Title: Declarative Recipes for Staged Survey Weighting with
Recipe-Aware Replicate Variances
Description: Builds survey analysis weights by declaring the whole weighting
process as an ordered recipe of explicit adjustments and estimating it in a
single call. Steps include within-cluster selection, second-phase
subsampling for two-phase sampling, nonresponse adjustment by weighting
classes or response-propensity models (including machine-learning learners
with optional cross-fitting), calibration to known totals following Deville
and Sarndal (1992) <doi:10.2307/2290268> with optional model-assisted
calibration following Wu and Sitter (2001)
<doi:10.1198/016214501750333054>, adjustment of non-probability samples by
pseudo-weighting, mass imputation and doubly robust estimators, and
range-restricted trimming. Variances come from a recipe-aware bootstrap and
jackknife that resample or delete primary sampling units and re-apply the
entire cascade on each replicate, following Rao and Wu (1988)
<doi:10.1080/01621459.1988.10478591>, and are separated into first- and
second-phase [...truncated...]
Author: Juan Pablo Ferreira [aut, cre, cph] ,
Andres Gutierrez [aut]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 1.1.0 dated 2026-08-19 and 1.2.0 dated 2026-08-29
DESCRIPTION | 46 - MD5 | 238 ++++--- NAMESPACE | 20 NEWS.md | 28 R/adjust-calibrate.R | 93 ++ R/adjust-ml.R | 8 R/adjust-nr-sensitivity.R |only R/adjust-poststrata.R | 69 ++ R/adjust-pseudoweight.R |only R/adjust-solve.R | 31 R/adjust-trim.R | 110 ++- R/adjustments.R | 35 - R/collect-propensities.R | 1 R/collect-step-detail.R | 16 R/data-defect.R |only R/disclosure-risk.R |only R/domain-summary.R | 43 + R/plots.R | 6 R/prep.R | 126 +++ R/print.R | 7 R/r-indicators.R | 9 R/recipe-io.R |only R/report-assets.R | 35 - R/report-cards.R | 441 ++++++++++--- R/report-helpers.R | 121 ++- R/report-narrative.R | 95 ++ R/report.R | 74 +- R/sae.R |only R/spec-steps-calibrate.R | 140 +++- R/spec-steps-cascade.R | 75 +- R/spec-steps-final.R | 171 ++++- R/spec-steps-subsample.R |only R/spec.R | 77 +- R/variance.R | 466 ++++++++++++-- R/weightflow-alerts.R |only R/weightflow-concepts.R | 20 README.md | 59 + build/vignette.rds |binary inst/WORDLIST | 68 ++ inst/doc/advanced-methods.html | 52 - inst/doc/calibration-totals.Rmd | 5 inst/doc/calibration-totals.html | 6 inst/doc/calibration.Rmd | 7 inst/doc/calibration.html | 32 inst/doc/inspecting-auditing.R |only inst/doc/inspecting-auditing.Rmd |only inst/doc/inspecting-auditing.html |only inst/doc/model-calibration.Rmd | 6 inst/doc/model-calibration.html | 7 inst/doc/nonprobability-samples.R |only inst/doc/nonprobability-samples.Rmd |only inst/doc/nonprobability-samples.html |only inst/doc/nonresponse-propensities.Rmd | 6 inst/doc/nonresponse-propensities.html | 13 inst/doc/preparing-the-sample.html | 76 +- inst/doc/quality-report.Rmd | 13 inst/doc/quality-report.html | 88 +- inst/doc/quickstart.html | 20 inst/doc/reference-survey.R |only inst/doc/reference-survey.Rmd |only inst/doc/reference-survey.html |only inst/doc/two-phase-sampling.R |only inst/doc/two-phase-sampling.Rmd |only inst/doc/two-phase-sampling.html |only inst/doc/validation-against-survey.R | 16 inst/doc/validation-against-survey.Rmd | 16 inst/doc/validation-against-survey.html | 16 inst/doc/variance-estimation.R | 19 inst/doc/variance-estimation.Rmd | 61 + inst/doc/variance-estimation.html | 896 +++------------------------ inst/doc/weightflow-in-production.R |only inst/doc/weightflow-in-production.Rmd |only inst/doc/weightflow-in-production.html |only inst/doc/weightflow.html | 36 - man/as_sae_input.Rd |only man/as_svydesign.Rd | 9 man/bootstrap_estimate.Rd | 35 - man/bootstrap_weights.Rd | 31 man/collect_propensities.Rd | 9 man/collect_replicate_weights.Rd | 20 man/collect_step_detail.Rd | 14 man/collect_weights.Rd | 10 man/data_defect.Rd |only man/disclosure_risk.Rd |only man/domain_summary.Rd | 23 man/jackknife_estimate.Rd | 26 man/jackknife_weights.Rd | 9 man/nr_sensitivity.Rd |only man/prep.Rd | 12 man/read_recipe.Rd |only man/reference_sample.Rd |only man/step_assert.Rd | 24 man/step_calibrate.Rd | 38 + man/step_drop_ineligible.Rd | 24 man/step_model_calibration.Rd | 30 man/step_nonresponse.Rd | 25 man/step_nr_sensitivity.Rd |only man/step_pseudoweight.Rd |only man/step_rescale.Rd | 24 man/step_round.Rd | 29 man/step_select_within.Rd | 30 man/step_subsample.Rd |only man/step_trim.Rd | 31 man/step_trim_calibrated.Rd | 39 + man/step_trim_weights.Rd | 25 man/step_unknown_eligibility.Rd | 24 man/two_phase_variance.Rd |only man/weight_factors.Rd | 10 man/weightflow-alerts.Rd |only man/weightflow-concepts.Rd | 21 man/weightflow-package.Rd | 4 man/weighting_alerts.Rd |only man/weighting_spec.Rd | 17 man/write_recipe.Rd |only tests/testthat/_snaps/snapshot.md | 22 tests/testthat/test-audit-2026-08b.R |only tests/testthat/test-audit-2026-08c.R |only tests/testthat/test-audit-2026-08d.R |only tests/testthat/test-audit-followups.R |only tests/testthat/test-audit-ronda2.R |only tests/testthat/test-audit-ronda2b.R |only tests/testthat/test-blindaje-reporte-en.R | 2 tests/testthat/test-calibrate-reference.R |only tests/testthat/test-data-defect.R |only tests/testthat/test-domain-gate-disclosure.R |only tests/testthat/test-fpc-ci.R |only tests/testthat/test-nr-sensitivity.R |only tests/testthat/test-pseudoweight.R |only tests/testthat/test-recipe-io.R |only tests/testthat/test-reference-sample.R |only tests/testthat/test-replication-card.R | 19 tests/testthat/test-report-reference-note.R |only tests/testthat/test-sae.R |only tests/testthat/test-step-id.R |only tests/testthat/test-subsample.R |only tests/testthat/test-trim-domain-and-alerts.R |only tests/testthat/test-unit-report-narrative.R | 2 tests/testthat/test-unit-spec-steps.R | 4 vignettes/calibration-totals.Rmd | 5 vignettes/calibration.Rmd | 7 vignettes/inspecting-auditing.Rmd |only vignettes/model-calibration.Rmd | 6 vignettes/nonprobability-samples.Rmd |only vignettes/nonresponse-propensities.Rmd | 6 vignettes/quality-report.Rmd | 13 vignettes/reference-survey.Rmd |only vignettes/two-phase-sampling.Rmd |only vignettes/validation-against-survey.Rmd | 16 vignettes/variance-estimation.Rmd | 61 + vignettes/weightflow-in-production.Rmd |only 150 files changed, 3377 insertions(+), 1498 deletions(-)
Title: Automatically Reduce Failing R Scripts to a Minimal Reproducible
Example
Description: Shrinks a failing R script to the smallest subset of statements
that still triggers the same error, using the delta debugging algorithm of
Zeller and Hildebrandt (2002) <doi:10.1109/32.988498>. Each candidate
reduction is evaluated in a separate R process, so dependencies between
statements and their side effects are respected. The result is a
one-minimal example, in which removing any remaining statement makes the
error disappear; this is the form most useful for bug reports and for
questions on community forums. When no statement can be removed, because
the failure is nested inside a function body, reduction continues within
the surviving statements. A general delta debugging routine and a
helper for reducing data frames to the rows that reproduce a failure are
also provided.
Author: Sandeep Bodduluri [aut, cph] ,
Sumanth Chandrupatla [aut, cre, cph]
Maintainer: Sumanth Chandrupatla <srchandr@uab.edu>
Diff between minex versions 0.1.0 dated 2026-07-16 and 0.2.0 dated 2026-08-29
DESCRIPTION | 32 +-- LICENSE | 2 MD5 | 71 ++++-- NAMESPACE | 4 NEWS.md | 61 +++++ R/cdd.R |only R/clipboard.R |only R/ddmin.R | 151 ++++++++++---- R/explain-prompt.R |only R/explain-verify.R |only R/explain.R |only R/hdd.R |only R/match.R |only R/minex.R | 368 ++++++++++++++++++++++++++++++----- R/oracle.R | 118 +++++------ R/parse-tree.R |only R/parse.R | 20 + R/print.R | 45 +++- R/reduce-rows.R | 12 - R/sweep.R |only R/trace.R |only R/truncate.R |only build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 23 ++ inst/doc/minex.html | 4 man/ddmin.Rd | 34 ++- man/explain_failure.Rd |only man/minex-package.Rd | 10 man/minex.Rd | 109 +++++++++- man/reduce_rows.Rd | 14 + tests/testthat.R | 14 + tests/testthat/test-auto-escalate.R |only tests/testthat/test-cdd.R |only tests/testthat/test-clipboard.R |only tests/testthat/test-ddmin.R | 77 +++++++ tests/testthat/test-explain-prompt.R |only tests/testthat/test-explain-verify.R |only tests/testthat/test-explain.R |only tests/testthat/test-hdd.R |only tests/testthat/test-match.R |only tests/testthat/test-minex.R | 220 ++++++++++++++++++++ tests/testthat/test-oracle.R |only tests/testthat/test-parse-error.R |only tests/testthat/test-parse-tree.R |only tests/testthat/test-print-axis.R |only tests/testthat/test-print.R |only tests/testthat/test-reduce-rows.R | 14 + tests/testthat/test-sweep.R |only tests/testthat/test-truncate.R |only 50 files changed, 1182 insertions(+), 221 deletions(-)
Title: Tools for Assessing Clustering
Description: A set of tools for evaluating clustering robustness using
proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014)
<doi:10.1038/srep06207>), as well as similarity across methods
and method stability using element-centric clustering comparison (Gates et
al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package
enables stability-based parameter assessment for graph-based clustering
pipelines typical in single-cell data analysis.
Author: Andi Munteanu [aut, cre],
Arash Shahsavari [aut],
Rafael Kollyfas [ctb],
Miguel Larraz Lopez de Novales [aut],
Liviu Ciortuz [ctb],
Irina Mohorianu [aut]
Maintainer: Andi Munteanu <am3019@cam.ac.uk>
Diff between ClustAssess versions 1.1.0 dated 2025-05-27 and 1.2.0 dated 2026-08-29
DESCRIPTION | 16 MD5 | 55 +- NAMESPACE | 6 NEWS.md | 26 + R/ECS.R | 87 ---- R/convert.R | 50 +- R/generics.R | 4 R/shiny-app.R | 29 + R/shiny-comparisons.R | 453 +++++++++++++++++----- R/shiny-feature-stability.R | 45 +- R/shiny-graph-clustering.R | 38 - R/shiny-info.R | 24 - R/shiny-sandbox.R | 31 - R/shiny-utils.R | 441 +++++++++++++++++---- R/stability-1-dim-reduction.R | 32 - R/stability-2-graph-construction.R | 54 -- R/stability-3-graph-clustering.R | 48 -- R/stability-based-parameter-assessment.R | 80 +-- R/utils.R | 86 ++++ README.md | 75 +-- man/add_metadata.Rd | 6 man/create_monocle_from_clustassess_app.Rd | 10 man/create_seurat_object_default.Rd | 6 man/plot_feature_overall_stability_incremental.Rd | 2 man/plot_n_neigh_ecs.Rd | 6 man/write_objects.Rd | 4 man/write_shiny_app.Rd | 8 src/optimise_snn.cpp | 32 - tests/testthat/test-calculate-markers.R |only 29 files changed, 1125 insertions(+), 629 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut] ,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.8.1 dated 2025-05-05 and 0.9.0 dated 2026-08-29
alcyon-0.8.1/alcyon/R/PointMap.R |only alcyon-0.8.1/alcyon/man/PointMap-class.Rd |only alcyon-0.8.1/alcyon/man/PointMap_subset.Rd |only alcyon-0.8.1/alcyon/man/as.Rd |only alcyon-0.8.1/alcyon/man/connections-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/linkCoords-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/linkRefs-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/links-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/makeVGAPointMap.Rd |only alcyon-0.8.1/alcyon/man/name-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/plot.PointMap.Rd |only alcyon-0.8.1/alcyon/man/unlinkCoords-PointMap-method.Rd |only alcyon-0.8.1/alcyon/man/unlinkRefs-PointMap-method.Rd |only alcyon-0.8.1/alcyon/src/libs/salalib/pointmap.cpp |only alcyon-0.8.1/alcyon/src/libs/salalib/pointmap.hpp |only alcyon-0.8.1/alcyon/src/libs/salalib/spacepix.cpp |only alcyon-0.8.1/alcyon/src/libs/salalib/spacepix.hpp |only alcyon-0.8.1/alcyon/src/rcpp_PointMap.cpp |only alcyon-0.8.1/alcyon/src/rcpp_PointMap.hpp |only alcyon-0.8.1/alcyon/tests/testthat/test-PointMap.R |only alcyon-0.9.0/alcyon/DESCRIPTION | 24 alcyon-0.9.0/alcyon/MD5 | 459 ++++----- alcyon-0.9.0/alcyon/NAMESPACE | 57 - 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alcyon-0.9.0/alcyon/src/libs/salalib/agents/agent.hpp | 14 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentanalysis.cpp | 27 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentanalysis.hpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentga.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentprogram.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/alllinemap.cpp | 29 alcyon-0.9.0/alcyon/src/libs/salalib/analysisresult.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/attributemap.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/attributetable.cpp | 11 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableindex.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableview.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableview.hpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/axialminimiser.cpp | 28 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialintegration.cpp | 17 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialintegration.hpp | 28 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axiallocal.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialstepdepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/axialpolygons.cpp | 31 alcyon-0.9.0/alcyon/src/libs/salalib/axialpolygons.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/connector.cpp | 29 alcyon-0.9.0/alcyon/src/libs/salalib/entityparsing.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/entityparsing.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/exportutils.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/bsptree.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/containerutils.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/exceptions.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/line4f.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/pafmath.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/pafmath.hpp | 33 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/point2f.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/poly.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/readwritehelpers.hpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/region4f.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/simplematrix.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/stringutils.cpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/xmlparse.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/geometrygenerators.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/importtypedefs.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/importutils.cpp | 61 - alcyon-0.9.0/alcyon/src/libs/salalib/importutils.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/isovist.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/latticemap.cpp |only alcyon-0.9.0/alcyon/src/libs/salalib/latticemap.hpp |only alcyon-0.9.0/alcyon/src/libs/salalib/layermanager.hpp | 9 alcyon-0.9.0/alcyon/src/libs/salalib/layermanagerimpl.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/linkutils.cpp | 28 alcyon-0.9.0/alcyon/src/libs/salalib/linkutils.hpp | 18 alcyon-0.9.0/alcyon/src/libs/salalib/mapconverter.cpp | 29 alcyon-0.9.0/alcyon/src/libs/salalib/metagraphreadwrite.cpp | 126 +- alcyon-0.9.0/alcyon/src/libs/salalib/metagraphreadwrite.hpp | 48 alcyon-0.9.0/alcyon/src/libs/salalib/ngraph.cpp | 11 alcyon-0.9.0/alcyon/src/libs/salalib/parsers/dxfp.cpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/parsers/mapinfodata.cpp | 15 alcyon-0.9.0/alcyon/src/libs/salalib/parsers/mapinfodata.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/parsers/ntfp.cpp | 9 alcyon-0.9.0/alcyon/src/libs/salalib/parsers/tigerp.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/pixelbase.cpp |only alcyon-0.9.0/alcyon/src/libs/salalib/pixelbase.hpp |only alcyon-0.9.0/alcyon/src/libs/salalib/point.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/point.hpp | 34 alcyon-0.9.0/alcyon/src/libs/salalib/pushvalues.cpp | 14 alcyon-0.9.0/alcyon/src/libs/salalib/pushvalues.hpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/resources/graph.grammar | 10 alcyon-0.9.0/alcyon/src/libs/salalib/resources/graph.hexpat | 16 alcyon-0.9.0/alcyon/src/libs/salalib/salaprogram.cpp | 27 alcyon-0.9.0/alcyon/src/libs/salalib/salaprogram.hpp | 20 alcyon-0.9.0/alcyon/src/libs/salalib/salashape.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/CMakeLists.txt | 2 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmangular.cpp | 9 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmmetric.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmmetricpd.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmmetricshortestpath.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtopological.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtopologicalpd.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtopologicalshortestpath.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulip.cpp | 484 +++++----- alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulip.hpp | 46 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulipdepth.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulipleafchoice.cpp |only alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulipleafchoice.hpp |only alcyon-0.9.0/alcyon/src/libs/salalib/segmmodules/segmtulipshortestpath.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/shapegraph.cpp | 72 - alcyon-0.9.0/alcyon/src/libs/salalib/shapegraph.hpp | 36 alcyon-0.9.0/alcyon/src/libs/salalib/shapemap.cpp | 435 +++----- alcyon-0.9.0/alcyon/src/libs/salalib/shapemap.hpp | 62 - alcyon-0.9.0/alcyon/src/libs/salalib/shapemapgroupdata.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/spacepixel.cpp |only alcyon-0.9.0/alcyon/src/libs/salalib/spacepixel.hpp |only alcyon-0.9.0/alcyon/src/libs/salalib/sparksieve2.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/tidylines.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/tidylines.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/extractlinkdata.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivga.hpp | 9 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgaangular.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgametric.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgatraversing.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgavisual.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangular.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangular.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.cpp | 22 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametric.cpp | 17 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametric.hpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.cpp | 34 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.hpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.cpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.cpp | 8 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/process_link.cpp | 114 +- alcyon-0.9.0/alcyon/src/rcpp_LatticeMap.cpp |only alcyon-0.9.0/alcyon/src/rcpp_LatticeMap.hpp |only alcyon-0.9.0/alcyon/src/rcpp_metagraphdata.cpp | 12 alcyon-0.9.0/alcyon/tests/testthat/helper-loadMaps.R | 8 alcyon-0.9.0/alcyon/tests/testthat/test-LatticeMap.R |only alcyon-0.9.0/alcyon/tests/testthat/test-MetaGraph.R | 12 alcyon-0.9.0/alcyon/tests/testthat/test-agentanalysis.R | 14 alcyon-0.9.0/alcyon/tests/testthat/test-prepareVGA.R | 28 alcyon-0.9.0/alcyon/tests/testthat/test-segmentAnalysis.R | 94 + alcyon-0.9.0/alcyon/tests/testthat/test-vga.R | 64 - alcyon-0.9.0/alcyon/tests/testthat/test-vgaCpp.R | 64 - alcyon-0.9.0/alcyon/vignettes/agentAnalysis.Rmd | 10 alcyon-0.9.0/alcyon/vignettes/vga.Rmd | 8 255 files changed, 2579 insertions(+), 2089 deletions(-)
Title: Polished, Editable Tables and Statistical Results
Description: Sends supported 'R' objects to the 'Mellio' web app and creates
polished, editable statistical tables in 'R'. The 'mellio_open' interface
handles common hypothesis tests, model objects, model comparisons,
descriptive summaries, tabular data, plots, and image files. The
'melliotab' interface formats data frames, model summaries, correlation
matrices, and side-by-side comparison tables with APA-style numeric
formatting, confidence intervals, table notes, and optional significance
markers. Manual table helpers can copy or save 'melliotab' output as
'HTML', 'LaTeX', or 'Markdown' when file-based handoff is needed.
