Title: Interactive Stability Analysis of Multi-Environment Trials
Description: A 'shiny' application for the stability analysis of
multi-environment trials of plant breeding with the package 'stability':
analyses of variance, Eberhart and Russell's and Finlay and Wilkinson's
regression, Wricke's, Shukla's, Kang's and Fox's statistics, Eskridge's
safety-first indices, Annicchiarico's, Lin and Binns' and Huehn's
statistics, AMMI analysis
and stability values, and the GGE biplot. Every analysis comes with its
tables, plots, the R code that repeats it and an interpretation specific to
the method, computed from the results; an optional longer written
interpretation can be requested from an external text service with the
user's own key.
Author: Muhammad Yaseen [aut, cre, cph] ,
Kent Eskridge [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between StabilityApp versions 0.1.0 dated 2024-11-01 and 1.0.0 dated 2026-11-10
StabilityApp-0.1.0/StabilityApp/R/StabilityApp.R |only StabilityApp-0.1.0/StabilityApp/inst/shinyapp |only StabilityApp-0.1.0/StabilityApp/tests/testthat/test-inst-apps.R |only StabilityApp-1.0.0/StabilityApp/DESCRIPTION | 67 ++-- StabilityApp-1.0.0/StabilityApp/MD5 | 66 ++-- StabilityApp-1.0.0/StabilityApp/NAMESPACE | 20 - StabilityApp-1.0.0/StabilityApp/NEWS.md | 46 ++ StabilityApp-1.0.0/StabilityApp/R/StabilityApp-package.R |only StabilityApp-1.0.0/StabilityApp/R/app.R |only StabilityApp-1.0.0/StabilityApp/R/app_module.R |only StabilityApp-1.0.0/StabilityApp/R/common-validate.R |only StabilityApp-1.0.0/StabilityApp/R/prompt.R |only StabilityApp-1.0.0/StabilityApp/R/registry.R |only StabilityApp-1.0.0/StabilityApp/R/services.R |only StabilityApp-1.0.0/StabilityApp/README.md | 164 +++++----- StabilityApp-1.0.0/StabilityApp/build |only StabilityApp-1.0.0/StabilityApp/inst/CITATION | 30 + StabilityApp-1.0.0/StabilityApp/inst/doc |only StabilityApp-1.0.0/StabilityApp/inst/services |only StabilityApp-1.0.0/StabilityApp/man/StabilityApp-package.Rd |only StabilityApp-1.0.0/StabilityApp/man/StabilityApp.Rd | 53 ++- StabilityApp-1.0.0/StabilityApp/man/sa_prompt.Rd |only StabilityApp-1.0.0/StabilityApp/man/sa_services.Rd |only StabilityApp-1.0.0/StabilityApp/tests/testthat.R | 8 StabilityApp-1.0.0/StabilityApp/tests/testthat/Rplots.pdf |only StabilityApp-1.0.0/StabilityApp/tests/testthat/helper-common.R |only StabilityApp-1.0.0/StabilityApp/tests/testthat/test-app.R |only StabilityApp-1.0.0/StabilityApp/tests/testthat/test-prompt.R |only StabilityApp-1.0.0/StabilityApp/tests/testthat/test-services.R |only StabilityApp-1.0.0/StabilityApp/vignettes |only 30 files changed, 294 insertions(+), 160 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a
headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
Posit Software, PBC [cph, fnd] ,
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinytest2 versions 0.5.1 dated 2026-02-25 and 0.6.0 dated 2026-11-10
shinytest2-0.5.1/shinytest2/man/figures/logo.svg |only shinytest2-0.6.0/shinytest2/DESCRIPTION | 21 shinytest2-0.6.0/shinytest2/MD5 | 235 - shinytest2-0.6.0/shinytest2/NAMESPACE | 26 shinytest2-0.6.0/shinytest2/NEWS.md | 58 shinytest2-0.6.0/shinytest2/R/R6-helper.R | 27 shinytest2-0.6.0/shinytest2/R/app-driver-dir.R | 2 shinytest2-0.6.0/shinytest2/R/app-driver-expect-download.R | 38 shinytest2-0.6.0/shinytest2/R/app-driver-expect-js.R | 4 shinytest2-0.6.0/shinytest2/R/app-driver-expect-screenshot.R | 2 shinytest2-0.6.0/shinytest2/R/app-driver-expect-unique-names.R | 32 shinytest2-0.6.0/shinytest2/R/app-driver-expect-values.R | 4 shinytest2-0.6.0/shinytest2/R/app-driver-get-log.R | 62 shinytest2-0.6.0/shinytest2/R/app-driver-initialize.R | 14 shinytest2-0.6.0/shinytest2/R/app-driver-log-message.R | 15 shinytest2-0.6.0/shinytest2/R/app-driver-message.R | 28 shinytest2-0.6.0/shinytest2/R/app-driver-node.R | 58 shinytest2-0.6.0/shinytest2/R/app-driver-set-inputs.R | 46 shinytest2-0.6.0/shinytest2/R/app-driver-start.R | 66 shinytest2-0.6.0/shinytest2/R/app-driver-stop.R | 23 shinytest2-0.6.0/shinytest2/R/app-driver-timeout.R | 24 shinytest2-0.6.0/shinytest2/R/app-driver-upload-file.R | 32 shinytest2-0.6.0/shinytest2/R/app-driver-variant.R | 2 shinytest2-0.6.0/shinytest2/R/app-driver-wait.R | 75 shinytest2-0.6.0/shinytest2/R/app-driver-window.R | 12 shinytest2-0.6.0/shinytest2/R/app-driver.R | 70 shinytest2-0.6.0/shinytest2/R/chromote-methods.R | 122 shinytest2-0.6.0/shinytest2/R/compare-screenshot-threshold.R | 24 shinytest2-0.6.0/shinytest2/R/httr2.R | 2 shinytest2-0.6.0/shinytest2/R/migrate.R | 432 +- shinytest2-0.6.0/shinytest2/R/pkg.R | 14 shinytest2-0.6.0/shinytest2/R/platform.R | 23 shinytest2-0.6.0/shinytest2/R/record-test.R | 10 shinytest2-0.6.0/shinytest2/R/save-app.R | 63 shinytest2-0.6.0/shinytest2/R/shiny-browser.R | 25 shinytest2-0.6.0/shinytest2/R/shinytest2-logs.R | 31 shinytest2-0.6.0/shinytest2/R/shinytest2-package.R | 3 shinytest2-0.6.0/shinytest2/R/test-app.R | 10 shinytest2-0.6.0/shinytest2/R/use.R | 2 shinytest2-0.6.0/shinytest2/R/utils.R | 10 shinytest2-0.6.0/shinytest2/README.md | 6 shinytest2-0.6.0/shinytest2/build/vignette.rds |binary shinytest2-0.6.0/shinytest2/inst/doc/in-depth.R | 6 shinytest2-0.6.0/shinytest2/inst/doc/in-depth.Rmd | 22 shinytest2-0.6.0/shinytest2/inst/doc/in-depth.html | 4 shinytest2-0.6.0/shinytest2/inst/doc/robust.R | 4 shinytest2-0.6.0/shinytest2/inst/doc/robust.Rmd | 13 shinytest2-0.6.0/shinytest2/inst/doc/robust.html | 2 shinytest2-0.6.0/shinytest2/inst/doc/shinytest2.R | 12 shinytest2-0.6.0/shinytest2/inst/doc/shinytest2.Rmd | 44 shinytest2-0.6.0/shinytest2/inst/doc/shinytest2.html | 14 shinytest2-0.6.0/shinytest2/inst/doc/use-application-audit.R | 6 shinytest2-0.6.0/shinytest2/inst/doc/use-application-audit.Rmd | 21 shinytest2-0.6.0/shinytest2/inst/doc/use-application-audit.html | 4 shinytest2-0.6.0/shinytest2/inst/doc/use-ci.R | 2 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shinytest2-0.6.0/shinytest2/tests/testthat/test-app-image.R | 17 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-logs.R | 1 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-renviron.R |only shinytest2-0.6.0/shinytest2/tests/testthat/test-app-screenshot-size.R | 7 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-shiny.R | 14 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-start.R |only shinytest2-0.6.0/shinytest2/tests/testthat/test-app-stop.R | 33 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-timeout.R | 88 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-upload.R | 7 shinytest2-0.6.0/shinytest2/tests/testthat/test-app-wait-get-value.R | 1 shinytest2-0.6.0/shinytest2/tests/testthat/test-known-names.R | 8 shinytest2-0.6.0/shinytest2/tests/testthat/test-pkg.R |only shinytest2-0.6.0/shinytest2/tests/testthat/test-shinytest2.R | 11 shinytest2-0.6.0/shinytest2/tests/testthat/test-stop.R | 33 shinytest2-0.6.0/shinytest2/tests/testthat/test-test-app-reporter.R | 10 shinytest2-0.6.0/shinytest2/tests/testthat/test-url.R | 50 shinytest2-0.6.0/shinytest2/vignettes/images/diffviewer-1.