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
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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
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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
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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
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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
tectonicr-0.4.8/tectonicr/man/Q4_to_euler.Rd |only tectonicr-0.4.8/tectonicr/man/conjugate_Q4.Rd |only tectonicr-0.4.8/tectonicr/man/is.Q4.Rd |only tectonicr-0.4.8/tectonicr/man/normalize_Q4.Rd |only tectonicr-0.4.8/tectonicr/man/product_Q4.Rd |only tectonicr-0.4.8/tectonicr/man/rayleigh_test.Rd |only tectonicr-0.4.8/tectonicr/man/rotation_Q4.Rd |only tectonicr-0.4.8/tectonicr/man/weighted_rayleigh.Rd |only tectonicr-0.4.9/tectonicr/DESCRIPTION | 14 tectonicr-0.4.9/tectonicr/MD5 | 195 tectonicr-0.4.9/tectonicr/NAMESPACE | 27 tectonicr-0.4.9/tectonicr/NEWS.md | 14 tectonicr-0.4.9/tectonicr/R/coordinates.R | 1023 ++-- tectonicr-0.4.9/tectonicr/R/data_stress.R | 45 tectonicr-0.4.9/tectonicr/R/distributions.R |only tectonicr-0.4.9/tectonicr/R/draw_eulerpole.R | 17 tectonicr-0.4.9/tectonicr/R/interpolation.R | 2673 ++++++----- tectonicr-0.4.9/tectonicr/R/model_shmax.R | 75 tectonicr-0.4.9/tectonicr/R/pb_distance.R | 11 tectonicr-0.4.9/tectonicr/R/plotting.R | 785 --- tectonicr-0.4.9/tectonicr/R/roll_statistics.R | 2 tectonicr-0.4.9/tectonicr/R/rose.R |only tectonicr-0.4.9/tectonicr/R/rotation.R | 909 ++- tectonicr-0.4.9/tectonicr/R/stat_tests.R | 1044 ++-- tectonicr-0.4.9/tectonicr/R/statistics.R | 2828 +++++------- tectonicr-0.4.9/tectonicr/R/trigonometry_degrees.R | 890 +-- tectonicr-0.4.9/tectonicr/R/various.R | 1024 ++-- tectonicr-0.4.9/tectonicr/README.md | 2 tectonicr-0.4.9/tectonicr/data/homing.rda |only tectonicr-0.4.9/tectonicr/data/striae.rda |only tectonicr-0.4.9/tectonicr/inst/doc/datasets.html | 11 tectonicr-0.4.9/tectonicr/inst/doc/interpolation.Rmd | 305 - 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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
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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(-)
Title: An MCMC Sampler Using the t-Walk Algorithm
Description: Implements the t-walk algorithm, a general-purpose, self-adjusting
Markov Chain Monte Carlo (MCMC) sampler for continuous distributions as
described by Christen & Fox (2010) <doi:10.1214/10-BA603>. The t-walk requires
no tuning and is robust for a wide range of target distributions, including
high-dimensional and multimodal problems. This implementation includes an
option for running multiple chains in parallel to accelerate sampling and
facilitate convergence diagnostics.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between Rtwalk versions 2.0.2 dated 2026-07-30 and 2.1.0 dated 2026-08-28
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 1 NEWS.md | 45 +++++ R/diagnostics.R | 91 +++++++++-- R/s3-methods.R | 14 + R/twalk_engine.R | 77 +++++++-- R/twalk_main.R | 298 ++++++++++++++++++++++++++++++------ README.md | 59 ++++++- inst/doc/validation_study.R | 44 +++-- inst/doc/validation_study.Rmd | 60 +++++-- inst/doc/validation_study.html | 79 ++++++--- man/calculate_diagnostics.Rd | 6 man/twalk.Rd | 45 ++++- man/visualize_results.Rd | 2 tests/testthat/test-diagnostics.R | 47 +++++ tests/testthat/test-kernels.R | 37 ++++ tests/testthat/test-methods.R | 51 ++++++ tests/testthat/test-twalk.R | 310 +++++++++++++++++++++++++++++++++++++- tests/testthat/test-visualize.R | 19 ++ vignettes/validation_study.Rmd | 60 +++++-- 21 files changed, 1182 insertions(+), 211 deletions(-)
Title: Taxonomic Hierarchy Distances and Lineage Analysis
Description: Computes distances between taxonomic hierarchy nodes using lineage
data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For
distinct nodes, distance is defined as the reciprocal of the depth of their
most recent common ancestor; identical nodes have distance zero. This
definition yields an ultrametric within each connected hierarchy. Functions
are provided for lineage retrieval and comparison, clade membership,
pairwise and matrix distance calculation, hierarchical clustering,
principal coordinates analysis, and cache management. Distance matrices are
returned as base R 'dist' objects. The distances represent classification
depth rather than evolutionary time or phylogenetic branch length.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between taxodist versions 0.6.0 dated 2026-08-19 and 0.7.0 dated 2026-08-28
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 22 ++++++ R/distance.R | 105 +++++++++++++++++++++++---------- R/fetch.R | 20 +++++- data/taxobase.rda |binary inst/CITATION | 2 inst/doc/introduction.html | 2 inst/doc/statistical-applications.html | 2 tests/testthat/test-distance.R | 97 +++++++++++++++++++++++++++++- 10 files changed, 224 insertions(+), 50 deletions(-)
Title: Extracts Risk Neutral Densities of Prices, Money Market Rates
and Government Bond Yields from Interest Rates Futures Options
Prices
Description: Provides with parametric Risk Neutral Densities (RNDs) and cumulative densities of futures prices on fixed-income products. It relies on options on Short Term Interest Rate futures or options on government bond futures. It models the futures price as a mixture of lognormal densities. Leveraging on this, the package provides with the RNDs and cumulative densities of the money market rate or the government bond yield inferred from the futures price, using the RND of the futures price. The package also extracts from the RND of the government bond futures price simultaneously the RND of the cheapest-to-deliver bond yield at options' maturity and the RND of the ctd bond repo rate from options' maturity to futures' maturity. The package also provides with the probability attached to each bond in the delivery basket of a government bond futures to be the cheapest at maturity, and also the non parametric distribution of the spread between two bond yields, using two RNDs based on options on bon [...truncated...]
Author: William Arrata [aut, cre]
Maintainer: William Arrata <william.arrata@gmail.com>
Diff between yrnd versions 0.1.5 dated 2026-07-21 and 0.1.6 dated 2026-08-28
DESCRIPTION | 12 MD5 | 40 NAMESPACE | 2 R/bond_fut_irr_ytm.R |only R/bond_future_charac_bbg.R | 2 R/bond_future_price.R | 106 R/bond_yield_spread.R | 3 R/ctd_bond_yield.R | 120 R/deliv_bonds_charac_bbg.R | 16 R/globals.R | 3 R/option_prices_bbg.R | 9 R/proba_ctd.R | 261 R/proba_ctd_opt.R | 15 R/stir_future_price.R | 102 R/stir_rate.R | 103 inst/doc/yrnd-functions.R | 53 inst/doc/yrnd-functions.Rmd | 70 inst/doc/yrnd-functions.html |101448 ++++-------------------------------------- man/bond_fut_irr_ytm.Rd |only man/bond_future_charac_bbg.Rd | 1 man/proba_ctd.Rd | 6 vignettes/yrnd-functions.Rmd | 70 22 files changed, 11053 insertions(+), 91389 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling
tools for developing cellular automata, dynamic raster models, and
agent based models in 'SpaDES'. Included are various methods for
spatial spreading, spatial agents, GIS operations, random map
generation, and others. See '?SpaDES.tools' for a categorized
overview of these additional tools.
Author: Eliot J B McIntire [aut] ,
Alex M Chubaty [aut, cre] ,
Yong Luo [ctb],
Ceres Barros [ctb] ,
Steve Cumming [ctb],
Jean Marchal [ctb],
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
This is a re-admission after prior archival of version 2.1.1 dated 2026-01-11
Diff between SpaDES.tools versions 2.1.1 dated 2026-01-11 and 2.1.3 dated 2026-08-28
SpaDES.tools-2.1.1/SpaDES.tools/man/wrap.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/DESCRIPTION | 29 SpaDES.tools-2.1.3/SpaDES.tools/MD5 | 210 ++++-- SpaDES.tools-2.1.3/SpaDES.tools/NAMESPACE | 185 ++--- SpaDES.tools-2.1.3/SpaDES.tools/NEWS.md | 106 +++ SpaDES.tools-2.1.3/SpaDES.tools/R/RcppExports.R | 48 + SpaDES.tools-2.1.3/SpaDES.tools/R/SELES.R | 31 SpaDES.tools-2.1.3/SpaDES.tools/R/distanceFromEachPoint.R | 6 SpaDES.tools-2.1.3/SpaDES.tools/R/heading.R | 12 SpaDES.tools-2.1.3/SpaDES.tools/R/helpers.R | 12 SpaDES.tools-2.1.3/SpaDES.tools/R/initialize.R | 238 ++----- SpaDES.tools-2.1.3/SpaDES.tools/R/mapReduce.R | 118 +-- SpaDES.tools-2.1.3/SpaDES.tools/R/movement.R | 90 +- SpaDES.tools-2.1.3/SpaDES.tools/R/neighbourhood.R | 132 +++ SpaDES.tools-2.1.3/SpaDES.tools/R/probability.R | 6 SpaDES.tools-2.1.3/SpaDES.tools/R/rastFromDF.R |only SpaDES.tools-2.1.3/SpaDES.tools/R/release-bullets.R |only SpaDES.tools-2.1.3/SpaDES.tools/R/rings.R | 4 SpaDES.tools-2.1.3/SpaDES.tools/R/spades-tools-deprecated.R | 3 SpaDES.tools-2.1.3/SpaDES.tools/R/spades-tools-package.R | 28 SpaDES.tools-2.1.3/SpaDES.tools/R/splitRaster.R | 2 SpaDES.tools-2.1.3/SpaDES.tools/R/spread.R | 30 SpaDES.tools-2.1.3/SpaDES.tools/R/spread2.R | 31 SpaDES.tools-2.1.3/SpaDES.tools/R/spread3.R | 4 SpaDES.tools-2.1.3/SpaDES.tools/R/studyArea.R | 5 SpaDES.tools-2.1.3/SpaDES.tools/README.md | 181 ++++- SpaDES.tools-2.1.3/SpaDES.tools/inst/WORDLIST | 23 SpaDES.tools-2.1.3/SpaDES.tools/inst/examples/example_spread.R | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/SELEStransitions.Rd | 22 SpaDES.tools-2.1.3/SpaDES.tools/man/SpaDES.tools-package.Rd | 24 SpaDES.tools-2.1.3/SpaDES.tools/man/adjPairsMatrix.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/adjPairsWithId.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/crw.Rd | 11 SpaDES.tools-2.1.3/SpaDES.tools/man/deprecated.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/distances.Rd | 7 SpaDES.tools-2.1.3/SpaDES.tools/man/dwrpnorm2.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/neutralLandscapeMap.Rd | 76 +- SpaDES.tools-2.1.3/SpaDES.tools/man/pkgEnv.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/rastFromDF.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/rings.Rd | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/specnumperpatch-probs.Rd | 8 SpaDES.tools-2.1.3/SpaDES.tools/man/splitRaster.Rd | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/spread.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/spread2.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/testEquivalentMetadata.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/wrapTorus.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/src/RcppExports.cpp | 31 SpaDES.tools-2.1.3/SpaDES.tools/src/adj_spread.cpp |only SpaDES.tools-2.1.3/SpaDES.tools/src/duplicated.cpp | 4 SpaDES.tools-2.1.3/SpaDES.tools/src/runif.cpp | 2 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/_spread_snapshots |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/setup.R | 1 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-SELES.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-adj-helpers.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-adj.R | 141 ++++ SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-distanceFromEachPoint.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-heading.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-initialize.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-misc-helpers.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-movement.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-neutralLandscapeMap.R | 5 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-probability.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-randomPolygon.R | 62 + SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-rastFromDF.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-rings.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spokes.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread-snapshots.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread.R | 335 +++++----- SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread2.R | 219 +++++- SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread3.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-studyArea.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-wrapTorus.R |only 72 files changed, 1778 insertions(+), 737 deletions(-)
Title: Hierarchical Piecewise Regression with Smoothed Change-Points
Description: Fits Bayesian hierarchical piecewise regression models with
multiple logistic-smoothed change-points. Non-linear parameters (change-point
locations and transition sharpness) and linear parameters can each be
conditioned on covariates and factors via flexible design matrices.
A random-intercept structure is supported for any parameter. Spike-and-slab
regularization is supported for selecting the number of breakpoints.
Posterior inference uses a Metropolis-within-Gibbs sampler implemented
in 'Rust' for speed. Methods are based on the smooth transition
piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389>
and variable selection spike-and-slab priors of Kuo and Mallick (1998)
<https://www.jstor.org/stable/25053023>. Methods are described in
Bindoff (2026) <doi:10.48550/arXiv.2606.19044>.
Author: Aidan D Bindoff [aut, cre]
Maintainer: Aidan D Bindoff <aidan.bindoff@utas.edu.au>
Diff between smoothbp versions 0.2.7 dated 2026-06-16 and 0.2.8 dated 2026-08-28
smoothbp-0.2.7/smoothbp/tools/test_vignette_params.R |only smoothbp-0.2.7/smoothbp/tools/verify_mixing_changes.R |only smoothbp-0.2.8/smoothbp/DESCRIPTION | 21 smoothbp-0.2.8/smoothbp/MD5 | 30 smoothbp-0.2.8/smoothbp/NAMESPACE | 1 smoothbp-0.2.8/smoothbp/NEWS.md | 128 ++ smoothbp-0.2.8/smoothbp/R/methods_text.R | 6 smoothbp-0.2.8/smoothbp/R/smoothbp.R | 7 smoothbp-0.2.8/smoothbp/R/smoothbp_ss.R | 91 + smoothbp-0.2.8/smoothbp/inst/CITATION |only smoothbp-0.2.8/smoothbp/man/reexports.Rd | 40 smoothbp-0.2.8/smoothbp/man/update.smoothbp_ss_fit.Rd |only smoothbp-0.2.8/smoothbp/src/Makevars.win.in | 4 smoothbp-0.2.8/smoothbp/src/rust/src/model.rs | 113 + smoothbp-0.2.8/smoothbp/src/rust/src/sampler.rs | 640 +++++++++- smoothbp-0.2.8/smoothbp/src/rust/src/sampler_re.rs | 619 ++++++++- smoothbp-0.2.8/smoothbp/tests/testthat/test-collapsed-indicator.R |only smoothbp-0.2.8/smoothbp/tests/testthat/test-reparameterise.R |only smoothbp-0.2.8/smoothbp/tests/testthat/test-update-recovery-hypothesis-bf.R | 44 19 files changed, 1594 insertions(+), 150 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.5 dated 2026-07-13 and 0.3.6 dated 2026-08-28
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 1 NEWS.md | 13 - R/pre_process.R | 222 +++++++++++++++++---------- README.md | 3 inst/doc/introduction-to-quickSentiment.html | 61 +++---- man/pre_process.Rd | 38 ++-- 8 files changed, 219 insertions(+), 139 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Access the 'Mobility Database' API to Discover Transit Feeds
Description: Search and access transit feed data from the
'Mobility Database' <https://mobilitydatabase.org>. The package wraps the 'Mobility Database'
API, allowing users to discover 'GTFS' (General Transit Feed Specification) and
'GBFS' (General Bikeshare Feed Specification) feeds from agencies worldwide.
Functions are designed to integrate seamlessly with
packages like 'tidytransit' and 'gtfstools' for subsequent feed analysis.
Author: Jason Adle [aut, cre, cph]
Maintainer: Jason Adle <developer@jasonadle.dev>
Diff between mobdb versions 1.0.1 dated 2026-08-07 and 1.0.3 dated 2026-08-28
DESCRIPTION | 6 LICENSE | 4 MD5 | 162 - NAMESPACE | 88 - NEWS.md | 321 +-- R/api-datasets.R | 232 +- R/api-feeds.R | 874 ++++----- R/api-metadata.R | 34 R/api-search.R | 346 +-- R/cache.R | 744 ++++---- R/geo-feeds.R | 470 ++--- R/integration-tidytransit.R | 2188 ++++++++++++------------- R/mobdb-package.R | 60 R/utils-auth.R | 344 +-- R/utils-conditions.R | 94 - R/utils-convenience.R | 380 ++-- R/utils-gtfs-format.R | 282 +-- R/utils-helpers.R | 1350 +++++++-------- R/utils-request.R | 244 +- README.md | 368 ++-- build/vignette.rds |binary inst/doc/gbfs-and-gtfs-rt.R | 148 - inst/doc/gbfs-and-gtfs-rt.Rmd | 332 +-- inst/doc/gbfs-and-gtfs-rt.html | 1062 ++++++------ inst/doc/mobdb.R | 432 ++-- inst/doc/mobdb.Rmd | 646 +++---- inst/doc/mobdb.html | 1308 +++++++------- man/download_best_feed.Rd | 270 +-- man/download_feed.Rd | 306 +-- man/feeds.Rd | 198 +- man/feeds_bbox.Rd | 188 +- man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/filter_by_validation.Rd | 156 - man/get_validation_report.Rd | 138 - man/gtfs_to_spec_format.Rd | 128 - man/mobdb-package.Rd | 62 man/mobdb_browse.Rd | 44 man/mobdb_cache_clear.Rd | 56 man/mobdb_cache_info.Rd | 46 man/mobdb_cache_list.Rd | 46 man/mobdb_cache_path.Rd | 78 man/mobdb_can_run_examples.Rd | 38 man/mobdb_datasets.Rd | 98 - man/mobdb_extract_datasets.Rd | 138 - man/mobdb_extract_locations.Rd | 114 - man/mobdb_extract_urls.Rd | 80 man/mobdb_feed_url.Rd | 60 man/mobdb_get_dataset.Rd | 48 man/mobdb_get_feed.Rd | 46 man/mobdb_has_internet.Rd | 38 man/mobdb_has_key.Rd | 42 man/mobdb_has_tidytransit.Rd | 38 man/mobdb_read_gtfs.Rd | 88 - man/mobdb_search.Rd | 210 +- man/mobdb_set_key.Rd | 70 man/view_validation_report.Rd | 102 - tests/testthat.R | 8 tests/testthat/README.md | 184 +- tests/testthat/setup.R | 64 tests/testthat/test-api-feeds.R | 466 ++--- tests/testthat/test-api-metadata.R | 60 tests/testthat/test-api-parameter-validation.R | 46 tests/testthat/test-api-search.R | 348 +-- tests/testthat/test-auth.R | 296 +-- tests/testthat/test-cache.R | 1260 +++++++------- tests/testthat/test-datasets.R | 332 +-- tests/testthat/test-download-best-feed.R | 300 +-- tests/testthat/test-export-gtfs.R | 392 ++-- tests/testthat/test-feed-quality-scoring.R | 736 ++++---- tests/testthat/test-format-feed-summary.R | 574 +++--- tests/testthat/test-geo-feeds.R | 406 ++-- tests/testthat/test-gtfs-format.R | 574 +++--- tests/testthat/test-helpers.R | 724 ++++---- tests/testthat/test-integration.R | 490 ++--- tests/testthat/test-utils-convenience.R | 94 - tests/testthat/test-utils-request.R | 556 +++--- tests/testthat/test-validation-helpers.R | 396 ++-- vignettes/gbfs-and-gtfs-rt.Rmd | 332 +-- vignettes/mobdb.Rmd | 646 +++---- 82 files changed, 12464 insertions(+), 12449 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.2 dated 2026-08-28 and 2.0.3 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/get_drainage_area_estimates.R | 15 +++++++++++---- man/get_drainage_area_estimates.Rd | 3 ++- 5 files changed, 27 insertions(+), 12 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.10 dated 2025-09-28 and 1.4.11 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 7 ++++++- src/meanderingTriangleC.cpp | 1 + 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Lindley Approximation for Capability Indices under Progressive
Censoring
Description: Implements Bayesian parameter and Generalized Process Capability
Indices (GPCIs) estimation using the Lindley approximation method (Lindley,
1980 <doi:10.2307/2345271>) under progressive Type-II censored data
(Balakrishnan & Aggarwala, 2000 <doi:10.1007/978-1-4612-1334-5>). Evaluates
point estimates and posterior expectations for classical and non-normal
capability indices, including Cpy (Maiti et al., 2010
<doi:10.1080/16843703.2010.11673233>), Spmk (Dey & Saha, 2019
<doi:10.1007/s41872-019-00081-4>), CpTk (Saha et al., 2019
<doi:10.1007/s13198-019-00789-7>), Cpc (Saha et al.,
2022 <doi:10.1080/02664763.2021.1971632>), CNpmc (Alotaibi et al., 2022
<doi:10.1155/2022/3135264>), CNpmkc (Saha et al., 2024
<doi:10.1142/S021853932450013X>), CNpk (Saha et al., 2018
<doi:10.1080/21681015.2018.1437793>), and Vannman's Cp(u,v) family (Vannman,
1995 <doi:10.1111/j.1467-9574.1995.tb01472.x>). Calculates point estimates,
bias, mea [...truncated...]
Author: Shikhar Tyagi [aut, cre] ,
Sumit Kumar [aut],
Arvind Pandey [aut],
Bhupendra Singh [aut],
Vrijesh Tripathi [aut]
Maintainer: Shikhar Tyagi <shikhar1093tyagi@gmail.com>
Diff between gpciLindApproxProgII versions 0.1.0 dated 2026-08-26 and 0.1.1 dated 2026-08-28
gpciLindApproxProgII-0.1.0/gpciLindApproxProgII/tests/testthat/Rplots.pdf |only gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/DESCRIPTION | 9 gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/MD5 | 9 gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/inst/WORDLIST | 50 +++- gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/inst/doc/GPCILindApproxProgII.html | 114 +++++----- gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/tests/testthat/test-all.R | 19 + 6 files changed, 119 insertions(+), 82 deletions(-)
More information about gpciLindApproxProgII at CRAN
Permanent link
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders,
truncated normal, mixture of inverse Gaussian, mixture of Birnbaum-Saunders,
generalized exponential, Jorgensen-Seshadri-Whitmore, weighted Akash, weighted Shanker and
weighted Sujatha as the distribution for frailty terms. For the basal model, it
is considered a parametric approach based on the exponential, Weibull and the
piecewise exponential distributions as well as a semiparametric approach. For
details, see Gallardo et al. (2024) <doi:10.1007/s11222-024-10458-w>,
Gallardo et al. (2025) <doi:10.1002/bimj.70044>, Kiprotich et al. (2025) <doi:10.1177/09622802251338984>,
Gallardo et al. (2025) <doi:10.1038/s41598-025-15903-y>, Kiprotich et al. (2026) <doi:10.1080/00949655.2025.2584734
and Mohammadi et al. (2026).
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut],
John Santibanez [ctb],
Gilbert Kiprotich [ctb],
Pedro Ramos [ctb],
Thomas Augustin [ctb],
Zohreh Mohammadi [ctb],
Paulo Ferreira [ctb],
Gerson Primo [ctb]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between extrafrail versions 1.14 dated 2025-08-24 and 1.15 dated 2026-08-28
DESCRIPTION | 34 - MD5 | 16 NAMESPACE | 2 NEWS.md | 10 R/frailty.fit.R | 1574 +++++++++++++++++++++++++++++++++++++++++++++++- R/print.extrafrail.R | 190 ----- R/summary.extrafrail.R | 51 + man/frailty.fit.Rd | 6 man/tools.extrafrail.Rd | 4 9 files changed, 1699 insertions(+), 188 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a widely used health-related quality-of-life instrument
developed by the EuroQol Group and used in the clinical and economic
evaluation of health care. Health is described using five dimensions
(mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression) rated on either a three-level (EQ-5D-3L and EQ-5D-Y-3L)
or five-level (EQ-5D-5L) scale. Responses can be reported as EQ-5D health
states or converted to utility index scores using country-specific value
sets. The package provides methods for the valuation, reporting and
analysis of EQ-5D data. Utility index scores can be calculated for
EQ-5D-3L, EQ-5D-5L and EQ-5D-Y-3L data using a wide range of value sets and
mapping approaches. Functionality is also provided for descriptive-system
reporting, severity and distributional summaries, informativity measures,
health-state distribution analysis, longitudinal change analysis,
probability of superiority analysis and Health Profile Grid visualisation.
Methods descr [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.16.3 dated 2026-03-30 and 0.17.0 dated 2026-08-28
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Title: Create (Advanced) Coupled Matrix and Tensor Factorization Models
Description: Creation and selection of (Advanced) Coupled Matrix and Tensor Factorization (ACMTF) and ACMTF-Regression (ACMTF-R) models. Selection of the optimal number of components can be done using 'ACMTF_modelSelection()' and 'ACMTFR_modelSelection()'. The CMTF and ACMTF methods were originally described by Acar et al., 2011 <doi:10.48550/arXiv.1105.3422> and Acar et al., 2014 <doi:10.1186/1471-2105-15-239>, respectively.
Author: Geert Roelof van der Ploeg [aut, cre] ,
Johan Westerhuis [ctb] ,
Anna Heintz-Buschart [ctb] ,
Age Smilde [ctb] ,
University of Amsterdam [cph, fnd]
Maintainer: Geert Roelof van der Ploeg <roel@simula.no>
This is a re-admission after prior archival of version 1.0.1 dated 2025-08-22
Diff between CMTFtoolbox versions 1.0.1 dated 2025-08-22 and 1.1.1 dated 2026-08-28
DESCRIPTION | 13 LICENSE | 4 MD5 | 122 +-- NAMESPACE | 66 - NEWS.md | 8 R/ACMTFR_modelSelection.R | 1008 ++++++++++++++-------------- R/ACMTF_modelSelection.R | 680 +++++++++--------- R/FMS_cv.R | 132 +-- R/FMS_random.R | 120 +-- R/acmtf_fg.R | 264 +++---- R/acmtf_fun.R | 142 +-- R/acmtf_gradient.R | 172 ++-- R/acmtf_opt.R | 174 ++-- R/acmtfr_fg.R | 324 ++++----- R/acmtfr_fun.R | 178 ++-- R/acmtfr_gradient.R | 196 ++--- R/acmtfr_opt.R | 188 ++--- R/cmtf_fg.R | 160 ++-- R/cmtf_fun.R | 96 +- R/cmtf_opt.R | 184 ++--- R/computeFMS.R | 154 ++-- R/data.R | 26 R/initializeCMTF.R | 146 ++-- R/npred.R | 240 +++--- R/reinflateFac.R | 132 +-- R/utils.R | 618 ++++++++--------- README.md | 2 build/vignette.rds |binary inst/doc/Introduction.Rmd | 270 +++---- inst/doc/Introduction.html | 38 - man/ACMTFR_modelSelection.Rd | 214 ++--- man/ACMTF_modelSelection.Rd | 192 ++--- man/FMS_cv.Rd | 76 +- man/FMS_random.Rd | 72 +- man/Georgiou2025.Rd | 54 - man/acmtf_fg.Rd | 86 +- man/acmtfr_fg.Rd | 118 +-- man/cmtf_fg.Rd | 74 +- man/npred.Rd | 94 +- man/reinflateMatrix.Rd | 48 - man/reinflateTensor.Rd | 54 - man/removeTwoNormCol.Rd | 42 - tests/testthat.R | 24 tests/testthat/test-ACMTFR_modelSelection.R | 122 +-- tests/testthat/test-ACMTF_modelSelection.R | 86 +- tests/testthat/test-FMS_cv.R | 182 ++--- tests/testthat/test-FMS_random.R | 182 ++--- tests/testthat/test-acmtf_fg.R | 92 +- tests/testthat/test-acmtf_fun.R | 54 - tests/testthat/test-acmtf_opt.R | 336 ++++----- tests/testthat/test-acmtfr_fg.R | 102 +- tests/testthat/test-acmtfr_fun.R | 88 +- tests/testthat/test-acmtfr_gradient.R | 180 ++--- tests/testthat/test-acmtfr_opt.R | 434 ++++++------ tests/testthat/test-cmtf_fg.R | 114 +-- tests/testthat/test-cmtf_opt.R | 314 ++++---- tests/testthat/test-degenScore.R | 8 tests/testthat/test-initializeCMTF.R | 212 ++--- tests/testthat/test-npred.R | 528 +++++++------- tests/testthat/test-reinflateFac.R | 136 +-- tests/testthat/test-utils.R | 19 vignettes/Introduction.Rmd | 270 +++---- 62 files changed, 5237 insertions(+), 5227 deletions(-)
Title: Bayesian Analyses for One- and Two-Sample Inference and
Regression Methods
Description: Perform fundamental analyses using Bayesian parametric and non-parametric inference (regression, anova, 1 and 2 sample inference, non-parametric tests, etc.). (Practically) no Markov chain Monte Carlo (MCMC) is used; all exact finite sample inference is completed via closed form solutions or else through posterior sampling automated to ensure precision in interval estimate bounds. Diagnostic plots for model assessment, and key inferential quantities (point and interval estimates, probability of direction, region of practical equivalence, and Bayes factors) and model visualizations are provided. Bayes factors are computed either by the Savage Dickey ratio given in Dickey (1971) <doi:10.1214/aoms/1177693507> or by Chib's method as given in <doi:10.1080/01621459.1995.10476635>. Interpretations are from Kass and Raftery (1995) <doi:10.1080/01621459.1995.10476572>. ROPE bounds are based on discussions in Kruschke (2018) <doi:10.1177/2515245918771304>. Methods for d [...truncated...]
Author: Daniel K. Sewell [aut, cre, cph] ,
Alan Arakkal [aut]
Maintainer: Daniel K. Sewell <daniel-sewell@uiowa.edu>
Diff between bayesics versions 3.0.1 dated 2026-08-26 and 3.0.2 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/mediate_b.R | 15 +++++++++++---- 4 files changed, 23 insertions(+), 10 deletions(-)
Title: Predict Energy Expenditure from Accelerometry Data
Description: Simplifies the application of various energy expenditure models. The
package is intended as a hub that brings together methods from a variety of
other, themed packages such as 'Sojourn' and 'TwoRegression'. Several methods
are supported locally as well, including the linear methods of
Hildebrand et al. (2014) <doi:10.1249/MSS.0000000000000289> and the
non-linear adaptation by Ellingson et al. (2017) <doi:10.1088/1361-6579/aa6d00>.
The package can combine output from different methods and produce standardized
output in a range of units.
Author: Paul R. Hibbing [aut, cre],
Children's Mercy Kansas City [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2026-05-12
Diff between accelEE versions 0.3.1 dated 2026-05-12 and 0.3.2 dated 2026-08-28
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 13 insertions(+), 8 deletions(-)
Title: Flexible, Interactive 'shiny' Modules for Almost Any Plot
Description: Offers a core selection of interactivity-first 'shiny' modules for many
plot types meant to serve as flexible building blocks for applications and
as the base for more complex modules. These modules
allow for the rapid and convenient construction of 'shiny' apps with very few lines
of code and decouple plotting from the underlying data. These modules allow
for full plot aesthetic customization by the end user through UI inputs. Utility
functions for simple UI organization, automated UI tooltips, and additional
plot enhancements are also provided. Includes a multi-panel figure builder app
for arranging multiple modules together in a free-form layout.
Author: Jared Andrews [aut, cre] ,
Jacob Martin [aut]
Maintainer: Jared Andrews <jared.andrews07@gmail.com>
Diff between VizModules versions 0.3.0 dated 2026-07-27 and 0.4.0 dated 2026-08-28
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VizModules-0.4.0/VizModules/R/dittoViz_ScatterPlot_module_ui.R | 197 --- VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_app.R |only VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_server.R |only VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_ui.R |only VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_server.R | 510 ++++++++-- VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_ui.R | 163 ++- VizModules-0.4.0/VizModules/R/dumbbellPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/dumbbellPlot_module_server.R | 64 - VizModules-0.4.0/VizModules/R/dumbbellPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/figureBuilder_module_app.R | 11 VizModules-0.4.0/VizModules/R/figureBuilder_module_server.R | 20 VizModules-0.4.0/VizModules/R/figureBuilder_module_ui.R | 12 VizModules-0.4.0/VizModules/R/globals.R | 5 VizModules-0.4.0/VizModules/R/linePlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/linePlot_module_server.R | 108 +- VizModules-0.4.0/VizModules/R/linePlot_module_ui.R | 43 VizModules-0.4.0/VizModules/R/multiColorPicker.R | 357 ------- VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot.R | 1 VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_server.R | 60 - VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/parse_utils.R | 449 ++++++++ VizModules-0.4.0/VizModules/R/piePlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/piePlot_module_server.R | 98 + VizModules-0.4.0/VizModules/R/piePlot_module_ui.R | 47 VizModules-0.4.0/VizModules/R/plot_facets.R | 13 VizModules-0.4.0/VizModules/R/plot_helpers.R | 181 +++ VizModules-0.4.0/VizModules/R/plot_source_data.R | 202 +++ VizModules-0.4.0/VizModules/R/plotly_annotation_utils.R | 191 +++ VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_server.R | 62 - VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_ui.R | 27 VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_server.R | 106 +- VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_ui.R | 36 VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_server.R | 117 +- VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_server.R | 64 - VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_ui.R | 28 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_server.R | 41 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_ui.R | 38 VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_server.R | 64 - VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_ui.R | 28 VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_server.R | 81 + VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_ui.R | 36 VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_server.R | 111 +- VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/radarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/radarPlot_module_server.R | 102 +- VizModules-0.4.0/VizModules/R/radarPlot_module_ui.R | 48 VizModules-0.4.0/VizModules/R/reactive_defaults.R |only VizModules-0.4.0/VizModules/R/reset_uniform_ui_inputs.R | 91 + VizModules-0.4.0/VizModules/R/select_inputs.R |only VizModules-0.4.0/VizModules/R/stat_helper.R | 395 ++++++- VizModules-0.4.0/VizModules/R/ui_utils.R | 99 + VizModules-0.4.0/VizModules/R/uniform_ui_inputs.R | 215 +++- VizModules-0.4.0/VizModules/R/use_skills.R |only VizModules-0.4.0/VizModules/README.md | 28 VizModules-0.4.0/VizModules/build/vignette.rds |binary VizModules-0.4.0/VizModules/data/example_bar.rda |binary VizModules-0.4.0/VizModules/data/example_composition.rda |only VizModules-0.4.0/VizModules/data/example_demographics.rda |binary VizModules-0.4.0/VizModules/data/example_heatmap_column_data.rda |only VizModules-0.4.0/VizModules/data/example_heatmap_matrix.rda |only VizModules-0.4.0/VizModules/data/example_iris.rda |binary VizModules-0.4.0/VizModules/data/example_markers.rda |binary VizModules-0.4.0/VizModules/data/example_mtcars.rda |binary VizModules-0.4.0/VizModules/data/example_population.rda |binary VizModules-0.4.0/VizModules/data/example_rnaseq.rda |binary VizModules-0.4.0/VizModules/data/example_sales.rda |binary VizModules-0.4.0/VizModules/data/example_school_earnings.rda |binary VizModules-0.4.0/VizModules/data/example_skills.rda |binary VizModules-0.4.0/VizModules/inst/apps/module-gallery/app.R | 57 + VizModules-0.4.0/VizModules/inst/doc/adding-a-new-module.Rmd | 214 ++++ VizModules-0.4.0/VizModules/inst/doc/adding-a-new-module.html | 288 +++++ VizModules-0.4.0/VizModules/inst/doc/custom-model-lines.Rmd | 2 VizModules-0.4.0/VizModules/inst/doc/custom-model-lines.html | 5 VizModules-0.4.0/VizModules/inst/doc/custom-modules.R | 26 VizModules-0.4.0/VizModules/inst/doc/custom-modules.Rmd | 43 VizModules-0.4.0/VizModules/inst/doc/custom-modules.html | 87 + VizModules-0.4.0/VizModules/inst/doc/data-filtering.R |only VizModules-0.4.0/VizModules/inst/doc/data-filtering.Rmd |only VizModules-0.4.0/VizModules/inst/doc/data-filtering.html |only VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.R | 31 VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.Rmd | 59 + VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.html | 282 +++-- VizModules-0.4.0/VizModules/inst/doc/quick-start.Rmd | 1 VizModules-0.4.0/VizModules/inst/doc/quick-start.html | 6 VizModules-0.4.0/VizModules/inst/skills |only VizModules-0.4.0/VizModules/inst/src/multiColorPicker.css | 84 + VizModules-0.4.0/VizModules/inst/src/multiColorPicker.js | 148 ++ VizModules-0.4.0/VizModules/inst/src/vizSelect.js |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapApp.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapInfoOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapInputsUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapMainOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapServer.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapSubOutputUI.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_apply_highlight_styling.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_axis_limit_clears.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_blank_to_null.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_calculate_range.Rd | 12 VizModules-0.4.0/VizModules/man/INTERNAL_create_highlight_annotations.Rd | 6 VizModules-0.4.0/VizModules/man/INTERNAL_create_selected_annotations.Rd | 6 VizModules-0.4.0/VizModules/man/INTERNAL_default_group_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_facet_check.Rd | 4 VizModules-0.4.0/VizModules/man/INTERNAL_freq_maps_one_per.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_sample_choices.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_selected_vars.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_stats_group_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_summary.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_y_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_has_group_names.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_spec.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_widget_id.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_build_annotation.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_default_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_resolve_data.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_resolve_split.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_scale_matrix.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_merge_annotation_sets.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_multivar_long_df.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_pairwise_layout.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_plotted_vars_from_attrs.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_plotted_vars_from_inputs.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_reapply_manual_edits.Rd | 9 VizModules-0.4.0/VizModules/man/INTERNAL_require_data_frame.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_reset_group_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_same_axis_range.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_should_include_trace.Rd | 7 VizModules-0.4.0/VizModules/man/INTERNAL_stat_bracket_headroom.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_viz_select_dependency.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_with_stable_seed.Rd |only VizModules-0.4.0/VizModules/man/apply_stat_annotations.Rd | 16 VizModules-0.4.0/VizModules/man/collect_source_data.Rd | 149 +- VizModules-0.4.0/VizModules/man/createModuleApp.Rd | 3 VizModules-0.4.0/VizModules/man/dataFilterServer.Rd | 52 - VizModules-0.4.0/VizModules/man/dittoViz_freqPlotApp.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotInputsUI.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotOutputUI.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotServer.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotInputsUI.Rd | 12 VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotServer.Rd | 11 VizModules-0.4.0/VizModules/man/dittoViz_yPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dittoViz_yPlotInputsUI.Rd | 49 VizModules-0.4.0/VizModules/man/dittoViz_yPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/dumbbellPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dumbbellPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/dumbbellPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/example_composition.Rd |only VizModules-0.4.0/VizModules/man/example_heatmap_column_data.Rd |only VizModules-0.4.0/VizModules/man/example_heatmap_matrix.Rd |only VizModules-0.4.0/VizModules/man/figureBuilderServer.Rd | 4 VizModules-0.4.0/VizModules/man/finalize_manual_edits.Rd | 15 VizModules-0.4.0/VizModules/man/get_default.Rd | 13 VizModules-0.4.0/VizModules/man/hide_input.Rd |only VizModules-0.4.0/VizModules/man/linePlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/linePlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/linePlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/multiColorPicker.Rd | 16 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/piePlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/piePlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/piePlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_BarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DotPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_DotPlotInputsUI.Rd | 6 VizModules-0.4.0/VizModules/man/plotthis_DotPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_HistogramApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_HistogramInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_HistogramServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/radarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/radarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/radarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/reset_annotation_inputs.Rd |only VizModules-0.4.0/VizModules/man/reset_axis_title_text.Rd |only VizModules-0.4.0/VizModules/man/resolve_column_targets.Rd |only VizModules-0.4.0/VizModules/man/resolve_palette.Rd | 25 VizModules-0.4.0/VizModules/man/setup_auto_update_logic.Rd | 22 VizModules-0.4.0/VizModules/man/setup_axis_range.Rd |only VizModules-0.4.0/VizModules/man/setup_group_colors.Rd |only VizModules-0.4.0/VizModules/man/setup_reactive_defaults.Rd |only VizModules-0.4.0/VizModules/man/show_input.Rd |only VizModules-0.4.0/VizModules/man/stat_bracket_y_max.Rd |only VizModules-0.4.0/VizModules/man/toggle_input_cell.Rd |only VizModules-0.4.0/VizModules/man/uniform_annotation_inputs_ui.Rd |only VizModules-0.4.0/VizModules/man/update_viz_select.Rd |only VizModules-0.4.0/VizModules/man/use_vizmodules_skills.Rd |only VizModules-0.4.0/VizModules/man/viz_select_input.Rd |only VizModules-0.4.0/VizModules/tests/testthat/test-dataFilter.R |only VizModules-0.4.0/VizModules/tests/testthat/test-figureBuilder.R | 7 VizModules-0.4.0/VizModules/tests/testthat/test-freqPlot.R |only VizModules-0.4.0/VizModules/tests/testthat/test-group_colors.R |only VizModules-0.4.0/VizModules/tests/testthat/test-heatmap.R |only VizModules-0.4.0/VizModules/tests/testthat/test-multiColorPicker.R | 205 ++-- VizModules-0.4.0/VizModules/tests/testthat/test-plot_mods.R | 149 ++ VizModules-0.4.0/VizModules/tests/testthat/test-plot_source_data.R |only VizModules-0.4.0/VizModules/tests/testthat/test-reactive_defaults.R |only VizModules-0.4.0/VizModules/tests/testthat/test-scatterPlot.R | 60 + VizModules-0.4.0/VizModules/tests/testthat/test-select_inputs.R |only VizModules-0.4.0/VizModules/tests/testthat/test-stat_helper.R | 80 + VizModules-0.4.0/VizModules/tests/testthat/test-yPlot.R |only VizModules-0.4.0/VizModules/vignettes/adding-a-new-module.Rmd | 214 ++++ VizModules-0.4.0/VizModules/vignettes/custom-model-lines.Rmd | 2 VizModules-0.4.0/VizModules/vignettes/custom-modules.Rmd | 43 VizModules-0.4.0/VizModules/vignettes/data-filtering.Rmd |only VizModules-0.4.0/VizModules/vignettes/defaults-and-hiding.Rmd | 59 + VizModules-0.4.0/VizModules/vignettes/quick-start.Rmd | 1 253 files changed, 6749 insertions(+), 2275 deletions(-)
Title: Interface to 'TexTra' from R
Description: A wrapper for the 'TexTra' API <https://mt-auto-minhon-mlt.ucri.jgn-x.jp/>,
a web service for translating texts between different languages.
