Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre] ,
Dong Wang [ths],
Yuan Miao [ths]
Maintainer: Yuxuan He <heyuxuan0525@outlook.com>
Diff between Nematode versions 0.3.0 dated 2026-04-07 and 0.3.1 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/nematode_metabolic_footprints.R | 8 ++++---- README.md | 5 ++++- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Make Your 'targets' Pipelines into a Package
Description: Runs 'targets' pipelines bundled inside a package and caches
the results in the R user cache directory, so that users of the package
do not need to rerun the pipeline themselves. Package authors can update
the cached results at any time by releasing a new package version.
Author: Mizuki Uchida [aut, cre, cph]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
This is a re-admission after prior archival of version 0.1.1 dated 2025-06-22
Diff between tarchives versions 0.1.1 dated 2025-06-22 and 0.2.0 dated 2026-07-12
DESCRIPTION | 26 +- LICENSE | 4 MD5 | 84 ++++-- NAMESPACE | 30 +- NEWS.md | 14 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/tar_archive.R | 106 +++++++- R/tar_archive_pipelines.R |only R/tar_destroy_archive.R |only R/tar_load_archive.R |only R/tar_make_archive.R | 12 R/tar_manifest_archive.R |only R/tar_meta_archive.R |only R/tar_read_archive.R | 19 + R/tar_source_archive.R | 13 - R/tar_target_archive.R | 87 ++++-- R/tarchives-package.R | 1 R/use_tarchives.R | 29 ++ README.md | 13 - inst/tarchives/R/utils.R | 10 inst/tarchives/example-model/_targets.R | 4 inst/tarchives/example-plot/R/plot.R | 13 - inst/tarchives/example-plot/_targets.R | 2 man/tar_archive.Rd | 143 ++++++----- man/tar_archive_pipelines.Rd |only man/tar_archive_script.Rd | 94 +++---- man/tar_archive_store.Rd | 62 ++-- man/tar_destroy_archive.Rd |only man/tar_load_archive.Rd |only man/tar_make_archive.Rd | 349 ++++++++++++++-------------- man/tar_manifest_archive.Rd |only man/tar_meta_archive.Rd |only man/tar_read_archive.Rd | 16 + man/tar_source_archive.Rd | 72 +++-- man/tar_target_archive.Rd | 37 ++ man/tarchives-package.Rd | 44 ++- man/use_tarchives.Rd | 54 ++-- tests/testthat/_snaps |only tests/testthat/setup.R |only tests/testthat/test-tar_archive.R | 5 tests/testthat/test-tar_archive_pipelines.R |only tests/testthat/test-tar_destroy_archive.R |only tests/testthat/test-tar_load_archive.R |only tests/testthat/test-tar_make_archive.R | 58 +++- tests/testthat/test-tar_manifest_archive.R |only tests/testthat/test-tar_meta_archive.R |only tests/testthat/test-tar_read_archive.R | 11 tests/testthat/test-tar_source_archive.R | 28 +- tests/testthat/test-tar_target_archive.R |only tests/testthat/test-use_tarchives.R |only 51 files changed, 896 insertions(+), 544 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.4-1 dated 2026-06-06 and 1.4-2 dated 2026-07-12
DESCRIPTION | 7 +++---- MD5 | 18 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary cleanup | 4 ++++ inst/NEWS.Rd | 8 ++++++++ inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.pdf |binary tests/bugfix-tests.R | 2 +- tests/bugfix-tests.Rout.save | 6 +++--- 10 files changed, 28 insertions(+), 17 deletions(-)
Title: Isotope Origin Clustering and Assignment Tools
Description: This resource provides tools to create, compare, and post-process
spatial isotope assignment models of animal origin. It generates
probability-of-origin maps for individuals based on user-provided tissue and
environment isotope values (e.g., as generated by IsoMAP, Bowen et al. [2013]
<doi:10.1111/2041-210X.12147>) using the framework established in Bowen et al.
