp | 16 spEDM-1.13/spEDM/src/GCCM4Grid.h | 12 spEDM-1.13/spEDM/src/GridExp.cpp | 318 ++++++++- spEDM-1.13/spEDM/src/LatticeExp.cpp | 8 spEDM-1.13/spEDM/src/Makevars | 4 spEDM-1.13/spEDM/src/Makevars.win | 4 spEDM-1.13/spEDM/src/RcppExports.cpp | 130 ++- spEDM-1.13/spEDM/src/SCPCM4Grid.cpp | 66 +- spEDM-1.13/spEDM/src/SCPCM4Grid.h | 22 spEDM-1.13/spEDM/src/SGC4Grid.cpp | 12 spEDM-1.13/spEDM/src/SGC4Grid.h | 4 spEDM-1.13/spEDM/vignettes/main1_pkgintro.Rmd | 404 ++++++------ spEDM-1.13/spEDM/vignettes/main1_pkgintro.Rmd.orig | 258 ++++--- spEDM-1.13/spEDM/vignettes/main2_ssr.Rmd | 282 ++++---- spEDM-1.13/spEDM/vignettes/main2_ssr.Rmd.orig | 176 ++--- spEDM-1.13/spEDM/vignettes/main3_gccm.Rmd | 46 - spEDM-1.13/spEDM/vignettes/main3_gccm.Rmd.orig | 364 +++++------ spEDM-1.13/spEDM/vignettes/main4_gpc.Rmd | 20 spEDM-1.13/spEDM/vignettes/main4_gpc.Rmd.orig | 356 +++++----- spEDM-1.13/spEDM/vignettes/main5_gcmc.Rmd | 58 - spEDM-1.13/spEDM/vignettes/main5_gcmc.Rmd.orig | 436 ++++++------- spEDM-1.13/spEDM/vignettes/main6_scpcm.Rmd | 191 ++--- spEDM-1.13/spEDM/vignettes/main6_scpcm.Rmd.orig | 335 ++++------ spEDM-1.13/spEDM/vignettes/si1_slm.Rmd | 378 +++++------ spEDM-1.13/spEDM/vignettes/si1_slm.Rmd.orig | 318 ++++----- spEDM-1.13/spEDM/vignettes/si2_sct.Rmd | 2 spEDM-1.13/spEDM/vignettes/si2_sct.Rmd.orig | 230 +++---- 96 files changed, 6992 insertions(+), 6572 deletions(-)
Title: Methods for Unweighted and Weighted Network Integration
Description: Implementation of network integration approaches
comprising unweighted and weighted integration methods. Unweighted integration
is performed considering the average, per-edge average, maximum and minimum of
networks edges. Weighted integration takes into account a weight for each
network during the fusion process, where the weights express
the ''predictiveness strength'' of each network considering a specific predictive
task. Weights can be learned using a machine learning algorithm able to associate
the weights to the assessment of the accuracy of the learning algorithm
trained on the network itself. The implemented methods can be applied to
effectively integrate different biological networks modelling a wide range
of problems in bioinformatics (e.g. disease gene prioritization, protein
function prediction, drug repurposing, clinical outcome prediction).
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between NetInt versions 1.0.1 dated 2025-05-03 and 1.0.2 dated 2026-09-09
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Calculate Hopkins Statistic for Clustering
Description: Calculate Hopkins statistic to assess the clusterability of data. See Wright (2023) <doi:10.32614/RJ-2022-055>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between hopkins versions 1.1 dated 2023-08-20 and 1.2 dated 2026-09-09
DESCRIPTION | 25 ++-- MD5 | 27 ++-- NAMESPACE | 20 +-- NEWS.md | 6 - R/hopkins.R | 76 +++++++------ build/vignette.rds |binary inst/doc/hopkins_optimization.R | 142 ++++++++++++------------- inst/doc/hopkins_optimization.html | 1 inst/doc/hopkins_protocol.R | 2 inst/doc/hopkins_protocol.Rmd | 17 ++- inst/doc/hopkins_protocol.html | 43 +++++-- man/hopkins.Rd | 206 ++++++++++++++++++------------------- man/hopkins.pval.Rd | 72 ++++++------ vignettes/hopkins_protocol.Rmd | 17 ++- vignettes/hopkins_protocol.html |only 15 files changed, 347 insertions(+), 307 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.4.0 dated 2026-08-05 and 1.5.0 dated 2026-09-09
DESCRIPTION | 33 MD5 | 151 +- NAMESPACE | 13 NEWS.md | 38 R/btw_chat_history_store.R |only R/btw_client_app.R | 1117 +---------------- R/btw_client_app_core.R |only R/btw_client_app_legacy.R |only R/btw_client_app_slash_commands.R |only R/btw_client_app_v05.R |only R/btw_project_db.R |only R/btw_this.R | 54 R/tool-agent-subagent.R | 172 ++ R/tool-cran.R | 262 +++ R/tool-docs-news.R | 85 - R/tool-docs.R | 24 R/tool-env-df.R | 16 R/tool-env.R | 4 R/tool-files-edit.R | 9 R/tool-files-list.R | 4 R/tool-files-patch.R | 7 R/tool-files-read.R | 14 R/tool-files-replace.R | 9 R/tool-files-search.R | 547 +++++++- R/tool-files-write.R | 29 R/tool-git.R | 42 R/tool-github.R | 8 R/tool-ide.R | 4 R/tool-pkg-covr.R | 2 R/tool-pkg-devtools.R | 8 R/tool-pkg-src.R | 18 R/tool-result.R | 17 R/tool-run.R | 107 + R/tool-session-package-installed.R | 2 R/tool-sessioninfo.R | 5 R/tool-skills.R | 359 +++-- R/tool-web.R | 7 R/utils-ellmer.R | 115 - R/utils-md.R | 74 + R/utils-shinychat.R |only R/zzz.R | 15 exec/btw.R | 193 ++ inst/cli-skill/r-btw-cli/SKILL.md | 3 inst/icons/construction.svg | 2 inst/icons/edit-document.svg |only inst/icons/find-replace.svg |only inst/icons/quick-reference.svg | 2 inst/js/app/btw_app.css | 46 inst/js/app/btw_app.js | 41 man/btw_client.Rd | 15 man/btw_skill_install_github.Rd | 2 man/btw_skill_install_package.Rd | 2 man/btw_skill_install_project.Rd | 2 man/btw_skill_prompt.Rd |only man/btw_skills_register_slash_commands.Rd |only man/btw_this.character.Rd | 10 man/btw_tool_cran_package.Rd | 3 man/btw_tool_cran_search.Rd | 3 man/btw_tool_cran_versions.Rd |only man/btw_tool_docs_package_news.Rd | 18 man/btw_tool_skill.Rd | 8 man/btw_tools.Rd | 1 tests/testthat/_snaps/btw_client.md | 4 tests/testthat/_snaps/btw_client_app_slash_commands.md |only tests/testthat/_snaps/tool-env-df.md | 3 tests/testthat/_snaps/tool_skills.md | 28 tests/testthat/_snaps/utils-md.md | 14 tests/testthat/_snaps/utils-shinychat.md |only tests/testthat/helpers.R | 61 tests/testthat/test-btw-project-db.R |only tests/testthat/test-btw_chat_history_store.R |only tests/testthat/test-btw_client_app.R | 96 + tests/testthat/test-btw_client_app_slash_commands.R |only tests/testthat/test-btw_this.R | 39 tests/testthat/test-cli.R | 195 ++ tests/testthat/test-deprecated.R | 2 tests/testthat/test-tool-agent-subagent.R | 139 ++ tests/testthat/test-tool-cran.R | 135 ++ tests/testthat/test-tool-docs-news.R | 41 tests/testthat/test-tool-files-read.R | 4 tests/testthat/test-tool-files-search.R |only tests/testthat/test-tool-pkg-src.R | 11 tests/testthat/test-tool-run.R | 94 + tests/testthat/test-tool_skills.R | 260 +++ tests/testthat/test-utils-md.R | 35 tests/testthat/test-utils-shinychat.R |only 86 files changed, 3104 insertions(+), 1779 deletions(-)
Title: Estimating Propensity Scores (PS), PS-Based Weights, and Effects
Description: Toolbox that provides a streamlined, end-to-end workflow for propensity
score analysis in generating real-world evidence from real-world data.
The package covers the full analytic pipeline - from estimating propensity scores
via logistic regression, to calculating weights or creating a matched cohort,
to generating publication-ready Table 1s with standardized mean
differences and weighted balance diagnostics. It also estimates incidence rates,
rate differences and rate ratios, hazard ratios, risks, risk ratios, and risk
differences, including competing-risk methods and optionally stratified hazard
models. Many functions can write formatted 'Excel' reports with method documentation,
making results immediately shareable with collaborators and stakeholders. Methods
are based on Rosenbaum and Rubin (1983)
<doi:10.1093/biomet/70.1.41>, Austin (2011) <doi:10.1080/00273171.2011.568786>,
and Desai et al. (2017) <doi:10.1097/EDE.0000000000000595>.
Author: Hanseul Cho [aut, cre],
Georg Hahn [aut],
Janinne Ortega-Montiel [aut],
Julie Paik [aut],
Elisabetta Patorno [aut]
Maintainer: Hanseul Cho <hanseul0618@gmail.com>
Diff between rwetools versions 0.4.0 dated 2026-08-01 and 0.5.0 dated 2026-09-09
rwetools-0.4.0/rwetools/R/effect_measures.R |only rwetools-0.4.0/rwetools/man/add_readme_sheet.Rd |only rwetools-0.4.0/rwetools/man/calc_c_statistic.Rd |only rwetools-0.4.0/rwetools/man/canonize_levels.Rd |only rwetools-0.4.0/rwetools/man/combine_named_list.Rd |only rwetools-0.4.0/rwetools/man/create_love_plot.Rd |only rwetools-0.4.0/rwetools/man/dot-is_balanced.Rd |only rwetools-0.4.0/rwetools/man/dot-plot_ps_distribution_set.Rd |only rwetools-0.4.0/rwetools/man/dot-trim_ps.Rd |only rwetools-0.4.0/rwetools/man/dot-truncate_ps_weights.Rd |only rwetools-0.4.0/rwetools/man/estimate_hr_ir.Rd |only rwetools-0.4.0/rwetools/man/estimate_rr_rd.Rd |only rwetools-0.4.0/rwetools/man/fmt_mean_sd.Rd |only rwetools-0.4.0/rwetools/man/fmt_n_pct.Rd |only rwetools-0.4.0/rwetools/man/fmt_num.Rd |only rwetools-0.4.0/rwetools/man/fmt_pct.Rd |only rwetools-0.4.0/rwetools/man/get_var_types.Rd |only rwetools-0.4.0/rwetools/man/get_weighted_prop.Rd |only rwetools-0.4.0/rwetools/man/get_weighted_stats.Rd |only rwetools-0.4.0/rwetools/man/levels_excl_zero.Rd |only rwetools-0.4.0/rwetools/man/process_catbin_direct.Rd |only rwetools-0.4.0/rwetools/man/summarize_ps_by_group.Rd |only rwetools-0.4.0/rwetools/tests/testthat/test-estimate_hr_ir.R |only rwetools-0.4.0/rwetools/tests/testthat/test-estimate_rr_rd.R |only rwetools-0.5.0/rwetools/DESCRIPTION | 15 rwetools-0.5.0/rwetools/MD5 | 84 rwetools-0.5.0/rwetools/NAMESPACE | 5 rwetools-0.5.0/rwetools/NEWS.md | 78 rwetools-0.5.0/rwetools/R/build_table1.R | 284 +-- rwetools-0.5.0/rwetools/R/create_psweights.R | 466 +++-- rwetools-0.5.0/rwetools/R/estimate_hr.R |only rwetools-0.5.0/rwetools/R/estimate_ir.R |only rwetools-0.5.0/rwetools/R/estimate_ps.R | 75 rwetools-0.5.0/rwetools/R/estimate_risk.R |only rwetools-0.5.0/rwetools/R/helpers_effect_engines.R | 274 --- rwetools-0.5.0/rwetools/R/helpers_effect_measures.R | 847 +++------- rwetools-0.5.0/rwetools/R/helpers_exposure.R |only rwetools-0.5.0/rwetools/R/helpers_ps_psweights.R | 42 rwetools-0.5.0/rwetools/R/helpers_table1.R | 91 - rwetools-0.5.0/rwetools/man/build_table1.Rd | 158 + rwetools-0.5.0/rwetools/man/create_ps_fs_weights.Rd | 127 - rwetools-0.5.0/rwetools/man/create_ps_matched_cohort.Rd | 192 +- rwetools-0.5.0/rwetools/man/estimate_hr.Rd |only rwetools-0.5.0/rwetools/man/estimate_ir.Rd |only rwetools-0.5.0/rwetools/man/estimate_ps.Rd | 6 rwetools-0.5.0/rwetools/man/estimate_risk.Rd |only rwetools-0.5.0/rwetools/tests/testthat/fixtures/make_v030_fixtures.R | 7 rwetools-0.5.0/rwetools/tests/testthat/helper.R | 18 rwetools-0.5.0/rwetools/tests/testthat/test-build_table1.R | 64 rwetools-0.5.0/rwetools/tests/testthat/test-create_ps_fs_weights.R | 48 rwetools-0.5.0/rwetools/tests/testthat/test-create_ps_matched_cohort.R | 108 + rwetools-0.5.0/rwetools/tests/testthat/test-create_psweights.R | 47 rwetools-0.5.0/rwetools/tests/testthat/test-estimate_hr.R |only rwetools-0.5.0/rwetools/tests/testthat/test-estimate_ir.R |only rwetools-0.5.0/rwetools/tests/testthat/test-estimate_ps.R | 31 rwetools-0.5.0/rwetools/tests/testthat/test-estimate_risk.R |only rwetools-0.5.0/rwetools/tests/testthat/test-finegray.R | 16 rwetools-0.5.0/rwetools/tests/testthat/test-helpers-engines.R | 124 - rwetools-0.5.0/rwetools/tests/testthat/test-irr.R | 37 rwetools-0.5.0/rwetools/tests/testthat/test-matched-block-guards.R |only rwetools-0.5.0/rwetools/tests/testthat/test-matched-cluster-se.R |only 61 files changed, 1652 insertions(+), 1592 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.3.0 dated 2026-08-31 and 1.4.0 dated 2026-09-09
DESCRIPTION | 14 MD5 | 49 - NAMESPACE | 7 NEWS.md | 22 R/KorAPCorpusStats.R | 31 R/KorAPQuery.R | 32 R/association-scores.R | 70 + R/cacheAs.R |only R/collocationAnalysis.R | 141 +++ R/collocationScoreQuery.R | 24 R/misc.R | 111 ++- R/textMetadata.R | 20 man/association-score-functions.Rd | 45 + man/blessCacheAs.Rd |only man/cacheAs.Rd |only man/cacheAsInfo.Rd |only man/collocationAnalysis-KorAPConnection-method.Rd | 45 + man/collocationScoreQuery-KorAPConnection-method.Rd | 5 man/corpusStats-KorAPConnection-method.Rd | 4 man/frequencyQuery-KorAPConnection-method.Rd | 3 man/textMetadata-KorAPConnection-method.Rd | 4 man/withCachedResults.Rd |only tests/testthat/test-association-score-functions.R | 31 tests/testthat/test-cache-as.R |only tests/testthat/test-collocation-cache-parameters.R |only tests/testthat/test-collocations.R | 36 - tests/testthat/test-common-affixes.R |only tests/testthat/test-readme-against-llm.R | 707 ++++++++++++++------ tests/testthat/test-readme-consistency.R |only tests/testthat/test-snippet-parsing.R |only tests/testthat/test-vc-labels.R |only 31 files changed, 1126 insertions(+), 275 deletions(-)
Title: An IMAP Client for R
Description: A session-based IMAP client that implements the full command sets of
the IMAP4rev2 (RFC 9051) and IMAP4rev1 (RFC 3501) protocols, along with the
optional extensions registered with the Internet Assigned Numbers
Authority, allowing virtually all e-mail operations to be performed from
within R, paving the way for e-mail data analysis.
Author: Allan Quadros [aut, cre] ,
Paul Smith [ctb],
Kurt Hornik [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 1.4.0 dated 2026-07-28 and 3.0.0 dated 2026-09-09
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Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.4 dated 2025-12-18 and 0.1.5 dated 2026-09-09
DESCRIPTION | 13 ++++-- MD5 | 73 +++++++++++++++++++++----------------- NEWS.md | 28 ++++++++++++++ R/MTDest-methods.R | 3 + R/MTDest.R | 2 - R/MTDmodel-methods.R | 4 ++ R/checkSample.R | 1 R/countsTab.R | 3 + R/empirical_probs.R | 3 + R/hdMTD-methods.R | 2 + R/hdMTD.R | 9 +++- R/hdMTD_BIC.R | 14 ++++++- R/hdMTD_CUT.R | 13 +++++- R/hdMTD_FS.R | 5 +- R/hdMTD_FSC.R | 67 ++++++++++++++++++++++++----------- R/oscillation.R | 3 + R/tempdata.R | 8 ++-- build |only inst |only man/MTD-methods.Rd | 17 +++++++- man/MTDest-methods.Rd | 14 ++++++- man/MTDest.Rd | 2 - man/countsTab.Rd | 3 + man/empirical_probs.Rd | 3 + man/hdMTD-methods.Rd | 11 ++++- man/hdMTD.Rd | 4 +- man/hdMTD_BIC.Rd | 16 +++++++- man/hdMTD_CUT.Rd | 15 ++++++- man/hdMTD_FS.Rd | 5 +- man/hdMTD_FSC.Rd | 45 ++++++++++++++++------- man/oscillation.Rd | 3 + man/tempdata.Rd | 76 ++++++++++++++++++++-------------------- tests/testthat/test-hdMTD.R | 14 ++++++- tests/testthat/test-hdMTD_FS.R | 9 ++++ tests/testthat/test-hdMTD_FSC.R | 15 +++++++ vignettes |only 36 files changed, 359 insertions(+), 144 deletions(-)
Title: DCC Models with GARCH and GARCH-MIDAS Specifications in the
Univariate Step, RiskMetrics, Moving Covariance and Scalar and
Diagonal BEKK Models
Description: Estimates a variety of Dynamic Conditional Correlation (DCC) models. More in detail, the 'dccmidas' package allows the estimation of the corrected DCC (cDCC) of Aielli (2013) <doi:10.1080/07350015.2013.771027>, the DCC-MIDAS of Colacito et al. (2011) <doi:10.1016/j.jeconom.2011.02.013>, the Asymmetric DCC of Cappiello et al. <doi:10.1093/jjfinec/nbl005>, and the Dynamic Equicorrelation (DECO) of Engle and Kelly (2012) <doi:10.1080/07350015.2011.652048>. 'dccmidas' offers the possibility of including standard GARCH <doi:10.1016/0304-4076(86)90063-1>, GARCH-MIDAS <doi:10.1162/REST_a_00300> and Double Asymmetric GARCH-MIDAS <doi:10.1016/j.econmod.2018.07.025> models in the univariate estimation. Moreover, also the scalar and diagonal BEKK <doi:10.1017/S0266466600009063> models can be estimated. Finally, the package calculates also the var-cov matrix under two non-parametric models: the Moving Covariance and the RiskMetrics specifications.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between dccmidas versions 0.1.2 dated 2024-02-21 and 0.1.3 dated 2026-09-09
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS.md | 4 + R/functions.R | 115 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary inst/CITATION | 2 man/bekk_fit.Rd | 2 man/cov_eval.Rd | 2 man/dcc_fit.Rd | 19 ++++---- man/plot_dccmidas.Rd | 2 man/riskmetrics_mat.Rd | 22 +++++++++ 11 files changed, 132 insertions(+), 64 deletions(-)
Title: Compute Moments Related to Beta-Wishart and Inverse Beta-Wishart
Distributions
Description: Provides functions for computing moments and coefficients related to the Beta-Wishart and Inverse Beta-Wishart distributions.
It includes functions for calculating the expectation of matrix-valued functions of the Beta-Wishart distribution,
coefficient matrices C_k and H_k, expectation of matrix-valued functions of the inverse Beta-Wishart distribution,
and coefficient matrices \tilde{C}_k and \tilde{H}_k. For more details, refer Hillier and Kan (2024) <https://www-2.rotman.utoronto.ca/~kan/papers/wishmom.pdf>,
"On the Expectations of Equivariant Matrix-valued Functions of Wishart and Inverse Wishart Matrices".
Author: Raymond Kan [aut, cre],
Preston Liang [aut]
Maintainer: Raymond Kan <raymond.kan@rotman.utoronto.ca>
Diff between wishmom versions 1.1.0 dated 2024-08-27 and 1.2.0 dated 2026-09-09
DESCRIPTION | 7 MD5 | 27 NEWS.md |only R/iwish_psr.R | 2 R/iwishmom.R | 14 R/iwishmom_sym.R | 2 R/wishmom.R | 4 R/wishmom_sym.R | 19 build/vignette.rds |binary inst/doc/wishmom_vignettes.Rmd | 2303 +++++++++++++++++++--------------------- inst/doc/wishmom_vignettes.html | 1898 ++++++++++++++++++++------------ man/iwish_psr.Rd | 2 man/iwishmom.Rd | 7 man/wishmom_sym.Rd | 4 vignettes/wishmom_vignettes.Rmd | 2303 +++++++++++++++++++--------------------- 15 files changed, 3508 insertions(+), 3084 deletions(-)
Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage
Priors
Description: Efficient variational inference methods for fully Bayesian univariate
and multivariate Gaussian and t-process regression models. Hierarchical shrinkage priors,
including the triple gamma prior, are used for effective variable selection and
covariance shrinkage in high-dimensional settings. The package leverages normalizing
flows to approximate complex posterior distributions. For details on implementation,
see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkGPR versions 2.0.0 dated 2026-03-30 and 2.1.0 dated 2026-09-09
DESCRIPTION | 9 MD5 | 55 ++-- NAMESPACE | 2 NEWS.md | 6 R/GPR_class.R | 4 R/IAF.R |only R/MVGPR_class.R | 5 R/NSF.R |only R/kernel_funcs.R | 178 +++++++------- R/pred_functions.R | 5 R/simGPR.R | 452 +++++++++++++++++++------------------- man/LPDS.Rd | 100 ++++---- man/calc_pred_moments.Rd | 122 +++++----- man/eval_pred_dens.Rd | 118 ++++----- man/gen_posterior_samples.Rd | 136 +++++------ man/iaf.Rd |only man/kernel_functions.Rd | 160 ++++++------- man/load_shrinkGPR.Rd | 100 ++++---- man/masked_linear.Rd |only man/nsf_cl.Rd |only man/predict.shrinkGPR.Rd | 96 ++++---- man/save_shrinkGPR.Rd | 106 ++++---- man/shrinkGPR.Rd | 406 +++++++++++++++++----------------- man/shrinkTPR.Rd | 406 +++++++++++++++++----------------- man/simGPR.Rd | 176 +++++++------- tests/testthat.R | 24 +- tests/testthat/Rplots.pdf |binary tests/testthat/test_shrinkGPR.R | 2 tests/testthat/test_shrinkMVGPR.R | 2 tests/testthat/test_shrinkMVTPR.R | 2 tests/testthat/test_shrinkTPR.R | 2 31 files changed, 1346 insertions(+), 1328 deletions(-)
More information about PricingBandits at CRAN
Permanent link
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Uses similarity graphs to estimate change-points and their p-values. The default data-level interface constructs a k-MST with k=floor(sqrt(N)) and reports the max-type scan. The generalized, original, and weighted scans remain available explicitly.