'TexTra' API account is required to use the service.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Diff between textrar versions 0.8.0 dated 2024-04-23 and 0.9.0 dated 2026-08-28
textrar-0.8.0/textrar/tools |only textrar-0.9.0/textrar/DESCRIPTION | 20 - textrar-0.9.0/textrar/LICENSE | 4 textrar-0.9.0/textrar/MD5 | 40 +- textrar-0.9.0/textrar/NAMESPACE | 16 textrar-0.9.0/textrar/NEWS.md | 34 + textrar-0.9.0/textrar/R/textra.R | 518 ++++++++++++++++++---------- textrar-0.9.0/textrar/README.md | 27 + textrar-0.9.0/textrar/inst/WORDLIST | 2 textrar-0.9.0/textrar/man/base_url.Rd | 46 +- textrar-0.9.0/textrar/man/extract_result.Rd | 62 ++- textrar-0.9.0/textrar/man/gen_params.Rd | 89 +++- textrar-0.9.0/textrar/man/get_token.Rd | 66 ++- textrar-0.9.0/textrar/man/post_request.Rd | 62 +-- textrar-0.9.0/textrar/man/textra.Rd | 76 ++-- textrar-0.9.0/textrar/tests/testthat |only textrar-0.9.0/textrar/tests/testthat.R |only 17 files changed, 683 insertions(+), 379 deletions(-)
Title: Perpendicular Line Transects for Geosciences
Description: Toolset to create perpendicular profile graphs and swath
profiles. Method are based on coordinate rotation algorithm by
Schaeben et al. (2024) <doi:10.1002/mma.9823>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between geoprofiler versions 0.0.3 dated 2025-12-11 and 0.0.4 dated 2026-08-28
geoprofiler-0.0.3/geoprofiler/man/geoprofiler.Rd |only geoprofiler-0.0.3/geoprofiler/man/profile_coords.Rd |only geoprofiler-0.0.4/geoprofiler/DESCRIPTION | 8 geoprofiler-0.0.4/geoprofiler/MD5 | 46 geoprofiler-0.0.4/geoprofiler/NAMESPACE | 3 geoprofiler-0.0.4/geoprofiler/NEWS.md | 12 geoprofiler-0.0.4/geoprofiler/R/geoprofiler-package.R | 6 geoprofiler-0.0.4/geoprofiler/R/profile_points.R | 614 +++++----- geoprofiler-0.0.4/geoprofiler/R/project.R | 26 geoprofiler-0.0.4/geoprofiler/R/swath.R | 7 geoprofiler-0.0.4/geoprofiler/README.md | 12 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.R | 2 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.Rmd | 2 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.html | 16 geoprofiler-0.0.4/geoprofiler/inst/doc/B_Swath.html | 4 geoprofiler-0.0.4/geoprofiler/man/figures/README-plot-1.png |binary geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-deprecated.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-experimental.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-stable.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-superseded.svg |only geoprofiler-0.0.4/geoprofiler/man/geoprofiler-package.Rd |only geoprofiler-0.0.4/geoprofiler/man/profile-coords.Rd |only geoprofiler-0.0.4/geoprofiler/man/profile_azimuth.Rd | 19 geoprofiler-0.0.4/geoprofiler/man/profile_line.Rd | 30 geoprofiler-0.0.4/geoprofiler/man/profile_points.Rd | 7 geoprofiler-0.0.4/geoprofiler/man/swath_profile.Rd | 8 geoprofiler-0.0.4/geoprofiler/tests/testthat/test_projection.R | 6 geoprofiler-0.0.4/geoprofiler/vignettes/A_Distances.Rmd | 2 28 files changed, 495 insertions(+), 335 deletions(-)
Title: Qualification of R Software Installations
Description: Qualify R software installations using R Markdown as the foundation
for the Installation Qualification (IQ) and Operational Qualification (OQ) when
used in environments (such as regulated clinical trials) where such
processes may be required.
Author: Donnie Musgrove [aut, cre],
Graeme L. Hickey [aut] ,
Marc Schwartz [aut] ,
Alan Haynes [ctb],
Bryan Martin [ctb],
Medtronic Inc. [cph]
Maintainer: Donnie Musgrove <donniemusgrove@gmail.com>
Diff between rqualify versions 1.0.2 dated 2026-04-16 and 1.1.0 dated 2026-08-28
DESCRIPTION | 22 MD5 | 53 NAMESPACE | 1 NEWS.md | 25 R/check_validation_results.R |only R/platform.R |only R/render_validation.R |only R/rqualify.R | 175 -- R/setup_pandoc_env.R |only R/setup_tinytex_env.R |only R/setup_validation_dirs.R |only README.md | 14 build/vignette.rds |binary inst/doc/rqualify-cran.Rmd | 2 inst/doc/rqualify-cran.html | 42 inst/qualify_r/R-validation.Rmd | 1606 ++++++++++++------------- inst/qualify_r/R-validation.qmd |only inst/qualify_r/example_success/CMDFile1Out.txt | 186 +- inst/qualify_r/example_success/CMDFile2Out.txt | 90 - inst/qualify_r/example_success/CMDFile3Out.txt | 86 - inst/qualify_r/example_success/CMDFile4Out.txt | 86 - inst/qualify_r/example_success/CMDFile5Out.txt | 100 - inst/qualify_r/example_success/CMDFile6Out.txt | 268 ++-- inst/qualify_r/example_success/CMDFile7Out.txt | 818 ++++++------ man/rqualify.Rd | 20 tests/testthat.R | 24 tests/testthat/test-check_validation_results.R |only tests/testthat/test-render_validation.R |only tests/testthat/test-rqualify-orchestration.R |only tests/testthat/test-rqualify.R | 12 tests/testthat/test-setup_pandoc_env.R |only tests/testthat/test-setup_tinytex_env.R |only tests/testthat/test-setup_validation_dirs.R |only vignettes/rqualify-cran.Rmd | 2 34 files changed, 1789 insertions(+), 1843 deletions(-)
Title: Conjoint Analysis with Reliability Correction and Visualization
Description: Provides tools for analyzing data generated from conjoint survey experiments, a method widely used in the social sciences for studying multidimensional preferences. The package implements estimation of marginal means (MMs) and average marginal component effects (AMCEs), with corrections for measurement error. Methods include profile-level and choice-level estimators, bias correction using intra-respondent reliability (IRR), and visualization utilities. For details on the methodology, see Clayton, Horiuchi, Kaufman, King, and Komisarchik (2025) <https://gking.harvard.edu/conjointE>.
Author: Yusaku Horiuchi [aut, cre] ,
Aaron Kaufman [aut] ,
Gary King [aut]
Maintainer: Yusaku Horiuchi <yusaku.horiuchi@gmail.com>
Diff between projoint versions 1.1.3 dated 2026-07-31 and 1.1.4 dated 2026-08-28
DESCRIPTION | 8 - MD5 | 33 ++-- NEWS.md | 11 + R/predict_tau.R | 2 R/reshape_projoint.R | 22 ++ README.md | 15 + inst/CITATION | 2 inst/doc/analyze.R | 6 inst/doc/analyze.Rmd | 13 + inst/doc/analyze.html | 14 + inst/doc/read.R | 6 inst/doc/read.Rmd | 43 ++++- inst/doc/read.html | 167 ++++++++++++---------- man/reshape_projoint.Rd | 22 ++ tests/testthat/test-predict_tau.R |only tests/testthat/test-reshape-projoint-validation.R | 4 vignettes/analyze.Rmd | 13 + vignettes/read.Rmd | 43 ++++- 18 files changed, 291 insertions(+), 133 deletions(-)
Title: Logic Forest
Description: Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
Author: Bethany Wolf [aut],
Melica Nikahd [ctb, cre],
Andrew Gothard [ctb],
Madison Hyer [ctb]
Maintainer: Melica Nikahd <melica.nikahd@osumc.edu>
Diff between LogicForest versions 2.1.4 dated 2026-04-03 and 2.1.5 dated 2026-08-28
DESCRIPTION | 6 MD5 | 18 +- R/a.frame.logreg2.R | 1 R/logforest.R | 12 + R/predict.logforest.R | 326 +++++++++++++++++++++++------------------------ R/predict.logreg2.R | 2 R/print.LFprediction.R | 27 +++ R/print.logforest.R | 8 - man/logforest.Rd | 5 man/predict.logforest.Rd | 6 10 files changed, 225 insertions(+), 186 deletions(-)
Title: Causal Distillation Trees
Description: Causal Distillation Tree (CDT) is a novel machine learning method
for estimating interpretable subgroups with heterogeneous treatment effects.
CDT allows researchers to fit any machine learning model (or metalearner) to
estimate heterogeneous treatment effects for each individual, and then
"distills" these predicted heterogeneous treatment effects into
interpretable subgroups by fitting an ordinary decision tree to predict the
previously-estimated heterogeneous treatment effects. This package
provides tools to estimate causal distillation trees (CDT), as detailed in
Huang, Tang, and Kenney (2025) <doi:10.48550/arXiv.2502.07275>.
Author: Tiffany Tang [aut, cre] ,
Melody Huang [aut],
Ana Kenney [aut]
Maintainer: Tiffany Tang <ttang4@nd.edu>
Diff between causalDT versions 1.0.0 dated 2025-09-03 and 1.0.1 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md |only R/RcppExports.R | 17 +++++++++++++++++ R/diagnostics-stability.R | 10 ---------- R/plot.R | 4 ++++ R/student.R | 2 +- R/teacher.R | 3 ++- README.md | 9 ++++++++- man/jaccardSSI.Rd |only man/plot_jaccard.Rd | 4 ++++ src/stability.cpp | 11 ++++++++--- 13 files changed, 61 insertions(+), 30 deletions(-)
Title: American Travel Behavior and Access Datasets
Description: Subsets of data from the National Household Travel Survey 2017. It includes personal trips, mobility, demographic, and household information. It is suitable for data visualization, data wrangling, joining datasets, exploratory data analysis, group comparisons, simple linear regression, categorical data analysis, and data ethics discussion in data science and statistics classes.
Author: Shiya Cao [aut, cre],
Amber Zhang [ctb],
Anna Zhao [ctb],
Smith College [cph]
Maintainer: Shiya Cao <scao53@smith.edu>
Diff between tripaccess versions 0.1.0 dated 2026-07-04 and 0.2.0 dated 2026-08-28
DESCRIPTION | 13 +++++---- MD5 | 16 +++++------ NEWS.md | 6 +++- R/tripaccess.R | 3 +- README.md | 49 +++++++++++++++++++++++++----------- data/tripaccess.rda |binary inst/doc/house.html | 2 - man/tripaccess.Rd | 3 +- tests/testthat/_snaps/tripaccess.md | 2 - 9 files changed, 61 insertions(+), 33 deletions(-)
Title: Extended Dynamic Quantile Linear Models
Description: Bayesian quantile-regression routines for dynamic state-space
models and static regression under the extended asymmetric Laplace
(exAL) error distribution. The dynamic state-space models are extended
dynamic quantile linear models (exDQLMs). The package combines dynamic
exDQLM inference via Laplace-delta variational Bayes (LDVB), Markov
chain Monte Carlo (MCMC), and legacy importance-sampling variational Bayes
(ISVB) with static exAL regression via LDVB and MCMC, reduced asymmetric
Laplace/dynamic quantile linear model (AL/DQLM) paths through fixed
skewness, component builders for trend/seasonality/regression blocks,
static shrinkage priors including ridge, regularized horseshoe, and
'rhs_ns', evidence lower bound (ELBO) diagnostics, optional C++
accelerators, and posterior predictive synthesis across separately fitted
quantiles through 'quantileSynthesis()'. Dynamic exDQLM methods are
described in Barata et al. (2020) <doi:10.1214/21-AOAS1497>.
Author: Raquel Barata [aut, cre],
Raquel Prado [ths],
Bruno Sanso [ths],
Antonio Aguirre [aut]
Maintainer: Raquel Barata <raquel.a.barata@gmail.com>
Diff between exdqlm versions 1.1.0 dated 2026-07-09 and 1.1.1 dated 2026-08-28
DESCRIPTION | 6 MD5 | 109 ++++--- NEWS.md | 27 + R/compPlot.R | 9 R/exalStaticDiagnostics.R | 2 R/exalStaticFit_methods.R | 11 R/exalStaticLDVB.R | 289 ++++++++++++++++----- R/exalStaticMCMC.R | 143 ++++++++-- R/exal_inference_config.R | 17 + R/exal_sigmagam_structured.R |only R/exdqlm-package.R | 27 + R/exdqlmFit_methods.R | 27 + R/exdqlmForecast.R | 6 R/exdqlmForecastDiagnostics.R | 2 R/exdqlmForecast_methods.R | 8 R/exdqlmLDVB.R | 157 +++++++++-- R/exdqlmMCMC.R | 187 ++++++++++--- R/exdqlmPlot.R | 6 R/exdqlmTransferLDVB.R | 12 R/exdqlmTransferMCMC.R | 2 R/utils.R | 21 + R/zzz.R | 2 README.md | 20 + man/compPlot.Rd | 9 man/diagnostics.exalStaticFit.Rd | 1 man/diagnostics.exdqlmForecast.Rd | 2 man/exalStaticDiagnostics.Rd | 1 man/exalStaticLDVB.Rd | 35 +- man/exalStaticMCMC.Rd | 25 + man/exal_make_vb_sigmagam_control.Rd | 14 + man/exdqlm-package.Rd | 29 +- man/exdqlmForecast.Rd | 6 man/exdqlmForecastDiagnostics.Rd | 2 man/exdqlmLDVB.Rd | 28 +- man/exdqlmMCMC.Rd | 33 +- man/exdqlmPlot.Rd | 6 man/exdqlmTransferLDVB.Rd | 19 + man/exdqlmTransferMCMC.Rd | 19 - man/plot.exalStaticFit.Rd | 4 man/plot.exalStaticLDVB.Rd | 3 man/plot.exalStaticMCMC.Rd | 3 man/plot.exdqlmFit.Rd | 13 man/plot.exdqlmForecast.Rd | 2 man/plot.exdqlmLDVB.Rd | 2 man/predict.exdqlmFit.Rd | 8 man/print.exdqlmForecast.Rd | 2 man/print.exdqlmLDVB.Rd | 2 man/summary.exdqlmForecast.Rd | 2 man/summary.exdqlmLDVB.Rd | 2 src/sampling_truncnorm.cpp | 51 +-- src/sampling_utils.cpp | 286 ++++---------------- tests/testthat/test-exal-inference-config.R | 13 tests/testthat/test-exal-sigmagam-structured.R |only tests/testthat/test-exdqlm-transfer-mcmc.R | 5 tests/testthat/test-rng-repeatability.R |only tests/testthat/test-static-diagnostics.R | 12 tests/testthat/test-vb-mcmc-convergence-controls.R | 33 ++ 57 files changed, 1155 insertions(+), 607 deletions(-)
Title: Coarse-to-Fine Spatial and Spatio-Temporal Modeling
Description: Provides functions for coarse-to-fine spatial and spatio-temporal modeling, enabling fast prediction, regression, and uncertainty quantification for moderate to large datasets. For methodological details, see Murakami et al. (2026) <doi:10.1111/gean.70034> and related work on generalized linear, downscaling, and dynamic spatio-temporal extensions.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut],
Jose Luis Blanco-Claraco [ctb, cph] ),
Marius Muja [cph] ,
David G. Lowe [cph]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.2.0 dated 2026-08-04 and 0.2.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 36 - NAMESPACE | 44 - R/cf_dglm.R | 10 R/cf_glm.R | 15 R/cf_lm.R | 13 R/spCFmap.R | 2 R/sp_map_core.R | 286 +++++++-- inst/doc/spCF_glm.html | 79 ++ inst/doc/spCF_lm.html | 48 + inst/shiny/spCFmap/app.R | 48 + inst/shiny/spCFmap/example_downscale.csv | 714 ++++++++++++------------ inst/shiny/spCFmap/example_downscale.geojson | 434 +++++++------- inst/shiny/spCFmap/example_downscale_ReadMe.txt |only inst/shiny/spCFmap/example_point_ReadMe.txt |only man/cf_dglm.Rd | 9 tests/testthat/test-cf_glm.R | 16 tests/testthat/test-cf_lm.R | 20 tests/testthat/test-mapping.R | 103 +++ tests/testthat/test-spCFmap.R | 24 20 files changed, 1195 insertions(+), 714 deletions(-)
Title: Wavelet Analysis
Description: Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholding, block thresholding, linear,...) with applications to data compression, denoising/regression or clustering. The core of the code is a port of 'MATLAB' Wavelab toolbox written by D. Donoho, A. Maleki and M. Shahram.
Author: Fabien Navarro [aut, cre],
Christophe Chesneau [aut]
Maintainer: Fabien Navarro <fnavarro@math.cnrs.fr>
Diff between rwavelet versions 0.4.1 dated 2020-12-12 and 0.4.2 dated 2026-08-28
DESCRIPTION | 31 +- MD5 | 38 +-- NAMESPACE | 1 NEWS.md | 23 + R/BlockThresh2d.R |only R/HardThresh.R | 3 R/SUREThresh.R | 2 R/SoftThresh.R | 3 R/WaveFEX.R |only R/cameraman.R |only R/lena.R |only build/vignette.rds |binary data/cameraman.rda |only data/lena.rda |only inst/doc/rwaveletvignette.R | 90 +++---- inst/doc/rwaveletvignette.html | 500 ++++++++++++++++++++--------------------- man/BlockThresh2d.Rd |only man/HardThresh.Rd | 3 man/RaphNMR.Rd | 4 man/SLphantom.Rd | 4 man/SUREThresh.Rd | 2 man/SoftThresh.Rd | 3 man/WaveFEX.Rd |only man/cameraman.Rd |only man/lena.Rd |only 25 files changed, 372 insertions(+), 335 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 1.1.0.3 dated 2026-04-13 and 1.1.0.4 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 5 +++-- man/print.MVL_INDEX.Rd |only src/libMVL_sort.cc | 1 + 4 files changed, 7 insertions(+), 5 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoglu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb] ,
Tuomas Borman [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.7.0 dated 2025-10-28 and 1.7.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 104 +- NAMESPACE | 46 - NEWS.md | 7 R/checks.R | 165 +++- R/compare_models.R | 38 - R/corr_feats.R | 49 - R/cross_val.R | 60 + R/feature_importance.R | 95 +- R/hyperparameters.R | 11 R/partition.R | 30 R/performance.R | 207 +++-- R/plot.R | 108 +- R/preprocess.R | 393 ++++++---- R/reexports.R | 4 R/run_ml.R | 129 ++- R/train.R | 21 README.md | 44 + build/partial.rdb |binary build/vignette.rds |binary inst/container |only inst/doc/introduction.Rmd | 26 inst/doc/introduction.html | 5 inst/doc/paper.Rmd | 2 inst/doc/paper.html | 143 +-- man/calc_perf_bootstrap_split.Rd | 2 man/calc_perf_metrics.Rd | 2 man/check_all.Rd | 2 man/define_cv.Rd | 2 man/find_permuted_perf_metric.Rd | 2 man/get_feature_importance.Rd | 2 man/get_performance_tbl.Rd | 2 man/mikropml-package.Rd | 1 man/preprocess_data.Rd | 2 man/reexports.Rd | 6 man/run_ml.Rd | 2 tests/testthat/fixtures/predict.R | 13 tests/testthat/fixtures/train-multi.R | 17 tests/testthat/test-checks.R | 137 ++- tests/testthat/test-compare_models.R | 14 tests/testthat/test-corr_feats.R | 143 ++- tests/testthat/test-cross_val.R | 223 +++++- tests/testthat/test-feature_importance.R | 147 +++ tests/testthat/test-hyperparameters.R | 215 ++++- tests/testthat/test-partition.R | 35 tests/testthat/test-performance.R | 136 ++- tests/testthat/test-plot.R | 337 ++++++--- tests/testthat/test-preprocess.R | 1150 +++++++++++++++++++++---------- tests/testthat/test-run_ml.R | 281 ++++++- tests/testthat/test-train.R | 89 +- vignettes/introduction.Rmd | 26 vignettes/paper.Rmd | 2 vignettes/paper.bib | 2 53 files changed, 3352 insertions(+), 1335 deletions(-)
Title: Download Insee French Institute of Statistics Open Data
Description: A wrapper for the French Institute of Statistics (Insee) API
Melodi <https://catalogue-donnees.insee.fr>. Download, search, filter data
and metadata from open data statistical public datasets,
in french or in english.
Author: Cedric Bobinec [aut, cre],
Christophe Goudeau [aut],
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Cedric Bobinec <cedric.bobinec@insee.fr>
Diff between melodi versions 1.1.0 dated 2026-07-29 and 1.1.2 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 6 +++++ R/get_all_data.R | 6 ++++- README.md | 3 +- tests/testthat/test-get_all_data.R | 39 ++++++++++++++++++++++++++++++++----- 6 files changed, 55 insertions(+), 15 deletions(-)
Title: Flexible Graphs for Analysis of Financial Data and Time Series
Description: Flexible wrappers around R graphics modules 'dygraphs' <https://dygraphs.com/> and 'ggplot2' <https://ggplot2.tidyverse.org/> to visualize data commonly found in Financial Studies, with an emphasis on time series.
Interactive time series plots include multiple options for incorporating external data such as forecasts and events. Other static plots useful for time
series data include an intuitive and generic scatter plotter, a boxplot generator suitable for multiple time series, and event study plotters for time series analysis
around sets of dates.
Author: Derek Holmes [aut, cre, cph]
Maintainer: Derek Holmes <derek@derekholmes.com>
Diff between FinanceGraphs versions 0.9.2 dated 2026-08-21 and 0.9.21 dated 2026-08-28
DESCRIPTION | 17 +++--- MD5 | 28 +++++----- NAMESPACE | 1 NEWS.md | 6 ++ R/event_helpers.R | 7 +- R/seas_ggplot.R | 4 - R/ts_ggplot.R | 12 ++-- data/eqtypx.rda |binary data/eqtypx_melt.rda |binary data/eqtyrtn.rda |binary data/example_fcst_set.rda |binary data/nomfxdta.rda |binary data/yc_CMSUST.rda |binary inst/doc/Time-Series-dygraph.html | 88 +++++++++++++++++----------------- inst/doc/Time-Series-scatterplot.html | 12 +--- 15 files changed, 87 insertions(+), 88 deletions(-)
Title: Guarded Resampling Workflows for Leakage-Aware Machine Learning
in R
Description: Provides a guarded resampling workflow for training and evaluating machine-learning models.
When the guarded resampling path is used, preprocessing and model fitting are re-estimated within
each resampling split to reduce leakage risk. Supports multiple resampling schemes, integrates
with established engines in the 'tidymodels' ecosystem, and aims to improve evaluation reliability by
coordinating preprocessing, fitting, and evaluation within supported workflows. Offers a lightweight
AutoML-style workflow by automating model training, resampling, and tuning across multiple algorithms,
while keeping evaluation design explicit and user-controlled.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.7.9 dated 2026-08-19 and 0.7.10 dated 2026-08-28
DESCRIPTION | 20 - MD5 | 52 +- NAMESPACE | 1 NEWS.md | 54 +++ R/engine_helpers.R | 1 R/evaluate_models.R | 2 R/fastml.R | 163 +++++++-- R/params_helpers.R | 263 ++++++++++++--- R/process_model.R | 23 + R/process_model_helpers.R | 47 ++ R/resampling_utils.R | 70 ++++ R/summary.fastml.R | 69 +++ R/train_models.R | 452 +++++++++++++++++++++----- R/tuning_config.R | 12 README.md | 4 man/fastml.Rd | 78 +++- man/summary.fastml.Rd | 9 man/train_models.Rd | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-algorithm-registry.R |only tests/testthat/test-bootstrap-ci-default.R |only tests/testthat/test-bugfixes-round2.R | 59 +-- tests/testthat/test-holdout-splitting.R | 73 ++++ tests/testthat/test-interface-hints.R |only tests/testthat/test-leakage-not-expressible.R |only tests/testthat/test-metric-set-prob.R |only tests/testthat/test-nested-cv-tuning.R |only tests/testthat/test-prediction-orientation.R |only tests/testthat/test-sanitize.R | 35 +- tests/testthat/test-survival-registry.R |only tests/testthat/test-tuning-grid-scale.R |only tests/testthat/test-xgboost-aft-bounds.R |only 32 files changed, 1229 insertions(+), 268 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<https://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored as JSON in a
database ('PostgreSQL', 'SQLite', 'DuckDB', 'MongoDB' or 'MariaDB';
via package 'nodbi'). Protocols, statistical analysis plans, informed
consent sheets and other documents in registers associated with trials
can also be downloaded. Other functions implement trial analysis
concepts canonically across registers, identify deduplicated records
across registers, easily find and extract variables (fields) of interest
e [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.26.2 dated 2026-07-12 and 1.26.3 dated 2026-08-28
DESCRIPTION | 39 +-- MD5 | 82 +++---- NAMESPACE | 196 ++++++++++-------- NEWS.md | 16 + R/ctrFindActiveSubstanceSynonyms.R | 196 ++++++++++++++---- R/ctrLoadQueryIntoDbEuctr.R | 62 ++--- R/ctrdata-package.R | 5 R/ctrdata-registers.R | 14 - R/dbFindIdsUniqueTrials.R | 11 - R/f_likelyPlatformTrial.R | 4 R/f_primaryEndpointResults.R | 24 +- R/f_sampleSize.R | 21 + R/f_trialObjectives.R | 2 R/util_functions.R | 175 +++++----------- R/zzz.R | 8 README.md | 98 +++++---- inst/WORDLIST | 4 inst/doc/ctrdata_install.R | 4 inst/doc/ctrdata_install.Rmd | 7 inst/doc/ctrdata_install.html | 21 + inst/doc/ctrdata_retrieve.html | 2 inst/doc/ctrdata_summarise.html | 2 inst/extdata/demo.sqlite |binary inst/tinytest/ctrdata_ctgov2.R | 13 - inst/tinytest/ctrdata_euctr.R | 41 --- inst/tinytest/more_test_ctrdata_duckdb_ctis.R | 3 inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 3 inst/tinytest/more_test_ctrdata_duckdb_isrctn.R | 3 inst/tinytest/setup_ctrdata.R | 10 inst/tinytest/test_ctrdata_duckdb_ctgov2.R | 3 inst/tinytest/test_ctrdata_function_activesubstance.R | 4 inst/tinytest/test_ctrdata_function_trial-concepts.R | 21 + inst/tinytest/test_ctrdata_function_various.R | 69 ++++-- inst/tinytest/test_ctrdata_mariadb_ctgov2.R |only inst/tinytest/test_ctrdata_mariadb_remote_ctgov2.R |only man/ctrDb.Rd | 3 man/ctrFindActiveSubstanceSynonyms.Rd | 19 - man/ctrdata-package.Rd | 2 man/ctrdata-registers.Rd | 14 - man/ctrdata.Rd | 5 man/f.likelyPlatformTrial.Rd | 4 man/f.sampleSize.Rd | 6 vignettes/ctrdata_install.Rmd | 7 43 files changed, 689 insertions(+), 534 deletions(-)
Title: Functions for Statistics Classes at Carleton College
Description: Includes commands for bootstrapping and permutation tests, a
command for created grouped bar plots, and a demo of the
quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara [aut],
Adam Loy [aut, cre]
Maintainer: Adam Loy <aloy@carleton.edu>
Diff between CarletonStats versions 2.2 dated 2023-08-22 and 2.3 dated 2026-08-28
DESCRIPTION | 16 MD5 | 111 +++--- NEWS.md | 10 R/Data.R | 20 + R/anovaSummarized.R | 86 ++-- R/boot.R | 33 + R/boot.default.R | 159 +++++--- R/boot.formula.R | 32 - R/bootCor.R | 10 R/bootCor.default.R | 101 ++--- R/bootCor.formula.R | 49 +- R/bootPaired.R | 8 R/bootPaired.default.R | 97 ++--- R/bootPaired.formula.R | 51 +- R/bootSlope.R | 8 R/bootSlope.default.R | 77 ++-- R/bootSlope.formula.R | 49 +- R/confIntDemo.R | 141 ++++--- R/confint.R | 2 R/corDemo.R | 48 +- R/groupedBar.R | 10 R/groupedBar.default.R | 160 ++++---- R/groupedBar.formula.R | 53 +- R/missingLevel.R | 24 - R/permTest.R | 26 - R/permTest.default.R | 131 +++---- R/permTest.formula.R | 24 - R/permTestAnova.R | 13 R/permTestAnova.default.R | 107 ++--- R/permTestAnova.formula.R | 26 - R/permTestCor.R | 8 R/permTestCor.default.R | 123 +++--- R/permTestCor.formula.R | 50 +- R/permTestPaired.R | 8 R/permTestPaired.default.R | 142 +++---- R/permTestPaired.formula.R | 50 +- R/permTestSlope.R | 10 R/permTestSlope.default.R | 115 ++---- R/permTestSlope.formula.R | 50 +- R/plot.R | 94 +++-- R/print.R | 198 +++++++--- R/pvalue.R | 13 R/qqPlotDemo.R | 110 ++++-- R/stemPlot.R | 10 R/stemPlot.default.R | 65 +-- R/stemPlot.formula.R | 50 +- R/summary.R | 43 +- R/utils-formula.R |only README.md | 1 data/penguin_survival.rda |only man/CarletonStats-package.Rd | 1 man/boot.Rd | 27 + man/bootSlope.Rd | 2 man/penguin_survival.Rd |only man/permTest.Rd | 19 - man/permTestSlope.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/_snaps |only tests/testthat/test-Carl.R | 785 ++++++++++++++++++++++++++++++++++++++++++- 59 files changed, 2359 insertions(+), 1299 deletions(-)
Title: Create and Install Custom 'RStudio' Themes
Description: Create, convert and install custom 'RStudio' editor themes
from 'Visual Studio Code', 'Positron' and 'TextMate' theme files.
Convert themes between 'TextMate', 'Visual Studio Code' and 'Positron'
formats and install bundled ports of popular themes for use in
'RStudio'. Inspect theme files as tabular data for custom conversion
workflows.
Author: Diego Hernangomez [aut, cre, cph] ,
Garrick Aden-Buie [cph] function)
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rstudiothemes versions 1.1.2 dated 2026-06-19 and 1.2.0 dated 2026-08-28
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rstudiothemes-1.2.0/rstudiothemes/tests/testthat/_snaps/utils.md | 38 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/helper.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-tm-to-vs.R | 114 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-to-rs.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-vs-to-tm.R | 173 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-generate-uuid.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-on-rstudio.R | 20 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-read-tm-theme.R | 65 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-read-vs-theme.R | 55 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-rstudiothemes-actions.R | 399 - rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-utils.R | 90 rstudiothemes-1.2.0/rstudiothemes/vignettes/rstudiothemes.qmd | 16 96 files changed, 6061 insertions(+), 6683 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Description: Provides nonparametric procedures for the analysis of longitudinal data in factorial experiments. The package implements hypothesis tests on marginal distribution functions and unweighted relative marginal effects. It supports arbitrary crossed factorial designs with longitudinal or repeated-measures factors, missing observations, dependent replicates, rank- and pseudo-rank-based inference, Wald-type and ANOVA-type statistics, multiple contrast tests, and simultaneous confidence intervals.
Author: Frank Konietschke [aut, cre],
Kimihiro Noguchi [ctb] ,
Mahbub Latif [ctb] ,
Karthinathan Thangavelu [ctb] ,
Yulia R. Gel [ctb] ,
Edgar Brunner [ctb]
Maintainer: Frank Konietschke <frank.konietschke@charite.de>
Diff between nparLD versions 2.3.0 dated 2026-08-22 and 2.3.1 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NEWS.md | 10 ++++++++- R/Statistics.R | 4 --- R/Utility.R | 18 ++++++++++++----- inst/doc/nparLD.html | 42 ++++++++++++++++++++--------------------- tests/testthat/test-examples.R | 31 ++++++++++++++++++++++++++++++ 7 files changed, 84 insertions(+), 39 deletions(-)
Title: Bayesian Super Imposition by Translation and Rotation Growth
Curve Analysis
Description: The Super Imposition by Translation and Rotation (SITAR) model
is a shape-invariant nonlinear mixed effect model that fits a natural cubic
spline mean curve to the growth data and aligns individual-specific growth
curves to the underlying mean curve via a set of random effects (see Cole,
2010 <doi:10.1093/ije/dyq115> for details). The non-Bayesian version of the
SITAR model can be fit by using the already available R package 'sitar'. Unlike
the 'sitar' package which allows modelling of a single outcome only, the 'bsitar'
package offers great flexibility in fitting models of varying complexities,
including joint modelling of multiple outcomes such as height and weight
(multivariate model). Additionally, the 'bsitar' package allows for the simultaneous
analysis of an outcome separately for subgroups defined by a factor variable such
as gender. This is achieved by fitting separate models for each subgroup
(for example males and females for gender variable). An advantage of this appr [...truncated...]
Author: Satpal Sandhu [aut, cre, cph]
Maintainer: Satpal Sandhu <satpal.sandhu@bristol.ac.uk>
Diff between bsitar versions 0.3.3 dated 2026-03-25 and 0.4.0 dated 2026-08-28
bsitar-0.3.3/bsitar/R/check_and_get_object.R |only bsitar-0.3.3/bsitar/tests/testthat/test-bsitar-rcs-settings.R |only bsitar-0.4.0/bsitar/DESCRIPTION | 46 bsitar-0.4.0/bsitar/MD5 | 200 bsitar-0.4.0/bsitar/NAMESPACE | 26 bsitar-0.4.0/bsitar/NEWS.md | 439 bsitar-0.4.0/bsitar/R/add_model_criterion.R | 45 bsitar-0.4.0/bsitar/R/bsitar.R | 5308 +++------ bsitar-0.4.0/bsitar/R/compare_models.R |only bsitar-0.4.0/bsitar/R/expose_model_functions.R | 91 bsitar-0.4.0/bsitar/R/fitted_draws.R | 177 bsitar-0.4.0/bsitar/R/getNsObject.R |only bsitar-0.4.0/bsitar/R/get_comparisons.R | 758 - bsitar-0.4.0/bsitar/R/get_growthparameters.R | 783 - bsitar-0.4.0/bsitar/R/get_model_criterion.R |only bsitar-0.4.0/bsitar/R/get_predictions.R | 661 - bsitar-0.4.0/bsitar/R/growthparameters.R | 223 bsitar-0.4.0/bsitar/R/hypothesis_test.R | 274 bsitar-0.4.0/bsitar/R/loo_validation.R | 34 bsitar-0.4.0/bsitar/R/modelbased_growthparameters.R | 441 bsitar-0.4.0/bsitar/R/optimize_model.R | 334 bsitar-0.4.0/bsitar/R/plot_caterpillar.R |only bsitar-0.4.0/bsitar/R/plot_conditional_effects.R | 135 bsitar-0.4.0/bsitar/R/plot_curves.R | 937 + bsitar-0.4.0/bsitar/R/plot_diagnostics.R |only bsitar-0.4.0/bsitar/R/plot_ppc.R | 148 bsitar-0.4.0/bsitar/R/predict_draws.R | 212 bsitar-0.4.0/bsitar/R/prior_conflict.R |only bsitar-0.4.0/bsitar/R/prior_sensitivity.R |only bsitar-0.4.0/bsitar/R/prior_table.R |only bsitar-0.4.0/bsitar/R/update_model.R | 205 bsitar-0.4.0/bsitar/R/utils-helper-1.R | 4933 ++++---- bsitar-0.4.0/bsitar/R/utils-helper-10.R | 750 - 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bsitar-0.4.0/bsitar/R/utils-helper-5.R | 5612 ++++------ bsitar-0.4.0/bsitar/R/utils-helper-6.R | 377 bsitar-0.4.0/bsitar/R/utils-helper-7.R | 1234 -- bsitar-0.4.0/bsitar/R/utils-helper-8.R | 244 bsitar-0.4.0/bsitar/R/utils-helper-9.R | 833 - bsitar-0.4.0/bsitar/R/zzz.R | 4 bsitar-0.4.0/bsitar/build/partial.rdb |binary bsitar-0.4.0/bsitar/build/vignette.rds |binary bsitar-0.4.0/bsitar/data/berkeley_exdata.rda |binary bsitar-0.4.0/bsitar/data/berkeley_exfit.rda |binary bsitar-0.4.0/bsitar/inst/REFERENCES.bib | 10 bsitar-0.4.0/bsitar/inst/WORDLIST | 12 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.Rmd | 34 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.html | 52 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.R | 2 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.Rmd | 11 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.html | 162 bsitar-0.4.0/bsitar/man/add_model_criterion.Rd | 27 bsitar-0.4.0/bsitar/man/bsitar.Rd | 2264 ++-- bsitar-0.4.0/bsitar/man/compare_models.Rd |only bsitar-0.4.0/bsitar/man/fitted_draws.Rd | 67 bsitar-0.4.0/bsitar/man/getNsObject.Rd | 2 bsitar-0.4.0/bsitar/man/get_comparisons.Rd | 112 bsitar-0.4.0/bsitar/man/get_growthparameters.Rd | 143 bsitar-0.4.0/bsitar/man/get_model_criterion.Rd |only bsitar-0.4.0/bsitar/man/get_predictions.Rd | 119 bsitar-0.4.0/bsitar/man/growthparameters.Rd | 79 bsitar-0.4.0/bsitar/man/hypothesis_test.Rd | 63 bsitar-0.4.0/bsitar/man/is.bgmfit.Rd | 7 bsitar-0.4.0/bsitar/man/loo_validation.Rd | 14 bsitar-0.4.0/bsitar/man/modelbased_growthparameters.Rd | 108 bsitar-0.4.0/bsitar/man/optimize_model.Rd | 17 bsitar-0.4.0/bsitar/man/plot_caterpillar.Rd |only bsitar-0.4.0/bsitar/man/plot_conditional_effects.Rd | 77 bsitar-0.4.0/bsitar/man/plot_curves.Rd | 203 bsitar-0.4.0/bsitar/man/plot_diagnostics.Rd |only bsitar-0.4.0/bsitar/man/plot_ppc.Rd | 132 bsitar-0.4.0/bsitar/man/predict_draws.Rd | 67 bsitar-0.4.0/bsitar/man/prior_conflict.Rd |only bsitar-0.4.0/bsitar/man/prior_sensitivity.Rd |only bsitar-0.4.0/bsitar/man/prior_table.Rd |only bsitar-0.4.0/bsitar/man/update_model.Rd | 34 bsitar-0.4.0/bsitar/tests/testthat/helper-data.R | 684 + bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-bsp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-isp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-msp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-nsk-settings.R | 6 bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-nsp-settings.R | 11 bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-autocor_all.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-corefuns-uvar.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-init_prior.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-knots_selection.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-parameterization_cp.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-plot_curves.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-plot_diagnostics.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-qr.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-vf_all.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-xyadj-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-hypothesis_test.R | 89 bsitar-0.4.0/bsitar/tests/testthat/test-prior_conflict.R |only bsitar-0.4.0/bsitar/tests/testthat/test-prior_sensitivity.R |only bsitar-0.4.0/bsitar/vignettes/Bayesian_SITAR_model_An_Introduction.Rmd | 34 bsitar-0.4.0/bsitar/vignettes/Bayesian_SITAR_model_fit.Rmd | 11 118 files changed, 16178 insertions(+), 25149 deletions(-)
Title: Interface to 'episensr' for Sensitivity Analysis of
Epidemiological Results
Description: API for using 'episensr', Basic sensitivity analysis of the
observed relative risks adjusting for unmeasured confounding and
misclassification of the exposure/outcome, or both. See
<https://cran.r-project.org/package=episensr>.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <cheval@zaclys.net>
Diff between apisensr versions 2.0.0 dated 2025-05-16 and 2.0.1 dated 2026-08-28
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++------------ NAMESPACE | 60 +++++++++++++++++++++++++++------------------- NEWS.md | 6 +++- R/mod_analysis.R | 8 +++--- R/mod_multi.R | 2 - R/mod_notable.R | 20 +++++++-------- R/mod_prob.R | 4 +-- README.md | 15 +++++------ build/vignette.rds |binary inst/CITATION | 6 ++-- inst/app/www/functions.md | 20 +++++++-------- inst/doc/apisensr.Rmd | 20 +++++++-------- inst/doc/apisensr.html | 20 +++++++-------- man/apisensr-package.Rd | 5 +++ vignettes/apisensr.Rmd | 20 +++++++-------- 16 files changed, 134 insertions(+), 114 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Twenty-seven nearest-neighbor parameter sets are provided, covering DNA, RNA and RNA/DNA hybrid duplexes. These include se [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.8 dated 2026-07-29 and 1.0.9 dated 2026-08-28
DESCRIPTION | 10 - MD5 | 21 +- NEWS.md |only R/sysdata.rda |binary R/tm_calculate.R | 146 +++++++++++++++--- R/tm_nn.R | 209 +++++++++++++++++++++++--- R/zzz.R | 287 ++++++++++++++++++++++++++++++++++++- README.md | 72 +++++++++ inst/doc/genome_wide_tm_ecoli.html | 46 ++--- man/TmCalculator-package.Rd | 2 man/tm_calculate.Rd | 131 +++++++++++++--- man/tm_nn.Rd | 132 +++++++++++++++-- 12 files changed, 921 insertions(+), 135 deletions(-)
Title: Reality Check and Predictive Ability Tests for Forecast
Evaluation
Description: Implements a comprehensive suite of statistical tests for
evaluating the accuracy of forecasting models against a benchmark.