(2010) <doi:10.1146/annurev-earth-040809-152429>). The package 'isocat' can then
quantitatively compare and cluster these maps to group individuals by
similar origin. It also includes techniques for applying four approaches
(cumulative sum, odds ratio, quantile only, and quantile simulation) with
which users can summarize geographic origins and probable distance traveled
by individuals. Campbell et al. [2020] establishes several of the functions
included in this package <doi:10.1515/ami-2020-0004>.
Author: Caitlin Campbell [aut, cre]
Maintainer: Caitlin Campbell <caitjcampbell@gmail.com>
Diff between isocat versions 1.0.0 dated 2026-07-09 and 1.0.1 dated 2026-07-12
DESCRIPTION | 6 +- MD5 | 20 ++++----- NEWS.md | 56 ++++++++++++++++++++++----- R/isotopeAssignmentModel.R | 2 R/schoenersD.R | 13 +++--- R/simmatrixMaker.R | 4 - README.md | 5 ++ inst/doc/isocat.html | 7 +-- tests/testthat/helper-isocat.R | 22 ++++++++++ tests/testthat/test-isotopeAssignmentModel.R | 12 +++++ tests/testthat/test-simmatrix.R | 43 ++++++++++++++++++++ 11 files changed, 156 insertions(+), 34 deletions(-)
Title: Set Alpha Based on Sample Size Using Bayes Factors
Description: Sets the alpha level for coefficients in a regression model
as a decreasing function of the sample size through the use of
Jeffreys' Approximate Bayes factor. You tell alphaN() your sample
size, and it tells you to which value you must lower alpha to avoid
Lindley's Paradox. For details, see Wulff and Taylor (2024)
<doi:10.1177/14761270231214429>. Alpha can also be calibrated to the
effect-size and moment Bayes factors of Klauer, Meyer-Grant, and
Kellen (2024) <doi:10.3758/s13423-024-02612-2>, which center the
alternative hypothesis on an effect size of your choosing.
Author: Jesper Wulff [aut, cre] ,
Luke Taylor [aut]
Maintainer: Jesper Wulff <jwulff@econ.au.dk>
Diff between alphaN versions 0.1.2 dated 2025-07-13 and 0.2.0 dated 2026-07-12
DESCRIPTION | 17 +++-- MD5 | 61 +++++++++++--------- NAMESPACE | 4 + NEWS.md | 53 +++++++++++++++++ R/JAB.R | 32 ++++++---- R/JAB_plot.R | 31 ++-------- R/JABp.R | 33 +++++++--- R/JABt.R | 19 ++---- R/alphaN.R | 86 +++++++++++++++++++++++----- R/alphaN_plot.R | 29 ++++++--- R/helper_functions.R | 35 ++++++++++- R/klauer.R |only README.md | 106 ++++++++++++++++++++++++++++++++++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 53 +++++++++-------- inst/doc/intro-alphaN.R | 12 +++ inst/doc/intro-alphaN.Rmd | 38 ++++++++++-- inst/doc/intro-alphaN.html | 79 +++++++++++++++++++------- man/JAB.Rd | 8 +- man/JAB_plot.Rd | 14 ++-- man/JABp.Rd | 13 ++-- man/JABt.Rd | 9 +- man/alphaN.Rd | 69 +++++++++++++++++++--- man/alphaN_plot.Rd | 5 + man/figures/README-JAB-plot-1.png |only man/figures/README-alphaN-plot-1.png |only tests/testthat/test-JAB.R | 33 ++++++++++ tests/testthat/test-JABp.R | 11 +++ tests/testthat/test-JABt.R | 21 ++++++ tests/testthat/test-alphaN.R | 25 ++++++++ tests/testthat/test-klauer.R |only tests/testthat/test-plots.R |only vignettes/intro-alphaN.Rmd | 38 ++++++++++-- 35 files changed, 735 insertions(+), 199 deletions(-)
Title: Robust Covariance Matrix Estimators
Description: Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic
robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC)
covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC)
covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators);
clustered covariances (one-way and multi-way); panel and panel-corrected covariances;
outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are
applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted
to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>,
Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Author: Achim Zeileis [aut, cre] ,
Thomas Lumley [aut] ,
Nathaniel Graham [ctb] ,
Susanne Koell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 3.1-1 dated 2024-09-15 and 3.1-2 dated 2026-07-12
DESCRIPTION | 15 +- MD5 | 50 ++++---- NAMESPACE | 1 NEWS.md | 14 ++ R/bread.R | 4 R/estfun.R | 20 +++ R/vcovHC.R | 1 R/vcovPC.R | 1 README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/sandwich-CL.R | 52 +++++--- inst/doc/sandwich-CL.Rnw | 7 + inst/doc/sandwich-CL.pdf |binary inst/doc/sandwich-OOP.R | 2 inst/doc/sandwich-OOP.Rnw | 2 inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.R | 2 inst/doc/sandwich.Rnw | 4 inst/doc/sandwich.pdf |binary man/figures/README-sandwich.svg | 232 ++++++++++++++++++---------------------- vignettes/hac.bib | 20 +-- vignettes/sandwich-CL.Rnw | 7 + vignettes/sandwich-CL.Rout.save | 3 vignettes/sandwich-OOP.Rnw | 2 vignettes/sandwich.Rnw | 4 26 files changed, 243 insertions(+), 206 deletions(-)
Title: Simultaneous Selection by Trait and WAASB Index
Description: This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the 'metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the 'metan' and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a c [...truncated...]
