Title: Spatial Empirical Dynamic Modeling
Description: Inferring causation from spatial cross-sectional data through empirical dynamic modeling (EDM), with methodological extensions including geographical convergent cross mapping from Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>, geographical cross mapping cardinality as introduced by Lyu et al. (2026) <doi:10.1080/13658816.2026.2687121>, as well as the spatial causality test following the approach of Herrera et al. (2016) <doi:10.1111/pirs.12144>, together with geographical pattern causality proposed in Zhang & Wang (2025) <doi:10.1080/13658816.2025.2581207>.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.12 dated 2026-04-05 and 1.13 dated 2026-09-09
spEDM-1.12/spEDM/man/figures/scpcm/fig3-1.png |only spEDM-1.13/spEDM/DESCRIPTION | 11 spEDM-1.13/spEDM/MD5 | 188 ++--- spEDM-1.13/spEDM/NAMESPACE | 56 - spEDM-1.13/spEDM/NEWS.md | 586 +++++++++--------- spEDM-1.13/spEDM/R/Agenerics.R | 26 spEDM-1.13/spEDM/R/RcppExports.R | 60 - spEDM-1.13/spEDM/R/detectThreads.R | 22 spEDM-1.13/spEDM/R/embedded.R | 108 +-- spEDM-1.13/spEDM/R/fnn.R | 98 +-- spEDM-1.13/spEDM/R/formatoutput.R | 502 +++++++-------- spEDM-1.13/spEDM/R/gccm.R | 207 +++--- spEDM-1.13/spEDM/R/gcmc.R | 223 +++--- spEDM-1.13/spEDM/R/globals.R | 10 spEDM-1.13/spEDM/R/gpc.R | 126 +-- spEDM-1.13/spEDM/R/ic.R | 96 +- spEDM-1.13/spEDM/R/internal_utility.R | 580 ++++++++--------- spEDM-1.13/spEDM/R/multiview.R | 98 +-- spEDM-1.13/spEDM/R/pc.R | 106 +-- spEDM-1.13/spEDM/R/scpcm.R | 202 +++--- spEDM-1.13/spEDM/R/sctest.R | 114 +-- spEDM-1.13/spEDM/R/simplex.R | 110 +-- spEDM-1.13/spEDM/R/slm.R | 124 +-- spEDM-1.13/spEDM/R/smap.R | 100 +-- spEDM-1.13/spEDM/R/zzz.R | 5 spEDM-1.13/spEDM/README.md | 145 ++-- spEDM-1.13/spEDM/inst/CITATION | 26 spEDM-1.13/spEDM/inst/doc/main1_pkgintro.Rmd | 404 ++++++------ spEDM-1.13/spEDM/inst/doc/main1_pkgintro.html | 77 +- spEDM-1.13/spEDM/inst/doc/main2_ssr.Rmd | 282 ++++---- spEDM-1.13/spEDM/inst/doc/main2_ssr.html | 38 - spEDM-1.13/spEDM/inst/doc/main3_gccm.Rmd | 46 - spEDM-1.13/spEDM/inst/doc/main3_gccm.html | 48 - spEDM-1.13/spEDM/inst/doc/main4_gpc.Rmd | 20 spEDM-1.13/spEDM/inst/doc/main4_gpc.html | 20 spEDM-1.13/spEDM/inst/doc/main5_gcmc.Rmd | 58 - spEDM-1.13/spEDM/inst/doc/main5_gcmc.html | 67 +- spEDM-1.13/spEDM/inst/doc/main6_scpcm.Rmd | 191 ++--- spEDM-1.13/spEDM/inst/doc/main6_scpcm.html | 226 +++--- spEDM-1.13/spEDM/inst/doc/si1_slm.Rmd | 378 +++++------ spEDM-1.13/spEDM/inst/doc/si1_slm.html | 64 - spEDM-1.13/spEDM/inst/doc/si2_sct.Rmd | 2 spEDM-1.13/spEDM/inst/doc/si2_sct.html | 2 spEDM-1.13/spEDM/man/detectThreads.Rd | 36 - spEDM-1.13/spEDM/man/embedded.Rd | 136 ++-- spEDM-1.13/spEDM/man/figures/gccm/fig1-1.png |binary spEDM-1.13/spEDM/man/figures/gcmc/fig1-1.png |binary spEDM-1.13/spEDM/man/figures/scpcm/fig2-1.png |binary spEDM-1.13/spEDM/man/figures/slm/sim_trispecies-1.png |binary spEDM-1.13/spEDM/man/figures/slm/slm1-1.png |binary spEDM-1.13/spEDM/man/figures/slm/slm2-1.png |binary spEDM-1.13/spEDM/man/figures/ssr/fig1-1.png |binary spEDM-1.13/spEDM/man/fnn.Rd | 182 ++--- spEDM-1.13/spEDM/man/gccm.Rd | 258 +++---- spEDM-1.13/spEDM/man/gcmc.Rd | 214 +++--- spEDM-1.13/spEDM/man/gpc.Rd | 275 ++++---- spEDM-1.13/spEDM/man/ic.Rd | 181 ++--- spEDM-1.13/spEDM/man/multiview.Rd | 207 +++--- spEDM-1.13/spEDM/man/pc.Rd | 215 +++--- spEDM-1.13/spEDM/man/sc.test.Rd | 195 +++-- spEDM-1.13/spEDM/man/scpcm.Rd | 270 ++++---- spEDM-1.13/spEDM/man/simplex.Rd | 200 +++--- spEDM-1.13/spEDM/man/slm.Rd | 234 +++---- spEDM-1.13/spEDM/man/smap.Rd | 212 +++--- spEDM-1.13/spEDM/src/CppGridUtils.cpp | 327 ++++++---- spEDM-1.13/spEDM/src/CppGridUtils.h | 48 + spEDM-1.13/spEDM/src/DelayedMI.cpp |only spEDM-1.13/spEDM/src/Forecast4Grid.cpp | 46 - spEDM-1.13/spEDM/src/Forecast4Grid.h | 26 spEDM-1.13/spEDM/src/GCCM4Grid.cpp | 16 spEDM-1.13/spEDM/src/GCCM4Grid.h | 12 spEDM-1.13/spEDM/src/GridExp.cpp | 318 ++++++++- spEDM-1.13/spEDM/src/LatticeExp.cpp | 8 spEDM-1.13/spEDM/src/Makevars | 4 spEDM-1.13/spEDM/src/Makevars.win | 4 spEDM-1.13/spEDM/src/RcppExports.cpp | 130 ++- spEDM-1.13/spEDM/src/SCPCM4Grid.cpp | 66 +- spEDM-1.13/spEDM/src/SCPCM4Grid.h | 22 spEDM-1.13/spEDM/src/SGC4Grid.cpp | 12 spEDM-1.13/spEDM/src/SGC4Grid.h | 4 spEDM-1.13/spEDM/vignettes/main1_pkgintro.Rmd | 404 ++++++------ spEDM-1.13/spEDM/vignettes/main1_pkgintro.Rmd.orig | 258 ++++--- spEDM-1.13/spEDM/vignettes/main2_ssr.Rmd | 282 ++++---- spEDM-1.13/spEDM/vignettes/main2_ssr.Rmd.orig | 176 ++--- spEDM-1.13/spEDM/vignettes/main3_gccm.Rmd | 46 - spEDM-1.13/spEDM/vignettes/main3_gccm.Rmd.orig | 364 +++++------ spEDM-1.13/spEDM/vignettes/main4_gpc.Rmd | 20 spEDM-1.13/spEDM/vignettes/main4_gpc.Rmd.orig | 356 +++++----- spEDM-1.13/spEDM/vignettes/main5_gcmc.Rmd | 58 - spEDM-1.13/spEDM/vignettes/main5_gcmc.Rmd.orig | 436 ++++++------- spEDM-1.13/spEDM/vignettes/main6_scpcm.Rmd | 191 ++--- spEDM-1.13/spEDM/vignettes/main6_scpcm.Rmd.orig | 335 ++++------ spEDM-1.13/spEDM/vignettes/si1_slm.Rmd | 378 +++++------ spEDM-1.13/spEDM/vignettes/si1_slm.Rmd.orig | 318 ++++----- spEDM-1.13/spEDM/vignettes/si2_sct.Rmd | 2 spEDM-1.13/spEDM/vignettes/si2_sct.Rmd.orig | 230 +++---- 96 files changed, 6992 insertions(+), 6572 deletions(-)
Title: Methods for Unweighted and Weighted Network Integration
Description: Implementation of network integration approaches
comprising unweighted and weighted integration methods. Unweighted integration
is performed considering the average, per-edge average, maximum and minimum of
networks edges. Weighted integration takes into account a weight for each
network during the fusion process, where the weights express
the ''predictiveness strength'' of each network considering a specific predictive
task. Weights can be learned using a machine learning algorithm able to associate
the weights to the assessment of the accuracy of the learning algorithm
trained on the network itself. The implemented methods can be applied to
effectively integrate different biological networks modelling a wide range
of problems in bioinformatics (e.g. disease gene prioritization, protein
function prediction, drug repurposing, clinical outcome prediction).
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between NetInt versions 1.0.1 dated 2025-05-03 and 1.0.2 dated 2026-09-09
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Calculate Hopkins Statistic for Clustering
Description: Calculate Hopkins statistic to assess the clusterability of data. See Wright (2023) <doi:10.32614/RJ-2022-055>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between hopkins versions 1.1 dated 2023-08-20 and 1.2 dated 2026-09-09
DESCRIPTION | 25 ++-- MD5 | 27 ++-- NAMESPACE | 20 +-- NEWS.md | 6 - R/hopkins.R | 76 +++++++------ build/vignette.rds |binary inst/doc/hopkins_optimization.R | 142 ++++++++++++------------- inst/doc/hopkins_optimization.html | 1 inst/doc/hopkins_protocol.R | 2 inst/doc/hopkins_protocol.Rmd | 17 ++- inst/doc/hopkins_protocol.html | 43 +++++-- man/hopkins.Rd | 206 ++++++++++++++++++------------------- man/hopkins.pval.Rd | 72 ++++++------ vignettes/hopkins_protocol.Rmd | 17 ++- vignettes/hopkins_protocol.html |only 15 files changed, 347 insertions(+), 307 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.4.0 dated 2026-08-05 and 1.5.0 dated 2026-09-09
DESCRIPTION | 33 MD5 | 151 +- NAMESPACE | 13 NEWS.md | 38 R/btw_chat_history_store.R |only R/btw_client_app.R | 1117 +---------------- R/btw_client_app_core.R |only R/btw_client_app_legacy.R |only R/btw_client_app_slash_commands.R |only R/btw_client_app_v05.R |only R/btw_project_db.R |only R/btw_this.R | 54 R/tool-agent-subagent.R | 172 ++ R/tool-cran.R | 262 +++ R/tool-docs-news.R | 85 - R/tool-docs.R | 24 R/tool-env-df.R | 16 R/tool-env.R | 4 R/tool-files-edit.R | 9 R/tool-files-list.R | 4 R/tool-files-patch.R | 7 R/tool-files-read.R | 14 R/tool-files-replace.R | 9 R/tool-files-search.R | 547 +++++++- R/tool-files-write.R | 29 R/tool-git.R | 42 R/tool-github.R | 8 R/tool-ide.R | 4 R/tool-pkg-covr.R | 2 R/tool-pkg-devtools.R | 8 R/tool-pkg-src.R | 18 R/tool-result.R | 17 R/tool-run.R | 107 + R/tool-session-package-installed.R | 2 R/tool-sessioninfo.R | 5 R/tool-skills.R | 359 +++-- R/tool-web.R | 7 R/utils-ellmer.R | 115 - R/utils-md.R | 74 + R/utils-shinychat.R |only R/zzz.R | 15 exec/btw.R | 193 ++ inst/cli-skill/r-btw-cli/SKILL.md | 3 inst/icons/construction.svg | 2 inst/icons/edit-document.svg |only inst/icons/find-replace.svg |only inst/icons/quick-reference.svg | 2 inst/js/app/btw_app.css | 46 inst/js/app/btw_app.js | 41 man/btw_client.Rd | 15 man/btw_skill_install_github.Rd | 2 man/btw_skill_install_package.Rd | 2 man/btw_skill_install_project.Rd | 2 man/btw_skill_prompt.Rd |only man/btw_skills_register_slash_commands.Rd |only man/btw_this.character.Rd | 10 man/btw_tool_cran_package.Rd | 3 man/btw_tool_cran_search.Rd | 3 man/btw_tool_cran_versions.Rd |only man/btw_tool_docs_package_news.Rd | 18 man/btw_tool_skill.Rd | 8 man/btw_tools.Rd | 1 tests/testthat/_snaps/btw_client.md | 4 tests/testthat/_snaps/btw_client_app_slash_commands.md |only tests/testthat/_snaps/tool-env-df.md | 3 tests/testthat/_snaps/tool_skills.md | 28 tests/testthat/_snaps/utils-md.md | 14 tests/testthat/_snaps/utils-shinychat.md |only tests/testthat/helpers.R | 61 tests/testthat/test-btw-project-db.R |only tests/testthat/test-btw_chat_history_store.R |only tests/testthat/test-btw_client_app.R | 96 + tests/testthat/test-btw_client_app_slash_commands.R |only tests/testthat/test-btw_this.R | 39 tests/testthat/test-cli.R | 195 ++ tests/testthat/test-deprecated.R | 2 tests/testthat/test-tool-agent-subagent.R | 139 ++ tests/testthat/test-tool-cran.R | 135 ++ tests/testthat/test-tool-docs-news.R | 41 tests/testthat/test-tool-files-read.R | 4 tests/testthat/test-tool-files-search.R |only tests/testthat/test-tool-pkg-src.R | 11 tests/testthat/test-tool-run.R | 94 + tests/testthat/test-tool_skills.R | 260 +++ tests/testthat/test-utils-md.R | 35 tests/testthat/test-utils-shinychat.R |only 86 files changed, 3104 insertions(+), 1779 deletions(-)
Title: Estimating Propensity Scores (PS), PS-Based Weights, and Effects
Description: Toolbox that provides a streamlined, end-to-end workflow for propensity
score analysis in generating real-world evidence from real-world data.
The package covers the full analytic pipeline - from estimating propensity scores
via logistic regression, to calculating weights or creating a matched cohort,
to generating publication-ready Table 1s with standardized mean
differences and weighted balance diagnostics. It also estimates incidence rates,
rate differences and rate ratios, hazard ratios, risks, risk ratios, and risk
differences, including competing-risk methods and optionally stratified hazard
models. Many functions can write formatted 'Excel' reports with method documentation,
making results immediately shareable with collaborators and stakeholders. Methods
are based on Rosenbaum and Rubin (1983)
<doi:10.1093/biomet/70.1.41>, Austin (2011) <doi:10.1080/00273171.2011.568786>,
and Desai et al. (2017) <doi:10.1097/EDE.0000000000000595>.
Author: Hanseul Cho [aut, cre],
Georg Hahn [aut],
Janinne Ortega-Montiel [aut],
Julie Paik [aut],
Elisabetta Patorno [aut]
Maintainer: Hanseul Cho <hanseul0618@gmail.com>
Diff between rwetools versions 0.4.0 dated 2026-08-01 and 0.5.0 dated 2026-09-09
rwetools-0.4.0/rwetools/R/effect_measures.R |only rwetools-0.4.0/rwetools/man/add_readme_sheet.Rd |only rwetools-0.4.0/rwetools/man/calc_c_statistic.Rd |only rwetools-0.4.0/rwetools/man/canonize_levels.Rd |only rwetools-0.4.0/rwetools/man/combine_named_list.Rd |only rwetools-0.4.0/rwetools/man/create_love_plot.Rd |only rwetools-0.4.0/rwetools/man/dot-is_balanced.Rd |only rwetools-0.4.0/rwetools/man/dot-plot_ps_distribution_set.Rd |only rwetools-0.4.0/rwetools/man/dot-trim_ps.Rd |only rwetools-0.4.0/rwetools/man/dot-truncate_ps_weights.Rd |only rwetools-0.4.0/rwetools/man/estimate_hr_ir.Rd |only rwetools-0.4.0/rwetools/man/estimate_rr_rd.Rd |only rwetools-0.4.0/rwetools/man/fmt_mean_sd.Rd |only rwetools-0.4.0/rwetools/man/fmt_n_pct.Rd |only rwetools-0.4.0/rwetools/man/fmt_num.Rd |only rwetools-0.4.0/rwetools/man/fmt_pct.Rd |only rwetools-0.4.0/rwetools/man/get_var_types.Rd |only rwetools-0.4.0/rwetools/man/get_weighted_prop.Rd |only rwetools-0.4.0/rwetools/man/get_weighted_stats.Rd |only rwetools-0.4.0/rwetools/man/levels_excl_zero.Rd |only rwetools-0.4.0/rwetools/man/process_catbin_direct.Rd |only rwetools-0.4.0/rwetools/man/summarize_ps_by_group.Rd |only rwetools-0.4.0/rwetools/tests/testthat/test-estimate_hr_ir.R |only rwetools-0.4.0/rwetools/tests/testthat/test-estimate_rr_rd.R |only rwetools-0.5.0/rwetools/DESCRIPTION | 15 rwetools-0.5.0/rwetools/MD5 | 84 rwetools-0.5.0/rwetools/NAMESPACE | 5 rwetools-0.5.0/rwetools/NEWS.md | 78 rwetools-0.5.0/rwetools/R/build_table1.R | 284 +-- rwetools-0.5.0/rwetools/R/create_psweights.R | 466 +++-- rwetools-0.5.0/rwetools/R/estimate_hr.R |only rwetools-0.5.0/rwetools/R/estimate_ir.R |only rwetools-0.5.0/rwetools/R/estimate_ps.R | 75 rwetools-0.5.0/rwetools/R/estimate_risk.R |only rwetools-0.5.0/rwetools/R/helpers_effect_engines.R | 274 --- rwetools-0.5.0/rwetools/R/helpers_effect_measures.R | 847 +++------- rwetools-0.5.0/rwetools/R/helpers_exposure.R |only rwetools-0.5.0/rwetools/R/helpers_ps_psweights.R | 42 rwetools-0.5.0/rwetools/R/helpers_table1.R | 91 - rwetools-0.5.0/rwetools/man/build_table1.Rd | 158 + rwetools-0.5.0/rwetools/man/create_ps_fs_weights.Rd | 127 - rwetools-0.5.0/rwetools/man/create_ps_matched_cohort.Rd | 192 +- rwetools-0.5.0/rwetools/man/estimate_hr.Rd |only rwetools-0.5.0/rwetools/man/estimate_ir.Rd |only rwetools-0.5.0/rwetools/man/estimate_ps.Rd | 6 rwetools-0.5.0/rwetools/man/estimate_risk.Rd |only rwetools-0.5.0/rwetools/tests/testthat/fixtures/make_v030_fixtures.R | 7 rwetools-0.5.0/rwetools/tests/testthat/helper.R | 18 rwetools-0.5.0/rwetools/tests/testthat/test-build_table1.R | 64 rwetools-0.5.0/rwetools/tests/testthat/test-create_ps_fs_weights.R | 48 rwetools-0.5.0/rwetools/tests/testthat/test-create_ps_matched_cohort.R | 108 + rwetools-0.5.0/rwetools/tests/testthat/test-create_psweights.R | 47 rwetools-0.5.0/rwetools/tests/testthat/test-estimate_hr.R |only rwetools-0.5.0/rwetools/tests/testthat/test-estimate_ir.R |only rwetools-0.5.0/rwetools/tests/testthat/test-estimate_ps.R | 31 rwetools-0.5.0/rwetools/tests/testthat/test-estimate_risk.R |only rwetools-0.5.0/rwetools/tests/testthat/test-finegray.R | 16 rwetools-0.5.0/rwetools/tests/testthat/test-helpers-engines.R | 124 - rwetools-0.5.0/rwetools/tests/testthat/test-irr.R | 37 rwetools-0.5.0/rwetools/tests/testthat/test-matched-block-guards.R |only rwetools-0.5.0/rwetools/tests/testthat/test-matched-cluster-se.R |only 61 files changed, 1652 insertions(+), 1592 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.3.0 dated 2026-08-31 and 1.4.0 dated 2026-09-09
DESCRIPTION | 14 MD5 | 49 - NAMESPACE | 7 NEWS.md | 22 R/KorAPCorpusStats.R | 31 R/KorAPQuery.R | 32 R/association-scores.R | 70 + R/cacheAs.R |only R/collocationAnalysis.R | 141 +++ R/collocationScoreQuery.R | 24 R/misc.R | 111 ++- R/textMetadata.R | 20 man/association-score-functions.Rd | 45 + man/blessCacheAs.Rd |only man/cacheAs.Rd |only man/cacheAsInfo.Rd |only man/collocationAnalysis-KorAPConnection-method.Rd | 45 + man/collocationScoreQuery-KorAPConnection-method.Rd | 5 man/corpusStats-KorAPConnection-method.Rd | 4 man/frequencyQuery-KorAPConnection-method.Rd | 3 man/textMetadata-KorAPConnection-method.Rd | 4 man/withCachedResults.Rd |only tests/testthat/test-association-score-functions.R | 31 tests/testthat/test-cache-as.R |only tests/testthat/test-collocation-cache-parameters.R |only tests/testthat/test-collocations.R | 36 - tests/testthat/test-common-affixes.R |only tests/testthat/test-readme-against-llm.R | 707 ++++++++++++++------ tests/testthat/test-readme-consistency.R |only tests/testthat/test-snippet-parsing.R |only tests/testthat/test-vc-labels.R |only 31 files changed, 1126 insertions(+), 275 deletions(-)
Title: An IMAP Client for R
Description: A session-based IMAP client that implements the full command sets of
the IMAP4rev2 (RFC 9051) and IMAP4rev1 (RFC 3501) protocols, along with the
optional extensions registered with the Internet Assigned Numbers
Authority, allowing virtually all e-mail operations to be performed from
within R, paving the way for e-mail data analysis.