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/gremlins-inject.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/gremlins-logs.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/gremlins-slider-handle.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/gremlins-start.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/plot-app.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/record-name.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/record-simple-app-2.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/record-simple-app.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/screenshot-exports-app.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/screenshot-recorder-random-seed.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/shinytest2-loadtest.png |binary shinytest2-0.6.0/shinytest2/vignettes/images/shinytest2-shinyloadtest-optimized.png |binary shinytest2-0.6.0/shinytest2/vignettes/in-depth.Rmd | 22 shinytest2-0.6.0/shinytest2/vignettes/robust.Rmd | 13 shinytest2-0.6.0/shinytest2/vignettes/shinytest2.Rmd | 44 shinytest2-0.6.0/shinytest2/vignettes/use-application-audit.Rmd | 21 shinytest2-0.6.0/shinytest2/vignettes/use-ci.Rmd | 6 shinytest2-0.6.0/shinytest2/vignettes/use-package.Rmd | 97 shinytest2-0.6.0/shinytest2/vignettes/using-monkey-testing.Rmd | 56 shinytest2-0.6.0/shinytest2/vignettes/z-migration.Rmd | 3 shinytest2-0.6.0/shinytest2/vignettes/zzz-faq.Rmd | 71 124 files changed, 3370 insertions(+), 1873 deletions(-)
Title: An 'Shiny' App for Exploring scRNA-seq Data Processed in
'Seurat'
Description: A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Author: Yongchao Zhang [aut, cre]
Maintainer: Yongchao Zhang <zhangyongchao@nibs.ac.cn>
Diff between SeuratExplorer versions 0.1.8 dated 2026-09-01 and 0.1.10 dated 2026-11-10
DESCRIPTION | 24 MD5 | 18 NAMESPACE | 58 R/functions.R | 1021 +++++++++++- R/launch.R | 83 R/server.R | 2862 +++++++++++++++++++++++----------- R/ui.R | 3680 +++++++++++++++++++++++--------------------- man/cellRatioPlot.Rd | 32 man/launchSeuratExplorer.Rd | 20 man/param_group_collapse.Rd | 3 10 files changed, 5056 insertions(+), 2745 deletions(-)
More information about SeuratExplorer at CRAN
Permanent link
Title: Trends and Indices for Monitoring Data
Description: The TRIM model is widely used for estimating growth and decline of
animal populations based on (possibly sparsely available) count data. The
current package is a reimplementation of the original TRIM software developed
at Statistics Netherlands by Jeroen Pannekoek.
See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d>
for more information about TRIM.
Author: Patrick Bogaart [aut, cre] ,
Mark van der Loo [aut],
Jeroen Pannekoek [aut],
Statistics Netherlands [cph]
Maintainer: Patrick Bogaart <rtrim@cbs.nl>
Diff between rtrim versions 2.3.1 dated 2026-02-13 and 2.4.0 dated 2026-11-10
DESCRIPTION | 14 MD5 | 149 NAMESPACE | 163 NEWS | 164 R/data_checks.R | 2723 +++++++++++++--- R/oystercatcher.R | 46 R/parse_outfile.R | 1022 +++--- R/read_icv.R | 114 R/read_tcf.R | 764 ++-- R/read_tdf.R | 326 - R/rtrim-pkg.R | 110 R/skylark.R | 82 R/trim.R | 951 ++--- R/trim_estimate.R | 235 - R/trim_gof.R | 212 - R/trim_heatmap.R | 338 +- R/trim_index.R | 1359 ++++---- R/trim_overall.R | 941 ++--- R/trim_post.R | 1878 +++++------ R/trim_refine.R | 547 +-- R/trim_smooth.R | 445 +- R/trim_wald.R | 622 +-- R/trim_workhorse.R | 3980 ++++++++++++------------ R/trim_workhorse_241.R |only R/utils.R | 52 build/vignette.rds |binary inst/doc/FAQ.html | 1556 ++++----- inst/doc/Skylark_example.R | 173 - inst/doc/Skylark_example.Rmd | 411 +- inst/doc/Skylark_example.html | 1653 ++++----- inst/doc/TRIM_methods_v2.pdf.asis | 8 inst/doc/rtrim_2_extensions.R | 442 +- inst/doc/rtrim_2_extensions.Rmd | 860 ++--- inst/doc/rtrim_2_extensions.html | 1931 +++++------ inst/doc/rtrim_confidence_intervals.R | 708 ++-- inst/doc/rtrim_confidence_intervals.Rmd | 990 ++--- inst/doc/rtrim_confidence_intervals.html | 1755 +++++----- inst/doc/rtrim_for_TRIM_users.R | 178 - inst/doc/rtrim_for_TRIM_users.Rmd | 436 +- inst/doc/rtrim_for_TRIM_users.html | 1305 +++---- inst/doc/taming_overdispersion.R | 296 - inst/doc/taming_overdispersion.Rmd | 466 +- inst/doc/taming_overdispersion.html | 1294 +++---- man/check_observations.Rd | 31 man/get_deletion.Rd |only man/overall.Rd | 2 man/pieces_from_changepoints.Rd |only man/read_tcf.Rd | 2 man/results.Rd | 8 man/rtrim-package.Rd | 2 man/set_trim_verbose.Rd | 2 man/trim.Rd | 1 man/trim_estimate.Rd | 9 man/trim_refine.Rd | 2 man/trim_workhorse.Rd | 36 man/trimcommand.Rd | 2 tests/testthat.R | 4 tests/testthat/outfiles/skylark-1a.tcf | 32 tests/testthat/outfiles/skylark-1c.tcf | 32 tests/testthat/outfiles/skylark-1d.tcf | 32 tests/testthat/outfiles/skylark-minimal.tcf | 24 tests/testthat/outfiles/skylark-model2-f.csv | 882 ++--- tests/testthat/outfiles/skylark_wt.dat | 880 ++--- tests/testthat/outfiles/skylark_yr.dat | 880 ++--- tests/testthat/outfiles/test_skylark_1a_to_2b.R | 402 +- tests/testthat/test_checks.R | 306 - tests/testthat/test_errors.R | 64 tests/testthat/test_tcf.R | 290 - tests/testthat/test_tdf.R | 100 tests/testthat/test_trim.R | 697 ++-- tests/testthat/test_utils.R | 20 vignettes/Skylark_example.Rmd | 411 +- vignettes/TRIM_methods_v2.pdf.asis | 8 vignettes/rtrim_2_extensions.Rmd | 860 ++--- vignettes/rtrim_confidence_intervals.Rmd | 990 ++--- vignettes/rtrim_for_TRIM_users.Rmd | 436 +- vignettes/taming_overdispersion.Rmd | 466 +- 77 files changed, 20958 insertions(+), 18654 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main references for rSPDE are Bolin, Simas and Xiong (2023) <doi:10.1080/10618600.2023.2231051> for the covariance-based method and Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537> for the operator-based rational approximation. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Finn Lindgren [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 2.6.0 dated 2026-08-31 and 2.7.0 dated 2026-11-10