Payloads include package-version metadata to support reproducible
reporting and software citation.
Author: Melih Sahin [aut, cre]
Maintainer: Melih Sahin <nicomelpro@pm.me>
Diff between mellio versions 1.0.2 dated 2026-07-08 and 1.1.0 dated 2026-08-29
DESCRIPTION | 15 ++-- MD5 | 19 ++--- NAMESPACE | 4 + NEWS.md | 12 +++ R/bridge-edit.R | 33 +++++++++ R/bridge-extract-interactions.R |only R/bridge-payload.R | 7 ++ R/edit.R | 4 - man/mellio_payload.Rd | 19 +++-- tests/testthat/test-bridge.R | 130 ++++++++++++++++++++++++++++++++++++++ tests/testthat/test-mellio-open.R | 14 ++++ 11 files changed, 232 insertions(+), 25 deletions(-)
Title: Access 'Hugging Face' Models and Datasets
Description: Access models and datasets hosted on the 'Hugging Face' Hub
through its Inference Application Programming Interface (API). Run text
classification, embeddings, chat, translation, image, audio, and other
tasks from tidy 'R' workflows without installing 'Python' by default.
Results are returned as data frames or simple 'R' objects so they can be
composed with 'dplyr', 'tidyr', and related tooling. Helpers also support
Hub search, file download, provider discovery, and guarded uploads for
authenticated workflows.
Author: Alex Farach [aut, cre, cph],
Sam Terfa [aut, cph],
Jack Penzer [aut, cph]
Maintainer: Alex Farach <alexfarach@gmail.com>
Diff between huggingfaceR versions 2.1.0 dated 2026-06-30 and 2.2.0 dated 2026-08-29
huggingfaceR-2.1.0/huggingfaceR/tools |only huggingfaceR-2.2.0/huggingfaceR/DESCRIPTION | 12 huggingfaceR-2.2.0/huggingfaceR/MD5 | 50 +-- huggingfaceR-2.2.0/huggingfaceR/NAMESPACE | 1 huggingfaceR-2.2.0/huggingfaceR/NEWS.md | 66 ++++ huggingfaceR-2.2.0/huggingfaceR/R/auth.R | 82 +++-- huggingfaceR-2.2.0/huggingfaceR/R/batch.R | 10 huggingfaceR-2.2.0/huggingfaceR/R/defaults.R | 2 huggingfaceR-2.2.0/huggingfaceR/R/hub.R | 70 +++- huggingfaceR-2.2.0/huggingfaceR/R/multimodal.R | 22 - huggingfaceR-2.2.0/huggingfaceR/R/providers.R |only huggingfaceR-2.2.0/huggingfaceR/R/request.R | 139 +++++++-- huggingfaceR-2.2.0/huggingfaceR/R/text-tasks.R | 15 - huggingfaceR-2.2.0/huggingfaceR/R/utils.R | 10 huggingfaceR-2.2.0/huggingfaceR/R/zzz.R | 4 huggingfaceR-2.2.0/huggingfaceR/README.md | 44 ++ huggingfaceR-2.2.0/huggingfaceR/man/hf_clear_provider_cache.Rd |only huggingfaceR-2.2.0/huggingfaceR/man/hf_list_providers.Rd | 17 - huggingfaceR-2.2.0/huggingfaceR/man/hf_set_token.Rd | 10 huggingfaceR-2.2.0/huggingfaceR/man/hf_text_to_speech.Rd | 2 huggingfaceR-2.2.0/huggingfaceR/man/hf_whoami.Rd | 3 huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-auth.R | 149 ++++++---- huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-multimodal.R | 4 huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-providers.R |only huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-request.R | 15 - huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-text-tasks.R | 20 - 26 files changed, 548 insertions(+), 199 deletions(-)
Title: Add the 'dann' Model and the 'sub_dann' Model to the
'tidymodels' Ecosystem
Description: Provides model specifications and tuning parameters that make the
models in the 'dann' package available to the 'tidymodels' ecosystem.
Models based on Hastie (1996)
<https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between tidydann versions 1.0.1 dated 2025-04-12 and 1.0.2 dated 2026-08-29
tidydann-1.0.1/tidydann/tests/testthat/testthat-problems.rds |only tidydann-1.0.2/tidydann/DESCRIPTION | 24 +- tidydann-1.0.2/tidydann/MD5 | 38 ++- tidydann-1.0.2/tidydann/NAMESPACE | 5 tidydann-1.0.2/tidydann/NEWS.md | 40 ++-- tidydann-1.0.2/tidydann/R/nearest_neighbor_adaptive.R | 98 ++++++++-- tidydann-1.0.2/tidydann/R/threads.R |only tidydann-1.0.2/tidydann/R/tunable.R | 75 +++++-- tidydann-1.0.2/tidydann/R/zzz.R | 20 +- tidydann-1.0.2/tidydann/README.md | 88 +++++--- tidydann-1.0.2/tidydann/man/check_args.nearest_neighbor_adaptive.Rd |only tidydann-1.0.2/tidydann/man/figures/README-Circle-1.png |binary tidydann-1.0.2/tidydann/man/matrix_diagonal.Rd | 13 - tidydann-1.0.2/tidydann/man/nearest_neighbor_adaptive.Rd | 48 +++- tidydann-1.0.2/tidydann/man/neighborhood.Rd | 19 + tidydann-1.0.2/tidydann/man/sphere.Rd | 12 - tidydann-1.0.2/tidydann/man/tidydann_set_threads.Rd |only tidydann-1.0.2/tidydann/man/tunable.nearest_neighbor_adaptive.Rd | 8 tidydann-1.0.2/tidydann/man/update.nearest_neighbor_adaptive.Rd | 46 +++- tidydann-1.0.2/tidydann/man/weighted.Rd | 11 - tidydann-1.0.2/tidydann/tests/testthat/setup.R |only tidydann-1.0.2/tidydann/tests/testthat/test_B_tunable.R | 66 ++++++ tidydann-1.0.2/tidydann/tests/testthat/test_D_threads.R |only 23 files changed, 431 insertions(+), 180 deletions(-)
Title: Self-Similarity Test for Normality
Description: Implements the Self-Similarity Test for Normality (SSTN), a new
statistical test designed to assess whether a given sample originates from
a normal distribution. The method exploits the self-similarity property of
the normal characteristic function by iteratively transforming and comparing
standardized empirical characteristic functions. The null distribution of
the test statistic is obtained via Monte Carlo simulation. Details of the
methodology are described in Anarat and Schwender (2026),
"A test for normality based on self-similarity", <doi:10.48550/arXiv.2604.03810>.
Author: Akin Anarat [aut, cre]
Maintainer: Akin Anarat <akin.anarat@hhu.de>
Diff between sstn versions 1.0.1 dated 2026-04-11 and 1.0.2 dated 2026-08-29
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/asymptotic_calibration.R | 4 ++-- R/calibration_data.R | 4 ++-- R/sstn.R | 10 +++++----- R/sysdata.rda |binary inst/doc/Introduction_to_SSTN.R | 4 ++-- inst/doc/Introduction_to_SSTN.Rmd | 4 ++-- inst/doc/Introduction_to_SSTN.html | 26 ++++++++++++++++++-------- man/calibration_data.Rd | 4 ++-- man/sstn.Rd | 4 ++-- vignettes/Introduction_to_SSTN.Rmd | 4 ++-- 13 files changed, 58 insertions(+), 42 deletions(-)
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 0.2.0 dated 2026-08-06 and 0.2.2 dated 2026-08-29
DESCRIPTION | 20 MD5 | 24 NAMESPACE | 2 NEWS.md | 29 + R/fitdistrBayes.R | 619 ++++++++++++++++++++-- R/model_spec.R |only README.md | 14 inst/examples/teaching.R | 21 inst/examples/tutorial_fitdistrBayes_all_models.R | 69 ++ man/fitdistrBayes.Rd | 61 +- man/fitdistrBayes_model.Rd |only man/fitdistrBayes_routes.Rd | 5 tests/tests_extension_api.R |only tests/tests_registry.R | 16 tests/tests_weighted_lindley.R |only 15 files changed, 786 insertions(+), 94 deletions(-)
Title: Remedy for Violations of the Proportional Hazards Assumption in
Cox Proportional Hazards Models
Description: Remedying proportional hazards
assumption violations of a Cox proportional hazards model using
stepwise changepoint and time-varying coefficient methods based on
Cox (1972) <doi:10.1111/j.2517-6161.1972.tb00899.x> and Klein
and Moeschberger (1997) <doi:10.1007/978-1-4757-2728-9>.
Author: Hamin Kim [aut, cre]
Maintainer: Hamin Kim <haaamin@korea.ac.kr>
Diff between cox.rvph versions 0.1.5 dated 2026-08-19 and 0.2.0 dated 2026-08-29
DESCRIPTION | 8 +- MD5 | 12 ++- NAMESPACE | 2 R/cox.rvph.R | 191 +++++++++++++++++++++++++++++------------------- R/print.cox.rvph.R |only R/summary.cox.rvph.R |only man/cox.rvph.Rd | 108 ++++++++++----------------- man/print.cox.rvph.Rd |only man/summary.cox.rvph.Rd |only 9 files changed, 174 insertions(+), 147 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.3.2 dated 2026-01-12 and 0.3.3 dated 2026-08-29
autoslider.core-0.3.2/autoslider.core/man/decorate-VTableTree-method.Rd |only autoslider.core-0.3.2/autoslider.core/man/decorate-listing_df-method.Rd |only autoslider.core-0.3.3/autoslider.core/DESCRIPTION | 29 autoslider.core-0.3.3/autoslider.core/MD5 | 94 autoslider.core-0.3.3/autoslider.core/NAMESPACE | 18 autoslider.core-0.3.3/autoslider.core/NEWS.md | 5 autoslider.core-0.3.3/autoslider.core/R/decorate.R | 733 ++--- autoslider.core-0.3.3/autoslider.core/R/generate_output.R | 276 +- autoslider.core-0.3.3/autoslider.core/R/save_output.R | 480 +-- autoslider.core-0.3.3/autoslider.core/R/to_ft_funs.R | 884 +++--- autoslider.core-0.3.3/autoslider.core/R/to_slides.R | 786 +++--- autoslider.core-0.3.3/autoslider.core/README.md | 86 autoslider.core-0.3.3/autoslider.core/build/vignette.rds |binary autoslider.core-0.3.3/autoslider.core/inst/WORDLIST | 224 - autoslider.core-0.3.3/autoslider.core/inst/doc/adding_templates.html | 342 +- autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.R | 88 autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.Rmd | 1074 ++++---- autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.html | 1275 ++++------ autoslider.core-0.3.3/autoslider.core/inst/doc/downstream.html | 193 - autoslider.core-0.3.3/autoslider.core/inst/doc/generate_placeholder_slides.html | 404 +-- autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.R |only autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.Rmd |only autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.html |only autoslider.core-0.3.3/autoslider.core/inst/doc/opensource.html | 505 ++- autoslider.core-0.3.3/autoslider.core/inst/doc/tlg_templates.html | 524 ++-- autoslider.core-0.3.3/autoslider.core/inst/doc/use_LLM.html | 390 +-- autoslider.core-0.3.3/autoslider.core/inst/doc/using_formats.html | 402 +-- autoslider.core-0.3.3/autoslider.core/inst/mcp |only autoslider.core-0.3.3/autoslider.core/man/autoslider.core-package.Rd | 97 autoslider.core-0.3.3/autoslider.core/man/decorate.Rd | 39 autoslider.core-0.3.3/autoslider.core/man/decorate.VTableTree.Rd |only autoslider.core-0.3.3/autoslider.core/man/decorate.autoslider_error.Rd | 38 autoslider.core-0.3.3/autoslider.core/man/decorate.default.Rd | 38 autoslider.core-0.3.3/autoslider.core/man/decorate.ggplot.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.grob.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.gtsummary.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.list.Rd | 62 autoslider.core-0.3.3/autoslider.core/man/decorate.listing_df.Rd |only autoslider.core-0.3.3/autoslider.core/man/decorate.tbl_roche_summary.Rd |only autoslider.core-0.3.3/autoslider.core/man/generate_outputs.Rd | 100 autoslider.core-0.3.3/autoslider.core/man/trial.Rd | 28 autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_eg_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_lb_chg_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_lb_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_mean_general_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_mean_nounit_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_vs_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/save_output.md | 6 autoslider.core-0.3.3/autoslider.core/tests/testthat/l_ae_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_slide_G34_X2PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_slide_X10PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_soc_slide_G34_X2PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_soc_slide_X10PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_summ_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_dd_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ds_slide_FAS.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-ai-offline.R |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-gtsummary.R |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-save_output.R | 73 autoslider.core-0.3.3/autoslider.core/vignettes/autoslideR.Rmd | 1074 ++++---- autoslider.core-0.3.3/autoslider.core/vignettes/mcp_server.Rmd |only 61 files changed, 5405 insertions(+), 5169 deletions(-)
More information about autoslider.core at CRAN
Permanent link
Title: Interventional Prediction Evaluation
Description: Provides methods to evaluate predictive performance of models that
estimate risks under hypothetical intervention scenarios
(interventional/causal/counterfactual predictions) with observational data
subject to treatment-outcome confounding. Inverse probability of treatment
weighting (IPTW) is used to construct a pseudopopulation in which all
individuals receive a specified intervention, enabling assessment of
agreement between predicted risks under the intervention and observed
outcomes in the pseudo-population corresponding to that intervention.