Author: Hao Chen [aut, cre] ,
Nancy R. Zhang [aut],
Lynna Chu [aut],
Hoseung Song [aut]
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 1.0 dated 2020-09-24 and 1.1 dated 2026-09-09
DESCRIPTION | 27 ++++-- MD5 | 26 +++-- NAMESPACE | 5 - NEWS.md |only R/NNL.R | 11 +- R/canonical-interface.R |only R/gSeg.r | 140 ++++++++++++++++++++++++-------- R/gSeg_discrete.R | 209 +++++++++++++++++++++++++++++++++--------------- man/gSeg-package.Rd | 7 - man/gseg1.Rd | 15 +-- man/gseg1_data.Rd |only man/gseg1_discrete.Rd | 18 ++-- man/gseg2.Rd | 9 -- man/gseg2_data.Rd |only man/gseg2_discrete.Rd | 12 +- man/gseg_kmst.Rd |only tests |only 17 files changed, 325 insertions(+), 154 deletions(-)
Title: Adaptive Trial Designs for Survival and Binary Endpoints
Description: Implements Goldilocks adaptive trial designs for time-to-event and
fixed-time binary endpoints. Outcomes are generated with a piecewise
exponential model, with conjugate Gamma priors used for predictive
imputation. Final analyses may use log-rank, Cox, or restricted mean
survival time tests, Bayesian piecewise-exponential inference, frequentist
risk differences, or Bayesian beta-binomial inference. The method closely
follows Broglio and colleagues (2014)
<doi:10.1080/10543406.2014.888569> and supports simulation of design
operating characteristics.
Author: Graeme L. Hickey [aut, cre] ,
Ying Wan [aut],
Thevaa Chandereng [aut] ,
Becton, Dickinson and Company [cph],
Tim Kacprowski [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between goldilocks versions 0.6.0 dated 2026-07-29 and 1.0.0 dated 2026-09-09
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Title: Objective Bayesian Distribution Fitting
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation. The
reference-prior framework follows Bernardo (1979)
<doi:10.1111/j.2517-6161.1979.tb01066.x>.
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.2.2 dated 2026-08-29 and 0.2.3 dated 2026-09-09
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 12 +++++++++++ R/fitdistrBayes.R | 14 ++++++++---- README.md | 10 ++++++--- inst/examples/teaching.R | 2 - inst/examples/tutorial_fitdistrBayes_all_models.R | 6 ++--- man/fitdistrBayes.Rd | 8 +++++-- tests/tests_review_regressions.R | 24 ++++++++++++++++++++++ 9 files changed, 73 insertions(+), 25 deletions(-)
More information about epistandardiseR at CRAN
Permanent link
Title: Combined Cluster and Discriminant Analysis
Description: Implements the combined cluster and discriminant analysis method for finding homogeneous groups of data with known origin as described in Kovacs et. al (2014): Classification into homogeneous groups using combined cluster and discriminant analysis (CCDA). Environmental Modelling & Software. <doi:10.1016/j.envsoft.2014.01.010>.
Author: Solt Kovacs [aut],
Jozsef Kovacs [aut],
Peter Tanos [aut, cre]
Maintainer: Peter Tanos <tanospeter@gmail.com>
This is a re-admission after prior archival of version 1.1.1 dated 2019-10-02
Diff between ccda versions 1.1.1 dated 2019-10-02 and 1.2 dated 2026-09-09
DESCRIPTION | 19 ++++-- MD5 | 8 +- NAMESPACE | 18 ++--- R/ccda.main.R | 168 ++++++++++++++++++++++++++----------------------------- man/ccda.main.Rd | 87 ++++++++++++++-------------- 5 files changed, 153 insertions(+), 147 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.18.1 dated 2026-05-24 and 0.19.0 dated 2026-09-09
DESCRIPTION | 28 +++--- MD5 | 89 +++++++++---------- NAMESPACE | 11 +- NEWS.md | 24 ++++- R/bayesfactor.R | 30 +++--- R/bci.R | 46 ++++++++-- R/check_prior.R | 86 +++++++++++------- R/contr.equalprior.R | 8 + R/effective_sample.R | 53 +---------- R/p_to_bf.R | 141 ++++++++++++++++++++----------- R/print.R | 17 +++ R/print_html.R | 11 ++ R/print_md.R | 11 ++ R/reshape_iterations.R | 13 +- R/sexit.R | 61 ++++++++++--- R/utils_check_collinearity.R | 13 +- README.md | 30 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 54 +---------- man/bayesfactor.Rd | 2 man/bayesfactor_inclusion.Rd | 8 - man/bayesfactor_models.Rd | 8 - man/bayesfactor_parameters.Rd | 8 - man/bayesfactor_restricted.Rd | 8 - man/bayestestR-package.Rd | 2 man/bci.Rd | 23 +++-- man/check_prior.Rd | 27 +++-- man/ci.Rd | 12 +- man/contr.equalprior.Rd | 9 - man/distribution.Rd | 5 - man/effective_sample.Rd | 2 man/eti.Rd | 12 +- man/hdi.Rd | 12 +- man/p_to_bf.Rd | 86 +++++++++++------- man/reexports.Rd | 2 man/reshape_iterations.Rd | 2 man/sexit.Rd | 2 man/si.Rd | 12 +- man/spi.Rd | 12 +- tests/testthat/test-bayesfactor_models.R | 28 ++++++ tests/testthat/test-bci.R |only tests/testthat/test-ci.R | 25 ++++- tests/testthat/test-effective_sample.R | 45 +++++++++ tests/testthat/test-p_to_bf.R | 30 +++++- tests/testthat/test-rope_range.R | 34 ++++++- 46 files changed, 721 insertions(+), 421 deletions(-)
Title: Robust Supervised Hierarchical Identification of Single Cells
Description: Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, The Tumor Profiler Consortium , Daniel Stekhoven, Franziska Singer, scROSHI: robust supervised hierarchical identification of single cells, NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad058, <doi:10.1093/nargab/lqad058>.
Author: Lars Bosshard [aut] ,
Dominik Burri [aut, cre] ,
Michael Prummer [aut]
Maintainer: Dominik Burri <burri@nexus.ethz.ch>
Diff between scROSHI versions 1.0.0.0 dated 2023-01-10 and 1.0.0.1 dated 2026-09-09
DESCRIPTION | 31 ++++--- MD5 | 23 ++--- NAMESPACE | 16 +-- R/config.R | 4 R/data.R | 4 R/scROSHI-package.R | 2 README.md | 151 ++++++++++++++++++------------------ build |only man/config.Rd | 4 man/f_annot_ctgenes.Rd | 60 +++++++------- man/f_my_wilcox_test.Rd | 48 +++++------ man/scROSHI.Rd | 198 +++++++++++++++++++++++++----------------------- man/test_sce_data.Rd | 4 13 files changed, 283 insertions(+), 262 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Jinwoo Jeong [ctb],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 2.0.0 dated 2026-09-01 and 2.0.1 dated 2026-09-09
DESCRIPTION | 31 +++++++++++++++---------------- MD5 | 6 +++--- NEWS.md | 14 +++++--------- R/fit_cmdstan.R | 6 +++--- 4 files changed, 26 insertions(+), 31 deletions(-)
Title: Double Constrained Correspondence Analysis for Trait-Environment
Analysis in Ecology
Description: Double constrained correspondence analysis (dc-CA) analyzes
(multi-)trait (multi-)environment ecological data by using the 'vegan'
package and native R code. Throughout the two step algorithm of ter Braak
et al. (2018) is used. This algorithm combines and extends community-
(sample-) and species-level analyses, i.e. the usual community weighted
means (CWM)-based regression analysis and the species-level analysis of
species-niche centroids (SNC)-based regression analysis. The two steps use
canonical correspondence analysis to regress the abundance data on to the
traits and (weighted) redundancy analysis to regress the CWM of the
orthonormalized traits on to the environmental predictors. The function
dc_CA() has an option to divide the abundance data of a site by the site
total, giving equal site weights. This division has the advantage that the
multivariate analysis corresponds with an unweighted (multi-trait)
community-level analysis, instead of being weighted. The first step of
the al [...truncated...]
Author: Cajo J.F ter Braak [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between douconca versions 1.2.5.1 dated 2026-08-24 and 1.2.6 dated 2026-09-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/douconca.html | 2 +- inst/tinytest/test_anova.dcca.R | 17 ++++++++++++++--- inst/tinytest/test_anova.dccav.R | 17 ++++++++++++++--- 6 files changed, 42 insertions(+), 16 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre] ,
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.19.0 dated 2026-03-19 and 0.21.1 dated 2026-09-09
DESCRIPTION | 24 + MD5 | 182 +++++++------- NAMESPACE | 66 +++-- NEWS.md | 11 R/impute_xifti.R | 414 ++++++++++++++++++++++----------- R/load_surf.R | 4 R/make_xifti_components.R | 2 R/onAttach.R | 16 - R/platform.R |only R/rox_args_docs.R | 19 - R/select_xifti.R | 3 R/smooth_cifti.R | 58 ++-- R/smooth_gifti.R | 10 R/utils_color.R | 2 R/utils_volume.R | 66 ++--- R/view_comp.R | 2 R/view_xifti.R | 5 R/view_xifti_surface.R | 145 +++++++---- R/wb_cmd.R | 12 R/write_nifti.R | 119 ++++++++- build/vignette.rds |binary inst/doc/ciftiTools_vignette_mini.R | 12 inst/doc/ciftiTools_vignette_mini.Rmd | 12 inst/doc/ciftiTools_vignette_mini.html | 81 +++--- man/ROY_BIG_BL.Rd | 8 man/add_surf.Rd | 74 +++-- man/apply_parc.Rd | 50 +-- man/apply_platform_overrides.Rd |only man/apply_xifti.Rd | 38 +-- man/as.xifti.Rd | 14 - man/boundary_mask_surf.Rd | 26 +- man/check_render_backend.Rd |only man/ciftiTools.Rd | 3 man/combine_xifti.Rd | 38 +-- man/convert_xifti.Rd | 38 +-- man/edit_mask_surf.Rd | 26 +- man/even_vert_samp.Rd | 26 +- man/expand_color_pal.Rd | 8 man/faces_Param.Rd | 1 man/impute_xifti.Rd | 91 ++++--- man/info_cifti.Rd | 14 - man/is.cifti.Rd | 12 man/is.surf.Rd | 26 +- man/is_tahoe.Rd |only man/load_parc.Rd | 26 +- man/load_sub_parc.Rd | 12 man/load_surf.Rd | 44 +-- man/make_color_pal.Rd | 8 man/mask_Param_vertices.Rd | 1 man/mask_surf.Rd | 26 +- man/merge_xifti.Rd | 38 +-- man/move_to_mwall.Rd | 38 +-- man/move_to_submask.Rd | 38 +-- man/newdata_xifti.Rd | 38 +-- man/parc_add_subcortex.Rd | 12 man/parc_borders.Rd | 12 man/parc_vals_to_xifti.Rd | 12 man/platform.Rd |only man/read_cifti.Rd | 26 +- man/read_surf.Rd | 40 +-- man/read_xifti2.Rd | 14 - man/remap_cifti.Rd | 38 +-- man/remap_gifti.Rd | 6 man/remove_xifti.Rd | 38 +-- man/resample_cifti.Rd | 50 +-- man/resample_cifti_from_template.Rd | 38 +-- man/resample_gifti.Rd | 6 man/resample_surf.Rd | 26 +- man/rotate_surf.Rd | 26 +- man/scale_xifti.Rd | 38 +-- man/select_xifti.Rd | 42 +-- man/separate_cifti.Rd | 12 man/set_names_xifti.Rd | 38 +-- man/smooth_cifti.Rd | 56 ++-- man/smooth_gifti.Rd | 8 man/surfL_Param_optional.Rd | 5 man/surfR_Param_optional.Rd | 5 man/surf_area.Rd | 26 +- man/transform_xifti.Rd | 38 +-- man/use_color_pal.Rd | 8 man/vertices_Param.Rd | 1 man/view_comp.Rd | 10 man/view_surf.Rd | 36 +- man/view_xifti.Rd | 22 - man/view_xifti_surface.Rd | 10 man/view_xifti_volume.Rd | 10 man/write_cifti.Rd | 24 - man/write_metric_gifti.Rd | 12 man/write_subcort_nifti.Rd | 12 man/write_surf_gifti.Rd | 38 +-- man/write_xifti2.Rd | 12 tests/testthat/test-misc.R | 39 ++- tests/testthat/test-plotting_sub.R | 3 tests/testthat/test-web_render.R |only vignettes/ciftiTools_vignette_mini.Rmd | 12 95 files changed, 1654 insertions(+), 1234 deletions(-)
Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data. Streams vector operations (spatial transforms,
point-in-polygon and nearest-feature joins including a two-sided
grid-partitioned join, select-by-location, clip, erase, dissolve,
'rasterization', 'polygonization', and contouring) through 'sf', and runs
raster operations (zonal statistics, focal windows, terrain derivatives,
resample or 'reproject' warp, polygon masking, map algebra, and 'mosaicking')
in native C or over the tiled '.vec' format, one batch or tile at [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.11.8 dated 2026-07-30 and 0.12.0 dated 2026-09-09
DESCRIPTION | 6 MD5 | 98 NEWS.md | 3850 +++++++++-------- R/expr.R | 12 R/index.R | 53 R/spatial.R | 7105 ++++++++++++++++----------------- R/spatial_more.R | 3 R/spatial_topology.R | 5 R/write.R | 49 inst/AGENTS.md | 6 inst/doc/coverage-topology.html | 4 inst/doc/engine.Rmd | 16 inst/doc/engine.html | 21 inst/doc/formats.html | 8 inst/doc/geometry-expressions.html | 4 inst/doc/indexing.Rmd | 35 inst/doc/indexing.html | 52 inst/doc/joins.html | 4 inst/doc/large-data.html | 4 inst/doc/networks.html | 4 inst/doc/offload.html | 4 inst/doc/quickstart.html | 4 inst/doc/schema.html | 4 inst/doc/sdm.html | 4 inst/doc/spatial.html | 4 inst/doc/streaming-spatial.html | 4 inst/doc/string-ops.html | 4 man/append_vtr.Rd | 39 man/create_index.Rd | 21 man/has_index.Rd | 7 src/file_map.c |only src/file_map.h |only src/init.c | 5 src/r_bridge.h | 5 src/r_bridge_index.c | 24 src/scan.c | 118 src/tdc/VENDORED_FROM | 2 src/tdc/include/tdc/format.h | 36 src/tdc/include/tdc/stream.h | 62 src/tdc/src/api/stream_encode.c | 355 + src/vtr1_tdc.c | 149 src/vtr1_tdc.h | 47 src/vtr_append.c | 91 src/vtr_append.h | 13 src/vtri.c | 545 +- src/vtri.h | 172 tests/testthat/test-append-delete.R | 72 tests/testthat/test-index.R | 331 + tests/testthat/test-spatial-topology.R | 49 vignettes/engine.Rmd | 16 vignettes/indexing.Rmd | 35 51 files changed, 7593 insertions(+), 5968 deletions(-)
Title: Interface the 'xts' API via 'Rcpp'
Description: Access to some of the C level functions of the 'xts' package.
In its current state, the package is mostly a proof-of-concept to support
adding useful functions, and does not yet add any of its own.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppXts versions 0.0.6 dated 2022-11-01 and 0.0.7 dated 2026-09-09
RcppXts-0.0.6/RcppXts/src/Makevars |only RcppXts-0.0.6/RcppXts/src/Makevars.win |only RcppXts-0.0.7/RcppXts/ChangeLog | 42 +++++++++++++++++++++++++++++++++ RcppXts-0.0.7/RcppXts/DESCRIPTION | 15 +++++++---- RcppXts-0.0.7/RcppXts/MD5 | 12 +++------ RcppXts-0.0.7/RcppXts/README.md | 8 +++--- RcppXts-0.0.7/RcppXts/inst/NEWS.Rd | 9 +++++++ RcppXts-0.0.7/RcppXts/src/xtsMod.cpp | 2 - 8 files changed, 71 insertions(+), 17 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For users with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph] ,
Andy Jacobson [ctb] ,
Jason Riedy [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.7.0 dated 2022-08-25 and 3.8.0 dated 2026-09-09
DESCRIPTION | 30 ++++--- MD5 | 26 +++--- NEWS.md | 39 +++++++++ R/999.package.R | 4 - R/Matlab.R | 14 +-- R/readMat.R | 133 ++++++++++++++++++---------------- R/utils.R | 36 +++++++++ inst/mat-files/CharUINT16-wide.mat |only inst/mat-files/CharUTF16-wide.mat |only inst/mat-files/CharUTF8-multibyte.mat |only man/Matlab.Rd | 30 +++---- man/R.matlab-package.Rd | 4 - man/readMat.Rd | 7 - man/setOption.Matlab.Rd | 2 tests/readMat.R | 76 +++++++++++++++++++ tests/setFunction.R |only 16 files changed, 283 insertions(+), 118 deletions(-)
Title: Principal Surface Contour Biplots
Description: Fits principal surfaces, the two-dimensional generalisation of the
principal curves of Hastie and Stuetzle (1989)
<doi:10.1080/01621459.1989.10478797>, and displays them as biplots in which
each variable is read off the contour lines of its fitted surface coordinate
function. Sample predictivity, the proportion of a sample's squared length
that is reconstructed by the fitted surface, is reported as a per-sample
diagnostic of how well the surface represents the data.
Author: Raeesa Ganey [aut, cre, cph]
Maintainer: Raeesa Ganey <raeesa.ganey@wits.ac.za>
Diff between prinsurf versions 1.0 dated 2025-03-12 and 2.0 dated 2026-09-09
prinsurf-1.0/prinsurf/R/principal.surface.R |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.R |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.Rmd |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.html |only prinsurf-1.0/prinsurf/man/figures/3d_plot.png |only prinsurf-1.0/prinsurf/man/figures/README-example-1.png |only prinsurf-1.0/prinsurf/man/principal.surface.Rd |only prinsurf-1.0/prinsurf/vignettes/Principal_Surfaces.Rmd |only prinsurf-2.0/prinsurf/DESCRIPTION | 37 +++++++++++------ prinsurf-2.0/prinsurf/LICENSE | 4 - prinsurf-2.0/prinsurf/MD5 | 34 +++++++++------ prinsurf-2.0/prinsurf/NAMESPACE | 8 +++ prinsurf-2.0/prinsurf/NEWS.md |only prinsurf-2.0/prinsurf/R/diagnostics.R |only prinsurf-2.0/prinsurf/R/methods.R |only prinsurf-2.0/prinsurf/R/prinsurf.R |only prinsurf-2.0/prinsurf/R/psaxis.R |only prinsurf-2.0/prinsurf/README.md | 32 -------------- prinsurf-2.0/prinsurf/build/vignette.rds |binary prinsurf-2.0/prinsurf/inst/doc/contour-biplots.R |only prinsurf-2.0/prinsurf/inst/doc/contour-biplots.Rmd |only prinsurf-2.0/prinsurf/inst/doc/contour-biplots.html |only prinsurf-2.0/prinsurf/man/contour_predictive_error.Rd |only prinsurf-2.0/prinsurf/man/figures/logo.png |only prinsurf-2.0/prinsurf/man/fitted.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/plot.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/predict.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/predictivity.Rd |only prinsurf-2.0/prinsurf/man/prinsurf.Rd |only prinsurf-2.0/prinsurf/vignettes/contour-biplots.Rmd |only 30 files changed, 56 insertions(+), 59 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Jeremie Dubois-Lacoste [aut],
Leslie Perez Caceres [aut],
Thomas Stuetzle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 4.4.2 dated 2026-04-23 and 4.4.4 dated 2026-09-09
DESCRIPTION | 8 MD5 | 64 +-- NEWS.md | 16 R/irace-options.R | 2 R/parameters.R | 7 R/psRace.R | 10 R/race.R | 8 R/scenario.R | 8 R/version.R | 2 README.md | 3 build/partial.rdb |binary inst/doc/irace-package.Rnw | 4 inst/doc/irace-package.pdf |binary inst/examples/acotsp/target-runner | 3 inst/examples/julia |only inst/exdata/irace-acotsp.Rdata |binary inst/exdata/log-ablation.Rdata |binary inst/exdata/sann.rda |binary inst/templates/scenario.txt.tmpl | 3 man/defaultScenario.Rd | 2 man/irace_cmdline.Rd | 5 man/irace_license.Rd | 5 man/irace_version.Rd | 5 tests/testthat/test-bug-10.R | 3 tests/testthat/test-bug-90.R | 1 tests/testthat/test-bug-94.R |only tests/testthat/test-bug1col.R | 1 tests/testthat/test-psrace-nothing-to-run.R |only vignettes/examples.Rdata |binary vignettes/irace-acotsp-stdout.txt | 523 ++++++++++++++-------------- vignettes/irace-package.Rnw | 4 vignettes/irace-package.bib | 2 vignettes/section/irace-options.Rnw | 2 33 files changed, 378 insertions(+), 313 deletions(-)
Title: Access and Analyse UN Comtrade International Trade Data
Description: Download and analyse international merchandise and services trade
data from the United Nations Comtrade database
<https://comtradeplus.un.org/>. Retrieve bilateral trade flows, compute
trade analytics (revealed comparative advantage, trade concentration,
trade balance), and convert between commodity classifications
(Harmonised System 'HS', Standard International Trade Classification
'SITC', Broad Economic Categories 'BEC'). Covers 200+ reporter
countries, 60+ years of goods trade data (1962-present), and services
trade via Extended Balance of Payments Services ('EBOPS'). Works
without registration for basic queries. A free Application Programming
Interface ('API') key from
<https://comtradedeveloper.un.org/> unlocks full access.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between comtrade versions 0.1.0 dated 2026-04-13 and 0.1.1 dated 2026-09-09
DESCRIPTION | 20 ++++++++++------- MD5 | 42 ++++++++++++++++++------------------ NEWS.md | 17 ++++++++++++++ R/analytics.R | 51 +++++++++++++++++++++++++++++++++++--------- R/reference.R | 10 ++++++-- R/trade.R | 20 ++++++++++++----- R/utils.R | 24 +++++++++++++++++++- README.md | 15 ++++++++++-- man/comtrade-package.Rd | 3 +- man/ct_available.Rd | 3 +- man/ct_balance.Rd | 8 ++++++ man/ct_compare.Rd | 7 +++++- man/ct_growth.Rd | 6 ++++- man/ct_hhi.Rd | 6 +++-- man/ct_rca.Rd | 6 +++-- man/ct_reporters.Rd | 7 ++++-- man/ct_services.Rd | 4 ++- man/ct_share.Rd | 6 ++++- man/ct_top_partners.Rd | 6 ++++- man/ct_top_products.Rd | 6 ++++- man/ct_trade.Rd | 16 ++++++++++--- tests/testthat/test-utils.R | 33 ++++++++++++++++++++++++++++ 22 files changed, 246 insertions(+), 70 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data.
