Title: Reusable Data Viewer Module for 'shiny'
Description: Provides a reusable 'shiny' module for viewing tabular data with a searchable 'reactable' table and a variable summary sidebar built with 'bslib'.
Author: Ryan Harrison [aut, cre, cph]
Maintainer: Ryan Harrison <harrison.ryan.w@gmail.com>
Diff between shinydataviewer versions 0.1.0 dated 2026-04-09 and 0.2.0 dated 2026-08-04
DESCRIPTION | 11 +- MD5 | 56 +++++++------ NEWS.md | 12 ++ R/data_summary.R | 77 ++++++++++++++++--- R/data_viewer_assets.R | 40 +++++++++ R/mod_data_viewer.R | 26 ++++-- R/ui_components.R | 46 +++++++++++ README.md | 28 ++++++ build/vignette.rds |binary inst/WORDLIST | 2 inst/app/www/data-viewer.css | 93 ++++++++++++++++++++--- inst/doc/customization.R | 6 + inst/doc/customization.Rmd | 18 ++++ inst/doc/customization.html | 49 +++++++----- inst/doc/get-started.R | 3 inst/doc/get-started.Rmd | 10 ++ inst/doc/get-started.html | 9 +- inst/examples/upload-dataset |only man/data_viewer_card_ui.Rd | 7 + man/data_viewer_server.Rd | 2 man/data_viewer_ui.Rd | 7 + man/shinydataviewer-package.Rd | 5 + man/summarize_columns.Rd | 13 ++- tests/spelling.R |only tests/testthat/helper-load-package.R | 18 ---- tests/testthat/test-data-summary-edge-cases.R | 56 +++++++++++++ tests/testthat/test-module-server.R | 18 ++++ tests/testthat/test-ui-components.R | 105 ++++++++++++++++++++++++++ vignettes/customization.Rmd | 18 ++++ vignettes/get-started.Rmd | 10 ++ 30 files changed, 640 insertions(+), 105 deletions(-)
More information about shinydataviewer at CRAN
Permanent link
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 5.0.2 dated 2026-06-11 and 5.1.0 dated 2026-08-04
nlmixr2plot-5.0.2/nlmixr2plot/R/nlmixr2PlotList.R |only nlmixr2plot-5.0.2/nlmixr2plot/tests/testthat/test-nlmixr2PlotList.R |only nlmixr2plot-5.1.0/nlmixr2plot/DESCRIPTION | 12 - nlmixr2plot-5.1.0/nlmixr2plot/MD5 | 34 +- nlmixr2plot-5.1.0/nlmixr2plot/NAMESPACE | 4 nlmixr2plot-5.1.0/nlmixr2plot/NEWS.md | 51 ++++ nlmixr2plot-5.1.0/nlmixr2plot/R/plot.bsv.R |only nlmixr2plot-5.1.0/nlmixr2plot/R/plot.nlmixr2.R | 108 ++++----- nlmixr2plot-5.1.0/nlmixr2plot/R/plot.nlmixr2AugPred.R | 69 +++--- nlmixr2plot-5.1.0/nlmixr2plot/R/vpcPlot.R | 114 ++++++++-- nlmixr2plot-5.1.0/nlmixr2plot/man/plot.nlmixr2AugPred.Rd | 6 nlmixr2plot-5.1.0/nlmixr2plot/man/plot.nlmixr2FitData.Rd | 19 + nlmixr2plot-5.1.0/nlmixr2plot/man/traceplot.Rd | 3 nlmixr2plot-5.1.0/nlmixr2plot/man/vpcPlot.Rd | 4 nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat.R | 60 +++++ nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-gglist-integration.R |only nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-bsv.R |only nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-cens.R | 49 +++- nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-multiple-endpoints.R | 18 + nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots.R | 26 +- nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-vpc-cens-cols.R |only 21 files changed, 422 insertions(+), 155 deletions(-)
Title: Save 'nlmixr2' Fits in a Format Readable Outside 'nlmixr2'
Description: Provides tools to save 'nlmixr2' fitted models in a portable format
readable outside of 'nlmixr2' and independent of the package version.
'nlmixr2' fits and compares nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving uses compiled
C code from the 'rxode2' package (Wang, Hallow, and James 2015
<doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2save versions 0.1.0 dated 2026-06-17 and 0.2.0 dated 2026-08-04
DESCRIPTION | 9 LICENSE | 4 MD5 | 77 NAMESPACE | 62 NEWS.md | 103 - R/RcppExports.R | 57 R/nlmixr2save-package.R | 10 R/save.R | 2782 +++++++++++++++++----------- R/simplify.R | 194 + README.md | 994 +++++----- build/vignette.rds |binary inst/doc/register-simulation-functions.R | 74 inst/doc/register-simulation-functions.Rmd | 258 +- inst/doc/register-simulation-functions.html | 915 ++++----- inst/doc/sharing-fits.R |only inst/doc/sharing-fits.Rmd |only inst/doc/sharing-fits.html |only inst/doc/uses.R | 78 inst/doc/uses.Rmd | 382 +-- inst/doc/uses.html | 1043 +++++----- inst/doc/version-tracking.R |only inst/doc/version-tracking.Rmd |only inst/doc/version-tracking.html |only man/colon-equals.Rd | 199 +- man/dot-assignParent.Rd | 48 man/dot-assignRestore.Rd | 44 man/dot-nlmixr2saveProps.Rd | 106 - man/loadFit.Rd | 38 man/nlmixr2saveInvalidate.Rd |only man/nlmixr2saveParFixedDf.Rd | 56 man/nlmixr2saveShare.Rd |only man/nlmixrDataSimplify.Rd | 79 man/saveFit.Rd | 149 - man/saveFitItem.Rd | 88 man/saveFitRandom.Rd | 60 src/RcppExports.cpp | 9 src/nlmixr2fix.cpp | 58 tests/testthat.R | 33 tests/testthat/test-save.R | 1416 ++++++++------ tests/testthat/test-simplify.R | 223 +- tests/testthat/test-vig-options.R |only vignettes/register-simulation-functions.Rmd | 258 +- vignettes/sharing-fits.Rmd |only vignettes/uses.Rmd | 382 +-- vignettes/version-tracking.Rmd |only 45 files changed, 5712 insertions(+), 4576 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Anne Keunecke [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Richard Hooijmaijers [ctb],
Michael Wayne Ke [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 5.0.0 dated 2025-11-30 and 7.0.1 dated 2026-08-04
DESCRIPTION | 22 +++++---- MD5 | 14 +++--- NAMESPACE | 2 NEWS.md | 35 +++++++++++++++ R/nlmixr2CheckInstall.R | 55 +++++++++++++++++++++--- R/verse.R | 102 +++++++++++++++++++++++++-------------------- README.md | 83 +++++++++++------------------------- man/nlmixr2CheckInstall.Rd | 4 + 8 files changed, 192 insertions(+), 125 deletions(-)
Title: Survey Sampling Algorithms
Description: Fast implementations of survey sampling algorithms for
single-stage probability sampling from finite populations,
written in C.
Provides equal probability methods (simple random sampling,
systematic, Bernoulli), unequal probability methods (conditional
Poisson / maximum entropy, Sampford, Brewer, systematic PPS, Pareto,
sequential Poisson, Poisson, Chromy's minimum replacement,
multinomial), balanced sampling via the cube method, and
spatially balanced sampling via the local pivotal method and
spatially correlated Poisson sampling.
All sampling functions return design objects carrying sample
indices, inclusion probabilities, and design metadata. Generics
compute joint inclusion probabilities, pairwise expectations, and
sampling covariances for variance estimation. Mostly based on
algorithms from Tillé (2006, <doi:10.1007/0-387-34240-0>).
Author: Ahmadou Dicko [aut, cre] ,
Thomas Lumley [ctb],
Wilmer Prentius [ctb, cph] cube implementation from which src/cube.c was ported)
Maintainer: Ahmadou Dicko <mail@ahmadoudicko.com>
Diff between sondage versions 0.9.0 dated 2026-08-03 and 0.9.1 dated 2026-08-04
DESCRIPTION | 6 ++-- MD5 | 42 +++++++++++++++++----------------- R/balanced_wor.R | 2 - R/constructors.R | 4 +-- R/equal_prob.R | 2 - R/generics.R | 8 ++++-- R/register.R | 2 - R/unequal_prob.R | 6 ++-- README.md | 52 ++++++++++++++++--------------------------- inst/doc/custom-methods.html | 42 +++++++++++++++++----------------- inst/doc/sondage.Rmd | 2 - inst/doc/sondage.html | 6 +++- man/balanced_wor.Rd | 2 - man/equal_prob_wor.Rd | 2 - man/joint_expected_hits.Rd | 2 - man/joint_inclusion_prob.Rd | 2 - man/register_method.Rd | 2 - man/sampling_cov.Rd | 5 ++++ man/sondage_sample.Rd | 4 +-- man/unequal_prob_wor.Rd | 6 ++-- src/joint_probs.c | 12 +++++---- vignettes/sondage.Rmd | 2 - 22 files changed, 107 insertions(+), 106 deletions(-)
Title: LLM Wiki Engine
Description: Personal wiki engine with a large language model (LLM) as
research assistant. Supports guided sessions through a 'Claude Code'
<https://github.com/anthropics/claude-code> skill bundle and
autonomous research runs from R via autoresearch(). Results land in
a structured vault of markdown pages with 'YAML' frontmatter and
wikilinks, ready for hand-editing in your favourite editor
alongside the LLM. Vaults are seeded with 'CLAUDE.md' and
'AGENTS.md' so 'Claude Code', 'Codex'
<https://github.com/openai/codex>, and other agents share the same
operating instructions. Can adopt an existing 'Obsidian'
<https://obsidian.md/> vault in place via init_vault(adopt = TRUE).
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between pensar versions 0.6.4 dated 2026-06-24 and 0.7.0 dated 2026-08-04
DESCRIPTION | 8 - MD5 | 91 ++++++------ NAMESPACE | 1 NEWS.md | 54 +++++++ R/audits.R | 1 R/autoresearch.R | 1 R/autoresearch_backends.R | 1 R/autoresearch_program.R | 1 R/autoresearch_steps.R | 25 ++- R/backlinks.R | 1 R/db.R | 1 R/export.R | 7 R/git.R | 299 +++++++++++++++++++++++++++++++++++++++--- R/index.R | 1 R/ingest.R | 1 R/ingest_agent_context.R | 1 R/ingest_briefing.R | 1 R/ingest_repo.R | 1 R/ingest_url.R | 1 R/lint.R | 1 R/log.R | 1 R/manifest.R | 98 +++++++++++++ R/merge.R |only R/migrate.R | 1 R/outlinks.R | 1 R/parse.R | 1 R/pensar-package.R | 1 R/pensarignore.R | 1 R/registry.R | 1 R/retrieval.R | 1 R/show_page.R | 1 R/skills.R | 1 R/status.R | 20 ++ R/vault.R | 90 ++++++++++-- R/vault_graph.R | 1 R/wiki_write.R | 1 README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/bin/pensar | 3 inst/scripts/merge.R |only inst/tinytest/test_git.R | 243 +++++++++++++++++++++++++++++++++- inst/tinytest/test_manifest.R | 81 +++++++++++ inst/tinytest/test_merge.R |only inst/tinytest/test_nested.R |only man/init_vault.Rd | 11 + man/status.Rd | 5 man/vault_commit.Rd | 41 ++++- man/vault_merge.Rd |only 49 files changed, 970 insertions(+), 139 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.8.0-1 dated 2026-06-04 and 0.9.0 dated 2026-08-04
DESCRIPTION | 10 MD5 | 68 - NAMESPACE | 1 NEWS.md | 10 R/convert-array.R | 4 R/ipc.R | 24 R/nanoarrow-package.R | 7 configure | 21 man/as_nanoarrow_schema.Rd | 4 man/as_nanoarrow_schema.python.builtin.object.Rd | 2 man/convert_array.Rd | 6 man/example_ipc_stream.Rd | 4 man/infer_nanoarrow_ptype.Rd | 2 man/na_vctrs.Rd | 2 man/nanoarrow-package.Rd | 1 man/nanoarrow_version.Rd | 4 src/Makevars.ucrt | 18 src/Makevars.win | 18 src/flatcc.c | 9 src/flatcc/flatcc_endian.h | 2 src/flatcc/flatcc_types.h | 5 src/flatcc/flatcc_verifier.h | 4 src/flatcc/portable/flatcc_portable.h |only src/flatcc/portable/pstdint.h | 2 src/init.c | 2 src/nanoarrow.c | 430 ++++++ src/nanoarrow.h | 145 ++ src/nanoarrow.hpp | 8 src/nanoarrow_ipc.c | 1505 ++++++++++++++++++----- src/nanoarrow_ipc.h | 318 ++++ src/nanoarrow_ipc.hpp | 54 src/version.c | 8 tests/testthat/test-convert-array-stream.R | 96 + tests/testthat/test-convert-array.R | 75 + tests/testthat/test-ipc.R | 160 ++ tools/test_lz4.c |only 36 files changed, 2578 insertions(+), 451 deletions(-)
Title: Basis Expansions for Regression Modeling
Description: Provides various basis expansions for flexible regression modeling,
including random Fourier features (Rahimi & Recht, 2007)
<https://proceedings.neurips.cc/paper_files/paper/2007/file/013a006f03dbc5392effeb8f18fda755-Paper.pdf>,
exact kernel / Gaussian process feature maps, prior features for Bayesian
Additive Regression Trees (BART) (McCartan & Huang, 2026) <doi:10.48550/arXiv.2607.28844>,
and a helpful interface for n-way interactions. The provided functions may
be used within any modeling formula, allowing the use of kernel methods and
other basis expansions in modeling functions that do not otherwise support
them. Along with the basis expansions, a number of kernel functions are also
provided, which support kernel arithmetic to form new kernels. Basic ridge
regression functionality is included as well.
Author: Cory McCartan [aut, cre, cph]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between bases versions 0.2.0 dated 2026-02-27 and 0.2.1 dated 2026-08-04
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/b_bart.R | 27 ++++++++++++++++----------- R/b_gff.R | 4 ++-- R/b_rff.R | 2 +- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary man/b_bart.Rd | 26 +++++++++++++++----------- man/b_gff.Rd | 2 +- man/bases-package.Rd | 7 ++++++- 12 files changed, 64 insertions(+), 45 deletions(-)
Title: Minimal R Documentation Generator
Description: A deterministic, dependency-free documentation generator for R
packages. Generates valid Rd files and NAMESPACE from 'roxygen2'-style comments
using only base R. Supports a strict subset of tags with no markdown parsing,
no inference magic, and explicit-only behavior.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between tinyrox versions 0.4.0 dated 2026-06-24 and 0.4.1 dated 2026-08-04
DESCRIPTION | 8 +- MD5 | 18 +++-- NEWS.md | 7 ++ R/rd.R | 130 ++++++++++++++++++++++++++--------------- README.md | 28 ++++++++ inst/tinytest/test_rd.R | 152 ++++++++++++++++++++++++++++++++++++++++++++++++ man/document.Rd | 9 ++ man/escape_percent.Rd |only man/format_usage.Rd | 6 + man/generate_rd.Rd | 7 +- man/wrap_usage_arg.Rd |only 11 files changed, 302 insertions(+), 63 deletions(-)
Title: 'OpenAI' Compatible Speech-to-Text API Client
Description: A minimal-dependency R client for 'OpenAI'-compatible speech-to-text
APIs (see <https://developers.openai.com/api/reference/resources/audio>) with
optional local fallbacks. Supports 'OpenAI', local servers, and the
'whisper' package for local transcription.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between stt.api versions 0.3.0 dated 2026-06-19 and 0.3.1 dated 2026-08-04
DESCRIPTION | 12 - LICENSE | 2 MD5 | 29 +++- NAMESPACE | 1 NEWS.md | 126 ++++++++++++++++++++ R/internal_api.R | 224 ++++++++++++++++++++++++++++++++---- R/internal_interop.R |only R/label_speakers.R |only R/stt.R | 170 +++++++++++++++++++++++++-- inst/audio |only inst/tinytest/test_diarize.R |only inst/tinytest/test_interop.R |only inst/tinytest/test_label_speakers.R |only man/dot-audio_data_uri.Rd |only man/dot-audio_mime.Rd |only man/dot-is_diarizing.Rd |only man/dot-parse_api_segments.Rd |only man/dot-validate_known_speakers.Rd |only man/label_speakers.Rd |only man/stt.Rd | 101 ++++++++++++++-- 20 files changed, 609 insertions(+), 56 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan Shumaker [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.5 dated 2026-07-28 and 5.1.6 dated 2026-08-04
DESCRIPTION | 14 - MD5 | 43 ++-- NAMESPACE | 1 NEWS.md | 77 ++++++++ R/eventSens.R | 62 +++++- R/rxode2.R | 85 ++++++++- R/rxode2_md5.R | 2 inst/doc/rxode2-syntax.html | 26 +- inst/include/rxode2.h | 14 + inst/include/rxode2parseVer.h | 4 inst/include/rxode2ptr.h | 75 +++++++- inst/tools/workaround.R | 28 ++- man/rxEventSensLoadModel.Rd | 4 man/rxStripModelSrc.Rd |only src/init.c | 54 +++++ src/linCmt.cpp | 10 + src/par_solve.cpp | 240 ++++++++++++++++++++++++++ src/rx2api.c | 37 +++- src/rxode2_sundials_stan_compat.h | 15 + src/rxthreefry.cpp | 130 +++++++++++++- tests/testthat/test-event-sensitivities-api.R |only tests/testthat/test-plot.R | 18 + tests/testthat/test-random.R | 35 +++ tests/testthat/test-rxpre-cache-key.R |only 24 files changed, 889 insertions(+), 85 deletions(-)
Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of
data to/from the file system. It builds one (or more) centralized
repository where R objects are stored with rich annotations,
including corresponding code chunks, and easily searched and
retrieved. See Napolitano (2017) <doi:10.1186/s12859-017-1510-6> for further
information.
Author: Francesco Napolitano [aut, cre]
Maintainer: Francesco Napolitano <franapoli@gmail.com>
This is a re-admission after prior archival of version 2.1.5 dated 2020-02-08
Diff between repo versions 2.1.5 dated 2020-02-08 and 2.1.7 dated 2026-08-04
DESCRIPTION | 22 - MD5 | 35 +- NEWS.md | 425 +++++++++++---------------- R/repo.R | 6 R/repo_private.R | 2 R/repo_public.R | 15 README.md | 58 ++- build/partial.rdb |only build/vignette.rds |binary inst/README-depgraph-1.png |binary inst/doc/index.R | 108 +++--- inst/doc/index.Rmd | 6 inst/doc/index.html | 707 ++++++++++++++++++++++++++------------------- man/repo-package.Rd | 5 man/repo_build.Rd | 9 man/repo_dependencies.Rd | 2 man/repo_open.Rd | 4 man/repo_pies.Rd | 4 vignettes/index.Rmd | 6 19 files changed, 762 insertions(+), 652 deletions(-)
Title: Matrix End-to-End Encryption Primitives
Description: 'Olm' and 'Megolm' encryption ratchet primitives for the
'Matrix' messaging protocol <https://matrix.org/>, wrapping the
'vodozemac' Rust crate. Provides device-key generation, one-time-key
management, 1:1 'Olm' sessions, and 'Megolm' group sessions. Pairs
with the 'mx.api' package, which handles 'Matrix' HTTP transport.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
The Matrix.org Foundation C.I.C. [ctb, cph] ,
Authors of the dependency Rust crates [ctb]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.crypto versions 0.2.0 dated 2026-06-12 and 0.2.1 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 13 +++++++++++++ build/vignette.rds |binary tools/configure.R | 43 +++++++++++++++++++++++++++++++++---------- 5 files changed, 54 insertions(+), 18 deletions(-)
Title: Stateful Matrix Client Helpers
Description: Stateful helpers for building 'Matrix' (<https://matrix.org>)
chat clients in R. Builds on the low-level 'mx.api' Client-Server API
bindings, adding local configuration persistence, room resolution,
sync cursor handling, sync-event extraction, invite acceptance, a
conservative Markdown-to-HTML converter for formatted messages, and
'Olm'/'Megolm' end-to-end encryption orchestration over the optional
'mx.crypto' package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.client versions 0.1.1 dated 2026-06-19 and 0.2.0 dated 2026-08-04
DESCRIPTION | 10 +- MD5 | 59 +++++++----- NAMESPACE | 5 + NEWS.md | 90 ++++++++++++++++++ R/config.R | 64 +++++++++++++ R/crypto.R | 131 +++++++++++++++++++++++++-- R/e2ee.R | 123 ++++++++++++++++++++++--- R/markdown.R | 167 +++++++++++++++++++++++++++++------ R/messages.R | 17 ++- R/profile.R |only R/tables.R |only R/transport.R | 104 ++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/skills |only inst/tinytest/test_crypto.R | 11 +- inst/tinytest/test_e2ee.R | 120 ++++++++++++++++++++++++- inst/tinytest/test_markdown.R | 40 ++++++++ inst/tinytest/test_mx.client.R | 47 +++++++++ inst/tinytest/test_relogin.R | 7 + inst/tinytest/test_tables.R |only inst/tinytest/test_transport.R |only man/mx_crypto_claim_otks.Rd | 9 + man/mx_crypto_encrypt_for_devices.Rd | 14 ++ man/mx_crypto_handle_to_device.Rd | 32 +++++- man/mx_crypto_known_devices.Rd | 9 + man/mx_crypto_process_sync.Rd | 10 +- man/mx_crypto_room_key_payload.Rd | 15 ++- man/mx_extract_text_events.Rd | 6 + man/mx_markdown_to_html.Rd | 2 man/mx_pill_mentions.Rd | 15 +-- man/mx_send_table.Rd |only man/mx_set_displayname.Rd |only man/mx_table_html.Rd |only man/print.mx_client_config.Rd |only 35 files changed, 975 insertions(+), 132 deletions(-)
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] ,
Chester Ismay [aut] ,
Andrew Bray [ctb] ,
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] ,
Will Hopper [ctb] ,
Benjamin S. Baumer [ctb] ,
Marium Tapal [ctb] ,
Wayne Ndlovu [ctb],
Catherine Peppers [ctb],
Annah Mutaya [ctb],
A [...truncated...]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.7.0 dated 2024-09-01 and 0.8.0 dated 2026-08-04
DESCRIPTION | 48 +- MD5 | 117 +++-- NAMESPACE | 13 NEWS.md | 19 R/datasets.R | 42 + R/geom_categorical_model.R | 21 R/get_correlation.R | 174 +++++-- R/moderndive.R | 12 R/plot_3d_regression.R |only R/regression_functions.R | 421 ++++++++++--------- R/view.R |only R/zzz.R |only build/partial.rdb |binary build/vignette.rds |binary data/pennies_resamples.rda |binary inst/doc/moderndive.R | 56 +- inst/doc/moderndive.Rmd | 2 inst/doc/moderndive.html | 61 +- inst/doc/paper.Rmd | 2 inst/doc/paper.pdf |binary man/MA_schools.Rd | 2 man/View.Rd |only man/early_january_2023_weather.Rd | 3 man/early_january_weather.Rd | 3 man/geom_categorical_model.Rd | 25 - man/geom_parallel_slopes.Rd | 8 man/get_correlation.Rd | 76 ++- man/get_regression_points.Rd | 38 - man/get_regression_summaries.Rd | 9 man/get_regression_table.Rd | 26 - man/house_prices.Rd | 4 man/ma_traffic_2020_vs_2019.Rd | 2 man/moderndive.Rd | 12 man/pennies_resamples.Rd | 2 man/pennies_sample.Rd | 2 man/plot_3d_regression.Rd |only man/reexports.Rd | 2 man/saratoga_houses.Rd | 4 man/spotify_52_original.Rd | 6 man/spotify_52_shuffled.Rd | 6 man/spotify_by_genre.Rd | 8 tests/testthat/_snaps |only tests/testthat/helper-utils.R | 4 tests/testthat/test-datasets.R |only tests/testthat/test-geom_categorical_model.R | 187 ++++++++ tests/testthat/test-geom_parallel_slopes.R | 51 ++ tests/testthat/test-get_correlation.R | 210 +++++++++ tests/testthat/test-get_regression_functions.R | 551 ++++++++++++++++++++++++- tests/testthat/test-plot_3d_regression.R |only tests/testthat/test-tidy_summary.R | 160 +++++++ tests/testthat/test-view.R |only vignettes/moderndive.Rmd | 2 vignettes/paper.Rmd | 2 vignettes/paper.html | 36 - vignettes/paper.md | 2 55 files changed, 1885 insertions(+), 546 deletions(-)
Title: A Fast and Lightweight Logging System for R, Based on 'log4j'
Description: Provides a fast, lightweight, object-oriented approach to
logging based on the widely-emulated 'log4j' system and etymology.
Loggers write messages to one or more destinations, such as the
console, a file, or a remote server, using a format you control.
Messages below the chosen severity threshold are discarded cheaply, so
logging calls can be left in production code.
Author: John Myles White [aut, cph],
Kenton White [ctb],
Kirill Mueller [ctb],
Aaron Jacobs [aut],
Posit Software, PBC [cph, fnd] ,
Hadley Wickham [cre]
Maintainer: Hadley Wickham <hadley@posit.co>
This is a re-admission after prior archival of version 0.4.4 dated 2024-10-12
Diff between log4r versions 0.4.4 dated 2024-10-12 and 0.5.0 dated 2026-08-04
log4r-0.4.4/log4r/R/create.logger.R |only log4r-0.4.4/log4r/R/level.logger.R |only log4r-0.4.4/log4r/R/logfile.logger.R |only log4r-0.4.4/log4r/R/logformat.logger.R |only log4r-0.4.4/log4r/R/loglevel.R |only log4r-0.4.4/log4r/man/create.logger.Rd |only log4r-0.4.4/log4r/man/levellog.Rd |only log4r-0.4.4/log4r/man/logfile.Rd |only log4r-0.4.4/log4r/man/logformat.Rd |only log4r-0.4.4/log4r/man/loglevel.Rd |only log4r-0.4.4/log4r/tests/testthat/test-loglevel.R |only log4r-0.4.4/log4r/tests/testthat/test-verbosity.R |only log4r-0.5.0/log4r/DESCRIPTION | 51 log4r-0.5.0/log4r/MD5 | 88 - log4r-0.5.0/log4r/NAMESPACE | 8 log4r-0.5.0/log4r/NEWS.md | 26 log4r-0.5.0/log4r/R/appenders.R | 129 +- log4r-0.5.0/log4r/R/deprecated.R |only log4r-0.5.0/log4r/R/layouts.R | 96 + log4r-0.5.0/log4r/R/level.R |only log4r-0.5.0/log4r/R/logfuncs.R | 90 - log4r-0.5.0/log4r/R/logger.R |only log4r-0.5.0/log4r/README.md | 51 log4r-0.5.0/log4r/build/vignette.rds |binary log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.R | 12 log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.Rmd | 6 log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.html | 13 log4r-0.5.0/log4r/inst/doc/performance.R | 19 log4r-0.5.0/log4r/inst/doc/performance.Rmd | 30 log4r-0.5.0/log4r/inst/doc/performance.html | 695 ++++++++++--- log4r-0.5.0/log4r/inst/doc/structured-logging.R | 4 log4r-0.5.0/log4r/inst/doc/structured-logging.Rmd | 6 log4r-0.5.0/log4r/inst/doc/structured-logging.html | 19 log4r-0.5.0/log4r/man/appenders.Rd | 14 log4r-0.5.0/log4r/man/figures |only log4r-0.5.0/log4r/man/http_appender.Rd | 11 log4r-0.5.0/log4r/man/layouts.Rd | 29 log4r-0.5.0/log4r/man/level.Rd | 36 log4r-0.5.0/log4r/man/log4r-deprecated.Rd |only log4r-0.5.0/log4r/man/log4r-package.Rd | 9 log4r-0.5.0/log4r/man/log_at.Rd |only log4r-0.5.0/log4r/man/logger.Rd | 25 log4r-0.5.0/log4r/man/syslog_appender.Rd | 18 log4r-0.5.0/log4r/man/tcp_appender.Rd | 19 log4r-0.5.0/log4r/src/log4r.c | 59 + log4r-0.5.0/log4r/tests/testthat/_snaps |only log4r-0.5.0/log4r/tests/testthat/test-acceptance.R | 8 log4r-0.5.0/log4r/tests/testthat/test-appenders.R | 30 log4r-0.5.0/log4r/tests/testthat/test-layouts.R | 7 log4r-0.5.0/log4r/tests/testthat/test-level.R |only log4r-0.5.0/log4r/vignettes/logging-beyond-local-files.Rmd | 6 log4r-0.5.0/log4r/vignettes/performance.Rmd | 30 log4r-0.5.0/log4r/vignettes/structured-logging.Rmd | 6 53 files changed, 1164 insertions(+), 486 deletions(-)
Title: Shared 'Shiny' Components for 'LLMR' Family Applications
Description: Reusable 'Shiny' user interface and server components from
which the graphical applications in the 'LLMR' package family are
assembled.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR.shiny versions 0.1.1 dated 2026-07-21 and 0.1.2 dated 2026-08-04
LLMR.shiny-0.1.1/LLMR.shiny/R/cost.R |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_add_usage.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_empty.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_set_plan.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_tile.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/github_remote_for.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/is_auth_error.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/llmr_error_banner.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/null-coalesce.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/pkg_available.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/DESCRIPTION | 21 LLMR.shiny-0.1.2/LLMR.shiny/MD5 | 82 +- LLMR.shiny-0.1.2/LLMR.shiny/NAMESPACE | 18 LLMR.shiny-0.1.2/LLMR.shiny/NEWS.md | 39 + LLMR.shiny-0.1.2/LLMR.shiny/R/LLMR.shiny-package.R | 4 LLMR.shiny-0.1.2/LLMR.shiny/R/display.R | 193 ++++- LLMR.shiny-0.1.2/LLMR.shiny/R/guards.R | 60 - LLMR.shiny-0.1.2/LLMR.shiny/R/io.R | 104 ++ LLMR.shiny-0.1.2/LLMR.shiny/R/keys.R | 44 - LLMR.shiny-0.1.2/LLMR.shiny/R/persona_selector.R | 56 + LLMR.shiny-0.1.2/LLMR.shiny/R/runners.R | 157 +++- LLMR.shiny-0.1.2/LLMR.shiny/R/theme.R |only LLMR.shiny-0.1.2/LLMR.shiny/R/usage.R |only LLMR.shiny-0.1.2/LLMR.shiny/README.md | 183 ++++- LLMR.shiny-0.1.2/LLMR.shiny/man/LLMR.shiny-package.Rd | 4 LLMR.shiny-0.1.2/LLMR.shiny/man/annotate_demo_result.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/as_display_table.Rd | 20 LLMR.shiny-0.1.2/LLMR.shiny/man/build_llm_config.Rd | 25 LLMR.shiny-0.1.2/LLMR.shiny/man/build_runner.Rd | 9 LLMR.shiny-0.1.2/LLMR.shiny/man/demo_banner_ui.Rd | 4 LLMR.shiny-0.1.2/LLMR.shiny/man/demo_runner.Rd | 18 LLMR.shiny-0.1.2/LLMR.shiny/man/extract_token_counts.Rd | 5 LLMR.shiny-0.1.2/LLMR.shiny/man/figures/logo.png |binary LLMR.shiny-0.1.2/LLMR.shiny/man/guess_column.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/help_tip.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/install_guidance_ui.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/is_demo_result.Rd | 6 LLMR.shiny-0.1.2/LLMR.shiny/man/llmr_theme.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/persona_selector_server.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/persona_selector_ui.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/provider_default_model.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/provider_registry.Rd | 16 LLMR.shiny-0.1.2/LLMR.shiny/man/shell_context.Rd | 7 LLMR.shiny-0.1.2/LLMR.shiny/man/shell_sidebar.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/text_block_output.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_add.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_empty.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_set_plan.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_tile.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-guess-column.R |only LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-persona-selector.R | 40 - LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-substrate.R | 347 ++++++++-- LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-ui-helpers.R |only 53 files changed, 1185 insertions(+), 328 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2025) <doi:10.1080/07350015.2024.2322090>,
Savi Virolainen (in press) <doi:10.1016/j.ecosta.2025.09.003>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between gmvarkit versions 2.2.1 dated 2025-10-06 and 2.2.2 dated 2026-08-04
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/gmvarkit-vignette.R | 2 -- inst/doc/gmvarkit-vignette.pdf |binary man/cond_moments.Rd | 8 ++++---- man/get_regime_autocovs.Rd | 8 ++++---- man/get_regime_means.Rd | 8 ++++---- man/gmvarkit-package.Rd | 7 ++++++- man/uncond_moments.Rd | 8 ++++---- vignettes/refs.bib | 2 +- 12 files changed, 44 insertions(+), 37 deletions(-)
Title: Publication-Ready Forest Plots with 'ggplot2'
Description: Transform model coefficients into flexible forest
plots using 'ggplot2'. Provides helpers to standardize
coefficient data from a range of modelling workflows and render
publication-ready forest plots with a consistent interface.
