Title: Tidy Tools for Chinese, Japanese and Korean Text
Description: A tidy toolkit for text that is written in Chinese, Japanese or
Korean. Most text tooling in R assumes that words are separated by
whitespace, which CJK writing does not use, so ordinary summaries of a text
column either treat a sentence as one undifferentiated blob or split it into
isolated characters. Word segmentation is a pluggable engine, with
dictionary-based segmentation for Chinese and Japanese supplied through
'ICU' and further engines registrable by the caller, because where a word
ends is a fact about a language and not about Unicode. 'tidycjk'
classifies characters by Unicode block, reports which script and which
language a text is written in, measures how much of a text is CJK, and
turns those measurements into tibbles that slot straight into a
'tidyverse' workflow. It also measures display width in terminal columns,
pads, truncates and wraps to a width rather than to a character
count, and normalises fullwidth and halfwidth forms surgically -- including
composing halfwidt [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidycjk versions 0.1.0 dated 2026-09-09 and 0.2.0 dated 2026-10-11
DESCRIPTION | 46 ++- MD5 | 107 ++++++-- NAMESPACE | 14 + NEWS.md | 400 ++++++++++++++++++++++++++++++++ R/collate.R |only R/detect.R | 34 ++ R/nlp.R |only R/normalize.R | 189 ++++++++++++++- R/ranges.R | 322 ++++++++++++++++++++++---- R/segment.R | 289 ++++++++++++++++++++--- R/summary.R | 26 +- R/tidycjk-package.R | 95 +++++-- R/transliterate.R |only R/width.R | 238 ++++++++++++++++++- README.md | 316 +++++--------------------- build |only inst |only man/cjk_blocks.Rd | 60 ++-- man/cjk_char_counts.Rd | 8 man/cjk_detect_language.Rd | 8 man/cjk_jamo.Rd |only man/cjk_ngrams.Rd |only man/cjk_normalize.Rd |only man/cjk_pad.Rd | 5 man/cjk_ratio.Rd | 7 man/cjk_romanize.Rd |only man/cjk_script.Rd | 5 man/cjk_segment.Rd | 25 +- man/cjk_segmenters.Rd | 75 +++++- man/cjk_sentences.Rd |only man/cjk_simplify.Rd |only man/cjk_sort.Rd |only man/cjk_strip_punct.Rd |only man/cjk_summary.Rd | 6 man/cjk_tokens.Rd | 17 + man/cjk_truncate.Rd | 13 - man/cjk_width.Rd | 5 man/cjk_wrap.Rd |only man/figures |only man/has_cjk.Rd | 5 man/tidycjk-package.Rd | 111 +++++---- man/to_halfwidth.Rd | 9 man/to_hiragana.Rd |only tests/testthat/test-collate.R |only tests/testthat/test-detect.R | 64 +++++ tests/testthat/test-differential.R |only tests/testthat/test-invariants.R |only tests/testthat/test-nlp.R |only tests/testthat/test-normalize.R | 198 ++++++++++++++++ tests/testthat/test-ranges.R | 437 ++++++++++++++++++++++++++++++++++-- tests/testthat/test-segment.R | 313 +++++++++++++++++++++++++ tests/testthat/test-transliterate.R |only tests/testthat/test-width.R | 79 ++++++ tests/testthat/test-wrap.R |only vignettes |only 55 files changed, 2962 insertions(+), 564 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc. From this
version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all,
see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb],
Patrick [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 2.2-3 dated 2026-07-19 and 2.2-4 dated 2026-10-11
DESCRIPTION | 6 - MD5 | 22 ++--- build/vignette.rds |binary inst/NEWS.Rd | 5 + inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/retiring_rgdal_geos_1.html | 2 inst/doc/sp_gallery.html | 43 +++++------ src/sp_xports.c | 1 tests/Rplots.pdf |binary tests/pass1.R | 20 ++--- tests/pass1.Rout.save | 138 +++--------------------------------- 12 files changed, 66 insertions(+), 171 deletions(-)
Title: A Shiny Dashboard Template Modular System with Chat Bot Support
Description: A template dashboard system with AI agent integrated.
Comes with default themes that can be customized.
Developers can upload modified templates on 'Github', and users can
easily download templates with 'RStudio' project wizard.
The key features of the default template include light and dark theme
switcher, resizing graphs, synchronizing inputs across sessions,
new notification system, fancy progress bars, and card-like flip
panels with back sides, as well as various of 'HTML' tool widgets.
Author: Zhengjia Wang [cph, aut, cre] ,
ColorlibHQ [cph] ,
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Ivan Sagalaev [ctb, cph] ,
Rene Haas [ctb, cph] ,
Zeno Rocha [ctb, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between shidashi versions 0.2.0 dated 2026-04-10 and 0.3.0 dated 2026-10-11
shidashi-0.2.0/shidashi/inst/builtin-templates/AdminLTE3-bare/ui.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/AdminLTE3-bare/www/bootstrap/js/bootstrap.bundle.min.js.map |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/_rs_job.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/global.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/ui.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/css/shidashi.css.map |only shidashi-0.3.0/shidashi/DESCRIPTION | 18 shidashi-0.3.0/shidashi/MD5 | 122 shidashi-0.3.0/shidashi/NAMESPACE | 12 shidashi-0.3.0/shidashi/NEWS.md | 117 shidashi-0.3.0/shidashi/R/aaa.R | 34 shidashi-0.3.0/shidashi/R/ask-user.R |only shidashi-0.3.0/shidashi/R/barebone.R | 28 shidashi-0.3.0/shidashi/R/chat-helpers.R | 115 shidashi-0.3.0/shidashi/R/chatbot.R | 29 shidashi-0.3.0/shidashi/R/colorpicker.R |only shidashi-0.3.0/shidashi/R/ellmer-helpers.R | 2 shidashi-0.3.0/shidashi/R/globals.R | 124 shidashi-0.3.0/shidashi/R/launcher.R |only shidashi-0.3.0/shidashi/R/mcp-catalog.R |only shidashi-0.3.0/shidashi/R/mcp-click.R |only shidashi-0.3.0/shidashi/R/mcp-handler.R | 1445 ++-------- shidashi-0.3.0/shidashi/R/mcp-http.R |only shidashi-0.3.0/shidashi/R/mcp-log.R |only shidashi-0.3.0/shidashi/R/mcp-module.R |only shidashi-0.3.0/shidashi/R/mcp-switch-module.R |only shidashi-0.3.0/shidashi/R/mcp-wrapper.R | 1096 ++++++- shidashi-0.3.0/shidashi/R/modules.R | 29 shidashi-0.3.0/shidashi/R/object-list.R |only shidashi-0.3.0/shidashi/R/render.R | 20 shidashi-0.3.0/shidashi/R/settings.R | 2 shidashi-0.3.0/shidashi/R/skill-parse.R | 115 shidashi-0.3.0/shidashi/R/skill-runner.R | 4 shidashi-0.3.0/shidashi/R/skill-wrapper.R | 516 ++- shidashi-0.3.0/shidashi/R/standalone-viewer.R | 6 shidashi-0.3.0/shidashi/R/zzz.R | 14 shidashi-0.3.0/shidashi/inst/builtin-templates/AdminLTE3-bare/www/shidashi/img/header-bg.png |binary shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/agents/skills/greet/SKILL.md | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/agents/tool-schema.yaml | 24 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/aiagent/agents.yaml | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/demo/R/demo-ui.R | 110 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/demo/agents.yaml | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/mcpsetup/R/mcpsetup-ui.R | 166 + shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/css/shidashi.css | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/img/header-bg.png |binary shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/js/index.js | 16 shidashi-0.3.0/shidashi/inst/mcp-proxy/README.md |only shidashi-0.3.0/shidashi/inst/mcp-proxy/shidashi-proxy.mjs | 1341 ++++++++- shidashi-0.3.0/shidashi/inst/rave.yaml |only shidashi-0.3.0/shidashi/man/colormapSelectInput.Rd |only shidashi-0.3.0/shidashi/man/mcp_call_active.Rd |only shidashi-0.3.0/shidashi/man/mcp_click.Rd |only shidashi-0.3.0/shidashi/man/mcp_wrapper.Rd | 4 shidashi-0.3.0/shidashi/man/module_info.Rd | 19 shidashi-0.3.0/shidashi/man/objectListInput.Rd |only shidashi-0.3.0/shidashi/man/register_input_state.Rd |only shidashi-0.3.0/shidashi/man/register_io.Rd | 39 shidashi-0.3.0/shidashi/man/render.Rd | 5 shidashi-0.3.0/shidashi/man/renderPlot2.Rd |only shidashi-0.3.0/shidashi/man/render_hidden_output.Rd |only shidashi-0.3.0/shidashi/man/save_launcher.Rd |only shidashi-0.3.0/shidashi/man/skill_wrapper.Rd | 46 shidashi-0.3.0/shidashi/man/template_settings.Rd | 5 shidashi-0.3.0/shidashi/tests/testthat/helper-mcp.R |only shidashi-0.3.0/shidashi/tests/testthat/setup-cache.R |only shidashi-0.3.0/shidashi/tests/testthat/test-colorpicker.R |only shidashi-0.3.0/shidashi/tests/testthat/test-fastmap.R |only shidashi-0.3.0/shidashi/tests/testthat/test-input-hints.R |only shidashi-0.3.0/shidashi/tests/testthat/test-launcher.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-catalog.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-http.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-log.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-module.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-plugin.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-server-info.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-switch-module.R |only shidashi-0.3.0/shidashi/tests/testthat/test-object-list.R |only shidashi-0.3.0/shidashi/tests/testthat/test-query-ui.R |only shidashi-0.3.0/shidashi/tests/testthat/test-register-input.R |only shidashi-0.3.0/shidashi/tests/testthat/test-render.R |only shidashi-0.3.0/shidashi/tests/testthat/test-safe-observe.R |only shidashi-0.3.0/shidashi/tests/testthat/test-skill-parse.R | 64 shidashi-0.3.0/shidashi/tests/testthat/test-skill-runner.R | 15 shidashi-0.3.0/shidashi/tests/testthat/test-skill-wrapper.R | 231 + 84 files changed, 3883 insertions(+), 2058 deletions(-)
Title: Restricted Bridge Estimation
Description: Implements bridge regression with linear coefficient restrictions
using the local quadratic approximation described by Yuzbasi, Arashi and
Akdeniz (2021) <doi:10.1007/s00500-021-05763-9>. Provides coefficient paths,
cross-validation, prediction and coefficient extraction for restricted and
unrestricted linear models.
Author: Bahadir Yuzbasi [aut, cre],
Mohammad Arashi [aut],
Fikri Akdeniz [aut],
Jerome Friedman [ctb] ,
Trevor Hastie [ctb] ,
Robert Tibshirani [ctb]
Maintainer: Bahadir Yuzbasi <b.yzb@hotmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2020-02-29
Diff between rbridge versions 1.0.2 dated 2020-02-29 and 1.0.3 dated 2026-10-11
DESCRIPTION | 44 + MD5 | 90 ++- NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 4 R/bridge.R | 126 +++-- R/cv.bridge.R | 183 +++++--- R/cv.rbridge.R | 263 +++++++---- R/methods.R | 879 +++++++++++++++++++++++---------------- R/rbridge.R | 196 +++++--- R/rbridge_info.R |only R/utilities.R | 33 + README.md |only build |only inst |only man/bridge.Rd | 131 ++++- man/coef.bridge.Rd | 48 +- man/coef.cv.bridge.Rd | 55 +- man/coef.cv.rbridge.Rd | 68 ++- man/coef.rbridge.Rd | 64 +- man/cv.bridge.Rd | 179 +++++-- man/cv.rbridge.Rd | 261 +++++++---- man/figures |only man/plot.cv.bridge.Rd | 49 +- man/plot.cv.rbridge.Rd | 53 ++ man/predict.bridge.Rd | 80 ++- man/predict.cv.bridge.Rd | 88 ++- man/predict.cv.rbridge.Rd | 104 +++- man/predict.rbridge.Rd | 93 ++-- man/rbridge.Rd | 201 +++++--- man/rbridge_info.Rd |only src/Main_functions.cpp | 427 +++++++----------- src/Makevars | 14 src/Makevars.win | 18 src/RcppExports.cpp | 16 tests/testthat/fixtures |only tests/testthat/helper-fixtures.R |only tests/testthat/test-engine.R |only tests/testthat/test-methods.R |only tests/testthat/test.R | 68 +-- vignettes |only 41 files changed, 2410 insertions(+), 1426 deletions(-)
Title: Bayesian Analysis of Finite Mixtures of Plackett-Luce Models for
Partial Rankings/Orderings
Description: Fit finite mixtures of Plackett-Luce models for partial top rankings/orderings within the Bayesian framework. It provides MAP point estimates via EM algorithm and posterior MCMC simulations via Gibbs Sampling. It also fits MLE as a special case of the noninformative Bayesian analysis with vague priors. In addition to inferential techniques, the package assists other fundamental phases of a model-based analysis for partial rankings/orderings, by including functions for data manipulation, simulation, descriptive summary, model selection and goodness-of-fit evaluation. Main references on the methods are Mollica and Tardella (2017) <doi:10.1007/s11336-016-9530-0> and Mollica and Tardella (2014) <doi:10.1002/sim.6224>.
Author: Cristina Mollica [aut, cre],
Luca Tardella [aut]
Maintainer: Cristina Mollica <cristina.mollica@uniroma1.it>
This is a re-admission after prior archival of version 2.2.0 dated 2025-06-30
Diff between PLMIX versions 2.2.0 dated 2025-06-30 and 2.2.1 dated 2026-10-11
PLMIX-2.2.0/PLMIX/src/dlb_sort.cpp |only PLMIX-2.2.1/PLMIX/DESCRIPTION | 24 +-- PLMIX-2.2.1/PLMIX/MD5 | 18 +- PLMIX-2.2.1/PLMIX/NAMESPACE | 86 +++++++----- PLMIX-2.2.1/PLMIX/NEWS | 3 PLMIX-2.2.1/PLMIX/R/PLMIXfunctions.R | 201 +++++++++++++++-------------- PLMIX-2.2.1/PLMIX/R/gibbsPLMIX_with_norm.R | 142 -------------------- PLMIX-2.2.1/PLMIX/man/plot.gsPLMIX.Rd | 8 - PLMIX-2.2.1/PLMIX/man/plot.mpPLMIX.Rd | 6 PLMIX-2.2.1/PLMIX/src/dbl_sort.cpp |only PLMIX-2.2.1/PLMIX/src/loglikPLMIX.cpp | 15 +- 11 files changed, 198 insertions(+), 305 deletions(-)
Title: Motif-Based Spectral Clustering of Weighted Directed Networks
Description: Tools for spectral clustering of weighted directed networks using motif
adjacency matrices. Methods perform well on large and sparse networks, and
random sampling methods for generating weighted directed networks are also
provided. Based on methodology detailed in Underwood, Elliott and Cucuringu
(2020) <doi:10.48550/arXiv.2004.01293>.
Author: William George Underwood [aut, cre]
Maintainer: William George Underwood <william.underwood@warwick.ac.uk>
Diff between motifcluster versions 0.2.3 dated 2022-11-18 and 0.2.4 dated 2026-10-11
DESCRIPTION | 14 ++++++------- MD5 | 32 +++++++++++++++---------------- NEWS.md | 4 +++ R/clustering.R | 4 +-- R/indicators.R | 22 ++++++++++----------- R/motifadjacency.R | 36 +++++++++++++++++------------------ R/sampling.R | 6 ++--- R/spectral.R | 8 +++---- R/utils.R | 12 +++++------ README.md | 4 +-- build/vignette.rds |binary inst/doc/motifcluster_vignette.R | 16 +++++++-------- inst/doc/motifcluster_vignette.Rmd | 5 +--- inst/doc/motifcluster_vignette.pdf |binary tests/testthat/test_motifadjacency.R | 12 +++++------ tests/testthat/test_spectral.R | 28 +++++++++++++-------------- vignettes/motifcluster_vignette.Rmd | 5 +--- 17 files changed, 105 insertions(+), 103 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal,
conservative, or deep-first search). The objective of this package is to
make it as simple as possible to identify global objects for the purpose
of exporting them in parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph] ,
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.19.1 dated 2026-03-13 and 0.20.0 dated 2026-10-11
.Rinstignore |only DESCRIPTION | 19 MD5 | 91 ++-- NAMESPACE | 17 NEWS.md | 37 + R/Globals-class.R | 54 ++ R/call_find_globals_with_dotdotdot.R | 2 R/cleanup.R | 5 R/findGlobals.R | 56 -- R/findGlobalsDFS.R | 36 - R/globalsByName.R | 26 - R/globalsOf.R | 27 - R/packagesOf.R | 27 + R/utils.R | 6 inst/testme/_epilogue/002.undo-state.R | 4 inst/testme/_epilogue/995.detritus-connections.R | 19 inst/testme/_prologue/090.context.R | 9 inst/testme/deploy.R | 2 inst/testme/run.R | 516 ++++++++++++----------- inst/testme/test-Globals.R | 114 +++++ inst/testme/test-codetools-bug16.R | 33 + inst/testme/test-debug-trace-paths.R |only inst/testme/test-dotdotdot.R | 13 inst/testme/test-findGlobals,dfs.R | 16 inst/testme/test-findGlobals.R | 14 inst/testme/test-globalsByName.R | 33 + inst/testme/test-globalsOf.R | 51 ++ inst/testme/test-packagesOf.R |only man/Globals.Rd | 4 man/cleanup.Globals.Rd | 9 man/globalsOf.Rd | 7 man/packagesOf.Globals.Rd | 6 man/print.Globals.Rd |only tests/test-Globals.R | 1 tests/test-cleanup.R | 1 tests/test-codetools-bug16.R | 1 tests/test-conservative.R | 1 tests/test-debug-trace-paths.R |only tests/test-dotdotdot.R | 1 tests/test-findGlobals,dfs.R | 1 tests/test-findGlobals.R | 1 tests/test-formulas.R | 1 tests/test-globalsByName.R | 1 tests/test-globalsOf,locals.R | 1 tests/test-globalsOf.R | 1 tests/test-liberal.R | 1 tests/test-packagesOf.R |only tests/test-utils.R | 1 tests/test-walkAST.R | 1 tests/test-zzz.R | 1 50 files changed, 844 insertions(+), 424 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.9.1 dated 2025-10-08 and 0.9.2 dated 2026-10-11
DESCRIPTION | 8 MD5 | 176 NEWS.md | 432 - R/accessor-functions.R | 222 R/add_inactive_replicates.R | 414 - R/as_bootstrap_design.R | 650 +- R/as_data_frame_with_weights.R | 262 R/as_jackknife_design.R | 1136 +-- R/calibrate_to_estimate.R | 790 +- R/calibrate_to_sample.R | 2 R/fays_generalized_replication.R | 17 R/generalized_bootstrap.R | 1626 ++--- R/libraries_data.R | 188 R/lou_vax_data.R | 216 R/make_bootstrap_weights.R | 1451 ++-- R/quadratic_forms.R | 3100 +++++----- R/redistribute_weights.R | 542 - R/rescale_replicates.R | 420 - R/shuffle_replicates.R | 170 R/stack_replicate_designs.R | 496 - R/subsample_replicates.R | 256 R/successive-difference-replication.R | 1100 +-- R/summarize_rep_weights.R | 658 +- R/svrep-package-options.R | 136 R/svrep-package.R | 78 R/svyby_repwts.R | 312 - R/variance-estimators.R | 466 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 inst/doc/bootstrap-replicates.Rmd | 1434 ++-- inst/doc/bootstrap-replicates.html | 23 inst/doc/sample-based-calibration.html | 2 inst/doc/two-phase-sampling.Rmd | 1928 +++--- inst/doc/two-phase-sampling.html | 21 man/add_inactive_replicates.Rd | 228 man/as_bootstrap_design.Rd | 368 - man/as_data_frame_with_weights.Rd | 130 man/as_fays_gen_rep_design.Rd | 420 - man/as_gen_boot_design.Rd | 660 +- man/as_random_group_jackknife_design.Rd | 462 - man/as_sdr_design.Rd | 346 - man/assign_hadamard_rows.Rd | 164 man/calibrate_to_estimate.Rd | 348 - man/calibrate_to_sample.Rd | 354 - man/draw_antal_tille_resample.Rd | 58 man/draw_doubled_half_sample.Rd | 52 man/estimate_boot_reps_for_target_cv.Rd | 270 man/estimate_boot_sim_cv.Rd | 220 man/get_design_quad_form.Rd | 400 - man/get_nearest_psd_matrix.Rd | 84 man/get_rep_scale_coefs.Rd | 152 man/get_rep_type.Rd | 84 man/ht_matrix_to_joint_probs.Rd | 52 man/is_psd_matrix.Rd | 86 man/libraries.Rd | 198 man/lou_pums_microdata.Rd | 108 man/lou_vax_survey.Rd | 62 man/lou_vax_survey_control_totals.Rd | 76 man/make_deville_tille_matrix.Rd | 124 man/make_doubled_half_bootstrap_weights.Rd | 248 man/make_fays_gen_rep_factors.Rd | 374 - man/make_gen_boot_factors.Rd | 388 - man/make_kernel_var_matrix.Rd | 176 man/make_ppswor_approx_matrix.Rd | 184 man/make_quad_form_matrix.Rd | 422 - man/make_rwyb_bootstrap_weights.Rd | 422 - man/make_sd_matrix.Rd | 78 man/make_sdr_replicate_factors.Rd | 132 man/make_twophase_quad_form.Rd | 618 - man/redistribute_weights.Rd | 136 man/rescale_replicates.Rd | 286 man/shuffle_replicates.Rd | 100 man/stack_replicate_designs.Rd | 140 man/subsample_replicates.Rd | 162 man/summarize_rep_weights.Rd | 194 man/svrep-package-options.Rd | 154 man/svrep-package.Rd | 5 man/svyby_repwts.Rd | 270 man/variance-estimators.Rd | 534 - tests/testthat/test-accessor-functions.R | 86 tests/testthat/test-add_inactive_replicates.R | 294 tests/testthat/test-doubled_half_bootstrap.R | 672 +- tests/testthat/test-fays-generalized-replication.R | 1134 +-- tests/testthat/test-quadratic-forms.R | 1708 ++--- tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 544 - tests/testthat/test-rwyb_bootstrap.R | 796 +- vignettes/bootstrap-replicates.Rmd | 1434 ++-- vignettes/two-phase-sampling.Rmd | 1928 +++--- 89 files changed, 18978 insertions(+), 18899 deletions(-)
Title: Rolling Eigenanalysis
Description: Fast and efficient computation of rolling and expanding
eigenanalysis for time-series data. The 'rolleigen' package decomposes
the covariance matrix of the explanatory variables into eigenvalues
and eigenvectors to perform principal component analysis (Pearson,
1901, <doi:10.1080/14786440109462720>; Hotelling, 1933,
<doi:10.1037/h0071325>) and principal component regression (Massy,
1965, <doi:10.1080/01621459.1965.10480787>) over rolling and expanding
windows. For each window, the eigenvalues and eigenvectors are
computed from the covariance matrix and, optionally, ordered from the
largest to smallest eigenvalue to summarize the directions of greatest
variation in the data. A subset of leading components is then used to
fit a regression that mitigates collinearity in the explanatory
variables. Use cases include dimensionality reduction, factor
extraction, and regression on collinear explanatory variables. The
package supports rolling and expanding windows, weights, a [...truncated...]