Author: Ali Arminian [aut, cre, cph]
Maintainer: Ali Arminian <abeyran@gmail.com>
Diff between rYWAASB versions 0.4 dated 2026-06-10 and 0.4.1 dated 2026-07-12
DESCRIPTION | 14 ++-- MD5 | 22 +++---- NEWS.md | 3 R/PCA_biplot.R | 3 R/bar_plot1.R | 2 R/bar_plot2.R | 2 R/nbclust.R | 2 R/ranki.R | 2 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/rYWAASB_manual.html | 134 +++++++++++++++++++++++-------------------- man/PCA_biplot.Rd | 1 12 files changed, 103 insertions(+), 82 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-27 dated 2026-03-13 and 1.2-28 dated 2026-07-12
partykit-1.2-27/partykit/tests/Rplots.pdf |only partykit-1.2-28/partykit/DESCRIPTION | 9 - partykit-1.2-28/partykit/MD5 | 73 +++++++------- partykit-1.2-28/partykit/R/modelparty.R | 4 partykit-1.2-28/partykit/R/party.R | 8 - partykit-1.2-28/partykit/R/simpleparty.R | 10 - partykit-1.2-28/partykit/build/partial.rdb |binary partykit-1.2-28/partykit/build/vignette.rds |binary partykit-1.2-28/partykit/inst/NEWS.Rd | 8 + partykit-1.2-28/partykit/inst/doc/constparty.R | 11 ++ partykit-1.2-28/partykit/inst/doc/constparty.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/constparty.pdf |binary partykit-1.2-28/partykit/inst/doc/ctree.R | 11 ++ partykit-1.2-28/partykit/inst/doc/ctree.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/ctree.pdf |binary partykit-1.2-28/partykit/inst/doc/mob.R | 11 ++ partykit-1.2-28/partykit/inst/doc/mob.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/mob.pdf |binary partykit-1.2-28/partykit/inst/doc/partykit.R | 11 ++ partykit-1.2-28/partykit/inst/doc/partykit.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/partykit.pdf |binary partykit-1.2-28/partykit/tests/bugfixes.R | 17 +-- partykit-1.2-28/partykit/tests/bugfixes.Rout.save | 21 ++-- partykit-1.2-28/partykit/tests/constparty.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-MIA.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-cforest.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-ctree.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-glmtree.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-nmax.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-node.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-party.Rout.save | 76 +++++++-------- partykit-1.2-28/partykit/tests/regtest-split.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-weights.Rout.save | 4 partykit-1.2-28/partykit/vignettes/constparty.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/ctree.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/mob.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/partykit.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/partykit.Rout.save | 11 +- 38 files changed, 285 insertions(+), 136 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut] ,
Carolin Strobl [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-20 dated 2026-03-26 and 1.3-21 dated 2026-07-12
DESCRIPTION | 9 +-- MD5 | 96 ++++++++++++++++---------------- R/AAA.R | 2 R/Classes.R | 2 R/ConditionalTree.R | 2 R/Plot.R | 2 R/Predict.R | 2 R/Print.R | 2 R/RandomForest.R | 2 R/Utils.R | 2 R/Variables.R | 2 R/zInitMethods.