The package is grounded in the reality check framework of White
(2000) <doi:10.1111/1468-0262.00152>, extended by Hansen (2005)
<doi:10.1198/073500105000000063> for Superior Predictive Ability
(SPA), Giacomini & White (2006) <doi:10.1111/j.1468-0262.2006.00718.x>
for Conditional Predictive Ability (CPA), and Corradi & Swanson
(2006) <doi:10.1016/j.jeconom.2005.07.026> for predictive density
evaluation via the Kullback-Leibler Information Criterion (KLIC) and
ZP Quantile Loss test, the Continuous Ranked Probability
Score (CRPS) (Gneiting & Raftery, 2007)
<doi:10.1198/016214506000001437>, coverage tests (Kupiec, 1995)
<doi:10.3905/jod.1995.407942>, HAC covariance estimation (Newey &
West, 1987) <doi:10.2307/1913610>, and Moving Block Bootstrap
resampling (Kunsch, 1989) <doi:10.1214/aos/1176347265>.
Author: Joanna Jedrzejewska [aut, cre] ,
Krzysztof Drachal [ctb]
Maintainer: Joanna Jedrzejewska <j.jedrzejewska3@uw.edu.pl>
Diff between RCtest versions 1.1 dated 2026-08-20 and 1.2 dated 2026-08-28
DESCRIPTION | 7 ++-- MD5 | 19 ++++++++--- NEWS.md | 50 ++++++++++++++++++++++-------- R/analysis_helpers.R | 80 ++++++++++++++++++++++++++++++++++--------------- R/workflow_functions.R | 48 ++++++++++++++++++++--------- man/compute_kupiec.Rd | 70 +++++++++++++++++++++++++++++++----------- tests |only 7 files changed, 197 insertions(+), 77 deletions(-)
Title: Project Risk Analysis
Description: Data analysis for Project Risk Management via the Second Moment Method,
Monte Carlo Simulation, Contingency Analysis, Sensitivity Analysis, Earned Value Management,
Learning Curves, Bayesian Methods, and more.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
This is a re-admission after prior archival of version 0.4.0 dated 2026-04-08
Diff between PRA versions 0.4.0 dated 2026-04-08 and 0.6.0 dated 2026-08-28
PRA-0.4.0/PRA/R/app.R |only PRA-0.4.0/PRA/R/chat.R |only PRA-0.4.0/PRA/R/rag.R |only PRA-0.4.0/PRA/build/vignette.rds |only PRA-0.4.0/PRA/inst/doc |only PRA-0.4.0/PRA/inst/eval |only PRA-0.4.0/PRA/inst/knowledge |only PRA-0.4.0/PRA/man/add_documents.Rd |only PRA-0.4.0/PRA/man/build_knowledge_base.Rd |only PRA-0.4.0/PRA/man/execute_command.Rd |only PRA-0.4.0/PRA/man/format_command_help.Rd |only PRA-0.4.0/PRA/man/format_help_overview.Rd |only PRA-0.4.0/PRA/man/get_ollama_models.Rd |only PRA-0.4.0/PRA/man/parse_command_args.Rd |only PRA-0.4.0/PRA/man/pra_app.Rd |only PRA-0.4.0/PRA/man/pra_chat.Rd |only PRA-0.4.0/PRA/man/pra_command_registry.Rd |only PRA-0.4.0/PRA/man/pra_shiny_app.Rd |only PRA-0.4.0/PRA/man/pra_system_prompt.Rd |only PRA-0.4.0/PRA/man/retrieve_context.Rd |only PRA-0.4.0/PRA/man/route_input.Rd |only PRA-0.4.0/PRA/tests/testthat/test-app.R |only PRA-0.4.0/PRA/tests/testthat/test-chat.R |only PRA-0.4.0/PRA/tests/testthat/test-rag.R |only PRA-0.4.0/PRA/vignettes |only PRA-0.6.0/PRA/DESCRIPTION | 16 PRA-0.6.0/PRA/LICENSE |only PRA-0.6.0/PRA/MD5 | 145 -- PRA-0.6.0/PRA/NAMESPACE | 15 PRA-0.6.0/PRA/NEWS.md | 41 PRA-0.6.0/PRA/R/cormat.R | 60 - PRA-0.6.0/PRA/R/data.R |only PRA-0.6.0/PRA/R/dsm.R | 27 PRA-0.6.0/PRA/R/inference.R | 32 PRA-0.6.0/PRA/R/learning.R | 97 + PRA-0.6.0/PRA/R/mcp.R |only PRA-0.6.0/PRA/R/mcs.R | 88 - PRA-0.6.0/PRA/R/network.R |only PRA-0.6.0/PRA/R/sensitivity.R | 35 PRA-0.6.0/PRA/R/sigmoidal.R | 11 PRA-0.6.0/PRA/R/smm.R | 13 PRA-0.6.0/PRA/R/tools.R | 975 ----------------- PRA-0.6.0/PRA/README.md | 140 -- PRA-0.6.0/PRA/build/partial.rdb |only PRA-0.6.0/PRA/data |only PRA-0.6.0/PRA/inst/CITATION | 12 PRA-0.6.0/PRA/inst/skills |only PRA-0.6.0/PRA/man/building_project.Rd |only PRA-0.6.0/PRA/man/cor_matrix.Rd | 14 PRA-0.6.0/PRA/man/cost_pdf.Rd | 8 PRA-0.6.0/PRA/man/cost_post_pdf.Rd | 22 PRA-0.6.0/PRA/man/figures/README-unnamed-chunk-5-1.png |binary PRA-0.6.0/PRA/man/grandparent_dsm.Rd | 21 PRA-0.6.0/PRA/man/mcs.Rd | 15 PRA-0.6.0/PRA/man/parent_dsm.Rd | 6 PRA-0.6.0/PRA/man/pra_mcp_server.Rd |only PRA-0.6.0/PRA/man/pra_tools.Rd | 9 PRA-0.6.0/PRA/man/prob_net.Rd |only PRA-0.6.0/PRA/man/prob_net_learn.Rd |only PRA-0.6.0/PRA/man/prob_net_sim.Rd |only PRA-0.6.0/PRA/man/prob_net_update.Rd |only PRA-0.6.0/PRA/man/risk_post_prob.Rd | 7 PRA-0.6.0/PRA/man/risk_prob.Rd | 8 PRA-0.6.0/PRA/man/sensitivity.Rd | 5 PRA-0.6.0/PRA/tests/testthat/Rplots.pdf |binary PRA-0.6.0/PRA/tests/testthat/test-cormat.R | 39 PRA-0.6.0/PRA/tests/testthat/test-data.R |only PRA-0.6.0/PRA/tests/testthat/test-inference.R | 29 PRA-0.6.0/PRA/tests/testthat/test-learning.R | 48 PRA-0.6.0/PRA/tests/testthat/test-mcp.R |only PRA-0.6.0/PRA/tests/testthat/test-mcs.R | 39 PRA-0.6.0/PRA/tests/testthat/test-network.R |only PRA-0.6.0/PRA/tests/testthat/test-sensitivity.R | 13 PRA-0.6.0/PRA/tests/testthat/test-sigmoidal.R | 2 PRA-0.6.0/PRA/tests/testthat/test-tools.R | 561 --------- 75 files changed, 723 insertions(+), 1830 deletions(-)
Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
Description: Many tools for making, manipulating, and modifying many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Tomas Diviak [ctb],
Henrique Sposito [ctb] ,
Christian Steglich [ctb],
Alvaro Uzaheta [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 2.2.3 dated 2026-07-30 and 2.3.1 dated 2026-08-28
manynet-2.2.3/manynet/R/manip_global.R |only manynet-2.2.3/manynet/R/modif_correlation.R |only manynet-2.2.3/manynet/man/manip_global.Rd |only manynet-2.2.3/manynet/man/modif_correlation.Rd |only manynet-2.2.3/manynet/tests/testthat/test-manip_correlation.R |only manynet-2.3.1/manynet/DESCRIPTION | 12 manynet-2.3.1/manynet/MD5 | 269 - manynet-2.3.1/manynet/NAMESPACE | 431 +- manynet-2.3.1/manynet/NEWS.md | 292 + manynet-2.3.1/manynet/R/class_describe.R | 131 manynet-2.3.1/manynet/R/class_marks.R | 16 manynet-2.3.1/manynet/R/class_measures.R | 81 manynet-2.3.1/manynet/R/class_missing.R |only manynet-2.3.1/manynet/R/class_networks.R | 10 manynet-2.3.1/manynet/R/class_stocnet.R | 183 - manynet-2.3.1/manynet/R/class_validate.R | 52 manynet-2.3.1/manynet/R/coerce_graph.R | 388 +- manynet-2.3.1/manynet/R/coerce_list.R | 329 + manynet-2.3.1/manynet/R/data_fict.R | 29 manynet-2.3.1/manynet/R/data_irps.R | 390 +- manynet-2.3.1/manynet/R/data_ison.R | 754 +++- manynet-2.3.1/manynet/R/make_collect.R | 10 manynet-2.3.1/manynet/R/make_create.R | 20 manynet-2.3.1/manynet/R/make_read.R | 815 ++++ manynet-2.3.1/manynet/R/manip_changes.R | 58 manynet-2.3.1/manynet/R/manip_globals.R |only manynet-2.3.1/manynet/R/manip_info.R | 284 + manynet-2.3.1/manynet/R/manip_nodes.R | 170 manynet-2.3.1/manynet/R/manip_ties.R | 26 manynet-2.3.1/manynet/R/manynet-data.R | 7 manynet-2.3.1/manynet/R/manynet-defunct.R | 69 manynet-2.3.1/manynet/R/manynet-glossary.R | 14 manynet-2.3.1/manynet/R/manynet-utils.R | 7 manynet-2.3.1/manynet/R/mark_changes.R | 130 manynet-2.3.1/manynet/R/mark_classes.R | 2 manynet-2.3.1/manynet/R/mark_features.R | 2 manynet-2.3.1/manynet/R/mark_format.R | 149 manynet-2.3.1/manynet/R/measure_attributes.R | 163 manynet-2.3.1/manynet/R/measure_properties.R | 193 - manynet-2.3.1/manynet/R/modif_backbone.R |only manynet-2.3.1/manynet/R/modif_direction.R | 137 manynet-2.3.1/manynet/R/modif_from.R | 144 manynet-2.3.1/manynet/R/modif_levels.R | 10 manynet-2.3.1/manynet/R/modif_miss.R | 761 ++++ manynet-2.3.1/manynet/R/modif_motifs.R | 84 manynet-2.3.1/manynet/R/modif_paths.R | 16 manynet-2.3.1/manynet/R/modif_permutation.R |only manynet-2.3.1/manynet/R/modif_plexity.R | 228 + manynet-2.3.1/manynet/R/modif_project.R | 535 ++- manynet-2.3.1/manynet/R/modif_proximity.R |only manynet-2.3.1/manynet/R/modif_scope.R | 490 +- manynet-2.3.1/manynet/R/modif_split.R | 250 + manynet-2.3.1/manynet/R/modif_weight.R | 243 + manynet-2.3.1/manynet/R/reexports_classes.R | 46 manynet-2.3.1/manynet/R/zzz.R | 40 manynet-2.3.1/manynet/README.md | 43 manynet-2.3.1/manynet/data/fict_marvel.rda |binary manynet-2.3.1/manynet/data/fict_potter.rda |binary manynet-2.3.1/manynet/data/fict_starwars.rda |binary manynet-2.3.1/manynet/data/irps_blogs.rda |binary manynet-2.3.1/manynet/data/irps_corruption.rda |only manynet-2.3.1/manynet/data/irps_nuclear.rda |binary manynet-2.3.1/manynet/data/irps_supremecourt.rda |only manynet-2.3.1/manynet/data/irps_tribes.rda |only manynet-2.3.1/manynet/data/ison_bankwiring.rda |only manynet-2.3.1/manynet/data/ison_classmates.rda |only manynet-2.3.1/manynet/data/ison_florentine.rda |only manynet-2.3.1/manynet/data/ison_fraternity.rda |only manynet-2.3.1/manynet/data/ison_koenigsberg.rda |binary manynet-2.3.1/manynet/data/ison_monks.rda |binary manynet-2.3.1/manynet/data/ison_tailorshop.rda |only manynet-2.3.1/manynet/inst/figures/cheatsheet.pdf |binary manynet-2.3.1/manynet/inst/tutorials/manynet1/making.Rmd | 28 manynet-2.3.1/manynet/inst/tutorials/manynet1/making.html | 169 manynet-2.3.1/manynet/inst/tutorials/manynet2/manipulating.Rmd | 704 +++- manynet-2.3.1/manynet/inst/tutorials/manynet2/manipulating.html | 1735 +++++++++- manynet-2.3.1/manynet/man/class_describe.Rd | 16 manynet-2.3.1/manynet/man/coerce_list.Rd | 113 manynet-2.3.1/manynet/man/defunct.Rd | 45 manynet-2.3.1/manynet/man/fict_actually.Rd | 13 manynet-2.3.1/manynet/man/fict_marvel.Rd | 58 manynet-2.3.1/manynet/man/fict_potter.Rd | 16 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manynet-2.3.1/manynet/man/modif_plexity.Rd | 61 manynet-2.3.1/manynet/man/modif_project.Rd | 205 + manynet-2.3.1/manynet/man/modif_proximity.Rd |only manynet-2.3.1/manynet/man/modif_scope.Rd | 132 manynet-2.3.1/manynet/man/modif_split.Rd | 83 manynet-2.3.1/manynet/man/modif_weight.Rd | 79 manynet-2.3.1/manynet/tests/testthat/helper-functional.R | 92 manynet-2.3.1/manynet/tests/testthat/sheets/gephi.gexf |only manynet-2.3.1/manynet/tests/testthat/sheets/gexfdynamic.gexf |only manynet-2.3.1/manynet/tests/testthat/sheets/networkcanvas.graphml |only manynet-2.3.1/manynet/tests/testthat/test-coercion.R | 215 + manynet-2.3.1/manynet/tests/testthat/test-functional_from.R | 72 manynet-2.3.1/manynet/tests/testthat/test-functional_impute.R |only manynet-2.3.1/manynet/tests/testthat/test-functional_manips.R | 20 manynet-2.3.1/manynet/tests/testthat/test-functional_marks.R | 46 manynet-2.3.1/manynet/tests/testthat/test-functional_measures.R | 9 manynet-2.3.1/manynet/tests/testthat/test-functional_prints.R | 124 manynet-2.3.1/manynet/tests/testthat/test-functional_to.R | 70 manynet-2.3.1/manynet/tests/testthat/test-make_read.R | 200 + manynet-2.3.1/manynet/tests/testthat/test-manip_add.R | 11 manynet-2.3.1/manynet/tests/testthat/test-manip_format.R | 176 - manynet-2.3.1/manynet/tests/testthat/test-manip_grab.R | 137 manynet-2.3.1/manynet/tests/testthat/test-manip_info.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_layers.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_miss.R | 314 + manynet-2.3.1/manynet/tests/testthat/test-manip_nodes.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_reformed.R | 14 manynet-2.3.1/manynet/tests/testthat/test-manip_split.R | 228 + manynet-2.3.1/manynet/tests/testthat/test-manip_transform.R | 678 +++ manynet-2.3.1/manynet/tests/testthat/test-manynet-data.R | 83 manynet-2.3.1/manynet/tests/testthat/test-mark_is.R | 133 manynet-2.3.1/manynet/tests/testthat/test-modif_proximity.R |only 154 files changed, 13125 insertions(+), 2385 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, KCF, and GlycoWorkbench formats. It
also provides an automatic parser to detect the format and parse the
structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.7.1 dated 2026-07-08 and 0.8.1 dated 2026-08-28
DESCRIPTION | 13 MD5 | 103 + NAMESPACE | 1 NEWS.md | 26 R/auto-parse.R | 13 R/furanose.R |only R/parse-glycam-iupac.R | 67 - R/parse-glycoct.R | 1489 ++++++++++++++++++++++++---- R/parse-gwb.R |only R/parse-iupac-compact.R | 129 +- R/parse-iupac-condensed.R | 9 R/parse-iupac-extended.R | 61 - R/parse-iupac-short.R | 31 R/parse-kcf.R | 24 R/parse-linear-code.R | 24 R/parse-linucs.R | 56 - R/parse-pglyco.R | 31 R/parse-strucgp.R | 62 - R/parse-wurcs.R | 725 ++++++++++++- R/struc-parser-wrapper.R | 187 ++- R/utils.R | 25 README.md | 14 build/partial.rdb |binary build/vignette.rds |binary inst/doc/glyparse.R | 51 inst/doc/glyparse.Rmd | 239 ++-- inst/doc/glyparse.html | 415 ++++--- man/auto_parse.Rd | 1 man/parse_glycoct.Rd | 13 man/parse_gwb.Rd |only man/parse_iupac_compact.Rd | 4 man/parse_kcf.Rd | 5 man/parse_linucs.Rd | 6 man/parse_pglyco_struc.Rd | 5 man/parse_strucgp_struc.Rd | 5 man/parse_wurcs.Rd | 15 tests/testthat/_snaps/parse-glycoct.md |only tests/testthat/test-auto-parse.R | 29 tests/testthat/test-furanose.R |only tests/testthat/test-mixed-residue-types.R |only tests/testthat/test-parse-glycam-iupac.R | 43 tests/testthat/test-parse-glycoct.R | 610 +++++++++++ tests/testthat/test-parse-gwb.R |only tests/testthat/test-parse-iupac-compact.R | 41 tests/testthat/test-parse-iupac-condensed.R | 39 tests/testthat/test-parse-iupac-extended.R | 51 tests/testthat/test-parse-iupac-short.R | 12 tests/testthat/test-parse-kcf.R | 53 tests/testthat/test-parse-linear-code.R | 13 tests/testthat/test-parse-linucs.R | 60 + tests/testthat/test-parse-pglyco.R | 51 tests/testthat/test-parse-strucgp.R | 51 tests/testthat/test-parse-wurcs.R | 649 ++++++++++++ tests/testthat/test-performance.R | 171 +++ tests/testthat/test-struc-parser-wrapper.R | 58 + vignettes/glyparse.Rmd | 239 ++-- 56 files changed, 5048 insertions(+), 971 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.2.4 dated 2026-06-02 and 1.3.0 dated 2026-08-28
epidatr-1.2.4/epidatr/inst/doc/epidatr.R |only epidatr-1.2.4/epidatr/inst/doc/signal-discovery.R |only epidatr-1.2.4/epidatr/inst/doc/v5-api-demo.R |only epidatr-1.2.4/epidatr/inst/doc/versioned-data.R |only epidatr-1.3.0/epidatr/DESCRIPTION | 12 epidatr-1.3.0/epidatr/MD5 | 124 - epidatr-1.3.0/epidatr/NAMESPACE | 3 epidatr-1.3.0/epidatr/NEWS.md | 39 epidatr-1.3.0/epidatr/R/auth.R | 17 epidatr-1.3.0/epidatr/R/cache.R | 50 epidatr-1.3.0/epidatr/R/check.R | 25 epidatr-1.3.0/epidatr/R/covidcast.R | 68 epidatr-1.3.0/epidatr/R/endpoints.R | 1012 +++++++++-- epidatr-1.3.0/epidatr/R/epidatacall.R | 84 epidatr-1.3.0/epidatr/R/epidatr-package.R | 5 epidatr-1.3.0/epidatr/R/model.R | 95 - epidatr-1.3.0/epidatr/R/request.R | 42 epidatr-1.3.0/epidatr/R/utils.R | 225 ++ epidatr-1.3.0/epidatr/README.md | 75 epidatr-1.3.0/epidatr/build/vignette.rds |binary epidatr-1.3.0/epidatr/inst/doc/epidatr.Rmd | 158 + epidatr-1.3.0/epidatr/inst/doc/epidatr.html | 389 ++++ epidatr-1.3.0/epidatr/inst/doc/migration-guide.Rmd |only epidatr-1.3.0/epidatr/inst/doc/migration-guide.html |only epidatr-1.3.0/epidatr/inst/doc/signal-discovery.Rmd | 372 +++- epidatr-1.3.0/epidatr/inst/doc/signal-discovery.html | 554 +++++- epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.Rmd | 205 ++ epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.html | 275 ++ epidatr-1.3.0/epidatr/inst/doc/versioned-data.Rmd | 87 epidatr-1.3.0/epidatr/inst/doc/versioned-data.html | 533 +++++ epidatr-1.3.0/epidatr/man/cast_api_queries.Rd | 39 epidatr-1.3.0/epidatr/man/covidcast_epidata.Rd | 8 epidatr-1.3.0/epidatr/man/dot-aux_key_columns.Rd |only epidatr-1.3.0/epidatr/man/dot-check_cast_empty.Rd |only epidatr-1.3.0/epidatr/man/dot-serialize_key_filters.Rd |only epidatr-1.3.0/epidatr/man/epidata_aux.Rd |only epidatr-1.3.0/epidatr/man/epidata_meta.Rd | 5 epidatr-1.3.0/epidatr/man/fetch_args_list.Rd | 6 epidatr-1.3.0/epidatr/man/note_frozen_endpoint.Rd |only epidatr-1.3.0/epidatr/man/pub_covidcast.Rd | 7 epidatr-1.3.0/epidatr/man/pub_covidcast_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pub_flusurv.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview_clinical.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pub_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pvt_quidel.Rd | 7 epidatr-1.3.0/epidatr/man/set_cache.Rd | 2 epidatr-1.3.0/epidatr/man/warn_v4_sunset.Rd |only epidatr-1.3.0/epidatr/tests/testthat/_snaps/endpoint-urls.md |only epidatr-1.3.0/epidatr/tests/testthat/_snaps/epidatacall.md | 14 epidatr-1.3.0/epidatr/tests/testthat/_snaps/fixtures.md |only epidatr-1.3.0/epidatr/tests/testthat/fixtures |only epidatr-1.3.0/epidatr/tests/testthat/helper-endpoints.R |only epidatr-1.3.0/epidatr/tests/testthat/helper-fixtures.R |only epidatr-1.3.0/epidatr/tests/testthat/helper-live.R | 29 epidatr-1.3.0/epidatr/tests/testthat/test-cache.R | 39 epidatr-1.3.0/epidatr/tests/testthat/test-endpoint-urls.R |only epidatr-1.3.0/epidatr/tests/testthat/test-endpoints.R | 485 +++++ epidatr-1.3.0/epidatr/tests/testthat/test-epidatacall.R | 78 epidatr-1.3.0/epidatr/tests/testthat/test-fixtures.R |only epidatr-1.3.0/epidatr/tests/testthat/test-live.R | 483 +---- epidatr-1.3.0/epidatr/tests/testthat/test-model.R | 11 epidatr-1.3.0/epidatr/tests/testthat/test-utils.R | 56 epidatr-1.3.0/epidatr/vignettes/epidatr.Rmd | 158 + epidatr-1.3.0/epidatr/vignettes/img |only epidatr-1.3.0/epidatr/vignettes/migration-guide.Rmd |only epidatr-1.3.0/epidatr/vignettes/signal-discovery.Rmd | 372 +++- epidatr-1.3.0/epidatr/vignettes/v5-api-demo.Rmd | 205 ++ epidatr-1.3.0/epidatr/vignettes/versioned-data.Rmd | 87 70 files changed, 5461 insertions(+), 1121 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, direct age standardization against
the bundled WHO World Standard Population, period life-table
construction, a snapshot helper for reproducible data pulls, and
convenience clients for the World Health Organization Global Health
Observatory (GHO) OData API <https://ghoapi.azureedge.net/api/> and
the United Nations Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
This is a re-admission after prior archival of version 0.8.0 dated 2026-07-02
Diff between DSIR versions 0.8.0 dated 2026-07-02 and 0.9.0 dated 2026-08-28
DESCRIPTION | 22 +++++---- MD5 | 64 +++++++++++++++++------------ NAMESPACE | 3 + NEWS.md | 54 ++++++++++++++++++++++++ R/age_standardize.R |only R/data.R | 75 +++++++++++++++++++++++++++++++++- R/gho.R | 16 ------- R/http.R |only R/life_table.R |only R/sdg.R | 21 ++++----- R/sdg_coverage.R | 18 +++++--- R/snapshot.R |only README.md | 2 build/vignette.rds |binary data/afro_cty.rda |binary data/amro_cty.rda |binary data/emro_cty.rda |binary data/euro_cty.rda |binary data/pic_cty.rda |binary data/searo_cty.rda |binary data/who_countries.rda |binary data/who_std_pop.rda |only data/wpro_cty.rda |binary inst/CITATION |only inst/WORDLIST | 32 ++++++++++++++ inst/doc/DSIR.html | 65 ++++++++++++++--------------- inst/doc/visualizing-indicators.html | 4 - man/age_standardize.Rd |only man/life_table.Rd |only man/snapshot.Rd |only man/who_countries.Rd | 18 +++++++- man/who_std_pop.Rd |only tests/testthat/test-age_standardize.R |only tests/testthat/test-gho-get-mock.R | 20 +++++++++ tests/testthat/test-life_table.R |only tests/testthat/test-sdg-coverage.R | 73 +++++++++++++++++++++++++++++++++ tests/testthat/test-sdg-get-mock.R | 34 +++++++++++++++ tests/testthat/test-snapshot.R |only tests/testthat/test-who_countries.R | 25 ++++++++++- tests/testthat/test-who_std_pop.R |only 40 files changed, 441 insertions(+), 105 deletions(-)
Title: Continuous-Time Subgrouping with GIMME
Description: Estimates group-, subgroup-, and individual-level dynamic
structures from multivariate intensive longitudinal data using
continuous-time state-space models. The subgrouping procedure combines
iterative shared-path searches with recurrent-evidence feature screening
and partitioning around medoids. The continuous-time group iterative
multiple model estimation method is described in Park et al. (2025)
<doi:10.1080/10705511.2024.2429544>.
Author: Jonathan J. Park [aut, cre, cph] ,
Nathan Xin Mills [aut, ctb]
Maintainer: Jonathan J. Park <imJPark@UCDavis.edu>
Diff between ctgimme versions 0.0.12 dated 2026-08-24 and 0.1.0 dated 2026-08-28
DESCRIPTION | 6 MD5 | 42 - NEWS.md | 80 +-- R/cleanup.R | 12 R/context.R | 449 ++++++++++--------- R/ctgimme-package.R | 2 R/ctgimme.R | 240 +++++----- R/data-preparation.R | 20 R/fit-helpers.R | 6 R/individual-models.R | 98 ++-- R/model-building.R | 22 R/shared-search.R | 108 ++-- R/subgroup-legacy.R | 26 - R/subgroup-model.R | 26 - README.md | 139 +++--- demo/quick-subgroups.R | 6 inst/WORDLIST | 38 - man/ctgimme.Rd | 18 tests/testthat/test-api.R | 504 +++++++++++----------- tests/testthat/test-core-helpers.R | 243 ++++++++-- tests/testthat/test-multisubject-subgroup-model.R | 56 +- tests/testthat/test-subgroup-time-and-cleanup.R | 72 +-- 22 files changed, 1223 insertions(+), 990 deletions(-)
Title: Join World Bank Data, Country Codes and Maps on the ISO Spine
Description: A complete toolkit for getting country data onto honest maps.
Country names rarely line up across data sources ("US", "U.S.",
"United States", "United States of America" are one country, but a
naive join treats them as four), so 'countryatlas' makes ISO codes the
universal join key. It generalises a one-call, map-ready table that
stitches together 'ggplot2' map geometry, 'WDI' World Bank indicators
and the 'countrycode' Rosetta stone; exposes the join machinery for the
user's own data; ships curated reference data (metadata, group
memberships, an indicator catalogue, flags and currencies); adds
analysis helpers (per-capita, regional roll-ups, ranking, inequality and
convergence statistics); and turns one hand-drawn choropleth into a full
vocabulary of projected, area-honest maps (binned and quantile
choropleths, proportional-symbol, spike, bivariate, cartogram, tile-grid,
flow, small-multiple, animated, globe and interactive), and can hand its
curated, ISO-reconciled tables to 'ggsql' [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between countryatlas versions 2.0.0 dated 2026-08-25 and 2.0.1 dated 2026-08-28
DESCRIPTION | 9 +++---- MD5 | 15 +++++++------ NEWS.md | 43 ++++++++++++++++++++++++++++++++++++++ R/cache.R | 9 +++++-- R/ggsql.R | 20 ++++++++++++++++- inst/doc/countryatlas.html | 2 - man/clear_wdi_cache.Rd | 9 +++++-- tests/testthat/setup-user-dirs.R |only tests/testthat/test-standardize.R | 17 ++++++++++----- 9 files changed, 99 insertions(+), 25 deletions(-)
Title: Tree-Based Scan Statistics
Description: Implementation of unconditional Bernoulli Scan Statistic developed
by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039>
for hierarchical tree structures. Tree-based Scan Statistics are an
exploratory method to identify event clusters across the space of a
hierarchical tree.
Author: Joshua P. Entrop [aut, cre, cph] ,
Viktor Wintzell [aut]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>
Diff between TreeMineR versions 1.1.0 dated 2026-08-25 and 1.1.1 dated 2026-08-28
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- NEWS.md | 4 +++ inst/doc/Tree-based-scan-statistics.R | 2 - inst/doc/Tree-based-scan-statistics.Rmd | 8 ++++-- inst/doc/Tree-based-scan-statistics.html | 38 ++++++++++++++++++++----------- vignettes/Tree-based-scan-statistics.Rmd | 8 ++++-- 7 files changed, 51 insertions(+), 27 deletions(-)
Title: Single-Cell Decomposition using Hierarchical Autoencoder
Description: Provides a fast and accurate pipeline for single-cell analyses.
The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).
Author: Ha Nguyen [cre],
Duc Tran [aut],
Tin Nguyen [fnd],
Hao Chen [ctb]
Maintainer: Ha Nguyen <hvn0006@wayne.edu>
Diff between scDHA versions 1.2.3 dated 2025-09-23 and 1.2.4 dated 2026-08-28
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/Example.html | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.1 dated 2026-08-21 and 2.0.2 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 8 +++---- NEWS.md | 5 ++++ tests/testthat/fixtures.tar.gz |binary tests/testthat/helper.R | 46 +++++++++++++++++++++++++++++++++++------ 5 files changed, 52 insertions(+), 13 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks
adjusting for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Fox M.P., MacLehose R.F., and Lash T.L. "Applying
Quantitative Bias Analysis to Epidemiologic Data, second ed.", ('Springer', 2021).
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <cheval@zaclys.net>
Diff between episensr versions 2.1.0 dated 2025-11-04 and 2.2.0 dated 2026-08-28
episensr-2.1.0/episensr/R/pipe.R |only episensr-2.1.0/episensr/R/rename.R |only episensr-2.1.0/episensr/man/rename.Rd |only episensr-2.2.0/episensr/DESCRIPTION | 16 - episensr-2.2.0/episensr/MD5 | 74 +++--- episensr-2.2.0/episensr/NAMESPACE | 89 +++---- episensr-2.2.0/episensr/NEWS.md | 2 episensr-2.2.0/episensr/R/confounding.R | 4 episensr-2.2.0/episensr/R/misclassification.R | 4 episensr-2.2.0/episensr/R/utils-pipe.R |only episensr-2.2.0/episensr/README.md | 24 +- episensr-2.2.0/episensr/build/vignette.rds |binary episensr-2.2.0/episensr/inst/CITATION | 6 episensr-2.2.0/episensr/inst/doc/b_probabilistic.Rmd | 4 episensr-2.2.0/episensr/inst/doc/b_probabilistic.html | 16 - episensr-2.2.0/episensr/inst/doc/c_multiple_bias.html | 4 episensr-2.2.0/episensr/inst/doc/d_other_sens.Rmd | 8 episensr-2.2.0/episensr/inst/doc/d_other_sens.html | 21 - episensr-2.2.0/episensr/inst/doc/episensr.Rmd | 6 episensr-2.2.0/episensr/inst/doc/episensr.html | 40 +-- episensr-2.2.0/episensr/man/confounders.Rd | 16 - episensr-2.2.0/episensr/man/confounders_array.Rd | 12 - episensr-2.2.0/episensr/man/confounders_evalue.Rd | 12 - episensr-2.2.0/episensr/man/confounders_ext.Rd | 12 - episensr-2.2.0/episensr/man/confounders_limit.Rd | 12 - episensr-2.2.0/episensr/man/episensr-package.Rd | 5 episensr-2.2.0/episensr/man/mbias.Rd | 4 episensr-2.2.0/episensr/man/misclass.Rd | 10 episensr-2.2.0/episensr/man/misclass_cov.Rd | 6 episensr-2.2.0/episensr/man/pipe.Rd | 28 +- episensr-2.2.0/episensr/man/plot.episensr_booted.Rd | 6 episensr-2.2.0/episensr/man/plot.episensr_probsens.Rd | 6 episensr-2.2.0/episensr/man/plot.mbias.Rd | 6 episensr-2.2.0/episensr/man/probsens_irr.Rd | 6 episensr-2.2.0/episensr/man/probsens_irr_conf.Rd | 12 - episensr-2.2.0/episensr/man/selection.Rd | 4 episensr-2.2.0/episensr/tests/testthat/test-probsens.R | 200 +++++++++++------ episensr-2.2.0/episensr/vignettes/b_probabilistic.Rmd | 4 episensr-2.2.0/episensr/vignettes/d_other_sens.Rmd | 8 episensr-2.2.0/episensr/vignettes/episensr.Rmd | 6 40 files changed, 382 insertions(+), 311 deletions(-)
Title: Discriminant Adaptive Nearest Neighbor Classification
Description: Discriminant Adaptive Nearest Neighbor Classification is a
variation of k nearest neighbors where the shape of the neighborhood is
data driven. The neighborhood is elongated along class boundaries and
shrunk in the orthogonal direction. This package implements dann and
sub_dann from Hastie (1996)
<https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between dann versions 1.2.0 dated 2026-08-22 and 1.3.0 dated 2026-08-28
DESCRIPTION | 6 +-- MD5 | 29 +++++++++++------- NAMESPACE | 3 + NEWS.md | 6 +++ R/RcppExports.R | 26 ++++++++++++++++ R/dann.R | 2 + R/sub_dann.R | 2 + R/threads.R |only README.md | 2 - man/dann_set_threads.Rd |only man/figures |only man/predict.dann.Rd | 2 + man/predict.sub_dann.Rd | 2 + src/RcppExports.cpp | 45 ++++++++++++++++++++++++++++ src/internal_armadillo_helpers.cpp | 59 ++++++++++++++++++++++++++++++++++++- tests/testthat/setup.R |only tests/testthat/test_G_threads.R |only 17 files changed, 168 insertions(+), 16 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.47 dated 2026-06-16 and 0.48 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gitbook.R | 2 +- R/html.R | 2 +- R/utils.R | 2 +- build/vignette.rds |binary inst/rstudio/templates/project/resources/common/book.bib | 2 +- 7 files changed, 14 insertions(+), 14 deletions(-)
Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from central bank
APIs including 'Banco Central do Brasil' (BCB), 'Banco de España'
(BdE), 'Banco de México' (Banxico), 'Banco de Portugal' (BdP), 'Bank
for International Settlements' (BIS), 'Bank of Canada' (BoC), 'Bank of
England' (BoE), 'Bank of Israel' (BoI), 'Bank of Japan' (BoJ), 'Banque
de France' (BdF), 'Czech National Bank' (CNB), 'Deutsche Bundesbank'
(BBk), 'European Central Bank' (ECB), 'National Bank of Poland' (NBP),
'Norges Bank' (NoB), 'Oesterreichische Nationalbank' (OeNB), 'Sveriges
Riksbank' (SRb), and 'Swiss National Bank' (SNB).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.12.0 dated 2026-07-10 and 0.13.0 dated 2026-08-28
DESCRIPTION | 22 - MD5 | 233 ++++++++++---------- NAMESPACE | 55 ++-- NEWS.md | 46 +++ R/assertions.R | 2 R/banxico.R | 10 R/bbk-package.R | 3 R/bbk.R | 41 ++- R/bcb.R | 4 R/bde.R | 47 +++- R/bdp.R | 119 ++++++++-- R/bis.R | 29 -- R/boc.R | 46 +-- R/boe.R | 12 - R/boi.R |only R/boj.R | 20 + R/cnb.R | 13 - R/ecb.R | 27 +- R/fx-rates.R | 31 ++ R/nbp.R | 32 +- R/nob.R | 90 ++++--- R/onb.R | 24 +- R/sdmx.R | 39 +++ R/snb.R | 14 - R/srb.R | 45 ++- R/utils.R | 34 ++ README.md | 7 man/banxico_data.Rd | 5 man/banxico_metadata.Rd | 6 man/bbk-package.Rd | 2 man/bbk_data.Rd | 1 man/bbk_dimension.Rd | 2 man/bbk_metadata.Rd | 2 man/bbk_series.Rd | 1 man/bcb_currencies.Rd | 2 man/bcb_data.Rd | 1 man/bcb_expectations.Rd | 1 man/bcb_fx_rates.Rd | 1 man/bcb_inflation.Rd | 1 man/bcb_selic.Rd | 1 man/bcb_top5.Rd | 1 man/bde_data.Rd | 1 man/bde_latest.Rd | 1 man/bdf_codelist.Rd | 1 man/bdf_data.Rd | 1 man/bdf_dataset.Rd | 1 man/bdf_dimension.Rd | 2 man/bdp_data.Rd | 7 man/bdp_dataset.Rd | 2 man/bdp_dimension.Rd | 2 man/bdp_domain.Rd | 2 man/bdp_series.Rd | 2 man/bis_data.Rd | 1 man/bis_dimension.Rd | 2 man/bis_metadata.Rd | 2 man/boc_data.Rd | 1 man/boc_metadata.Rd | 4 man/boe_data.Rd | 1 man/boi_data.Rd |only man/boi_dimension.Rd |only man/boi_metadata.Rd |only man/boj_data.Rd | 5 man/boj_metadata.Rd | 2 man/cnb_czeonia.Rd | 1 man/cnb_data.Rd | 1 man/cnb_dimension.Rd | 2 man/cnb_fx_other_rates.Rd | 8 man/cnb_fx_rates.Rd | 1 man/cnb_indicators.Rd | 2 man/cnb_pribor.Rd | 1 man/cnb_snapshots.Rd | 2 man/cnb_tree.Rd | 2 man/ecb_data.Rd | 1 man/ecb_dimension.Rd | 2 man/ecb_metadata.Rd | 2 man/figures/README-plotting-1.png |binary man/nbp_fx_rates.Rd | 6 man/nbp_gold.Rd | 6 man/nob_data.Rd | 1 man/nob_dimension.Rd | 2 man/nob_metadata.Rd | 2 man/onb_data.Rd | 1 man/onb_dimension.Rd | 2 man/onb_frequency.Rd | 2 man/onb_hierarchy.Rd | 2 man/onb_metadata.Rd | 2 man/onb_toc.Rd | 2 man/snb_data.Rd | 1 man/snb_dimension.Rd | 2 man/snb_metadata.Rd | 2 man/snb_toc.Rd | 2 man/srb_calendar.Rd | 2 man/srb_cross_rates.Rd | 1 man/srb_data.Rd | 1 man/srb_series.Rd | 2 tests/testthat/_snaps/banxico.md | 17 + tests/testthat/_snaps/bcb.md |only tests/testthat/_snaps/boi.md |only tests/testthat/fixtures/bbk-series-short-header.rds |only tests/testthat/fixtures/bde-data-es.rds |only tests/testthat/fixtures/bdp-data-multi.rds |only tests/testthat/fixtures/boi-data.xml |only tests/testthat/fixtures/boi-dimension.xml |only tests/testthat/fixtures/boi-metadata.xml |only tests/testthat/fixtures/nob-data.xml | 29 -- tests/testthat/test-banxico.R | 12 + tests/testthat/test-bbk.R | 55 ++++ tests/testthat/test-bcb.R | 4 tests/testthat/test-bde.R | 12 + tests/testthat/test-bdp.R | 134 +++++++++++ tests/testthat/test-bis.R | 65 +++++ tests/testthat/test-boc.R | 47 ++++ tests/testthat/test-boe.R | 20 + tests/testthat/test-boi.R |only tests/testthat/test-boj.R | 7 tests/testthat/test-cnb.R | 4 tests/testthat/test-ecb.R | 52 ++++ tests/testthat/test-exchange-rates.R | 36 +++ tests/testthat/test-nbp.R | 17 + tests/testthat/test-nob.R | 68 +++++ tests/testthat/test-onb.R | 41 +++ tests/testthat/test-sdmx.R | 118 +++++++++- tests/testthat/test-snb.R | 16 + tests/testthat/test-srb.R | 30 ++ 124 files changed, 1536 insertions(+), 426 deletions(-)
Title: Structured Covariances Estimators for Pairwise and Spatial
Covariates
Description: Implements estimators for structured covariance matrices in the
presence of pairwise and spatial covariates.
Metodiev, Perrot-Dockès,
Ouadah, Fosdick, Robin, Latouche & Raftery (2026)
<doi:10.1214/26-AOAS2183>.
Author: Martin Metodiev [aut, cre, cph] ,
Marie Perrot-Dockes [aut],
Stephane Robin [aut]
Maintainer: Martin Metodiev <m.metodiev@tutanota.com>
Diff between scov versions 2.0.0 dated 2026-03-18 and 2.0.2 dated 2026-08-28
DESCRIPTION | 15 ++++--- MD5 | 20 +++++----- NAMESPACE | 48 +++++++++++++++--------- NEWS.md | 12 ++---- R/scov.R | 11 +++-- build/vignette.rds |binary inst/doc/scov_vignette.R | 2 - inst/doc/scov_vignette.Rmd | 2 - inst/doc/scov_vignette.html | 85 +++++++++++++++++++++++++++++++++++++++----- man/scov.Rd | 11 +++-- vignettes/scov_vignette.Rmd | 2 - 11 files changed, 144 insertions(+), 64 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Carlos C. Ra [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.45 dated 2026-05-21 and 3.46 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 25 +++++++++++++++++++++++++ R/HLfit.R | 2 +- R/plotCoeffs.R | 6 ++++++ R/varImp.R | 39 +++++++++++++++++++++++++++++++-------- man/Miller.Rd | 2 +- man/mod2obspred.Rd | 4 ++-- man/modEvA-package.Rd | 4 ++-- man/plotCoeffs.Rd | 8 ++++---- man/threshMeasures.Rd | 6 ++++++ man/varImp.Rd | 12 +++++++----- 12 files changed, 100 insertions(+), 38 deletions(-)
Title: Perform Logistic Normal Multinomial Clustering for Microbiome
Compositional Data
Description: An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <doi:10.1038/s41598-023-41318-8>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2023) <doi:10.1007/s00357-023-09452-0> and Tu and Subedi (2022) <doi:10.3329/jsr.v56i2.67469>. It also include a Biclustering algorithm that applies to multivariate normal data: T [...truncated...]