Supports interventions with binary or categorical treatment levels, applied
at a single time point. Performance measures supported are AUC (Area
Under the receiving operating characteristic Curve), Brier score,
observed-expected ratio, and calibration plots. Methods implemented in this
package are based on work by Keogh and Van Geloven (2024)
<DOI:10.1097/EDE.0000000000001713>.
Author: Jasper van Egeraat [aut, cre],
Nan van Geloven [aut, cph],
Ruth Keogh [aut, cph],
Leiden University Medical Center [fnd]
Maintainer: Jasper van Egeraat <j.w.a.van_egeraat@lumc.nl>
Diff between ipeval versions 0.1.0 dated 2026-05-06 and 0.1.1 dated 2026-08-29
DESCRIPTION | 32 - MD5 | 62 +- NAMESPACE | 1 NEWS.md | 7 R/bootstrap.R | 93 +-- R/helpers.R | 96 ++++ R/ip_score.R | 687 ++++++++++++++++++----------- R/ipc_weights.R | 31 - R/ipeval-package.R |only R/ipt_weights.R | 72 ++- R/metrics.R | 59 -- R/observed_score.R | 95 ++-- R/print.R | 333 +++++++++++--- README.md | 94 ++- build/partial.rdb |only build/vignette.rds |binary inst/doc/ipeval.Rmd | 8 inst/doc/ipeval.html | 91 ++- inst/doc/time-to-event.html | 159 ++++-- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/ip_score.Rd | 231 ++++++--- man/ipeval-package.Rd |only man/observed_score.Rd | 38 + man/plot.ip_score.Rd |only tests/testthat/_snaps |only tests/testthat/test-helpers.R | 44 + tests/testthat/test-ip_score-categorical.R |only tests/testthat/test-ip_score.R | 241 +++++----- tests/testthat/test-ipc_weights.R | 110 +--- tests/testthat/test-ipt_weights.R | 18 tests/testthat/test-metrics.R | 148 +----- tests/testthat/test-observed_score.R | 23 tests/testthat/test-predict_CF.R |only tests/testthat/test-print.R |only vignettes/ipeval.Rmd | 8 36 files changed, 1777 insertions(+), 1004 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 1.6.0 dated 2026-06-04 and 1.7.0 dated 2026-08-29
DESCRIPTION | 12 ++--- MD5 | 38 +++++++++------ NAMESPACE | 3 + NEWS.md | 11 ++++ R/download_td_file.R | 4 + R/globals.R | 1 R/gtdd_get_yield_curve.R | 3 - R/plots.R |only R/read_td_file.R | 48 ++++++++++++-------- R/td_get.R | 7 -- R/td_get_current.R | 53 ++++++++++++---------- R/utils.R | 74 ++++++++++++++++++++++++++++--- README.md | 13 +++++ man/figures/README-unnamed-chunk-3-1.png |only man/get_asset_info.Rd |only man/get_cache_folder.Rd | 5 +- man/get_td_names.Rd | 5 +- man/plot_td_series.Rd |only man/plot_yield_curve.Rd |only man/td_get_current.Rd | 14 ++++- tests/testthat/test-importing-data.R | 35 ++------------ tests/testthat/test-new-features.R |only tests/testthat/test-yc.R | 2 23 files changed, 218 insertions(+), 110 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.2.4 dated 2026-02-02 and 0.2.5 dated 2026-08-29
DESCRIPTION | 8 MD5 | 122 +++---- NAMESPACE | 198 ++++++----- NEWS.md | 314 +++++++++--------- R/bib-ggtree.R | 520 +++++++++++++++---------------- R/bib-knownledge.R | 649 +++++++++++++++++++-------------------- R/biorxiv.R | 88 ++--- R/cache.R | 444 +++++++++++++------------- R/combinations.R | 28 - R/concat.r | 261 +++++++++------ R/download.R | 160 ++++----- R/error-utils.r | 712 +++++++++++++++++++++---------------------- R/file.R | 314 +++++++++--------- R/install_zip.R | 134 ++++---- R/list.R | 62 +-- R/load-orgdb.r | 36 +- R/matrix-utils.R | 74 ++-- R/os.R | 194 +++++------ R/parse_ratio.R | 44 +- R/pkg-utils.R | 482 ++++++++++++++--------------- R/regexpr.R | 134 ++++---- R/scale.R | 28 - R/scihub-dl.R | 52 +-- R/str-utils.R | 214 ++++++------ R/sudo-install.R | 42 +- R/utilities.R | 108 +++--- R/yulab-msg.R | 206 ++++++------ R/yulab-utils-package.R | 6 R/zzz.R | 20 - inst/prototype/GEO.r | 66 +-- inst/prototype/sra.r | 24 - man/as_chunked_array.Rd |only man/c2.Rd | 14 man/check_directory.Rd | 10 man/check_file.Rd | 10 man/check_input.Rd | 10 man/check_packages.Rd | 10 man/check_range.Rd | 10 man/cran-bioc-pkg.Rd | 68 ++-- man/exec.Rd | 6 man/get_dependencies.Rd | 16 man/get_fun_from_pkg.Rd | 72 ++-- man/github-pkg.Rd | 16 man/has_internet.Rd | 6 man/install_zip.Rd | 48 +- man/install_zip_gh.Rd | 68 ++-- man/is.installed.Rd | 68 ++-- man/mat2df.Rd | 52 +-- man/mypkg.Rd | 66 +-- man/o.Rd | 66 +-- man/packageTitle.Rd | 16 man/pload.Rd | 16 man/read.cb.Rd | 58 +-- man/scihub-dl.Rd | 48 +- man/show_in_excel.Rd | 54 +-- man/str-detect.Rd | 8 man/str-extract.Rd | 8 man/str-starts-ends.Rd | 68 ++-- man/str_wrap.Rd | 58 +-- man/user_dir.Rd | 6 man/yread.Rd | 13 man/yulab.utils-package.Rd | 5 tests/testthat/test-concat.R |only 63 files changed, 3402 insertions(+), 3316 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight deviations
(differences from totals, comparisons between lines or columns, contributions to
variance, odds ratios, etc.) and significance (confidence intervals, stars, etc.).
Create the same kind of tables for regression models, with a framework to compare
model effects with their crude/observed counterpart systematically.
All functions render data frames which can be easily manipulated.
All tables can be exported with formats and colors to 'Excel', html and markdown.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@protonmail.com>
Diff between tabxplor versions 1.3.1 dated 2025-09-26 and 2.0.0 dated 2026-08-29
tabxplor-1.3.1/tabxplor/man/bind_datas_for_tab.Rd |only tabxplor-1.3.1/tabxplor/man/compare_levels.Rd |only tabxplor-1.3.1/tabxplor/man/fct_case_when_recode.Rd |only tabxplor-1.3.1/tabxplor/man/fct_clean.Rd |only tabxplor-1.3.1/tabxplor/man/fct_detect_replace.Rd |only tabxplor-1.3.1/tabxplor/man/fct_levels_from_vector.Rd |only tabxplor-1.3.1/tabxplor/man/fct_rename.Rd |only tabxplor-1.3.1/tabxplor/man/fct_replace.Rd |only tabxplor-1.3.1/tabxplor/man/fct_to_na.Rd |only tabxplor-1.3.1/tabxplor/man/formats_SAS_to_R.Rd |only tabxplor-1.3.1/tabxplor/man/get_ci_type.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/get_ci_type.default.Rd |only tabxplor-1.3.1/tabxplor/man/get_ci_type.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/get_col_var.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/get_col_var.default.Rd |only tabxplor-1.3.1/tabxplor/man/get_col_var.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/get_color.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/get_color.default.Rd |only tabxplor-1.3.1/tabxplor/man/get_color.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/get_ref_type.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/get_ref_type.default.Rd |only tabxplor-1.3.1/tabxplor/man/get_ref_type.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/get_type.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/get_type.default.Rd |only tabxplor-1.3.1/tabxplor/man/get_type.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/is_refcol.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/is_refcol.default.Rd |only tabxplor-1.3.1/tabxplor/man/is_refcol.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/is_refrow.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/is_refrow.default.Rd |only tabxplor-1.3.1/tabxplor/man/is_refrow.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/is_totcol.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/is_totcol.default.Rd |only tabxplor-1.3.1/tabxplor/man/is_totcol.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/is_totrow.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/is_totrow.default.Rd |only tabxplor-1.3.1/tabxplor/man/is_totrow.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/is_tottab.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/is_tottab.default.Rd |only tabxplor-1.3.1/tabxplor/man/is_tottab.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/map2_if.Rd |only tabxplor-1.3.1/tabxplor/man/new_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/pillar_shaft.tab_chi2_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/pipe.Rd |only tabxplor-1.3.1/tabxplor/man/pmap_if.Rd |only tabxplor-1.3.1/tabxplor/man/prepare_fct_recode.Rd |only tabxplor-1.3.1/tabxplor/man/set_display.data.frame.Rd |only tabxplor-1.3.1/tabxplor/man/set_display.default.Rd |only tabxplor-1.3.1/tabxplor/man/set_display.tabxplor_fmt.Rd |only tabxplor-1.3.1/tabxplor/man/tab_kable.Rd |only tabxplor-1.3.1/tabxplor/tests/testthat/test-fmt_class.R |only tabxplor-1.3.1/tabxplor/tests/testthat/test-tab_classes.R |only tabxplor-1.3.1/tabxplor/tests/testthat/test-tab_xl.R |only tabxplor-2.0.0/tabxplor/DESCRIPTION | 61 tabxplor-2.0.0/tabxplor/MD5 | 463 tabxplor-2.0.0/tabxplor/NAMESPACE | 473 tabxplor-2.0.0/tabxplor/NEWS.md | 237 tabxplor-2.0.0/tabxplor/R/aaa-grid.R |only tabxplor-2.0.0/tabxplor/R/data.R |only tabxplor-2.0.0/tabxplor/R/fmt_class.R | 8197 +++++- tabxplor-2.0.0/tabxplor/R/jmvtab-cache.R |only tabxplor-2.0.0/tabxplor/R/jmvtab-export.R |only tabxplor-2.0.0/tabxplor/R/jmvtab.b.R | 728 tabxplor-2.0.0/tabxplor/R/jmvtab.h.R | 620 tabxplor-2.0.0/tabxplor/R/jmvtabreg-cache.R |only tabxplor-2.0.0/tabxplor/R/jmvtabreg.b.R |only tabxplor-2.0.0/tabxplor/R/jmvtabreg.h.R |only tabxplor-2.0.0/tabxplor/R/plots.R |only tabxplor-2.0.0/tabxplor/R/reg-assumptions.R |only tabxplor-2.0.0/tabxplor/R/reg-cross.R |only tabxplor-2.0.0/tabxplor/R/reg-digest.R |only tabxplor-2.0.0/tabxplor/R/reg-empirical.R |only tabxplor-2.0.0/tabxplor/R/reg-estimand.R |only tabxplor-2.0.0/tabxplor/R/reg-influence.R |only tabxplor-2.0.0/tabxplor/R/reg-resolve.R |only tabxplor-2.0.0/tabxplor/R/reg-spec-build.R |only tabxplor-2.0.0/tabxplor/R/row-model.R |only tabxplor-2.0.0/tabxplor/R/survey-design.R |only tabxplor-2.0.0/tabxplor/R/survey-variance.R |only tabxplor-2.0.0/tabxplor/R/tab-agg.R |only tabxplor-2.0.0/tabxplor/R/tab-args.R |only tabxplor-2.0.0/tabxplor/R/tab-chi2.R |only tabxplor-2.0.0/tabxplor/R/tab-counts.R |only tabxplor-2.0.0/tabxplor/R/tab-cross.R |only tabxplor-2.0.0/tabxplor/R/tab-css.R |only tabxplor-2.0.0/tabxplor/R/tab-deprecate.R |only tabxplor-2.0.0/tabxplor/R/tab-display.R |only tabxplor-2.0.0/tabxplor/R/tab-export-prep.R |only tabxplor-2.0.0/tabxplor/R/tab-export.R |only tabxplor-2.0.0/tabxplor/R/tab-leaf.R |only tabxplor-2.0.0/tabxplor/R/tab-options.R |only tabxplor-2.0.0/tabxplor/R/tab-palettes.R |only tabxplor-2.0.0/tabxplor/R/tab-parallel.R |only tabxplor-2.0.0/tabxplor/R/tab-render-html.R |only tabxplor-2.0.0/tabxplor/R/tab-resolve.R |only tabxplor-2.0.0/tabxplor/R/tab-steps-legacy.R |only tabxplor-2.0.0/tabxplor/R/tab-structure.R |only tabxplor-2.0.0/tabxplor/R/tab-test-display.R |only tabxplor-2.0.0/tabxplor/R/tab-theme-detect.R |only tabxplor-2.0.0/tabxplor/R/tab-tooltip.R |only tabxplor-2.0.0/tabxplor/R/tab-transpose-render.R |only tabxplor-2.0.0/tabxplor/R/tab-xl-backend.R |only tabxplor-2.0.0/tabxplor/R/tab.R | 7416 +----- tabxplor-2.0.0/tabxplor/R/tab_classes.R | 4579 +-- tabxplor-2.0.0/tabxplor/R/tab_md.R |only tabxplor-2.0.0/tabxplor/R/tab_reg.R |only tabxplor-2.0.0/tabxplor/R/tab_xl.R | 5272 +--- tabxplor-2.0.0/tabxplor/R/table-spec.R |only tabxplor-2.0.0/tabxplor/R/tabxplor-package.R |only tabxplor-2.0.0/tabxplor/R/utils.R | 1623 - tabxplor-2.0.0/tabxplor/R/var-shape.R |only tabxplor-2.0.0/tabxplor/R/zzz-fact-keys.R |only tabxplor-2.0.0/tabxplor/README.md | 685 tabxplor-2.0.0/tabxplor/build/vignette.rds |binary tabxplor-2.0.0/tabxplor/data |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-programming.R |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-programming.Rmd |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-programming.html |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reading-a-regression.R |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reading-a-regression.Rmd |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reading-a-regression.html |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reg.R |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reg.Rmd |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-reg.html |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-weights.R |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-weights.Rmd |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor-weights.html |only tabxplor-2.0.0/tabxplor/inst/doc/tabxplor.R | 392 tabxplor-2.0.0/tabxplor/inst/doc/tabxplor.Rmd | 676 tabxplor-2.0.0/tabxplor/inst/doc/tabxplor.html |11734 +++++++--- tabxplor-2.0.0/tabxplor/inst/i18n/fr.json | 830 tabxplor-2.0.0/tabxplor/inst/po |only tabxplor-2.0.0/tabxplor/inst/tab.css | 6 tabxplor-2.0.0/tabxplor/inst/tabxplor-1.0 |only tabxplor-2.0.0/tabxplor/man/arrange.tabxplor_tab.Rd | 5 tabxplor-2.0.0/tabxplor/man/car_arrests.Rd |only tabxplor-2.0.0/tabxplor/man/car_salaries.Rd |only tabxplor-2.0.0/tabxplor/man/cash-.