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/MOB.R | 12 ++++ inst/doc/MOB.Rnw | 13 ++++ inst/doc/MOB.pdf |binary inst/doc/party.R | 20 +++++- inst/doc/party.Rnw | 13 ++++ inst/doc/party.pdf |binary src/Classes.c | 4 - src/Convenience.c | 4 - src/Distributions.c | 4 - src/IndependenceTest.c | 4 - src/LinearStatistic.c | 4 - src/Node.c | 4 - src/Predict.c | 4 - src/RandomForest.c | 4 - src/S3Classes.c | 4 - src/Splits.c | 4 - src/SurrogateSplits.c | 4 - src/TestStatistic.c | 4 - src/TreeGrow.c | 4 - src/Utils.c | 4 - tests/Distributions.Rout.save | 8 +- tests/LinearStatistic-regtest.Rout.save | 8 +- tests/Predict-regtest.Rout.save | 8 +- tests/RandomForest-regtest.Rout.save | 8 +- tests/TestStatistic-regtest.Rout.save | 8 +- tests/TreeGrow-regtest.Rout.save | 8 +- tests/Utils-regtest.Rout.save | 8 +- tests/bugfixes.R | 13 ++-- tests/bugfixes.Rout.save | 21 +++---- tests/mob.Rout.save | 8 +- vignettes/MOB.Rnw | 13 ++++ vignettes/MOB.Rout.save | 19 ++++-- vignettes/party.Rnw | 13 ++++ vignettes/party.Rout.save | 11 +++ 49 files changed, 246 insertions(+), 153 deletions(-)
Title: Access the U.S. National Provider Identifier Registry API
Description: Access the United States National Provider Identifier
Registry API <https://npiregistry.cms.hhs.gov/api/>. Obtain and transform
administrative data linked to a specific individual or organizational
healthcare provider, or perform advanced searches based on provider name,
location, type of service, credentials, and other attributes exposed by
the API.
Author: Frank Farach [cre, aut, cph] ,
Sam Parmar [ctb],
Matthias Grenie [rev] ,
Emily C. Zabor [rev]
Maintainer: Frank Farach <frank.farach@gmail.com>
Diff between npi versions 0.2.0 dated 2022-11-14 and 0.3.0 dated 2026-07-12
DESCRIPTION | 17 +- MD5 | 37 ++--- NEWS.md | 33 +++- R/extractors.R | 2 R/npi_results_s3.R | 147 ++++++++++++++++---- R/npi_search.R | 73 ++++++---- R/utils.R | 14 - README.md | 250 ++++++++++++++++------------------ build/vignette.rds |binary inst/CITATION | 13 - inst/doc/advanced-use.R | 2 inst/doc/advanced-use.html | 159 ++++++++++------------ inst/doc/npi.R | 2 inst/doc/npi.html | 281 +++++++++++++++++++-------------------- man/npi_search.Rd | 15 -- man/npi_summarize.Rd | 4 man/npi_summarize.npi_results.Rd | 4 tests/spelling.Rout.save |only tests/testthat/test-api.R | 40 +++++ tests/testthat/test-validators.R | 8 + 20 files changed, 626 insertions(+), 475 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] ,
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb],
Christian Ritz [ctb],
Christian B. Pipper [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-30 dated 2026-03-09 and 1.4-31 dated 2026-07-12
multcomp-1.4-30/multcomp/inst/NEWS |only multcomp-1.4-31/multcomp/DESCRIPTION | 9 - multcomp-1.4-31/multcomp/MD5 | 82 +++++----- multcomp-1.4-31/multcomp/R/contrMat.R | 2 multcomp-1.4-31/multcomp/R/expressions.R | 2 multcomp-1.4-31/multcomp/R/glht.R | 2 multcomp-1.4-31/multcomp/R/helpers.R | 2 multcomp-1.4-31/multcomp/R/maxsets.R | 2 multcomp-1.4-31/multcomp/R/mcp.R | 2 multcomp-1.4-31/multcomp/R/methods.R | 2 multcomp-1.4-31/multcomp/R/parm.R | 2 multcomp-1.4-31/multcomp/R/plot.R | 2 multcomp-1.4-31/multcomp/R/pqfunctions.R | 2 multcomp-1.4-31/multcomp/R/print.R | 2 multcomp-1.4-31/multcomp/build/partial.rdb |binary multcomp-1.4-31/multcomp/build/vignette.rds |binary multcomp-1.4-31/multcomp/data/cholesterol.rda |binary multcomp-1.4-31/multcomp/data/litter.rda |binary multcomp-1.4-31/multcomp/inst/NEWS.Rd | 8 multcomp-1.4-31/multcomp/inst/NEWS.old |only multcomp-1.4-31/multcomp/inst/doc/chfls1.R | 12 + multcomp-1.4-31/multcomp/inst/doc/chfls1.Rnw | 21 ++ multcomp-1.4-31/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.4-31/multcomp/inst/doc/generalsiminf.R | 12 + multcomp-1.4-31/multcomp/inst/doc/generalsiminf.Rnw | 19 ++ multcomp-1.4-31/multcomp/inst/doc/generalsiminf.pdf |binary multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.R | 12 + multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.Rnw | 17 +- multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.pdf |binary multcomp-1.4-31/multcomp/man/mmm.Rd | 4 multcomp-1.4-31/multcomp/tests/Examples/multcomp-Ex.Rout.save | 8 multcomp-1.4-31/multcomp/tests/bugfix.R | 4 multcomp-1.4-31/multcomp/tests/bugfix.