DESCRIPTION | 14 MD5 | 125 ++- NAMESPACE | 10 NEWS.md | 128 +++ R/covariance.functions.R | 71 +- R/fractional.computations.R | 75 +- R/fractional.operators.R | 559 +++++++++++++--- R/inla_rspde.R | 451 ++++++++++-- R/inla_rspde_1d.R | 168 +++- R/inla_rspde_intrinsic.R | 17 R/inla_rspde_spacetime.R | 10 R/inla_safe.R | 15 R/inlabru_rspde.R | 99 ++ R/intrinsic.R | 216 ++---- R/posterior_crossvalidation.R | 145 ++-- R/print.summary.R | 33 R/rSPDE-package.R | 2 R/rational_wl2.R |only R/rspde_lme.R | 34 R/stationary1d.R | 197 ++++- R/sysdata.rda |binary R/util.R | 351 ++++++++-- inst/CITATION | 4 inst/doc/rSPDE_package.html | 4 man/bru_get_mapper.inla_rspde.Rd | 6 man/cross_validation.Rd | 13 man/fractional.operators.Rd | 38 + man/intrinsic.matern.operators.Rd | 44 - man/intrinsic.operators.Rd | 38 - man/matern.operators.Rd | 111 ++- man/matern.rational.Rd | 8 man/matern.rational.cov.Rd | 11 man/posterior_crossvalidation.Rd | 143 ---- man/posterior_crossvalidation.rspde_lme.Rd |only man/precision.intrinsicCBrSPDEobj.Rd | 18 man/predict.intrinsicCBrSPDEobj.Rd | 32 man/rational.coefficients.wl2.Rd |only man/rspde.cache.Rd |only man/rspde.intrinsic.Rd | 8 man/rspde.make.A.Rd | 7 man/rspde.make.index.Rd | 7 man/rspde.matern.Rd | 89 +- man/rspde.matern.precision.Rd | 10 man/rspde.matern.precision.opt.Rd | 11 man/rspde.matern1d.Rd | 66 + man/rspde.mesh.project.Rd | 16 man/rspde.wl2.table.Rd |only man/rspde.xmin.Rd |only man/spde.matern.operators.Rd | 58 + man/update.CBrSPDEobj.Rd | 14 man/update.intrinsicCBrSPDEobj.Rd | 18 man/update.rSPDEobj.Rd | 12 man/update_rational_coefficients.Rd |only man/variogram.intrinsic.spde.Rd | 40 - src |only tests/testthat/helper-inlabru.R |only tests/testthat/helper-optim-warnings.R |only tests/testthat/test-cross-validation-routing.R |only tests/testthat/test-positive-transformed-density.R |only tests/testthat/test.CBrSPDE.R | 2 tests/testthat/test.cgeneric_builtin.R | 6 tests/testthat/test.fractional.operators.R | 179 +++++ tests/testthat/test.inlabru_rspde.R | 4 tests/testthat/test.posterior_crossvalidation.R | 8 tests/testthat/test.posterior_crossvalidation_generic.R |only tests/testthat/test.rational.wl2.R |only tests/testthat/test.rational.wl2.inla.R |only tests/testthat/test.rspde_lme_predict_precompute.R | 8 tests/testthat/test_hybrid_spde.R | 18 tests/testthat/test_inla_rspde_hybrid.R | 61 + 70 files changed, 2846 insertions(+), 986 deletions(-)
Title: R Client for 'iRODS'
Description: The open sourced data management software 'Integrated
Rule-Oriented Data System' ('iRODS') offers solutions for the whole
data life cycle (<https://irods.org/>). The loosely constructed and
highly configurable architecture of 'iRODS' frees the user from strict
formatting constraints and single-vendor solutions. This package
provides an interface to the 'iRODS' HTTP API, allowing you to manage
your data and metadata in 'iRODS' with R. Storage of annotated files
and R objects in 'iRODS' ensures findability, accessibility,
interoperability, and reusability of data.
Author: iRODS Consortium [cph],
Martin Schobben [aut] ,
Mariana Montes [aut],
Terrell Russell [cre],
Christine Staiger [ctb],
Ton Smeele [ctb],
Alan King [ctb]
Maintainer: Terrell Russell <rirods@irods.org>
Diff between rirods versions 0.3.0 dated 2026-07-19 and 0.3.1 dated 2026-11-10
rirods-0.3.0/rirods/inst/irods_demo |only rirods-0.3.1/rirods/DESCRIPTION | 20 +++---- rirods-0.3.1/rirods/MD5 | 72 +++++++------------------- rirods-0.3.1/rirods/NEWS.md | 6 ++ rirods-0.3.1/rirods/README.md | 41 -------------- rirods-0.3.1/rirods/build/partial.rdb |binary rirods-0.3.1/rirods/build/vignette.rds |binary rirods-0.3.1/rirods/inst/WORDLIST | 4 + rirods-0.3.1/rirods/inst/doc/demo.Rmd | 4 + rirods-0.3.1/rirods/inst/doc/demo.html | 17 +----- rirods-0.3.1/rirods/inst/doc/develop.Rmd | 5 - rirods-0.3.1/rirods/inst/doc/develop.html | 13 +--- rirods-0.3.1/rirods/inst/doc/icommands.Rmd | 4 + rirods-0.3.1/rirods/inst/doc/icommands.html | 17 +----- rirods-0.3.1/rirods/inst/doc/local-irods.Rmd | 4 + rirods-0.3.1/rirods/inst/doc/local-irods.html | 17 +----- rirods-0.3.1/rirods/inst/doc/metadata.Rmd | 4 + rirods-0.3.1/rirods/inst/doc/metadata.html | 17 +----- rirods-0.3.1/rirods/vignettes/demo.Rmd | 4 + rirods-0.3.1/rirods/vignettes/develop.Rmd | 5 - rirods-0.3.1/rirods/vignettes/icommands.Rmd | 4 + rirods-0.3.1/rirods/vignettes/local-irods.Rmd | 4 + rirods-0.3.1/rirods/vignettes/metadata.Rmd | 4 + 23 files changed, 92 insertions(+), 174 deletions(-)
Title: Estimating Effective Migration Surfaces from Single Nucleotide
Polymorphism Data
Description: Wrapper and plotting utilities for the spatial population genetics tool 'EEMS' (Estimated Effective Migration Surfaces) for SNP (Single Nucleotide Polymorphism) data, originally provided as a command-line tool written in 'C++' together with an accompanying 'R' package for plotting the output of the 'EEMS' tool itself (<https://github.com/dipetkov/eems/>). There are four main motivations for offering this to 'R' users as a package. Firstly, to remove the installation and configuration burden for the 'EEMS' command-line tool, which relies on manually installed 'Boost' and 'Eigen' system libraries and configuring their location; secondly, to streamline the workflow by having a singe environment (the 'R' system) for the entire analysis rather than a file-based command-line executable whose output files are then to be imported and analysed by a separate 'R' script; thirdly, to make the input formats compatible with other, 'R'-based spatial population genetics tools such as the 'ConStr [...truncated...]