Author: Allan Quadros [aut, cre] ,
Paul Smith [ctb],
Kurt Hornik [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 1.4.0 dated 2026-07-28 and 3.0.0 dated 2026-09-09
mRpostman-1.4.0/mRpostman/R/delete-msg-int-new.R |only mRpostman-1.4.0/mRpostman/R/execute-attachment-fetch.R |only mRpostman-1.4.0/mRpostman/R/extract-MIME-level-and-filenames.R |only mRpostman-1.4.0/mRpostman/vignettes/xoauth2.0 |only mRpostman-3.0.0/mRpostman/DESCRIPTION | 28 mRpostman-3.0.0/mRpostman/MD5 | 340 mRpostman-3.0.0/mRpostman/NAMESPACE | 18 mRpostman-3.0.0/mRpostman/R/AND.R | 6 mRpostman-3.0.0/mRpostman/R/OR.R | 6 mRpostman-3.0.0/mRpostman/R/R6.R | 2099 ++- mRpostman-3.0.0/mRpostman/R/acl-int.R |only mRpostman-3.0.0/mRpostman/R/add-flags-int.R | 43 mRpostman-3.0.0/mRpostman/R/adjust-folder-name.R | 8 mRpostman-3.0.0/mRpostman/R/append-int.R | 71 mRpostman-3.0.0/mRpostman/R/assert-capability.R | 4 mRpostman-3.0.0/mRpostman/R/before.R | 6 mRpostman-3.0.0/mRpostman/R/charset-fallback.R |only mRpostman-3.0.0/mRpostman/R/check-args.R | 7 mRpostman-3.0.0/mRpostman/R/check-int.R |only mRpostman-3.0.0/mRpostman/R/close-folder-int.R | 44 mRpostman-3.0.0/mRpostman/R/conditions.R 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Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.4 dated 2025-12-18 and 0.1.5 dated 2026-09-09
DESCRIPTION | 13 ++++-- MD5 | 73 +++++++++++++++++++++----------------- NEWS.md | 28 ++++++++++++++ R/MTDest-methods.R | 3 + R/MTDest.R | 2 - R/MTDmodel-methods.R | 4 ++ R/checkSample.R | 1 R/countsTab.R | 3 + R/empirical_probs.R | 3 + R/hdMTD-methods.R | 2 + R/hdMTD.R | 9 +++- R/hdMTD_BIC.R | 14 ++++++- R/hdMTD_CUT.R | 13 +++++- R/hdMTD_FS.R | 5 +- R/hdMTD_FSC.R | 67 ++++++++++++++++++++++++----------- R/oscillation.R | 3 + R/tempdata.R | 8 ++-- build |only inst |only man/MTD-methods.Rd | 17 +++++++- man/MTDest-methods.Rd | 14 ++++++- man/MTDest.Rd | 2 - man/countsTab.Rd | 3 + man/empirical_probs.Rd | 3 + man/hdMTD-methods.Rd | 11 ++++- man/hdMTD.Rd | 4 +- man/hdMTD_BIC.Rd | 16 +++++++- man/hdMTD_CUT.Rd | 15 ++++++- man/hdMTD_FS.Rd | 5 +- man/hdMTD_FSC.Rd | 45 ++++++++++++++++------- man/oscillation.Rd | 3 + man/tempdata.Rd | 76 ++++++++++++++++++++-------------------- tests/testthat/test-hdMTD.R | 14 ++++++- tests/testthat/test-hdMTD_FS.R | 9 ++++ tests/testthat/test-hdMTD_FSC.R | 15 +++++++ vignettes |only 36 files changed, 359 insertions(+), 144 deletions(-)
Title: DCC Models with GARCH and GARCH-MIDAS Specifications in the
Univariate Step, RiskMetrics, Moving Covariance and Scalar and
Diagonal BEKK Models
Description: Estimates a variety of Dynamic Conditional Correlation (DCC) models. More in detail, the 'dccmidas' package allows the estimation of the corrected DCC (cDCC) of Aielli (2013) <doi:10.1080/07350015.2013.771027>, the DCC-MIDAS of Colacito et al. (2011) <doi:10.1016/j.jeconom.2011.02.013>, the Asymmetric DCC of Cappiello et al. <doi:10.1093/jjfinec/nbl005>, and the Dynamic Equicorrelation (DECO) of Engle and Kelly (2012) <doi:10.1080/07350015.2011.652048>. 'dccmidas' offers the possibility of including standard GARCH <doi:10.1016/0304-4076(86)90063-1>, GARCH-MIDAS <doi:10.1162/REST_a_00300> and Double Asymmetric GARCH-MIDAS <doi:10.1016/j.econmod.2018.07.025> models in the univariate estimation. Moreover, also the scalar and diagonal BEKK <doi:10.1017/S0266466600009063> models can be estimated. Finally, the package calculates also the var-cov matrix under two non-parametric models: the Moving Covariance and the RiskMetrics specifications.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between dccmidas versions 0.1.2 dated 2024-02-21 and 0.1.3 dated 2026-09-09
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS.md | 4 + R/functions.R | 115 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary inst/CITATION | 2 man/bekk_fit.Rd | 2 man/cov_eval.Rd | 2 man/dcc_fit.Rd | 19 ++++---- man/plot_dccmidas.Rd | 2 man/riskmetrics_mat.Rd | 22 +++++++++ 11 files changed, 132 insertions(+), 64 deletions(-)
Title: Compute Moments Related to Beta-Wishart and Inverse Beta-Wishart
Distributions
Description: Provides functions for computing moments and coefficients related to the Beta-Wishart and Inverse Beta-Wishart distributions.
It includes functions for calculating the expectation of matrix-valued functions of the Beta-Wishart distribution,
coefficient matrices C_k and H_k, expectation of matrix-valued functions of the inverse Beta-Wishart distribution,
and coefficient matrices \tilde{C}_k and \tilde{H}_k. For more details, refer Hillier and Kan (2024) <https://www-2.rotman.utoronto.ca/~kan/papers/wishmom.pdf>,
"On the Expectations of Equivariant Matrix-valued Functions of Wishart and Inverse Wishart Matrices".
Author: Raymond Kan [aut, cre],
Preston Liang [aut]
Maintainer: Raymond Kan <raymond.kan@rotman.utoronto.ca>
Diff between wishmom versions 1.1.0 dated 2024-08-27 and 1.2.0 dated 2026-09-09
DESCRIPTION | 7 MD5 | 27 NEWS.md |only R/iwish_psr.R | 2 R/iwishmom.R | 14 R/iwishmom_sym.R | 2 R/wishmom.R | 4 R/wishmom_sym.R | 19 build/vignette.rds |binary inst/doc/wishmom_vignettes.Rmd | 2303 +++++++++++++++++++--------------------- inst/doc/wishmom_vignettes.html | 1898 ++++++++++++++++++++------------ man/iwish_psr.Rd | 2 man/iwishmom.Rd | 7 man/wishmom_sym.Rd | 4 vignettes/wishmom_vignettes.Rmd | 2303 +++++++++++++++++++--------------------- 15 files changed, 3508 insertions(+), 3084 deletions(-)
Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage
Priors
Description: Efficient variational inference methods for fully Bayesian univariate
and multivariate Gaussian and t-process regression models. Hierarchical shrinkage priors,
including the triple gamma prior, are used for effective variable selection and
covariance shrinkage in high-dimensional settings. The package leverages normalizing
flows to approximate complex posterior distributions. For details on implementation,
see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkGPR versions 2.0.0 dated 2026-03-30 and 2.1.0 dated 2026-09-09
DESCRIPTION | 9 MD5 | 55 ++-- NAMESPACE | 2 NEWS.md | 6 R/GPR_class.R | 4 R/IAF.R |only R/MVGPR_class.R | 5 R/NSF.R |only R/kernel_funcs.R | 178 +++++++------- R/pred_functions.R | 5 R/simGPR.R | 452 +++++++++++++++++++------------------- man/LPDS.Rd | 100 ++++---- man/calc_pred_moments.Rd | 122 +++++----- man/eval_pred_dens.Rd | 118 ++++----- man/gen_posterior_samples.Rd | 136 +++++------ man/iaf.Rd |only man/kernel_functions.Rd | 160 ++++++------- man/load_shrinkGPR.Rd | 100 ++++---- man/masked_linear.Rd |only man/nsf_cl.Rd |only man/predict.shrinkGPR.Rd | 96 ++++---- man/save_shrinkGPR.Rd | 106 ++++---- man/shrinkGPR.Rd | 406 +++++++++++++++++----------------- man/shrinkTPR.Rd | 406 +++++++++++++++++----------------- man/simGPR.Rd | 176 +++++++------- tests/testthat.R | 24 +- tests/testthat/Rplots.pdf |binary tests/testthat/test_shrinkGPR.R | 2 tests/testthat/test_shrinkMVGPR.R | 2 tests/testthat/test_shrinkMVTPR.R | 2 tests/testthat/test_shrinkTPR.R | 2 31 files changed, 1346 insertions(+), 1328 deletions(-)
More information about PricingBandits at CRAN
Permanent link
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Uses similarity graphs to estimate change-points and their p-values. The default data-level interface constructs a k-MST with k=floor(sqrt(N)) and reports the max-type scan. The generalized, original, and weighted scans remain available explicitly.
Author: Hao Chen [aut, cre] ,
Nancy R. Zhang [aut],
Lynna Chu [aut],
Hoseung Song [aut]
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 1.0 dated 2020-09-24 and 1.1 dated 2026-09-09
DESCRIPTION | 27 ++++-- MD5 | 26 +++-- NAMESPACE | 5 - NEWS.md |only R/NNL.R | 11 +- R/canonical-interface.R |only R/gSeg.r | 140 ++++++++++++++++++++++++-------- R/gSeg_discrete.R | 209 +++++++++++++++++++++++++++++++++--------------- man/gSeg-package.Rd | 7 - man/gseg1.Rd | 15 +-- man/gseg1_data.Rd |only man/gseg1_discrete.Rd | 18 ++-- man/gseg2.Rd | 9 -- man/gseg2_data.Rd |only man/gseg2_discrete.Rd | 12 +- man/gseg_kmst.Rd |only tests |only 17 files changed, 325 insertions(+), 154 deletions(-)
Title: Adaptive Trial Designs for Survival and Binary Endpoints
Description: Implements Goldilocks adaptive trial designs for time-to-event and
fixed-time binary endpoints. Outcomes are generated with a piecewise
exponential model, with conjugate Gamma priors used for predictive
imputation. Final analyses may use log-rank, Cox, or restricted mean
survival time tests, Bayesian piecewise-exponential inference, frequentist
risk differences, or Bayesian beta-binomial inference. The method closely
follows Broglio and colleagues (2014)
<doi:10.1080/10543406.2014.888569> and supports simulation of design
operating characteristics.
Author: Graeme L. Hickey [aut, cre] ,
Ying Wan [aut],
Thevaa Chandereng [aut] ,
Becton, Dickinson and Company [cph],
Tim Kacprowski [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between goldilocks versions 0.6.0 dated 2026-07-29 and 1.0.0 dated 2026-09-09
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Title: Objective Bayesian Distribution Fitting
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation. The
reference-prior framework follows Bernardo (1979)
<doi:10.1111/j.2517-6161.1979.tb01066.x>.
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.2.2 dated 2026-08-29 and 0.2.3 dated 2026-09-09
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 12 +++++++++++ R/fitdistrBayes.R | 14 ++++++++---- README.md | 10 ++++++--- inst/examples/teaching.R | 2 - inst/examples/tutorial_fitdistrBayes_all_models.R | 6 ++--- man/fitdistrBayes.Rd | 8 +++++-- tests/tests_review_regressions.R | 24 ++++++++++++++++++++++ 9 files changed, 73 insertions(+), 25 deletions(-)
More information about epistandardiseR at CRAN
Permanent link
Title: Combined Cluster and Discriminant Analysis
Description: Implements the combined cluster and discriminant analysis method for finding homogeneous groups of data with known origin as described in Kovacs et. al (2014): Classification into homogeneous groups using combined cluster and discriminant analysis (CCDA). Environmental Modelling & Software. <doi:10.1016/j.envsoft.2014.01.010>.
Author: Solt Kovacs [aut],
Jozsef Kovacs [aut],
Peter Tanos [aut, cre]
Maintainer: Peter Tanos <tanospeter@gmail.com>
This is a re-admission after prior archival of version 1.1.1 dated 2019-10-02
Diff between ccda versions 1.1.1 dated 2019-10-02 and 1.2 dated 2026-09-09
DESCRIPTION | 19 ++++-- MD5 | 8 +- NAMESPACE | 18 ++--- R/ccda.main.R | 168 ++++++++++++++++++++++++++----------------------------- man/ccda.main.Rd | 87 ++++++++++++++-------------- 5 files changed, 153 insertions(+), 147 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.18.1 dated 2026-05-24 and 0.19.0 dated 2026-09-09
DESCRIPTION | 28 +++--- MD5 | 89 +++++++++---------- NAMESPACE | 11 +- NEWS.md | 24 ++++- R/bayesfactor.R | 30 +++--- R/bci.R | 46 ++++++++-- R/check_prior.R | 86 +++++++++++------- R/contr.equalprior.R | 8 + R/effective_sample.R | 53 +---------- R/p_to_bf.R | 141 ++++++++++++++++++++----------- R/print.R | 17 +++ R/print_html.R | 11 ++ R/print_md.R | 11 ++ R/reshape_iterations.R | 13 +- R/sexit.R | 61 ++++++++++--- R/utils_check_collinearity.R | 13 +- README.md | 30 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 54 +---------- man/bayesfactor.Rd | 2 man/bayesfactor_inclusion.Rd | 8 - man/bayesfactor_models.Rd | 8 - man/bayesfactor_parameters.Rd | 8 - man/bayesfactor_restricted.Rd | 8 - man/bayestestR-package.Rd | 2 man/bci.Rd | 23 +++-- man/check_prior.Rd | 27 +++-- man/ci.Rd | 12 +- man/contr.equalprior.Rd | 9 - man/distribution.Rd | 5 - man/effective_sample.Rd | 2 man/eti.Rd | 12 +- man/hdi.Rd | 12 +- man/p_to_bf.Rd | 86 +++++++++++------- man/reexports.Rd | 2 man/reshape_iterations.Rd | 2 man/sexit.Rd | 2 man/si.Rd | 12 +- man/spi.Rd | 12 +- tests/testthat/test-bayesfactor_models.R | 28 ++++++ tests/testthat/test-bci.R |only tests/testthat/test-ci.R | 25 ++++- tests/testthat/test-effective_sample.R | 45 +++++++++ tests/testthat/test-p_to_bf.R | 30 +++++- tests/testthat/test-rope_range.R | 34 ++++++- 46 files changed, 721 insertions(+), 421 deletions(-)
Title: Robust Supervised Hierarchical Identification of Single Cells
Description: Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, The Tumor Profiler Consortium , Daniel Stekhoven, Franziska Singer, scROSHI: robust supervised hierarchical identification of single cells, NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad058, <doi:10.1093/nargab/lqad058>.
Author: Lars Bosshard [aut] ,
Dominik Burri [aut, cre] ,
Michael Prummer [aut]
Maintainer: Dominik Burri <burri@nexus.ethz.ch>
Diff between scROSHI versions 1.0.0.0 dated 2023-01-10 and 1.0.0.1 dated 2026-09-09
DESCRIPTION | 31 ++++--- MD5 | 23 ++--- NAMESPACE | 16 +-- R/config.R | 4 R/data.R | 4 R/scROSHI-package.R | 2 README.md | 151 ++++++++++++++++++------------------ build |only man/config.Rd | 4 man/f_annot_ctgenes.Rd | 60 +++++++------- man/f_my_wilcox_test.Rd | 48 +++++------ man/scROSHI.Rd | 198 +++++++++++++++++++++++++----------------------- man/test_sce_data.Rd | 4 13 files changed, 283 insertions(+), 262 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Jinwoo Jeong [ctb],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 2.0.0 dated 2026-09-01 and 2.0.1 dated 2026-09-09
DESCRIPTION | 31 +++++++++++++++---------------- MD5 | 6 +++--- NEWS.md | 14 +++++--------- R/fit_cmdstan.R | 6 +++--- 4 files changed, 26 insertions(+), 31 deletions(-)
Title: Double Constrained Correspondence Analysis for Trait-Environment
Analysis in Ecology
Description: Double constrained correspondence analysis (dc-CA) analyzes
(multi-)trait (multi-)environment ecological data by using the 'vegan'
package and native R code. Throughout the two step algorithm of ter Braak
et al. (2018) is used. This algorithm combines and extends community-
(sample-) and species-level analyses, i.e. the usual community weighted
means (CWM)-based regression analysis and the species-level analysis of
species-niche centroids (SNC)-based regression analysis. The two steps use
canonical correspondence analysis to regress the abundance data on to the
traits and (weighted) redundancy analysis to regress the CWM of the
orthonormalized traits on to the environmental predictors. The function
dc_CA() has an option to divide the abundance data of a site by the site
total, giving equal site weights. This division has the advantage that the
multivariate analysis corresponds with an unweighted (multi-trait)
community-level analysis, instead of being weighted. The first step of
the al [...truncated...]