Author: Carson Richardson [aut, cre, cph]
Maintainer: Carson Richardson <carson.richardson@outlook.com>
Diff between ggforestplotR versions 0.3.0 dated 2026-07-07 and 0.3.1 dated 2026-08-04
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 7 ++++++ R/add_forest_table.R | 17 ++++++++++----- R/as_forest_data.R | 6 +++-- R/ggforestplot.R | 8 ++++--- R/utils.R | 5 ++++ build/vignette.rds |binary tests/testthat/test-forest-table.R | 40 ++++++++++++++++++++++++++++++++----- 9 files changed, 78 insertions(+), 27 deletions(-)
Title: Bayesian Treed Distributed Lag Models
Description: Estimation of distributed lag models (DLMs) based on a Bayesian additive regression trees framework. Includes several extensions of DLMs: treed DLMs and distributed lag mixture models (Mork and Wilson, 2023) <doi:10.1111/biom.13568>; treed distributed lag nonlinear models (Mork and Wilson, 2022) <doi:10.1093/biostatistics/kxaa051>; heterogeneous DLMs (Mork, et. al., 2024) <doi:10.1080/01621459.2023.2258595>; monotone DLMs (Mork and Wilson, 2024) <doi:10.1214/23-BA1412>. The package also includes visualization tools and a 'shiny' interface to check model convergence and to help interpret results.
Author: Daniel Mork [aut, cre, cph] ,
Seongwon Im [aut] ,
Ander Wilson [aut]
Maintainer: Daniel Mork <dmork@hsph.harvard.edu>
Diff between dlmtree versions 1.1.1 dated 2026-02-02 and 1.2.0 dated 2026-08-04
dlmtree-1.1.1/dlmtree/man/dlmtreeGPFixedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeGPGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeHDLMGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeHDLMMGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLMFixedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLMNestedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLM_cpp.Rd |only dlmtree-1.1.1/dlmtree/src/dlmtreeGPFixedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeGPGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeHDLMGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeHDLMMGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLMFixedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLMNestedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLM_cpp.cpp |only dlmtree-1.2.0/dlmtree/DESCRIPTION | 6 dlmtree-1.2.0/dlmtree/MD5 | 52 +--- dlmtree-1.2.0/dlmtree/NEWS.md | 12 + dlmtree-1.2.0/dlmtree/R/RcppExports.R | 52 ---- dlmtree-1.2.0/dlmtree/R/control.R | 1 dlmtree-1.2.0/dlmtree/R/dlmtree.R | 44 +++ dlmtree-1.2.0/dlmtree/R/estDLM.R | 2 dlmtree-1.2.0/dlmtree/man/dlmtree.Rd | 3 dlmtree-1.2.0/dlmtree/man/dlmtreeMixtures.Rd |only dlmtree-1.2.0/dlmtree/man/dlmtreeNested.Rd |only dlmtree-1.2.0/dlmtree/man/dlmtreeShared.Rd |only dlmtree-1.2.0/dlmtree/src/Fncs.cpp | 6 dlmtree-1.2.0/dlmtree/src/Node.cpp | 47 +++- dlmtree-1.2.0/dlmtree/src/Node.h | 1 dlmtree-1.2.0/dlmtree/src/RcppExports.cpp | 78 +----- dlmtree-1.2.0/dlmtree/src/dlmtreeMixtures.cpp |only dlmtree-1.2.0/dlmtree/src/dlmtreeNested.cpp |only dlmtree-1.2.0/dlmtree/src/dlmtreeShared.cpp |only dlmtree-1.2.0/dlmtree/src/modelCtr.h | 52 ++-- dlmtree-1.2.0/dlmtree/src/modelEst.cpp | 186 ++++++---------- dlmtree-1.2.0/dlmtree/src/monotdlnm_Cpp.cpp | 40 +++ dlmtree-1.2.0/dlmtree/src/tdlmm_Cpp.cpp | 45 +++ dlmtree-1.2.0/dlmtree/src/tdlnm_Cpp.cpp | 61 +++-- 37 files changed, 374 insertions(+), 314 deletions(-)
Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data
within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing
and discovery tool that facilitates exploration of HIV immunological data
from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut],
Sean Hughes [rev],
Jason Taylor [aut, cre],
Helen Miller [aut],
Kellie MacPhee [rev],
CAVD DataSpace [cph]
Maintainer: Jason Taylor <jmtaylor@fredhutch.org>
Diff between DataSpaceR versions 1.0.0 dated 2026-06-26 and 1.0.1 dated 2026-08-04
DataSpaceR-1.0.0/DataSpaceR/inst/doc/Accessing_CDS_DAASH.Rmd |only DataSpaceR-1.0.0/DataSpaceR/inst/doc/Accessing_CDS_DAASH.html |only DataSpaceR-1.0.0/DataSpaceR/vignettes/Accessing_CDS_DAASH.Rmd |only DataSpaceR-1.0.0/DataSpaceR/vignettes/Accessing_CDS_DAASH.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/DESCRIPTION | 8 DataSpaceR-1.0.1/DataSpaceR/MD5 | 82 - DataSpaceR-1.0.1/DataSpaceR/NAMESPACE | 1 DataSpaceR-1.0.1/DataSpaceR/NEWS.md | 6 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceConnection.R | 77 + DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceDaash.R | 4 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceR.R | 4 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceStudies.R | 30 DataSpaceR-1.0.1/DataSpaceR/R/helpers.R | 118 ++ DataSpaceR-1.0.1/DataSpaceR/README.md | 13 DataSpaceR-1.0.1/DataSpaceR/build/vignette.rds |binary DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpaceR.Rmd | 433 ------- DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpaceR.html | 547 +--------- DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpace_DAASH.Rmd |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpace_DAASH.html |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Monoconal_Antibody_Data.Rmd | 6 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Monoconal_Antibody_Data.html | 8 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Publication_Data.Rmd | 16 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Publication_Data.html | 64 - DataSpaceR-1.0.1/DataSpaceR/inst/doc/Studies_Groups.Rmd |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Studies_Groups.html |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Virus_Name_Mapping_Tables.Rmd | 2 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Virus_Name_Mapping_Tables.html | 4 DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceConnection.Rd | 413 ++++--- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceDaash.Rd | 217 ++- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceDonors.Rd | 153 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceGroups.Rd | 139 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceMabs.Rd | 160 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceStudies.Rd | 180 +-- DataSpaceR-1.0.1/DataSpaceR/tests/testthat/setup.R | 2 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-connection.R | 8 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-daash.R | 8 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-mabs-donors.R | 28 DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpaceR.Rmd | 433 ------- DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpaceR.Rmd.orig | 136 -- DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpace_DAASH.Rmd |only DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpace_DAASH.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Monoconal_Antibody_Data.Rmd | 6 DataSpaceR-1.0.1/DataSpaceR/vignettes/Monoconal_Antibody_Data.Rmd.orig | 4 DataSpaceR-1.0.1/DataSpaceR/vignettes/Publication_Data.Rmd | 16 DataSpaceR-1.0.1/DataSpaceR/vignettes/Studies_Groups.Rmd |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Studies_Groups.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Virus_Name_Mapping_Tables.Rmd | 2 DataSpaceR-1.0.1/DataSpaceR/vignettes/precompile.R | 3 48 files changed, 1174 insertions(+), 2157 deletions(-)
Title: Biomonitoring and Bioassessment Calculations
Description: An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa,
subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) <https://archive.epa.gov/water/archive/web/html/index-14.html>.
Author: Erik W. Leppo [aut, cre] ,
Jen Stamp [ctb],
John van Sickles [ctb],
Ben Block [ctb]
Maintainer: Erik W. Leppo <Erik.Leppo@tetratech.com>
Diff between BioMonTools versions 1.3.1 dated 2026-07-22 and 1.3.2 dated 2026-08-04
DESCRIPTION | 6 +- MD5 | 22 ++++---- NEWS | 47 ++++++++++++++++++ NEWS.md | 47 ++++++++++++++++++ R/metric_values_excel.R | 24 ++++++--- R/qc_taxa_phylo.R | 92 ++++++++++++++++++++++++++----------- README.md | 12 ++-- inst/doc/vignette_BioMonTools.html | 4 - inst/doc/vignette_MapTaxaObs.html | 4 - inst/doc/vignette_NewIndex.html | 4 - man/metvalgrpxl.Rd | 2 man/qc_taxa_phylo.Rd | 63 ++++++++++++++++--------- 12 files changed, 239 insertions(+), 88 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-4 dated 2025-12-18 and 0.10-0 dated 2026-08-04
OncoBayes2-0.10-0/OncoBayes2/DESCRIPTION | 20 OncoBayes2-0.10-0/OncoBayes2/MD5 | 107 - OncoBayes2-0.10-0/OncoBayes2/NAMESPACE | 4 OncoBayes2-0.10-0/OncoBayes2/NEWS.md | 23 OncoBayes2-0.10-0/OncoBayes2/R/OncoBayes2-package.R | 3 OncoBayes2-0.10-0/OncoBayes2/R/blrm_exnex.R | 221 +-- OncoBayes2-0.10-0/OncoBayes2/R/blrm_trial.R | 2 OncoBayes2-0.10-0/OncoBayes2/R/diagnostics.R | 38 OncoBayes2-0.10-0/OncoBayes2/R/draws_backend.R |only OncoBayes2-0.10-0/OncoBayes2/R/nsamples.R | 8 OncoBayes2-0.10-0/OncoBayes2/R/plot_blrm.R | 116 - OncoBayes2-0.10-0/OncoBayes2/R/posterior.R | 75 - OncoBayes2-0.10-0/OncoBayes2/R/posterior_interval.R | 2 OncoBayes2-0.10-0/OncoBayes2/R/pp_data.R | 7 OncoBayes2-0.10-0/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.10-0/OncoBayes2/build/partial.rdb |binary OncoBayes2-0.10-0/OncoBayes2/build/vignette.rds |binary OncoBayes2-0.10-0/OncoBayes2/data/codata_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/dose_info_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/drug_info_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_SA.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_combo3.rda |binary OncoBayes2-0.10-0/OncoBayes2/inst/REFERENCES.bib |only OncoBayes2-0.10-0/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.10-0/OncoBayes2/inst/doc/introduction.Rmd | 53 OncoBayes2-0.10-0/OncoBayes2/inst/doc/introduction.html | 727 +++++----- OncoBayes2-0.10-0/OncoBayes2/inst/doc/map_approach.Rmd | 10 OncoBayes2-0.10-0/OncoBayes2/inst/doc/map_approach.html | 283 ++- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.10-0/OncoBayes2/inst/sbc/make_reference_rankhist.R | 282 ++- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/sbc_report.html | 657 ++++----- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/sbc_tools.R | 49 OncoBayes2-0.10-0/OncoBayes2/man/OncoBayes2.Rd | 25 OncoBayes2-0.10-0/OncoBayes2/man/blrm_exnex.Rd | 32 OncoBayes2-0.10-0/OncoBayes2/man/blrm_formula_saturating.Rd | 5 OncoBayes2-0.10-0/OncoBayes2/man/blrm_trial.Rd | 10 OncoBayes2-0.10-0/OncoBayes2/man/codata_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/dose_info_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/draws-OncoBayes2.Rd | 5 OncoBayes2-0.10-0/OncoBayes2/man/drug_info_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo2_trial.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo3.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-single-agent.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/hist_SA.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/hist_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/plot_blrm.Rd | 10 OncoBayes2-0.10-0/OncoBayes2/src/stanExports_blrm_exnex.cc | 34 OncoBayes2-0.10-0/OncoBayes2/tests/testthat/helper-fixtures.R |only OncoBayes2-0.10-0/OncoBayes2/tests/testthat/helper-sampling.R | 135 - OncoBayes2-0.10-0/OncoBayes2/tests/testthat/test-blrm_exnex.R | 89 - OncoBayes2-0.10-0/OncoBayes2/tests/testthat/test-posterior.R | 12 OncoBayes2-0.10-0/OncoBayes2/vignettes/introduction.Rmd | 53 OncoBayes2-0.10-0/OncoBayes2/vignettes/map_approach.Rmd | 10 OncoBayes2-0.10-0/OncoBayes2/vignettes/references.bib |only OncoBayes2-0.9-4/OncoBayes2/man/dot-label_index.Rd |only 57 files changed, 1653 insertions(+), 1496 deletions(-)
Title: Minimal LLM Chat Interface
Description: A minimal-dependency client for Large Language Model chat APIs.
Supports 'OpenAI' <https://openai.com/>, 'Anthropic' 'Claude'
<https://claude.com/>, 'Moonshot' 'Kimi' <https://www.moonshot.ai/>,
'OpenAI' 'Codex' subscription endpoints, 'Ollama'
<https://ollama.com/>, and other 'OpenAI'-compatible endpoints.
Includes an agent loop with tool use and a 'Model Context
Protocol' client <https://modelcontextprotocol.io/>. API design is
derived from the 'ellmer' package, reimplemented with only base R,
'curl', 'jsonlite', and 'tinyoauth'.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
ellmer team [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between llm.api versions 0.1.8 dated 2026-06-26 and 0.1.9 dated 2026-08-04
DESCRIPTION | 8 +-- MD5 | 47 +++++++++--------- NEWS.md | 24 +++++++++ R/agent.R | 33 +++++++++--- R/chat.R | 15 +++-- R/config.R | 53 +++++++++++++++++--- R/cost.R | 4 + R/providers.R | 52 +++++++++++++++++++- R/session.R | 5 + README.md | 79 ++++++++++++++++++++++++++++++- inst/tinytest/test_config.R | 44 ++++++++++++++--- inst/tinytest/test_moonshot_web_search.R | 2 inst/tinytest/test_openai_codex.R | 4 - inst/tinytest/test_openai_compatible.R |only inst/tinytest/test_openai_responses.R | 2 inst/tinytest/test_providers.R | 4 - man/agent.Rd | 13 +++-- man/anthropic_claude_credentials.Rd | 4 - man/chat.Rd | 7 +- man/chat_session.Rd | 6 +- man/create_agent.Rd | 5 + man/llm_base.Rd | 2 man/llm_key.Rd | 2 man/provider_default_model.Rd | 7 +- man/usage_cost.Rd | 4 + 25 files changed, 338 insertions(+), 88 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Diff between castor versions 1.8.6 dated 2026-07-24 and 1.8.7 dated 2026-08-04
castor-1.8.6/castor/R/correlate_discrete_traits.R |only castor-1.8.6/castor/man/correlate_discrete_traits.Rd |only castor-1.8.7/castor/DESCRIPTION | 8 - castor-1.8.7/castor/MD5 | 24 +-- castor-1.8.7/castor/NAMESPACE | 2 castor-1.8.7/castor/R/auxiliary_routines.R | 97 ++++++++++++- castor-1.8.7/castor/R/correlate_categorical_traits.R |only castor-1.8.7/castor/R/fit_mk.R | 77 ++++++---- castor-1.8.7/castor/R/get_random_mk_transition_matrix.R | 2 castor-1.8.7/castor/R/simulate_mk_model.R | 8 - castor-1.8.7/castor/man/correlate_categorical_traits.Rd |only castor-1.8.7/castor/man/fit_mk.Rd | 2 castor-1.8.7/castor/man/get_random_mk_transition_matrix.Rd | 2 castor-1.8.7/castor/src/RcppExports.cpp | 4 castor-1.8.7/castor/src/phylogenetics_cpp_routines.cpp | 30 +++- 15 files changed, 193 insertions(+), 63 deletions(-)
Title: Runs Allelematch Regression Tests
Description: Automates regression testing of package 'allelematch'. Over
2500 tests cover all functions in 'allelematch', reproduce the
examples from the documentation, and include negative tests. The
implementation is based on 'testthat'.
Author: Department of Wildlife, Fish and Environmental Studies at Swedish
University of Agricultural Sciences [cph],
Goeran Spong [cph] ,
Paul Galpern [ctb] ,
Torvald Staxler [aut, cre]
Maintainer: Torvald Staxler <torvald.staxler@telia.com>
Diff between amregtest versions 1.2.0 dated 2026-07-13 and 1.3.2 dated 2026-08-04
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amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique.R | 13 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique_negative.R | 16 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique_print.R | 18 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_7-amUniqueProfile.R | 12 amregtest-1.3.2/amregtest/tests/testthat/test-amExample1.R | 4 amregtest-1.3.2/amregtest/tests/testthat/test-amExample2.R | 8 amregtest-1.3.2/amregtest/tests/testthat/test-amExample3.R | 4 amregtest-1.3.2/amregtest/tests/testthat/test-amExample4.R | 9 amregtest-1.3.2/amregtest/tests/testthat/test-ggData.R | 1 85 files changed, 11795 insertions(+), 10472 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldNet versions 1.3 dated 2021-10-29 and 1.4 dated 2026-08-04
DESCRIPTION | 26 - MD5 | 65 ++-- NAMESPACE | 74 ++-- R/RcppExports.R |only R/asTensor.R | 53 +-- R/cpDecomposition.R | 412 +++++++++++++-------------- R/cpmNormalization.R | 130 ++++---- R/dModularity.R | 57 --- R/dRegulation.R | 274 +++++++++--------- R/makeNetworks.R | 218 ++++++++------ R/manifoldAlignment.R | 216 +++++++------- R/pcNet.R | 492 ++++++++++++++++++++++----------- R/scQC.R | 269 ++++++++++-------- R/scTenifoldNet.R | 479 ++++++++++++++++---------------- R/tensorDecomposition.R | 372 +++++++++++------------- README.md | 482 +++++++++++++------------------- inst/CITATION | 32 +- man/cpDecomposition.Rd | 85 +++-- man/cpmNormalization.Rd | 141 +++++---- man/dRegulation.Rd | 165 +++++------ man/makeNetworks.Rd | 213 +++++++------- man/manifoldAlignment.Rd | 181 ++++++------ man/pcNet.Rd | 160 +++++----- man/pcNetCoreRcpp.Rd |only man/scQC.Rd | 226 ++++++++------- man/scTenifoldNet.Rd | 422 ++++++++++++++-------------- man/tensorDecomposition.Rd | 185 ++++++------ src |only tests/testthat.R | 8 tests/testthat/test-cpmNormalization.R | 86 ++--- tests/testthat/test-makeNetworks.R | 56 +-- tests/testthat/test-pcNet.R | 120 ++++---- tests/testthat/test-pcNetRcpp.R |only tests/testthat/test-scQC.R | 98 +++--- 34 files changed, 3014 insertions(+), 2783 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut] ,
Omar Elashkar [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 5.1.0 dated 2026-06-07 and 5.2.0 dated 2026-08-04
DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 3 NEWS.md | 62 +++++ R/AICHelpers.R |only R/SCM.R | 12 - R/computingutil.R | 321 ++++++++++++++++++++---------- R/setCov.R | 8 R/theoFitOde.R | 42 +++ data/theoFitOde.rda |binary man/getMinAICFit.Rd |only man/isBoundaryFit.Rd |only man/listModelsTested.Rd |only man/theoFitOde.Rd | 8 tests/testthat/test-AICHelpers.R |only tests/testthat/test-SCM-covarSearchAuto.R |only tests/testthat/test-bootstrap.R | 264 ++++++++++++++++++++++++ tests/testthat/test-computing.R | 23 ++ 18 files changed, 650 insertions(+), 131 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 6.0.1 dated 2026-06-03 and 7.0.2 dated 2026-08-04
nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-fo.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-foce.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-focei-fast.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-focei.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-foi.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-lag-focei.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-lag-saem.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-posthoc.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-saem-cwres.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-saem.rds |only nlmixr2est-7.0.2/nlmixr2est/DESCRIPTION | 24 nlmixr2est-7.0.2/nlmixr2est/MD5 | 712 nlmixr2est-7.0.2/nlmixr2est/NAMESPACE | 215 nlmixr2est-7.0.2/nlmixr2est/NEWS.md | 1854 + nlmixr2est-7.0.2/nlmixr2est/R/RcppExports.R | 451 nlmixr2est-7.0.2/nlmixr2est/R/addCwres.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/augPred.R | 6 nlmixr2est-7.0.2/nlmixr2est/R/bobyqa.R | 155 nlmixr2est-7.0.2/nlmixr2est/R/cloneNlmixr.R | 13 nlmixr2est-7.0.2/nlmixr2est/R/compat.R | 83 nlmixr2est-7.0.2/nlmixr2est/R/complete.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/cov.R | 297 nlmixr2est-7.0.2/nlmixr2est/R/covRecompute.R |only nlmixr2est-7.0.2/nlmixr2est/R/deparse.R | 10 nlmixr2est-7.0.2/nlmixr2est/R/emviControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/fbvi.R |only nlmixr2est-7.0.2/nlmixr2est/R/fitSim.R | 4 nlmixr2est-7.0.2/nlmixr2est/R/fo.R | 7 nlmixr2est-7.0.2/nlmixr2est/R/focei.R | 1363 - nlmixr2est-7.0.2/nlmixr2est/R/foceiControl.R | 1182 nlmixr2est-7.0.2/nlmixr2est/R/foceiCov.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiCovAnalytic.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiCovFdFull.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiFast.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiGradAnalytic.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiLik.R |only nlmixr2est-7.0.2/nlmixr2est/R/focep.R |only nlmixr2est-7.0.2/nlmixr2est/R/foi.R | 7 nlmixr2est-7.0.2/nlmixr2est/R/hook.R | 117 nlmixr2est-7.0.2/nlmixr2est/R/iagq.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifoce.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifocei.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifocep.R |only nlmixr2est-7.0.2/nlmixr2est/R/ilaplace.R |only nlmixr2est-7.0.2/nlmixr2est/R/imp.R |only nlmixr2est-7.0.2/nlmixr2est/R/impPsis.R |only nlmixr2est-7.0.2/nlmixr2est/R/impmap.R |only nlmixr2est-7.0.2/nlmixr2est/R/impmapThetaSens.R |only nlmixr2est-7.0.2/nlmixr2est/R/iov.R | 33 nlmixr2est-7.0.2/nlmixr2est/R/iterPrintControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/lbfgsb3c.R | 161 nlmixr2est-7.0.2/nlmixr2est/R/magq.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfoce.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfocei.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfocep.R |only nlmixr2est-7.0.2/nlmixr2est/R/mix.R | 453 nlmixr2est-7.0.2/nlmixr2est/R/mlaplace.R |only nlmixr2est-7.0.2/nlmixr2est/R/mu2.R | 62 nlmixr2est-7.0.2/nlmixr2est/R/muRefClassify.R |only nlmixr2est-7.0.2/nlmixr2est/R/muRefControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/muRefLinear.R |only nlmixr2est-7.0.2/nlmixr2est/R/n1qn1.R | 120 nlmixr2est-7.0.2/nlmixr2est/R/newuoa.R | 115 nlmixr2est-7.0.2/nlmixr2est/R/nlm.R | 308 nlmixr2est-7.0.2/nlmixr2est/R/nlmShared.R | 311 nlmixr2est-7.0.2/nlmixr2est/R/nlme.R | 117 nlmixr2est-7.0.2/nlmixr2est/R/nlmeRxUiGet.R | 4 nlmixr2est-7.0.2/nlmixr2est/R/nlminb.R | 138 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2.R | 18 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2Est.R | 111 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2EstType.R |only nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2global.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2output.R | 667 nlmixr2est-7.0.2/nlmixr2est/R/nlmixrGrad.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/nls.R | 229 nlmixr2est-7.0.2/nlmixr2est/R/nmObjGet.R | 198 nlmixr2est-7.0.2/nlmixr2est/R/nmObjHandle.R | 8 nlmixr2est-7.0.2/nlmixr2est/R/npBox.R |only nlmixr2est-7.0.2/nlmixr2est/R/npCommon.R |only nlmixr2est-7.0.2/nlmixr2est/R/npInner.R |only nlmixr2est-7.0.2/nlmixr2est/R/npMuExpand.R |only nlmixr2est-7.0.2/nlmixr2est/R/npag.R |only nlmixr2est-7.0.2/nlmixr2est/R/npb.R |only nlmixr2est-7.0.2/nlmixr2est/R/odeSwapVerify.R |only nlmixr2est-7.0.2/nlmixr2est/R/ofv.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/omegaBlock.R |only nlmixr2est-7.0.2/nlmixr2est/R/optim.R | 227 nlmixr2est-7.0.2/nlmixr2est/R/preProcessBoundedTransform.R | 160 nlmixr2est-7.0.2/nlmixr2est/R/preProcessCovariatesPresent.R | 11 nlmixr2est-7.0.2/nlmixr2est/R/preProcessLinCmtOde.R |only nlmixr2est-7.0.2/nlmixr2est/R/preProcessLiteralFix.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/preProcessVaeNonMuTheta.R |only nlmixr2est-7.0.2/nlmixr2est/R/preProcessZeroOmega.R | 13 nlmixr2est-7.0.2/nlmixr2est/R/preProcessZeroTheta.R |only nlmixr2est-7.0.2/nlmixr2est/R/print.R | 10 nlmixr2est-7.0.2/nlmixr2est/R/qrpem.R |only nlmixr2est-7.0.2/nlmixr2est/R/resid.R | 249 nlmixr2est-7.0.2/nlmixr2est/R/rxNamedModel.R |only nlmixr2est-7.0.2/nlmixr2est/R/rxsolve.R | 41 nlmixr2est-7.0.2/nlmixr2est/R/saem.R | 576 nlmixr2est-7.0.2/nlmixr2est/R/saemControl.R | 273 nlmixr2est-7.0.2/nlmixr2est/R/saemRxUiGet.R | 177 nlmixr2est-7.0.2/nlmixr2est/R/saemRxUiGetModel.R | 150 nlmixr2est-7.0.2/nlmixr2est/R/saem_fit.R | 214 nlmixr2est-7.0.2/nlmixr2est/R/saem_fit_aux.R | 88 nlmixr2est-7.0.2/nlmixr2est/R/sharedControl.R | 88 nlmixr2est-7.0.2/nlmixr2est/R/timing.R | 15 nlmixr2est-7.0.2/nlmixr2est/R/uninformativeEtas.R | 108 nlmixr2est-7.0.2/nlmixr2est/R/uobyqa.R | 126 nlmixr2est-7.0.2/nlmixr2est/R/utils.R | 163 nlmixr2est-7.0.2/nlmixr2est/R/vae.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeCovSelectL0.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeCovShapes.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeData.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeDecoder.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeFit.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeGrad.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeInner.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeOutput.R |only nlmixr2est-7.0.2/nlmixr2est/R/vi.R |only nlmixr2est-7.0.2/nlmixr2est/R/viData.R |only nlmixr2est-7.0.2/nlmixr2est/R/vpc.R | 33 nlmixr2est-7.0.2/nlmixr2est/R/zzz.R | 64 nlmixr2est-7.0.2/nlmixr2est/configure | 1 nlmixr2est-7.0.2/nlmixr2est/configure.win | 2 nlmixr2est-7.0.2/nlmixr2est/inst/COPYRIGHT | 9 nlmixr2est-7.0.2/nlmixr2est/inst/tools/workaround.R | 21 nlmixr2est-7.0.2/nlmixr2est/man/agqControl.Rd | 41 nlmixr2est-7.0.2/nlmixr2est/man/bobyqaControl.Rd | 325 nlmixr2est-7.0.2/nlmixr2est/man/dot-absorbIterPrintControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-collectWarn.Rd | 31 nlmixr2est-7.0.2/nlmixr2est/man/dot-deparseDifferent.Rd | 6 nlmixr2est-7.0.2/nlmixr2est/man/dot-deparseFinal.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-iniS3.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-loadSymengine.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmFamilyControlGeneric.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmFamilyFitGeneric.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmSetupEnv.Rd | 66 nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmeGetNonMuRefNames.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmixr0preProcessNpMuExpand.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessLinCmtOde.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessVaeNonMuTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessZeroTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-saemDropMuRefFromModel.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-sensEtaOrTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/emviControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/fbviControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/foceControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/foceiControl.Rd | 907 nlmixr2est-7.0.2/nlmixr2est/man/foceiGradPooledDirect_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiGradPooledSetupLoad_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikLoad.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikRun.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikUnload.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/focepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foiControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/formatMinWidth.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/getBaseSimModelFit.Rd | 3 nlmixr2est-7.0.2/nlmixr2est/man/getValidNlmixrControl.Rd | 132 nlmixr2est-7.0.2/nlmixr2est/man/iagqControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifoceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifoceiControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifocepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ilaplaceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/impControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/impmapControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/iterPrintControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/iterPrintParams.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/laplaceControl.Rd | 39 nlmixr2est-7.0.2/nlmixr2est/man/lbfgsb3cControl.Rd | 325 nlmixr2est-7.0.2/nlmixr2est/man/magqControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfoceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfoceiControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfocepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mlaplaceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/n1qn1Control.Rd | 298 nlmixr2est-7.0.2/nlmixr2est/man/newuoaControl.Rd | 336 nlmixr2est-7.0.2/nlmixr2est/man/nlmControl.Rd | 336 nlmixr2est-7.0.2/nlmixr2est/man/nlmGetParHist.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlmerSolveGrad.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlminbControl.Rd | 331 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2AllEstType.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Est.Rd | 134 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Gill83.Rd | 10 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2GradFun.Rd | 23 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2NlmeControl.Rd | 123 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Print.Rd | 8 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2fix.Rd | 32 nlmixr2est-7.0.2/nlmixr2est/man/nlmixrWithTiming.Rd | 7 nlmixr2est-7.0.2/nlmixr2est/man/nlsControl.Rd | 297 nlmixr2est-7.0.2/nlmixr2est/man/nmGetDistributionSaemLines.Rd | 6 nlmixr2est-7.0.2/nlmixr2est/man/nmNearPD.Rd | 9 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGet.Rd | 15 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGetControl.Rd | 78 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGetFoceiControl.Rd | 66 nlmixr2est-7.0.2/nlmixr2est/man/nmObjHandleControlObject.Rd | 50 nlmixr2est-7.0.2/nlmixr2est/man/nmSuppressMsg.Rd | 14 nlmixr2est-7.0.2/nlmixr2est/man/npBuildPsi.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npCondense_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npIpmBurke.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npObjAtGamma_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npSobolGrid_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npagControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npagCycle_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npbControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/optimControl.Rd | 312 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooksAdd.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/posthocControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooksAdd.Rd | 23 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooksAdd.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/predict.nlmixr2FitCore.Rd | 5 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nlmixr2est-7.0.2/nlmixr2est/src/inner.h | 9 nlmixr2est-7.0.2/nlmixr2est/src/nearPD.cpp | 2 nlmixr2est-7.0.2/nlmixr2est/src/nlm.cpp | 328 nlmixr2est-7.0.2/nlmixr2est/src/nmMcmcRng.h |only nlmixr2est-7.0.2/nlmixr2est/src/np.h |only nlmixr2est-7.0.2/nlmixr2est/src/npCommon.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npCommon.h |only nlmixr2est-7.0.2/nlmixr2est/src/npag.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npb.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npde.cpp | 99 nlmixr2est-7.0.2/nlmixr2est/src/odeSwap.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/odeSwap.h |only nlmixr2est-7.0.2/nlmixr2est/src/rxProtect.h | 6 nlmixr2est-7.0.2/nlmixr2est/src/rxcmp.cpp | 12 nlmixr2est-7.0.2/nlmixr2est/src/rxomp.h | 9 nlmixr2est-7.0.2/nlmixr2est/src/saem.cpp | 2536 +- nlmixr2est-7.0.2/nlmixr2est/src/scale.h | 522 nlmixr2est-7.0.2/nlmixr2est/src/shi21.cpp | 25 nlmixr2est-7.0.2/nlmixr2est/src/shi21.h | 4 nlmixr2est-7.0.2/nlmixr2est/src/solveWarnHelper.h |only nlmixr2est-7.0.2/nlmixr2est/src/utilc.c | 48 nlmixr2est-7.0.2/nlmixr2est/src/utilc.h | 3 nlmixr2est-7.0.2/nlmixr2est/src/vaeEncoder.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/vaeEncoder.h |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat.R | 168 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/baselines |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/fixtures/README.md | 7 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/fixtures/npag |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-gradref.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-quiet.R | 24 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-vae-resid.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-wang2007.R | 25 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-zzz-fits.R | 48 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-agq-cov.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-agq-fast-grad.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-ar-est.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-augpred.R | 64 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nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-vpcSim.R | 50 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-vpcSimExpand.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-warfarin.R | 20 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-zero-omega-restore.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/testthat-problems.rds |only 466 files changed, 31074 insertions(+), 9146 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness. Supports generalized linear models, Weibull accelerated
failure time (AFT) models, Cox proportional hazards models,
quadratic programming constraints, and customizable working-correlation
structures, with options for parallel fitting. The core spline construction
builds on Ezhov et al. (2018) <doi:10.1515/jag-2017-0029>.