Author: Jason Foster [aut, cre]
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between rolleigen versions 1.0.0 dated 2026-06-19 and 1.0.1 dated 2026-10-11
DESCRIPTION | 32 +- MD5 | 28 +- NAMESPACE | 6 NEWS.md | 8 R/rolleigen.R | 238 +++++++++--------- README.md | 176 ++++++------- build/partial.rdb |binary inst/include/rolleigen.h | 9 man/rolleigen-package.Rd | 46 +-- tests/testthat.R | 6 tests/testthat/helper-data.R | 60 ++-- tests/testthat/helper-eigen.R | 236 ++++++++++------- tests/testthat/helper-pcr.R | 552 +++++++++++++++++++++--------------------- tests/testthat/test-eigen.R | 105 +++++-- tests/testthat/test-pcr.R | 108 ++++---- 15 files changed, 843 insertions(+), 767 deletions(-)
Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.callr versions 1.0.0 dated 2026-06-22 and 1.0.1 dated 2026-10-11
DESCRIPTION | 8 +-- MD5 | 70 ++++++++++++++++------------ NAMESPACE | 48 ++++++++++--------- NEWS.md | 19 +++++++ R/CallrFutureBackend-class.R | 42 +++++++++++++++- R/utils-debug.R | 3 - build/vignette.rds |binary inst/doc/future.callr.html | 18 ++++--- inst/testme/deploy.R | 21 ++------ inst/testme/run.R | 16 ++++++ inst/testme/test-callr,backend-validation.R |only inst/testme/test-callr,call-stack.R |only inst/testme/test-callr,cancel-interrupt.R |only inst/testme/test-callr,conditions.R |only inst/testme/test-callr,connections.R |only inst/testme/test-callr,timeout.R |only inst/testme/test-callr,worker-termination.R | 17 ++++++ inst/testme/test-utils.R | 18 +++++++ man/callr.Rd | 6 ++ tests/test-callr,backend-validation.R |only tests/test-callr,call-stack.R |only tests/test-callr,cancel-interrupt.R |only tests/test-callr,conditions.R |only tests/test-callr,connections.R |only tests/test-callr,launch-failure.R | 1 tests/test-callr,timeout.R |only tests/test-callr,worker-termination.R | 1 tests/test-demo.R | 1 tests/test-dotdotdot.R | 1 tests/test-future,labels.R | 1 tests/test-future,lazy.R | 1 tests/test-globals,formulas.R | 1 tests/test-globals,manual.R | 1 tests/test-globals,subassignment.R | 1 tests/test-globals,tricky.R | 1 tests/test-immediateCondition.R | 1 tests/test-nbrOfWorkers.R | 1 tests/test-plan.R | 1 tests/test-rng.R | 1 tests/test-stdout.R | 1 tests/test-utils.R | 1 tests/test-zzz,future_lapply.R | 1 42 files changed, 220 insertions(+), 83 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.2.3 dated 2026-08-21 and 0.2.4 dated 2026-10-11
DESCRIPTION | 8 MD5 | 55 ++-- NAMESPACE | 13 - NEWS.md | 16 + R/RcppExports.R | 36 ++ R/bind.R | 7 R/class-filearray.R | 193 +++++++++------ R/filearray-package.R | 6 R/lock.R | 423 +++++++++++++++++++++++++++++++++ R/method-map.R | 17 + R/methods-subsetAssign.R | 26 -- R/write.R | 149 +++++++++++ man/FileArray-class.Rd | 64 ++++ man/S3-filearray.Rd | 6 man/with_filelock.Rd |only src/RcppExports.cpp | 111 ++++++++ src/conversion.cpp | 6 src/core.cpp | 68 +++-- src/load.cpp | 13 - src/lock.cpp |only src/lock.h |only src/lockExports.cpp |only src/map.cpp | 63 +++- src/mapreduce.cpp | 25 + src/save.cpp | 2 src/serialize.cpp | 53 ++-- src/utils.cpp | 14 - tests/testthat/helper-lock.R |only tests/testthat/test-filelock.R |only tests/testthat/test-lock-process.R |only tests/testthat/test-lock.R |only tests/testthat/test-map.R | 111 ++++++++ tests/testthat/test-partition-create.R |only 33 files changed, 1268 insertions(+), 217 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There
is also an experimental extension for survival analysis, clustering
and general, example-specific cost-sensitive learning. Generic
resampling, including cross-validation, bootstrapping and subsampling.
Hyperparameter tuning with modern optimization techniques, for single-
and multi-objective problems. Filter and wrapper methods for feature
selection. Extension of basic learners with additional operations
common in machine learning, also allowing for easy nested resampling.
Most operations can be parallelized.
Author: Bernd Bischl [aut] ,
Michel Lang [aut] ,
Lars Kotthoff [aut],
Patrick Schratz [aut] ,
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut] ,
Mason Gallo [aut],
Jakob Bossek [ctb] ,
Erich Studerus [ctb] ,
Leonard [...truncated...]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr versions 2.19.3 dated 2025-08-22 and 2.19.4 dated 2026-10-11
mlr-2.19.3/mlr/tests/testthat/xgboost.model |only mlr-2.19.4/mlr/DESCRIPTION | 6 +- mlr-2.19.4/mlr/MD5 | 63 +++++++++++++-------------- mlr-2.19.4/mlr/NEWS.md | 11 ++++ mlr-2.19.4/mlr/R/ClassifTask.R | 2 mlr-2.19.4/mlr/R/ClusterTask.R | 2 mlr-2.19.4/mlr/R/CostSensTask.R | 10 +++- mlr-2.19.4/mlr/R/MultilabelTask.R | 2 mlr-2.19.4/mlr/R/RLearner_regr_km.R | 14 +++++- mlr-2.19.4/mlr/R/RegrTask.R | 2 mlr-2.19.4/mlr/R/SurvTask.R | 2 mlr-2.19.4/mlr/R/Task.R | 51 +-------------------- mlr-2.19.4/mlr/R/TuneControl.R | 25 ---------- mlr-2.19.4/mlr/R/TuneControlCMAES.R | 5 +- mlr-2.19.4/mlr/R/TuneControlDesign.R | 3 - mlr-2.19.4/mlr/R/TuneControlGenSA.R | 3 - mlr-2.19.4/mlr/R/TuneControlGrid.R | 3 - mlr-2.19.4/mlr/R/TuneControlIrace.R | 3 - mlr-2.19.4/mlr/R/TuneControlMBO.R | 3 - mlr-2.19.4/mlr/R/TuneControlRandom.R | 3 - mlr-2.19.4/mlr/R/TuneMultiCritControl.R | 2 mlr-2.19.4/mlr/R/batchmark.R | 8 +-- mlr-2.19.4/mlr/R/crossover.R | 2 mlr-2.19.4/mlr/R/datasets.R | 4 - mlr-2.19.4/mlr/R/getFeatureImportance.R | 2 mlr-2.19.4/mlr/build/partial.rdb |binary mlr-2.19.4/mlr/build/vignette.rds |binary mlr-2.19.4/mlr/man/Task.Rd | 62 +------------------------- mlr-2.19.4/mlr/man/TuneControl.Rd | 56 ------------------------ mlr-2.19.4/mlr/man/crossover.Rd | 4 + mlr-2.19.4/mlr/man/mlrFamilies.Rd | 4 + mlr-2.19.4/mlr/man/pid.task.Rd | 4 - mlr-2.19.4/mlr/tests/testthat/test_regr_km.R | 18 +++++++ 33 files changed, 135 insertions(+), 244 deletions(-)
Title: Nadaraya-Watson Kernel Regression
Description: Fast implementation of Nadaraya-Watson kernel regression for either univariate or multivariate responses, with one or more bandwidths. K-fold cross-validation is also performed.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between kernreg versions 1.0 dated 2026-02-16 and 1.1 dated 2026-10-11
kernreg-1.0/kernreg/src/Makevars.win |only kernreg-1.1/kernreg/DESCRIPTION | 8 ++++---- kernreg-1.1/kernreg/MD5 | 5 ++--- kernreg-1.1/kernreg/src/kern_reg_cpp.cpp | 5 +---- 4 files changed, 7 insertions(+), 11 deletions(-)
Title: Grouped Hyper Data Frame
Description: Extensions of "hyper data frame" (from package 'spatstat.geom') with a grouping structure. The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.4.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.4.5 dated 2026-08-25 and 0.4.6 dated 2026-10-11
DESCRIPTION | 10 +++++----- MD5 | 3 ++- README.md |only 3 files changed, 7 insertions(+), 6 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.2.1 dated 2026-07-27 and 2.3.0 dated 2026-10-11
crmPack-2.2.1/crmPack/inst/doc/comparison_decider.html |only crmPack-2.3.0/crmPack/DESCRIPTION | 12 crmPack-2.3.0/crmPack/MD5 | 315 +- crmPack-2.3.0/crmPack/NAMESPACE | 155 - crmPack-2.3.0/crmPack/NEWS.md | 64 crmPack-2.3.0/crmPack/R/Design-methods.R | 229 +- crmPack-2.3.0/crmPack/R/HierarchicalModel-class.R | 216 +- crmPack-2.3.0/crmPack/R/Model-methods.R | 2 crmPack-2.3.0/crmPack/R/Model-validity.R | 20 crmPack-2.3.0/crmPack/R/Rules-class.R | 80 crmPack-2.3.0/crmPack/R/Rules-methods.R | 482 +++- crmPack-2.3.0/crmPack/R/Rules-validity.R | 4 crmPack-2.3.0/crmPack/R/Samples-methods.R | 8 crmPack-2.3.0/crmPack/R/Simulations-class.R | 38 crmPack-2.3.0/crmPack/R/Simulations-methods.R | 677 +++++- crmPack-2.3.0/crmPack/R/Simulations-validity.R | 14 crmPack-2.3.0/crmPack/R/helpers_broom.R | 2 crmPack-2.3.0/crmPack/R/helpers_knitr_Stopping.R | 31 crmPack-2.3.0/crmPack/R/helpers_rules.R | 642 +++++ crmPack-2.3.0/crmPack/R/helpers_simulations.R | 93 crmPack-2.3.0/crmPack/build/partial.rdb |binary crmPack-2.3.0/crmPack/build/vignette.rds |binary crmPack-2.3.0/crmPack/inst/WORDLIST | 5 crmPack-2.3.0/crmPack/inst/doc/combo_designs.Rmd | 180 - crmPack-2.3.0/crmPack/inst/doc/combo_designs.html | 355 +-- crmPack-2.3.0/crmPack/inst/doc/comparison_decider.Rmd | 1077 ++++++++-- crmPack-2.3.0/crmPack/inst/doc/comparison_decider.pdf |only crmPack-2.3.0/crmPack/inst/doc/crmPack-jss-paper.Rmd | 27 crmPack-2.3.0/crmPack/inst/doc/crmPack-jss-paper.html | 43 crmPack-2.3.0/crmPack/inst/doc/example.Rmd | 43 crmPack-2.3.0/crmPack/inst/doc/example.html | 122 - crmPack-2.3.0/crmPack/inst/doc/knit_print.Rmd | 2 crmPack-2.3.0/crmPack/inst/doc/knit_print.html | 4 crmPack-2.3.0/crmPack/inst/doc/ordinal-crm.Rmd | 159 - crmPack-2.3.0/crmPack/inst/doc/ordinal-crm.html | 165 - crmPack-2.3.0/crmPack/inst/doc/parallel_computing_with_extensions.Rmd | 5 crmPack-2.3.0/crmPack/inst/doc/parallel_computing_with_extensions.html | 93 crmPack-2.3.0/crmPack/inst/doc/rolling-crm.html | 2 crmPack-2.3.0/crmPack/inst/doc/simulations.Rmd | 71 crmPack-2.3.0/crmPack/inst/doc/simulations.html | 69 crmPack-2.3.0/crmPack/inst/doc/tidy_method.Rmd | 100 crmPack-2.3.0/crmPack/inst/doc/tidy_method.html | 106 crmPack-2.3.0/crmPack/inst/doc/trial_analysis.html | 4 crmPack-2.3.0/crmPack/inst/doc/trial_backfill.Rmd | 127 - crmPack-2.3.0/crmPack/inst/doc/trial_backfill.html | 143 - crmPack-2.3.0/crmPack/inst/doc/trial_definition.html | 2 crmPack-2.3.0/crmPack/inst/doc/trial_sanity_checks.Rmd | 22 crmPack-2.3.0/crmPack/inst/doc/trial_sanity_checks.html | 68 crmPack-2.3.0/crmPack/inst/doc/upgrading_from_the_old_crmPack.Rmd | 15 crmPack-2.3.0/crmPack/inst/doc/upgrading_from_the_old_crmPack.html | 33 crmPack-2.3.0/crmPack/man/GeneralSimulationsSummary-class.Rd | 3 crmPack-2.3.0/crmPack/man/HierarchicalModel-class.Rd | 21 crmPack-2.3.0/crmPack/man/Simulations-class.Rd | 19 crmPack-2.3.0/crmPack/man/SimulationsSummary-class.Rd | 4 crmPack-2.3.0/crmPack/man/Stopping-class.Rd | 8 crmPack-2.3.0/crmPack/man/StoppingDoseStabilized-class.Rd |only crmPack-2.3.0/crmPack/man/examine.Rd | 45 crmPack-2.3.0/crmPack/man/h_arrange_plots_aligned.Rd |only crmPack-2.3.0/crmPack/man/h_barplot_percentages.Rd | 17 crmPack-2.3.0/crmPack/man/h_dose_axis_labels.Rd |only crmPack-2.3.0/crmPack/man/h_dose_plot_position.Rd |only crmPack-2.3.0/crmPack/man/h_hierarchical_compile_init.Rd | 4 crmPack-2.3.0/crmPack/man/h_hierarchical_compile_priormodel.Rd | 5 crmPack-2.3.0/crmPack/man/h_hierarchical_supported_refs.Rd | 4 crmPack-2.3.0/crmPack/man/h_histogram_percentages.Rd |only crmPack-2.3.0/crmPack/man/h_next_best_marker.Rd |only crmPack-2.3.0/crmPack/man/h_next_best_ncrm_loss_plot.Rd | 26 crmPack-2.3.0/crmPack/man/h_next_best_probability_plot.Rd |only crmPack-2.3.0/crmPack/man/h_next_best_reference_lines.Rd |only crmPack-2.3.0/crmPack/man/h_next_best_safety_marker.Rd |only crmPack-2.3.0/crmPack/man/h_overdose_prob.Rd |only crmPack-2.3.0/crmPack/man/h_overdose_threshold.Rd |only crmPack-2.3.0/crmPack/man/h_plot_doses_tried.Rd | 23 crmPack-2.3.0/crmPack/man/h_plot_simulation_trajectory.Rd | 25 crmPack-2.3.0/crmPack/man/knit_print.Rd | 5 crmPack-2.3.0/crmPack/man/nextBest.Rd | 92 crmPack-2.3.0/crmPack/man/plot-DualSimulations-missing-method.Rd | 23 crmPack-2.3.0/crmPack/man/plot-DualSimulationsSummary-missing-method.Rd | 4 crmPack-2.3.0/crmPack/man/plot-GeneralSimulations-missing-method.Rd | 31 crmPack-2.3.0/crmPack/man/plot-GeneralSimulationsSummary-missing-method.Rd | 48 crmPack-2.3.0/crmPack/man/plot-PseudoDualFlexiSimulations-missing-method.Rd | 23 crmPack-2.3.0/crmPack/man/plot-PseudoDualSimulations-missing-method.Rd | 23 crmPack-2.3.0/crmPack/man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 4 crmPack-2.3.0/crmPack/man/plot-PseudoSimulationsSummary-missing-method.Rd | 4 crmPack-2.3.0/crmPack/man/plot-SimulationsSummary-missing-method.Rd | 11 crmPack-2.3.0/crmPack/man/simulate-Design-method.Rd | 2 crmPack-2.3.0/crmPack/man/stopTrial.Rd | 45 crmPack-2.3.0/crmPack/man/tidy.Rd | 4 crmPack-2.3.0/crmPack/man/v_general_simulations.Rd | 3 crmPack-2.3.0/crmPack/man/v_stopping.Rd | 4 crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_da_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_dual_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_pseudo_dual_flexi_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_pseudo_dual_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_pseudo_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/default_simulations.Rds |binary crmPack-2.3.0/crmPack/tests/testthat/fixtures/make_persistent_objects_for_mocked_constructors.R | 29 crmPack-2.3.0/crmPack/tests/testthat/helper-HierarchicalDesign-methods.R | 13 crmPack-2.3.0/crmPack/tests/testthat/test-Design-methods.R | 14 crmPack-2.3.0/crmPack/tests/testthat/test-HierarchicalDesign-methods.R | 14 crmPack-2.3.0/crmPack/tests/testthat/test-HierarchicalModel.R | 278 ++ crmPack-2.3.0/crmPack/tests/testthat/test-Rules-class.R | 36 crmPack-2.3.0/crmPack/tests/testthat/test-Rules-methods.R | 437 +++- crmPack-2.3.0/crmPack/tests/testthat/test-Rules-validity.R | 3 crmPack-2.3.0/crmPack/tests/testthat/test-Simulations-class.R | 35 crmPack-2.3.0/crmPack/tests/testthat/test-Simulations-methods.R | 421 +++ crmPack-2.3.0/crmPack/tests/testthat/test-TwoDrugsCombo-class.R | 24 crmPack-2.3.0/crmPack/tests/testthat/test-examine-DADesign.R |only crmPack-2.3.0/crmPack/tests/testthat/test-helpers-simulations.R | 59 crmPack-2.3.0/crmPack/tests/testthat/test-helpers_knitr_Stopping.R | 27 crmPack-2.3.0/crmPack/tests/testthat/test-helpers_rules.R | 194 + crmPack-2.3.0/crmPack/vignettes/combo_designs-figures/unnamed-chunk-15-1.png |binary crmPack-2.3.0/crmPack/vignettes/combo_designs-figures/unnamed-chunk-4-1.png |binary crmPack-2.3.0/crmPack/vignettes/combo_designs.Rmd | 180 - crmPack-2.3.0/crmPack/vignettes/comparison_decider-figures |only crmPack-2.3.0/crmPack/vignettes/comparison_decider.Rmd | 1077 ++++++++-- crmPack-2.3.0/crmPack/vignettes/comparison_decider.html |only crmPack-2.3.0/crmPack/vignettes/crmPack-jss-paper.Rmd | 27 crmPack-2.3.0/crmPack/vignettes/example-figures/DLTSim-plotsummary-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/DLTsampSim-plotsummary-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/Design-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/cohort-size-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/datastruct-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/dual-nextdose-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/dual-sim-sum-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/dual-sims-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/increments-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/model-classes-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/next-best-results-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotDLTSim-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotDLTsampSim-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotGain-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotsimulationresults1-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotsimulationresults2-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/plotsimulationresults3-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/rules-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/sim-future-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/sim-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/sim-sum-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/summarysimulationresults1-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/summarysimulationresults2-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/summarysimulationresults3-1.png |binary crmPack-2.3.0/crmPack/vignettes/example-figures/three-sims-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/example.Rmd | 43 crmPack-2.3.0/crmPack/vignettes/jss-figures/nextBest-ncrm-1.png |binary crmPack-2.3.0/crmPack/vignettes/jss-figures/plot-model-fit-1.png |binary crmPack-2.3.0/crmPack/vignettes/jss-figures/plot-model-fit-2.png |binary crmPack-2.3.0/crmPack/vignettes/jss-figures/sim-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/jss-figures/sim-summary-plot-1.png |binary crmPack-2.3.0/crmPack/vignettes/knit_print.Rmd | 2 crmPack-2.3.0/crmPack/vignettes/ordinal-crm-figures/plot1-1.png |binary crmPack-2.3.0/crmPack/vignettes/ordinal-crm-figures/plot2-1.png |binary crmPack-2.3.0/crmPack/vignettes/ordinal-crm-figures/plot3-1.png |binary crmPack-2.3.0/crmPack/vignettes/ordinal-crm.Rmd | 159 - crmPack-2.3.0/crmPack/vignettes/parallel_computing_with_extensions.Rmd | 5 crmPack-2.3.0/crmPack/vignettes/rolling-crm-figures/Recommend-1.png |binary crmPack-2.3.0/crmPack/vignettes/simulations.Rmd | 71 crmPack-2.3.0/crmPack/vignettes/tidy_method-figures/unnamed-chunk-7-1.png |binary crmPack-2.3.0/crmPack/vignettes/tidy_method.Rmd | 100 crmPack-2.3.0/crmPack/vignettes/trial_analysis-figures/unnamed-chunk-10-1.png |binary crmPack-2.3.0/crmPack/vignettes/trial_analysis-figures/unnamed-chunk-36-1.png |binary crmPack-2.3.0/crmPack/vignettes/trial_backfill.Rmd | 127 - crmPack-2.3.0/crmPack/vignettes/trial_definition-figures/unnamed-chunk-5-1.png |binary crmPack-2.3.0/crmPack/vignettes/trial_sanity_checks.Rmd | 22 crmPack-2.3.0/crmPack/vignettes/upgrading_from_the_old_crmPack.Rmd | 15 crmPack-2.3.0/crmPack/vignettes/vignettes.bib | 2 166 files changed, 7650 insertions(+), 2420 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Citations are:
* Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
* Luis F.S. Castro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and Timothy Charles Bates (2026). umx version 4.5: Extending Twin and Path-Based SEM in R with CLPM, MR-DoC, Definition Variables, Onyx Integration, and Censored Distributions. Twin Research and Human Genetics, 1-6. <doi:10.1017/thg.2026.10056>.