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-Tukey.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-anova.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-interface-extended.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-interface.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-lme.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-mmm.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-survival.Rout.save | 4 multcomp-1.4-31/multcomp/vignettes/chfls1.Rnw | 21 ++ multcomp-1.4-31/multcomp/vignettes/generalsiminf.Rnw | 19 ++ multcomp-1.4-31/multcomp/vignettes/multcomp-examples.Rnw | 17 +- 43 files changed, 246 insertions(+), 101 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.1-2 dated 2025-09-22 and 2.1-3 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 7 +++++++ R/hcl_palettes.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/colorspace.html | 16 ++++++++-------- inst/doc/hcl-colors.R | 8 ++++---- inst/doc/hcl-colors.Rnw | 10 ++++++---- inst/doc/hcl-colors.pdf |binary vignettes/hcl-colors.Rnw | 10 ++++++---- vignettes/hcl-colors.Rout.save | 4 ++-- 12 files changed, 51 insertions(+), 40 deletions(-)
Title: 115 Data Sets from "Introductory Econometrics: A Modern
Approach, 8e" by Jeffrey M. Wooldridge
Description: Students learning both econometrics and R may find the introduction
to both challenging. The wooldridge data package aims to lighten the task by efficiently
loading any data set found in the text with a single command. Data sets have been
compressed to a fraction of their original size. Documentation files contain page numbers,
the original source, time of publication, and notes from the author suggesting avenues for
further analysis and research. If one needs an introduction to R model syntax, a
vignette contains solutions to examples from chapters of the text.
Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0),
and are backwards compatible with all previous versions of the text.
Author: Justin M. Shea [aut, cre],
Kennth H. Brown [ctb]
Maintainer: Justin M. Shea <jshea01@uic.edu>
Diff between wooldridge versions 1.4-4 dated 2024-12-04 and 1.4-7 dated 2026-07-12
DESCRIPTION | 14 MD5 | 58 +-- NEWS.md | 15 + R/approval.R | 2 R/beveridge.R | 8 R/catholic.R | 2 R/census2000.R | 2 R/countymurders.R | 2 R/econmath.R | 2 R/happiness.R | 10 R/jtrain98.R | 2 R/labsup.R | 2 R/meapsingle.R | 2 R/ncaa_rpi.R | 2 R/school93_98.R | 2 README.md | 23 - build/vignette.rds |binary inst/doc/Introductory-Econometrics-Examples.html | 343 +++++++++++------------ man/approval.Rd | 2 man/beveridge.Rd | 8 man/catholic.Rd | 2 man/census2000.Rd | 2 man/countymurders.Rd | 2 man/econmath.Rd | 2 man/happiness.Rd | 10 man/jtrain98.Rd | 2 man/labsup.Rd | 2 man/meapsingle.Rd | 2 man/ncaa_rpi.Rd | 2 man/school93_98.Rd | 2 30 files changed, 268 insertions(+), 261 deletions(-)
Title: R Interface to the 'OKX' REST API
Description: Provides lightweight R wrappers for the 'OKX' REST API, covering
endpoints for market data, trading, account management, asset balances,
and copy trading. The upstream API reference is available at
<https://www.okx.com/docs-v5/en/>.