Author: Wangshu Tu [aut, cre],
Sanjeena Subedi [aut],
Yuan Fang [aut]
Maintainer: Wangshu Tu <wangshu.tu@carleton.ca>
Diff between lnmCluster versions 0.3.1 dated 2022-07-20 and 1.0.0 dated 2026-08-28
DESCRIPTION | 17 +- MD5 | 45 +++--- NAMESPACE | 5 R/Micro_bi_PGMM.R | 8 - R/Micro_bi_jensens.R | 4 R/Micro_bi_lasso.R | 6 R/bmm.R |only R/initial_and_main_bmm.R |only R/lnmbiclust.R | 36 ++-- R/lnmfa.R | 29 ++- R/model_selection_bmm.R |only R/plnmfa.R | 27 +-- README.md |only build/vignette.rds |binary inst/doc/lnm-bicluster.R | 200 +++++++++++++++------------ inst/doc/lnm-bicluster.Rmd | 41 ++++- inst/doc/lnm-bicluster.html | 321 ++++++++++++++++++++++++-------------------- man/Mico_bi_PGMM.Rd | 2 man/Mico_bi_jensens.Rd | 2 man/Mico_bi_lasso.Rd | 2 man/bi_fa_T.Rd |only man/bmm.Rd |only man/lnmbiclust.Rd | 30 ++-- man/lnmfa.Rd | 26 +-- man/model_selection_bmm.Rd |only man/plnmfa.Rd | 28 ++- vignettes/lnm-bicluster.Rmd | 41 ++++- 27 files changed, 506 insertions(+), 364 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.54 dated 2026-05-21 and 4.59 dated 2026-08-28
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS.md | 93 ++++++++++++++++++++++++ R/clampVars.R |only R/corSelect.R | 7 + R/pairwiseRangemaps.R | 178 +++++++++++++++++++++++++++++------------------ R/rangemapSim.R | 27 +++++-- R/selectAbsences.R | 24 +++--- man/biasLayer.Rd | 3 man/clampVars.Rd |only man/corSelect.Rd | 8 +- man/fuzzySim-package.Rd | 4 - man/pairwiseRangemaps.Rd | 42 ++++++----- man/rangemapSim.Rd | 20 ++--- man/selectAbsences.Rd | 10 ++ man/simMat.Rd | 33 +------- 16 files changed, 321 insertions(+), 164 deletions(-)
Title: Kernelized Stein Discrepancy for Goodness-of-Fit Tests and Stein
Sampling
Description: Provides Stein-discrepancy goodness-of-fit tests and
Stein-method-based sampling tools. The tests include kernel Stein
discrepancy U- and V-statistics following Liu et al. (2016)
<doi:10.48550/arXiv.1602.03253> and Chwialkowski et al. (2016)
<doi:10.48550/arXiv.1602.02964>, plus the finite set Stein discrepancy
test of Jitkrittum et al. (2017) <doi:10.48550/arXiv.1705.07673>. The
sampling tools include Stein thinning, Stein Points, Stein Point Markov
chain Monte Carlo, and Stein variational gradient descent following
Riabiz et al. (2022) <doi:10.48550/arXiv.2005.03952>, Chen et al. (2018)
<doi:10.48550/arXiv.1803.10161>, Chen et al. (2019)
<doi:10.48550/arXiv.1905.03673>, and Liu and Wang (2016)
<doi:10.48550/arXiv.1608.04471>. Gaussian mixture utilities are included
for constructing example targets, simulation, density evaluation, and
score callbacks.
Author: Junhao Gao [aut, cre],
Ery Arias-Castro [aut]
Maintainer: Junhao Gao <jug049@ucsd.edu>
Diff between steinsampling versions 0.1.0 dated 2026-07-21 and 0.1.1 dated 2026-08-28
steinsampling-0.1.0/steinsampling/man/compute_fssd_null_pvalue.Rd |only steinsampling-0.1.0/steinsampling/man/compute_fssd_unbiased_stat.Rd |only steinsampling-0.1.0/steinsampling/man/custom_adjusted_gradient.Rd |only steinsampling-0.1.0/steinsampling/man/grw.Rd |only steinsampling-0.1.0/steinsampling/man/grwmetrop.Rd |only steinsampling-0.1.0/steinsampling/man/kernel_generics.Rd |only steinsampling-0.1.0/steinsampling/man/likelihoodgmm.Rd |only steinsampling-0.1.0/steinsampling/man/perturbgmm.Rd |only steinsampling-0.1.0/steinsampling/man/plotgmm.Rd |only steinsampling-0.1.0/steinsampling/man/posteriorgmm.Rd |only steinsampling-0.1.0/steinsampling/man/scorefunctiongmm.Rd |only steinsampling-0.1.0/steinsampling/man/update_svgd.Rd |only steinsampling-0.1.1/steinsampling/DESCRIPTION | 19 steinsampling-0.1.1/steinsampling/MD5 | 138 steinsampling-0.1.1/steinsampling/NAMESPACE | 50 steinsampling-0.1.1/steinsampling/R/bootstrap.R | 282 - steinsampling-0.1.1/steinsampling/R/fssd_test.R | 1210 +++----- steinsampling-0.1.1/steinsampling/R/gmm_model.R | 745 +--- steinsampling-0.1.1/steinsampling/R/kernel_classes.R | 1499 ++++------ steinsampling-0.1.1/steinsampling/R/ksd_u_test.R | 534 --- steinsampling-0.1.1/steinsampling/R/ksd_v_test.R | 581 +-- steinsampling-0.1.1/steinsampling/R/stein_helpers.R | 341 -- steinsampling-0.1.1/steinsampling/R/stein_point_mcmc.R | 1141 +++---- steinsampling-0.1.1/steinsampling/R/stein_points.R | 1061 +++---- steinsampling-0.1.1/steinsampling/R/stein_thinning.R | 247 - steinsampling-0.1.1/steinsampling/R/steinsampling-package.R | 25 steinsampling-0.1.1/steinsampling/R/svgd.R | 448 +- steinsampling-0.1.1/steinsampling/man/compute_tau.Rd | 70 steinsampling-0.1.1/steinsampling/man/cross_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/custom_stein_kernel.Rd | 123 steinsampling-0.1.1/steinsampling/man/densitygmm.Rd |only steinsampling-0.1.1/steinsampling/man/eval_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/find_median_distance.Rd | 54 steinsampling-0.1.1/steinsampling/man/fmin_grid.Rd | 4 steinsampling-0.1.1/steinsampling/man/fmin_mc.Rd | 4 steinsampling-0.1.1/steinsampling/man/fmin_nm.Rd | 15 steinsampling-0.1.1/steinsampling/man/fssd_null_pvalue.Rd |only steinsampling-0.1.1/steinsampling/man/fssd_opt_test.Rd | 123 steinsampling-0.1.1/steinsampling/man/fssd_rand_test.Rd | 74 steinsampling-0.1.1/steinsampling/man/fssd_statistic.Rd |only steinsampling-0.1.1/steinsampling/man/fssd_test.Rd | 120 steinsampling-0.1.1/steinsampling/man/get_score_evaluator.Rd | 35 steinsampling-0.1.1/steinsampling/man/gmm.Rd | 49 steinsampling-0.1.1/steinsampling/man/grad_theta_v_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/grad_x_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/kernel_scale2.Rd |only steinsampling-0.1.1/steinsampling/man/ksd_u_bootstrap.Rd | 55 steinsampling-0.1.1/steinsampling/man/ksd_u_statistic.Rd | 42 steinsampling-0.1.1/steinsampling/man/ksd_u_test.Rd | 116 steinsampling-0.1.1/steinsampling/man/ksd_uq_matrix.Rd | 54 steinsampling-0.1.1/steinsampling/man/ksd_v_bootstrap.Rd | 71 steinsampling-0.1.1/steinsampling/man/ksd_v_statistic.Rd | 43 steinsampling-0.1.1/steinsampling/man/ksd_v_test.Rd | 150 - steinsampling-0.1.1/steinsampling/man/ksd_vq_matrix.Rd | 50 steinsampling-0.1.1/steinsampling/man/mala.Rd | 47 steinsampling-0.1.1/steinsampling/man/print.SteinKernel.Rd |only steinsampling-0.1.1/steinsampling/man/print.stein_points.Rd |only steinsampling-0.1.1/steinsampling/man/rgmm.Rd | 31 steinsampling-0.1.1/steinsampling/man/rwm.Rd | 51 steinsampling-0.1.1/steinsampling/man/sp_mcmc.Rd | 174 - steinsampling-0.1.1/steinsampling/man/sp_mcmc_criterion.Rd | 36 steinsampling-0.1.1/steinsampling/man/sp_mcmc_eval_candidates.Rd | 17 steinsampling-0.1.1/steinsampling/man/sp_mcmc_select_start.Rd | 17 steinsampling-0.1.1/steinsampling/man/sp_mcmc_state.Rd | 14 steinsampling-0.1.1/steinsampling/man/stein_codescent.Rd | 39 steinsampling-0.1.1/steinsampling/man/stein_kernel.Rd | 69 steinsampling-0.1.1/steinsampling/man/stein_kernel_imq_score.Rd | 29 steinsampling-0.1.1/steinsampling/man/stein_kernel_inverse_log.Rd | 33 steinsampling-0.1.1/steinsampling/man/stein_kernel_matrix.Rd | 69 steinsampling-0.1.1/steinsampling/man/stein_points.Rd | 136 steinsampling-0.1.1/steinsampling/man/stein_thinning.Rd | 177 - steinsampling-0.1.1/steinsampling/man/steinsampling-package.Rd | 23 steinsampling-0.1.1/steinsampling/man/svgd.Rd | 134 steinsampling-0.1.1/steinsampling/man/trace_mixed_kernel.Rd |only steinsampling-0.1.1/steinsampling/tests/testthat/helper-test-utils.R | 52 steinsampling-0.1.1/steinsampling/tests/testthat/test-fssd.R | 80 steinsampling-0.1.1/steinsampling/tests/testthat/test-gmm.R | 72 steinsampling-0.1.1/steinsampling/tests/testthat/test-gof-scale-contract.R |only steinsampling-0.1.1/steinsampling/tests/testthat/test-kernels.R | 79 steinsampling-0.1.1/steinsampling/tests/testthat/test-ksd.R | 50 steinsampling-0.1.1/steinsampling/tests/testthat/test-optimizers-and-sampling.R | 164 + steinsampling-0.1.1/steinsampling/tests/testthat/test-svgd-spmcmc.R | 176 - 82 files changed, 4749 insertions(+), 6593 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.17.1 dated 2026-06-30 and 0.18.0 dated 2026-08-28
DESCRIPTION | 41 + MD5 | 70 +-- NAMESPACE | 25 - NEWS.md | 50 ++ R/binned_residuals.R | 22 - R/check_collinearity.R | 55 +- R/check_group_variation.R | 72 ++- R/check_heteroscedasticity.R | 41 + R/check_model_diagnostics.R | 21 R/compare_performance.R | 8 R/icc.R | 3 R/model_performance.lavaan.R | 16 R/performance_ior.R |only R/performance_mor.R |only R/performance_poor.R |only R/r2.R | 142 +++--- R/r2_mcfadden.R | 5 R/test_performance.R | 2 man/binned_residuals.Rd | 23 - man/check_group_variation.Rd | 9 man/check_heteroscedasticity.Rd | 6 man/icc.Rd | 4 man/performance-package.Rd | 1 man/performance_ior.Rd |only man/performance_mor.Rd |only man/performance_poor.Rd |only man/r2.Rd | 8 man/test_performance.Rd | 2 tests/testthat/test-binned_residuals.R | 426 +++---------------- tests/testthat/test-check_collinearity.R | 20 tests/testthat/test-check_group_variation.R | 222 ++++------ tests/testthat/test-check_heteroskedasticity.R | 30 + tests/testthat/test-compare_performance.R | 56 ++ tests/testthat/test-model_performance.gam.R | 18 tests/testthat/test-performance_mor.R |only tests/testthat/test-performance_poor.R |only tests/testthat/test-performance_roc.R | 103 ---- tests/testthat/test-r2.R | 35 + tests/testthat/test-r2_mcfadden.R | 41 + tests/testthat/test-r2_nakagawa.R | 536 ++----------------------- 40 files changed, 905 insertions(+), 1208 deletions(-)
Title: R Binding for the 'Certifiably Optimal RulE ListS (Corels)'
Learner
Description: The 'Certifiably Optimal RulE ListS (Corels)' learner by
Angelino et al described in <doi:10.48550/arXiv.1704.01701> provides interpretable decision
rules with an optimality guarantee, and is made available to R with this package.
See the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Dirk Eddelbuettel [aut, cre] ,
Nicholas Larus-Stone [aut] ,
Elaine Angelino [aut] ,
Daniel Alabi [ctb] ,
Cynthia Rudin [ctb] ,
Margo Seltzer [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between corels versions 0.0.5 dated 2024-12-04 and 0.0.6 dated 2026-08-28
ChangeLog | 22 DESCRIPTION | 19 MD5 | 12 README.md | 3 build/partial.rdb |binary configure | 3376 ++++++++++++++++++++++++++++++++---------------------- configure.ac | 4 7 files changed, 2091 insertions(+), 1345 deletions(-)
Title: (Bifactor) ESEM with Continuous (MLR) or Ordered (WLSMV) Data
Description: Fits bifactor exploratory structural equation models (B-ESEM),
together with standard exploratory structural equation modeling (ESEM)
and confirmatory factor analysis (CFA), for continuous and
ordered-categorical data. Continuous models use 'lavaan' native efa()
blocks with robust maximum likelihood (MLR) estimation.
Ordered-categorical ESEM defaults to the 'lavaan' weighted least squares
mean- and variance-adjusted (WLSMV) estimator; ordered B-ESEM uses a
custom diagonally weighted least squares (DWLS) path with polychoric
correlations from 'psych', rotation-delta standard errors via 'numDeriv',
and a mean- and variance-adjusted chi-square. Target, geomin, and oblimin
rotations use 'GPArotation'; the bifactor ESEM approach follows Morin,
Arens and Marsh (2016) <doi:10.1080/10705511.2014.961800>. Additional
features include multi-group measurement invariance (configural through
strict, with partial invariance), ESEM-within-CFA conversion, McDonald's
omega reliability suite, and t [...truncated...]
Author: Leon T. De Beer [aut, cre]
Maintainer: Leon T. De Beer <leondb@gmail.com>
Diff between bifactory versions 0.5.1 dated 2026-07-11 and 0.5.2 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 29 +++++++++++++++++++++++++++++ R/bifactor.R | 8 ++++++++ R/esem.R | 11 +++++++---- R/factor_scores.R | 44 +++++++++++++++++++++++++++++++++++--------- R/methods.R | 30 +++++++++++++++++++++++------- R/ordered_esem.R | 34 ++++++++++++++++++++++------------ R/pipeline.R | 11 +++++++---- R/reliability.R | 11 +++++++---- R/utils.R | 8 ++++---- man/factor_scores.Rd | 9 +++++++++ man/parameters.Rd | 15 ++++++++++++--- 13 files changed, 178 insertions(+), 62 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett [aut],
Amanda Ellis [aut],
Wanda Lauth [aut, cre]
Maintainer: Wanda Lauth <wanda.lauth@pmu.ac.at>
Diff between npmv versions 2.4.1 dated 2025-01-07 and 2.5.0 dated 2026-08-28
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/basenonpartest.R | 24 +++++++++++++++++------- R/nonpartest.R | 32 ++++++++++++++++++++++++-------- man/nonpartest.Rd | 15 +++++++++------ man/npmv-package.Rd | 4 ++-- man/ssnonpartest.Rd | 6 +++--- 8 files changed, 78 insertions(+), 42 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.16.0 dated 2026-06-30 and 0.17.0 dated 2026-08-28
DESCRIPTION | 22 +- MD5 | 97 +++++---- NAMESPACE | 16 + NEWS.md | 63 ++++++ R/estimate_contrasts.R | 38 +++ R/estimate_grouplevel.R | 6 R/estimate_means.R | 60 ++++-- R/estimate_predicted.R | 3 R/estimate_slopes.R | 1 R/format.R | 117 +++++++++++- R/get_contexteffects.R | 8 R/get_emcontrasts.R | 82 +++++--- R/get_emmeans.R | 58 +++++ R/get_inequalitycontrasts.R | 27 +- R/get_marginalcontrasts.R | 20 +- R/get_marginalmeans.R | 122 ++++++++++++ R/get_marginaltrends.R | 17 + R/options.R | 10 + R/p_adjust.R | 4 R/pool.R | 4 R/print.R | 22 +- R/summary.R | 2 R/tinyplot.R | 116 +++++++++++ R/utils.R | 2 R/visualisation_recipe.R | 10 - R/visualisation_recipe_internal.R | 1 inst/doc/overview_of_vignettes.Rmd | 4 inst/doc/overview_of_vignettes.html | 7 man/estimate_contrasts.Rd | 82 +++++--- man/estimate_expectation.Rd | 4 man/estimate_means.Rd | 57 ++++- man/estimate_slopes.Rd | 57 ++++- man/get_emmeans.Rd | 85 ++++++-- man/modelbased-options.Rd | 8 man/print.estimate_contrasts.Rd | 8 man/visualisation_recipe.estimate_predicted.Rd | 73 +++++++ tests/testthat/test-brms.R | 37 +++ tests/testthat/test-estimate_contrasts.R | 156 ++++++++++++++-- tests/testthat/test-estimate_contrasts_context.R | 4 tests/testthat/test-estimate_contrasts_counterfactual.R | 11 + tests/testthat/test-estimate_means.R | 38 +++ tests/testthat/test-estimate_means_ci.R | 126 ++++++++++-- tests/testthat/test-estimate_means_mixed.R | 67 +++++- tests/testthat/test-estimate_slopes.R | 32 +++ tests/testthat/test-glmmTMB.R | 113 ++++++++--- tests/testthat/test-mgcv.R | 20 +- tests/testthat/test-vcov.R | 2 tests/testthat/test-weighted_datagrid.R |only vignettes/bibliography.bib | 85 ++++++++ vignettes/overview_of_vignettes.Rmd | 4 50 files changed, 1668 insertions(+), 340 deletions(-)
Title: Improved Text Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables the rendering of
complex formatted plot labels (titles, subtitles, facet labels,
axis labels, etc.). Text boxes with automatic word wrap are also
supported.
Author: Claus O. Wilke [aut] ,
Brenton M. Wiernik [aut, cre]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between ggtext versions 0.1.2 dated 2022-09-16 and 0.2.0 dated 2026-08-28
DESCRIPTION | 14 MD5 | 60 ++- NAMESPACE | 1 NEWS.md | 4 R/draw-keys.R |only R/element-textbox.R | 17 - R/geom-richtext.R | 2 R/ggtext.R | 3 README.md | 27 - build/vignette.rds |binary inst/doc/plotting_text.R | 2 inst/doc/plotting_text.html | 424 +++++++++++++------------- inst/doc/theme_elements.R | 2 inst/doc/theme_elements.html | 473 +++++++++++++++--------------- man/draw_key_richtext.Rd |only man/element_markdown.Rd | 4 man/element_textbox.Rd | 21 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/geom_richtext.Rd | 94 ++++- man/geom_textbox.Rd | 78 +++- man/ggtext.Rd | 19 + tests/testthat/_snaps |only tests/testthat/test-draw-keys.R |only 29 files changed, 687 insertions(+), 558 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.8 dated 2026-07-20 and 0.4.9 dated 2026-08-28
DESCRIPTION | 12 MD5 | 78 ++--- NAMESPACE | 1 NEWS.md | 11 R/cms_catalogue_entry.R | 2 R/cms_cite_product.r | 2 R/cms_download_native.R | 580 +++++++++++++++++++++---------------------- R/cms_download_subset.r | 89 ++++-- R/cms_glossary.R | 2 R/cms_login.r | 4 R/cms_ncdf.R |only R/cms_product_details.r | 2 R/cms_product_metadata.r | 2 R/cms_product_services.r | 2 R/cms_products_list.r | 2 R/cms_wmts.r | 2 R/init.R | 52 ++- R/translate.R | 2 README.md | 53 ++- inst/doc/glossary.html | 4 inst/doc/product-info.html | 2 inst/doc/proxy.html | 2 man/account.Rd | 2 man/cms_cite_product.Rd | 2 man/cms_download_native.Rd | 4 man/cms_download_subset.Rd | 6 man/cms_get_client_info.Rd | 5 man/cms_glossary.Rd | 5 man/cms_login.Rd | 2 man/cms_native_proxy.Rd | 4 man/cms_native_s3.Rd | 8 man/cms_product_details.Rd | 2 man/cms_product_metadata.Rd | 2 man/cms_product_services.Rd | 2 man/cms_products_list.Rd | 2 man/cms_translate.Rd | 3 man/cms_wmts.Rd | 2 man/cms_write_ncdf.Rd |only man/cms_zarr_proxy.Rd | 2 tests/testthat/test_native.r | 4 tests/testthat/test_subset.r | 52 +++ 41 files changed, 574 insertions(+), 441 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Search Download and Handle Data from the Copernicus Data Space
Ecosystem
Description: The Copernicus Data Space Ecosystem, is an open
ecosystem that provides free instant access to a wide range
of data and services from the Copernicus Sentinel missions and
more on our planet’s land, oceans and atmosphere. This package
provides entry points to several APIs allowing users to access
the data directly in R.
Author: Pepijn de Vries [aut, cre] ,
Alicia Hamer [rtm] ,
LVVN
[fnd] ,
WMR [ctr]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusDataspace versions 0.0.4 dated 2026-07-20 and 0.0.5 dated 2026-08-28
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/init.R | 7 ++++--- R/login.R | 2 +- R/odata_products.R | 5 +++-- R/s3.R | 2 +- R/sentinelhub.R | 4 +++- R/stac.R | 9 +++++++-- R/tidyverse.R | 2 +- inst/doc/OData.html | 16 ++++++++-------- inst/doc/STAC.html | 24 ++++++++++++------------ inst/doc/SentinelHub.html | 28 ++++++++++++++-------------- 13 files changed, 78 insertions(+), 62 deletions(-)
More information about CopernicusDataspace at CRAN
Permanent link
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.10.2 dated 2026-01-07 and 4.10.3 dated 2026-08-28
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 4 R/export2md.R | 14 -- R/prepare.r | 9 - inst/app/server.R | 35 ++--- inst/doc/compareGroups_vignette.html | 237 +++++++++++++++++------------------ man/compareGroups-package.Rd | 4 8 files changed, 162 insertions(+), 163 deletions(-)
Title: ARAchnid KNowledge Online
Description: Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Author: Pedro Cardoso [aut, cre]
Maintainer: Pedro Cardoso <pmcardoso@ciencias.ulisboa.pt>
Diff between arakno versions 1.3.2 dated 2026-04-20 and 1.3.3 dated 2026-08-28
arakno-1.3.2/arakno/data/wscmap.csv |only arakno-1.3.2/arakno/man/buildtree.Rd |only arakno-1.3.2/arakno/man/checknames.Rd |only arakno-1.3.3/arakno/DESCRIPTION | 12 +- arakno-1.3.3/arakno/MD5 | 29 ++-- arakno-1.3.3/arakno/NAMESPACE | 4 arakno-1.3.3/arakno/R/arakno.R | 190 ++++++++++++++------------------ arakno-1.3.3/arakno/R/globals.R |only arakno-1.3.3/arakno/data/wscmap.csv.gz |only arakno-1.3.3/arakno/man/authors.Rd | 4 arakno-1.3.3/arakno/man/buildTree.Rd |only arakno-1.3.3/arakno/man/checkNames.Rd |only arakno-1.3.3/arakno/man/countries.Rd | 4 arakno-1.3.3/arakno/man/distribution.Rd | 4 arakno-1.3.3/arakno/man/endemics.Rd | 6 - arakno-1.3.3/arakno/man/lsid.Rd | 4 arakno-1.3.3/arakno/man/map.Rd | 4 arakno-1.3.3/arakno/man/species.Rd | 4 arakno-1.3.3/arakno/man/taxonomy.Rd | 4 19 files changed, 128 insertions(+), 141 deletions(-)
Title: Programmatic Access to Data and Statistics from the World Bank
API
Description: Search and download data from the World Bank Data API. Includes
support for mutliple languages, access to annual, quarterly, and monthly
data.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Jesse Piburn [aut] ,
The World Bank [dtc]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between wbstats versions 1.1 dated 2025-09-14 and 1.2 dated 2026-08-28
wbstats-1.1/wbstats/R/utils-pipe.R |only wbstats-1.1/wbstats/data/wb_cachelist.RData |only wbstats-1.1/wbstats/man/figures/ggplot2-1.png |only wbstats-1.1/wbstats/man/figures/readme-chart-1.png |only wbstats-1.1/wbstats/man/pipe.Rd |only wbstats-1.1/wbstats/tests/testthat |only wbstats-1.1/wbstats/tests/testthat.R |only wbstats-1.1/wbstats/tools |only wbstats-1.2/wbstats/DESCRIPTION | 25 wbstats-1.2/wbstats/MD5 | 93 +- wbstats-1.2/wbstats/NAMESPACE | 25 wbstats-1.2/wbstats/NEWS.md | 13 wbstats-1.2/wbstats/R/build_urls.R | 133 +-- wbstats-1.2/wbstats/R/end_points.R | 34 wbstats-1.2/wbstats/R/format-data.R | 125 +- wbstats-1.2/wbstats/R/search.R | 51 - wbstats-1.2/wbstats/R/sysdata.rda |binary wbstats-1.2/wbstats/R/update_cache.R | 20 wbstats-1.2/wbstats/R/utils.R | 28 wbstats-1.2/wbstats/R/wb_country_coverage.R |only wbstats-1.2/wbstats/R/wb_data.R | 218 ++--- wbstats-1.2/wbstats/R/wbstats-package.R | 14 wbstats-1.2/wbstats/R/zzz.R | 6 wbstats-1.2/wbstats/README.md | 158 ++- wbstats-1.2/wbstats/build/vignette.rds |binary wbstats-1.2/wbstats/data/wb_cachelist.rda |only wbstats-1.2/wbstats/inst/doc/wbstats.Rmd | 500 +++++++---- wbstats-1.2/wbstats/inst/doc/wbstats.html | 553 ++++++++----- wbstats-1.2/wbstats/inst/tinytest |only wbstats-1.2/wbstats/man/figures/logo.svg | 48 - wbstats-1.2/wbstats/man/figures/readme-gdppc-vs-lifexp.png |only wbstats-1.2/wbstats/man/wb_cache.Rd | 25 wbstats-1.2/wbstats/man/wb_cachelist.Rd | 13 wbstats-1.2/wbstats/man/wb_country_coverage.Rd |only wbstats-1.2/wbstats/man/wb_data.Rd | 183 ++-- wbstats-1.2/wbstats/man/wb_end_point_info.Rd | 28 wbstats-1.2/wbstats/man/wb_indicators.Rd | 40 wbstats-1.2/wbstats/man/wb_search.Rd | 48 - wbstats-1.2/wbstats/man/wbstats.Rd | 35 wbstats-1.2/wbstats/tests/tinytest.R |only wbstats-1.2/wbstats/vignettes/wbstats.Rmd | 500 +++++++---- 41 files changed, 1684 insertions(+), 1232 deletions(-)
More information about VanillaCalendar at CRAN
Permanent link
Title: Parse 'User-Agent' Strings
Description: Parses HTTP user agent strings and returns user agent, device and OS information.
This is a ‘V8’-backed package that uses the UA, device and OS definitions from the ‘ua-parser’
project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb],
Jim Vine [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.4.0 dated 2026-07-02 and 0.4.1 dated 2026-08-28
uaparserjs-0.4.0/uaparserjs/README.md |only uaparserjs-0.4.1/uaparserjs/DESCRIPTION | 13 ++-- uaparserjs-0.4.1/uaparserjs/MD5 | 24 +++++--- uaparserjs-0.4.1/uaparserjs/NEWS.md | 5 + uaparserjs-0.4.1/uaparserjs/R/uaparser.R | 15 ++--- uaparserjs-0.4.1/uaparserjs/R/utils.R | 2 uaparserjs-0.4.1/uaparserjs/R/zzz.r | 6 -- uaparserjs-0.4.1/uaparserjs/inst/js/bundle.js | 2 uaparserjs-0.4.1/uaparserjs/inst/tinytest/test_exhaustive.R | 27 ++++------ uaparserjs-0.4.1/uaparserjs/inst/tinytest/test_multirow.R | 21 ++++--- uaparserjs-0.4.1/uaparserjs/inst/tinytest/tests/test_device.yaml | 10 +++ uaparserjs-0.4.1/uaparserjs/man/figures |only uaparserjs-0.4.1/uaparserjs/tests/test_device.yaml |only uaparserjs-0.4.1/uaparserjs/tests/test_os.yaml |only uaparserjs-0.4.1/uaparserjs/tests/test_ua.yaml |only 15 files changed, 73 insertions(+), 52 deletions(-)
Title: Design and Analysis Tools for Target Trial Emulation
Description: Design and analysis tools for target trial emulation using longitudinal observational data. Functions are provided for checking person-period data, expanding longitudinal data into sequentially nested trials, estimating inverse probability weights for intention-to-treat and per-protocol analyses, and assessing weight distributions and covariate balance. Additional functions fit weighted pooled discrete-time outcome models, obtain standardized risks and treatment contrasts, and estimate weighted Kaplan-Meier and Aalen-Johansen curves. Two worked examples based on fully synthetic data illustrate an active-comparator new-user study comparing sodium-glucose cotransporter 2 inhibitors with dipeptidyl peptidase-4 inhibitors and an analysis of sequentially nested trials comparing angiotensin receptor blocker and calcium channel blocker strategies.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between TTE versions 1.1.1 dated 2026-08-02 and 1.1.2 dated 2026-08-28
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- man/SGLT2.Rd | 2 +- man/TTE-package.Rd | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Statistical Framework for Co-Mediators of Zero-Inflated
Single-Cell Data
Description: A causal mediation framework for single-cell data that incorporates two key features ('MedZIsc', pronounced Magics): (1) zero-inflation using beta regression and (2) overdispersed expression counts using negative binomial regression. This approach also includes a screening step based on penalized and marginal models to handle high-dimensionality. Full methodological details are available in our recent preprint by Ahn S et al. (2025) <doi:10.48550/arXiv.2507.06113>.
Author: Seungjun Ahn [cre, aut] ,
Zhigang Li [ctb]
Maintainer: Seungjun Ahn <seungjun.ahn@mountsinai.org>
Diff between MedZIsc versions 0.0.4 dated 2025-07-16 and 0.0.5 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 1 + R/Magics.R | 9 +++++---- R/compute_M.R |only man/Magics.Rd | 9 +++++---- man/compute_M.Rd |only 7 files changed, 21 insertions(+), 16 deletions(-)
Title: Download and Visualize Essential Global Heating Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, CMIP6 projections, sea levels, Arctic/Antarctic sea-ice, Hurricanes, Wildfires, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.htm [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.9.1 dated 2026-07-08 and 1.0.0 dated 2026-08-28
DESCRIPTION | 16 +++--- MD5 | 79 +++++++++++++++++--------------- NAMESPACE | 76 +++++++++++++++++++------------ NEWS.md | 6 ++ R/2kyears_temp.R | 2 R/carbon.R | 2 R/daily_temp.R | 8 +-- R/data_cache.R | 3 + R/emissions.R | 2 R/fires.R | 16 +++--- R/future_climate.R |only R/hurricanes.R | 5 -- R/icecurves.R | 2 R/instrumental_temp.R | 2 R/methane.R | 2 R/paleo.R | 4 - R/seaice.R | 2 R/sealevel.R | 4 - README.md | 46 ++++++++++++------ inst/WORDLIST | 20 ++++++++ inst/doc/usinghockeystick.R | 14 +++++ inst/doc/usinghockeystick.html | 88 ++++++++++++++++++++++-------------- inst/doc/usinghockeystick.qmd | 17 ++++++ man/figures/README-carbon-1.png |binary man/figures/README-cmip6-1.png |only man/figures/README-cmip6anom-1.png |only man/figures/README-dailytemp-1.png |binary man/figures/README-fires-1.png |binary man/figures/README-fires-2.png |binary man/figures/README-grid-1.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-si-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/get_cmip6.Rd |only man/get_cmip6_anom.Rd |only man/hockeystick-package.Rd | 4 - man/plot_cmip6.Rd |only man/plot_cmip6_anom.Rd |only man/plot_dailytemp.Rd | 2 vignettes/usinghockeystick.qmd | 17 ++++++ 44 files changed, 291 insertions(+), 148 deletions(-)
Title: Numerical Tools for 'Rcpp' and Lambda Functions
Description: Provides a 'C++' API for routinely used numerical tools such as integration,
root-finding, and optimization, where function arguments are given as
lambdas. This facilitates 'Rcpp' programming, enabling the development of
'R'-like code in 'C++' where functions can be defined on the fly and use
variables in the surrounding environment.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between fntl versions 0.1.3.1 dated 2026-07-30 and 0.1.3.2 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/fntl.pdf |binary inst/doc/fntl.qmd | 2 +- inst/include/util.h | 2 ++ vignettes/fntl.qmd | 2 +- 6 files changed, 13 insertions(+), 11 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests, directed and
covariate-space tests, smoothing and resampling tests, and calibration
tests. Each is obtained from its own package where installed and
attributed to its authors. The package also implements the author's own
procedures for sparse data, where the Hosmer-Lemeshow test loses power:
the omnibus Ebrahim-Farrington test, the directed 'EDGE' test,
'DeepGOF-1' (a pretrained convolutional statistic whose level comes from the
analyst's own parametric bootstrap rather than from the network), a
Cauchy-combination ensemble, 'legoft()' (a pretrained combination whose
weights are fixed offline and ship frozen, so two analysts obtain the same
p-value), and 'shrink. [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.4.0 dated 2026-07-22 and 2.6.0 dated 2026-08-28
DESCRIPTION | 40 MD5 | 24 NAMESPACE | 88 NEWS.md | 750 +++++--- R/deepgof.R |only R/legoft.R |only R/run_all_gof.R | 2925 ++++++++++++++++++--------------- R/shrink_gof.R |only R/sysdata.rda |only inst/doc/ebrahim-farrington-intro.html | 4 man/deepgof1.Rd |only man/legoft.Rd |only man/legoft.localize.Rd |only man/run.all.gof.Rd | 356 +++- man/shrink.gof.Rd |only tests/testthat/test-deepgof1.R |only tests/testthat/test-lecessie-algebra.R |only tests/testthat/test-run-all-gof.R | 354 ++- 18 files changed, 2636 insertions(+), 1905 deletions(-)
Title: Data from the GLM Book by Dobson and Barnett
Description: Example datasets from the book "An Introduction to Generalised Linear Models" (4th edition) (Year: 2018, <isbn:9781138741515>) by Dobson and Barnett.
Author: Adrian Barnett [aut, cre, cph]
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>
Diff between dobson versions 0.4 dated 2018-11-20 and 0.4.1 dated 2026-08-28
dobson-0.4.1/dobson/DESCRIPTION | 18 +++--- dobson-0.4.1/dobson/MD5 | 92 ++++++++++++++++---------------- dobson-0.4.1/dobson/NAMESPACE | 2 dobson-0.4.1/dobson/NEWS.md |only dobson-0.4.1/dobson/README.md |only dobson-0.4.1/dobson/data/achieve.rda |only dobson-0.4.1/dobson/data/anthers.rda |binary dobson-0.4.1/dobson/data/doctors.rda |binary dobson-0.4.1/dobson/man/Cars.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/PLOS.Rd | 2 dobson-0.4.1/dobson/man/achieve.Rd |only dobson-0.4.1/dobson/man/aids.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/anthers.Rd | 60 ++++++++++---------- dobson-0.4.1/dobson/man/balanced.Rd | 6 +- dobson-0.4.1/dobson/man/beetle.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/birthweight.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/carbohydrate.Rd | 58 ++++++++++---------- dobson-0.4.1/dobson/man/cholesterol.Rd | 4 - dobson-0.4.1/dobson/man/chronic.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/doctors.Rd | 57 ++++++++++--------- dobson-0.4.1/dobson/man/dogs.Rd | 58 ++++++++++---------- dobson-0.4.1/dobson/man/ear.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/failure.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/graduates.Rd | 2 dobson-0.4.1/dobson/man/hepatitis.Rd | 60 ++++++++++---------- dobson-0.4.1/dobson/man/hiroshima.Rd | 2 dobson-0.4.1/dobson/man/housing.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/insurance.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/leukemia.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/machine.Rd | 4 - dobson-0.4.1/dobson/man/melanoma.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/mortality.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/moths.Rd | 62 ++++++++++----------- dobson-0.4.1/dobson/man/plant.dried.Rd | 9 +-- dobson-0.4.1/dobson/man/plants.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/plasma.Rd | 6 +- dobson-0.4.1/dobson/man/poisson.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/remission.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/senility.Rd | 50 ++++++++--------- dobson-0.4.1/dobson/man/stroke.wide.Rd | 30 ++++------ dobson-0.4.1/dobson/man/sugar.Rd | 6 +- dobson-0.4.1/dobson/man/survival.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/tumor.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/ulcer.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/unbalanced.Rd | 4 - dobson-0.4.1/dobson/man/vaccine.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/waist.Rd | 60 ++++++++++---------- dobson-0.4/dobson/R |only dobson-0.4/dobson/data/achievement.rda |only dobson-0.4/dobson/man/achievement.Rd |only dobson-0.4/dobson/man/dobson.Rd |only 51 files changed, 826 insertions(+), 820 deletions(-)
Title: Deep Compositional Spatial Models
Description: Deep compositional spatial models are standard spatial covariance
models coupled with an injective warping function of the spatial
domain. The warping function is constructed through a composition
of multiple elemental injective functions in a deep-learning
framework. The package implements two cases for the univariate setting; first,
when these warping functions are known up to some weights that
need to be estimated, and, second, when the weights in each layer are random.
In the multivariate setting only the former case is available.
Estimation and inference is done using `tensorflow`, which makes use of
graphics processing units.
For more details see Zammit-Mangion et al. (2022) <doi:10.1080/01621459.2021.1887741>,
Vu et al. (2022) <doi:10.5705/ss.202020.0156>,
Vu et al. (2023) <doi:10.1016/j.spasta.2023.100742>, and
Shao et al. (2025) <doi:10.48550/arXiv.2505.12548>.
Author: Andrew Zammit-Mangion [aut],
Quan Vu [aut, cre],
Xuanjie Shao [aut]
Maintainer: Quan Vu <quanvustats@gmail.com>
Diff between deepspat versions 0.3.1 dated 2025-11-25 and 0.3.2 dated 2026-08-28
deepspat-0.3.1/deepspat/R/NMLL_nn_ST.R |only deepspat-0.3.1/deepspat/R/summary.deepspat_MSP.R |only deepspat-0.3.1/deepspat/R/summary.deepspat_rPP.R |only deepspat-0.3.1/deepspat/R/tent.R |only deepspat-0.3.1/deepspat/man/summary.deepspat_MSP.Rd |only deepspat-0.3.1/deepspat/man/summary.deepspat_rPP.Rd |only deepspat-0.3.2/deepspat/DESCRIPTION | 12 deepspat-0.3.2/deepspat/MD5 | 111 deepspat-0.3.2/deepspat/NAMESPACE | 29 deepspat-0.3.2/deepspat/NEWS.md | 27 deepspat-0.3.2/deepspat/R/AFF.R | 250 - deepspat-0.3.2/deepspat/R/NMLL.R | 48 deepspat-0.3.2/deepspat/R/RBF.R | 70 deepspat-0.3.2/deepspat/R/bisquare.R | 90 deepspat-0.3.2/deepspat/R/bisquare_basis.R | 198 - deepspat-0.3.2/deepspat/R/cov_fns.R | 235 - deepspat-0.3.2/deepspat/R/cov_fns_nn.R | 156 - deepspat-0.3.2/deepspat/R/deepspat.R | 16 deepspat-0.3.2/deepspat/R/deepspat_main.R | 541 ++-- deepspat-0.3.2/deepspat/R/deepspat_main_GP.R | 721 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_MSP.R | 851 +++--- deepspat-0.3.2/deepspat/R/deepspat_main_bivar_GP.R | 1739 ++++++------- deepspat-0.3.2/deepspat/R/deepspat_main_nn_GP.R | 685 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_nn_ST_GP.R | 1114 ++++---- deepspat-0.3.2/deepspat/R/deepspat_main_rPP.R | 764 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_trivar_GP.R | 1871 +++++++------- deepspat-0.3.2/deepspat/R/init_learn_rates.R | 62 deepspat-0.3.2/deepspat/R/plot.deepspat.R |only deepspat-0.3.2/deepspat/R/predict.deepspat.R | 8 deepspat-0.3.2/deepspat/R/predict.deepspat_GP.R | 229 - deepspat-0.3.2/deepspat/R/predict.deepspat_MSP.R |only deepspat-0.3.2/deepspat/R/predict.deepspat_bivar_GP.R | 545 ++-- deepspat-0.3.2/deepspat/R/predict.deepspat_nn_GP.R | 244 + deepspat-0.3.2/deepspat/R/predict.deepspat_nn_ST_GP.R | 346 +- deepspat-0.3.2/deepspat/R/predict.deepspat_rPP.R |only deepspat-0.3.2/deepspat/R/predict.deepspat_trivar_GP.R | 85 deepspat-0.3.2/deepspat/R/print.deepspat.R |only deepspat-0.3.2/deepspat/R/sigmoid.R | 38 deepspat-0.3.2/deepspat/R/sim_data.R | 328 +- deepspat-0.3.2/deepspat/R/summary.deepspat.R |only deepspat-0.3.2/deepspat/R/train_step.R | 53 deepspat-0.3.2/deepspat/R/utils.R | 626 ++-- deepspat-0.3.2/deepspat/R/utils_error.R |only deepspat-0.3.2/deepspat/R/utils_tf.R | 161 - deepspat-0.3.2/deepspat/R/zzz.R | 142 - deepspat-0.3.2/deepspat/README.md | 108 deepspat-0.3.2/deepspat/man/deepspat.Rd | 30 deepspat-0.3.2/deepspat/man/deepspat_GP.Rd | 6 deepspat-0.3.2/deepspat/man/deepspat_MSP.Rd | 5 deepspat-0.3.2/deepspat/man/deepspat_bivar_GP.Rd | 6 deepspat-0.3.2/deepspat/man/deepspat_nn_GP.Rd | 4 deepspat-0.3.2/deepspat/man/deepspat_nn_ST_GP.Rd | 4 deepspat-0.3.2/deepspat/man/deepspat_rPP.Rd | 2 deepspat-0.3.2/deepspat/man/deepspat_trivar_GP.Rd | 4 deepspat-0.3.2/deepspat/man/plot.deepspat.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat.Rd | 4 deepspat-0.3.2/deepspat/man/predict.deepspat_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_MSP.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat_bivar_GP.Rd | 12 deepspat-0.3.2/deepspat/man/predict.deepspat_nn_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_nn_ST_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_rPP.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat_trivar_GP.Rd | 12 deepspat-0.3.2/deepspat/man/print.deepspat.Rd |only deepspat-0.3.2/deepspat/man/summary.deepspat.Rd |only 65 files changed, 6673 insertions(+), 5949 deletions(-)
Title: Bayesian Essentials with R
Description: Allows the reenactment of the R programs used in
the book Bayesian Essentials with R without further programming.