Author: Timothy C. Bates [aut, cre] ,
Luis De Araujo [ctb],
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.65.0 dated 2026-05-18 and 4.80.0 dated 2026-10-11
umx-4.65.0/umx/R/deprecated.R |only umx-4.65.0/umx/man/figures/umx_help_figures.graffle |only umx-4.65.0/umx/man/fin_CAGR.Rd |only umx-4.65.0/umx/man/fin_FIF.Rd |only umx-4.65.0/umx/man/fin_JustifiedPE.Rd |only umx-4.65.0/umx/man/fin_NI.Rd |only umx-4.65.0/umx/man/fin_StockCAGR.Rd |only umx-4.65.0/umx/man/fin_carryCost.Rd |only umx-4.65.0/umx/man/fin_expected.Rd |only umx-4.65.0/umx/man/fin_interest.Rd |only umx-4.65.0/umx/man/fin_net_present_value.Rd |only umx-4.65.0/umx/man/fin_option.Rd |only umx-4.65.0/umx/man/fin_percent.Rd |only umx-4.65.0/umx/man/fin_ticker.Rd |only umx-4.65.0/umx/man/fin_valuation.Rd |only umx-4.65.0/umx/man/umx-deprecated.Rd |only umx-4.65.0/umx/man/umx_get_alphas.Rd |only umx-4.65.0/umx/man/umx_paste_names.Rd |only umx-4.65.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd |only umx-4.65.0/umx/tests/testthat/test_residuals.MxModel.r |only umx-4.65.0/umx/tests/testthat/test_umx_APA_pval.r |only umx-4.65.0/umx/tests/testthat/test_umx_datasets.r |only umx-4.80.0/umx/DESCRIPTION | 23 umx-4.80.0/umx/INSTALL | 1 umx-4.80.0/umx/MD5 | 961 +- umx-4.80.0/umx/NAMESPACE | 360 - umx-4.80.0/umx/NEWS.md | 106 umx-4.80.0/umx/R/TRHG_code.R | 3 umx-4.80.0/umx/R/build_run_modify.R | 3401 ---------- umx-4.80.0/umx/R/datasets.R | 190 umx-4.80.0/umx/R/double_entry.R |only umx-4.80.0/umx/R/fin_volatility_helper.R |only umx-4.80.0/umx/R/financial_functions.R | 1236 ++- umx-4.80.0/umx/R/fit_and_reporting.R | 2327 +++--- umx-4.80.0/umx/R/gh.R |only umx-4.80.0/umx/R/lavanify2ram.R | 39 umx-4.80.0/umx/R/misc_and_utility.R | 3332 +++++++-- umx-4.80.0/umx/R/package.R | 13 umx-4.80.0/umx/R/tmx.R | 132 umx-4.80.0/umx/R/umx-package.R |only umx-4.80.0/umx/R/umxAPA.R |only umx-4.80.0/umx/R/umxCLPM.R | 7 umx-4.80.0/umx/R/umxCloud.R |only umx-4.80.0/umx/R/umxCompare.R |only umx-4.80.0/umx/R/umxDoC.R | 34 umx-4.80.0/umx/R/umxDoCbyPath.R | 37 umx-4.80.0/umx/R/umxGSEM.R |only umx-4.80.0/umx/R/umxGSEM_std.R |only umx-4.80.0/umx/R/umxLISREL.R |only umx-4.80.0/umx/R/umxMRDoC.R | 8 umx-4.80.0/umx/R/umxMatrixFree.R | 1 umx-4.80.0/umx/R/umxMeasurementInvariance.R |only umx-4.80.0/umx/R/umxPower.R | 15 umx-4.80.0/umx/R/umxRAM.R |only umx-4.80.0/umx/R/umxRAM_DE.R |only umx-4.80.0/umx/R/umxRAM_GLM.R |only umx-4.80.0/umx/R/umxSummary.MxModel.R |only umx-4.80.0/umx/R/umx_ICA_report.R |only umx-4.80.0/umx/R/umx_build_high_level_models.R | 66 umx-4.80.0/umx/R/umx_build_polychoricMatrix3.R | 404 - umx-4.80.0/umx/R/umx_build_umxACE.R |only umx-4.80.0/umx/R/umx_build_umxACEv.R | 21 umx-4.80.0/umx/R/umx_build_umxCP.R |only umx-4.80.0/umx/R/umx_build_umxGxE.R |only umx-4.80.0/umx/R/umx_build_umxGxEbiv.R | 8 umx-4.80.0/umx/R/umx_build_umxIP.R |only umx-4.80.0/umx/R/umx_build_umxSexLim.R | 278 umx-4.80.0/umx/R/umx_build_umxSimplex.R | 14 umx-4.80.0/umx/R/umx_data.R |only umx-4.80.0/umx/R/umx_fit_stash_CIs.R | 4 umx-4.80.0/umx/R/umx_fit_umxFitIndices.R | 1 umx-4.80.0/umx/R/xmu.R | 1211 ++- umx-4.80.0/umx/R/xmuGSEM.R |only umx-4.80.0/umx/R/xmuWLS.R |only umx-4.80.0/umx/R/xmu_build_model_helpers.R |only umx-4.80.0/umx/R/xmu_make_top_twin_models.R | 47 umx-4.80.0/umx/R/xmu_robust_SB_savalei.R |only umx-4.80.0/umx/README.md | 15 umx-4.80.0/umx/build/partial.rdb |binary umx-4.80.0/umx/build/vignette.rds |only umx-4.80.0/umx/data/Anthro_LDSC.rda |only umx-4.80.0/umx/data/HSwls.rda |only umx-4.80.0/umx/data/Psych_LDSC.rda |only umx-4.80.0/umx/inst/CITATION | 4 umx-4.80.0/umx/inst/WORDLIST | 221 umx-4.80.0/umx/inst/doc |only umx-4.80.0/umx/man/Anthro_LDSC.Rd |only umx-4.80.0/umx/man/Fischbein_wt.Rd | 5 umx-4.80.0/umx/man/FishersMethod.Rd | 40 umx-4.80.0/umx/man/GFF.Rd | 5 umx-4.80.0/umx/man/HSwls.Rd |only umx-4.80.0/umx/man/Psych_LDSC.Rd |only umx-4.80.0/umx/man/RMSEA.MxModel.Rd | 37 umx-4.80.0/umx/man/RMSEA.Rd | 33 umx-4.80.0/umx/man/RMSEA.summary.mxmodel.Rd | 37 umx-4.80.0/umx/man/SE_from_p.Rd | 34 umx-4.80.0/umx/man/aic_weights.Rd |only umx-4.80.0/umx/man/bucks.Rd | 6 umx-4.80.0/umx/man/calculateStrictSb.Rd |only umx-4.80.0/umx/man/deg2rad.Rd | 20 umx-4.80.0/umx/man/dl_from_dropbox.Rd | 16 umx-4.80.0/umx/man/docData.Rd | 11 umx-4.80.0/umx/man/extractAIC.MxModel.Rd | 33 umx-4.80.0/umx/man/fin_options_Greeks.Rd |only umx-4.80.0/umx/man/fin_options_LeapSimulate.Rd |only umx-4.80.0/umx/man/fin_options_plotGreeks.Rd |only umx-4.80.0/umx/man/fin_options_teach.Rd |only umx-4.80.0/umx/man/fin_resolveVolatility.Rd |only umx-4.80.0/umx/man/fin_stock_CAGR.Rd |only umx-4.80.0/umx/man/fin_stock_justifiedPE.Rd |only umx-4.80.0/umx/man/fin_stock_target.Rd |only umx-4.80.0/umx/man/fin_stock_ticker.Rd |only umx-4.80.0/umx/man/fin_stock_valuation.Rd |only umx-4.80.0/umx/man/fin_tax_FIF.Rd |only umx-4.80.0/umx/man/fin_tax_NI.Rd |only umx-4.80.0/umx/man/fin_value_CAGR.Rd |only umx-4.80.0/umx/man/fin_value_CarryCost.Rd |only umx-4.80.0/umx/man/fin_value_NPV.Rd |only umx-4.80.0/umx/man/fin_value_interest.Rd |only umx-4.80.0/umx/man/fin_value_percent.Rd |only umx-4.80.0/umx/man/geometric_mean.Rd | 81 umx-4.80.0/umx/man/ggAddR.Rd | 36 umx-4.80.0/umx/man/gh_feature_branch.Rd |only umx-4.80.0/umx/man/gh_message_search.Rd |only umx-4.80.0/umx/man/gh_open_PR_url.Rd |only umx-4.80.0/umx/man/harmonic_mean.Rd | 58 umx-4.80.0/umx/man/install.OpenMx.Rd | 106 umx-4.80.0/umx/man/iqdat.Rd | 33 umx-4.80.0/umx/man/libs.Rd | 40 umx-4.80.0/umx/man/loadings.MxModel.Rd | 37 umx-4.80.0/umx/man/loadings.Rd | 37 umx-4.80.0/umx/man/mx_make.Rd |only umx-4.80.0/umx/man/noNAs.Rd | 51 umx-4.80.0/umx/man/oddsratio.Rd | 38 umx-4.80.0/umx/man/plot.MxLISRELModel.Rd | 65 umx-4.80.0/umx/man/plot.MxModel.Rd | 62 umx-4.80.0/umx/man/plot.MxModelTwinMaker.Rd | 36 umx-4.80.0/umx/man/plot.percent.Rd | 10 umx-4.80.0/umx/man/plot.umx_GWAS.Rd |only umx-4.80.0/umx/man/power.ACE.test.Rd | 70 umx-4.80.0/umx/man/print.percent.Rd | 10 umx-4.80.0/umx/man/prolific_anonymize.Rd | 57 umx-4.80.0/umx/man/prolific_check_ID.Rd | 59 umx-4.80.0/umx/man/prolific_read_demog.Rd | 55 umx-4.80.0/umx/man/prolific_scoring_stub.Rd |only umx-4.80.0/umx/man/qm.Rd | 39 umx-4.80.0/umx/man/rad2deg.Rd | 20 umx-4.80.0/umx/man/reliability.Rd | 40 umx-4.80.0/umx/man/residuals.MxModel.Rd | 37 umx-4.80.0/umx/man/tmx_genotypic_effect.Rd | 10 umx-4.80.0/umx/man/tmx_is.identified.Rd | 15 umx-4.80.0/umx/man/tmx_show.MxMatrix.Rd | 33 umx-4.80.0/umx/man/tmx_show.MxModel.Rd | 14 umx-4.80.0/umx/man/tmx_show.MxModelGSEM.Rd |only umx-4.80.0/umx/man/tmx_show.Rd | 33 umx-4.80.0/umx/man/tvars.Rd |only umx-4.80.0/umx/man/umx.Rd | 460 - umx-4.80.0/umx/man/umxACE.Rd | 69 umx-4.80.0/umx/man/umxACE_DE.Rd |only umx-4.80.0/umx/man/umxACE_GLM.Rd |only umx-4.80.0/umx/man/umxACEcov.Rd | 76 umx-4.80.0/umx/man/umxACEv.Rd | 68 umx-4.80.0/umx/man/umxAPA.Rd | 54 umx-4.80.0/umx/man/umxAlgebra.Rd | 17 umx-4.80.0/umx/man/umxBrownie.Rd | 20 umx-4.80.0/umx/man/umxCI.Rd | 37 umx-4.80.0/umx/man/umxCI_boot.Rd | 33 umx-4.80.0/umx/man/umxCLPM.Rd | 6 umx-4.80.0/umx/man/umxCP.Rd | 68 umx-4.80.0/umx/man/umxCloud.Rd |only umx-4.80.0/umx/man/umxCompare.Rd | 100 umx-4.80.0/umx/man/umxConfint.Rd | 37 umx-4.80.0/umx/man/umxCov2cor.Rd | 38 umx-4.80.0/umx/man/umxDiagnose.Rd | 10 umx-4.80.0/umx/man/umxDiffMZ.Rd | 65 umx-4.80.0/umx/man/umxDiscTwin.Rd | 63 umx-4.80.0/umx/man/umxDoC.Rd | 66 umx-4.80.0/umx/man/umxDoCp.Rd | 61 umx-4.80.0/umx/man/umxEFA.Rd | 49 umx-4.80.0/umx/man/umxEquate.Rd | 18 umx-4.80.0/umx/man/umxExamples.Rd | 4 umx-4.80.0/umx/man/umxExpCov.Rd | 33 umx-4.80.0/umx/man/umxExpMeans.Rd | 33 umx-4.80.0/umx/man/umxFactor.Rd | 67 umx-4.80.0/umx/man/umxFactorScores.Rd | 27 umx-4.80.0/umx/man/umxFitIndices.Rd | 33 umx-4.80.0/umx/man/umxFixAll.Rd | 21 umx-4.80.0/umx/man/umxGSEM.Rd |only umx-4.80.0/umx/man/umxGSEM_GWAS.Rd |only umx-4.80.0/umx/man/umxGSEM_dl_tutorial_files.Rd |only umx-4.80.0/umx/man/umxGSEM_label_ldsc.Rd |only umx-4.80.0/umx/man/umxGSEM_ldsc.Rd |only umx-4.80.0/umx/man/umxGSEM_munge.Rd |only umx-4.80.0/umx/man/umxGSEM_sim_snps.Rd |only umx-4.80.0/umx/man/umxGSEM_std.Rd |only umx-4.80.0/umx/man/umxGSEM_sumstats.Rd |only umx-4.80.0/umx/man/umxGetLatents.Rd | 20 umx-4.80.0/umx/man/umxGetManifests.Rd | 20 umx-4.80.0/umx/man/umxGetModel.Rd | 20 umx-4.80.0/umx/man/umxGetParameters.Rd | 24 umx-4.80.0/umx/man/umxGxE.Rd | 133 umx-4.80.0/umx/man/umxGxE_window.Rd | 72 umx-4.80.0/umx/man/umxGxEbiv.Rd | 61 umx-4.80.0/umx/man/umxHetCor.Rd | 91 umx-4.80.0/umx/man/umxIP.Rd | 69 umx-4.80.0/umx/man/umxJiggle.Rd | 21 umx-4.80.0/umx/man/umxLISREL.Rd |only umx-4.80.0/umx/man/umxLav2RAM.Rd | 35 umx-4.80.0/umx/man/umxMI.Rd | 29 umx-4.80.0/umx/man/umxMRDoC.Rd | 63 umx-4.80.0/umx/man/umxMatrix.Rd | 16 umx-4.80.0/umx/man/umxMeasurementInvariance.Rd |only umx-4.80.0/umx/man/umxModel.Rd | 191 umx-4.80.0/umx/man/umxModelNames.Rd | 35 umx-4.80.0/umx/man/umxModify.Rd | 20 umx-4.80.0/umx/man/umxParameters.Rd | 24 umx-4.80.0/umx/man/umxParan.Rd | 40 umx-4.80.0/umx/man/umxPath.Rd | 29 umx-4.80.0/umx/man/umxPlot.Rd | 46 umx-4.80.0/umx/man/umxPlotACE.Rd | 40 umx-4.80.0/umx/man/umxPlotACE_DE.Rd |only umx-4.80.0/umx/man/umxPlotACE_GLM.Rd |only umx-4.80.0/umx/man/umxPlotACEcov.Rd | 40 umx-4.80.0/umx/man/umxPlotACEv.Rd | 40 umx-4.80.0/umx/man/umxPlotCP.Rd | 48 umx-4.80.0/umx/man/umxPlotDoC.Rd | 40 umx-4.80.0/umx/man/umxPlotFun.Rd | 42 umx-4.80.0/umx/man/umxPlotGxE.Rd | 40 umx-4.80.0/umx/man/umxPlotGxEbiv.Rd | 40 umx-4.80.0/umx/man/umxPlotIP.Rd | 43 umx-4.80.0/umx/man/umxPlotPredict.Rd | 49 umx-4.80.0/umx/man/umxPlotSexLim.Rd | 43 umx-4.80.0/umx/man/umxPlotSimplex.Rd | 36 umx-4.80.0/umx/man/umxPower.Rd | 8 umx-4.80.0/umx/man/umxPrint_double_entry_data.Rd |only umx-4.80.0/umx/man/umxRAM.Rd | 104 umx-4.80.0/umx/man/umxRAM2Lav.Rd | 41 umx-4.80.0/umx/man/umxRAM_DE.Rd |only umx-4.80.0/umx/man/umxRAM_GLM.Rd |only umx-4.80.0/umx/man/umxReduce.Rd | 79 umx-4.80.0/umx/man/umxReduceACE.Rd | 65 umx-4.80.0/umx/man/umxReduceGxE.Rd | 65 umx-4.80.0/umx/man/umxRenameMatrix.Rd | 185 umx-4.80.0/umx/man/umxRotate.MxModelCP.Rd | 62 umx-4.80.0/umx/man/umxRotate.Rd | 33 umx-4.80.0/umx/man/umxRun.Rd | 21 umx-4.80.0/umx/man/umxSetParameters.Rd | 18 umx-4.80.0/umx/man/umxSexLim.Rd | 66 umx-4.80.0/umx/man/umxSimplex.Rd | 65 umx-4.80.0/umx/man/umxSummarizeTwinData.Rd | 75 umx-4.80.0/umx/man/umxSummary.MxDataStatic.Rd |only umx-4.80.0/umx/man/umxSummary.MxLISRELModel.Rd |only umx-4.80.0/umx/man/umxSummary.MxModel.Rd | 112 umx-4.80.0/umx/man/umxSummary.MxModelGLM.Rd |only umx-4.80.0/umx/man/umxSummary.Rd | 18 umx-4.80.0/umx/man/umxSummary.list.Rd |only umx-4.80.0/umx/man/umxSummaryACE.Rd | 65 umx-4.80.0/umx/man/umxSummaryACE_DE.Rd |only umx-4.80.0/umx/man/umxSummaryACE_GLM.Rd |only umx-4.80.0/umx/man/umxSummaryACEcov.Rd | 16 umx-4.80.0/umx/man/umxSummaryACEv.Rd | 65 umx-4.80.0/umx/man/umxSummaryCP.Rd | 16 umx-4.80.0/umx/man/umxSummaryDoC.Rd | 61 umx-4.80.0/umx/man/umxSummaryGxE.Rd | 16 umx-4.80.0/umx/man/umxSummaryGxEbiv.Rd | 65 umx-4.80.0/umx/man/umxSummaryIP.Rd | 16 umx-4.80.0/umx/man/umxSummaryMRDoC.Rd | 12 umx-4.80.0/umx/man/umxSummarySexLim.Rd | 66 umx-4.80.0/umx/man/umxSummarySimplex.Rd | 65 umx-4.80.0/umx/man/umxSuperModel.Rd | 26 umx-4.80.0/umx/man/umxThresholdMatrix.Rd | 21 umx-4.80.0/umx/man/umxTwinMaker.Rd | 81 umx-4.80.0/umx/man/umxTwoStage.Rd | 21 umx-4.80.0/umx/man/umxUnexplainedCausalNexus.Rd | 21 umx-4.80.0/umx/man/umxVersion.Rd | 44 umx-4.80.0/umx/man/umxWeightedAIC.Rd | 42 umx-4.80.0/umx/man/umx_APA_pval.Rd | 185 umx-4.80.0/umx/man/umx_ICA_report.Rd |only umx-4.80.0/umx/man/umx_aggregate.Rd | 44 umx-4.80.0/umx/man/umx_apply.Rd | 43 umx-4.80.0/umx/man/umx_array_shift.Rd | 35 umx-4.80.0/umx/man/umx_as_numeric.Rd | 59 umx-4.80.0/umx/man/umx_check.Rd | 33 umx-4.80.0/umx/man/umx_check_OS.Rd | 33 umx-4.80.0/umx/man/umx_check_model.Rd | 39 umx-4.80.0/umx/man/umx_check_names.Rd | 49 umx-4.80.0/umx/man/umx_check_parallel.Rd | 35 umx-4.80.0/umx/man/umx_complete_dollar.Rd |only umx-4.80.0/umx/man/umx_cont_2_quantiles.Rd | 68 umx-4.80.0/umx/man/umx_cor.Rd | 51 umx-4.80.0/umx/man/umx_data.Rd |only umx-4.80.0/umx/man/umx_detect_cores.Rd |only umx-4.80.0/umx/man/umx_explode.Rd | 22 umx-4.80.0/umx/man/umx_explode_twin_names.Rd | 26 umx-4.80.0/umx/man/umx_file_load_pseudo.Rd | 14 umx-4.80.0/umx/man/umx_find_object.Rd | 42 umx-4.80.0/umx/man/umx_fun_mean_sd.Rd | 189 umx-4.80.0/umx/man/umx_get_bracket_addresses.Rd | 189 umx-4.80.0/umx/man/umx_get_checkpoint.Rd | 40 umx-4.80.0/umx/man/umx_get_options.Rd | 39 umx-4.80.0/umx/man/umx_grep.Rd | 22 umx-4.80.0/umx/man/umx_has_CIs.Rd | 33 umx-4.80.0/umx/man/umx_has_been_run.Rd | 33 umx-4.80.0/umx/man/umx_has_means.Rd | 33 umx-4.80.0/umx/man/umx_has_square_brackets.Rd | 34 umx-4.80.0/umx/man/umx_is_GSEM.Rd |only umx-4.80.0/umx/man/umx_is_LISREL.Rd |only umx-4.80.0/umx/man/umx_is_MxData.Rd | 37 umx-4.80.0/umx/man/umx_is_MxMatrix.Rd | 33 umx-4.80.0/umx/man/umx_is_MxModel.Rd | 33 umx-4.80.0/umx/man/umx_is_RAM.Rd | 33 umx-4.80.0/umx/man/umx_is_class.Rd | 16 umx-4.80.0/umx/man/umx_is_cov.Rd | 35 umx-4.80.0/umx/man/umx_is_endogenous.Rd | 16 umx-4.80.0/umx/man/umx_is_exogenous.Rd | 16 umx-4.80.0/umx/man/umx_is_numeric.Rd | 16 umx-4.80.0/umx/man/umx_is_ordered.Rd | 16 umx-4.80.0/umx/man/umx_long2wide.Rd | 18 umx-4.80.0/umx/man/umx_lower.tri.Rd | 35 umx-4.80.0/umx/man/umx_lower2full.Rd | 63 umx-4.80.0/umx/man/umx_make.Rd | 209 umx-4.80.0/umx/man/umx_make_GxE_data.Rd |only umx-4.80.0/umx/man/umx_make_MR_data.Rd | 55 