Title: Two-Part Estimation of Treatment Rules for Semi-Continuous Data
Description: Implements the methodology of Huling, Smith, and
Chen (2020) <doi:10.1080/01621459.2020.1801449>, which allows for subgroup identification
for semi-continuous outcomes by estimating individualized treatment rules. It uses a two-part
modeling framework to handle semi-continuous data by separately modeling the positive part
of the outcome and an indicator of whether each outcome is positive, but still results in a
single treatment rule. High dimensional data is handled with a cooperative lasso penalty,
which encourages the coefficients in the two models to have the same sign.
Author: Jared Huling [aut, cre]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized2part versions 0.0.1 dated 2020-09-10 and 0.0.2 dated 2026-01-13
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/fit_two_part.R | 2 +- R/predict_two_part.R | 13 +++++++------ README.md | 4 ++-- inst/CITATION | 4 ++-- man/hdgamma.Rd | 2 +- src/Makevars | 2 +- src/RcppExports.cpp | 5 +++++ 9 files changed, 33 insertions(+), 27 deletions(-)
More information about personalized2part at CRAN
Permanent link
Title: Complementary Package to 'nicheROVER' and 'SIBER'
Description: Provides functions complementary to packages 'nicheROVER' and 'SIBER'
allowing the user to extract Bayesian estimates from data objects created
by the packages 'nicheROVER' and 'SIBER'. Please see the following
publications for detailed methods on 'nicheROVER' and 'SIBER'
Hansen et al. (2015) <doi:10.1890/14-0235.1>,
Jackson et al. (2011) <do i:10.1111/j.1365-2656.2011.01806.x>, and
Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>,
respectfully.
Author: Benjamin L. Hlina [aut, cre]
Maintainer: Benjamin L. Hlina <benjamin.hlina@gmail.com>
Diff between nichetools versions 0.3.2 dated 2024-09-30 and 0.3.3 dated 2026-01-13
DESCRIPTION | 12 - MD5 | 22 +- R/niche_ellipse.R | 8 R/zzz.R | 57 ++++- README.md | 101 ++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/using-nichetools-with-the-package-SIBER.html | 15 - inst/doc/using-nichetools-with-the-package-nicheROVER.html | 19 + man/niche_ellipse.Rd | 6 man/nichetools-package.Rd | 2 vignettes/using-nichetools-and-nicheROVER-with-three-isotopes.R |only vignettes/using-nichetools-and-nicheROVER-with-three-isotopes.html |only 13 files changed, 160 insertions(+), 82 deletions(-)
More information about BayesianInference at CRAN
Permanent link
Title: Compute Neural Fragility for Ictal iEEG Time Series
Description: Provides tools to compute the neural fragility matrix from intracranial electrocorticographic (iEEG) recordings, enabling the analysis of brain dynamics during seizures. The package implements the method described by Li et al. (2017) <doi:10.23919/ACC.2017.7963378> and includes functions for data preprocessing ('Epoch'), fragility computation ('calcAdjFrag'), and visualization.
Author: Jiefei Wang [aut, cre] ,
Patrick Karas [aut],
Anne-Cecile Lesage [aut] ,
Ioannis Malagaris [aut] ,
Oliver Zhou [aut],
Liliana Camarillo Rodriguez [aut] ,
Sean O'Leary [aut] ,
Yuanyi Zhang [aut]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between EZFragility versions 2.0.1 dated 2025-09-07 and 2.1.1 dated 2026-01-13
EZFragility-2.0.1/EZFragility/man/plotFragHeatmap.Rd |only EZFragility-2.1.1/EZFragility/DESCRIPTION | 8 EZFragility-2.1.1/EZFragility/MD5 | 33 EZFragility-2.1.1/EZFragility/NAMESPACE | 1 EZFragility-2.1.1/EZFragility/NEWS.md |only EZFragility-2.1.1/EZFragility/R/visualization.R | 56 EZFragility-2.1.1/EZFragility/build/vignette.rds |binary EZFragility-2.1.1/EZFragility/data/pt01EcoG.rda |binary EZFragility-2.1.1/EZFragility/data/pt01Frag.rda |binary EZFragility-2.1.1/EZFragility/inst/doc/Intro_to_EZFragility.R | 6 EZFragility-2.1.1/EZFragility/inst/doc/Intro_to_EZFragility.Rmd | 11 EZFragility-2.1.1/EZFragility/inst/doc/Intro_to_EZFragility.html | 584 +----- EZFragility-2.1.1/EZFragility/inst/doc/manuscript_reproducible.R | 176 + EZFragility-2.1.1/EZFragility/inst/doc/manuscript_reproducible.Rmd | 214 +- EZFragility-2.1.1/EZFragility/inst/doc/manuscript_reproducible.html | 891 +++------- EZFragility-2.1.1/EZFragility/man/plotFrag.Rd |only EZFragility-2.1.1/EZFragility/tests/testthat/test-visualization.R | 10 EZFragility-2.1.1/EZFragility/vignettes/Intro_to_EZFragility.Rmd | 11 EZFragility-2.1.1/EZFragility/vignettes/manuscript_reproducible.Rmd | 214 +- 19 files changed, 931 insertions(+), 1284 deletions(-)
Title: Bindings to 'Tree-Sitter'
Description: Provides bindings to 'Tree-sitter', an incremental parsing
system for programming tools. 'Tree-sitter' builds concrete syntax
trees for source files of any language, and can efficiently update
those syntax trees as the source file is edited. It also includes a
robust error recovery system that provides useful parse results even
in the presence of syntax errors.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd],
Tree-sitter authors [cph]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between treesitter versions 0.3.0 dated 2025-06-06 and 0.3.1 dated 2026-01-13
treesitter-0.3.0/treesitter/src/rlang/altrep.h |only treesitter-0.3.1/treesitter/DESCRIPTION | 6 treesitter-0.3.1/treesitter/MD5 | 101 ++++++------ treesitter-0.3.1/treesitter/NEWS.md | 4 treesitter-0.3.1/treesitter/src/rlang/arg.h | 3 treesitter-0.3.1/treesitter/src/rlang/attrib.c | 42 ----- treesitter-0.3.1/treesitter/src/rlang/attrib.h | 28 ++- treesitter-0.3.1/treesitter/src/rlang/c-utils.h | 34 ++++ treesitter-0.3.1/treesitter/src/rlang/call.h | 4 treesitter-0.3.1/treesitter/src/rlang/cnd.h | 5 treesitter-0.3.1/treesitter/src/rlang/debug.h | 3 treesitter-0.3.1/treesitter/src/rlang/decl/env-decl.h | 4 treesitter-0.3.1/treesitter/src/rlang/df.c | 2 treesitter-0.3.1/treesitter/src/rlang/df.h | 4 treesitter-0.3.1/treesitter/src/rlang/dict.c | 2 treesitter-0.3.1/treesitter/src/rlang/dict.h | 4 treesitter-0.3.1/treesitter/src/rlang/dyn-array.c | 15 + treesitter-0.3.1/treesitter/src/rlang/dyn-array.h | 10 + treesitter-0.3.1/treesitter/src/rlang/dyn-list-of.c | 6 treesitter-0.3.1/treesitter/src/rlang/dyn-list-of.h | 4 treesitter-0.3.1/treesitter/src/rlang/env-binding.c | 4 treesitter-0.3.1/treesitter/src/rlang/env-binding.h | 3 treesitter-0.3.1/treesitter/src/rlang/env.c | 149 +++++------------- treesitter-0.3.1/treesitter/src/rlang/env.h | 96 +++++++++-- treesitter-0.3.1/treesitter/src/rlang/eval.c | 6 treesitter-0.3.1/treesitter/src/rlang/eval.h | 5 treesitter-0.3.1/treesitter/src/rlang/export.c | 13 - treesitter-0.3.1/treesitter/src/rlang/export.h | 12 - treesitter-0.3.1/treesitter/src/rlang/fn.h | 38 ++-- treesitter-0.3.1/treesitter/src/rlang/formula.c | 2 treesitter-0.3.1/treesitter/src/rlang/formula.h | 3 treesitter-0.3.1/treesitter/src/rlang/globals.h | 3 treesitter-0.3.1/treesitter/src/rlang/node.c | 11 - treesitter-0.3.1/treesitter/src/rlang/node.h | 17 +- treesitter-0.3.1/treesitter/src/rlang/obj.c | 4 treesitter-0.3.1/treesitter/src/rlang/obj.h | 27 +-- treesitter-0.3.1/treesitter/src/rlang/parse.h | 3 treesitter-0.3.1/treesitter/src/rlang/quo.h | 3 treesitter-0.3.1/treesitter/src/rlang/rlang-types.h | 10 - treesitter-0.3.1/treesitter/src/rlang/rlang.c | 30 +-- treesitter-0.3.1/treesitter/src/rlang/rlang.h | 16 - treesitter-0.3.1/treesitter/src/rlang/session.h | 3 treesitter-0.3.1/treesitter/src/rlang/stack.h | 3 treesitter-0.3.1/treesitter/src/rlang/state.h | 8 treesitter-0.3.1/treesitter/src/rlang/sym.h | 3 treesitter-0.3.1/treesitter/src/rlang/vec-chr.h | 5 treesitter-0.3.1/treesitter/src/rlang/vec-lgl.h | 4 treesitter-0.3.1/treesitter/src/rlang/vec.c | 122 +++++++------- treesitter-0.3.1/treesitter/src/rlang/vec.h | 85 +++++++--- treesitter-0.3.1/treesitter/src/rlang/vendor.h | 2 treesitter-0.3.1/treesitter/src/rlang/walk.c | 28 --- treesitter-0.3.1/treesitter/src/rlang/walk.h | 5 52 files changed, 561 insertions(+), 443 deletions(-)
Title: Makes 'R' Easier for Everyone
Description: A meta-package that aims to make 'R' easier for everyone,
especially programmers who have a background in 'SAS®' software.
This set of packages brings many useful concepts to 'R', including
data libraries, data dictionaries, formats
and format catalogs, a data step, and a traceable log. The system
also includes a package that replicates several commonly-used 'SAS®' procedures,
like 'PROC FREQ', 'PROC MEANS', and 'PROC REG'.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between sassy versions 1.2.9 dated 2025-10-07 and 1.3.0 dated 2026-01-13
sassy-1.2.9/sassy/man/images/vs_pg3.png |only sassy-1.3.0/sassy/DESCRIPTION | 14 sassy-1.3.0/sassy/MD5 | 77 +-- sassy-1.3.0/sassy/NAMESPACE | 1 sassy-1.3.0/sassy/NEWS.md | 8 sassy-1.3.0/sassy/R/iq.R | 2 sassy-1.3.0/sassy/R/oq.R | 83 +++ sassy-1.3.0/sassy/R/sassy.R | 3 sassy-1.3.0/sassy/README.md | 8 sassy-1.3.0/sassy/inst/doc/sassy-faq.Rmd | 9 sassy-1.3.0/sassy/inst/doc/sassy-faq.html | 5 sassy-1.3.0/sassy/inst/doc/sassy-figureby.R | 157 +++--- sassy-1.3.0/sassy/inst/doc/sassy-figureby.Rmd | 608 +++++++---------------- sassy-1.3.0/sassy/inst/doc/sassy-figureby.html | 636 +++++++------------------ sassy-1.3.0/sassy/inst/doc/sassy-plisting.R | 1 sassy-1.3.0/sassy/inst/doc/sassy-plisting.Rmd | 1 sassy-1.3.0/sassy/inst/doc/sassy-plisting.html | 5 sassy-1.3.0/sassy/inst/doc/sassy-training.Rmd | 1 sassy-1.3.0/sassy/inst/doc/sassy-training.html | 2 sassy-1.3.0/sassy/inst/doc/sassy.Rmd | 2 sassy-1.3.0/sassy/inst/doc/sassy.html | 4 sassy-1.3.0/sassy/inst/extdata/macro.R |only sassy-1.3.0/sassy/man/images/vs_pg1.png |binary sassy-1.3.0/sassy/man/images/vs_pg2.png |binary sassy-1.3.0/sassy/man/run_oq.Rd | 6 sassy-1.3.0/sassy/man/sassy.Rd | 1 sassy-1.3.0/sassy/tests/testthat/IQ |only sassy-1.3.0/sassy/tests/testthat/OQ |only sassy-1.3.0/sassy/tests/testthat/test-oq.R | 20 sassy-1.3.0/sassy/vignettes/sassy-faq.Rmd | 9 sassy-1.3.0/sassy/vignettes/sassy-figureby.Rmd | 608 +++++++---------------- sassy-1.3.0/sassy/vignettes/sassy-plisting.Rmd | 1 sassy-1.3.0/sassy/vignettes/sassy-training.Rmd | 1 sassy-1.3.0/sassy/vignettes/sassy.Rmd | 2 34 files changed, 890 insertions(+), 1385 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.5 dated 2025-03-06 and 0.2.6 dated 2026-01-13
DESCRIPTION | 8 MD5 | 64 ++-- NAMESPACE | 4 NEWS.md | 4 R/assess_export_help.R | 27 + R/assess_last_30_bugs_status.R | 10 R/metric_score.R | 7 R/pkg_ref_cache.R | 2 R/pkg_ref_cache_archive_release_date.R | 4 R/pkg_ref_cache_bug_reports.R | 5 R/pkg_ref_cache_description.R | 4 R/pkg_ref_cache_examples.R | 2 R/pkg_ref_cache_help_aliases.R | 4 R/pkg_ref_cache_license.R | 3 R/pkg_ref_cache_maintainer.R | 5 R/pkg_ref_cache_news.R | 9 R/pkg_ref_cache_r_cmd_check.R | 1 R/pkg_ref_cache_release_date.R | 6 R/pkg_ref_cache_repo_base_url.R | 3 R/pkg_ref_cache_tarball_url.R | 3 R/pkg_ref_cache_vignettes.R | 8 R/pkg_ref_cache_web_url.R | 4 R/pkg_ref_cache_website_urls.R | 6 R/pkg_ref_class.R | 4 R/pkg_ref_class_coersion.R | 2 R/utils_memoised.R | 2 README.md | 14 inst/doc/extending-riskmetric.R | 19 - inst/doc/extending-riskmetric.Rmd | 13 inst/doc/extending-riskmetric.html | 426 ++++++++++++++++------------- inst/doc/riskmetric.R | 16 - inst/doc/riskmetric.html | 484 ++++++++++++++++++++------------- vignettes/extending-riskmetric.Rmd | 13 33 files changed, 692 insertions(+), 494 deletions(-)
Title: Random Survival Forest for Recurrent Events
Description: A tool designed to analyze recurrent events when dealing with right-censored data and the potential presence of a terminal event (that prevents further occurrences, like death). It extends the random survival forest algorithm, adapting splitting rules and node estimators to handle complexities of recurrent events. The methodology is fully described in Murris, J., Bouaziz, O., Jakubczak, M., Katsahian, S., & Lavenu, A. (2024) (<https://hal.science/hal-04612431v1/document>).