Author: Felix Weitkaemper [aut, cre, cph] ,
Grace Zawadi [aut],
Desislava Petkova [cph]
Maintainer: Felix Weitkaemper <felix.weitkaemper@german-uds.de>
Diff between reems versions 0.1.0 dated 2026-05-05 and 0.1.1 dated 2026-11-10
DESCRIPTION | 16 +- MD5 | 60 ++++--- NAMESPACE | 16 +- NEWS.md | 7 R/RcppExports.R | 8 - R/color.funcs.R | 48 ++++++ R/contour.funcs.R | 215 +++++++++++++++++++++++++++ R/contour.with.holes.R | 39 ++++ R/cpp.tests.R |only R/eems.resid.heatmap.R | 37 ++++ R/eems.run.R | 60 ++++++- R/eems.voronoi.samples.R | 22 ++ R/plot.dissimilarities.R | 41 +++++ R/plot.inputs.R | 111 +++++++++++++ R/plot.logposterior.R | 9 + R/plot.utils.R | 27 +++ R/recenter.longitudes.R | 42 ++++- R/reems-package.R | 9 + R/utils.R | 20 ++ R/zzz.R | 6 README.md | 2 build/vignette.rds |binary man/eems.Rd | 7 man/eems.from.files.Rd | 4 src/RcppExports.cpp | 3 src/test-draw.cpp |only src/test-graph.cpp |only src/test-runner.cpp |only src/test-util.cpp |only src/util.cpp | 4 tests/testthat/test-check.greatcirc.coords.R |only tests/testthat/test-cpp.R |only tests/testthat/test-eems.R | 83 ++++++++++ tests/testthat/test-eems.from.files.R | 56 +++++++ tests/testthat/test-which.dist.metric.R |only 35 files changed, 889 insertions(+), 63 deletions(-)
Title: Readmission Risk Pool Platform
Description: Provides the R implementation of the Readmission Risk Pool (RRP)
analytical platform for reassessing the remaining probability of a first
hospital readmission through 30 days after discharge. Distributed as the
'readmit' package, it creates user-owned projects, applies shared eligibility
rules at explicit assessment times, retains completed assessments as
history, and generates CSV analytical products for a project-owned
interactive application. Project authors supply clinical source-mapping
and risk-provider functions; no clinically validated prediction model is
included.
Author: Alex Zajichek [aut, cre],
CentralStatz Statistical & Data Sciences LLC [cph]
Maintainer: Alex Zajichek <alex@centralstatz.com>
Diff between readmit versions 1.0.0 dated 2026-11-03 and 1.1.0 dated 2026-11-10
DESCRIPTION | 8 - MD5 | 64 ++++---- NEWS.md | 13 + R/canonical-source.R | 33 ++-- R/episode-eligibility.R | 12 - R/product-refresh.R | 3 R/project-history.R | 6 R/project-inspection.R | 6 R/rrp-run.R | 13 + README.md | 39 ++-- build/vignette.rds |binary inst/doc/getting-started.R | 3 inst/doc/getting-started.Rmd | 69 +++++--- inst/doc/getting-started.html | 222 ++++++++++++++++------------ inst/project-template/R/produce-canonical.R | 17 +- inst/project-template/README.md | 22 +- man/readmit-package.Rd | 5 man/rrp_inspect_history.Rd | 6 man/rrp_produce_project_canonical.Rd | 13 + man/rrp_refresh_products.Rd | 3 man/rrp_run.Rd | 13 + tests/stage3-installed-workflow.R | 23 +- tests/stage5-installed-workflow.R | 8 - tests/testthat/test-analytical-products.R | 3 tests/testthat/test-authoring-workflow.R | 7 tests/testthat/test-canonical-source.R | 40 ++++- tests/testthat/test-episode-eligibility.R | 71 ++++---- tests/testthat/test-product-refresh.R | 2 tests/testthat/test-project-history.R | 13 + tests/testthat/test-project-inspection.R | 11 - tests/testthat/test-provider-assessment.R | 6 tests/testthat/test-rrp-run.R | 89 ++++++++--- vignettes/getting-started.Rmd | 69 +++++--- 33 files changed, 545 insertions(+), 367 deletions(-)
Title: Read 'SBML' Models and Convert Them to Simulation Code
Description: Reads models in the Systems Biology Markup Language ('SBML')
(Hucka et al. (2003) <doi:10.1093/bioinformatics/btg015>) through the
bundled 'libSBML' library (Bornstein et al. (2008)
<doi:10.1093/bioinformatics/btn051>). Lists a model's species,
parameters, compartments, reactions, rules, events and function
definitions, and converts the model into ready-to-run simulation code
for 'deSolve', 'mrgsolve', 'rxode2', 'MATLAB', 'Julia' or 'ubiquity'.
Models are read, not modified.
Author: Satyaprakash Nayak [aut, cre, cph],
Sarah M. Keating [ctb] ,
Frank T. Bergmann [ctb] ,
Lucian P. Smith [ctb] ,
Brett G. Olivier [ctb] ,
Akiya Jouraku [ctb] ,
Michael Hucka [ctb] ,
Ben Bornstein [ctb] ,
Jeroen Ooms [ctb] ,
California Institute of Tech [...truncated...]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between r2sbml versions 0.1.0 dated 2026-11-03 and 0.1.1 dated 2026-11-10
DESCRIPTION | 8 MD5 | 24 - NEWS.md | 20 + README.md | 4 configure | 596 ++++++++++++++++++----------------- configure.ac | 10 configure.win | 5 inst/doc/limitations.html | 8 inst/doc/r2sbml.html | 12 src/convertReactions.cpp | 135 +++---- src/formulaToInfix.h | 6 tests/testthat/test-initial-values.R | 8 tools/cmake_call.sh | 67 +++ 13 files changed, 496 insertions(+), 407 deletions(-)
Title: Nonparametric Quantile Density Estimation and Structural
Analysis of First-Price Auctions
Description: Nonparametric estimators of the quantile density function
(the derivative of the quantile function): kernel, boundary-corrected
kernel, Poisson-weight and Bernstein-polynomial smoothers, indirect
estimators (Jones (1992)
<https://www.ism.ac.jp/editsec/aism/pdf/044_4_0721.pdf>; Soni, Dewan and
Jain (2012) <doi:10.1016/j.csda.2012.04.014>; Chaubey, Dewan and Li (2024)
<doi:10.1080/03610926.2023.2222922>), and linear, hard-thresholded and
block-thresholded wavelet estimators (Chesneau, Dewan and Doosti (2016)
<doi:10.1016/j.csda.2015.08.006>; Shirazi and Doosti (2022)
<doi:10.1080/03610918.2019.1656250>), with smoothing parameters chosen by
biased, robust likelihood (Wu (2019) <doi:10.1080/07350015.2018.1424633>)
or least-squares cross-validation. The estimators are applied to the
structural analysis of first-price sealed-bid auctions: recovery of
private values for independent or affiliated values and risk-neutral or
risk-averse bidders (Doosti, Dewan [...truncated...]