umx-4.80.0/umx/man/umx_make_TwinData.Rd | 134 umx-4.80.0/umx/man/umx_make_double_entry_data.Rd |only umx-4.80.0/umx/man/umx_make_fake_data.Rd | 71 umx-4.80.0/umx/man/umx_make_raw_from_cov.Rd | 55 umx-4.80.0/umx/man/umx_make_sql_from_excel.Rd | 18 umx-4.80.0/umx/man/umx_make_twin_data_nice.Rd | 18 umx-4.80.0/umx/man/umx_means.Rd | 38 umx-4.80.0/umx/man/umx_merge_randomized_columns.Rd | 51 umx-4.80.0/umx/man/umx_move_file.Rd | 14 umx-4.80.0/umx/man/umx_msg.Rd | 67 umx-4.80.0/umx/man/umx_names.Rd | 38 umx-4.80.0/umx/man/umx_open.Rd | 18 umx-4.80.0/umx/man/umx_open_CRAN_page.Rd | 35 umx-4.80.0/umx/man/umx_pad.Rd | 41 umx-4.80.0/umx/man/umx_polychoric.Rd | 57 umx-4.80.0/umx/man/umx_polypairwise.Rd | 66 umx-4.80.0/umx/man/umx_polytriowise.Rd | 63 umx-4.80.0/umx/man/umx_print.Rd | 35 umx-4.80.0/umx/man/umx_r_test.Rd | 34 umx-4.80.0/umx/man/umx_read_lower.Rd | 55 umx-4.80.0/umx/man/umx_rename.Rd | 51 umx-4.80.0/umx/man/umx_rename_file.Rd | 14 umx-4.80.0/umx/man/umx_reorder.Rd | 57 umx-4.80.0/umx/man/umx_residualize.Rd | 18 umx-4.80.0/umx/man/umx_rot.Rd | 23 umx-4.80.0/umx/man/umx_round.Rd | 38 umx-4.80.0/umx/man/umx_scale.Rd | 38 umx-4.80.0/umx/man/umx_scale_reliabilities.Rd |only umx-4.80.0/umx/man/umx_scale_wide_twin_data.Rd | 18 umx-4.80.0/umx/man/umx_score_scale.Rd | 59 umx-4.80.0/umx/man/umx_select_valid.Rd | 51 umx-4.80.0/umx/man/umx_set_auto_plot.Rd | 39 umx-4.80.0/umx/man/umx_set_auto_run.Rd | 35 umx-4.80.0/umx/man/umx_set_checkpoint.Rd | 50 umx-4.80.0/umx/man/umx_set_condensed_slots.Rd | 39 umx-4.80.0/umx/man/umx_set_cores.Rd | 68 umx-4.80.0/umx/man/umx_set_data_variance_check.Rd | 39 umx-4.80.0/umx/man/umx_set_dollar_symbol.Rd | 45 umx-4.80.0/umx/man/umx_set_optimization_options.Rd | 39 umx-4.80.0/umx/man/umx_set_optimizer.Rd | 58 umx-4.80.0/umx/man/umx_set_plot_file_suffix.Rd | 39 umx-4.80.0/umx/man/umx_set_plot_format.Rd | 39 umx-4.80.0/umx/man/umx_set_separator.Rd | 41 umx-4.80.0/umx/man/umx_set_silent.Rd | 39 umx-4.80.0/umx/man/umx_set_table_format.Rd | 39 umx-4.80.0/umx/man/umx_stack.Rd | 57 umx-4.80.0/umx/man/umx_standardize.Rd | 185 umx-4.80.0/umx/man/umx_str_chars.Rd | 22 umx-4.80.0/umx/man/umx_str_from_object.Rd | 22 umx-4.80.0/umx/man/umx_string_to_algebra.Rd | 189 umx-4.80.0/umx/man/umx_strings2numeric.Rd | 51 umx-4.80.0/umx/man/umx_tail.Rd |only umx-4.80.0/umx/man/umx_time.Rd | 28 umx-4.80.0/umx/man/umx_trim.Rd | 23 umx-4.80.0/umx/man/umx_tutorials.Rd |only umx-4.80.0/umx/man/umx_var.Rd | 38 umx-4.80.0/umx/man/umx_wide2long.Rd | 35 umx-4.80.0/umx/man/umx_wide2longTwinData.Rd | 22 umx-4.80.0/umx/man/umx_wide4lmer.Rd | 40 umx-4.80.0/umx/man/umx_write_to_clipboard.Rd | 14 umx-4.80.0/umx/man/umx_yj_wide_twin_data.Rd | 19 umx-4.80.0/umx/man/us_skinfold_data.Rd | 11 umx-4.80.0/umx/man/xgh_check_base_name.Rd |only umx-4.80.0/umx/man/xgh_get_current_branch.Rd |only umx-4.80.0/umx/man/xgh_git.Rd |only umx-4.80.0/umx/man/xmuCalculateSRMR.Rd |only umx-4.80.0/umx/man/xmuHasSquareBrackets.Rd | 185 umx-4.80.0/umx/man/xmuLabel.Rd | 23 umx-4.80.0/umx/man/xmuLabel_MATRIX_Model.Rd | 185 umx-4.80.0/umx/man/xmuLabel_Matrix.Rd | 185 umx-4.80.0/umx/man/xmuLabel_RAM_Model.Rd | 185 umx-4.80.0/umx/man/xmuMI.Rd | 185 umx-4.80.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 185 umx-4.80.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 185 umx-4.80.0/umx/man/xmuMaxLevels.Rd | 185 umx-4.80.0/umx/man/xmuMinLevels.Rd | 185 umx-4.80.0/umx/man/xmuPropagateLabels.Rd | 185 umx-4.80.0/umx/man/xmuRAM2Ordinal.Rd | 189 umx-4.80.0/umx/man/xmuTwinSuper_Continuous.Rd | 185 umx-4.80.0/umx/man/xmuTwinSuper_NoBinary.Rd | 185 umx-4.80.0/umx/man/xmuTwinUpgradeMeansToCovariateModel.Rd | 185 umx-4.80.0/umx/man/xmuValues.Rd | 23 umx-4.80.0/umx/man/xmu_CI_merge.Rd | 191 umx-4.80.0/umx/man/xmu_CI_stash.Rd | 189 umx-4.80.0/umx/man/xmu_DF_to_mxData_TypeCov.Rd | 189 umx-4.80.0/umx/man/xmu_PadAndPruneForDefVars.Rd | 185 umx-4.80.0/umx/man/xmu_WLS_align_jacobian.Rd |only umx-4.80.0/umx/man/xmu_WLS_align_weight.Rd |only umx-4.80.0/umx/man/xmu_WLS_polycor_names.Rd |only umx-4.80.0/umx/man/xmu_ace_de_apply_censor_thresholds.Rd |only umx-4.80.0/umx/man/xmu_ace_de_parse_censor_meta.Rd |only umx-4.80.0/umx/man/xmu_ace_de_parse_censor_rule.Rd |only umx-4.80.0/umx/man/xmu_ace_de_release_binary_v1.Rd |only umx-4.80.0/umx/man/xmu_bracket_address2rclabel.Rd | 189 umx-4.80.0/umx/man/xmu_catml_df3_diagnostic.Rd |only umx-4.80.0/umx/man/xmu_catml_discrepancy_at_WLS.Rd |only umx-4.80.0/umx/man/xmu_catml_eval_model.Rd |only umx-4.80.0/umx/man/xmu_catml_implied_correlation.Rd |only umx-4.80.0/umx/man/xmu_catml_wls_v.Rd |only umx-4.80.0/umx/man/xmu_cell_is_on.Rd | 189 umx-4.80.0/umx/man/xmu_check_levels_identical.Rd | 185 umx-4.80.0/umx/man/xmu_check_needs_means.Rd | 185 umx-4.80.0/umx/man/xmu_check_variance.Rd | 185 umx-4.80.0/umx/man/xmu_clean_label.Rd | 185 umx-4.80.0/umx/man/xmu_compare_WLS.Rd |only umx-4.80.0/umx/man/xmu_compare_constraint_note.Rd |only umx-4.80.0/umx/man/xmu_compare_robust_ML.Rd |only umx-4.80.0/umx/man/xmu_custom_completer.Rd |only umx-4.80.0/umx/man/xmu_data_missing.Rd | 185 umx-4.80.0/umx/man/xmu_data_swap_a_block.Rd | 185 umx-4.80.0/umx/man/xmu_describe_data_WLS.Rd | 189 umx-4.80.0/umx/man/xmu_dot_define_shapes.Rd | 16 umx-4.80.0/umx/man/xmu_dot_make_paths.Rd | 217 umx-4.80.0/umx/man/xmu_dot_make_residuals.Rd | 217 umx-4.80.0/umx/man/xmu_dot_maker.Rd | 203 umx-4.80.0/umx/man/xmu_dot_mat2dot.Rd | 17 umx-4.80.0/umx/man/xmu_dot_move_ranks.Rd | 185 umx-4.80.0/umx/man/xmu_dot_rank.Rd | 12 umx-4.80.0/umx/man/xmu_dot_rank_str.Rd | 189 umx-4.80.0/umx/man/xmu_equate_threshold_values.Rd | 4 umx-4.80.0/umx/man/xmu_extract_column.Rd | 185 umx-4.80.0/umx/man/xmu_genomicmx_binary_url.Rd |only umx-4.80.0/umx/man/xmu_genomicmx_release_page_url.Rd |only umx-4.80.0/umx/man/xmu_get_CI.Rd | 189 umx-4.80.0/umx/man/xmu_gsem_expand_snp.Rd |only umx-4.80.0/umx/man/xmu_gsem_extract_snp_path.Rd |only umx-4.80.0/umx/man/xmu_gsem_prepare_WLS.Rd |only umx-4.80.0/umx/man/xmu_gsem_subset_covstruc.Rd |only umx-4.80.0/umx/man/xmu_has_summary_mxData.Rd |only umx-4.80.0/umx/man/xmu_invert_matrix.Rd |only umx-4.80.0/umx/man/xmu_is_gsem_covstruc.Rd |only umx-4.80.0/umx/man/xmu_is_ordinal_WLS.Rd |only umx-4.80.0/umx/man/xmu_is_wls.Rd |only umx-4.80.0/umx/man/xmu_lavaan_process_group.Rd | 185 umx-4.80.0/umx/man/xmu_make_TwinSuperModel.Rd | 191 umx-4.80.0/umx/man/xmu_make_bin_cont_pair_data.Rd | 199 umx-4.80.0/umx/man/xmu_make_mxData.Rd | 185 umx-4.80.0/umx/man/xmu_match.arg.Rd | 189 umx-4.80.0/umx/man/xmu_matrix_for_print.Rd |only umx-4.80.0/umx/man/xmu_mxData_summary.Rd |only umx-4.80.0/umx/man/xmu_mxRefModels.Rd |only umx-4.80.0/umx/man/xmu_mx_make_run.Rd |only umx-4.80.0/umx/man/xmu_name_from_lavaan_str.Rd | 189 umx-4.80.0/umx/man/xmu_openmx_engine_status.Rd |only umx-4.80.0/umx/man/xmu_openmx_install_message.Rd |only umx-4.80.0/umx/man/xmu_parse_completion_context.Rd |only umx-4.80.0/umx/man/xmu_path2twin.Rd | 185 umx-4.80.0/umx/man/xmu_path_regex.Rd | 189 umx-4.80.0/umx/man/xmu_print_algebras.Rd | 185 umx-4.80.0/umx/man/xmu_ram_de_apply_censor_thresholds.Rd |only umx-4.80.0/umx/man/xmu_ram_de_parse_censor_meta.Rd |only umx-4.80.0/umx/man/xmu_rclabel_2_bracket_address.Rd | 189 umx-4.80.0/umx/man/xmu_relevel_factors.Rd | 191 umx-4.80.0/umx/man/xmu_require_summary_mxData.Rd |only umx-4.80.0/umx/man/xmu_robust_ML_fit.Rd |only umx-4.80.0/umx/man/xmu_robust_WLS_fit.Rd |only umx-4.80.0/umx/man/xmu_safe_run_summary.Rd | 186 umx-4.80.0/umx/man/xmu_savalei_fit_cfi.Rd |only umx-4.80.0/umx/man/xmu_savalei_fit_rmsea.Rd |only umx-4.80.0/umx/man/xmu_savalei_fit_tli.Rd |only umx-4.80.0/umx/man/xmu_savalei_null_scaling_factor.Rd |only umx-4.80.0/umx/man/xmu_savalei_polycor_blocks.Rd |only umx-4.80.0/umx/man/xmu_savalei_scaling_factor.Rd |only umx-4.80.0/umx/man/xmu_set_sep_from_suffix.Rd | 189 umx-4.80.0/umx/man/xmu_show_fit_or_comparison.Rd | 187 umx-4.80.0/umx/man/xmu_simplex_corner.Rd | 185 umx-4.80.0/umx/man/xmu_standardize_ACE.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_ACEcov.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_ACEv.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_CP.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_IP.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_LISREL.Rd |only umx-4.80.0/umx/man/xmu_standardize_RAM.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_SexLim.Rd | 185 umx-4.80.0/umx/man/xmu_standardize_Simplex.Rd | 189 umx-4.80.0/umx/man/xmu_start_value_list.Rd | 185 umx-4.80.0/umx/man/xmu_starts.Rd | 185 umx-4.80.0/umx/man/xmu_summary_RAM_group_parameters.Rd | 185 umx-4.80.0/umx/man/xmu_threshold_id_RAM.Rd |only umx-4.80.0/umx/man/xmu_threshold_id_twin_check.Rd |only umx-4.80.0/umx/man/xmu_topo_sort.Rd |only umx-4.80.0/umx/man/xmu_twin_add_WeightMatrices.Rd | 185 umx-4.80.0/umx/man/xmu_twin_check.Rd | 189 umx-4.80.0/umx/man/xmu_twin_get_var_names.Rd | 185 umx-4.80.0/umx/man/xmu_twin_make_def_means_mats_and_alg.Rd | 185 umx-4.80.0/umx/man/xmu_twin_upgrade_selDvs2SelVars.Rd | 185 umx-4.80.0/umx/man/xmu_umxSummary_print_matrix.Rd |only umx-4.80.0/umx/man/xmu_update_covar.Rd | 191 umx-4.80.0/umx/man/xmu_utils_completeToken.Rd |only umx-4.80.0/umx/man/xmu_wls_block_diag.Rd |only umx-4.80.0/umx/man/xmu_wls_data_models.Rd |only umx-4.80.0/umx/man/xmu_wls_display_chi.Rd |only umx-4.80.0/umx/man/xmu_wls_extract_WV.Rd |only umx-4.80.0/umx/tests/testthat.R | 22 umx-4.80.0/umx/tests/testthat/Rplots.pdf |only umx-4.80.0/umx/tests/testthat/fixtures |only umx-4.80.0/umx/tests/testthat/test_GSEM_goldens.R |only umx-4.80.0/umx/tests/testthat/test_MLR_fit_and_compare.R |only umx-4.80.0/umx/tests/testthat/test_MxModel_residuals.r |only umx-4.80.0/umx/tests/testthat/test_SRMR-test.r |only umx-4.80.0/umx/tests/testthat/test_WLS_HSwls_catML_scale.R |only umx-4.80.0/umx/tests/testthat/test_WLS_Savalei_lavaan_parity.R |only umx-4.80.0/umx/tests/testthat/test_WLS_chi_consistency.R |only umx-4.80.0/umx/tests/testthat/test_WLS_lavaan.R |only umx-4.80.0/umx/tests/testthat/test_WLS_ordinal_robust.R |only umx-4.80.0/umx/tests/testthat/test_WLS_summary_compare_workflow.R |only umx-4.80.0/umx/tests/testthat/test_WLS_umxCompare_WLS_routing.R |only umx-4.80.0/umx/tests/testthat/test_WLS_umxSummary_WLS_routing.R |only umx-4.80.0/umx/tests/testthat/test_WLS_xmu_compare_WLS.R |only umx-4.80.0/umx/tests/testthat/test_data_HSwls.R |only umx-4.80.0/umx/tests/testthat/test_data_gxeData.R |only umx-4.80.0/umx/tests/testthat/test_datasets_in_umx.r |only umx-4.80.0/umx/tests/testthat/test_double_entry.r |only umx-4.80.0/umx/tests/testthat/test_fin_.r |only umx-4.80.0/umx/tests/testthat/test_lavaan.r | 21 umx-4.80.0/umx/tests/testthat/test_openmx_engine_status.R |only umx-4.80.0/umx/tests/testthat/test_plot.MxLISRELModel.r |only umx-4.80.0/umx/tests/testthat/test_prolific_scoring_stub.R |only umx-4.80.0/umx/tests/testthat/test_umxACE_GLM.R |only umx-4.80.0/umx/tests/testthat/test_umxACE_GLM_vs_threshold.R |only umx-4.80.0/umx/tests/testthat/test_umxAPA.r |only umx-4.80.0/umx/tests/testthat/test_umxAPA_pval.r |only umx-4.80.0/umx/tests/testthat/test_umxBuild_run_modify.r | 47 umx-4.80.0/umx/tests/testthat/test_umxCP.r | 32 umx-4.80.0/umx/tests/testthat/test_umxCloud.R |only umx-4.80.0/umx/tests/testthat/test_umxCompare_constraint_note.R |only umx-4.80.0/umx/tests/testthat/test_umxConfint.r | 2 umx-4.80.0/umx/tests/testthat/test_umxFactorScores.r | 2 umx-4.80.0/umx/tests/testthat/test_umxFitAndReporting.r | 205 umx-4.80.0/umx/tests/testthat/test_umxGSEM_dl_tutorial_files.R |only umx-4.80.0/umx/tests/testthat/test_umxGSEM_ldsc.R |only umx-4.80.0/umx/tests/testthat/test_umxGSEM_std.R |only umx-4.80.0/umx/tests/testthat/test_umxGxE.r |only umx-4.80.0/umx/tests/testthat/test_umxGxE_cov.R |only umx-4.80.0/umx/tests/testthat/test_umxLISREL.r |only umx-4.80.0/umx/tests/testthat/test_umxMeasurementInvariance.R |only umx-4.80.0/umx/tests/testthat/test_umxPath.r | 4 umx-4.80.0/umx/tests/testthat/test_umxPower.r | 2 umx-4.80.0/umx/tests/testthat/test_umxRAM_DE.R |only umx-4.80.0/umx/tests/testthat/test_umxRAM_GLM.R |only umx-4.80.0/umx/tests/testthat/test_umxRAM_etc.r | 57 umx-4.80.0/umx/tests/testthat/test_umxRAM_weight.R |only umx-4.80.0/umx/tests/testthat/test_umx_ACE_etc.r | 37 umx-4.80.0/umx/tests/testthat/test_umx_has_CI.r | 2 umx-4.80.0/umx/tests/testthat/test_umx_has_means.r | 8 umx-4.80.0/umx/tests/testthat/test_umx_lower2full.r | 19 umx-4.80.0/umx/tests/testthat/test_umx_make.R |only umx-4.80.0/umx/tests/testthat/test_umx_misc.r | 192 umx-4.80.0/umx/tests/testthat/test_umx_reorder.r | 2 umx-4.80.0/umx/tests/testthat/test_umx_score_scale.r | 88 umx-4.80.0/umx/tests/testthat/test_umx_set.r | 1 umx-4.80.0/umx/tests/testthat/test_umx_stack.R |only umx-4.80.0/umx/tests/testthat/test_uncertainty_reporting.R |only umx-4.80.0/umx/tests/testthat/test_xmu_make_mxData.r | 53 umx-4.80.0/umx/tests/testthat/test_xmu_safe_run_summary.r |only umx-4.80.0/umx/vignettes |only 579 files changed, 21897 insertions(+), 16980 deletions(-)
Title: Media File Preprocessing and Metadata for the 'tidyverse'
Description: Batch preprocessing and metadata extraction for audio,
video and image files, built on the command-line programs 'FFmpeg'
(<https://ffmpeg.org/>) and 'MediaInfo'
(<https://mediaarea.net/en/MediaInfo>). Trim, crop, scale, convert and
standardize files one at a time or across a whole directory, and read
container and stream metadata back as tibbles for use with the
'tidyverse'.