Author: Juliette Murris [aut, cre] ,
Guillaume Desachy [aut] ,
Colin Fay [aut] ,
Yohann Mansiaux [aut] ,
Audrey Lavenu [aut] ,
Sandrine Katsahian [aut]
Maintainer: Juliette Murris <murris.juliette@gmail.com>
Diff between recforest versions 1.0.0 dated 2024-12-05 and 1.0.2 dated 2026-01-13
DESCRIPTION | 23 ++++++----- MD5 | 40 ++++++++++---------- NEWS.md | 11 +++++ R/0_s3_methods.R | 65 +++++++++++++++------------------ R/forest.R | 49 +++++++++++++----------- R/globals.R | 3 + README.md | 51 +++++++++++++++++-------- build/vignette.rds |binary inst/doc/explain.html | 3 + inst/doc/method.html | 2 - inst/doc/predict.R | 3 - inst/doc/predict.Rmd | 3 - inst/doc/predict.html | 42 ++++++++++----------- man/plot.recforest.Rd | 3 - man/predict.recforest.Rd | 58 +++++++++++++++-------------- man/print.recforest.Rd | 8 ---- man/recforest-package.Rd | 2 - man/train_forest.Rd | 49 +++++++++++++----------- tests/testthat/_snaps/golden_master.md | 2 - tests/testthat/test-train_forest.R | 38 +++++++++---------- vignettes/predict.Rmd | 3 - 21 files changed, 243 insertions(+), 215 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.7 dated 2025-11-25 and 0.8.8 dated 2026-01-13
paws.common-0.8.7/paws.common/R/populate.R |only paws.common-0.8.8/paws.common/DESCRIPTION | 16 - paws.common-0.8.8/paws.common/MD5 | 27 +- paws.common-0.8.8/paws.common/NAMESPACE | 1 paws.common-0.8.8/paws.common/NEWS.md | 4 paws.common-0.8.8/paws.common/R/RcppExports.R | 24 ++ paws.common-0.8.8/paws.common/man/populate.Rd | 6 paws.common-0.8.8/paws.common/src/RcppExports.cpp | 16 + paws.common-0.8.8/paws.common/src/json_builder.cpp | 58 +++-- paws.common-0.8.8/paws.common/src/json_escape.cpp | 1 paws.common-0.8.8/paws.common/src/populate.cpp |only paws.common-0.8.8/paws.common/tests/testthat/test_config.R | 32 ++- paws.common-0.8.8/paws.common/tests/testthat/test_credential_providers.R | 10 paws.common-0.8.8/paws.common/tests/testthat/test_net.R | 12 - paws.common-0.8.8/paws.common/tests/testthat/test_populate.R |only paws.common-0.8.8/paws.common/tests/testthat/test_signer_bearer.R | 105 ++++++---- 16 files changed, 199 insertions(+), 113 deletions(-)
Title: Multiple Time Series Scanner
Description: Generate interactive html reports that enable quick visual review of multiple related time series stored in a data frame. For static datasets, this can help to identify any temporal artefacts that may affect the validity of subsequent analyses. For live data feeds, regularly scheduled reports can help to pro-actively identify data feed problems or unexpected trends that may require action. The reports are self-contained and shareable without a web server.
Author: T. Phuong Quan [aut, cre] ,
University of Oxford [cph],
National Institute for Health Research [fnd],
Rodrigo Pires [rev],
Margaret Siple [rev]
Maintainer: T. Phuong Quan <phuongquan567@outlook.com>
Diff between mantis versions 1.0.0 dated 2025-10-27 and 1.0.1 dated 2026-01-13
DESCRIPTION | 12 ++-- MD5 | 22 +++---- NEWS.md | 8 ++ R/construct.R | 4 + R/prepare.R | 20 ++++++- README.md | 28 ++++++--- man/bespoke_rmd_output.Rd | 4 + man/mantis-package.Rd | 6 +- tests/testthat/test-prepare.R | 45 ++++++++++++++++ vignettes/articles/example-report-interactive.Rmd | 2 vignettes/articles/example-report-static-heatmap.Rmd | 2 vignettes/articles/example-report-static-multipanel.Rmd | 2 12 files changed, 118 insertions(+), 37 deletions(-)
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between clock versions 0.7.3 dated 2025-03-21 and 0.7.4 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/clock.html | 5 +++-- inst/doc/faq.html | 7 ++++--- inst/doc/recipes.html | 5 +++-- src/clock.h | 9 +++++++++ src/rcrd.cpp | 6 +++--- 9 files changed, 37 insertions(+), 21 deletions(-)
Title: Bayesian Flexible Parametric Survival Modelling and
Extrapolation
Description: Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a prior on the coefficients that controls over-fitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Additive hazards (relative survival) models, waning treatment effects, and mixture cure models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using 'Stan', and outputs are arranged in a tidy format. See Jackson (2023) <doi:10.1186/s12874-023-02094-1>.
Author: Christopher Jackson [aut, cre, cph] ,
Iain Timmins [ctb] ,
Michael Sweeting [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between survextrap versions 1.0 dated 2025-06-10 and 1.0.1 dated 2026-01-13
DESCRIPTION | 8 MD5 | 85 +- NAMESPACE | 1 NEWS.md | 5 R/loo.R | 24 R/priors.R | 51 + R/rstpm2.R | 3 R/survextrap.R | 3 README.md | 353 +++++++++--- inst/doc/examples.R | 2 inst/doc/examples.Rmd | 6 inst/doc/examples.html | 136 ++-- inst/doc/methods.Rmd | 5 inst/doc/methods.html | 18 inst/doc/priors.Rmd | 6 inst/doc/priors.html | 8 man/prior_sample.Rd | 2 man/prior_sample_hazard.Rd | 2 src/stanExports_survextrap.cc | 34 - tests/testthat/test_priorsample.R | 4 vignettes/examples.Rmd | 6 vignettes/examples_files/figure-html/unnamed-chunk-11-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-18-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-22-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-23-2.png |binary vignettes/examples_files/figure-html/unnamed-chunk-27-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-28-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-31-2.png |binary vignettes/examples_files/figure-html/unnamed-chunk-31-3.png |binary vignettes/examples_files/figure-html/unnamed-chunk-35-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-35-2.png |binary vignettes/examples_files/figure-html/unnamed-chunk-38-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-40-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/examples_files/figure-html/unnamed-chunk-6-1.png |binary vignettes/methods.Rmd | 5 vignettes/methods_files |only vignettes/priors.Rmd | 6 vignettes/priors_files |only 41 files changed, 522 insertions(+), 251 deletions(-)
Title: Create Phantom Variables in Structural Equation Models for
Sensitivity Analyses
Description: Create phantom variables, which are variables that were not observed, for the purpose of sensitivity analyses for structural equation models. The package makes it easier for a user to test different combinations of covariances between the phantom variable(s) and observed variables. The package may be used to assess a model's or effect's sensitivity to temporal bias (e.g., if cross-sectional data were collected) or confounding bias.
Author: Alexis Georgeson [aut, cre, cph]
Maintainer: Alexis Georgeson <georgeson.alexis@gmail.com>
Diff between phantSEM versions 1.0.0.0 dated 2023-09-07 and 1.0.1 dated 2026-01-13
phantSEM-1.0.0.0/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_4039354938aecf96582338b6664894ad.RData |only phantSEM-1.0.0.0/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_4039354938aecf96582338b6664894ad.rdb |only phantSEM-1.0.0.0/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_4039354938aecf96582338b6664894ad.rdx |only phantSEM-1.0.1/phantSEM/DESCRIPTION | 12 phantSEM-1.0.1/phantSEM/MD5 | 34 - phantSEM-1.0.1/phantSEM/NEWS.md |only phantSEM-1.0.1/phantSEM/R/SA_step1.R | 6 phantSEM-1.0.1/phantSEM/R/SA_step2.R | 8 phantSEM-1.0.1/phantSEM/R/ghost_par_ests.R | 2 phantSEM-1.0.1/phantSEM/R/utils.R |only phantSEM-1.0.1/phantSEM/README.md | 27 phantSEM-1.0.1/phantSEM/build/vignette.rds |binary phantSEM-1.0.1/phantSEM/inst/doc/my-vignette.R | 31 - phantSEM-1.0.1/phantSEM/inst/doc/my-vignette.Rmd | 42 - phantSEM-1.0.1/phantSEM/inst/doc/my-vignette.html | 296 ++++------ phantSEM-1.0.1/phantSEM/man/cor2cov_lavaan.Rd |only phantSEM-1.0.1/phantSEM/man/ghost_par_ests.Rd | 2 phantSEM-1.0.1/phantSEM/vignettes/my-vignette.Rmd | 42 - phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_60746649f94fdc0626d802431f70d6f7.RData |only phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_60746649f94fdc0626d802431f70d6f7.rdb |only phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-13_60746649f94fdc0626d802431f70d6f7.rdx |only phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-8_276549b4e4bb2b762323abbd9ea9c64f.RData |only phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-8_276549b4e4bb2b762323abbd9ea9c64f.rdb |only phantSEM-1.0.1/phantSEM/vignettes/my-vignette_cache/html/unnamed-chunk-8_276549b4e4bb2b762323abbd9ea9c64f.rdx |only 24 files changed, 179 insertions(+), 323 deletions(-)
Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: Volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2020, <doi:10.1002/jae.2742>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between mfGARCH versions 0.2.1 dated 2021-06-17 and 0.2.2 dated 2026-01-13
DESCRIPTION | 14 +++++--- MD5 | 20 ++++++------ NEWS.md | 23 ++++++++------ R/data.R | 4 -- R/fit_mfgarch.R | 79 +++++++++++++++++++++++++++----------------------- R/generic_functions.R | 8 ++--- R/helper_functions.R | 9 ++++- inst/CITATION | 52 ++++++++++++++++++++++---------- man/df_financial.Rd | 4 -- man/df_mfgarch.Rd | 4 -- src/RcppExports.cpp | 5 +++ 11 files changed, 126 insertions(+), 96 deletions(-)
Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Seunghyun Kim [aut [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.4.3 dated 2025-07-15 and 0.5.0 dated 2026-01-13
xportr |only 1 file changed
Title: The SHAPBoost Feature Selection Algorithm
Description: The implementation of SHAPBoost, a boosting-based feature selection technique that ranks features iteratively based on Shapley values.
Author: Oemer Tarik Oezyilmaz [aut, cre, cph] ,
Tamas Szili-Toeroek [aut, cph]
Maintainer: Oemer Tarik Oezyilmaz <o.t.ozyilmaz@umcg.nl>
Diff between SHAPBoost versions 1.0.1 dated 2025-12-04 and 1.0.2 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/shapboost_estimator.R | 18 ++++++++++++++++-- man/SHAPBoostEstimator-class.Rd | 2 ++ 5 files changed, 30 insertions(+), 9 deletions(-)
Title: Add Even More Interactivity to Interactive Charts
Description: Like package 'manipulate' does for static graphics, this package
helps to easily add controls like sliders, pickers, checkboxes, etc. that
can be used to modify the input data or the parameters of an interactive
chart created with package 'htmlwidgets'.