Author: Oliver Zhou [aut, cre],
Lily Li [aut]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between okxr versions 0.4.5 dated 2026-05-08 and 0.4.7 dated 2026-07-12
DESCRIPTION | 8 MD5 | 125 ++++++------- NAMESPACE | 7 NEWS.md | 19 ++ R/def_constants.R | 209 ++++++++++++++++------ R/wrappers_get_account.R | 22 ++ R/wrappers_get_asset.R | 8 R/wrappers_get_market.R | 128 +++++++++++++ R/wrappers_post_trade.R | 167 +++++++++++++++-- README.md | 11 + man/dot-execute_get_action.Rd | 7 man/dot-gets.Rd | 4 man/dot-okx_default_tz.Rd | 4 man/dot-posts.Rd | 4 man/get_account_bill_types.Rd |only man/get_account_instruments.Rd | 6 man/get_account_interest_rate.Rd | 6 man/get_account_leverage_info.Rd | 7 man/get_account_max_withdrawal.Rd | 6 man/get_account_mmp_config.Rd | 6 man/get_account_position_risk.Rd | 6 man/get_account_precheck_set_delta_neutral.Rd | 6 man/get_account_set_account_switch_precheck.Rd | 6 man/get_account_subaccount_balances.Rd | 6 man/get_account_trade_fee.Rd | 2 man/get_asset_asset_valuation.Rd | 6 man/get_asset_bills.Rd | 3 man/get_asset_bills_history.Rd | 3 man/get_asset_non_tradable_assets.Rd | 6 man/get_copy_trade_instruments.Rd | 6 man/get_copy_trade_public_config.Rd | 5 man/get_market_block_ticker.Rd | 6 man/get_market_books.Rd | 7 man/get_market_books_rpi.Rd |only man/get_market_index_components.Rd | 6 man/get_market_platform_24_volume.Rd | 5 man/get_market_trades.Rd | 7 man/get_public_block_trades.Rd | 6 man/get_public_event_contract_events.Rd |only man/get_public_event_contract_markets.Rd |only man/get_public_event_contract_series.Rd |only man/get_public_funding_rate.Rd | 6 man/get_public_instrument_tick_bands.Rd | 2 man/get_public_instruments.Rd | 6 man/get_public_mm_instrument_types.Rd |only man/get_public_price_limit.Rd | 6 man/get_public_underlying.Rd | 6 man/get_trade_one_click_repay_currency_list_v2.Rd | 5 man/get_trade_orders_history_7d.Rd | 6 man/okxr-package.Rd | 1 man/post_account_set_account_level.Rd | 6 man/post_account_set_auto_loan.Rd | 6 man/post_account_set_auto_repay.Rd | 6 man/post_account_set_greeks.Rd | 6 man/post_account_set_position_mode.Rd | 6 man/post_trade_amend_algos.Rd | 3 man/post_trade_amend_batch_orders.Rd | 10 - man/post_trade_amend_order.Rd | 4 man/post_trade_batch_orders.Rd | 4 man/post_trade_cancel_all_after.Rd | 7 man/post_trade_cancel_batch_orders.Rd | 6 man/post_trade_order.Rd | 15 + man/post_trade_order_algo.Rd |only man/post_trade_order_precheck.Rd | 8 man/set_okxr_options.Rd | 4 tests/testthat/test-request-helpers.R | 6 tests/testthat/test-wrapper-queries.R | 102 ++++++++++ 67 files changed, 750 insertions(+), 333 deletions(-)
Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.5.6 dated 2025-12-07 and 1.5.8 dated 2026-07-12