Author: Jeffrey Girard [aut, cre]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between tidymedia versions 0.2.1 dated 2026-10-10 and 0.2.2 dated 2026-10-11
DESCRIPTION | 6 MD5 | 112 ++++--- NAMESPACE | 1 NEWS.md | 79 +++++ R/cache.R | 42 ++ R/ffm.R | 82 +++++ R/ffm_batch.R | 110 +++++++ R/ffm_manifest.R | 6 R/ffmpeg.R | 242 +++++++++++++++-- R/program_management.R | 268 +++++++++++++++---- R/tidymedia-package.R | 6 R/timeout.R | 12 inst/doc/batch.html | 8 inst/doc/tidymedia.html | 24 - inst/doc/verification.R | 22 + inst/doc/verification.Rmd | 23 + inst/doc/verification.html | 19 - inst/doc/workflow.html | 14 man/ffm_batch.Rd | 28 + man/ffm_manifest.Rd | 6 man/ffm_run.Rd | 36 ++ man/ffmpeg_codecs.Rd | 1 man/ffmpeg_encoders.Rd | 1 man/find_ffmpeg.Rd | 17 - man/hardware_encoder.Rd | 1 man/has_encoder.Rd |only man/normalize_audio_batch.Rd | 7 man/program_status.Rd | 9 man/refresh_ffmpeg_capabilities.Rd | 21 + man/set_program.Rd | 8 man/tidymedia-package.Rd | 6 man/with_timeout.Rd | 12 tests/testthat/helper-media.R | 18 - tests/testthat/helper-program-config.R | 36 +- tests/testthat/helper-skip.R | 27 + tests/testthat/helper-timeout-sweep.R | 58 +++- tests/testthat/test-anonymize-video-batch.R | 6 tests/testthat/test-anonymize-video.R | 2 tests/testthat/test-audio-stream-normalize.R | 8 tests/testthat/test-convert-audio-batch.R | 2 tests/testthat/test-encoder-diagnosis.R |only tests/testthat/test-ffm-batch.R | 10 tests/testthat/test-ffm-manifest.R | 2 tests/testthat/test-ffm.R | 2 tests/testthat/test-ffmpeg.R | 4 tests/testthat/test-format-for-web-batch.R | 3 tests/testthat/test-has-encoder.R |only tests/testthat/test-input-path-front-door.R | 11 tests/testthat/test-location-portability.R |only tests/testthat/test-normalize-audio.R | 2 tests/testthat/test-program-management.R | 119 ++++---- tests/testthat/test-separate-av-multitrack.R | 72 ++++- tests/testthat/test-standardize-video-batch.R | 5 tests/testthat/test-timeout-refusal-blame.R | 5 tests/testthat/test-timeout-silence.R | 21 + tests/testthat/test-unguarded-argument-front-doors.R | 21 + tests/testthat/test-verify.R | 4 tests/testthat/test-video-codec.R | 1 vignettes/verification.Rmd | 23 + 59 files changed, 1355 insertions(+), 336 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.4.3 dated 2026-05-27 and 5.5.1 dated 2026-10-11
secr-5.4.3/secr/R/telemetry.R |only secr-5.5.1/secr/DESCRIPTION | 13 secr-5.5.1/secr/MD5 | 154 secr-5.5.1/secr/NAMESPACE | 3 secr-5.5.1/secr/NEWS | 2258 +++++++------- secr-5.5.1/secr/R/RSE.R | 101 secr-5.5.1/secr/R/RcppExports.R | 32 secr-5.5.1/secr/R/addSightings.R | 151 secr-5.5.1/secr/R/addTelemetry.R | 627 ++-- secr-5.5.1/secr/R/autoini.R | 412 +- secr-5.5.1/secr/R/chatmarking.R |only secr-5.5.1/secr/R/derivedDcoef.R | 2 secr-5.5.1/secr/R/derivedDcw.R |only secr-5.5.1/secr/R/derivedDsurface.R | 479 +-- secr-5.5.1/secr/R/derivedMS.R | 13 secr-5.5.1/secr/R/fastsecrloglik.R | 669 ++-- secr-5.5.1/secr/R/fxi.R | 929 +++--- secr-5.5.1/secr/R/generalsecrloglik.R | 645 +++- secr-5.5.1/secr/R/homerange.R | 1454 ++++----- secr-5.5.1/secr/R/join2.R | 766 ++-- secr-5.5.1/secr/R/loglikhelperfn.R | 21 secr-5.5.1/secr/R/logmultinom.R | 89 secr-5.5.1/secr/R/makeStart.R | 52 secr-5.5.1/secr/R/methods.R | 121 secr-5.5.1/secr/R/plot.popn.R | 214 - secr-5.5.1/secr/R/preparedata.R | 126 secr-5.5.1/secr/R/regionN.R | 1297 ++++---- secr-5.5.1/secr/R/secr.design.MS.R | 1598 +++++----- secr-5.5.1/secr/R/secr.fit.R | 122 secr-5.5.1/secr/R/secr.refit.R | 212 - secr-5.5.1/secr/R/sim.capthist.R | 2311 +++++++-------- secr-5.5.1/secr/R/sim.detect.R | 6 secr-5.5.1/secr/R/summary.capthist.R | 591 +-- secr-5.5.1/secr/R/telemGH.R |only secr-5.5.1/secr/R/usagePlot.R | 271 - secr-5.5.1/secr/R/utility.R | 207 + secr-5.5.1/secr/R/verify.R | 2124 +++++++------ secr-5.5.1/secr/inst/doc/secr-datainput.pdf |binary secr-5.5.1/secr/inst/doc/secr-overview.Rmd | 1160 +++---- secr-5.5.1/secr/inst/doc/secr-overview.pdf |binary secr-5.5.1/secr/inst/extdata/telemetrydemo.txt |only secr-5.5.1/secr/man/AICcompatible.Rd | 145 secr-5.5.1/secr/man/RSE.Rd | 130 secr-5.5.1/secr/man/addTelemetry.Rd | 373 +- secr-5.5.1/secr/man/blackbear.Rd | 20 secr-5.5.1/secr/man/derivedMS.Rd | 10 secr-5.5.1/secr/man/details.Rd | 647 ++-- secr-5.5.1/secr/man/expected.n.Rd | 236 - secr-5.5.1/secr/man/homerange.Rd | 494 +-- secr-5.5.1/secr/man/read.telemetry.Rd | 137 secr-5.5.1/secr/man/region.N.Rd | 466 +-- secr-5.5.1/secr/man/secr-package.Rd | 368 +- secr-5.5.1/secr/man/secr.fit.Rd | 767 ++-- secr-5.5.1/secr/man/sighting.Rd | 30 secr-5.5.1/secr/man/usagePlot.Rd | 251 - secr-5.5.1/secr/man/userdist.Rd | 245 - secr-5.5.1/secr/man/verify.Rd | 257 - secr-5.5.1/secr/src/RcppExports.cpp | 121 secr-5.5.1/secr/src/autils.cpp | 2 secr-5.5.1/secr/src/detectfn.cpp | 30 secr-5.5.1/secr/src/poly.h | 4 secr-5.5.1/secr/src/prwifastproximity.cpp | 210 - secr-5.5.1/secr/src/prwisignal.cpp | 165 - secr-5.5.1/secr/src/prwisimple.cpp | 450 ++ secr-5.5.1/secr/src/prwisimplefxi.cpp | 85 secr-5.5.1/secr/src/secr.h | 14 secr-5.5.1/secr/src/sighting.cpp | 37 secr-5.5.1/secr/src/sightingchat.cpp | 247 - secr-5.5.1/secr/src/sightingexpectedmusk.cpp | 134 secr-5.5.1/secr/tests/testthat.R | 12 secr-5.5.1/secr/tests/testthat/telemetry_marking_ch.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_dx.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_q.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_sex.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_metrescale.RDS |only secr-5.5.1/secr/tests/testthat/test-fixedpmix.R |only secr-5.5.1/secr/tests/testthat/test-getpmix.R |only secr-5.5.1/secr/tests/testthat/test-markresight.R | 18 secr-5.5.1/secr/tests/testthat/test-relativeD.R | 48 secr-5.5.1/secr/tests/testthat/test-signaldetector.R | 50 secr-5.5.1/secr/tests/testthat/test-start.R | 118 secr-5.5.1/secr/tests/testthat/test-telemetry.R |only secr-5.5.1/secr/tests/testthat/test-telemetrymarking.R |only secr-5.5.1/secr/tests/testthat/test-telemetrymarkingD.R |only secr-5.5.1/secr/tests/testthat/test-uselog.R |only secr-5.5.1/secr/vignettes/secr-overview.Rmd | 1160 +++---- 86 files changed, 14227 insertions(+), 12484 deletions(-)
Title: Object-Oriented Interface for Offline Change-Point Detection
Description: A collection of efficient implementations of popular offline change-point detection algorithms, featuring a consistent, object-oriented interface for practical use.
Author: Minh Long Nguyen [aut, cre],
Toby Hocking [aut],
Charles Truong [aut],
Huy Nhat Minh Nguyen [ctb]
Maintainer: Minh Long Nguyen <edelweiss611428@gmail.com>
Diff between rupturesRcpp versions 1.0.3 dated 2026-09-18 and 2.0.0 dated 2026-10-11
rupturesRcpp-1.0.3/rupturesRcpp/src/L1_cwMed.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/L1_cwMed.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/L2.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/L2.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/LinearL2.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/LinearL2.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/SIGMA.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/SIGMA.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/VAR.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/VAR.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/baseClass.h |only rupturesRcpp-2.0.0/rupturesRcpp/DESCRIPTION | 24 rupturesRcpp-2.0.0/rupturesRcpp/LICENSE |only rupturesRcpp-2.0.0/rupturesRcpp/MD5 | 62 +- rupturesRcpp-2.0.0/rupturesRcpp/NAMESPACE | 15 rupturesRcpp-2.0.0/rupturesRcpp/R/DynpR6.R |only rupturesRcpp-2.0.0/rupturesRcpp/R/PeltR6.R | 172 +++++- rupturesRcpp-2.0.0/rupturesRcpp/R/WindowR6.R | 283 +++++++++- rupturesRcpp-2.0.0/rupturesRcpp/R/binSegR6.R | 281 +++++++++ rupturesRcpp-2.0.0/rupturesRcpp/R/costFactoryR6.R |only rupturesRcpp-2.0.0/rupturesRcpp/R/costFuncR6.R | 239 ++++++++ rupturesRcpp-2.0.0/rupturesRcpp/R/zzz.R | 25 rupturesRcpp-2.0.0/rupturesRcpp/README.md | 264 +-------- rupturesRcpp-2.0.0/rupturesRcpp/man/Dynp.Rd |only rupturesRcpp-2.0.0/rupturesRcpp/man/PELT.Rd | 71 ++ rupturesRcpp-2.0.0/rupturesRcpp/man/Window.Rd | 127 +++- rupturesRcpp-2.0.0/rupturesRcpp/man/binSeg.Rd | 125 +++- rupturesRcpp-2.0.0/rupturesRcpp/man/costFactory.Rd |only rupturesRcpp-2.0.0/rupturesRcpp/man/costFunc.Rd | 68 ++ rupturesRcpp-2.0.0/rupturesRcpp/src/RcppExports.cpp | 44 + rupturesRcpp-2.0.0/rupturesRcpp/src/costs.cpp |only rupturesRcpp-2.0.0/rupturesRcpp/src/costs.h |only rupturesRcpp-2.0.0/rupturesRcpp/src/tmplBinSeg.cpp | 208 ++++++- rupturesRcpp-2.0.0/rupturesRcpp/src/tmplDynp.cpp |only rupturesRcpp-2.0.0/rupturesRcpp/src/tmplPelt.cpp | 187 +++++- rupturesRcpp-2.0.0/rupturesRcpp/src/tmplWindow.cpp | 277 ++++++++- rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_Custom.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_LinearL1.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_LinearSIGMA.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_costFactory.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_Dynp.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_PELT.R | 52 + rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_Window.R | 150 +++++ rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_binSeg.R | 150 +++++ 44 files changed, 2341 insertions(+), 483 deletions(-)
Title: A Legacy Package
Description: The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1186/s12859-023-05408-8>, <doi:10.1016/j.labinv.2023.100158> and <doi:10.1093/bioinformatics/btaf182> is not maintained in versions >= 0.4.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex versions 0.2.1 dated 2026-08-26 and 0.2.2 dated 2026-10-11
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- R/0PACKAGE.R | 1 + README.md |only man/Qindex-package.Rd | 3 ++- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: An interactive HTML widget of the perspective plot for generalized additive models; an alternative solution of the function mgcv::vis.gam(). This R package author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf182> and <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.3.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre],
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.3.3 dated 2026-08-25 and 0.3.4 dated 2026-10-11
DESCRIPTION | 10 +++++----- MD5 | 3 ++- README.md |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Logistic Regression Trees
Description: A logistic regression tree is a decision tree with logistic regressions at its leaves. A particular stochastic expectation maximization algorithm is used to draw a few good trees, that are then assessed via the user's criterion of choice among BIC / AIC / test set Gini. The formal development is given in a PhD chapter, see Ehrhardt (2019) <https://github.com/adimajo/manuscrit_these/releases/>.
Author: Adrien Ehrhardt [aut, cre]
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@polytechnique.edu>
This is a re-admission after prior archival of version 0.3.1 dated 2024-03-06
Diff between glmtree versions 0.3.1 dated 2024-03-06 and 0.4.0 dated 2026-10-11
glmtree-0.3.1/glmtree/R/predict_tweaked.R |only glmtree-0.3.1/glmtree/inst/document.R |only glmtree-0.3.1/glmtree/inst/lint.R |only glmtree-0.3.1/glmtree/inst/rhubcheck.R |only glmtree-0.3.1/glmtree/man/glmdisc-class.Rd |only glmtree-0.3.1/glmtree/man/predict_tweaked.Rd |only glmtree-0.3.1/glmtree/tests/testthat/test-predict_tweaked.R |only glmtree-0.4.0/glmtree/DESCRIPTION | 25 glmtree-0.4.0/glmtree/MD5 | 74 - glmtree-0.4.0/glmtree/NAMESPACE | 6 glmtree-0.4.0/glmtree/NEWS.md |only glmtree-0.4.0/glmtree/R/allClasses.R | 14 glmtree-0.4.0/glmtree/R/cutDataset.R | 103 - glmtree-0.4.0/glmtree/R/generateData.R | 119 - glmtree-0.4.0/glmtree/R/glmtree.R | 385 ++--- glmtree-0.4.0/glmtree/R/helpers.R |only glmtree-0.4.0/glmtree/R/initialization.R | 6 glmtree-0.4.0/glmtree/R/normalizedGini.R | 32 glmtree-0.4.0/glmtree/R/predict.R |only glmtree-0.4.0/glmtree/build/vignette.rds |binary glmtree-0.4.0/glmtree/inst/CITATION | 20 glmtree-0.4.0/glmtree/inst/doc/glmtree.R | 171 -- glmtree-0.4.0/glmtree/inst/doc/glmtree.Rmd | 260 +-- glmtree-0.4.0/glmtree/inst/doc/glmtree.html | 821 +++--------- glmtree-0.4.0/glmtree/man/align_features.Rd |only glmtree-0.4.0/glmtree/man/bernoulli_loglik.Rd |only glmtree-0.4.0/glmtree/man/check_features.Rd |only glmtree-0.4.0/glmtree/man/cutDataset.Rd |only glmtree-0.4.0/glmtree/man/design_matrix.Rd |only glmtree-0.4.0/glmtree/man/draw_segments.Rd |only glmtree-0.4.0/glmtree/man/encode_response.Rd |only glmtree-0.4.0/glmtree/man/feature_description.Rd |only glmtree-0.4.0/glmtree/man/fit_logit.Rd |only glmtree-0.4.0/glmtree/man/fit_segments.Rd |only glmtree-0.4.0/glmtree/man/glmtree-class.Rd |only glmtree-0.4.0/glmtree/man/glmtree.Rd | 56 glmtree-0.4.0/glmtree/man/holdout_criterion.Rd |only glmtree-0.4.0/glmtree/man/initialization.Rd | 4 glmtree-0.4.0/glmtree/man/normalizedGini.Rd | 4 glmtree-0.4.0/glmtree/man/predict.Rd |only glmtree-0.4.0/glmtree/man/predict_core.Rd |only glmtree-0.4.0/glmtree/man/segment_probabilities.Rd |only glmtree-0.4.0/glmtree/man/training_criterion.Rd |only glmtree-0.4.0/glmtree/man/tree_segments.Rd |only glmtree-0.4.0/glmtree/tests/testthat/Rplots.pdf |only glmtree-0.4.0/glmtree/tests/testthat/test-cutdataset.R | 76 - glmtree-0.4.0/glmtree/tests/testthat/test-generatedata.R | 44 glmtree-0.4.0/glmtree/tests/testthat/test-glmtree.R | 152 ++ glmtree-0.4.0/glmtree/tests/testthat/test-helpers.R |only glmtree-0.4.0/glmtree/tests/testthat/test-initialization.R | 8 glmtree-0.4.0/glmtree/tests/testthat/test-normalizedgini.R | 31 glmtree-0.4.0/glmtree/tests/testthat/test-predict.R |only glmtree-0.4.0/glmtree/vignettes/glmtree.Rmd | 260 +-- 53 files changed, 1123 insertions(+), 1548 deletions(-)
Title: Deal with Country Data in an Easy Way
Description: Wrangle country data more effectively and quickly.
This package contains functions to easily identify and convert country names,
download country information, merge country data from different sources,
and make quick world maps.
Author: Francesco Saverio Bellelli [aut, cre, cph]
Maintainer: Francesco Saverio Bellelli <fsabellelli@gmail.com>
Diff between countries versions 1.2.4 dated 2026-07-18 and 1.2.5 dated 2026-10-11
countries-1.2.4/countries/man/figures/unnamed-chunk-8-1.png |only countries-1.2.5/countries/DESCRIPTION | 8 - countries-1.2.5/countries/MD5 | 15 +- countries-1.2.5/countries/NEWS.md | 3 countries-1.2.5/countries/README.md | 27 ++-- countries-1.2.5/countries/data/country_reference_list.rda |binary countries-1.2.5/countries/data/country_reference_list_long.rda |binary countries-1.2.5/countries/inst/doc/auto_merge.html | 60 +++++----- countries-1.2.5/countries/inst/doc/dealing_with_names.html | 14 +- 9 files changed, 63 insertions(+), 64 deletions(-)
Title: Idealisation of Patch Clamp Recordings
Description: Implements the model-free multiscale idealisation approaches: Jump-Segmentation by MUltiResolution Filter (JSMURF), Hotz et al. (2013) <doi:10.1109/TNB.2013.2284063>, JUmp Local dEconvolution Segmentation filter (JULES), Pein et al. (2018) <doi:10.1109/TNB.2018.2845126>, and Heterogeneous Idealization by Local testing and DEconvolution (HILDE), Pein et al. (2021) <doi:10.1109/TNB.2020.3031202>. Further details on how to use them are given in Pein, Eltzner and Munk (2021) <doi:10.1007/s00249-021-01506-8>.
Author: Florian Pein [aut, cre],
Timo Aspelmeier [ctb]
Maintainer: Florian Pein <f.pein@lancaster.ac.uk>
Diff between clampSeg versions 1.3-0 dated 2026-10-08 and 1.3-1 dated 2026-10-11
ChangeLog | 8 ++++++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary tests/testthat/test_cacheLocation.R | 19 ++++++++++++++++--- 5 files changed, 31 insertions(+), 10 deletions(-)
Title: Health Geography Toolbox for Model-Based Analysis of Infections
Panel Data
Description: Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. Cluster and hotspot analyses can be conducted using neighborhood matrices. See Wieland (2020) <doi:10.18335/region.v7i2.324> for an application of some of the mentioned analysis methods. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the [...truncated...]
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 3.0.0 dated 2026-10-02 and 3.0.1 dated 2026-10-11
swash-3.0.0/swash/NEWS.md |only swash-3.0.1/swash/DESCRIPTION | 12 - swash-3.0.1/swash/MD5 | 24 +- swash-3.0.1/swash/NAMESPACE | 2 swash-3.0.1/swash/R/config.R | 6 swash-3.0.1/swash/R/growthmodels.R | 14 + swash-3.0.1/swash/R/stathelp.R | 30 ++- swash-3.0.1/swash/man/K4kant20260101gf_ch2007Poly.Rd | 2 swash-3.0.1/swash/man/exponential_growth.Rd | 30 ++- swash-3.0.1/swash/man/growth_initial.Rd | 29 ++- swash-3.0.1/swash/man/logistic_growth.Rd | 19 +- swash-3.0.1/swash/man/metrics.Rd | 6 swash-3.0.1/swash/man/swash-package.Rd | 166 +++++++++++++------ swash-3.0.1/swash/tests |only 14 files changed, 239 insertions(+), 101 deletions(-)
Title: Fast Spatial Species Accumulation Curves
Description: High-performance spatial species accumulation curves using
fixed-focus spatially constrained rarefaction, nearest-centroid expansion,
and nearest-neighbor walks with a C++ backend for speed. Supports Hill
numbers (q=0,1,2), beta diversity partitioning (turnover/nestedness) at
site and pooled resolution, coverage-based rarefaction and extrapolation
of alpha and beta diversity, phylogenetic diversity (PD; Faith's PD,
EvoHeritage, mean pairwise distance, mean nearest taxon distance),
functional diversity accumulation including aggregated functional
diversity and intraspecific trait variation, phylogenetic and functional
redundancy, interaction network accumulation, diversity-area
relationships (DAR), endemism-area curves, sampling-effort correction and
fragmentation analysis, species-area relationship (SAR) models based on
extreme value theory (EVT), and area-based richness extrapolation via the
total-species curve. Total richness is also estimated from frequency
counts, including the acc [...truncated...]