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Francois Guillem [aut],
RTE [cph],
JJ Allaire [ctb],
Marion Praz [ctb] ,
Benoit Thieurmel [ctb],
Titouan Robert [ctb],
Duncan Murdoch [ctb]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between manipulateWidget versions 0.11.1 dated 2021-10-05 and 0.11.2 dated 2026-01-13
DESCRIPTION | 32 LICENSE | 2 MD5 | 152 NAMESPACE | 125 NEWS.md | 287 R/combine_widgets.R | 676 +- R/compare_options.R | 104 R/controller.R | 668 +- R/debug.R | 34 R/get_output_and_render_func.R | 66 R/get_row_and_cols.R | 36 R/input_class.R | 570 - R/input_env.R | 484 - R/input_list_class.R | 512 - R/inputs.R | 1436 ++-- R/manipulate_widget.R | 394 - R/module_ui.R | 122 R/mw_ui.R | 262 R/on_done.R | 38 R/shiny_module.R | 128 R/shiny_module_compare_inputs.R | 200 R/shiny_module_grid.R | 118 R/shiny_module_inputarea.R | 218 R/shiny_module_menu.R | 344 - R/static_image.R | 118 R/translations.R | 88 R/zzz.R | 240 build/vignette.rds |binary inst/doc/manipulateWidgets.R | 298 inst/doc/manipulateWidgets.Rmd | 500 - inst/doc/manipulateWidgets.html | 6904 +++++++++++++++++++++-- inst/lib/export/Blob/Blob.js | 422 - inst/lib/export/Blob/LICENSE.md | 50 inst/lib/export/FileSaver/FileSaver.min.js | 4 inst/lib/export/FileSaver/LICENSE.md | 18 inst/lib/export/canvas-toBlob/LICENSE.md | 62 inst/lib/export/canvas-toBlob/canvas-toBlob.js | 250 inst/lib/export/html2canvas/html2canvas.js | 40 inst/manipulate_widget/manipulate_widget.css | 642 +- inst/manipulate_widget/manipulate_widget.js | 104 man/MWController-class.Rd | 158 man/combineWidgets-shiny.Rd | 60 man/combineWidgets.Rd | 338 - man/compareOptions.Rd | 112 man/manipulateWidget-package.Rd | 152 man/manipulateWidget.Rd | 582 - man/mwCheckbox.Rd | 110 man/mwCheckboxGroup.Rd | 118 man/mwDate.Rd | 106 man/mwDateRange.Rd | 118 man/mwGroup.Rd | 110 man/mwModule.Rd | 220 man/mwNumeric.Rd | 108 man/mwPassword.Rd | 116 man/mwRadio.Rd | 116 man/mwSelect.Rd | 162 man/mwSelectize.Rd | 150 man/mwSharedValue.Rd | 134 man/mwSlider.Rd | 138 man/mwText.Rd | 106 man/mwTranslations.Rd | 100 man/staticPlot.Rd | 108 man/worldEnergyUse.Rd | 86 tests/testthat.R | 8 tests/testthat/helper-input_class.R | 78 tests/testthat/test-controller.R | 182 tests/testthat/test-get_output_and_render_func.R | 44 tests/testthat/test-input_class.R | 88 tests/testthat/test-input_env.R | 516 - tests/testthat/test-input_list_class.R | 322 - tests/testthat/test-inputs.R | 194 tests/testthat/test-manipulate_widget.R | 268 tests/testthat/test-mwGroup.R | 144 tests/testthat/test-mwModuleUI.R | 46 tests/testthat/test-on_done.R | 90 tests/testthat/test-staticPlot.R | 50 vignettes/manipulateWidgets.Rmd | 500 - 77 files changed, 14470 insertions(+), 8316 deletions(-)
More information about manipulateWidget at CRAN
Permanent link
Title: Dynamic Bayesian Network Learning and Inference
Description: Learning and inference over dynamic Bayesian networks of arbitrary
Markovian order. Extends some of the functionality offered by the 'bnlearn'
package to learn the networks from data and perform exact inference.
It offers three structure learning algorithms for dynamic Bayesian networks:
Trabelsi G. (2013) <doi:10.1007/978-3-642-41398-8_34>, Santos F.P. and Maciel C.D. (2014)
<doi:10.1109/BRC.2014.6880957>, Quesada D., Bielza C. and Larrañaga P. (2021)
<doi:10.1007/978-3-030-86271-8_14>. It also offers the possibility to perform
forecasts of arbitrary length. A tool for visualizing the structure of the
net is also provided via the 'visNetwork' package. Further detailed information
and examples can be found in our Journal of Statistical Software paper
Quesada D., Larrañaga P. and Bielza C. (2025) <doi:10.18637/jss.v115.i06>.
Author: David Quesada [aut, cre],
Gabriel Valverde [ctb]
Maintainer: David Quesada <dkesada@gmail.com>
Diff between dbnR versions 0.7.9 dated 2024-06-19 and 0.8.0 dated 2026-01-13
DESCRIPTION | 10 ++++++---- MD5 | 7 ++++--- NEWS.md | 6 ++++++ README.md | 11 ++++++----- inst |only 5 files changed, 22 insertions(+), 12 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 2.2.0 dated 2025-09-17 and 2.2.1 dated 2026-01-13
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/cctest.R | 5 ++- build/partial.rdb |binary man/cctest.Rd | 74 ++++++++++++++++++++++++++++++++---------------------- 5 files changed, 54 insertions(+), 39 deletions(-)
Title: Dairy Farm Carbon Footprint Assessment
Description: Calculates the carbon footprint of dairy farms based on methodologies of the International Dairy Federation and the Intergovernmental Panel on Climate Change. Includes tools for single-farm and batch analysis, report generation, and visualization. Methods follow International Dairy Federation (2022) "The IDF global Carbon Footprint standard for the dairy sector" (Bulletin of the IDF n° 520/2022) <doi:10.56169/FKRK7166> and IPCC (2019) "2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management" <https://www.ipcc-nggip.iges.or.jp/public/2019rf/pdf/4_Volume4/19R_V4_Ch10_Livestock.pdf> guidelines.
Author: Juan Moreno [aut, cre]
Maintainer: Juan Moreno <juanmarcosmoreno@gmail.com>
Diff between cowfootR versions 0.1.2 dated 2025-09-22 and 0.1.3 dated 2026-01-13
cowfootR-0.1.2/cowfootR/inst/doc/Complete_Parameter_Reference_Guide.R |only cowfootR-0.1.2/cowfootR/inst/doc/Complete_Parameter_Reference_Guide.Rmd |only cowfootR-0.1.2/cowfootR/inst/doc/Complete_Parameter_Reference_Guide.html |only cowfootR-0.1.2/cowfootR/inst/doc/IPCC_Methodology_Tiers_cowfootR.R |only cowfootR-0.1.2/cowfootR/inst/doc/IPCC_Methodology_Tiers_cowfootR.Rmd |only cowfootR-0.1.2/cowfootR/inst/doc/IPCC_Methodology_Tiers_cowfootR.html |only cowfootR-0.1.2/cowfootR/inst/doc/Introduction_to_Dairy_LCA_cowfootR.R |only cowfootR-0.1.2/cowfootR/inst/doc/Introduction_to_Dairy_LCA_cowfootR.Rmd |only cowfootR-0.1.2/cowfootR/inst/doc/Introduction_to_Dairy_LCA_cowfootR.html |only cowfootR-0.1.2/cowfootR/inst/doc/Single_Farm_Analysis_cowfootR.R |only cowfootR-0.1.2/cowfootR/inst/doc/Single_Farm_Analysis_cowfootR.Rmd |only cowfootR-0.1.2/cowfootR/inst/doc/Single_Farm_Analysis_cowfootR.html |only cowfootR-0.1.2/cowfootR/man/figures/logo.png |only cowfootR-0.1.2/cowfootR/vignettes/Complete_Parameter_Reference_Guide.Rmd |only cowfootR-0.1.2/cowfootR/vignettes/IPCC_Methodology_Tiers_cowfootR.Rmd |only cowfootR-0.1.2/cowfootR/vignettes/Introduction_to_Dairy_LCA_cowfootR.Rmd |only cowfootR-0.1.2/cowfootR/vignettes/Single_Farm_Analysis_cowfootR.Rmd |only cowfootR-0.1.3/cowfootR/DESCRIPTION | 6 cowfootR-0.1.3/cowfootR/MD5 | 136 - cowfootR-0.1.3/cowfootR/NEWS.md | 51 cowfootR-0.1.3/cowfootR/R/calc_batch.R | 1066 +++++----- cowfootR-0.1.3/cowfootR/R/calc_emissions_energy.R | 171 - cowfootR-0.1.3/cowfootR/R/calc_emissions_enteric.R | 120 - cowfootR-0.1.3/cowfootR/R/calc_emissions_inputs.R | 361 --- cowfootR-0.1.3/cowfootR/R/calc_emissions_manure.R | 153 - cowfootR-0.1.3/cowfootR/R/calc_emissions_soil.R | 140 - cowfootR-0.1.3/cowfootR/R/calc_intensity_area.R | 86 cowfootR-0.1.3/cowfootR/R/calc_intensity_litre.R | 27 cowfootR-0.1.3/cowfootR/R/calc_total_emissions.R | 101 cowfootR-0.1.3/cowfootR/R/download_template.R | 16 cowfootR-0.1.3/cowfootR/R/inputs_helpers.R |only cowfootR-0.1.3/cowfootR/R/set_system_boundaries.R | 6 cowfootR-0.1.3/cowfootR/README.md | 381 ++- cowfootR-0.1.3/cowfootR/build/vignette.rds |binary cowfootR-0.1.3/cowfootR/inst/doc/get-started.R |only cowfootR-0.1.3/cowfootR/inst/doc/get-started.Rmd |only cowfootR-0.1.3/cowfootR/inst/doc/get-started.html |only cowfootR-0.1.3/cowfootR/inst/doc/introduction-lca.R |only cowfootR-0.1.3/cowfootR/inst/doc/introduction-lca.Rmd |only cowfootR-0.1.3/cowfootR/inst/doc/introduction-lca.html |only cowfootR-0.1.3/cowfootR/inst/doc/ipcc-tiers.R |only cowfootR-0.1.3/cowfootR/inst/doc/ipcc-tiers.Rmd |only cowfootR-0.1.3/cowfootR/inst/doc/ipcc-tiers.html |only cowfootR-0.1.3/cowfootR/inst/doc/parameter-reference.R |only cowfootR-0.1.3/cowfootR/inst/doc/parameter-reference.Rmd |only cowfootR-0.1.3/cowfootR/inst/doc/parameter-reference.html |only cowfootR-0.1.3/cowfootR/inst/doc/single-farm-analysis.R |only cowfootR-0.1.3/cowfootR/inst/doc/single-farm-analysis.Rmd |only cowfootR-0.1.3/cowfootR/inst/doc/single-farm-analysis.html |only cowfootR-0.1.3/cowfootR/man/benchmark_area_intensity.Rd | 9 cowfootR-0.1.3/cowfootR/man/calc_batch.Rd | 79 cowfootR-0.1.3/cowfootR/man/calc_emissions_energy.Rd | 39 cowfootR-0.1.3/cowfootR/man/calc_emissions_enteric.Rd | 27 cowfootR-0.1.3/cowfootR/man/calc_emissions_inputs.Rd | 8 cowfootR-0.1.3/cowfootR/man/calc_emissions_manure.Rd | 30 cowfootR-0.1.3/cowfootR/man/calc_emissions_soil.Rd | 26 cowfootR-0.1.3/cowfootR/man/calc_intensity_area.Rd | 32 cowfootR-0.1.3/cowfootR/man/calc_intensity_litre.Rd | 11 cowfootR-0.1.3/cowfootR/man/calc_total_emissions.Rd | 22 cowfootR-0.1.3/cowfootR/man/cf_download_template.Rd | 2 cowfootR-0.1.3/cowfootR/man/export_hdc_report.Rd | 7 cowfootR-0.1.3/cowfootR/man/figures/diagram.png |only cowfootR-0.1.3/cowfootR/man/print.cf_area_intensity.Rd | 17 cowfootR-0.1.3/cowfootR/man/print.cf_intensity.Rd | 16 cowfootR-0.1.3/cowfootR/man/print.cf_total.Rd | 13 cowfootR-0.1.3/cowfootR/man/set_system_boundaries.Rd | 4 cowfootR-0.1.3/cowfootR/tests/testthat/helper-utils.R | 36 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_batch.R | 34 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_emissions_energy.R | 32 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_emissions_enteric.R | 28 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_emissions_inputs.R | 8 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_emissions_manure.R | 25 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_emissions_soil.R | 24 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_intensity.R | 35 cowfootR-0.1.3/cowfootR/tests/testthat/test-calc_total_emissions.R | 47 cowfootR-0.1.3/cowfootR/tests/testthat/test-energy.R | 87 cowfootR-0.1.3/cowfootR/tests/testthat/test-enteric-reference.R |only cowfootR-0.1.3/cowfootR/tests/testthat/test-export_functions.R | 27 cowfootR-0.1.3/cowfootR/tests/testthat/test-helpers.R | 7 cowfootR-0.1.3/cowfootR/tests/testthat/test-integration.R | 71 cowfootR-0.1.3/cowfootR/tests/testthat/test-intensities.R | 235 -- cowfootR-0.1.3/cowfootR/tests/testthat/test-manure.R | 156 - cowfootR-0.1.3/cowfootR/tests/testthat/test-system_boundaries.R | 71 cowfootR-0.1.3/cowfootR/tests/testthat/test-total.R | 148 - cowfootR-0.1.3/cowfootR/vignettes/get-started.Rmd |only cowfootR-0.1.3/cowfootR/vignettes/introduction-lca.Rmd |only cowfootR-0.1.3/cowfootR/vignettes/ipcc-tiers.Rmd |only cowfootR-0.1.3/cowfootR/vignettes/parameter-reference.Rmd |only cowfootR-0.1.3/cowfootR/vignettes/single-farm-analysis.Rmd |only 89 files changed, 2266 insertions(+), 1968 deletions(-)
Title: Dose-Response Network Meta-Analysis in a Frequentist Way
Description: A set of functions providing the implementation of the network meta-analysis model with dose-response relationships, predicted values of the fitted model and dose-response plots in a frequentist way.
Author: Maria Petropoulou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Maria Petropoulou <m.petropoulou.a@gmail.com>
Diff between netdose versions 0.7-2 dated 2025-10-10 and 0.7-3 dated 2026-01-13
DESCRIPTION | 8 +-- MD5 | 16 +++--- R/netdose-internal.R | 9 ++- R/netdose.R | 64 ++++++++++++++++---------- R/nma_dose.R | 2 R/plot.netdose.R | 62 ++++++++++++++++++------- R/predict.netdose.R | 75 +++++++++++++++++++++++-------- R/prepare.R | 123 +++++++++++++++++++++++++++++++++++++++++++-------- man/netdose.Rd | 12 +++- 9 files changed, 276 insertions(+), 95 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods for defining, detecting, and categorising the extreme events
known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) <doi: 10.1016/j.pocean.2015.12.014>
and Hobday et al. (2018) <https://www.jstor.org/stable/26542662>. The functions in this package work on both air
and water temperature data of hourly and daily temporal resolution. These detection algorithms may be used on
non-temperature data as well.