Author: Hassan Doosti [aut, cre, cph] ,
Yogendra P. Chaubey [ctb, cph] ,
Isha Dewan [ctb, cph] ,
Jun Li [ctb, cph] ,
Brent R. Hickman [ctb, cph] ),
Timothy P. Hubbard [ctb, cph] ),
Brani Vidakovic [ctb, cph] , phi_jk,
dwt_periodic, idwt_periodic and loclin_s [...truncated...]
Maintainer: Hassan Doosti <Hassan.doosti@mq.edu.au>
Diff between qdfauction versions 0.2.0 dated 2026-10-22 and 0.3.0 dated 2026-11-10
DESCRIPTION | 11 +- MD5 | 143 ++++++++++++++------------ NAMESPACE | 14 ++ NEWS.md | 94 +++++++++++++++++ R/bandwidth.R | 6 - R/blocks.R |only R/copula.R | 34 ++++++ R/fpa_density_boot.R | 23 +++- R/fpa_revenue.R | 36 +++++- R/fpa_values.R | 8 + R/proc_cost_boot_blocks.R |only R/procurement.R |only R/qdf.R | 25 +++- inst/CITATION |only inst/doc/timber.html | 2 man/bcv_criterion.Rd | 71 ++++++------ man/bid_icc.Rd |only man/block_length_auto.Rd |only man/copula_fit.Rd | 6 - man/copula_psi.Rd | 20 +-- man/copula_psi_np.Rd | 12 +- man/copula_spec_test.Rd | 16 +- man/copula_tau_to_theta.Rd | 2 man/density_marmer_shneyerov.Rd | 6 - man/dwt_periodic.Rd | 16 +- man/fpa_bid_function.Rd | 16 +- man/fpa_block_boot.Rd |only man/fpa_corner_test.Rd | 48 ++++---- man/fpa_density.Rd | 94 ++++++++--------- man/fpa_density_boot.Rd | 34 ++++-- man/fpa_density_ci.Rd | 40 +++---- man/fpa_density_cv.Rd | 32 ++--- man/fpa_evaluate_values.Rd | 26 ++-- man/fpa_montecarlo.Rd | 22 ++-- man/fpa_optimal_reserve.Rd | 12 +- man/fpa_revenue.Rd | 10 - man/fpa_revenue_boot.Rd | 47 +++++--- man/fpa_revenue_model.Rd | 26 ++-- man/fpa_revenue_qd.Rd | 20 +-- man/fpa_simulate.Rd | 16 +- man/fpa_values.Rd | 94 +++++++++-------- man/fpa_virtual_value_model.Rd | 22 ++-- man/kde_hh.Rd | 16 +- man/loclin_smooth.Rd | 6 - man/make_kernel.Rd | 16 +- man/phi_jk.Rd | 6 - man/plot.fpa_density.Rd | 8 - man/plot.fpa_density_ci.Rd | 8 - man/plot.fpa_revenue_boot.Rd | 10 - man/plot.fpa_values.Rd | 10 - man/plot.qdf.Rd | 10 - man/predict.qdf.Rd | 4 man/proc_M.Rd |only man/proc_check_winning_bid.Rd |only man/proc_cost.Rd |only man/proc_cost_boot.Rd |only man/proc_optimal_ceiling.Rd |only man/proc_simulate.Rd |only man/proc_values.Rd |only man/psi_jk.Rd | 12 +- man/qdf.Rd | 80 ++++++++------ man/qdf_jones.Rd | 71 ++++++------ man/qdf_kernel.Rd | 29 ++--- man/qdf_poisson.Rd | 35 +++--- man/qdf_wavelet.Rd | 44 +++----- man/qdf_wavelet_nl.Rd | 56 ++++------ man/quantile_indirect_poisson.Rd | 18 +-- man/rcopula_archimedean.Rd | 4 man/resample_blocks.Rd |only man/scaling_function.Rd | 8 - man/select_bandwidth.Rd | 68 ++++++------ man/select_fpa_density.Rd | 54 ++++----- man/select_wavelet.Rd | 16 +- man/threshold_coefficients.Rd | 35 +++--- man/timber.Rd | 20 +-- man/wavelet_filter.Rd | 4 tests/testthat/test-blocks.R |only tests/testthat/test-input-and-extensibility.R | 16 ++ tests/testthat/test-jns-pseudovalues.R |only tests/testthat/test-merge-020.R | 4 tests/testthat/test-procurement.R |only tests/testthat/test-revenue-blocks-proc.R |only 82 files changed, 1020 insertions(+), 752 deletions(-)
Title: Post-Processing Tools for GC-MS Volatile Organic Compound Data
Description: Provides functions for processing Shimadzu gas
chromatography-mass spectrometry (GC-MS) exported text files,
extracting Chemical Abstracts Service (CAS) numbers and peak areas,
building abundance matrices, annotating compounds, and screening
based on occurrence frequency. The package is designed for
organizing, identifying, and screening volatile compounds in
metabolomics and environmental studies.
Author: Xiaotao Han [aut, cre]
Maintainer: Xiaotao Han <postvocs.r@gmail.com>
Diff between postvocs versions 0.2.5 dated 2026-09-12 and 0.2.6 dated 2026-11-10
DESCRIPTION | 6 MD5 | 8 NEWS.md | 14 + R/filter_by_frequency.R | 401 ++++++++++++++++++++------------------------- man/filter_by_frequency.Rd | 79 ++------ 5 files changed, 228 insertions(+), 280 deletions(-)
Title: SQL Parsing, Analysis and Dialect Translation
Description: Parse, tokenize, validate, format, analyze and translate SQL
between more than 30 dialects ('PostgreSQL', 'MySQL', 'BigQuery',
'Snowflake', 'DuckDB', 'T-SQL', and others) using the 'polyglot-sql'
Rust crate <https://github.com/tobilg/polyglot>, a Rust port of the
'SQLGlot' 'Python' library. All processing happens locally in the R
session; no database connection, 'Python' runtime or external service
is required. Includes column-level lineage, structural query
analysis, query optimization, 'AST' diffing and 'OpenLineage' facet
generation.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
Tobias Mueller [cph] ),
Toby Mao [cph] ,
The authors of the vendored Rust dependencies [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between polyglotSQL versions 0.1.2 dated 2026-10-08 and 0.1.3 dated 2026-11-10
DESCRIPTION | 8 ++--- MD5 | 32 ++++++++++---------- NEWS.md | 40 +++++++++++++++++++++++++ README.md | 5 +-- inst/COPYRIGHTS | 4 +- inst/WORDLIST | 3 + inst/doc/getting-started.html | 2 - inst/doc/installation-and-troubleshooting.Rmd | 7 +++- inst/doc/installation-and-troubleshooting.html | 9 +++++ src/rust/Cargo.lock | 8 ++--- src/rust/Cargo.toml | 2 - src/rust/src/lib.rs | 2 + src/rust/vendor.tar.xz |binary tests/testthat/test-compiled-code.R | 8 +++++ tests/testthat/test-metadata.R | 5 +-- tools/config.R | 24 +++++++++++++++ vignettes/installation-and-troubleshooting.Rmd | 7 +++- 17 files changed, 131 insertions(+), 35 deletions(-)
Title: Estimate Pollinator Body Size and Co-Varying Ecological Traits
Description: Tools to estimate pollinator body size and co-varying traits. This package contains
Bayesian predictive models of pollinator body size (for bees and hoverflies) and
bee foraging range, as well as preexisting predictive models for pollinator body size
(currently implemented for ants, bees, butterflies, flies, moths and wasps), bee tongue
length, foraging range, total field nectar loads and wing loading. An additional GitHub
repository <https://github.com/liamkendall/pollimetrydata> provides model objects to use
the bodysize and foraging.range functions internally. The Bayesian models are described in Kendall
et al. (2019) <doi:10.1002/ece3.4835> & Kendall et al. (2022) <doi:10.1002/ecy.3809>.