'caret' is a frequently used package for model training and prediction using machine learning.
CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'.
It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate
the performance of spatial prediction models and allows for spatial variable selection to selects
suitable predictor variables in view to their contribution to the spatial model performance.
CAST further includes functionality to estimate the (spatial) area of applicability of prediction models.
Methods are described in
Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>;
Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>;
Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>;
Milà et al. (2022) <doi:10.1111/2041-210X.13851>;
Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>;
L [...truncated...]
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Fabian Schumacher [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Jakub Nowosad [ctb],
Darius Goergen [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 1.1.1 dated 2026-07-15 and 1.1.2 dated 2026-09-09
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++-------- NEWS.md | 3 ++ inst/doc/cast01-CAST-intro.html | 4 +-- inst/doc/cast02-plotgeodist.html | 4 +-- inst/doc/cast03-CV.R | 39 +++++++++++++++++++------------- inst/doc/cast03-CV.Rmd | 43 ++++++++++++++++++++++-------------- inst/doc/cast03-CV.html | 45 +++++++++++++++++++------------------- inst/doc/cast04-AOA-tutorial.html | 4 +-- inst/doc/cast05-parallel.html | 4 +-- vignettes/cast03-CV.Rmd | 43 ++++++++++++++++++++++-------------- 11 files changed, 124 insertions(+), 91 deletions(-)
Title: (Bifactor) ESEM with Continuous (MLR) or Ordinal (WLSMV) Data
Description: Fits bifactor exploratory structural equation models (B-ESEM),
together with standard exploratory structural equation modeling (ESEM)
and confirmatory factor analysis (CFA), for continuous and
ordinal data. Continuous models use 'lavaan' native efa()
blocks with robust maximum likelihood (MLR) estimation.
Ordinal ESEM defaults to the 'lavaan' weighted least squares
mean- and variance-adjusted (WLSMV) estimator; ordinal B-ESEM uses a
custom diagonally weighted least squares (DWLS) path with polychoric
correlations from 'psych', rotation-delta standard errors via 'numDeriv',
and a mean- and variance-adjusted chi-square. Target, geomin, and oblimin
rotations use 'GPArotation'; the bifactor ESEM approach follows Morin,
Arens and Marsh (2016) <doi:10.1080/10705511.2014.961800>. Additional
features include multi-group measurement invariance (configural through
strict, with partial invariance), ESEM-within-CFA conversion, McDonald's
omega reliability suite, and the Mehrvarz and Rouder ( [...truncated...]
Author: Leon T. De Beer [aut, cre]
Maintainer: Leon T. De Beer <leondb@gmail.com>
Diff between bifactory versions 0.5.2 dated 2026-08-28 and 0.6.0 dated 2026-09-09
DESCRIPTION | 20 MD5 | 151 - NAMESPACE | 6 NEWS.md | 148 + R/align_loadings.R | 150 - R/alignment_check.R | 3 R/bifactor.R | 1148 ++++---- R/bifactory-package.R | 1 R/compare.R | 28 R/esem.R | 704 ++--- R/ewc.R | 211 - R/factor_scores.R | 995 +++---- R/invariance.R | 4146 +++++++++++++++++-------------- R/methods.R | 96 R/ordered_esem.R | 2812 ++++++++++----------- R/partial_invariance.R | 184 + R/pipeline.R | 2700 ++++++++++---------- R/reliability.R | 65 R/srmr_mplus.R |only inst/VALIDATION.md | 127 inst/templates/template.R | 479 +-- man/align_loadings.Rd | 51 man/alignment_check.Rd | 58 man/besem.Rd | 115 man/besem_ordered.Rd | 68 man/bifactory_template.Rd | 2 man/chisq_decomp.Rd | 6 man/coef.esem_fit.Rd | 4 man/compare_ewc.Rd | 2 man/compare_loadings.Rd | 14 man/compute_indices.Rd | 64 man/doc_estimator_paths.Rd | 56 man/esem.Rd | 115 man/esem_compare.Rd | 8 man/esem_invariance.Rd | 170 - man/esem_ordered.Rd | 75 man/ewc_syntax.Rd | 20 man/extract_mplus_loadings.Rd | 2 man/factor_scores.Rd | 44 man/find_ewc_referents.Rd | 2 man/fitMeasures.esem_fit.Rd | 2 man/fit_ewc.Rd | 16 man/fit_indices.Rd | 8 man/generate_mplus_besem_syntax.Rd | 2 man/generate_mplus_syntax.Rd | 2 man/lavaan_fit.Rd | 2 man/make_bifactor_target.Rd | 2 man/make_target.Rd | 21 man/modindices.esem_fit.Rd | 2 man/parameters.Rd | 12 man/parse_mplus_polychoric.Rd | 4 man/partial_invariance.Rd | 40 man/plot.alignment_check.Rd | 2 man/print.aligned_loadings.Rd | 2 man/print.alignment_check.Rd | 2 man/print.besem_fit.Rd | 2 man/print.esem_comparison.Rd | 2 man/print.esem_comparison_pipeline.Rd | 2 man/print.esem_fit.Rd | 2 man/print.esem_invariance.Rd | 2 man/print.esem_partial_invariance.Rd | 2 man/print.esem_spec.Rd | 2 man/print.esem_target.Rd | 2 man/print.reliability_indices.Rd | 2 man/refine_rotation.Rd | 16 man/run_comparison.Rd | 14 man/run_mplus_besem_invariance.Rd | 8 man/save_results.Rd | 20 man/specify_model.Rd | 20 man/summary.esem_fit.Rd | 2 tests/testthat/test-align_loadings.R |only tests/testthat/test-compare.R |only tests/testthat/test-console_colour.R |only tests/testthat/test-ewc.R |only tests/testthat/test-fit_retry.R |only tests/testthat/test-inv_notes.R |only tests/testthat/test-invariance.R |only tests/testthat/test-parallel_starts.R |only tests/testthat/test-parameters.R | 5 tests/testthat/test-partial_invariance.R |only tests/testthat/test-rd_markdown.R |only tests/testthat/test-reliability.R |only tests/testthat/test-srmr.R |only 83 files changed, 8136 insertions(+), 7136 deletions(-)
Title: Simple Power Simulations for ANOVAs
Description: A-priori power simulations and power-calculations for within, between and mixed ANOVAs based on target (partial) eta-squared values. Supports complex designs with more than two factors and their interactions with a single function call.
Author: Shaheed Azaad [aut, cre]
Maintainer: Shaheed Azaad <sazaad@uni-muenster.de>
Diff between anovapowersim versions 1.1.0 dated 2026-05-31 and 1.2.0 dated 2026-09-09
DESCRIPTION | 9 MD5 | 92 + NAMESPACE | 17 NEWS.md | 156 ++ R/anovapowersim-package.R | 23 R/f_to_pes.R |only R/power_curve.R | 1509 +++++++++++++++----------- R/power_effect.R |only R/power_effect_calc.R |only R/power_n_calc.R |only R/power_unbalanced.R |only R/print_methods.R | 414 +++++++ R/utils.R | 45 R/within_covariance.R |only README.md | 65 - build/vignette.rds |binary inst/CITATION |only inst/doc/anovapowersim.R | 37 inst/doc/anovapowersim.Rmd | 107 - inst/doc/anovapowersim.html | 166 +- inst/doc/calculated-power.R |only inst/doc/calculated-power.Rmd |only inst/doc/calculated-power.html |only inst/doc/comparison-with-gpower.R |only inst/doc/comparison-with-gpower.Rmd |only inst/doc/comparison-with-gpower.html |only inst/doc/covariance.R |only inst/doc/covariance.Rmd |only inst/doc/covariance.html |only inst/doc/fixed-sample-power.R |only inst/doc/fixed-sample-power.Rmd |only inst/doc/fixed-sample-power.html |only inst/doc/unbalanced-designs.R |only inst/doc/unbalanced-designs.Rmd |only inst/doc/unbalanced-designs.html |only man/anovapowersim-package.Rd | 24 man/cell_design.Rd |only man/design_term_means.Rd | 34 man/f_to_pes.Rd |only man/means_pattern.Rd |only man/power_achieved.Rd |only man/power_achieved_calc.Rd |only man/power_curve.Rd | 110 + man/power_n.Rd | 65 - man/power_n_calc.Rd |only man/power_sensitivity.Rd |only man/power_sensitivity_calc.Rd |only man/power_unbalanced.Rd |only man/print.anovapowersim_achieved_power.Rd |only man/print.anovapowersim_sensitivity.Rd |only man/print.anovapowersim_unbalanced_power.Rd |only man/simulate_design_dataset.Rd | 8 man/summary.anovapowersim_achieved_power.Rd |only man/summary.anovapowersim_sensitivity.Rd |only man/summary.anovapowersim_unbalanced_power.Rd |only man/unbalanced_covariance.Rd |only man/within_covariance.Rd |only tests/testthat/_snaps |only tests/testthat/helper-covariance.R |only tests/testthat/test-calibration-scale.R |only tests/testthat/test-f_to_pes.R |only tests/testthat/test-means-pattern.R |only tests/testthat/test-power-effect-calc.R |only tests/testthat/test-power-effect.R |only tests/testthat/test-power-tail.R |only tests/testthat/test-power-unbalanced.R |only tests/testthat/test-power_curve.R | 777 ++++++++++++- tests/testthat/test-within_covariance.R |only vignettes/anovapowersim.Rmd | 107 - vignettes/calculated-power.Rmd |only vignettes/comparison-with-gpower.Rmd |only vignettes/covariance.Rmd |only vignettes/fixed-sample-power.Rmd |only vignettes/unbalanced-designs.Rmd |only 74 files changed, 2817 insertions(+), 948 deletions(-)
Title: Analysis of Event Data with Two Time Scales
Description: Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales. If covariates are available, estimate a proportional hazards model with such a two-dimensional baseline hazard.
Functions are provided to prepare the raw data for estimation, to fit the model and to plot the two-dimensional smooth hazard.
Extension to a competing risks model is implemented. For details about the method please refer to Carollo et al. (2025) <doi:10.1002/sim.10297>.
Author: Angela Carollo [aut, cre, cph] ,
Paul H.C. Eilers [aut],
Jutta Gampe [aut]
Maintainer: Angela Carollo <carollo@demogr.mpg.de>
Diff between TwoTimeScales versions 1.2.1 dated 2026-03-30 and 1.3.1 dated 2026-09-09
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++++------ NAMESPACE | 6 ++++++ NEWS.md | 9 +++++++++ R/boot_cuminc2ts.R |only R/competing_risks_methods.R | 3 ++- R/plot_boot_cuminc2ts.R |only R/predict_haz2ts_pointwise.R | 2 +- README.md | 8 +++++--- man/boot_cuminc2ts.Rd |only man/plot_boot_cuminc2ts.Rd |only 11 files changed, 39 insertions(+), 16 deletions(-)
Title: A Data Interface Between 'GAMS' and R
Description: Read, analyze, modify, and write 'GAMS' (General Algebraic
Modeling System) data. The main focus of 'gamstransfer' is the
highly efficient transfer of data with 'GAMS' <https://www.gams.com/>,
while keeping these operations as simple as possible for the user. The
transfer of data usually takes place via an intermediate GDX (GAMS Data
Exchange) file. Additionally, 'gamstransfer' provides utility
functions to get an overview of 'GAMS' data and to check its validity.
Author: Atharv Bhosekar [aut, cre],
GAMS Development Corp. [cph, fnd],
GAMS Software GmbH [cph, fnd]
Maintainer: Atharv Bhosekar <abhosekar@gams.com>
Diff between gamstransfer versions 3.0.8 dated 2026-01-09 and 3.0.9 dated 2026-09-09
gamstransfer-3.0.8/gamstransfer/src/gdx/src/rtl/p3platform.cpp |only gamstransfer-3.0.9/gamstransfer/DESCRIPTION | 10 gamstransfer-3.0.9/gamstransfer/LICENSE | 4 gamstransfer-3.0.9/gamstransfer/MD5 | 241 gamstransfer-3.0.9/gamstransfer/NAMESPACE | 20 gamstransfer-3.0.9/gamstransfer/NEWS.md | 86 gamstransfer-3.0.9/gamstransfer/R/Alias.R | 758 gamstransfer-3.0.9/gamstransfer/R/BaseAlias.R | 286 gamstransfer-3.0.9/gamstransfer/R/Container.R | 3539 +-- gamstransfer-3.0.9/gamstransfer/R/DomainViolation.R | 144 gamstransfer-3.0.9/gamstransfer/R/Equation.R | 1108 - gamstransfer-3.0.9/gamstransfer/R/Parameter.R | 674 gamstransfer-3.0.9/gamstransfer/R/RcppExports.R | 38 gamstransfer-3.0.9/gamstransfer/R/Set.R | 414 gamstransfer-3.0.9/gamstransfer/R/SpecialValues.R | 128 gamstransfer-3.0.9/gamstransfer/R/Super.R | 340 gamstransfer-3.0.9/gamstransfer/R/Symbol.R | 4208 ++-- gamstransfer-3.0.9/gamstransfer/R/UniverseAlias.R | 456 gamstransfer-3.0.9/gamstransfer/R/Variable.R | 1122 - gamstransfer-3.0.9/gamstransfer/R/gamstransfer-package.R | 12 gamstransfer-3.0.9/gamstransfer/R/symbolTypes.R | 120 gamstransfer-3.0.9/gamstransfer/R/utility.R | 62 gamstransfer-3.0.9/gamstransfer/README.md | 298 gamstransfer-3.0.9/gamstransfer/configure | 1 gamstransfer-3.0.9/gamstransfer/configure.ac | 1 gamstransfer-3.0.9/gamstransfer/man/Alias.Rd | 36 gamstransfer-3.0.9/gamstransfer/man/Container.Rd | 95 gamstransfer-3.0.9/gamstransfer/man/DomainViolation.Rd | 66 gamstransfer-3.0.9/gamstransfer/man/Equation.Rd | 40 gamstransfer-3.0.9/gamstransfer/man/Parameter.Rd | 40 gamstransfer-3.0.9/gamstransfer/man/Set.Rd | 38 gamstransfer-3.0.9/gamstransfer/man/SpecialValues.Rd | 56 gamstransfer-3.0.9/gamstransfer/man/UniverseAlias.Rd | 32 gamstransfer-3.0.9/gamstransfer/man/Variable.Rd | 38 gamstransfer-3.0.9/gamstransfer/man/dot-Symbol.Rd | 24 gamstransfer-3.0.9/gamstransfer/man/gamstransfer-package.Rd | 58 gamstransfer-3.0.9/gamstransfer/man/readGDX.Rd | 52 gamstransfer-3.0.9/gamstransfer/man/writeGDX.Rd | 82 gamstransfer-3.0.9/gamstransfer/src/Makevars.in | 2 gamstransfer-3.0.9/gamstransfer/src/Makevars.win | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/LICENSE | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/batchalloc.hpp | 14 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/datastorage.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/datastorage.hpp | 49 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/dblutil.cpp | 31 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/dblutil.hpp | 14 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsdata.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsdata.hpp | 10 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsobj.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsobj.hpp | 57 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsstrm.cpp | 43 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsstrm.hpp | 55 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strhash.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strhash.hpp | 141 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strindexbuf.hpp | 35 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strutilx.cpp | 564 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strutilx.hpp | 34 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/utils.cpp | 46 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/utils.hpp | 52 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdx.hpp | 51 gamstransfer-3.0.9/gamstransfer/src/gdx/src/global/delphitypes.hpp | 37 gamstransfer-3.0.9/gamstransfer/src/gdx/src/global/unit.h | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gxfile.cpp | 660 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gxfile.hpp | 42 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/dtoaLoc.h | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/math_p3.cpp | 312 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/math_p3.hpp | 17 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3io.cpp | 166 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3io.hpp | 21 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3platform.hpp | 79 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3process.cpp | 545 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3process.hpp | 32 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3utils.cpp | 1026 - gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3utils.hpp | 46 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/system_p3.cpp | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/system_p3.hpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/sysutils_p3.cpp | 491 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/sysutils_p3.hpp | 73 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/LICENSE | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/compress.c | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/crc32.c | 164 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/deflate.c | 145 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/deflate.h | 5 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzguts.h | 5 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzlib.c | 78 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzread.c | 293 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzwrite.c | 267 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/infback.c | 69 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inffast.c | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inffixed.h | 182 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inflate.c | 155 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inftrees.c | 143 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inftrees.h | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/trees.c | 24 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/uncompr.c | 62 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zconf.h | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zconf.h.in | 1095 - gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zlib.h | 260 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zutil.c | 84 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zutil.h | 82 gamstransfer-3.0.9/gamstransfer/src/utilities.hpp | 6 gamstransfer-3.0.9/gamstransfer/tests/testthat.R | 58 gamstransfer-3.0.9/gamstransfer/tests/testthat/data.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/diffile.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/empty.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.gms | 30 gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.lst | 62 gamstransfer-3.0.9/gamstransfer/tests/testthat/foo_1.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/gt.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/out.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_equation.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_parameter.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar_equation.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar_variable.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_set.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_variable.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_write.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/test-alias-family.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-container-methods.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-read.R | 9582 +++++----- gamstransfer-3.0.9/gamstransfer/tests/testthat/test-setrecords-and-super.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-symbol-methods.R |only 124 files changed, 17705 insertions(+), 14825 deletions(-)
Title: Download and Tidy Data from the 'OECD'
Description: Provides clean, tidy access to key economic indicators published
by the 'Organisation for Economic Co-operation and Development' ('OECD'),
covering GDP, CPI inflation, unemployment, tax revenue, government deficit,
health expenditure, education expenditure, income inequality, labour
productivity, and current account balance across all
38 'OECD' member countries. Data is downloaded from the 'OECD Data Explorer'
API <https://data-explorer.oecd.org> on first use and cached locally for
subsequent calls. Returns tidy long-format data frames ready for analysis
and visualisation.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readoecd versions 0.3.3 dated 2026-03-18 and 0.3.4 dated 2026-09-09
DESCRIPTION | 9 ++-- MD5 | 45 ++++++++++++------------ NEWS.md | 67 ++++++++++++++++++++++++++++++++++++- R/deficit.R | 2 - R/gdp.R | 2 - R/health.R | 4 +- R/labour.R | 2 - R/productivity.R | 29 ++++++++++++++-- R/tax.R | 19 +++++++--- R/trade.R | 2 - R/utils.R | 42 ++++++++++++++++++++--- man/readoecd-package.Rd | 1 tests/testthat/helper-oecd.R |only tests/testthat/test-cpi.R | 4 +- tests/testthat/test-deficit.R | 4 +- tests/testthat/test-education.R | 4 +- tests/testthat/test-gdp.R | 8 ++-- tests/testthat/test-health.R | 4 +- tests/testthat/test-inequality.R | 4 +- tests/testthat/test-productivity.R | 4 +- tests/testthat/test-tax.R | 4 +- tests/testthat/test-trade.R | 4 +- tests/testthat/test-unemployment.R | 14 +++---- tests/testthat/test-utils.R | 4 +- 24 files changed, 208 insertions(+), 74 deletions(-)
Title: Access 'European Central Bank' Data
Description: Provides clean, tidy access to statistical data published by the
'European Central Bank' ('ECB') via the 'ECB Data Portal' API
<https://data.ecb.europa.eu>. Covers policy interest rates, 'EURIBOR',
euro exchange rates, harmonised consumer price inflation ('HICP'), euro area
yield curves, the euro short-term rate ('ESTR'), monetary aggregates (M1,
M2, M3), mortgage and lending rates, GDP, unemployment, and government
debt-to-GDP. Each dataset has a dedicated function that abstracts away the
underlying 'SDMX' key structure, so users do not need to know series codes.
A generic fetcher is also provided for direct access to any of the 'ECB'
100-plus dataflows. Data is downloaded on first use and cached locally for
subsequent calls.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readecb versions 0.1.2 dated 2026-03-19 and 0.1.4 dated 2026-09-09
DESCRIPTION | 9 +- MD5 | 97 +++++++++++++++--------------- NEWS.md | 55 +++++++++++++++++ R/cache.R | 3 R/ecb_estr.R | 4 - R/ecb_euribor.R | 6 + R/ecb_exchange_rate.R | 17 ++++- R/ecb_gdp.R | 4 - R/ecb_get.R | 6 + R/ecb_government_debt.R | 4 - R/ecb_hicp.R | 11 ++- R/ecb_lending_rates.R | 4 - R/ecb_money_supply.R | 4 - R/ecb_mortgage_rates.R | 4 - R/ecb_policy_rates.R | 4 - R/ecb_unemployment.R | 4 - R/ecb_yield_curve.R | 6 + R/list_helpers.R | 4 - R/utils.R | 50 +++++++++++++-- README.md | 22 ++---- man/ecb_estr.Rd | 4 - man/ecb_euribor.Rd | 6 + man/ecb_exchange_rate.Rd | 6 + man/ecb_gdp.Rd | 4 - man/ecb_get.Rd | 6 + man/ecb_government_debt.Rd | 4 - man/ecb_hicp.Rd | 6 + man/ecb_lending_rates.Rd | 4 - man/ecb_money_supply.Rd | 4 - man/ecb_mortgage_rates.Rd | 4 - man/ecb_policy_rates.Rd | 4 - man/ecb_unemployment.Rd | 4 - man/ecb_yield_curve.Rd | 6 + man/list_ecb_dataflows.Rd | 4 - man/readecb-package.Rd | 1 tests/testthat/helper-ecb.R |only tests/testthat/test-ecb_estr.R | 4 - tests/testthat/test-ecb_euribor.R | 6 - tests/testthat/test-ecb_exchange_rate.R | 8 +- tests/testthat/test-ecb_gdp.R | 4 - tests/testthat/test-ecb_get.R | 2 tests/testthat/test-ecb_government_debt.R | 4 - tests/testthat/test-ecb_hicp.R | 6 - tests/testthat/test-ecb_lending_rates.R | 4 - tests/testthat/test-ecb_money_supply.R | 4 - tests/testthat/test-ecb_mortgage_rates.R | 4 - tests/testthat/test-ecb_policy_rates.R | 6 - tests/testthat/test-ecb_unemployment.R | 4 - tests/testthat/test-ecb_yield_curve.R | 6 - tests/testthat/test-list_helpers.R | 2 50 files changed, 307 insertions(+), 142 deletions(-)
Title: Download Data from the 'Office for National Statistics'
Description: Provides functions to download and tidy statistical data
published by the 'Office for National Statistics'
<https://www.ons.gov.uk>. Covers GDP, inflation (CPI, CPIH, RPI),
unemployment, employment, wages, trade, retail sales, house prices,
productivity, population, and public sector finances. Most series are
fetched from the 'ONS' website using its CSV time series endpoint.