Author: Gilles Colling [aut, cre, cph] ,
Marius Muja [ctb, cph] ),
David G. Lowe [ctb, cph] ),
Jose Luis Blanco [ctb, cph] )
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between spacc versions 0.8.3 dated 2026-06-20 and 0.11.0 dated 2026-10-11
spacc-0.11.0/spacc/DESCRIPTION | 83 spacc-0.11.0/spacc/MD5 | 345 - spacc-0.11.0/spacc/NAMESPACE | 70 spacc-0.11.0/spacc/NEWS.md | 555 + spacc-0.11.0/spacc/R/RcppExports.R | 192 spacc-0.11.0/spacc/R/arc.R |only spacc-0.11.0/spacc/R/as_spacc.R |only spacc-0.11.0/spacc/R/autoplot.R | 184 spacc-0.11.0/spacc/R/beta.R | 1206 +--- spacc-0.11.0/spacc/R/compare.R | 2 spacc-0.11.0/spacc/R/coverage.R | 1022 +-- spacc-0.11.0/spacc/R/curves-utils.R |only spacc-0.11.0/spacc/R/custom.R | 45 spacc-0.11.0/spacc/R/diversity.R | 429 - spacc-0.11.0/spacc/R/estimators.R | 1452 ++--- spacc-0.11.0/spacc/R/extrapolate.R | 1246 ++-- spacc-0.11.0/spacc/R/extrapolate_area.R |only spacc-0.11.0/spacc/R/hill.R | 928 +-- spacc-0.11.0/spacc/R/hill_coverage.R | 478 - spacc-0.11.0/spacc/R/methods.R | 1110 +-- spacc-0.11.0/spacc/R/metrics.R | 703 +- spacc-0.11.0/spacc/R/network.R |only spacc-0.11.0/spacc/R/phylofunc.R | 1153 ++-- spacc-0.11.0/spacc/R/rarefy.R | 415 - spacc-0.11.0/spacc/R/redundancy.R |only spacc-0.11.0/spacc/R/sar.R | 1572 ++--- spacc-0.11.0/spacc/R/ses.R | 1335 ++-- spacc-0.11.0/spacc/R/spacc.R | 1646 ++--- spacc-0.11.0/spacc/R/spatial-orders.R |only spacc-0.11.0/spacc/R/zzz.R | 205 spacc-0.11.0/spacc/README.md | 75 spacc-0.11.0/spacc/build/partial.rdb |binary spacc-0.11.0/spacc/build/vignette.rds |binary spacc-0.11.0/spacc/inst/CITATION | 7 spacc-0.11.0/spacc/inst/COPYRIGHTS |only spacc-0.11.0/spacc/inst/WORDLIST | 12 spacc-0.11.0/spacc/inst/doc/community-assembly.R | 11 spacc-0.11.0/spacc/inst/doc/community-assembly.Rmd | 14 spacc-0.11.0/spacc/inst/doc/community-assembly.html | 207 spacc-0.11.0/spacc/inst/doc/diversity.R | 65 spacc-0.11.0/spacc/inst/doc/diversity.Rmd | 143 spacc-0.11.0/spacc/inst/doc/diversity.html | 708 +- spacc-0.11.0/spacc/inst/doc/extrapolation.R | 73 spacc-0.11.0/spacc/inst/doc/extrapolation.Rmd | 255 spacc-0.11.0/spacc/inst/doc/extrapolation.html | 602 +- spacc-0.11.0/spacc/inst/doc/quickstart.R | 17 spacc-0.11.0/spacc/inst/doc/quickstart.Rmd | 70 spacc-0.11.0/spacc/inst/doc/quickstart.html | 558 - spacc-0.11.0/spacc/inst/doc/rarefaction-standardization.R | 17 spacc-0.11.0/spacc/inst/doc/rarefaction-standardization.Rmd | 30 spacc-0.11.0/spacc/inst/doc/rarefaction-standardization.html | 350 - spacc-0.11.0/spacc/inst/doc/richness-estimation.R | 22 spacc-0.11.0/spacc/inst/doc/richness-estimation.Rmd | 87 spacc-0.11.0/spacc/inst/doc/richness-estimation.html | 573 +- spacc-0.11.0/spacc/inst/doc/spatial-analysis.R | 13 spacc-0.11.0/spacc/inst/doc/spatial-analysis.Rmd | 20 spacc-0.11.0/spacc/inst/doc/spatial-analysis.html | 301 - spacc-0.11.0/spacc/inst/doc/theory.R |only spacc-0.11.0/spacc/inst/doc/theory.Rmd |only spacc-0.11.0/spacc/inst/doc/theory.html |only spacc-0.11.0/spacc/man/ace.Rd | 82 spacc-0.11.0/spacc/man/alphaDiversity.Rd | 98 spacc-0.11.0/spacc/man/analytical.Rd | 18 spacc-0.11.0/spacc/man/arc.Rd |only spacc-0.11.0/spacc/man/as_sf.Rd | 64 spacc-0.11.0/spacc/man/as_spacc.Rd |only spacc-0.11.0/spacc/man/autoplot.spacc.Rd | 58 spacc-0.11.0/spacc/man/betaDecay.Rd | 176 spacc-0.11.0/spacc/man/bootstrap_richness.Rd | 76 spacc-0.11.0/spacc/man/c.spacc.Rd | 34 spacc-0.11.0/spacc/man/c.spacc_beta.Rd | 36 spacc-0.11.0/spacc/man/c.spacc_coverage.Rd | 36 spacc-0.11.0/spacc/man/c.spacc_hill.Rd | 36 spacc-0.11.0/spacc/man/chao1.Rd | 108 spacc-0.11.0/spacc/man/chao2.Rd | 100 spacc-0.11.0/spacc/man/coleman.Rd | 44 spacc-0.11.0/spacc/man/collector.Rd | 38 spacc-0.11.0/spacc/man/compare.Rd | 132 spacc-0.11.0/spacc/man/compareModels.Rd | 86 spacc-0.11.0/spacc/man/completenessProfile.Rd | 152 spacc-0.11.0/spacc/man/confint.spacc_fit.Rd |only spacc-0.11.0/spacc/man/dar.Rd | 229 spacc-0.11.0/spacc/man/distanceDecay.Rd | 88 spacc-0.11.0/spacc/man/distances.Rd | 116 spacc-0.11.0/spacc/man/diversityPartition.Rd | 160 spacc-0.11.0/spacc/man/diversityProfile.Rd | 177 spacc-0.11.0/spacc/man/evenness.Rd | 162 spacc-0.11.0/spacc/man/extrapolate.Rd | 164 spacc-0.11.0/spacc/man/extrapolateArea.Rd |only spacc-0.11.0/spacc/man/extrapolateCoverage.Rd | 127 spacc-0.11.0/spacc/man/gammaDiversity.Rd | 74 spacc-0.11.0/spacc/man/iChao1.Rd | 98 spacc-0.11.0/spacc/man/iChao2.Rd | 98 spacc-0.11.0/spacc/man/interpolateCoverage.Rd | 50 spacc-0.11.0/spacc/man/jackknife.Rd | 90 spacc-0.11.0/spacc/man/mao_tau.Rd | 46 spacc-0.11.0/spacc/man/plot.spacc.Rd | 112 spacc-0.11.0/spacc/man/plot.spacc_metrics.Rd | 100 spacc-0.11.0/spacc/man/predict.spacc.Rd | 88 spacc-0.11.0/spacc/man/predict.spacc_area.Rd |only spacc-0.11.0/spacc/man/predict.spacc_fit.Rd |only spacc-0.11.0/spacc/man/rarefy.Rd | 124 spacc-0.11.0/spacc/man/ses.Rd | 270 spacc-0.11.0/spacc/man/sesars.Rd | 116 spacc-0.11.0/spacc/man/sfar.Rd | 124 spacc-0.11.0/spacc/man/spacc-package.Rd | 63 spacc-0.11.0/spacc/man/spacc.Rd | 361 - spacc-0.11.0/spacc/man/spaccBeta.Rd | 232 spacc-0.11.0/spacc/man/spaccCoverage.Rd | 251 spacc-0.11.0/spacc/man/spaccDiversity.Rd | 15 spacc-0.11.0/spacc/man/spaccEndemism.Rd | 178 spacc-0.11.0/spacc/man/spaccFunc.Rd | 243 spacc-0.11.0/spacc/man/spaccHill.Rd | 204 spacc-0.11.0/spacc/man/spaccHillBeta.Rd | 221 spacc-0.11.0/spacc/man/spaccHillCoverage.Rd | 208 spacc-0.11.0/spacc/man/spaccMetrics.Rd | 179 spacc-0.11.0/spacc/man/spaccNetwork.Rd |only spacc-0.11.0/spacc/man/spaccPhylo.Rd | 235 spacc-0.11.0/spacc/man/spaccRedundancy.Rd |only spacc-0.11.0/spacc/man/spaccWavefront.Rd |only spacc-0.11.0/spacc/man/spatialEigenvectors.Rd | 144 spacc-0.11.0/spacc/man/spatialPartition.Rd | 112 spacc-0.11.0/spacc/man/spatialRarefaction.Rd | 58 spacc-0.11.0/spacc/man/subsample.Rd | 130 spacc-0.11.0/spacc/man/zetaDiversity.Rd | 196 spacc-0.11.0/spacc/src/Makevars | 1 spacc-0.11.0/spacc/src/Makevars.win | 1 spacc-0.11.0/spacc/src/RcppExports.cpp | 758 -- spacc-0.11.0/spacc/src/accumulate.cpp |only spacc-0.11.0/spacc/src/arc.cpp |only spacc-0.11.0/spacc/src/balltree.h | 115 spacc-0.11.0/spacc/src/beta.cpp | 362 - spacc-0.11.0/spacc/src/core/accumulation_core.h | 377 - spacc-0.11.0/spacc/src/core/arc_core.h |only spacc-0.11.0/spacc/src/core/coverage_core.h | 46 spacc-0.11.0/spacc/src/core/distance_core.h | 30 spacc-0.11.0/spacc/src/core/func_core.h |only spacc-0.11.0/spacc/src/core/geometry_core.h |only spacc-0.11.0/spacc/src/core/hill_core.h | 25 spacc-0.11.0/spacc/src/core/inext_core.h |only spacc-0.11.0/spacc/src/core/phylo_core.h |only spacc-0.11.0/spacc/src/coverage.cpp | 328 - spacc-0.11.0/spacc/src/distance.cpp | 72 spacc-0.11.0/spacc/src/hill.cpp | 550 - spacc-0.11.0/spacc/src/kdtree_adapter.h | 76 spacc-0.11.0/spacc/src/orders.cpp | 283 spacc-0.11.0/spacc/src/parallel_utils.h | 134 spacc-0.11.0/spacc/src/phylofunc.cpp |only spacc-0.11.0/spacc/tests/testthat/test-arc.R |only spacc-0.11.0/spacc/tests/testthat/test-as-spacc-external.R |only spacc-0.11.0/spacc/tests/testthat/test-as_spacc.R |only spacc-0.11.0/spacc/tests/testthat/test-autoplot.R | 166 spacc-0.11.0/spacc/tests/testthat/test-beta-decay.R | 288 - spacc-0.11.0/spacc/tests/testthat/test-beta-pool.R |only spacc-0.11.0/spacc/tests/testthat/test-beta.R | 28 spacc-0.11.0/spacc/tests/testthat/test-comprehensive-coverage.R | 2851 +++++----- spacc-0.11.0/spacc/tests/testthat/test-coverage-boost.R | 1738 +++--- spacc-0.11.0/spacc/tests/testthat/test-coverage.R | 990 +-- spacc-0.11.0/spacc/tests/testthat/test-cpp-backends.R | 578 +- spacc-0.11.0/spacc/tests/testthat/test-dar-curves.R |only spacc-0.11.0/spacc/tests/testthat/test-diversity-custom.R | 2 spacc-0.11.0/spacc/tests/testthat/test-diversity-profiles.R | 378 - spacc-0.11.0/spacc/tests/testthat/test-evoheritage.R |only spacc-0.11.0/spacc/tests/testthat/test-extended-coverage.R | 1318 ++-- spacc-0.11.0/spacc/tests/testthat/test-extrapolate.R | 14 spacc-0.11.0/spacc/tests/testthat/test-func-itv.R |only spacc-0.11.0/spacc/tests/testthat/test-func-k.R |only spacc-0.11.0/spacc/tests/testthat/test-hill-beta-coverage.R |only spacc-0.11.0/spacc/tests/testthat/test-more.R |only spacc-0.11.0/spacc/tests/testthat/test-network.R |only spacc-0.11.0/spacc/tests/testthat/test-phylofunc.R | 772 +- spacc-0.11.0/spacc/tests/testthat/test-plot-methods.R | 758 +- spacc-0.11.0/spacc/tests/testthat/test-rarefy-inext.R |only spacc-0.11.0/spacc/tests/testthat/test-recovery.R |only spacc-0.11.0/spacc/tests/testthat/test-redundancy.R |only spacc-0.11.0/spacc/tests/testthat/test-sar.R | 954 +-- spacc-0.11.0/spacc/tests/testthat/test-ses-shift-rotate.R |only spacc-0.11.0/spacc/tests/testthat/test-spacc.R | 1136 +-- spacc-0.11.0/spacc/tests/testthat/test-spatial-order-semantics.R |only spacc-0.11.0/spacc/tests/testthat/test-spatiotemporal.R | 232 spacc-0.11.0/spacc/tests/testthat/test-wavefront-decay.R | 114 spacc-0.11.0/spacc/tests/testthat/test-zeta.R | 346 - spacc-0.11.0/spacc/vignettes/community-assembly.Rmd | 14 spacc-0.11.0/spacc/vignettes/diversity.Rmd | 143 spacc-0.11.0/spacc/vignettes/extrapolation.Rmd | 255 spacc-0.11.0/spacc/vignettes/quickstart.Rmd | 70 spacc-0.11.0/spacc/vignettes/rarefaction-standardization.Rmd | 30 spacc-0.11.0/spacc/vignettes/richness-estimation.Rmd | 87 spacc-0.11.0/spacc/vignettes/spatial-analysis.Rmd | 20 spacc-0.11.0/spacc/vignettes/theory.Rmd |only spacc-0.8.3/spacc/man/diversityProfileFunc.Rd |only spacc-0.8.3/spacc/man/diversityProfilePhylo.Rd |only spacc-0.8.3/spacc/man/spaccBetaFunc.Rd |only spacc-0.8.3/spacc/man/spaccBetaPhylo.Rd |only spacc-0.8.3/spacc/man/wavefront.Rd |only spacc-0.8.3/spacc/src/hill_coverage.cpp |only spacc-0.8.3/spacc/src/kncn.cpp |only spacc-0.8.3/spacc/src/knn.cpp |only spacc-0.8.3/spacc/src/methods.cpp |only spacc-0.8.3/spacc/src/metrics.cpp |only spacc-0.8.3/spacc/src/phylo.cpp |only spacc-0.8.3/spacc/src/random.cpp |only 202 files changed, 22669 insertions(+), 21394 deletions(-)
Title: Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions ('GloBI')
(<https://www.globalbioticinteractions.org/>). 'GloBI' provides
access to spatial-temporal species interaction records from
sources all over the world. 'rglobi' provides methods to search
species interactions by location, interaction type, and
taxonomic name.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut],
Helen Waters [aut]
Maintainer: Jorrit Poelen <jhpoelen@jhpoelen.nl>
This is a re-admission after prior archival of version 0.3.4 dated 2023-10-06
Diff between rglobi versions 0.3.4 dated 2023-10-06 and 0.3.6 dated 2026-10-11
rglobi-0.3.4/rglobi/tests/testthat/cache/c60a4c30c129aac24d6978d589d75332d26084c7e3523a7c91fb27b8efdeaf12 |only rglobi-0.3.6/rglobi/DESCRIPTION | 16 rglobi-0.3.6/rglobi/MD5 | 36 - rglobi-0.3.6/rglobi/NEWS.md | 9 rglobi-0.3.6/rglobi/R/rglobi.R | 84 ++- rglobi-0.3.6/rglobi/build/vignette.rds |binary rglobi-0.3.6/rglobi/inst/doc/rglobi_vignette.Rmd | 4 rglobi-0.3.6/rglobi/inst/doc/rglobi_vignette.html | 216 ++++------ rglobi-0.3.6/rglobi/man/get_interaction_areas.Rd | 8 rglobi-0.3.6/rglobi/man/get_interaction_matrix.Rd | 14 rglobi-0.3.6/rglobi/man/get_interaction_types.Rd | 14 rglobi-0.3.6/rglobi/man/get_interactions.Rd | 14 rglobi-0.3.6/rglobi/man/get_interactions_by_taxa.Rd | 22 - rglobi-0.3.6/rglobi/man/get_interactions_by_type.Rd | 14 rglobi-0.3.6/rglobi/man/get_interactions_in_area.Rd | 4 rglobi-0.3.6/rglobi/man/get_predators_of.Rd | 14 rglobi-0.3.6/rglobi/man/get_prey_of.Rd | 14 rglobi-0.3.6/rglobi/tests/testthat/cache/ecb75972c528f18171aac8400639135363af1aace862f70accd2d9c761af1712 |only rglobi-0.3.6/rglobi/tests/testthat/test-globi.R | 19 rglobi-0.3.6/rglobi/vignettes/rglobi_vignette.Rmd | 4 20 files changed, 276 insertions(+), 230 deletions(-)
Title: R Repositories Data
Description: Retrieve metadata about packages from repositories to explore
package dependencies, links between help pages, aliases, package
availability on a given date, and other repository-dependent outcome.
In addition, it provides access to information about the processes at CRAN.
This metadata can be used to help package maintainers and users navigate
changes to dependencies and with reproducibility.
Author: Lluis Revilla Sancho [aut, cre, cph]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between repo.data versions 0.2.2 dated 2026-06-20 and 0.2.6 dated 2026-10-11
repo.data-0.2.2/repo.data/inst/scripts/pkg4.2.rds |only repo.data-0.2.2/repo.data/inst/scripts/pkgstats-CRAN-current.Rds |only repo.data-0.2.6/repo.data/DESCRIPTION | 8 repo.data-0.2.6/repo.data/MD5 | 127 - repo.data-0.2.6/repo.data/NAMESPACE | 21 repo.data-0.2.6/repo.data/NEWS.md | 5 repo.data-0.2.6/repo.data/R/aaa.R | 20 repo.data-0.2.6/repo.data/R/alias_utils.R | 106 - repo.data-0.2.6/repo.data/R/arch_utils.R | 240 +-- repo.data-0.2.6/repo.data/R/base_alias.R | 28 repo.data-0.2.6/repo.data/R/base_help.R | 161 +- repo.data-0.2.6/repo.data/R/base_xrefs.R | 127 - repo.data-0.2.6/repo.data/R/bioconductor.R | 161 +- repo.data-0.2.6/repo.data/R/cran_actions.R | 153 +- repo.data-0.2.6/repo.data/R/cran_alias.R | 83 - repo.data-0.2.6/repo.data/R/cran_archive.R | 178 +- repo.data-0.2.6/repo.data/R/cran_comments.R | 214 +-- repo.data-0.2.6/repo.data/R/cran_doom.R | 121 + repo.data-0.2.6/repo.data/R/cran_help.R | 300 ++-- repo.data-0.2.6/repo.data/R/cran_maintainers.R | 109 - repo.data-0.2.6/repo.data/R/cran_snapshot.R | 190 +- repo.data-0.2.6/repo.data/R/cran_xrefs.R | 221 +-- repo.data-0.2.6/repo.data/R/dependencies.R | 648 +++++----- repo.data-0.2.6/repo.data/R/environment.R | 68 - repo.data-0.2.6/repo.data/R/issues.R | 101 - repo.data-0.2.6/repo.data/R/meta.R | 304 ++-- repo.data-0.2.6/repo.data/R/package_date.R | 367 ++--- repo.data-0.2.6/repo.data/R/repos.R | 139 +- repo.data-0.2.6/repo.data/R/utils.R | 375 +++-- repo.data-0.2.6/repo.data/R/versions.R | 8 repo.data-0.2.6/repo.data/R/xrefs_utils.R | 396 +++--- repo.data-0.2.6/repo.data/README.md | 20 repo.data-0.2.6/repo.data/build/vignette.rds |binary repo.data-0.2.6/repo.data/inst/doc/repo.data.R | 22 repo.data-0.2.6/repo.data/inst/doc/repo.data.Rmd | 14 repo.data-0.2.6/repo.data/inst/doc/repo.data.html | 71 - repo.data-0.2.6/repo.data/man/base_help_cliques.Rd | 2 repo.data-0.2.6/repo.data/man/bioc_cran_archived.Rd | 2 repo.data-0.2.6/repo.data/man/check_repos.Rd |only repo.data-0.2.6/repo.data/man/cran_archive.Rd | 10 repo.data-0.2.6/repo.data/man/cran_help_cliques.Rd | 4 repo.data-0.2.6/repo.data/man/cran_help_pages_not_linked.Rd | 8 repo.data-0.2.6/repo.data/man/cran_help_pages_wo_links.Rd | 8 repo.data-0.2.6/repo.data/man/cran_issues.Rd | 2 repo.data-0.2.6/repo.data/man/cran_snapshot.Rd | 2 repo.data-0.2.6/repo.data/man/duplicated_alias.Rd | 4 repo.data-0.2.6/repo.data/man/package_repos.Rd | 2 repo.data-0.2.6/repo.data/tests/spelling.R | 3 repo.data-0.2.6/repo.data/tests/test-actions.R | 2 repo.data-0.2.6/repo.data/tests/test-alias.R | 60 repo.data-0.2.6/repo.data/tests/test-bioconductor.R | 3 repo.data-0.2.6/repo.data/tests/test-cran_actions.R | 4 repo.data-0.2.6/repo.data/tests/test-cran_archive.R | 3 repo.data-0.2.6/repo.data/tests/test-cran_doom.R | 1 repo.data-0.2.6/repo.data/tests/test-cran_history.R | 1 repo.data-0.2.6/repo.data/tests/test-cran_issues.R | 8 repo.data-0.2.6/repo.data/tests/test-cran_targets_links.R | 3 repo.data-0.2.6/repo.data/tests/test-cran_version.R | 1 repo.data-0.2.6/repo.data/tests/test-dates.R | 2 repo.data-0.2.6/repo.data/tests/test-help.R | 34 repo.data-0.2.6/repo.data/tests/test-links.R | 2 repo.data-0.2.6/repo.data/tests/test-maintainers.R | 7 repo.data-0.2.6/repo.data/tests/test-package_date.R | 3 repo.data-0.2.6/repo.data/tests/test-package_repos.R | 2 repo.data-0.2.6/repo.data/tests/test-update_dependencies.R | 10 repo.data-0.2.6/repo.data/vignettes/repo.data.Rmd | 14 66 files changed, 2801 insertions(+), 2512 deletions(-)
Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2026) <doi:10.18637/jss.v116.i04> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.6.6 dated 2026-10-10 and 1.6.7 dated 2026-10-11
DESCRIPTION | 11 - MD5 | 67 +++++----- NAMESPACE | 4 NEWS.md | 13 +- R/Q_function.R | 2 R/blip.R | 2 R/drql.R | 2 R/fit_functions.R | 2 R/g_function.R | 4 R/g_models.R | 163 ++++++++++++-------------- R/policy_eval.R | 2 R/policy_eval_online.R | 2 R/policy_learn.R | 4 R/q_models.R | 200 ++++++++++++++++---------------- R/sl_models.R | 125 +++++++++++++------- inst/doc/policy_data.html | 2 inst/doc/policy_eval.R | 6 inst/doc/policy_eval.Rmd | 8 - inst/doc/policy_eval.html | 47 +++---- inst/doc/policy_learn.html | 35 ++--- man/control_blip.Rd | 2 man/control_drql.Rd | 2 man/fit_g_functions.Rd | 2 man/g_model.Rd | 39 ++++-- man/policy_eval.Rd | 2 man/policy_eval_online.Rd | 2 man/policy_learn.Rd | 4 man/q_model.Rd | 48 +++++-- tests/testthat/test-Q-function.R | 3 tests/testthat/test-g_models.R | 74 +++++++++++ tests/testthat/test-policy_learn-blip.R | 15 +- tests/testthat/test-policy_learn-drql.R | 8 - tests/testthat/test-q_models.R | 74 +++++++++++ tests/testthat/test-q_sl.R |only vignettes/policy_eval.Rmd | 8 - 35 files changed, 607 insertions(+), 377 deletions(-)
Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Description: A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user,
which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class.
Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.