nebula-1.5.6/nebula/data/sample_seurat.rda |only nebula-1.5.6/nebula/man/sample_seurat.Rd |only nebula-1.5.8/nebula/DESCRIPTION | 20 +- nebula-1.5.8/nebula/LICENSE |only nebula-1.5.8/nebula/MD5 | 49 +++--- nebula-1.5.8/nebula/NAMESPACE | 7 nebula-1.5.8/nebula/R/data.R | 28 +-- nebula-1.5.8/nebula/R/group_cell.R | 4 nebula-1.5.8/nebula/R/nbresidual.R | 4 nebula-1.5.8/nebula/R/nebula.R | 16 -- nebula-1.5.8/nebula/R/scToNeb.R | 24 ++- nebula-1.5.8/nebula/R/utils.R | 46 +++++ nebula-1.5.8/nebula/README.md | 164 +++++++++----------- nebula-1.5.8/nebula/build/partial.rdb |binary nebula-1.5.8/nebula/build/vignette.rds |binary nebula-1.5.8/nebula/inst/doc/nebula_example.R | 45 +++-- nebula-1.5.8/nebula/inst/doc/nebula_example.Rmd | 17 +- nebula-1.5.8/nebula/inst/doc/nebula_example.html | 90 ++++++----- nebula-1.5.8/nebula/inst/extdata |only nebula-1.5.8/nebula/man/group_cell.Rd | 75 ++++----- nebula-1.5.8/nebula/man/load_sample_seurat.Rd |only nebula-1.5.8/nebula/man/nbresidual.Rd | 77 +++++---- nebula-1.5.8/nebula/man/nebula.Rd | 183 +++++++++++------------ nebula-1.5.8/nebula/man/sample_data.Rd | 6 nebula-1.5.8/nebula/man/scToNeb.Rd | 89 +++++------ nebula-1.5.8/nebula/src/optimization.cpp | 6 nebula-1.5.8/nebula/tests |only nebula-1.5.8/nebula/vignettes/nebula_example.Rmd | 17 +- 28 files changed, 541 insertions(+), 426 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.1.2 dated 2026-05-20 and 1.1.3 dated 2026-07-12
DESCRIPTION | 8 MD5 | 18 - R/lmeb.R | 52 +++- inst/doc/lmebreed.gxe.html | 8 inst/doc/lmebreed.qg.R | 32 ++ inst/doc/lmebreed.qg.Rmd | 42 +++ inst/doc/lmebreed.qg.html | 427 +++++++++++++++++++++------------------ inst/doc/lmebreed.summaries.html | 4 man/lmeb.Rd | 44 +--- vignettes/lmebreed.qg.Rmd | 42 +++ 10 files changed, 423 insertions(+), 254 deletions(-)
Title: Kabaila and Giri (2009) Confidence Interval
Description: Computes a confidence interval for a specified linear combination of
the regression parameters in a linear regression model with iid normal
errors with unknown variance when there is uncertain prior information
that a distinct specified linear combination of the regression
parameters takes a specified number. This confidence interval, found by
numerical nonlinear constrained optimization, has the required minimum coverage
and utilizes this uncertain prior information through desirable
expected length properties. This confidence interval is proposed by
Kabaila, P. and Giri, K. (2009) <doi:10.1016/j.jspi.2009.03.018>.
Author: Nishika Ranathunga [aut],
Paul Kabaila [aut, cre]
Maintainer: Paul Kabaila <P.Kabaila@latrobe.edu.au>
Diff between ciuupi2 versions 1.0.1 dated 2021-03-11 and 1.0.2 dated 2026-07-12
DESCRIPTION | 9 +- MD5 | 8 +- R/optimize_knots.R | 21 ++--- build/vignette.rds |binary inst/doc/description-ciuupi2.html | 151 +++++++++++++++++++++++++++++--------- 5 files changed, 136 insertions(+), 53 deletions(-)