Author: Cajo J.F ter Braak [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between douconca versions 1.2.5.1 dated 2026-08-24 and 1.2.6 dated 2026-09-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/douconca.html | 2 +- inst/tinytest/test_anova.dcca.R | 17 ++++++++++++++--- inst/tinytest/test_anova.dccav.R | 17 ++++++++++++++--- 6 files changed, 42 insertions(+), 16 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre] ,
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.19.0 dated 2026-03-19 and 0.21.1 dated 2026-09-09
DESCRIPTION | 24 + MD5 | 182 +++++++------- NAMESPACE | 66 +++-- NEWS.md | 11 R/impute_xifti.R | 414 ++++++++++++++++++++++----------- R/load_surf.R | 4 R/make_xifti_components.R | 2 R/onAttach.R | 16 - R/platform.R |only R/rox_args_docs.R | 19 - R/select_xifti.R | 3 R/smooth_cifti.R | 58 ++-- R/smooth_gifti.R | 10 R/utils_color.R | 2 R/utils_volume.R | 66 ++--- R/view_comp.R | 2 R/view_xifti.R | 5 R/view_xifti_surface.R | 145 +++++++---- R/wb_cmd.R | 12 R/write_nifti.R | 119 ++++++++- build/vignette.rds |binary inst/doc/ciftiTools_vignette_mini.R | 12 inst/doc/ciftiTools_vignette_mini.Rmd | 12 inst/doc/ciftiTools_vignette_mini.html | 81 +++--- man/ROY_BIG_BL.Rd | 8 man/add_surf.Rd | 74 +++-- man/apply_parc.Rd | 50 +-- man/apply_platform_overrides.Rd |only man/apply_xifti.Rd | 38 +-- man/as.xifti.Rd | 14 - man/boundary_mask_surf.Rd | 26 +- man/check_render_backend.Rd |only man/ciftiTools.Rd | 3 man/combine_xifti.Rd | 38 +-- man/convert_xifti.Rd | 38 +-- man/edit_mask_surf.Rd | 26 +- man/even_vert_samp.Rd | 26 +- man/expand_color_pal.Rd | 8 man/faces_Param.Rd | 1 man/impute_xifti.Rd | 91 ++++--- man/info_cifti.Rd | 14 - man/is.cifti.Rd | 12 man/is.surf.Rd | 26 +- man/is_tahoe.Rd |only man/load_parc.Rd | 26 +- man/load_sub_parc.Rd | 12 man/load_surf.Rd | 44 +-- man/make_color_pal.Rd | 8 man/mask_Param_vertices.Rd | 1 man/mask_surf.Rd | 26 +- man/merge_xifti.Rd | 38 +-- man/move_to_mwall.Rd | 38 +-- man/move_to_submask.Rd | 38 +-- man/newdata_xifti.Rd | 38 +-- man/parc_add_subcortex.Rd | 12 man/parc_borders.Rd | 12 man/parc_vals_to_xifti.Rd | 12 man/platform.Rd |only man/read_cifti.Rd | 26 +- man/read_surf.Rd | 40 +-- man/read_xifti2.Rd | 14 - man/remap_cifti.Rd | 38 +-- man/remap_gifti.Rd | 6 man/remove_xifti.Rd | 38 +-- man/resample_cifti.Rd | 50 +-- man/resample_cifti_from_template.Rd | 38 +-- man/resample_gifti.Rd | 6 man/resample_surf.Rd | 26 +- man/rotate_surf.Rd | 26 +- man/scale_xifti.Rd | 38 +-- man/select_xifti.Rd | 42 +-- man/separate_cifti.Rd | 12 man/set_names_xifti.Rd | 38 +-- man/smooth_cifti.Rd | 56 ++-- man/smooth_gifti.Rd | 8 man/surfL_Param_optional.Rd | 5 man/surfR_Param_optional.Rd | 5 man/surf_area.Rd | 26 +- man/transform_xifti.Rd | 38 +-- man/use_color_pal.Rd | 8 man/vertices_Param.Rd | 1 man/view_comp.Rd | 10 man/view_surf.Rd | 36 +- man/view_xifti.Rd | 22 - man/view_xifti_surface.Rd | 10 man/view_xifti_volume.Rd | 10 man/write_cifti.Rd | 24 - man/write_metric_gifti.Rd | 12 man/write_subcort_nifti.Rd | 12 man/write_surf_gifti.Rd | 38 +-- man/write_xifti2.Rd | 12 tests/testthat/test-misc.R | 39 ++- tests/testthat/test-plotting_sub.R | 3 tests/testthat/test-web_render.R |only vignettes/ciftiTools_vignette_mini.Rmd | 12 95 files changed, 1654 insertions(+), 1234 deletions(-)
Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data. Streams vector operations (spatial transforms,
point-in-polygon and nearest-feature joins including a two-sided
grid-partitioned join, select-by-location, clip, erase, dissolve,
'rasterization', 'polygonization', and contouring) through 'sf', and runs
raster operations (zonal statistics, focal windows, terrain derivatives,
resample or 'reproject' warp, polygon masking, map algebra, and 'mosaicking')
in native C or over the tiled '.vec' format, one batch or tile at [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.11.8 dated 2026-07-30 and 0.12.0 dated 2026-09-09
DESCRIPTION | 6 MD5 | 98 NEWS.md | 3850 +++++++++-------- R/expr.R | 12 R/index.R | 53 R/spatial.R | 7105 ++++++++++++++++----------------- R/spatial_more.R | 3 R/spatial_topology.R | 5 R/write.R | 49 inst/AGENTS.md | 6 inst/doc/coverage-topology.html | 4 inst/doc/engine.Rmd | 16 inst/doc/engine.html | 21 inst/doc/formats.html | 8 inst/doc/geometry-expressions.html | 4 inst/doc/indexing.Rmd | 35 inst/doc/indexing.html | 52 inst/doc/joins.html | 4 inst/doc/large-data.html | 4 inst/doc/networks.html | 4 inst/doc/offload.html | 4 inst/doc/quickstart.html | 4 inst/doc/schema.html | 4 inst/doc/sdm.html | 4 inst/doc/spatial.html | 4 inst/doc/streaming-spatial.html | 4 inst/doc/string-ops.html | 4 man/append_vtr.Rd | 39 man/create_index.Rd | 21 man/has_index.Rd | 7 src/file_map.c |only src/file_map.h |only src/init.c | 5 src/r_bridge.h | 5 src/r_bridge_index.c | 24 src/scan.c | 118 src/tdc/VENDORED_FROM | 2 src/tdc/include/tdc/format.h | 36 src/tdc/include/tdc/stream.h | 62 src/tdc/src/api/stream_encode.c | 355 + src/vtr1_tdc.c | 149 src/vtr1_tdc.h | 47 src/vtr_append.c | 91 src/vtr_append.h | 13 src/vtri.c | 545 +- src/vtri.h | 172 tests/testthat/test-append-delete.R | 72 tests/testthat/test-index.R | 331 + tests/testthat/test-spatial-topology.R | 49 vignettes/engine.Rmd | 16 vignettes/indexing.Rmd | 35 51 files changed, 7593 insertions(+), 5968 deletions(-)
Title: Interface the 'xts' API via 'Rcpp'
Description: Access to some of the C level functions of the 'xts' package.
In its current state, the package is mostly a proof-of-concept to support
adding useful functions, and does not yet add any of its own.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppXts versions 0.0.6 dated 2022-11-01 and 0.0.7 dated 2026-09-09
RcppXts-0.0.6/RcppXts/src/Makevars |only RcppXts-0.0.6/RcppXts/src/Makevars.win |only RcppXts-0.0.7/RcppXts/ChangeLog | 42 +++++++++++++++++++++++++++++++++ RcppXts-0.0.7/RcppXts/DESCRIPTION | 15 +++++++---- RcppXts-0.0.7/RcppXts/MD5 | 12 +++------ RcppXts-0.0.7/RcppXts/README.md | 8 +++--- RcppXts-0.0.7/RcppXts/inst/NEWS.Rd | 9 +++++++ RcppXts-0.0.7/RcppXts/src/xtsMod.cpp | 2 - 8 files changed, 71 insertions(+), 17 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For users with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph] ,
Andy Jacobson [ctb] ,
Jason Riedy [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.7.0 dated 2022-08-25 and 3.8.0 dated 2026-09-09
DESCRIPTION | 30 ++++--- MD5 | 26 +++--- NEWS.md | 39 +++++++++ R/999.package.R | 4 - R/Matlab.R | 14 +-- R/readMat.R | 133 ++++++++++++++++++---------------- R/utils.R | 36 +++++++++ inst/mat-files/CharUINT16-wide.mat |only inst/mat-files/CharUTF16-wide.mat |only inst/mat-files/CharUTF8-multibyte.mat |only man/Matlab.Rd | 30 +++---- man/R.matlab-package.Rd | 4 - man/readMat.Rd | 7 - man/setOption.Matlab.Rd | 2 tests/readMat.R | 76 +++++++++++++++++++ tests/setFunction.R |only 16 files changed, 283 insertions(+), 118 deletions(-)
Title: Principal Surface Contour Biplots
Description: Fits principal surfaces, the two-dimensional generalisation of the
principal curves of Hastie and Stuetzle (1989)
<doi:10.1080/01621459.1989.10478797>, and displays them as biplots in which
each variable is read off the contour lines of its fitted surface coordinate
function. Sample predictivity, the proportion of a sample's squared length
that is reconstructed by the fitted surface, is reported as a per-sample
diagnostic of how well the surface represents the data.
Author: Raeesa Ganey [aut, cre, cph]
Maintainer: Raeesa Ganey <raeesa.ganey@wits.ac.za>
Diff between prinsurf versions 1.0 dated 2025-03-12 and 2.0 dated 2026-09-09
prinsurf-1.0/prinsurf/R/principal.surface.R |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.R |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.Rmd |only prinsurf-1.0/prinsurf/inst/doc/Principal_Surfaces.html |only prinsurf-1.0/prinsurf/man/figures/3d_plot.png |only prinsurf-1.0/prinsurf/man/figures/README-example-1.png |only prinsurf-1.0/prinsurf/man/principal.surface.Rd |only prinsurf-1.0/prinsurf/vignettes/Principal_Surfaces.Rmd |only prinsurf-2.0/prinsurf/DESCRIPTION | 37 +++++++++++------ prinsurf-2.0/prinsurf/LICENSE | 4 - prinsurf-2.0/prinsurf/MD5 | 34 +++++++++------ prinsurf-2.0/prinsurf/NAMESPACE | 8 +++ prinsurf-2.0/prinsurf/NEWS.md |only prinsurf-2.0/prinsurf/R/diagnostics.R |only prinsurf-2.0/prinsurf/R/methods.R |only prinsurf-2.0/prinsurf/R/prinsurf.R |only prinsurf-2.0/prinsurf/R/psaxis.R |only prinsurf-2.0/prinsurf/README.md | 32 -------------- prinsurf-2.0/prinsurf/build/vignette.rds |binary prinsurf-2.0/prinsurf/inst/doc/contour-biplots.R |only prinsurf-2.0/prinsurf/inst/doc/contour-biplots.Rmd |only prinsurf-2.0/prinsurf/inst/doc/contour-biplots.html |only prinsurf-2.0/prinsurf/man/contour_predictive_error.Rd |only prinsurf-2.0/prinsurf/man/figures/logo.png |only prinsurf-2.0/prinsurf/man/fitted.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/plot.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/predict.prinsurf.Rd |only prinsurf-2.0/prinsurf/man/predictivity.Rd |only prinsurf-2.0/prinsurf/man/prinsurf.Rd |only prinsurf-2.0/prinsurf/vignettes/contour-biplots.Rmd |only 30 files changed, 56 insertions(+), 59 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Jeremie Dubois-Lacoste [aut],
Leslie Perez Caceres [aut],
Thomas Stuetzle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 4.4.2 dated 2026-04-23 and 4.4.4 dated 2026-09-09
DESCRIPTION | 8 MD5 | 64 +-- NEWS.md | 16 R/irace-options.R | 2 R/parameters.R | 7 R/psRace.R | 10 R/race.R | 8 R/scenario.R | 8 R/version.R | 2 README.md | 3 build/partial.rdb |binary inst/doc/irace-package.Rnw | 4 inst/doc/irace-package.pdf |binary inst/examples/acotsp/target-runner | 3 inst/examples/julia |only inst/exdata/irace-acotsp.Rdata |binary inst/exdata/log-ablation.Rdata |binary inst/exdata/sann.rda |binary inst/templates/scenario.txt.tmpl | 3 man/defaultScenario.Rd | 2 man/irace_cmdline.Rd | 5 man/irace_license.Rd | 5 man/irace_version.Rd | 5 tests/testthat/test-bug-10.R | 3 tests/testthat/test-bug-90.R | 1 tests/testthat/test-bug-94.R |only tests/testthat/test-bug1col.R | 1 tests/testthat/test-psrace-nothing-to-run.R |only vignettes/examples.Rdata |binary vignettes/irace-acotsp-stdout.txt | 523 ++++++++++++++-------------- vignettes/irace-package.Rnw | 4 vignettes/irace-package.bib | 2 vignettes/section/irace-options.Rnw | 2 33 files changed, 378 insertions(+), 313 deletions(-)
Title: Access and Analyse UN Comtrade International Trade Data
Description: Download and analyse international merchandise and services trade
data from the United Nations Comtrade database
<https://comtradeplus.un.org/>. Retrieve bilateral trade flows, compute
trade analytics (revealed comparative advantage, trade concentration,
trade balance), and convert between commodity classifications
(Harmonised System 'HS', Standard International Trade Classification
'SITC', Broad Economic Categories 'BEC'). Covers 200+ reporter
countries, 60+ years of goods trade data (1962-present), and services
trade via Extended Balance of Payments Services ('EBOPS'). Works
without registration for basic queries. A free Application Programming
Interface ('API') key from
<https://comtradedeveloper.un.org/> unlocks full access.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between comtrade versions 0.1.0 dated 2026-04-13 and 0.1.1 dated 2026-09-09
DESCRIPTION | 20 ++++++++++------- MD5 | 42 ++++++++++++++++++------------------ NEWS.md | 17 ++++++++++++++ R/analytics.R | 51 +++++++++++++++++++++++++++++++++++--------- R/reference.R | 10 ++++++-- R/trade.R | 20 ++++++++++++----- R/utils.R | 24 +++++++++++++++++++- README.md | 15 ++++++++++-- man/comtrade-package.Rd | 3 +- man/ct_available.Rd | 3 +- man/ct_balance.Rd | 8 ++++++ man/ct_compare.Rd | 7 +++++- man/ct_growth.Rd | 6 ++++- man/ct_hhi.Rd | 6 +++-- man/ct_rca.Rd | 6 +++-- man/ct_reporters.Rd | 7 ++++-- man/ct_services.Rd | 4 ++- man/ct_share.Rd | 6 ++++- man/ct_top_partners.Rd | 6 ++++- man/ct_top_products.Rd | 6 ++++- man/ct_trade.Rd | 16 ++++++++++--- tests/testthat/test-utils.R | 33 ++++++++++++++++++++++++++++ 22 files changed, 246 insertions(+), 70 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data.
'caret' is a frequently used package for model training and prediction using machine learning.
CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'.
It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate
the performance of spatial prediction models and allows for spatial variable selection to selects
suitable predictor variables in view to their contribution to the spatial model performance.
CAST further includes functionality to estimate the (spatial) area of applicability of prediction models.
Methods are described in
Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>;
Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>;
Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>;
Milà et al. (2022) <doi:10.1111/2041-210X.13851>;
Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>;
L [...truncated...]
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Fabian Schumacher [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Jakub Nowosad [ctb],
Darius Goergen [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 1.1.1 dated 2026-07-15 and 1.1.2 dated 2026-09-09
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++-------- NEWS.md | 3 ++ inst/doc/cast01-CAST-intro.html | 4 +-- inst/doc/cast02-plotgeodist.html | 4 +-- inst/doc/cast03-CV.R | 39 +++++++++++++++++++------------- inst/doc/cast03-CV.Rmd | 43 ++++++++++++++++++++++-------------- inst/doc/cast03-CV.html | 45 +++++++++++++++++++------------------- inst/doc/cast04-AOA-tutorial.html | 4 +-- inst/doc/cast05-parallel.html | 4 +-- vignettes/cast03-CV.Rmd | 43 ++++++++++++++++++++++-------------- 11 files changed, 124 insertions(+), 91 deletions(-)
Title: (Bifactor) ESEM with Continuous (MLR) or Ordinal (WLSMV) Data
Description: Fits bifactor exploratory structural equation models (B-ESEM),
together with standard exploratory structural equation modeling (ESEM)
and confirmatory factor analysis (CFA), for continuous and
ordinal data. Continuous models use 'lavaan' native efa()
blocks with robust maximum likelihood (MLR) estimation.
Ordinal ESEM defaults to the 'lavaan' weighted least squares
mean- and variance-adjusted (WLSMV) estimator; ordinal B-ESEM uses a
custom diagonally weighted least squares (DWLS) path with polychoric
correlations from 'psych', rotation-delta standard errors via 'numDeriv',
and a mean- and variance-adjusted chi-square. Target, geomin, and oblimin
rotations use 'GPArotation'; the bifactor ESEM approach follows Morin,
Arens and Marsh (2016) <doi:10.1080/10705511.2014.961800>. Additional
features include multi-group measurement invariance (configural through
strict, with partial invariance), ESEM-within-CFA conversion, McDonald's
omega reliability suite, and the Mehrvarz and Rouder ( [...truncated...]