Author: Liam Kendall [aut, cre],
Ignasi Bartomeus [aut]
Maintainer: Liam Kendall <liam.k.kendall@gmail.com>
Diff between pollimetry versions 1.1.1 dated 2026-11-03 and 1.1.1-1 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 4 ++++ R/bodysize.R | 18 +++++++++++------- R/forage_dataset.R | 38 +++++++++++++++++++------------------- R/foragedist.R | 27 +++++++++++++-------------- R/foraging.range.R | 18 ++++++++++++------ R/pollimetry_dataset.R | 44 ++++++++++++++++++++++---------------------- R/tongue_dataset.R | 8 ++++---- R/tonguelength.R | 9 +++------ README.md | 28 +++++++--------------------- man/bodysize.Rd | 6 +++--- man/forage_dataset.Rd | 38 +++++++++++++++++++------------------- man/foragedist.Rd | 9 ++++----- man/foraging.range.Rd | 8 ++++---- man/pollimetry_dataset.Rd | 44 ++++++++++++++++++++++---------------------- man/tongue_dataset.Rd | 6 +++--- man/tonguelength.Rd | 6 +++--- 18 files changed, 173 insertions(+), 178 deletions(-)
Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API
<https://api.opengwas.io/api/>. Includes a wrapper to make generic
calls to the API, plus convenience functions for specific queries.
Author: Gibran Hemani [aut, cph] ,
Ben Elsworth [aut] ,
Tom Palmer [aut, cre] ,
Rita Rasteiro [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between ieugwasr versions 1.2.0 dated 2026-10-07 and 1.2.1 dated 2026-11-10
DESCRIPTION | 16 ++++---- MD5 | 23 ++++++------ NEWS.md | 10 +++++ R/ld_clump.R | 75 ++++++++++++++++++++++++++++++++++++++--- R/ld_matrix.R | 23 +++++++++--- R/query.R | 3 + build/vignette.rds |binary man/ld_clump.Rd | 9 ++++ man/ld_clump_local.Rd | 18 +++++++++ man/ld_matrix.Rd | 9 ++++ man/ld_matrix_local.Rd | 16 ++++++++ tests/testthat/test_fix_n.r | 20 ++++++++++ tests/testthat/test_ld_local.r |only 13 files changed, 191 insertions(+), 31 deletions(-)
Title: 'REST' API Client for Accessing Data on 'WEkEO HDA V2'
Description: Provides seamless access to the WEkEO Harmonised Data Access (HDA) API, enabling
users to query, download, and process data efficiently from the HDA platform.
With 'hdar', researchers and data scientists can integrate the extensive HDA
datasets into their R workflows, enhancing their data analysis capabilities.
Comprehensive information on the API functionality and usage is available
at <https://gateway.prod.wekeo2.eu/hda-broker/docs>.
Author: Matteo Mattiuzzi [aut, cre]
Maintainer: Matteo Mattiuzzi <matteo.mattiuzzi@eea.europa.eu>
Diff between hdar versions 1.0.7 dated 2025-06-17 and 1.0.9 dated 2026-11-10
hdar |only 1 file changed
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Centofanti et al. (2025) <doi:10.1080/00224065.2024.2430978>,
Capezza et al. (2025) <doi:10.48550/arXiv.2410.20138>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Davide Forcina [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.8.1 dated 2026-01-18 and 1.8.2 dated 2026-11-10
funcharts-1.8.1/funcharts/man/RoMFCC_PhaseII_casewise.Rd |only funcharts-1.8.1/funcharts/man/RoMFCC_PhaseI_casewise.Rd |only funcharts-1.8.2/funcharts/DESCRIPTION | 8 funcharts-1.8.2/funcharts/MD5 | 156 - funcharts-1.8.2/funcharts/NAMESPACE | 2 funcharts-1.8.2/funcharts/NEWS.md | 7 funcharts-1.8.2/funcharts/R/04_phaseII.R | 2 funcharts-1.8.2/funcharts/R/05_fault_detection.R | 65 funcharts-1.8.2/funcharts/R/FRTM_scamfunctions.R | 2 funcharts-1.8.2/funcharts/R/RcppExports.R | 8 funcharts-1.8.2/funcharts/R/RoAMFEWMA.R |only funcharts-1.8.2/funcharts/R/amfewma.R | 111 - funcharts-1.8.2/funcharts/R/rmfcc.R | 1095 ---------- funcharts-1.8.2/funcharts/build/partial.rdb |binary funcharts-1.8.2/funcharts/build/vignette.rds |binary funcharts-1.8.2/funcharts/man/AMFEWMA_PhaseI.Rd | 420 +-- funcharts-1.8.2/funcharts/man/AMFEWMA_PhaseII.Rd | 41 funcharts-1.8.2/funcharts/man/FRTM_PhaseI.Rd | 248 +- funcharts-1.8.2/funcharts/man/FRTM_PhaseII.Rd | 160 - funcharts-1.8.2/funcharts/man/OEBFDTW.Rd | 262 +- funcharts-1.8.2/funcharts/man/RoAMFEWMA_PhaseI.Rd | 336 +-- funcharts-1.8.2/funcharts/man/RoAMFEWMA_PhaseII.Rd | 179 - funcharts-1.8.2/funcharts/man/RoMFDI.Rd | 182 - funcharts-1.8.2/funcharts/man/air.Rd | 100 funcharts-1.8.2/funcharts/man/cbind_mfd.Rd | 70 funcharts-1.8.2/funcharts/man/cont_plot.Rd | 139 - funcharts-1.8.2/funcharts/man/control_charts_pca.Rd | 378 +-- funcharts-1.8.2/funcharts/man/control_charts_pca_mfd_real_time.Rd | 216 - funcharts-1.8.2/funcharts/man/control_charts_sof_pc.Rd | 328 +- funcharts-1.8.2/funcharts/man/control_charts_sof_pc_real_time.Rd | 204 - funcharts-1.8.2/funcharts/man/data_sim_mfd.Rd | 62 funcharts-1.8.2/funcharts/man/fof_pc.Rd | 300 +- funcharts-1.8.2/funcharts/man/fof_pc_real_time.Rd | 156 - funcharts-1.8.2/funcharts/man/funcharts-package.Rd | 127 - funcharts-1.8.2/funcharts/man/get_mfd_array.Rd | 120 - funcharts-1.8.2/funcharts/man/get_mfd_array_real_time.Rd | 138 - funcharts-1.8.2/funcharts/man/get_mfd_df.Rd | 282 +- funcharts-1.8.2/funcharts/man/get_mfd_df_real_time.Rd | 184 - funcharts-1.8.2/funcharts/man/get_mfd_fd.Rd | 58 funcharts-1.8.2/funcharts/man/get_mfd_list.Rd | 232 +- funcharts-1.8.2/funcharts/man/get_mfd_list_real_time.Rd | 144 - funcharts-1.8.2/funcharts/man/get_ooc.Rd | 98 funcharts-1.8.2/funcharts/man/get_sof_pc_outliers.Rd | 86 funcharts-1.8.2/funcharts/man/inprod_mfd.Rd | 90 funcharts-1.8.2/funcharts/man/inprod_mfd_diag.Rd | 94 funcharts-1.8.2/funcharts/man/is.mfd.Rd | 36 funcharts-1.8.2/funcharts/man/mFPCA.Rd | 162 - funcharts-1.8.2/funcharts/man/mfd.Rd | 196 - funcharts-1.8.2/funcharts/man/norm.mfd.Rd | 56 funcharts-1.8.2/funcharts/man/par.FDTW.Rd | 148 - funcharts-1.8.2/funcharts/man/par.mFPCA.Rd | 50 funcharts-1.8.2/funcharts/man/par.rtr.Rd | 100 funcharts-1.8.2/funcharts/man/pca_mfd.Rd | 84 funcharts-1.8.2/funcharts/man/pca_mfd_real_time.Rd | 96 funcharts-1.8.2/funcharts/man/plot.FRTM_PhaseI.Rd | 120 - funcharts-1.8.2/funcharts/man/plot.mFPCA.Rd | 80 funcharts-1.8.2/funcharts/man/plot_bifd.Rd | 82 funcharts-1.8.2/funcharts/man/plot_bootstrap_sof_pc.Rd | 86 funcharts-1.8.2/funcharts/man/plot_control_charts.Rd | 120 - funcharts-1.8.2/funcharts/man/plot_control_charts_real_time.Rd | 134 - funcharts-1.8.2/funcharts/man/plot_mfd.Rd | 152 - funcharts-1.8.2/funcharts/man/plot_mon.Rd | 144 - funcharts-1.8.2/funcharts/man/plot_pca_mfd.Rd | 68 funcharts-1.8.2/funcharts/man/predict_fof_pc.Rd | 118 - funcharts-1.8.2/funcharts/man/predict_sof_pc.Rd | 144 - funcharts-1.8.2/funcharts/man/rbind_mfd.Rd | 68 funcharts-1.8.2/funcharts/man/regr_cc_fof.Rd | 254 +- funcharts-1.8.2/funcharts/man/regr_cc_fof_real_time.Rd | 248 +- funcharts-1.8.2/funcharts/man/regr_cc_sof.Rd | 280 +- funcharts-1.8.2/funcharts/man/scale_mfd.Rd | 110 - funcharts-1.8.2/funcharts/man/sim_funcharts.Rd | 96 funcharts-1.8.2/funcharts/man/simulate_mfd.Rd | 408 +-- funcharts-1.8.2/funcharts/man/sof_pc.Rd | 252 +- funcharts-1.8.2/funcharts/man/sof_pc_real_time.Rd | 150 - funcharts-1.8.2/funcharts/man/sub-.mfd.Rd | 166 - funcharts-1.8.2/funcharts/man/tensor_product_mfd.Rd | 82 funcharts-1.8.2/funcharts/man/which_ooc.Rd | 106 funcharts-1.8.2/funcharts/src/RcppExports.cpp | 18 funcharts-1.8.2/funcharts/src/src.cpp | 37 funcharts-1.8.2/funcharts/tests/testthat/Rplots.pdf |binary funcharts-1.8.2/funcharts/tests/testthat/test-amfewma-contributions.R |only 81 files changed, 5222 insertions(+), 6119 deletions(-)
Title: Fast Utilities for Year Month Day Objects
Description: A collection of utility functions for working with
Year Month Day objects. Includes functions for fast parsing of numeric
and character input based on algorithms described in Hinnant, H. (2021)
<https://howardhinnant.github.io/date_algorithms.html> as well as a branchless
calculation of leap years by Jerichaux (2025) <https://stackoverflow.com/a/79564914>.
Author: Tim Taylor [aut, cre] ,
Howard Hinnant [aut] ,
jerichaux [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between fastymd versions 0.1.5 dated 2026-02-27 and 0.2.0 dated 2026-11-10
fastymd-0.1.5/fastymd/R/accessors.R |only fastymd-0.1.5/fastymd/man/accessors.Rd |only fastymd-0.1.5/fastymd/src/api.c |only fastymd-0.1.5/fastymd/src/epochdays.c |only fastymd-0.1.5/fastymd/src/epochdays.h |only fastymd-0.2.0/fastymd/DESCRIPTION | 8 +- fastymd-0.2.0/fastymd/MD5 | 39 +++++++----- fastymd-0.2.0/fastymd/NAMESPACE | 13 ++++ fastymd-0.2.0/fastymd/NEWS.md | 15 ++++ fastymd-0.2.0/fastymd/R/generics.R |only fastymd-0.2.0/fastymd/R/yearweek.R |only fastymd-0.2.0/fastymd/build/partial.rdb |binary fastymd-0.2.0/fastymd/build/vignette.rds |binary fastymd-0.2.0/fastymd/inst/doc/fastymd.html | 66 +++++++++++---------- fastymd-0.2.0/fastymd/inst/tinytest/test_fastymd.R | 66 ++++++++++++++++++++- fastymd-0.2.0/fastymd/man/fastymd-package.Rd | 1 fastymd-0.2.0/fastymd/man/fymd.Rd | 4 - fastymd-0.2.0/fastymd/man/generics.Rd |only fastymd-0.2.0/fastymd/man/yearweek.Rd |only fastymd-0.2.0/fastymd/src/api-leapyear.c |only fastymd-0.2.0/fastymd/src/api-yearweek.c |only fastymd-0.2.0/fastymd/src/api-ymd.c |only fastymd-0.2.0/fastymd/src/civil_from_days.c | 17 +++++ fastymd-0.2.0/fastymd/src/civil_from_days.h | 2 fastymd-0.2.0/fastymd/src/init.c | 35 ++++++++--- fastymd-0.2.0/fastymd/src/leapyear.h |only fastymd-0.2.0/fastymd/src/utils.c |only fastymd-0.2.0/fastymd/src/utils.h |only 28 files changed, 204 insertions(+), 62 deletions(-)
Title: Fast QR Decomposition and Update
Description: Efficient algorithms for performing, updating, and removing rows or columns from the QR decomposition, R decomposition, or the inverse of the R decomposition of a matrix as rows or columns are added or removed. It also includes functions for solving linear systems of equations, normal equations for linear regression models, and normal equations for linear regression with a RIDGE penalty. For a detailed introduction to these methods, the monograph Matrix Computations (2013, <doi:10.1007/978-3-319-05089-8>) for complete introduction to the methods.