Quadratic-programming and SQP details follow Goldfarb & Idnani (1983)
<doi:10.1007/BF02591962> and Nocedal & Wright (2006)
<doi:10.1007/978-0-387-40065-5>. For smoothing spline and penalized spline
background, see Wahba (1990) <doi:10.1137/1.9781611970128> and Wood (2017)
<doi:10.1201/9781315370279>. For variance-component and correlation-parameter
estimation, see Searle et al. (2006) <ISBN:978-04700 [...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 1.1.0 dated 2026-05-08 and 1.2.1 dated 2026-08-04
DESCRIPTION | 10 MD5 | 63 - NAMESPACE | 4 NEWS.md | 10 R/HelperFunctions.R | 71 + R/additive_lgspline.R |only R/blockfit_solve.R | 90 + R/cox_helpers.R | 1459 ++++++++++++++-------------- R/get_B.R | 105 -- R/integrate.R | 95 + R/leave_one_out.R | 168 ++- R/lgspline-details.R | 158 +-- R/lgspline.R | 168 ++- R/methods.R | 433 ++++++-- R/prior_loglik.R | 34 R/process_input.R | 159 ++- README.md | 41 inst/WORDLIST | 6 inst/simulations |only man/Details.Rd | 122 +- man/equation.Rd | 19 man/generate_posterior.Rd | 3 man/generate_posterior_correlation.Rd | 5 man/get_B.Rd | 11 man/integrate.lgspline.Rd | 4 man/leave_one_out.Rd | 45 man/lgspline.Rd | 43 man/lgspline.fit.Rd | 33 man/lgspline_cox.Rd | 1 man/logLik.lgspline.Rd | 9 man/print.additive_lgspline.Rd |only man/process_input.Rd | 19 man/summary.additive_lgspline.Rd |only tests/testthat/test-additive-splines.R |only tests/testthat/test_correlation_structure.R | 25 35 files changed, 2171 insertions(+), 1242 deletions(-)
Title: Analysis of Ecological Dynamic Regimes
Description: A toolbox for implementing the Ecological Dynamic Regime framework,
including functions to characterize and compare groups of ecological trajectories
(Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>); assess the ecological
resilience of a disturbed system using a reference dynamic regime (Sánchez-Pinillos
et al., 2024 <doi:10.1016/j.biocon.2023.110409>); and forecast ecological
trajectories from a dynamic regime (Sánchez-Pinillos et al. 2026,
<doi:10.1111/2041-210x.70372>). Additional functions are also available for
visualizing ecological dynamic regimes, their representative trajectories,
as well as predicted trajectories in a multidimensional state space.
Author: Martina Sanchez-Pinillos [aut, cre, cph]
Maintainer: Martina Sanchez-Pinillos <martina.sanchez.pinillos@gmail.com>
Diff between ecoregime versions 0.3.1 dated 2026-06-07 and 0.4.1 dated 2026-08-04
ecoregime-0.3.1/ecoregime/R/deviation_metrics.R |only ecoregime-0.3.1/ecoregime/R/plot.R |only ecoregime-0.3.1/ecoregime/R/summary.R |only ecoregime-0.3.1/ecoregime/man/deviation_metrics.Rd |only ecoregime-0.3.1/ecoregime/tests/testthat/Rplots.pdf |only ecoregime-0.3.1/ecoregime/tests/testthat/test-deviation_metrics.R |only ecoregime-0.3.1/ecoregime/tests/testthat/test-plot.R |only ecoregime-0.3.1/ecoregime/tests/testthat/test-summary.R |only ecoregime-0.4.1/ecoregime/DESCRIPTION | 30 +- ecoregime-0.4.1/ecoregime/MD5 | 75 +++-- ecoregime-0.4.1/ecoregime/NAMESPACE | 5 ecoregime-0.4.1/ecoregime/NEWS.md | 28 + ecoregime-0.4.1/ecoregime/R/EDR_metrics.R | 2 ecoregime-0.4.1/ecoregime/R/MPD.R |only ecoregime-0.4.1/ecoregime/R/dist_edr.R | 29 -- ecoregime-0.4.1/ecoregime/R/ecoregime-package.R | 2 ecoregime-0.4.1/ecoregime/R/petra_edr.R |only ecoregime-0.4.1/ecoregime/R/plot_PETRA.R |only ecoregime-0.4.1/ecoregime/R/plot_RETRA.R |only ecoregime-0.4.1/ecoregime/R/plot_edr.R | 2 ecoregime-0.4.1/ecoregime/R/resilience_metrics.R |only ecoregime-0.4.1/ecoregime/R/summary_RETRA.R |only ecoregime-0.4.1/ecoregime/README.md | 80 +++++ ecoregime-0.4.1/ecoregime/build/vignette.rds |binary ecoregime-0.4.1/ecoregime/inst/CITATION | 15 + ecoregime-0.4.1/ecoregime/inst/doc/EDR_framework.Rmd | 43 ++- ecoregime-0.4.1/ecoregime/inst/doc/EDR_framework.html | 142 ++++++---- ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.R |only ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.Rmd |only ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.html |only ecoregime-0.4.1/ecoregime/inst/doc/Resilience.Rmd | 8 ecoregime-0.4.1/ecoregime/inst/doc/Resilience.html | 57 ++-- ecoregime-0.4.1/ecoregime/man/EDR_metrics.Rd | 2 ecoregime-0.4.1/ecoregime/man/MPD.Rd |only ecoregime-0.4.1/ecoregime/man/dist_edr.Rd | 29 -- ecoregime-0.4.1/ecoregime/man/ecoregime-package.Rd | 2 ecoregime-0.4.1/ecoregime/man/figures/README-predict-1.png |only ecoregime-0.4.1/ecoregime/man/petra_edr.Rd |only ecoregime-0.4.1/ecoregime/man/plot.PETRA.Rd |only ecoregime-0.4.1/ecoregime/man/plot.RETRA.Rd | 5 ecoregime-0.4.1/ecoregime/man/plot_edr.Rd | 2 ecoregime-0.4.1/ecoregime/man/resilience_metrics.Rd |only ecoregime-0.4.1/ecoregime/man/summary.RETRA.Rd | 2 ecoregime-0.4.1/ecoregime/tests/testthat/test-MPD.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-dist_edr.R | 4 ecoregime-0.4.1/ecoregime/tests/testthat/test-petra_edr.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-plot_PETRA.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-plot_RETRA.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-resilience_metrics.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-summary_RETRA.R |only ecoregime-0.4.1/ecoregime/vignettes/EDR_framework.Rmd | 43 ++- ecoregime-0.4.1/ecoregime/vignettes/Predicting_trajectories.Rmd |only ecoregime-0.4.1/ecoregime/vignettes/Resilience.Rmd | 8 53 files changed, 406 insertions(+), 209 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre],
Antonio Canale [ctb],
Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 1.2.1 dated 2026-03-06 and 1.2.3 dated 2026-08-04
DESCRIPTION | 8 ++-- MD5 | 6 +-- inst/doc/BNPmix.pdf |binary vignettes/BNPmix_ref.bib | 86 +++++++++++++++++++++++++---------------------- 4 files changed, 54 insertions(+), 46 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2023) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2022) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between uGMAR versions 3.6.0 dated 2025-06-19 and 3.6.1 dated 2026-08-04
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/uGMARpaper.R | 2 -- inst/doc/uGMARpaper.Rnw | 1 + inst/doc/uGMARpaper.pdf |binary man/cond_moments.Rd | 10 +++++----- man/get_regime_autocovs.Rd | 10 +++++----- man/get_regime_means.Rd | 10 +++++----- man/get_regime_vars.Rd | 10 +++++----- man/uGMAR-package.Rd | 7 ++++++- man/uncond_moments.Rd | 10 +++++----- vignettes/refs.bib | 24 +++++++++++++----------- vignettes/uGMARpaper.Rnw | 1 + 15 files changed, 71 insertions(+), 59 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph] ,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 8.0.0 dated 2026-05-01 and 8.1.0 dated 2026-08-04
roxygen2-8.0.0/roxygen2/man/markdown_pass1.Rd |only roxygen2-8.1.0/roxygen2/DESCRIPTION | 12 roxygen2-8.1.0/roxygen2/MD5 | 135 +++--- roxygen2-8.1.0/roxygen2/NAMESPACE | 34 - roxygen2-8.1.0/roxygen2/NEWS.md | 21 - roxygen2-8.1.0/roxygen2/R/markdown-code.R | 8 roxygen2-8.1.0/roxygen2/R/markdown-escaping.R | 9 roxygen2-8.1.0/roxygen2/R/markdown-link-resolve.R | 119 ----- roxygen2-8.1.0/roxygen2/R/markdown-link.R | 17 roxygen2-8.1.0/roxygen2/R/markdown.R | 201 ---------- roxygen2-8.1.0/roxygen2/R/namespace.R | 116 ++++- roxygen2-8.1.0/roxygen2/R/object-from-call.R | 14 roxygen2-8.1.0/roxygen2/R/options.R | 26 + roxygen2-8.1.0/roxygen2/R/rd-describe-in.R | 2 roxygen2-8.1.0/roxygen2/R/rd-examples.R | 2 roxygen2-8.1.0/roxygen2/R/rd-family.R | 2 roxygen2-8.1.0/roxygen2/R/rd-inherit.R | 49 +- roxygen2-8.1.0/roxygen2/R/rd-params.R | 2 roxygen2-8.1.0/roxygen2/R/rd-r6-external.R | 2 roxygen2-8.1.0/roxygen2/R/rd-raw.R | 2 roxygen2-8.1.0/roxygen2/R/rd-s4.R | 4 roxygen2-8.1.0/roxygen2/R/rd-s7.R | 2 roxygen2-8.1.0/roxygen2/R/rd-section.R | 27 + roxygen2-8.1.0/roxygen2/R/rd-template.R | 2 roxygen2-8.1.0/roxygen2/R/rd-usage.R | 25 + roxygen2-8.1.0/roxygen2/R/rd.R | 5 roxygen2-8.1.0/roxygen2/R/roxygenize-setup.R | 35 + roxygen2-8.1.0/roxygen2/R/roxygenize.R | 1 roxygen2-8.1.0/roxygen2/R/tag-parser.R | 95 +++- roxygen2-8.1.0/roxygen2/R/utils-rd.R | 20 roxygen2-8.1.0/roxygen2/build/vignette.rds |binary roxygen2-8.1.0/roxygen2/inst/doc/namespace.Rmd | 1 roxygen2-8.1.0/roxygen2/inst/doc/namespace.html | 5 roxygen2-8.1.0/roxygen2/inst/doc/rd-S3.Rmd | 2 roxygen2-8.1.0/roxygen2/inst/doc/rd-S3.html | 2 roxygen2-8.1.0/roxygen2/inst/doc/rd-S4.Rmd | 29 + roxygen2-8.1.0/roxygen2/inst/doc/rd-S4.html | 35 + roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.R | 4 roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.Rmd | 2 roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.html | 2 roxygen2-8.1.0/roxygen2/inst/roxygen2-tags.yml | 4 roxygen2-8.1.0/roxygen2/man/markdown-internals.Rd | 10 roxygen2-8.1.0/roxygen2/man/tag_parsers.Rd | 25 - roxygen2-8.1.0/roxygen2/man/tags-namespace.Rd | 2 roxygen2-8.1.0/roxygen2/src/isComplete.cpp | 45 +- roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/markdown.md | 9 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/namespace.md | 20 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/options.md |only roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/rd-inherit.md | 4 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/roxygenize-setup.md | 14 roxygen2-8.1.0/roxygen2/tests/testthat/helper-test.R | 2 roxygen2-8.1.0/roxygen2/tests/testthat/test-markdown-link-resolve.R | 25 - roxygen2-8.1.0/roxygen2/tests/testthat/test-markdown.R | 9 roxygen2-8.1.0/roxygen2/tests/testthat/test-namespace.R | 157 +++++++ roxygen2-8.1.0/roxygen2/tests/testthat/test-object-from-call.R | 20 roxygen2-8.1.0/roxygen2/tests/testthat/test-options.R | 11 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-examples.R | 7 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-inherit.R | 66 +++ roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-markdown-escaping.R | 11 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-section.R | 18 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-usage.R | 46 ++ roxygen2-8.1.0/roxygen2/tests/testthat/test-roxygenize-setup.R | 37 + roxygen2-8.1.0/roxygen2/tests/testthat/test-select-args.R | 5 roxygen2-8.1.0/roxygen2/tests/testthat/test-tag-parser.R | 9 roxygen2-8.1.0/roxygen2/tests/testthat/testImportFrom |only roxygen2-8.1.0/roxygen2/vignettes/namespace.Rmd | 1 roxygen2-8.1.0/roxygen2/vignettes/rd-S3.Rmd | 2 roxygen2-8.1.0/roxygen2/vignettes/rd-S4.Rmd | 29 + roxygen2-8.1.0/roxygen2/vignettes/roxygen2.Rmd | 2 69 files changed, 1057 insertions(+), 604 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and n-grams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Paul Nulty [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
William Lowe [aut] ,
Christian Mueller [ctb],
Olivier Delmarcelle [ctb] ,
European Research [...truncated...]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 4.4 dated 2026-04-06 and 4.5.0 dated 2026-08-04
quanteda-4.4/quanteda/man/dictionary_tokenize.Rd |only quanteda-4.4/quanteda/tests/testthat/testthat-problems.rds |only quanteda-4.5.0/quanteda/DESCRIPTION | 18 quanteda-4.5.0/quanteda/MD5 | 218 +++++----- quanteda-4.5.0/quanteda/NAMESPACE | 28 + quanteda-4.5.0/quanteda/NEWS.md | 41 + quanteda-4.5.0/quanteda/R/RcppExports.R | 36 + quanteda-4.5.0/quanteda/R/aaa.R | 2 quanteda-4.5.0/quanteda/R/casechange-functions.R | 50 +- quanteda-4.5.0/quanteda/R/corpus-methods.R | 24 - quanteda-4.5.0/quanteda/R/corpus_segment.R | 3 quanteda-4.5.0/quanteda/R/data-documentation.R | 79 +-- quanteda-4.5.0/quanteda/R/dfm-classes.R | 13 quanteda-4.5.0/quanteda/R/dfm-print.R | 27 - quanteda-4.5.0/quanteda/R/dfm.R | 25 - quanteda-4.5.0/quanteda/R/dfm_match.R | 34 - quanteda-4.5.0/quanteda/R/dfm_replace.R | 6 quanteda-4.5.0/quanteda/R/dfm_trim.R | 19 quanteda-4.5.0/quanteda/R/dictionaries.R | 69 +-- quanteda-4.5.0/quanteda/R/docvars.R | 19 quanteda-4.5.0/quanteda/R/fcm-classes.R | 9 quanteda-4.5.0/quanteda/R/fcm-print.R | 22 - quanteda-4.5.0/quanteda/R/fcm.R | 2 quanteda-4.5.0/quanteda/R/kwic.R | 13 quanteda-4.5.0/quanteda/R/message.R | 58 ++ quanteda-4.5.0/quanteda/R/meta.R | 18 quanteda-4.5.0/quanteda/R/object-builder.R | 23 - quanteda-4.5.0/quanteda/R/quanteda_options.R | 2 quanteda-4.5.0/quanteda/R/spacyr-methods.R | 11 quanteda-4.5.0/quanteda/R/tokenizers.R | 6 quanteda-4.5.0/quanteda/R/tokens-methods.R | 132 ++---- quanteda-4.5.0/quanteda/R/tokens.R | 101 ---- quanteda-4.5.0/quanteda/R/tokens_compound.R | 1 quanteda-4.5.0/quanteda/R/tokens_lookup.R | 2 quanteda-4.5.0/quanteda/R/tokens_match.R |only quanteda-4.5.0/quanteda/R/tokens_recompile.R |only quanteda-4.5.0/quanteda/R/tokens_replace.R | 5 quanteda-4.5.0/quanteda/R/tokens_segment.R | 1 quanteda-4.5.0/quanteda/R/tokens_trim.R | 14 quanteda-4.5.0/quanteda/R/tokens_xptr.R | 40 - quanteda-4.5.0/quanteda/R/validator.R | 22 - quanteda-4.5.0/quanteda/R/wordstem.R | 6 quanteda-4.5.0/quanteda/README.md | 2 quanteda-4.5.0/quanteda/build/partial.rdb |binary quanteda-4.5.0/quanteda/build/vignette.rds |binary quanteda-4.5.0/quanteda/inst/doc/quickstart.html | 32 - quanteda-4.5.0/quanteda/inst/include/lib.h | 5 quanteda-4.5.0/quanteda/inst/include/tokens.h | 79 ++- quanteda-4.5.0/quanteda/man/as.tokens.Rd | 18 quanteda-4.5.0/quanteda/man/check_integer.Rd | 22 - quanteda-4.5.0/quanteda/man/corpus.Rd | 4 quanteda-4.5.0/quanteda/man/data_char_sampletext.Rd | 7 quanteda-4.5.0/quanteda/man/data_char_ukimmig2010.Rd | 6 quanteda-4.5.0/quanteda/man/data_corpus_inaugural.Rd | 2 quanteda-4.5.0/quanteda/man/data_dfm_lbgexample.Rd | 2 quanteda-4.5.0/quanteda/man/data_dictionary_LSD2015.Rd | 8 quanteda-4.5.0/quanteda/man/dfm-class.Rd | 11 quanteda-4.5.0/quanteda/man/dfm.Rd | 8 quanteda-4.5.0/quanteda/man/dfm_match.Rd | 30 - quanteda-4.5.0/quanteda/man/dfm_trim.Rd | 5 quanteda-4.5.0/quanteda/man/fcm-class.Rd | 3 quanteda-4.5.0/quanteda/man/inflect.Rd |only quanteda-4.5.0/quanteda/man/make_meta.Rd | 2 quanteda-4.5.0/quanteda/man/msg.Rd | 6 quanteda-4.5.0/quanteda/man/print-methods.Rd | 3 quanteda-4.5.0/quanteda/man/quanteda-package.Rd | 8 quanteda-4.5.0/quanteda/man/reexports.Rd | 2 quanteda-4.5.0/quanteda/man/spacyr-methods.Rd | 9 quanteda-4.5.0/quanteda/man/split_values.Rd | 6 quanteda-4.5.0/quanteda/man/tokenize_dictionary.Rd |only quanteda-4.5.0/quanteda/man/tokens_match.Rd |only quanteda-4.5.0/quanteda/man/tokens_recompile.Rd | 55 -- quanteda-4.5.0/quanteda/man/tokens_tolower.Rd | 7 quanteda-4.5.0/quanteda/man/tokens_trim.Rd | 5 quanteda-4.5.0/quanteda/man/valuetype.Rd | 2 quanteda-4.5.0/quanteda/man/wrap.Rd |only quanteda-4.5.0/quanteda/src/RcppExports.cpp | 110 ++++- quanteda-4.5.0/quanteda/src/dfm.cpp |only quanteda-4.5.0/quanteda/src/fcm.cpp | 16 quanteda-4.5.0/quanteda/src/index.cpp | 11 quanteda-4.5.0/quanteda/src/kwic.cpp | 18 quanteda-4.5.0/quanteda/src/serialize.cpp | 12 quanteda-4.5.0/quanteda/src/tokens_chunk.cpp | 15 quanteda-4.5.0/quanteda/src/tokens_combine.cpp | 20 quanteda-4.5.0/quanteda/src/tokens_compound.cpp | 55 -- quanteda-4.5.0/quanteda/src/tokens_group.cpp | 10 quanteda-4.5.0/quanteda/src/tokens_lookup.cpp | 65 +- quanteda-4.5.0/quanteda/src/tokens_match.cpp |only quanteda-4.5.0/quanteda/src/tokens_ngrams.cpp | 29 - 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Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of chromosomal segments shared
identical-by-descent (IBD) among pedigree members. Using sex-specific
recombination rates along the human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.3.2 dated 2025-11-23 and 2.3.3 dated 2026-08-04
ibdsim2-2.3.2/ibdsim2/inst/shiny/R/rcode.R |only ibdsim2-2.3.2/ibdsim2/inst/shiny/www/scripts.js |only ibdsim2-2.3.3/ibdsim2/DESCRIPTION | 20 - ibdsim2-2.3.3/ibdsim2/MD5 | 100 ++++----- ibdsim2-2.3.3/ibdsim2/NAMESPACE | 1 ibdsim2-2.3.3/ibdsim2/NEWS.md | 24 +- ibdsim2-2.3.3/ibdsim2/R/estimateCoeffs.R | 26 +- ibdsim2-2.3.3/ibdsim2/R/findPattern.R | 44 +--- ibdsim2-2.3.3/ibdsim2/R/genedrop.R | 2 ibdsim2-2.3.3/ibdsim2/R/haploDraw.R | 16 - ibdsim2-2.3.3/ibdsim2/R/ibdsim.R | 70 ++++-- ibdsim2-2.3.3/ibdsim2/R/ibdsim2-package.R | 3 ibdsim2-2.3.3/ibdsim2/R/karyogram.R | 23 +- ibdsim2-2.3.3/ibdsim2/R/launchApp.R | 6 ibdsim2-2.3.3/ibdsim2/R/map_constructors.R | 71 +++--- ibdsim2-2.3.3/ibdsim2/R/map_utils.R | 73 ++++-- ibdsim2-2.3.3/ibdsim2/R/plotSegmentDistribution.R | 12 - ibdsim2-2.3.3/ibdsim2/R/profileSimIBD.R | 110 ++++++---- ibdsim2-2.3.3/ibdsim2/R/realisedCoeffs.R | 29 +- ibdsim2-2.3.3/ibdsim2/R/segment_utils.R | 102 ++++----- ibdsim2-2.3.3/ibdsim2/R/utils.R | 16 + ibdsim2-2.3.3/ibdsim2/R/zeroIBD.R | 37 +-- ibdsim2-2.3.3/ibdsim2/README.md | 29 +- ibdsim2-2.3.3/ibdsim2/build/partial.rdb |binary ibdsim2-2.3.3/ibdsim2/inst/shiny/R/builtin-peds.R | 21 + ibdsim2-2.3.3/ibdsim2/inst/shiny/R/plot-functions.R | 6 ibdsim2-2.3.3/ibdsim2/inst/shiny/R/saveData.R | 11 - ibdsim2-2.3.3/ibdsim2/inst/shiny/R/utils.R | 17 + ibdsim2-2.3.3/ibdsim2/inst/shiny/app.R | 49 ++-- ibdsim2-2.3.3/ibdsim2/inst/shiny/www/custom.css | 36 --- ibdsim2-2.3.3/ibdsim2/man/convertPos.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/customMap.Rd | 2 ibdsim2-2.3.3/ibdsim2/man/estimateCoeffs.Rd | 10 ibdsim2-2.3.3/ibdsim2/man/figures/README-ibdsim2-example-distplot-1.png |binary ibdsim2-2.3.3/ibdsim2/man/findPattern.Rd | 2 ibdsim2-2.3.3/ibdsim2/man/haploDraw.Rd | 8 ibdsim2-2.3.3/ibdsim2/man/ibdsim.Rd | 17 + ibdsim2-2.3.3/ibdsim2/man/ibdsim2-package.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/karyoHaploid.Rd | 5 ibdsim2-2.3.3/ibdsim2/man/launchApp.Rd | 5 ibdsim2-2.3.3/ibdsim2/man/loadMap.Rd | 8 ibdsim2-2.3.3/ibdsim2/man/plotSegmentDistribution.Rd | 10 ibdsim2-2.3.3/ibdsim2/man/profileSimIBD.Rd | 17 - ibdsim2-2.3.3/ibdsim2/man/realised.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/zeroIBD.Rd | 4 ibdsim2-2.3.3/ibdsim2/src/ibdsim2.cpp | 29 +- ibdsim2-2.3.3/ibdsim2/tests/testthat/test-estimates.R |only ibdsim2-2.3.3/ibdsim2/tests/testthat/test-maps.R | 31 ++ ibdsim2-2.3.3/ibdsim2/tests/testthat/test-meisosis.R | 7 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-patterns.R | 10 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-profilesim-ibd.R |only ibdsim2-2.3.3/ibdsim2/tests/testthat/test-recombine.R | 1 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-segments.R | 29 ++ 53 files changed, 693 insertions(+), 477 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene set collections. It stores gene set membership, names, gene identifiers, species, versions, and source metadata, with utilities for reading, writing, validating, and converting gene set data for enrichment analysis and related workflows.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.2.0 dated 2026-07-01 and 0.2.1 dated 2026-08-04
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NAMESPACE | 1 - NEWS.md | 4 ++++ R/GMT.R | 20 ++++++++++++-------- 5 files changed, 24 insertions(+), 18 deletions(-)
Title: Bayesian Generalized Linear Models (IID Samples)
Description: Provides Bayesian linear and generalized linear model fitting
with independent and identically distributed (iid) posterior samples. The
main functions mirror R's lm() and glm() interfaces while adding prior
family specifications for Gaussian, Poisson, binomial, and Gamma models
with log-concave likelihoods. Sampling for supported non-conjugate models
uses accept-reject methods based on likelihood subgradients as in Nygren
and Nygren (2006) <doi:10.1198/016214506000000357>. The package also
includes tools for prior setup, posterior summaries, prediction,
diagnostics, simulation, vignettes, and optional 'OpenCL' acceleration for
larger models.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
This is a re-admission after prior archival of version 0.9.72 dated 2026-07-26
Diff between glmbayes versions 0.9.72 dated 2026-07-26 and 0.9.75 dated 2026-08-04
glmbayes-0.9.72/glmbayes/src/glmbayes_getRegisteredNamespace.cpp |only glmbayes-0.9.72/glmbayes/src/glmbayes_getRegisteredNamespace.h |only glmbayes-0.9.72/glmbayes/tools |only glmbayes-0.9.75/glmbayes/DESCRIPTION | 8 glmbayes-0.9.75/glmbayes/MD5 | 98 - glmbayes-0.9.75/glmbayes/NEWS.md | 675 ++++---- glmbayes-0.9.75/glmbayes/README.md | 794 +++++----- glmbayes-0.9.75/glmbayes/build/partial.rdb |binary glmbayes-0.9.75/glmbayes/configure | 92 - glmbayes-0.9.75/glmbayes/configure.win | 41 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-01.html | 12 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S01.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S02.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S03.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S05.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-03.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-05.html | 166 +- glmbayes-0.9.75/glmbayes/inst/doc/Chapter-06.html | 162 +- glmbayes-0.9.75/glmbayes/inst/doc/Chapter-07.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-08.html | 50 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-09.html | 84 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-10.html | 84 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-11.html | 56 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-13.html | 8 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-14.html | 34 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-16.R | 9 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-16.Rmd | 6 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-17.html | 18 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-18.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A01.html | 26 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A02.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A03.html | 122 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A05.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A06.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A07.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A08.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A09.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A10.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A11.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A12.html | 4 glmbayes-0.9.75/glmbayes/inst/examples/Ex_Boston_centered.R | 38 glmbayes-0.9.75/glmbayes/inst/examples/Ex_Cleveland.R | 8 glmbayes-0.9.75/glmbayes/inst/examples/Ex_load_kernel_source.R | 4 glmbayes-0.9.75/glmbayes/man/Boston_centered.Rd | 38 glmbayes-0.9.75/glmbayes/man/Cleveland.Rd | 8 glmbayes-0.9.75/glmbayes/man/gpu_diagnostics.Rd | 4 glmbayes-0.9.75/glmbayes/src/Makevars.win | 3 glmbayes-0.9.75/glmbayes/vignettes/Chapter-16.Rmd | 6 51 files changed, 1377 insertions(+), 1353 deletions(-)
Title: Heteroskedasticity-Consistent Inference for Linear Models
Description: Computes heteroskedasticity-consistent covariance matrix
estimators for ordinary least squares regression models. The published HC0
through HC5m estimators implemented in the package follow White (1980)
<doi:10.2307/1912934>, Hinkley (1977)
<doi:10.1080/00401706.1977.10489550>, MacKinnon and White (1985)
<doi:10.1016/0304-4076(85)90158-7>, Cribari-Neto (2004)
<doi:10.1016/S0167-9473(02)00366-3>, Cribari-Neto and da Silva
(2011) <doi:10.1007/s10182-010-0141-2>, Cribari-Neto et al. (2007)
<doi:10.1080/03610920601126589>, and Li et al. (2016)
<doi:10.1080/00949655.2016.1198906>. The package also includes HCbeta, a
new estimator proposed by the package authors. It provides normal Wald tests,
confidence intervals, diagnostics, and S3 output for applied inference.