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/cash-.tabxplor_tab.Rd |only tabxplor-2.0.0/tabxplor/man/complete_partial_totals.Rd | 10 tabxplor-2.0.0/tabxplor/man/conf_level_to_z.Rd |only tabxplor-2.0.0/tabxplor/man/dplyr_col_modify.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/dplyr_reconstruct.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/dplyr_row_slice.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/facto_tea.Rd |only tabxplor-2.0.0/tabxplor/man/fct_recode_helper.Rd | 33 tabxplor-2.0.0/tabxplor/man/figures |only tabxplor-2.0.0/tabxplor/man/fmt.Rd | 876 tabxplor-2.0.0/tabxplor/man/fmt_attr.Rd |only tabxplor-2.0.0/tabxplor/man/fmt_attributes.Rd |only tabxplor-2.0.0/tabxplor/man/fmt_fields.Rd |only tabxplor-2.0.0/tabxplor/man/fmt_get_color_code.Rd | 19 tabxplor-2.0.0/tabxplor/man/forest_plot.Rd |only tabxplor-2.0.0/tabxplor/man/format.tabxplor_fmt.Rd | 50 tabxplor-2.0.0/tabxplor/man/get_test.Rd |only tabxplor-2.0.0/tabxplor/man/group_by.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/gss_cat_data_formatting.Rd |only tabxplor-2.0.0/tabxplor/man/is_tab.Rd |only tabxplor-2.0.0/tabxplor/man/jmvtab.Rd | 476 tabxplor-2.0.0/tabxplor/man/jmvtabreg.Rd |only tabxplor-2.0.0/tabxplor/man/kable_tabxplor_style.Rd | 68 tabxplor-2.0.0/tabxplor/man/mutate.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/new_lvl.Rd |only tabxplor-2.0.0/tabxplor/man/new_tab.Rd | 129 tabxplor-2.0.0/tabxplor/man/pillar_shaft.tabxplor_fmt.Rd | 8 tabxplor-2.0.0/tabxplor/man/print.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/print.tabxplor_kable.Rd |only tabxplor-2.0.0/tabxplor/man/print.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/print.tabxplor_tabs.Rd |only tabxplor-2.0.0/tabxplor/man/questionr_hdv.Rd |only tabxplor-2.0.0/tabxplor/man/reg_check_plots.Rd |only tabxplor-2.0.0/tabxplor/man/reg_formulas.Rd |only tabxplor-2.0.0/tabxplor/man/reg_measures.Rd |only tabxplor-2.0.0/tabxplor/man/relocate.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/rename.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/rename_with.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/rowwise.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/rowwise.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/score_from_lv1.Rd | 27 tabxplor-2.0.0/tabxplor/man/select.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/set_caption.Rd |only tabxplor-2.0.0/tabxplor/man/set_color_palette.Rd |only tabxplor-2.0.0/tabxplor/man/shape_numeric_var.Rd |only tabxplor-2.0.0/tabxplor/man/sub-.tabxplor_grouped_tab.Rd | 5 tabxplor-2.0.0/tabxplor/man/sub-subset-.tabxplor_grouped_tab.Rd | 3 tabxplor-2.0.0/tabxplor/man/subset-.tabxplor_grouped_tab.Rd | 3 tabxplor-2.0.0/tabxplor/man/summarise.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/tab.Rd | 652 tabxplor-2.0.0/tabxplor/man/tab_cast.Rd | 478 tabxplor-2.0.0/tabxplor/man/tab_chi2.Rd | 95 tabxplor-2.0.0/tabxplor/man/tab_ci.Rd | 193 tabxplor-2.0.0/tabxplor/man/tab_color_legend.Rd |only tabxplor-2.0.0/tabxplor/man/tab_columns.Rd |only tabxplor-2.0.0/tabxplor/man/tab_compact.Rd | 6 tabxplor-2.0.0/tabxplor/man/tab_counts.Rd |only tabxplor-2.0.0/tabxplor/man/tab_css.Rd |only tabxplor-2.0.0/tabxplor/man/tab_estimates.Rd |only tabxplor-2.0.0/tabxplor/man/tab_export.Rd |only tabxplor-2.0.0/tabxplor/man/tab_get_vars.Rd |only tabxplor-2.0.0/tabxplor/man/tab_get_wrapped_dimensions.Rd | 4 tabxplor-2.0.0/tabxplor/man/tab_html.Rd |only tabxplor-2.0.0/tabxplor/man/tab_many.Rd | 516 tabxplor-2.0.0/tabxplor/man/tab_md.Rd |only tabxplor-2.0.0/tabxplor/man/tab_num.Rd | 225 tabxplor-2.0.0/tabxplor/man/tab_parallel_stop.Rd |only tabxplor-2.0.0/tabxplor/man/tab_pct.Rd | 126 tabxplor-2.0.0/tabxplor/man/tab_plain.Rd | 232 tabxplor-2.0.0/tabxplor/man/tab_plot.Rd | 55 tabxplor-2.0.0/tabxplor/man/tab_prepare.Rd | 100 tabxplor-2.0.0/tabxplor/man/tab_pvalue_lines.Rd | 1 tabxplor-2.0.0/tabxplor/man/tab_reg.Rd |only tabxplor-2.0.0/tabxplor/man/tab_spread.Rd | 94 tabxplor-2.0.0/tabxplor/man/tab_structure.Rd |only tabxplor-2.0.0/tabxplor/man/tab_supports.Rd |only tabxplor-2.0.0/tabxplor/man/tab_tot.Rd | 96 tabxplor-2.0.0/tabxplor/man/tab_totaltab.Rd | 90 tabxplor-2.0.0/tabxplor/man/tab_transpose.Rd |only tabxplor-2.0.0/tabxplor/man/tab_wrap_text.Rd | 15 tabxplor-2.0.0/tabxplor/man/tab_xl.Rd | 271 tabxplor-2.0.0/tabxplor/man/tabxplor-base-coercion.Rd |only tabxplor-2.0.0/tabxplor/man/tabxplor-display.Rd |only tabxplor-2.0.0/tabxplor/man/tabxplor-options.Rd |only tabxplor-2.0.0/tabxplor/man/tabxplor-package.Rd |only tabxplor-2.0.0/tabxplor/man/tabxplor-type.Rd |only tabxplor-2.0.0/tabxplor/man/tabxplor-vctrs.Rd | 18 tabxplor-2.0.0/tabxplor/man/tbl_format_body.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/tbl_format_footer.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/tbl_sum.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/tbl_sum.tabxplor_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/ungroup.tabxplor_grouped_tab.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_arith.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.character.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.double.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.integer.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.tabxplor_fmt.double.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.tabxplor_fmt.integer.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_cast.tabxplor_fmt.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_math.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_proxy_compare.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_proxy_equal.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype2.double.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype2.integer.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype2.tabxplor_fmt.double.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype2.tabxplor_fmt.integer.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype2.tabxplor_fmt.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype_abbr.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/man/vec_ptype_full.tabxplor_fmt.Rd | 1 tabxplor-2.0.0/tabxplor/po/R-fr.po | 2028 + tabxplor-2.0.0/tabxplor/po/R-tabxplor.pot | 1574 + tabxplor-2.0.0/tabxplor/tests/testthat.R | 30 tabxplor-2.0.0/tabxplor/tests/testthat/_color_golden |only tabxplor-2.0.0/tabxplor/tests/testthat/_golden |only tabxplor-2.0.0/tabxplor/tests/testthat/_snaps |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-color-golden.R |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-fixtures.R |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-golden.R |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-i18n.R |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-reg.R |only tabxplor-2.0.0/tabxplor/tests/testthat/helper-source.R |only tabxplor-2.0.0/tabxplor/tests/testthat/setup.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-color-golden.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-edge-cases.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-fact-keys.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-fmt.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-golden.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-i18n.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-jmvtab.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-jmvtabreg.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-non-ascii.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-plots.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-reg-assumptions.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-reg-cross.R |only 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tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-cross.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-deprecate.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-display.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-export-prep.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-export.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-leaf.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-md.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-options.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-palettes.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-reg.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-render-html.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-steps-legacy.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-test-display.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-theme-detect.R |only tabxplor-2.0.0/tabxplor/tests/testthat/test-tab-tooltip.R |only 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Title: Encrypt and Decrypt Strings, R Objects and Files
Description: A consistent interface to encrypt and decrypt strings, R objects and files using symmetric and asymmetric key encryption.
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Diff between safer versions 0.2.2 dated 2026-03-24 and 0.2.3 dated 2026-08-29
DESCRIPTION | 9 +++-- MD5 | 11 +++---- NAMESPACE | 1 NEWS.md | 5 +++ R/keypair.R | 77 +++++++++++++++++++++++++++++++++++++++++++++------ man/read_keypair.Rd |only man/safer-package.Rd | 2 - 7 files changed, 87 insertions(+), 18 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut, cre],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Visruth Srimath Kandali [ctb],
Trustees of Columbia University [cph]
Maintainer: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Diff between rstantools versions 2.7.0 dated 2026-07-25 and 2.7.1 dated 2026-08-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 12 +++++++----- R/stanc_exceptions.R | 4 ++-- inst/doc/developer-guidelines.html | 2 +- inst/doc/minimal-rstan-package.html | 4 ++-- 6 files changed, 21 insertions(+), 19 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.10.1 dated 2026-07-19 and 3.11.0 dated 2026-08-29
gsDesign-3.10.1/gsDesign/vignettes/gsDesignAISkills.html |only gsDesign-3.11.0/gsDesign/DESCRIPTION | 6 gsDesign-3.11.0/gsDesign/MD5 | 140 gsDesign-3.11.0/gsDesign/NAMESPACE | 2 gsDesign-3.11.0/gsDesign/NEWS.md | 119 gsDesign-3.11.0/gsDesign/R/binomialExactPValues.R | 22 gsDesign-3.11.0/gsDesign/R/gsDesign.R | 283 - gsDesign-3.11.0/gsDesign/R/gsMethods.R | 251 gsDesign-3.11.0/gsDesign/R/gsSurv-nSurv.R | 35 gsDesign-3.11.0/gsDesign/R/gsSurv-utils.R | 127 gsDesign-3.11.0/gsDesign/R/gsSurv.R | 37 gsDesign-3.11.0/gsDesign/R/gsSurvCalendar.R | 17 gsDesign-3.11.0/gsDesign/R/gsSurvPower.R | 913 ++- gsDesign-3.11.0/gsDesign/R/gsUtilities.R | 10 gsDesign-3.11.0/gsDesign/R/gsqplot.R | 32 gsDesign-3.11.0/gsDesign/R/minMedianFollowUp.R |only gsDesign-3.11.0/gsDesign/R/sequentialPValue.R | 13 gsDesign-3.11.0/gsDesign/R/toBinomialExact.R | 341 + gsDesign-3.11.0/gsDesign/R/toInteger.R | 105 gsDesign-3.11.0/gsDesign/build/vignette.rds |binary gsDesign-3.11.0/gsDesign/inst/doc/ConditionalErrorSpending.html | 345 - gsDesign-3.11.0/gsDesign/inst/doc/HarmBound.R | 6 gsDesign-3.11.0/gsDesign/inst/doc/HarmBound.Rmd | 47 gsDesign-3.11.0/gsDesign/inst/doc/HarmBound.html | 240 gsDesign-3.11.0/gsDesign/inst/doc/MultiSeasonRareEvents.html | 345 - gsDesign-3.11.0/gsDesign/inst/doc/PoissonMixtureModel.html | 119 gsDesign-3.11.0/gsDesign/inst/doc/SelectiveBoundTesting.R | 203 gsDesign-3.11.0/gsDesign/inst/doc/SelectiveBoundTesting.Rmd | 356 - gsDesign-3.11.0/gsDesign/inst/doc/SelectiveBoundTesting.html | 2763 ++++++++-- gsDesign-3.11.0/gsDesign/inst/doc/SurvivalEnrollmentPlanning.R |only gsDesign-3.11.0/gsDesign/inst/doc/SurvivalEnrollmentPlanning.Rmd |only gsDesign-3.11.0/gsDesign/inst/doc/SurvivalEnrollmentPlanning.html |only gsDesign-3.11.0/gsDesign/inst/doc/VaccineEfficacy.Rmd | 10 gsDesign-3.11.0/gsDesign/inst/doc/VaccineEfficacy.html | 646 +- gsDesign-3.11.0/gsDesign/inst/doc/binomialSPRTExample.R | 20 gsDesign-3.11.0/gsDesign/inst/doc/binomialSPRTExample.html | 230 gsDesign-3.11.0/gsDesign/inst/doc/binomialTwoSample.R | 44 gsDesign-3.11.0/gsDesign/inst/doc/binomialTwoSample.html | 982 +-- gsDesign-3.11.0/gsDesign/inst/doc/gsSurvBasicExamples.html | 340 - gsDesign-3.11.0/gsDesign/inst/doc/gsSurvPower.R | 152 gsDesign-3.11.0/gsDesign/inst/doc/gsSurvPower.Rmd | 583 +- gsDesign-3.11.0/gsDesign/inst/doc/gsSurvPower.html | 1431 +++-- gsDesign-3.11.0/gsDesign/inst/doc/nNormal.html | 2 gsDesign-3.11.0/gsDesign/inst/doc/toInteger.html | 10 gsDesign-3.11.0/gsDesign/inst/slides |only gsDesign-3.11.0/gsDesign/man/gsBoundSummary.Rd | 17 gsDesign-3.11.0/gsDesign/man/gsDesign.Rd | 17 gsDesign-3.11.0/gsDesign/man/gsSurvCalendar.Rd | 16 gsDesign-3.11.0/gsDesign/man/gsSurvPower.Rd | 296 - gsDesign-3.11.0/gsDesign/man/minMedianFollowUp.Rd |only gsDesign-3.11.0/gsDesign/man/nSurv.Rd | 38 gsDesign-3.11.0/gsDesign/man/plot.gsDesign.Rd | 7 gsDesign-3.11.0/gsDesign/man/repeatedPValueBinomialExact.Rd | 8 gsDesign-3.11.0/gsDesign/man/sequentiaPValue.Rd | 7 gsDesign-3.11.0/gsDesign/man/sequentialPValueBinomialExact.Rd | 6 gsDesign-3.11.0/gsDesign/man/toBinomialExact.Rd | 38 gsDesign-3.11.0/gsDesign/man/toInteger.Rd | 17 gsDesign-3.11.0/gsDesign/src/gsdensity.c | 17 gsDesign-3.11.0/gsDesign/tests/testthat/Rplots.pdf |only gsDesign-3.11.0/gsDesign/tests/testthat/_snaps/independent-test-print.gsSurv.md | 68 gsDesign-3.11.0/gsDesign/tests/testthat/test-developer-test-toBinomialExact.R | 2 gsDesign-3.11.0/gsDesign/tests/testthat/test-gsSurv-N-enrollment.R |only gsDesign-3.11.0/gsDesign/tests/testthat/test-gsSurvPower.R | 735 ++ gsDesign-3.11.0/gsDesign/tests/testthat/test-independent-test-binomialExactPValues.R | 37 gsDesign-3.11.0/gsDesign/tests/testthat/test-independent-test-plotgsPower.R | 36 gsDesign-3.11.0/gsDesign/tests/testthat/test-independent-test-toBinomialExact.R | 202 gsDesign-3.11.0/gsDesign/tests/testthat/test-independent-test-toInteger.R | 29 gsDesign-3.11.0/gsDesign/tests/testthat/test-k1-survival-designs.R |only gsDesign-3.11.0/gsDesign/tests/testthat/test-minMedianFollowUp.R |only gsDesign-3.11.0/gsDesign/tests/testthat/test-selective-bounds.R | 237 gsDesign-3.11.0/gsDesign/tests/testthat/test-sequentialPValue.R | 29 gsDesign-3.11.0/gsDesign/vignettes/HarmBound.Rmd | 47 gsDesign-3.11.0/gsDesign/vignettes/SelectiveBoundTesting.Rmd | 356 - gsDesign-3.11.0/gsDesign/vignettes/SurvivalEnrollmentPlanning.Rmd |only gsDesign-3.11.0/gsDesign/vignettes/VaccineEfficacy.Rmd | 10 gsDesign-3.11.0/gsDesign/vignettes/gsDesignVsProcSeqdesign.html |only gsDesign-3.11.0/gsDesign/vignettes/gsSurvPower.Rmd | 583 +- 77 files changed, 10547 insertions(+), 3635 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 1.2.1 dated 2026-08-26 and 1.2.2 dated 2026-08-29