Author: Robert W. Schlegel [aut, cre, ctb] ,
Albertus J. Smit [aut, ctb]
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.5.4 dated 2025-04-10 and 0.5.5 dated 2026-01-13
DESCRIPTION | 20 +++--- MD5 | 40 ++++++------- NEWS.md | 11 +++ R/detect_event.R | 2 R/ts2clm3.R | 10 +-- README.md | 88 ++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Download_SST_v2.html | 9 +-- inst/doc/MHW_metric_trends.html | 9 +-- inst/doc/MHW_to_nc.html | 9 +-- inst/doc/OISST_preparation.html | 9 +-- inst/doc/complex_clims.html | 17 +++-- inst/doc/detection_and_visualisation.html | 35 ++++++----- inst/doc/event_categories.html | 19 +++--- inst/doc/exceedance.html | 13 ++-- inst/doc/gridded_event_detection.html | 9 +-- inst/doc/internal_workflow.html | 4 - man/detect_event.Rd | 2 man/heatwaveR-package.Rd | 2 src/Makevars | 6 +- 21 files changed, 167 insertions(+), 147 deletions(-)
Title: Genome Polarization via Diagnostic Index Expectation
Maximization
Description: Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.5.2 dated 2025-12-11 and 1.5.3 dated 2026-01-13
DESCRIPTION | 6 +- MD5 | 28 +++++----- NEWS.md | 8 ++ R/diem.r | 19 ++++-- R/hybridIndex.r | 6 +- R/plotPolarized.r | 5 + inst/doc/Importing-data-for-genome-polarisation.html | 4 - inst/doc/Understanding-genome-polarisation-output-files.html | 4 - inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 - inst/extdata/testBarrier.txt | 4 - man/diem.Rd | 7 ++ man/figures |only man/hybridIndex.Rd | 6 +- man/plotPolarized.Rd | 3 - tests/testthat/test_hybridIndex.r | 6 +- tests/testthat/test_rank2map.r |only 16 files changed, 68 insertions(+), 42 deletions(-)
Title: Confidentiality of Spatial Point Data
Description: Provides an automatic aggregation tool to manage point data privacy,
intended to be helpful for the production of official spatial data and for researchers.
The package pursues the data accuracy at the smallest possible areas preventing
individual information disclosure. The methodology, based on hierarchical geographic
data structures performs aggregation and local suppression of point data to ensure privacy
as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>.
The data structures are created following the guidelines for grid datasets from the
European Forum for Geography and Statistics.
Author: Raymond Lagonigro [aut, cre] ,
Ramon Oller [aut] ,
Joan Carles Martori [aut]
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>
Diff between AQuadtree versions 1.0.4 dated 2023-07-19 and 1.0.5 dated 2026-01-13
DESCRIPTION | 16 +++++++++------- MD5 | 40 ++++++++++++++++++++-------------------- NEWS | 6 ++++++ R/AQuadtree-class.R | 4 ++-- R/AQuadtree.R | 4 ++-- R/createAQuadtree.R | 4 ++-- R/createGrid.R | 4 ++-- R/data.R | 2 +- R/spatialPointsCellCodes.R | 4 ++-- R/splitCellNum.R | 4 ++-- build/vignette.rds |binary inst/doc/AQuadtreeUse.R | 14 +++++++------- inst/doc/AQuadtreeUse.pdf |binary man/AQuadtree-class.Rd | 4 ++-- man/AQuadtree-package.Rd | 4 ++-- man/BarcelonaPop.Rd | 2 +- man/createAQuadtree.Rd | 4 ++-- man/createGrid.Rd | 4 ++-- man/spatialPointsCellCodes.Rd | 4 ++-- man/splitCellNum.Rd | 4 ++-- vignettes/References.bib | 7 +++---- 21 files changed, 71 insertions(+), 64 deletions(-)
Title: Graphic Styles and Colours for Scottish Government Plots
Description: A 'ggplot2' theme and colour palettes to create accessible
data visualisations in the Scottish Government.
Author: Scottish Government [cph, fnd],
Alice Hannah [aut, cre]
Maintainer: Alice Hannah <alice.hannah@gov.scot>
Diff between sgplot versions 0.4.0 dated 2025-05-27 and 0.5.0 dated 2026-01-13
sgplot-0.4.0/sgplot/build |only sgplot-0.4.0/sgplot/inst |only sgplot-0.4.0/sgplot/vignettes |only sgplot-0.5.0/sgplot/DESCRIPTION | 16 sgplot-0.5.0/sgplot/MD5 | 53 - sgplot-0.5.0/sgplot/NEWS.md | 110 +-- sgplot-0.5.0/sgplot/R/colour_table.R | 2 sgplot-0.5.0/sgplot/R/data.R | 24 sgplot-0.5.0/sgplot/R/scale_continuous_sg.R | 36 - sgplot-0.5.0/sgplot/R/use_sgplot.R | 44 - sgplot-0.5.0/sgplot/README.md | 66 +- sgplot-0.5.0/sgplot/man/af_colour_values.Rd | 6 sgplot-0.5.0/sgplot/man/figures/README-ex1-1.svg | 591 +++++++++--------- sgplot-0.5.0/sgplot/man/figures/README-ex2-1.svg | 554 +++++++++------- sgplot-0.5.0/sgplot/man/scale_colour_continuous_sg.Rd | 15 sgplot-0.5.0/sgplot/man/sg_colour_values.Rd | 6 sgplot-0.5.0/sgplot/man/sgplot-package.Rd | 2 sgplot-0.5.0/sgplot/man/sss_colour_values.Rd | 6 sgplot-0.5.0/sgplot/man/use_sgplot.Rd | 11 sgplot-0.5.0/sgplot/tests/testthat/test-use_sgplot.R |only 20 files changed, 842 insertions(+), 700 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Koslik [aut, cre]
Maintainer: Jan-Ole Koslik <jan-ole.koslik@uni-bielefeld.de>
Diff between RTMBdist versions 0.1.0 dated 2025-10-07 and 1.0.0 dated 2026-01-13
DESCRIPTION | 8 - MD5 | 58 ++++--- NAMESPACE | 20 ++ R/aaa_utils.R | 28 +++ R/copulas.R | 363 ++++++++++++++++++++++++++++++++++++++++++++++--- R/laplace.R | 19 +- R/pgweibull.R |only R/skewnorm.R | 17 +- R/skewnorm2.R | 2 R/skewt.R | 16 +- R/skewt2.R |only R/wishart.R | 130 +++++++++++++++-- README.md | 24 ++- build/vignette.rds |binary inst/doc/Examples.html | 10 - inst/doc/distlist.Rmd | 23 ++- inst/doc/distlist.html | 38 ++++- man/abs_smooth.Rd |only man/cclayton.Rd | 12 + man/cfrank.Rd | 8 - man/cgaussian.Rd | 2 man/cgmrf.Rd |only man/cgumbel.Rd | 15 +- man/cmvgauss.Rd |only man/dcopula.Rd | 3 man/ddcopula.Rd |only man/dmvcopula.Rd |only man/laplace.Rd | 5 man/pgweibull.Rd |only man/skewnorm.Rd | 3 man/skewnorm2.Rd | 3 man/skewt.Rd | 11 - man/skewt2.Rd |only man/wishart.Rd |only vignettes/distlist.Rmd | 23 ++- 35 files changed, 732 insertions(+), 109 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.8.0 dated 2025-02-21 and 1.9.0 dated 2026-01-13
DESCRIPTION | 12 +-- MD5 | 21 +++--- NAMESPACE | 6 + NEWS | 15 ++++ R/image.R | 49 +++++++++++++++ README.md | 84 +++++++++++--------------- build/partial.rdb |binary inst/include/RNifti.h | 2 inst/include/RNifti/NiftiImage.h | 59 +++++++++++------- inst/include/RNifti/NiftiImage_impl.h | 108 ++++++++++++++++++++-------------- inst/tinytest/test-55-fuzz.R |only src/main.cpp | 99 +++++++++++++++++++++++++++++++ 12 files changed, 327 insertions(+), 128 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.2.6 dated 2024-11-20 and 4.2.7 dated 2026-01-13
ChangeLog | 4 DESCRIPTION | 6 MD5 | 16 - build/vignette.rds |binary inst/doc/browseMovebank.R | 210 +++++++++--------- inst/doc/browseMovebank.html | 7 inst/doc/move.R | 186 ++++++++-------- inst/doc/move.html | 494 +++++++++++++++++++++---------------------- tests/testthat/test.emd.R | 174 +++++++++++---- 9 files changed, 596 insertions(+), 501 deletions(-)
Title: Estimate Latent Classes on a Mixture of Continuous and
Dichotomous Data
Description: EQ-5D value set estimation can be done using the hybrid model likelihood as described by
Oppe and van Hout (2010) <doi:10.1002/hec.3560> and Ramos-Goñi et al. (2017) <doi:10.1097/MLR.0000000000000283>.
The package is based on 'flexmix' and among others contains an M-step-driver as described by Leisch (2004) <doi:10.18637/jss.v011.i08>.
Users can estimate latent classes and address preference heterogeneity. Both uncensored and censored data are supported.
Furthermore, heteroscedasticity can be taken into account. It is possible to control for different covariates on the continuous and dichotomous parts of the data and start values can differ
between the expected latent classes.
Author: Svenja Elkenkamp [aut, cre],
Kim Rand [aut],
John Grosser [aut],
EuroQol [fnd]
Maintainer: Svenja Elkenkamp <svenja.elkenkamp@uni-bielefeld.de>
Diff between hyreg2 versions 1.1.0 dated 2025-12-19 and 1.1.1 dated 2026-01-13
DESCRIPTION | 6 ++--- MD5 | 8 +++---- inst/doc/hyreg2_basics-vignette.Rmd | 8 +++---- inst/doc/hyreg2_basics-vignette.html | 39 +++++++++++++++++------------------ vignettes/hyreg2_basics-vignette.Rmd | 8 +++---- 5 files changed, 34 insertions(+), 35 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2024)
<doi:10.1016/j.alcr.2024.100617>. The package supports joint modeling of
multiple measurements per individual, time-varying and time-invariant
effects, and a wide range of discrete and continuous distributions.
Estimation of these dynamic multivariate panel models is carried out via
'Stan'. For an in-depth tutorial of the package, see
(Tikka and Helske, 2025) <doi:10.18637/jss.v115.i05>.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D'Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.5.6 dated 2025-04-07 and 1.6.2 dated 2026-01-13
dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-10-1.png |only dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-11-1.png |only dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-7-1.png |only dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-8-1.png |only dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-9-1.png |only dynamite-1.6.2/dynamite/DESCRIPTION | 17 dynamite-1.6.2/dynamite/MD5 | 116 dynamite-1.6.2/dynamite/NEWS.md | 24 dynamite-1.6.2/dynamite/R/deterministic.R | 465 dynamite-1.6.2/dynamite/R/dynamice.R | 20 dynamite-1.6.2/dynamite/R/dynamite.R | 2533 ++--- dynamite-1.6.2/dynamite/R/dynamiteformula.R | 1878 +-- dynamite-1.6.2/dynamite/R/fitted.R | 209 dynamite-1.6.2/dynamite/R/getters.R | 735 - dynamite-1.6.2/dynamite/R/lags.R | 1196 +- dynamite-1.6.2/dynamite/R/lfo.R | 7 dynamite-1.6.2/dynamite/R/loo.R | 3 dynamite-1.6.2/dynamite/R/model_matrix.R | 286 dynamite-1.6.2/dynamite/R/plot.R | 7 dynamite-1.6.2/dynamite/R/predict.R | 1366 +- dynamite-1.6.2/dynamite/R/predict_helpers.R | 26 dynamite-1.6.2/dynamite/R/prepare_stan_input.R | 4 dynamite-1.6.2/dynamite/R/print.R | 20 dynamite-1.6.2/dynamite/R/specials.R | 6 dynamite-1.6.2/dynamite/R/stan_utilities.R | 860 - dynamite-1.6.2/dynamite/R/stanblocks.R | 1920 +-- dynamite-1.6.2/dynamite/R/stanblocks_families.R | 4895 ++++------ dynamite-1.6.2/dynamite/R/sysdata.rda |binary dynamite-1.6.2/dynamite/R/update.R | 294 dynamite-1.6.2/dynamite/R/utilities.R | 990 +- dynamite-1.6.2/dynamite/README.md | 54 dynamite-1.6.2/dynamite/build/vignette.rds |binary dynamite-1.6.2/dynamite/data/categorical_example_fit.rda |binary dynamite-1.6.2/dynamite/data/gaussian_example_fit.rda |binary dynamite-1.6.2/dynamite/data/multichannel_example_fit.rda |binary dynamite-1.6.2/dynamite/inst/CITATION | 75 dynamite-1.6.2/dynamite/inst/doc/dynamite.html | 340 dynamite-1.6.2/dynamite/inst/doc/dynamite.qmd | 2020 ++-- dynamite-1.6.2/dynamite/inst/doc/dynamite_custom.html | 180 dynamite-1.6.2/dynamite/inst/doc/dynamite_priors.html | 225 dynamite-1.6.2/dynamite/inst/doc/dynamite_priors.qmd | 218 dynamite-1.6.2/dynamite/inst/doc/dynamite_simulation.html | 180 dynamite-1.6.2/dynamite/inst/doc/dynamite_simulation.qmd | 488 dynamite-1.6.2/dynamite/man/dynamice.Rd | 13 dynamite-1.6.2/dynamite/man/dynamite.Rd | 21 dynamite-1.6.2/dynamite/man/figures/README-dag-1.png |only dynamite-1.6.2/dynamite/man/figures/README-posterior-1.png |only dynamite-1.6.2/dynamite/man/figures/README-prediction-1.png |only dynamite-1.6.2/dynamite/man/figures/README-random-1.png |only dynamite-1.6.2/dynamite/man/figures/README-trace-1.png |only dynamite-1.6.2/dynamite/man/fitted.dynamitefit.Rd | 5 dynamite-1.6.2/dynamite/man/plot.dynamiteformula.Rd | 130 dynamite-1.6.2/dynamite/man/predict.dynamitefit.Rd | 5 dynamite-1.6.2/dynamite/tests/testthat/test-cmdstanr.R | 1194 +- dynamite-1.6.2/dynamite/tests/testthat/test-edgecases.R | 20 dynamite-1.6.2/dynamite/tests/testthat/test-extended.R | 1817 +-- dynamite-1.6.2/dynamite/tests/testthat/test-internals.R | 468 dynamite-1.6.2/dynamite/tests/testthat/test-output.R | 1012 +- dynamite-1.6.2/dynamite/tests/testthat/test-predict.R | 41 dynamite-1.6.2/dynamite/tests/testthat/test-random.R | 15 dynamite-1.6.2/dynamite/tests/testthat/test-warnings.R | 8 dynamite-1.6.2/dynamite/vignettes/dynamite.qmd | 2020 ++-- dynamite-1.6.2/dynamite/vignettes/dynamite_priors.qmd | 218 dynamite-1.6.2/dynamite/vignettes/dynamite_simulation.qmd | 488 64 files changed, 14915 insertions(+), 14217 deletions(-)
Title: A User-Friendly 'shiny' Application for Exploring Associations
and Visual Patterns
Description: A user-friendly 'shiny' application to explore statistical associations and visual patterns in multivariate datasets. The app provides interactive correlation networks, bivariate plots, and summary tables for different types of variables (numeric and categorical). It also supports optional survey weights and range-based filters on association strengths, making it suitable for the exploration of survey and public data by non-technical users, journalists, educators, and researchers. For background and methodological details, see Soetewey et al. (2025) <doi:10.1016/j.softx.2025.102483>.