House price data is sourced from 'HM Land Registry'
<https://www.gov.uk/government/organisations/land-registry>.
Data is cached locally between sessions.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between ons versions 0.1.3 dated 2026-03-18 and 0.1.4 dated 2026-09-09
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/ons_search.R | 1 + README.md | 25 ++++++++++++++----------- man/ons-package.Rd | 1 + 6 files changed, 31 insertions(+), 20 deletions(-)
Title: Inflation Adjustment for Historical Currency Values
Description: Convert historical monetary values into their present-day equivalents
using bundled CPI (Consumer Price Index) and GDP deflator data sourced from the
World Bank Development Indicators. Supports British pounds (GBP), Australian
dollars (AUD), US dollars (USD), Euro (EUR), Canadian dollars (CAD), Japanese
yen (JPY), Chinese yuan (CNY), Swiss francs (CHF), New Zealand dollars (NZD),
Indian rupees (INR), South Korean won (KRW), Brazilian reais (BRL), and
Norwegian krone (NOK). Currency codes and country names are both accepted as
input.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between inflateR versions 0.1.3 dated 2026-03-04 and 0.2.0 dated 2026-09-09
DESCRIPTION | 11 +- MD5 | 143 +++++++++++++++++++++----------------- NAMESPACE | 2 NEWS.md | 65 +++++++++++++++++ R/adjust.R | 96 +++++-------------------- R/adjust_real.R | 90 ++++-------------------- R/data.R | 102 +++++++++++++-------------- R/historical_real.R | 92 ++++-------------------- R/historical_value.R | 95 ++++--------------------- R/inflateR-package.R |only R/inflation_rate.R |only R/list_currencies.R |only R/utils.R |only README.md | 178 ++++++++++++++++++++++++++++++++---------------- data/aud_cpi.rda |binary data/aud_gdp_def.rda |binary data/brl_cpi.rda |binary data/brl_gdp_def.rda |binary data/cad_cpi.rda |binary data/cad_gdp_def.rda |binary data/chf_cpi.rda |binary data/chf_gdp_def.rda |binary data/cny_cpi.rda |binary data/cny_gdp_def.rda |binary data/eur_cpi.rda |binary data/eur_gdp_def.rda |binary data/inr_cpi.rda |binary data/inr_gdp_def.rda |binary data/jpy_cpi.rda |binary data/jpy_gdp_def.rda |binary data/krw_cpi.rda |binary data/krw_gdp_def.rda |binary data/nok_cpi.rda |binary data/nok_gdp_def.rda |binary data/nzd_cpi.rda |binary data/nzd_gdp_def.rda |binary data/uk_cpi.rda |binary data/uk_gdp_def.rda |binary data/usd_cpi.rda |binary data/usd_gdp_def.rda |binary inst/CITATION |only man/adjust_inflation.Rd | 22 ++++- man/adjust_real.Rd | 17 +++- man/aud_cpi.Rd | 4 - man/aud_gdp_def.Rd | 4 - man/brl_cpi.Rd | 6 - man/brl_gdp_def.Rd | 4 - man/cad_cpi.Rd | 4 - man/cad_gdp_def.Rd | 4 - man/chf_cpi.Rd | 4 - man/chf_gdp_def.Rd | 4 - man/cny_cpi.Rd | 4 - man/cny_gdp_def.Rd | 4 - man/eur_cpi.Rd | 4 - man/eur_gdp_def.Rd | 4 - man/historical_real.Rd | 19 ++++- man/historical_value.Rd | 21 ++++- man/inflateR-package.Rd |only man/inflation_rate.Rd |only man/inr_cpi.Rd | 4 - man/inr_gdp_def.Rd | 4 - man/jpy_cpi.Rd | 4 - man/jpy_gdp_def.Rd | 4 - man/krw_cpi.Rd | 4 - man/krw_gdp_def.Rd | 4 - man/list_currencies.Rd |only man/nok_cpi.Rd | 4 - man/nok_gdp_def.Rd | 4 - man/nzd_cpi.Rd | 4 - man/nzd_gdp_def.Rd | 4 - man/uk_cpi.Rd | 4 - man/uk_gdp_def.Rd | 4 - man/usd_gdp_def.Rd | 4 - tests |only 74 files changed, 507 insertions(+), 548 deletions(-)
Title: Compute Global Sensitivity Analysis Indices Using Optimal
Transport
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
Author: Leonardo Chiani [aut, cre, cph] ,
Emanuele Borgonovo [rev],
Elmar Plischke [rev],
Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Diff between gsaot versions 1.1.1 dated 2025-09-17 and 1.2.0 dated 2026-09-09
DESCRIPTION | 6 MD5 | 50 +++--- NAMESPACE | 1 NEWS.md | 18 ++ R/build_partition.R | 10 - R/check_solver_optns.R | 12 - R/gsaot_indices.R | 6 R/ot_indices.R | 21 +- R/ot_indices_1d.R | 4 R/plot_functions.R | 5 R/utils.R | 244 ++++++++++++++----------------- README.md | 37 ++-- build/partial.rdb |binary inst/doc/gaussian-model-sensitivity.html | 38 ++-- man/confint.gsaot_indices.Rd | 4 man/entropic_bound.Rd | 4 man/irrelevance_threshold.Rd | 14 + man/ot_indices.Rd | 13 - man/ot_indices_1d.Rd | 7 man/ot_indices_wb.Rd | 7 man/residual_gap.Rd |only src/sinkhorn.cpp | 73 +++++---- src/sinkhorn_stable.cpp | 35 ++-- tests |only 24 files changed, 331 insertions(+), 278 deletions(-)
Title: Access Carbon Market Data from Emissions Trading Systems and
Voluntary Registries
Description: Unified access to carbon market data from compliance
emissions trading systems ('EU ETS', 'UK ETS', 'RGGI', California
Cap-and-Trade) and voluntary carbon markets (Verra, Gold Standard,
American Carbon Registry, Climate Action Reserve, via the Berkeley
Voluntary Registry Offsets Database and the 'CarbonPlan' 'OffsetsDB'
API). Includes cross-market price data from the 'International
Carbon Action Partnership' ('ICAP') Allowance Price Explorer
<https://icapcarbonaction.com/en/ets-prices>, global carbon pricing
from the World Bank Carbon Pricing Dashboard
<https://carbonpricingdashboard.worldbank.org/>, and the historical
'RFF' World Carbon Pricing Database following Dolphin, Pollitt and
Newbery (2020) <doi:10.1038/s41597-022-01659-x>. Data is downloaded
from public sources on first use and cached locally.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between carbondata versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-09-09
DESCRIPTION | 11 MD5 | 70 +++--- NAMESPACE | 2 NEWS.md | 193 +++++++++++++++++ R/aggregators.R | 423 +++++++++++++++++++++++++++++++------- R/compliance.R | 111 +++++++-- R/euets.R | 275 +++++++++++++++++++----- R/markets.R | 18 - R/utils.R | 135 ++++++++++-- R/voluntary.R | 122 ++++++++-- inst |only man/carbondata-package.Rd | 1 man/co2_cad_trust.Rd | 8 man/co2_california_caps.Rd | 8 man/co2_california_prices.Rd | 8 man/co2_ecp_prices.Rd |only man/co2_euets_allocations.Rd | 18 + man/co2_euets_emissions.Rd | 17 + man/co2_euets_files.Rd | 8 man/co2_euets_installations.Rd | 21 + man/co2_euets_price.Rd | 8 man/co2_euets_surrendered.Rd | 8 man/co2_icap_prices.Rd | 23 +- man/co2_icap_systems.Rd |only man/co2_offsets_db.Rd | 30 ++ man/co2_rff_pricing.Rd | 31 ++ man/co2_rggi_allowances.Rd | 8 man/co2_rggi_state_proceeds.Rd | 8 man/co2_ukets.Rd | 8 man/co2_ukets_allocations.Rd | 8 man/co2_vrod.Rd | 18 + man/co2_world_bank.Rd | 31 ++ tests/testthat/test-aggregators.R | 84 +++++++ tests/testthat/test-compliance.R | 23 ++ tests/testthat/test-euets.R | 59 +++++ tests/testthat/test-utils.R | 112 ++++++++++ tests/testthat/test-voluntary.R | 31 ++ 37 files changed, 1627 insertions(+), 312 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, aut] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between bigalgebra versions 3.1.0 dated 2026-03-24 and 3.1.1 dated 2026-09-09
DESCRIPTION | 10 +++--- MD5 | 18 ++++++------ NEWS.md | 6 +++- README.md | 45 +++++++++++++++++++------------ build/vignette.rds |binary inst/doc/big-matrix-workflows.html | 32 +++++++++++----------- inst/doc/level-1-blas-style-helpers.html | 4 +- inst/doc/matrix-wrapper-helpers.html | 8 ++--- inst/doc/z_lapack-decompositions.html | 17 ++++++----- src/bigalgebra.cpp | 2 + 10 files changed, 80 insertions(+), 62 deletions(-)
Title: Download Australian Energy Market Operator Data
Description: Fetch Australian Energy Market Operator (AEMO)
public data from 'NEMweb' <http://nemweb.com.au> and the
Market Management System Data Model (MMSDM) historical
archive. Provides tidy access to 5-minute and 30-minute
wholesale electricity prices, regional demand, dispatch-unit
output, interconnector flows, rooftop photovoltaic generation,
generator bids, predispatch forecasts, frequency control
ancillary services markets, and gas market data across the
National Electricity Market (NEM) regions. Data is published
by AEMO under its Copyright Permissions Notice
<https://www.aemo.com.au/privacy-and-legal-notices/copyright-permissions>.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between aemo versions 0.4.1 dated 2026-05-27 and 0.4.2 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 16 ++++++++++++++++ R/dispatch.R | 23 +++++++++++++++-------- R/forecasts.R | 8 +++++++- man/aemo_pasa.Rd | 8 +++++++- 6 files changed, 53 insertions(+), 18 deletions(-)
Title: Create Interactive Web Exercises
Description: Functions for easily creating interactive web exercises in
'R Markdown', 'Quarto', and package vignettes that students can use in
self-guided learning.
Author: Dale Barr [aut],
Lisa DeBruine [aut],
Caspar J. Van Lissa [aut, cre]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between webexercises versions 1.1.0 dated 2023-05-15 and 1.2.0 dated 2026-09-09
webexercises-1.1.0/webexercises/R/webexercises_fns.R |only webexercises-1.2.0/webexercises/DESCRIPTION | 39 webexercises-1.2.0/webexercises/MD5 | 140 webexercises-1.2.0/webexercises/NAMESPACE | 49 webexercises-1.2.0/webexercises/NEWS.md | 77 webexercises-1.2.0/webexercises/R/add_latex_support.R |only webexercises-1.2.0/webexercises/R/add_to_bookdown.R | 332 - webexercises-1.2.0/webexercises/R/add_to_pkgdown.R |only webexercises-1.2.0/webexercises/R/add_to_quarto.R | 190 - webexercises-1.2.0/webexercises/R/awesomebox.R |only webexercises-1.2.0/webexercises/R/fns_questions.R |only webexercises-1.2.0/webexercises/R/mc_to_quiz.R |only webexercises-1.2.0/webexercises/R/quarto.R | 56 webexercises-1.2.0/webexercises/R/quiz.R |only webexercises-1.2.0/webexercises/R/ui.R |only webexercises-1.2.0/webexercises/R/webex_vignette.R |only webexercises-1.2.0/webexercises/R/webexercises.R |only webexercises-1.2.0/webexercises/R/webexercises_default.R | 122 webexercises-1.2.0/webexercises/R/zzz.R | 8 webexercises-1.2.0/webexercises/README.md | 74 webexercises-1.2.0/webexercises/build |only webexercises-1.2.0/webexercises/inst/doc |only webexercises-1.2.0/webexercises/inst/reports/default/index.Rmd | 330 - webexercises-1.2.0/webexercises/inst/reports/default/index.qmd | 286 - webexercises-1.2.0/webexercises/inst/reports/default/webex.R | 2 webexercises-1.2.0/webexercises/inst/reports/default/webex.css | 240 - webexercises-1.2.0/webexercises/inst/reports/default/webex.js | 412 +- webexercises-1.2.0/webexercises/inst/reports/default/webexercises.qmd | 268 - webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/skeleton/skeleton.Rmd | 274 - webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/skeleton/skeleton.html | 1782 +++++----- webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/template.yaml | 4 webexercises-1.2.0/webexercises/man/add_html_support.Rd |only webexercises-1.2.0/webexercises/man/add_latex_support.Rd |only webexercises-1.2.0/webexercises/man/add_to_bookdown.Rd | 76 webexercises-1.2.0/webexercises/man/add_to_pkgdown.Rd |only webexercises-1.2.0/webexercises/man/add_to_quarto.Rd | 58 webexercises-1.2.0/webexercises/man/add_to_quarto_file.Rd |only webexercises-1.2.0/webexercises/man/answer.Rd |only webexercises-1.2.0/webexercises/man/box_args.Rd |only webexercises-1.2.0/webexercises/man/cli_msg.Rd |only webexercises-1.2.0/webexercises/man/create_quarto_doc.Rd | 38 webexercises-1.2.0/webexercises/man/determine_output_format.Rd |only webexercises-1.2.0/webexercises/man/escape_regex.Rd | 40 webexercises-1.2.0/webexercises/man/figures/unnamed-chunk-18-1.png |only webexercises-1.2.0/webexercises/man/fitb.Rd | 120 webexercises-1.2.0/webexercises/man/hide.Rd | 72 webexercises-1.2.0/webexercises/man/is_quiet.Rd |only webexercises-1.2.0/webexercises/man/longmcq.Rd | 74 webexercises-1.2.0/webexercises/man/mcq.Rd | 62 webexercises-1.2.0/webexercises/man/quiz.Rd |only webexercises-1.2.0/webexercises/man/quiz_from_cvs.Rd |only webexercises-1.2.0/webexercises/man/rmd_webex_support.Rd |only webexercises-1.2.0/webexercises/man/round2.Rd | 62 webexercises-1.2.0/webexercises/man/strip_lzero.Rd | 40 webexercises-1.2.0/webexercises/man/style_widgets.Rd | 80 webexercises-1.2.0/webexercises/man/torf.Rd | 56 webexercises-1.2.0/webexercises/man/total_correct.Rd | 39 webexercises-1.2.0/webexercises/man/unhide.Rd | 54 webexercises-1.2.0/webexercises/man/use_webex_vignette.Rd |only webexercises-1.2.0/webexercises/man/webex_vignette.Rd |only webexercises-1.2.0/webexercises/man/webexercises_default.Rd | 82 webexercises-1.2.0/webexercises/man/with_cli_try.Rd |only webexercises-1.2.0/webexercises/tests/testthat.R | 8 webexercises-1.2.0/webexercises/tests/testthat/_problems |only webexercises-1.2.0/webexercises/tests/testthat/helper_usethis.R |only webexercises-1.2.0/webexercises/tests/testthat/helpers.R |only webexercises-1.2.0/webexercises/tests/testthat/test-add_to_bookdown.R | 340 - webexercises-1.2.0/webexercises/tests/testthat/test-add_to_quarto.R | 131 webexercises-1.2.0/webexercises/tests/testthat/test-compilation.R | 72 webexercises-1.2.0/webexercises/tests/testthat/test-create_quarto_doc.R | 103 webexercises-1.2.0/webexercises/tests/testthat/test-fitb.R | 142 webexercises-1.2.0/webexercises/tests/testthat/test-longmcq.R | 16 webexercises-1.2.0/webexercises/tests/testthat/test-mcq.R | 28 webexercises-1.2.0/webexercises/tests/testthat/test-quarto_renders_pdf.R |only webexercises-1.2.0/webexercises/tests/testthat/test-round2.R | 44 webexercises-1.2.0/webexercises/tests/testthat/test-special_characters.R |only webexercises-1.2.0/webexercises/tests/testthat/test-strip_lzero.R | 28 webexercises-1.2.0/webexercises/tests/testthat/testthat-problems.rds |only webexercises-1.2.0/webexercises/vignettes |only 79 files changed, 3319 insertions(+), 3231 deletions(-)
Title: Collapsed Variational Inference for Dirichlet Process (DP)
Mixture Model
Description: Collapsed Variational Inference for a Dirichlet Process (DP) mixture model with unknown covariance matrix structure and DP concentration parameter. It enables efficient clustering of high-dimensional data with significantly improved computational speed than traditional MCMC methods. The package incorporates 8 parameterisations and corresponding prior choices for the unknown covariance matrix, from which the user can choose and apply accordingly.
Author: Annesh Pal [aut, cre] ,
Boris Hejblum [aut]
Maintainer: Annesh Pal <sistm.soft.maintain@gmail.com>
Diff between vimixr versions 0.1.2 dated 2026-01-12 and 0.1.3 dated 2026-09-09
DESCRIPTION | 13 +-- MD5 | 46 ++++++----- NAMESPACE | 54 ++++++++----- NEWS.md | 4 - R/CVI_update_function.R | 54 +++++++------ R/ELBO_function_type.R | 39 +++------ R/RcppExports.R | 37 +++++++-- R/cvi_npmm.R | 49 +++++++----- R/cvi_singlerun.R | 4 - R/empiricalBayesa0.R | 2 R/log_sum_exp.R |only build/vignette.rds |binary inst/doc/vimixr_userguide.R | 43 ++++------ inst/doc/vimixr_userguide.Rmd | 43 ++++------ inst/doc/vimixr_userguide.html | 164 +++++++++++++++++++---------------------- man/cvi_npmm.Rd | 7 + man/log_sum_exp.Rd |only man/lower_tri_stats.Rd |only man/mat_mult.Rd | 14 ++- man/sparse_cov_op.Rd |only src/RcppExports.cpp | 41 ++++++++-- src/lower_tri_stats.cpp |only src/mat_mult.cpp | 43 +++++++++- src/mat_mult_t.cpp | 5 + src/sparse_cov_op.cpp |only src/t_mat_mult.cpp | 5 + vignettes/vimixr_userguide.Rmd | 43 ++++------ 27 files changed, 401 insertions(+), 309 deletions(-)
Title: Access 'NOAA' Climate and Weather Data
Description: Provides clean, tidy access to climate and weather data from the
'National Oceanic and Atmospheric Administration' ('NOAA') via the 'National
Centers for Environmental Information' ('NCEI') Data Service API
<https://www.ncei.noaa.gov/support/access-data-service-api-user-documentation>. Covers daily weather
observations, monthly and annual summaries, and 30-year climate normals from
over 100,000 stations across 180 countries. No API key is required.
Dedicated functions handle the most common datasets, while a generic fetcher
provides access to all 'NCEI' datasets. Station discovery functions help
users find stations by location or name. Data is downloaded on first use
and cached locally for subsequent calls. This package is not endorsed or
certified by 'NOAA'.
Author: Charles Coverdale [aut, cre, cph]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readnoaa versions 0.1.1 dated 2026-03-19 and 0.2.1 dated 2026-09-09
DESCRIPTION | 11 MD5 | 72 +++--- NAMESPACE | 2 NEWS.md | 154 +++++++++++++ R/annual.R | 20 + R/cache.R | 60 +++++ R/coverage.R |only R/daily.R | 37 ++- R/get.R | 38 ++- R/list_helpers.R | 112 ++++++++-- R/monthly.R | 20 + R/normals.R | 108 ++++++++- R/request.R | 408 ++++++++++++++++++++++++++++++------- R/stations.R | 184 ++++++++++++---- R/utils.R | 240 ++++++++++++++++++--- README.md | 244 ++++++++++++++-------- man/cache_info.Rd |only man/clear_cache.Rd | 3 man/list_datasets.Rd | 7 man/list_datatypes.Rd | 42 +++ man/noaa_annual.Rd | 14 + man/noaa_coverage.Rd |only man/noaa_daily.Rd | 30 ++ man/noaa_get.Rd | 37 ++- man/noaa_monthly.Rd | 14 + man/noaa_nearby.Rd | 37 ++- man/noaa_normals.Rd | 71 +++++- man/noaa_stations.Rd | 58 ++++- man/readnoaa-package.Rd | 3 tests/testthat/test-annual.R | 26 +- tests/testthat/test-cache.R | 77 ++++++ tests/testthat/test-coverage.R |only tests/testthat/test-daily.R | 74 ++++-- tests/testthat/test-get.R | 62 ++++- tests/testthat/test-list_helpers.R | 42 ++- tests/testthat/test-monthly.R | 24 +- tests/testthat/test-normals.R | 39 ++- tests/testthat/test-stations.R | 87 ++++--- tests/testthat/test-utils.R | 209 +++++++++++------- 39 files changed, 2102 insertions(+), 564 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb],
Mads Fjeld Wold [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 1.9.0 dated 2026-02-02 and 2.0.0 dated 2026-09-09
DESCRIPTION | 16 ++-- MD5 | 16 ++-- NAMESPACE | 28 ++++--- NEWS.md | 14 +++ R/query_url.R | 24 ++++++ build/vignette.rds |binary inst/doc/pxwebapi_v1.html | 110 +++++++++++++++---------------- inst/doc/pxwebapi_v2.html | 162 +++++++++++++++++++++++----------------------- man/query_url.Rd | 11 +++ 9 files changed, 219 insertions(+), 162 deletions(-)
Title: Generalized Linear Models Adjusting for Misrepresentation
Description: Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.
Author: Patrick Rafael [cre, aut],
Xia Michelle [aut],
Rexford Akakpo [aut]
Maintainer: Patrick Rafael <pbr2608@vt.edu>
Diff between glmMisrep versions 0.1.2 dated 2026-08-20 and 0.1.3 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 8 ++++++++ tests/LN-testing.R | 10 +++++----- tests/NB-testing.R | 10 ++++++---- tests/Norm-testing.R | 11 ++++++----- tests/Pois-testing.R | 44 ++++++++++++++++++++++++++------------------ tests/gamma-testing.R | 16 +++++++++++----- 8 files changed, 72 insertions(+), 47 deletions(-)
Title: Access 'Federal Reserve Economic Data'
Description: Provides clean, tidy access to economic data from the 'Federal
Reserve Economic Data' ('FRED') API <https://fred.stlouisfed.org/docs/api/fred/>.