R code being available as well, they can be modified by the user
to conduct one's own simulations.
Marin J.-M. and Robert C. P. (2014) <doi:10.1007/978-1-4614-8687-9>.
Author: Jean-Michel Marin [aut, cre],
Christian P. Robert [aut]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
This is a re-admission after prior archival of version 1.6 dated 2024-03-06
Diff between bayess versions 1.6 dated 2024-03-06 and 1.7 dated 2026-08-28
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 19 insertions(+), 10 deletions(-)
Title: Optimal Confidence Intervals for Visual Testing
Description: Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.
Author: Dave Armstrong [aut, cre] ,
William Poirier [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between VizTest versions 0.7 dated 2026-03-03 and 0.8 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/functions.R | 14 +++++++++++++- build/vignette.rds |binary inst/doc/compact_letter_displays.html | 12 ++++++------ inst/doc/creating_forest_plots.html | 18 +++++++++--------- inst/doc/heatmaps.html | 19 +++++++++---------- inst/doc/sig_diffs_explanation.html | 20 ++++++++++---------- inst/doc/significance_brackets.html | 10 +++++----- man/geom_forestpoint.Rd | 5 +++++ man/geom_foreststripe.Rd | 5 +++++ man/geom_foresttable.Rd | 5 +++++ 12 files changed, 81 insertions(+), 55 deletions(-)
Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and
semi-supervised classification with mixture modelling <doi: 10.18637/jss.v067.i06>.
Author: Florent Langrognet [aut],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [aut],
Parmeet Bhatia [ctb],
Anwuli Echenim [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb],
Gerard Govaert [ctb],
Julien Schueller [ctb],
Q [...truncated...]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between Rmixmod versions 2.1.10 dated 2023-12-13 and 2.1.12 dated 2026-08-28
DESCRIPTION | 10 MD5 | 119 +- R/Mixmod.R | 451 +++++----- R/MixmodResults.R | 23 R/Strategy.R | 2 configure | 24 man/Rmixmod-package.Rd | 7 man/extract-methods.Rd | 60 - man/initialize-methods.Rd | 14 man/mixmodStrategy.Rd | 2 src/Makevars.in | 8 src/Makevars.win | 10 src/mixmod/Clustering/ClusteringMain.cpp | 11 src/mixmod/Clustering/ClusteringOutput.cpp | 54 - src/mixmod/Clustering/ClusteringStrategy.cpp | 8 src/mixmod/Clustering/ClusteringStrategyInit.cpp | 24 src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.cpp | 54 - src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.cpp | 50 - src/mixmod/Kernel/Algo/Algo.cpp | 2 src/mixmod/Kernel/Algo/CEMAlgo.cpp | 4 src/mixmod/Kernel/Algo/EMAlgo.cpp | 6 src/mixmod/Kernel/Algo/MAPAlgo.cpp | 2 src/mixmod/Kernel/Algo/MAlgo.cpp | 2 src/mixmod/Kernel/Algo/SEMAlgo.cpp | 8 src/mixmod/Kernel/Criterion/CVCriterion.cpp | 34 src/mixmod/Kernel/Criterion/CriterionOutput.cpp | 2 src/mixmod/Kernel/IO/BinaryData.cpp | 42 src/mixmod/Kernel/IO/GaussianData.cpp | 8 src/mixmod/Kernel/IO/Input.cpp | 2 src/mixmod/Kernel/IO/Label.cpp | 4 src/mixmod/Kernel/IO/Partition.cpp | 8 src/mixmod/Kernel/IO/ProbaOutput.cpp | 2 src/mixmod/Kernel/Model/Model.cpp | 74 - src/mixmod/Kernel/Parameter/BinaryEParameter.cpp | 8 src/mixmod/Kernel/Parameter/BinaryEjParameter.cpp | 6 src/mixmod/Kernel/Parameter/BinaryEkParameter.cpp | 6 src/mixmod/Kernel/Parameter/BinaryEkjParameter.cpp | 18 src/mixmod/Kernel/Parameter/BinaryEkjhParameter.cpp | 4 src/mixmod/Kernel/Parameter/BinaryParameter.cpp | 24 src/mixmod/Kernel/Parameter/CompositeParameter.cpp | 8 src/mixmod/Kernel/Parameter/GaussianEDDAParameter.cpp | 24 src/mixmod/Kernel/Parameter/GaussianGeneralParameter.cpp | 2 src/mixmod/Kernel/Parameter/GaussianHDDAParameter.cpp | 68 - src/mixmod/Kernel/Parameter/GaussianParameter.cpp | 2 src/mixmod/Kernel/Parameter/GaussianSphericalParameter.cpp | 8 src/mixmod/Kernel/Parameter/Parameter.cpp | 4 src/mixmod/Matrix/DiagMatrix.cpp | 2 src/mixmod/Matrix/SymmetricMatrix.cpp | 4 src/mixmod/Utilities/OutputAdapter.h |only src/mixmod/Utilities/Random.cpp | 12 src/mixmod/Utilities/Util.cpp | 14 src/mixmod/Utilities/Util.h | 1 src/mixmod/Utilities/exceptions/DCVException.h | 2 src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.h | 2 src/mixmod/Utilities/exceptions/Exception.h | 4 src/mixmod/Utilities/exceptions/InputException.h | 2 src/mixmod/Utilities/exceptions/NumericException.h | 2 src/mixmod/Utilities/exceptions/OtherException.h | 2 src/mixmod/Utilities/maths/Eigen.h | 8 src/mixmod_iostream/IOStreamUtil.cpp | 35 src/mixmod_iostream/NodeOpInput.cpp | 2 61 files changed, 706 insertions(+), 699 deletions(-)
Title: Lean Analytics and Robust Exploration Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.4.0 dated 2026-04-23 and 5.4.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 368 ++++++++++++------------- NAMESPACE | 592 +++++++++++++++++++++-------------------- R/confidence.R | 8 R/correlations.R | 6 R/google_sheets.R | 74 ++--- R/lares.R | 61 ++-- R/onehotencoding.R | 2 R/stocks.R | 2 R/utils_data.R | 50 ++- R/utils_system.R | 14 R/wrangling.R | 6 inst/doc/api-integrations.html | 4 inst/doc/data-wrangling.html | 22 - inst/doc/games.html | 4 inst/doc/machine-learning.html | 102 +++---- inst/doc/robyn_lares.html | 4 man/ROC.Rd | 38 +- man/autoline.Rd | 74 ++--- man/balance_data.Rd | 46 +-- man/bind_files.Rd | 74 ++--- man/bring_api.Rd | 100 +++--- man/cal_split.Rd | 74 ++--- man/categ_reducer.Rd | 46 +-- man/chr2num.Rd | 74 ++--- man/ci_lower.Rd | 4 man/ci_var.Rd | 4 man/clean_text.Rd | 64 ++-- man/clusterKmeans.Rd | 10 man/clusterOptimalK.Rd | 10 man/clusterVisualK.Rd | 10 man/conf_mat.Rd | 38 +- man/corr.Rd | 16 - man/corr_cross.Rd | 16 - man/corr_var.Rd | 34 +- man/crosstab.Rd | 28 - man/dalex_local.Rd | 8 man/dalex_residuals.Rd | 8 man/dalex_variable.Rd | 8 man/date_cuts.Rd | 46 +-- man/date_feats.Rd | 60 ++-- man/db_download.Rd | 98 +++--- man/db_upload.Rd | 98 +++--- man/df_str.Rd | 28 - man/dfr.Rd | 2 man/dft.Rd | 2 man/dist2d.Rd | 10 man/distr.Rd | 48 +-- man/dont_sleep.Rd | 74 ++--- man/encrypt_file.Rd | 20 - man/errors.Rd | 12 man/etf_sector.Rd | 10 man/export_plot.Rd | 74 ++--- man/export_results.Rd | 100 +++--- man/fb_accounts.Rd | 42 +- man/fb_ads.Rd | 42 +- man/fb_creatives.Rd | 42 +- man/fb_insights.Rd | 42 +- man/fb_process.Rd | 42 +- man/fb_report_check.Rd | 42 +- man/fb_rf.Rd | 42 +- man/fb_token.Rd | 42 +- man/file_name.Rd | 70 +--- man/filesGD.Rd | 24 - man/files_functions.Rd | 74 ++--- man/filterdata.Rd | 94 +----- man/font_exists.Rd | 74 ++--- man/forecast_arima.Rd | 4 man/formatColoured.Rd | 74 ++--- man/format_string.Rd | 120 ++++---- man/freqs.Rd | 56 +-- man/freqs_df.Rd | 56 +-- man/freqs_list.Rd | 56 +-- man/freqs_plot.Rd | 56 +-- man/gain_lift.Rd | 38 +- man/gemini_ask.Rd | 32 +- man/get_credentials.Rd | 20 - man/get_tweets.Rd | 20 - man/gg_fill_customs.Rd | 8 man/glued.Rd | 74 ++--- man/google_sheets.Rd | 24 - man/google_trends.Rd | 24 - man/gpt_ask.Rd | 36 +- man/gpt_prompter.Rd | 10 man/grepm.Rd | 74 ++--- man/h2o_automl.Rd | 26 - man/h2o_explainer.Rd | 8 man/h2o_predict.Rd | 26 - man/h2o_selectmodel.Rd | 100 +++--- man/h2o_shap.Rd | 4 man/haveInternet.Rd | 74 ++--- man/holidays.Rd | 78 ++--- man/image_metadata.Rd | 74 ++--- man/importxlsx.Rd | 74 ++--- man/impute.Rd | 76 ++--- man/ip_data.Rd | 103 +++---- man/iter_seeds.Rd | 26 - man/json2vector.Rd | 74 ++--- man/lares_pal.Rd | 8 man/lasso_vars.Rd | 54 +-- man/left_right.Rd | 46 +-- man/list_cats.Rd | 74 ++--- man/listfiles.Rd | 74 ++--- man/loglossBinary.Rd | 12 man/mail_send.Rd | 94 +++--- man/markdown2df.Rd | 74 ++--- man/maze_solve.Rd | 8 man/missingness.Rd | 32 +- man/model_metrics.Rd | 48 +-- man/model_preprocess.Rd | 26 - man/move_files.Rd | 74 ++--- man/mp3_get.Rd | 22 - man/mp3_trim.Rd | 6 man/mp3_update_tags.Rd | 6 man/mplot_conf.Rd | 26 - man/mplot_cuts.Rd | 26 - man/mplot_cuts_error.Rd | 26 - man/mplot_density.Rd | 26 - man/mplot_full.Rd | 26 - man/mplot_gain.Rd | 26 - man/mplot_importance.Rd | 26 - man/mplot_lineal.Rd | 26 - man/mplot_metrics.Rd | 26 - man/mplot_response.Rd | 26 - man/mplot_roc.Rd | 26 - man/mplot_splits.Rd | 26 - man/mplot_topcats.Rd | 26 - man/msplit.Rd | 100 +++--- man/myip.Rd | 76 ++--- man/ngrams.Rd | 18 - man/noPlot.Rd | 20 - man/normalize.Rd | 46 +-- man/num_abbr.Rd | 46 +-- man/ohe_commas.Rd | 54 +-- man/ohse.Rd | 60 ++-- man/outlier_tukey.Rd | 8 man/outlier_zscore.Rd | 8 man/outlier_zscore_plot.Rd | 8 man/plot_cats.Rd | 28 - man/plot_chord.Rd | 20 - man/plot_df.Rd | 28 - man/plot_nums.Rd | 28 - man/plot_palette.Rd | 8 man/plot_survey.Rd | 20 - man/plot_timeline.Rd | 20 - man/prophesize.Rd | 4 man/quants.Rd | 56 +-- man/queryDB.Rd | 20 - man/queryGA.Rd | 54 +-- man/quiet.Rd | 74 ++--- man/read.file.Rd | 74 ++--- man/reduce_pca.Rd | 14 man/reduce_tsne.Rd | 14 man/remove_stopwords.Rd | 18 - man/replaceall.Rd | 64 ++-- man/replacefactor.Rd | 46 +-- man/robyn_hypsbuilder.Rd | 8 man/robyn_marginal.Rd | 8 man/robyn_modelselector.Rd | 8 man/robyn_performance.Rd | 8 man/scrabble.Rd | 8 man/sentimentBreakdown.Rd | 18 - man/shap_var.Rd | 4 man/slackSend.Rd | 46 +-- man/statusbar.Rd | 74 ++--- man/stocks_hist.Rd | 24 - man/stocks_plots.Rd | 24 - man/stocks_report.Rd | 28 - man/sudoku_solver.Rd | 8 man/textCloud.Rd | 18 - man/textFeats.Rd | 64 ++-- man/textTokenizer.Rd | 64 ++-- man/theme_lares.Rd | 8 man/tic.Rd | 74 ++--- man/topics_rake.Rd | 18 - man/tree_var.Rd | 48 +-- man/try_require.Rd | 74 ++--- man/updateLares.Rd | 74 ++--- man/vector2text.Rd | 46 +-- man/warnifnot.Rd | 74 ++--- man/what_size.Rd | 74 ++--- man/winsorize.Rd | 8 man/wordle.Rd | 8 man/year_month.Rd | 46 +-- man/zerovar.Rd | 46 +-- 185 files changed, 4021 insertions(+), 4009 deletions(-)
Title: Direct Labels for Multicolor Plots
Description: An extensible framework
for automatically placing direct labels onto multicolor 'lattice' or
'ggplot2' plots.
Label positions are described using Positioning Methods
which can be re-used across several different plots.
There are heuristics for examining "trellis" and "ggplot" objects
and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between directlabels versions 2026.4.23 dated 2026-04-23 and 2026.8.27 dated 2026-08-28
DESCRIPTION | 13 ++++----- MD5 | 29 +++++++++++++------- NAMESPACE | 4 ++ NEWS | 4 ++ R/RcppExports.R |only R/isoreg_dp.R |only R/utility.function.R | 48 ++++++--------------------------- build/vignette.rds |binary inst/doc/examples.R | 2 - inst/doc/examples.Rmd | 2 - inst/doc/examples.html | 65 +++++++++++++++++++++++++++++---------------- man/aligned_labels_dp.Rd |only man/isoreg_dp.Rd |only man/qp.labels.Rd | 2 - src |only tests/testthat/test-CRAN.R |only vignettes/examples.Rmd | 2 - 17 files changed, 89 insertions(+), 82 deletions(-)
Title: 'Lifebit' Platform 'API' Client
Description: Interacts with the 'Lifebit' Platform Cohort Browser 'API'
<https://cloudos.lifebit.ai>. Enables schema discovery, table exploration,
and read-only 'SQL' query execution with policy-aware behavior and team-based
access control for cohort data analysis. Requires bastion-enabled workspaces
for 'API' access.
Author: Leila Mansouri [aut, cre]
Maintainer: Leila Mansouri <leila.mansouri@lifebit.ai>
Diff between cloudosR versions 0.2.0 dated 2026-06-01 and 0.2.4 dated 2026-08-28
cloudosR-0.2.0/cloudosR/man/build_query_string.Rd |only cloudosR-0.2.0/cloudosR/man/http_request_with_retry.Rd |only cloudosR-0.2.0/cloudosR/man/paginate_results.Rd |only cloudosR-0.2.4/cloudosR/DESCRIPTION | 11 cloudosR-0.2.4/cloudosR/MD5 | 55 cloudosR-0.2.4/cloudosR/NAMESPACE | 3 cloudosR-0.2.4/cloudosR/NEWS.md | 59 cloudosR-0.2.4/cloudosR/R/config.R | 3 cloudosR-0.2.4/cloudosR/R/http.R | 329 +-- cloudosR-0.2.4/cloudosR/R/query.R | 741 ++++--- cloudosR-0.2.4/cloudosR/R/utils.R | 161 + cloudosR-0.2.4/cloudosR/inst/WORDLIST | 6 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.R | 27 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.Rmd | 33 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.html | 151 - cloudosR-0.2.4/cloudosR/man/cloudos.query.Rd | 21 cloudosR-0.2.4/cloudosR/man/cloudos.query_count.Rd |only cloudosR-0.2.4/cloudosR/man/cloudos.query_count_results.Rd |only cloudosR-0.2.4/cloudosR/man/cloudos.query_results.Rd | 15 cloudosR-0.2.4/cloudosR/man/cloudos.query_submit_async.Rd | 11 cloudosR-0.2.4/cloudosR/man/cloudos.query_submit_count_async.Rd |only cloudosR-0.2.4/cloudosR/man/error_body_text.Rd |only cloudosR-0.2.4/cloudosR/man/extract_error_message.Rd |only cloudosR-0.2.4/cloudosR/man/handle_api_error.Rd | 2 cloudosR-0.2.4/cloudosR/man/http_get_parallel.Rd |only cloudosR-0.2.4/cloudosR/man/parse_json_response.Rd | 5 cloudosR-0.2.4/cloudosR/man/process_response.Rd |only cloudosR-0.2.4/cloudosR/man/resolve_max_parallel.Rd |only cloudosR-0.2.4/cloudosR/man/results_response_to_df.Rd |only cloudosR-0.2.4/cloudosR/man/truncate_error_text.Rd |only cloudosR-0.2.4/cloudosR/tests/testthat/helper-config.R |only cloudosR-0.2.4/cloudosR/tests/testthat/test-config.R | 83 cloudosR-0.2.4/cloudosR/tests/testthat/test-http.R |only cloudosR-0.2.4/cloudosR/tests/testthat/test-query.R | 936 +++++++++- cloudosR-0.2.4/cloudosR/tests/testthat/test-utils.R | 43 cloudosR-0.2.4/cloudosR/vignettes/getting-started.Rmd | 33 36 files changed, 1888 insertions(+), 840 deletions(-)
Title: Climate Exposure Relative to a Species' Climatic Niche
Description: Quantifies projected climatic change relative to the climatic
niche represented by a species' current distribution. A weighted current
reference defines the niche centre and empirical radial boundary. Present
and projected conditions at each location give local climatic displacement,
signed change in niche distance, a derived non-radial reconfiguration term,
and exceedance beyond the niche boundary. Occurrence records, range maps,
and binary or continuous species distribution model outputs can define
reference weights. Matrix and spatial workflows return location-level
values, weighted summaries, maps and climatic-variable contributions.
Author: Bohao He [aut, cre]
Maintainer: Bohao He <bohao.he@polimi.it>
Diff between climniche versions 0.0.1 dated 2026-05-29 and 0.3.8 dated 2026-08-28
climniche-0.0.1/climniche/R/diagram.R |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_clean_obis_records.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_classes.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_summary.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_top_variables.csv |only climniche-0.0.1/climniche/man/climniche_diagram_data.Rd |only climniche-0.0.1/climniche/man/climniche_showcase_data.Rd |only climniche-0.0.1/climniche/man/plot_climniche_class_summary.Rd |only climniche-0.0.1/climniche/man/plot_climniche_classes.Rd |only climniche-0.0.1/climniche/man/plot_climniche_diagram.Rd |only climniche-0.0.1/climniche/man/plot_climniche_showcase.Rd |only climniche-0.0.1/climniche/man/plot_variable_contribution.Rd |only climniche-0.0.1/climniche/vignettes/figures/anchovy-climniche-diagram.png |only climniche-0.0.1/climniche/vignettes/figures/anchovy-climniche-showcase.png |only climniche-0.3.8/climniche/DESCRIPTION | 28 climniche-0.3.8/climniche/LICENSE |only climniche-0.3.8/climniche/MD5 | 175 +- climniche-0.3.8/climniche/NAMESPACE | 70 climniche-0.3.8/climniche/NEWS.md | 162 + climniche-0.3.8/climniche/R/aliases.R | 438 +++-- climniche-0.3.8/climniche/R/classify.R | 139 - climniche-0.3.8/climniche/R/contribution_map.R |only climniche-0.3.8/climniche/R/core.R | 303 ++- climniche-0.3.8/climniche/R/departure.R |only climniche-0.3.8/climniche/R/dynamic_plot.R |only climniche-0.3.8/climniche/R/dynamic_report.R |only climniche-0.3.8/climniche/R/metric.R | 141 + climniche-0.3.8/climniche/R/priority.R |only climniche-0.3.8/climniche/R/range.R |only climniche-0.3.8/climniche/R/raster_workflow.R | 241 +- climniche-0.3.8/climniche/R/reference.R |only climniche-0.3.8/climniche/R/report.R | 495 ++++- climniche-0.3.8/climniche/R/series_fit.R |only climniche-0.3.8/climniche/R/showcase.R | 501 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files changed, 5353 insertions(+), 1549 deletions(-)
Title: Fast, Weighted ROC Curves
Description: Fast computation of
Receiver Operating Characteristic (ROC) curves
and Area Under the Curve (AUC)
for weighted binary classification problems
(weights are example-specific cost values).
Author: Toby Dylan Hocking [cre, aut]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between WeightedROC versions 2020.1.31 dated 2020-02-01 and 2026.8.27 dated 2026-08-28
DESCRIPTION | 14 + MD5 | 30 +-- NAMESPACE | 8 NEWS | 128 +++++++------- R/AUC.R | 130 +++++++------- R/ROC.R | 376 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/Definition.R | 42 ++-- inst/doc/Definition.Rnw | 286 ++++++++++++++++---------------- inst/doc/Definition.pdf |binary man/WeightedAUC.Rd | 122 ++++++------- man/WeightedROC.Rd | 288 ++++++++++++++++---------------- tests/testthat.R | 4 tests/testthat/test-auc.R | 332 ++++++++++++++++++------------------- tests/testthat/test-errors.R | 94 +++++----- vignettes/Definition.Rnw | 286 ++++++++++++++++---------------- 16 files changed, 1074 insertions(+), 1066 deletions(-)
Title: Make Data Based on Different Geographies Comparable
Description: Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between tongfen versions 0.3.7 dated 2026-06-05 and 0.3.8 dated 2026-08-28
DESCRIPTION | 6 MD5 | 64 ++-- NAMESPACE | 1 NEWS.md | 63 ++++ R/helpers.R | 262 +++++++++++------ R/tongfen.R | 82 +++-- R/tongfen_ca.R | 104 ++++-- R/tongfen_ca_deprecated.R | 16 - R/tongfen_ca_estimate.R | 4 R/tongfen_estimate.R | 29 - R/tongfen_us.R | 373 +++++++++++++++++++++---- README.md | 4 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/tongfen.html | 6 inst/doc/tongfen_ca.R | 4 inst/doc/tongfen_ca.Rmd | 4 inst/doc/tongfen_ca.html | 12 inst/doc/tongfen_us.R | 21 + inst/doc/tongfen_us.Rmd | 34 ++ inst/doc/tongfen_us.html | 49 +++ man/check_tongfen_areas.Rd | 4 man/get_tongfen_ca_census.Rd | 11 man/get_tongfen_correspondence_ca_census.Rd | 12 man/get_tongfen_correspondence_us_census.Rd |only man/get_tongfen_us_census.Rd | 17 + man/tongfen_aggregate.Rd | 11 tests/testthat/test-aggregate.R | 81 +++++ tests/testthat/test-correspondence-estimate.R |only tests/testthat/test-estimate.R |only tests/testthat/test-helpers.R | 138 +++++++++ tests/testthat/test-proportional-reaggregate.R | 32 ++ tests/testthat/test-us-correspondence.R |only vignettes/tongfen_ca.Rmd | 4 vignettes/tongfen_us.Rmd | 34 ++ 35 files changed, 1167 insertions(+), 315 deletions(-)
Title: Latent Dirichlet Allocation Using 'tidyverse' Conventions
Description: Implements an algorithm for Latent Dirichlet
Allocation (LDA), Blei et al. (2003) <https://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf>,
using style conventions from the 'tidyverse',
Wickham et al. (2019)<doi:10.21105/joss.01686>,
and 'tidymodels', Kuhn et al.<https://tidymodels.github.io/model-implementation-principles/>.
Fitting is done via 'warpLDA', a Metropolis-Hastings sampler,
Chen et al. (2016) <doi:10.48550/arXiv.1510.08628>.
Also implements several novel features for LDA such as guided models and
transfer learning.
Author: Tommy Jones [aut, cre] ,
Brendan Knapp [ctb] ,
Barum Park [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between tidylda versions 0.0.7 dated 2025-11-14 and 0.1.0 dated 2026-08-28
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Title: Stability Assessment of Statistical Learning Methods
Description: Graphical and computational methods that can be used to assess the
stability of results from supervised statistical learning.
Author: Michel Philipp [aut],
Carolin Strobl [aut] ,
Achim Zeileis [aut, cre] ,
Thomas Rusch [aut] ,
Kurt Hornik [aut] ,
Lennart Schneider [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between stablelearner versions 0.1-8 dated 2026-07-30 and 0.1-9 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 10 +++++++++- NEWS.md | 8 ++++++++ R/stabletree-coercion.R | 2 +- R/stabletree.R | 2 +- inst/doc/forests.html | 4 ++-- man/stabletree-coercion.Rd | 2 +- 8 files changed, 33 insertions(+), 17 deletions(-)
Title: Humane Interface to Amazon Web Services
Description: An opinionated interface to Amazon Web Services <https://aws.amazon.com>,
with functions for interacting with 'IAM' (Identity and Access Management),
'S3' (Simple Storage Service), 'RDS' (Relational Data Service), Redshift, and Billing.
Lower level functions ('aws_' prefix) are for do it yourself workflows, while
higher level functions ('six_' prefix) automate common tasks.
Author: Sean Kross [aut],
Scott Chamberlain [aut, cre] ,
Fred Hutchinson Cancer Center [fnd]
Maintainer: Scott Chamberlain <sachamber@fredhutch.org>
Diff between sixtyfour versions 0.2.0 dated 2025-03-31 and 0.2.4 dated 2026-08-28
DESCRIPTION | 28 ++- LICENSE | 2 MD5 | 242 +++++++++++++++++----------------- NAMESPACE | 158 ++++++++++++---------- NEWS.md | 4 R/clients.R | 17 ++ R/configure.R | 3 R/database-misc.R | 4 R/database-rds.R | 13 + R/database-redshift.R | 7 R/internal.R | 2 R/policies.R | 8 - R/s3.R | 9 - R/secrets_manager.R | 16 +- R/sixtyfour-package.R | 1 R/users.R | 4 R/utils.R | 4 R/vpc_security_groups.R | 8 - R/wait.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/contributing.Rmd | 6 inst/doc/contributing.html | 10 - man/as_policy_arn.Rd | 26 +-- man/aws_billing.Rd | 6 man/aws_billing_raw.Rd | 6 man/aws_bucket_create.Rd | 22 +-- man/aws_bucket_delete.Rd | 22 +-- man/aws_bucket_download.Rd | 24 +-- man/aws_bucket_exists.Rd | 22 +-- man/aws_bucket_list_objects.Rd | 22 +-- man/aws_bucket_tree.Rd | 22 +-- man/aws_bucket_upload.Rd | 24 +-- man/aws_buckets.Rd | 22 +-- man/aws_db_cluster_status.Rd | 14 - man/aws_db_instance_status.Rd | 14 - man/aws_db_rds_con.Rd | 14 - man/aws_db_rds_create.Rd | 14 - man/aws_db_rds_list.Rd | 16 +- man/aws_db_redshift_con.Rd | 16 +- man/aws_db_redshift_create.Rd | 14 - man/aws_file_attr.Rd | 20 +- man/aws_file_copy.Rd | 18 +- man/aws_file_delete.Rd | 18 +- man/aws_file_download.Rd | 20 +- man/aws_file_exists.Rd | 18 +- man/aws_file_rename.Rd | 18 +- man/aws_file_upload.Rd | 18 +- man/aws_group.Rd | 14 - man/aws_group_create.Rd | 14 - man/aws_group_delete.Rd | 14 - man/aws_group_exists.Rd | 14 - man/aws_groups.Rd | 14 - man/aws_policies.Rd | 28 +-- man/aws_policy.Rd | 26 +-- man/aws_policy_attach.Rd | 26 +-- man/aws_policy_create.Rd | 26 +-- man/aws_policy_delete.Rd | 26 +-- man/aws_policy_delete_version.Rd | 26 +-- man/aws_policy_detach.Rd | 26 +-- man/aws_policy_document_create.Rd | 2 man/aws_policy_exists.Rd | 26 +-- man/aws_policy_list_entities.Rd | 26 +-- man/aws_policy_list_versions.Rd | 26 +-- man/aws_policy_update.Rd | 26 +-- man/aws_role.Rd | 12 - man/aws_role_create.Rd | 12 - man/aws_role_delete.Rd | 12 - man/aws_role_exists.Rd | 12 - man/aws_roles.Rd | 12 - man/aws_secrets_all.Rd | 2 man/aws_secrets_create.Rd | 2 man/aws_secrets_delete.Rd | 2 man/aws_secrets_get.Rd | 2 man/aws_secrets_list.Rd | 2 man/aws_secrets_pwd.Rd | 2 man/aws_secrets_rotate.Rd | 2 man/aws_secrets_update.Rd | 2 man/aws_user.Rd | 24 +-- man/aws_user_access_key.Rd | 22 +-- man/aws_user_access_key_delete.Rd | 22 +-- man/aws_user_add_to_group.Rd | 24 +-- man/aws_user_create.Rd | 24 +-- man/aws_user_current.Rd | 22 +-- man/aws_user_delete.Rd | 24 +-- man/aws_user_exists.Rd | 24 +-- man/aws_users.Rd | 24 +-- man/aws_vpc_sec_group_rules_mod.Rd | 14 - man/aws_vpc_security_group.Rd | 12 - man/aws_vpc_security_group_create.Rd | 12 - man/aws_vpc_security_group_ingress.Rd | 12 - man/aws_vpc_security_groups.Rd | 14 - man/aws_vpc_sg_with_ingress.Rd | 12 - man/aws_vpcs.Rd | 2 man/con_iam.Rd | 2 man/con_s3fs.Rd | 2 man/figure_out_policy_arn.Rd | 2 man/reexports.Rd | 4 man/six_admin_setup.Rd | 12 - man/six_bucket_add_user.Rd | 2 man/six_bucket_change_user.Rd | 2 man/six_bucket_delete.Rd | 34 ++-- man/six_bucket_permissions.Rd | 2 man/six_bucket_remove_user.Rd | 2 man/six_bucket_upload.Rd | 34 ++-- man/six_file_upload.Rd | 34 ++-- man/six_group_delete.Rd | 14 - man/six_user_create.Rd | 36 ++--- man/six_user_creds.Rd | 2 man/six_user_delete.Rd | 36 ++--- man/sixtyfour-package.Rd | 3 tests/testthat/helper-vcr.R | 1 tests/testthat/test-buckets.R | 12 + tests/testthat/test-db-rds.R | 2 tests/testthat/test-db-redshift.R | 2 tests/testthat/test-files.R | 28 ++- tests/testthat/test-policies.R | 9 - tests/testthat/test-s3.R | 21 -- tests/testthat/test-users.R | 3 tests/testthat/test-utils.R | 16 +- tests/testthat/test-vpc.R | 8 - vignettes/contributing.Rmd | 6 122 files changed, 1083 insertions(+), 976 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Tom Palmer [aut] ,
Paul Madley-Dowd [aut] ,
Alejandro Szmulewicz [aut] ,
Miguel A. Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.4.3 dated 2026-06-23 and 1.4.4 dated 2026-08-28
DESCRIPTION | 28 ++-- MD5 | 88 ++++++++----- NAMESPACE | 63 +++++---- NEWS.md | 6 R/SEQexpand.R | 10 + R/SEQopts.R | 27 +++- R/SEQuential.R | 94 ++++++++++++-- R/class_definitions.R | 16 ++ R/class_methods.R | 130 +++++++++++++++++--- R/class_setters.R | 48 ++++++- R/internal_analysis.R | 68 ++++++++-- R/internal_endoffup.R |only R/internal_glmHelpers.R | 19 ++ R/internal_misc.R | 10 + R/internal_weights.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/ITT.R | 5 inst/doc/ITT.Rmd | 5 inst/doc/ITT.html | 191 +++++++++++++++--------------- inst/doc/SEQuential.R | 1 inst/doc/SEQuential.Rmd | 1 inst/doc/SEQuential.html | 177 +++++++++++++-------------- inst/doc/doseresponse.R | 5 inst/doc/doseresponse.Rmd | 5 inst/doc/doseresponse.html | 191 +++++++++++++++--------------- inst/doc/endoffollowup.R |only inst/doc/endoffollowup.Rmd |only inst/doc/endoffollowup.html |only inst/doc/seqopts.Rmd | 4 inst/doc/seqopts.html | 35 +++++ man/SEQTaRget-package.Rd | 4 man/SEQopts.Rd | 16 ++ man/SEQoutput-class.Rd | 6 man/SEQuential.Rd | 22 +++ man/cached_cols.Rd |only man/clean_models.Rd |only man/create.endoffup.Rd |only man/diagnostics.Rd | 16 ++ man/end_of_fup.Rd |only man/endoffup.counts.Rd |only man/endoffup.estimate.Rd |only man/endoffup.measure.Rd |only man/endoffup.summary.Rd |only man/prepare.output.Rd | 4 man/select_cached_level.Rd |only tests/testthat/test_armspecific_weights.R |only tests/testthat/test_end_of_fup.R |only vignettes/ITT.Rmd | 5 vignettes/SEQuential.Rmd | 1 vignettes/doseresponse.Rmd | 5 vignettes/endoffollowup.Rmd |only vignettes/seqopts.Rmd | 4 53 files changed, 891 insertions(+), 423 deletions(-)
Title: Wrapper for 'run_example()'
Description: Captures errors or missing examples encountered when iteratively running 'run_examplez()', and archives them.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between runExamplesWrapper versions 1.1 dated 2026-01-16 and 2.0 dated 2026-08-28
runExamplesWrapper-1.1/runExamplesWrapper/R/runExamplesWrapper.R |only runExamplesWrapper-1.1/runExamplesWrapper/man/RunExamples.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/balanceCurly.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/parseRunExamples.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/retrieveExamplesFromMan.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/retrieveMan.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/startExample.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/DESCRIPTION | 16 +-- runExamplesWrapper-2.0/runExamplesWrapper/MD5 | 24 ++--- runExamplesWrapper-2.0/runExamplesWrapper/NAMESPACE | 10 -- runExamplesWrapper-2.0/runExamplesWrapper/R/run_example.R |only runExamplesWrapper-2.0/runExamplesWrapper/build/vignette.rds |binary runExamplesWrapper-2.0/runExamplesWrapper/inst/doc/runExamplesWrapper.Rmd | 23 ++--- runExamplesWrapper-2.0/runExamplesWrapper/inst/doc/runExamplesWrapper.html | 45 ++++------ runExamplesWrapper-2.0/runExamplesWrapper/man/runExamplesWrapper.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/man/run_examplez.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/vignettes/Figure1.jpg |binary runExamplesWrapper-2.0/runExamplesWrapper/vignettes/runExamplesWrapper.Rmd | 23 ++--- 18 files changed, 58 insertions(+), 83 deletions(-)
More information about runExamplesWrapper at CRAN
Permanent link
Title: Hypothesis Tests for Quantiles and Quantile-Based Measures
Description: Functions to conduct hypothesis tests and derive confidence intervals
for quantiles, linear combinations of quantiles,
ratios of dependent linear combinations and differences
and ratios of all of the above for comparisons between independent samples.
Additionally, quantile-based measures of inequality are also considered.
Author: Shenal Dedduwakumara [aut, cre],
Luke Prendergast [aut],
Robert Staudte [aut]
Maintainer: Shenal Dedduwakumara <shenal.dedduwakumara@adelaide.edu.au>
Diff between rquest versions 1.0.5 dated 2025-06-11 and 1.1.0 dated 2026-08-28
rquest-1.0.5/rquest/R/R.R |only rquest-1.0.5/rquest/R/qor.ln.R |only rquest-1.1.0/rquest/DESCRIPTION | 8 rquest-1.1.0/rquest/MD5 | 43 - rquest-1.1.0/rquest/NAMESPACE | 9 rquest-1.1.0/rquest/NEWS.md | 20 rquest-1.1.0/rquest/R/get.coefs.R |only rquest-1.1.0/rquest/R/q.test.R | 44 - rquest-1.1.0/rquest/R/qcov.R | 98 +-- rquest-1.1.0/rquest/R/qden.R |only rquest-1.1.0/rquest/R/qineq.R | 175 ++++- rquest-1.1.0/rquest/R/qor.R |only rquest-1.1.0/rquest/R/qrcov.R |only rquest-1.1.0/rquest/R/rcv.test.R |only rquest-1.1.0/rquest/R/rquest-package.R | 14 rquest-1.1.0/rquest/README.md | 488 +++++++++++++-- rquest-1.1.0/rquest/man/q.test.Rd | 18 rquest-1.1.0/rquest/man/qcov.Rd | 55 + rquest-1.1.0/rquest/man/qden.Rd |only rquest-1.1.0/rquest/man/qineq.Rd | 50 + rquest-1.1.0/rquest/man/qor.Rd |only rquest-1.1.0/rquest/man/qrcov.Rd |only rquest-1.1.0/rquest/man/rcv.test.Rd |only rquest-1.1.0/rquest/tests/testthat/test-q.test.R | 643 +++++++++++++++++---- rquest-1.1.0/rquest/tests/testthat/test-qcov.R | 111 +++ rquest-1.1.0/rquest/tests/testthat/test-qden.R |only rquest-1.1.0/rquest/tests/testthat/test-qineq.R | 203 ++++++ rquest-1.1.0/rquest/tests/testthat/test-qor.R |only rquest-1.1.0/rquest/tests/testthat/test-qrcov.R |only rquest-1.1.0/rquest/tests/testthat/test-rcv.test.R |only 30 files changed, 1591 insertions(+), 388 deletions(-)
Title: Random Hazard Forests
Description: Random Hazard Forests (RHF) extend Random Survival
Forests (RSF) by directly estimating the hazard function and by
accommodating time-dependent covariates through counting-process
style inputs. The package fits tree ensembles for dynamic survival
prediction, returning hazard, cumulative hazard, integrated hazard,
and related performance summaries for training and test data. The
methods build on Random Survival Forests described by Ishwaran et
al. (2008) <doi:10.1214/08-AOAS169> and on nonparametric hazard
modeling with time-dependent covariates described by Lee et
al. (2021) <doi:10.1214/20-AOS2028>.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestRHF versions 1.0.1 dated 2026-04-28 and 2.0.0 dated 2026-08-28
DESCRIPTION | 8 MD5 | 104 ++-- NAMESPACE | 2 NEWS.md | 11 R/auct.rhf.R | 506 ++++++++++++++++++++-- R/importance.rhf_plot.R | 885 +++++++++++++++++++++++++++++++++------- R/plot.rhf.R | 14 R/predict.rhf.R | 32 + R/predict.rhf.workhorse.R | 244 ++++++++++- R/print.rhf.R | 13 R/rhf.R | 12 R/rhf.workhorse.R | 197 ++++++++ R/tune.treesize.rhf.R | 369 ++++++++++++++-- R/utilities_additional.R | 497 ++++++++++++++++------ R/utilities_hazard_simulation.R | 637 +++++++++++++++++++--------- R/utilities_importance.R | 101 ++++ R/utilities_importance_plot.R | 740 +++++++++++++++++++++++++++------ R/utilities_lot.R | 20 R/utilities_tdc.R | 680 +++++++++++++++++++++++++++--- man/auct.rhf.Rd | 14 man/importance.rhf.Rd | 285 +++++++++--- man/plot.rhf.Rd | 6 man/predict.rhf.Rd | 59 ++ man/rhf.Rd | 219 ++++++--- man/tune.treesize.rhf.Rd | 56 ++ man/utilities_internal.Rd | 10 src/Makevars | 1 src/Makevars.win | 1 src/R_init_randomForestRHF.c | 9 src/entry.c | 55 ++ src/entry.h | 4 src/entryGeneric.c | 3 src/external.h | 21 src/internal.c | 21 src/medianLogStitchedHazard.c | 24 - src/processEnsemble.c | 345 ++++++++++++--- src/processEnsemble.h | 7 src/processEnsembleCOE.c |only src/processEnsembleCOE.h |only src/rhfMain.c | 130 +++++ src/sexpOutgoing.c | 14 src/sexpOutgoing.h | 24 - src/shared/stackForestObjects.c | 2 src/splitTDC.c | 42 - src/stackOutput.c | 112 ++++- src/stackOutputQQ.c | 103 ++++ src/stackOutputQQ.h | 19 src/survivalTDC.c | 163 +++++++ src/survivalTDC.h | 1 src/termOps.c | 33 + src/termOps.h | 2 src/terminal.h | 4 src/treeOps.c | 35 + src/weightedStitchedHazard.c | 26 - 54 files changed, 5662 insertions(+), 1260 deletions(-)
More information about randomForestRHF at CRAN
Permanent link
Title: Proportional Apportionment
Description: Calculate seat apportionment for legislative bodies with
various methods. The algorithms include divisor or highest averages methods
(e.g. Jefferson, Webster or Adams), largest remainder methods and
biproportional apportionment.