Author: Antoine Soetewey [aut, cre] ,
Cedric Heuchenne [aut] ,
Arnaud Claes [aut] ,
Antonin Descampe [aut]
Maintainer: Antoine Soetewey <antoine.soetewey@uclouvain.be>
Diff between AssociationExplorer2 versions 0.1.4 dated 2026-01-09 and 0.1.5 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 ++- README.md | 5 +++-- inst/CITATION | 2 +- inst/app/app.R | 10 +++++++--- 6 files changed, 21 insertions(+), 15 deletions(-)
More information about AssociationExplorer2 at CRAN
Permanent link
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.1.1 dated 2025-12-13 and 1.2.0 dated 2026-01-13
qol-1.1.1/qol/man/args_to_char.Rd |only qol-1.1.1/qol/man/convert_numeric.Rd |only qol-1.2.0/qol/DESCRIPTION | 6 qol-1.2.0/qol/MD5 | 171 qol-1.2.0/qol/NAMESPACE | 45 qol-1.2.0/qol/NEWS.md | 133 qol-1.2.0/qol/R/any_table.R | 4079 ++++++++--------- qol-1.2.0/qol/R/apply_format.R | 63 qol-1.2.0/qol/R/build_master.R | 175 qol-1.2.0/qol/R/build_rstheme.R | 26 qol-1.2.0/qol/R/content_report.R |only qol-1.2.0/qol/R/conversion.R | 267 - qol-1.2.0/qol/R/create_format.R | 70 qol-1.2.0/qol/R/crosstabs.R | 484 +- qol-1.2.0/qol/R/dummy_data.R | 311 - qol-1.2.0/qol/R/error_handling.R |only qol-1.2.0/qol/R/excel_helpers.R | 79 qol-1.2.0/qol/R/export_with_style.R | 162 qol-1.2.0/qol/R/frequencies.R | 436 + qol-1.2.0/qol/R/globals.R | 24 qol-1.2.0/qol/R/if_else.R | 484 +- qol-1.2.0/qol/R/import_export.R |only qol-1.2.0/qol/R/internal.R | 295 - qol-1.2.0/qol/R/keep_drop.R | 346 - qol-1.2.0/qol/R/loading.R |only qol-1.2.0/qol/R/monitor.R | 474 - qol-1.2.0/qol/R/multi_join.R | 81 qol-1.2.0/qol/R/options.R |only qol-1.2.0/qol/R/qol.R | 57 qol-1.2.0/qol/R/recode.R | 89 qol-1.2.0/qol/R/renaming.R |only qol-1.2.0/qol/R/retain.R | 414 + qol-1.2.0/qol/R/small_helpers.R | 349 - qol-1.2.0/qol/R/sort_plus.R |only qol-1.2.0/qol/R/split_by.R | 306 - qol-1.2.0/qol/R/statistics.R | 66 qol-1.2.0/qol/R/summarise_plus.R | 550 +- qol-1.2.0/qol/R/transpose_plus.R |only qol-1.2.0/qol/R/variable_selection.R |only qol-1.2.0/qol/README.md | 123 qol-1.2.0/qol/inst |only qol-1.2.0/qol/man/add_extension.Rd | 4 qol-1.2.0/qol/man/add_variable_range.Rd |only qol-1.2.0/qol/man/any_table.Rd | 114 qol-1.2.0/qol/man/build_master.Rd | 16 qol-1.2.0/qol/man/build_rstheme.Rd | 14 qol-1.2.0/qol/man/content_report.Rd |only qol-1.2.0/qol/man/convert_arguments.Rd |only qol-1.2.0/qol/man/convert_variables.Rd |only qol-1.2.0/qol/man/crosstabs.Rd | 65 qol-1.2.0/qol/man/dummy_data.Rd | 2 qol-1.2.0/qol/man/error_handling.Rd |only qol-1.2.0/qol/man/excel_output_style.Rd | 20 qol-1.2.0/qol/man/export_with_style.Rd | 63 qol-1.2.0/qol/man/figures/output.png |binary qol-1.2.0/qol/man/first_row_as_names.Rd |only qol-1.2.0/qol/man/formats.Rd | 2 qol-1.2.0/qol/man/frequencies.Rd | 65 qol-1.2.0/qol/man/get_integer_length.Rd |only qol-1.2.0/qol/man/import_export.Rd |only qol-1.2.0/qol/man/inverse.Rd | 8 qol-1.2.0/qol/man/keep_dropp.Rd | 114 qol-1.2.0/qol/man/libname.Rd | 4 qol-1.2.0/qol/man/modify_number_formats.Rd | 2 qol-1.2.0/qol/man/modify_output_style.Rd | 2 qol-1.2.0/qol/man/multi_join.Rd | 2 qol-1.2.0/qol/man/number_format_style.Rd | 2 qol-1.2.0/qol/man/qol-package.Rd | 57 qol-1.2.0/qol/man/qol_news.Rd |only qol-1.2.0/qol/man/qol_options.Rd |only qol-1.2.0/qol/man/remove_stat_extension.Rd | 2 qol-1.2.0/qol/man/rename_multi.Rd |only qol-1.2.0/qol/man/rename_pattern.Rd | 2 qol-1.2.0/qol/man/replace_except.Rd | 4 qol-1.2.0/qol/man/retain.Rd | 43 qol-1.2.0/qol/man/set.Rd |only qol-1.2.0/qol/man/sort_plus.Rd |only qol-1.2.0/qol/man/split_by.Rd | 75 qol-1.2.0/qol/man/style_options.Rd |only qol-1.2.0/qol/man/summarise_plus.Rd | 12 qol-1.2.0/qol/man/transpose_plus.Rd |only qol-1.2.0/qol/man/vars_between.Rd |only qol-1.2.0/qol/tests/testthat/test-any_table.R | 272 - qol-1.2.0/qol/tests/testthat/test-build_master.R | 14 qol-1.2.0/qol/tests/testthat/test-build_rstheme.R | 14 qol-1.2.0/qol/tests/testthat/test-content_report.R |only qol-1.2.0/qol/tests/testthat/test-conversion.R | 72 qol-1.2.0/qol/tests/testthat/test-crosstabs.R | 776 +-- qol-1.2.0/qol/tests/testthat/test-export_with_style.R | 17 qol-1.2.0/qol/tests/testthat/test-frequencies.R | 679 +- qol-1.2.0/qol/tests/testthat/test-if_else.R | 248 - qol-1.2.0/qol/tests/testthat/test-import_export.R |only qol-1.2.0/qol/tests/testthat/test-keep_drop.R | 346 - qol-1.2.0/qol/tests/testthat/test-loading.R |only qol-1.2.0/qol/tests/testthat/test-multi_join.R | 22 qol-1.2.0/qol/tests/testthat/test-options.R |only qol-1.2.0/qol/tests/testthat/test-renaming.R |only qol-1.2.0/qol/tests/testthat/test-retain.R | 193 qol-1.2.0/qol/tests/testthat/test-small_helpers.R | 51 qol-1.2.0/qol/tests/testthat/test-sort_plus.R |only qol-1.2.0/qol/tests/testthat/test-split_by.R | 167 qol-1.2.0/qol/tests/testthat/test-summarise_plus.R | 382 - qol-1.2.0/qol/tests/testthat/test-transpose_plus.R |only qol-1.2.0/qol/tests/testthat/test-variable_selection.R |only 104 files changed, 8075 insertions(+), 6037 deletions(-)
Title: Multi-Purpose and High-Performance Routing
Description: Provides routing based on the 'path-tree' 'Rust' crate. The routing
is general purpose in the sense that any type of R object can be associated
with a path, not just a handler function.
Author: Thomas Lin Pedersen [aut, cre] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between waysign versions 0.1.0 dated 2025-12-16 and 0.1.1 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/signpost.R | 29 ++++++++++++++++++++--------- 4 files changed, 31 insertions(+), 15 deletions(-)
Title: Calculate and Track Dates and Medications During Pregnancy
Description: Provides functionality for calculating pregnancy-related dates and
tracking medications during pregnancy and fertility treatment. Calculates
due dates from various starting points including last menstrual period and
IVF (In Vitro Fertilisation) transfer dates, determines pregnancy progress
on any given date, and identifies when specific pregnancy weeks are
reached. Includes medication tracking capabilities for individuals
undergoing fertility treatment or during pregnancy, allowing users to
monitor remaining doses and quantities needed over specified time periods.
Designed for those tracking their own pregnancies or supporting partners
through the process, making use of options to personalise output messages.
For details on due date calculations, see
<https://www.acog.org/clinical/clinical-guidance/committee-opinion/articles/2017/05/methods-for-estimating-the-due-date>.
Author: Ella Kaye [aut, cre, cph]
Maintainer: Ella Kaye <ella.kaye@gmail.com>
Diff between pregnancy versions 0.2.0 dated 2025-11-19 and 0.2.1 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/pregnancy.html | 42 +++++++++++++++++++++--------------------- tests/testthat/test-how_far.R | 2 ++ 6 files changed, 35 insertions(+), 29 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables
for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
Kenward-Roger method is also available via the pbkrtest package. Model selection
methods include step, drop1 and anova-like tables for random effects (ranova).
Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut, cre] ,
Sofie Poedenphant Jensen [ctb]
Maintainer: Rune Haubo Bojesen Christensen <Rune.Haubo@gmail.com>
Diff between lmerTest versions 3.1-3 dated 2020-10-23 and 3.2-0 dated 2026-01-13
lmerTest-3.1-3/lmerTest/man/containment.Rd |only lmerTest-3.1-3/lmerTest/man/devfun_vp.Rd |only lmerTest-3.1-3/lmerTest/man/doolittle.Rd |only lmerTest-3.1-3/lmerTest/man/ensure_full_rank.Rd |only lmerTest-3.1-3/lmerTest/man/get_Fstat_ddf.Rd |only lmerTest-3.1-3/lmerTest/man/get_contrasts_type1.Rd |only lmerTest-3.1-3/lmerTest/man/get_contrasts_type3.Rd |only lmerTest-3.1-3/lmerTest/man/get_covbeta.Rd |only lmerTest-3.1-3/lmerTest/man/get_model_matrix.Rd |only lmerTest-3.1-3/lmerTest/man/get_rdX.Rd |only lmerTest-3.1-3/lmerTest/man/is_estimable.Rd |only lmerTest-3.1-3/lmerTest/man/nullspace.Rd |only lmerTest-3.1-3/lmerTest/man/qform.Rd |only lmerTest-3.1-3/lmerTest/man/rbindall.Rd |only lmerTest-3.1-3/lmerTest/man/rm_complete_terms.Rd |only lmerTest-3.1-3/lmerTest/man/single_anova.Rd |only lmerTest-3.1-3/lmerTest/man/term_contain.Rd |only lmerTest-3.2-0/lmerTest/DESCRIPTION | 22 +-- lmerTest-3.2-0/lmerTest/MD5 | 74 ++++------ lmerTest-3.2-0/lmerTest/NAMESPACE | 11 + lmerTest-3.2-0/lmerTest/NEWS.md | 18 +- lmerTest-3.2-0/lmerTest/R/anova_contrasts.R | 4 lmerTest-3.2-0/lmerTest/R/contest.R | 3 lmerTest-3.2-0/lmerTest/R/contrast_utils.R | 7 lmerTest-3.2-0/lmerTest/R/data_documentation.R | 4 lmerTest-3.2-0/lmerTest/R/drop1.R | 6 lmerTest-3.2-0/lmerTest/R/estimability.R | 4 lmerTest-3.2-0/lmerTest/R/legacy.R | 2 lmerTest-3.2-0/lmerTest/R/lmer.R | 42 ++++- lmerTest-3.2-0/lmerTest/R/lmerTest.R | 5 lmerTest-3.2-0/lmerTest/R/lmer_anova.R | 9 - lmerTest-3.2-0/lmerTest/R/lmer_summary.R | 5 lmerTest-3.2-0/lmerTest/R/ls_means.R | 3 lmerTest-3.2-0/lmerTest/R/ranova.R | 108 ++++++++++----- lmerTest-3.2-0/lmerTest/R/step.R | 4 lmerTest-3.2-0/lmerTest/R/terms_utils.R | 3 lmerTest-3.2-0/lmerTest/R/utils.R | 4 lmerTest-3.2-0/lmerTest/R/zzz.R |only lmerTest-3.2-0/lmerTest/man/ham.Rd | 2 lmerTest-3.2-0/lmerTest/man/lmer.Rd | 52 +++++-- lmerTest-3.2-0/lmerTest/man/lmerTest-package.Rd | 9 + lmerTest-3.2-0/lmerTest/man/ranova.Rd | 14 + lmerTest-3.2-0/lmerTest/man/show_tests.Rd | 2 lmerTest-3.2-0/lmerTest/tests/test_devfun_vp.R |only lmerTest-3.2-0/lmerTest/tests/test_legacy.R | 8 - lmerTest-3.2-0/lmerTest/tests/test_lmer.R | 4 lmerTest-3.2-0/lmerTest/tests/test_ranova_step.R | 29 ++++ lmerTest-3.2-0/lmerTest/tests/test_re_covar_structures.R |only 48 files changed, 309 insertions(+), 149 deletions(-)
Title: Core 'hubverse' Utilities
Description: Core set of low-level utilities common across the
'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files
and model outputs and designed to be primarily used internally by other
'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831>
for an overview of Collaborative Hubs.