Author: Alem Gusinac [aut, cre] ,
Thomas Ederveen [aut] ,
Annemarie Boleij [aut, fnd]
Maintainer: Alem Gusinac <alem.gusinac@gmail.com>
Diff between OmicFlow versions 1.6.0 dated 2026-05-19 and 1.7.0 dated 2026-10-11
OmicFlow-1.6.0/OmicFlow/R/diversity_plot.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/alpha_diversity.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/composition.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/dfe.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/distances.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/hill.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/ordination.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/subsetting.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/sync.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/_snaps/transformations.md |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-alpha_diversity.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-autoflow.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-colormap.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-composition.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-dfe.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-distances.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-diversity.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-diversity_plot.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-hill.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-ordination.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-ordination_plot.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-pairwise_stats.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-plot_pairwise_stats.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-rankstat.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-subsetting.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-sync.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-transformations.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-utils.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-volcano_plot.R |only OmicFlow-1.6.0/OmicFlow/tests/testthat/test-write_biom.R |only OmicFlow-1.7.0/OmicFlow/DESCRIPTION | 25 OmicFlow-1.7.0/OmicFlow/LICENSE | 4 OmicFlow-1.7.0/OmicFlow/MD5 | 233 OmicFlow-1.7.0/OmicFlow/NAMESPACE | 119 OmicFlow-1.7.0/OmicFlow/NEWS.md |only OmicFlow-1.7.0/OmicFlow/R/OmicFlow-package.R | 30 OmicFlow-1.7.0/OmicFlow/R/RcppExports.R | 70 OmicFlow-1.7.0/OmicFlow/R/boxjitter_test.R |only OmicFlow-1.7.0/OmicFlow/R/bray.R | 148 OmicFlow-1.7.0/OmicFlow/R/canberra.R | 147 OmicFlow-1.7.0/OmicFlow/R/colormap.R | 129 OmicFlow-1.7.0/OmicFlow/R/composition_plot.R | 327 OmicFlow-1.7.0/OmicFlow/R/cosine.R | 146 OmicFlow-1.7.0/OmicFlow/R/dependencies.R |only OmicFlow-1.7.0/OmicFlow/R/diversity.R | 216 OmicFlow-1.7.0/OmicFlow/R/euclidean.R | 143 OmicFlow-1.7.0/OmicFlow/R/hill_taxa.R | 176 OmicFlow-1.7.0/OmicFlow/R/jaccard.R | 144 OmicFlow-1.7.0/OmicFlow/R/jsd.R | 152 OmicFlow-1.7.0/OmicFlow/R/manhattan.R | 146 OmicFlow-1.7.0/OmicFlow/R/metagenomics-class.R | 1216 +- OmicFlow-1.7.0/OmicFlow/R/omics-class.R | 4774 +++++----- OmicFlow-1.7.0/OmicFlow/R/ordination_plot.R | 262 OmicFlow-1.7.0/OmicFlow/R/pairwise_adonis.R | 252 OmicFlow-1.7.0/OmicFlow/R/pairwise_anosim.R | 218 OmicFlow-1.7.0/OmicFlow/R/plot_pairwise_stats.R | 236 OmicFlow-1.7.0/OmicFlow/R/proteomics-class.R | 288 OmicFlow-1.7.0/OmicFlow/R/unifrac.R | 193 OmicFlow-1.7.0/OmicFlow/R/utils.R | 388 OmicFlow-1.7.0/OmicFlow/R/volcano_plot.R | 372 OmicFlow-1.7.0/OmicFlow/exec/autoFlow.R | 172 OmicFlow-1.7.0/OmicFlow/inst/extdata/biomv2.biom |only OmicFlow-1.7.0/OmicFlow/inst/extdata/counts.tsv | 486 - OmicFlow-1.7.0/OmicFlow/inst/extdata/counts_dense.tsv | 486 - OmicFlow-1.7.0/OmicFlow/inst/extdata/counts_with_rownames.tsv | 486 - OmicFlow-1.7.0/OmicFlow/inst/extdata/features.tsv | 486 - OmicFlow-1.7.0/OmicFlow/inst/extdata/metadata.tsv | 10 OmicFlow-1.7.0/OmicFlow/inst/extdata/tree.newick | 2 OmicFlow-1.7.0/OmicFlow/inst/metadata_schema.json | 76 OmicFlow-1.7.0/OmicFlow/inst/report.Rmd | 444 OmicFlow-1.7.0/OmicFlow/inst/styles.css | 74 OmicFlow-1.7.0/OmicFlow/man/OmicFlow-package.Rd | 5 OmicFlow-1.7.0/OmicFlow/man/boxjitter_test.Rd |only OmicFlow-1.7.0/OmicFlow/man/bray.Rd | 104 OmicFlow-1.7.0/OmicFlow/man/canberra.Rd | 104 OmicFlow-1.7.0/OmicFlow/man/colormap.Rd | 17 OmicFlow-1.7.0/OmicFlow/man/column_exists.Rd | 6 OmicFlow-1.7.0/OmicFlow/man/composition_plot.Rd | 174 OmicFlow-1.7.0/OmicFlow/man/cosine.Rd | 104 OmicFlow-1.7.0/OmicFlow/man/diversity.Rd | 143 OmicFlow-1.7.0/OmicFlow/man/diversity_plot.Rd | 116 OmicFlow-1.7.0/OmicFlow/man/euclidean.Rd | 98 OmicFlow-1.7.0/OmicFlow/man/figures |only OmicFlow-1.7.0/OmicFlow/man/hill_taxa.Rd | 108 OmicFlow-1.7.0/OmicFlow/man/jaccard.Rd | 100 OmicFlow-1.7.0/OmicFlow/man/jsd.Rd | 106 OmicFlow-1.7.0/OmicFlow/man/manhattan.Rd | 104 OmicFlow-1.7.0/OmicFlow/man/matrix_to_dtable.Rd | 34 OmicFlow-1.7.0/OmicFlow/man/metagenomics.Rd | 630 - OmicFlow-1.7.0/OmicFlow/man/omics.Rd | 2864 +++-- OmicFlow-1.7.0/OmicFlow/man/ordination_plot.Rd | 123 OmicFlow-1.7.0/OmicFlow/man/pairwise_adonis.Rd | 134 OmicFlow-1.7.0/OmicFlow/man/pairwise_anosim.Rd | 129 OmicFlow-1.7.0/OmicFlow/man/plot_pairwise_stats.Rd | 18 OmicFlow-1.7.0/OmicFlow/man/proteomics.Rd | 382 OmicFlow-1.7.0/OmicFlow/man/unifrac.Rd | 140 OmicFlow-1.7.0/OmicFlow/man/volcano_plot.Rd | 163 OmicFlow-1.7.0/OmicFlow/src/Makevars | 1 OmicFlow-1.7.0/OmicFlow/src/Makevars.win | 3 OmicFlow-1.7.0/OmicFlow/tests/testthat.R | 34 OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/metagenomics-write_biom.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/metagenomics.md | 259 OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/metrics-distances.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/metrics-diversity.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/metrics-hill.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-alpha_diversity.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-autoflow.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-composition.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-feature_merge.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-foldchange.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-ordination.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-rankstat.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-subsetting.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics-transformations.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/omics.md | 208 OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/proteomics.md | 162 OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/statistics-pairwise_stats.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/util-colormap.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/util-column_exists.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/util-combine_conditions.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/util-matrix_to_dtable.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/visualisation-boxjitter_test.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/visualisation-composition_plot.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/visualisation-ordination_plot.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/visualisation-plot_pairwise_stats.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/_snaps/visualisation-volcano_plot.md |only OmicFlow-1.7.0/OmicFlow/tests/testthat/input/metagenomics/biom_with_taxonomy_json.biom | 108 OmicFlow-1.7.0/OmicFlow/tests/testthat/input/metagenomics/rooted_tree.newick | 2 OmicFlow-1.7.0/OmicFlow/tests/testthat/input/proteomics/counts.csv | 102 OmicFlow-1.7.0/OmicFlow/tests/testthat/input/proteomics/counts_without_rownames.csv | 102 OmicFlow-1.7.0/OmicFlow/tests/testthat/input/proteomics/metadata.csv | 22 OmicFlow-1.7.0/OmicFlow/tests/testthat/input/proteomics/tree.newick | 2 OmicFlow-1.7.0/OmicFlow/tests/testthat/test-metagenomics-write_biom.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-metagenomics.R | 151 OmicFlow-1.7.0/OmicFlow/tests/testthat/test-metrics-distances.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-metrics-diversity.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-metrics-hill.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-alpha_diversity.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-autoflow.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-composition.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-feature_merge.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-foldchange.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-ordination.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-rankstat.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-subsetting.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics-transformations.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-omics.R | 215 OmicFlow-1.7.0/OmicFlow/tests/testthat/test-proteomics.R | 119 OmicFlow-1.7.0/OmicFlow/tests/testthat/test-statistics-pairwise_stats.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-util-colormap.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-util-column_exists.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-util-combine_conditions.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-util-is.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-util-matrix_to_dtable.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-visualisation-boxjitter_test.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-visualisation-composition_plot.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-visualisation-ordination_plot.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-visualisation-plot_pairwise_stats.R |only OmicFlow-1.7.0/OmicFlow/tests/testthat/test-visualisation-volcano_plot.R |only 159 files changed, 11457 insertions(+), 9215 deletions(-)
Title: Regularized Bayesian Estimator for Two-Level Latent Variable
Models
Description: Implements a regularized Bayesian estimator that optimizes the estimation
of between-group coefficients for multilevel latent variable models by minimizing
mean squared error (MSE) and balancing variance and bias. The package provides more reliable
estimates in scenarios with limited data, offering a robust solution for accurate
parameter estimation in two-level latent variable models. It is designed for
researchers in psychology, education, and related fields who face challenges in
estimating between-group effects under small sample sizes and low intraclass
correlation coefficients. The package includes comprehensive S3 methods for result
objects: print(), summary(), coef(), se(), vcov(), confint(), as.data.frame(),
dim(), length(), names(), and update() for enhanced usability and integration
with standard R workflows. Dashuk et al. (2025a) <doi:10.1017/psy.2025.10045>
derived the optimal regularized Bayesian estimator;
Dashuk et al. (2025b) <doi:10.1007/s41237-025-00264-7> [...truncated...]
Author: Valerii Dashuk [aut, cre],
Binayak Timilsina [aut],
Martin Hecht [aut],
Steffen Zitzmann [aut]
Maintainer: Valerii Dashuk <vadashuk@gmail.com>
Diff between MultiLevelOptimalBayes versions 0.0.4.0 dated 2025-09-23 and 0.1.0.0 dated 2026-10-11
DESCRIPTION | 9 MD5 | 34 - NEWS.md |only R/estimation-bayes.R | 661 +++++------------------------ R/mlob.R | 34 + README.md | 126 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MultiLevelOptimalBayes-Intro.Rmd | 555 ++++++++++++------------ inst/doc/MultiLevelOptimalBayes-Intro.html | 260 +++++------ man/estimate_Bay_CV.Rd | 11 man/mlob.Rd | 18 man/ratio_moments.Rd |only man/ratio_se.Rd |only tests/testthat/helper-anova-moments.R |only tests/testthat/helper-reference-fits.R |only tests/testthat/helper-simulate-alcd.R |only tests/testthat/test-mlob.R | 19 tests/testthat/test-numeric-estimators.R |only tests/testthat/test-numeric-invariance.R |only tests/testthat/test-numeric-properties.R |only tests/testthat/test-numeric-reference.R |only vignettes/MultiLevelOptimalBayes-Intro.Rmd | 555 ++++++++++++------------ 23 files changed, 943 insertions(+), 1339 deletions(-)
More information about MultiLevelOptimalBayes at CRAN
Permanent link
Title: Mobility Network Analysis
Description: Implements the method to analyse weighted mobility networks or distribution networks as outlined in:
Block, P., Stadtfeld, C., & Robins, G. (2022) <doi:10.1016/j.socnet.2021.08.003>.
The purpose of the model is to analyse the structure of mobility,
incorporating exogenous predictors pertaining to individuals and locations
known from classical mobility analyses, as well as modelling emergent mobility
patterns akin to structural patterns known from the statistical analysis of social networks.
Version 2 runs the simulations in 'C++' (using 'Rcpp') and, besides stochastic
approximation (Robbins-Monro), can estimate parameters with Geyer-Thompson MCMC
maximum likelihood estimation.
Author: Per Block [cre, aut, cph] ,
Christoph Stadtfeld [aut] ,
Nico Keiser [aut] ,
Marion Hoffman [aut] ,
Jingying Wang [aut]
Maintainer: Per Block <block@soziologie.uzh.ch>
Diff between MoNAn versions 1.1.0 dated 2024-09-12 and 2.0.0 dated 2026-10-11
MoNAn-1.1.0/MoNAn/man/concentration_basic_squared.Rd |only MoNAn-1.1.0/MoNAn/man/concentration_norm.Rd |only MoNAn-1.1.0/MoNAn/man/concentration_norm_squared.Rd |only MoNAn-1.1.0/MoNAn/man/concentration_prop_orig_cov.Rd |only MoNAn-1.1.0/MoNAn/man/concentration_rankGW.Rd |only MoNAn-1.1.0/MoNAn/man/in_weights_exponent.Rd |only MoNAn-2.0.0/MoNAn/DESCRIPTION | 37 MoNAn-2.0.0/MoNAn/MD5 | 211 +-- MoNAn-2.0.0/MoNAn/NAMESPACE | 23 MoNAn-2.0.0/MoNAn/NEWS.md | 108 + MoNAn-2.0.0/MoNAn/R/1_hiddenFunctions.R | 595 +++++++- MoNAn-2.0.0/MoNAn/R/1b_cppSampler.R |only MoNAn-2.0.0/MoNAn/R/2_effectFunctions.R | 151 +- MoNAn-2.0.0/MoNAn/R/2b_effectFunctions_loops.R | 4 MoNAn-2.0.0/MoNAn/R/2c_effectFunctions_concentration.R | 671 ++++++---- MoNAn-2.0.0/MoNAn/R/2d_effectFunctions_reciprocity.R | 28 MoNAn-2.0.0/MoNAn/R/2e_effectFunctions_transitivity.R | 432 +++--- MoNAn-2.0.0/MoNAn/R/2f_effectFunctions_endogenousCovariateBased.R | 26 MoNAn-2.0.0/MoNAn/R/3_coreFunctions.R | 142 +- MoNAn-2.0.0/MoNAn/R/3b_wrapperFunctions.R | 94 + MoNAn-2.0.0/MoNAn/R/4_auxiliaryFunctions.R | 4 MoNAn-2.0.0/MoNAn/R/RcppExports.R |only MoNAn-2.0.0/MoNAn/R/zzz.R | 6 MoNAn-2.0.0/MoNAn/README.md | 109 - MoNAn-2.0.0/MoNAn/build/partial.rdb |binary MoNAn-2.0.0/MoNAn/data/myEffects.rda |binary MoNAn-2.0.0/MoNAn/man/MoNAn-package.Rd | 12 MoNAn-2.0.0/MoNAn/man/addDummyEffects.Rd |only MoNAn-2.0.0/MoNAn/man/addEffect.Rd | 2 MoNAn-2.0.0/MoNAn/man/alter_covariate.Rd | 21 MoNAn-2.0.0/MoNAn/man/associativity_all_AC_covar_bin.Rd | 21 MoNAn-2.0.0/MoNAn/man/associativity_one_AC_covar_bin.Rd | 21 MoNAn-2.0.0/MoNAn/man/avoiding_dissimilar_covar_bin.Rd | 19 MoNAn-2.0.0/MoNAn/man/avoiding_dissimilar_covar_cont.Rd | 19 MoNAn-2.0.0/MoNAn/man/concentration_AC.Rd | 19 MoNAn-2.0.0/MoNAn/man/concentration_AC_dyad_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/concentration_AC_resource_covar_bin.Rd | 23 MoNAn-2.0.0/MoNAn/man/concentration_GW.Rd | 19 MoNAn-2.0.0/MoNAn/man/concentration_GW_dyad_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/concentration_GW_resource_covar_bin.Rd | 23 MoNAn-2.0.0/MoNAn/man/concentration_basic.Rd | 17 MoNAn-2.0.0/MoNAn/man/concentration_basic_cube.Rd | 17 MoNAn-2.0.0/MoNAn/man/concentration_max.Rd |only MoNAn-2.0.0/MoNAn/man/concentration_prop.Rd | 19 MoNAn-2.0.0/MoNAn/man/concentration_prop_AC.Rd |only MoNAn-2.0.0/MoNAn/man/createAlgorithm.Rd | 34 MoNAn-2.0.0/MoNAn/man/crowding_out_prop_covar_bin.Rd | 19 MoNAn-2.0.0/MoNAn/man/dyadic_covariate.Rd | 19 MoNAn-2.0.0/MoNAn/man/dyadic_covariate_resource_attribute.Rd | 21 MoNAn-2.0.0/MoNAn/man/estimateMobilityNetwork.Rd | 9 MoNAn-2.0.0/MoNAn/man/extractTraces.Rd | 2 MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-17-1.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-17-2.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-17-3.png |only MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-17-4.png |only MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-18-1.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-18-2.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-18-3.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-18-4.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-19-1.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-19-2.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-20-1.png |binary MoNAn-2.0.0/MoNAn/man/figures/README-unnamed-chunk-20-2.png |binary MoNAn-2.0.0/MoNAn/man/gofMobilityNetwork.Rd | 2 MoNAn-2.0.0/MoNAn/man/in_ties_loops.Rd | 17 MoNAn-2.0.0/MoNAn/man/in_weights_AC.Rd | 19 MoNAn-2.0.0/MoNAn/man/in_weights_GW.Rd | 19 MoNAn-2.0.0/MoNAn/man/joining_similar_avoiding_dissimilar_covar_bin.Rd | 19 MoNAn-2.0.0/MoNAn/man/joining_similar_avoiding_dissimilar_covar_cont.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops.Rd | 17 MoNAn-2.0.0/MoNAn/man/loops_AC.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops_GW.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops_additional_origin.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops_node_covar.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops_resource_covar.Rd | 19 MoNAn-2.0.0/MoNAn/man/loops_resource_covar_node_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/loops_x_loops_additional_origin.Rd | 19 MoNAn-2.0.0/MoNAn/man/monanDataCreate.Rd | 12 MoNAn-2.0.0/MoNAn/man/present_relations.Rd | 17 MoNAn-2.0.0/MoNAn/man/reciprocity_AC.Rd | 19 MoNAn-2.0.0/MoNAn/man/reciprocity_AC_dyad_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/reciprocity_AC_dyad_covar_bin.Rd | 21 MoNAn-2.0.0/MoNAn/man/reciprocity_GW.Rd | 19 MoNAn-2.0.0/MoNAn/man/reciprocity_GW_dyad_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/reciprocity_GW_dyad_covar_bin.Rd | 21 MoNAn-2.0.0/MoNAn/man/reciprocity_basic.Rd | 17 MoNAn-2.0.0/MoNAn/man/reciprocity_min.Rd | 17 MoNAn-2.0.0/MoNAn/man/reciprocity_min_dyad_covar.Rd | 21 MoNAn-2.0.0/MoNAn/man/reciprocity_min_resource_covar.Rd | 19 MoNAn-2.0.0/MoNAn/man/resource_covar_to_node_covar.Rd | 23 MoNAn-2.0.0/MoNAn/man/same_covariate.Rd | 19 MoNAn-2.0.0/MoNAn/man/sim_covariate.Rd | 19 MoNAn-2.0.0/MoNAn/man/simulateMobilityNetworks.Rd | 2 MoNAn-2.0.0/MoNAn/man/staying_by_prop_bin_inflow.Rd | 19 MoNAn-2.0.0/MoNAn/man/target_change_match.Rd | 9 MoNAn-2.0.0/MoNAn/man/test_effect.Rd | 5 MoNAn-2.0.0/MoNAn/man/transitivity_AC.Rd | 19 MoNAn-2.0.0/MoNAn/man/transitivity_GW.Rd | 19 MoNAn-2.0.0/MoNAn/man/transitivity_basic.Rd | 17 MoNAn-2.0.0/MoNAn/man/transitivity_min.Rd | 17 MoNAn-2.0.0/MoNAn/man/transitivity_netflow.Rd | 17 MoNAn-2.0.0/MoNAn/man/triad120C.Rd | 17 MoNAn-2.0.0/MoNAn/man/triad120D.Rd | 17 MoNAn-2.0.0/MoNAn/man/triad120U.Rd | 17 MoNAn-2.0.0/MoNAn/src |only MoNAn-2.0.0/MoNAn/tests |only 106 files changed, 1835 insertions(+), 1912 deletions(-)
Title: Calculation of Low Flow Statistics for Daily Stream Flow Data
Description: The "Manual on Low-flow Estimation and Prediction" (Gustard & Demuth (2009, ISBN:978-92-63-11029-9)), published by the World Meteorological Organisation, gives a comprehensive summary on how to analyse stream flow data focusing on low-flows. This packages provides functions to compute the described statistics and produces plots similar to the ones in the manual.
Author: Tobias Gauster [ctb, cre],
Gregor Laaha [aut] ,
Daniel Koffler [aut]
Maintainer: Tobias Gauster <t.gauster@gmail.com>
Diff between lfstat versions 0.9.13 dated 2025-09-04 and 0.9.15 dated 2026-10-11
DESCRIPTION | 11 +- MD5 | 10 +- NAMESPACE | 208 +++++++++++++++++++++++-------------------- NEWS.md | 6 + build/partial.rdb |binary tests/testthat/test-import.R | 9 + 6 files changed, 136 insertions(+), 108 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] ,
Jiawei Zhang [ctb, cph] ,
Jie Ding [ctb, cph] ,
Yuhong Yang [ctb, cph]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.9.0 dated 2026-10-01 and 2.10.0 dated 2026-10-11
DESCRIPTION | 19 MD5 | 122 NAMESPACE | 32 NEWS.md | 1988 +++++++------ R/bagoft_fast.R | 4 R/battery_summary.R |only R/calm_gof.R | 770 ++--- R/cdef_gof.R | 456 +-- R/cubic_calib_gof.R |only R/deepgof.R | 1371 ++++----- R/deepgof_certificate.R |only R/deepgof_plot.R |only R/def_ensemble_gof.R | 368 +- R/def_gof.R | 879 +++-- R/ebrahim.gof-package.R | 9 R/ebrahim_farrington_test.R | 807 +++-- R/edge_belt.R |only R/edge_gof.R | 451 ++- R/legoft.R | 498 +-- R/localize_gof.R |only R/localize_plot.R |only R/proj_gof.R | 428 +- R/run_all_external.R | 34 R/run_all_gof.R | 3897 +++++++++++++------------- R/shrink_gof.R | 444 +- README.md | 61 build/vignette.rds |binary inst/CITATION | 109 inst/doc/ebrahim-farrington-intro.Rmd | 6 inst/doc/ebrahim-farrington-intro.html | 97 inst/doc/ebrahim-gof-toolbox.R | 39 inst/doc/ebrahim-gof-toolbox.Rmd | 113 inst/doc/ebrahim-gof-toolbox.html | 435 ++ inst/doc/extensions.R |only inst/doc/extensions.Rmd |only inst/doc/extensions.html |only man/calm.gof.Rd | 6 man/cubic.calib.gof.Rd |only man/deepgof1.Rd | 5 man/deepgof1.external.Rd | 4 man/def.gof.Rd | 36 man/ebrahim.gof-package.Rd | 9 man/edge.belt.Rd |only man/edge.gof.Rd | 41 man/ef.gof.Rd | 157 - man/gof_certificate.Rd |only man/localize.external.Rd |only man/localize.gof.Rd |only man/plot.deepgof1.Rd |only man/plot.edge_gof.Rd |only man/plot.gof_battery.Rd | 7 man/plot.gof_localize.Rd |only man/print.gof_battery.Rd | 10 man/run.all.external.Rd | 10 man/run.all.gof.Rd | 104 man/shrink.gof.Rd | 6 man/summary.gof_battery.Rd |only tests/testthat/helper-ef-reference.R |only tests/testthat/test-battery-input.R |only tests/testthat/test-battery-summary.R |only tests/testthat/test-cubic-calib.R |only tests/testthat/test-deepgof-plot.R |only tests/testthat/test-deepgof1.R | 15 tests/testthat/test-def-gof.R | 480 +-- tests/testthat/test-ebrahim-farrington.R | 371 +- tests/testthat/test-edge-belt.R |only tests/testthat/test-edge-plot.R |only tests/testthat/test-ef-method.R | 47 tests/testthat/test-ef-paper.R |only tests/testthat/test-gof_certificate.R |only tests/testthat/test-localize.R |only tests/testthat/test-mccullagh-copas-algebra.R |only tests/testthat/test-na-exclude.R |only tests/testthat/test-run-all-external.R | 35 tests/testthat/test-run-all-gof.R | 644 ++-- vignettes/ebrahim-farrington-intro.Rmd | 6 vignettes/ebrahim-gof-toolbox.Rmd | 113 vignettes/extensions.Rmd |only 78 files changed, 8644 insertions(+), 6899 deletions(-)
Title: Data-Driven Locally Weighted Regression for Trend and
Seasonality in TS
Description: Various methods for the identification of trend and seasonal
components in time series (TS) are provided. Among them is a data-driven locally
weighted regression approach with automatically selected bandwidth for
equidistant short-memory time series. The approach is a
combination / extension of the algorithms by
Feng (2013) <doi:10.1080/02664763.2012.740626> and Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598> and a brief
description of this new method is provided in the package documentation and in
more detail in Schulz (2026) <doi:10.32614/RJ-2026-025>.