Gaffke, N. & Pukelsheim, F. (2008) <doi:10.1016/j.mathsocsci.2008.01.004>
Oelbermann, K. F. (2016) <doi:10.1016/j.mathsocsci.2016.02.003>.
Author: Flavio Poletti [aut, cre, cph]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between proporz versions 1.5.2 dated 2025-10-10 and 1.5.3 dated 2026-08-28
proporz-1.5.2/proporz/inst/bazi |only proporz-1.5.2/proporz/man/proporz_methods.Rd |only proporz-1.5.3/proporz/DESCRIPTION | 8 proporz-1.5.3/proporz/MD5 | 150 +-- proporz-1.5.3/proporz/NAMESPACE | 4 proporz-1.5.3/proporz/NEWS.md | 7 proporz-1.5.3/proporz/R/S3.R | 34 proporz-1.5.3/proporz/R/bazi.R |only proporz-1.5.3/proporz/R/biproportional-check.R | 103 +- proporz-1.5.3/proporz/R/biproportional-divisors.R | 8 proporz-1.5.3/proporz/R/biproportional-lower.R | 94 +- proporz-1.5.3/proporz/R/biproportional-upper.R | 49 - proporz-1.5.3/proporz/R/biproportional-wto.R | 17 proporz-1.5.3/proporz/R/biproportional.R | 49 - proporz-1.5.3/proporz/R/data.R | 9 proporz-1.5.3/proporz/R/divisor-check.R | 21 proporz-1.5.3/proporz/R/divisor_methods.R | 34 proporz-1.5.3/proporz/R/matrix.R | 9 proporz-1.5.3/proporz/R/proporz.R | 31 proporz-1.5.3/proporz/R/quorum.R | 116 +- proporz-1.5.3/proporz/R/quota_methods.R | 5 proporz-1.5.3/proporz/R/round.R | 20 proporz-1.5.3/proporz/R/shinyapp.R | 439 ++++++---- proporz-1.5.3/proporz/R/utils.R | 53 + proporz-1.5.3/proporz/README.md | 4 proporz-1.5.3/proporz/build/vignette.rds |binary proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.R | 14 proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.Rmd | 14 proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.html | 25 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.R | 3 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.Rmd | 26 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.html | 93 +- proporz-1.5.3/proporz/inst/run_additional_tests.R |only proporz-1.5.3/proporz/inst/test-bazi |only proporz-1.5.3/proporz/man/apply_quorum.Rd | 15 proporz-1.5.3/proporz/man/biproporz.Rd | 37 proporz-1.5.3/proporz/man/ceil_at.Rd | 8 proporz-1.5.3/proporz/man/district_winner_matrix.Rd | 5 proporz-1.5.3/proporz/man/divide_votes_matrix.Rd | 12 proporz-1.5.3/proporz/man/divisor_methods.Rd | 9 proporz-1.5.3/proporz/man/figures/shinyapp-example.gif |binary proporz-1.5.3/proporz/man/find_divisor.Rd | 15 proporz-1.5.3/proporz/man/find_matrix_divisors.Rd | 9 proporz-1.5.3/proporz/man/get_divisors.Rd | 6 proporz-1.5.3/proporz/man/highest_averages_method.Rd | 9 proporz-1.5.3/proporz/man/largest_remainder_method.Rd | 9 proporz-1.5.3/proporz/man/lower_apportionment.Rd | 6 proporz-1.5.3/proporz/man/pivot_to_matrix.Rd | 9 proporz-1.5.3/proporz/man/proporz.Rd | 9 proporz-1.5.3/proporz/man/pukelsheim.Rd | 19 proporz-1.5.3/proporz/man/quorum_functions.Rd | 22 proporz-1.5.3/proporz/man/reached_quorum_any_district.Rd | 4 proporz-1.5.3/proporz/man/reached_quorum_total.Rd | 4 proporz-1.5.3/proporz/man/reached_quorums.Rd | 21 proporz-1.5.3/proporz/man/read_bazi.Rd |only proporz-1.5.3/proporz/man/run_app.Rd | 11 proporz-1.5.3/proporz/man/upper_apportionment.Rd | 14 proporz-1.5.3/proporz/man/uri2020.Rd | 6 proporz-1.5.3/proporz/man/weight_votes_matrix.Rd | 17 proporz-1.5.3/proporz/man/zug2018.Rd | 4 proporz-1.5.3/proporz/tests/testthat/data |only proporz-1.5.3/proporz/tests/testthat/helper.R |only proporz-1.5.3/proporz/tests/testthat/test-biproportional-data.R | 6 proporz-1.5.3/proporz/tests/testthat/test-biproportional-errors.R | 39 proporz-1.5.3/proporz/tests/testthat/test-biproportional.R | 49 - proporz-1.5.3/proporz/tests/testthat/test-divisor.R | 10 proporz-1.5.3/proporz/tests/testthat/test-fuzzy.R |only proporz-1.5.3/proporz/tests/testthat/test-proporz-parameters.R | 34 proporz-1.5.3/proporz/tests/testthat/test-proporz.R | 18 proporz-1.5.3/proporz/tests/testthat/test-quorum.R | 37 proporz-1.5.3/proporz/tests/testthat/test-read_bazi.R |only proporz-1.5.3/proporz/tests/testthat/test-round.R | 12 proporz-1.5.3/proporz/tests/testthat/test-shiny.R |only proporz-1.5.3/proporz/tests/testthat/test-utils.R | 2 proporz-1.5.3/proporz/vignettes/apportionment_scenarios.Rmd | 14 proporz-1.5.3/proporz/vignettes/modifying_biproporz.Rmd | 26 76 files changed, 1220 insertions(+), 746 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Christophe Dervieux [ctb] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Atsushi Yasumoto [ctb] ,
Posit Software, PBC [cph, fnd],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.24 dated 2026-04-09 and 0.25 dated 2026-08-28
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/chrome.R | 10 ++++++++-- README.md | 2 +- inst/resources/lua/loft.lua | 29 ++++++++++++++++++++++++++++- tests/test-ci/test-chrome.R | 19 +++++++++++++++---- 8 files changed, 69 insertions(+), 19 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalised,
sequential, and standard IB clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2026) <doi:10.1016/j.patcog.2026.113580>. The standard IB method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
the generalised IB from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>,
and the sequential IB from Slonim et al. (2002) <doi:10.1145/564376.564401>. Diagnostic and plotting functions are provided to summarise, visualise, and predict from the resulting clusteri [...truncated...]
Author: Angelos Markos [aut, cre],
Efthymios Costa [aut],
Ioanna Papatsouma [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.4 dated 2026-07-14 and 1.5 dated 2026-08-28
DESCRIPTION | 8 +- MD5 | 38 ++++++------ NAMESPACE | 1 R/IBclust-package.R | 2 R/aibclust-methods.R | 2 R/as_hclust.R | 2 R/find_elbow.R | 2 R/gibclust-methods.R | 119 ++++++++++++++++++++++++++++++++++++---- R/info_metrics.R | 2 R/make_dendrogram.R | 12 ++-- R/sibclust-methods.R | 136 +++++++++++++++++++++++++++++++++++++++------- build/partial.rdb |binary man/aibclust-methods.Rd | 2 man/as.hclust.aibclust.Rd | 2 man/find_elbow.Rd | 2 man/gibclust-methods.Rd | 45 ++++++++++++--- man/info_metrics.Rd | 2 man/predict.gibclust.Rd | 2 man/predict.sibclust.Rd | 2 man/sibclust-methods.Rd | 46 ++++++++++++--- 20 files changed, 336 insertions(+), 91 deletions(-)
Title: Interactive Forest Plot
Description: Interactive forest plot for clinical trial safety analysis
using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM)
datasets. Includes functionality for adverse event filtering,
incidence-based group filtering, hover-over reveals, and search and sort
operations. The workflow allows for metadata construction, data preparation,
output formatting, and interactive plot generation.
Author: Yilong Zhang [aut],
Benjamin Wang [aut],
Yujie Zhao [aut, cre],
Nan Xiao [ctb],
Hiroaki Fukuda [aut],
Yulia Sidi [ctb],
Xuan Deng [ctb],
Jeetener Chauhan [ctb],
Li Ma [ctb],
Chen Wang [ctb],
Madhusudhan Ginnaram [ctb],
Merck & Co., Inc., Rahway, NJ, [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between forestly versions 0.1.5 dated 2026-06-12 and 0.1.6 dated 2026-08-28
forestly-0.1.5/forestly/R/meta_forestly.R |only forestly-0.1.5/forestly/man/meta_forestly.Rd |only forestly-0.1.5/forestly/tests/testthat/helper-meta_forestly.R |only forestly-0.1.5/forestly/tests/testthat/test-independent-testing-meta_forestly.R |only forestly-0.1.6/forestly/DESCRIPTION | 8 forestly-0.1.6/forestly/MD5 | 73 ++-- forestly-0.1.6/forestly/NAMESPACE | 1 forestly-0.1.6/forestly/NEWS.md | 6 forestly-0.1.6/forestly/R/ae_forestly.R | 62 +++ forestly-0.1.6/forestly/R/ae_listing.R | 114 ++++++ forestly-0.1.6/forestly/R/format_ae_forestly.R | 62 +++ forestly-0.1.6/forestly/R/plot.R | 165 ++++++++-- forestly-0.1.6/forestly/R/prepare_ae_forestly.R | 61 +++ forestly-0.1.6/forestly/R/rtf_static_forestly.R | 51 ++- forestly-0.1.6/forestly/README.md | 82 ++++ forestly-0.1.6/forestly/build/vignette.rds |binary forestly-0.1.6/forestly/inst/doc/customize-ae-specific-columns.html | 16 forestly-0.1.6/forestly/inst/doc/customize-color.html | 16 forestly-0.1.6/forestly/inst/doc/customize-diff-label.html | 16 forestly-0.1.6/forestly/inst/doc/customize-digits.html | 16 forestly-0.1.6/forestly/inst/doc/customize-display-only-soc.html | 16 forestly-0.1.6/forestly/inst/doc/customize-listing-columns.html | 16 forestly-0.1.6/forestly/inst/doc/customize-toggle-buttons.html | 18 - forestly-0.1.6/forestly/inst/doc/customize-width.html | 28 - forestly-0.1.6/forestly/inst/doc/customize-xlimit.html | 12 forestly-0.1.6/forestly/inst/doc/forest-plot-static.R | 54 ++- forestly-0.1.6/forestly/inst/doc/forest-plot-static.Rmd | 54 ++- forestly-0.1.6/forestly/inst/doc/forest-plot-static.html | 66 +++- forestly-0.1.6/forestly/man/ae_forestly.Rd | 62 +++ forestly-0.1.6/forestly/man/format_ae_forestly.Rd | 62 +++ forestly-0.1.6/forestly/man/plot_dot.Rd | 55 ++- forestly-0.1.6/forestly/man/plot_errorbar.Rd | 55 ++- forestly-0.1.6/forestly/man/prepare_ae_forestly.Rd | 61 +++ forestly-0.1.6/forestly/man/rtf_static_forestly.Rd | 51 ++- forestly-0.1.6/forestly/man/table_panel.Rd | 55 ++- forestly-0.1.6/forestly/tests/testthat/helper-ae_forestly.R | 2 forestly-0.1.6/forestly/tests/testthat/helper-format_ae_forestly.R | 2 forestly-0.1.6/forestly/tests/testthat/helper-meta_ae.R |only forestly-0.1.6/forestly/tests/testthat/test-ae_forestly.R | 4 forestly-0.1.6/forestly/vignettes/forest-plot-static.Rmd | 54 ++- 40 files changed, 1200 insertions(+), 276 deletions(-)
Title: Data Mining and R Programming for Beginners
Description: Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Author: Alexandre Blansche [aut, cre]
Maintainer: Alexandre Blansche <alexandre.blansche@univ-lorraine.fr>
Diff between fdm2id versions 0.9.9 dated 2023-06-12 and 1.0.0 dated 2026-08-28
DESCRIPTION | 23 MD5 | 428 +++--- NAMESPACE | 38 NEWS.md |only R/association.R | 170 +- R/classification.R | 2475 +++++++++++++++++++++++++++++---------- R/clustering.R | 1558 ++++++++++++++++++------ R/dataset.R | 144 +- R/factorial.R | 279 ++++ R/feature.R | 748 ++++++++--- R/misc.R | 419 +++++- R/regression.R | 387 ++++-- R/text.R | 324 ++--- R/visualization.R | 711 +++++++---- build |only data/accident2014.rda |binary data/alcohol.rda |binary data/autompg.rda |binary data/beetles.rda |binary data/birth.rda |binary data/britpop.rda |binary data/capitals.rda |only data/cookies.desc.test.rda |binary data/cookies.desc.train.rda |binary data/cookies.rda |binary data/cookies.y.test.rda |binary data/cookies.y.train.rda |binary data/credit.rda |binary data/data1.rda |binary data/data2.rda |binary data/data3.rda |binary data/decathlon.rda |binary data/eucalyptus.rda |binary data/ionosphere.rda |binary data/linsep.rda |binary data/movies.rda |binary data/ozone.rda |binary data/reg1.rda |binary data/reg1.test.rda |binary data/reg1.train.rda |binary data/reg2.rda |binary data/reg2.test.rda |binary data/reg2.train.rda |binary data/snore.rda |binary data/spine.rda |binary data/spine.test.rda |binary data/spine.train.rda |binary data/temperature.rda |binary data/titanic.rda |binary data/universite.rda |binary data/vowels.rda |binary data/vowels.test.rda |binary data/vowels.train.rda |binary data/wheat.rda |binary data/wine.rda |binary data/zoo.rda |binary inst |only man/ADABOOST.Rd | 14 man/APRIORI.Rd | 17 man/BAGGING.Rd | 14 man/CA.Rd | 8 man/CART.Rd | 22 man/CDA.Rd | 34 man/DBSCAN.Rd | 13 man/EM.Rd | 6 man/FEATURESELECTION.Rd | 27 man/GBREG.Rd |only man/GRADIENTBOOSTING.Rd | 20 man/HCA.Rd | 26 man/KERREG.Rd | 25 man/KMEANS.Rd | 38 man/KNN.Rd | 31 man/LDA.Rd | 24 man/LINREG.Rd | 42 man/LR.Rd | 55 man/MCA.Rd | 12 man/MEANSHIFT.Rd | 8 man/MLP.Rd | 25 man/MLPREG.Rd | 29 man/NB.Rd | 24 man/NMF.Rd | 4 man/PAM.Rd |only man/PCA.Rd | 5 man/POLYREG.Rd | 25 man/QDA.Rd | 24 man/RANDOMFOREST.Rd | 22 man/SOM.Rd | 3 man/SPECTRAL.Rd | 6 man/STUMP.Rd | 28 man/SVM.Rd | 19 man/SVMl.Rd | 20 man/SVMr.Rd | 20 man/SVR.Rd | 27 man/SVRl.Rd | 24 man/SVRr.Rd | 24 man/TEXTMINING.Rd | 13 man/TSNE.Rd | 14 man/alcohol.Rd | 4 man/apriori-class.Rd | 26 man/augmentation.Rd | 6 man/autompg.Rd | 2 man/average.doc.Rd |only man/beetles.Rd | 2 man/boosting-class.Rd | 22 man/boxclus.Rd | 4 man/capitals.Rd |only man/cartdepth.Rd | 2 man/cda-class.Rd | 43 man/check.classes.Rd |only man/closegraphics.Rd | 9 man/compare.Rd | 11 man/compare.accuracy.Rd | 10 man/compare.jaccard.Rd | 18 man/compare.kappa.Rd | 21 man/confusion.Rd | 18 man/cookplot.Rd | 2 man/cost.curves.Rd | 37 man/data.diag.Rd | 10 man/data.gauss.Rd | 8 man/data.parabol.Rd | 8 man/data.target1.Rd | 8 man/data.target2.Rd | 8 man/data.twomoons.Rd | 8 man/data.xor.Rd | 8 man/dataset-class.Rd | 20 man/dbs-class.Rd | 23 man/em-class.Rd | 38 man/eucalyptus.Rd | 2 man/evaluation.adjr2.Rd | 13 man/evaluation.fmeasure.Rd | 36 man/evaluation.fowlkesmallows.Rd | 35 man/evaluation.goodness.Rd | 36 man/evaluation.jaccard.Rd | 29 man/evaluation.kappa.Rd | 5 man/evaluation.precision.Rd | 31 man/evaluation.recall.Rd | 31 man/exportgraphics.Rd | 19 man/factorial-class.Rd | 11 man/filter.rules.Rd | 5 man/frequentwords.Rd | 21 man/general.rules.Rd | 5 man/getvocab.Rd | 19 man/intern.Rd | 8 man/intern.dunn.Rd | 9 man/intern.interclass.Rd | 2 man/intern.intraclass.Rd | 2 man/ionosphere.Rd | 4 man/kmeans.getk.Rd | 35 man/knn-class.Rd | 17 man/leverageplot.Rd | 2 man/loadtext.Rd | 24 man/meanshift-class.Rd | 35 man/model-class.Rd | 14 man/movies.Rd | 8 man/ozone.Rd | 9 man/params-class.Rd | 23 man/performance.Rd | 61 man/plot.apriori.Rd |only man/plot.cda.Rd | 10 man/plot.factorial.Rd | 29 man/plot.selection.Rd |only man/plotcloud.Rd | 13 man/plotclus.Rd | 2 man/plotdata.Rd | 65 - man/plotzipf.Rd | 8 man/predict.factorial.Rd |only man/predict.hca.Rd |only man/predict.pam.Rd |only man/predict.som.Rd |only man/predict.spectral.Rd |only man/predict.textmining.Rd | 7 man/print.boosting.Rd |only man/print.cda.Rd |only man/print.dataset.Rd |only man/print.dbs.Rd |only man/print.em.Rd |only man/print.knn.Rd |only man/print.meanshift.Rd |only man/print.model.Rd |only man/print.params.Rd |only man/print.selection.Rd |only man/print.som.Rd |only man/print.spectral.Rd |only man/query.docs.Rd | 13 man/query.words.Rd | 9 man/regplot.Rd | 2 man/resplot.Rd | 8 man/roc.curves.Rd | 50 man/scatterplot.Rd | 4 man/selectfeatures.Rd | 6 man/selection-class.Rd | 40 man/snore.Rd | 6 man/som-class.Rd | 20 man/spectral-class.Rd | 20 man/spine.Rd | 2 man/splitdata.Rd | 18 man/summary.model.Rd |only man/textmining-class.Rd | 17 man/titanic.Rd | 2 man/treeplot.Rd | 2 man/tune.doc.Rd |only man/vectorize.docs.Rd | 31 man/vectorize.words.Rd | 20 man/vectorizer-class.Rd | 26 man/vowels.Rd | 2 man/wheat.Rd | 2 man/wine.Rd | 2 man/zoo.Rd | 2 tests |only vignettes |only 210 files changed, 7239 insertions(+), 2622 deletions(-)
Title: Survey Analysis Tools for the Chilean Social Observatory
Description: Provides high-level functions to compute estimates (means,
proportions, totals, ratios and quantiles) for complex survey designs,
with automatic classification of statistical reliability, between-year
significance tests and standardised report generation in 'Excel' format
(via 'openxlsx'). It was developed for the Social Observatory
('Observatorio Social') of the Chilean Ministry of Social Development
and implements its data-quality criteria, but it can be applied to any
complex-survey design (for example the Chilean 'CASEN' household survey,
included as example data). The reliability criteria follow Division
Observatorio Social (2023)
<https://bidat.gob.cl/details/ficha/dato/manual-para-la-investigacion-casen-2022>
and Instituto Nacional de Estadisticas (2020)
<https://www.ine.gob.cl/inicio/documentos-de-trabajo/documento/fundamentos-del-est%C3%A1ndar-para-la-evaluaci%C3%B3n-de-la-calidad-de-las-estimaciones-en-encuestas-de-hogares>;
complex-survey estimation methods follo [...truncated...]
Author: Gabriel Sotomayor [aut, cre]
Maintainer: Gabriel Sotomayor <gabrielsotomayorl@gmail.com>
Diff between dosr versions 0.3.4 dated 2026-07-06 and 0.3.6 dated 2026-08-28
DESCRIPTION | 12 - MD5 | 72 +++--- NEWS.md | 130 ++++++++--- R/api_helpers.R | 60 +++++ R/data.R | 12 - R/engine.R | 97 ++++---- R/globals.R | 1 R/multi_bin.R | 157 ++++++++----- R/public_api.R | 152 ++++++++---- R/reporting.R | 244 ++++++++++++-------- R/significance.R | 4 R/survey_direct.R |only R/utils.R | 93 +++++++ data/casen_2022.rda |binary data/casen_2024.rda |binary inst/CITATION |only inst/doc/introduccion.R | 6 inst/doc/introduccion.Rmd | 15 + inst/doc/introduccion.html | 352 +++++++++++++++--------------- inst/doc/metodologia.R | 2 inst/doc/metodologia.Rmd | 5 inst/doc/metodologia.html | 41 +-- man/casen_2022.Rd | 6 man/casen_2024.Rd | 6 man/multi_bin.Rd | 18 + man/obs_cuantil.Rd | 22 + man/obs_media.Rd | 22 + man/obs_prop.Rd | 26 +- man/obs_ratio.Rd | 22 + man/obs_total.Rd | 22 + tests/testthat/helper-synthetic-designs.R |only tests/testthat/test-engine.R | 43 +++ tests/testthat/test-multi-bin.R | 82 ++++++ tests/testthat/test-public-api.R | 132 +++++++++++ tests/testthat/test-significance.R | 26 ++ tests/testthat/test-survey-direct.R |only tests/testthat/test-utils.R | 46 +++ vignettes/introduccion.Rmd | 15 + vignettes/metodologia.Rmd | 5 39 files changed, 1408 insertions(+), 540 deletions(-)
Title: Models Spatially Continuous and Discrete Population Genetic
Structure
Description: A method for modeling genetic data as a combination of discrete
layers, within each of which relatedness may decay continuously with geographic
distance. This package contains code for running analyses (which are implemented
in the modeling language 'rstan') and visualizing and interpreting output. See the
paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@umich.edu>
Diff between conStruct versions 1.0.6 dated 2024-01-08 and 1.0.7 dated 2026-08-28
CHANGELOG | 2 DESCRIPTION | 10 MD5 | 54 - NAMESPACE | 2 NEWS.md | 5 R/conStruct-package.R | 3 R/model.comparison.R | 10 R/plot.output.R | 56 - R/run.conStruct.R | 16 build/vignette.rds |binary inst/doc/format-data.R | 46 inst/doc/format-data.html | 7 inst/doc/model-comparison.R | 254 ++--- inst/doc/model-comparison.html | 31 inst/doc/run-conStruct.R | 94 - inst/doc/run-conStruct.html | 11 inst/doc/visualize-results.R | 78 - inst/doc/visualize-results.html | 25 man/compare.two.runs.Rd | 10 man/conStruct-package.Rd | 9 src/stanExports_multiK.cc | 34 src/stanExports_multiK.h | 1368 +++++++++++++--------------- src/stanExports_oneK.cc | 34 src/stanExports_oneK.h | 904 ++++++++---------- src/stanExports_space_multiK.cc | 34 src/stanExports_space_multiK.h | 1907 ++++++++++++++++++---------------------- src/stanExports_space_oneK.cc | 34 src/stanExports_space_oneK.h | 1169 +++++++++++------------- 28 files changed, 2887 insertions(+), 3320 deletions(-)
Title: Scraper for Chess-Results.com
Description: Scrape data from <https://chess-results.com> and get a clean
'tibble'. Currently supports tournament information, starting rank,
playing schedule, pairings/results for rounds, and closing rank.
Author: Sirf Haru [aut, cre, cph]
Maintainer: Sirf Haru <sirfharu@proton.me>
Diff between chessResults versions 2026.07.05 dated 2026-07-11 and 2026.08.27 dated 2026-08-28
chessResults-2026.07.05/chessResults/tests/testthat.R |only chessResults-2026.08.27/chessResults/DESCRIPTION | 31 chessResults-2026.08.27/chessResults/MD5 | 12 chessResults-2026.08.27/chessResults/NEWS.md |only chessResults-2026.08.27/chessResults/R/chess_results.R | 548 ++++++++++---- chessResults-2026.08.27/chessResults/README.md | 87 +- chessResults-2026.08.27/chessResults/inst |only chessResults-2026.08.27/chessResults/man/chess_results.Rd | 29 chessResults-2026.08.27/chessResults/tests/spelling.R |only 9 files changed, 509 insertions(+), 198 deletions(-)
Title: Interactive Training App for Data Science and AI Skills
Description: An interactive 'shiny' training companion for people who are
new to data, developed for World Health Organization data trainings.
Bundles hands-on modules for importing data, missing values, outliers,
text cleaning, merging, visualization, and basic statistics, plus a set
of AI-skills pages (prompting levels, a prompt gallery, AI safety rules,
and a methodology case study) and an interactive quiz with per-session
topic filters. Launch the app with run_cata().
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between cataScience versions 2.1.2 dated 2026-07-30 and 2.1.3 dated 2026-08-28
DESCRIPTION | 6 MD5 | 8 NEWS.md | 58 +++-- README.md | 120 ++++++------ inst/app/R/app-function.R | 455 +++++++++++++++++++++++----------------------- 5 files changed, 337 insertions(+), 310 deletions(-)
Title: Bootstrap Methods for Complete Survey Data
Description: Bootstrap resampling methods have been widely studied in the context of survey data. This package implements various bootstrap resampling techniques tailored for survey data, with a focus on stratified simple random sampling and stratified two-stage cluster sampling. It provides tools for precise and consistent bootstrap variance estimation for population totals, means, and quartiles. Additionally, it enables easy generation of bootstrap samples for in-depth analysis.
Author: Zeinab Mashreghi [aut, cre]
Maintainer: Zeinab Mashreghi <z.mashreghi@uwinnipeg.ca>
Diff between bootsurv versions 0.0.1 dated 2024-05-17 and 0.1.0 dated 2026-08-28
DESCRIPTION | 13 MD5 | 25 NAMESPACE | 17 NEWS.md |only R/BootReplicates.R |only R/BootstrapWeightsMethods.R | 150 ++++- R/DirectBootstrapMethods.R | 139 ++++ R/PseudoPopBootstrapMethods.R | 110 +++ R/TwoStageBootsrtrapMethods.R | 1180 +++++++++++++++++++++++------------------- man/All.data.Rd | 7 man/boot.replicates.Rd |only man/boot.twostage.Rd | 102 ++- man/boot.weights.stsrs.Rd | 48 + man/direct.boot.stsrs.Rd | 40 + man/pseudopop.boot.stsrs.Rd | 49 + 15 files changed, 1191 insertions(+), 689 deletions(-)
Title: Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri', 'dwi'
Description: Defines the method extract and provides 'openMP' support as needed in several packages.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between awsMethods versions 1.1-1 dated 2019-05-08 and 1.1-2 dated 2026-08-28
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- src/omp_funcs.c | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Access Live Sports Odds from the Odds API
Description: A utility to quickly obtain clean and tidy sports odds from
The Odds API <https://the-odds-api.com>. Provides wrappers for every
version 4 endpoint -- featured-market and single-event odds (including
player props and alternate lines), historical odds snapshots, scores,
events, participants, and usage-quota reporting -- returning tidy
tibbles ready for analysis.
Author: Saiem Gilani [aut, cre, cph]
Maintainer: Saiem Gilani <saiem.gilani@gmail.com>
Diff between oddsapiR versions 1.0.0 dated 2026-08-24 and 1.0.1 dated 2026-08-27
DESCRIPTION | 6 +- MD5 | 67 +++++++++++------------ NAMESPACE | 104 ++++++++++++++++++------------------ NEWS.md | 23 +++++++ R/data.R | 30 +++++----- R/toa_event_markets.R | 3 - R/toa_event_odds.R | 4 + R/toa_event_odds_history.R | 4 + R/toa_requests.R | 3 - R/toa_sports.R | 3 - R/toa_sports_events.R | 3 - R/toa_sports_events_history.R | 3 - R/toa_sports_odds.R | 3 - R/toa_sports_odds_history.R | 3 - R/toa_sports_participants.R | 3 - R/toa_sports_scores.R | 3 - R/utils.R | 40 +++++++++++-- man/csv_from_url.Rd | 36 ++++++------ man/progressively.Rd | 46 +++++++-------- man/rds_from_url.Rd | 36 ++++++------ man/toa_event_markets.Rd | 2 man/toa_event_odds.Rd | 2 man/toa_event_odds_history.Rd | 2 man/toa_quota.Rd | 2 man/toa_requests.Rd | 2 man/toa_sports.Rd | 2 man/toa_sports_events.Rd | 2 man/toa_sports_events_history.Rd | 2 man/toa_sports_keys.Rd | 44 +++++++-------- man/toa_sports_odds.Rd | 2 man/toa_sports_odds_history.Rd | 2 man/toa_sports_participants.Rd | 2 man/toa_sports_scores.Rd | 2 tests/testthat.R | 10 +-- tests/testthat/test-quota-headers.R |only 35 files changed, 294 insertions(+), 207 deletions(-)
Title: Lists of Numeric Atomic Objects
Description: Create and manipulate numeric list ('nlist') objects. An
'nlist' is an S3 list of uniquely named numeric objects. An numeric
object is an integer or double vector, matrix or array. An 'nlists'
object is a S3 class list of 'nlist' objects with the same names,
dimensionalities and typeofs. Numeric list objects are of interest
because they are the raw data inputs for analytic engines such as
'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for
storing multiple realizations of of simulated data sets, can be
converted to coda::mcmc and coda::mcmc.list objects.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Ayla Pearson [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between nlist versions 0.4.0 dated 2025-05-11 and 0.5.0 dated 2026-08-27
nlist-0.4.0/nlist/R/as-list.R |only nlist-0.4.0/nlist/R/extras.R |only nlist-0.4.0/nlist/R/utils.R |only nlist-0.4.0/nlist/tests/testthat/test-as-list.R |only nlist-0.4.0/nlist/tests/testthat/tests-fill-all.R |only nlist-0.5.0/nlist/DESCRIPTION | 15 nlist-0.5.0/nlist/MD5 | 192 +-- nlist-0.5.0/nlist/NAMESPACE | 66 - nlist-0.5.0/nlist/NEWS.md | 36 nlist-0.5.0/nlist/R/aggregate.R | 37 nlist-0.5.0/nlist/R/as-nlist.R | 8 nlist-0.5.0/nlist/R/as-nlists.R | 4 nlist-0.5.0/nlist/R/as-term-frame.R | 4 nlist-0.5.0/nlist/R/as-term.R | 3 nlist-0.5.0/nlist/R/brackets.R | 8 nlist-0.5.0/nlist/R/c.R | 9 nlist-0.5.0/nlist/R/chk.R | 29 nlist-0.5.0/nlist/R/collapse-chains.R | 6 nlist-0.5.0/nlist/R/complete-terms.R | 4 nlist-0.5.0/nlist/R/deprecated.R | 20 nlist-0.5.0/nlist/R/internal.R | 20 nlist-0.5.0/nlist/R/nlist.R | 2 nlist-0.5.0/nlist/R/params.R | 8 nlist-0.5.0/nlist/R/pars.R | 94 - nlist-0.5.0/nlist/R/pdims.R | 1 nlist-0.5.0/nlist/R/print.R | 9 nlist-0.5.0/nlist/R/relist-nlist.R | 3 nlist-0.5.0/nlist/R/set-pars.R | 13 nlist-0.5.0/nlist/R/sort.R | 24 nlist-0.5.0/nlist/R/split-chains.R | 4 nlist-0.5.0/nlist/R/subset.R | 77 - nlist-0.5.0/nlist/R/tidy.R | 105 +- nlist-0.5.0/nlist/R/unlist-nlist.R | 8 nlist-0.5.0/nlist/R/vld.R | 11 nlist-0.5.0/nlist/build/stage23.rdb |binary nlist-0.5.0/nlist/build/vignette.rds |binary nlist-0.5.0/nlist/inst/doc/nlist-objects-and-coercions.R | 2 nlist-0.5.0/nlist/inst/doc/nlist-objects-and-coercions.Rmd | 5 nlist-0.5.0/nlist/inst/doc/nlist-objects-and-coercions.html | 158 +-- nlist-0.5.0/nlist/man/aggregate.nlist.Rd | 11 nlist-0.5.0/nlist/man/aggregate.nlists.Rd | 12 nlist-0.5.0/nlist/man/as_mcmc.Rd | 6 nlist-0.5.0/nlist/man/as_mcmc_list.Rd | 4 nlist-0.5.0/nlist/man/as_nlist.Rd | 4 nlist-0.5.0/nlist/man/as_nlists.Rd | 4 nlist-0.5.0/nlist/man/as_term.mcmc.Rd | 15 nlist-0.5.0/nlist/man/as_term.nlist.Rd | 15 nlist-0.5.0/nlist/man/as_term.nlists.Rd | 15 nlist-0.5.0/nlist/man/as_term_frame.Rd | 12 nlist-0.5.0/nlist/man/as_term_frame.nlist.Rd | 12 nlist-0.5.0/nlist/man/as_term_frame.nlists.Rd | 12 nlist-0.5.0/nlist/man/collapse_chains.mcmc.Rd | 7 nlist-0.5.0/nlist/man/collapse_chains.mcmc.list.Rd | 14 nlist-0.5.0/nlist/man/collapse_chains.nlist.Rd | 7 nlist-0.5.0/nlist/man/collapse_chains.nlists.Rd | 7 nlist-0.5.0/nlist/man/deprecated.Rd | 8 nlist-0.5.0/nlist/man/fill_all.nlist.Rd | 4 nlist-0.5.0/nlist/man/fill_all.nlists.Rd | 4 nlist-0.5.0/nlist/man/fill_na.nlist.Rd | 4 nlist-0.5.0/nlist/man/fill_na.nlists.Rd | 4 nlist-0.5.0/nlist/man/nlist-package.Rd | 6 nlist-0.5.0/nlist/man/params.Rd | 9 nlist-0.5.0/nlist/man/pars.mcmc.Rd | 3 nlist-0.5.0/nlist/man/pars.mcmc.list.Rd | 3 nlist-0.5.0/nlist/man/reexports.Rd | 12 nlist-0.5.0/nlist/man/set_pars.mcmc.Rd | 3 nlist-0.5.0/nlist/man/set_pars.mcmc.list.Rd | 3 nlist-0.5.0/nlist/man/sort.mcmc.Rd |only nlist-0.5.0/nlist/man/sort.mcmc.list.Rd |only nlist-0.5.0/nlist/man/tidy.mcmc.Rd | 11 nlist-0.5.0/nlist/man/tidy.mcmc.list.Rd | 11 nlist-0.5.0/nlist/man/tidy.nlists.Rd | 17 nlist-0.5.0/nlist/tests/testthat/test-aggregate.R | 80 - nlist-0.5.0/nlist/tests/testthat/test-as-mcmc-list.R | 596 +++++++++--- nlist-0.5.0/nlist/tests/testthat/test-as-mcmc.R | 408 ++++++-- nlist-0.5.0/nlist/tests/testthat/test-as-nlist.R | 73 + nlist-0.5.0/nlist/tests/testthat/test-as-nlists.R | 23 nlist-0.5.0/nlist/tests/testthat/test-as-term-frame.R | 197 +++ nlist-0.5.0/nlist/tests/testthat/test-bind-iterations.R |only nlist-0.5.0/nlist/tests/testthat/test-brackets.R | 139 ++ nlist-0.5.0/nlist/tests/testthat/test-c.R | 58 - nlist-0.5.0/nlist/tests/testthat/test-chk.R | 41 nlist-0.5.0/nlist/tests/testthat/test-deprecated.R | 24 nlist-0.5.0/nlist/tests/testthat/test-estimates.R | 80 + nlist-0.5.0/nlist/tests/testthat/test-fill-all.R |only nlist-0.5.0/nlist/tests/testthat/test-is.R | 8 nlist-0.5.0/nlist/tests/testthat/test-niters.R | 8 nlist-0.5.0/nlist/tests/testthat/test-nlist.R | 2 nlist-0.5.0/nlist/tests/testthat/test-nlists.R | 33 nlist-0.5.0/nlist/tests/testthat/test-nsams.R | 11 nlist-0.5.0/nlist/tests/testthat/test-nterms.R | 11 nlist-0.5.0/nlist/tests/testthat/test-pars.R | 47 nlist-0.5.0/nlist/tests/testthat/test-print.R | 37 nlist-0.5.0/nlist/tests/testthat/test-relist-nlist.R | 9 nlist-0.5.0/nlist/tests/testthat/test-set-pars.R | 46 nlist-0.5.0/nlist/tests/testthat/test-sort.R |only nlist-0.5.0/nlist/tests/testthat/test-split-chains.R | 19 nlist-0.5.0/nlist/tests/testthat/test-subset.R | 181 ++- nlist-0.5.0/nlist/tests/testthat/test-thin.R | 20 nlist-0.5.0/nlist/tests/testthat/test-tidy.R | 348 +++++-- nlist-0.5.0/nlist/tests/testthat/test-unlist-nlist.R | 2 nlist-0.5.0/nlist/vignettes/nlist-objects-and-coercions.Rmd | 5 102 files changed, 2601 insertions(+), 1149 deletions(-)
Title: A Graph-Based Cross-Fitting Engine in R
Description: Provides a general cross-fitting engine for semiparametric estimation
(e.g., double/debiased machine learning). Supports user-defined target
functionals and directed acyclic graphs of nuisance learners with per-node
training fold widths, target-specific evaluation windows, and
fold-allocation modes ("overlap", "disjoint", "independence"). Returns
either numeric estimates (mode = "estimate") or cross-fitted prediction
functions (mode = "predict"), with configurable aggregation over panels
and repetitions, reuse-aware caching, and failure isolation, making it
well-suited for simulation studies and large benchmarks.
Author: Etienne Peyrot [aut, cre]
Maintainer: Etienne Peyrot <etienne.peyrot@inserm.fr>
Diff between crossfit versions 0.1.3 dated 2026-03-04 and 0.1.4 dated 2026-08-27
crossfit-0.1.3/crossfit/man/fun_code_sig.Rd |only crossfit-0.1.3/crossfit/tests/tests |only crossfit-0.1.3/crossfit/tests/testthat/test-failure-isolation-max_fail.R |only crossfit-0.1.4/crossfit/DESCRIPTION | 8 crossfit-0.1.4/crossfit/MD5 | 62 +- crossfit-0.1.4/crossfit/NAMESPACE | 1 crossfit-0.1.4/crossfit/NEWS.md | 24 - crossfit-0.1.4/crossfit/R/engine.R | 108 ++-- crossfit-0.1.4/crossfit/R/failure-control.R |only crossfit-0.1.4/crossfit/R/plan.R | 70 +-- crossfit-0.1.4/crossfit/R/validation.R | 26 - crossfit-0.1.4/crossfit/README.md | 56 +- crossfit-0.1.4/crossfit/build/vignette.rds |binary crossfit-0.1.4/crossfit/inst/doc/crossfit-intro.R | 2 crossfit-0.1.4/crossfit/inst/doc/crossfit-intro.Rmd | 85 ++- crossfit-0.1.4/crossfit/inst/doc/crossfit-intro.html | 87 ++- crossfit-0.1.4/crossfit/man/create_method.Rd | 15 crossfit-0.1.4/crossfit/man/crossfit-package.Rd | 5 crossfit-0.1.4/crossfit/man/crossfit.Rd | 19 crossfit-0.1.4/crossfit/man/crossfit_failure_control.Rd |only crossfit-0.1.4/crossfit/man/crossfit_multi.Rd | 13 crossfit-0.1.4/crossfit/man/ensure_model.Rd | 7 crossfit-0.1.4/crossfit/man/fun_registry_id.Rd | 18 crossfit-0.1.4/crossfit/man/fun_registry_new.Rd | 8 crossfit-0.1.4/crossfit/man/validate_failure_control.Rd |only crossfit-0.1.4/crossfit/man/validate_method.Rd | 2 crossfit-0.1.4/crossfit/tests/testthat/test-crossfit.R | 34 - crossfit-0.1.4/crossfit/tests/testthat/test-failure-control.R |only crossfit-0.1.4/crossfit/tests/testthat/test-failure-isolation.R |only crossfit-0.1.4/crossfit/tests/testthat/test-no-leakage-trace.R | 226 +++++----- crossfit-0.1.4/crossfit/vignettes/crossfit-intro.Rmd | 85 ++- 31 files changed, 546 insertions(+), 415 deletions(-)
Title: Bayesian Output Analysis Program (BOA) for MCMC
Description: A menu-driven program and library of functions for carrying out
convergence diagnostics and statistical and graphical analysis of Markov
chain Monte Carlo sampling output.