Author: Anna Krystalli [aut, cre] ,
Li Shandross [aut],
Nicholas G. Reich [ctb] ,
Evan L. Ray [ctb],
Zhian N. Kamvar [ctb] ,
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Anna Krystalli <annakrystalli@googlemail.com>
Diff between hubUtils versions 0.1.7 dated 2024-09-18 and 1.2.0 dated 2026-01-13
hubUtils-0.1.7/hubUtils/inst/testhubs/flusight/forecasts/umass_ens |only hubUtils-1.2.0/hubUtils/DESCRIPTION | 23 hubUtils-1.2.0/hubUtils/MD5 | 256 ++++++++-- hubUtils-1.2.0/hubUtils/NAMESPACE | 35 + hubUtils-1.2.0/hubUtils/NEWS.md | 79 +++ hubUtils-1.2.0/hubUtils/R/as_config.R |only hubUtils-1.2.0/hubUtils/R/as_model_out_tbl.R | 92 ++- hubUtils-1.2.0/hubUtils/R/back-compatibility.R | 9 hubUtils-1.2.0/hubUtils/R/check_deprecated_schema.R | 24 hubUtils-1.2.0/hubUtils/R/convert_output_type.R |only hubUtils-1.2.0/hubUtils/R/model_id_merge.R | 21 hubUtils-1.2.0/hubUtils/R/read_config.R | 207 ++++++-- hubUtils-1.2.0/hubUtils/R/utils-config.R | 6 hubUtils-1.2.0/hubUtils/R/utils-get_hub.R |only hubUtils-1.2.0/hubUtils/R/utils-model_out_tbl.R |only hubUtils-1.2.0/hubUtils/R/utils-round-config.R | 6 hubUtils-1.2.0/hubUtils/R/utils-round_ids.R | 17 hubUtils-1.2.0/hubUtils/R/utils-schema-versions.R |only hubUtils-1.2.0/hubUtils/R/utils-schema.R | 113 +++- hubUtils-1.2.0/hubUtils/R/utils-target-data.R |only hubUtils-1.2.0/hubUtils/R/utils-task_ids.R |only hubUtils-1.2.0/hubUtils/R/utils-url.R |only hubUtils-1.2.0/hubUtils/R/v3-schema-utils.R | 18 hubUtils-1.2.0/hubUtils/R/zzz.R | 4 hubUtils-1.2.0/hubUtils/README.md | 23 hubUtils-1.2.0/hubUtils/inst/schemas |only hubUtils-1.2.0/hubUtils/inst/testhubs/flusight/forecasts/hub-baseline/2023-05-08-hub-baseline.parquet |binary hubUtils-1.2.0/hubUtils/inst/testhubs/flusight/forecasts/hub-ensemble/2023-04-24-hub-ensemble.csv | 76 +- hubUtils-1.2.0/hubUtils/inst/testhubs/flusight/forecasts/hub-ensemble/2023-05-01-hub-ensemble.arrow |binary hubUtils-1.2.0/hubUtils/inst/testhubs/flusight/forecasts/hub-ensemble/2023-05-08-hub-ensemble.parquet |binary hubUtils-1.2.0/hubUtils/inst/testhubs/flusight/forecasts/umass-ens |only hubUtils-1.2.0/hubUtils/inst/testhubs/v4 |only hubUtils-1.2.0/hubUtils/inst/testhubs/v5 |only hubUtils-1.2.0/hubUtils/inst/testhubs/v6 |only hubUtils-1.2.0/hubUtils/man/as_config.Rd |only hubUtils-1.2.0/hubUtils/man/convert_output_type.Rd |only hubUtils-1.2.0/hubUtils/man/create_s3_url.Rd |only hubUtils-1.2.0/hubUtils/man/extract_schema_version.Rd | 3 hubUtils-1.2.0/hubUtils/man/get_config_tid.Rd | 7 hubUtils-1.2.0/hubUtils/man/get_hub_timezone.Rd |only hubUtils-1.2.0/hubUtils/man/get_schema_url.Rd | 9 hubUtils-1.2.0/hubUtils/man/get_schema_version_latest.Rd | 2 hubUtils-1.2.0/hubUtils/man/get_version_config.Rd |only hubUtils-1.2.0/hubUtils/man/is_github_repo_url.Rd |only hubUtils-1.2.0/hubUtils/man/is_github_url.Rd |only hubUtils-1.2.0/hubUtils/man/is_s3_base_fs.Rd |only hubUtils-1.2.0/hubUtils/man/is_url.Rd |only hubUtils-1.2.0/hubUtils/man/is_v3_config.Rd | 2 hubUtils-1.2.0/hubUtils/man/is_v3_config_file.Rd | 9 hubUtils-1.2.0/hubUtils/man/is_v3_hub.Rd | 10 hubUtils-1.2.0/hubUtils/man/is_valid_url.Rd |only hubUtils-1.2.0/hubUtils/man/read_config.Rd | 22 hubUtils-1.2.0/hubUtils/man/read_config_file.Rd | 28 - hubUtils-1.2.0/hubUtils/man/subset_task_id_cols.Rd |only hubUtils-1.2.0/hubUtils/man/subset_task_id_names.Rd |only hubUtils-1.2.0/hubUtils/man/target-data-utils.Rd |only hubUtils-1.2.0/hubUtils/man/version_equal.Rd |only hubUtils-1.2.0/hubUtils/tests/testthat/_snaps/as_config.md |only hubUtils-1.2.0/hubUtils/tests/testthat/_snaps/check_deprecated_schema.md | 2 hubUtils-1.2.0/hubUtils/tests/testthat/_snaps/read_config.md | 75 ++ hubUtils-1.2.0/hubUtils/tests/testthat/_snaps/utils-schema-versions.md |only hubUtils-1.2.0/hubUtils/tests/testthat/helper-test_data.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-as_config.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-as_model_out_tbl.R | 20 hubUtils-1.2.0/hubUtils/tests/testthat/test-convert_output_type.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-model_id_merge.R | 33 - hubUtils-1.2.0/hubUtils/tests/testthat/test-read_config.R | 112 ++++ hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-get_hub.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-model_out_tbl.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-round-config.R | 6 hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-schema-versions.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-schema.R | 94 +++ hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-target-data.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-task_ids.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-utils-url.R |only hubUtils-1.2.0/hubUtils/tests/testthat/test-v3-schema-utils.R | 38 + hubUtils-1.2.0/hubUtils/tests/testthat/testdata/tasks-append.json |only 77 files changed, 1224 insertions(+), 257 deletions(-)
Title: MASCOTNUM / RT-UQ Algorithms Template Tools
Description: Helper functions for MASCOTNUM / RT-UQ <https://uq.math.cnrs.fr/> algorithm template, for design of numerical experiments practice:
algorithm template parser to support MASCOTNUM specification <https://github.com/MASCOTNUM/algorithms>,
'ask & tell' decoupling injection (inspired by <https://search.r-project.org/CRAN/refmans/sensitivity/html/decoupling.html>)
to use "crimped" algorithms (like uniroot(), optim(), ...) from outside R,
basic template examples: Brent algorithm for 1 dim root finding and L-BFGS-B from base optim().
Author: Yann Richet [aut, cre]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between templr versions 0.2-2 dated 2026-01-12 and 0.2-3 dated 2026-01-13
DESCRIPTION | 6 +-- MD5 | 5 +-- R/import.R | 66 +++++++++++++++++++++++++------------------ tests/testthat/test-import.R |only 4 files changed, 45 insertions(+), 32 deletions(-)
Title: Provider-Agnostic OAuth Authentication for 'shiny' Applications
Description: Provides a simple, configurable, provider-agnostic 'OAuth 2.0' and
'OpenID Connect' (OIDC) authentication framework for 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval, asynchronous
flows, and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.1.4 dated 2025-11-24 and 0.2.0 dated 2026-01-13
DESCRIPTION | 8 MD5 | 200 - NAMESPACE | 1 NEWS.md | 214 + R/classes__OAuthClient.R | 259 + R/classes__OAuthProvider.R | 234 + R/custom_cache.R | 3 R/errors.R | 16 R/methods__client_bearer_req.R | 12 R/methods__login.R | 851 +++++- R/methods__token.R | 632 ++++ R/methods__userinfo.R | 83 R/oauth_module_server.R | 555 +++- R/providers.R | 25 R/providers__oidc_discovery.R | 53 R/use_shinyOAuth.R | 35 R/utils.R | 278 +- R/utils__crypt.R | 17 R/utils__http.R | 316 ++ R/utils__jwks.R | 105 R/utils__jwt.R | 125 R/utils__random.R | 8 R/utils__scopes.R | 67 R/utils__shiny.R | 170 + R/utils__state.R | 60 R/utils__url.R | 128 README.md | 2 inst/doc/audit-logging.Rmd | 128 inst/doc/audit-logging.html | 211 + inst/doc/authentication-flow.Rmd | 108 inst/doc/authentication-flow.html | 248 + inst/doc/example-spotify.R | 32 inst/doc/example-spotify.Rmd | 32 inst/doc/example-spotify.html | 2068 +++++++-------- inst/doc/usage.R | 15 inst/doc/usage.Rmd | 147 - inst/doc/usage.html | 246 + inst/examples/call_methods.R | 6 inst/examples/oauth_module_server.R | 77 inst/examples/oauth_provider_microsoft.R | 24 man/OAuthClient.Rd | 134 man/OAuthProvider.Rd | 29 man/client_bearer_req.Rd | 14 man/custom_cache.Rd | 3 man/handle_callback.Rd | 171 - man/introspect_token.Rd | 15 man/oauth_client.Rd | 134 man/oauth_module_server.Rd | 104 man/oauth_provider.Rd | 29 man/oauth_provider_keycloak.Rd | 2 man/oauth_provider_microsoft.Rd | 28 man/oauth_provider_oidc_discover.Rd | 17 man/oauth_provider_spotify.Rd | 12 man/prepare_call.Rd | 120 man/refresh_token.Rd | 56 man/revoke_token.Rd |only man/state_payload_decrypt_validate.Rd | 52 man/state_store_get_remove.Rd | 50 man/use_shinyOAuth.Rd | 9 tests/testthat/helper-login.R | 15 tests/testthat/test-absolute-url-validation.R |only tests/testthat/test-alg-confusion.R | 22 tests/testthat/test-audit-all-events.R | 20 tests/testthat/test-audit-async-options.R |only tests/testthat/test-audit-async-session-context.R |only tests/testthat/test-audit-shiny-context.R | 43 tests/testthat/test-audit-state-failures.R | 2 tests/testthat/test-auth-url-scope-reserved.R |only tests/testthat/test-callback-query-size-options.R |only tests/testthat/test-client-bearer-req.R | 82 tests/testthat/test-client-jwt-auth.R | 176 + tests/testthat/test-client-secret-pkce.R | 99 tests/testthat/test-defaults-and-validation.R | 241 + tests/testthat/test-discovery-issuer-mismatch.R | 36 tests/testthat/test-error-response-state.R |only tests/testthat/test-errors-and-audit.R | 404 ++ tests/testthat/test-introspect-on-login.R |only tests/testthat/test-introspect-token.R | 9 tests/testthat/test-issued-at-boundary.R | 44 tests/testthat/test-issued-at-independent-of-store-ttl.R |only tests/testthat/test-jwks-force-refresh-rate-limit.R |only tests/testthat/test-jwks-malformed-and-pinning.R | 5 tests/testthat/test-jwks.R | 130 tests/testthat/test-jwt-malformed-and-claims.R | 22 tests/testthat/test-login-callback.R | 232 + tests/testthat/test-module-server.R | 614 ++++ tests/testthat/test-oauth-client-shiny-warning.R |only tests/testthat/test-oauth-module-introspection-args.R |only tests/testthat/test-provider-fingerprint.R |only tests/testthat/test-random-and-validators.R | 2 tests/testthat/test-redirect-following-disabled.R |only tests/testthat/test-refresh-races.R | 123 tests/testthat/test-refresh-token.R | 1512 ++++++++++ tests/testthat/test-revoke-on-session-end.R |only tests/testthat/test-revoke-token.R |only tests/testthat/test-scope-validation.R |only tests/testthat/test-state-envelope-roundtrip.R | 1 tests/testthat/test-state-fail-delay.R | 2 tests/testthat/test-state-store-strict.R | 103 tests/testthat/test-token-type-policy.R | 57 tests/testthat/test-use-shinyOAuth-referrer-meta.R |only tests/testthat/test-userinfo-after-id-token-validation.R |only tests/testthat/test-userinfo-parsing.R |only tests/testthat/test-utils-crypt-decrypt-rejects.R | 46 tests/testthat/test-utils-http-helpers.R | 218 + tests/testthat/test-utils-url-and-scopes.R | 68 tests/testthat/test_chromote_cookie.R | 47 vignettes/audit-logging.Rmd | 128 vignettes/authentication-flow.Rmd | 108 vignettes/example-spotify.Rmd | 32 vignettes/usage.Rmd | 147 - 111 files changed, 11234 insertions(+), 2334 deletions(-)
Title: Methods for High-Dimensional Repeated Measures Data
Description: A toolkit for the analysis of high-dimensional repeated measurements, providing functions
for outlier detection, differential expression analysis, gene-set tests, and binary random data generation.