Author: Pedro Rafael D. Marinho [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Marina Oliveira Cunha [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between hcinfer versions 0.1.1 dated 2026-07-13 and 0.2.0 dated 2026-08-04
hcinfer-0.1.1/hcinfer/man/figures/README-unnamed-chunk-5-1.png |only hcinfer-0.1.1/hcinfer/man/figures/README-unnamed-chunk-6-1.png |only hcinfer-0.2.0/hcinfer/DESCRIPTION | 13 hcinfer-0.2.0/hcinfer/MD5 | 93 - hcinfer-0.2.0/hcinfer/NAMESPACE | 6 hcinfer-0.2.0/hcinfer/NEWS.md | 7 hcinfer-0.2.0/hcinfer/R/boot-pairs.R |only hcinfer-0.2.0/hcinfer/R/data.R | 75 + hcinfer-0.2.0/hcinfer/R/hc-weights.R | 68 - hcinfer-0.2.0/hcinfer/R/hcinfer.R | 14 hcinfer-0.2.0/hcinfer/R/methods.R | 2 hcinfer-0.2.0/hcinfer/R/model-info.R | 9 hcinfer-0.2.0/hcinfer/R/plot.R | 118 ++ hcinfer-0.2.0/hcinfer/R/tests.R | 5 hcinfer-0.2.0/hcinfer/R/utils-validation.R | 15 hcinfer-0.2.0/hcinfer/R/vcov-hc.R | 31 hcinfer-0.2.0/hcinfer/README.md | 77 - hcinfer-0.2.0/hcinfer/build/vignette.rds |binary hcinfer-0.2.0/hcinfer/data/Crime2009.rda |only hcinfer-0.2.0/hcinfer/data/Hprice.rda |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.R |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.Rmd |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.html |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.R | 27 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.Rmd | 48 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.html | 192 +-- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.R |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.Rmd |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.html |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.R | 113 -- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.Rmd | 221 +-- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.html | 561 ++++------ hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.R | 7 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.Rmd | 120 -- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.html | 132 -- hcinfer-0.2.0/hcinfer/inst/doc/introduction.R | 21 hcinfer-0.2.0/hcinfer/inst/doc/introduction.Rmd | 59 - hcinfer-0.2.0/hcinfer/inst/doc/introduction.html | 95 - hcinfer-0.2.0/hcinfer/man/Crime2009.Rd |only hcinfer-0.2.0/hcinfer/man/Hprice.Rd |only hcinfer-0.2.0/hcinfer/man/boot_pairs.Rd |only hcinfer-0.2.0/hcinfer/man/figures/README-readme-ci-plot-1.png |only hcinfer-0.2.0/hcinfer/man/figures/README-readme-diagnostics-plot-1.png |only hcinfer-0.2.0/hcinfer/man/hcinfer.Rd | 14 hcinfer-0.2.0/hcinfer/man/hcinfer_boot-methods.Rd |only hcinfer-0.2.0/hcinfer/man/plot.hcinfer_boot.Rd |only hcinfer-0.2.0/hcinfer/man/tests.Rd | 5 hcinfer-0.2.0/hcinfer/man/vcov_hc.Rd | 31 hcinfer-0.2.0/hcinfer/tests/testthat/_snaps/boot-pairs.md |only hcinfer-0.2.0/hcinfer/tests/testthat/_snaps/hc-weights.md |only hcinfer-0.2.0/hcinfer/tests/testthat/test-boot-pairs.R |only hcinfer-0.2.0/hcinfer/tests/testthat/test-hc-methods.R | 2 hcinfer-0.2.0/hcinfer/tests/testthat/test-hc-weights.R | 228 ++++ hcinfer-0.2.0/hcinfer/vignettes/hcinfer-bootstrap.Rmd |only hcinfer-0.2.0/hcinfer/vignettes/hcinfer-comparison.Rmd | 48 hcinfer-0.2.0/hcinfer/vignettes/hcinfer-hcbeta-algorithm.Rmd |only hcinfer-0.2.0/hcinfer/vignettes/hcinfer-hcbeta.Rmd | 221 +-- hcinfer-0.2.0/hcinfer/vignettes/hcinfer-methodology.Rmd | 120 -- hcinfer-0.2.0/hcinfer/vignettes/introduction.Rmd | 59 - 59 files changed, 1372 insertions(+), 1485 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.0 dated 2026-07-01 and 0.2.1 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/gsea.R | 7 ++++++- R/utilities.R | 1 + build/partial.rdb |binary man/enrichit_params.Rd | 1 + 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for
the 'zip' function, that does not require any additional external
tools on any platform.
Author: Gabor Csardi [aut, cre],
Kuba Podgorski [ctb],
Rich Geldreich [ctb],
Arm Limited [ctb, cph] ),
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zip versions 3.0.1 dated 2026-07-13 and 3.0.2 dated 2026-08-04
DESCRIPTION | 6 ++-- MD5 | 11 ++++---- NEWS.md | 5 +++ src/unixutils.c | 2 - src/zip.c | 41 +++++++++++++++++++++++--------- tests/testthat/fixtures/symlink-dir.zip |only tests/testthat/test-unzip.R | 18 ++++++++++++++ 7 files changed, 63 insertions(+), 20 deletions(-)
Title: Declarative API for Staged Survey Weights
Description: Builds survey weights from design base weights by chaining the
stages of a weighting workflow (unknown-eligibility redistribution,
nonresponse adjustment, calibration to known population totals, and weight
trimming) through a declarative, pipeable, 'tidymodels'-style API, with
nonresponse handled by weighting classes, by response-propensity
models fitted with logistic regression or machine-learning learners (trees,
random forests and gradient boosting), or by calibration. Calibration
follows Deville and Sarndal (1992) <doi:10.2307/2290268>, and a
range-restricted variant trims the weights into a fixed interval while
preserving the calibration totals, following the generalized exponential
method of Folsom and Singh (2000). Variances are obtained with a
recipe-aware bootstrap and jackknife that resample primary sampling units
and re-apply the whole cascade on each replicate, following the rescaling
bootstrap of Rao and Wu (1988) <doi:10.1080/01621459.1988.10478591>, so the
re [...truncated...]
Author: Juan Pablo Ferreira [aut, cre],
Andres Gutierrez [ctb]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 0.2.0 dated 2026-07-22 and 1.0.0 dated 2026-08-04
DESCRIPTION | 46 - MD5 | 87 +- NAMESPACE | 2 NEWS.md | 149 ++++ R/adjustments.R | 406 +++++++++-- R/prep.R | 21 R/r-indicators.R | 5 R/report.R | 836 ++++++++++++++++++++++-- R/spec.R | 225 +++++- R/variance.R | 138 +++ build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 25 inst/doc/advanced-methods.R | 25 inst/doc/advanced-methods.Rmd | 51 + inst/doc/advanced-methods.html | 52 + inst/doc/model-calibration.html | 4 inst/doc/nonresponse-propensities.R | 31 inst/doc/nonresponse-propensities.Rmd | 70 +- inst/doc/nonresponse-propensities.html | 111 ++- inst/doc/quality-report.R |only inst/doc/quality-report.Rmd |only inst/doc/quality-report.html |only inst/doc/validation-against-survey.R | 15 inst/doc/validation-against-survey.Rmd | 28 inst/doc/validation-against-survey.html | 27 inst/doc/variance-estimation.Rmd | 13 inst/doc/variance-estimation.html | 29 man/bootstrap_weights.Rd | 18 man/jackknife_weights.Rd | 20 man/report_weighting.Rd | 39 + man/step_nonresponse.Rd | 71 +- man/step_trim_calibrated.Rd |only man/step_trim_weights.Rd | 17 man/weightflow-package.Rd | 5 tests/testthat/test-bootstrap.R | 33 tests/testthat/test-calibrate-reconcile.R |only tests/testthat/test-calibrate-totals.R | 19 tests/testthat/test-jackknife.R | 16 tests/testthat/test-nonresponse-calibration.R |only tests/testthat/test-nonresponse-weight-model.R |only tests/testthat/test-replication-card.R |only tests/testthat/test-report-diagnostics.R |only tests/testthat/test-report-scatter.R |only tests/testthat/test-report.R |only tests/testthat/test-trim-calibrated.R |only tests/testthat/test-trim-weights-redistribute.R |only vignettes/advanced-methods.Rmd | 51 + vignettes/nonresponse-propensities.Rmd | 70 +- vignettes/quality-report.Rmd |only vignettes/validation-against-survey.Rmd | 28 vignettes/variance-estimation.Rmd | 13 52 files changed, 2542 insertions(+), 254 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.7.2 dated 2026-04-28 and 0.7.3 dated 2026-08-04
DESCRIPTION | 10 - MD5 | 251 +++++++++++++++--------------- NEWS.md | 226 +++++++++++++-------------- R/heat_colours.R | 5 R/network_p2p.R | 114 ++++++++++--- inst/discovery |only man/IV_report.Rd | 18 +- man/afterhours_dist.Rd | 134 ++++++++-------- man/afterhours_fizz.Rd | 134 ++++++++-------- man/afterhours_line.Rd | 134 ++++++++-------- man/afterhours_rank.Rd | 134 ++++++++-------- man/afterhours_summary.Rd | 134 ++++++++-------- man/afterhours_trend.Rd | 134 ++++++++-------- man/any_idate.Rd | 34 ++-- man/camel_clean.Rd | 34 ++-- man/check_inputs.Rd | 34 ++-- man/check_query.Rd | 40 ++-- man/collaboration_area.Rd | 134 ++++++++-------- man/collaboration_dist.Rd | 134 ++++++++-------- man/collaboration_fizz.Rd | 134 ++++++++-------- man/collaboration_line.Rd | 134 ++++++++-------- man/collaboration_rank.Rd | 134 ++++++++-------- man/collaboration_sum.Rd | 134 ++++++++-------- man/collaboration_trend.Rd | 134 ++++++++-------- man/copy_df.Rd | 10 - man/create_IV.Rd | 8 man/create_bar.Rd | 160 +++++++++---------- man/create_bar_asis.Rd | 160 +++++++++---------- man/create_boxplot.Rd | 160 +++++++++---------- man/create_bubble.Rd | 160 +++++++++---------- man/create_density.Rd | 40 ++-- man/create_dist.Rd | 160 +++++++++---------- man/create_dt.Rd | 10 - man/create_fizz.Rd | 160 +++++++++---------- man/create_hist.Rd | 40 ++-- man/create_inc.Rd | 160 +++++++++---------- man/create_line.Rd | 168 ++++++++++---------- man/create_line_asis.Rd | 168 ++++++++++---------- man/create_period_scatter.Rd | 168 ++++++++++---------- man/create_radar.Rd | 160 +++++++++---------- man/create_rank.Rd | 160 +++++++++---------- man/create_rogers.Rd | 120 +++++++------- man/create_sankey.Rd | 160 +++++++++---------- man/create_scatter.Rd | 160 +++++++++---------- man/create_stacked.Rd | 160 +++++++++---------- man/create_survival.Rd | 160 +++++++++---------- man/create_tracking.Rd | 160 +++++++++---------- man/create_trend.Rd | 168 ++++++++++---------- man/cut_hour.Rd | 34 ++-- man/email_dist.Rd | 132 +++++++-------- man/email_fizz.Rd | 132 +++++++-------- man/email_line.Rd | 132 +++++++-------- man/email_rank.Rd | 132 +++++++-------- man/email_summary.Rd | 132 +++++++-------- man/email_trend.Rd | 132 +++++++-------- man/export.Rd | 10 - man/external_dist.Rd | 128 +++++++-------- man/external_fizz.Rd | 128 +++++++-------- man/external_line.Rd | 128 +++++++-------- man/external_rank.Rd | 134 ++++++++-------- man/external_sum.Rd | 128 +++++++-------- man/extract_date_range.Rd | 34 ++-- man/extract_hr.Rd | 74 ++++---- man/flag_ch_ratio.Rd | 40 ++-- man/flag_em_ratio.Rd | 40 ++-- man/flag_extreme.Rd | 40 ++-- man/flag_outlooktime.Rd | 40 ++-- man/g2g_data.Rd | 14 - man/generate_report.Rd | 10 - man/heat_colours.Rd | 40 ++-- man/hr_trend.Rd | 160 +++++++++---------- man/hrvar_count.Rd | 160 +++++++++---------- man/hrvar_count_all.Rd | 40 ++-- man/hrvar_trend.Rd | 160 +++++++++---------- man/identify_churn.Rd | 40 ++-- man/identify_holidayweeks.Rd | 40 ++-- man/identify_inactiveweeks.Rd | 40 ++-- man/identify_nkw.Rd | 40 ++-- man/identify_outlier.Rd | 40 ++-- man/identify_privacythreshold.Rd | 40 ++-- man/identify_shifts.Rd | 40 ++-- man/identify_tenure.Rd | 40 ++-- man/import_query.Rd | 10 - man/is_date_format.Rd | 34 ++-- man/keymetrics_scan.Rd | 120 +++++++------- man/maxmin.Rd | 34 ++-- man/meeting_dist.Rd | 134 ++++++++-------- man/meeting_fizz.Rd | 134 ++++++++-------- man/meeting_line.Rd | 134 ++++++++-------- man/meeting_rank.Rd | 134 ++++++++-------- man/meeting_summary.Rd | 134 ++++++++-------- man/meeting_tm_report.Rd | 36 ++-- man/meeting_trend.Rd | 134 ++++++++-------- man/mt_data.Rd | 4 man/network_g2g.Rd | 8 man/network_p2p.Rd | 20 +- man/network_summary.Rd | 8 man/one2one_dist.Rd | 134 ++++++++-------- man/one2one_fizz.Rd | 134 ++++++++-------- man/one2one_freq.Rd | 134 ++++++++-------- man/one2one_line.Rd | 134 ++++++++-------- man/one2one_rank.Rd | 134 ++++++++-------- man/one2one_sum.Rd | 134 ++++++++-------- man/one2one_trend.Rd | 134 ++++++++-------- man/p2p_data.Rd | 14 - man/p2p_data_sim.Rd | 10 - man/pairwise_count.Rd | 46 ++--- man/pq_data.Rd | 4 man/prep_query.Rd | 10 - man/read_preamble.Rd | 44 ++--- man/rgb2hex.Rd | 34 ++-- man/theme_wpa.Rd | 4 man/theme_wpa_basic.Rd | 4 man/tm_clean.Rd | 12 - man/tm_cooc.Rd | 12 - man/tm_freq.Rd | 12 - man/tm_wordcloud.Rd | 12 - man/totals_bind.Rd | 34 ++-- man/totals_col.Rd | 34 ++-- man/track_HR_change.Rd | 40 ++-- man/tstamp.Rd | 34 ++-- man/us_to_space.Rd | 34 ++-- man/validation_report.Rd | 50 ++--- man/vivainsights-package.Rd | 1 man/wrap.Rd | 34 ++-- tests/testthat/test_discovery_catalogue.R |only tests/testthat/test_network_p2p.R | 113 +++++++++++++ 127 files changed, 5545 insertions(+), 5365 deletions(-)
Title: Compare and Verify File Contents
Description: Extendable 'R6' file comparison classes, including a 'shiny' app for combining the comparison functionality into a file comparison application. The package idea originates from pharma companies' drug development processes, where statisticians and statistical programmers need to review and compare different versions of the same outputs and datasets. The package implementation itself is not tied to any specific industry and can be used in any context for easy file comparisons between different file version sets.
Author: Juha Javanainen [aut, cre],
Tiina Kirsilae [ctb],
Anna Wiksten [ctb]
Maintainer: Juha Javanainen <ejuhjav@gmail.com>
Diff between verifyr2 versions 1.2.0 dated 2026-05-23 and 1.3.0 dated 2026-08-04
DESCRIPTION | 18 MD5 | 72 +-- NAMESPACE | 2 NEWS.md | 15 R/Config.R | 35 + R/FileComparatorFactory.R | 14 R/ImgFileComparator.R | 96 ++++ R/PdfFileComparator.R | 19 R/TxtFileComparator.R | 15 R/XlsxFileComparator.R |only README.md | 30 - inst/extdata/base_files/file12.xlsx |only inst/extdata/compare_files/file12.xlsx |only inst/shiny_examples/app/app.R | 85 --- inst/shiny_examples/app/image_diff_styles.css |only inst/shiny_examples/app/report_styles.css | 26 + inst/shiny_examples/app/report_template.Rmd | 384 ++++++++++-------- inst/shiny_examples/app/styles.css | 94 ---- man/ImgFileComparator.Rd | 22 + man/PdfFileComparator.Rd | 28 + man/RtfFileComparator.Rd | 1 man/TxtFileComparator.Rd | 25 + man/TxtWithImagesFileComparator.Rd | 1 man/XlsxFileComparator.Rd |only tests/testthat/_snaps/app-app/file_compare-001_.png |binary tests/testthat/_snaps/app-app/folder_compare-001.json | 3 tests/testthat/_snaps/app-app/folder_compare-001_.png |binary tests/testthat/_snaps/app-app/options_reset-001.json | 4 tests/testthat/test-details_comparison_bin.R | 26 - tests/testthat/test-details_comparison_img.R | 78 ++- tests/testthat/test-details_comparison_json.R | 32 - tests/testthat/test-details_comparison_pdf.R | 67 ++- tests/testthat/test-details_comparison_rtf.R | 75 ++- tests/testthat/test-details_comparison_txt.R | 66 +-- tests/testthat/test-details_comparison_xlsx.R |only tests/testthat/test-summary_comparison_img.R | 18 tests/testthat/test-summary_comparison_pdf.R | 6 tests/testthat/test-summary_comparison_xlsx.R |only tests/testthat/test-vrf_contents_xlsx.R |only tests/testthat/test_outputs/xlsx |only 40 files changed, 836 insertions(+), 521 deletions(-)
Title: Discover, Count, Categorise, Score, Translate and Relate Emoji
in Text
Description: A tidy toolkit for working with the emoji in any text column, such
as social-media posts, product reviews, chat logs or survey responses.
Unicode is awkward to handle and not every code point is an emoji, which
makes emoji statistics fiddly to obtain. 'tidyEmoji' extracts, counts,
categorises, sentiment-scores and emotion-scores emoji, converts them to and
from text (for accessibility and NLP preprocessing), searches the emoji
catalogue, maps emoji co-occurrence and sequences (graph-ready edge lists
and n-grams), measures where and how densely emoji are used, and builds
document-by-emoji feature tables for machine learning, with grapheme-aware
detection (so skin-tone and multi-person sequences stay intact), returning
tidy data frames that slot straight into a 'tidyverse' workflow. The
bundled emoji sentiment lexicon is from the Emoji
Sentiment Ranking of Kralj Novak et al. (2015)
<doi:10.1371/journal.pone.0144296>, released under CC BY-SA 4.0; the emotion
lexicon is from EmoTag12 [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidyEmoji versions 0.2.0 dated 2026-06-17 and 0.3.0 dated 2026-08-04
tidyEmoji-0.2.0/tidyEmoji/vignettes/ata_tweets.rda |only tidyEmoji-0.3.0/tidyEmoji/DESCRIPTION | 31 tidyEmoji-0.3.0/tidyEmoji/MD5 | 97 - tidyEmoji-0.3.0/tidyEmoji/NAMESPACE | 18 tidyEmoji-0.3.0/tidyEmoji/NEWS.md | 154 ++ tidyEmoji-0.3.0/tidyEmoji/R/data.R | 43 tidyEmoji-0.3.0/tidyEmoji/R/emoji-categorize.R | 9 tidyEmoji-0.3.0/tidyEmoji/R/emoji-dfm.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-emotion.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-engine.R | 178 ++ tidyEmoji-0.3.0/tidyEmoji/R/emoji-extraction.R | 12 tidyEmoji-0.3.0/tidyEmoji/R/emoji-lexicon-api.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-metrics.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-relate.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-search.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-sentiment.R | 54 tidyEmoji-0.3.0/tidyEmoji/R/emoji-summary.R | 27 tidyEmoji-0.3.0/tidyEmoji/R/emoji-translate.R |only tidyEmoji-0.3.0/tidyEmoji/R/tidyEmoji.R | 28 tidyEmoji-0.3.0/tidyEmoji/R/top-n-emojis.R | 60 tidyEmoji-0.3.0/tidyEmoji/README.md | 175 ++ tidyEmoji-0.3.0/tidyEmoji/data/category_unicode_crosswalk.rda |binary tidyEmoji-0.3.0/tidyEmoji/data/emoji_emotion_lexicon.rda |only tidyEmoji-0.3.0/tidyEmoji/data/emoji_unicode_crosswalk.rda |binary tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.R | 111 + tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.Rmd | 264 +++- tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.html | 655 +++++++--- tidyEmoji-0.3.0/tidyEmoji/man/as_emoji_name.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_cooccurrence.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_density.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_dfm.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion_label.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion_lexicon.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_extract_unnest.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_filter.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_frequency.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_lexicons.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_ngrams.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_pairs.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_position.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_ratio.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_score.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_search.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_sentiment.Rd | 24 tidyEmoji-0.3.0/tidyEmoji/man/emoji_sentiment_lexicon.Rd | 20 tidyEmoji-0.3.0/tidyEmoji/man/emoji_summary.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_to_text.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_unicode_crosswalk.Rd | 3 tidyEmoji-0.3.0/tidyEmoji/man/figures |only tidyEmoji-0.3.0/tidyEmoji/man/register_emoji_lexicon.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/text_to_emoji.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/tidyEmoji-package.Rd | 20 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-dfm.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-dimensions.R | 8 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-edge-cases.R | 6 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-emotion.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-extraction.R | 8 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-frequency-categorize.R | 21 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-metrics.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-regression-0.2.1.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-regression-0.3.0.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-relate.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-sentiment.R | 2 tidyEmoji-0.3.0/tidyEmoji/vignettes/ata_tweets.csv |only tidyEmoji-0.3.0/tidyEmoji/vignettes/introduction.Rmd | 264 +++- 66 files changed, 1940 insertions(+), 368 deletions(-)
Title: 'OpenCL' Tools for R Package Developers
Description: Runtime 'OpenCL' support for R package developers: probe hardware
and drivers, load and concatenate kernel sources, and manage
dependency-annotated '.cl' libraries, so packages like 'nmathopencl' and
other ported libraries can offer GPU acceleration without each re-implementing
and related helpers. Vignettes illustrate integration with suggested package
'nmathopencl' and with downstream applications such as 'glmbayes';
production kernels for those applications ship in those packages rather
than here.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between opencltools versions 0.8.2 dated 2026-07-11 and 0.8.3 dated 2026-08-04
opencltools-0.8.2/opencltools/src/glmbayes_getRegisteredNamespace.cpp |only opencltools-0.8.2/opencltools/src/glmbayes_getRegisteredNamespace.h |only opencltools-0.8.2/opencltools/tools/patch_rcpp_function_h.R |only opencltools-0.8.2/opencltools/tools/rcpp_include.R |only opencltools-0.8.3/opencltools/DESCRIPTION | 18 opencltools-0.8.3/opencltools/MD5 | 18 opencltools-0.8.3/opencltools/NEWS.md | 353 +++++----- opencltools-0.8.3/opencltools/configure | 21 opencltools-0.8.3/opencltools/configure.win | 39 - opencltools-0.8.3/opencltools/src/Makevars | 4 opencltools-0.8.3/opencltools/src/Makevars.win | 3 opencltools-0.8.3/opencltools/tools/README.md | 30 12 files changed, 213 insertions(+), 273 deletions(-)
Title: Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics
Description: A lightweight interchange layer for single-cell and spatial omics
data, built on the L-star model of labelled axes and typed fields over them,
serialized to the 'Zarr' format. Provides bidirectional converters
("profiles") for 'Seurat', 'SingleCellExperiment', 'Conos', and 'pagoda2'
objects, including collections of heterogeneous samples, via a shared C++
core ('libstar') so the same store is readable from R, 'Python', and C++.
Author: Peter Kharchenko [aut, cre]
Maintainer: Peter Kharchenko <pk.restricted@gmail.com>
Diff between lstar versions 0.2.1 dated 2026-07-22 and 0.2.2 dated 2026-08-04
DESCRIPTION | 8 ++--- MD5 | 10 +++--- NEWS.md | 29 ++++++++++++++++++ R/viewer.R | 42 ++++++++++++++++++++++++--- man/extend_for_viewer.Rd | 14 +++++++-- tests/testthat/test-viewer-export.R | 56 ++++++++++++++++++++++++++++++++++++ 6 files changed, 144 insertions(+), 15 deletions(-)
Title: Processing, Visualizing, and Labeling Americas Barometer Data
Description: Labeling, weighting, and plotting data following custom style guidelines for use in reports, presentations, and social media posts. The Center for Global Democracy (formerly the Latin American Public Opinion Project) at Vanderbilt University is a leader in public survey research, best known for the Americas Barometer project. The publicly available data can be downloaded from: <https://www.vanderbilt.edu/lapop/data-access.php>.
Author: Robert Vidigal [cre, aut] ,
Luke Plutowski [ctb, aut]
Maintainer: Robert Vidigal <robert.vidigal@vanderbilt.edu>
Diff between lapop versions 2.1.5 dated 2026-04-29 and 2.1.7 dated 2026-08-04
DESCRIPTION | 18 - LICENSE | 2 MD5 | 66 ++--- NAMESPACE | 2 NEWS.md | 8 R/globals.R | 7 R/lapop_cc.R | 268 +++++++++++++++------- R/lapop_ccm.R | 451 +++++++++++++++++++++---------------- R/lapop_coef.R | 167 +++++++++---- R/lapop_hist.R | 9 R/lapop_mover.R | 37 ++- R/lapop_save.R | 60 ++-- R/lapop_stack.R | 458 ++++++++++++++++++++++---------------- R/lpr_cc.R | 171 ++++++++++---- R/lpr_ccm.R | 214 +++++++++++------ R/lpr_dumb.R | 191 ++++++++++----- R/lpr_hist.R | 64 +++-- R/lpr_mline.R | 153 ++++++++---- R/lpr_mover.R | 137 ++++++----- R/lpr_na_attributes.R |only R/lpr_ts.R | 101 +++++--- README.md | 37 ++- build/vignette.rds |binary inst/cran_preflight.R | 2 inst/doc/lapop-visualization.R | 2 inst/doc/lapop-visualization.Rmd | 2 inst/doc/lapop-visualization.html | 10 man/lapop-deprecated.Rd | 1 man/lapop_cc.Rd | 35 ++ man/lapop_ccm.Rd | 14 - man/lapop_coef.Rd | 17 + man/lapop_stack.Rd | 24 + man/lpr_ccm.Rd | 29 +- man/lpr_na_attributes.Rd |only vignettes/lapop-visualization.Rmd | 2 35 files changed, 1779 insertions(+), 980 deletions(-)
Title: A Copy Number and Expression-Based Classifier for Breast Tumours
Description: Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.
Author: Oscar M Rueda [aut, cre]
Maintainer: Oscar M Rueda <Oscar.Rueda@mrc-bsu.cam.ac.uk>
Diff between iC10 versions 2.0.2 dated 2024-07-19 and 2.0.3 dated 2026-08-04
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS | 2 ++ R/compare.R | 10 +++++++++- build/partial.rdb |binary 5 files changed, 21 insertions(+), 10 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
'ggplot2' figures suitab [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 1.1.0 dated 2026-07-14 and 1.1.1 dated 2026-08-04
DESCRIPTION | 6 - MD5 | 28 ++--- NEWS.md | 29 ++++++ R/conditional_infit.R | 151 ++++++++++++++++++++++---------- R/infit_cutoff.R | 4 R/targeting_plot.R | 7 - README.md | 8 - inst/doc/easyRasch2.Rmd | 7 + inst/doc/easyRasch2.html | 10 +- man/RMitemInfit.Rd | 33 +++++- man/RMitemInfitCutoff.Rd | 4 man/RMtargeting.Rd | 2 tests/testthat/test-infit_pvalue.R | 61 ++++++++++++ vignettes/easyRasch2.Rmd | 7 + vignettes/figures/rasch-targeting-1.png |binary 15 files changed, 268 insertions(+), 89 deletions(-)
Title: Reading, Formatting, and Organizing the Panel Study of Income
Dynamics (PSID)
Description: Provides various functions for reading and preparing the Panel Study of Income Dynamics (PSID) for longitudinal analysis, including functions that read the PSID's fixed width format files directly into R, rename all of the PSID's longitudinal variables so that recurring variables have consistent names across years, simplify assembling longitudinal datasets from cross sections of the PSID Family Files, and export the resulting PSID files into file formats common among other statistical programming languages ('SAS', 'STATA', and 'SPSS').
Author: Brian Aronson [aut, cre]
Maintainer: Brian Aronson <bdaronson@gmail.com>
Diff between easyPSID versions 0.1.2 dated 2021-10-03 and 0.1.3 dated 2026-08-04
DESCRIPTION | 11 +-- LICENSE | 2 MD5 | 35 ++++++----- NAMESPACE | 3 NEWS.md | 25 +++++++- R/10find_desc.R | 8 -- R/2convert_to_rds.R | 152 +++++++++++++++++++++++++++++-------------------- R/3rename_fam_vars.R | 87 ++++++++++++++++------------ R/4rename_ind_vars.R | 51 ++++++++++------ R/8find_name.R | 35 +++-------- R/9find_years.R | 36 +++-------- R/reference_lookup.R |only R/sysdata.rda |binary README.md | 75 ++++++++++++++---------- man/convert_to_rds.Rd | 2 man/rename_ind_vars.Rd | 5 - tests |only 17 files changed, 302 insertions(+), 225 deletions(-)
Title: Das Gupta Standardisation and Decomposition
Description: Implementation of Das Gupta's standardisation and decomposition of population rates, as set out "Standardization and decomposition of rates: A user’s manual", Das Gupta (1993) <https://www2.census.gov/library/publications/1993/demographics/p23-186.pdf>. The goal of these methods is to calculate adjusted rates based on compositional 'factors' and quantify the contribution of each factor to the difference in crude rates between populations. The package offers functionality to handle various scenarios for any number of factors and populations, where said factors can be comprised of vectors across sub-populations (including cross-classified population breakdowns), and with the option to specify user-defined rate functions.
Author: Josiah King [aut, cre],
Ben Matthews [aut],
Prithwis Das Gupta [aut]
Maintainer: Josiah King <josiah.king@ed.ac.uk>
Diff between DasGuptR versions 2.1.0 dated 2025-04-07 and 2.2.0 dated 2026-08-04
DasGuptR-2.1.0/DasGuptR/R/uspop.R |only DasGuptR-2.1.0/DasGuptR/data/uspop.RData |only DasGuptR-2.1.0/DasGuptR/man/uspop.Rd |only DasGuptR-2.2.0/DasGuptR/DESCRIPTION | 18 DasGuptR-2.2.0/DasGuptR/MD5 | 94 + DasGuptR-2.2.0/DasGuptR/NAMESPACE | 30 DasGuptR-2.2.0/DasGuptR/NEWS.md | 12 DasGuptR-2.2.0/DasGuptR/R/dg2pop.R | 1 DasGuptR-2.2.0/DasGuptR/R/dg354.R | 6 DasGuptR-2.2.0/DasGuptR/R/dg611.R | 2 DasGuptR-2.2.0/DasGuptR/R/dg612.R | 57 - DasGuptR-2.2.0/DasGuptR/R/dg_check.R |only DasGuptR-2.2.0/DasGuptR/R/dg_plot.R | 16 DasGuptR-2.2.0/DasGuptR/R/dg_table.R | 3 DasGuptR-2.2.0/DasGuptR/R/dgeg2_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_2.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_4.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg3_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_4.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg5_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg5_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg6_5.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg6_6.R |only DasGuptR-2.2.0/DasGuptR/R/dgnpop.R | 329 ++---- DasGuptR-2.2.0/DasGuptR/R/reconv.R | 31 DasGuptR-2.2.0/DasGuptR/R/split_popstr.R | 82 - DasGuptR-2.2.0/DasGuptR/README.md | 34 DasGuptR-2.2.0/DasGuptR/build/vignette.rds |binary DasGuptR-2.2.0/DasGuptR/data/dgeg2_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_2.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_4.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg3_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_4.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg5_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg5_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg6_5.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg6_6.RData |only DasGuptR-2.2.0/DasGuptR/inst/doc/category_effects.html | 524 ++++------ DasGuptR-2.2.0/DasGuptR/inst/doc/choosing_comparison_years.html |only DasGuptR-2.2.0/DasGuptR/inst/doc/choosing_comparison_years.html.asis |only DasGuptR-2.2.0/DasGuptR/man/dg611.Rd | 2 DasGuptR-2.2.0/DasGuptR/man/dg612.Rd | 6 DasGuptR-2.2.0/DasGuptR/man/dg_check.Rd |only DasGuptR-2.2.0/DasGuptR/man/dg_plot.Rd | 18 DasGuptR-2.2.0/DasGuptR/man/dg_table.Rd | 2 DasGuptR-2.2.0/DasGuptR/man/dgeg2_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_2.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_4.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg3_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_4.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg5_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg5_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg6_5.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg6_6.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgnpop.Rd | 473 +++------ DasGuptR-2.2.0/DasGuptR/man/reconv.Rd | 30 DasGuptR-2.2.0/DasGuptR/tests |only DasGuptR-2.2.0/DasGuptR/vignettes/choosing_comparison_years.html.asis |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/bsamps_2004_2016.rds |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/bsamps_2015_2016.rds |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/category_effects.qmd | 28 DasGuptR-2.2.0/DasGuptR/vignettes/qmd/choosing_comparison_years.qmd |only 71 files changed, 870 insertions(+), 928 deletions(-)
Title: Fast and Portable Character String Processing Facilities
Description: A collection of character string/text/natural language
processing tools for pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms. Documentation about 'stringi' is
provided via its website at <https://stringi.gagolewski.com/> and
the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).