Author: Leon T. De Beer [aut, cre]
Maintainer: Leon T. De Beer <leondb@gmail.com>
Diff between bifactory versions 0.5.2 dated 2026-08-28 and 0.6.0 dated 2026-09-09
DESCRIPTION | 20 MD5 | 151 - NAMESPACE | 6 NEWS.md | 148 + R/align_loadings.R | 150 - R/alignment_check.R | 3 R/bifactor.R | 1148 ++++---- R/bifactory-package.R | 1 R/compare.R | 28 R/esem.R | 704 ++--- R/ewc.R | 211 - R/factor_scores.R | 995 +++---- R/invariance.R | 4146 +++++++++++++++++-------------- R/methods.R | 96 R/ordered_esem.R | 2812 ++++++++++----------- R/partial_invariance.R | 184 + R/pipeline.R | 2700 ++++++++++---------- R/reliability.R | 65 R/srmr_mplus.R |only inst/VALIDATION.md | 127 inst/templates/template.R | 479 +-- man/align_loadings.Rd | 51 man/alignment_check.Rd | 58 man/besem.Rd | 115 man/besem_ordered.Rd | 68 man/bifactory_template.Rd | 2 man/chisq_decomp.Rd | 6 man/coef.esem_fit.Rd | 4 man/compare_ewc.Rd | 2 man/compare_loadings.Rd | 14 man/compute_indices.Rd | 64 man/doc_estimator_paths.Rd | 56 man/esem.Rd | 115 man/esem_compare.Rd | 8 man/esem_invariance.Rd | 170 - man/esem_ordered.Rd | 75 man/ewc_syntax.Rd | 20 man/extract_mplus_loadings.Rd | 2 man/factor_scores.Rd | 44 man/find_ewc_referents.Rd | 2 man/fitMeasures.esem_fit.Rd | 2 man/fit_ewc.Rd | 16 man/fit_indices.Rd | 8 man/generate_mplus_besem_syntax.Rd | 2 man/generate_mplus_syntax.Rd | 2 man/lavaan_fit.Rd | 2 man/make_bifactor_target.Rd | 2 man/make_target.Rd | 21 man/modindices.esem_fit.Rd | 2 man/parameters.Rd | 12 man/parse_mplus_polychoric.Rd | 4 man/partial_invariance.Rd | 40 man/plot.alignment_check.Rd | 2 man/print.aligned_loadings.Rd | 2 man/print.alignment_check.Rd | 2 man/print.besem_fit.Rd | 2 man/print.esem_comparison.Rd | 2 man/print.esem_comparison_pipeline.Rd | 2 man/print.esem_fit.Rd | 2 man/print.esem_invariance.Rd | 2 man/print.esem_partial_invariance.Rd | 2 man/print.esem_spec.Rd | 2 man/print.esem_target.Rd | 2 man/print.reliability_indices.Rd | 2 man/refine_rotation.Rd | 16 man/run_comparison.Rd | 14 man/run_mplus_besem_invariance.Rd | 8 man/save_results.Rd | 20 man/specify_model.Rd | 20 man/summary.esem_fit.Rd | 2 tests/testthat/test-align_loadings.R |only tests/testthat/test-compare.R |only tests/testthat/test-console_colour.R |only tests/testthat/test-ewc.R |only tests/testthat/test-fit_retry.R |only tests/testthat/test-inv_notes.R |only tests/testthat/test-invariance.R |only tests/testthat/test-parallel_starts.R |only tests/testthat/test-parameters.R | 5 tests/testthat/test-partial_invariance.R |only tests/testthat/test-rd_markdown.R |only tests/testthat/test-reliability.R |only tests/testthat/test-srmr.R |only 83 files changed, 8136 insertions(+), 7136 deletions(-)
Title: Simple Power Simulations for ANOVAs
Description: A-priori power simulations and power-calculations for within, between and mixed ANOVAs based on target (partial) eta-squared values. Supports complex designs with more than two factors and their interactions with a single function call.
Author: Shaheed Azaad [aut, cre]
Maintainer: Shaheed Azaad <sazaad@uni-muenster.de>
Diff between anovapowersim versions 1.1.0 dated 2026-05-31 and 1.2.0 dated 2026-09-09
DESCRIPTION | 9 MD5 | 92 + NAMESPACE | 17 NEWS.md | 156 ++ R/anovapowersim-package.R | 23 R/f_to_pes.R |only R/power_curve.R | 1509 +++++++++++++++----------- R/power_effect.R |only R/power_effect_calc.R |only R/power_n_calc.R |only R/power_unbalanced.R |only R/print_methods.R | 414 +++++++ R/utils.R | 45 R/within_covariance.R |only README.md | 65 - build/vignette.rds |binary inst/CITATION |only inst/doc/anovapowersim.R | 37 inst/doc/anovapowersim.Rmd | 107 - inst/doc/anovapowersim.html | 166 +- inst/doc/calculated-power.R |only inst/doc/calculated-power.Rmd |only inst/doc/calculated-power.html |only inst/doc/comparison-with-gpower.R |only inst/doc/comparison-with-gpower.Rmd |only inst/doc/comparison-with-gpower.html |only inst/doc/covariance.R |only inst/doc/covariance.Rmd |only inst/doc/covariance.html |only inst/doc/fixed-sample-power.R |only inst/doc/fixed-sample-power.Rmd |only inst/doc/fixed-sample-power.html |only inst/doc/unbalanced-designs.R |only inst/doc/unbalanced-designs.Rmd |only inst/doc/unbalanced-designs.html |only man/anovapowersim-package.Rd | 24 man/cell_design.Rd |only man/design_term_means.Rd | 34 man/f_to_pes.Rd |only man/means_pattern.Rd |only man/power_achieved.Rd |only man/power_achieved_calc.Rd |only man/power_curve.Rd | 110 + man/power_n.Rd | 65 - man/power_n_calc.Rd |only man/power_sensitivity.Rd |only man/power_sensitivity_calc.Rd |only man/power_unbalanced.Rd |only man/print.anovapowersim_achieved_power.Rd |only man/print.anovapowersim_sensitivity.Rd |only man/print.anovapowersim_unbalanced_power.Rd |only man/simulate_design_dataset.Rd | 8 man/summary.anovapowersim_achieved_power.Rd |only man/summary.anovapowersim_sensitivity.Rd |only man/summary.anovapowersim_unbalanced_power.Rd |only man/unbalanced_covariance.Rd |only man/within_covariance.Rd |only tests/testthat/_snaps |only tests/testthat/helper-covariance.R |only tests/testthat/test-calibration-scale.R |only tests/testthat/test-f_to_pes.R |only tests/testthat/test-means-pattern.R |only tests/testthat/test-power-effect-calc.R |only tests/testthat/test-power-effect.R |only tests/testthat/test-power-tail.R |only tests/testthat/test-power-unbalanced.R |only tests/testthat/test-power_curve.R | 777 ++++++++++++- tests/testthat/test-within_covariance.R |only vignettes/anovapowersim.Rmd | 107 - vignettes/calculated-power.Rmd |only vignettes/comparison-with-gpower.Rmd |only vignettes/covariance.Rmd |only vignettes/fixed-sample-power.Rmd |only vignettes/unbalanced-designs.Rmd |only 74 files changed, 2817 insertions(+), 948 deletions(-)
Title: Analysis of Event Data with Two Time Scales
Description: Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales. If covariates are available, estimate a proportional hazards model with such a two-dimensional baseline hazard.
Functions are provided to prepare the raw data for estimation, to fit the model and to plot the two-dimensional smooth hazard.
Extension to a competing risks model is implemented. For details about the method please refer to Carollo et al. (2025) <doi:10.1002/sim.10297>.
Author: Angela Carollo [aut, cre, cph] ,
Paul H.C. Eilers [aut],
Jutta Gampe [aut]
Maintainer: Angela Carollo <carollo@demogr.mpg.de>
Diff between TwoTimeScales versions 1.2.1 dated 2026-03-30 and 1.3.1 dated 2026-09-09
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++++------ NAMESPACE | 6 ++++++ NEWS.md | 9 +++++++++ R/boot_cuminc2ts.R |only R/competing_risks_methods.R | 3 ++- R/plot_boot_cuminc2ts.R |only R/predict_haz2ts_pointwise.R | 2 +- README.md | 8 +++++--- man/boot_cuminc2ts.Rd |only man/plot_boot_cuminc2ts.Rd |only 11 files changed, 39 insertions(+), 16 deletions(-)
Title: A Data Interface Between 'GAMS' and R
Description: Read, analyze, modify, and write 'GAMS' (General Algebraic
Modeling System) data. The main focus of 'gamstransfer' is the
highly efficient transfer of data with 'GAMS' <https://www.gams.com/>,
while keeping these operations as simple as possible for the user. The
transfer of data usually takes place via an intermediate GDX (GAMS Data
Exchange) file. Additionally, 'gamstransfer' provides utility
functions to get an overview of 'GAMS' data and to check its validity.
Author: Atharv Bhosekar [aut, cre],
GAMS Development Corp. [cph, fnd],
GAMS Software GmbH [cph, fnd]
Maintainer: Atharv Bhosekar <abhosekar@gams.com>
Diff between gamstransfer versions 3.0.8 dated 2026-01-09 and 3.0.9 dated 2026-09-09
gamstransfer-3.0.8/gamstransfer/src/gdx/src/rtl/p3platform.cpp |only gamstransfer-3.0.9/gamstransfer/DESCRIPTION | 10 gamstransfer-3.0.9/gamstransfer/LICENSE | 4 gamstransfer-3.0.9/gamstransfer/MD5 | 241 gamstransfer-3.0.9/gamstransfer/NAMESPACE | 20 gamstransfer-3.0.9/gamstransfer/NEWS.md | 86 gamstransfer-3.0.9/gamstransfer/R/Alias.R | 758 gamstransfer-3.0.9/gamstransfer/R/BaseAlias.R | 286 gamstransfer-3.0.9/gamstransfer/R/Container.R | 3539 +-- gamstransfer-3.0.9/gamstransfer/R/DomainViolation.R | 144 gamstransfer-3.0.9/gamstransfer/R/Equation.R | 1108 - gamstransfer-3.0.9/gamstransfer/R/Parameter.R | 674 gamstransfer-3.0.9/gamstransfer/R/RcppExports.R | 38 gamstransfer-3.0.9/gamstransfer/R/Set.R | 414 gamstransfer-3.0.9/gamstransfer/R/SpecialValues.R | 128 gamstransfer-3.0.9/gamstransfer/R/Super.R | 340 gamstransfer-3.0.9/gamstransfer/R/Symbol.R | 4208 ++-- gamstransfer-3.0.9/gamstransfer/R/UniverseAlias.R | 456 gamstransfer-3.0.9/gamstransfer/R/Variable.R | 1122 - gamstransfer-3.0.9/gamstransfer/R/gamstransfer-package.R | 12 gamstransfer-3.0.9/gamstransfer/R/symbolTypes.R | 120 gamstransfer-3.0.9/gamstransfer/R/utility.R | 62 gamstransfer-3.0.9/gamstransfer/README.md | 298 gamstransfer-3.0.9/gamstransfer/configure | 1 gamstransfer-3.0.9/gamstransfer/configure.ac | 1 gamstransfer-3.0.9/gamstransfer/man/Alias.Rd | 36 gamstransfer-3.0.9/gamstransfer/man/Container.Rd | 95 gamstransfer-3.0.9/gamstransfer/man/DomainViolation.Rd | 66 gamstransfer-3.0.9/gamstransfer/man/Equation.Rd | 40 gamstransfer-3.0.9/gamstransfer/man/Parameter.Rd | 40 gamstransfer-3.0.9/gamstransfer/man/Set.Rd | 38 gamstransfer-3.0.9/gamstransfer/man/SpecialValues.Rd | 56 gamstransfer-3.0.9/gamstransfer/man/UniverseAlias.Rd | 32 gamstransfer-3.0.9/gamstransfer/man/Variable.Rd | 38 gamstransfer-3.0.9/gamstransfer/man/dot-Symbol.Rd | 24 gamstransfer-3.0.9/gamstransfer/man/gamstransfer-package.Rd | 58 gamstransfer-3.0.9/gamstransfer/man/readGDX.Rd | 52 gamstransfer-3.0.9/gamstransfer/man/writeGDX.Rd | 82 gamstransfer-3.0.9/gamstransfer/src/Makevars.in | 2 gamstransfer-3.0.9/gamstransfer/src/Makevars.win | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/LICENSE | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/batchalloc.hpp | 14 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/datastorage.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/datastorage.hpp | 49 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/dblutil.cpp | 31 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/dblutil.hpp | 14 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsdata.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsdata.hpp | 10 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsobj.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsobj.hpp | 57 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsstrm.cpp | 43 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/gmsstrm.hpp | 55 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strhash.cpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strhash.hpp | 141 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strindexbuf.hpp | 35 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strutilx.cpp | 564 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/strutilx.hpp | 34 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/utils.cpp | 46 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdlib/utils.hpp | 52 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gdx.hpp | 51 gamstransfer-3.0.9/gamstransfer/src/gdx/src/global/delphitypes.hpp | 37 gamstransfer-3.0.9/gamstransfer/src/gdx/src/global/unit.h | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gxfile.cpp | 660 gamstransfer-3.0.9/gamstransfer/src/gdx/src/gxfile.hpp | 42 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/dtoaLoc.h | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/math_p3.cpp | 312 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/math_p3.hpp | 17 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3io.cpp | 166 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3io.hpp | 21 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3platform.hpp | 79 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3process.cpp | 545 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3process.hpp | 32 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3utils.cpp | 1026 - gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/p3utils.hpp | 46 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/system_p3.cpp | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/system_p3.hpp | 6 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/sysutils_p3.cpp | 491 gamstransfer-3.0.9/gamstransfer/src/gdx/src/rtl/sysutils_p3.hpp | 73 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/LICENSE | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/compress.c | 44 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/crc32.c | 164 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/deflate.c | 145 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/deflate.h | 5 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzguts.h | 5 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzlib.c | 78 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzread.c | 293 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/gzwrite.c | 267 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/infback.c | 69 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inffast.c | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inffixed.h | 182 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inflate.c | 155 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inftrees.c | 143 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/inftrees.h | 4 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/trees.c | 24 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/uncompr.c | 62 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zconf.h | 9 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zconf.h.in | 1095 - gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zlib.h | 260 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zutil.c | 84 gamstransfer-3.0.9/gamstransfer/src/gdx/zlib/zutil.h | 82 gamstransfer-3.0.9/gamstransfer/src/utilities.hpp | 6 gamstransfer-3.0.9/gamstransfer/tests/testthat.R | 58 gamstransfer-3.0.9/gamstransfer/tests/testthat/data.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/diffile.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/empty.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.gms | 30 gamstransfer-3.0.9/gamstransfer/tests/testthat/foo.lst | 62 gamstransfer-3.0.9/gamstransfer/tests/testthat/foo_1.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/gt.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/out.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_equation.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_parameter.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar_equation.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_scalar_variable.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_set.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_variable.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/partial_write.gdx |binary gamstransfer-3.0.9/gamstransfer/tests/testthat/test-alias-family.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-container-methods.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-read.R | 9582 +++++----- gamstransfer-3.0.9/gamstransfer/tests/testthat/test-setrecords-and-super.R |only gamstransfer-3.0.9/gamstransfer/tests/testthat/test-symbol-methods.R |only 124 files changed, 17705 insertions(+), 14825 deletions(-)
Title: Download and Tidy Data from the 'OECD'
Description: Provides clean, tidy access to key economic indicators published
by the 'Organisation for Economic Co-operation and Development' ('OECD'),
covering GDP, CPI inflation, unemployment, tax revenue, government deficit,
health expenditure, education expenditure, income inequality, labour
productivity, and current account balance across all
38 'OECD' member countries. Data is downloaded from the 'OECD Data Explorer'
API <https://data-explorer.oecd.org> on first use and cached locally for
subsequent calls. Returns tidy long-format data frames ready for analysis
and visualisation.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readoecd versions 0.3.3 dated 2026-03-18 and 0.3.4 dated 2026-09-09
DESCRIPTION | 9 ++-- MD5 | 45 ++++++++++++------------ NEWS.md | 67 ++++++++++++++++++++++++++++++++++++- R/deficit.R | 2 - R/gdp.R | 2 - R/health.R | 4 +- R/labour.R | 2 - R/productivity.R | 29 ++++++++++++++-- R/tax.R | 19 +++++++--- R/trade.R | 2 - R/utils.R | 42 ++++++++++++++++++++--- man/readoecd-package.Rd | 1 tests/testthat/helper-oecd.R |only tests/testthat/test-cpi.R | 4 +- tests/testthat/test-deficit.R | 4 +- tests/testthat/test-education.R | 4 +- tests/testthat/test-gdp.R | 8 ++-- tests/testthat/test-health.R | 4 +- tests/testthat/test-inequality.R | 4 +- tests/testthat/test-productivity.R | 4 +- tests/testthat/test-tax.R | 4 +- tests/testthat/test-trade.R | 4 +- tests/testthat/test-unemployment.R | 14 +++---- tests/testthat/test-utils.R | 4 +- 24 files changed, 208 insertions(+), 74 deletions(-)
Title: Access 'European Central Bank' Data
Description: Provides clean, tidy access to statistical data published by the
'European Central Bank' ('ECB') via the 'ECB Data Portal' API
<https://data.ecb.europa.eu>. Covers policy interest rates, 'EURIBOR',
euro exchange rates, harmonised consumer price inflation ('HICP'), euro area
yield curves, the euro short-term rate ('ESTR'), monetary aggregates (M1,
M2, M3), mortgage and lending rates, GDP, unemployment, and government
debt-to-GDP. Each dataset has a dedicated function that abstracts away the
underlying 'SDMX' key structure, so users do not need to know series codes.
A generic fetcher is also provided for direct access to any of the 'ECB'
100-plus dataflows. Data is downloaded on first use and cached locally for
subsequent calls.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readecb versions 0.1.2 dated 2026-03-19 and 0.1.4 dated 2026-09-09
DESCRIPTION | 9 +- MD5 | 97 +++++++++++++++--------------- NEWS.md | 55 +++++++++++++++++ R/cache.R | 3 R/ecb_estr.R | 4 - R/ecb_euribor.R | 6 + R/ecb_exchange_rate.R | 17 ++++- R/ecb_gdp.R | 4 - R/ecb_get.R | 6 + R/ecb_government_debt.R | 4 - R/ecb_hicp.R | 11 ++- R/ecb_lending_rates.R | 4 - R/ecb_money_supply.R | 4 - R/ecb_mortgage_rates.R | 4 - R/ecb_policy_rates.R | 4 - R/ecb_unemployment.R | 4 - R/ecb_yield_curve.R | 6 + R/list_helpers.R | 4 - R/utils.R | 50 +++++++++++++-- README.md | 22 ++---- man/ecb_estr.Rd | 4 - man/ecb_euribor.Rd | 6 + man/ecb_exchange_rate.Rd | 6 + man/ecb_gdp.Rd | 4 - man/ecb_get.Rd | 6 + man/ecb_government_debt.Rd | 4 - man/ecb_hicp.Rd | 6 + man/ecb_lending_rates.Rd | 4 - man/ecb_money_supply.Rd | 4 - man/ecb_mortgage_rates.Rd | 4 - man/ecb_policy_rates.Rd | 4 - man/ecb_unemployment.Rd | 4 - man/ecb_yield_curve.Rd | 6 + man/list_ecb_dataflows.Rd | 4 - man/readecb-package.Rd | 1 tests/testthat/helper-ecb.R |only tests/testthat/test-ecb_estr.R | 4 - tests/testthat/test-ecb_euribor.R | 6 - tests/testthat/test-ecb_exchange_rate.R | 8 +- tests/testthat/test-ecb_gdp.R | 4 - tests/testthat/test-ecb_get.R | 2 tests/testthat/test-ecb_government_debt.R | 4 - tests/testthat/test-ecb_hicp.R | 6 - tests/testthat/test-ecb_lending_rates.R | 4 - tests/testthat/test-ecb_money_supply.R | 4 - tests/testthat/test-ecb_mortgage_rates.R | 4 - tests/testthat/test-ecb_policy_rates.R | 6 - tests/testthat/test-ecb_unemployment.R | 4 - tests/testthat/test-ecb_yield_curve.R | 6 - tests/testthat/test-list_helpers.R | 2 50 files changed, 307 insertions(+), 142 deletions(-)
Title: Download Data from the 'Office for National Statistics'
Description: Provides functions to download and tidy statistical data
published by the 'Office for National Statistics'
<https://www.ons.gov.uk>. Covers GDP, inflation (CPI, CPIH, RPI),
unemployment, employment, wages, trade, retail sales, house prices,
productivity, population, and public sector finances. Most series are
fetched from the 'ONS' website using its CSV time series endpoint.