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS.md | 14 +++++++ R/graph_aes.R | 21 +++++++++- R/graph_legends.R | 74 ++++++++++++++++++++++++------------- R/graph_nodes.R | 28 +++++++++----- R/graphr.R | 4 ++ R/grapht.R | 15 +++++++ R/zzz.R | 41 +++++++++++++++++--- man/plot_graphr.Rd | 4 ++ man/plot_grapht.Rd | 4 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test-graphr.R | 86 +++++++++++++++++++++++++++++++++++++++++-- tests/testthat/test-grapht.R | 9 ++++ 14 files changed, 269 insertions(+), 63 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb],
Wouter van der Bijl [ctb],
Hugo Gruson [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.4 dated 2025-11-10 and 0.2.5 dated 2026-08-29
uwot-0.2.4/uwot/inst/include/RcppPerpendicular.h |only uwot-0.2.5/uwot/DESCRIPTION | 9 uwot-0.2.5/uwot/MD5 | 89 ++++---- uwot-0.2.5/uwot/NEWS.md | 21 + uwot-0.2.5/uwot/R/neighbors.R | 43 ++++ uwot-0.2.5/uwot/R/nn_hnsw.R | 10 uwot-0.2.5/uwot/R/nn_nndescent.R | 21 + uwot-0.2.5/uwot/R/transform.R | 9 uwot-0.2.5/uwot/R/umap2.R | 11 - uwot-0.2.5/uwot/R/uwot.R | 139 +++++++++---- uwot-0.2.5/uwot/build/partial.rdb |binary uwot-0.2.5/uwot/build/vignette.rds |binary uwot-0.2.5/uwot/inst/include/pforr.h |only uwot-0.2.5/uwot/inst/include/uwot/connected_components.h | 4 uwot-0.2.5/uwot/inst/include/uwot/coords.h | 28 +- uwot-0.2.5/uwot/inst/include/uwot/epoch.h | 15 - uwot-0.2.5/uwot/inst/include/uwot/gradient.h | 33 +-- uwot-0.2.5/uwot/inst/include/uwot/optimize.h | 17 + uwot-0.2.5/uwot/inst/include/uwot/smooth_knn.h | 2 uwot-0.2.5/uwot/inst/include/uwot/tauprng.h | 3 uwot-0.2.5/uwot/inst/include/uwot/transform.h | 4 uwot-0.2.5/uwot/inst/include/uwot/update.h | 41 +-- uwot-0.2.5/uwot/man/lvish.Rd | 25 +- uwot-0.2.5/uwot/man/similarity_graph.Rd | 27 +- uwot-0.2.5/uwot/man/tumap.Rd | 25 +- uwot-0.2.5/uwot/man/umap.Rd | 25 +- uwot-0.2.5/uwot/man/umap2.Rd | 11 - uwot-0.2.5/uwot/src/Makevars | 1 uwot-0.2.5/uwot/src/nn_parallel.cpp | 4 uwot-0.2.5/uwot/src/perplexity.cpp | 4 uwot-0.2.5/uwot/src/r_uwot.cpp | 55 ++--- uwot-0.2.5/uwot/src/rparallel.h | 17 - uwot-0.2.5/uwot/src/smooth_knn.cpp | 4 uwot-0.2.5/uwot/src/transform.cpp | 4 uwot-0.2.5/uwot/tests/testthat/test_curve.R | 24 +- uwot-0.2.5/uwot/tests/testthat/test_epochs.R | 2 uwot-0.2.5/uwot/tests/testthat/test_errors.R | 36 +++ uwot-0.2.5/uwot/tests/testthat/test_fuzzy_simplicial_set.R | 38 +-- uwot-0.2.5/uwot/tests/testthat/test_knn_aff.R | 2 uwot-0.2.5/uwot/tests/testthat/test_neighbors.R | 68 +++--- uwot-0.2.5/uwot/tests/testthat/test_nndescent.R |only uwot-0.2.5/uwot/tests/testthat/test_output.R | 23 +- uwot-0.2.5/uwot/tests/testthat/test_perplexity.R | 20 - uwot-0.2.5/uwot/tests/testthat/test_saveload.R | 10 uwot-0.2.5/uwot/tests/testthat/test_smooth_knn_dists.R | 32 +- uwot-0.2.5/uwot/tests/testthat/test_supervised.R | 10 uwot-0.2.5/uwot/tests/testthat/test_transform.R | 4 47 files changed, 610 insertions(+), 360 deletions(-)
Title: Fast Raster Summary and Manipulation
Description: Fast alternatives to several relatively slow 'raster' package
functions. For large rasters, the functions run from 5 to
approximately 100 times faster than the 'raster' package functions
they replace. The 'fasterize' package, on which one function in this
package depends, includes an implementation of the scan line
algorithm attributed to Wylie et al. (1967)
<doi:10.1145/1465611.1465619>.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between rasterDT versions 0.3.2 dated 2022-12-15 and 0.3.3 dated 2026-08-29
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 15 ++++++++------- NAMESPACE | 42 +++++++++++++++++++++++++++--------------- NEWS.md | 14 +++++++++++--- R/crosstabDT.R | 2 +- R/subsDT.R | 12 +++++++----- build/partial.rdb |binary man/figures |only man/subsDT.Rd | 5 ----- 9 files changed, 69 insertions(+), 46 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/en-us>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Tyler Littlefield [ctb],
httr development team [ctb] ,
Scott Holden [ctb] ,
Chris Stone [ctb] ,
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureAuth versions 1.3.4 dated 2025-12-20 and 1.3.5 dated 2026-08-29
DESCRIPTION | 9 +++++---- MD5 | 18 +++++++++--------- NAMESPACE | 7 +++++++ NEWS.md | 4 ++++ R/cert_creds.R | 7 +++++++ R/managed_token.R | 4 ++++ R/token_manual.R | 31 +++++++++---------------------- man/AzureManualToken.Rd | 48 ++++++++++-------------------------------------- man/AzureToken.Rd | 4 ++-- man/get_azure_token.Rd | 2 +- 10 files changed, 58 insertions(+), 76 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.8 dated 2025-12-12 and 0.4.9 dated 2026-08-29
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tectonicr-0.4.9/tectonicr/vignettes/statistics.Rmd | 77 tectonicr-0.4.9/tectonicr/vignettes/tectonicr.Rmd | 586 +- 110 files changed, 7449 insertions(+), 6974 deletions(-)
Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that [...truncated...]
Author: Michael Dumelle [aut, cre] ,
Tom Kincaid [aut],
Anthony R. Olsen [aut],
Marc Weber [aut],
Don Stevens [ctb],
Denis White [ctb],
Amanda M. Nahlik [ctb],
Sarah Lehmann [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spsurvey versions 5.6.1 dated 2026-05-04 and 5.7.0 dated 2026-08-29
DESCRIPTION | 8 MD5 | 189 ++++++++--------- NEWS.md | 16 + R/adjwgt.R | 1 R/adjwgtNR.R | 17 + R/ash1_wgt.R | 57 +++++ R/attrisk_analysis.R | 85 ++++++- R/attrisk_var.R | 65 +++++ R/bootfcn.R | 8 R/cat_analysis.R | 29 ++ R/cat_localmean_prop.R | 58 ++++- R/cat_localmean_total.R | 64 ++++- R/category_est.R | 52 +++- R/catvar_prop.R | 70 +++++- R/catvar_total.R | 51 ++++ R/cdf_est.R | 36 ++- R/cdf_localmean_prop.R | 70 +++++- R/cdf_localmean_total.R | 66 ++++- R/cdf_nresp.R | 1 R/cdf_plot.R | 1 R/cdf_prop.R | 4 R/cdftest_localmean_prop.R | 70 +++++- R/cdftest_localmean_total.R | 80 +++++-- R/cdftestvar_prop.R | 103 +++++++-- R/cdftestvar_total.R | 98 +++++++- R/cdfvar_prop.R | 53 ++++ R/cdfvar_total.R | 49 +++- R/change_analysis.R | 49 ++-- R/change_est.R | 486 ++++++++++++++++++++++++++++---------------- R/changevar_mean.R | 21 + R/changevar_prop.R | 15 - R/changevar_total.R | 13 - R/cont_analysis.R | 41 ++- R/cont_cdfplot.R | 1 R/cont_cdftest.R | 39 ++- R/diffrisk_analysis.R | 80 ++++++- R/dsgn_check.R | 9 R/grts.R | 27 +- R/grts_stratum.R | 22 + R/grtspts_ip.R | 1 R/grtspts_ipleg.R | 5 R/grtspts_mindis.R | 6 R/input_check.R | 11 R/insideAreaGridCell.R | 5 R/insideLinearGridCell.R | 5 R/interp_axis.R | 9 R/interp_cdf.R | 7 R/irs.R | 19 + R/irs_stratum.R | 13 + R/irspts_mindis.R | 6 R/localmean_cov.R | 12 + R/localmean_var.R | 10 R/localmean_weight.R | 33 ++ R/mean_est.R | 30 +- R/mean_localmean.R | 79 ++++++- R/mean_var.R | 62 ++++- R/percentile_est.R | 47 ++-- R/plot.R | 34 +-- R/power_dsgn.R | 2 R/ppd_plot.R | 1 R/print.R | 10 R/relrisk_analysis.R | 72 +++++- R/relrisk_var.R | 70 +++++- R/replace_near.R | 32 +- R/revisit_bibd.R | 6 R/revisit_dsgn.R | 3 R/rho.R | 11 R/sp_balance.R | 121 ++++++++++ R/sp_frame.R | 10 R/sp_plot.R | 6 R/sp_summary.R | 39 +++ R/summary.R | 4 R/survey_design.R | 22 + R/svychisq_localmean.R | 15 + R/total_est.R | 27 +- R/total_localmean.R | 94 ++++++-- R/total_var.R | 47 +++- R/trend_analysis.R | 97 ++++++-- R/uniqueID.R | 4 R/utils.R | 150 ++++++++++++- R/vecprint.R | 5 R/warnprnt.R | 1 inst/doc/start-here.Rmd | 8 inst/doc/start-here.html | 13 - inst/references.bib |only man/attrisk_analysis.Rd | 19 + man/cat_analysis.Rd | 18 + man/change_analysis.Rd | 25 +- man/cont_analysis.Rd | 26 +- man/cont_cdftest.Rd | 13 - man/diffrisk_analysis.Rd | 19 + man/plot.sp_CDF.Rd | 2 man/relrisk_analysis.Rd | 19 + man/sp_balance.Rd | 4 man/trend_analysis.Rd | 20 + vignettes/start-here.Rmd | 8 96 files changed, 2846 insertions(+), 795 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.13.1 dated 2026-07-09 and 0.14.0 dated 2026-08-29
DESCRIPTION | 12 MD5 | 160 +++++----- NEWS.md | 35 ++ R/areaplot.R | 5 R/barplot.R | 10 R/boxviolinplot.R | 11 R/chordplot.R | 6 R/clustreeplot.R | 6 R/common_args.R | 7 R/densityplot.R | 40 ++ R/dimplot.R | 136 ++++++-- R/dotplot.R | 10 R/gsea.R | 1 R/heatmap-utils.R | 344 ++++++++++++++++++++-- R/heatmap.R | 511 +++++++++++++++++++++++++++++---- R/jitterplot.R | 206 ++++++++++--- R/lineplot.R | 6 R/linkedheatmap.R | 22 + R/network.R | 9 R/piechart.R | 5 R/radarplot.R | 10 R/ringplot.R | 5 R/roccurve.R | 2 R/scatterplot.R | 5 R/trendplot.R | 5 R/utils.R | 55 +++ R/volcanoplot.R | 374 +++++++++++++++++------- man/ClustreePlot.Rd | 5 man/DimPlotAtomic.Rd | 10 man/DimPlotAtomic3D.Rd | 6 man/Heatmap.Rd | 120 +++++++ man/HeatmapAtomic.Rd | 55 ++- man/JitterPlotAtomic.Rd | 12 man/LinkedHeatmap.Rd | 24 + man/LinkedHeatmapAtomic.Rd | 15 man/Network.Rd | 16 - man/QQPlot.Rd | 9 man/RidgePlot.Rd | 11 man/RidgePlotAtomic.Rd | 2 man/ScatterPlot.Rd | 3 man/ScatterPlotAtomic.Rd | 3 man/VolcanoPlot.Rd | 136 ++++---- man/VolcanoPlotAtomic.Rd | 48 ++- man/WordCloudPlot.Rd | 9 man/common_args.Rd | 9 man/densityhistoplot.Rd | 9 man/dimplot.Rd | 6 man/dot-prep_annotations.Rd | 3 man/dot-resolve_show_modes.Rd |only man/dot-setup_annos.Rd | 5 man/enrichmap1.Rd | 9 man/sankeyplot.Rd | 9 man/validate_common_args.Rd | 9 tests/testthat/test-areaplot.R | 18 + tests/testthat/test-barplot.R | 64 ++++ tests/testthat/test-boxviolinplot.R | 45 ++ tests/testthat/test-chordplot.R | 18 + tests/testthat/test-clustreeplot.R | 53 +++ tests/testthat/test-corplot.R | 14 tests/testthat/test-densityhistoplot.R | 33 ++ tests/testthat/test-dimplot.R | 36 ++ tests/testthat/test-dotplot.R | 38 ++ tests/testthat/test-enrich.R | 32 ++ tests/testthat/test-heatmap.R | 332 +++++++++++++++++++++ tests/testthat/test-jitterplot.R | 96 ++++++ tests/testthat/test-lineplot.R | 12 tests/testthat/test-linkedheatmap.R |only tests/testthat/test-manhattanplot.R | 18 + tests/testthat/test-network.R | 55 +++ tests/testthat/test-piechart.R | 28 + tests/testthat/test-qqplot.R | 18 + tests/testthat/test-radarplot.R | 36 ++ tests/testthat/test-rarefactionplot.R | 16 + tests/testthat/test-roccurve.R | 20 + tests/testthat/test-sankeyplot.R | 22 + tests/testthat/test-scatterplot.R | 18 + tests/testthat/test-trendplot.R | 26 + tests/testthat/test-upsetplot.R | 32 ++ tests/testthat/test-utils-extra.R | 40 ++ tests/testthat/test-venndiagram.R | 32 ++ tests/testthat/test-volcanoplot.R | 100 ++++++ tests/testthat/test-wordcloudplot.R | 20 + 82 files changed, 3305 insertions(+), 508 deletions(-)
Title: Adverse Events Analysis Using 'metalite'
Description: Analyzes adverse events in clinical trials using the 'metalite'
data structure. The package simplifies the workflow to create
production-ready tables, listings, and figures discussed in the
adverse events analysis chapters of
"R for Clinical Study Reports and Submission"
by Zhang et al. (2022) <https://r4csr.org/>.