Author: Marek Gagolewski [aut, cre, cph] ,
Bartek Tartanus [ctb],
Unicode, Inc. and others [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.8.7 dated 2025-03-27 and 1.8.9 dated 2026-08-04
stringi-1.8.7/stringi/tools |only stringi-1.8.9/stringi/DESCRIPTION | 14 stringi-1.8.9/stringi/INSTALL | 9 stringi-1.8.9/stringi/LICENSE | 2 stringi-1.8.9/stringi/MD5 | 554 +-- stringi-1.8.9/stringi/NEWS | 7 stringi-1.8.9/stringi/R/ICU_settings.R | 2 stringi-1.8.9/stringi/R/compare.R | 2 stringi-1.8.9/stringi/R/encoding.R | 2 stringi-1.8.9/stringi/R/encoding_conversion.R | 2 stringi-1.8.9/stringi/R/encoding_detection.R | 2 stringi-1.8.9/stringi/R/encoding_management.R | 2 stringi-1.8.9/stringi/R/escape.R | 2 stringi-1.8.9/stringi/R/files.R | 2 stringi-1.8.9/stringi/R/install.R | 2 stringi-1.8.9/stringi/R/internal_prepare_arg.R | 2 stringi-1.8.9/stringi/R/internal_test.R | 2 stringi-1.8.9/stringi/R/join.R | 2 stringi-1.8.9/stringi/R/length.R | 2 stringi-1.8.9/stringi/R/locale.R | 2 stringi-1.8.9/stringi/R/locale_management.R | 2 stringi-1.8.9/stringi/R/opts.R | 2 stringi-1.8.9/stringi/R/pad.R | 2 stringi-1.8.9/stringi/R/random.R | 2 stringi-1.8.9/stringi/R/reverse.R | 2 stringi-1.8.9/stringi/R/search.R | 4 stringi-1.8.9/stringi/R/search_count_4.R | 2 stringi-1.8.9/stringi/R/search_count_bound.R | 2 stringi-1.8.9/stringi/R/search_detect_4.R | 2 stringi-1.8.9/stringi/R/search_extract_4.R | 2 stringi-1.8.9/stringi/R/search_extract_bound.R | 2 stringi-1.8.9/stringi/R/search_locate_4.R | 2 stringi-1.8.9/stringi/R/search_locate_bound.R | 2 stringi-1.8.9/stringi/R/search_match_4.R | 2 stringi-1.8.9/stringi/R/search_replace_4.R | 2 stringi-1.8.9/stringi/R/search_split_4.R | 2 stringi-1.8.9/stringi/R/search_split_bound.R | 2 stringi-1.8.9/stringi/R/search_startsendswith_4.R | 2 stringi-1.8.9/stringi/R/search_subset_4.R | 2 stringi-1.8.9/stringi/R/sort.R | 2 stringi-1.8.9/stringi/R/sprintf.R | 2 stringi-1.8.9/stringi/R/stats.R | 2 stringi-1.8.9/stringi/R/stringi_package.R | 2 stringi-1.8.9/stringi/R/sub.R | 2 stringi-1.8.9/stringi/R/time_calendar.R | 2 stringi-1.8.9/stringi/R/time_format.R | 8 stringi-1.8.9/stringi/R/time_symbols.R | 2 stringi-1.8.9/stringi/R/time_zone.R | 2 stringi-1.8.9/stringi/R/trans_casemap.R | 2 stringi-1.8.9/stringi/R/trans_normalization.R | 2 stringi-1.8.9/stringi/R/trans_other.R | 2 stringi-1.8.9/stringi/R/trans_transliterate.R | 2 stringi-1.8.9/stringi/R/trim.R | 2 stringi-1.8.9/stringi/R/utils.R | 2 stringi-1.8.9/stringi/R/wrap.R | 2 stringi-1.8.9/stringi/build/partial.rdb |binary stringi-1.8.9/stringi/configure | 1554 +++------- stringi-1.8.9/stringi/configure.ac | 203 - stringi-1.8.9/stringi/configure.win | 2 stringi-1.8.9/stringi/man/about_arguments.Rd | 2 stringi-1.8.9/stringi/man/about_encoding.Rd | 38 stringi-1.8.9/stringi/man/about_locale.Rd | 44 stringi-1.8.9/stringi/man/about_search.Rd | 94 stringi-1.8.9/stringi/man/about_search_boundaries.Rd | 54 stringi-1.8.9/stringi/man/about_search_charclass.Rd | 8 stringi-1.8.9/stringi/man/about_search_coll.Rd | 40 stringi-1.8.9/stringi/man/about_search_fixed.Rd | 6 stringi-1.8.9/stringi/man/about_search_regex.Rd | 6 stringi-1.8.9/stringi/man/operator_add.Rd | 10 stringi-1.8.9/stringi/man/operator_compare.Rd | 32 stringi-1.8.9/stringi/man/operator_dollar.Rd | 14 stringi-1.8.9/stringi/man/stri_compare.Rd | 32 stringi-1.8.9/stringi/man/stri_count.Rd | 4 stringi-1.8.9/stringi/man/stri_count_boundaries.Rd | 52 stringi-1.8.9/stringi/man/stri_datetime_add.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_create.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_fields.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_format.Rd | 26 stringi-1.8.9/stringi/man/stri_datetime_fstr.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_now.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_symbols.Rd | 20 stringi-1.8.9/stringi/man/stri_detect.Rd | 4 stringi-1.8.9/stringi/man/stri_dup.Rd | 10 stringi-1.8.9/stringi/man/stri_duplicated.Rd | 32 stringi-1.8.9/stringi/man/stri_enc_detect.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_detect2.Rd | 42 stringi-1.8.9/stringi/man/stri_enc_fromutf32.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_info.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_isascii.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_isutf16.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_isutf8.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_list.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_mark.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_set.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_toascii.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_tonative.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_toutf32.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_toutf8.Rd | 12 stringi-1.8.9/stringi/man/stri_encode.Rd | 12 stringi-1.8.9/stringi/man/stri_escape_unicode.Rd | 4 stringi-1.8.9/stringi/man/stri_extract.Rd | 6 stringi-1.8.9/stringi/man/stri_extract_boundaries.Rd | 54 stringi-1.8.9/stringi/man/stri_flatten.Rd | 10 stringi-1.8.9/stringi/man/stri_isempty.Rd | 14 stringi-1.8.9/stringi/man/stri_join.Rd | 10 stringi-1.8.9/stringi/man/stri_join_list.Rd | 10 stringi-1.8.9/stringi/man/stri_length.Rd | 14 stringi-1.8.9/stringi/man/stri_list2matrix.Rd | 8 stringi-1.8.9/stringi/man/stri_locale_info.Rd | 6 stringi-1.8.9/stringi/man/stri_locale_list.Rd | 6 stringi-1.8.9/stringi/man/stri_locale_set.Rd | 6 stringi-1.8.9/stringi/man/stri_locate.Rd | 12 stringi-1.8.9/stringi/man/stri_locate_boundaries.Rd | 60 stringi-1.8.9/stringi/man/stri_match.Rd | 6 stringi-1.8.9/stringi/man/stri_na2empty.Rd | 8 stringi-1.8.9/stringi/man/stri_numbytes.Rd | 14 stringi-1.8.9/stringi/man/stri_opts_brkiter.Rd | 16 stringi-1.8.9/stringi/man/stri_opts_collator.Rd | 34 stringi-1.8.9/stringi/man/stri_opts_fixed.Rd | 2 stringi-1.8.9/stringi/man/stri_opts_regex.Rd | 2 stringi-1.8.9/stringi/man/stri_order.Rd | 32 stringi-1.8.9/stringi/man/stri_pad.Rd | 14 stringi-1.8.9/stringi/man/stri_rand_lipsum.Rd | 6 stringi-1.8.9/stringi/man/stri_rand_shuffle.Rd | 6 stringi-1.8.9/stringi/man/stri_rand_strings.Rd | 6 stringi-1.8.9/stringi/man/stri_rank.Rd | 32 stringi-1.8.9/stringi/man/stri_read_lines.Rd | 6 stringi-1.8.9/stringi/man/stri_read_raw.Rd | 6 stringi-1.8.9/stringi/man/stri_remove_empty.Rd | 8 stringi-1.8.9/stringi/man/stri_replace.Rd | 6 stringi-1.8.9/stringi/man/stri_replace_na.Rd | 8 stringi-1.8.9/stringi/man/stri_replace_rstr.Rd | 6 stringi-1.8.9/stringi/man/stri_sort.Rd | 32 stringi-1.8.9/stringi/man/stri_sort_key.Rd | 32 stringi-1.8.9/stringi/man/stri_split.Rd | 6 stringi-1.8.9/stringi/man/stri_split_boundaries.Rd | 54 stringi-1.8.9/stringi/man/stri_split_lines.Rd | 22 stringi-1.8.9/stringi/man/stri_sprintf.Rd | 14 stringi-1.8.9/stringi/man/stri_startsendswith.Rd | 4 stringi-1.8.9/stringi/man/stri_stats_general.Rd | 4 stringi-1.8.9/stringi/man/stri_stats_latex.Rd | 4 stringi-1.8.9/stringi/man/stri_sub.Rd | 8 stringi-1.8.9/stringi/man/stri_sub_all.Rd | 8 stringi-1.8.9/stringi/man/stri_subset.Rd | 2 stringi-1.8.9/stringi/man/stri_timezone_info.Rd | 26 stringi-1.8.9/stringi/man/stri_timezone_list.Rd | 26 stringi-1.8.9/stringi/man/stri_timezone_set.Rd | 26 stringi-1.8.9/stringi/man/stri_trans_casemap.Rd | 58 stringi-1.8.9/stringi/man/stri_trans_char.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_general.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_list.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_nf.Rd | 10 stringi-1.8.9/stringi/man/stri_trim.Rd | 8 stringi-1.8.9/stringi/man/stri_unescape_unicode.Rd | 4 stringi-1.8.9/stringi/man/stri_unique.Rd | 32 stringi-1.8.9/stringi/man/stri_width.Rd | 14 stringi-1.8.9/stringi/man/stri_wrap.Rd | 48 stringi-1.8.9/stringi/man/stri_write_lines.Rd | 6 stringi-1.8.9/stringi/man/stringi-package.Rd | 2 stringi-1.8.9/stringi/src/Makevars.in | 2 stringi-1.8.9/stringi/src/Makevars.win | 2 stringi-1.8.9/stringi/src/icu74/common/udata.cpp | 54 stringi-1.8.9/stringi/src/install.libs.R.in | 2 stringi-1.8.9/stringi/src/stri_ICU_settings.cpp | 2 stringi-1.8.9/stringi/src/stri_brkiter.cpp | 2 stringi-1.8.9/stringi/src/stri_brkiter.h | 2 stringi-1.8.9/stringi/src/stri_bytesearch_matcher.h | 2 stringi-1.8.9/stringi/src/stri_callables.cpp | 2 stringi-1.8.9/stringi/src/stri_callables.h | 2 stringi-1.8.9/stringi/src/stri_collator.cpp | 2 stringi-1.8.9/stringi/src/stri_common.cpp | 2 stringi-1.8.9/stringi/src/stri_compare.cpp | 2 stringi-1.8.9/stringi/src/stri_container_base.cpp | 4 stringi-1.8.9/stringi/src/stri_container_base.h | 5 stringi-1.8.9/stringi/src/stri_container_bytesearch.cpp | 2 stringi-1.8.9/stringi/src/stri_container_bytesearch.h | 2 stringi-1.8.9/stringi/src/stri_container_charclass.h | 2 stringi-1.8.9/stringi/src/stri_container_double.h | 2 stringi-1.8.9/stringi/src/stri_container_integer.h | 2 stringi-1.8.9/stringi/src/stri_container_listint.cpp | 2 stringi-1.8.9/stringi/src/stri_container_listint.h | 2 stringi-1.8.9/stringi/src/stri_container_listraw.cpp | 22 stringi-1.8.9/stringi/src/stri_container_listraw.h | 6 stringi-1.8.9/stringi/src/stri_container_listutf8.cpp | 2 stringi-1.8.9/stringi/src/stri_container_listutf8.h | 2 stringi-1.8.9/stringi/src/stri_container_logical.h | 2 stringi-1.8.9/stringi/src/stri_container_regex.cpp | 2 stringi-1.8.9/stringi/src/stri_container_regex.h | 2 stringi-1.8.9/stringi/src/stri_container_usearch.cpp | 2 stringi-1.8.9/stringi/src/stri_container_usearch.h | 2 stringi-1.8.9/stringi/src/stri_container_utf16.cpp | 2 stringi-1.8.9/stringi/src/stri_container_utf16.h | 2 stringi-1.8.9/stringi/src/stri_container_utf8.cpp | 16 stringi-1.8.9/stringi/src/stri_container_utf8.h | 6 stringi-1.8.9/stringi/src/stri_container_utf8_indexable.cpp | 4 stringi-1.8.9/stringi/src/stri_container_utf8_indexable.h | 2 stringi-1.8.9/stringi/src/stri_encoding_conversion.cpp | 2 stringi-1.8.9/stringi/src/stri_encoding_detection.cpp | 2 stringi-1.8.9/stringi/src/stri_encoding_management.cpp | 2 stringi-1.8.9/stringi/src/stri_escape.cpp | 2 stringi-1.8.9/stringi/src/stri_exception.cpp | 2 stringi-1.8.9/stringi/src/stri_exception.h | 2 stringi-1.8.9/stringi/src/stri_exports.h | 2 stringi-1.8.9/stringi/src/stri_external.h | 2 stringi-1.8.9/stringi/src/stri_interval.h | 2 stringi-1.8.9/stringi/src/stri_intvec.h | 2 stringi-1.8.9/stringi/src/stri_join.cpp | 2 stringi-1.8.9/stringi/src/stri_length.cpp | 2 stringi-1.8.9/stringi/src/stri_macros.h | 2 stringi-1.8.9/stringi/src/stri_messages.h | 2 stringi-1.8.9/stringi/src/stri_pad.cpp | 2 stringi-1.8.9/stringi/src/stri_prepare_arg.cpp | 2 stringi-1.8.9/stringi/src/stri_random.cpp | 2 stringi-1.8.9/stringi/src/stri_reverse.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_trim.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_common.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_in.cpp | 2 stringi-1.8.9/stringi/src/stri_search_other_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_match.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_sort.cpp | 2 stringi-1.8.9/stringi/src/stri_sprintf.cpp | 2 stringi-1.8.9/stringi/src/stri_stats.cpp | 2 stringi-1.8.9/stringi/src/stri_string8.cpp | 2 stringi-1.8.9/stringi/src/stri_string8.h | 2 stringi-1.8.9/stringi/src/stri_string8buf.h | 2 stringi-1.8.9/stringi/src/stri_stringi.cpp | 2 stringi-1.8.9/stringi/src/stri_stringi.h | 2 stringi-1.8.9/stringi/src/stri_sub.cpp | 2 stringi-1.8.9/stringi/src/stri_test.cpp | 2 stringi-1.8.9/stringi/src/stri_time_calendar.cpp | 11 stringi-1.8.9/stringi/src/stri_time_format.cpp | 12 stringi-1.8.9/stringi/src/stri_time_symbols.cpp | 2 stringi-1.8.9/stringi/src/stri_time_zone.cpp | 5 stringi-1.8.9/stringi/src/stri_trans_casemap.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_normalization.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_other.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_transliterate.cpp | 2 stringi-1.8.9/stringi/src/stri_ucnv.cpp | 2 stringi-1.8.9/stringi/src/stri_ucnv.h | 2 stringi-1.8.9/stringi/src/stri_uloc.cpp | 2 stringi-1.8.9/stringi/src/stri_utils.cpp | 2 stringi-1.8.9/stringi/src/stri_wrap.cpp | 2 stringi-1.8.9/stringi/src/uconfig_local.h.in | 6 278 files changed, 1989 insertions(+), 2559 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality
is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
Author: Francois Michonneau [aut, cre] ,
Ben Bolker [aut] ,
Mark Holder [aut] ,
Paul Lewis [aut] ,
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.8.9 dated 2026-01-21 and 0.8.10 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ README.md | 2 +- build/partial.rdb |binary src/ncl/nxscxxdiscretematrix.h | 6 +++--- src/ncl/nxsstring.h | 9 +++------ 7 files changed, 24 insertions(+), 19 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.10-0 dated 2026-07-02 and 1.11-0 dated 2026-08-04
DESCRIPTION | 9 MD5 | 105 ++--- NAMESPACE | 1 NEWS.md | 51 ++ R/AS.R | 2 R/BinaryExactCI.R | 3 R/RBesT-package.R | 4 R/asthma.R | 2 R/automixfit.R | 4 R/colitis.R | 4 R/crohn.R | 2 R/decision1S.R | 4 R/decision2S.R | 4 R/decision2S_boundary.R | 596 +++++++++++++++++++++++------- R/gMAP.R | 14 R/mixess.R | 9 R/mixfit.R | 4 R/oc2S.R | 6 R/pos2S.R | 2 R/postmix.R | 4 R/robustify.R | 5 R/sysdata.rda |binary R/transplant.R | 4 R/uniroot_int.R | 48 +- build/partial.rdb |only inst/REFERENCES.bib |only inst/doc/RBesT.pdf |binary inst/doc/introduction.Rmd | 22 - inst/doc/introduction.html | 169 +++++--- inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 590 ++++++++++++++--------------- inst/sbc/sbc_tools.R | 38 + man/AS.Rd | 2 man/BinaryExactCI.Rd | 3 man/RBesT-package.Rd | 3 man/asthma.Rd | 2 man/automixfit.Rd | 4 man/colitis.Rd | 4 man/crohn.Rd | 2 man/decision1S.Rd | 4 man/decision2S.Rd | 4 man/decision2S_boundary.Rd | 2 man/ess.Rd | 9 man/gMAP.Rd | 13 man/mixfit.Rd | 4 man/oc2S.Rd | 6 man/pos2S.Rd | 2 man/postmix.Rd | 4 man/robustify.Rd | 5 man/transplant.Rd | 4 man/uniroot_int.Rd | 10 tests/testthat/test-decision2S.R | 6 tests/testthat/test-decision2S_boundary.R | 160 +++++++- vignettes/REFERENCES.bib |only vignettes/introduction.Rmd | 22 - 55 files changed, 1282 insertions(+), 705 deletions(-)
Title: Optimize PTSD Diagnostic Criteria
Description: Provides tools for analyzing and optimizing PTSD (Post-Traumatic
Stress Disorder) diagnostic criteria using PCL-5 (PTSD Checklist for DSM-5)
and CAPS-5 (Clinician-Administered PTSD Scale for DSM-5) data. Functions
identify optimal subsets of PCL-5 items that maintain diagnostic accuracy
while reducing assessment burden. Includes tools for both hierarchical
(cluster-based) and non-hierarchical symptom combinations, calculation of
diagnostic metrics, and comparison with standard DSM-5 criteria. Redundancy
analysis quantifies how many item subsets perform equivalently, through
plateau sizes and bootstrap stability, and reports item selection against
the chance baseline of the searched candidate space. A transport layer
allows a site to evaluate subsets derived elsewhere and return only
aggregate summaries, supporting multi-site validation without sharing
individual-level data. Model validation is conducted using holdout and
cross-validation methods to assess robustness and generalizabilit [...truncated...]
Author: Laura Weidmann [aut] ,
Tobias R. Spiller [aut, cre] ,
Flavio A. Schueepp [aut]
Maintainer: Tobias R. Spiller <tobias.spiller@access.uzh.ch>
Diff between PTSDdiag versions 0.4.1 dated 2026-07-13 and 0.5.0 dated 2026-08-04
DESCRIPTION | 36 ++++--- MD5 | 73 +++++++++++--- NAMESPACE | 31 ++++++ NEWS.md | 148 ++++++++++++++++++++++++++++++ R/bootstrap_stability.R |only R/compare_rule_forms.R |only R/diagnostic_metrics.R |only R/evaluate_sets.R |only R/internals.R | 14 ++ R/internals_stability.R |only R/plateau.R |only R/plot_symptom_selection.R |only R/scenario_plots.R | 56 +++++++++-- R/scenario_tables.R | 61 ++++++++++-- R/symptom_selection.R |only R/transport.R |only inst/doc/multi-site-validation.html | 2 inst/doc/validation.R | 19 +++ inst/doc/validation.Rmd | 34 ++++++ inst/doc/validation.html | 83 ++++++++++++++++ man/as_set_matrix.Rd |only man/ba_ci.Rd |only man/bootstrap_stability.Rd |only man/chance_baseline.Rd |only man/compare_rule_forms.Rd |only man/compute_plateau.Rd |only man/diagnostic_metrics.Rd |only man/diagnostic_metrics_family.Rd |only man/evaluate_sets.Rd |only man/exact_ci.Rd |only man/five_number.Rd |only man/fmt_est_ci.Rd |only man/fmt_ratio_ci.Rd |only man/icd11_items.Rd |only man/icd11_performance.Rd |only man/kappa_ci.Rd |only man/lr_ci.Rd |only man/n_candidates.Rd |only man/pcl5_item_labels.Rd |only man/plot_symptom_frequency.Rd | 22 +++- man/plot_symptom_selection.Rd |only man/print.ptsdiag_plateau.Rd |only man/print.ptsdiag_rule_forms.Rd |only man/print.ptsdiag_stability.Rd |only man/print.ptsdiag_transport.Rd |only man/read_transport.Rd |only man/set_id_to_items.Rd |only man/symptom_frequency.Rd | 21 +++- man/symptom_selection.Rd |only man/transport_plateau.Rd |only man/wilson_ci.Rd |only man/write_transport.Rd |only tests/testthat/test-analysis.R | 53 ++++++++++ tests/testthat/test-bootstrap_stability.R |only tests/testthat/test-diagnostic_metrics.R |only tests/testthat/test-evaluate_sets.R |only tests/testthat/test-plateau.R |only tests/testthat/test-symptom_selection.R |only tests/testthat/test-transport.R |only vignettes/validation.Rmd | 34 ++++++ 60 files changed, 630 insertions(+), 57 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.4.1 dated 2026-04-04 and 1.4.2 dated 2026-08-04
DESCRIPTION | 8 MD5 | 89 +-- NEWS.md | 5 R/datastep.R | 2 R/utilities.R | 19 build/vignette.rds |binary inst/doc/libr-basics.R | 162 ++--- inst/doc/libr-datastep.R | 1130 ++++++++++++++++++++--------------------- inst/doc/libr-example1.R | 236 ++++---- inst/doc/libr-example2.R | 354 ++++++------ inst/doc/libr-faq.R | 114 ++-- inst/doc/libr-management.R | 254 ++++----- inst/doc/libr.R | 216 +++---- man/datastep.Rd | 14 man/delete.Rd | 14 man/dsarray.Rd | 14 man/dsattr.Rd | 14 man/import_spec.Rd | 10 man/is.lib.Rd | 32 - man/length.dsarray.Rd | 14 man/lib_add.Rd | 32 - man/lib_copy.Rd | 32 - man/lib_delete.Rd | 32 - man/lib_export.Rd | 32 - man/lib_info.Rd | 32 - man/lib_load.Rd | 32 - man/lib_path.Rd | 32 - man/lib_remove.Rd | 32 - man/lib_replace.Rd | 32 - man/lib_size.Rd | 32 - man/lib_sync.Rd | 32 - man/lib_unload.Rd | 32 - man/lib_write.Rd | 32 - man/libname.Rd | 32 - man/libr.Rd | 5 man/output.Rd | 14 man/print.lib.Rd | 32 - man/print.specs.Rd | 10 man/read.specs.Rd | 10 man/specs.Rd | 10 man/sub-.dsarray.Rd | 14 man/write.specs.Rd | 10 tests/testthat/data/types |only tests/testthat/test-datastep.R | 1 tests/testthat/test-libname.R | 15 tests/testthat/test-specs.R | 14 46 files changed, 1663 insertions(+), 1621 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualizations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.4.0 dated 2026-07-02 and 3.5.0 dated 2026-08-04
DESCRIPTION | 22 LICENSE | 4 MD5 | 240 NAMESPACE | 16 NEWS.md | 205 R/autoplot_methods.R | 13 R/calc_roc.R | 4 R/gg_beta_varpro.R | 17 R/gg_brier.R | 17 R/gg_error.R | 64 R/gg_isopro.R | 25 R/gg_ivarpro.R | 6 R/gg_partial.R | 39 R/gg_partial_rfsrc.R | 11 R/gg_partial_varpro.R | 161 R/gg_rfsrc.R | 7 R/gg_roc.R | 4 R/gg_shap.R |only R/gg_variable.R | 9 R/gg_varpro.R | 12 R/gg_vimp.R | 269 R/help.R | 123 R/plot.gg_beta_uvarpro.R | 2 R/plot.gg_beta_varpro.R | 6 R/plot.gg_error.R | 40 R/plot.gg_isopro.R | 10 R/plot.gg_ivarpro.R | 2 R/plot.gg_partial.R | 23 R/plot.gg_partial_varpro.R | 4 R/plot.gg_rfsrc.R | 12 R/plot.gg_roc.R | 10 R/plot.gg_sdependent.R | 6 R/plot.gg_shap.R |only R/plot.gg_udependent.R | 8 R/plot.gg_variable.R | 16 R/plot.gg_varpro.R | 13 R/plot.gg_vimp.R | 8 R/print_methods.R | 10 R/quantile_pts.R | 20 R/ribbon_style.R | 2 R/summary_methods.R | 31 build/vignette.rds |binary inst/doc/ggRandomForests-classification.R |only inst/doc/ggRandomForests-classification.html |only inst/doc/ggRandomForests-classification.qmd |only inst/doc/ggRandomForests-regression.R | 25 inst/doc/ggRandomForests-regression.html | 216 inst/doc/ggRandomForests-regression.qmd | 82 inst/doc/ggRandomForests-survival.R | 7 inst/doc/ggRandomForests-survival.html | 56 inst/doc/ggRandomForests-survival.qmd | 9 inst/doc/ggRandomForests.R | 3 inst/doc/ggRandomForests.html | 10 inst/doc/ggRandomForests.qmd | 3 inst/doc/uvarpro.R | 3 inst/doc/uvarpro.html | 12 inst/doc/uvarpro.qmd | 5 inst/doc/varpro.R | 32 inst/doc/varpro.html | 7010 ---------- inst/doc/varpro.qmd | 117 man/autoplot.gg.Rd | 10 man/dot-varpro_imp_stats.Rd | 4 man/ggRandomForests-package.Rd | 129 man/gg_beta_varpro.Rd | 15 man/gg_brier.Rd | 8 man/gg_error.Rd | 52 man/gg_isopro.Rd | 25 man/gg_ivarpro.Rd | 4 man/gg_partial.Rd | 34 man/gg_partial_rfsrc.Rd | 12 man/gg_partial_varpro.Rd | 72 man/gg_roc.rfsrc.Rd | 2 man/gg_shap.Rd |only man/gg_varpro.Rd | 8 man/gg_vimp.Rd | 66 man/plot.gg_beta_uvarpro.Rd | 2 man/plot.gg_beta_varpro.Rd | 6 man/plot.gg_error.Rd | 30 man/plot.gg_isopro.Rd | 2 man/plot.gg_ivarpro.Rd | 2 man/plot.gg_partial.Rd | 2 man/plot.gg_partial_rfsrc.Rd | 4 man/plot.gg_partial_varpro.Rd | 4 man/plot.gg_rfsrc.Rd | 6 man/plot.gg_roc.Rd | 4 man/plot.gg_sdependent.Rd | 6 man/plot.gg_shap.Rd |only man/plot.gg_udependent.Rd | 8 man/plot.gg_variable.Rd | 2 man/plot.gg_varpro.Rd | 6 man/plot.gg_vimp.Rd | 6 man/print.gg.Rd | 3 man/quantile_pts.Rd | 18 man/shap_beeswarm.Rd |only man/shap_dependence.Rd |only man/shap_importance.Rd |only man/summary.gg.Rd | 3 tests/testthat/_snaps/snapshots/gg-isopro-default.svg |only tests/testthat/_snaps/snapshots/gg-isopro-predict-overlay.svg |only tests/testthat/_snaps/snapshots/gg-isopro-threshold.svg |only tests/testthat/_snaps/snapshots/gg-roc-multiclass-facet.svg |only tests/testthat/_snaps/snapshots/gg-roc-multiclass-overlay.svg |only tests/testthat/_snaps/snapshots/gg-shap-beeswarm.svg |only tests/testthat/_snaps/snapshots/gg-shap-dependence.svg |only tests/testthat/_snaps/snapshots/gg-shap-importance.svg |only tests/testthat/_snaps/snapshots/gg-udependent-default.svg |only tests/testthat/_snaps/snapshots/gg-udependent-undirected.svg |only tests/testthat/_snaps/snapshots/gg-variable-rf-classification-default.svg |only tests/testthat/_snaps/snapshots/gg-variable-rf-classification-smooth.svg |only tests/testthat/_snaps/snapshots/gg-vimp-classification-rf.svg | 184 tests/testthat/_snaps/snapshots/gg-vimp-regression-rf.svg | 48 tests/testthat/test_default_dispatch.R |only tests/testthat/test_gg_error.R | 2 tests/testthat/test_gg_isopro.R | 6 tests/testthat/test_gg_partial.R | 53 tests/testthat/test_gg_partial_rfsrc.R | 2 tests/testthat/test_gg_partial_varpro.R | 179 tests/testthat/test_gg_shap.R |only tests/testthat/test_gg_varpro.R | 35 tests/testthat/test_gg_vimp.R | 210 tests/testthat/test_plot_layer_data.R | 10 tests/testthat/test_print_summary.R | 96 tests/testthat/test_snapshots.R | 26 tests/testthat/test_surv_partial.R | 2 vignettes/_fig_optim.R |only vignettes/ggRandomForests-classification.qmd |only vignettes/ggRandomForests-regression.qmd | 82 vignettes/ggRandomForests-survival.qmd | 9 vignettes/ggRandomForests.bib | 19 vignettes/ggRandomForests.qmd | 3 vignettes/precompute_varpro.R | 23 vignettes/uvarpro.qmd | 5 vignettes/varpro.qmd | 117 vignettes/varpro_precomputed.rds |binary 134 files changed, 2992 insertions(+), 7755 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Enhanced Office Open XML Charting for 'openxlsx2'
Description: Provides a high-level 'R6' interface for creating complex
Office Open XML (OOXML) charts. Allows users to build
multi-series combo charts with secondary axes and granular styling
options, designed to integrate seamlessly with 'openxlsx2'.