House price data is sourced from 'HM Land Registry'
<https://www.gov.uk/government/organisations/land-registry>.
Data is cached locally between sessions.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between ons versions 0.1.3 dated 2026-03-18 and 0.1.4 dated 2026-09-09
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/ons_search.R | 1 + README.md | 25 ++++++++++++++----------- man/ons-package.Rd | 1 + 6 files changed, 31 insertions(+), 20 deletions(-)
Title: Inflation Adjustment for Historical Currency Values
Description: Convert historical monetary values into their present-day equivalents
using bundled CPI (Consumer Price Index) and GDP deflator data sourced from the
World Bank Development Indicators. Supports British pounds (GBP), Australian
dollars (AUD), US dollars (USD), Euro (EUR), Canadian dollars (CAD), Japanese
yen (JPY), Chinese yuan (CNY), Swiss francs (CHF), New Zealand dollars (NZD),
Indian rupees (INR), South Korean won (KRW), Brazilian reais (BRL), and
Norwegian krone (NOK). Currency codes and country names are both accepted as
input.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between inflateR versions 0.1.3 dated 2026-03-04 and 0.2.0 dated 2026-09-09
DESCRIPTION | 11 +- MD5 | 143 +++++++++++++++++++++----------------- NAMESPACE | 2 NEWS.md | 65 +++++++++++++++++ R/adjust.R | 96 +++++-------------------- R/adjust_real.R | 90 ++++-------------------- R/data.R | 102 +++++++++++++-------------- R/historical_real.R | 92 ++++-------------------- R/historical_value.R | 95 ++++--------------------- R/inflateR-package.R |only R/inflation_rate.R |only R/list_currencies.R |only R/utils.R |only README.md | 178 ++++++++++++++++++++++++++++++++---------------- data/aud_cpi.rda |binary data/aud_gdp_def.rda |binary data/brl_cpi.rda |binary data/brl_gdp_def.rda |binary data/cad_cpi.rda |binary data/cad_gdp_def.rda |binary data/chf_cpi.rda |binary data/chf_gdp_def.rda |binary data/cny_cpi.rda |binary data/cny_gdp_def.rda |binary data/eur_cpi.rda |binary data/eur_gdp_def.rda |binary data/inr_cpi.rda |binary data/inr_gdp_def.rda |binary data/jpy_cpi.rda |binary data/jpy_gdp_def.rda |binary data/krw_cpi.rda |binary data/krw_gdp_def.rda |binary data/nok_cpi.rda |binary data/nok_gdp_def.rda |binary data/nzd_cpi.rda |binary data/nzd_gdp_def.rda |binary data/uk_cpi.rda |binary data/uk_gdp_def.rda |binary data/usd_cpi.rda |binary data/usd_gdp_def.rda |binary inst/CITATION |only man/adjust_inflation.Rd | 22 ++++- man/adjust_real.Rd | 17 +++- man/aud_cpi.Rd | 4 - man/aud_gdp_def.Rd | 4 - man/brl_cpi.Rd | 6 - man/brl_gdp_def.Rd | 4 - man/cad_cpi.Rd | 4 - man/cad_gdp_def.Rd | 4 - man/chf_cpi.Rd | 4 - man/chf_gdp_def.Rd | 4 - man/cny_cpi.Rd | 4 - man/cny_gdp_def.Rd | 4 - man/eur_cpi.Rd | 4 - man/eur_gdp_def.Rd | 4 - man/historical_real.Rd | 19 ++++- man/historical_value.Rd | 21 ++++- man/inflateR-package.Rd |only man/inflation_rate.Rd |only man/inr_cpi.Rd | 4 - man/inr_gdp_def.Rd | 4 - man/jpy_cpi.Rd | 4 - man/jpy_gdp_def.Rd | 4 - man/krw_cpi.Rd | 4 - man/krw_gdp_def.Rd | 4 - man/list_currencies.Rd |only man/nok_cpi.Rd | 4 - man/nok_gdp_def.Rd | 4 - man/nzd_cpi.Rd | 4 - man/nzd_gdp_def.Rd | 4 - man/uk_cpi.Rd | 4 - man/uk_gdp_def.Rd | 4 - man/usd_gdp_def.Rd | 4 - tests |only 74 files changed, 507 insertions(+), 548 deletions(-)
Title: Compute Global Sensitivity Analysis Indices Using Optimal
Transport
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
Author: Leonardo Chiani [aut, cre, cph] ,
Emanuele Borgonovo [rev],
Elmar Plischke [rev],
Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Diff between gsaot versions 1.1.1 dated 2025-09-17 and 1.2.0 dated 2026-09-09
DESCRIPTION | 6 MD5 | 50 +++--- NAMESPACE | 1 NEWS.md | 18 ++ R/build_partition.R | 10 - R/check_solver_optns.R | 12 - R/gsaot_indices.R | 6 R/ot_indices.R | 21 +- R/ot_indices_1d.R | 4 R/plot_functions.R | 5 R/utils.R | 244 ++++++++++++++----------------- README.md | 37 ++-- build/partial.rdb |binary inst/doc/gaussian-model-sensitivity.html | 38 ++-- man/confint.gsaot_indices.Rd | 4 man/entropic_bound.Rd | 4 man/irrelevance_threshold.Rd | 14 + man/ot_indices.Rd | 13 - man/ot_indices_1d.Rd | 7 man/ot_indices_wb.Rd | 7 man/residual_gap.Rd |only src/sinkhorn.cpp | 73 +++++---- src/sinkhorn_stable.cpp | 35 ++-- tests |only 24 files changed, 331 insertions(+), 278 deletions(-)
Title: Access Carbon Market Data from Emissions Trading Systems and
Voluntary Registries
Description: Unified access to carbon market data from compliance
emissions trading systems ('EU ETS', 'UK ETS', 'RGGI', California
Cap-and-Trade) and voluntary carbon markets (Verra, Gold Standard,
American Carbon Registry, Climate Action Reserve, via the Berkeley
Voluntary Registry Offsets Database and the 'CarbonPlan' 'OffsetsDB'
API). Includes cross-market price data from the 'International
Carbon Action Partnership' ('ICAP') Allowance Price Explorer
<https://icapcarbonaction.com/en/ets-prices>, global carbon pricing
from the World Bank Carbon Pricing Dashboard
<https://carbonpricingdashboard.worldbank.org/>, and the historical
'RFF' World Carbon Pricing Database following Dolphin, Pollitt and
Newbery (2020) <doi:10.1038/s41597-022-01659-x>. Data is downloaded
from public sources on first use and cached locally.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between carbondata versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-09-09
DESCRIPTION | 11 MD5 | 70 +++--- NAMESPACE | 2 NEWS.md | 193 +++++++++++++++++ R/aggregators.R | 423 +++++++++++++++++++++++++++++++------- R/compliance.R | 111 +++++++-- R/euets.R | 275 +++++++++++++++++++----- R/markets.R | 18 - R/utils.R | 135 ++++++++++-- R/voluntary.R | 122 ++++++++-- inst |only man/carbondata-package.Rd | 1 man/co2_cad_trust.Rd | 8 man/co2_california_caps.Rd | 8 man/co2_california_prices.Rd | 8 man/co2_ecp_prices.Rd |only man/co2_euets_allocations.Rd | 18 + man/co2_euets_emissions.Rd | 17 + man/co2_euets_files.Rd | 8 man/co2_euets_installations.Rd | 21 + man/co2_euets_price.Rd | 8 man/co2_euets_surrendered.Rd | 8 man/co2_icap_prices.Rd | 23 +- man/co2_icap_systems.Rd |only man/co2_offsets_db.Rd | 30 ++ man/co2_rff_pricing.Rd | 31 ++ man/co2_rggi_allowances.Rd | 8 man/co2_rggi_state_proceeds.Rd | 8 man/co2_ukets.Rd | 8 man/co2_ukets_allocations.Rd | 8 man/co2_vrod.Rd | 18 + man/co2_world_bank.Rd | 31 ++ tests/testthat/test-aggregators.R | 84 +++++++ tests/testthat/test-compliance.R | 23 ++ tests/testthat/test-euets.R | 59 +++++ tests/testthat/test-utils.R | 112 ++++++++++ tests/testthat/test-voluntary.R | 31 ++ 37 files changed, 1627 insertions(+), 312 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, aut] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between bigalgebra versions 3.1.0 dated 2026-03-24 and 3.1.1 dated 2026-09-09
DESCRIPTION | 10 +++--- MD5 | 18 ++++++------ NEWS.md | 6 +++- README.md | 45 +++++++++++++++++++------------ build/vignette.rds |binary inst/doc/big-matrix-workflows.html | 32 +++++++++++----------- inst/doc/level-1-blas-style-helpers.html | 4 +- inst/doc/matrix-wrapper-helpers.html | 8 ++--- inst/doc/z_lapack-decompositions.html | 17 ++++++----- src/bigalgebra.cpp | 2 + 10 files changed, 80 insertions(+), 62 deletions(-)
Title: Download Australian Energy Market Operator Data
Description: Fetch Australian Energy Market Operator (AEMO)
public data from 'NEMweb' <http://nemweb.com.au> and the
Market Management System Data Model (MMSDM) historical
archive. Provides tidy access to 5-minute and 30-minute
wholesale electricity prices, regional demand, dispatch-unit
output, interconnector flows, rooftop photovoltaic generation,
generator bids, predispatch forecasts, frequency control
ancillary services markets, and gas market data across the
National Electricity Market (NEM) regions. Data is published
by AEMO under its Copyright Permissions Notice
<https://www.aemo.com.au/privacy-and-legal-notices/copyright-permissions>.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between aemo versions 0.4.1 dated 2026-05-27 and 0.4.2 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 16 ++++++++++++++++ R/dispatch.R | 23 +++++++++++++++-------- R/forecasts.R | 8 +++++++- man/aemo_pasa.Rd | 8 +++++++- 6 files changed, 53 insertions(+), 18 deletions(-)
Title: Create Interactive Web Exercises
Description: Functions for easily creating interactive web exercises in
'R Markdown', 'Quarto', and package vignettes that students can use in
self-guided learning.
Author: Dale Barr [aut],
Lisa DeBruine [aut],
Caspar J. Van Lissa [aut, cre]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between webexercises versions 1.1.0 dated 2023-05-15 and 1.2.0 dated 2026-09-09
webexercises-1.1.0/webexercises/R/webexercises_fns.R |only webexercises-1.2.0/webexercises/DESCRIPTION | 39 webexercises-1.2.0/webexercises/MD5 | 140 webexercises-1.2.0/webexercises/NAMESPACE | 49 webexercises-1.2.0/webexercises/NEWS.md | 77 webexercises-1.2.0/webexercises/R/add_latex_support.R |only webexercises-1.2.0/webexercises/R/add_to_bookdown.R | 332 - webexercises-1.2.0/webexercises/R/add_to_pkgdown.R |only webexercises-1.2.0/webexercises/R/add_to_quarto.R | 190 - webexercises-1.2.0/webexercises/R/awesomebox.R |only webexercises-1.2.0/webexercises/R/fns_questions.R |only webexercises-1.2.0/webexercises/R/mc_to_quiz.R |only webexercises-1.2.0/webexercises/R/quarto.R | 56 webexercises-1.2.0/webexercises/R/quiz.R |only webexercises-1.2.0/webexercises/R/ui.R |only webexercises-1.2.0/webexercises/R/webex_vignette.R |only webexercises-1.2.0/webexercises/R/webexercises.R |only webexercises-1.2.0/webexercises/R/webexercises_default.R | 122 webexercises-1.2.0/webexercises/R/zzz.R | 8 webexercises-1.2.0/webexercises/README.md | 74 webexercises-1.2.0/webexercises/build |only webexercises-1.2.0/webexercises/inst/doc |only webexercises-1.2.0/webexercises/inst/reports/default/index.Rmd | 330 - webexercises-1.2.0/webexercises/inst/reports/default/index.qmd | 286 - webexercises-1.2.0/webexercises/inst/reports/default/webex.R | 2 webexercises-1.2.0/webexercises/inst/reports/default/webex.css | 240 - webexercises-1.2.0/webexercises/inst/reports/default/webex.js | 412 +- webexercises-1.2.0/webexercises/inst/reports/default/webexercises.qmd | 268 - webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/skeleton/skeleton.Rmd | 274 - webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/skeleton/skeleton.html | 1782 +++++----- webexercises-1.2.0/webexercises/inst/rmarkdown/templates/webexercises/template.yaml | 4 webexercises-1.2.0/webexercises/man/add_html_support.Rd |only webexercises-1.2.0/webexercises/man/add_latex_support.Rd |only webexercises-1.2.0/webexercises/man/add_to_bookdown.Rd | 76 webexercises-1.2.0/webexercises/man/add_to_pkgdown.Rd |only webexercises-1.2.0/webexercises/man/add_to_quarto.Rd | 58 webexercises-1.2.0/webexercises/man/add_to_quarto_file.Rd |only webexercises-1.2.0/webexercises/man/answer.Rd |only webexercises-1.2.0/webexercises/man/box_args.Rd |only webexercises-1.2.0/webexercises/man/cli_msg.Rd |only webexercises-1.2.0/webexercises/man/create_quarto_doc.Rd | 38 webexercises-1.2.0/webexercises/man/determine_output_format.Rd |only webexercises-1.2.0/webexercises/man/escape_regex.Rd | 40 webexercises-1.2.0/webexercises/man/figures/unnamed-chunk-18-1.png |only webexercises-1.2.0/webexercises/man/fitb.Rd | 120 webexercises-1.2.0/webexercises/man/hide.Rd | 72 webexercises-1.2.0/webexercises/man/is_quiet.Rd |only webexercises-1.2.0/webexercises/man/longmcq.Rd | 74 webexercises-1.2.0/webexercises/man/mcq.Rd | 62 webexercises-1.2.0/webexercises/man/quiz.Rd |only webexercises-1.2.0/webexercises/man/quiz_from_cvs.Rd |only webexercises-1.2.0/webexercises/man/rmd_webex_support.Rd |only webexercises-1.2.0/webexercises/man/round2.Rd | 62 webexercises-1.2.0/webexercises/man/strip_lzero.Rd | 40 webexercises-1.2.0/webexercises/man/style_widgets.Rd | 80 webexercises-1.2.0/webexercises/man/torf.Rd | 56 webexercises-1.2.0/webexercises/man/total_correct.Rd | 39 webexercises-1.2.0/webexercises/man/unhide.Rd | 54 webexercises-1.2.0/webexercises/man/use_webex_vignette.Rd |only webexercises-1.2.0/webexercises/man/webex_vignette.Rd |only webexercises-1.2.0/webexercises/man/webexercises_default.Rd | 82 webexercises-1.2.0/webexercises/man/with_cli_try.Rd |only webexercises-1.2.0/webexercises/tests/testthat.R | 8 webexercises-1.2.0/webexercises/tests/testthat/_problems |only webexercises-1.2.0/webexercises/tests/testthat/helper_usethis.R |only webexercises-1.2.0/webexercises/tests/testthat/helpers.R |only webexercises-1.2.0/webexercises/tests/testthat/test-add_to_bookdown.R | 340 - webexercises-1.2.0/webexercises/tests/testthat/test-add_to_quarto.R | 131 webexercises-1.2.0/webexercises/tests/testthat/test-compilation.R | 72 webexercises-1.2.0/webexercises/tests/testthat/test-create_quarto_doc.R | 103 webexercises-1.2.0/webexercises/tests/testthat/test-fitb.R | 142 webexercises-1.2.0/webexercises/tests/testthat/test-longmcq.R | 16 webexercises-1.2.0/webexercises/tests/testthat/test-mcq.R | 28 webexercises-1.2.0/webexercises/tests/testthat/test-quarto_renders_pdf.R |only webexercises-1.2.0/webexercises/tests/testthat/test-round2.R | 44 webexercises-1.2.0/webexercises/tests/testthat/test-special_characters.R |only webexercises-1.2.0/webexercises/tests/testthat/test-strip_lzero.R | 28 webexercises-1.2.0/webexercises/tests/testthat/testthat-problems.rds |only webexercises-1.2.0/webexercises/vignettes |only 79 files changed, 3319 insertions(+), 3231 deletions(-)
Title: Collapsed Variational Inference for Dirichlet Process (DP)
Mixture Model
Description: Collapsed Variational Inference for a Dirichlet Process (DP) mixture model with unknown covariance matrix structure and DP concentration parameter. It enables efficient clustering of high-dimensional data with significantly improved computational speed than traditional MCMC methods. The package incorporates 8 parameterisations and corresponding prior choices for the unknown covariance matrix, from which the user can choose and apply accordingly.
Author: Annesh Pal [aut, cre] ,
Boris Hejblum [aut]
Maintainer: Annesh Pal <sistm.soft.maintain@gmail.com>
Diff between vimixr versions 0.1.2 dated 2026-01-12 and 0.1.3 dated 2026-09-09
DESCRIPTION | 13 +-- MD5 | 46 ++++++----- NAMESPACE | 54 ++++++++----- NEWS.md | 4 - R/CVI_update_function.R | 54 +++++++------ R/ELBO_function_type.R | 39 +++------ R/RcppExports.R | 37 +++++++-- R/cvi_npmm.R | 49 +++++++----- R/cvi_singlerun.R | 4 - R/empiricalBayesa0.R | 2 R/log_sum_exp.R |only build/vignette.rds |binary inst/doc/vimixr_userguide.R | 43 ++++------ inst/doc/vimixr_userguide.Rmd | 43 ++++------ inst/doc/vimixr_userguide.html | 164 +++++++++++++++++++---------------------- man/cvi_npmm.Rd | 7 + man/log_sum_exp.Rd |only man/lower_tri_stats.Rd |only man/mat_mult.Rd | 14 ++- man/sparse_cov_op.Rd |only src/RcppExports.cpp | 41 ++++++++-- src/lower_tri_stats.cpp |only src/mat_mult.cpp | 43 +++++++++- src/mat_mult_t.cpp | 5 + src/sparse_cov_op.cpp |only src/t_mat_mult.cpp | 5 + vignettes/vimixr_userguide.Rmd | 43 ++++------ 27 files changed, 401 insertions(+), 309 deletions(-)
Title: Access 'NOAA' Climate and Weather Data
Description: Provides clean, tidy access to climate and weather data from the
'National Oceanic and Atmospheric Administration' ('NOAA') via the 'National
Centers for Environmental Information' ('NCEI') Data Service API
<https://www.ncei.noaa.gov/support/access-data-service-api-user-documentation>. Covers daily weather
observations, monthly and annual summaries, and 30-year climate normals from
over 100,000 stations across 180 countries. No API key is required.