'FRED' is maintained by the 'Federal Reserve Bank of St. Louis' and contains over
800,000 time series from 118 sources covering GDP, employment, inflation,
interest rates, trade, and more. Dedicated functions fetch series observations,
search for series, browse categories, releases, and tags, and retrieve series
metadata. Multiple series can be fetched in a single call, in long or wide
format. Server-side unit transformations (percent change, log, etc.) and
frequency aggregation are supported, with readable transform aliases such as
'yoy_pct' and 'log_diff'. Real-time and vintage helpers (built on 'ALFRED')
return a series as it appeared on a given date, the first-release version,
every revision, or a panel of selected vintages. An offline curated catalogue
of around fifty popular series, NBER recession reference dates, and FOMC
meeting [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between fred versions 0.2.0 dated 2026-04-11 and 0.3.1 dated 2026-09-09
DESCRIPTION | 26 ++++--- MD5 | 120 +++++++++++++++++++++++----------- NAMESPACE | 14 ++++ NEWS.md | 113 ++++++++++++++++++++++++++++++++ R/auth.R | 4 - R/cache.R | 3 R/catalogue.R |only R/categories.R | 34 ++++++--- R/cite.R |only R/class.R | 138 ++++++++++++++++++++++++++++++++-------- R/dates.R |only R/manifest.R |only R/plot.R |only R/releases.R | 24 ++++-- R/request.R | 4 - R/search.R | 24 ++++-- R/series.R | 38 ++++++----- R/sources.R | 16 +++- R/tags.R | 18 +++-- R/updates.R | 8 +- R/utilities.R |only R/vintages.R | 26 ++++--- build |only inst/CITATION | 2 inst/WORDLIST | 37 ++++++++++ inst/doc |only man/fred-package.Rd | 3 man/fred_aggregate.Rd |only man/fred_all_vintages.Rd | 6 + man/fred_as_of.Rd | 6 + man/fred_browse.Rd |only man/fred_catalogue.Rd |only man/fred_category.Rd | 10 +- man/fred_category_children.Rd | 6 + man/fred_category_series.Rd | 4 - man/fred_cite_series.Rd |only man/fred_event_window.Rd |only man/fred_first_release.Rd | 6 + man/fred_fomc_dates.Rd |only man/fred_get_key.Rd | 4 - man/fred_info.Rd | 4 - man/fred_interpolate.Rd |only man/fred_manifest.Rd |only man/fred_real_time_panel.Rd | 8 +- man/fred_recession_dates.Rd |only man/fred_related_tags.Rd | 4 - man/fred_release_dates.Rd | 4 - man/fred_release_series.Rd | 6 + man/fred_releases.Rd | 4 - man/fred_request.Rd | 4 - man/fred_search.Rd | 16 ++-- man/fred_series.Rd | 22 +++--- man/fred_source_releases.Rd | 6 + man/fred_sources.Rd | 4 - man/fred_tags.Rd | 6 + man/fred_updates.Rd | 4 - man/fred_vintage_revisions.Rd |only man/fred_vintages.Rd | 4 - man/plot.fred_tbl.Rd |only man/print.fred_manifest.Rd |only man/print.fred_tbl.Rd | 7 +- man/sub-.fred_tbl.Rd |only man/summary.fred_tbl.Rd |only tests/testthat/test-catalogue.R |only tests/testthat/test-cite.R |only tests/testthat/test-class.R |only tests/testthat/test-dates.R |only tests/testthat/test-manifest.R |only tests/testthat/test-plot.R |only tests/testthat/test-utilities.R |only vignettes |only 71 files changed, 602 insertions(+), 195 deletions(-)
Title: Measuring the Stability of Dimension Reduction and Cluster
Assignment in scRNA-Seq Experiments
Description: Provides functions for evaluating the stability of low-dimensional embeddings and cluster assignments in single‑cell RNA sequencing (scRNA‑seq) datasets. Starting from a principal component analysis (PCA) object, users can generate multiple replicates of t‑Distributed Stochastic Neighbor Embedding (t‑SNE) or Uniform Manifold Approximation and Projection (UMAP) embeddings. Embedding stability is quantified by computing pairwise Kendall’s Tau correlations across replicates and summarizing the distribution of correlation coefficients. In addition to dimensionality reduction, 'scStability' assesses clustering consistency using either Louvain or Leiden algorithms and calculating the Normalized Mutual Information (NMI) between all pairs of cluster assignments. For background on UMAP and t-SNE algorithms, see McInnes et al. (2020, <doi:10.21105/joss.00861>) and van der Maaten & Hinton (2008, <https://github.com/lvdmaaten/bhtsne>), respectively.
Author: Ben Abrahams [aut, cre]
Maintainer: Ben Abrahams <benabrahams52@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2025-06-23
Diff between scStability versions 1.0.3 dated 2025-06-23 and 1.0.4 dated 2026-09-09
DESCRIPTION | 12 +- MD5 | 29 +++--- R/clustStable.r | 4 R/createEmb.r | 5 - R/scStability.r | 39 +++----- inst/doc/Introduction-to-scStability.R | 12 +- inst/doc/Introduction-to-scStability.Rmd | 14 +- inst/doc/Introduction-to-scStability.html | 141 ++++++++++++++++-------------- man/clustStable.Rd | 2 man/scStability.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-clustStable.R | 38 +++++--- tests/testthat/test-compareEmb.R | 20 ++-- tests/testthat/test-createEmb.R | 4 tests/testthat/test-scStability.R | 37 +++++-- vignettes/Introduction-to-scStability.Rmd | 14 +- 16 files changed, 212 insertions(+), 163 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.2 dated 2026-08-28 and 2.0.4 dated 2026-09-09
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- NEWS.md | 26 +++++++++++++++++++++----- R/get_drainage_area_estimates.R | 15 +++++++++++---- R/get_vaa.R | 2 +- README.md | 10 +++++----- inst/doc/hydrogeofetch.Rmd | 2 +- inst/doc/hydrogeofetch.html | 2 +- inst/extdata/3dhp_yahara_flowlines.R | 2 +- inst/extdata/new_hope_data.R | 4 ++-- inst/extdata/nhdplushr_data.R | 2 +- inst/extdata/sample_data.R | 2 +- inst/extdata/sample_flines.R | 2 +- inst/extdata/walker_data.R | 2 +- man/get_drainage_area_estimates.Rd | 3 ++- tests/testthat/helper.R | 2 +- tests/testthat/test_get_nhdplus.R | 6 +++--- vignettes/hydrogeofetch.Rmd | 2 +- 18 files changed, 77 insertions(+), 53 deletions(-)
Title: Imputation of Multivariate Time Series Based on Dynamic Time
Warping
Description: Functions to impute large gaps within multivariate time series based on Dynamic Time Warping methods. Gaps of size 1 or inferior to a defined threshold are filled using simple average and weighted moving average respectively. Larger gaps are filled using the methodology provided by Phan et al. (2017) <DOI:10.1109/MLSP.2017.8168165>: a query is built immediately before/after a gap and a moving window is used to find the most similar sequence to this query using Dynamic Time Warping. To lower the calculation time, similar sequences are pre-selected using global features. Contrary to the univariate method (package 'DTWBI'), these global features are not estimated over the sequence containing the gap(s), but a feature matrix is built to summarize general features of the whole multivariate signal. Once the most similar sequence to the query has been identified, the adjacent sequence to this window is used to fill the gap considered. This function can deal with multiple gaps over all t [...truncated...]
Author: Camille Dezecache [aut],
Thi Thu Hong Phan [aut],
Emilie Poisson-Caillault [aut, cre]
Maintainer: Emilie Poisson-Caillault <emilie.poisson@univ-littoral.fr>
Diff between DTWUMI versions 1.0 dated 2018-07-13 and 1.1 dated 2026-09-09
DTWUMI-1.0/DTWUMI/R/XXXX_4Local_derivative_DDTW.R |only DTWUMI-1.0/DTWUMI/build |only DTWUMI-1.0/DTWUMI/man/DTWUMI-package.Rd |only DTWUMI-1.1/DTWUMI/DESCRIPTION | 24 +++- DTWUMI-1.1/DTWUMI/MD5 | 53 +++++----- DTWUMI-1.1/DTWUMI/NAMESPACE | 7 + DTWUMI-1.1/DTWUMI/R/4_1_1Estimate_global_features.R | 48 ++++----- DTWUMI-1.1/DTWUMI/R/4_1_2Features_matrix.R | 32 ++---- DTWUMI-1.1/DTWUMI/R/4_2Indexes_size_missing.R | 6 - DTWUMI-1.1/DTWUMI/R/4_3_1Imputing_1NA.R | 5 DTWUMI-1.1/DTWUMI/R/4_3_2Imputing_SmallNAgaps.R | 5 DTWUMI-1.1/DTWUMI/R/4_4Find_global_threshold_multivariate.R | 3 DTWUMI-1.1/DTWUMI/R/4_5Find_similar_window_multivariate.R | 3 DTWUMI-1.1/DTWUMI/R/4_5Find_similar_window_multivariate_AFBDTW.R | 3 DTWUMI-1.1/DTWUMI/R/4_6DTWUMI_1gap.R | 25 ++-- DTWUMI-1.1/DTWUMI/R/4_7DTWUMI_general.R | 6 - DTWUMI-1.1/DTWUMI/R/DATA.R | 4 DTWUMI-1.1/DTWUMI/R/XXXX_1Trapezoid.R | 10 + DTWUMI-1.1/DTWUMI/R/XXXX_3Dist_AFBDTW_matrix.R | 6 - DTWUMI-1.1/DTWUMI/inst/CITATION | 4 DTWUMI-1.1/DTWUMI/man/DTWUMI_1gap_imputation.Rd | 31 +++-- DTWUMI-1.1/DTWUMI/man/DTWUMI_imputation.Rd | 16 +-- DTWUMI-1.1/DTWUMI/man/Indexes_size_missing_multi.Rd | 5 DTWUMI-1.1/DTWUMI/man/dataDTWUMI.Rd | 8 - DTWUMI-1.1/DTWUMI/man/dot-DTW_threshold_global_multivariate.Rd |only DTWUMI-1.1/DTWUMI/man/dot-Finding_similar_window_multivariate.Rd |only DTWUMI-1.1/DTWUMI/man/dot-Finding_similar_window_multivariate_AFBDTW.Rd |only DTWUMI-1.1/DTWUMI/man/dot-dist_afbdtw_matrix.Rd |only DTWUMI-1.1/DTWUMI/man/dot-features_matrix.Rd |only DTWUMI-1.1/DTWUMI/man/dot-globalfeatures.Rd |only DTWUMI-1.1/DTWUMI/man/dot-imp_NA_WMA.Rd |only DTWUMI-1.1/DTWUMI/man/dot-trapezoid.Rd |only DTWUMI-1.1/DTWUMI/man/imp_1NA.Rd | 5 33 files changed, 162 insertions(+), 147 deletions(-)
Title: Imputation of Time Series Based on Dynamic Time Warping
Description: Functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).
Author: Camille Dezecache [aut],
Thi Thu Hong Phan [aut],
Emilie Poisson-Caillault [aut, cre]
Maintainer: Emilie Poisson-Caillault <emilie.poisson@univ-littoral.fr>
Diff between DTWBI versions 1.1 dated 2018-07-11 and 1.2 dated 2026-09-09
DTWBI-1.1/DTWBI/build |only DTWBI-1.1/DTWBI/man/DTWBI-package.Rd |only DTWBI-1.2/DTWBI/DESCRIPTION | 24 ++- DTWBI-1.2/DTWBI/MD5 | 68 +++++----- DTWBI-1.2/DTWBI/NAMESPACE | 13 + DTWBI-1.2/DTWBI/R/1_1Similarity.R | 8 - DTWBI-1.2/DTWBI/R/1_2NMAE.R | 6 DTWBI-1.2/DTWBI/R/1_4RMSE.R | 6 DTWBI-1.2/DTWBI/R/1_5FSD.R | 6 DTWBI-1.2/DTWBI/R/1_6FB.R | 6 DTWBI-1.2/DTWBI/R/1_7FA2.R | 6 DTWBI-1.2/DTWBI/R/2_1DDTW.R | 4 DTWBI-1.2/DTWBI/R/2_2AFBDTW.R | 24 +-- DTWBI-1.2/DTWBI/R/2_3DTWcost.R | 6 DTWBI-1.2/DTWBI/R/3_1Create_large_gaps.R | 20 +- DTWBI-1.2/DTWBI/R/3_2Estimate_global_features.R | 46 +++--- DTWBI-1.2/DTWBI/R/3_3Find_global_threshold_univariate.R | 3 DTWBI-1.2/DTWBI/R/3_4Find_similar_windows_univariate.R | 3 DTWBI-1.2/DTWBI/R/3_4Find_similar_windows_univariate_AFBDTW.R | 3 DTWBI-1.2/DTWBI/R/3_5DTWBI_algorithm_simple_univariate.R | 26 +-- DTWBI-1.2/DTWBI/R/DATA.R | 4 DTWBI-1.2/DTWBI/inst/CITATION | 6 DTWBI-1.2/DTWBI/man/DTWBI_univariate.Rd | 37 ++--- DTWBI-1.2/DTWBI/man/compute.fa2.Rd | 5 DTWBI-1.2/DTWBI/man/compute.fb.Rd | 5 DTWBI-1.2/DTWBI/man/compute.fsd.Rd | 5 DTWBI-1.2/DTWBI/man/compute.nmae.Rd | 5 DTWBI-1.2/DTWBI/man/compute.rmse.Rd | 5 DTWBI-1.2/DTWBI/man/compute.sim.Rd | 7 - DTWBI-1.2/DTWBI/man/dataDTWBI.Rd | 10 - DTWBI-1.2/DTWBI/man/dist_afbdtw.Rd | 23 +-- DTWBI-1.2/DTWBI/man/dot-DTW_threshold_global_univariate.Rd |only DTWBI-1.2/DTWBI/man/dot-Finding_similar_window_univariate.Rd |only DTWBI-1.2/DTWBI/man/dot-Finding_similar_window_univariate_AFBDTW.Rd |only DTWBI-1.2/DTWBI/man/dot-globalfeatures.Rd |only DTWBI-1.2/DTWBI/man/gapCreation.Rd | 19 +- DTWBI-1.2/DTWBI/man/local.derivative.ddtw.Rd | 3 DTWBI-1.2/DTWBI/man/minCost.Rd | 3 38 files changed, 197 insertions(+), 218 deletions(-)
Title: Unified Climate Indices for Temperature, Precipitation, and
Drought
Description: Compute the standard suite of climate indices from daily
weather observations. Provides the canonical 'ETCCDI' 27 (Expert
Team on Climate Change Detection and Indices), the 'ET-SCI'
heatwave and cold-wave families plus the Excess Heat Factor of
Nairn and Fawcett (2013), and agroclimatic, drought, and
human-comfort families. Drought indices ('SPI', 'SPEI') accept a
choice of distribution (gamma or Pearson III for SPI; log-logistic
or generalised extreme value for SPEI). Reference
evapotranspiration is available via Hargreaves and the FAO-56
Penman-Monteith method (Allen et al. 1998). Percentile-based
indices support the Zhang (2005) in-base bootstrap. Daily inputs
are numeric vectors plus a 'Date' vector; outputs are tidy data
frames. Optional gridded support via 'terra' applies any index
over a 'SpatRaster' and reads 'netCDF' input. No external API
calls; pairs with data packages such as 'readnoaa'. References:
Alexander et al. (2006) <doi:10.1029/2005JD006290>; Zhang et al.
(201 [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between climatekit versions 0.2.0 dated 2026-05-09 and 0.2.2 dated 2026-09-09
DESCRIPTION | 8 - MD5 | 67 ++++---- NAMESPACE | 1 NEWS.md | 105 +++++++++++++ R/agroclimatic.R | 15 + R/bootstrap.R | 4 R/climatekit-package.R | 1 R/comfort.R | 10 - R/compute.R | 77 +-------- R/convert.R | 37 ++-- R/drought.R | 47 +++-- R/ehf.R | 13 + R/gridded.R | 4 R/heatwave.R | 20 +- R/index-table.R |only R/metadata.R | 260 +++------------------------------ R/precipitation.R | 37 +++- R/temperature.R | 72 +++------ R/utils.R | 60 +++++++ README.md | 114 ++++---------- inst/doc/climdex-migration.Rmd | 15 + inst/doc/climdex-migration.html | 21 ++ man/ck_apply_grid.Rd | 4 man/ck_compute.Rd | 9 + man/ck_dry_days.Rd | 7 man/ck_spei.Rd | 12 + man/ck_spi.Rd | 2 man/ck_warm_spell.Rd | 5 man/ck_wet_days.Rd | 9 + man/clear_cache.Rd | 21 +- tests/testthat/test-drought.R | 4 tests/testthat/test-ehf.R | 2 tests/testthat/test-index-table.R |only tests/testthat/test-precipitation.R | 4 tests/testthat/test-v022-regressions.R |only vignettes/climdex-migration.Rmd | 15 + 36 files changed, 525 insertions(+), 557 deletions(-)
Title: Bayesian Instrumental Regression for Disparity Estimation
Description: Bayesian models for accurately estimating conditional
distributions by race, using Bayesian Improved Surname Geocoding (BISG)
probability estimates of individual race. Implements the methods described
in McCartan, Fisher, Goldin, Ho and Imai (2025) <doi:10.1080/01621459.2025.2526695>.
Author: Cory McCartan [aut, cre],
Kosuke Imai [ctb],
Daniel Ho [ctb],
Jacob Goldin [ctb],
Robin Fisher [ctb],
The Stan Development Team [cph]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between birdie versions 0.7.1 dated 2025-07-24 and 0.8.0 dated 2026-09-09
birdie-0.7.1/birdie/inst/extdata/natl_race.rds |only birdie-0.7.1/birdie/inst/include/rstan/boost_random_R.hpp |only birdie-0.7.1/birdie/inst/include/rstan/rcpp_module_def_for_rstan.hpp |only birdie-0.8.0/birdie/DESCRIPTION | 22 birdie-0.8.0/birdie/MD5 | 57 - birdie-0.8.0/birdie/NEWS.md | 12 birdie-0.8.0/birdie/R/birdie.R | 26 birdie-0.8.0/birdie/R/bisg.R | 499 ++++++---- birdie-0.8.0/birdie/R/census.R | 20 birdie-0.8.0/birdie/R/generics.R | 7 birdie-0.8.0/birdie/R/sysdata.rda |binary birdie-0.8.0/birdie/R/utils.R | 4 birdie-0.8.0/birdie/README.md | 50 - birdie-0.8.0/birdie/build/partial.rdb |binary birdie-0.8.0/birdie/build/vignette.rds |binary birdie-0.8.0/birdie/inst/doc/birdie.html | 128 +- birdie-0.8.0/birdie/inst/extdata/names_2020_counts.rds |only birdie-0.8.0/birdie/inst/extdata/state_race_2020.rds |only birdie-0.8.0/birdie/inst/extdata/zip_race_2020.rds |only birdie-0.8.0/birdie/inst/include/rstan/stan_fit.hpp | 9 birdie-0.8.0/birdie/man/birdie-package.Rd | 2 birdie-0.8.0/birdie/man/birdie.Rd | 26 birdie-0.8.0/birdie/man/bisg.Rd | 59 + birdie-0.8.0/birdie/man/census_race_geo_table.Rd | 3 birdie-0.8.0/birdie/man/p_r_natl.Rd | 14 birdie-0.8.0/birdie/man/reexports.Rd | 1 birdie-0.8.0/birdie/src/Makevars | 4 birdie-0.8.0/birdie/src/stanExports_multinom.cc | 34 birdie-0.8.0/birdie/src/stanExports_multinom.h | 272 +++-- birdie-0.8.0/birdie/tests/testthat/_snaps/birdie.md | 2 birdie-0.8.0/birdie/tests/testthat/test-birdie.R | 2 birdie-0.8.0/birdie/tests/testthat/test-bisg.R | 83 + birdie-0.8.0/birdie/tests/testthat/test-census-premade.R |only 33 files changed, 913 insertions(+), 423 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) with the goal of maximizing between-group similarity or within-group heterogeneity. The anticlustering approach thereby reverses the logic of cluster analysis that strives for high within-group homogeneity and clear separation between groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The main function anticlustering() gives access to optimal and heuristic anticlustering methods described in Papenberg and Klau (2021; <doi:10.1037/met0000301>), Brusco et al. (2020; <doi:10.1111/bmsp.12186>), Papenberg (2024; <doi:10.1111/bmsp.12315>), Papenberg, Wang, et al. (2025; <doi:10.1016/j.crmeth.2025.101137>), Papenberg, Breuer, et al. (2025; <doi:10.1017/psy.2025.10052>), Yang et al. (202 [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb] ,
Dimitry Wintermantel [ctb] ),
David Buczynski [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.14 dated 2026-04-15 and 0.8.16 dated 2026-09-09
DESCRIPTION | 24 +++- LICENSE | 2 MD5 | 59 +++++++----- NAMESPACE | 5 + R/Optimal_Dispersion.R | 2 R/bicriterion_iterated_local_search_call.R | 2 R/c-anticlustering.R | 17 +++ R/categories_to_binary.R | 23 ++++ R/experimental_allocation.R |only R/fast_anticlustering.R | 26 ++++- R/input-validation.R | 12 +- R/md.R |only R/optimal_anticlustering.R | 2 R/wrapper-anticlustering.R | 41 +++++--- R/wrapper-feasible-and-infeasible-region-search.R |only build/vignette.rds |binary inst/doc/Anticlustering_in_2025.Rmd | 2 inst/doc/Anticlustering_in_2025.html | 2 inst/doc/Speeding_up_anticlustering.html | 28 ++--- inst/tinytest/test-fifr.R |only inst/tinytest/test-md.R |only man/anticlustering.Rd | 23 +++- man/bicriterion_anticlustering.Rd | 2 man/categories_to_binary.Rd | 11 ++ man/experimental_allocation.Rd |only man/fast_anticlustering.Rd | 9 + man/feasible_and_infeasible_region_search_anticlustering.Rd |only man/mahalanobis_distance.Rd |only man/optimal_anticlustering.Rd | 2 man/optimal_dispersion.Rd | 2 src/anticlust_init.c | 7 + src/declarations.h | 13 ++ src/fast-MD-anticlustering.c |only src/feasible_and_infeasible_region_search.c |only src/fifr_header.h |only vignettes/Anticlustering_in_2025.Rmd | 2 36 files changed, 223 insertions(+), 95 deletions(-)
Title: Parse, Clean, and Normalize URLs
Description: A lightweight toolkit for extracting structured information from URLs.