Author: Jan Marvin Garbuszus [aut, cre]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between encharter versions 0.9.1 dated 2026-06-27 and 0.10 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md |only R/encharter.R | 22 ++++++++++++---------- R/encharter_chart.R | 18 +++++++++++------- inst/AUTHORS | 1 + man/EncharterBase.Rd | 4 ++++ man/encharter.Rd | 4 ++++ src/pugixml.cpp | 4 ++-- tests/testthat/test-axis_logic.R | 39 +++++++++++++++++++++++++++++++++++++++ 10 files changed, 85 insertions(+), 30 deletions(-)
Title: Bayesian Parameter Estimation and Forecasting for
Epidemiological Models
Description: Methods for Bayesian parameter estimation and forecasting in epidemiological models.
Functions enable model fitting using Bayesian methods and generate forecasts with uncertainty quantification.
Implements approaches described in <doi:10.48550/arXiv.2411.05371> and <doi:10.1002/sim.9164>.
Author: Hamed Karami [aut],
Amanda Bleichrodt [aut],
Ruiyan Luo [aut],
Gerardo Chowell [aut, cre]
Maintainer: Gerardo Chowell <gchowell@gsu.edu>
Diff between BayesianFitForecast versions 1.1.0 dated 2025-08-19 and 1.1.1 dated 2026-08-04
DESCRIPTION | 11 +++--- MD5 | 14 +++++--- NEWS.md |only R/Imports.R |only R/Run_analyzeResults.R | 1 inst/doc/BayesianFitForecast.html | 5 +-- inst/extdata/ode_model.stan | 60 ++++++++++++++++++++------------------ inst/scripts/run_analyzeResults.R | 14 +++----- inst/scripts/stancreator.R | 2 - 9 files changed, 55 insertions(+), 52 deletions(-)
More information about BayesianFitForecast at CRAN
Permanent link
Title: Inference for Functions of Multinomial Parameters
Description: We consider the problem where we observe k vectors (possibly of different lengths), each representing an independent multinomial random vector. For a given function that takes in the concatenated vector of multinomial probabilities and outputs a real number, this is a Monte Carlo estimation procedure of an exact p-value and confidence interval. The resulting inference is valid even in small samples, when the parameter is on the boundary, and when the function is not differentiable at the parameter value, all situations where asymptotic methods and the bootstrap would fail. For more details see Sachs, Fay, and Gabriel (2025) <doi:10.48550/arXiv.2406.19141>.
Author: Michael C Sachs [aut, cre],
Michael P Fay [aut],
Erin E Gabriel [aut],
David B Dahl [ctb] )
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between xactonomial versions 1.2.1 dated 2026-07-30 and 1.2.2 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.in | 1 - 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 3.2.0 dated 2026-07-19 and 3.2.1 dated 2026-08-04
mizer-3.2.0/mizer/tests/testthat/Rplots.pdf |only mizer-3.2.1/mizer/DESCRIPTION | 6 mizer-3.2.1/mizer/MD5 | 31 mizer-3.2.1/mizer/NAMESPACE | 8 mizer-3.2.1/mizer/NEWS.md | 105 +++ mizer-3.2.1/mizer/R/helpers.R | 14 mizer-3.2.1/mizer/R/matchGrowth.R | 13 mizer-3.2.1/mizer/R/setFishing.R | 21 mizer-3.2.1/mizer/R/species_params.R | 420 ++++++++++-- mizer-3.2.1/mizer/R/zzz.R | 27 mizer-3.2.1/mizer/man/print.mizer_plot.Rd |only mizer-3.2.1/mizer/man/record_given_species_params.Rd |only mizer-3.2.1/mizer/man/species_params.Rd | 53 + mizer-3.2.1/mizer/tests/testthat/test-matchGrowth.R | 18 mizer-3.2.1/mizer/tests/testthat/test-setFishing.R | 14 mizer-3.2.1/mizer/tests/testthat/test-species_params.R | 439 ++++++++++++- mizer-3.2.1/mizer/tests/testthat/test-validSpeciesParams.R | 9 mizer-3.2.1/mizer/tests/testthat/test-zzz.R | 24 18 files changed, 1046 insertions(+), 156 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Shejuty Devnath [aut],
Cen Wu [aut]
Maintainer: Kun Fan <fzt0428@gmail.com>
Diff between mixedBayes versions 0.2.5 dated 2026-04-23 and 0.2.6 dated 2026-08-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/mixedBayes-package.R | 6 ++++++ build/partial.rdb |binary man/mixedBayes-package.Rd | 6 ++++++ 6 files changed, 26 insertions(+), 10 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and computing. Includes functions for logging, parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.4.7 dated 2026-05-24 and 0.4.9 dated 2026-08-04
thisutils-0.4.7/thisutils/tests/testthat/test-package-startup.R |only thisutils-0.4.9/thisutils/DESCRIPTION | 16 thisutils-0.4.9/thisutils/MD5 | 52 thisutils-0.4.9/thisutils/NAMESPACE | 6 thisutils-0.4.9/thisutils/NEWS.md | 24 thisutils-0.4.9/thisutils/R/BiocNeighborsKNN.R |only thisutils-0.4.9/thisutils/R/ClassificationMetrics.R |only thisutils-0.4.9/thisutils/R/MatrixTopK.R |only thisutils-0.4.9/thisutils/R/RcppExports.R | 12 thisutils-0.4.9/thisutils/R/log_message.R | 10 thisutils-0.4.9/thisutils/R/package_management.R | 406 +++- thisutils-0.4.9/thisutils/R/parallelize_fun.R | 860 +++++++--- thisutils-0.4.9/thisutils/R/row_variance.R |only thisutils-0.4.9/thisutils/README.md | 2 thisutils-0.4.9/thisutils/inst/include |only thisutils-0.4.9/thisutils/inst/python |only thisutils-0.4.9/thisutils/man/check_r.Rd | 33 thisutils-0.4.9/thisutils/man/classification_metrics_compute.Rd |only thisutils-0.4.9/thisutils/man/fast_row_vars.Rd |only thisutils-0.4.9/thisutils/man/filter_nonzero_variance_features.Rd |only thisutils-0.4.9/thisutils/man/log_message.Rd | 2 thisutils-0.4.9/thisutils/man/parallelize_fun.Rd | 27 thisutils-0.4.9/thisutils/man/run_biocneighbors_knn.Rd |only thisutils-0.4.9/thisutils/man/run_dense_topk_by_column.Rd |only thisutils-0.4.9/thisutils/man/run_sparse_topk_by_column.Rd |only thisutils-0.4.9/thisutils/src/ClassificationMetrics.cpp |only thisutils-0.4.9/thisutils/src/MatrixTopK.cpp |only thisutils-0.4.9/thisutils/src/RcppExports.cpp | 43 thisutils-0.4.9/thisutils/tests/testthat/test-biocneighbors-knn.R |only thisutils-0.4.9/thisutils/tests/testthat/test-classification-metrics.R |only thisutils-0.4.9/thisutils/tests/testthat/test-matrix-topk.R |only thisutils-0.4.9/thisutils/tests/testthat/test-package-management.R |only thisutils-0.4.9/thisutils/tests/testthat/test-parallelize_fun.R | 819 +++++++++ thisutils-0.4.9/thisutils/tests/testthat/test-row-variance.R |only 34 files changed, 2007 insertions(+), 305 deletions(-)
Title: Spectral Preprocessing and Chemometric Calibration of NIR
Sensors
Description: Provides tools to build quantitative chemometric models and
applications for near-infrared (NIR) sensors. Chemometric regression
models are based on partial least squares regression as described by
Wold (1975) <doi:10.1016/B978-0-12-103950-9.50017-4> and modified
partial least squares regression as described by Shenk and Westerhaus
(1991) <doi:10.2135/cropsci1991.0011183X003100020049x>, with further
discussion by Westerhaus (2014) <doi:10.1255/nirn.1492>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Claudio Orellano [aut] ,
Nicolae Cudlenco [aut] ,
Mai Said [aut] ,
Mohamed Abushosha [aut],
Marcal Plans [aut]
Maintainer: Leonardo Ramirez-Lopez <ramirez-lopez.l@buchi.com>
Diff between proximetricsR versions 0.6.5 dated 2026-07-17 and 0.7.0 dated 2026-08-04
DESCRIPTION | 17 LICENSE | 2 MD5 | 81 NAMESPACE | 1 NEWS | 10 R/AAA.R | 11 R/calibrate_models.R | 8 R/plot.spectral_model.R | 71 R/proximate_read_data.R | 57 R/proxiscout_read_data.R | 188 - R/proxiscout_write_model_info.R |only R/write_rtf.R | 60 README.md | 8 build/stage23.rdb |binary inst/CITATION | 2 inst/doc/aa-intro.html | 4 inst/doc/ab-pre-processing-recipes.html | 4 inst/doc/ac-mathematical-overview-of-regression-algorithms.html | 4 inst/doc/ad-proximate-building-applications.R | 21 inst/doc/ad-proximate-building-applications.html | 27 inst/doc/ad-proximate-building-applications.qmd | 21 inst/doc/ae-proxiscout-building-applications.html | 4 inst/doc/af-proximate-structure-of-the-applications.html | 6 inst/doc/ag-proxiscout-structure-of-the-applications.html | 4 inst/doc/ah-read-and-recalibrate-applications.html | 4 inst/figure_xls.qmd |only inst/logo.R | 99 inst/model_plot_template.qmd | 1484 ++++++---- inst/zebra_handdrawn-wb.png |only man/figures/logo.png |binary man/plot.spectral_model.Rd | 35 man/proximate_read_data.Rd | 6 man/proximetricsR-package.Rd | 7 man/proxiscout_read_data.Rd | 46 man/proxiscout_write_model_info.Rd |only tests/testthat/_snaps/write_nax/test_nax.CBD.rtf | 34 tests/testthat/_snaps/write_nax/test_nax.CBDA.rtf | 22 tests/testthat/_snaps/write_nax/test_nax1.THC.rtf | 36 tests/testthat/_snaps/write_rtf/test_rtf1.THC.rtf | 140 tests/testthat/test-plot.spectral_model.R | 1 tests/testthat/test-proxiscout_read_data.R | 152 + tests/testthat/test-proxiscout_write_model_info.R |only tests/testthat/test-write_rtf.R | 2 vignettes/ad-proximate-building-applications.qmd | 21 44 files changed, 1878 insertions(+), 822 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
Staysail Systems, Inc. [cph] ,
Capitar IT Group BV [cph] ,
The Mbed TLS Contributors [cph] ,
Pierre L'Ecuyer [cph] ,
sakura authors [cph] ,
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.10.1 dated 2026-07-09 and 1.10.2 dated 2026-08-04
DESCRIPTION | 8 MD5 | 44 - NEWS.md | 10 R/dispatcher.R | 6 R/ncurl.R | 14 build/vignette.rds |binary inst/doc/nanonext.html | 20 inst/doc/v01-messaging.html | 20 inst/doc/v02-protocols.html | 20 inst/doc/v03-configuration.html | 20 inst/doc/v04-web.html | 20 man/dot-dispatcher_start.Rd | 4 man/ncurl.Rd | 14 src/aio.c | 58 - src/dispatcher.c | 1077 ++++++++++++++++++------------ src/init.c | 2 src/nanonext.h | 3 src/nng/src/core/msgqueue.c | 2 src/nng/src/supplemental/tls/tls_common.c | 3 src/server.c | 12 src/sync.c | 4 tests/tests.R | 70 + tools/patch_nng.sh | 42 + 23 files changed, 933 insertions(+), 540 deletions(-)
Title: MRI Tissue Classification
Description: Implements various methods for tissue classification in magnetic
resonance (MR) images of the brain, including normal mixture models
and hidden Markov normal mixture models, as outlined in Feng &
Tierney (2011) <doi:10.18637/jss.v044.i07>. These methods allow a
structural MR image to be classified into gray matter, white matter
and cerebrospinal fluid tissue types.
Author: Dai Feng [aut],
Luke Tierney [aut],
Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between mritc versions 0.6.0 dated 2026-07-24 and 0.6.1 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ src/registerDynamicSymbol.c | 4 ++++ src/updateDistanceUnit_omp.c | 4 ++-- 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Inference on Granger-Causality in the Frequency Domain
Description: Implements unconditional and conditional Granger-causality spectra in the frequency domain, bootstrap inference for both spectra and their difference, and the Breitung-Candelon parametric tests. The bootstrap procedures follow Farnè and Montanari (2022) <doi:10.1007/s10614-021-10112-x>.
Author: Matteo Farne [aut, cre],
Angela Montanari [aut]
Maintainer: Matteo Farne <matteo.farne@unibo.it>
Diff between grangers versions 0.1.0 dated 2019-06-03 and 0.1.1 dated 2026-08-04
DESCRIPTION | 26 ++++++++++++++++------- MD5 | 37 +++++++++++++++++---------------- R/Granger_conditional.R | 6 ++--- R/Granger_inference_conditional.R | 12 +++++----- R/Granger_inference_difference.R | 18 ++++++++-------- R/Granger_inference_unconditional.R | 12 +++++----- R/Granger_unconditional.R | 6 ++--- R/bc_test_cond.R | 6 ++--- R/bc_test_uncond.R | 6 ++--- R/euro_area_indicators.R | 6 ++--- README.md |only build |only inst |only man/Granger.conditional.Rd | 19 ++++++++++++---- man/Granger.inference.conditional.Rd | 29 +++++++++++++++++-------- man/Granger.inference.difference.Rd | 36 +++++++++++++++++++++----------- man/Granger.inference.unconditional.Rd | 26 ++++++++++++++++------- man/Granger.unconditional.Rd | 17 ++++++++++----- man/bc_test_cond.Rd | 19 ++++++++++++---- man/bc_test_uncond.Rd | 18 +++++++++++----- man/euro_area_indicators.Rd | 10 +++++--- 21 files changed, 195 insertions(+), 114 deletions(-)
More information about blockr.session at CRAN
Permanent link
Title: Parse and Manipulate R Code
Description: Parsing R code is key to build tools such as linters and stylers.
This package provides a binding to the 'Rust' crate 'ast-grep' so that one
can parse and explore R code.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between astgrepr versions 0.1.1 dated 2025-06-07 and 0.1.2 dated 2026-08-04
DESCRIPTION | 10 ++--- MD5 | 32 +++++++++--------- NEWS.md | 4 ++ R/rule.R | 2 - README.md | 24 +++++++++----- build/vignette.rds |binary inst/doc/astgrepr.R | 8 ++-- inst/doc/astgrepr.Rmd | 40 +++++++++++------------ inst/doc/astgrepr.html | 13 ++++--- man/pattern_rule.Rd | 2 - src/Makevars.win.in | 2 - src/rust/Cargo.lock | 21 +++--------- src/rust/Cargo.toml | 2 - src/rust/src/language.rs | 80 +++++++++++++++++++++++------------------------ src/rust/vendor.tar.xz |binary tools/config.R | 12 +++++++ vignettes/astgrepr.Rmd | 40 +++++++++++------------ 17 files changed, 155 insertions(+), 137 deletions(-)
Title: Creating Composite Plots using 'aplot'
Description: Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Chun-Hui Gao [ctb] ,
Shensuo Li [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplotExtra versions 0.0.5 dated 2026-07-13 and 0.0.6 dated 2026-08-04
DESCRIPTION | 6 +-- MD5 | 9 +++-- NAMESPACE | 1 NEWS.md | 5 +++ R/oncoplot.r | 75 ++++++++++++++++++++++++++++++++------------- man/oncoplot_components.Rd |only 6 files changed, 68 insertions(+), 28 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, counterfactual analysis, and
computation of impulse response functions, generalized impulse response functions,
generalized forecast error variance decompositions, as well as historical
decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.1016/j.jedc.2025.105162>,
Savi Virolainen (2026) <doi:10.1080/07474938.2026.2673986>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between sstvars versions 1.2.4 dated 2026-05-29 and 1.2.5 dated 2026-08-04
DESCRIPTION | 12 ++--- MD5 | 88 ++++++++++++++++++++--------------------- NEWS.md | 5 ++ R/LSest.R | 4 - R/MAINest.R | 4 - R/STVARconstruction.R | 4 - R/argumentChecks.R | 4 - R/data.R | 4 - R/distributionFuns.R | 4 - R/jointSpectralRadius.R | 4 - R/loglikelihood.R | 4 - R/moreEst.R | 4 - README.md | 6 +- inst/doc/sstvars-vignette.pdf |binary man/STVAR.Rd | 4 - man/alt_stvar.Rd | 4 - man/bound_JSR.Rd | 4 - man/bound_jsr_G.Rd | 4 - man/change_regime.Rd | 4 - man/check_params.Rd | 4 - man/diagnostic_plot.Rd | 4 - man/estim_NLS.Rd | 4 - man/fitSSTVAR.Rd | 4 - man/fitSTVAR.Rd | 4 - man/fitbsSSTVAR.Rd | 4 - man/get_alpha_mt.Rd | 4 - man/get_residuals.Rd | 4 - man/in_paramspace.Rd | 4 - man/iterate_more.Rd | 4 - man/loglikelihood.Rd | 4 - man/n_params.Rd | 4 - man/plot_struct_shocks.Rd | 4 - man/predict.stvar.Rd | 4 - man/profile_logliks.Rd | 4 - man/reform_constrained_pars.Rd | 4 - man/regime_distance.Rd | 4 - man/simulate.stvar.Rd | 4 - man/simulate_from_regime.Rd | 4 - man/simulate_stvar_int.Rd | 4 - man/sstvars-package.Rd | 4 - man/stand_t_dens.Rd | 4 - man/standard_errors.Rd | 4 - man/swap_parametrization.Rd | 4 - man/usacpu.Rd | 4 - vignettes/refs.bib | 6 ++ 45 files changed, 141 insertions(+), 132 deletions(-)
Title: Robust Estimation for Multi-Study High-Dimensional Elliptical
Factor Analytics
Description: We introduce a multi-study high-dimensional factor analysis toolbox 'MultiEFM' based on the elliptical factor model framework, which learns latent heterogeneous features and accounts for cross-study variation among sources. It provides robust estimation algorithms for heterogeneous datasets, particularly tailored for multi-study RNA sequencing arrays and complex spatial multi-omics layers. The package implements highly efficient initialization strategies, identifiability constraints alignment, and computationally scalable parameter estimation paradigms.
Author: Ruihan Zhang [aut, cre],
Wei Liu [aut]
Maintainer: Ruihan Zhang <ruihanzhang6166@gmail.com>
Diff between MultiEFM versions 0.1.3 dated 2026-07-28 and 0.1.4 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/main.R | 10 +++++----- inst/doc/simu_high_dim.html | 10 +++++----- inst/doc/simu_low_dim.html | 10 +++++----- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Multi-Armed Qini
Description: Fits generalized Qini curves for evaluating treatment allocation
policies with one or more mutually exclusive treatment arms. Given
estimated conditional treatment effects and treatment costs, 'maq'
computes the optimal treatment allocation over a range of budget levels
and estimates the resulting policy value using doubly robust or
inverse-propensity weighted scores. The underlying optimization exploits
the linear multiple-choice knapsack structure of the allocation problem
to compute the full solution path efficiently.
For details see Sverdrup, Wu, Athey, and Wager (2025) <doi:10.1080/10618600.2024.2418820>.
Author: Erik Sverdrup [aut, cre],
Han Wu [aut],
Susan Athey [aut],
Stefan Wager [aut]
Maintainer: Erik Sverdrup <erik.sverdrup@gmail.com>
Diff between maq versions 0.6.0 dated 2025-04-14 and 0.6.1 dated 2026-08-04
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- R/get_aipw_scores.R | 2 +- R/maq.R | 25 ++++++++++++++----------- R/plot.R | 15 +++++++++------ man/get_aipw_scores.Rd | 2 +- man/maq.Rd | 25 ++++++++++++++----------- man/plot.maq.Rd | 15 +++++++++------ 8 files changed, 70 insertions(+), 52 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] ,
Matt Wand [ctb] ,
Jose Chacon [ctb] ,
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.15.2 dated 2026-05-09 and 1.15.3 dated 2026-08-04
CHANGELOG | 4 ++ DESCRIPTION | 15 +++---- MD5 | 94 +++++++++++++++++++++++++------------------------- R/kcopula.R | 2 - R/kdde.R | 4 +- R/kde-boundary.R | 2 - R/kde.R | 3 - R/kfs.R | 2 - README.md | 24 +++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ks.Rmd | 4 +- inst/doc/ks.html | 6 +-- inst/pkgdown.yml | 2 - man/Hbcv.Rd | 10 ++--- man/Hlscv.Rd | 4 +- man/Hnm.Rd | 6 +-- man/Hns.Rd | 4 +- man/Hpi.Rd | 10 ++--- man/Hscv.Rd | 6 +-- man/as.kde.Rd | 4 +- man/binning.Rd | 2 - man/hsct.Rd | 2 - man/ise.mixt.Rd | 2 - man/kcde.Rd | 2 - man/kcopula.Rd | 2 - man/kdcde.Rd | 7 +-- man/kdde.Rd | 2 - man/kde.boundary.Rd | 8 ++-- man/kde.local.test.Rd | 8 ++-- man/kde.test.Rd | 2 - man/kdr.Rd | 8 ++-- man/kfe.Rd | 4 +- man/kfs.Rd | 12 +++--- man/kms.Rd | 10 ++--- man/kroc.Rd | 4 +- man/ks-package.Rd | 15 ++++--- man/ksupp.Rd | 4 +- man/plot.kcde.Rd | 4 +- man/plot.kda.Rd | 4 +- man/plot.kdde.Rd | 4 +- man/plot.kde.Rd | 6 +-- man/plotmixt.Rd | 4 +- man/quake.Rd | 2 - man/tempb.Rd | 5 -- man/unicef.Rd | 2 - man/vkde.Rd | 8 ++-- vignettes/ks.Rmd | 4 +- 48 files changed, 173 insertions(+), 170 deletions(-)
Title: Induced Priors in Bayesian Mixture Models
Description: Computes implicitly induced quantities from prior/hyperparameter
specifications of three Mixtures of Finite Mixtures models: Dirichlet
Process Mixtures (DPMs; Escobar and West (1995)
<doi:10.1080/01621459.1995.10476550>), Static Mixtures of Finite Mixtures
(Static MFMs; Miller and Harrison (2018)
<doi:10.1080/01621459.2016.1255636>), and Dynamic Mixtures of Finite
Mixtures (Dynamic MFMs; Frühwirth-Schnatter, Malsiner-Walli and Grün (2021)
<doi:10.1214/21-ba1294>). For methodological details, please refer to
Greve, Grün, Malsiner-Walli and Frühwirth-Schnatter (2022)
<doi:10.1111/anzs.12350>) as well as the package vignette.
Author: Jan Greve [aut, cre],
Bettina Gruen [ctb] ,
Gertraud Malsiner-Walli [ctb] ,
Sylvia Fruehwirth-Schnatter [ctb]
Maintainer: Jan Greve <jangre@uio.no>
This is a re-admission after prior archival of version 1.0.0 dated 2021-02-11
Diff between fipp versions 1.0.0 dated 2021-02-11 and 1.0.1 dated 2026-08-04
fipp-1.0.0/fipp/man/figures |only fipp-1.0.1/fipp/DESCRIPTION | 34 - fipp-1.0.1/fipp/MD5 | 28 - fipp-1.0.1/fipp/NEWS.md | 7 fipp-1.0.1/fipp/R/fipp.R | 38 - fipp-1.0.1/fipp/R/utils.R | 7 fipp-1.0.1/fipp/build/partial.rdb |only fipp-1.0.1/fipp/build/vignette.rds |binary fipp-1.0.1/fipp/inst/doc/fippCrashCourse.R | 18 fipp-1.0.1/fipp/inst/doc/fippCrashCourse.html | 718 +++++++++++++++++--------- fipp-1.0.1/fipp/man/dbnb.Rd | 7 fipp-1.0.1/fipp/man/fipp.Rd | 19 fipp-1.0.1/fipp/man/nClusters.Rd | 19 fipp-1.0.1/fipp/src/Makevars | 1 fipp-1.0.1/fipp/src/Makevars.win | 1 fipp-1.0.1/fipp/src/RcppExports.cpp | 5 16 files changed, 583 insertions(+), 319 deletions(-)
Title: Financial Instrument Modeling Infrastructure
Description: Provides infrastructure for defining, storing, and managing
financial instrument metadata independently of market data sources.
Models instrument identities, contract specifications, identifiers, and
relationships among financial instruments, including currencies,
equities, funds, bonds, futures, options, spreads, exchange rates, and
synthetic instruments. Supports reusable instrument definitions for
research, portfolio management, trading, and quantitative finance
applications.
Author: Peter Carl [aut],
Brian G. Peterson [aut],
Garrett See [aut],
Ross Bennett [aut],
Justin M. Shea [cre, ctb]
Maintainer: Justin M. Shea <jshea01@uic.edu>
This is a re-admission after prior archival of version 1.3.1 dated 2018-01-10
Diff between FinancialInstrument versions 1.3.1 dated 2018-01-10 and 1.4.1 dated 2026-08-04
FinancialInstrument-1.3.1/FinancialInstrument/data/currencies.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/data/future_series.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/data/root_contracts.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/inst/tests |only FinancialInstrument-1.3.1/FinancialInstrument/tests/test-all.R |only FinancialInstrument-1.4.1/FinancialInstrument/DESCRIPTION | 73 FinancialInstrument-1.4.1/FinancialInstrument/MD5 | 181 +- FinancialInstrument-1.4.1/FinancialInstrument/NAMESPACE | 3 FinancialInstrument-1.4.1/FinancialInstrument/NEWS | 122 + FinancialInstrument-1.4.1/FinancialInstrument/R/CompareInstrumentFiles.R | 84 FinancialInstrument-1.4.1/FinancialInstrument/R/FinancialInstrument-package.R | 373 ---- FinancialInstrument-1.4.1/FinancialInstrument/R/FindCommonInstrumentAttributes.R | 15 FinancialInstrument-1.4.1/FinancialInstrument/R/Tick2Sec.R | 178 +- FinancialInstrument-1.4.1/FinancialInstrument/R/all.equal.instrument.R | 49 FinancialInstrument-1.4.1/FinancialInstrument/R/build_symbols.R | 33 FinancialInstrument-1.4.1/FinancialInstrument/R/expires.R | 133 - FinancialInstrument-1.4.1/FinancialInstrument/R/find.instrument.R | 68 FinancialInstrument-1.4.1/FinancialInstrument/R/instrument.R | 849 +++++----- FinancialInstrument-1.4.1/FinancialInstrument/R/load.instruments.R | 328 ++- FinancialInstrument-1.4.1/FinancialInstrument/R/ls_by_currency.R | 250 +- FinancialInstrument-1.4.1/FinancialInstrument/R/ls_instruments.R | 177 -- FinancialInstrument-1.4.1/FinancialInstrument/R/parse_id.R | 162 - FinancialInstrument-1.4.1/FinancialInstrument/R/redenominate.R | 103 - FinancialInstrument-1.4.1/FinancialInstrument/R/saveInstruments.R | 174 +- FinancialInstrument-1.4.1/FinancialInstrument/R/saveSymbols.R | 75 FinancialInstrument-1.4.1/FinancialInstrument/R/splice.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/splooth.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.iShares.R | 40 FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.morningstar.R | 24 FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.yahoo.R | 179 +- FinancialInstrument-1.4.1/FinancialInstrument/R/utils_quantmod.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/volep.R | 7 FinancialInstrument-1.4.1/FinancialInstrument/README.md |only FinancialInstrument-1.4.1/FinancialInstrument/data/currencies.csv |only FinancialInstrument-1.4.1/FinancialInstrument/data/future_series.csv |only FinancialInstrument-1.4.1/FinancialInstrument/data/root_contracts.csv |only FinancialInstrument-1.4.1/FinancialInstrument/inst/tinytest |only FinancialInstrument-1.4.1/FinancialInstrument/man/C2M.Rd | 1 FinancialInstrument-1.4.1/FinancialInstrument/man/CompareInstrumentFiles.Rd | 80 FinancialInstrument-1.4.1/FinancialInstrument/man/FinancialInstrument-package.Rd | 294 +-- FinancialInstrument-1.4.1/FinancialInstrument/man/FindCommonInstrumentAttributes.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/Tick2Sec.Rd | 56 FinancialInstrument-1.4.1/FinancialInstrument/man/add.defined.by.Rd | 14 FinancialInstrument-1.4.1/FinancialInstrument/man/add.identifier.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/all.equal.instrument.Rd | 22 FinancialInstrument-1.4.1/FinancialInstrument/man/buildRatio.Rd | 6 FinancialInstrument-1.4.1/FinancialInstrument/man/buildSpread.Rd | 20 FinancialInstrument-1.4.1/FinancialInstrument/man/build_series_symbols.Rd | 7 FinancialInstrument-1.4.1/FinancialInstrument/man/build_spread_symbols.Rd | 26 FinancialInstrument-1.4.1/FinancialInstrument/man/exchange_rate.Rd | 47 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.Rd | 29 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.character.Rd | 24 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.instrument.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.spread.Rd | 21 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.xts.Rd | 18 FinancialInstrument-1.4.1/FinancialInstrument/man/find.instrument.Rd | 71 FinancialInstrument-1.4.1/FinancialInstrument/man/fn_SpreadBuilder.Rd | 20 FinancialInstrument-1.4.1/FinancialInstrument/man/getInstrument.Rd | 29 FinancialInstrument-1.4.1/FinancialInstrument/man/getSymbols.FI.Rd | 111 - FinancialInstrument-1.4.1/FinancialInstrument/man/get_rate.Rd | 10 FinancialInstrument-1.4.1/FinancialInstrument/man/instrument.Rd | 171 +- FinancialInstrument-1.4.1/FinancialInstrument/man/instrument.auto.Rd | 72 FinancialInstrument-1.4.1/FinancialInstrument/man/instrument_attr.Rd | 24 FinancialInstrument-1.4.1/FinancialInstrument/man/is.currency.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/is.currency.name.Rd | 8 FinancialInstrument-1.4.1/FinancialInstrument/man/is.instrument.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/is.instrument.name.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/load.instruments.Rd | 65 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_by_currency.Rd | 102 - FinancialInstrument-1.4.1/FinancialInstrument/man/ls_by_expiry.Rd | 1 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_expiries.Rd | 17 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_instruments.Rd | 53 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_instruments_by.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/next.future_id.Rd | 8 FinancialInstrument-1.4.1/FinancialInstrument/man/option_series.yahoo.Rd | 33 FinancialInstrument-1.4.1/FinancialInstrument/man/parse_id.Rd | 14 FinancialInstrument-1.4.1/FinancialInstrument/man/parse_suffix.Rd | 7 FinancialInstrument-1.4.1/FinancialInstrument/man/print.id.list.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/print.instrument.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/print.suffix.list.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/redenominate.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/saveInstruments.Rd | 63 FinancialInstrument-1.4.1/FinancialInstrument/man/saveSymbols.days.Rd | 57 FinancialInstrument-1.4.1/FinancialInstrument/man/series_instrument.Rd | 83 FinancialInstrument-1.4.1/FinancialInstrument/man/setSymbolLookup.FI.Rd | 40 FinancialInstrument-1.4.1/FinancialInstrument/man/sort.instrument.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/synthetic.instrument.Rd | 101 - FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.iShares.Rd | 18 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.instrument.Rd | 35 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.masterDATA.Rd | 32 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.morningstar.Rd | 15 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.yahoo.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/volep.Rd | 5 FinancialInstrument-1.4.1/FinancialInstrument/tests/tinytest.R |only 94 files changed, 3084 insertions(+), 2622 deletions(-)
More information about FinancialInstrument at CRAN
Permanent link
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] ,
James Manton [aut] ,
Dominik Krzeminski [ctb]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.25 dated 2025-08-18 and 1.8.26 dated 2026-08-04
DESCRIPTION | 6 - MD5 | 42 ++++---- NEWS | 5 + R/neuron-io-neuroml.R | 2 R/neuron-io.R | 4 R/neuronlistfh.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Installation.html | 9 + inst/doc/neurons-intro.R | 38 +++---- inst/doc/neurons-intro.html | 168 ++++++++++++++++++----------------- tests/testthat/test-cmtk.R | 14 +- tests/testthat/test-cmtk_io.R | 2 tests/testthat/test-dotprops.R | 2 tests/testthat/test-hxsurf.R | 4 tests/testthat/test-im3d.R | 6 - tests/testthat/test-landmarks-io.R | 2 tests/testthat/test-neuron-fiji-io.R | 4 tests/testthat/test-neuron-io.R | 20 ++-- tests/testthat/test-neuron.R | 2 tests/testthat/test-ngraph.R | 4 tests/testthat/test-xformimage.R | 16 +-- 22 files changed, 183 insertions(+), 169 deletions(-)
Title: Testing, Monitoring, and Dating Structural Changes
Description: Testing, monitoring and dating structural changes in (linear)
regression models. strucchange features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM,
recursive/moving estimates) and F statistics, respectively.