Dedicated functions handle the most common datasets, while a generic fetcher
provides access to all 'NCEI' datasets. Station discovery functions help
users find stations by location or name. Data is downloaded on first use
and cached locally for subsequent calls. This package is not endorsed or
certified by 'NOAA'.
Author: Charles Coverdale [aut, cre, cph]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readnoaa versions 0.1.1 dated 2026-03-19 and 0.2.1 dated 2026-09-09
DESCRIPTION | 11 MD5 | 72 +++--- NAMESPACE | 2 NEWS.md | 154 +++++++++++++ R/annual.R | 20 + R/cache.R | 60 +++++ R/coverage.R |only R/daily.R | 37 ++- R/get.R | 38 ++- R/list_helpers.R | 112 ++++++++-- R/monthly.R | 20 + R/normals.R | 108 ++++++++- R/request.R | 408 ++++++++++++++++++++++++++++++------- R/stations.R | 184 ++++++++++++---- R/utils.R | 240 ++++++++++++++++++--- README.md | 244 ++++++++++++++-------- man/cache_info.Rd |only man/clear_cache.Rd | 3 man/list_datasets.Rd | 7 man/list_datatypes.Rd | 42 +++ man/noaa_annual.Rd | 14 + man/noaa_coverage.Rd |only man/noaa_daily.Rd | 30 ++ man/noaa_get.Rd | 37 ++- man/noaa_monthly.Rd | 14 + man/noaa_nearby.Rd | 37 ++- man/noaa_normals.Rd | 71 +++++- man/noaa_stations.Rd | 58 ++++- man/readnoaa-package.Rd | 3 tests/testthat/test-annual.R | 26 +- tests/testthat/test-cache.R | 77 ++++++ tests/testthat/test-coverage.R |only tests/testthat/test-daily.R | 74 ++++-- tests/testthat/test-get.R | 62 ++++- tests/testthat/test-list_helpers.R | 42 ++- tests/testthat/test-monthly.R | 24 +- tests/testthat/test-normals.R | 39 ++- tests/testthat/test-stations.R | 87 ++++--- tests/testthat/test-utils.R | 209 +++++++++++------- 39 files changed, 2102 insertions(+), 564 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb],
Mads Fjeld Wold [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 1.9.0 dated 2026-02-02 and 2.0.0 dated 2026-09-09
DESCRIPTION | 16 ++-- MD5 | 16 ++-- NAMESPACE | 28 ++++--- NEWS.md | 14 +++ R/query_url.R | 24 ++++++ build/vignette.rds |binary inst/doc/pxwebapi_v1.html | 110 +++++++++++++++---------------- inst/doc/pxwebapi_v2.html | 162 +++++++++++++++++++++++----------------------- man/query_url.Rd | 11 +++ 9 files changed, 219 insertions(+), 162 deletions(-)
Title: Generalized Linear Models Adjusting for Misrepresentation
Description: Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.
Author: Patrick Rafael [cre, aut],
Xia Michelle [aut],
Rexford Akakpo [aut]
Maintainer: Patrick Rafael <pbr2608@vt.edu>
Diff between glmMisrep versions 0.1.2 dated 2026-08-20 and 0.1.3 dated 2026-09-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 8 ++++++++ tests/LN-testing.R | 10 +++++----- tests/NB-testing.R | 10 ++++++---- tests/Norm-testing.R | 11 ++++++----- tests/Pois-testing.R | 44 ++++++++++++++++++++++++++------------------ tests/gamma-testing.R | 16 +++++++++++----- 8 files changed, 72 insertions(+), 47 deletions(-)
Title: Access 'Federal Reserve Economic Data'
Description: Provides clean, tidy access to economic data from the 'Federal
Reserve Economic Data' ('FRED') API <https://fred.stlouisfed.org/docs/api/fred/>.
'FRED' is maintained by the 'Federal Reserve Bank of St. Louis' and contains over
800,000 time series from 118 sources covering GDP, employment, inflation,
interest rates, trade, and more. Dedicated functions fetch series observations,
search for series, browse categories, releases, and tags, and retrieve series
metadata. Multiple series can be fetched in a single call, in long or wide
format. Server-side unit transformations (percent change, log, etc.) and
frequency aggregation are supported, with readable transform aliases such as
'yoy_pct' and 'log_diff'. Real-time and vintage helpers (built on 'ALFRED')
return a series as it appeared on a given date, the first-release version,
every revision, or a panel of selected vintages. An offline curated catalogue
of around fifty popular series, NBER recession reference dates, and FOMC
meeting [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between fred versions 0.2.0 dated 2026-04-11 and 0.3.1 dated 2026-09-09
DESCRIPTION | 26 ++++--- MD5 | 120 +++++++++++++++++++++++----------- NAMESPACE | 14 ++++ NEWS.md | 113 ++++++++++++++++++++++++++++++++ R/auth.R | 4 - R/cache.R | 3 R/catalogue.R |only R/categories.R | 34 ++++++--- R/cite.R |only R/class.R | 138 ++++++++++++++++++++++++++++++++-------- R/dates.R |only R/manifest.R |only R/plot.R |only R/releases.R | 24 ++++-- R/request.R | 4 - R/search.R | 24 ++++-- R/series.R | 38 ++++++----- R/sources.R | 16 +++- R/tags.R | 18 +++-- R/updates.R | 8 +- R/utilities.R |only R/vintages.R | 26 ++++--- build |only inst/CITATION | 2 inst/WORDLIST | 37 ++++++++++ inst/doc |only man/fred-package.Rd | 3 man/fred_aggregate.Rd |only man/fred_all_vintages.Rd | 6 + man/fred_as_of.Rd | 6 + man/fred_browse.Rd |only man/fred_catalogue.Rd |only man/fred_category.Rd | 10 +- man/fred_category_children.Rd | 6 + man/fred_category_series.Rd | 4 - man/fred_cite_series.Rd |only man/fred_event_window.Rd |only man/fred_first_release.Rd | 6 + man/fred_fomc_dates.Rd |only man/fred_get_key.Rd | 4 - man/fred_info.Rd | 4 - man/fred_interpolate.Rd |only man/fred_manifest.Rd |only man/fred_real_time_panel.Rd | 8 +- man/fred_recession_dates.Rd |only man/fred_related_tags.Rd | 4 - man/fred_release_dates.Rd | 4 - man/fred_release_series.Rd | 6 + man/fred_releases.Rd | 4 - man/fred_request.Rd | 4 - man/fred_search.Rd | 16 ++-- man/fred_series.Rd | 22 +++--- man/fred_source_releases.Rd | 6 + man/fred_sources.Rd | 4 - man/fred_tags.Rd | 6 + man/fred_updates.Rd | 4 - man/fred_vintage_revisions.Rd |only man/fred_vintages.Rd | 4 - man/plot.fred_tbl.Rd |only man/print.fred_manifest.Rd |only man/print.fred_tbl.Rd | 7 +- man/sub-.fred_tbl.Rd |only man/summary.fred_tbl.Rd |only tests/testthat/test-catalogue.R |only tests/testthat/test-cite.R |only tests/testthat/test-class.R |only tests/testthat/test-dates.R |only tests/testthat/test-manifest.R |only tests/testthat/test-plot.R |only tests/testthat/test-utilities.R |only vignettes |only 71 files changed, 602 insertions(+), 195 deletions(-)
Title: Measuring the Stability of Dimension Reduction and Cluster
Assignment in scRNA-Seq Experiments
Description: Provides functions for evaluating the stability of low-dimensional embeddings and cluster assignments in single‑cell RNA sequencing (scRNA‑seq) datasets. Starting from a principal component analysis (PCA) object, users can generate multiple replicates of t‑Distributed Stochastic Neighbor Embedding (t‑SNE) or Uniform Manifold Approximation and Projection (UMAP) embeddings. Embedding stability is quantified by computing pairwise Kendall’s Tau correlations across replicates and summarizing the distribution of correlation coefficients. In addition to dimensionality reduction, 'scStability' assesses clustering consistency using either Louvain or Leiden algorithms and calculating the Normalized Mutual Information (NMI) between all pairs of cluster assignments. For background on UMAP and t-SNE algorithms, see McInnes et al. (2020, <doi:10.21105/joss.00861>) and van der Maaten & Hinton (2008, <https://github.com/lvdmaaten/bhtsne>), respectively.
Author: Ben Abrahams [aut, cre]
Maintainer: Ben Abrahams <benabrahams52@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2025-06-23
Diff between scStability versions 1.0.3 dated 2025-06-23 and 1.0.4 dated 2026-09-09
DESCRIPTION | 12 +- MD5 | 29 +++--- R/clustStable.r | 4 R/createEmb.r | 5 - R/scStability.r | 39 +++----- inst/doc/Introduction-to-scStability.R | 12 +- inst/doc/Introduction-to-scStability.Rmd | 14 +- inst/doc/Introduction-to-scStability.html | 141 ++++++++++++++++-------------- man/clustStable.Rd | 2 man/scStability.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-clustStable.R | 38 +++++--- tests/testthat/test-compareEmb.R | 20 ++-- tests/testthat/test-createEmb.R | 4 tests/testthat/test-scStability.R | 37 +++++-- vignettes/Introduction-to-scStability.Rmd | 14 +- 16 files changed, 212 insertions(+), 163 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.2 dated 2026-08-28 and 2.0.4 dated 2026-09-09
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- NEWS.md | 26 +++++++++++++++++++++----- R/get_drainage_area_estimates.R | 15 +++++++++++---- R/get_vaa.R | 2 +- README.md | 10 +++++----- inst/doc/hydrogeofetch.Rmd | 2 +- inst/doc/hydrogeofetch.html | 2 +- inst/extdata/3dhp_yahara_flowlines.R | 2 +- inst/extdata/new_hope_data.R | 4 ++-- inst/extdata/nhdplushr_data.R | 2 +- inst/extdata/sample_data.R | 2 +- inst/extdata/sample_flines.R | 2 +- inst/extdata/walker_data.R | 2 +- man/get_drainage_area_estimates.Rd | 3 ++- tests/testthat/helper.R | 2 +- tests/testthat/test_get_nhdplus.R | 6 +++--- vignettes/hydrogeofetch.Rmd | 2 +- 18 files changed, 77 insertions(+), 53 deletions(-)
Title: Imputation of Multivariate Time Series Based on Dynamic Time
Warping
Description: Functions to impute large gaps within multivariate time series based on Dynamic Time Warping methods. Gaps of size 1 or inferior to a defined threshold are filled using simple average and weighted moving average respectively. Larger gaps are filled using the methodology provided by Phan et al. (2017) <DOI:10.1109/MLSP.2017.8168165>: a query is built immediately before/after a gap and a moving window is used to find the most similar sequence to this query using Dynamic Time Warping. To lower the calculation time, similar sequences are pre-selected using global features. Contrary to the univariate method (package 'DTWBI'), these global features are not estimated over the sequence containing the gap(s), but a feature matrix is built to summarize general features of the whole multivariate signal. Once the most similar sequence to the query has been identified, the adjacent sequence to this window is used to fill the gap considered. This function can deal with multiple gaps over all t [...truncated...]
Author: Camille Dezecache [aut],
Thi Thu Hong Phan [aut],
Emilie Poisson-Caillault [aut, cre]
Maintainer: Emilie Poisson-Caillault <emilie.poisson@univ-littoral.fr>
Diff between DTWUMI versions 1.0 dated 2018-07-13 and 1.1 dated 2026-09-09
DTWUMI-1.0/DTWUMI/R/XXXX_4Local_derivative_DDTW.R |only DTWUMI-1.0/DTWUMI/build |only DTWUMI-1.0/DTWUMI/man/DTWUMI-package.Rd |only DTWUMI-1.1/DTWUMI/DESCRIPTION | 24 +++- DTWUMI-1.1/DTWUMI/MD5 | 53 +++++----- DTWUMI-1.1/DTWUMI/NAMESPACE | 7 + DTWUMI-1.1/DTWUMI/R/4_1_1Estimate_global_features.R | 48 ++++----- DTWUMI-1.1/DTWUMI/R/4_1_2Features_matrix.R | 32 ++---- DTWUMI-1.1/DTWUMI/R/4_2Indexes_size_missing.R | 6 - DTWUMI-1.1/DTWUMI/R/4_3_1Imputing_1NA.R | 5 DTWUMI-1.1/DTWUMI/R/4_3_2Imputing_SmallNAgaps.R | 5 DTWUMI-1.1/DTWUMI/R/4_4Find_global_threshold_multivariate.R | 3 DTWUMI-1.1/DTWUMI/R/4_5Find_similar_window_multivariate.R | 3 DTWUMI-1.1/DTWUMI/R/4_5Find_similar_window_multivariate_AFBDTW.R | 3 DTWUMI-1.1/DTWUMI/R/4_6DTWUMI_1gap.R | 25 ++-- DTWUMI-1.1/DTWUMI/R/4_7DTWUMI_general.R | 6 - DTWUMI-1.1/DTWUMI/R/DATA.R | 4 DTWUMI-1.1/DTWUMI/R/XXXX_1Trapezoid.R | 10 + DTWUMI-1.1/DTWUMI/R/XXXX_3Dist_AFBDTW_matrix.R | 6 - DTWUMI-1.1/DTWUMI/inst/CITATION | 4 DTWUMI-1.1/DTWUMI/man/DTWUMI_1gap_imputation.Rd | 31 +++-- DTWUMI-1.1/DTWUMI/man/DTWUMI_imputation.Rd | 16 +-- DTWUMI-1.1/DTWUMI/man/Indexes_size_missing_multi.Rd | 5 DTWUMI-1.1/DTWUMI/man/dataDTWUMI.Rd | 8 - DTWUMI-1.1/DTWUMI/man/dot-DTW_threshold_global_multivariate.Rd |only DTWUMI-1.1/DTWUMI/man/dot-Finding_similar_window_multivariate.Rd |only DTWUMI-1.1/DTWUMI/man/dot-Finding_similar_window_multivariate_AFBDTW.Rd |only DTWUMI-1.1/DTWUMI/man/dot-dist_afbdtw_matrix.Rd |only DTWUMI-1.1/DTWUMI/man/dot-features_matrix.Rd |only DTWUMI-1.1/DTWUMI/man/dot-globalfeatures.Rd |only DTWUMI-1.1/DTWUMI/man/dot-imp_NA_WMA.Rd |only DTWUMI-1.1/DTWUMI/man/dot-trapezoid.Rd |only DTWUMI-1.1/DTWUMI/man/imp_1NA.Rd | 5 33 files changed, 162 insertions(+), 147 deletions(-)
Title: Imputation of Time Series Based on Dynamic Time Warping
Description: Functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).
Author: Camille Dezecache [aut],
Thi Thu Hong Phan [aut],
Emilie Poisson-Caillault [aut, cre]
Maintainer: Emilie Poisson-Caillault <emilie.poisson@univ-littoral.fr>
Diff between DTWBI versions 1.1 dated 2018-07-11 and 1.2 dated 2026-09-09
DTWBI-1.1/DTWBI/build |only DTWBI-1.1/DTWBI/man/DTWBI-package.Rd |only DTWBI-1.2/DTWBI/DESCRIPTION | 24 ++- DTWBI-1.2/DTWBI/MD5 | 68 +++++----- DTWBI-1.2/DTWBI/NAMESPACE | 13 + DTWBI-1.2/DTWBI/R/1_1Similarity.R | 8 - DTWBI-1.2/DTWBI/R/1_2NMAE.R | 6 DTWBI-1.2/DTWBI/R/1_4RMSE.R | 6 DTWBI-1.2/DTWBI/R/1_5FSD.R | 6 DTWBI-1.2/DTWBI/R/1_6FB.R | 6 DTWBI-1.2/DTWBI/R/1_7FA2.R | 6 DTWBI-1.2/DTWBI/R/2_1DDTW.R | 4 DTWBI-1.2/DTWBI/R/2_2AFBDTW.R | 24 +-- DTWBI-1.2/DTWBI/R/2_3DTWcost.R | 6 DTWBI-1.2/DTWBI/R/3_1Create_large_gaps.R | 20 +- DTWBI-1.2/DTWBI/R/3_2Estimate_global_features.R | 46 +++--- DTWBI-1.2/DTWBI/R/3_3Find_global_threshold_univariate.R | 3 DTWBI-1.2/DTWBI/R/3_4Find_similar_windows_univariate.R | 3 DTWBI-1.2/DTWBI/R/3_4Find_similar_windows_univariate_AFBDTW.R | 3 DTWBI-1.2/DTWBI/R/3_5DTWBI_algorithm_simple_univariate.R | 26 +-- DTWBI-1.2/DTWBI/R/DATA.R | 4 DTWBI-1.2/DTWBI/inst/CITATION | 6 DTWBI-1.2/DTWBI/man/DTWBI_univariate.Rd | 37 ++--- DTWBI-1.2/DTWBI/man/compute.fa2.Rd | 5 DTWBI-1.2/DTWBI/man/compute.fb.Rd | 5 DTWBI-1.2/DTWBI/man/compute.fsd.Rd | 5 DTWBI-1.2/DTWBI/man/compute.nmae.Rd | 5 DTWBI-1.2/DTWBI/man/compute.rmse.Rd | 5 DTWBI-1.2/DTWBI/man/compute.sim.Rd | 7 - DTWBI-1.2/DTWBI/man/dataDTWBI.Rd | 10 - DTWBI-1.2/DTWBI/man/dist_afbdtw.Rd | 23 +-- DTWBI-1.2/DTWBI/man/dot-DTW_threshold_global_univariate.Rd |only DTWBI-1.2/DTWBI/man/dot-Finding_similar_window_univariate.Rd |only DTWBI-1.2/DTWBI/man/dot-Finding_similar_window_univariate_AFBDTW.Rd |only DTWBI-1.2/DTWBI/man/dot-globalfeatures.Rd |only DTWBI-1.2/DTWBI/man/gapCreation.Rd | 19 +- DTWBI-1.2/DTWBI/man/local.derivative.ddtw.Rd | 3 DTWBI-1.2/DTWBI/man/minCost.Rd | 3 38 files changed, 197 insertions(+), 218 deletions(-)
Title: Unified Climate Indices for Temperature, Precipitation, and
Drought
Description: Compute the standard suite of climate indices from daily
weather observations. Provides the canonical 'ETCCDI' 27 (Expert
Team on Climate Change Detection and Indices), the 'ET-SCI'
heatwave and cold-wave families plus the Excess Heat Factor of
Nairn and Fawcett (2013), and agroclimatic, drought, and
human-comfort families. Drought indices ('SPI', 'SPEI') accept a
choice of distribution (gamma or Pearson III for SPI; log-logistic
or generalised extreme value for SPEI). Reference
evapotranspiration is available via Hargreaves and the FAO-56
Penman-Monteith method (Allen et al. 1998). Percentile-based
indices support the Zhang (2005) in-base bootstrap. Daily inputs
are numeric vectors plus a 'Date' vector; outputs are tidy data
frames. Optional gridded support via 'terra' applies any index
over a 'SpatRaster' and reads 'netCDF' input. No external API
calls; pairs with data packages such as 'readnoaa'. References:
Alexander et al. (2006) <doi:10.1029/2005JD006290>; Zhang et al.