Author: Yilong Zhang [aut],
Yujie Zhao [aut, cre],
Hiroaki Fukuda [aut],
Benjamin Wang [aut],
Nan Xiao [aut],
Sarad Nepal [aut],
Madhusudhan Ginnaram [aut],
Venkatesh Burla [ctb],
Ruchitbhai Patel [aut],
Brian Lang [aut],
Xuan Deng [aut],
Bing Liu [aut],
Jee [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between metalite.ae versions 0.1.3 dated 2024-10-23 and 0.1.4 dated 2026-08-29
metalite.ae-0.1.3/metalite.ae/R/meta_ae_example.R |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-listing.R |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-listing.Rmd |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-listing.html |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-specific.R |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-specific.Rmd |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-specific.html |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-summary.R |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-summary.Rmd |only metalite.ae-0.1.3/metalite.ae/inst/doc/ae-summary.html |only metalite.ae-0.1.3/metalite.ae/man/meta_ae_example.Rd |only metalite.ae-0.1.3/metalite.ae/tests/testthat/test-independent-testing-meta_ae_dummy.R |only metalite.ae-0.1.3/metalite.ae/tests/testthat/test-rate_compare.R |only metalite.ae-0.1.3/metalite.ae/tests/testthat/test-rate_compare_sum.R |only metalite.ae-0.1.3/metalite.ae/vignettes/ae-listing.Rmd |only 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metalite.ae-0.1.4/metalite.ae/vignettes/rtf/ae0summary2.rtf | 262 metalite.ae-0.1.4/metalite.ae/vignettes/rtf/ae0summary3.rtf |only metalite.ae-0.1.4/metalite.ae/vignettes/rtf/mock_ae0specific1.rtf | 20 162 files changed, 7186 insertions(+), 8939 deletions(-)
Title: Bayesian Analysis of Dynamic Generalized Linear Models
Description: Provide routines for filtering and smoothing, forecasting, sampling and Bayesian analysis of Dynamic Generalized Linear Models using the methodology described in Alves et al. (2024)<doi:10.48550/arXiv.2201.05387> and dos Santos Jr. et al. (2024)<doi:10.48550/arXiv.2403.13069>.
Author: Silvaneo dos Santos Jr. [aut, cre],
Mariane Branco Alves [aut],
Helio dos Santos Migon [aut]
Maintainer: Silvaneo dos Santos Jr. <silvaneojunior@utexas.edu>
Diff between kDGLM versions 1.2.14 dated 2026-04-10 and 1.2.15 dated 2026-08-29
kDGLM-1.2.14/kDGLM/inst/doc/example1.R |only kDGLM-1.2.14/kDGLM/inst/doc/example1.Rmd |only kDGLM-1.2.14/kDGLM/inst/doc/example1.html |only kDGLM-1.2.14/kDGLM/vignettes/example1.Rmd |only kDGLM-1.2.15/kDGLM/DESCRIPTION | 12 kDGLM-1.2.15/kDGLM/MD5 | 42 kDGLM-1.2.15/kDGLM/R/kernel_multinormal.R | 4 kDGLM-1.2.15/kDGLM/R/plot_helper.R | 5 kDGLM-1.2.15/kDGLM/README.md | 1 kDGLM-1.2.15/kDGLM/build/partial.rdb |binary kDGLM-1.2.15/kDGLM/build/vignette.rds |binary kDGLM-1.2.15/kDGLM/inst/doc/fitting.Rmd | 4 kDGLM-1.2.15/kDGLM/inst/doc/fitting.html | 36 kDGLM-1.2.15/kDGLM/inst/doc/intro.R | 2 kDGLM-1.2.15/kDGLM/inst/doc/intro.Rmd | 9 kDGLM-1.2.15/kDGLM/inst/doc/intro.html | 47 kDGLM-1.2.15/kDGLM/inst/doc/outcomes.Rmd | 9 kDGLM-1.2.15/kDGLM/inst/doc/outcomes.html | 1934 ++++++++++++++++++++++++++-- kDGLM-1.2.15/kDGLM/inst/doc/structures.Rmd | 6 kDGLM-1.2.15/kDGLM/inst/doc/structures.html | 30 kDGLM-1.2.15/kDGLM/vignettes/fitting.Rmd | 4 kDGLM-1.2.15/kDGLM/vignettes/intro.Rmd | 9 kDGLM-1.2.15/kDGLM/vignettes/outcomes.Rmd | 9 kDGLM-1.2.15/kDGLM/vignettes/structures.Rmd | 6 24 files changed, 1937 insertions(+), 232 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not
fun. It contains functions for designing studies such as Simon
2-stage and group sequential designs and for data analysis such
as Jonckheere-Terpstra test and estimating survival quantiles.
Author: Venkatraman E. Seshan [aut, cre],
Karissa Whiting [aut]
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.1.5 dated 2023-10-19 and 1.1.6 dated 2026-08-29
clinfun-1.1.5/clinfun/src/fdwilcox.c |only clinfun-1.1.6/clinfun/DESCRIPTION | 6 clinfun-1.1.6/clinfun/MD5 | 35 clinfun-1.1.6/clinfun/NEWS.md | 7 clinfun-1.1.6/clinfun/R/jonkheere.R | 14 clinfun-1.1.6/clinfun/R/ph2simon.R | 3 clinfun-1.1.6/clinfun/build/vignette.rds |binary clinfun-1.1.6/clinfun/inst/doc/clinical-trial-functions.R | 2 clinfun-1.1.6/clinfun/inst/doc/clinical-trial-functions.Rmd | 14 clinfun-1.1.6/clinfun/inst/doc/clinical-trial-functions.html | 702 +++++++---- clinfun-1.1.6/clinfun/man/coxphQuantile.Rd | 6 clinfun-1.1.6/clinfun/man/deltaAUC.Rd | 3 clinfun-1.1.6/clinfun/man/ph2simon.Rd | 4 clinfun-1.1.6/clinfun/man/ph2single.Rd | 2 clinfun-1.1.6/clinfun/man/roc.area.test.Rd | 2 clinfun-1.1.6/clinfun/man/roc.curve.Rd | 4 clinfun-1.1.6/clinfun/src/init.c | 4 clinfun-1.1.6/clinfun/src/jtpdf.f | 50 clinfun-1.1.6/clinfun/vignettes/clinical-trial-functions.Rmd | 14 19 files changed, 549 insertions(+), 323 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://www.lens.org/>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.4.1 dated 2026-06-16 and 5.5.0 dated 2026-08-29
DESCRIPTION | 10 MD5 | 97 ++- NAMESPACE | 576 +++++++++++------------ NEWS | 47 + R/authorProdOverTime.R | 2 R/bib2df.R | 13 R/biblioAnalysis.R | 2 R/bradford.R | 2 R/cocMatrix.R | 4 R/collabByRegionPlot.R | 2 R/completeMetadata.R | 198 +++++-- R/conceptualStructure.R | 2 R/couplingMap.R | 2 R/csvOA2df.R | 152 ++++-- R/csvScopus2df.R | 9 R/dimensions2df.R | 2 R/fieldByYear.R | 2 R/histNetwork.R | 141 +++-- R/histPlot.R | 2 R/isi2df.R | 39 + R/mergeDbSources.R | 88 ++- R/metaTagExtraction.R | 51 +- R/missingData.R | 5 R/rpys.R | 2 R/termExtraction.R | 2 R/thematicMap.R | 2 build/partial.rdb |binary inst/biblioshiny/Htmlboxformat.R | 12 inst/biblioshiny/biblioAI.R | 310 +++++++++--- inst/biblioshiny/contentAnalysisServer.R | 84 +-- inst/biblioshiny/contentAnalysisUI.R | 10 inst/biblioshiny/helpContent.R | 561 ++++++++++++---------- inst/biblioshiny/libraries.R | 32 + inst/biblioshiny/lifeCycleUI.R | 6 inst/biblioshiny/openalex_api.R | 158 +++++- inst/biblioshiny/server.R | 377 ++++++++++++--- inst/biblioshiny/ui.R | 16 inst/biblioshiny/utils.R | 363 +++++++++++--- man/completeMetadata.Rd | 22 man/match_citations_fast.Rd |only man/mergeDbSources.Rd | 32 + tests/testthat/fixtures/wos_bibtex_sample.bib |only tests/testthat/fixtures/wos_newformat_sample.txt |only tests/testthat/helper-load-fixtures.R | 16 tests/testthat/test-biblioshiny-ranking.R |only tests/testthat/test-biblioshiny-startup.R |only tests/testthat/test-completeMetadata.R | 63 +- tests/testthat/test-convert2df.R | 75 ++ tests/testthat/test-data-merge.R | 107 ++++ tests/testthat/test-data-quality.R | 20 tests/testthat/test-network.R | 22 tests/testthat/test-visualization.R | 42 + 52 files changed, 2703 insertions(+), 1079 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.32 dated 2026-03-20 and 2.4.0 dated 2026-08-29
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++------------ NAMESPACE | 1 + NEWS.md | 5 +++++ R/chi2.R |only man/tgs_chi2.Rd |only src/HashFunc.h | 1 + src/ProgressReporter.cpp | 1 + src/chi2.cpp |only src/corgraph.cpp | 3 ++- src/graph2cluster.h | 1 + src/knn.cpp | 10 ++++++---- src/matrix_tapply.cpp | 2 ++ src/tgstat-init.cpp | 2 ++ src/tgstat.cpp | 2 ++ src/tgstat.h | 1 + tests/testthat/test-chi2.R |only 17 files changed, 44 insertions(+), 21 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include ordinary least-squares
regression, binomial regression, multinomial regression, and Poisson
regression. Both dense and sparse predictor matrices are supported. In
addition, the package features predictor screening rules that enable fast
and efficient solutions to high-dimensional problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johan@jolars.co>
Diff between SLOPE versions 2.1.0 dated 2026-03-28 and 2.1.1 dated 2026-08-29
SLOPE-2.1.0/SLOPE/src/slope/DO_NOT_MODIFY |only SLOPE-2.1.1/SLOPE/DESCRIPTION | 37 SLOPE-2.1.1/SLOPE/MD5 | 157 ++-- SLOPE-2.1.1/SLOPE/NEWS.md | 9 SLOPE-2.1.1/SLOPE/R/coef.R | 23 SLOPE-2.1.1/SLOPE/R/cv.R | 33 SLOPE-2.1.1/SLOPE/R/data.R | 160 ++-- SLOPE-2.1.1/SLOPE/R/deviance.R | 5 SLOPE-2.1.1/SLOPE/R/interpolate_coefficients.R | 9 SLOPE-2.1.1/SLOPE/R/interpolate_penalty.R | 6 SLOPE-2.1.1/SLOPE/R/plot.R | 143 +-- SLOPE-2.1.1/SLOPE/R/plot_diagnostics.R | 16 SLOPE-2.1.1/SLOPE/R/predict.R | 46 - SLOPE-2.1.1/SLOPE/R/refit.R | 18 SLOPE-2.1.1/SLOPE/R/regularization_weights.R | 19 SLOPE-2.1.1/SLOPE/R/score.R | 38 - SLOPE-2.1.1/SLOPE/R/setup_diagnostics.R | 4 SLOPE-2.1.1/SLOPE/R/slope.R | 242 +++--- SLOPE-2.1.1/SLOPE/R/sorted_l1_prox.R | 5 SLOPE-2.1.1/SLOPE/R/summary.R | 18 SLOPE-2.1.1/SLOPE/R/train_slope.R | 67 - SLOPE-2.1.1/SLOPE/R/utils.R | 36 SLOPE-2.1.1/SLOPE/build/partial.rdb |binary SLOPE-2.1.1/SLOPE/build/vignette.rds |binary SLOPE-2.1.1/SLOPE/inst/COPYRIGHTS | 18 SLOPE-2.1.1/SLOPE/inst/doc/introduction.html | 12 SLOPE-2.1.1/SLOPE/inst/doc/models.html | 36 SLOPE-2.1.1/SLOPE/inst/doc/solvers.html | 8 SLOPE-2.1.1/SLOPE/inst/include/slope/clusters.h | 32 SLOPE-2.1.1/SLOPE/inst/include/slope/cv.h | 15 SLOPE-2.1.1/SLOPE/inst/include/slope/diagnostics.h | 205 ++++- SLOPE-2.1.1/SLOPE/inst/include/slope/estimate_alpha.h | 1 SLOPE-2.1.1/SLOPE/inst/include/slope/losses/logistic.h | 18 SLOPE-2.1.1/SLOPE/inst/include/slope/losses/loss.h | 29 SLOPE-2.1.1/SLOPE/inst/include/slope/losses/multinomial.h | 18 SLOPE-2.1.1/SLOPE/inst/include/slope/losses/poisson.h | 4 SLOPE-2.1.1/SLOPE/inst/include/slope/losses/quadratic.h | 16 SLOPE-2.1.1/SLOPE/inst/include/slope/math.h | 180 ++++ SLOPE-2.1.1/SLOPE/inst/include/slope/screening.h | 87 -- SLOPE-2.1.1/SLOPE/inst/include/slope/slope.h | 188 +++-- SLOPE-2.1.1/SLOPE/inst/include/slope/slope_path.h | 1 SLOPE-2.1.1/SLOPE/inst/include/slope/solvers/hybrid.h | 6 SLOPE-2.1.1/SLOPE/inst/include/slope/solvers/hybrid_cd.h | 373 ++++++++-- SLOPE-2.1.1/SLOPE/inst/include/slope/solvers/setup_solver.h | 5 SLOPE-2.1.1/SLOPE/inst/include/slope/solvers/slope_threshold.h | 21 SLOPE-2.1.1/SLOPE/inst/include/slope/sorted_l1_norm.h | 18 SLOPE-2.1.1/SLOPE/inst/include/slope/utils.h | 1 SLOPE-2.1.1/SLOPE/inst/licenses |only SLOPE-2.1.1/SLOPE/src/Makevars | 3 SLOPE-2.1.1/SLOPE/src/slope/VENDORED |only SLOPE-2.1.1/SLOPE/src/slope/clusters.cpp | 1 SLOPE-2.1.1/SLOPE/src/slope/kkt_check.cpp | 55 + SLOPE-2.1.1/SLOPE/src/slope/kkt_check.h | 9 SLOPE-2.1.1/SLOPE/src/slope/losses/logistic.cpp | 110 ++ SLOPE-2.1.1/SLOPE/src/slope/losses/loss.cpp | 50 + SLOPE-2.1.1/SLOPE/src/slope/losses/multinomial.cpp | 96 ++ SLOPE-2.1.1/SLOPE/src/slope/losses/poisson.cpp | 46 + SLOPE-2.1.1/SLOPE/src/slope/math.cpp | 23 SLOPE-2.1.1/SLOPE/src/slope/regularization_sequence.cpp | 4 SLOPE-2.1.1/SLOPE/src/slope/screening.cpp | 80 -- SLOPE-2.1.1/SLOPE/src/slope/solvers/slope_threshold.cpp | 71 + SLOPE-2.1.1/SLOPE/src/slope/sorted_l1_norm.cpp | 30 SLOPE-2.1.1/SLOPE/tests/spelling.R | 10 SLOPE-2.1.1/SLOPE/tests/testthat/setup.R | 6 SLOPE-2.1.1/SLOPE/tests/testthat/test-alpha-scaling.R | 7 SLOPE-2.1.1/SLOPE/tests/testthat/test-assertions.R | 31 SLOPE-2.1.1/SLOPE/tests/testthat/test-binomial.R | 8 SLOPE-2.1.1/SLOPE/tests/testthat/test-coef.R | 8 SLOPE-2.1.1/SLOPE/tests/testthat/test-cv.R | 29 SLOPE-2.1.1/SLOPE/tests/testthat/test-gaussian.R | 17 SLOPE-2.1.1/SLOPE/tests/testthat/test-lasso.R | 54 - SLOPE-2.1.1/SLOPE/tests/testthat/test-multinomial.R | 67 + SLOPE-2.1.1/SLOPE/tests/testthat/test-pattern.R | 3 SLOPE-2.1.1/SLOPE/tests/testthat/test-plotting.R | 24 SLOPE-2.1.1/SLOPE/tests/testthat/test-poisson.R | 28 SLOPE-2.1.1/SLOPE/tests/testthat/test-prox.R | 2 SLOPE-2.1.1/SLOPE/tests/testthat/test-relax.R | 4 SLOPE-2.1.1/SLOPE/tests/testthat/test-sparsity.R | 1 SLOPE-2.1.1/SLOPE/tests/testthat/test-summary.R | 29 SLOPE-2.1.1/SLOPE/tools |only 80 files changed, 2050 insertions(+), 1239 deletions(-)
Title: Reading FRE Corporate Data of Public Traded Companies from B3
Description: Reads corporate data such as board composition and compensation for companies traded at B3,
the Brazilian exchange <https://www.b3.com.br/>. All data is downloaded and imported from the ftp site <https://dados.cvm.gov.br/dados/CIA_ABERTA/DOC/FRE/>.