It is possible to monitor incoming data online using
fluctuation processes.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals.
Emphasis is always given to methods for visualizing the data.
Author: Achim Zeileis [aut, cre] ,
Friedrich Leisch [aut] ,
Kurt Hornik [aut] ,
Christian Kleiber [aut] ,
Bruce E. Hansen [ctb],
Edgar C. Merkle [ctb] ,
Nikolaus Umlauf [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between strucchange versions 1.5-4 dated 2024-09-02 and 1.6-0 dated 2026-08-04
strucchange-1.5-4/strucchange/NEWS |only strucchange-1.6-0/strucchange/DESCRIPTION | 45 +++--- strucchange-1.6-0/strucchange/MD5 | 51 +++---- strucchange-1.6-0/strucchange/NEWS.md |only strucchange-1.6-0/strucchange/R/critvals-monitoring.R | 6 strucchange-1.6-0/strucchange/R/critvals.R | 10 - strucchange-1.6-0/strucchange/R/gefp.R | 37 +++-- strucchange-1.6-0/strucchange/R/monitoring.R | 18 +- strucchange-1.6-0/strucchange/R/pvalue.Fstats.R | 8 - strucchange-1.6-0/strucchange/README.md |only strucchange-1.6-0/strucchange/build/partial.rdb |binary strucchange-1.6-0/strucchange/build/vignette.rds |binary strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.R | 2 strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.Rnw | 57 ++++--- strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.pdf |binary strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.R |only strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.Rmd |only strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.html |only strucchange-1.6-0/strucchange/man/GermanM1.Rd | 10 - strucchange-1.6-0/strucchange/man/Grossarl.Rd | 6 strucchange-1.6-0/strucchange/man/USIncExp.Rd | 2 strucchange-1.6-0/strucchange/man/breakpoints.Rd | 4 strucchange-1.6-0/strucchange/man/efp.Rd | 13 - strucchange-1.6-0/strucchange/man/gefp.Rd | 1 strucchange-1.6-0/strucchange/man/plot.efp.Rd | 6 strucchange-1.6-0/strucchange/man/sctest.efp.Rd | 6 strucchange-1.6-0/strucchange/tests/Examples/strucchange-Ex.Rout.save | 2 strucchange-1.6-0/strucchange/vignettes/strucchange-intro.Rnw | 57 ++++--- strucchange-1.6-0/strucchange/vignettes/strucchange-seatbelt.Rmd |only strucchange-1.6-0/strucchange/vignettes/strucchange.bib | 72 ++++++++-- 30 files changed, 243 insertions(+), 170 deletions(-)
Title: Character String Operations and Interpolation, Magic Edition
Description: Performs complex string operations compactly and efficiently. Supports string interpolation jointly with over 50 string operations. Also enhances regular string functions (like grep() and co). See an introduction at <https://lrberge.github.io/stringmagic/>.
Author: Laurent R Berge [aut, cre] ,
Morgan Jacob [ctb]
Maintainer: Laurent R Berge <laurent.berge@u-bordeaux.fr>
Diff between stringmagic versions 1.2.0 dated 2025-04-18 and 1.3.0 dated 2026-08-04
DESCRIPTION | 9 + MD5 | 50 +++++----- NEWS.md | 18 +++ R/AUTO_help.R | 4 R/check.R | 39 +++++--- R/string_magic_doc.R | 15 ++- R/string_magic_main.R | 56 +++++++---- R/string_tools.R | 18 ++- R/to_index.R | 5 - build/vignette.rds |binary inst/doc/guide_customization.R | 4 inst/doc/guide_customization.html | 34 +++---- inst/doc/guide_string_magic.html | 25 ++--- inst/doc/guide_string_tools.html | 5 - inst/doc/ref_operations.R | 10 +- inst/doc/ref_operations.html | 58 +++++++++--- inst/doc/ref_operations.rmd | 22 ++++ inst/doc/ref_regex_flags.html | 5 - inst/doc/ref_regex_logic.html | 5 - inst/doc/ref_string_magic_special_operations.html | 27 ++--- man/cat_magic.Rd | 10 +- man/string_magic.Rd | 15 ++- man/string_magic_alias.Rd | 2 man/string_vec.Rd | 8 + src/to_index.cpp | 104 +++++++++++++--------- vignettes/ref_operations.rmd | 22 ++++ 26 files changed, 377 insertions(+), 193 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph] ,
Martin Leitner-Ankerl [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.19.0 dated 2026-04-21 and 0.19.2 dated 2026-08-04
ChangeLog | 5 ++ DESCRIPTION | 22 +++++--- MD5 | 56 ++++++++++++---------- R/zz_help_files.R | 2 build/vignette.rds |binary inst/doc/vignette.html | 7 +- inst/include/ankerl |only inst/include/rstring_indexer.h | 28 ++--------- inst/include/sf_internal/slice_store.h | 56 +++++++++++----------- inst/include/sf_internal/string_types.h | 80 ++++++++++++++++++++++++-------- inst/include/simple_array |only man/sf_vector.Rd | 2 src/exported_functions/c_sf_paste.h | 4 - src/exported_functions/sf_collapse.h | 6 +- src/exported_functions/sf_compare.h | 2 src/exported_functions/sf_grepl.h | 2 src/exported_functions/sf_gsub.h | 4 - src/exported_functions/sf_iconv.h | 4 - src/exported_functions/sf_match.h | 56 ++++++++++++++++------ src/exported_functions/sf_nchar.h | 2 src/exported_functions/sf_split.h | 2 src/exported_functions/sf_substr.h | 4 - src/sf_altrep/common.h | 5 +- src/sf_altrep/slice_st_altrep.h | 4 - src/sf_encoding_helpers.h | 8 +-- src/sf_functions.cpp | 3 - src/sf_utility.h | 7 ++ vignettes/bench_v3.png |binary 28 files changed, 223 insertions(+), 148 deletions(-)
Title: Species Sensitivity Distribution Data
Description: Reference data sets of species sensitivities to compare the
results of fitting species sensitivity distributions using software
such as 'ssdtools' and 'Burrlioz'. It consists of curated data sets
for individual chemicals from Australian, New Zealand and Canadian
organizations, several data sets from anonymous sources, and larger
uncurated compilations drawn from the ANZTOX, WQBench and EnviroTox
databases. It also includes a data set of the results of fitting
various distributions using different software.
Author: Rebecca Fisher [aut, cre],
Joe Thorley [aut] ,
Ayla Pearson [aut] ,
Carl Schwarz [ctb],
David Fox [ctb]
Maintainer: Rebecca Fisher <R.Fisher@aims.gov.au>
Diff between ssddata versions 1.0.0 dated 2021-11-05 and 2.0.0 dated 2026-08-04
DESCRIPTION | 37 - MD5 | 323 ++++++-- NAMESPACE | 21 NEWS.md | 131 +++ R/aims_aluminium_marine.R | 68 - R/aims_data.R | 83 +- R/aims_gallium_marine.R | 68 - R/aims_molybdenum_marine.R | 68 - R/anon_a.R | 55 - R/anon_b.R | 55 - R/anon_c.R | 55 - R/anon_d.R | 55 - R/anon_data.R | 52 - R/anon_e.R | 55 - R/anzg_alpha_cypermethrin_fresh.R |only R/anzg_aluminium_marine.R |only R/anzg_ametryn_fresh.R |only R/anzg_ammonia_fresh.R |only R/anzg_bisphenol_a_fresh.R |only R/anzg_bisphenol_a_marine.R |only R/anzg_boron_fresh.R |only R/anzg_chlorine_marine.R |only R/anzg_chromium_III_fresh.R |only R/anzg_copper_marine.R |only R/anzg_data.R | 138 ++- R/anzg_dioxins_fresh.R |only R/anzg_diuron_fresh.R |only R/anzg_diuron_marine.R |only R/anzg_fipronil_fresh.R |only R/anzg_fluoride_fresh.R |only R/anzg_glyphosate_fresh.R |only R/anzg_iron_fresh.R |only R/anzg_iron_marine.R |only R/anzg_mancozeb_fresh.R |only R/anzg_manganese_marine.R |only R/anzg_mcpa_fresh.R |only R/anzg_metolachlor_fresh.R | 92 +- R/anzg_metsulfuron_methyl_fresh.R |only R/anzg_nickel_marine.R |only R/anzg_nitrate_hard_fresh.R |only R/anzg_nitrate_moderate_fresh.R |only R/anzg_nitrate_soft_fresh.R |only R/anzg_paraquat_fresh.R |only R/anzg_perfluorooctane_sulfonate_pfos_fresh.R |only R/anzg_picloram_fresh.R |only R/anzg_simazine_fresh.R |only R/anzg_simazine_marine.R |only R/anzg_sulfometuron_methyl_fresh.R |only R/anzg_zinc_marine.R |only R/anztox_data.R |only R/ccme_boron.R | 59 - R/ccme_cadmium.R | 59 - R/ccme_chloride.R | 59 - R/ccme_data.R | 79 +- R/ccme_endosulfan.R | 59 - R/ccme_glyphosate.R | 59 - R/ccme_silver.R | 59 - R/ccme_uranium.R | 59 - R/csiro_chlorine_marine.R | 76 +- R/csiro_cobalt_marine.R | 80 +- R/csiro_data.R | 101 +- R/csiro_lead_marine.R | 80 +- R/csiro_nickel_fresh.R | 78 +- R/envirotox_acute.R |only R/envirotox_chemical.R |only R/envirotox_chronic.R |only R/envirotox_data.R |only R/get_ssddata.R | 777 +++++++++++++++++---- R/namespace.R | 8 R/ssd-fits.R | 86 +- R/ssddata-package.R | 12 R/wqbench_data.R |only README.md | 49 - build/partial.rdb |binary build/vignette.rds |only data/aims_aluminium_marine.rda |binary data/aims_data.rda |binary data/aims_gallium_marine.rda |binary data/aims_molybdenum_marine.rda |binary data/anon_a.rda |binary data/anon_b.rda |binary data/anon_c.rda |binary data/anon_d.rda |binary data/anon_data.rda |binary data/anon_e.rda |binary data/anzg_alpha_cypermethrin_fresh.rda |only data/anzg_aluminium_marine.rda |only data/anzg_ametryn_fresh.rda |only data/anzg_ammonia_fresh.rda |only data/anzg_bisphenol_a_fresh.rda |only data/anzg_bisphenol_a_marine.rda |only data/anzg_boron_fresh.rda |only data/anzg_chlorine_marine.rda |only data/anzg_chromium_III_fresh.rda |only data/anzg_copper_marine.rda |only data/anzg_data.rda |binary data/anzg_dioxins_fresh.rda |only data/anzg_diuron_fresh.rda |only data/anzg_diuron_marine.rda |only data/anzg_fipronil_fresh.rda |only data/anzg_fluoride_fresh.rda |only data/anzg_glyphosate_fresh.rda |only data/anzg_iron_fresh.rda |only data/anzg_iron_marine.rda |only data/anzg_mancozeb_fresh.rda |only data/anzg_manganese_marine.rda |only data/anzg_mcpa_fresh.rda |only data/anzg_metolachlor_fresh.rda |binary data/anzg_metsulfuron_methyl_fresh.rda |only data/anzg_nickel_marine.rda |only data/anzg_nitrate_hard_fresh.rda |only data/anzg_nitrate_moderate_fresh.rda |only data/anzg_nitrate_soft_fresh.rda |only data/anzg_paraquat_fresh.rda |only data/anzg_perfluorooctane_sulfonate_pfos_fresh.rda |only data/anzg_picloram_fresh.rda |only data/anzg_simazine_fresh.rda |only data/anzg_simazine_marine.rda |only data/anzg_sulfometuron_methyl_fresh.rda |only data/anzg_zinc_marine.rda |only data/anztox_data.rda |only data/ccme_boron.rda |binary data/ccme_cadmium.rda |binary data/ccme_chloride.rda |binary data/ccme_data.rda |binary data/ccme_endosulfan.rda |binary data/ccme_glyphosate.rda |binary data/ccme_silver.rda |binary data/ccme_uranium.rda |binary data/csiro_chlorine_marine.rda |binary data/csiro_cobalt_marine.rda |binary data/csiro_data.rda |binary data/csiro_lead_marine.rda |binary data/csiro_nickel_fresh.rda |binary data/envirotox_acute.rda |only data/envirotox_chemical.rda |only data/envirotox_chronic.rda |only data/envirotox_data.rda |only data/ssd_fits.rda |binary data/wqbench_data.rda |only inst/REFERENCES.bib | 712 +++++++++++++++---- inst/doc |only man/aims_aluminium_marine.Rd | 81 +- man/aims_data.Rd | 101 +- man/aims_gallium_marine.Rd | 81 +- man/aims_molybdenum_marine.Rd | 81 +- man/anon_a.Rd | 66 - man/anon_b.Rd | 66 - man/anon_c.Rd | 66 - man/anon_d.Rd | 66 - man/anon_data.Rd | 70 - man/anon_e.Rd | 66 - man/anzg_alpha_cypermethrin_fresh.Rd |only man/anzg_aluminium_marine.Rd |only man/anzg_ametryn_fresh.Rd |only man/anzg_ammonia_fresh.Rd |only man/anzg_bisphenol_a_fresh.Rd |only man/anzg_bisphenol_a_marine.Rd |only man/anzg_boron_fresh.Rd |only man/anzg_chlorine_marine.Rd |only man/anzg_chromium_III_fresh.Rd |only man/anzg_copper_marine.Rd |only man/anzg_data.Rd | 154 ++-- man/anzg_dioxins_fresh.Rd |only man/anzg_diuron_fresh.Rd |only man/anzg_diuron_marine.Rd |only man/anzg_fipronil_fresh.Rd |only man/anzg_fluoride_fresh.Rd |only man/anzg_glyphosate_fresh.Rd |only man/anzg_iron_fresh.Rd |only man/anzg_iron_marine.Rd |only man/anzg_mancozeb_fresh.Rd |only man/anzg_manganese_marine.Rd |only man/anzg_mcpa_fresh.Rd |only man/anzg_metolachlor_fresh.Rd | 103 +- man/anzg_metsulfuron_methyl_fresh.Rd |only man/anzg_nickel_marine.Rd |only man/anzg_nitrate_hard_fresh.Rd |only man/anzg_nitrate_moderate_fresh.Rd |only man/anzg_nitrate_soft_fresh.Rd |only man/anzg_paraquat_fresh.Rd |only man/anzg_perfluorooctane_sulfonate_pfos_fresh.Rd |only man/anzg_picloram_fresh.Rd |only man/anzg_simazine_fresh.Rd |only man/anzg_simazine_marine.Rd |only man/anzg_sulfometuron_methyl_fresh.Rd |only man/anzg_zinc_marine.Rd |only man/anztox_data.Rd |only man/ccme_boron.Rd | 72 - man/ccme_cadmium.Rd | 72 - man/ccme_chloride.Rd | 72 - man/ccme_data.Rd | 97 +- man/ccme_endosulfan.Rd | 72 - man/ccme_glyphosate.Rd | 72 - man/ccme_silver.Rd | 72 - man/ccme_uranium.Rd | 72 - man/csiro_chlorine_marine.Rd | 87 +- man/csiro_cobalt_marine.Rd | 91 +- man/csiro_data.Rd | 117 +-- man/csiro_lead_marine.Rd | 91 +- man/csiro_nickel_fresh.Rd | 89 +- man/envirotox_acute.Rd |only man/envirotox_chemical.Rd |only man/envirotox_chronic.Rd |only man/envirotox_data.Rd |only man/envirotox_data_sets.Rd |only man/get_ssddata.Rd | 80 +- man/getdata.Rd | 36 man/gm_mean.Rd | 48 - man/list_datasets.Rd |only man/ssd_data_sets.Rd |only man/ssd_fits.Rd | 78 +- man/ssddata-package.Rd | 68 - man/wqbench_data.Rd |only tests/testthat/helper-datasets.R |only tests/testthat/test-data-aggregates.R |only tests/testthat/test-data-integrity.R |only tests/testthat/test-envirotox.R |only tests/testthat/test-get_ssddata-args.R |only tests/testthat/test-get_ssddata.R | 147 ++- tests/testthat/test-getdata.R | 4 tests/testthat/test-ssd-data-sets.R |only tests/testthat/test-ssd_fits.R |only tests/testthat/test-units-consistency.R |only vignettes |only 225 files changed, 3943 insertions(+), 2502 deletions(-)
Title: Interface to 'NetCDF' Datasets
Description: An interface to the 'NetCDF' file formats designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
Most capabilities of 'NetCDF' version 4 are supported. Optional conversions
of time units are enabled by 'UDUNITS' version 2, also from Unidata.
Author: Pavel Michna [aut],
Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>
Diff between RNetCDF versions 2.11-1 dated 2025-04-30 and 2.11-2 dated 2026-08-04
DESCRIPTION | 12 ++--- INSTALL | 4 - LICENSE | 2 MD5 | 108 +++++++++++++++++++++++++-------------------------- NEWS | 3 + R/RNetCDF.R | 2 R/config.R.in | 2 configure | 18 ++++---- configure.ac | 2 man/00RNetCDF.Rd | 4 - man/att.copy.nc.Rd | 2 man/att.delete.nc.Rd | 2 man/att.get.nc.Rd | 2 man/att.inq.nc.Rd | 2 man/att.put.nc.Rd | 2 man/att.rename.nc.Rd | 2 man/close.nc.Rd | 2 man/create.nc.Rd | 2 man/dim.def.nc.Rd | 2 man/dim.inq.nc.Rd | 2 man/dim.rename.nc.Rd | 2 man/file.inq.nc.Rd | 2 man/grp.def.nc.Rd | 2 man/grp.inq.nc.Rd | 2 man/grp.rename.nc.Rd | 2 man/open.nc.Rd | 2 man/print.nc.Rd | 2 man/read.nc.Rd | 2 man/sync.nc.Rd | 2 man/type.def.nc.Rd | 2 man/type.inq.nc.Rd | 2 man/utcal.nc.Rd | 6 +- man/utinit.nc.Rd | 2 man/utinvcal.nc.Rd | 2 man/var.def.nc.Rd | 2 man/var.get.nc.Rd | 2 man/var.inq.nc.Rd | 2 man/var.par.nc.Rd | 2 man/var.put.nc.Rd | 2 man/var.rename.nc.Rd | 2 src/RNetCDF.h | 4 - src/attribute.c | 4 - src/common.c | 6 +- src/common.h | 4 - src/convert.c | 4 - src/convert.h | 4 - src/dataset.c | 4 - src/dimension.c | 4 - src/group.c | 4 - src/init.c | 4 - src/type.c | 4 - src/udunits.c | 4 - src/variable.c | 4 - tests/RNetCDF-test.R | 4 - tools/convert.m4 | 4 - 55 files changed, 143 insertions(+), 140 deletions(-)
Title: Policy Learning via Doubly Robust Empirical Welfare Maximization
over Trees
Description: Learn optimal policies via doubly robust empirical welfare
maximization over trees. Given reward estimates, the algorithm finds a
rule-based treatment allocation, where the policy takes the form of a
shallow decision tree that is globally optimal (or nearly so). Methods are
described in Sverdrup, Kanodia, Zhou, Athey, and Wager (2020)
<doi:10.21105/joss.02232>, Athey and Wager (2021)
<doi:10.3982/ECTA15732>, and Zhou, Athey, and Wager (2023)
<doi:10.1287/opre.2022.2271>.
Author: Erik Sverdrup [aut, cre],
Ayush Kanodia [aut],
Zhengyuan Zhou [aut],
Susan Athey [aut],
Stefan Wager [aut]
Maintainer: Erik Sverdrup <erik.sverdrup@gmail.com>
Diff between policytree versions 1.2.4 dated 2026-02-18 and 1.2.5 dated 2026-08-04
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 10 +++++----- R/hybrid_policy_tree.R | 2 +- R/policy_tree.R | 6 +++--- man/policy_tree.Rd | 2 +- man/policytree-package.Rd | 2 +- 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Various Methods for the Two Sample Problem in D>1 Dimensions
Description: The routine twosample_test() in this package runs the
two-sample test using various test statistic for multivariate data.
The user can also run several tests and then find a p value adjusted for simultaneous inference.
The p values are found via permutation or via the parametric bootstrap.
The routine twosample_power() allows the estimation of the power of the tests.
The routine run.studies() allows a user to quickly study the power of a new method and
how it compares to those included in the package.
For details of the methods and references see the included vignettes.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MD2sample versions 1.2.2 dated 2026-06-25 and 1.3.0 dated 2026-08-04
MD2sample-1.2.2/MD2sample/R/signif.digits.R |only MD2sample-1.2.2/MD2sample/man/signif.digits.Rd |only MD2sample-1.3.0/MD2sample/DESCRIPTION | 9 - MD2sample-1.3.0/MD2sample/MD5 | 36 +++-- MD2sample-1.3.0/MD2sample/NAMESPACE | 1 MD2sample-1.3.0/MD2sample/NEWS.md | 7 + MD2sample-1.3.0/MD2sample/R/MD2sample-package.R | 22 +-- MD2sample-1.3.0/MD2sample/R/case.studies.R | 2 MD2sample-1.3.0/MD2sample/R/change.marginals.R | 2 MD2sample-1.3.0/MD2sample/R/rDalitz.R | 2 MD2sample-1.3.0/MD2sample/R/run.studies.R | 2 MD2sample-1.3.0/MD2sample/R/signif_digits.R |only MD2sample-1.3.0/MD2sample/R/twosample_power.R | 2 MD2sample-1.3.0/MD2sample/R/twosample_test.R | 4 MD2sample-1.3.0/MD2sample/R/twosample_test_adjusted_pvalue.R | 2 MD2sample-1.3.0/MD2sample/inst/doc/CaseStudies.html | 68 +++++------ MD2sample-1.3.0/MD2sample/inst/legacy-tests |only MD2sample-1.3.0/MD2sample/man/MD2sample-package.Rd | 5 MD2sample-1.3.0/MD2sample/man/signif_digits.Rd |only MD2sample-1.3.0/MD2sample/tests |only 20 files changed, 92 insertions(+), 72 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 2.0.0 dated 2026-07-26 and 2.0.1 dated 2026-08-04
DESCRIPTION | 6 +- MD5 | 16 ++--- NEWS.md | 17 ++++++ R/huge.select.R | 17 ++++-- configure | 18 +++--- configure.ac | 2 inst/doc/huge.pdf |binary src/huge_core.cpp | 33 +++++++++++ tests/testthat/test-regressions.R | 105 ++++++++++++++++++++++++++++++++++++++ 9 files changed, 187 insertions(+), 27 deletions(-)
Title: Graphical Markov Models with Mixed Graphs
Description: Provides functions for defining
mixed graphs containing three types of edges, directed,
undirected and bi-directed, with possibly multiple edges.
These graphs are useful because they capture fundamental
independence structures in multivariate distributions
and in the induced distributions after marginalization
and conditioning.
The package is especially concerned with Gaussian graphical
models for
(i) ML estimation for directed acyclic graphs, undirected and
bi-directed graphs and ancestral graph models
(ii) testing several conditional independencies
(iii) checking global identification of DAG Gaussian models
with one latent variable
(iv) testing Markov equivalences and generating Markov
equivalent graphs of specific types.
Author: Giovanni M. Marchetti [aut, cre] ,
Mathias Drton [aut] ,
Kayvan Sadeghi [aut]
Maintainer: Giovanni M. Marchetti <giovanni.marchetti@unifi.it>
Diff between ggm versions 2.5.2 dated 2025-07-25 and 2.5.4 dated 2026-08-04
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ man/drawGraph.Rd | 8 +++++--- man/fitAncestralGraph.Rd | 4 ++-- man/fitDag.Rd | 4 ++-- man/ggm.Rd | 3 ++- man/plotGraph.Rd | 20 +++++++++++++++++++- 8 files changed, 49 insertions(+), 20 deletions(-)
Title: GDP - Workflow Management
Description: Tools, methods and processes for the management
of analysis workflows. These lightweight solutions facilitate
structuring R&D activities. These solutions were developed to comply
with Good Documentation Practice (GDP),
with ALCOA+ principles as proposed by the U.S. FDA, and
with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.
Author: Gregoire Thomas [aut, cre, cph] ,
Metabolomic Diagnostics Ltd. [fnd]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between D4TAlink.light versions 2.1.22 dated 2026-07-21 and 2.1.23 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/taskFiles.R | 20 +++++++++++++++++++- inst/doc/D4TAlink_basics.html | 4 ++-- inst/doc/D4TAlink_quickstart.html | 4 ++-- man/saveReportXls.Rd | 10 ++++++++-- 7 files changed, 46 insertions(+), 17 deletions(-)
More information about D4TAlink.light at CRAN
Permanent link
Title: Brazilian Maps from Different Geographic Levels
Description: Provides simplified Brazilian territorial meshes derived from
official data published by the Brazilian Institute of Geography and
Statistics (IBGE) <https://www.ibge.gov.br/> as local spatial objects,
with no download required at use time. Municipal meshes cover selected
official editions from 2000 onwards whenever the number of municipalities
changes, and current meshes are available for states, regions and other
geographic levels. Convenience functions support filtering, joining and
plotting the maps, as well as consulting Brazilian territorial codes.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2017-09-21
Diff between brazilmaps versions 0.1.0 dated 2017-09-21 and 1.0.0 dated 2026-08-04
brazilmaps-0.1.0/brazilmaps/inst/maps/Brazil.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/City.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/MesoRegion.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/MicroRegion.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/Region.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/State.rds |only brazilmaps-0.1.0/brazilmaps/man/join_data.Rd |only brazilmaps-0.1.0/brazilmaps/man/theme_map.Rd |only brazilmaps-1.0.0/brazilmaps/DESCRIPTION | 40 - brazilmaps-1.0.0/brazilmaps/MD5 | 87 ++- brazilmaps-1.0.0/brazilmaps/NAMESPACE | 12 brazilmaps-1.0.0/brazilmaps/NEWS.md | 61 ++ brazilmaps-1.0.0/brazilmaps/R/brmap_years.R |only brazilmaps-1.0.0/brazilmaps/R/datasets.R | 114 +--- brazilmaps-1.0.0/brazilmaps/R/get_brmap.R | 226 ++++---- brazilmaps-1.0.0/brazilmaps/R/get_dtb_info.R |only brazilmaps-1.0.0/brazilmaps/R/get_dtb_lvl.R |only brazilmaps-1.0.0/brazilmaps/R/join_data.R | 89 +-- brazilmaps-1.0.0/brazilmaps/R/plot_brmap.R | 273 +++++----- brazilmaps-1.0.0/brazilmaps/R/utils.R |only brazilmaps-1.0.0/brazilmaps/R/zzz.R |only brazilmaps-1.0.0/brazilmaps/README.md | 162 +++++ brazilmaps-1.0.0/brazilmaps/build |only brazilmaps-1.0.0/brazilmaps/data/deaths.rda |binary brazilmaps-1.0.0/brazilmaps/data/gini2015.rda |binary brazilmaps-1.0.0/brazilmaps/data/pop2017.rda |binary brazilmaps-1.0.0/brazilmaps/inst/COPYRIGHTS |only brazilmaps-1.0.0/brazilmaps/inst/doc |only brazilmaps-1.0.0/brazilmaps/inst/dtb |only brazilmaps-1.0.0/brazilmaps/inst/maps/Brazil.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Imediate.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Intermediary.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/MesoRegion.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/MicroRegion.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Region.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/State.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/StateHex.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/StateReg.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/municipality |only brazilmaps-1.0.0/brazilmaps/man/brmap_editions.Rd |only brazilmaps-1.0.0/brazilmaps/man/deaths.Rd | 51 - brazilmaps-1.0.0/brazilmaps/man/get_brmap.Rd | 118 ++-- brazilmaps-1.0.0/brazilmaps/man/get_dtb.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_info.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_levels.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_lvl.Rd |only brazilmaps-1.0.0/brazilmaps/man/gini2015.Rd | 52 - brazilmaps-1.0.0/brazilmaps/man/join_brmap.Rd |only brazilmaps-1.0.0/brazilmaps/man/plot_brmap.Rd | 123 ++-- brazilmaps-1.0.0/brazilmaps/man/pop2017.Rd | 53 - brazilmaps-1.0.0/brazilmaps/man/theme_brmap.Rd |only brazilmaps-1.0.0/brazilmaps/tests |only brazilmaps-1.0.0/brazilmaps/vignettes |only 53 files changed, 842 insertions(+), 619 deletions(-)
Title: Regime-Switching Dynamic Correlation Models
Description: Estimation, forecasting, simulation, and portfolio construction for
regime-switching models with exogenous variables as in
Pelletier (2006) <doi:10.1016/j.jeconom.2005.01.013>.