Furthermore, the package allows its users to apply the base model of the
Berlin procedure, version 4.1, as described in Speth (2004) <https://www.destatis.de/DE/Methoden/Saisonbereinigung/BV41-methodenbericht-Heft3_2004.pdf?__blob=publicationFile>.
Permission to include this procedure was kindly provided by the Federal
Statistical Office of Germany.
Author: Yuanhua Feng [aut] ,
Dominik Schulz [aut, cre]
Maintainer: Dominik Schulz <dominik.schulz.r@gmail.com>
Diff between deseats versions 1.1.2 dated 2026-03-16 and 1.1.3 dated 2026-10-11
DESCRIPTION | 22 +- MD5 | 46 +++--- NAMESPACE | 60 ++++---- NEWS.md | 15 ++ R/AttachMessage.R | 3 R/class-s_semiarma.R | 19 ++ R/forecasting_functions.R | 2 README.md | 11 + build/vignette.rds |binary inst/CITATION |only inst/doc/deseats-workflow-example.html | 5 man/ENERGY.Rd | 56 +++---- man/GDP.Rd | 54 +++---- man/HOUSES.Rd | 54 +++---- man/RAINFALL.Rd | 52 +++---- man/RETAIL.Rd | 56 +++---- man/create_gain.Rd | 244 ++++++++++++++++----------------- man/deseats-package.Rd | 7 man/llin_decomp.Rd | 162 ++++++++++----------- man/plot-decomp-method.Rd | 130 ++++++++--------- man/plot-deseats_fc-method.Rd | 88 +++++------ man/plot-hfilter-method.Rd | 82 +++++------ man/predict-s_semiarma-method.Rd | 10 + man/run_decomposition.Rd | 58 +++---- tests/testthat/test-cores_prediction.R |only 25 files changed, 655 insertions(+), 581 deletions(-)
Title: Fast and Unified Synthetic Control Methods
Description: A unified 'Formula' interface to the Synthetic Control Method
(SCM) and related panel-data causal inference estimators: Synthetic
Difference-in-Differences (SDID), Generalized Synthetic Control (GSC),
Matrix Completion (MC), Time-Aware Synthetic Control (TASC), and Synthetic
Interventions (SI), together with an experimental-design variant.
Computational bottlenecks (quadratic programming, singular value
decomposition, and Kalman filtering) are implemented in 'C++' via
'RcppArmadillo'. Methods are described in Abadie, Diamond and Hainmueller
(2010) <doi:10.1198/jasa.2009.ap08746>, Arkhangelsky, Athey, Hirshberg,
Imbens and Wager (2021) <doi:10.1257/aer.20190159>, Xu (2017)
<doi:10.1017/pan.2016.2>, Athey, Bayati, Doudchenko, Imbens and Khosravi
(2021) <doi:10.1080/01621459.2021.1891924>, and Agarwal, Shah and Shen
(2025) <doi:10.1287/opre.2025.1590>.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between coresynth versions 0.5.0 dated 2026-08-25 and 1.0.1 dated 2026-10-11
DESCRIPTION | 6 MD5 | 104 NAMESPACE | 9 NEWS.md | 1973 +++--- R/RcppExports.R | 47 R/accessors.R | 23 R/broom.R | 713 +- R/conformal.R | 533 - R/coresynth-package.R | 11 R/export.R | 9 R/gsc.R | 137 R/mc.R | 233 R/plot.R | 1960 +++-- R/scm.R | 1104 ++- R/scm_fit.R | 1056 +-- R/scm_frontier.R |only R/scm_rank.R |only R/sdid.R | 1604 ++-- R/si.R | 1957 +++-- R/tasc.R | 18 R/utils.R | 323 README.md | 101 inst/doc/coresynth.Rmd | 307 inst/doc/coresynth.html | 15 man/coresynth-package.Rd | 10 man/figures/README-placebo-gaps-1.png |binary man/figures/README-plot-gap-1.png |binary man/figures/README-plot-trend-1.png |binary man/figures/README-plot-weights-1.png |binary man/gsc_boot.Rd | 5 man/mspe_ratio_pval.Rd | 24 man/plot.coresynth.Rd | 20 man/plot.scm_frontier.Rd |only man/plot.scm_placebo.Rd | 33 man/plot_data.Rd | 12 man/scm_balance_frontier.Rd |only man/scm_fit.Rd | 176 man/scm_inference.Rd | 90 man/scm_rank_pval.Rd |only man/sdid_inference.Rd | 4 man/soft_impute_cpp.Rd | 11 man/soft_impute_fe_cpp.Rd |only man/treated_outcomes.Rd | 15 src/RcppExports.cpp | 27 src/gsc.cpp | 34 src/inference.cpp | 30 src/mc.cpp | 107 src/optim.cpp | 149 src/scm.cpp | 244 src/sdid.cpp | 22 src/si.cpp | 14 src/tasc.cpp | 36 src/threads.h |only tests/testthat.R |only tests/testthat/test-integration.R |11156 +++++++++++++++++++--------------- tests/testthat/test-object-model.R | 25 vignettes/coresynth.Rmd | 307 57 files changed, 14527 insertions(+), 10267 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
Paul Schmidt [ctb] ,
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.29 dated 2026-08-20 and 1.30 dated 2026-10-11
DESCRIPTION | 10 MD5 | 56 +-- NEWS.md | 22 + R/class-color.R | 10 R/class-workbook-wrappers.R | 21 - R/class-workbook.R | 491 ++++++++++++++------------- R/conditional_formatting.R | 57 +++ R/deprecate.R | 2 R/read.R | 2 R/utils.R | 20 + R/wb_styles.R | 2 R/write.R | 11 inst/WORDLIST | 1 man/col_widths-wb.Rd | 4 man/convertToExcelDate.Rd | 3 man/create_colors_xml.Rd | 2 man/openxlsx2-package.Rd | 1 man/wbWorkbook.Rd | 10 man/wb_add_conditional_formatting.Rd | 2 man/wb_base_colors.Rd | 4 man/wb_color.Rd | 10 man/wb_save.Rd | 17 man/write_xlsx.Rd | 4 src/helper_functions.cpp | 94 ++++- tests/testthat/test-class-workbook.R | 24 + tests/testthat/test-conditional_formatting.R | 491 +++++++++++++++++++++++++++ tests/testthat/test-read_sources.R | 4 tests/testthat/test-save.R | 57 +++ tests/testthat/test-write.R | 25 + 29 files changed, 1164 insertions(+), 293 deletions(-)
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgstats versions 0.2.4 dated 2026-07-21 and 0.2.5 dated 2026-10-11
pkgstats-0.2.4/pkgstats/vignettes/installation.md |only pkgstats-0.2.4/pkgstats/vignettes/pkgstats.md |only pkgstats-0.2.5/pkgstats/DESCRIPTION | 14 +-- pkgstats-0.2.5/pkgstats/MD5 | 38 +++++---- pkgstats-0.2.5/pkgstats/NEWS.md | 6 + pkgstats-0.2.5/pkgstats/R/cran-data-archive.R | 45 +++++++---- pkgstats-0.2.5/pkgstats/R/cran-data-update.R | 47 ++++++++---- pkgstats-0.2.5/pkgstats/R/cran-data-utils.R |only pkgstats-0.2.5/pkgstats/R/pkgstats-summary.R | 3 pkgstats-0.2.5/pkgstats/build/vignette.rds |binary pkgstats-0.2.5/pkgstats/inst/doc/installation.html | 6 - pkgstats-0.2.5/pkgstats/inst/doc/pkgstats-data.html |only pkgstats-0.2.5/pkgstats/inst/doc/pkgstats-data.qmd |only pkgstats-0.2.5/pkgstats/inst/doc/pkgstats.html | 10 +- pkgstats-0.2.5/pkgstats/inst/extdata/pkgstats-col-types.csv |only pkgstats-0.2.5/pkgstats/tests/testthat/test-archive-trawl.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-col-types.R |only pkgstats-0.2.5/pkgstats/tests/testthat/test-cran-update.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-ctags.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-desc-stats.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-pkgstats.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-plot-network.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-summary.R | 2 pkgstats-0.2.5/pkgstats/vignettes/pkgstats-data.qmd |only 24 files changed, 116 insertions(+), 67 deletions(-)
Title: Identifies Package Differences
Description: Identifies differences between
versions of a package. Specifically, the functions help
determine if there are breaking changes from one package version
to the next. The package also includes a stability assessment,
to help you determine the overall stability of a package, or even
an entire repository.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Kevin Putschko [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between pkgdiff versions 1.0.4 dated 2026-07-14 and 1.0.5 dated 2026-10-11
DESCRIPTION | 11 MD5 | 44 +- NEWS.md | 5 R/pkgrepo.R | 17 R/utilities.R | 20 - build/vignette.rds |binary inst/doc/pkgdiff.R | 908 +++++++++++++++++++++++------------------------ man/pkg_cache.Rd | 18 man/pkg_diff.Rd | 18 man/pkg_info.Rd | 18 man/pkg_repo.Rd | 12 man/pkg_stability.Rd | 18 man/pkg_versions.Rd | 18 man/pkgdiff.Rd | 5 man/print.pcache.Rd | 18 man/print.pdiff.Rd | 18 man/print.pdiff_score.Rd | 18 man/print.pinfo.Rd | 18 man/print.prepo.Rd | 12 man/print.rbreak.Rd | 12 man/print.rstability.Rd | 12 man/repo_breakages.Rd | 12 man/repo_stability.Rd | 12 23 files changed, 634 insertions(+), 610 deletions(-)
Title: Spherical k-Means Clustering
Description: Algorithms to compute spherical k-means partitions.
Features several methods, including a genetic and a fixed-point
algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre] ,
Ingo Feinerer [aut] ,
Martin Kober [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between skmeans versions 0.2-20 dated 2026-03-26 and 0.2-21 dated 2026-10-11
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- R/skmeans.R | 21 --------------------- build/partial.rdb |binary man/skmeans.Rd | 20 -------------------- 5 files changed, 8 insertions(+), 50 deletions(-)
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted, optional
persistence of the look, named wallpaper scenes, helpers to
match 'ggplot2', 'plotly', 'gt', and 'DT' output to the glass pack,
a flatten mode for print and screenshots, and documented CSS tokens.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.4.0 dated 2026-09-20 and 0.5.0 dated 2026-10-11
DESCRIPTION | 12 MD5 | 159 +- NAMESPACE | 3 NEWS.md | 239 +++ R/glass-accent.R | 35 R/glass-flatten.R | 10 R/glass-intensity.R | 48 R/glass-page.R | 47 R/glass-plots.R | 57 R/glass-react.R |only R/glass-theme.R | 409 ++++- R/glass-tokens.R | 124 + R/shinyglass-package.R | 166 +- README.md | 96 + build/vignette.rds |binary inst/WORDLIST | 43 inst/doc/compatibility.Rmd | 14 inst/doc/compatibility.html | 39 inst/doc/migrating.R |only inst/doc/migrating.Rmd |only inst/doc/migrating.html |only inst/doc/playground.Rmd | 7 inst/doc/playground.html | 5 inst/doc/shinychat.R |only inst/doc/shinychat.Rmd |only inst/doc/shinychat.html |only inst/doc/shinyglass.R |only inst/doc/shinyglass.Rmd |only inst/doc/shinyglass.html |only inst/doc/shinyreact.R |only inst/doc/shinyreact.Rmd |only inst/doc/shinyreact.html |only inst/doc/theming.R | 17 inst/doc/theming.Rmd | 56 inst/doc/theming.html | 69 inst/examples/_shared |only inst/examples/apple-glass-reference.R | 38 inst/examples/bslib-dashboard.R | 32 inst/examples/compat-glass.R |only inst/examples/demo-app.R | 28 inst/examples/inputs-gallery.R | 28 inst/examples/intensity-slider-demo.R | 6 inst/examples/shinychat-glass |only inst/examples/shinyreact-glass |only inst/js/glass-intensity-head.js |only inst/js/glass-ios27.js |only inst/js/shiny-glass.js | 539 +++++-- inst/js/shinyglass-react.js |only inst/scss/glass.scss | 2288 +++++++++++++++++++++++++++++--- man/dt_options_glass.Rd | 12 man/figures |only man/glass_accent_input.Rd | 24 man/glass_add_tokens.Rd | 9 man/glass_css_tokens.Rd | 11 man/glass_flatten.Rd | 8 man/glass_intensity_slider.Rd | 22 man/glass_page.Rd | 27 man/glass_page_react.Rd |only man/glass_plot_colors.Rd | 17 man/glass_plot_surface_input.Rd | 20 man/glass_preset_input.Rd | 20 man/glass_react_dependency.Rd |only man/glass_resolved_preset.Rd | 23 man/glass_scene_input.Rd | 20 man/glass_scenes.Rd | 13 man/glass_system_colors.Rd | 24 man/glass_theme.Rd | 91 + man/glass_theme_dependencies.Rd |only man/glass_theme_toggle.Rd | 23 man/glass_token_pack.Rd | 9 man/gt_theme_glass.Rd | 15 man/observe_glass.Rd | 37 man/observe_glass_accent.Rd | 30 man/observe_glass_intensity.Rd | 33 man/observe_glass_plot_surface.Rd | 42 man/observe_glass_preset_input.Rd | 33 man/observe_glass_scene.Rd | 41 man/observe_glass_theme_toggle.Rd | 33 man/plotly_glass.Rd | 14 man/shinyglass-package.Rd | 176 ++ man/theme_glass.Rd | 12 man/update_glass_theme.Rd | 27 tests/testthat/test-deploy-core5.R |only tests/testthat/test-glass-theme.R | 569 +++++++ tests/testthat/test-phone-preview.R |only tests/testthat/test-pkgdown-reference.R |only tests/testthat/test-shinyreact.R |only vignettes/compatibility.Rmd | 14 vignettes/migrating.Rmd |only vignettes/playground.Rmd | 7 vignettes/shinychat.Rmd |only vignettes/shinyglass.Rmd |only vignettes/shinyreact.Rmd |only vignettes/theming.Rmd | 56 94 files changed, 5454 insertions(+), 672 deletions(-)
Title: H3 Extension of 'DuckDB'
Description: Fast & memory-efficient functions to analyze and manipulate large
data sets. It leverages the fast analytical
capabilities of 'DuckDB' and its spatial extension (see <https://duckdb.org/community_extensions/extensions/h3>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckh3 versions 0.1.0 dated 2026-04-24 and 0.2.0 dated 2026-10-11
DESCRIPTION | 11 MD5 | 105 - NAMESPACE | 64 NEWS.md | 32 R/h3_extension.R | 224 +- R/h3_geom_to.R |only R/h3_get_resolution.R | 154 - R/h3_h3_to.R | 656 +++--- R/h3_hierarchy.R | 864 ++++---- R/h3_is.R | 460 ++-- R/h3_lonlat_to.R | 408 ++-- R/h3_points_to.R | 596 +++--- R/h3_templates.R | 679 ++++-- R/h3_vertex.R | 634 +++--- R/utils_not_exported.R | 494 +++-- README.md | 222 +- inst/extdata/example_pts.csv | 202 +- man/ddbh3_create_conn.Rd | 102 - man/ddbh3_geom_to.Rd |only man/ddbh3_get_child_pos.Rd | 174 - man/ddbh3_get_hierarchy.Rd | 374 +-- man/ddbh3_get_icosahedron_faces.Rd | 200 +- man/ddbh3_get_resolution.Rd | 182 - man/ddbh3_h3_to.Rd | 400 ++-- man/ddbh3_is.Rd | 342 +-- man/ddbh3_lonlat_to.Rd | 350 +-- man/ddbh3_points_to.Rd | 250 +- man/ddbh3_vertex.Rd | 390 +-- man/roxygen/templates/conn_null.R | 4 man/roxygen/templates/desc_formats.R | 8 man/roxygen/templates/h3.R | 4 man/roxygen/templates/h3vertex.R | 4 man/roxygen/templates/lat.R | 2 man/roxygen/templates/lon.R | 2 man/roxygen/templates/memory_limit_gb.R | 2 man/roxygen/templates/name.R | 8 man/roxygen/templates/nested.R | 6 man/roxygen/templates/new_column.R | 4 man/roxygen/templates/output.R | 20 man/roxygen/templates/overwrite.R | 4 man/roxygen/templates/quiet.R | 4 man/roxygen/templates/resolution.R | 4 man/roxygen/templates/returns_tbl.R | 18 man/roxygen/templates/threads.R | 2 man/roxygen/templates/x.R | 18 tests/testthat.R | 24 tests/testthat/setup.R | 22 tests/testthat/test-h3_geom_to.R |only tests/testthat/test-h3_get_resolution.R | 449 ++-- tests/testthat/test-h3_h3_to.R | 2114 ++++++++++----------- tests/testthat/test-h3_hierarchy.R | 3153 ++++++++++++++++---------------- tests/testthat/test-h3_is.R | 1814 +++++++++--------- tests/testthat/test-h3_lonlat_to.R | 1150 +++++------ tests/testthat/test-h3_points_to.R | 998 +++++----- tests/testthat/test-h3_vertex.R | 2400 ++++++++++++------------ 55 files changed, 10644 insertions(+), 10163 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [ctb]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.2.4 dated 2026-08-31 and 0.2.5 dated 2026-10-11
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- NAMESPACE | 46 +++++++++++++++++++++++--------------- NEWS.md | 9 +++++++ R/mff.R | 5 ++-- R/tune.mff.R | 19 +++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mff-workflow.html | 4 +-- man/mff.Rd | 3 +- tests/testthat/test-mff-predict.R | 2 - tests/testthat/test-tune-mff.R | 36 +++++++++++++++++++++++++++++ 12 files changed, 109 insertions(+), 45 deletions(-)
Title: Measurement and Linear Hypothesis Models for Lambda Star
Description: Estimates intrinsic and captured noncentrality from parallel
measurements and evaluates the numerical parsimony functional for an
explicitly encoded hypothesis matrix, formula, or compatible linear model.
Includes common-case model comparisons, quantized entropy capacity,
controlled temperature integration, and explicit singularity diagnostics.
Uses manuscript projection estimates by default, with an explicit alternative
population estimator. Supports common nuisance adjustment and ordinary case
or cluster percentile bootstrap intervals, with diagnostics for undefined
estimates and preserved model coding.
Provides reusable row-bound design specifications and explicit conditional
term blocks, named linear restrictions, explicit predictor-grid contrasts,
and fixed or reevaluated basis recipes under a homogeneous isotropic
measurement-fluctuation assumption. Supports explicit known-reference
mean hypotheses and paired differences from parallel measurement pairs.
Encodes fixed person-by-oc [...truncated...]
Author: Mike Hammes [aut, cre, cph]
Maintainer: Mike Hammes <mike.hammes@mikehammes.name>
Diff between lambdastar versions 0.8.1 dated 2026-10-07 and 0.8.2 dated 2026-10-11
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS.md | 13 ++++++++++ R/measurement.R | 13 ++++++---- README.md | 28 ++++++++++++++++++----- tests/cases/measurement.R | 55 ++++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 106 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-01 1.1
2024-12-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-27 1.0.0
2026-05-20 0.9.8
2026-04-28 0.9.7
Title: Prophet Modelling Interface for 'fable'
Description: Allows prophet models from the 'prophet' package to be used in a tidy workflow with the modelling interface of 'fabletools'. This extends 'prophet' to provide enhanced model specification and management, performance evaluation methods, and model combination tools.
Author: Mitchell O'Hara-Wild [aut, cre],
Sean Taylor [ctb] ,
Ben Letham [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fable.prophet versions 0.1.1 dated 2026-10-02 and 1.0.0 dated 2026-10-11
DESCRIPTION | 14 MD5 | 42 +- NAMESPACE | 3 NEWS.md | 30 ++ R/model.R | 462 ++++++++++++++++++++++++++----- R/prophet.R | 1 README.md | 85 +++-- inst/doc/intro.R | 24 + inst/doc/intro.Rmd | 42 ++ inst/doc/intro.html | 95 +++++- man/components.fbl_prophet.Rd | 5 man/fable.prophet-package.Rd | 1 man/figures/README-components-plot-1.png |binary man/figures/README-components-plot-2.png |binary man/figures/README-fable-1.png |binary man/figures/README-plot-1.png |binary man/forecast.fbl_prophet.Rd | 13 man/generate.fbl_prophet.Rd |only man/prophet.Rd | 83 +++++ man/refit.fbl_prophet.Rd |only man/tidy.fbl_prophet.Rd | 10 tests/testthat/test-prophet.R | 324 +++++++++++++++++++++ vignettes/intro.Rmd | 42 ++ 23 files changed, 1124 insertions(+), 152 deletions(-)