Includes functions for parsing, normalizing protocols, extracting domains, and constructing clean URLs.
Domain and public-suffix extraction is delegated to the 'pslr' package,
which implements the Public Suffix List from <https://publicsuffix.org>.
Punycode and IDNA encoding is handled by the 'punycoder' package.
Author: Bart Turczynski [aut, cre]
Maintainer: Bart Turczynski <bartek@turczynski.pl>
Diff between rurl versions 1.2.0 dated 2026-06-19 and 3.0.1 dated 2026-09-09
rurl-1.2.0/rurl/R/sysdata.rda |only rurl-3.0.1/rurl/DESCRIPTION | 47 rurl-3.0.1/rurl/LICENSE | 2 rurl-3.0.1/rurl/LICENSE.note |only rurl-3.0.1/rurl/MD5 | 255 rurl-3.0.1/rurl/NAMESPACE | 29 rurl-3.0.1/rurl/NEWS.md | 3021 ++++++++ rurl-3.0.1/rurl/R/accessors.R | 1611 ++++ rurl-3.0.1/rurl/R/canonical_join.R | 445 - rurl-3.0.1/rurl/R/diagnostics.R |only rurl-3.0.1/rurl/R/domain.R | 638 + rurl-3.0.1/rurl/R/email-diagnostics.R |only rurl-3.0.1/rurl/R/format.R |only rurl-3.0.1/rurl/R/host-policy.R |only rurl-3.0.1/rurl/R/parse-phases.R | 3500 ++++++++-- rurl-3.0.1/rurl/R/parse-state.R |only rurl-3.0.1/rurl/R/parse-web.R |only rurl-3.0.1/rurl/R/parse.R | 2713 +++++++ rurl-3.0.1/rurl/R/path-query.R | 536 + rurl-3.0.1/rurl/R/percent-coding.R |only rurl-3.0.1/rurl/R/profiles.R |only rurl-3.0.1/rurl/R/query-denylist.R |only rurl-3.0.1/rurl/R/resolve.R |only rurl-3.0.1/rurl/R/rurl-package.R |only rurl-3.0.1/rurl/R/scheme-policy.R |only rurl-3.0.1/rurl/R/serialize.R |only rurl-3.0.1/rurl/R/status-constants.R |only rurl-3.0.1/rurl/R/url-join.R |only rurl-3.0.1/rurl/R/url-key.R |only rurl-3.0.1/rurl/R/utils.R | 468 + rurl-3.0.1/rurl/R/verdicts.R |only rurl-3.0.1/rurl/R/zzz.R | 441 - 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Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss, (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate, and (c) racing
diffusion model (RDM; Tillman, Van Zandt, & Logan, 2020,
<doi:10.3758/s13423-020-01719-6>).
Author: Henrik Singmann [aut, cre] ,
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Kiante Fernandez [aut] ,
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb],
Trisha Van Zandt [ctb],
Gabriel Tillman [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between rtdists versions 0.11-6 dated 2026-06-10 and 0.12-0 dated 2026-09-09
rtdists-0.11-6/rtdists/NEWS |only rtdists-0.12-0/rtdists/DESCRIPTION | 29 - rtdists-0.12-0/rtdists/MD5 | 46 + rtdists-0.12-0/rtdists/NAMESPACE | 44 + rtdists-0.12-0/rtdists/NEWS.md |only rtdists-0.12-0/rtdists/R/diffusion.R | 243 +++++----- rtdists-0.12-0/rtdists/R/lba.r | 43 + rtdists-0.12-0/rtdists/R/lba_race.R | 29 - rtdists-0.12-0/rtdists/R/rdm.R |only rtdists-0.12-0/rtdists/R/rtdists-package.R | 25 - rtdists-0.12-0/rtdists/R/single-lba.r | 50 +- rtdists-0.12-0/rtdists/R/single-rdm.R |only rtdists-0.12-0/rtdists/inst/doc/reanalysis_rr98.html | 46 - rtdists-0.12-0/rtdists/man/Diffusion.Rd | 15 rtdists-0.12-0/rtdists/man/LBA-race.Rd | 13 rtdists-0.12-0/rtdists/man/LBA.Rd | 47 + rtdists-0.12-0/rtdists/man/RDM.Rd |only rtdists-0.12-0/rtdists/man/rtdists-package.Rd | 22 rtdists-0.12-0/rtdists/man/single-RDM.Rd |only rtdists-0.12-0/rtdists/src/CDF_no_variability.h | 20 rtdists-0.12-0/rtdists/tests/testthat/test-diffusion-bugs.R | 64 ++ rtdists-0.12-0/rtdists/tests/testthat/test-diffusion-math.R | 104 +++- rtdists-0.12-0/rtdists/tests/testthat/test-diffusion.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-lba-bugs-A-small.R |only rtdists-0.12-0/rtdists/tests/testthat/test-lba_basics.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-pdiffusion_rng.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-rdiffusion.R | 6 rtdists-0.12-0/rtdists/tests/testthat/test-rdm.R |only 28 files changed, 543 insertions(+), 309 deletions(-)
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Description: 'Rcpp' bindings for 'PLANC', a highly parallel
and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library.
Wraps algorithms described in
Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and
Eswar et. al (2021) <doi:10.1145/3432185>.
Implements algorithms described in
Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>,
Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and
Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Author: Andrew Robbins [aut, cre] ,
Yichen Wang [aut],
Joshua Welch [cph] ,
Ramakrishnan Kannan [cph] ,
Conrad Sanderson [cph] ,
Blue Brain Project/EPFL [cph] ,
UT-Batelle [cph] ,
LibHwloc Contributors [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between RcppPlanc versions 2.0.15 dated 2026-02-26 and 2.0.16 dated 2026-09-09
DESCRIPTION | 16 ++-- MD5 | 21 +++--- NEWS.md | 4 + build/vignette.rds |binary configure | 4 - inst/COPYRIGHTS | 98 ++++++++++++++++++++++++++++ inst/doc/RcppPlanc.html | 10 +- man/data.Rd | 6 - man/onlineINMF.Rd | 2 src/planc/CMakeLists.txt | 4 - tools/patches/04_discarded_qualifiers.patch |only tools/patches/series | 1 12 files changed, 134 insertions(+), 32 deletions(-)
Title: Tools for Working with the National Hydrography Dataset
Description: Tools for working with the National Hydrography Dataset, with
functions for querying, downloading, and networking both the NHD
<https://www.usgs.gov/national-hydrography>
and NHDPlus <https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus> datasets.
Author: Jemma Stachelek [aut, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between nhdR versions 0.6.1 dated 2023-08-11 and 0.6.2 dated 2026-09-09
DESCRIPTION | 18 MD5 | 56 +- NAMESPACE | 154 +++--- NEWS.md | 168 +++--- R/load.R | 718 ++++++++++++++-------------- R/nhdR-package.R | 6 R/query.R | 678 +++++++++++++------------- R/utils.R | 780 +++++++++++++++---------------- README.md | 485 +++++++++---------- build/vignette.rds |binary inst/CITATION | 34 - inst/doc/demo.R | 32 - inst/doc/demo.html | 560 ++++++++++++++-------- inst/doc/flow.R | 104 ++-- inst/doc/flow.html | 652 ++++++++++++++++--------- inst/doc/network.R | 68 +- inst/doc/network.html | 610 ++++++++++++++++-------- man/figures/README-unnamed-chunk-4-1.png |binary man/find_state.Rd | 44 - man/nhdR-package.Rd | 11 man/nhd_dl_state.Rd | 86 +-- man/nhd_load.Rd | 124 ++-- man/nhd_plus_load.Rd | 166 +++--- man/nhd_plus_query.Rd | 144 ++--- man/nhd_query.Rd | 126 ++--- man/select_point_overlay.Rd | 68 +- tests/testthat/test-list.R | 50 - tests/testthat/test-load.R | 190 +++---- tests/testthat/test-query.R | 176 +++--- 29 files changed, 3473 insertions(+), 2835 deletions(-)
Title: Evaluation Platform in Chronic Obstructive Pulmonary Disease
Description: Evaluation Platform in Chronic Obstructive Pulmonary Disease (EPIC) is a Discrete Event Simulation (DES) model that simulates health outcomes of patients with Chronic Obstructive Pulmonary Disease (COPD) based on demographics and individual-level risk factors, based on the model published in Sadatsafavi et al. (2019) <doi:10.1177/0272989X18824098>.
Author: Mohsen Sadatsafavi [aut, cph],
Kate Johnson [aut, cre],
Amin Adibi [aut],
Kevin Yan [aut]
Maintainer: Kate Johnson <kate.johnson@ubc.ca>
Diff between epicR versions 1.0.1 dated 2026-03-24 and 1.0.2 dated 2026-09-09
epicR-1.0.1/epicR/NEWS.md |only epicR-1.0.2/epicR/DESCRIPTION | 20 - epicR-1.0.2/epicR/MD5 | 23 - epicR-1.0.2/epicR/R/validation.R | 87 ++---- epicR-1.0.2/epicR/build/vignette.rds |binary epicR-1.0.2/epicR/inst/config/config_us.json | 8 epicR-1.0.2/epicR/inst/doc/AddingNewCountry.html | 3 epicR-1.0.2/epicR/inst/doc/GettingStarted.html | 3 epicR-1.0.2/epicR/inst/doc/InputsOutputsStructure.html | 246 ++++++++--------- epicR-1.0.2/epicR/man/epicR-package.Rd | 6 epicR-1.0.2/epicR/src/model.cpp | 4 epicR-1.0.2/epicR/src/model_events.cpp | 17 - epicR-1.0.2/epicR/tests/testthat/testExacerbations.R | 4 13 files changed, 195 insertions(+), 226 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests such as
Hosmer-Lemeshow, directed and covariate-space tests, smoothing and
resampling tests, and calibration tests. Each is obtained from its own
package where installed and attributed to its authors. The package also
implements the author's own procedures for sparse data, where the
Hosmer-Lemeshow test loses power: the omnibus Ebrahim-Farrington test
'ef.gof()', the directed 'edge.gof()' and its covariate-space variant
'cdef.gof()', the Cauchy-combination ensemble 'edges.gof()', 'DeepGOF-1'
(a pretrained convolutional statistic whose level comes from the analyst's
own parametric bootstrap rather than from the network), and 'legoft()'
(a frozen-weight combination [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.6.0 dated 2026-08-28 and 2.7.0 dated 2026-09-09
DESCRIPTION | 48 - MD5 | 83 +- NAMESPACE | 3 NEWS.md | 114 +++ R/calm_gof.R |only R/cdef_gof.R | 23 R/deepgof.R | 23 R/def_ensemble_gof.R | 301 ++++----- R/def_gof.R | 378 ++++++----- R/ebrahim.gof-package.R | 74 +- R/ebrahim_farrington_test.R | 659 ++++++++++---------- R/edge_gof.R | 17 R/legoft.R | 30 R/run_all_gof.R | 56 + R/shrink_gof.R | 64 + README.md | 1080 ++++++++++++++++----------------- inst/CITATION | 6 inst/WORDLIST | 134 ++-- inst/doc/ebrahim-farrington-intro.R | 67 -- inst/doc/ebrahim-farrington-intro.Rmd | 652 +++++++++---------- inst/doc/ebrahim-farrington-intro.html | 100 +-- inst/doc/ebrahim-gof-toolbox.R | 9 inst/doc/ebrahim-gof-toolbox.Rmd | 47 + inst/doc/ebrahim-gof-toolbox.html | 60 + man/calm.gof.Rd |only man/cdef.gof.Rd | 7 man/deepgof1.Rd | 16 man/def.ensemble.gof.Rd | 23 man/def.gof.Rd | 36 - man/deploy.gof.Rd | 7 man/ebrahim.gof-package.Rd | 75 +- man/edge.gof.Rd | 17 man/edges.gof.Rd | 6 man/ef.gof.Rd | 45 + man/figures |only man/gof.features.Rd | 7 man/legoft.Rd | 9 man/legoft.localize.Rd | 7 man/run.all.gof.Rd | 56 + man/shrink.gof.Rd | 51 + tests/testthat/test-exports-smoke.R |only vignettes/ebrahim-farrington-intro.Rmd | 652 +++++++++---------- vignettes/ebrahim-gof-toolbox.Rmd | 47 + 43 files changed, 2856 insertions(+), 2233 deletions(-)
Title: Multi-Context Colocalization Analysis for QTL and GWAS Studies
Description: A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects,
based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero
effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS)
and quantitative trait loci (QTL) studies.
The ColocBoost model is described in Cao et. al. (2025) <doi:10.1101/2025.04.17.25326042>.
Author: Xuewei Cao [cre, aut, cph],
Haochen Sun [aut, cph],
Ru Feng [aut, cph],
Daniel Nachun [aut, cph],
Kushal Dey [aut, cph],
Gao Wang [aut, cph]
Maintainer: Xuewei Cao <xc2270@cumc.columbia.edu>
Diff between colocboost versions 1.0.9 dated 2026-06-08 and 1.0.10 dated 2026-09-09
colocboost-1.0.10/colocboost/DESCRIPTION | 8 colocboost-1.0.10/colocboost/MD5 | 77 - colocboost-1.0.10/colocboost/R/colocboost_assemble_cos.R | 31 colocboost-1.0.10/colocboost/R/colocboost_check_update_jk.R | 162 +- colocboost-1.0.10/colocboost/R/colocboost_init.R | 2 colocboost-1.0.10/colocboost/R/colocboost_output.R | 4 colocboost-1.0.10/colocboost/R/colocboost_plot.R | 5 colocboost-1.0.10/colocboost/R/colocboost_update.R | 52 colocboost-1.0.10/colocboost/R/colocboost_utils.R | 112 + colocboost-1.0.10/colocboost/R/colocboost_workhorse.R | 1 colocboost-1.0.10/colocboost/build/vignette.rds |binary colocboost-1.0.10/colocboost/inst/WORDLIST | 20 colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.R |only colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.Rmd |only colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.html |only colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.R | 2 colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.Rmd | 4 colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.html | 2 colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.R |only colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.Rmd |only colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.html |only colocboost-1.0.10/colocboost/inst/doc/Individual_Level_Colocalization.html | 10 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.R | 6 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.Rmd | 44 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.html | 67 - colocboost-1.0.10/colocboost/inst/doc/Partial_Overlap_Variants.Rmd | 7 colocboost-1.0.10/colocboost/inst/doc/Partial_Overlap_Variants.html | 6 colocboost-1.0.10/colocboost/inst/doc/announcements.Rmd | 5 colocboost-1.0.10/colocboost/inst/doc/announcements.html | 13 colocboost-1.0.10/colocboost/tests/testthat/test_Xref.R | 54 colocboost-1.0.10/colocboost/tests/testthat/test_large_outcome_inference.R |only colocboost-1.0.10/colocboost/tests/testthat/test_optimization_phase1.R | 631 ++++++++++ colocboost-1.0.10/colocboost/tests/testthat/test_utils.R | 10 colocboost-1.0.10/colocboost/vignettes/Advanced_Colocalization_Scenarios.Rmd |only colocboost-1.0.10/colocboost/vignettes/ColocBoost_Update.Rmd | 4 colocboost-1.0.10/colocboost/vignettes/Conceptual_Multi_Trait_Colocalization.Rmd |only colocboost-1.0.10/colocboost/vignettes/Interpret_ColocBoost_Output.Rmd | 44 colocboost-1.0.10/colocboost/vignettes/Partial_Overlap_Variants.Rmd | 7 colocboost-1.0.10/colocboost/vignettes/announcements.Rmd | 5 colocboost-1.0.10/colocboost/vignettes/figures |only colocboost-1.0.9/colocboost/man/figures/ColocBoost_update.gif |only colocboost-1.0.9/colocboost/man/figures/missing_representation.png |only 42 files changed, 1195 insertions(+), 200 deletions(-)
Title: Resolving Plant Taxon Names Using the Australian Plant Census
Description: The process of resolving and updating taxon names is necessary when
working with biodiversity data. 'APCalign' uses the Australian Plant Census
(APC) and the Australian Plant Name Index (APNI) to align and update plant
taxon names to current, accepted standards. 'APCalign' also supplies
information about the establishment status (i.e. native or introduced) of
plant taxa across different states/territories.
Author: Elizabeth Wenk [aut, cre, cph] ,
Daniel Falster [aut, ctb] ,
Will Cornwell [aut, ctb] ,
Fonti Kar [aut, ctb] ,
Carl Boettiger [ctb]
Maintainer: Elizabeth Wenk <e.wenk@unsw.edu.au>
Diff between APCalign versions 2.0.0 dated 2026-03-27 and 2.0.1 dated 2026-09-09
DESCRIPTION | 8 MD5 | 57 NEWS.md | 11 R/APCalign-package.R | 3 R/fuzzy_match.R | 24 R/load_taxonomic_resources.R | 4 R/match_taxa.R | 2698 +++------- R/native_anywhere_in_australia.R | 35 R/standardise_names.R | 145 R/strip_names.R | 40 R/synonyms_for_accepted_names.R | 34 R/utils.R |only README.md | 55 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST |only inst/doc/APCalign.Rmd | 6 inst/doc/APCalign.html | 6 man/default_version.Rd | 2 man/get_versions.Rd | 2 man/standardise_names.Rd | 9 tests/testthat/_snaps |only tests/testthat/benchmarks/standardise_names.csv | 8 tests/testthat/benchmarks/test_matches_alignments_updates.csv | 461 - tests/testthat/test-connection.R | 12 tests/testthat/test-functions-fuzzy_match.R |only tests/testthat/test-functions-standardise_names.R | 56 tests/testthat/test-match_branches.R |only tests/testthat/test-operation_outputs.R | 4 tests/testthat/test-state_diversity.R | 27 vignettes/APCalign.Rmd | 6 32 files changed, 1472 insertions(+), 2243 deletions(-)
Title: Generates Aoristic Probability Distributions
Description: It can sometimes be difficult to ascertain when some events (such as property crime)
occur because the victim is not present when the crime happens. As a result, police databases often
record a 'start' (or 'from') date and time, and an 'end' (or 'to') date and time. The time span between
these date/times can be minutes, hours, or sometimes days, hence the term 'Aoristic'.
Aoristic is one of the past tenses in Greek and represents an uncertain occurrence in time.
For events with a location described by either a latitude/longitude or X/Y coordinate pair,
and a start and end date/time, this package generates an aoristic data frame with aoristic weighted
probability values for each hour of the week, for each observation. The coordinates are not
necessary for the program to calculate aoristic weights; however, they are part of this package
because a spatial component has been integral to aoristic analysis from the start. Dummy
coordinates can be introduced if the user only has temporal data [...truncated...]
Author: Jerry Ratcliffe [aut, cre]
Maintainer: Jerry Ratcliffe <jerryr@sas.upenn.edu>
Diff between aoristic versions 1.1.1 dated 2022-10-20 and 2.0.0 dated 2026-09-09
DESCRIPTION | 24 ++- MD5 | 44 +++-- NAMESPACE | 1 NEWS.md |only R/aoristic.datacheck.R | 193 +++++++++----------------- R/aoristic.df.R | 341 ++++++++++++---------------------------------- R/aoristic.graph.R | 2 R/aoristic.plot.R | 4 R/aoristic.summary.R | 4 R/validation.R |only README.md | 272 ++++++++++++------------------------ man/CouncilDistrict.Rd | 24 +-- man/NYburg.Rd | 56 +++---- man/aoristic.all.graph.Rd | 52 +++---- man/aoristic.datacheck.Rd | 37 ++-- man/aoristic.density.Rd | 24 +-- man/aoristic.df.Rd | 36 ++-- man/aoristic.grid.Rd | 24 +-- man/aoristic.plot.Rd | 60 ++++---- man/aoristic.shp.Rd | 24 +-- man/aoristic.spdf.Rd | 24 +-- man/arlington.Rd | 24 +-- tests |only 23 files changed, 492 insertions(+), 778 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control
of Research Outputs.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [aut, ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.7 dated 2026-02-02 and 1.0.0 dated 2026-09-09
DESCRIPTION | 38 +-- MD5 | 54 +++-- NAMESPACE | 10 NEWS.md | 10 R/acro_init.R | 11 - R/acro_tables.R | 339 +++++++++++++++++++++++++++++++-- R/output_commands.R | 26 ++ R/utils.R |only R/zzz.R |only inst/AI_POLICY.md |only inst/WORDLIST | 7 inst/doc/welcome.html | 2 inst/notebooks |only man/acro_crosstab.Rd | 28 ++ man/acro_disable_rounding.Rd |only man/acro_enable_rounding.Rd |only man/acro_hist.Rd | 4 man/acro_init.Rd | 9 man/acro_pie.Rd |only man/acro_summarise.Rd |only man/acro_table.Rd | 14 + man/create_factors.Rd |only man/is_excluded.Rd |only man/is_invalid.Rd |only man/to_pandas_categorical.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-acro_crosstab.R | 54 +++++ tests/testthat/test-acro_hist.R | 80 +++++++ tests/testthat/test-acro_pie.R |only tests/testthat/test-acro_pivot_table.R | 14 + tests/testthat/test-acro_rounding.R |only tests/testthat/test-acro_summarise.R |only tests/testthat/test-acro_table.R | 219 ++++++++++++++++++++- tests/testthat/test-install_acro.R | 12 - 34 files changed, 854 insertions(+), 77 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural Bayes estimators, which are neural networks that map data to a point summary of the posterior distribution (Sainsbury-Dale et al., 2024, <doi:10.1080/00031305.2023.2249522>). These estimators are likelihood-free and amortised, in the sense that, once the neural networks are trained on simulated data, inference from observed data can be made in a fraction of the time required by conventional approaches. The package also supports amortised Bayesian or frequentist inference using neural networks that approximate the posterior or likelihood-to-evidence ratio (Zammit-Mangion et al., 2025, Sec. 3.2, 5.2, <doi:10.48550/arXiv.2404.12484>). The package accommodates any model for which simulation is feasible by allowing users to define models implicitly through simulated data.