Author: David Ardia [aut, cre, cph, fnd] ,
Benjamin Seguin [aut],
Roosevelt Ymele Nguemo [aut]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between RSDC versions 1.1-2 dated 2025-09-03 and 1.7-0 dated 2026-08-04
RSDC-1.1-2/RSDC/inst/extdata/green-brown-ptf.xlsx |only RSDC-1.7-0/RSDC/DESCRIPTION | 36 RSDC-1.7-0/RSDC/MD5 | 113 +- RSDC-1.7-0/RSDC/NAMESPACE | 54 + RSDC-1.7-0/RSDC/NEWS.md | 215 +++++ RSDC-1.7-0/RSDC/R/RcppExports.R |only RSDC-1.7-0/RSDC/R/bands.R |only RSDC-1.7-0/RSDC/R/bootstrap.R |only RSDC-1.7-0/RSDC/R/broom.R |only RSDC-1.7-0/RSDC/R/ff5ind.R |only RSDC-1.7-0/RSDC/R/forecast_ahead.R |only RSDC-1.7-0/RSDC/R/global_search.R |only RSDC-1.7-0/RSDC/R/greenbrown.R | 5 RSDC-1.7-0/RSDC/R/inference.R |only RSDC-1.7-0/RSDC/R/mccc.R |only RSDC-1.7-0/RSDC/R/methods.R |only RSDC-1.7-0/RSDC/R/model_estimate.R | 716 +++++++++++++---- RSDC-1.7-0/RSDC/R/model_fit.R | 276 ++++-- RSDC-1.7-0/RSDC/R/parallel.R |only RSDC-1.7-0/RSDC/R/partial_corr.R |only RSDC-1.7-0/RSDC/R/pf_optimize.R | 175 ++-- RSDC-1.7-0/RSDC/R/predict_corr.R | 139 ++- RSDC-1.7-0/RSDC/R/rsdc.R | 37 RSDC-1.7-0/RSDC/R/simulate_data.R | 99 +- RSDC-1.7-0/RSDC/R/starts.R |only RSDC-1.7-0/RSDC/R/unpack.R |only RSDC-1.7-0/RSDC/R/viterbi.R |only RSDC-1.7-0/RSDC/build/partial.rdb |binary RSDC-1.7-0/RSDC/build/vignette.rds |only RSDC-1.7-0/RSDC/data/ff5ind.rda |only RSDC-1.7-0/RSDC/data/mccc.rda |only RSDC-1.7-0/RSDC/inst/CITATION | 7 RSDC-1.7-0/RSDC/inst/REFERENCES.bib | 35 RSDC-1.7-0/RSDC/inst/WORDLIST |only RSDC-1.7-0/RSDC/inst/doc |only RSDC-1.7-0/RSDC/inst/extdata/mccc-monthly.csv |only RSDC-1.7-0/RSDC/inst/simulation |only RSDC-1.7-0/RSDC/man/RSDC.Rd | 34 RSDC-1.7-0/RSDC/man/augment.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/autoplot.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/ff5ind.Rd |only RSDC-1.7-0/RSDC/man/glance.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/greenbrown.Rd | 5 RSDC-1.7-0/RSDC/man/mccc.Rd |only RSDC-1.7-0/RSDC/man/rsdc_bootstrap.Rd |only RSDC-1.7-0/RSDC/man/rsdc_corr_bands.Rd |only RSDC-1.7-0/RSDC/man/rsdc_estimate.Rd | 102 ++ RSDC-1.7-0/RSDC/man/rsdc_fit-methods.Rd |only RSDC-1.7-0/RSDC/man/rsdc_forecast.Rd | 26 RSDC-1.7-0/RSDC/man/rsdc_forecast_ahead.Rd |only RSDC-1.7-0/RSDC/man/rsdc_hamilton.Rd | 49 - RSDC-1.7-0/RSDC/man/rsdc_likelihood.Rd | 19 RSDC-1.7-0/RSDC/man/rsdc_maxdiv.Rd | 15 RSDC-1.7-0/RSDC/man/rsdc_minvar.Rd | 63 - RSDC-1.7-0/RSDC/man/rsdc_simulate.Rd | 46 - RSDC-1.7-0/RSDC/man/rsdc_starts.Rd |only RSDC-1.7-0/RSDC/man/rsdc_viterbi.Rd |only RSDC-1.7-0/RSDC/man/tidy.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/src |only RSDC-1.7-0/RSDC/tests/testthat/test-additions.R |only RSDC-1.7-0/RSDC/tests/testthat/test-bootstrap.R |only RSDC-1.7-0/RSDC/tests/testthat/test-controls-forward.R |only RSDC-1.7-0/RSDC/tests/testthat/test-correctness.R |only RSDC-1.7-0/RSDC/tests/testthat/test-cpp-equivalence.R |only RSDC-1.7-0/RSDC/tests/testthat/test-forecast.R | 72 + RSDC-1.7-0/RSDC/tests/testthat/test-global-search.R |only RSDC-1.7-0/RSDC/tests/testthat/test-guards.R |only RSDC-1.7-0/RSDC/tests/testthat/test-hamilton.R | 19 RSDC-1.7-0/RSDC/tests/testthat/test-inference.R |only RSDC-1.7-0/RSDC/tests/testthat/test-likelihood.R | 21 RSDC-1.7-0/RSDC/tests/testthat/test-methods.R |only RSDC-1.7-0/RSDC/tests/testthat/test-minvar-maxdiv.R | 26 RSDC-1.7-0/RSDC/tests/testthat/test-parallel.R |only RSDC-1.7-0/RSDC/tests/testthat/test-partial-corr.R |only RSDC-1.7-0/RSDC/tests/testthat/test-rsdc-estimate.R | 54 + RSDC-1.7-0/RSDC/tests/testthat/test-simulate.R | 7 RSDC-1.7-0/RSDC/tests/testthat/test-starts.R |only RSDC-1.7-0/RSDC/vignettes |only 78 files changed, 2001 insertions(+), 464 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp [aut, cre]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.16.9 dated 2026-07-16 and 0.17.8 dated 2026-08-04
DESCRIPTION | 6 MD5 | 75 ++--- NAMESPACE | 5 NEWS | 226 ++++++++++++++++ R/03_modelformation_matrixSetup_mu.R | 90 +++++- R/18_dlvm1_derivatives.R | 47 ++- R/18_dlvm1_implied.R | 23 + R/25_panelvar_derivatives.R | 23 + R/25_panelvar_implied.R | 12 R/a_models_dlvm1.R | 103 ++++++- R/a_models_name_aliases.R | 14 + R/a_models_panelvar.R | 71 ++++- R/a_models_ri_clpm.R | 43 +++ R/e_modelmodifications_ri_clpm_stationarity.R | 360 ++++++++++++++++++++++---- R/f_convenience_CIplot.R | 95 ++++++ R/f_convenience_getmatrix.R | 83 +++++ R/f_convenience_plot.R |only R/f_convenience_ri_clpm_blocks.R |only build/partial.rdb |binary inst/tinytest/_helpers.R |only inst/tinytest/test_dlvm1_beta_epsilon.R | 12 inst/tinytest/test_free_means.R |only inst/tinytest/test_meta.R | 22 - inst/tinytest/test_ml_lvm_2L.R | 8 inst/tinytest/test_ml_var1.R | 10 inst/tinytest/test_ml_varcov.R | 8 inst/tinytest/test_pdc_temporal.R | 20 - inst/tinytest/test_plot.R |only inst/tinytest/test_ri_clpm.R |only inst/tinytest/test_robust_ml.R | 5 inst/tinytest/test_var_panel.R | 32 +- man/CIplot.Rd | 12 man/dlvm1_family.Rd | 23 + man/getmatrix.Rd | 22 + man/panelvar_family.Rd | 31 +- man/plot.psychonetrics.Rd |only man/psychonetrics-package.Rd | 2 man/ri_clpm.Rd | 100 +++++-- src/18_dlvm1_derivatives_cpp.cpp | 60 ++-- src/18_dlvm1_implied_cpp.cpp | 24 + src/25_panelvar_derivatives_cpp.cpp | 24 + src/25_panelvar_implied_cpp.cpp | 22 + 42 files changed, 1429 insertions(+), 284 deletions(-)
Title: Expected Value of Information Based Sample Size Calculation
Description: Computes sample sizes for trial-based cost-effectiveness analyses using the expected value of information. The implementation follows the method described by Bader et al. (2018) <doi:10.1186/s12874-018-0571-1>.
Author: Audrey Cordon [aut, cre],
Clement Bader [ctb],
Morgane Donadel [ctb],
Aline Maillard [ctb],
Sebastien Cossin [ctb],
Mohamedou Sow [ctb],
Antoine Benard [ctb]
Maintainer: Audrey Cordon <audrey.cordon@chu-bordeaux.fr>
This is a re-admission after prior archival of version 0.1 dated 2016-10-02
Diff between EBASS versions 0.1 dated 2016-10-02 and 0.1.1 dated 2026-08-04
EBASS-0.1.1/EBASS/DESCRIPTION | 34 - EBASS-0.1.1/EBASS/MD5 | 76 +- EBASS-0.1.1/EBASS/NAMESPACE | 26 EBASS-0.1.1/EBASS/NEWS.md |only EBASS-0.1.1/EBASS/R/EVPI.R | 462 ++++++++--------- EBASS-0.1.1/EBASS/R/INMB.R | 232 ++++---- EBASS-0.1.1/EBASS/R/INMB_DIRECT.R | 116 ++-- EBASS-0.1.1/EBASS/R/Lambda.R | 102 +-- EBASS-0.1.1/EBASS/R/POP.R | 268 ++++----- EBASS-0.1.1/EBASS/R/VAR_INMB.R | 280 +++++----- EBASS-0.1.1/EBASS/R/VAR_INMB_DIFF.R | 369 ++++++------- EBASS-0.1.1/EBASS/R/VAR_INMB_DIRECT.R | 146 ++--- EBASS-0.1.1/EBASS/R/fonctions_sujets.R | 448 +++++++++------- EBASS-0.1.1/EBASS/R/internal.R | 200 +++---- EBASS-0.1.1/EBASS/README.md |only EBASS-0.1.1/EBASS/build/vignette.rds |binary EBASS-0.1.1/EBASS/inst/doc/my-vignette.R | 197 +++---- EBASS-0.1.1/EBASS/inst/doc/my-vignette.Rmd | 384 +++++++------- EBASS-0.1.1/EBASS/inst/doc/my-vignette.html |only EBASS-0.1.1/EBASS/man/EBASS-internal.Rd | 26 EBASS-0.1.1/EBASS/man/EVPI_DECREASE.Rd | 76 +- EBASS-0.1.1/EBASS/man/INMB.Rd | 94 +-- EBASS-0.1.1/EBASS/man/INMB_DIRECT.Rd | 56 +- EBASS-0.1.1/EBASS/man/Lambda.Rd | 50 - EBASS-0.1.1/EBASS/man/POP.Rd | 72 +- EBASS-0.1.1/EBASS/man/VAR_INMB.Rd | 96 +-- EBASS-0.1.1/EBASS/man/VAR_INMB_DIFF.Rd | 97 +-- EBASS-0.1.1/EBASS/man/VAR_INMB_DIRECT.Rd | 70 +- EBASS-0.1.1/EBASS/man/create_object_evpi_decrease.Rd | 86 +-- EBASS-0.1.1/EBASS/man/create_object_inmb.Rd | 75 +- EBASS-0.1.1/EBASS/man/create_object_inmb_direct.Rd | 49 - EBASS-0.1.1/EBASS/man/create_object_lambda.Rd | 49 - EBASS-0.1.1/EBASS/man/create_object_pop.Rd | 65 +- EBASS-0.1.1/EBASS/man/create_object_var_inmb.Rd | 81 +- EBASS-0.1.1/EBASS/man/create_object_var_inmb_diff.Rd | 87 +-- EBASS-0.1.1/EBASS/man/create_object_var_inmb_direct.Rd | 57 +- EBASS-0.1.1/EBASS/man/gamma_risk.Rd | 36 - EBASS-0.1.1/EBASS/man/graph_gain_n.Rd | 38 - EBASS-0.1.1/EBASS/man/sample_size.Rd | 45 - EBASS-0.1.1/EBASS/vignettes/my-vignette.Rmd | 384 +++++++------- EBASS-0.1/EBASS/inst/doc/my-vignette.pdf |only 41 files changed, 2575 insertions(+), 2454 deletions(-)
Title: Twin Support Vector Machines
Description: Provides twin support vector machine classifiers and visualization
tools for small to moderate classification problems. Includes one-vs-one
multi-class classification and a standard support vector machine baseline
for comparison.
Author: Shamika Tissera [aut, cre]
Maintainer: Shamika Tissera <nimeshshamika@gmail.com>
This is a re-admission after prior archival of version 0.0.2 dated 2026-06-09
Diff between twinsvm versions 0.0.2 dated 2026-06-09 and 0.0.4 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++++------ NAMESPACE | 4 ++++ NEWS.md | 25 +++++++++++++++++++++++++ R/resample.R |only man/plot.resample_accuracy.Rd |only man/resample_accuracy.Rd |only tests/testthat/test-baselines.R | 16 ++++++++++++++-- tests/testthat/test-multiclass.R | 18 ++++++++++++------ tests/testthat/test-phase0.R | 1 + tests/testthat/test-resample.R |only 11 files changed, 69 insertions(+), 17 deletions(-)
Title: Coarse-to-Fine Spatial and Spatio-Temporal Modeling
Description: Provides functions for coarse-to-fine spatial and spatio-temporal modeling, enabling fast prediction, regression, and uncertainty quantification for moderate to large datasets. For methodological details, see Murakami et al. (2026) <doi:10.1111/gean.70034> and related work on generalized linear, downscaling, and dynamic spatio-temporal extensions.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut],
Jose Luis Blanco-Claraco [ctb, cph] ),
Marius Muja [cph] ,
David G. Lowe [cph]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.1.2 dated 2026-06-29 and 0.2.0 dated 2026-08-04
DESCRIPTION | 37 +++- MD5 | 100 ++++++++---- NAMESPACE | 8 - R/RcppExports.R | 8 + R/cf_dglm.R |only R/cf_dglm_hv.R |only R/cf_downscale.R | 13 - R/cf_downscale_hv.R | 28 ++- R/cf_glm.R | 76 ++++++++- R/cf_glm_hv.R | 49 ++++-- R/cf_lm.R | 81 ++++++++-- R/cf_lm_hv.R | 33 ++-- R/internal_prediction_se.R |only R/internal_utils_dglm.R |only R/internal_utils_glm.R | 198 ++++++++++++++++++------- R/internal_utils_lm.R | 111 ++++++-------- R/internal_validate.R |only R/spCFmap.R |only R/sp_map_core.R |only R/sp_scalewise.R | 131 +++++++++++++--- build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/spCF_dglm.R |only inst/doc/spCF_dglm.Rmd |only inst/doc/spCF_dglm.html |only inst/doc/spCF_downscale.Rmd | 2 inst/doc/spCF_downscale.html | 145 +++++++++--------- inst/doc/spCF_glm.R | 6 inst/doc/spCF_glm.Rmd | 18 ++ inst/doc/spCF_glm.html | 335 ++++++++++++++++++------------------------- inst/doc/spCF_lm.R | 6 inst/doc/spCF_lm.Rmd | 18 ++ inst/doc/spCF_lm.html | 182 +++++++++++------------ inst/shiny |only man/cf_dglm.Rd |only man/cf_dglm_hv.Rd |only man/cf_downscale.Rd | 2 man/cf_glm.Rd | 28 +++ man/cf_lm.Rd | 30 +++ man/cf_lm_hv.Rd | 3 man/spCF.Rd | 16 ++ man/spCFmap.Rd |only man/sp_scalewise.Rd | 45 +++-- src/RcppExports.cpp | 48 ++++++ src/dglm_chunk.cpp |only src/lwr_chunk_glm_fused.cpp |only src/nanoflann.h |only tests |only vignettes/spCF_dglm.Rmd |only vignettes/spCF_downscale.Rmd | 2 vignettes/spCF_glm.Rmd | 18 ++ vignettes/spCF_lm.Rmd | 18 ++ 52 files changed, 1158 insertions(+), 637 deletions(-)
Title: Individual-Based Forest Growth Simulator 'TROLL'
Description: 'TROLL' is coded in C++ and it typically simulates hundreds of
thousands of individuals over hundreds of years. The 'rcontroll' R package
is a wrapper of 'TROLL'. 'rcontroll' includes functions that generate inputs
for simulations and run simulations. Finally, it is possible to analyse
the 'TROLL' outputs through tables, figures, and maps taking advantage of
other R visualisation packages. 'rcontroll' also offers the possibility to
generate a virtual LiDAR point cloud that corresponds to a snapshot of
the simulated forest.
Author: Sylvain Schmitt [aut, cre] ,
Guillaume Salzet [aut] ,
Fabian Fischer [aut] ,
Isabelle Marechaux [aut] ,
Jerome Chave [aut]
Maintainer: Sylvain Schmitt <sylvain.m.schmitt@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2024-09-30
Diff between rcontroll versions 0.1.2 dated 2024-09-30 and 0.1.3 dated 2026-08-04
rcontroll-0.1.2/rcontroll/man/rcontroll.Rd |only rcontroll-0.1.3/rcontroll/DESCRIPTION | 25 rcontroll-0.1.3/rcontroll/MD5 | 60 +- rcontroll-0.1.3/rcontroll/NAMESPACE | 5 rcontroll-0.1.3/rcontroll/NEWS.md | 11 rcontroll-0.1.3/rcontroll/R/generate_climate.R | 23 rcontroll-0.1.3/rcontroll/R/get_chm.trollsim.R | 13 rcontroll-0.1.3/rcontroll/R/load_output.R | 9 rcontroll-0.1.3/rcontroll/R/rcontroll.R | 6 rcontroll-0.1.3/rcontroll/R/trollsim.R | 5 rcontroll-0.1.3/rcontroll/R/trollstack.R | 3 rcontroll-0.1.3/rcontroll/R/zzz.R | 12 rcontroll-0.1.3/rcontroll/build/vignette.rds |binary rcontroll-0.1.3/rcontroll/inst/doc/climate.R | 205 +++---- rcontroll-0.1.3/rcontroll/inst/doc/climate.Rmd | 24 rcontroll-0.1.3/rcontroll/inst/doc/climate.html | 86 +-- rcontroll-0.1.3/rcontroll/inst/doc/lidar.R | 8 rcontroll-0.1.3/rcontroll/inst/doc/lidar.Rmd | 10 rcontroll-0.1.3/rcontroll/inst/doc/lidar.html | 285 +++++----- rcontroll-0.1.3/rcontroll/inst/doc/troll.html | 16 rcontroll-0.1.3/rcontroll/inst/doc/workflow.R | 34 - rcontroll-0.1.3/rcontroll/inst/doc/workflow.html | 29 - rcontroll-0.1.3/rcontroll/inst/extdata/ERA5land_hr_Nouragues_2022.nc |binary rcontroll-0.1.3/rcontroll/inst/extdata/ERA5land_mth_Nouragues_2021_2022.nc |binary rcontroll-0.1.3/rcontroll/man/option.rcontroll.Rd | 17 rcontroll-0.1.3/rcontroll/man/rcontroll-package.Rd |only rcontroll-0.1.3/rcontroll/man/trollCpp.Rd | 16 rcontroll-0.1.3/rcontroll/man/trollsim-class.Rd | 2 rcontroll-0.1.3/rcontroll/man/trollsim.Rd | 2 rcontroll-0.1.3/rcontroll/man/trollstack.Rd | 2 rcontroll-0.1.3/rcontroll/vignettes/climate.Rmd | 24 rcontroll-0.1.3/rcontroll/vignettes/lidar.Rmd | 10 32 files changed, 484 insertions(+), 458 deletions(-)
Title: Nonparametric Multiple Change Point Detection Using Wild Binary
Segmentation
Description: Implements nonparametric multiple change-point detection for
univariate sequences using Wild Binary Segmentation, as described in
Ross (2026) "Nonparametric Detection of Multiple Location-Scale Change
Points via Wild Binary Segmentation"
<doi:10.48550/arXiv.2107.01742>. The package provides Mann--Whitney,
Mood, Lepage, Cramér--von Mises, modified Baumgartner, and standardised
Zhang Z_C rank-based statistics, together with method-specific thresholds for controlling
the probability of incorrectly detecting a change point in a homogeneous
sequence.
Author: Gordon J. Ross [aut, cre]
Maintainer: Gordon J. Ross <gordon.ross@ed.ac.uk>
Diff between npwbs versions 0.4.0 dated 2026-07-28 and 0.5.0 dated 2026-08-04
DESCRIPTION | 14 ++-- MD5 | 20 +++--- NAMESPACE | 1 R/RcppExports.R | 4 + R/package-functions.R | 34 ++++++++-- R/sysdata.rda |binary R/zhang.R |only inst/extdata |only man/detectChanges.Rd | 6 + man/download_zhang_moments.Rd |only src/RcppExports.cpp | 17 +++++ src/zhang.cpp |only tests/test-package.R | 140 ++++++++++++++++++++++++++++++++++++++++-- 13 files changed, 210 insertions(+), 26 deletions(-)
Title: Kernel Independent Component Analysis
Description: The kernel independent component analysis (kernel ICA) method introduced by Bach and Jordan (2002) <doi:10.1162/153244303768966085>. A separate function for the incomplete Cholesky decomposition used in kernel ICA is also provided.
Author: Christoph L. Koesner [aut] ,
Juho Eagling [aut] ,
Klaus Nordhausen [aut, cre]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2021-03-01
Diff between KernelICA versions 0.1.0 dated 2021-03-01 and 2.0.0 dated 2026-08-04
DESCRIPTION | 37 +++++++++++++++++----------- MD5 | 53 ++++++++++++++++++++--------------------- NAMESPACE | 1 NEWS.md |only R/MD_distant_matrices.R | 13 +++++----- R/RcppExports.R | 38 ++++++++++++++--------------- R/incomplete_cholesky.R | 15 ++++++----- R/kernel_ica.R | 25 ++++++++----------- R/kernel_matrix.R | 16 ++++-------- R/load_modules.R | 2 - R/package.R | 18 +++++-------- build/partial.rdb |binary man/KernelICA-package.Rd | 15 +++++++++-- man/MD_distant_matrices.Rd | 5 --- man/incomplete_cholesky.Rd | 13 +++------- man/kernel_ica.Rd | 24 +++++++----------- man/kernel_matrix.Rd | 7 +---- src/Debugging.h | 2 - src/IncompleteCholesky.cpp | 2 - src/KernelGauss.cpp | 1 src/KernelHermite.cpp | 4 ++- src/KernelHermite.h | 2 - src/KernelICAProblem.cpp | 23 +++++++++-------- src/Makevars | 14 +--------- src/Makevars.win | 16 ++---------- src/RcppExports.cpp | 5 +++ src/RcppIncompleteCholesky.cpp | 21 +++------------- src/RcppKernelMatrices.cpp | 7 ++--- 28 files changed, 176 insertions(+), 203 deletions(-)
Title: Spectral Density Estimation and Comparison for Functional Time
Series
Description: Functions for estimating spectral density operator of functional
time series (FTS) and comparing the spectral density operator of two
functional time series, in a way that allows detection of differences of
the spectral density operator in frequencies and along the curve length.
A description of the implemented tests can be found in the paper
Tavakoli & Panaretos (2016) <doi:10.1080/01621459.2016.1147355>.
Author: Shahin Tavakoli [aut, cre]
Maintainer: Shahin Tavakoli <shahin.tavakoli@unige.ch>
This is a re-admission after prior archival of version 1.0.0 dated 2015-09-08
Diff between ftsspec versions 1.0.0 dated 2015-09-08 and 1.0.1 dated 2026-08-04
DESCRIPTION | 17 ++++++---- MD5 | 43 +++++++++++++------------- NAMESPACE | 2 - R/functional-spectral-density.R | 12 +++---- README.md |only man/Epanechnikov_kernel.Rd | 3 - man/Generate_filterMA.Rd | 16 ++++++--- man/Get_noise_sd.Rd | 3 - man/Marginal_basis_pval.Rd | 7 +--- man/PvalAdjust.Rd | 3 - man/Simulate_new_MA.Rd | 8 ++-- man/Spec.Rd | 20 ++++++++---- man/SpecMA.Rd | 3 - man/Spec_compare_fixed_freq.Rd | 20 ++++++++---- man/Spec_compare_localize_freq.Rd | 29 ++++++++++++----- man/Spec_compare_localize_freq_curvelength.Rd | 25 +++++++++------ man/ftsspec.Rd | 14 ++++++-- man/lines.SampleSpecDiffFreq.Rd | 6 +-- man/plot.SampleSpec.Rd | 3 - man/plot.SampleSpecDiffFreq.Rd | 3 - man/plot.SampleSpecDiffFreqCurvelength.Rd | 3 - man/plot.SpecMA.Rd | 3 - man/print.SampleSpecDiffFreqCurvelength.Rd | 3 - 23 files changed, 141 insertions(+), 105 deletions(-)
Title: Bioinformatic Distances
Description: A collection of high-performance methods for computing distance
measures for bioinformatics data. The weighted Euclidean distance can be
computed using 'OpenCL' on a GPU or a parallelized implementation on a CPU.
Other important distance measures for bioinformatics data are provided by
the R package 'parallelDist'. A specialized distance measure for the Gene
Ontology is also available.
Author: Quirin Stier [aut, rev, ctb] ,
Michael Thrun [aut, cre] ,
Luca Brinkmann [ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between BIDistances versions 0.1.3 dated 2025-05-10 and 0.1.5 dated 2026-08-04
BIDistances-0.1.3/BIDistances/inst/NEWS.md |only BIDistances-0.1.5/BIDistances/DESCRIPTION | 50 BIDistances-0.1.5/BIDistances/MD5 | 77 - BIDistances-0.1.5/BIDistances/NAMESPACE | 18 BIDistances-0.1.5/BIDistances/R/Dist2All.R | 150 +- BIDistances-0.1.5/BIDistances/R/DistanceDistributions.R | 1 BIDistances-0.1.5/BIDistances/R/DistanceMatrix.R | 516 +++++++--- BIDistances-0.1.5/BIDistances/R/EuclideanDistances_GPU.R |only BIDistances-0.1.5/BIDistances/R/Hellinger4ConditionalPDF.R |only BIDistances-0.1.5/BIDistances/R/Kullback_Leibler_div.R |only BIDistances-0.1.5/BIDistances/R/TransformSimilarity2MetricDistance.R | 16 BIDistances-0.1.5/BIDistances/R/calculateMemoryDemandGPU.R |only BIDistances-0.1.5/BIDistances/R/fastPdist.R | 1 BIDistances-0.1.5/BIDistances/R/knneighborDistances.R |only BIDistances-0.1.5/BIDistances/R/nearest.R | 21 BIDistances-0.1.5/BIDistances/R/ocl4BID.R |only BIDistances-0.1.5/BIDistances/R/pdistToroid.R |only BIDistances-0.1.5/BIDistances/build/partial.rdb |binary BIDistances-0.1.5/BIDistances/build/vignette.rds |binary BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanBatchOCL.cl |only BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanBlockOCL.cl |only BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanOCL.cl |only BIDistances-0.1.5/BIDistances/inst/doc/BIDistances.html | 9 BIDistances-0.1.5/BIDistances/man/CosinusDistance.Rd | 23 BIDistances-0.1.5/BIDistances/man/Dist2All.Rd | 87 - BIDistances-0.1.5/BIDistances/man/DistanceDistributions.Rd | 8 BIDistances-0.1.5/BIDistances/man/DistanceMatrix.Rd | 497 +++++++-- BIDistances-0.1.5/BIDistances/man/EuclideanDistances_GPU.Rd |only BIDistances-0.1.5/BIDistances/man/GiniDist.Rd | 32 BIDistances-0.1.5/BIDistances/man/Hellinger4ConditionalPDF.Rd |only BIDistances-0.1.5/BIDistances/man/Kullback_Leibler_div.Rd |only BIDistances-0.1.5/BIDistances/man/Mahalanobis.Rd | 8 BIDistances-0.1.5/BIDistances/man/Tfidf_dist.Rd | 5 BIDistances-0.1.5/BIDistances/man/ToroidDist2All.Rd | 125 ++ BIDistances-0.1.5/BIDistances/man/TransformSimilarity2MetricDistance.Rd | 9 BIDistances-0.1.5/BIDistances/man/VariablePrecision.Rd | 2 BIDistances-0.1.5/BIDistances/man/calculateMemoryDemandGPU.Rd |only BIDistances-0.1.5/BIDistances/man/fastPdist.Rd | 6 BIDistances-0.1.5/BIDistances/man/fastPdistC.Rd | 4 BIDistances-0.1.5/BIDistances/man/jaccard.Rd | 5 BIDistances-0.1.5/BIDistances/man/knneighborDistances.Rd |only BIDistances-0.1.5/BIDistances/man/msmd.Rd | 4 BIDistances-0.1.5/BIDistances/man/nearest.Rd | 5 BIDistances-0.1.5/BIDistances/man/pdistToroid.Rd |only BIDistances-0.1.5/BIDistances/man/twed.Rd | 4 BIDistances-0.1.5/BIDistances/src/InnerVariableDifferencesRcpp.cpp | 4 BIDistances-0.1.5/BIDistances/src/SND.cpp | 2 BIDistances-0.1.5/BIDistances/src/fastPdistC.cpp | 74 + 48 files changed, 1236 insertions(+), 527 deletions(-)
Title: Helper Functions for Package 'secr'
Description: Functions are provided for internal use by the spatial
capture-recapture package 'secr' (from version 5.4.0). The idea is to speed up
the installation of 'secr', and possibly reduce its size. Initially the functions
are those for area and transect search that use numerical integration code from
'RcppNumerical' and 'RcppEigen'. The functions are not intended to be user-friendly
and require considerable preprocessing of data.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrfunc versions 1.0.0 dated 2025-12-01 and 1.1.4 dated 2026-08-04
DESCRIPTION | 8 - MD5 | 23 ++- NAMESPACE | 19 +-- NEWS | 28 +++- R/RcppExports.R | 21 --- man/hdotpolycpp.Rd | 154 ++++++++++++------------- man/polygonhistoriescpp.Rd | 250 ++++++++++++++++++++++-------------------- man/secrfunc-package.Rd | 131 +++++++++++----------- src/RcppExports.cpp | 37 ++++++ src/hdot.cpp | 2 src/prwipolygon2.cpp |only src/prwipolygonfxi.cpp | 31 +++-- tests/testthat/test-initial.R | 182 ++++++++++++++++++------------ 13 files changed, 498 insertions(+), 388 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.3 dated 2026-03-31 and 0.8.4 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- src/htslib-1.21/config.status | 10 +++++----- src/htslib-1.21/cram/cram_decode.c | 2 +- src/htslib-1.21/cram/cram_io.c | 4 ++-- src/htslib-1.21/faidx.c | 2 +- src/htslib-1.21/hts.c | 17 ++++++++++------- src/htslib-1.21/sam.c | 3 ++- 8 files changed, 31 insertions(+), 27 deletions(-)
Title: Simple Unified Wrappers for Hosted Foundation Model Inference
APIs
Description: Provides lightweight R wrappers for querying and listing models
from several hosted foundation model inference platforms, currently
including 'OpenAI' <https://developers.openai.com/api/docs/>,
'Google Gemini' <https://ai.google.dev/gemini-api/docs>,
'Groq' <https://console.groq.com/docs/>,
'OpenRouter' <https://openrouter.ai/docs/>,
'Cerebras' <https://inference-docs.cerebras.ai/>, and
'Ollama Cloud' <https://docs.ollama.com/cloud>.
The package is designed for simple inference workflows and quick
experimentation, with minimal abstraction and a consistent interface
across providers. It includes helper functions for model discovery, text
generation, embeddings, image generation, and multimodal inputs, while
leaving room for future support of provider-specific parameters and
advanced options.
Author: Oliver Zhou [aut, cre]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between inferencer versions 0.1.4.5 dated 2026-07-10 and 0.2.0 dated 2026-08-04
DESCRIPTION | 13 MD5 | 37 +- NAMESPACE | 3 NEWS.md | 26 + R/inferencer-package.R | 13 R/llm_cerebras.R | 31 -- R/llm_groq.R | 37 +- R/llm_helpers.R | 354 +++++++++++++++++++++++++ R/llm_multimodal.R | 59 ++-- R/llm_openai.R |only R/llm_openrouter.R | 68 ++++ README.md | 85 ++++++ man/inferencer-package.Rd | 13 man/list_openai_models.Rd |only man/list_openrouter_benchmarks.Rd |only man/query_cerebras.Rd | 3 man/query_groq.Rd | 9 man/query_openai.Rd |only man/query_openrouter.Rd | 8 man/query_openrouter_content.Rd | 8 tests/testthat/test-api-wrappers.R | 479 ++++++++++++++++++++++++++++++++++- tests/testthat/test-live-providers.R |only 22 files changed, 1149 insertions(+), 97 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-21 0.1.0