Author: Brian J. Smith [aut, cre]
Maintainer: Brian J. Smith <brian-j-smith@uiowa.edu>
Diff between boa versions 1.1.8-2 dated 2016-06-22 and 1.1.9 dated 2026-08-27
boa-1.1.8-2/boa/data/line.rda |only boa-1.1.9/boa/DESCRIPTION | 10 - boa-1.1.9/boa/MD5 | 80 +++++------ boa-1.1.9/boa/NAMESPACE | 3 boa-1.1.9/boa/R/boa.chain.add.R | 3 boa-1.1.9/boa/R/boa.chain.import.R | 5 boa-1.1.9/boa/R/boa.core.R | 226 ++++++++++++++++---------------- boa-1.1.9/boa/R/boa.handw.R | 4 boa-1.1.9/boa/R/boa.license.R | 2 boa-1.1.9/boa/R/boa.menu.R | 5 boa-1.1.9/boa/R/boa.menu.analysis.R | 4 boa-1.1.9/boa/R/boa.menu.chains.R | 10 - boa-1.1.9/boa/R/boa.menu.coda.R | 16 -- boa-1.1.9/boa/R/boa.menu.file.R | 21 +- boa-1.1.9/boa/R/boa.menu.import.R | 12 - boa-1.1.9/boa/R/boa.menu.par.R | 18 +- boa-1.1.9/boa/R/boa.menu.plot.R | 4 boa-1.1.9/boa/R/boa.menu.plotcoda.R | 4 boa-1.1.9/boa/R/boa.menu.plotdesc.R | 4 boa-1.1.9/boa/R/boa.menu.setpar.R | 6 boa-1.1.9/boa/R/boa.menu.stats.R | 4 boa-1.1.9/boa/R/boa.pardesc.R | 2 boa-1.1.9/boa/R/boa.plot.acf.R | 8 - boa-1.1.9/boa/R/boa.plot.bandg.R | 12 - boa-1.1.9/boa/R/boa.plot.density.R | 9 - boa-1.1.9/boa/R/boa.plot.gandr.R | 11 - boa-1.1.9/boa/R/boa.plot.geweke.R | 18 -- boa-1.1.9/boa/R/boa.plot.history.R | 8 - boa-1.1.9/boa/R/boa.plot.par.R | 9 - boa-1.1.9/boa/R/boa.plot.trace.R | 8 - boa-1.1.9/boa/R/boa.print.gandr.R | 4 boa-1.1.9/boa/R/boa.print.info.R | 14 - boa-1.1.9/boa/R/boa.print.par.R | 15 +- boa-1.1.9/boa/R/boa.randl.R | 4 boa-1.1.9/boa/R/boa.version.R | 2 boa-1.1.9/boa/R/spectrum0.R | 61 ++++---- boa-1.1.9/boa/data/line.R |only boa-1.1.9/boa/inst/CITATION | 25 +-- boa-1.1.9/boa/man/boa.chain.Rd | 2 boa-1.1.9/boa/man/boa.chain.collapse.Rd | 2 boa-1.1.9/boa/man/boa.par.Rd | 2 boa-1.1.9/boa/man/boa.save.Rd | 4 42 files changed, 310 insertions(+), 351 deletions(-)
Title: Trace Function Parameter Types
Description: The 'R' language includes a set of defined types, but the language
itself is "absurdly dynamic" (Turcotte & Vitek (2019)
<doi:10.1145/3340670.3342426>), and lacks any way to specify which types are
expected by any expression. The 'typetracer' package enables code to be
traced to extract detailed information on the properties of parameters
passed to 'R' functions. 'typetracer' can trace individual functions or
entire packages.
Author: Mark Padgham [aut, cre] ,
Filip Krikava [ctb] ,
Antoine Soetewey [ctb] ,
covr authors [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between typetracer versions 0.2.4 dated 2026-07-30 and 0.2.5 dated 2026-08-27
DESCRIPTION | 9 - MD5 | 19 +- NEWS.md | 13 + R/install.R | 12 + R/trace-package.R | 18 ++ R/tracer-define.R | 58 +++++++- README.md | 250 ++++++++++++++++++++----------------- inst/doc/nse.html | 6 tests/testthat/_snaps/trace-fns.md | 27 +++ tests/testthat/test-install.R |only tests/testthat/test-trace-fns.R | 157 +++++++++++++++++++++++ 11 files changed, 425 insertions(+), 144 deletions(-)
Title: Fitting Multivariate Bidirectional Mendelian Randomization
Networks Using Bayesian Directed Cyclic Graphical Models
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. The [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitansarkar010899@gmail.com>
Diff between MR.RGM versions 0.1.0 dated 2026-01-22 and 0.1.1 dated 2026-08-27
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Generalized Multicomponent Latent Trait Model for Diagnosis
Description: Provides Bayesian estimation of Item Response Theory models
that decompose item difficulty into cognitive operations or rules.
Implements the Linear Logistic Test Model (LLTM; Fischer (1973)
<doi:10.1016/0001-6918(73)90003-6>), the Multicomponent Latent
Trait Model for Diagnosis (MLTM-D; Embretson and Yang (2013)
<doi:10.1007/s11336-012-9296-y>), and the Generalized Multicomponent
Latent Trait Model for Diagnosis (GMLTM-D; Ramirez et al. (2024)
<doi:10.3390/jintelligence12070067>), including a variant with
correlated latent components. All models are estimated via Hamiltonian
Monte Carlo using 'Stan' through the 'rstan' interface. Includes tools
for prior predictive checks (Gelman et al., 2020), model validation,
conditional reliability estimation, examinee mastery classification
following Embretson (2019) <doi:10.1007/978-3-030-05584-4_9>, and
individual diagnostic reports at the rule and component level.
Supports user-defined prior distributions for all model [...truncated...]
Author: Eduar Ramirez [aut, cre],
Marcos Jimenez [aut],
Vithor R. Franco [aut],
Jesus Alvarado [aut]
Maintainer: Eduar Ramirez <edrami02@ucm.es>
Diff between GMLTM versions 0.1.0 dated 2026-06-30 and 2.0.0 dated 2026-08-27
DESCRIPTION | 23 MD5 | 133 +-- NAMESPACE | 15 NEWS.md | 59 + R/GMLTM-package.R |only R/GMLTM.R | 58 + R/GMLTM_corr.R |only R/LLTM.R | 37 R/MLTM.R | 45 - R/Q_extended.R | 31 R/conditional-reliability-compare.R |only R/conditional_reliability.R | 420 --------- R/data.R | 3 R/extract_correlation.R |only R/model_validation.R | 26 R/plot_ICC.R | 12 R/ppchecks.R | 34 R/prior_predictive_check.R |only R/reliability-diagnostics.R |only R/reliability-enhanced.R |only R/reliability.R | 1195 --------------------------- R/student_report.R |only R/student_report_batch.R |only inst/GMLTM.stan | 9 inst/GMLTM_corr.stan |only man/GMLTM-package.Rd |only man/GMLTM.Rd | 32 man/GMLTM_corr.Rd |only man/LLTM.Rd | 20 man/MLTM.Rd | 25 man/analogy.Rd | 3 man/bayesian_reliability_fast.Rd | 2 man/check_reliability_data_quality.Rd | 33 man/compare_conditional_reliability.Rd | 33 man/compute_basic_diagnostics.Rd | 2 man/compute_model_validation.Rd | 11 man/conditional_reliability_fast.Rd | 2 man/conditional_reliability_tif.Rd | 31 man/demo_reliability_analysis.Rd | 14 man/enhanced_mltm_reliability.Rd | 33 man/export_reliability_results.Rd | 33 man/extract_correlation.Rd |only man/generate_Q_with_interactions.Rd | 1 man/hierarchical_reliability_fast.Rd | 2 man/informe_estudiante.Rd |only man/integrate_with_enhanced_reliability.Rd | 34 man/marginal_Pchecks.Rd | 30 man/plot.enhanced_mltm_reliability.Rd | 2 man/plot_ICC_grouped.Rd | 13 man/plot_ICC_individual.Rd | 7 man/plot_all_components.Rd | 33 man/plot_comparison_base.Rd | 2 man/plot_components_comparison.Rd | 33 man/plot_conditional_base.Rd | 2 man/plot_conditional_reliability.Rd | 31 man/plot_marginal_base.Rd | 2 man/plot_prior_predictive_check.Rd |only man/ppchecks.Rd | 13 man/print.GMLTM.Rd |only man/print.GMLTM_batch_report.Rd |only man/print.GMLTM_corr.Rd |only man/print.GMLTM_correlation.Rd |only man/print.GMLTM_prior_predictive_check.Rd |only man/print.GMLTM_student_report.Rd |only man/print.LLTM.Rd |only man/print.MLTM.Rd |only man/print.enhanced_mltm_reliability.Rd | 2 man/print.reliability_data_quality.Rd | 2 man/print.reliability_profile.Rd | 2 man/prior_predictive_check.Rd |only man/quick_reliability_check.Rd | 14 man/reliability.Rd | 51 + man/reliability_comparison_fast.Rd | 2 man/reliability_profile.Rd | 33 man/reliability_usage_instructions.Rd | 16 man/student_report.Rd |only man/student_report_batch.Rd |only tests/testthat/helper-mock-fit.R |only tests/testthat/test-data-input.R |only tests/testthat/test-prior_predictive_check.R |only tests/testthat/test-priors.R | 56 + tests/testthat/test-student_report.R |only tests/testthat/test-student_report_batch.R |only 83 files changed, 1045 insertions(+), 1712 deletions(-)
Title: Vehicle Routing Problem Solver Built on 'PyVRP'
Description: A 'tidyverse'-style interface to high-performance vehicle routing
problem (VRP) solving. Vendors the C++ core of the 'PyVRP' solver
(<https://github.com/PyVRP/PyVRP>) and rewires it through 'cpp11', with no
'Python' runtime dependency. Supports the capacitated VRP, time windows,
multiple depots, heterogeneous fleets, prize-collecting and multi-trip
variants, driven by an iterated local search metaheuristic.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut],
Niels Wouda [ctb, cph] ,
Thibaut Vidal [cph] ,
ORTEC [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between vrpr versions 0.1.0 dated 2026-07-04 and 0.1.1 dated 2026-08-27
DESCRIPTION | 10 +++++----- MD5 | 26 ++++++++++++++------------ NEWS.md | 19 +++++++++++++++++++ README.md | 10 ++++++++++ inst/CITATION | 2 +- inst/doc/vrpr.html | 2 +- man/figures/vrpr-rpkg.svg |only man/vrpr-package.Rd | 2 +- src/vendor/pyvrp/CostEvaluator.h | 7 ++++--- src/vendor/pyvrp/Route.h | 5 +++++ src/vendor/pyvrp/Solution.cpp | 1 + src/vendor/pyvrp/pyvrp_version.txt | 3 ++- src/vendor/pyvrp/search/LocalSearch.cpp | 1 + src/vendor/pyvrp/search/Route.h | 7 ++++--- src/vendor/pyvrp/vrpr_compat.h |only 15 files changed, 68 insertions(+), 27 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 1.1.0 dated 2026-06-16 and 1.1.1 dated 2026-08-27
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 139 +++++++++++++------------ R/summariseClinicalRecords.R | 40 ++++--- R/summariseConceptSetCounts.R | 6 - R/summariseInternal.R | 4 R/utilities.R | 21 ++- tests/testthat/test-summariseClinicalRecords.R | 4 tests/testthat/test-summariseTrend.R | 19 +++ 9 files changed, 152 insertions(+), 105 deletions(-)
Title: Interface for Large Language Models via 'llama.cpp'
Description: Provides R bindings to 'llama.cpp' for running large language
models locally, with optional GPU acceleration via 'ggmlR'. Supports text
generation, embeddings, chat-based workflows, tool calling, and multimodal
(vision) inference. Includes 'OpenAI'- and 'Anthropic'-compatible HTTP
servers for serving local models, along with device selection and
multi-GPU support.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between llamaR versions 0.2.5 dated 2026-07-02 and 0.2.6 dated 2026-08-27
DESCRIPTION | 10 MD5 | 182 +- NAMESPACE | 44 NEWS.md | 7 R/llama.R | 1199 ++++++++++++++++- R/serve.R | 289 +++- README.md | 122 + build/vignette.rds |binary inst/doc/multi-gpu.R |only inst/doc/multi-gpu.Rmd |only inst/doc/multi-gpu.html |only inst/examples/bench_pp_tp_dp.sh |only inst/examples/bench_replica.R |only inst/examples/claude_code_launcher.sh | 9 inst/examples/serve_openai_tools.R |only man/llama_apply_control_vector.Rd |only man/llama_context_flash_attn.Rd |only man/llama_flash_attn_type_name.Rd |only man/llama_gen_begin.Rd | 23 man/llama_gen_begin_at.Rd | 23 man/llama_generate.Rd | 23 man/llama_generate_batch.Rd | 20 man/llama_load_model_from_splits.Rd |only man/llama_lora_alora_invocation_tokens.Rd |only man/llama_lora_meta.Rd |only man/llama_max_parallel_sequences.Rd |only man/llama_max_tensor_buft_overrides.Rd |only man/llama_model_cls_labels.Rd |only man/llama_model_decoder_start_token.Rd |only man/llama_model_info.Rd | 15 man/llama_model_sampling_meta.Rd |only man/llama_perf_sampler.Rd |only man/llama_sampler_accept.Rd |only man/llama_sampler_chain_add.Rd |only man/llama_sampler_chain_from_params.Rd |only man/llama_sampler_chain_get.Rd |only man/llama_sampler_chain_n.Rd |only man/llama_sampler_chain_new.Rd |only man/llama_sampler_chain_remove.Rd |only man/llama_sampler_clone.Rd |only man/llama_sampler_free.Rd |only man/llama_sampler_get_seed.Rd |only man/llama_sampler_name.Rd |only man/llama_sampler_new.Rd |only man/llama_sampler_params.Rd |only man/llama_sampler_reset.Rd |only man/llama_serve_openai.Rd | 6 man/llama_split_path.Rd |only man/llama_split_prefix.Rd |only man/llama_state_data.Rd |only man/llama_state_seq.Rd |only man/llama_state_seq_file.Rd |only man/llama_vocab_add_special.Rd |only man/llama_vocab_get_attr.Rd |only man/llama_vocab_special_tokens.Rd |only src/common.h | 3 src/common_chat_support.cpp | 1 src/jinja/lexer.cpp | 1 src/jinja/parser.cpp | 1 src/jinja/string.cpp | 1 src/jinja/string.h | 1 src/jinja/value.h | 2 src/llama-adapter.cpp | 2 src/llama-adapter.h | 1 src/llama-batch.cpp | 1 src/llama-chat.cpp | 1 src/llama-context.cpp | 3 src/llama-context.h | 1 src/llama-grammar.h | 1 src/llama-graph.cpp | 3 src/llama-graph.h | 2 src/llama-impl.cpp | 1 src/llama-impl.h | 2 src/llama-kv-cache.cpp | 1 src/llama-kv-cache.h | 2 src/llama-memory-hybrid-iswa.cpp | 4 src/llama-memory-hybrid.cpp | 4 src/llama-memory-recurrent.h | 1 src/llama-mmap.cpp | 1 src/llama-model-loader.cpp | 3 src/llama-model-loader.h | 3 src/llama-model-saver.cpp | 1 src/llama-model.cpp | 1 src/llama-model.h | 2 src/llama-vocab.cpp | 4 src/llama.h | 5 src/log.cpp | 1 src/models/models.h | 6 src/mtmd/clip-impl.h | 3 src/mtmd/models/models.h | 4 src/mtmd/mtmd-helper.cpp | 2 src/mtmd/mtmd-image.cpp | 2 src/mtmd/mtmd.cpp | 1 src/mtmd/mtmd.h | 1 src/peg-parser.h | 2 src/r_chat_interface.cpp | 75 - src/r_llama_compat.h | 1 src/r_llama_interface.cpp | 2105 ++++++++++++++++++++++++------ src/r_llama_ptr.h |only src/r_llama_throw.h |only src/r_mtmd_interface.cpp | 66 src/regex-partial.cpp | 1 src/regex-partial.h | 2 src/unicode-data.cpp | 2 src/unicode-data.h | 2 src/unicode.cpp | 1 tests/testthat.R | 7 tests/testthat/test-cvec-perf-sampler.R |only tests/testthat/test-flash-attn.R |only tests/testthat/test-lora-multi.R | 60 tests/testthat/test-model-introspection.R |only tests/testthat/test-ptr-args.R |only tests/testthat/test-sampler-chain.R |only tests/testthat/test-sampler-params.R |only tests/testthat/test-serve-openai-e2e.R |only tests/testthat/test-splits.R |only tests/testthat/test-state-seq.R |only vignettes/multi-gpu.Rmd |only 118 files changed, 3783 insertions(+), 593 deletions(-)
Title: High-Performance HTTP Server for R via 'Drogon'
Description: Provides an 'R' interface to the 'Drogon' high-performance
'C++' 'HTTP' server framework
(<https://github.com/drogonframework/drogon>). Offers a 'plumber'-style
application programming interface for building 'REST' services from
'R' with substantially higher throughput, including streaming
responses and full-duplex 'WebSocket' endpoints.
Author: Yuri Baramykov [aut, cre] ,
An Tao [ctb, cph] ,
Shuo Chen [ctb, cph] ,
Baptiste Lepilleur [ctb, cph] ,
Christopher Dunn [ctb] ,
JsonCpp Contributors [ctb, cph] ,
Bert Belder [ctb, cph] ),
mman-win32 contributors [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between drogonR versions 0.1.8 dated 2026-07-04 and 0.1.9 dated 2026-08-27
DESCRIPTION | 6 - MD5 | 46 ++++---- NEWS.md | 9 + R/server.R | 32 +++++- README.md | 19 +++ inst/doc/mode-native.html | 4 man/dr_serve.Rd | 17 +++ src/drogon/lib/src/HttpAppFrameworkImpl.h | 1 src/drogon/lib/src/HttpServer.cc | 6 + src/drogon/lib/src/RequestStream.cc | 1 src/drogon/lib/src/WebSocketConnectionImpl.h | 1 src/drogon/lib/src/drogon_test.cc | 1 src/drogon/trantor/net/EventLoopThread.h | 1 src/drogon/trantor/net/TcpConnection.h | 13 ++ src/drogon/trantor/net/inner/RateLimitBucket.h |only src/drogon/trantor/net/inner/TcpConnectionImpl.cc | 115 ++++++++++++++++++++-- src/drogon/trantor/net/inner/TcpConnectionImpl.h | 16 +++ src/drogon/trantor/net/inner/Timer.cc | 1 src/drogon/trantor/utils/ConcurrentTaskQueue.h | 1 src/drogon_server.cpp | 23 ++++ src/r_bridge.cpp | 1 src/r_bridge.h | 1 tests/testthat.R | 1 tests/testthat/server-script.R | 5 tests/testthat/test-bandwidth.R |only 25 files changed, 282 insertions(+), 39 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] ,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.3.2 dated 2025-12-16 and 0.3.3 dated 2026-08-27
DESCRIPTION | 10 MD5 | 44 NAMESPACE | 6 NEWS.md | 6 R/base_api.R | 67 R/get_data.R | 17 R/get_map_data.R | 26 R/utils.R | 50 README.md | 14 build/vignette.rds |binary inst/doc/dawaR.html | 44 inst/doc/status.html | 18 man/connection_check.Rd | 4 man/get_data.Rd | 4 man/get_map_data.Rd | 4 man/status_check.Rd | 4 tests/testthat/_snaps/get_data.md |17120 ++++++++++----------- tests/testthat/_snaps/get_map_data-kommuner.md | 50 tests/testthat/_snaps/get_map_data-politikredse.md | 150 tests/testthat/_snaps/get_map_data-regioner.md | 80 tests/testthat/_snaps/get_map_data-vote.md | 70 tests/testthat/_snaps/status_check.md | 8 tests/testthat/setup-deprecation-warning.R |only tests/testthat/test-deprecation-warning.R |only 24 files changed, 8937 insertions(+), 8859 deletions(-)
Title: Parallel Runs of Reverse Depends
Description: Reverse depends for a given package are queued such that multiple
workers can run the reverse-dependency tests in parallel.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between prrd versions 0.0.6 dated 2024-03-06 and 0.0.7 dated 2026-08-27
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 15 +++++++++------ MD5 | 14 +++++++------- R/db.R | 2 +- R/summarise.R | 26 ++++++++++++++++++++++---- README.md | 6 +++--- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ 8 files changed, 80 insertions(+), 21 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Produce pdf, rtf, text report files.
6) Produce Installation and Operational Qualification (IQ/OQ) reports in pdf.
After installation, qualify the package in your own environment:
run pdfIQ() for Installation Qualification and pdfOQ() for Operational
Qualification. Run writeMD5() once after installation so the IQ
file-integrity check passes. To approve a report, sign it digitally in
Adobe Acrobat Reader (generate with sigField=TRUE, or run addSigField(),
to add click-to-sign fields), instead of printing and scanning; or use
signPDF()/verifyPDF() for a scriptable signature.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (I [...truncated...]
Author: Kyun-Seop Bae [aut, cre],
Michael E. Schaffer [ctb, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.7.0 dated 2026-07-20 and 0.7.1 dated 2026-08-27
DESCRIPTION | 10 MD5 | 19 - R/Res2Txt.R | 15 - R/pdfNCA.R | 3 R/pdfOQ.R | 185 +++++++++++++++- R/pdfPQ.R | 109 +++++++-- R/rtfNCA.R | 3 inst/NEWS.Rd | 13 + inst/OQ/Reference_Analytic_BLQ_Extravascular_Linear.csv |only man/pdfOQ.Rd | 31 +- tests |only 11 files changed, 330 insertions(+), 58 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Infrastructure for working with censored or truncated normal, logistic,
and Student-t distributions, i.e., d/p/q/r functions and distributions3
objects.
Author: Achim Zeileis [aut, cre] ,
Jakob W. Messner [aut] ,
Reto Stauffer [aut] ,
Ioannis Kosmidis [ctb] ,
Georg J. Mayr [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between crch versions 1.2-2 dated 2025-03-14 and 1.2-3 dated 2026-08-27
DESCRIPTION | 25 ++--- MD5 | 50 +++++----- NAMESPACE | 30 ++---- NEWS.md | 25 ++++- R/CensoredLogistic.R | 50 ++++++++-- R/CensoredNormal.R | 32 +++++- R/CensoredStudentsT.R | 61 ++++++++++-- R/TruncatedLogistic.R | 50 ++++++++-- R/TruncatedNormal.R | 32 +++++- R/TruncatedStudentsT.R | 56 +++++++++-- R/clogis.R | 108 ++++++++++++++-------- R/cnorm.R | 108 ++++++++++++++-------- R/crch.R | 26 ++--- R/crch.boost.R | 6 - R/ct.R | 131 ++++++++++++++++++--------- R/tlogis.R | 108 ++++++++++++++-------- R/tnorm.R | 108 ++++++++++++++-------- R/tt.R | 129 ++++++++++++++++++--------- README.md | 30 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/crch.R | 14 +- inst/doc/crch.html | 198 ++++++++++++++++++++++++++++++++---------- man/CensoredStudentsT.Rd | 3 man/TruncatedStudentsT.Rd | 3 tests/score-hessian.R |only tests/score-hessian.Rout.save |only 27 files changed, 930 insertions(+), 453 deletions(-)
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] ,
Natacha Turck [aut],
Alexandre Hainard [aut],
Natalia Tiberti [aut],
Frederique Lisacek [aut],
Jean-Charles Sanchez [aut],
Markus Mueller [aut],
Stefan Siegert [ctb] ,
Matthias Doering [ctb] ,
Zane Billings [ctb]
Maintainer: Xavier Robin <pROC-cran@xavamail.net>
Diff between pROC versions 1.19.0.1 dated 2025-07-31 and 1.19.1 dated 2026-08-27
DESCRIPTION | 16 ++++--- MD5 | 41 ++++++++++--------- NEWS | 6 ++ README.md | 35 +++++++++------- build/partial.rdb |binary build/vignette.rds |only inst/doc |only inst/extra/sos_clashes.R | 18 +++++--- man/coords_transpose.Rd | 2 man/geom_polygon_auc.roc.Rd | 3 - man/pROC-package.Rd | 9 +--- man/smooth.Rd | 10 ++++ tests/testthat/helper-deLongPlacementsCpp-expected.R | 12 ++--- tests/testthat/helper-roc.utils-expected.R | 4 - tests/testthat/test-are-paired.R | 1 tests/testthat/test-coords.R | 4 - tests/testthat/test-ggroc.R | 13 ++++-- tests/testthat/test-plot.R | 10 ++++ tests/testthat/test-print.R | 8 +++ tests/testthat/test-roc.R | 6 ++ tests/testthat/test-smooth.R | 3 + vignettes |only 22 files changed, 133 insertions(+), 68 deletions(-)
Title: Analyze Results Generated by the 'SqueezeMeta' Pipeline
Description: 'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
Author: Fernando Puente-Sanchez [aut, cre],
Natalia Garcia-Garcia [aut]
Maintainer: Fernando Puente-Sanchez <fernando.puente.sanchez@slu.se>
Diff between SQMtools versions 1.8.0 dated 2026-06-11 and 1.8.1 dated 2026-08-27
DESCRIPTION | 9 +++---- MD5 | 35 ++++++++++++++-------------- NAMESPACE | 60 ++++++++++++++++++++++++++++-------------------- R/CheckMProkaryote.R | 3 +- R/Hadza.R | 2 - R/MGKOs.R | 4 ++- R/MGOGs.R | 4 ++- R/USiCGs.R | 4 +-- R/aggregate_methods.R | 14 +++++------ R/loadSQM.R | 31 +++++++++++++++++++++--- R/loadSQMlite.R | 2 - build |only man/CheckMProkaryote.Rd | 5 +++- man/Hadza.Rd | 2 - man/MGKOs.Rd | 5 +++- man/MGOGs.Rd | 5 +++- man/USiCGs.Rd | 4 +-- man/loadSQM.Rd | 2 - man/loadSQMlite.Rd | 2 - 19 files changed, 121 insertions(+), 72 deletions(-)
Title: Recursive Construction of Nested Resolvable Designs and
Associated Uniform Designs over GF(p)
Description: Recursive construction of balanced incomplete block designs
(BIBDs), their successive generations, resolvable BIBDs (RBIBDs) and
associated uniform designs (UDs), derived from finite projective
geometries PG(m, p) over a Galois field GF(p) of any prime order p.
Implements and generalises the method of Boudraa, Gheribi-Aoulmi and
Laib (2013, International Journal of Research and Reviews in Applied
Sciences, 17(2), 167-176), which was previously available only for
p = 2, and the uniform design constructions of Fang et al. (2004)
<doi:10.1016/S0012-365X(03)00100-6>. Designs of every recursion stage
can be extracted, and all constructions are validated against the
parameters published in the original paper.
Author: Mohamed Laib [aut, cre],
Abla Boudraa [aut],
Zebida Gheribi-Aoulmi [aut]
Maintainer: Mohamed Laib <laib.med@gmail.com>
Diff between PGM2 versions 2.0.0 dated 2026-07-30 and 2.0.1 dated 2026-08-27
PGM2-2.0.0/PGM2/tests/testthat/lr2.log |only PGM2-2.0.0/PGM2/tests/testthat/texput.log |only PGM2-2.0.1/PGM2/DESCRIPTION | 9 - PGM2-2.0.1/PGM2/MD5 | 31 ++--- PGM2-2.0.1/PGM2/NAMESPACE | 1 PGM2-2.0.1/PGM2/NEWS.md | 30 ++++ PGM2-2.0.1/PGM2/R/Qn.R | 26 ++-- PGM2-2.0.1/PGM2/R/Steps.R | 14 ++ PGM2-2.0.1/PGM2/R/Uniform.R | 147 ++++++++++++++++-------- PGM2-2.0.1/PGM2/inst/CITATION | 1 PGM2-2.0.1/PGM2/inst/doc/PGM2-paper.Rmd | 17 +- PGM2-2.0.1/PGM2/inst/doc/PGM2-paper.html | 80 ++++++------- PGM2-2.0.1/PGM2/man/Qn.Rd | 26 ++-- PGM2-2.0.1/PGM2/man/Uniform.Rd | 23 +++ PGM2-2.0.1/PGM2/tests/testthat/paper-supplement |only PGM2-2.0.1/PGM2/tests/testthat/test-Qn.R | 4 PGM2-2.0.1/PGM2/tests/testthat/test-designs.R | 62 ++++++++++ PGM2-2.0.1/PGM2/vignettes/PGM2-paper.Rmd | 17 +- 18 files changed, 346 insertions(+), 142 deletions(-)
Title: Continuous Norming
Description: A toolbox for continuous norming of psychological and educational tests, supporting regression-based norming where norms can vary as a continuous function of age or another norm predictor. Norms are estimated using Generalized Additive Models for Location, Scale, and Shape (GAMLSS), enabling flexible modelling of the full score distribution in a normative sample. The package supports applications in psychometrics and psychological testing, and includes functions for model selection, reliability estimation, norm calculation, including confidence intervals, and sample size planning. For more details, see Timmerman et al. (2021) <doi:10.1037/met0000348>.
Author: Klazien de Vries [aut] ,
Hannah Heister [aut] ,
Julian Urban [aut] ,
Lieke Voncken [ctb] ,
Marieke Timmerman [aut, cre]
Maintainer: Marieke Timmerman <m.e.timmerman@rug.nl>
Diff between normref versions 0.1.1 dated 2026-04-10 and 0.1.2 dated 2026-08-27
normref-0.1.1/normref/README.md |only normref-0.1.1/normref/inst/extdata |only normref-0.1.2/normref/DESCRIPTION | 6 normref-0.1.2/normref/MD5 | 46 - normref-0.1.2/normref/NEWS.md | 17 normref-0.1.2/normref/R/evaluate.R | 36 - normref-0.1.2/normref/R/model_selection.R | 243 +++----- normref-0.1.2/normref/R/plot_results.R | 2 normref-0.1.2/normref/R/preprocess.R | 44 + normref-0.1.2/normref/R/utilities.R | 299 +++++----- normref-0.1.2/normref/build/partial.rdb |binary normref-0.1.2/normref/build/vignette.rds |binary normref-0.1.2/normref/inst/doc/intro_to_normref.R | 16 normref-0.1.2/normref/inst/doc/intro_to_normref.Rmd | 30 - normref-0.1.2/normref/inst/doc/intro_to_normref.html | 77 +- normref-0.1.2/normref/man/capture_family_env.Rd |only normref-0.1.2/normref/man/composite_shape.Rd | 18 normref-0.1.2/normref/man/fb_select.Rd | 29 normref-0.1.2/normref/man/normtable_create.Rd | 9 normref-0.1.2/normref/man/shape_data.Rd | 4 normref-0.1.2/normref/tests/testthat/_snaps/plot_results/normtable-plot.svg | 3 normref-0.1.2/normref/tests/testthat/setup.R | 1 normref-0.1.2/normref/tests/testthat/test-evaluate.R | 4 normref-0.1.2/normref/tests/testthat/test-model_selection.R | 186 ++++-- normref-0.1.2/normref/vignettes/intro_to_normref.Rmd | 30 - 25 files changed, 612 insertions(+), 488 deletions(-)
Title: Download 'Eurostat' 'GISCO' Spatial Data
Description: Tools to download global and European spatial data from the
'Eurostat' 'GISCO' (Geographic Information System of the Commission)
data distribution <https://ec.europa.eu/eurostat/web/gisco>. The
package provides helpers for country boundaries, 'NUTS' regions,
administrative units, statistical units, transport networks, basic
service locations and other 'GISCO' datasets. This package is not
officially related to or endorsed by 'Eurostat'.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 1.1.1 dated 2026-06-17 and 1.2.0 dated 2026-08-27
giscoR-1.1.1/giscoR/tests/testthat/helpers.R |only giscoR-1.2.0/giscoR/DESCRIPTION | 10 giscoR-1.2.0/giscoR/MD5 | 291 +++++----- giscoR-1.2.0/giscoR/NAMESPACE | 8 giscoR-1.2.0/giscoR/NEWS.md | 38 - giscoR-1.2.0/giscoR/R/data.R | 60 +- giscoR-1.2.0/giscoR/R/docs.R | 8 giscoR-1.2.0/giscoR/R/gisco-address-api.R | 28 giscoR-1.2.0/giscoR/R/gisco-attributions.R | 48 - giscoR-1.2.0/giscoR/R/gisco-bulk-download.R | 26 giscoR-1.2.0/giscoR/R/gisco-cache.R | 86 +- giscoR-1.2.0/giscoR/R/gisco-check-access.R | 10 giscoR-1.2.0/giscoR/R/gisco-get-airports.R | 50 + giscoR-1.2.0/giscoR/R/gisco-get-cached-db.R | 56 - giscoR-1.2.0/giscoR/R/gisco-get-census.R | 19 giscoR-1.2.0/giscoR/R/gisco-get-coastal-lines.R | 44 - giscoR-1.2.0/giscoR/R/gisco-get-communes.R | 21 giscoR-1.2.0/giscoR/R/gisco-get-countries.R | 27 giscoR-1.2.0/giscoR/R/gisco-get-education.R | 23 giscoR-1.2.0/giscoR/R/gisco-get-grid.R | 70 +- giscoR-1.2.0/giscoR/R/gisco-get-healthcare.R | 26 giscoR-1.2.0/giscoR/R/gisco-get-lau.R | 26 giscoR-1.2.0/giscoR/R/gisco-get-metadata.R | 10 giscoR-1.2.0/giscoR/R/gisco-get-nuts.R | 27 giscoR-1.2.0/giscoR/R/gisco-get-ports.R | 18 giscoR-1.2.0/giscoR/R/gisco-get-postal-codes.R | 53 + giscoR-1.2.0/giscoR/R/gisco-get-unit-country.R | 27 giscoR-1.2.0/giscoR/R/gisco-get-unit-nuts.R | 3 giscoR-1.2.0/giscoR/R/gisco-get-unit-urban-audit.R | 44 - giscoR-1.2.0/giscoR/R/gisco-get-units.R | 11 giscoR-1.2.0/giscoR/R/gisco-get-urban-audit.R | 19 giscoR-1.2.0/giscoR/R/gisco-id-api.R | 45 + giscoR-1.2.0/giscoR/R/giscoR-package.R | 1 giscoR-1.2.0/giscoR/R/utils-country.R | 20 giscoR-1.2.0/giscoR/R/utils-dataset.R | 9 giscoR-1.2.0/giscoR/R/utils-request.R | 49 + giscoR-1.2.0/giscoR/R/utils-sf.R | 10 giscoR-1.2.0/giscoR/R/utils-units.R | 26 giscoR-1.2.0/giscoR/R/utils-url.R | 30 - giscoR-1.2.0/giscoR/R/utils.R | 37 + giscoR-1.2.0/giscoR/README.md | 43 - giscoR-1.2.0/giscoR/build/stage23.rdb |binary giscoR-1.2.0/giscoR/build/vignette.rds |binary giscoR-1.2.0/giscoR/data/gisco_coastal_lines.rda |binary giscoR-1.2.0/giscoR/data/gisco_countries_2024.rda |binary giscoR-1.2.0/giscoR/data/gisco_countrycode.rda |binary giscoR-1.2.0/giscoR/data/gisco_db.rda |binary giscoR-1.2.0/giscoR/data/gisco_nuts_2024.rda |binary giscoR-1.2.0/giscoR/inst/WORDLIST | 148 ++--- giscoR-1.2.0/giscoR/inst/doc/apis.html |only giscoR-1.2.0/giscoR/inst/doc/apis.qmd |only giscoR-1.2.0/giscoR/inst/doc/giscoR.html | 25 giscoR-1.2.0/giscoR/inst/doc/giscoR.qmd | 33 - giscoR-1.2.0/giscoR/inst/schemaorg.json | 4 giscoR-1.2.0/giscoR/man/chunks/address_api.Rmd | 4 giscoR-1.2.0/giscoR/man/chunks/education_meta.Rmd | 5 giscoR-1.2.0/giscoR/man/chunks/healthcare_meta.Rmd | 6 giscoR-1.2.0/giscoR/man/figures/README-thematic-map-1.png |binary giscoR-1.2.0/giscoR/man/giscoR-package.Rd | 1 giscoR-1.2.0/giscoR/man/gisco_address_api.Rd | 17 giscoR-1.2.0/giscoR/man/gisco_attributions.Rd | 19 giscoR-1.2.0/giscoR/man/gisco_bulk_download.Rd | 18 giscoR-1.2.0/giscoR/man/gisco_clear_cache.Rd | 9 giscoR-1.2.0/giscoR/man/gisco_coastal_lines.Rd | 16 giscoR-1.2.0/giscoR/man/gisco_countries_2024.Rd | 14 giscoR-1.2.0/giscoR/man/gisco_countrycode.Rd | 7 giscoR-1.2.0/giscoR/man/gisco_db.Rd | 13 giscoR-1.2.0/giscoR/man/gisco_get_airports.Rd | 34 - giscoR-1.2.0/giscoR/man/gisco_get_cached_db.Rd | 4 giscoR-1.2.0/giscoR/man/gisco_get_census.Rd | 18 giscoR-1.2.0/giscoR/man/gisco_get_coastal_lines.Rd | 42 - giscoR-1.2.0/giscoR/man/gisco_get_communes.Rd | 22 giscoR-1.2.0/giscoR/man/gisco_get_countries.Rd | 22 giscoR-1.2.0/giscoR/man/gisco_get_education.Rd | 31 - giscoR-1.2.0/giscoR/man/gisco_get_grid.Rd | 68 +- giscoR-1.2.0/giscoR/man/gisco_get_healthcare.Rd | 46 - giscoR-1.2.0/giscoR/man/gisco_get_lau.Rd | 23 giscoR-1.2.0/giscoR/man/gisco_get_metadata.Rd | 8 giscoR-1.2.0/giscoR/man/gisco_get_nuts.Rd | 26 giscoR-1.2.0/giscoR/man/gisco_get_ports.Rd | 19 giscoR-1.2.0/giscoR/man/gisco_get_postal_codes.Rd | 57 + giscoR-1.2.0/giscoR/man/gisco_get_unit.Rd | 71 +- giscoR-1.2.0/giscoR/man/gisco_get_units.Rd | 29 giscoR-1.2.0/giscoR/man/gisco_get_urban_audit.Rd | 16 giscoR-1.2.0/giscoR/man/gisco_id_api.Rd | 14 giscoR-1.2.0/giscoR/man/gisco_nuts_2024.Rd | 26 giscoR-1.2.0/giscoR/man/gisco_set_cache_dir.Rd | 9 giscoR-1.2.0/giscoR/man/roxygen/meta.R | 9 giscoR-1.2.0/giscoR/tests/testthat/_snaps/docs.md | 4 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-address-api.md | 102 +++ giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-attributions.md | 8 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-bulk-download.md | 51 + giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-cache.md | 13 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-airports.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-cached-db.md | 27 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-census.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-coastal-lines.md | 13 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-communes.md | 73 ++ giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-countries.md | 13 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-education.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-grid.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-healthcare.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-lau.md | 34 + giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-metadata.md | 13 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-nuts.md | 21 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-ports.md |only giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-postal-codes.md | 20 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-unit-country.md | 23 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-unit-nuts.md | 21 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-unit-urban-audit.md | 21 giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-get-urban-audit.md | 63 ++ giscoR-1.2.0/giscoR/tests/testthat/_snaps/gisco-id-api.md | 45 + giscoR-1.2.0/giscoR/tests/testthat/_snaps/utils-country.md | 20 giscoR-1.2.0/giscoR/tests/testthat/_snaps/utils-url.md | 18 giscoR-1.2.0/giscoR/tests/testthat/_snaps/utils.md | 77 ++ giscoR-1.2.0/giscoR/tests/testthat/helper.R |only giscoR-1.2.0/giscoR/tests/testthat/setup-cache.R |only giscoR-1.2.0/giscoR/tests/testthat/test-docs.R | 27 giscoR-1.2.0/giscoR/tests/testthat/test-gisco-address-api.R | 45 - giscoR-1.2.0/giscoR/tests/testthat/test-gisco-attributions.R | 18 giscoR-1.2.0/giscoR/tests/testthat/test-gisco-bulk-download.R | 92 +-- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-cache.R | 224 ++++--- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-check-access.R | 18 giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-airports.R | 181 +++--- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-cached-db.R | 146 ++--- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-census.R | 218 +++---- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-coastal-lines.R | 49 - giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-communes.R | 46 - giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-countries.R | 93 +-- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-education.R | 290 ++++----- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-grid.R | 113 +-- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-healthcare.R | 248 ++++---- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-lau.R | 29 giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-metadata.R | 264 ++++----- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-nuts.R | 108 +-- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-ports.R | 191 +++--- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-postal-codes.R | 51 + giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-unit-country.R | 73 -- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-unit-nuts.R | 65 -- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-unit-urban-audit.R | 92 +-- giscoR-1.2.0/giscoR/tests/testthat/test-gisco-get-urban-audit.R | 48 - giscoR-1.2.0/giscoR/tests/testthat/test-gisco-id-api.R | 96 +-- giscoR-1.2.0/giscoR/tests/testthat/test-issues.R | 20 giscoR-1.2.0/giscoR/tests/testthat/test-utils-country.R | 27 giscoR-1.2.0/giscoR/tests/testthat/test-utils-request.R |only giscoR-1.2.0/giscoR/tests/testthat/test-utils-sf.R | 25 giscoR-1.2.0/giscoR/tests/testthat/test-utils-units.R | 25 giscoR-1.2.0/giscoR/tests/testthat/test-utils-url.R | 213 ++----- giscoR-1.2.0/giscoR/tests/testthat/test-utils.R | 66 +- giscoR-1.2.0/giscoR/vignettes/apis.qmd |only giscoR-1.2.0/giscoR/vignettes/fig-address-api-1.png |only giscoR-1.2.0/giscoR/vignettes/fig-api-id-1.png |only giscoR-1.2.0/giscoR/vignettes/fig-giscor-1.png |binary giscoR-1.2.0/giscoR/vignettes/giscoR.qmd | 33 - 154 files changed, 3646 insertions(+), 2658 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-28 1.0.0
Title: Superlatively Fast Fuzzy Joins
Description: Empowers users to fuzzily-merge data frames with millions or tens of millions of rows in minutes with low memory usage. The package uses the locality sensitive hashing algorithms developed by Datar, Immorlica, Indyk and Mirrokni (2004) <doi:10.1145/997817.997857>, and Broder (1998) <doi:10.1109/SEQUEN.1997.666900> to avoid having to compare every pair of records in each dataset, resulting in fuzzy-merges that finish in linear time.