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.2.1 dated 2026-04-28 and 0.2.2 dated 2026-09-09
DESCRIPTION | 6 MD5 | 32 +++-- NAMESPACE | 7 + R/core.R | 252 +++++++++++++++++++++++++++++++---------- R/estimators.R |only README.md | 52 +++++--- inst/doc/NeuralEstimators.html | 6 man/PointEstimator.Rd |only man/PosteriorEstimator.Rd |only man/RatioEstimator.Rd |only man/assess.Rd | 10 + man/cpu_device.Rd |only man/estimate.Rd | 8 - man/gpu_device.Rd |only man/infer.Rd |only man/logratio.Rd | 2 man/reactant_device.Rd |only man/sampleposterior.Rd | 4 man/savestate.Rd | 2 man/train.Rd | 40 +++++- tests/testthat/test-core.R | 123 ++++++++++++++++++-- 21 files changed, 419 insertions(+), 125 deletions(-)
More information about NeuralEstimators at CRAN
Permanent link
Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Arthur Garcia [aut],
Cristiane Gea [aut],
Diego Carvalho [ctb],
Diogo Santos [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Fernando Alexandrino [aut],
Luciano Mello [aut],
Rebecca Salles [a [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 2.0.707 dated 2026-05-22 and 2.0.717 dated 2026-09-09
DESCRIPTION | 19 ++- MD5 | 30 +++--- NAMESPACE | 113 +++++++++++++---------- R/ts_fil_fft.R | 159 +++++++++++++++++++++++++++----- R/ts_fil_gabor.R |only R/ts_fil_hp.R | 18 +++ R/ts_fil_remd.R | 141 +++++++++++++++++++++++------ R/ts_fil_spline.R | 47 ++++++++- R/ts_fil_winsor.R | 7 + R/tspredbench.R | 2 README.md | 246 +++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/m1.Rd | 2 man/ts_fil_fft.Rd | 25 ++++- man/ts_fil_gabor.Rd |only man/ts_fil_remd.Rd | 18 +++ man/ts_fil_spline.Rd | 12 +- 17 files changed, 578 insertions(+), 261 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 2.0.16 dated 2026-07-24 and 2.0.17 dated 2026-09-09
DESCRIPTION | 12 +- MD5 | 58 ++++++++++---- NAMESPACE | 13 +++ NEWS.md | 38 +++++++++ R/RcppExports.R | 48 +++++++++++ R/llik.R | 12 +- R/llikNew.R |only R/ptr.R |only inst/include |only man/dot-rxode2llPtr.Rd |only man/llikBetaProportion.Rd |only man/llikDblExp.Rd |only man/llikFrechet.Rd |only man/llikGumbel.Rd |only man/llikInvChisq.Rd |only man/llikInvGamma.Rd |only man/llikLnorm.Rd |only man/llikLogis.Rd |only man/llikNbinom.Rd | 2 man/llikNbinomMu.Rd | 2 man/llikPareto.Rd |only man/llikParetoType2.Rd |only man/llikRayleigh.Rd |only man/llikScaledInvChisq.Rd |only src/RcppExports.cpp | 155 ++++++++++++++++++++++++++++++++++++++ src/init.c | 63 +++++++++++++++ src/llik.h | 36 ++++++++ src/llik2.h | 12 ++ src/llikBetaProportion.cpp |only src/llikDblExp.cpp |only src/llikFrechet.cpp |only src/llikGumbel.cpp |only src/llikInvChisq.cpp |only src/llikInvGamma.cpp |only src/llikLnorm.cpp |only src/llikLogis.cpp |only src/llikNbinom.cpp | 51 ++++++++++-- src/llikNbinom2.cpp | 31 ++++++- src/llikPareto.cpp |only src/llikParetoType2.cpp |only src/llikRayleigh.cpp |only src/llikScaledInvChisq.cpp |only src/ptr.c |only tests/testthat/test-llik.R | 106 ++++++++++++++++++++++++- tests/testthat/test-newFamilies.R |only 45 files changed, 590 insertions(+), 49 deletions(-)
Title: Principal Components Analysis using NIPALS or Weighted EMPCA,
with Gram-Schmidt Orthogonalization
Description: Principal Components Analysis of a matrix using Non-linear
Iterative Partial Least Squares or weighted Expectation Maximization
PCA with Gram-Schmidt orthogonalization of the scores and loadings.
Optimized for speed. See Andrecut (2009) <doi:10.1089/cmb.2008.0221>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between nipals versions 1.0 dated 2024-12-02 and 1.2 dated 2026-09-09
DESCRIPTION | 11 - MD5 | 30 +-- NAMESPACE | 10 - NEWS.md | 9 + R/empca.R | 256 ++++++++++++++++-------------- R/nipals.R | 316 +++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/empca_notes.html | 8 inst/doc/nipals_algorithm.html | 26 +-- inst/doc/nipals_comparisons.html | 5 inst/doc/nipals_optimization.html | 5 man/empca.Rd | 14 - man/nipals.Rd | 13 - tests/testthat/test-empca.R | 163 ++++++++++--------- tests/testthat/test-nipals.R | 171 +++++++++++--------- tests/testthat/test-uscrime.R | 49 +++-- 16 files changed, 596 insertions(+), 490 deletions(-)
Title: 'NetCDF' Geometry and Time Series
Description: Tools to create time series and geometry 'NetCDF' files.
Author: David Blodgett [aut, cre],
Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between ncdfgeom versions 1.2.2 dated 2026-04-22 and 1.2.3 dated 2026-09-09
DESCRIPTION | 17 +-- MD5 | 44 ++++----- NEWS.md | 9 + R/calculate_area_intersection_weights.R | 6 - R/read_timeseries_dsg.R | 10 +- R/write_geometry.R | 12 +- R/write_point_dsg.R | 3 R/write_timeseries_dsg.R | 8 - build/vignette.rds |binary inst/CITATION | 8 + inst/WORDLIST | 1 inst/doc/geometry.html | 93 -------------------- inst/doc/ncdfgeom.Rmd | 15 +-- inst/doc/ncdfgeom.html | 110 +++--------------------- inst/doc/polygon_intersection.R | 10 +- inst/doc/polygon_intersection.Rmd | 10 +- inst/doc/polygon_intersection.html | 19 +--- inst/doc/timeseries.html | 58 +----------- man/calculate_area_intersection_weights.Rd | 2 tests/testthat/test_geom_examples.R | 19 +--- tests/testthat/test_read-write_timeseries_dsg.R | 9 + vignettes/ncdfgeom.Rmd | 15 +-- vignettes/polygon_intersection.Rmd | 10 +- 23 files changed, 145 insertions(+), 343 deletions(-)
Title: Automatic Plotting and Theming of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 1.2.2 dated 2026-08-29 and 1.2.3 dated 2026-09-09
autograph-1.2.2/autograph/R/graph_costs.R |only autograph-1.2.3/autograph/DESCRIPTION | 13 autograph-1.2.3/autograph/MD5 | 42 - autograph-1.2.3/autograph/NAMESPACE | 8 autograph-1.2.3/autograph/NEWS.md | 26 autograph-1.2.3/autograph/R/layout_aesthetics.R |only autograph-1.2.3/autograph/R/scale_mdate.R |only autograph-1.2.3/autograph/R/theme_aesthetics.R |only autograph-1.2.3/autograph/R/theme_colorblind.R | 123 --- autograph-1.2.3/autograph/R/zzz.R | 10 autograph-1.2.3/autograph/inst/tutorials/autograph1/visualisation.Rmd | 111 +- autograph-1.2.3/autograph/inst/tutorials/autograph1/visualisation.html | 392 ++++++---- autograph-1.2.3/autograph/man/check_colors.Rd |only autograph-1.2.3/autograph/man/check_layout.Rd | 236 ++++-- autograph-1.2.3/autograph/man/list_fonts.Rd | 1 autograph-1.2.3/autograph/man/mdate_scales.Rd |only autograph-1.2.3/autograph/man/theme_colorblind.Rd | 69 - autograph-1.2.3/autograph/man/theme_medium.Rd | 1 autograph-1.2.3/autograph/man/theme_set.Rd | 1 autograph-1.2.3/autograph/tests/testthat/Rplots.pdf |binary autograph-1.2.3/autograph/tests/testthat/helper-manynet.R | 32 autograph-1.2.3/autograph/tests/testthat/test-functional_coverage.R | 8 autograph-1.2.3/autograph/tests/testthat/test-functional_layouts.R | 55 + autograph-1.2.3/autograph/tests/testthat/test-grapht.R | 13 autograph-1.2.3/autograph/tests/testthat/test-layout_aesthetics.R |only autograph-1.2.3/autograph/tests/testthat/test-scale_mdate.R |only 26 files changed, 698 insertions(+), 443 deletions(-)
Title: Taxonomic Name Reconciliation Against the 'WCVP' Backbone
Description: Standardizes and reconciles scientific plant names against
a World Checklist of Vascular Plants ('WCVP')-style taxonomic
backbone. The package parses names into taxonomic components and
applies staged exact and fuzzy matching for binomial and trinomial
inputs, including infraspecific rank-aware checks. It also returns
accepted-name context and row-level matching flags to support
reproducible, auditable preprocessing for downstream biodiversity,
spatial, and trait analyses. A user-supplied backbone can be passed
through 'target_df'; when the optional companion package 'wcvpdata'
is installed, its default checklist can also be used.
Author: Paul Efren Santos Andrade [aut, cre, cph]
Maintainer: Paul Efren Santos Andrade <paulefrens@gmail.com>
Diff between wcvpmatch versions 0.0.1 dated 2026-03-23 and 0.0.2 dated 2026-09-08
DESCRIPTION | 16 MD5 | 92 +-- NAMESPACE | 10 R/build_tbl.R | 2 R/direct_match.R | 186 ++---- R/direct_match_species_within_genus.R | 29 R/distribution.R |only R/fuzzy_match_genus.R | 64 +- R/fuzzy_match_species_within_genus.R | 60 -- R/genus_match.R | 5 R/global.R | 53 + R/match_infraspecies_within_species.R | 32 - R/matching.R | 59 +- R/prefilter_target_by_genus.R | 129 +++- R/setup_info.R | 11 R/suffix_match_species_within_genus.R | 54 + R/synonyms.R |only R/utils.R | 283 ++++++++- README.md | 468 ++++------------ build |only inst |only man/build_genus_index.Rd | 9 man/classify_spnames.Rd | 2 man/prefilter_target_by_genus.Rd | 9 man/wcvp_direct_match.Rd | 10 man/wcvp_direct_match_species_within_genus.Rd | 3 man/wcvp_distribution.Rd |only man/wcvp_fuzzy_match_genus.Rd | 9 man/wcvp_fuzzy_match_species_within_genus.Rd | 3 man/wcvp_genus_match.Rd | 3 man/wcvp_matching.Rd | 22 man/wcvp_setup_info.Rd | 3 man/wcvp_suffix_match_species_within_genus.Rd | 9 man/wcvp_synonyms.Rd |only man/wcvpmatch-package.Rd | 6 tests/testthat/helper-wcvpdata.R | 6 tests/testthat/test-direct_match.R | 6 tests/testthat/test-direct_match_species_within_genus.R | 62 +- tests/testthat/test-distribution.R |only tests/testthat/test-fuzzy_match_genus.R | 16 tests/testthat/test-fuzzy_match_species_within_genus.R | 14 tests/testthat/test-genus_match.R | 8 tests/testthat/test-matching-infraspecies.R | 4 tests/testthat/test-matching.R | 99 +++ tests/testthat/test-performance-internals.R |only tests/testthat/test-prefilter-target-by-genus.R | 66 ++ tests/testthat/test-suffix_match_species_within_genus.R | 35 - tests/testthat/test-synonyms.R |only vignettes |only 49 files changed, 1184 insertions(+), 773 deletions(-)
Title: Worked Derivations for Classical Epidemiological Measures
Description: Computes classical epidemiological measures and returns the
complete worked derivation alongside the result: every intermediate
quantity, the formula, and the formula with the observed numbers
substituted in. Intended for teaching, for checking hand calculations,
and for generating worked solutions in course materials. Scope is
deliberately limited to methods a student can compute by hand on paper.
Methods follow Mantel and Haenszel (1959) <doi:10.1093/jnci/22.4.719>,
Greenland and Robins (1985, Biometrics 41, 55-68), Robins, Breslow and
Greenland (1986, Biometrics 42, 311-323), and Breslow and Day (1980,
IARC Scientific Publications No. 32).
Author: Raj Subedi [aut, cre]
Maintainer: Raj Subedi <rajsubediresearch@gmail.com>
Diff between epibyhand versions 0.1.0 dated 2026-08-05 and 0.2.0 dated 2026-09-08
DESCRIPTION | 8 +-- MD5 | 33 +++++++------ NAMESPACE | 1 NEWS.md | 24 +++++++++ R/derivation.R | 24 +++++++++ R/epi2x2.R | 21 ++++++++ R/measures.R | 8 +-- R/screening.R |only README.md | 39 ++++++++++++++- inst/CITATION | 1 inst/doc/epibyhand.R | 18 +++++++ inst/doc/epibyhand.Rmd | 35 ++++++++++++++ inst/doc/epibyhand.html | 90 ++++++++++++++++++++++++++++++++---- man/confint.epibyhand_derivation.Rd | 13 ++++- man/epibyhand-package.Rd | 5 ++ man/predictive_value.Rd |only tests/testthat/test-confint.R |only tests/testthat/test-labels.R |only tests/testthat/test-screening.R |only vignettes/epibyhand.Rmd | 35 ++++++++++++++ 20 files changed, 317 insertions(+), 38 deletions(-)
Title: Generalized Propensity Score Estimation and Matching for
Multiple Groups
Description: Implements the Vector Matching algorithm to match multiple
treatment groups based on previously estimated generalized propensity
scores. The package includes tools for visualizing initial confounder
imbalances, estimating treatment assignment probabilities using various
methods, defining the common support region, performing matching across
multiple groups, and evaluating matching quality. For more details, see
Lopez and Gutman (2017) <doi:10.1214/17-STS612>.
Author: Mateusz Kolek [aut, cre, cph]
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>
Diff between vecmatch versions 1.3.0 dated 2025-12-01 and 1.4.0 dated 2026-09-08
DESCRIPTION | 9 MD5 | 46 ++-- NEWS.md | 108 +++++++++ R/balqual.R | 302 +++++++++++++++++++++++++-- R/chk-utils.R | 21 - R/csregion.R | 43 +++ R/match_gps.R | 38 ++- R/optimize_gps.R | 26 ++ R/raincloud.R | 11 - R/utils.R | 343 +++++++++++++++++++++++++++++++ README.md | 9 inst/doc/optimizing-matching.html | 64 ++--- inst/doc/vecmatch.R | 17 + inst/doc/vecmatch.Rmd | 39 +++ inst/doc/vecmatch.html | 262 ++++++++++++++++++++---- man/balqual.Rd | 89 +++++++- man/match_gps.Rd | 6 man/vecmatch-package.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-balqual.R | 403 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-csregion.R | 76 ++++++ tests/testthat/test-match_gps.R | 176 ++++++++++++++++ tests/testthat/test-optimize_gps.R | 49 ++++ vignettes/vecmatch.Rmd | 39 +++ 24 files changed, 2005 insertions(+), 172 deletions(-)
Title: Feature-Based Clustering of Longitudinal Trajectories
Description: Identifies clusters of individual longitudinal trajectories. In the spirit of Leffondre et al. (2004), the procedure involves identifying each trajectory to a point in the space of measures. In this context, a measure is a quantity meant to capture a certain characteristic feature of the trajectory. The points in the space of measures are then clustered using a version of the Spectral Clustering algorithm.
Author: Marie-Pierre Sylvestre [aut],
Laurence Boulanger [aut, cre],
Jean-Benoit Bergeron [ctb],
Gillis Delmas [ctb],
Tchouangue Dinkou [ctb],
Dan Vatnik [ctb]
Maintainer: Laurence Boulanger <laurence.boulanger@umontreal.ca>
Diff between traj versions 3.0.1 dated 2026-03-15 and 3.1.0 dated 2026-09-08
traj-3.0.1/traj/data/trajdata.rda |only traj-3.1.0/traj/DESCRIPTION | 21 - traj-3.1.0/traj/MD5 | 47 +- traj-3.1.0/traj/NAMESPACE | 41 +- traj-3.1.0/traj/NEWS.md | 12 traj-3.1.0/traj/R/CubeRoot.R | 1 traj-3.1.0/traj/R/Der.R | 14 traj-3.1.0/traj/R/FctMean.R | 5 traj-3.1.0/traj/R/First.R | 3 traj-3.1.0/traj/R/FirstMode.R | 3 traj-3.1.0/traj/R/Last.R | 3 traj-3.1.0/traj/R/data.R | 14 traj-3.1.0/traj/R/plot.trajClusters.R | 499 +++++++++++++++++++++---------- traj-3.1.0/traj/R/quiet.R | 2 traj-3.1.0/traj/R/spect.R | 103 +++--- traj-3.1.0/traj/R/trajClusters.R | 386 ++++++++++++++--------- traj-3.1.0/traj/R/trajMeasures.R | 344 ++++++++------------- traj-3.1.0/traj/R/trajReduce.R | 55 +-- traj-3.1.0/traj/R/zzz.R |only traj-3.1.0/traj/data/trajdata.RData |only traj-3.1.0/traj/man/plot.trajClusters.Rd | 16 traj-3.1.0/traj/man/traj-package.Rd | 5 traj-3.1.0/traj/man/trajClusters.Rd | 18 - traj-3.1.0/traj/man/trajMeasures.Rd | 29 + traj-3.1.0/traj/man/trajReduce.Rd | 7 traj-3.1.0/traj/man/trajdata.Rd | 14 26 files changed, 970 insertions(+), 672 deletions(-)
Title: Methods for Penetrance Estimation in Family-Based Studies
Description: Implements statistical methods for estimating disease penetrance in
family-based studies. Penetrance refers to the probability of disease
manifestation in individuals carrying specific genetic variants. The package
provides tools for age-specific penetrance estimation, handling missing data,
and accounting for ascertainment bias in family studies.
Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2025) <doi:10.1093/bioadv/vbaf154>.
Author: Sol Rosito [cre],
Nicolas Kubista [aut],
BayesMendel Lab [aut],
Giovanni Parmigiani [aut],
Danielle Braun [aut],
Zaid Al-Ississ [aut],
Alice Zhang [aut]
Maintainer: Sol Rosito <bmendel@jimmy.harvard.edu>
Diff between penetrance versions 0.1.3 dated 2026-05-15 and 0.1.4 dated 2026-09-08
DESCRIPTION | 10 - MD5 | 28 +-- R/imputeAges.R | 63 +----- R/mhChain.R | 358 +++++++++++++++++---------------------- R/mhLoglikehood.r | 194 ++++++++------------- R/outputHelpers.R | 254 +++++++-------------------- R/penetranceMain.R | 4 R/priorElicitation.R | 19 +- README.md | 286 ++++++++++++++++--------------- data/simulated_families.RData |binary data/test_fam2.RData |binary man/apply_burn_in.Rd | 2 man/calculateEmpiricalDensity.Rd | 15 + man/makePriors.Rd | 2 man/penetrance.Rd | 1 15 files changed, 541 insertions(+), 695 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.2.7 dated 2026-03-19 and 0.2.8 dated 2026-09-08
NMsim-0.2.7/NMsim/R/NMwriteSectionOne.R |only NMsim-0.2.7/NMsim/inst/examples/data/xgxr032_bs.csv |only NMsim-0.2.7/NMsim/inst/examples/data/xgxr032_bs.rds |only NMsim-0.2.7/NMsim/inst/examples/data/xgxr032_bs_meta.txt |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033.coi |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033.cor |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033.phi |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033.pnm |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033.shk |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033_etas.txt |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033_input.rds |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr033_res.txt |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr044.mod |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr044.pnm |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr044_input.rds |only NMsim-0.2.7/NMsim/inst/examples/nonmem/xgxr132.mod |only NMsim-0.2.7/NMsim/inst/examples/outputs |only NMsim-0.2.7/NMsim/man/figures/ACOP_logo_transp.png |only NMsim-0.2.7/NMsim/tests/simres |only NMsim-0.2.7/NMsim/tests/testOutput2 |only NMsim-0.2.7/NMsim/tests/testthat/simres |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/pred_data1.csv |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/pred_data1.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/pred_data1_meta.txt |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/xgxr12.csv |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/xgxr12.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/data/xgxr12_meta.txt |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/NMsim_xgxr021_default_01_paths.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/NMsim_xgxr021_default_01_paths_res.fst |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd3_NWPRI |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd3_NWPRI_MetaData.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01.73 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01.73_MetaData.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01.74 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01.74_MetaData.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01_paths.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01_paths_res.fst |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01_paths.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01_paths_res.fst |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_paths.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr025_noname |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04_MetaData.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04_ResultsData.fst |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/backup_xgxr057 |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/pred030.pnm |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/pred030.shk |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/pred030_input.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/pred030_res.txt |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/xgxr021_sd1_NMreadSim |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/xgxr021com.mod |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/xgxr033_input.rds |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/xgxr053.coi |only 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NMsim-0.2.8/NMsim/R/NMsim_NWPRI.R | 9 NMsim-0.2.8/NMsim/R/NMsim_VarCov.R | 2 NMsim-0.2.8/NMsim/R/NMsim_helpers.R | 43 NMsim-0.2.8/NMsim/R/NMwriteInits.R | 26 NMsim-0.2.8/NMsim/R/NMwriteInitsOne.R | 335 ++-- NMsim-0.2.8/NMsim/R/NMwriteSizes.R | 4 NMsim-0.2.8/NMsim/R/addEVID2.R | 14 NMsim-0.2.8/NMsim/R/cleaningPatterns.R | 9 NMsim-0.2.8/NMsim/R/forestSummarize.R | 3 NMsim-0.2.8/NMsim/R/isSame.R |only NMsim-0.2.8/NMsim/R/prioritizePaths.R | 2 NMsim-0.2.8/NMsim/R/sampleCovs.R | 116 + NMsim-0.2.8/NMsim/R/simPopEtas.R | 7 NMsim-0.2.8/NMsim/R/stringToSection.R |only NMsim-0.2.8/NMsim/R/typicalize.R | 22 NMsim-0.2.8/NMsim/README.md | 75 - NMsim-0.2.8/NMsim/inst/examples/derived/dat_sim1.rds |binary NMsim-0.2.8/NMsim/man/NMreadSim.Rd | 110 - NMsim-0.2.8/NMsim/man/NMreadSimModTab.Rd | 80 - NMsim-0.2.8/NMsim/man/NMreadSimModTabOne.Rd | 83 - NMsim-0.2.8/NMsim/man/NMsim.Rd | 159 +- NMsim-0.2.8/NMsim/man/NMwriteInits.Rd | 2 NMsim-0.2.8/NMsim/man/figures/README-simple-sim-1.png |binary 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Title: Native and Extensible R Driver for 'Zarr'
Description: The 'Zarr' specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native 'Zarr' implementation in R with support for all required features of 'Zarr' version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between zarr versions 0.5.0 dated 2026-08-30 and 0.5.1 dated 2026-09-08
DESCRIPTION | 6 ++-- MD5 | 30 +++++++++++------------ NEWS.md | 6 ++++ R/api.R | 5 +-- R/array.R | 53 ++++++++++++++++++++++++++++++---------- R/chunking.R | 36 ++++++++++++++++++++++++++- R/chunking_regular.R | 56 +++++++++++++++++++++++++++---------------- R/store_s3.R | 3 +- R/utils.R | 7 +++-- R/zzz.R | 1 README.md | 4 +-- man/chunk_grid_regular.Rd | 22 ++++++++++++++++ man/create_zarr.Rd | 5 +-- man/s3_list_dir.Rd | 3 +- man/zarr_array.Rd | 29 ++++++++++++++++++++-- tests/testthat/test-resize.R | 4 +++ 16 files changed, 201 insertions(+), 69 deletions(-)
Title: Reproducible Data Capsules with Provenance and Fallback
Description: Tools for building brick-proof, reproducible, self-contained
data capsules.