Author: Klaus Jung [aut, cre],
Jochen Kruppa [aut],
Sergej Ruff [aut]
Maintainer: Klaus Jung <klaus.jung@tiho-hannover.de>
Diff between RepeatedHighDim versions 2.4.0 dated 2025-04-14 and 2.5.0 dated 2026-01-13
RepeatedHighDim-2.4.0/RepeatedHighDim/R/check_limma.R |only RepeatedHighDim-2.5.0/RepeatedHighDim/DESCRIPTION | 16 ++++++------- RepeatedHighDim-2.5.0/RepeatedHighDim/MD5 | 14 ++++++----- RepeatedHighDim-2.5.0/RepeatedHighDim/NAMESPACE | 13 ++++++++++ RepeatedHighDim-2.5.0/RepeatedHighDim/R/helper_f.R |only RepeatedHighDim-2.5.0/RepeatedHighDim/R/scTC_trim_effect.R | 3 ++ RepeatedHighDim-2.5.0/RepeatedHighDim/R/scTrimDist.R |only RepeatedHighDim-2.5.0/RepeatedHighDim/build/partial.rdb |binary RepeatedHighDim-2.5.0/RepeatedHighDim/man/check_limma.Rd | 2 - RepeatedHighDim-2.5.0/RepeatedHighDim/man/scTrimDist.Rd |only 10 files changed, 33 insertions(+), 15 deletions(-)
More information about RepeatedHighDim at CRAN
Permanent link
Title: Estimate and Simulate from Location Dependent Marked Point
Processes
Description: A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern.
You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model.
'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools.
Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results.
Documentation for the package 'ldmppr' is available in the form of a vignette.
Author: Lane Drew [aut, cre, cph] ,
Andee Kaplan [aut]
Maintainer: Lane Drew <lanetdrew@gmail.com>
Diff between ldmppr versions 1.1.0 dated 2026-01-08 and 1.1.1 dated 2026-01-13
DESCRIPTION | 6 MD5 | 80 +++--- NAMESPACE | 3 NEWS.md | 6 R/check_model_fit.R | 458 +++++++++++++++++------------------- R/data.R | 12 R/estimate_helpers.R | 358 ++++++++++++++++++---------- R/estimate_process_parameters.R | 132 +++++----- R/extra.R | 1 R/generate_mpp.R | 2 R/internal_helpers.R | 227 +++++++++++++++++ R/mark_model_s3.R | 45 +-- R/model_check_s3.R | 35 +- R/plot_mpp.R | 4 R/predict_marks.R | 20 - R/process_fit_s3.R | 54 ++-- R/sim_s3.R | 36 +- R/simulate_mpp.R | 115 +++++---- R/train_mark_model.R | 448 +++++++++++++++++------------------ inst/doc/ldmppr_howto.R | 64 ++--- inst/doc/ldmppr_howto.Rmd | 66 ++--- inst/doc/ldmppr_howto.html | 294 ++++++++++------------- inst/extdata/example_mark_model.rds |binary man/check_model_fit.Rd | 74 +++-- man/estimate_process_parameters.Rd | 55 ++-- man/generate_mpp.Rd | 2 man/ldmppr-internal.Rd | 34 ++ man/ldmppr_fit.Rd | 34 +- man/ldmppr_mark_model.Rd | 48 +-- man/ldmppr_model_check.Rd | 31 +- man/ldmppr_sim.Rd | 28 +- man/medium_example_data.Rd | 6 man/plot_mpp.Rd | 4 man/predict_marks.Rd | 16 - man/simulate_mpp.Rd | 49 ++- man/small_example_data.Rd | 6 man/train_mark_model.Rd | 53 ++-- tests/testthat/test-mark_model_io.R | 12 tests/testthat/test-model_check.R | 5 tests/testthat/test-simulate_mpp.R | 4 vignettes/ldmppr_howto.Rmd | 66 ++--- 41 files changed, 1693 insertions(+), 1300 deletions(-)
Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized (adaptive) elastic net S and M estimators for
linear regression. The methods are proposed in
Cohen Freue, G. V., Kepplinger, D., Salibián-Barrera, M., and Smucler, E.
(2019) <https://projecteuclid.org/euclid.aoas/1574910036>.
The package implements the extensions and algorithms described in
Kepplinger, D. (2020) <doi:10.14288/1.0392915>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pense versions 2.2.2 dated 2024-07-27 and 2.5.0 dated 2026-01-13
pense-2.2.2/pense/R/deprecated-functions.R |only pense-2.2.2/pense/R/pensem_regression.R |only pense-2.2.2/pense/build/stage23.rdb |only pense-2.2.2/pense/inst/doc/migration_guide.R |only pense-2.2.2/pense/inst/doc/migration_guide.Rmd |only pense-2.2.2/pense/inst/doc/migration_guide.html |only pense-2.2.2/pense/man/consistency_const.Rd |only pense-2.2.2/pense/man/deprecated_en_options.Rd |only pense-2.2.2/pense/man/enpy.Rd |only pense-2.2.2/pense/man/initest_options.Rd |only pense-2.2.2/pense/man/mstep_options.Rd |only pense-2.2.2/pense/man/pense_options.Rd |only pense-2.2.2/pense/man/pensem.Rd |only pense-2.2.2/pense/man/pensem_cv.Rd |only pense-2.2.2/pense/tests/testthat/snap/pense_algo_mt.json |only pense-2.2.2/pense/tests/testthat/snap/regmest_algo_mt.json |only pense-2.2.2/pense/vignettes/migration_guide.Rmd |only pense-2.5.0/pense/DESCRIPTION | 14 pense-2.5.0/pense/LICENSE | 2 pense-2.5.0/pense/MD5 | 219 pense-2.5.0/pense/NAMESPACE | 16 pense-2.5.0/pense/NEWS.md | 7 pense-2.5.0/pense/R/change_cv_measure.R |only pense-2.5.0/pense/R/coef-methods.R | 70 pense-2.5.0/pense/R/constants.R | 4 pense-2.5.0/pense/R/control_options.R | 23 pense-2.5.0/pense/R/cv_utilities.R |only pense-2.5.0/pense/R/elnet.R | 28 pense-2.5.0/pense/R/enpy.R | 2 pense-2.5.0/pense/R/pense_regression.R | 247 pense-2.5.0/pense/R/pense_regression_args.R | 79 pense-2.5.0/pense/R/plot-methods.R | 30 pense-2.5.0/pense/R/print-methods.R | 19 pense-2.5.0/pense/R/regmest_regression.R | 286 - pense-2.5.0/pense/R/residuals-methods.R | 38 pense-2.5.0/pense/R/utilities-internal.R | 332 - pense-2.5.0/pense/R/utilities.R | 270 pense-2.5.0/pense/build/partial.rdb |only pense-2.5.0/pense/build/vignette.rds |binary pense-2.5.0/pense/inst/doc/computing_adapense.R | 61 pense-2.5.0/pense/inst/doc/computing_adapense.Rmd | 94 pense-2.5.0/pense/inst/doc/computing_adapense.html | 345 - pense-2.5.0/pense/inst/doc/computing_adapense_fits.RData |binary pense-2.5.0/pense/inst/doc/lambda_grids.R | 27 pense-2.5.0/pense/inst/doc/lambda_grids.Rmd | 6 pense-2.5.0/pense/inst/doc/lambda_grids.html | 18 pense-2.5.0/pense/man/cd_algorithm_options.Rd | 4 pense-2.5.0/pense/man/change_cv_measure.Rd |only pense-2.5.0/pense/man/coef.pense_cvfit.Rd | 7 pense-2.5.0/pense/man/coef.pense_fit.Rd | 16 pense-2.5.0/pense/man/dot-bisquare_consistency_const.Rd | 4 pense-2.5.0/pense/man/dot-bisquare_efficiency_const.Rd |only pense-2.5.0/pense/man/dot-find_stable_bdb_bisquare.Rd | 5 pense-2.5.0/pense/man/dot-huber_efficiency_const.Rd |only pense-2.5.0/pense/man/dot-mopt_consistency_const.Rd |only pense-2.5.0/pense/man/dot-mopt_efficiency_const.Rd |only pense-2.5.0/pense/man/dot-run_replicated_cv.Rd | 2 pense-2.5.0/pense/man/dot-run_replicated_cv_ris.Rd |only pense-2.5.0/pense/man/dot-standardize_data.Rd | 3 pense-2.5.0/pense/man/elnet_cv.Rd | 10 pense-2.5.0/pense/man/en_admm_options.Rd | 5 pense-2.5.0/pense/man/en_algorithm_options.Rd | 8 pense-2.5.0/pense/man/en_cd_options.Rd | 5 pense-2.5.0/pense/man/en_dal_options.Rd | 5 pense-2.5.0/pense/man/en_lars_options.Rd | 5 pense-2.5.0/pense/man/enpy_initial_estimates.Rd | 1 pense-2.5.0/pense/man/enpy_options.Rd | 7 pense-2.5.0/pense/man/mloc.Rd | 11 pense-2.5.0/pense/man/mlocscale.Rd | 19 pense-2.5.0/pense/man/mm_algorithm_options.Rd | 4 pense-2.5.0/pense/man/mscale.Rd | 18 pense-2.5.0/pense/man/mscale_algorithm_options.Rd | 11 pense-2.5.0/pense/man/mscale_derivative.Rd | 49 pense-2.5.0/pense/man/pense.Rd | 18 pense-2.5.0/pense/man/pense_cv.Rd | 36 pense-2.5.0/pense/man/plot.pense_cvfit.Rd | 3 pense-2.5.0/pense/man/plot.pense_fit.Rd | 3 pense-2.5.0/pense/man/predict.pense_cvfit.Rd | 16 pense-2.5.0/pense/man/predict.pense_fit.Rd | 15 pense-2.5.0/pense/man/prinsens.Rd | 1 pense-2.5.0/pense/man/regmest.Rd | 42 pense-2.5.0/pense/man/regmest_cv.Rd | 76 pense-2.5.0/pense/man/residuals.pense_cvfit.Rd | 15 pense-2.5.0/pense/man/residuals.pense_fit.Rd | 14 pense-2.5.0/pense/man/rho-tuning-constants.Rd |only pense-2.5.0/pense/man/rho_function.Rd | 11 pense-2.5.0/pense/man/starting_point.Rd | 1 pense-2.5.0/pense/src/Makevars.in | 3 pense-2.5.0/pense/src/Makevars.win | 2 pense-2.5.0/pense/src/cd_pense.hpp | 8 pense-2.5.0/pense/src/constants.hpp | 15 pense-2.5.0/pense/src/m_loss.hpp | 18 pense-2.5.0/pense/src/nsoptim/armadillo.hpp | 4 pense-2.5.0/pense/src/nsoptim/container/data.hpp | 22 pense-2.5.0/pense/src/r_enpy.cc | 4 pense-2.5.0/pense/src/r_interface.cc | 2 pense-2.5.0/pense/src/r_interface_utils.cc | 19 pense-2.5.0/pense/src/r_interface_utils.hpp | 6 pense-2.5.0/pense/src/r_mesten_regression.cc | 14 pense-2.5.0/pense/src/r_pense_regression.cc | 24 pense-2.5.0/pense/src/r_robust_utils.cc | 250 pense-2.5.0/pense/src/r_robust_utils.hpp | 10 pense-2.5.0/pense/src/r_utilities.cc | 75 pense-2.5.0/pense/src/r_utilities.hpp | 9 pense-2.5.0/pense/src/rcpp_utils.hpp | 16 pense-2.5.0/pense/src/regularization_path.hpp | 10 pense-2.5.0/pense/src/rho.cc | 494 - pense-2.5.0/pense/src/rho.hpp | 241 pense-2.5.0/pense/src/robust_scale_location.cc | 227 pense-2.5.0/pense/src/robust_scale_location.hpp | 268 pense-2.5.0/pense/src/s_loss.hpp | 24 pense-2.5.0/pense/tests/testthat/helper.R |only pense-2.5.0/pense/tests/testthat/snap/pense_algo_st-mopt.json |only pense-2.5.0/pense/tests/testthat/snap/pense_algo_st.json | 2725 +++++----- pense-2.5.0/pense/tests/testthat/snap/regmest_algo_st-mopt.json |only pense-2.5.0/pense/tests/testthat/snap/regmest_algo_st.json | 2700 +++++---- pense-2.5.0/pense/tests/testthat/test_discrete_response.R | 4 pense-2.5.0/pense/tests/testthat/test_elnet_algorithms.R | 9 pense-2.5.0/pense/tests/testthat/test_mest_algorithm.R | 141 pense-2.5.0/pense/tests/testthat/test_multiple_alpha.R | 36 pense-2.5.0/pense/tests/testthat/test_pense_algorithm.R | 156 pense-2.5.0/pense/tests/testthat/test_predict.R |only pense-2.5.0/pense/tests/testthat/test_rho.R |only pense-2.5.0/pense/tests/testthat/test_ris_cv.R |only pense-2.5.0/pense/vignettes/computing_adapense.Rmd | 94 pense-2.5.0/pense/vignettes/computing_adapense_fits.RData |binary pense-2.5.0/pense/vignettes/lambda_grids.Rmd | 6 127 files changed, 5434 insertions(+), 4889 deletions(-)
Title: Geographically Weighted Partial Correlation Coefficient
Description: Implements a geographically weighted partial correlation which is
an extension from gwss() function in the 'GWmodel' package
(Percival and Tsutsumida (2017) <doi:10.1553/giscience2017_01_s36>).