(201 [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between climatekit versions 0.2.0 dated 2026-05-09 and 0.2.2 dated 2026-09-09
DESCRIPTION | 8 - MD5 | 67 ++++---- NAMESPACE | 1 NEWS.md | 105 +++++++++++++ R/agroclimatic.R | 15 + R/bootstrap.R | 4 R/climatekit-package.R | 1 R/comfort.R | 10 - R/compute.R | 77 +-------- R/convert.R | 37 ++-- R/drought.R | 47 +++-- R/ehf.R | 13 + R/gridded.R | 4 R/heatwave.R | 20 +- R/index-table.R |only R/metadata.R | 260 +++------------------------------ R/precipitation.R | 37 +++- R/temperature.R | 72 +++------ R/utils.R | 60 +++++++ README.md | 114 ++++---------- inst/doc/climdex-migration.Rmd | 15 + inst/doc/climdex-migration.html | 21 ++ man/ck_apply_grid.Rd | 4 man/ck_compute.Rd | 9 + man/ck_dry_days.Rd | 7 man/ck_spei.Rd | 12 + man/ck_spi.Rd | 2 man/ck_warm_spell.Rd | 5 man/ck_wet_days.Rd | 9 + man/clear_cache.Rd | 21 +- tests/testthat/test-drought.R | 4 tests/testthat/test-ehf.R | 2 tests/testthat/test-index-table.R |only tests/testthat/test-precipitation.R | 4 tests/testthat/test-v022-regressions.R |only vignettes/climdex-migration.Rmd | 15 + 36 files changed, 525 insertions(+), 557 deletions(-)
Title: Bayesian Instrumental Regression for Disparity Estimation
Description: Bayesian models for accurately estimating conditional
distributions by race, using Bayesian Improved Surname Geocoding (BISG)
probability estimates of individual race. Implements the methods described
in McCartan, Fisher, Goldin, Ho and Imai (2025) <doi:10.1080/01621459.2025.2526695>.
Author: Cory McCartan [aut, cre],
Kosuke Imai [ctb],
Daniel Ho [ctb],
Jacob Goldin [ctb],
Robin Fisher [ctb],
The Stan Development Team [cph]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between birdie versions 0.7.1 dated 2025-07-24 and 0.8.0 dated 2026-09-09
birdie-0.7.1/birdie/inst/extdata/natl_race.rds |only birdie-0.7.1/birdie/inst/include/rstan/boost_random_R.hpp |only birdie-0.7.1/birdie/inst/include/rstan/rcpp_module_def_for_rstan.hpp |only birdie-0.8.0/birdie/DESCRIPTION | 22 birdie-0.8.0/birdie/MD5 | 57 - birdie-0.8.0/birdie/NEWS.md | 12 birdie-0.8.0/birdie/R/birdie.R | 26 birdie-0.8.0/birdie/R/bisg.R | 499 ++++++---- birdie-0.8.0/birdie/R/census.R | 20 birdie-0.8.0/birdie/R/generics.R | 7 birdie-0.8.0/birdie/R/sysdata.rda |binary birdie-0.8.0/birdie/R/utils.R | 4 birdie-0.8.0/birdie/README.md | 50 - birdie-0.8.0/birdie/build/partial.rdb |binary birdie-0.8.0/birdie/build/vignette.rds |binary birdie-0.8.0/birdie/inst/doc/birdie.html | 128 +- birdie-0.8.0/birdie/inst/extdata/names_2020_counts.rds |only birdie-0.8.0/birdie/inst/extdata/state_race_2020.rds |only birdie-0.8.0/birdie/inst/extdata/zip_race_2020.rds |only birdie-0.8.0/birdie/inst/include/rstan/stan_fit.hpp | 9 birdie-0.8.0/birdie/man/birdie-package.Rd | 2 birdie-0.8.0/birdie/man/birdie.Rd | 26 birdie-0.8.0/birdie/man/bisg.Rd | 59 + birdie-0.8.0/birdie/man/census_race_geo_table.Rd | 3 birdie-0.8.0/birdie/man/p_r_natl.Rd | 14 birdie-0.8.0/birdie/man/reexports.Rd | 1 birdie-0.8.0/birdie/src/Makevars | 4 birdie-0.8.0/birdie/src/stanExports_multinom.cc | 34 birdie-0.8.0/birdie/src/stanExports_multinom.h | 272 +++-- birdie-0.8.0/birdie/tests/testthat/_snaps/birdie.md | 2 birdie-0.8.0/birdie/tests/testthat/test-birdie.R | 2 birdie-0.8.0/birdie/tests/testthat/test-bisg.R | 83 + birdie-0.8.0/birdie/tests/testthat/test-census-premade.R |only 33 files changed, 913 insertions(+), 423 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) with the goal of maximizing between-group similarity or within-group heterogeneity. The anticlustering approach thereby reverses the logic of cluster analysis that strives for high within-group homogeneity and clear separation between groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The main function anticlustering() gives access to optimal and heuristic anticlustering methods described in Papenberg and Klau (2021; <doi:10.1037/met0000301>), Brusco et al. (2020; <doi:10.1111/bmsp.12186>), Papenberg (2024; <doi:10.1111/bmsp.12315>), Papenberg, Wang, et al. (2025; <doi:10.1016/j.crmeth.2025.101137>), Papenberg, Breuer, et al. (2025; <doi:10.1017/psy.2025.10052>), Yang et al. (202 [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb] ,
Dimitry Wintermantel [ctb] ),
David Buczynski [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.14 dated 2026-04-15 and 0.8.16 dated 2026-09-09
DESCRIPTION | 24 +++- LICENSE | 2 MD5 | 59 +++++++----- NAMESPACE | 5 + R/Optimal_Dispersion.R | 2 R/bicriterion_iterated_local_search_call.R | 2 R/c-anticlustering.R | 17 +++ R/categories_to_binary.R | 23 ++++ R/experimental_allocation.R |only R/fast_anticlustering.R | 26 ++++- R/input-validation.R | 12 +- R/md.R |only R/optimal_anticlustering.R | 2 R/wrapper-anticlustering.R | 41 +++++--- R/wrapper-feasible-and-infeasible-region-search.R |only build/vignette.rds |binary inst/doc/Anticlustering_in_2025.Rmd | 2 inst/doc/Anticlustering_in_2025.html | 2 inst/doc/Speeding_up_anticlustering.html | 28 ++--- inst/tinytest/test-fifr.R |only inst/tinytest/test-md.R |only man/anticlustering.Rd | 23 +++- man/bicriterion_anticlustering.Rd | 2 man/categories_to_binary.Rd | 11 ++ man/experimental_allocation.Rd |only man/fast_anticlustering.Rd | 9 + man/feasible_and_infeasible_region_search_anticlustering.Rd |only man/mahalanobis_distance.Rd |only man/optimal_anticlustering.Rd | 2 man/optimal_dispersion.Rd | 2 src/anticlust_init.c | 7 + src/declarations.h | 13 ++ src/fast-MD-anticlustering.c |only src/feasible_and_infeasible_region_search.c |only src/fifr_header.h |only vignettes/Anticlustering_in_2025.Rmd | 2 36 files changed, 223 insertions(+), 95 deletions(-)
Title: Parse, Clean, and Normalize URLs
Description: A lightweight toolkit for extracting structured information from URLs.
Includes functions for parsing, normalizing protocols, extracting domains, and constructing clean URLs.
Domain and public-suffix extraction is delegated to the 'pslr' package,
which implements the Public Suffix List from <https://publicsuffix.org>.
Punycode and IDNA encoding is handled by the 'punycoder' package.
Author: Bart Turczynski [aut, cre]
Maintainer: Bart Turczynski <bartek@turczynski.pl>
Diff between rurl versions 1.2.0 dated 2026-06-19 and 3.0.1 dated 2026-09-09
rurl-1.2.0/rurl/R/sysdata.rda |only rurl-3.0.1/rurl/DESCRIPTION | 47 rurl-3.0.1/rurl/LICENSE | 2 rurl-3.0.1/rurl/LICENSE.note |only rurl-3.0.1/rurl/MD5 | 255 rurl-3.0.1/rurl/NAMESPACE | 29 rurl-3.0.1/rurl/NEWS.md | 3021 ++++++++ rurl-3.0.1/rurl/R/accessors.R | 1611 ++++ rurl-3.0.1/rurl/R/canonical_join.R | 445 - rurl-3.0.1/rurl/R/diagnostics.R |only rurl-3.0.1/rurl/R/domain.R | 638 + rurl-3.0.1/rurl/R/email-diagnostics.R |only rurl-3.0.1/rurl/R/format.R |only rurl-3.0.1/rurl/R/host-policy.R |only rurl-3.0.1/rurl/R/parse-phases.R | 3500 ++++++++-- rurl-3.0.1/rurl/R/parse-state.R |only rurl-3.0.1/rurl/R/parse-web.R |only rurl-3.0.1/rurl/R/parse.R | 2713 +++++++ rurl-3.0.1/rurl/R/path-query.R | 536 + rurl-3.0.1/rurl/R/percent-coding.R |only rurl-3.0.1/rurl/R/profiles.R |only rurl-3.0.1/rurl/R/query-denylist.R |only rurl-3.0.1/rurl/R/resolve.R |only rurl-3.0.1/rurl/R/rurl-package.R |only rurl-3.0.1/rurl/R/scheme-policy.R |only rurl-3.0.1/rurl/R/serialize.R |only rurl-3.0.1/rurl/R/status-constants.R |only rurl-3.0.1/rurl/R/url-join.R |only rurl-3.0.1/rurl/R/url-key.R |only rurl-3.0.1/rurl/R/utils.R | 468 + rurl-3.0.1/rurl/R/verdicts.R |only rurl-3.0.1/rurl/R/zzz.R | 441 - 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Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss, (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate, and (c) racing
diffusion model (RDM; Tillman, Van Zandt, & Logan, 2020,
<doi:10.3758/s13423-020-01719-6>).
Author: Henrik Singmann [aut, cre] ,
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Kiante Fernandez [aut] ,
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb],
Trisha Van Zandt [ctb],
Gabriel Tillman [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between rtdists versions 0.11-6 dated 2026-06-10 and 0.12-0 dated 2026-09-09
rtdists-0.11-6/rtdists/NEWS |only rtdists-0.12-0/rtdists/DESCRIPTION | 29 - rtdists-0.12-0/rtdists/MD5 | 46 + rtdists-0.12-0/rtdists/NAMESPACE | 44 + rtdists-0.12-0/rtdists/NEWS.md |only rtdists-0.12-0/rtdists/R/diffusion.R | 243 +++++----- rtdists-0.12-0/rtdists/R/lba.r | 43 + rtdists-0.12-0/rtdists/R/lba_race.R | 29 - rtdists-0.12-0/rtdists/R/rdm.R |only rtdists-0.12-0/rtdists/R/rtdists-package.R | 25 - rtdists-0.12-0/rtdists/R/single-lba.r | 50 +- rtdists-0.12-0/rtdists/R/single-rdm.R |only rtdists-0.12-0/rtdists/inst/doc/reanalysis_rr98.html | 46 - rtdists-0.12-0/rtdists/man/Diffusion.Rd | 15 rtdists-0.12-0/rtdists/man/LBA-race.Rd | 13 rtdists-0.12-0/rtdists/man/LBA.Rd | 47 + rtdists-0.12-0/rtdists/man/RDM.Rd |only rtdists-0.12-0/rtdists/man/rtdists-package.Rd | 22 rtdists-0.12-0/rtdists/man/single-RDM.Rd |only rtdists-0.12-0/rtdists/src/CDF_no_variability.h | 20 rtdists-0.12-0/rtdists/tests/testthat/test-diffusion-bugs.R | 64 ++ rtdists-0.12-0/rtdists/tests/testthat/test-diffusion-math.R | 104 +++- rtdists-0.12-0/rtdists/tests/testthat/test-diffusion.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-lba-bugs-A-small.R |only rtdists-0.12-0/rtdists/tests/testthat/test-lba_basics.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-pdiffusion_rng.R | 2 rtdists-0.12-0/rtdists/tests/testthat/test-rdiffusion.R | 6 rtdists-0.12-0/rtdists/tests/testthat/test-rdm.R |only 28 files changed, 543 insertions(+), 309 deletions(-)
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Description: 'Rcpp' bindings for 'PLANC', a highly parallel
and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library.
Wraps algorithms described in
Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and
Eswar et. al (2021) <doi:10.1145/3432185>.
Implements algorithms described in
Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>,
Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and
Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Author: Andrew Robbins [aut, cre] ,
Yichen Wang [aut],
Joshua Welch [cph] ,
Ramakrishnan Kannan [cph] ,
Conrad Sanderson [cph] ,
Blue Brain Project/EPFL [cph] ,
UT-Batelle [cph] ,
LibHwloc Contributors [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between RcppPlanc versions 2.0.15 dated 2026-02-26 and 2.0.16 dated 2026-09-09
DESCRIPTION | 16 ++-- MD5 | 21 +++--- NEWS.md | 4 + build/vignette.rds |binary configure | 4 - inst/COPYRIGHTS | 98 ++++++++++++++++++++++++++++ inst/doc/RcppPlanc.html | 10 +- man/data.Rd | 6 - man/onlineINMF.Rd | 2 src/planc/CMakeLists.txt | 4 - tools/patches/04_discarded_qualifiers.patch |only tools/patches/series | 1 12 files changed, 134 insertions(+), 32 deletions(-)
Title: Tools for Working with the National Hydrography Dataset
Description: Tools for working with the National Hydrography Dataset, with
functions for querying, downloading, and networking both the NHD
<https://www.usgs.gov/national-hydrography>
and NHDPlus <https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus> datasets.
Author: Jemma Stachelek [aut, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between nhdR versions 0.6.1 dated 2023-08-11 and 0.6.2 dated 2026-09-09
DESCRIPTION | 18 MD5 | 56 +- NAMESPACE | 154 +++--- NEWS.md | 168 +++--- R/load.R | 718 ++++++++++++++-------------- R/nhdR-package.R | 6 R/query.R | 678 +++++++++++++------------- R/utils.R | 780 +++++++++++++++---------------- README.md | 485 +++++++++---------- build/vignette.rds |binary inst/CITATION | 34 - inst/doc/demo.R | 32 - inst/doc/demo.html | 560 ++++++++++++++-------- inst/doc/flow.R | 104 ++-- inst/doc/flow.html | 652 ++++++++++++++++--------- inst/doc/network.R | 68 +- inst/doc/network.html | 610 ++++++++++++++++-------- man/figures/README-unnamed-chunk-4-1.png |binary man/find_state.Rd | 44 - man/nhdR-package.Rd | 11 man/nhd_dl_state.Rd | 86 +-- man/nhd_load.Rd | 124 ++-- man/nhd_plus_load.Rd | 166 +++--- man/nhd_plus_query.Rd | 144 ++--- man/nhd_query.Rd | 126 ++--- man/select_point_overlay.Rd | 68 +- tests/testthat/test-list.R | 50 - tests/testthat/test-load.R | 190 +++---- tests/testthat/test-query.R | 176 +++--- 29 files changed, 3473 insertions(+), 2835 deletions(-)
Title: Evaluation Platform in Chronic Obstructive Pulmonary Disease
Description: Evaluation Platform in Chronic Obstructive Pulmonary Disease (EPIC) is a Discrete Event Simulation (DES) model that simulates health outcomes of patients with Chronic Obstructive Pulmonary Disease (COPD) based on demographics and individual-level risk factors, based on the model published in Sadatsafavi et al. (2019) <doi:10.1177/0272989X18824098>.
Author: Mohsen Sadatsafavi [aut, cph],
Kate Johnson [aut, cre],
Amin Adibi [aut],
Kevin Yan [aut]
Maintainer: Kate Johnson <kate.johnson@ubc.ca>
Diff between epicR versions 1.0.1 dated 2026-03-24 and 1.0.2 dated 2026-09-09
epicR-1.0.1/epicR/NEWS.md |only epicR-1.0.2/epicR/DESCRIPTION | 20 - epicR-1.0.2/epicR/MD5 | 23 - epicR-1.0.2/epicR/R/validation.R | 87 ++---- epicR-1.0.2/epicR/build/vignette.rds |binary epicR-1.0.2/epicR/inst/config/config_us.json | 8 epicR-1.0.2/epicR/inst/doc/AddingNewCountry.html | 3 epicR-1.0.2/epicR/inst/doc/GettingStarted.html | 3 epicR-1.0.2/epicR/inst/doc/InputsOutputsStructure.html | 246 ++++++++--------- epicR-1.0.2/epicR/man/epicR-package.Rd | 6 epicR-1.0.2/epicR/src/model.cpp | 4 epicR-1.0.2/epicR/src/model_events.cpp | 17 - epicR-1.0.2/epicR/tests/testthat/testExacerbations.R | 4 13 files changed, 195 insertions(+), 226 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests such as
Hosmer-Lemeshow, directed and covariate-space tests, smoothing and
resampling tests, and calibration tests. Each is obtained from its own
package where installed and attributed to its authors. The package also
implements the author's own procedures for sparse data, where the
Hosmer-Lemeshow test loses power: the omnibus Ebrahim-Farrington test
'ef.gof()', the directed 'edge.gof()' and its covariate-space variant
'cdef.gof()', the Cauchy-combination ensemble 'edges.gof()', 'DeepGOF-1'
(a pretrained convolutional statistic whose level comes from the analyst's
own parametric bootstrap rather than from the network), and 'legoft()'
(a frozen-weight combination [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.6.0 dated 2026-08-28 and 2.7.0 dated 2026-09-09
DESCRIPTION | 48 - MD5 | 83 +- NAMESPACE | 3 NEWS.md | 114 +++ R/calm_gof.R |only R/cdef_gof.R | 23 R/deepgof.R | 23 R/def_ensemble_gof.R | 301 ++++----- R/def_gof.R | 378 ++++++----- R/ebrahim.gof-package.R | 74 +- R/ebrahim_farrington_test.R | 659 ++++++++++---------- R/edge_gof.R | 17 R/legoft.R | 30 R/run_all_gof.R | 56 + R/shrink_gof.R | 64 + README.md | 1080 ++++++++++++++++----------------- inst/CITATION | 6 inst/WORDLIST | 134 ++-- inst/doc/ebrahim-farrington-intro.R | 67 -- inst/doc/ebrahim-farrington-intro.Rmd | 652 +++++++++---------- inst/doc/ebrahim-farrington-intro.html | 100 +-- inst/doc/ebrahim-gof-toolbox.R | 9 inst/doc/ebrahim-gof-toolbox.Rmd | 47 + inst/doc/ebrahim-gof-toolbox.html | 60 + man/calm.gof.Rd |only man/cdef.gof.Rd | 7 man/deepgof1.Rd | 16 man/def.ensemble.gof.Rd | 23 man/def.gof.Rd | 36 - man/deploy.gof.Rd | 7 man/ebrahim.gof-package.Rd | 75 +- man/edge.gof.Rd | 17 man/edges.gof.Rd | 6 man/ef.gof.Rd | 45 + man/figures |only man/gof.features.Rd | 7 man/legoft.Rd | 9 man/legoft.localize.Rd | 7 man/run.all.gof.Rd | 56 + man/shrink.gof.Rd | 51 + tests/testthat/test-exports-smoke.R |only vignettes/ebrahim-farrington-intro.Rmd | 652 +++++++++---------- vignettes/ebrahim-gof-toolbox.Rmd | 47 + 43 files changed, 2856 insertions(+), 2233 deletions(-)
Title: Multi-Context Colocalization Analysis for QTL and GWAS Studies
Description: A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects,
based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero
effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS)
and quantitative trait loci (QTL) studies.