Author: Marcelo Perlin [aut, cre],
Guilherme Kirch [aut]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetFREData versions 1.0.1 dated 2026-06-03 and 1.1.0 dated 2026-08-29
GetFREData-1.0.1/GetFREData/R/fct_get_fre_links.R |only GetFREData-1.0.1/GetFREData/R/fct_read_fre_zip_file.R |only GetFREData-1.0.1/GetFREData/R/fct_utils.R |only GetFREData-1.0.1/GetFREData/R/fcts_xml.R |only GetFREData-1.0.1/GetFREData/man/gdfpd.read.zip.file.type.fre.Rd |only GetFREData-1.0.1/GetFREData/man/my_fix_cols.Rd |only GetFREData-1.1.0/GetFREData/DESCRIPTION | 13 GetFREData-1.1.0/GetFREData/MD5 | 38 -- GetFREData-1.1.0/GetFREData/NAMESPACE | 2 GetFREData-1.1.0/GetFREData/NEWS.md | 33 + GetFREData-1.1.0/GetFREData/R/GetFREData-package.R |only GetFREData-1.1.0/GetFREData/R/fct_download_file.R | 33 - GetFREData-1.1.0/GetFREData/R/fct_get_fre_data.R | 133 ------- GetFREData-1.1.0/GetFREData/R/fct_get_fre_data2.R | 184 +++++++--- GetFREData-1.1.0/GetFREData/R/fct_get_fre_ftp_contents.R | 8 GetFREData-1.1.0/GetFREData/build/vignette.rds |binary GetFREData-1.1.0/GetFREData/inst/doc/GetFREData-vignette-introduction.html | 4 GetFREData-1.1.0/GetFREData/man/GetFREData-package.Rd |only GetFREData-1.1.0/GetFREData/man/get_fre_data.Rd | 32 - GetFREData-1.1.0/GetFREData/man/get_fre_data2.Rd | 41 +- GetFREData-1.1.0/GetFREData/man/get_info_companies.Rd | 2 GetFREData-1.1.0/GetFREData/man/search_company.Rd | 2 GetFREData-1.1.0/GetFREData/tests/testthat/test-fredata2.R | 16 GetFREData-1.1.0/GetFREData/tests/testthat/test-input-validation.R |only GetFREData-1.1.0/GetFREData/tests/testthat/test-parsing.R |only 25 files changed, 278 insertions(+), 263 deletions(-)
Title: Basic Statistics
Description: Basic statistical analyses. The package provides comprehensive functions and
datasets for teaching introductory statistics courses. It has been developed
to be used in undergraduate statistics courses at Bocconi University
(Milan, Italy), and constitutes the core software tool used throughout the
textbook by Piccarreta, R., Tonini, D., & Trentini, F. (2026) "From Data to
Decisions. An Introduction to Applied Statistics", BUP, ISBN:9788823824096.
Author: Raffaella Piccarreta [aut],
Sergio Venturini [cre]
Maintainer: Sergio Venturini <sergio.venturini@unicatt.it>
Diff between UBStats versions 0.3.0 dated 2025-08-27 and 0.4.3 dated 2026-08-29
UBStats-0.3.0/UBStats/R/UBStats_Main_Visible_ALL_202508.R |only UBStats-0.3.0/UBStats/R/UBStats_Utility_Invisible_202508.R |only UBStats-0.3.0/UBStats/data/Banner.RData |only UBStats-0.3.0/UBStats/data/CallCentre_KPI.RData |only UBStats-0.3.0/UBStats/data/Grocery_NE.RData |only UBStats-0.3.0/UBStats/data/Marketing_Mix.RData |only UBStats-0.3.0/UBStats/data/Time_Social.RData |only UBStats-0.3.0/UBStats/data/Transition.RData |only UBStats-0.4.3/UBStats/DESCRIPTION | 22 UBStats-0.4.3/UBStats/MD5 | 84 - UBStats-0.4.3/UBStats/NAMESPACE | 32 UBStats-0.4.3/UBStats/R/UBStats_Main_Visible_ALL_202608.R |only UBStats-0.4.3/UBStats/R/UBStats_Utility_Invisible_202608.R |only UBStats-0.4.3/UBStats/R/zz_datasets.R | 708 ++++++++----- UBStats-0.4.3/UBStats/R/zz_package.R | 10 UBStats-0.4.3/UBStats/README.md | 4 UBStats-0.4.3/UBStats/data/Banner.rda |only UBStats-0.4.3/UBStats/data/BasketValue.rda |only UBStats-0.4.3/UBStats/data/CallCentre_KPI.rda |only UBStats-0.4.3/UBStats/data/ESG_Returns.rda |only UBStats-0.4.3/UBStats/data/Grocery_NE.rda |only UBStats-0.4.3/UBStats/data/JobEngage.rda |only UBStats-0.4.3/UBStats/data/Marketing_Mix.rda |only UBStats-0.4.3/UBStats/data/Spending.rda |only UBStats-0.4.3/UBStats/data/Time_Social.rda |only UBStats-0.4.3/UBStats/data/Transition.rda |only UBStats-0.4.3/UBStats/man/Banner.Rd | 34 UBStats-0.4.3/UBStats/man/BasketValue.Rd |only UBStats-0.4.3/UBStats/man/CI.diffmean.Rd | 2 UBStats-0.4.3/UBStats/man/CI.diffprop.Rd | 2 UBStats-0.4.3/UBStats/man/CI.mean.Rd | 2 UBStats-0.4.3/UBStats/man/CI.prop.Rd | 2 UBStats-0.4.3/UBStats/man/CallCentre_KPI.Rd | 86 - UBStats-0.4.3/UBStats/man/ESG_Returns.Rd |only UBStats-0.4.3/UBStats/man/Grocery_NE.Rd | 115 +- UBStats-0.4.3/UBStats/man/JobEngage.Rd |only UBStats-0.4.3/UBStats/man/LM.output.Rd | 2 UBStats-0.4.3/UBStats/man/Marketing_Mix.Rd | 96 - UBStats-0.4.3/UBStats/man/MktDATA.Orig.Rd | 66 - UBStats-0.4.3/UBStats/man/MktDATA.Rd | 4 UBStats-0.4.3/UBStats/man/Spending.Rd |only UBStats-0.4.3/UBStats/man/TEST.diffmean.Rd | 2 UBStats-0.4.3/UBStats/man/TEST.diffprop.Rd | 2 UBStats-0.4.3/UBStats/man/TEST.diffvar.Rd | 2 UBStats-0.4.3/UBStats/man/TEST.mean.Rd | 2 UBStats-0.4.3/UBStats/man/TEST.prop.Rd | 2 UBStats-0.4.3/UBStats/man/Time_Social.Rd | 31 UBStats-0.4.3/UBStats/man/Transition.Rd | 40 UBStats-0.4.3/UBStats/man/UBStats-package.Rd | 21 UBStats-0.4.3/UBStats/man/distr.plot.x.Rd | 2 UBStats-0.4.3/UBStats/man/distr.plot.xy.Rd | 2 UBStats-0.4.3/UBStats/man/distr.summary.x.Rd | 2 UBStats-0.4.3/UBStats/man/distr.table.x.Rd | 2 UBStats-0.4.3/UBStats/man/distr.table.xy.Rd | 2 UBStats-0.4.3/UBStats/man/summaries.plot.x.Rd | 2 55 files changed, 849 insertions(+), 536 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system to
implement a complete data-to-decisions, reproducible workflow.
The core components facilitate the development of modular pieces,
and enable the user to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the within-project dependencies.
Author: Alex M Chubaty [aut] ,
Eliot J B McIntire [aut, cre] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
This is a re-admission after prior archival of version 3.1.2 dated 2026-05-23
Diff between SpaDES.core versions 3.1.2 dated 2026-05-23 and 3.2.1 dated 2026-08-29
DESCRIPTION | 28 MD5 | 182 +++-- NAMESPACE | 300 ++++---- NEWS.md | 164 ++++ R/Plots.R | 40 - R/cache.R | 31 R/check.R | 9 R/codecheck-api.R | 125 +++ R/codecheck-engine.R | 284 +++++++ R/codecheck-report.R | 84 +- R/codecheck-rules.R | 287 +++++++- R/debugging.R | 7 R/helpers.R | 30 R/module-define.R | 37 - R/module-dependencies-class.R | 7 R/module-template.R | 10 R/options.R | 59 - R/paths.R | 92 ++ R/progress.R | 4 R/reexports.R | 4 R/restart.R | 543 +++++++++++---- R/saveLoadSimList.R | 219 +++++- R/simList-accessors.R | 35 R/simulation-parseModule.R | 107 ++ R/simulation-simInit.R | 644 ++++++++++++----- R/simulation-spades.R | 680 ++++++++++++------- R/spades-core-deprecated.R | 12 R/spades-core-package.R | 13 R/times.R | 5 R/urlLog.R |only build/vignette.rds |binary inst/WORDLIST | 15 inst/doc/i-introduction.html | 2 inst/doc/ii-modules.html | 4 inst/doc/iii-cache.html | 2 inst/doc/iv-advanced.html | 2 inst/doc/v-automated-testing.html | 2 inst/sampleModules/caribouMovement/caribouMovement.R | 2 inst/templates/module.Rmd.template | 2 man/SpaDES.core-package.Rd | 13 man/checkParams.Rd | 5 man/codeCheckModule.Rd | 86 ++ man/defineEvent.Rd | 16 man/deprecated.Rd | 5 man/dot-charLiteralsIn.Rd |only man/dot-fillDotParams.Rd |only man/dot-finishSimInit.Rd |only man/dot-fnsReachableFrom.Rd |only man/dot-reparseModules.Rd |only man/dot-restartModuleToReparse.Rd |only man/dot-restartRefreshBindings.Rd |only man/dot-restartResolveSim.Rd |only man/dot-restartRestoreEventObjs.Rd |only man/dot-runInputObjectsPhase.Rd |only man/dot-stepEvent.Rd |only man/findProjectPath.Rd |only man/globals.Rd | 6 man/inputObjectNames.Rd |only man/restartSpades.Rd | 44 - man/saveSimList.Rd | 66 + man/saveSimOnExitSimInit.Rd |only man/savedSimEnv.Rd | 4 man/simInitConditionHandlers.Rd |only man/simList-accessors-metadata.Rd | 7 man/singularPlural.Rd |only man/spadesOptions.Rd | 40 - tests/test-all.R | 1 tests/testthat/fixtures/inputObjects-golden.rds |only tests/testthat/helper-initTests.R | 14 tests/testthat/helper-inputObjectsGolden.R |only tests/testthat/test-1memory.R | 2 tests/testthat/test-Plots.R | 138 +++ tests/testthat/test-cache.R | 2 tests/testthat/test-cacheModulePathInEvent.R |only tests/testthat/test-cacheParamMetadata.R |only tests/testthat/test-check.R |only tests/testthat/test-clearCacheEventsOnly.R |only tests/testthat/test-codecheck-helpers.R |only tests/testthat/test-codecheck-report.R |only tests/testthat/test-codecheck-rules.R |only tests/testthat/test-codecheck.R | 432 ++++++++++++ tests/testthat/test-copyModule.R |only tests/testthat/test-debugging.R |only tests/testthat/test-defineEvent.R |only tests/testthat/test-deprecated.R |only tests/testthat/test-downloadData.R | 22 tests/testthat/test-eventReturnGuard.R |only tests/testthat/test-fileBackedAnchors.R |only tests/testthat/test-findProjectPath.R |only tests/testthat/test-futureEvents.R | 14 tests/testthat/test-inputObjects-golden.R |only tests/testthat/test-inputObjectsPhase.R |only tests/testthat/test-memory.R |only tests/testthat/test-misc-methods.R |only tests/testthat/test-mod.R | 494 +++++++++++++ tests/testthat/test-module-define-extras.R |only tests/testthat/test-module-deps-methods.R | 22 tests/testthat/test-module-template-extras.R |only tests/testthat/test-outputs-rmDups.R |only tests/testthat/test-parameters-accessor.R |only tests/testthat/test-paths.R | 26 tests/testthat/test-plotting-diagrams.R |only tests/testthat/test-progress.R |only tests/testthat/test-progressThrottle.R |only tests/testthat/test-rasterToMemory.R |only tests/testthat/test-save.R | 14 tests/testthat/test-saveLoadSimList-helpers.R |only tests/testthat/test-saveLoadSimList.R |only tests/testthat/test-scheduleConditionalEvent.R |only tests/testthat/test-setupDebugger.R |only tests/testthat/test-simList-accessors-sweep.R |only tests/testthat/test-simList-show.R |only tests/testthat/test-simList.R | 2 tests/testthat/test-simulation.R | 92 ++ tests/testthat/test-singularPlural.R |only tests/testthat/test-times-conversion.R |only tests/testthat/test-urlLog.R |only tests/testthat/test-useCacheArgs.R | 40 + vignettes/bibliography.bib | 3 119 files changed, 4614 insertions(+), 1069 deletions(-)
Title: Evaluating Phylogeny as a Proxy for Ecological Similarity
Description: Provides a trait-based workflow for evaluating whether phylogenetic relatedness is informative about similarity in measured quantitative traits within focal species pools and across multiple communities. Functions support trait data integration, taxon-specific trait extraction, coverage assessment, optional principal component analysis, and estimation of phylogenetic signal using Pagel's lambda or Blomberg's K. Curated quantitative trait datasets are included for plants, birds, mammals, reptiles, amphibians, and fishes. Paired simulations assess how observed patterns of missing trait data affect Pagel's lambda estimates and significance classifications for individual traits. Methods for quantifying phylogenetic signal are based on Pagel (1999) <doi:10.1038/44766>, Blomberg et al. (2003) <doi:10.1111/j.0014-3820.2003.tb00285.x>, and Münkemüller et al. (2012) <doi:10.1111/j.2041-210X.2012.00196.x>.