Author: Narumasa Tsutsumida [aut, cre] ,
Joseph Percival [aut]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>
Diff between GWpcor versions 0.1.7 dated 2021-11-26 and 0.1.8 dated 2026-01-13
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 6 +++--- README.md | 1 - man/gwpcor.Rd | 6 +++--- 4 files changed, 20 insertions(+), 17 deletions(-)
Title: Geographically Weighted Non-Negative Principal Components
Analysis
Description: Implements a geographically weighted non-negative principal
components analysis, which consists of the fusion of geographically
weighted and sparse non-negative principal components analyses
<doi:10.17608/k6.auckland.9850826.v1>.
Author: Narumasa Tsutsumida [aut, cre]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>
Diff between GWnnegPCA versions 0.0.5 dated 2025-02-05 and 0.0.6 dated 2026-01-13
DESCRIPTION | 13 ++++++------- MD5 | 2 +- 2 files changed, 7 insertions(+), 8 deletions(-)
Title: Compute Effect Sizes
Description: Several functions are available for calculating the most
widely used effect sizes (ES), along with their variances, confidence
intervals and p-values. The output includes ES's of d (mean difference), g
(unbiased estimate of d), r (correlation coefficient), z' (Fisher's z), and
OR (odds ratio and log odds ratio). In addition, NNT (number needed to
treat), U3, CLES (Common Language Effect Size) and Cliff's Delta are
computed. This package uses recommended formulas as described in The
Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, &
Valentine, 2009). A free web application is available at
<https://acdelre.github.io/apps/compute_es/>.
Author: AC Del Re [aut, cre]
Maintainer: AC Del Re <stats@acdelre.com>
Diff between compute.es versions 0.2-5 dated 2020-04-01 and 0.2-6 dated 2026-01-13
DESCRIPTION | 19 +++++++++++-------- MD5 | 10 ++++++---- NEWS | 4 +++- R/paired-t.R |only README.md |only inst/CITATION | 20 ++++++++++---------- man/compute.es-package.Rd | 10 +++++++--- 7 files changed, 37 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-14 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-28 0.5.3
2021-02-01 0.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-03 1.2.0
2024-07-05 1.1.0
2023-12-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-11 2.11.0
2019-06-12 2.10.0
2018-08-14 2.9.1
2016-04-23 2.8.0
2015-09-17 2.7.0
2015-04-28 2.6.0
2014-11-04 2.4.0
2014-04-09 2.3.2
2014-04-08 2.3.1
2013-09-12 2.1.2
2013-05-17 2.0
2013-03-19 1.5
2013-02-25 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-06 0.3.2
2020-05-31 0.3.1
2020-05-28 0.3.0
2019-12-02 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-25 0.1.4
2021-10-29 0.1.3
2020-01-24 0.1.2
2018-10-26 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 1.5
2019-01-11 1.4
2018-10-18 1.3
2017-10-07 1.2
2016-01-19 1.0.0
Title: Group Dates
Description: Tooling to group dates by a variety of periods including:
yearly, monthly, by second, by week of the month, and more. The
groups are defined in such a way that they also represent the distance
between dates in terms of the period. This extracts valuable
information that can be used in further calculations that rely on a
specific temporal spacing between observations.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between warp versions 0.2.2 dated 2025-11-14 and 0.2.3 dated 2026-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/vignette.rds |binary src/coercion.c | 2 +- 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Data Twinning
Description: An efficient algorithm for data twinning. This work is supported by U.S. National Science
Foundation grants DMREF-1921873 and CMMI-1921646.
Author: Akhil Vakayil [aut, cre],
Roshan Joseph [aut, ths]
Maintainer: Akhil Vakayil <akhilv@gatech.edu>
Diff between twinning versions 1.0 dated 2022-01-28 and 1.1 dated 2026-01-13
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/RcppExports.R | 30 +++++++++++++++--------------- src/Makevars | 1 - 4 files changed, 23 insertions(+), 24 deletions(-)
Title: Trust Region Optimization for Nonlinear Functions with Sparse
Hessians
Description: Trust region algorithm for nonlinear optimization. Efficient when
the Hessian of the objective function is sparse (i.e., relatively few nonzero
cross-partial derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>
Diff between trustOptim versions 0.8.7.3 dated 2021-10-11 and 0.8.7.4 dated 2026-01-13
DESCRIPTION | 14 MD5 | 27 - NEWS | 6 R/callTrust.R | 3 R/trustOptim-package.R |only R/trustOptim.R | 52 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 17 inst/doc/trustOptim-demo.R | 6 inst/doc/trustOptim-demo.html | 725 +++++++++++++++++++++++++++------- inst/doc/trustOptim-quick.R | 2 inst/doc/trustOptim-quick.html | 871 ++++++++++++++++++++++++++--------------- man/trustOptim-package.Rd |only man/trustOptim.Rd | 3 tests/testthat/test_binary.R | 2 16 files changed, 1206 insertions(+), 522 deletions(-)
Title: Recurrent Neural Network
Description: Implementation of a Recurrent Neural Network architectures in native R, including Long Short-Term Memory (Hochreiter and Schmidhuber, <doi:10.1162/neco.1997.9.8.1735>), Gated Recurrent Unit (Chung et al.) and vanilla RNN.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between rnn versions 1.9.0 dated 2023-04-21 and 1.9.1 dated 2026-01-13
DESCRIPTION | 15 ++++++++------- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 7 +++++++ R/rnn.R | 3 +-- README.md | 4 +--- build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/GRU_units.Rmd | 2 -- inst/doc/GRU_units.html | 10 ++++------ inst/doc/LSTM_units.html | 8 ++++---- inst/doc/basic_rnn.html | 25 +++++++++++++------------ inst/doc/rnn.R | 4 ++-- inst/doc/rnn.html | 41 +++++++++++++++++++++-------------------- inst/doc/rnn_units.html | 8 ++++---- inst/doc/simple_attention.R | 2 +- inst/doc/simple_attention.Rmd | 4 ++-- inst/doc/simple_attention.html | 28 +++++++++++++--------------- inst/doc/sinus.html | 7 ++++--- man/rnn.Rd | 5 +---- vignettes/GRU_units.Rmd | 2 -- vignettes/simple_attention.Rmd | 4 ++-- 21 files changed, 109 insertions(+), 112 deletions(-)
Title: Multivariate Normality Tests
Description: A comprehensive suite for assessing multivariate normality using six statistical tests
(Mardia, Henze–Zirkler, Henze–Wagner, Royston, Doornik–Hansen, Energy).
Also includes univariate diagnostics, bivariate density visualization, robust outlier
detection, power transformations (e.g., Box–Cox, Yeo–Johnson), and imputation strategies
("mean", "median", "mice") for handling missing data. Bootstrap resampling is supported
for selected tests to improve p-value accuracy in small samples.
Diagnostic plots are available via both 'ggplot2' and interactive 'plotly' visualizations. See Korkmaz et al. (2014) <https://journal.r-project.org/articles/RJ-2014-031/RJ-2014-031.pdf>.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut],
Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 6.2 dated 2025-10-10 and 6.3 dated 2026-01-13
DESCRIPTION | 19 ++-- MD5 | 20 ++-- R/mv_outlier.R | 18 +++- R/mvn.R | 45 ++++++---- R/power_transform.R | 34 ++++--- inst/CITATION | 2 inst/mvn-shiny-app/rsconnect/shinyapps.io/biosoft/mvn-shiny-app.dcf | 2 man/mv_outlier.Rd | 3 man/mvn.Rd | 5 - tests |only 10 files changed, 94 insertions(+), 54 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between maotai versions 0.2.7 dated 2025-09-24 and 0.3.0 dated 2026-01-13
maotai-0.2.7/maotai/R/later_findmed.R |only maotai-0.2.7/maotai/R/later_install_scipy.R |only maotai-0.2.7/maotai/R/later_matrix1F1.R |only maotai-0.2.7/maotai/R/later_matrix2F1.R |only maotai-0.2.7/maotai/R/later_mbeta.R |only maotai-0.2.7/maotai/R/later_mgamma.R |only maotai-0.2.7/maotai/R/later_scalar0F1.R |only maotai-0.2.7/maotai/R/later_scalar1F1.R |only maotai-0.2.7/maotai/R/later_scalar2F1.R |only maotai-0.2.7/maotai/R/later_scalarpFq.R |only maotai-0.2.7/maotai/R/lgpa.R |only maotai-0.2.7/maotai/man/lgpa.Rd |only maotai-0.3.0/maotai/DESCRIPTION | 12 +-- maotai-0.3.0/maotai/MD5 | 37 ++++------- maotai-0.3.0/maotai/NAMESPACE | 3 maotai-0.3.0/maotai/NEWS.md | 4 + maotai-0.3.0/maotai/R/RcppExports.R | 8 ++ maotai-0.3.0/maotai/R/bwproj.R |only maotai-0.3.0/maotai/R/later_caml_mean.R |only maotai-0.3.0/maotai/R/movMF_info.R | 6 + maotai-0.3.0/maotai/R/package-maotai.R | 1 maotai-0.3.0/maotai/R/zzz.R | 14 +++- maotai-0.3.0/maotai/build/partial.rdb |binary maotai-0.3.0/maotai/man/bwproj.Rd |only maotai-0.3.0/maotai/man/movMF_info.Rd | 1 maotai-0.3.0/maotai/src/RcppExports.cpp | 43 +++++++++++++ maotai-0.3.0/maotai/src/cpp_BuresWassersteinProjection.cpp |only maotai-0.3.0/maotai/src/cpp_caml.cpp |only 28 files changed, 92 insertions(+), 37 deletions(-)
Title: bartMachine JARs
Description: These are bartMachine's Java dependency libraries. Note: this package has no functionality of its own and should not be installed as a standalone package without bartMachine.
Author: Adam Kapelner [aut, cre] ,
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachineJARs versions 1.2.1 dated 2022-09-19 and 1.2.2 dated 2026-01-13
bartMachineJARs-1.2.1/bartMachineJARs/inst/java/fastutil-core-8.5.8.jar |only bartMachineJARs-1.2.2/bartMachineJARs/DESCRIPTION | 19 +++-- bartMachineJARs-1.2.2/bartMachineJARs/MD5 | 12 +-- bartMachineJARs-1.2.2/bartMachineJARs/NAMESPACE | 2 bartMachineJARs-1.2.2/bartMachineJARs/R/onLoad.R | 6 - bartMachineJARs-1.2.2/bartMachineJARs/inst/COPYRIGHTS | 37 ++++------ bartMachineJARs-1.2.2/bartMachineJARs/inst/java/fastutil-core-8.5.18.jar |only bartMachineJARs-1.2.2/bartMachineJARs/java/README | 14 +-- 8 files changed, 46 insertions(+), 44 deletions(-)
More information about bartMachineJARs at CRAN
Permanent link
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre] ,
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.9.0 dated 2025-12-17 and 0.9.1 dated 2026-01-13
DESCRIPTION | 6 MD5 | 38 NEWS.md | 5 R/auk-rollup.R | 30 R/data.R | 14 build/vignette.rds |binary data/ebird_taxonomy.rda |binary inst/doc/auk.R | 2 inst/doc/auk.Rmd | 2 inst/doc/auk.html | 212 ++--- inst/extdata/ebd-rollup-ex.txt | 46 - inst/extdata/ebd-sample.txt | 802 +++++++++---------- inst/extdata/zerofill-ex_ebd.txt | 536 ++++++------ inst/extdata/zerofill-ex_sampling.txt | 1417 +++++++++++++++++----------------- man/auk_rollup.Rd | 8 man/ebird_taxonomy.Rd | 14 tests/testthat/test_auk-filter.r | 10 tests/testthat/test_auk-keep-drop.r | 6 tests/testthat/test_auk-select.r | 2 vignettes/auk.Rmd | 2 20 files changed, 1623 insertions(+), 1529 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 <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.12 dated 2025-12-20 and 0.2.0 dated 2026-01-13
DESCRIPTION | 8 ++--- MD5 | 37 +++++++++++++++---------- NAMESPACE | 3 ++ NEWS.md | 9 ++++++ R/GE.R |only R/LONBGLSS.R | 34 +++++++++++++++++++++-- R/LONBGLSS_1.R | 34 +++++++++++++++++++++-- R/LONRBGLSS.R | 33 ++++++++++++++++++++--- R/LONRBGLSS_1.R | 35 +++++++++++++++++++++--- R/data.R | 4 +- R/make_Zblock.R |only R/mixedBayes.R | 66 +++++++++++++++++++++++----------------------- R/predict_mixedBayes.R |only R/reformat.R |only R/selection.R | 6 +--- R/selection_nonsparse.R | 15 +++++----- R/selection_sparse.R | 4 -- README.md | 50 ++++++++++++++++++++++++++++++++-- man/GE.Rd |only man/data.Rd | 4 ++ man/mixedBayes.Rd | 34 +++++++++++++++-------- man/predict_mixedBayes.Rd |only man/reformat.Rd |only 23 files changed, 279 insertions(+), 97 deletions(-)