The ColocBoost model is described in Cao et. al. (2025) <doi:10.1101/2025.04.17.25326042>.
Author: Xuewei Cao [cre, aut, cph],
Haochen Sun [aut, cph],
Ru Feng [aut, cph],
Daniel Nachun [aut, cph],
Kushal Dey [aut, cph],
Gao Wang [aut, cph]
Maintainer: Xuewei Cao <xc2270@cumc.columbia.edu>
Diff between colocboost versions 1.0.9 dated 2026-06-08 and 1.0.10 dated 2026-09-09
colocboost-1.0.10/colocboost/DESCRIPTION | 8 colocboost-1.0.10/colocboost/MD5 | 77 - colocboost-1.0.10/colocboost/R/colocboost_assemble_cos.R | 31 colocboost-1.0.10/colocboost/R/colocboost_check_update_jk.R | 162 +- colocboost-1.0.10/colocboost/R/colocboost_init.R | 2 colocboost-1.0.10/colocboost/R/colocboost_output.R | 4 colocboost-1.0.10/colocboost/R/colocboost_plot.R | 5 colocboost-1.0.10/colocboost/R/colocboost_update.R | 52 colocboost-1.0.10/colocboost/R/colocboost_utils.R | 112 + colocboost-1.0.10/colocboost/R/colocboost_workhorse.R | 1 colocboost-1.0.10/colocboost/build/vignette.rds |binary colocboost-1.0.10/colocboost/inst/WORDLIST | 20 colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.R |only colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.Rmd |only colocboost-1.0.10/colocboost/inst/doc/Advanced_Colocalization_Scenarios.html |only colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.R | 2 colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.Rmd | 4 colocboost-1.0.10/colocboost/inst/doc/ColocBoost_Update.html | 2 colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.R |only colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.Rmd |only colocboost-1.0.10/colocboost/inst/doc/Conceptual_Multi_Trait_Colocalization.html |only colocboost-1.0.10/colocboost/inst/doc/Individual_Level_Colocalization.html | 10 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.R | 6 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.Rmd | 44 colocboost-1.0.10/colocboost/inst/doc/Interpret_ColocBoost_Output.html | 67 - colocboost-1.0.10/colocboost/inst/doc/Partial_Overlap_Variants.Rmd | 7 colocboost-1.0.10/colocboost/inst/doc/Partial_Overlap_Variants.html | 6 colocboost-1.0.10/colocboost/inst/doc/announcements.Rmd | 5 colocboost-1.0.10/colocboost/inst/doc/announcements.html | 13 colocboost-1.0.10/colocboost/tests/testthat/test_Xref.R | 54 colocboost-1.0.10/colocboost/tests/testthat/test_large_outcome_inference.R |only colocboost-1.0.10/colocboost/tests/testthat/test_optimization_phase1.R | 631 ++++++++++ colocboost-1.0.10/colocboost/tests/testthat/test_utils.R | 10 colocboost-1.0.10/colocboost/vignettes/Advanced_Colocalization_Scenarios.Rmd |only colocboost-1.0.10/colocboost/vignettes/ColocBoost_Update.Rmd | 4 colocboost-1.0.10/colocboost/vignettes/Conceptual_Multi_Trait_Colocalization.Rmd |only colocboost-1.0.10/colocboost/vignettes/Interpret_ColocBoost_Output.Rmd | 44 colocboost-1.0.10/colocboost/vignettes/Partial_Overlap_Variants.Rmd | 7 colocboost-1.0.10/colocboost/vignettes/announcements.Rmd | 5 colocboost-1.0.10/colocboost/vignettes/figures |only colocboost-1.0.9/colocboost/man/figures/ColocBoost_update.gif |only colocboost-1.0.9/colocboost/man/figures/missing_representation.png |only 42 files changed, 1195 insertions(+), 200 deletions(-)
Title: Resolving Plant Taxon Names Using the Australian Plant Census
Description: The process of resolving and updating taxon names is necessary when
working with biodiversity data. 'APCalign' uses the Australian Plant Census
(APC) and the Australian Plant Name Index (APNI) to align and update plant
taxon names to current, accepted standards. 'APCalign' also supplies
information about the establishment status (i.e. native or introduced) of
plant taxa across different states/territories.
Author: Elizabeth Wenk [aut, cre, cph] ,
Daniel Falster [aut, ctb] ,
Will Cornwell [aut, ctb] ,
Fonti Kar [aut, ctb] ,
Carl Boettiger [ctb]
Maintainer: Elizabeth Wenk <e.wenk@unsw.edu.au>
Diff between APCalign versions 2.0.0 dated 2026-03-27 and 2.0.1 dated 2026-09-09
DESCRIPTION | 8 MD5 | 57 NEWS.md | 11 R/APCalign-package.R | 3 R/fuzzy_match.R | 24 R/load_taxonomic_resources.R | 4 R/match_taxa.R | 2698 +++------- R/native_anywhere_in_australia.R | 35 R/standardise_names.R | 145 R/strip_names.R | 40 R/synonyms_for_accepted_names.R | 34 R/utils.R |only README.md | 55 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST |only inst/doc/APCalign.Rmd | 6 inst/doc/APCalign.html | 6 man/default_version.Rd | 2 man/get_versions.Rd | 2 man/standardise_names.Rd | 9 tests/testthat/_snaps |only tests/testthat/benchmarks/standardise_names.csv | 8 tests/testthat/benchmarks/test_matches_alignments_updates.csv | 461 - tests/testthat/test-connection.R | 12 tests/testthat/test-functions-fuzzy_match.R |only tests/testthat/test-functions-standardise_names.R | 56 tests/testthat/test-match_branches.R |only tests/testthat/test-operation_outputs.R | 4 tests/testthat/test-state_diversity.R | 27 vignettes/APCalign.Rmd | 6 32 files changed, 1472 insertions(+), 2243 deletions(-)
Title: Generates Aoristic Probability Distributions
Description: It can sometimes be difficult to ascertain when some events (such as property crime)
occur because the victim is not present when the crime happens. As a result, police databases often
record a 'start' (or 'from') date and time, and an 'end' (or 'to') date and time. The time span between
these date/times can be minutes, hours, or sometimes days, hence the term 'Aoristic'.
Aoristic is one of the past tenses in Greek and represents an uncertain occurrence in time.
For events with a location described by either a latitude/longitude or X/Y coordinate pair,
and a start and end date/time, this package generates an aoristic data frame with aoristic weighted
probability values for each hour of the week, for each observation. The coordinates are not
necessary for the program to calculate aoristic weights; however, they are part of this package
because a spatial component has been integral to aoristic analysis from the start. Dummy
coordinates can be introduced if the user only has temporal data [...truncated...]
Author: Jerry Ratcliffe [aut, cre]
Maintainer: Jerry Ratcliffe <jerryr@sas.upenn.edu>
Diff between aoristic versions 1.1.1 dated 2022-10-20 and 2.0.0 dated 2026-09-09
DESCRIPTION | 24 ++- MD5 | 44 +++-- NAMESPACE | 1 NEWS.md |only R/aoristic.datacheck.R | 193 +++++++++----------------- R/aoristic.df.R | 341 ++++++++++++---------------------------------- R/aoristic.graph.R | 2 R/aoristic.plot.R | 4 R/aoristic.summary.R | 4 R/validation.R |only README.md | 272 ++++++++++++------------------------ man/CouncilDistrict.Rd | 24 +-- man/NYburg.Rd | 56 +++---- man/aoristic.all.graph.Rd | 52 +++---- man/aoristic.datacheck.Rd | 37 ++-- man/aoristic.density.Rd | 24 +-- man/aoristic.df.Rd | 36 ++-- man/aoristic.grid.Rd | 24 +-- man/aoristic.plot.Rd | 60 ++++---- man/aoristic.shp.Rd | 24 +-- man/aoristic.spdf.Rd | 24 +-- man/arlington.Rd | 24 +-- tests |only 23 files changed, 492 insertions(+), 778 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control
of Research Outputs.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [aut, ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.7 dated 2026-02-02 and 1.0.0 dated 2026-09-09
DESCRIPTION | 38 +-- MD5 | 54 +++-- NAMESPACE | 10 NEWS.md | 10 R/acro_init.R | 11 - R/acro_tables.R | 339 +++++++++++++++++++++++++++++++-- R/output_commands.R | 26 ++ R/utils.R |only R/zzz.R |only inst/AI_POLICY.md |only inst/WORDLIST | 7 inst/doc/welcome.html | 2 inst/notebooks |only man/acro_crosstab.Rd | 28 ++ man/acro_disable_rounding.Rd |only man/acro_enable_rounding.Rd |only man/acro_hist.Rd | 4 man/acro_init.Rd | 9 man/acro_pie.Rd |only man/acro_summarise.Rd |only man/acro_table.Rd | 14 + man/create_factors.Rd |only man/is_excluded.Rd |only man/is_invalid.Rd |only man/to_pandas_categorical.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-acro_crosstab.R | 54 +++++ tests/testthat/test-acro_hist.R | 80 +++++++ tests/testthat/test-acro_pie.R |only tests/testthat/test-acro_pivot_table.R | 14 + tests/testthat/test-acro_rounding.R |only tests/testthat/test-acro_summarise.R |only tests/testthat/test-acro_table.R | 219 ++++++++++++++++++++- tests/testthat/test-install_acro.R | 12 - 34 files changed, 854 insertions(+), 77 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural Bayes estimators, which are neural networks that map data to a point summary of the posterior distribution (Sainsbury-Dale et al., 2024, <doi:10.1080/00031305.2023.2249522>). These estimators are likelihood-free and amortised, in the sense that, once the neural networks are trained on simulated data, inference from observed data can be made in a fraction of the time required by conventional approaches. The package also supports amortised Bayesian or frequentist inference using neural networks that approximate the posterior or likelihood-to-evidence ratio (Zammit-Mangion et al., 2025, Sec. 3.2, 5.2, <doi:10.48550/arXiv.2404.12484>). The package accommodates any model for which simulation is feasible by allowing users to define models implicitly through simulated data.
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.2.1 dated 2026-04-28 and 0.2.2 dated 2026-09-09
DESCRIPTION | 6 MD5 | 32 +++-- NAMESPACE | 7 + R/core.R | 252 +++++++++++++++++++++++++++++++---------- R/estimators.R |only README.md | 52 +++++--- inst/doc/NeuralEstimators.html | 6 man/PointEstimator.Rd |only man/PosteriorEstimator.Rd |only man/RatioEstimator.Rd |only man/assess.Rd | 10 + man/cpu_device.Rd |only man/estimate.Rd | 8 - man/gpu_device.Rd |only man/infer.Rd |only man/logratio.Rd | 2 man/reactant_device.Rd |only man/sampleposterior.Rd | 4 man/savestate.Rd | 2 man/train.Rd | 40 +++++- tests/testthat/test-core.R | 123 ++++++++++++++++++-- 21 files changed, 419 insertions(+), 125 deletions(-)
More information about NeuralEstimators at CRAN
Permanent link
Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Arthur Garcia [aut],
Cristiane Gea [aut],
Diego Carvalho [ctb],
Diogo Santos [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Fernando Alexandrino [aut],
Luciano Mello [aut],
Rebecca Salles [a [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 2.0.707 dated 2026-05-22 and 2.0.717 dated 2026-09-09
DESCRIPTION | 19 ++- MD5 | 30 +++--- NAMESPACE | 113 +++++++++++++---------- R/ts_fil_fft.R | 159 +++++++++++++++++++++++++++----- R/ts_fil_gabor.R |only R/ts_fil_hp.R | 18 +++ R/ts_fil_remd.R | 141 +++++++++++++++++++++++------ R/ts_fil_spline.R | 47 ++++++++- R/ts_fil_winsor.R | 7 + R/tspredbench.R | 2 README.md | 246 +++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/m1.Rd | 2 man/ts_fil_fft.Rd | 25 ++++- man/ts_fil_gabor.Rd |only man/ts_fil_remd.Rd | 18 +++ man/ts_fil_spline.Rd | 12 +- 17 files changed, 578 insertions(+), 261 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.16 dated 2026-07-24 and 2.0.17 dated 2026-09-09
DESCRIPTION | 12 +- MD5 | 58 ++++++++++---- NAMESPACE | 13 +++ NEWS.md | 38 +++++++++ R/RcppExports.R | 48 +++++++++++ R/llik.R | 12 +- R/llikNew.R |only R/ptr.R |only inst/include |only man/dot-rxode2llPtr.Rd |only man/llikBetaProportion.Rd |only man/llikDblExp.Rd |only man/llikFrechet.Rd |only man/llikGumbel.Rd |only man/llikInvChisq.Rd |only man/llikInvGamma.Rd |only man/llikLnorm.Rd |only man/llikLogis.Rd |only man/llikNbinom.Rd | 2 man/llikNbinomMu.Rd | 2 man/llikPareto.Rd |only man/llikParetoType2.Rd |only man/llikRayleigh.Rd |only man/llikScaledInvChisq.Rd |only src/RcppExports.cpp | 155 ++++++++++++++++++++++++++++++++++++++ src/init.c | 63 +++++++++++++++ src/llik.h | 36 ++++++++ src/llik2.h | 12 ++ src/llikBetaProportion.cpp |only src/llikDblExp.cpp |only src/llikFrechet.cpp |only src/llikGumbel.cpp |only src/llikInvChisq.cpp |only src/llikInvGamma.cpp |only src/llikLnorm.cpp |only src/llikLogis.cpp |only src/llikNbinom.cpp | 51 ++++++++++-- src/llikNbinom2.cpp | 31 ++++++- src/llikPareto.cpp |only src/llikParetoType2.cpp |only src/llikRayleigh.cpp |only src/llikScaledInvChisq.cpp |only src/ptr.c |only tests/testthat/test-llik.R | 106 ++++++++++++++++++++++++- tests/testthat/test-newFamilies.R |only 45 files changed, 590 insertions(+), 49 deletions(-)
Title: Principal Components Analysis using NIPALS or Weighted EMPCA,
with Gram-Schmidt Orthogonalization
Description: Principal Components Analysis of a matrix using Non-linear
Iterative Partial Least Squares or weighted Expectation Maximization
PCA with Gram-Schmidt orthogonalization of the scores and loadings.
Optimized for speed. See Andrecut (2009) <doi:10.1089/cmb.2008.0221>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between nipals versions 1.0 dated 2024-12-02 and 1.2 dated 2026-09-09
DESCRIPTION | 11 - MD5 | 30 +-- NAMESPACE | 10 - NEWS.md | 9 + R/empca.R | 256 ++++++++++++++++-------------- R/nipals.R | 316 +++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/empca_notes.html | 8 inst/doc/nipals_algorithm.html | 26 +-- inst/doc/nipals_comparisons.html | 5 inst/doc/nipals_optimization.html | 5 man/empca.Rd | 14 - man/nipals.Rd | 13 - tests/testthat/test-empca.R | 163 ++++++++++--------- tests/testthat/test-nipals.R | 171 +++++++++++--------- tests/testthat/test-uscrime.R | 49 +++-- 16 files changed, 596 insertions(+), 490 deletions(-)
Title: 'NetCDF' Geometry and Time Series
Description: Tools to create time series and geometry 'NetCDF' files.
Author: David Blodgett [aut, cre],
Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between ncdfgeom versions 1.2.2 dated 2026-04-22 and 1.2.3 dated 2026-09-09
DESCRIPTION | 17 +-- MD5 | 44 ++++----- NEWS.md | 9 + R/calculate_area_intersection_weights.R | 6 - R/read_timeseries_dsg.R | 10 +- R/write_geometry.R | 12 +- R/write_point_dsg.R | 3 R/write_timeseries_dsg.R | 8 - build/vignette.rds |binary inst/CITATION | 8 + inst/WORDLIST | 1 inst/doc/geometry.html | 93 -------------------- inst/doc/ncdfgeom.Rmd | 15 +-- inst/doc/ncdfgeom.html | 110 +++--------------------- inst/doc/polygon_intersection.R | 10 +- inst/doc/polygon_intersection.Rmd | 10 +- inst/doc/polygon_intersection.html | 19 +--- inst/doc/timeseries.html | 58 +----------- man/calculate_area_intersection_weights.Rd | 2 tests/testthat/test_geom_examples.R | 19 +--- tests/testthat/test_read-write_timeseries_dsg.R | 9 + vignettes/ncdfgeom.Rmd | 15 +-- vignettes/polygon_intersection.Rmd | 10 +- 23 files changed, 145 insertions(+), 343 deletions(-)
Title: Automatic Plotting and Theming of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 1.2.2 dated 2026-08-29 and 1.2.3 dated 2026-09-09
autograph-1.2.2/autograph/R/graph_costs.R |only autograph-1.2.3/autograph/DESCRIPTION | 13 autograph-1.2.3/autograph/MD5 | 42 - autograph-1.2.3/autograph/NAMESPACE | 8 autograph-1.2.3/autograph/NEWS.md | 26 autograph-1.2.3/autograph/R/layout_aesthetics.R |only autograph-1.2.3/autograph/R/scale_mdate.R |only autograph-1.2.3/autograph/R/theme_aesthetics.R |only autograph-1.2.3/autograph/R/theme_colorblind.R | 123 --- autograph-1.2.3/autograph/R/zzz.R | 10 autograph-1.2.3/autograph/inst/tutorials/autograph1/visualisation.Rmd | 111 +- autograph-1.2.3/autograph/inst/tutorials/autograph1/visualisation.html | 392 ++++++---- autograph-1.2.3/autograph/man/check_colors.Rd |only autograph-1.2.3/autograph/man/check_layout.Rd | 236 ++++-- autograph-1.2.3/autograph/man/list_fonts.Rd | 1 autograph-1.2.3/autograph/man/mdate_scales.Rd |only autograph-1.2.3/autograph/man/theme_colorblind.Rd | 69 - autograph-1.2.3/autograph/man/theme_medium.Rd | 1 autograph-1.2.3/autograph/man/theme_set.Rd | 1 autograph-1.2.3/autograph/tests/testthat/Rplots.pdf |binary autograph-1.2.3/autograph/tests/testthat/helper-manynet.R | 32 autograph-1.2.3/autograph/tests/testthat/test-functional_coverage.R | 8 autograph-1.2.3/autograph/tests/testthat/test-functional_layouts.R | 55 + autograph-1.2.3/autograph/tests/testthat/test-grapht.R | 13 autograph-1.2.3/autograph/tests/testthat/test-layout_aesthetics.R |only autograph-1.2.3/autograph/tests/testthat/test-scale_mdate.R |only 26 files changed, 698 insertions(+), 443 deletions(-)