Author: Yan He [aut, cre],
Yu Xia [aut],
Rui Yang [aut],
Lingfeng Mao [aut]
Maintainer: Yan He <heyaneco@163.com>
Diff between PNC versions 0.1.0 dated 2025-11-07 and 0.2.0 dated 2026-08-29
PNC-0.1.0/PNC/R/Fishlife.R |only PNC-0.1.0/PNC/R/simulate_K_trait.R |only PNC-0.1.0/PNC/R/simulate_lambda_trait.R |only PNC-0.1.0/PNC/data/Fishlife.rda |only PNC-0.1.0/PNC/man/Fishlife.Rd |only PNC-0.1.0/PNC/man/simulate_K_trait.Rd |only PNC-0.1.0/PNC/man/simulate_lambda_trait.Rd |only PNC-0.2.0/PNC/DESCRIPTION | 19 PNC-0.2.0/PNC/MD5 | 72 - PNC-0.2.0/PNC/NAMESPACE | 16 PNC-0.2.0/PNC/NEWS.md | 11 PNC-0.2.0/PNC/R/AVONET.R | 110 + PNC-0.2.0/PNC/R/AmphiBIO.R | 115 + PNC-0.2.0/PNC/R/COMBINE.R | 220 ++- PNC-0.2.0/PNC/R/FishLife.R |only PNC-0.2.0/PNC/R/ReptTraits.R | 115 + PNC-0.2.0/PNC/R/TRY.R | 151 +- PNC-0.2.0/PNC/R/compnc.R | 1276 ++++++++++++++++----- PNC-0.2.0/PNC/R/compnc_robustness.R | 1753 ++++++++++++++++++++++++----- PNC-0.2.0/PNC/R/coverage.R | 229 +++ PNC-0.2.0/PNC/R/extract_traits.R | 652 +++++++++- PNC-0.2.0/PNC/R/merge_dataset.R | 444 +++++-- PNC-0.2.0/PNC/R/pnc.R | 843 ++++++++++--- PNC-0.2.0/PNC/R/pnc_robustness.R | 1421 ++++++++++++++++++++--- PNC-0.2.0/PNC/README.md | 308 +++-- PNC-0.2.0/PNC/data/COMBINE.rda |binary PNC-0.2.0/PNC/data/FishLife.rda |only PNC-0.2.0/PNC/data/TRY.rda |binary PNC-0.2.0/PNC/man/AVONET.Rd | 110 + PNC-0.2.0/PNC/man/AmphiBIO.Rd | 117 + PNC-0.2.0/PNC/man/COMBINE.Rd | 221 ++- PNC-0.2.0/PNC/man/FishLife.Rd |only PNC-0.2.0/PNC/man/ReptTraits.Rd | 116 + PNC-0.2.0/PNC/man/TRY.Rd | 145 +- PNC-0.2.0/PNC/man/compnc.Rd | 185 ++- PNC-0.2.0/PNC/man/compnc_robustness.Rd | 224 ++- PNC-0.2.0/PNC/man/coverage.Rd | 59 PNC-0.2.0/PNC/man/extract_traits.Rd | 154 +- PNC-0.2.0/PNC/man/figures/Figure1.jpg |binary PNC-0.2.0/PNC/man/merge_dataset.Rd | 114 + PNC-0.2.0/PNC/man/pnc.Rd | 146 +- PNC-0.2.0/PNC/man/pnc_robustness.Rd | 187 ++- 42 files changed, 7532 insertions(+), 2001 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet,
Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be
used for a variety of multivariate problems when count data are at
play, including principal component analysis for count data,
discriminant analysis, model-based clustering and network inference.
Implements variational algorithms to fit such models accompanied with
a set of functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] ,
Mahendra Mariadassou [aut] ,
Stephane Robin [aut],
Francois Gindraud [aut],
Julie Aubert [ctb],
Bastien Batardiere [ctb],
Giovanni Poggiato [ctb],
Cole Trapnell [ctb],
Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 1.3.0 dated 2026-07-27 and 1.3.1 dated 2026-08-29
DESCRIPTION | 8 +-- MD5 | 24 +++++----- NAMESPACE | 108 ++++++++++++++++++++++++--------------------- NEWS.md | 9 +++ R/PLNnetworkfamily-class.R | 31 +++++++++++- inst/doc/Import_data.html | 4 - inst/doc/PLN.html | 4 - inst/doc/PLNLDA.html | 4 - inst/doc/PLNPCA.html | 4 - inst/doc/PLNmixture.html | 4 - inst/doc/PLNnetwork.html | 8 +-- inst/doc/Trichoptera.html | 4 - inst/doc/ZIPLN.html | 10 ++-- 13 files changed, 132 insertions(+), 90 deletions(-)
Title: Mining Rigs for Problems in the Subset Sum Family
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to [...truncated...]
Author: Charlie Wusuo Liu [aut, cre]
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 9.2.9 dated 2026-08-26 and 9.3.0 dated 2026-08-29
FLSSS-9.2.9/FLSSS/src/legacy/Makevars |only FLSSS-9.3.0/FLSSS/DESCRIPTION | 6 +++--- FLSSS-9.3.0/FLSSS/MD5 | 11 +++++------ FLSSS-9.3.0/FLSSS/configure | 2 +- FLSSS-9.3.0/FLSSS/configure.ac | 2 +- FLSSS-9.3.0/FLSSS/src/GAgap.cpp | 7 ------- FLSSS-9.3.0/FLSSS/src/arbitraryDimFLSSS/arithmetic.hpp | 2 +- 7 files changed, 11 insertions(+), 19 deletions(-)
Title: Versatile R Server
Description: Rserve is a versatile, scalable server enabling the
efficient use of R from other applications through
variety of protocols including QAP, WebSockets, HTTP
and HTTPS. It acts as a server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for many popular languages allowing applications
to use facilities of R without the need of linking to
the R binary. Rserve supports remote connections,
user authentication and file transfer. A simple R client
is included in this package as well. It also supports
OCAP mode for secure remote procedure calls,
including support for full event loop, asynchronous
results/graphics and console I/O.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-19 dated 2026-03-24 and 1.8-19.1 dated 2026-08-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Rserv.c | 2 +- src/proxy/rscript.c | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Maxwell Control Charts
Description: Computes Control limits, coefficients of control limits, various performance metrics and depicts control charts for monitoring Maxwell-distributed quality characteristics.
Author: Zahid Khan [aut],
Zsolt T. Kosztyan [aut, cre]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between mxcc versions 0.0.5 dated 2026-04-10 and 0.0.6 dated 2026-08-29
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NAMESPACE | 1 + R/plot.R | 36 ++++++++++++++---------------------- README.md |only 5 files changed, 22 insertions(+), 28 deletions(-)
Title: I/O Tools for Streaming
Description: Basic I/O tools for streaming and data parsing.
Author: Simon Urbanek [aut, cre] ,
Taylor Arnold [aut]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between iotools versions 0.4-0 dated 2026-02-19 and 0.4-0.1 dated 2026-08-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/strutil.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant
versions of 'install.packages' and 'require' for CRAN packages, packages
no longer on CRAN (i.e., archived), specific versions of packages,
and GitHub packages. This approach is developed to create reproducible
workflows that are flexible and fast enough to use while in development stages,
while able to build snapshots once a stable package collection is found.
As with other functions in a reproducible workflow, this package
emphasizes functions that return the same result whether it is
the first or subsequent times running the function, with subsequent times being
sufficiently fast that they can be run every time without undue waiting burden on
the user or developer.
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 2.0.0 dated 2026-05-15 and 2.1.0 dated 2026-08-29
Require-2.0.0/Require/inst/snapshot.txt |only Require-2.1.0/Require/DESCRIPTION | 15 Require-2.1.0/Require/MD5 | 137 Require-2.1.0/Require/NAMESPACE | 89 Require-2.1.0/Require/NEWS.md | 185 + Require-2.1.0/Require/R/CRAN.R | 24 Require-2.1.0/Require/R/Require-helpers.R | 86 Require-2.1.0/Require/R/Require-package.R | 22 Require-2.1.0/Require/R/Require2.R | 379 +- Require-2.1.0/Require/R/RequireOptions.R | 74 Require-2.1.0/Require/R/extract.R | 84 Require-2.1.0/Require/R/helpers.R | 16 Require-2.1.0/Require/R/messages.R | 23 Require-2.1.0/Require/R/pak.R | 1730 ++++++++-- Require-2.1.0/Require/R/pkgDep.R | 169 Require-2.1.0/Require/R/pkgDep3.R | 17 Require-2.1.0/Require/R/pkgSnapshot.R | 83 Require-2.1.0/Require/R/setLibPaths.R | 44 Require-2.1.0/Require/R/setup.R | 17 Require-2.1.0/Require/R/zzz.R | 25 Require-2.1.0/Require/build/vignette.rds |binary Require-2.1.0/Require/inst/WORDLIST | 16 Require-2.1.0/Require/inst/snapshots |only Require-2.1.0/Require/man/DESCRIPTION-helpers.Rd | 3 Require-2.1.0/Require/man/GETWauthThenNonAuth.Rd |only Require-2.1.0/Require/man/GitHubTools.Rd | 8 Require-2.1.0/Require/man/Require.Rd | 107 Require-2.1.0/Require/man/RequireOptions.Rd | 74 Require-2.1.0/Require/man/availableVersions.Rd | 6 Require-2.1.0/Require/man/cacheGetOptionCachePkgDir.Rd | 4 Require-2.1.0/Require/man/clearRequire.Rd | 4 Require-2.1.0/Require/man/compareVersion2.Rd | 8 Require-2.1.0/Require/man/extractPkgName.Rd | 7 Require-2.1.0/Require/man/getCRANrepos.Rd | 3 Require-2.1.0/Require/man/getGitCredsToken.Rd |only Require-2.1.0/Require/man/modifyList2.Rd | 3 Require-2.1.0/Require/man/pkgDep.Rd | 45 Require-2.1.0/Require/man/pkgDepIfDepRemoved.Rd | 13 Require-2.1.0/Require/man/pkgSnapshot.Rd | 67 Require-2.1.0/Require/man/setLibPaths.Rd | 45 Require-2.1.0/Require/man/setLinuxBinaryRepo.Rd | 3 Require-2.1.0/Require/man/setup.Rd | 3 Require-2.1.0/Require/man/stripGitHubToRepos.Rd |only Require-2.1.0/Require/man/tempdir2.Rd | 3 Require-2.1.0/Require/man/tempfile2.Rd | 3 Require-2.1.0/Require/man/trimRedundancies.Rd |only Require-2.1.0/Require/man/trimVersionNumber.Rd | 10 Require-2.1.0/Require/tests/testthat/fixtures/smallSnapshot.txt | 11 Require-2.1.0/Require/tests/testthat/fixtures/smallSnapshotNoDeps.txt |only Require-2.1.0/Require/tests/testthat/helper_0.R | 117 Require-2.1.0/Require/tests/testthat/setup.R | 68 Require-2.1.0/Require/tests/testthat/test-00pkgSnapshot_testthat.R | 4 Require-2.1.0/Require/tests/testthat/test-01packages_testthat.R | 25 Require-2.1.0/Require/tests/testthat/test-02extract_testthat.R | 30 Require-2.1.0/Require/tests/testthat/test-03helpers_testthat.R | 2 Require-2.1.0/Require/tests/testthat/test-04other_testthat.R | 8 Require-2.1.0/Require/tests/testthat/test-05packagesLong_testthat.R | 32 Require-2.1.0/Require/tests/testthat/test-06pkgDep_testthat.R | 11 Require-2.1.0/Require/tests/testthat/test-08modules_testthat.R | 36 Require-2.1.0/Require/tests/testthat/test-09pkgSnapshotLong_testthat.R | 373 -- Require-2.1.0/Require/tests/testthat/test-10DifferentPkgs_testthat.R | 14 Require-2.1.0/Require/tests/testthat/test-11misc_testthat.R | 20 Require-2.1.0/Require/tests/testthat/test-12offlineMode_testthat.R | 15 Require-2.1.0/Require/tests/testthat/test-14coverage2_testthat.R | 63 Require-2.1.0/Require/tests/testthat/test-15bugfixes_testthat.R | 630 +++ Require-2.1.0/Require/tests/testthat/test-16installFailureMetadata_testthat.R | 110 Require-2.1.0/Require/tests/testthat/test-17usePak.R | 596 +++ Require-2.1.0/Require/tests/testthat/test-18nosudo_testthat.R | 11 Require-2.1.0/Require/tests/testthat/test-19smallSnapshot_testthat.R | 42 Require-2.1.0/Require/tests/testthat/test-20ghToken_testthat.R |only Require-2.1.0/Require/tests/testthat/test-21snapshotInstallPackages_testthat.R |only Require-2.1.0/Require/tests/testthat/test-22lessThanToAt_testthat.R |only Require-2.1.0/Require/tests/testthat/test-23snapshotRversion_testthat.R |only 73 files changed, 4680 insertions(+), 1192 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-26 1.0.2
2026-02-20 1.0
Title: Sample Size and Power Calculation for Two Co-Primary Endpoints
Description: Comprehensive functions to calculate sample size and power for
clinical trials with two co-primary endpoints. The package supports five
endpoint combinations: two continuous endpoints (Sozu et al. 2011
<doi:10.1080/10543406.2011.551329>), two binary endpoints using asymptotic
methods (Sozu et al. 2010 <doi:10.1002/sim.3972>) and exact methods (Homma
and Yoshida 2025 <doi:10.1177/09622802251368697>), mixed continuous and
binary endpoints (Sozu et al. 2012 <doi:10.1002/bimj.201100221>), and mixed
count and continuous endpoints (Homma and Yoshida 2024
<doi:10.1002/pst.2337>). All methods appropriately account for correlation
between endpoints and provide both sample size and power calculation
capabilities.
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between twoCoprimary versions 1.0.0 dated 2025-11-21 and 1.1.0 dated 2026-08-29
DESCRIPTION | 17 MD5 | 125 +-- NAMESPACE | 100 +- NEWS.md | 194 +++-- R/RcppExports.R |only R/dbibinom.R | 204 ++--- R/design_table.R | 879 ++++++++++++----------- R/power2BinaryExact.R | 362 ++++----- R/power2Continuous.R | 343 ++++----- R/power2MixedContinuousBinary.R | 666 +++++++++-------- R/rr1Binary.R | 425 ++++++----- R/ss2BinaryApprox.R | 350 ++++----- R/ss2BinaryExact.R | 324 ++++---- R/ss2Continuous.R | 346 ++++----- R/ss2MixedContinuousBinary.R | 377 +++++----- R/ss2MixedCountContinuous.R | 384 +++++----- R/twoCoprimary-package.R |only R/twoCoprimary2BinaryExact.R | 208 ++--- R/twoCoprimary2MixedContinuousBinary.R | 202 ++--- R/utils_dbibinom_g.R |only R/utils_tie_groups.R |only README.md | 367 +++++---- build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST |only inst/doc/mixed-continuous-binary.R | 21 inst/doc/mixed-continuous-binary.Rmd | 1021 ++++++++++++++------------- inst/doc/mixed-continuous-binary.html | 457 +++++++----- inst/doc/mixed-count-continuous.Rmd | 960 ++++++++++++------------- inst/doc/mixed-count-continuous.html | 7 inst/doc/overview.Rmd | 740 +++++++++---------- inst/doc/overview.html | 15 inst/doc/two-binary-endpoints-approx.R | 5 inst/doc/two-binary-endpoints-approx.Rmd | 1026 +++++++++++++-------------- inst/doc/two-binary-endpoints-approx.html | 284 +++---- inst/doc/two-binary-endpoints-exact.R | 10 inst/doc/two-binary-endpoints-exact.Rmd | 1038 ++++++++++++++-------------- inst/doc/two-binary-endpoints-exact.html | 462 +++++++----- inst/doc/two-continuous-endpoints.R | 8 inst/doc/two-continuous-endpoints.Rmd | 776 ++++++++++---------- inst/doc/two-continuous-endpoints.html | 90 +- man/dbibinom.Rd | 114 +-- man/design_table.Rd | 17 man/figures |only man/power2BinaryExact.Rd | 254 +++--- man/power2Continuous.Rd | 255 +++--- man/power2MixedContinuousBinary.Rd | 252 +++--- man/rr1Binary.Rd | 174 ++-- man/ss2BinaryApprox.Rd | 248 +++--- man/ss2BinaryExact.Rd | 240 +++--- man/ss2Continuous.Rd | 268 +++---- man/ss2MixedContinuousBinary.Rd | 296 ++++--- man/ss2MixedCountContinuous.Rd | 14 man/twoCoprimary-package.Rd |only man/twoCoprimary2BinaryExact.Rd | 11 src |only tests/spelling.R |only tests/testthat/test-continuous_variance.R |only tests/testthat/test-exact_binary.R |only tests/testthat/test-invariance.R |only tests/testthat/test-mixed_fisher.R |only tests/testthat/test-power_functions.R | 570 +++++++-------- tests/testthat/test-print_method.R | 430 +++++------ tests/testthat/test-sample_size_functions.R | 586 +++++++-------- vignettes/mixed-continuous-binary.Rmd | 1021 ++++++++++++++------------- vignettes/mixed-count-continuous.Rmd | 960 ++++++++++++------------- vignettes/overview.Rmd | 740 +++++++++---------- vignettes/two-binary-endpoints-approx.Rmd | 1026 +++++++++++++-------------- vignettes/two-binary-endpoints-exact.Rmd | 1038 ++++++++++++++-------------- vignettes/two-continuous-endpoints.Rmd | 776 ++++++++++---------- 70 files changed, 11391 insertions(+), 10692 deletions(-)