Resolves open-data sources through the Comprehensive Knowledge
Archive Network ('CKAN', <https://ckan.org/>) package_show and
package_search endpoints, records and verifies provenance with
Secure Hash Algorithm 256 ('SHA-256') digests and Internet Archive
'Wayback Machine' (<https://web.archive.org/>) snapshots, validates
downloaded data against a pinned schema, and falls back to
schema-driven synthetic data when the real source is unreachable.
Run records are captured in a manifest plus a plain-language summary
so any result can be traced back to its inputs. Also ships a small
compiled C core (fast summary statistics and a self-contained
'SHA-256') that sibling packages in the 'rmorie' ecosystem reach
through 'LinkingTo' for a single, shared numeric and
provenance-hashing backend.
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriebricklayer versions 0.3.7 dated 2026-08-05 and 0.3.9 dated 2026-09-08
DESCRIPTION | 11 +++++---- MD5 | 41 +++++++++++++++++++++--------------- NAMESPACE | 2 + NEWS.md | 33 ++++++++++++++++++++++++++++ R/agent_bundle.R | 26 +++++++++++++++------- R/json_native.R |only R/lib_data_loader.R | 14 ++++++------ R/lib_helpers.R | 25 +++++++++++++++++++++ R/lib_manifest.R | 10 +++++--- R/sha256_native.R |only README.md | 9 +++++++ inst/CITATION | 1 inst/doc/capsules.html | 2 - inst/scripts/setup_and_run.R | 15 ++++--------- man/agent_bundle.Rd | 18 +++++++++++---- man/bricklayer_json_from_json.Rd |only man/bricklayer_json_to_json.Rd |only man/write_manifest_json.Rd | 6 ++--- tests/testthat/test-agent-bundle.R |only tests/testthat/test-capsule.R | 12 ++++------ tests/testthat/test-data-loader.R | 31 +++++++++++---------------- tests/testthat/test-fetch-native.R | 20 +++++++++++++++++ tests/testthat/test-json-branches.R |only tests/testthat/test-json-native.R |only tests/testthat/test-json-parity.R |only tests/testthat/test-sha256-native.R |only 26 files changed, 191 insertions(+), 85 deletions(-)
More information about rmoriebricklayer at CRAN
Permanent link
Title: NHS and Healthcare-Related Data for Education and Training
Description: Free United Kingdom National Health Service (NHS) and other healthcare, or population health-related data for education and training purposes. This package contains synthetic data based on real healthcare datasets, or cuts of open-licenced official data. This package exists to support skills development in the NHS-R community: <https://nhsrcommunity.com/>.
Author: Zoe Turner [aut, cre] ,
Chris Mainey [aut] ,
Tom Jemmett [aut] ,
Fran Barton [aut] ,
Gary Hutson [aut] ,
NHS-R community [cph]
Maintainer: Zoe Turner <zoe.turner3@nhs.net>
Diff between NHSRdatasets versions 0.3.0 dated 2021-03-13 and 1.0.0 dated 2026-09-08
NHSRdatasets-0.3.0/NHSRdatasets/man/figures |only NHSRdatasets-1.0.0/NHSRdatasets/DESCRIPTION | 38 NHSRdatasets-1.0.0/NHSRdatasets/MD5 | 112 NHSRdatasets-1.0.0/NHSRdatasets/NEWS.md | 82 NHSRdatasets-1.0.0/NHSRdatasets/R/LOS_model.R | 67 NHSRdatasets-1.0.0/NHSRdatasets/R/ae_attendances.R | 156 - NHSRdatasets-1.0.0/NHSRdatasets/R/apha_cpd_survey.R |only NHSRdatasets-1.0.0/NHSRdatasets/R/covid19.R |only NHSRdatasets-1.0.0/NHSRdatasets/R/ons_mortality.R | 89 NHSRdatasets-1.0.0/NHSRdatasets/R/ons_uk_population_2023.R |only NHSRdatasets-1.0.0/NHSRdatasets/R/stranded_patient_model.R | 74 NHSRdatasets-1.0.0/NHSRdatasets/R/synthetic_news_data.R | 75 NHSRdatasets-1.0.0/NHSRdatasets/README.md | 286 +- NHSRdatasets-1.0.0/NHSRdatasets/build/vignette.rds |binary NHSRdatasets-1.0.0/NHSRdatasets/data/apha_cpd_survey.rda |only NHSRdatasets-1.0.0/NHSRdatasets/data/covid19.rda |only NHSRdatasets-1.0.0/NHSRdatasets/data/ons_uk_population_2023.rda |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/LOS_model.R | 53 NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/LOS_model.Rmd | 514 ++-- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/LOS_model.html | 1167 ++++++---- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/NHSRdatasets.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/NHSRdatasets.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/NHSRdatasets.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ae_attendances.R | 248 +- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ae_attendances.Rmd | 515 ++-- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ae_attendances.html | 869 ++++--- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/apha_cpd_survey.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/apha_cpd_survey.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/apha_cpd_survey.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/contributing.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/contributing.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/contributing.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/covid19.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/covid19.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/covid19.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_apha_cpd_survey.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_apha_cpd_survey.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_apha_cpd_survey.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_mortality.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_mortality.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_mortality.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_uk_population_2023.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_uk_population_2023.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/create_ons_uk_population_2023.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_mortality.R | 421 --- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_mortality.Rmd | 639 ----- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_mortality.html | 953 +++----- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_uk_population_2023.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_uk_population_2023.Rmd |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/ons_uk_population_2023.html |only NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/stranded_model.R | 62 NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/stranded_model.Rmd | 286 +- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/stranded_model.html | 634 +++-- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/synthetic_news_data.R | 93 NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/synthetic_news_data.Rmd | 266 +- NHSRdatasets-1.0.0/NHSRdatasets/inst/doc/synthetic_news_data.html | 634 +++-- NHSRdatasets-1.0.0/NHSRdatasets/inst/hex_logo.R |only NHSRdatasets-1.0.0/NHSRdatasets/inst/images |only NHSRdatasets-1.0.0/NHSRdatasets/man/LOS_model.Rd | 80 NHSRdatasets-1.0.0/NHSRdatasets/man/ae_attendances.Rd | 171 - 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Title: eXtensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Ross Bennett [ctb],
Corwin Joy [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between xts versions 0.14.2 dated 2026-02-28 and 0.14.3 dated 2026-09-08
DESCRIPTION | 6 +-- MD5 | 37 +++++++++++----------- NEWS.md | 12 ++++++- R/axTicksByTime.R | 2 - R/list.R | 2 - R/na.R | 4 +- R/parse8601.R | 47 ++++++++++++++++++++++++++++ R/xts.methods.R | 60 +++--------------------------------- build/vignette.rds |binary inst/doc/xts-faq.R | 2 - inst/doc/xts-faq.pdf |binary inst/doc/xts.R | 2 - inst/doc/xts.pdf |binary inst/tinytest/test-merge.R | 4 +- inst/tinytest/test-parseTimeOfDay.R |only inst/tinytest/test-tclass.R | 4 +- inst/tinytest/test-tformat.R | 2 - inst/tinytest/test-tzone.R | 2 - inst/tinytest/test-xts.methods.R | 2 - inst/tinytest/test-zoo.R | 16 --------- 20 files changed, 96 insertions(+), 108 deletions(-)
Title: More Flexible Form of Boolean Verbose
Description: R functions are not supposed to print text without giving
the user the option to turn the printing off or on using a Boolean
'verbose' in a construct like 'if(verbose) print(...)'. But this black/white
approach is rather rigid, and an approach with shades of gray might be more
appropriate in many circumstances. As of Version 1.4, also supports text
and background colors, as well as text styles.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between vprint versions 1.3 dated 2026-07-23 and 1.4 dated 2026-09-08
DESCRIPTION | 14 +++++++------ MD5 | 17 ++++++++-------- NAMESPACE | 1 R/vprint.R | 52 ++++++++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/vprint.Rmd | 11 ++++++++-- inst/doc/vprint.html | 16 +++++++++------ man/vprint.Rd | 13 +++++++++--- vignettes/colors.jpg |only vignettes/vprint.Rmd | 11 ++++++++-- 10 files changed, 87 insertions(+), 48 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 10.1.0 dated 2025-11-17 and 11.1.0 dated 2026-09-08
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SimInf-11.1.0/SimInf/man/u0_SIS.Rd | 81 - SimInf-11.1.0/SimInf/man/u0_SISe3.Rd | 118 + SimInf-11.1.0/SimInf/man/u0_from_individual_events.Rd |only SimInf-11.1.0/SimInf/man/v0-set.Rd | 89 - SimInf-11.1.0/SimInf/src/SimInf.c | 197 ++ SimInf-11.1.0/SimInf/src/SimInf_internal.h | 25 SimInf-11.1.0/SimInf/src/misc/SimInf_trajectory.c | 626 ++++++--- SimInf-11.1.0/SimInf/src/models/SEIR.c | 8 SimInf-11.1.0/SimInf/src/models/SIR.c | 8 SimInf-11.1.0/SimInf/src/models/SIS.c | 8 SimInf-11.1.0/SimInf/src/models/SISe.c | 8 SimInf-11.1.0/SimInf/src/models/SISe3.c | 8 SimInf-11.1.0/SimInf/src/models/SISe3_sp.c | 8 SimInf-11.1.0/SimInf/src/models/SISe_sp.c | 8 SimInf-11.1.0/SimInf/src/solvers/SimInf_solver.c | 41 SimInf-11.1.0/SimInf/src/solvers/SimInf_solver_aem.c | 98 - SimInf-11.1.0/SimInf/src/solvers/SimInf_solver_mssm.c | 143 +- SimInf-11.1.0/SimInf/src/solvers/SimInf_solver_mssm_crn.c |only SimInf-11.1.0/SimInf/src/solvers/SimInf_solver_ssm.c | 124 + SimInf-11.1.0/SimInf/tests/SEIR.R | 33 SimInf-11.1.0/SimInf/tests/SIR.R | 76 - SimInf-11.1.0/SimInf/tests/SIS.R | 12 SimInf-11.1.0/SimInf/tests/SISe.R | 16 SimInf-11.1.0/SimInf/tests/SISe3.R | 24 SimInf-11.1.0/SimInf/tests/SISe3_sp.R | 24 SimInf-11.1.0/SimInf/tests/SISe_sp.R | 14 SimInf-11.1.0/SimInf/tests/SimInf.R | 18 SimInf-11.1.0/SimInf/tests/SimInf_events.R | 68 SimInf-11.1.0/SimInf/tests/SimInf_model.R | 13 SimInf-11.1.0/SimInf/tests/abc-ldata.R | 6 SimInf-11.1.0/SimInf/tests/individual_events.R | 101 + SimInf-11.1.0/SimInf/tests/ldata_sp.R | 8 SimInf-11.1.0/SimInf/tests/match_compartments.R | 50 SimInf-11.1.0/SimInf/tests/mparse.R | 55 SimInf-11.1.0/SimInf/tests/pfilter.R | 24 SimInf-11.1.0/SimInf/tests/punchcard.R | 90 + SimInf-11.1.0/SimInf/tests/sample_select.R | 20 SimInf-11.1.0/SimInf/tests/solver_aem.R | 16 SimInf-11.1.0/SimInf/tests/v0.R | 17 SimInf-11.1.0/SimInf/vignettes/SimInf.Rnw | 35 SimInf-11.1.0/SimInf/vignettes/SimInf.bib | 4 SimInf-11.1.0/SimInf/vignettes/mparse.Rmd |only SimInf-11.1.0/SimInf/vignettes/post-process-data.Rmd | 174 +- SimInf-11.1.0/SimInf/vignettes/scheduled-events.Rmd | 594 +++++++- 195 files changed, 11932 insertions(+), 5322 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational
algebra, and on production experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as 'Spark',
databases, and 'data.table'. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 1.4.99 dated 2023-08-19 and 1.5.1 dated 2026-09-08
DESCRIPTION | 10 - MD5 | 44 +++--- NAMESPACE | 26 ++-- NEWS.md | 6 R/sql_node.R | 2 R/wrap_ex.R | 2 README.md | 28 ++-- build/vignette.rds |binary inst/doc/AssigmentPartitioner.html | 234 ++++++++++++++++++------------------- inst/doc/Parameterized_rquery.R | 2 inst/doc/Parameterized_rquery.html | 5 inst/doc/PipeableSQL.R | 4 inst/doc/PipeableSQL.html | 8 - inst/doc/QueryGeneration.html | 5 inst/doc/R_mapping.R | 12 - inst/doc/R_mapping.html | 15 +- inst/doc/rquery_intro.R | 2 inst/doc/rquery_intro.html | 9 - inst/doc/rquery_many_columns.html | 5 inst/doc/sql_quoting.html | 5 man/ex.Rd | 2 man/rquery-package.Rd | 5 man/sql_node.Rd | 2 23 files changed, 235 insertions(+), 198 deletions(-)
Title: Read/Write Files in Key-Value-Hierarchy Format
Description: The format KVH is a lightweight format that can be read/written both by humans and machines.
It can be useful in situations where XML or alike formats seem to be an overkill.
We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between kvh versions 1.4.2 dated 2022-01-26 and 1.5.0 dated 2026-09-08
DESCRIPTION | 18 +++++++----- MD5 | 21 +++++++-------- NEWS | 61 +++++++++++++++++++------------------------ R/RcppExports.R | 10 +++++-- R/kvh.R | 20 +++++++++----- inst/include/kvh.h | 4 +- man/kvh_read.Rd | 10 +++++-- man/obj2kvh.Rd | 2 - src/RcppExports.cpp | 9 +++--- src/rcpp_kvh.cpp | 64 ++++++++++++++++++++++++++++++++++++++-------- tests/testthat/res.RData |only tests/testthat/test_kvh.R | 27 +++++++++++++------ 12 files changed, 157 insertions(+), 89 deletions(-)
Title: Composite-Based Structural Equation Modeling
Description: Estimate, assess, test, and study linear, nonlinear, hierarchical
and multigroup structural equation models using composite-based approaches
and procedures, including estimation techniques such as partial least squares
path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc),
generalized structured component analysis (GSCA), generalized structured
component analysis with uniqueness terms (GSCAm), generalized canonical
correlation analysis (GCCA), principal component analysis (PCA),
factor score regression (FSR) using sum score, regression or
Bartlett scores (including bias correction using Croon’s approach),
as well as several tests and typical postestimation procedures
(e.g., verify admissibility of the estimates, assess the model fit,
test the model fit etc.).
Author: Manuel E. Rademaker [aut] ,
Florian Schuberth [aut, cre] ,
Tamara Schamberger [ctb] ,
Michael Klesel [ctb] ,
Huu Phuc Nguyen [ctb] ,
Theo K. Dijkstra [ctb],
Joerg Henseler [ctb] ,
Gloria Pietropolli [ctb] ,
Kjell S. Slupphaug [ctb] ,
Jason J. Berger [ [...truncated...]
Maintainer: Florian Schuberth <f.schuberth@utwente.nl>
Diff between cSEM versions 0.6.1 dated 2025-05-16 and 0.7.1 dated 2026-09-08
DESCRIPTION | 43 +- MD5 | 151 ++++--- NAMESPACE | 8 R/00_csem.R | 2 R/csem_data.R | 9 R/csem_fit.R | 4 R/csem_resample.R | 23 - R/estimators_paths.R | 4 R/helper_assess.R | 360 +++++++++++++++---- R/helper_csem.R | 4 R/helper_doModelSearch.R |only R/helper_estimators_paths.R | 22 - R/helper_foreman.R | 59 +-- R/helper_infer.R | 9 R/helper_matrix.R |only R/helper_polycor.R |only R/helper_test_MGD.R | 23 + R/plot.cSEMNonlinearEffects.R | 15 R/postestimate_assess.R | 30 - R/postestimate_doModelSearch.R |only R/postestimate_doRedundancyAnalysis.R | 2 R/postestimate_predict.R | 10 R/postestimate_test_MGD.R | 89 ++-- R/postestimate_test_MICOM.R | 37 + R/postestimate_test_OMF.R | 13 R/postestimate_verify.R | 10 R/print.cSEMAssess.R | 42 +- R/print.cSEMModelSearch.R |only R/zz_arguments.R | 41 +- R/zz_datasets.R | 96 ++++- README.md | 303 +++++++++------ build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary data/LeDang2022.RData |only data/corp_rep_data.rda |only inst/REFERENCES.bib | 173 ++++++--- inst/doc/Notation.html | 2 inst/doc/Terminology.html | 4 inst/doc/Using-assess.Rmd | 2 inst/doc/Using-assess.html | 103 ++--- inst/doc/cSEM.Rmd | 2 inst/doc/cSEM.html | 111 ++--- inst/examples/example_doModelSearch.R |only inst/examples/example_predict.R | 4 inst/examples/example_resampleData.R | 2 inst/examples/example_resamplecSEMResults.R | 2 inst/examples/example_testMICOM.R | 2 man/BergamiBagozzi2000.Rd | 8 man/LeDang2022.Rd |only man/args_assess_dotdotdot.Rd | 5 man/cSEM-package.Rd | 4 man/calculateCorVCV.Rd |only man/calculateFitness.Rd |only man/calculateHTMT.Rd | 28 - man/calculateHTMTasymptoticSE.Rd |only man/calculateIndicatorCor.Rd | 4 man/checkCycles.Rd |only man/checkIsolatedConstruct.Rd |only man/corp_rep_data.Rd |only man/csem.Rd | 2 man/csem_arguments.Rd | 26 + man/dbinorm.Rd |only man/doModelSearch.Rd |only man/doRedundancyAnalysis.Rd | 2 man/dropNAResamples.Rd |only man/fastIntTab.Rd |only man/isPositiveSemiDefinite.Rd |only man/mutateVector.Rd |only man/polychor.Rd |only man/polyserial.Rd |only man/predict.Rd | 2 man/print.cSEMModelSearch.Rd |only man/processData.Rd | 4 man/resampleData.Rd | 2 man/resamplecSEMResults.Rd | 2 man/snlminb.Rd |only man/testCVPAT.Rd | 2 man/testMGD.Rd | 37 + man/testMICOM.Rd | 2 man/trace.Rd |only tests/other_tests/test_nlin_second_order_issue_624.R |only tests/other_tests/test_polychor_performance.R |only tests/testthat/test-assess.R | 85 ++-- tests/testthat/test-csem.r | 140 ++++++- tests/testthat/test-helper_assess.R |only tests/testthat/test-main.R | 15 tests/testthat/test-testMGD.R | 93 ++++ tests/testthat/test-testMICOM.R | 59 +++ vignettes/Using-assess.Rmd | 2 vignettes/cSEM.Rmd | 2 91 files changed, 1606 insertions(+), 736 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] ,
Andrew Brown [aut] ,
A. Marcia Barbosa [aut] ,
Emanuele Cordano [aut] ,
Krzysztof Dyba [aut] ,
Roger Bivand [ctb] ,
Michael Chirico [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.9-46 dated 2026-08-22 and 1.9-50 dated 2026-09-08
DESCRIPTION | 10 +- MD5 | 87 +++++++++---------- NAMESPACE | 2 NEWS.md | 28 +++++- R/RcppExports.R | 4 R/animate.R | 11 ++ R/gdal.R | 4 R/generics.R | 65 +++++++------- configure | 52 ++++++++++- configure.ac | 49 +++++++++- inst/tinytest/test_cats.R | 26 +++-- man/RGB.Rd | 2 man/centroids.Rd | 4 man/crop.Rd | 4 man/dimensions.Rd | 4 man/extract.Rd | 4 man/focal3D.Rd | 2 man/focalCpp.Rd | 2 man/gdal.Rd | 4 man/plotRGB.Rd | 2 man/project.Rd | 13 +- man/same.crs.Rd | 2 man/subst.Rd | 2 man/terra-package.Rd | 4 man/terraOptions.Rd | 6 - man/union.Rd | 5 - man/writeRaster.Rd | 2 src/RcppExports.cpp | 11 ++ src/RcppFunctions.cpp | 25 +++++ src/RcppModule.cpp | 6 - src/catchments.cpp | 73 ++++++++++++---- src/crs.cpp | 64 ++++++++++---- src/gdal_algs.cpp | 190 +++++++++++++++++++++++++----------------- src/gdal_compat.h |only src/gdal_multidimensional.cpp | 133 +++++++++++++++++++++-------- src/gdalio.cpp | 20 ++++ src/gdalio.h | 2 src/geos_methods.cpp | 32 ++++--- src/geos_spat.h | 2 src/read_gdal.cpp | 64 +++++++++++--- src/spatRaster.h | 11 +- src/spatSources.cpp | 1 src/spatVector.h | 4 src/tessellate.cpp | 3 src/write_gdal.cpp | 1 45 files changed, 730 insertions(+), 312 deletions(-)
Title: Additional Documentation and Regression Tests for
'stats::free1way()'
Description: Function 'stats::free1way()' implements semiparametrically
efficient population- and permutation-based inference in
distribution-free stratified K-sample oneway layouts. This package
provides additional documentation, including a detailed description
of the implementation, and serves as a home for extensive regression tests.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Frank E Harrell Jr [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between free1way.docreg versions 1.0-2 dated 2026-06-30 and 1.0-3 dated 2026-09-08
DESCRIPTION | 8 +++---- MD5 | 16 +++++++------- inst/NEWS.Rd | 9 ++++++++ inst/doc/free1way.R | 45 ------------------------------------------ inst/doc/free1way.Rnw | 47 +++----------------------------------------- inst/doc/free1way.pdf |binary inst/nuweb/free1way.w | 47 +++----------------------------------------- tests/free1way-Ex.Rout.save | 43 ++++++++++++++++++++++++---------------- vignettes/free1way.Rnw | 47 +++----------------------------------------- 9 files changed, 60 insertions(+), 202 deletions(-)
More information about free1way.docreg at CRAN
Permanent link
Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Author: Paolo Frumento [aut, cre]
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between qrcm versions 3.3 dated 2026-06-22 and 3.4 dated 2026-09-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++--- R/iqrL1_fit.R | 22 ++++++++++++---------- man/qrcm-package.Rd | 4 ++-- 5 files changed, 25 insertions(+), 23 deletions(-)
More information about PseudoVoigtMixt at CRAN
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