Author: Beniamino Green [aut, cre, cph],
Etienne Bacher [ctb] ,
The authors of the dependency Rust crates [ctb, cph]
Maintainer: Beniamino Green <beniamino.green@yale.edu>
Diff between zoomerjoin versions 0.2.3 dated 2026-03-14 and 0.2.4 dated 2026-08-27
DESCRIPTION | 8 +-- MD5 | 36 +++++++-------- NEWS.md | 4 + R/join_core.R | 2 R/on_load.R | 4 - README.md | 40 ++++++++-------- inst/doc/guided_tour.html | 16 +++--- inst/doc/matching_vectors.html | 2 src/Makevars.win.in | 2 src/rust/Cargo.lock | 51 ++++++++++++++------- src/rust/Cargo.toml | 2 src/rust/prepare_vendors.sh | 2 src/rust/src/lib.rs | 10 ++++ src/rust/vendor.tar.xz |binary tests/testthat.R | 6 ++ tests/testthat/test-test_logical_euclid_join.R | 14 ++--- tests/testthat/test-test_logical_lsh_join.R | 60 ++++++++++++------------- tests/testthat/test-test_string_group.R | 4 - tools/config.R | 11 ++++ 19 files changed, 162 insertions(+), 112 deletions(-)
Title: Functions and Datasets for Math Used in School
Description: Contains functions for math taught in school. A main focus is set to prime-calculation. The package also contains a dataset of all primes between 1 and 99,999,999.
Author: Joerg grosse Schlarmann [aut, cre]
Maintainer: Joerg grosse Schlarmann <schlarmann@produnis.de>
Diff between schoolmath versions 0.5.0 dated 2026-07-07 and 0.5.1 dated 2026-08-27
schoolmath-0.5.0/schoolmath/R/zzz.R |only schoolmath-0.5.1/schoolmath/DESCRIPTION | 16 - schoolmath-0.5.1/schoolmath/MD5 | 29 ++ schoolmath-0.5.1/schoolmath/NAMESPACE | 7 schoolmath-0.5.1/schoolmath/NEWS.md | 9 schoolmath-0.5.1/schoolmath/R/RcppExports.R | 28 ++ schoolmath-0.5.1/schoolmath/R/functions.R | 199 +++++++++++++++++++ schoolmath-0.5.1/schoolmath/README.md | 1 schoolmath-0.5.1/schoolmath/man/is.decimal.Rd |only schoolmath-0.5.1/schoolmath/man/is.even.Rd |only schoolmath-0.5.1/schoolmath/man/is.negative.Rd |only schoolmath-0.5.1/schoolmath/man/is.odd.Rd |only schoolmath-0.5.1/schoolmath/man/is.positive.Rd |only schoolmath-0.5.1/schoolmath/man/is.real.positive.Rd |only schoolmath-0.5.1/schoolmath/man/is.whole.Rd |only schoolmath-0.5.1/schoolmath/src/RcppExports.cpp | 84 ++++++++ schoolmath-0.5.1/schoolmath/src/is_decimal.cpp |only schoolmath-0.5.1/schoolmath/src/is_even.cpp |only schoolmath-0.5.1/schoolmath/src/is_negative.cpp |only schoolmath-0.5.1/schoolmath/src/is_odd.cpp |only schoolmath-0.5.1/schoolmath/src/is_positive.cpp |only schoolmath-0.5.1/schoolmath/src/is_real_positive.cpp |only schoolmath-0.5.1/schoolmath/src/is_whole.cpp |only 23 files changed, 356 insertions(+), 17 deletions(-)
Title: Flags Spatial Errors in Biological Collection Data Using
Specialists' Information
Description: Automatically flags common spatial errors in biological collection data using metadata and specialists' information. RuHere implements a workflow to manage occurrence data through six steps: dataset merging, metadata flagging, validation against expert-derived distribution maps, visualization of flagged records, and sampling bias exploration. It specifically integrates specialist-curated range information to identify geographic errors and introductions that often escape standard automated validation procedures. For details on the methodology, see: Trindade & Caron (2026) <doi:10.64898/2026.02.02.703373>.
Author: Weverton C. F. Trindade [aut, cre] ,
Fernanda S. Caron [aut]
Maintainer: Weverton C. F. Trindade <wevertonf1993@gmail.com>
Diff between RuHere versions 1.0.1 dated 2026-02-17 and 1.1.0 dated 2026-08-27
DESCRIPTION | 12 MD5 | 177 +++++---- NAMESPACE | 34 + NEWS.md | 19 + R/RcppExports.R | 4 R/bien_here.R | 17 R/bind_here.R | 7 R/check_countries.R | 5 R/check_states.R | 7 R/cite_datapaper.R |only R/count_flags.R |only R/data.R | 104 +++++ R/faunabr_here.R | 2 R/flag_bien.R | 15 R/flag_consensus.R | 24 - R/flag_cultivated.R | 7 R/flag_duplicates.R | 4 R/flag_env_moran.R | 11 R/flag_faunabr.R | 21 - R/flag_florabr.R | 16 R/flag_fossil.R | 6 R/flag_geo_moran.R | 7 R/flag_inaturalist.R | 6 R/flag_iucn.R | 16 R/flag_wcvp.R | 16 R/flag_year.R | 8 R/florabr_here.R | 4 R/format_atlanticR.R |only R/format_columns.R | 7 R/get_bien.R | 500 +++++++++++++++++++++------- R/get_datapaper.R |only R/get_specieslink.R | 13 R/inventory_completeness.R |only R/iucn_here.R | 14 R/remove_flagged.R | 4 R/remove_invalid_coordinates.R | 32 + R/request_gbif.R | 26 + R/request_gbif_specieslist.R |only R/set_specieslink_credentials.R | 23 + R/summarize_flags.R | 4 R/thin_env.R | 10 R/thin_geo.R | 9 R/utils_BIEN.R |only R/wcvp_here.R | 3 R/zzz.R | 3 README.md | 7 data/atlantic_amphibians.rda |only inst/doc/flagging_records.html | 23 - inst/doc/flagging_records_species_list.Rmd | 2 inst/doc/flagging_records_species_list.html | 18 - inst/doc/obtaining_data.R | 76 +++- inst/doc/obtaining_data.Rmd | 116 ++++++ inst/doc/obtaining_data.html | 291 +++++++++++----- inst/doc/sampling_bias.html | 21 - inst/doc/spatial_consistency.html | 5 man/atlantic_amphibians.Rd |only man/bien_here.Rd | 13 man/bind_here.Rd | 5 man/check_countries.Rd | 127 +++---- man/check_states.Rd | 137 +++---- man/cite_datapaper.Rd |only man/count_flags.Rd |only man/faunabr_here.Rd | 2 man/flag_bien.Rd | 152 ++++---- man/flag_consensus.Rd | 22 - man/flag_cultivated.Rd | 96 ++--- man/flag_duplicates.Rd | 4 man/flag_env_moran.Rd | 11 man/flag_faunabr.Rd | 20 - man/flag_florabr.Rd | 16 man/flag_fossil.Rd | 84 ++-- man/flag_geo_moran.Rd | 7 man/flag_inaturalist.Rd | 106 +++-- man/flag_iucn.Rd | 186 +++++----- man/flag_wcvp.Rd | 166 ++++----- man/flag_year.Rd | 98 ++--- man/florabr_here.Rd | 4 man/get_datapaper.Rd |only man/get_specieslink.Rd | 25 - man/inventory_completeness.Rd |only man/iucn_here.Rd | 12 man/occ_flagged.Rd | 5 man/occ_gbif.Rd | 4 man/occurrences.Rd | 3 man/remove_invalid_coordinates.Rd | 142 ++++--- man/request_gbif.Rd | 7 man/request_gbif_specieslist.Rd |only man/set_specieslink_credentials.Rd | 23 + man/summarize_flags.Rd | 4 man/thin_env.Rd | 166 ++++----- man/thin_geo.Rd | 9 man/wcvp_here.Rd | 2 src/Makevars | 1 src/RcppExports.cpp | 12 src/get_rarefaction_components.cpp |only vignettes/flagging_records_species_list.Rmd | 2 vignettes/obtaining_data.Rmd | 116 ++++++ 97 files changed, 2331 insertions(+), 1214 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: Kevin Ushey [aut, cre] ,
JJ Allaire [aut],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Dirk Eddelbuettel [aut] ,
Intel [aut, cph] ,
UXL Foundation [aut, cph] ,
Microsoft [cph],
Posit, PB [...truncated...]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 6.2.0 dated 2026-07-30 and 6.2.1 dated 2026-08-27
DESCRIPTION | 6 +-- MD5 | 15 ++++--- NEWS.md | 13 ++++++ R/tbb-autodetected.R.in | 3 + R/tbb.R | 3 + src/Makevars.in | 4 +- src/tbb/include/oneapi/tbb/concurrent_queue.h | 2 + tests/test-cxx-flags.R |only tools/config/configure.R | 50 ++++++++++++++++++++++++-- 9 files changed, 82 insertions(+), 14 deletions(-)
Title: Easy-to-Use Tools for Common Forms of Random Assignment and
Sampling
Description: Generates random assignments for common experimental designs and
random samples for common sampling designs.
Author: Alexander Coppock [aut, cre] ,
Jasper Cooper [ctb] ,
Neal Fultz [ctb] ,
Graeme Blair [ctb] ,
Macartan Humphreys [ctb]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 1.0.1 dated 2026-02-02 and 2.0.1 dated 2026-08-27
randomizr-1.0.1/randomizr/R/zzz.R |only randomizr-1.0.1/randomizr/man/custom_ra.Rd |only randomizr-1.0.1/randomizr/man/custom_ra_probabilities.Rd |only randomizr-1.0.1/randomizr/man/randomizr.Rd |only randomizr-2.0.1/randomizr/DESCRIPTION | 23 randomizr-2.0.1/randomizr/LICENSE | 2 randomizr-2.0.1/randomizr/MD5 | 167 - randomizr-2.0.1/randomizr/NAMESPACE | 30 randomizr-2.0.1/randomizr/NEWS.md | 92 randomizr-2.0.1/randomizr/R/RcppExports.R |only randomizr-2.0.1/randomizr/R/balanced_ra.R |only randomizr-2.0.1/randomizr/R/block_and_cluster_ra.R | 119 - randomizr-2.0.1/randomizr/R/block_ra.R | 177 + randomizr-2.0.1/randomizr/R/cluster_ra.R | 82 randomizr-2.0.1/randomizr/R/cluster_rs.R | 75 randomizr-2.0.1/randomizr/R/complete_ra.R | 107 randomizr-2.0.1/randomizr/R/complete_rs.R | 60 randomizr-2.0.1/randomizr/R/custom_ra.R | 28 randomizr-2.0.1/randomizr/R/declare_ra.R | 482 +++- randomizr-2.0.1/randomizr/R/declare_rs.R | 136 - randomizr-2.0.1/randomizr/R/generated_methods.R | 379 +-- randomizr-2.0.1/randomizr/R/helper_functions.R | 153 - 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Title: Panel Sample Selection Models
Description: Extends the Heckman selection framework to panel data with individual random effects. The first stage models participation via a panel Probit specification, while the second stage can take a panel linear, Probit, Poisson, or Poisson log-normal form. Model details are provided in Bailey and Peng (2025) <doi:10.2139/ssrn.5475626> and Peng and Van den Bulte (2024) <doi:10.1287/mnsc.2019.01897>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between PanelSelect versions 1.0.0 dated 2025-10-25 and 1.0.1 dated 2026-08-27
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 2 ++ R/imported.R | 4 ++-- R/probitRE_linearRE.R | 33 ++++++++++++++++++++++++++------- R/probitRE_probitRE.R | 36 ++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/vignette.html | 4 ++-- man/predict_probitRE_linearRE.Rd |only man/predict_probitRE_probitRE.Rd |only man/probitRE_PLNRE.Rd | 12 ++++++------ man/probitRE_PoissonRE.Rd | 8 ++++---- man/probitRE_linearRE.Rd | 15 ++++++++------- man/probitRE_probitRE.Rd | 17 +++++++++-------- 14 files changed, 104 insertions(+), 59 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph],
Noah Greifer [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.1.1 dated 2026-06-07 and 0.1.2 dated 2026-08-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- inst/doc/count-firth-fastglm.html | 18 +++++++++--------- inst/doc/fastglm-overview.html | 12 ++++++------ inst/doc/fastglm.html | 12 ++++++------ inst/doc/firth-fastglm.html | 20 ++++++++++---------- inst/doc/large-data-fastglm.html | 4 ++-- src/bigmemory.cpp | 5 +++++ src/fit_glm_dense.cpp | 6 ++++++ 9 files changed, 55 insertions(+), 44 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Ger Inberg [aut, cre] ,
Adam Black [aut] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between CDMConnector versions 2.6.0 dated 2026-06-16 and 2.7.0 dated 2026-08-27
DESCRIPTION | 6 +- MD5 | 16 ++++--- NEWS.md | 5 ++ R/cdm.R | 3 - R/dateadd.R | 2 inst/breast_cancer.json |only inst/doc/a01_getting-started.html | 70 ++++++++++++++++----------------- inst/doc/a06_using_cdm_attributes.html | 4 - inst/testv1.json |only man/CDMConnector-package.Rd | 3 - 10 files changed, 59 insertions(+), 50 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-02 0.8.0
2026-05-23 0.7.1
2026-05-21 0.7.0
2026-04-21 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-06 0.5.2
2025-12-05 0.5.1
2025-10-26 0.5.0
2025-08-19 0.4.1
2025-05-11 0.4.0
2025-03-31 0.3.0
2024-05-02 0.2.1
2024-03-01 0.2.0
2024-02-13 0.1.1
Title: Frequentist Confidence Analysis for Clinical Trials
Description: Frequentist confidence analysis answers the question: How
confident are we in a particular treatment effect? This package calculates
the frequentist confidence in a treatment effect of interest given observed data,
and returns the family of
confidence curves associated with that data.
Author: Freda Werdiger [aut, cre]
Maintainer: Freda Werdiger <freda.werdiger@unimelb.edu.au>
Diff between confidenceCurves versions 0.2.0 dated 2025-10-01 and 0.2.1 dated 2026-08-27
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS.md |only R/confidenceCurves.R | 22 ++++++++++++---------- 4 files changed, 18 insertions(+), 15 deletions(-)
More information about confidenceCurves at CRAN
Permanent link
Title: Fit Probability Models to Forensic Survey Data
Description: Fits probability models to P- and S-type count data arising
from forensic surveys of clothing for the background presence of glass,
paint, and related trace material. Built-in models include zeta,
zero-inflated zeta, and logarithmic distributions, with a public extension
interface for additional models. Inference is available by maximum
likelihood, parametric Bayesian methods, the ordinary nonparametric
bootstrap, and Rubin's Bayesian Bootstrap. The clothing-survey setting is
described by Coulson, Buckleton, Gummer, and Triggs (2001)
<doi:10.1016/S1355-0306(01)71847-3>.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between fitPS versions 1.0.6 dated 2026-06-10 and 1.1.4 dated 2026-08-26
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Title: Microsoft Finance Time Series Forecasting Framework
Description: Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time
Series Forecasting Framework, aka Finn, can be used to forecast any component of the income
statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time,
Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built
to meet the needs of financial analysts to better forecast their businesses within a company, and has
a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!
Author: Mike Tokic [aut, cre] ,
Aadharsh Kannan [aut]
Maintainer: Mike Tokic <mftokic@gmail.com>
Diff between finnts versions 0.6.0 dated 2025-09-04 and 0.7.0 dated 2026-08-26
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Title: Large Language Model (LLM) Tools for Psychological Text Analysis
Description: A collection of large language model (LLM) text analysis methods
designed with psychological data in mind. Currently, LLMing (aka "lemming")
includes a text anomaly detection method based on the angle-based subspace
approach described by Zhang, Lin, and Karim (2015) and a text generation method.
<doi:10.1016/j.ress.2015.05.025>.
Author: Lindley Slipetz [aut, cre],
Teague Henry [aut],
Siqi Sun [ctb]
Maintainer: Lindley Slipetz <ddj6tu@virginia.edu>
Diff between LLMing versions 1.2.1 dated 2026-03-27 and 1.3.0 dated 2026-08-26
DESCRIPTION | 14 MD5 | 31 - NAMESPACE | 2 NEWS.md | 5 R/clean_texts.R |only R/construct_validity.R |only R/embed.R | 948 ++++++++++++++++++------------------- R/text_datagen.R | 977 +++++++++++++++++++++++++++++++------- R/vector_SNN.R | 1 README.md | 15 build/partial.rdb |binary inst/python/embed.py |only inst/python/text_datagen.py | 1116 ++++++++++++++++++++++++++++++-------------- man/LLMing-package.Rd | 1 man/clean_texts.Rd |only man/construct_validity.Rd |only man/embed.Rd | 111 +--- man/text_datagen.Rd | 162 +++--- tests |only 19 files changed, 2198 insertions(+), 1185 deletions(-)
Title: Graphical Multiple Comparison Procedures
Description: Multiple comparison procedures (MCPs) control the familywise error
rate in clinical trials. Graphical MCPs include many commonly used
procedures as special cases; see Bretz et al. (2011)
<doi:10.1002/bimj.201000239>, Lu (2016) <doi:10.1002/sim.6985>, and Xi et
al. (2017) <doi:10.1002/bimj.201600233>. This package is a low-dependency
implementation of graphical MCPs which allow mixed types of tests. It also
includes power simulations and visualization of graphical MCPs.
Author: Dong Xi [aut, cre],
Ethan Brockmann [aut],
Gilead Sciences, Inc. [cph, fnd]
Maintainer: Dong Xi <dong.xi1@gilead.com>
Diff between graphicalMCP versions 0.2.9 dated 2026-03-21 and 0.3.0 dated 2026-08-26
DESCRIPTION | 15 MD5 | 251 + NAMESPACE | 110 NEWS.md | 142 R/adjust_p.R | 408 +- R/adjust_weights.R | 414 +- R/adjust_weights_parametric_util.R | 314 +- R/as_graph.R | 272 - R/edge_pairs.R | 66 R/example_graphs.R | 884 +++--- R/graph_calculate_power.R | 968 +++--- R/graph_create.R | 453 +-- R/graph_generate_weights.R | 264 - R/graph_rejection_orderings.R | 240 - R/graph_test_closure.R | 900 +++--- R/graph_test_shortcut.R | 550 +-- R/graph_test_shortcut_gsd.R |only R/graph_update.R | 362 +- R/graphicalMCP-package.R | 4 R/gs_boundaries.R |only R/gs_corr.R |only R/plot.initial_graph.R | 476 +-- R/plot.updated_graph.R | 110 R/power_tests.R | 152 - R/print.graph_report.R | 580 ++-- R/print.gsd_graph_report.R |only R/print.initial_graph.R | 196 - R/print.power_report.R | 485 +-- R/print.updated_graph.R | 226 - R/repeated_p.R |only R/sequential_p.R |only R/spending_functions.R |only R/test_power_input_val.R | 430 +-- R/test_values.R | 322 +- README.md | 198 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 inst/WORDLIST | 206 - inst/doc/closed-testing.R | 630 ++-- inst/doc/closed-testing.Rmd | 854 ++--- inst/doc/closed-testing.html | 2455 ++++++++--------- inst/doc/glossary.R | 12 inst/doc/glossary.Rmd | 134 inst/doc/glossary.html | 998 +++--- inst/doc/graph-examples.R | 1083 +++---- inst/doc/graph-examples.Rmd | 1305 ++++----- inst/doc/graph-examples.html | 2440 ++++++++--------- inst/doc/graphicalMCP.R | 126 inst/doc/graphicalMCP.Rmd | 216 - inst/doc/graphicalMCP.html | 1140 +++---- inst/doc/group-sequential-testing.R |only inst/doc/group-sequential-testing.Rmd |only inst/doc/group-sequential-testing.html |only inst/doc/gsd-validation.R |only inst/doc/gsd-validation.Rmd |only inst/doc/gsd-validation.html |only inst/doc/internal-validation.R | 1062 +++---- inst/doc/internal-validation.Rmd | 1166 ++++---- inst/doc/internal-validation.html | 1007 +++---- inst/doc/shortcut-testing.R | 397 +- inst/doc/shortcut-testing.Rmd | 588 ++-- inst/doc/shortcut-testing.html | 1949 ++++++------- inst/references.bib | 520 +-- man/adjust_p.Rd | 216 - man/adjust_weights.Rd | 292 +- man/adjust_weights_parametric_util.Rd | 242 - man/as_graph.Rd | 156 - man/edge_pairs.Rd | 40 man/example_graphs.Rd | 370 +- man/graph_calculate_power.Rd | 412 +- man/graph_create.Rd | 266 - man/graph_generate_weights.Rd | 146 - man/graph_rejection_orderings.Rd | 146 - man/graph_test_closure.Rd | 374 +- man/graph_test_fast.Rd | 94 man/graph_test_shortcut.Rd | 216 - man/graph_test_shortcut_gsd.Rd |only man/graph_update.Rd | 186 - man/graphicalMCP-package.Rd | 71 man/gs_boundaries.Rd |only man/gs_corr.Rd |only man/gsd_boundary_table.Rd |only man/gsd_input_val.Rd |only man/gsd_test.Rd |only man/gsd_test_values_details.Rd |only man/gsd_test_values_look_back.Rd |only man/input_val.Rd | 164 - man/plot.initial_graph.Rd | 308 +- man/plot.updated_graph.Rd | 170 - man/print.graph_report.Rd | 104 man/print.gsd_graph_report.Rd |only man/print.initial_graph.Rd | 102 man/print.power_report.Rd | 159 - man/print.updated_graph.Rd | 114 man/repeated_p.Rd |only man/sequential_p.Rd |only man/spending_functions.Rd |only man/spending_with_time.Rd |only man/spending_wt.Rd |only man/test_values.Rd | 170 - tests/testthat.R | 24 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/print.graph_report.md | 3010 ++++++++++----------- tests/testthat/_snaps/print.initial_graph.md | 92 tests/testthat/_snaps/print.power_report.md | 830 ++--- tests/testthat/_snaps/print.updated_graph.md | 444 +-- tests/testthat/test-adjust_weights.R | 140 tests/testthat/test-as_graph.R | 28 tests/testthat/test-edge_pairs.R | 6 tests/testthat/test-example_graphs.R | 614 ++-- tests/testthat/test-graph_calculate_power.R | 308 +- tests/testthat/test-graph_create.R | 418 +- tests/testthat/test-graph_generate_weights.R | 86 tests/testthat/test-graph_test_closure.R | 894 +++--- tests/testthat/test-graph_test_shortcut.R | 374 +- tests/testthat/test-graph_test_shortcut_gsd.R |only tests/testthat/test-graph_update.R | 160 - tests/testthat/test-gs_boundaries.R |only tests/testthat/test-gs_corr.R |only tests/testthat/test-plot.initial_graph.R | 48 tests/testthat/test-plot.updated_graph.R | 48 tests/testthat/test-power_tests.R | 224 - tests/testthat/test-print.graph_report.R | 234 - tests/testthat/test-print.initial_graph.R | 26 tests/testthat/test-print.power_report.R | 168 - tests/testthat/test-print.updated_graph.R | 53 tests/testthat/test-repeated_p.R |only tests/testthat/test-sequential_p.R |only tests/testthat/test-spending_functions.R |only tests/testthat/test-test_values.R |only vignettes/closed-testing.Rmd | 854 ++--- vignettes/glossary.Rmd | 134 vignettes/graph-examples.Rmd | 1305 ++++----- vignettes/graphicalMCP.Rmd | 216 - vignettes/group-sequential-testing.Rmd |only vignettes/gsd-validation.Rmd |only vignettes/internal-validation.Rmd | 1166 ++++---- vignettes/internal-validation_bonferroni.csv | 2002 ++++++------- vignettes/internal-validation_hochberg.csv | 2002 ++++++------- vignettes/internal-validation_mixed.csv | 2002 ++++++------- vignettes/internal-validation_parametric-mixed.csv | 2002 ++++++------- vignettes/internal-validation_parametric.csv | 2002 ++++++------- vignettes/internal-validation_simes.csv | 2002 ++++++------- vignettes/shortcut-testing.Rmd | 588 ++-- 145 files changed, 28640 insertions(+), 28482 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 9.2.8 dated 2025-06-22 and 9.2.9 dated 2026-08-26
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/header/singleDstack.hpp | 1 + src/legacy/singleDstack.hpp | 1 + 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Download and Extract BlueTopo Bathymetry with Terra
Description: Discovers, downloads, verifies, and opens bathymetry assets from
the National Oceanic and Atmospheric Administration (NOAA) BlueTopo product
for user supplied areas of interest. The package keeps source files intact
by default, uses 'terra' for spatial data access, supports explicit
native-resolution selection policies, and records provenance for
reproducible extraction workflows. It accesses the NOAA BlueTopo web
service at <https://noaa-ocs-nationalbathymetry-pds.s3.amazonaws.com/> and
references product documentation at
<https://nauticalcharts.noaa.gov/data/bluetopo.html>.
Author: Elvin Cordero [aut, cre, cph]
Maintainer: Elvin Cordero <elvin.cordero@seamountgeo.com>
Diff between bluertopo versions 0.0.1 dated 2026-08-04 and 0.0.2 dated 2026-08-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/cache.R | 25 ++++++++++++++++++++++++- README.md | 8 ++++++-- tests/testthat/test-cache.R | 3 +-- 6 files changed, 45 insertions(+), 13 deletions(-)
Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data
within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing
and discovery tool that facilitates exploration of HIV immunological data
from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut],
Sean Hughes [rev],
Jason Taylor [aut, cre],
Helen Miller [aut],
Kellie MacPhee [rev],
CAVD DataSpace [cph]
Maintainer: Jason Taylor <jmtaylor@fredhutch.org>
Diff between DataSpaceR versions 1.0.1 dated 2026-08-04 and 1.0.2 dated 2026-08-26
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/DataSpaceConnection.R | 6 +++--- R/DataSpaceStudies.R | 23 ++++++++++++----------- build/vignette.rds |binary tests/testthat/test-studies-groups.R | 17 ++++++++++++++--- 7 files changed, 43 insertions(+), 26 deletions(-)
Title: A Graphical User Interface for Antitrust and Trade Practitioners
Description: A graphical user interface for simulating the effects of mergers, tariffs, and quotas under an
assortment of different economic models. The interface is powered by the 'Shiny' web application framework from
'RStudio'.
Author: Charles Taragin [aut, cre],
Kenneth Rios [aut],
Paulette Wolak [aut]
Maintainer: Charles Taragin <ctaragin+competitiontoolbox@gmail.com>
Diff between competitiontoolbox versions 0.7.1 dated 2022-08-25 and 0.7.4 dated 2026-08-26
competitiontoolbox-0.7.1/competitiontoolbox/inst/ct_shiny/www/emergency.pdf |only competitiontoolbox-0.7.1/competitiontoolbox/inst/ct_shiny/www/health.pdf |only competitiontoolbox-0.7.4/competitiontoolbox/DESCRIPTION | 22 competitiontoolbox-0.7.4/competitiontoolbox/MD5 | 49 competitiontoolbox-0.7.4/competitiontoolbox/NAMESPACE | 7 competitiontoolbox-0.7.4/competitiontoolbox/R/ct_shiny.R | 2 competitiontoolbox-0.7.4/competitiontoolbox/build/partial.rdb |binary competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Details/mergersNoPurch.R | 20 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Details/tradeNoPurch.R | 20 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Diagnostics/mergersDiag.R | 6 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Diagnostics/tradeDiag.R | 2 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Inputs/mergersInputs.R | 2 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Inputs/reactiveInputs.R | 109 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Inputs/tradeInputs.R | 2 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Output/mergersOutput.R | 64 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Output/tradeOutput.R | 40 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/R/mergersTemplateCode.R | 81 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/R/modelRegistry.R |only competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/R/tradeTemplateCode.R | 48 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Simulations/mergersSims.R | 224 - competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Simulations/tradeSims.R | 250 - competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Summary/mergersSummary.R | 31 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/Summary/tradeSummary.R | 7 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/rsconnect/shinyapps.io/daag/ct_shiny.dcf | 6 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/server.R | 9 competitiontoolbox-0.7.4/competitiontoolbox/inst/ct_shiny/ui.R | 1752 ++++------ competitiontoolbox-0.7.4/competitiontoolbox/tests |only 27 files changed, 1065 insertions(+), 1688 deletions(-)
More information about competitiontoolbox at CRAN
Permanent link
Title: Data from Japan Meteorological Agency
Description: Includes climate data from Japan Meteorological Agency ('JMA') <https://www.jma.go.jp/jma/indexe.html>.
Can download climate data from 'JMA'.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Diff between clidatajp versions 0.5.2 dated 2023-03-04 and 0.5.3 dated 2026-08-26
DESCRIPTION | 15 +- MD5 | 40 +++-- NAMESPACE | 20 ++ NEWS.md | 24 ++- R/data.R | 115 ++++++++++++++++- R/download_detail.R |only R/wi_ci.R | 4 README.md | 34 ++++- build/vignette.rds |binary data/climate_jp_full.rda |only data/mean_cli.rda |only data/station_jp_full.rda |only inst/WORDLIST | 69 +++++++++- inst/doc/clidatajp.R | 112 ++++++++-------- inst/doc/clidatajp.html | 277 ++++++++++++++++++++--------------------- man/climate_jp_full.Rd |only man/detail_colnames.Rd |only man/detail_url.Rd |only man/download_detail.Rd |only man/download_prec_no.Rd |only man/mean_cli.Rd |only man/station_jp.Rd | 4 man/station_jp_full.Rd |only man/wi.Rd | 4 tests/spelling.R | 6 tests/testthat/test-detail.R |only tests/testthat/test-download.R | 2 27 files changed, 488 insertions(+), 238 deletions(-)
Title: 'Yandex Clickhouse' Interface for R with Basic 'dplyr' Support
Description: 'Yandex Clickhouse' (<https://clickhouse.com/>) is a high-performance relational column-store database to enable
big data exploration and 'analytics' scaling to petabytes of data. Methods are
provided that enable working with 'Yandex Clickhouse' databases via
'DBI' methods and using 'dplyr'/'dbplyr' idioms.
Author: Christian Hotz-Behofsits [aut, cre],
Daniel Winkler [aut],
Luca Rauchenberger [aut],
Peter Knaus [aut],
Clemens Danninger [aut],
Daria Yudaeva [aut],
Simon Stiebellehner [aut],
Dan Egnor [aut],
Vlad Losev [aut],
Keith Ray [aut],
Zhanyong Wan [aut],
M [...truncated...]
Maintainer: Christian Hotz-Behofsits <christian.hotz-behofsits@wu.ac.at>
Diff between RClickhouse versions 0.6.11 dated 2026-06-23 and 0.6.12 dated 2026-08-26
DESCRIPTION | 6 +++--- MD5 | 5 +++-- inst/include/RClickhouse_RcppExports.h |only src/vendor/clickhouse-cpp/clickhouse/base/compressed.cpp | 1 + 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Optimal Binning and Weight of Evidence Framework for Modeling
Description: High-performance implementation of 37 optimal binning algorithms
(16 categorical, 21 numerical) for Weight of Evidence ('WoE') transformation,
credit scoring, and risk modeling. Includes advanced methods such as Mixed
Integer Linear Programming ('MILP'), Genetic Algorithms, Simulated Annealing,
and Monotonic Regression. Features automatic method selection based on
Information Value ('IV') maximization, strict monotonicity enforcement, and
efficient handling of large datasets via 'Rcpp'. Provides automated variable
screening by Information Value strength and bin ordering, and generation of
the equivalent 'SQL' 'CASE' expressions for in-database scoring. Fully
integrated with the 'tidymodels' ecosystem for building robust machine
learning pipelines.
Based on methods described in Siddiqi (2006) <doi:10.1002/9781119201731>
and Navas-Palencia (2020) <doi:10.48550/arXiv.2001.08025>.
Author: Jose Evandeilton Lopes [aut, cre, cph]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between OptimalBinningWoE versions 1.13.3 dated 2026-08-23 and 1.13.4 dated 2026-08-26
DESCRIPTION | 8 - MD5 | 21 ++--- NEWS.md | 59 ++++++++++++++ R/obwoe_sql.R | 144 +++++++++++++++++++++++++++-------- inst/doc/algorithms.html | 36 ++++---- inst/doc/industrial-pipeline.html | 8 - inst/doc/introduction.html | 10 +- man/dot-ob_sql_decimal.Rd |only man/dot-ob_sql_num.Rd | 34 ++++++-- man/obwoe_sql.Rd | 18 ++-- tests/testthat/helper-germancredit.R | 56 +++++++++++++ tests/testthat/test-obwoe-sql.R | 70 +++++++++++++++-- 12 files changed, 371 insertions(+), 93 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Title: Synthetic Our Future Health Data Generator
Description: Generates synthetic Our Future Health cohort datasets for method development,
including participant, questionnaire, clinic measurements, outpatient,
inpatient, emergency, mortality, primary care medication, and geography
outputs. Supports reproducible generation with configurable cohort size and
user-defined International Classification of Diseases, Tenth Revision
(ICD-10), Office of Population Censuses and Surveys Classification of
Interventions and Procedures, version 4 (OPCS-4), and British National
Formulary (BNF) code pools.
Author: Hannah Nicholls [aut, cre]
Maintainer: Hannah Nicholls <hlnichollsdev@outlook.com>
Diff between ofhsyn versions 0.1.1 dated 2026-06-09 and 0.1.3 dated 2026-08-26
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Animated Biplots
Description: Create animated biplots that enables dynamic visualisation of temporal or sequential changes in multivariate data by animating a single biplot across the levels of a time variable. It builds on objects from the 'biplotEZ' package, Lubbe S, le Roux N, Nienkemper-Swanepoel J, Ganey R, Buys R, Adams Z, Manefeldt P (2024) <doi:10.32614/CRAN.package.biplotEZ>, allowing users to create animated biplots that reveal how both samples and variables evolve over time.
Author: Raeesa Ganey [aut, cre, cph] ,
Johane Nienkemper-Swanepoel [aut, cph]
Maintainer: Raeesa Ganey <raeesa.ganey@wits.ac.za>
Diff between moveEZ versions 1.2.0 dated 2026-05-13 and 1.3.0 dated 2026-08-26
moveEZ-1.2.0/moveEZ/vignettes/anim1_moveplot.gif |only moveEZ-1.3.0/moveEZ/DESCRIPTION | 9 moveEZ-1.3.0/moveEZ/MD5 | 41 +- moveEZ-1.3.0/moveEZ/NAMESPACE | 5 moveEZ-1.3.0/moveEZ/NEWS.md | 4 moveEZ-1.3.0/moveEZ/R/evaluation_func.R | 24 - moveEZ-1.3.0/moveEZ/R/globals.R | 3 moveEZ-1.3.0/moveEZ/R/moveEZ-package.R | 1 moveEZ-1.3.0/moveEZ/R/moveplot_func.R |only moveEZ-1.3.0/moveEZ/R/plot.R | 374 ++++++++++++++++------- moveEZ-1.3.0/moveEZ/README.md | 9 moveEZ-1.3.0/moveEZ/build/partial.rdb |binary moveEZ-1.3.0/moveEZ/build/vignette.rds |binary moveEZ-1.3.0/moveEZ/inst/doc/moveEZ.R | 17 - moveEZ-1.3.0/moveEZ/inst/doc/moveEZ.Rmd | 19 - moveEZ-1.3.0/moveEZ/inst/doc/moveEZ.html | 310 +++++++++---------- moveEZ-1.3.0/moveEZ/man/evaluation.Rd | 6 moveEZ-1.3.0/moveEZ/man/figures/logo.png |binary moveEZ-1.3.0/moveEZ/man/moveplot.Rd | 27 + moveEZ-1.3.0/moveEZ/man/moveplot2.Rd | 15 moveEZ-1.3.0/moveEZ/man/reexports.Rd | 4 moveEZ-1.3.0/moveEZ/vignettes/anim1.gif |only moveEZ-1.3.0/moveEZ/vignettes/moveEZ.Rmd | 19 - 23 files changed, 550 insertions(+), 337 deletions(-)
Title: Missing Person Identification Tools
Description: A comprehensive toolkit for missing person identification combining
genetic and non-genetic evidence within a Bayesian framework. Computes
likelihood ratios (LRs) for DNA profiles, biological sex, age, hair color,
and birthdate evidence. Provides decision analysis tools including optimal
LR thresholds, error rate calculations, and ROC curve visualization.
Includes interactive Shiny applications for exploring evidence combinations.
For methodological details see Marsico et al. (2023) <doi:10.1016/j.fsigen.2023.102891>
and Marsico, Vigeland et al. (2021) <doi:10.1016/j.fsigen.2021.102519>.
Author: Franco Marsico [aut, cre] ,
Suisei Nakagawa [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between mispitools versions 2.0.0 dated 2026-08-25 and 2.0.1 dated 2026-08-26
DESCRIPTION | 6 +- MD5 | 24 ++++---- NEWS.md | 39 +++++++++++++ R/lr_distribution.R | 10 +++ R/r_ref_per_marker.R | 47 ++++++++++++++-- README.md | 121 +++++++++++++++++++++++++++++++++++++++++- inst/doc/belief_dynamics.html | 4 - inst/doc/introduction.html | 4 - inst/doc/workflow.html | 6 +- man/lr_distribution.Rd | 10 +++ src/core/evidence_combine.cpp | 11 +-- src/core/lr_dist.cpp | 34 +++++------ src/core/lr_dist.h | 48 +++++++++++++++- 13 files changed, 309 insertions(+), 55 deletions(-)
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding
Description: Methods for analyzing DNA methylation data via Most Recurrent
Methylation Patterns (MRMPs). Supports cell-type annotation, spatial
deconvolution, unsupervised clustering, and cancer cell-of-origin inference.
Includes C-backed summaries for YAME ".cg/.cm" files (overlap counts, log2
odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS
deconvolution, and plotting utilities. Scales to large spatial and
single-cell methylomes and is robust to extreme sparsity.
Author: Hongxiang Fu [aut, cre] ,
Wanding Zhou [cph, fnd],
The SAMtools/HTSlib authors [ctb, cph] ,
Attractive Chaos [ctb, cph] )
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Diff between MethScope versions 1.0.3 dated 2026-06-16 and 1.0.4 dated 2026-08-26
MethScope-1.0.3/MethScope/LICENSE |only MethScope-1.0.3/MethScope/inst/COPYRIGHTS |only MethScope-1.0.3/MethScope/inst/WORDLIST |only MethScope-1.0.3/MethScope/tests/spelling.R |only MethScope-1.0.4/MethScope/DESCRIPTION | 18 MethScope-1.0.4/MethScope/MD5 | 82 +- MethScope-1.0.4/MethScope/NEWS.md |only MethScope-1.0.4/MethScope/R/GenerateInput.R | 63 - MethScope-1.0.4/MethScope/R/ModelTraining.R | 55 + MethScope-1.0.4/MethScope/R/PredictCellType.R | 10 MethScope-1.0.4/MethScope/R/VisualizeOutput.R | 2 MethScope-1.0.4/MethScope/R/globals.R |only MethScope-1.0.4/MethScope/R/utils.R | 6 MethScope-1.0.4/MethScope/README.md | 174 ++++- MethScope-1.0.4/MethScope/build/vignette.rds |binary MethScope-1.0.4/MethScope/inst/doc/MethScope-Input.R |only MethScope-1.0.4/MethScope/inst/doc/MethScope-Input.Rmd |only MethScope-1.0.4/MethScope/inst/doc/MethScope-Input.html |only MethScope-1.0.4/MethScope/inst/doc/MethScope-MRMP.R | 5 MethScope-1.0.4/MethScope/inst/doc/MethScope-MRMP.Rmd | 51 + MethScope-1.0.4/MethScope/inst/doc/MethScope-MRMP.html | 89 +- MethScope-1.0.4/MethScope/inst/doc/MethScope-Tutorial.R | 122 ++- MethScope-1.0.4/MethScope/inst/doc/MethScope-Tutorial.Rmd | 230 +++++- MethScope-1.0.4/MethScope/inst/doc/MethScope-Tutorial.html | 366 ++++++++--- MethScope-1.0.4/MethScope/inst/doc/agent-skill.R |only MethScope-1.0.4/MethScope/inst/doc/agent-skill.Rmd |only MethScope-1.0.4/MethScope/inst/doc/agent-skill.html |only MethScope-1.0.4/MethScope/inst/doc/methscope-cli.R |only MethScope-1.0.4/MethScope/inst/doc/methscope-cli.Rmd |only MethScope-1.0.4/MethScope/inst/doc/methscope-cli.html |only MethScope-1.0.4/MethScope/inst/doc/pretrained-models.R |only MethScope-1.0.4/MethScope/inst/doc/pretrained-models.Rmd |only MethScope-1.0.4/MethScope/inst/doc/pretrained-models.html |only MethScope-1.0.4/MethScope/inst/extdata/example_label.csv |only MethScope-1.0.4/MethScope/inst/extdata/hg38_Zhou2025_ref.rds |only MethScope-1.0.4/MethScope/inst/extdata/mm10_Liu2021_ref.rds |only MethScope-1.0.4/MethScope/man/GenerateInput.Rd | 7 MethScope-1.0.4/MethScope/man/GenerateReference.Rd | 25 MethScope-1.0.4/MethScope/man/PlotConfusion.Rd | 2 MethScope-1.0.4/MethScope/man/PlotUMAP.Rd | 2 MethScope-1.0.4/MethScope/man/PlotUMAP_fixedwindow.Rd | 2 MethScope-1.0.4/MethScope/man/PredictCellType.Rd | 10 MethScope-1.0.4/MethScope/man/figures/logo.svg |only MethScope-1.0.4/MethScope/man/figures/overview.png |only MethScope-1.0.4/MethScope/src/Makevars | 1 MethScope-1.0.4/MethScope/src/bgzf.c | 30 MethScope-1.0.4/MethScope/src/format3.c | 44 - MethScope-1.0.4/MethScope/src/summary.c | 34 - MethScope-1.0.4/MethScope/vignettes/MethScope-Input.Rmd |only MethScope-1.0.4/MethScope/vignettes/MethScope-MRMP.Rmd | 51 + MethScope-1.0.4/MethScope/vignettes/MethScope-Tutorial.Rmd | 230 +++++- MethScope-1.0.4/MethScope/vignettes/agent-skill.Rmd |only MethScope-1.0.4/MethScope/vignettes/figures |only MethScope-1.0.4/MethScope/vignettes/methscope-cli.Rmd |only MethScope-1.0.4/MethScope/vignettes/pretrained-models.Rmd |only 55 files changed, 1221 insertions(+), 490 deletions(-)