Author: Mauro Bernardi [aut, cre],
Claudio Busatto [aut],
Manuela Cattelan [aut]
Maintainer: Mauro Bernardi <mauro.bernardi@unipd.it>
Diff between fastQR versions 1.1.4 dated 2026-02-13 and 1.1.5 dated 2026-11-10
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/RcppExports.R | 7 +++++++ build/partial.rdb |binary man/qr.Rd | 3 +++ man/qrmls.Rd | 3 +++ man/qrmridge.Rd | 3 +++ man/qrmridge_cv.Rd | 3 +++ man/qrridge_cv.Rd | 3 +++ man/rchol.Rd | 3 +++ man/rupdate.Rd | 3 +++ src/QR_utils_wrap.cpp | 5 +++++ src/QR_wrap.cpp | 1 + src/thinQR_wrap.cpp | 1 + src/utils.cpp | 6 +++--- 15 files changed, 56 insertions(+), 21 deletions(-)
Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers
including 'Claude' <https://claude.ai>, 'OpenAI'
<https://chatgpt.com>, and more. Supports streaming, asynchronous
calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] ,
Joe Cheng [aut],
Aaron Jacobs [aut],
Garrick Aden-Buie [aut] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between ellmer versions 0.5.1 dated 2026-11-08 and 0.5.2 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/otel.R | 26 ++++++++++++++++---------- R/provider-aws-api.R | 2 ++ R/sysdata.rda |binary tests/testthat/test-otel.R | 33 ++++++++++++++++++++++++++++++--- 7 files changed, 61 insertions(+), 22 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.3.9 dated 2026-09-11 and 0.3.10 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++++++++----------- NEWS.md | 5 +++++ R/guides.R | 4 ++-- build/vignette.rds |binary tests/_helper/init.R | 13 +++++++++++-- tests/_helper/objs-str-r90805 |only tests/test-diffStr.R | 20 +++++++++++++++----- tests/test-diffStr.Rout.save | 20 +++++++++++++++----- tests/test-guide.R | 12 ++++++++++++ tests/test-guide.Rout.save | 20 +++++++++++++++++--- tests/test-ses.R | 3 +-- tests/test-ses.Rout.save | 3 +-- 13 files changed, 105 insertions(+), 35 deletions(-)
Title: Distance-Correlation Based Methods for Blind Source Separation
and Dependence Analysis
Description: Independent component analysis based on distance correlation, including a robust variant using the bowl transformation. The package provides user-facing implementations of distance covariance and distance correlation, including memory-efficient blockwise computations for large data sets. It includes a sequential ICA estimator based on minimizing distance correlation, as well as tools for analyzing serial dependence via distance autocorrelation, dependograms, and permutation-based tests. In addition, it provides functions for testing serial dependence based on distance correlation and the Hilbert–Schmidt independence criterion. The methodology is related to Matteson and Tsay (2017) <doi:10.1080/01621459.2016.1150851> and to the robust framework of Leyder et al. (2026) <doi:10.1007/s11634-026-00674-9>.
Author: Sarah Leyder [aut] ,
Klaus Nordhausen [aut, cre]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between dcorBSS versions 1.0-0 dated 2026-06-10 and 1.0-1 dated 2026-11-10
DESCRIPTION | 6 +- MD5 | 44 +++++++++---------- R/biloop_transform.R | 7 ++- R/bowl_transform.R | 4 + R/dcorBSS-package.R | 4 - R/dcorICA.R | 4 - R/dcor_serial_test.R | 82 +++++++++++++++++++++---------------- R/dcov_large.R | 10 ++++ R/hsic_serial_test_curve.R | 39 ++++++++++++----- R/internal_dcor_helpers.R | 36 ++++++++++++++++ R/package.R | 3 - R/sdt.R | 44 +++++++++++-------- inst/ChangeLog | 16 +++++++ inst/doc/dcorBSS-introduction.Rmd | 8 +-- inst/doc/dcorBSS-introduction.html | 15 +++--- man/biloop_transform.Rd | 5 +- man/bowl_transform.Rd | 2 man/dcorBSS-package.Rd | 7 +-- man/dcorICA.Rd | 2 man/dcor_serial_test.Rd | 36 +++++++++------- man/hsic_serial_test.Rd | 18 ++++---- man/sdt.Rd | 14 +++--- vignettes/dcorBSS-introduction.Rmd | 8 +-- 23 files changed, 262 insertions(+), 152 deletions(-)
Title: Algorithms for Routing and Solving the Traffic Assignment
Problem
Description: Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm.
Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>),
bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://www.cs.princeton.edu/courses/archive/spr06/cos423/Handouts/EPP%20shortest%20path%20algorithms.pdf>),
A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>),
new bidirectional A* (Pijls & Post (2009) <https://repub.eur.nl/pub/16100/ei2009-10.pdf>),
Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>),
PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>).
Algorithms for solving the traffic assignment problem are All-or-Nothing assignment,
Method of Successive Averages,
Frank-Wolfe algorithm (M. Fukus [...truncated...]
Author: Vincent Larmet [aut, cre]
Maintainer: Vincent Larmet <larmet.vincent@gmail.com>
Diff between cppRouting versions 3.2 dated 2025-11-28 and 4.0 dated 2026-11-10
DESCRIPTION | 20 - MD5 | 154 +++++++-- NAMESPACE | 7 NEWS.md | 18 + R/RcppExports.R | 92 +++++ R/assign_traffic.R | 80 +++-- R/aux_helpers.R |only R/cch.R |only R/contract.R | 80 ++++- R/cpp_extract.R |only R/geom_graph_shared.R |only R/get_aon.R | 38 ++ R/get_detour.R | 3 R/get_distance_mat.R | 171 ++++++++++ R/get_distance_pair.R | 133 ++++++++ R/get_isochrone.R | 3 R/get_multi_paths.R | 3 R/get_path_pair.R | 19 + R/globalVariables.R |only R/graph_from_osmdata.R |only R/graph_from_osmpbf.R |only R/graph_from_sf.R |only R/graph_from_shapefile.R |only R/graphs.R | 29 + R/osm_profiles.R |only R/simplify.R | 46 ++ R/to_df.R | 24 + R/to_igraph.R |only R/zzz.R | 7 inst/doc/cppRouting.html | 4 man/assign_traffic.Rd | 15 man/cpp_contract.Rd | 35 ++ man/cpp_customize.Rd |only man/cpp_extract.Rd |only man/cpp_simplify.Rd | 5 man/get_distance_matrix.Rd | 18 - man/get_distance_pair.Rd | 16 - man/get_path_pair.Rd | 5 man/makegraph.Rd | 3 man/osm_bike_profile.Rd |only man/osm_car_profile.Rd |only man/osm_foot_profile.Rd |only man/osm_hgv_profile.Rd |only man/to_df.Rd | 17 - man/to_igraph.Rd |only src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 506 ++++++++++++++++++++++++++++++++ src/aggc.cpp | 108 ++++++ src/aggc.h | 17 + src/cch.h |only src/cch_assign.cpp |only src/cch_customize.cpp |only src/cch_internal.h |only src/cch_prepare.cpp |only src/cch_query.cpp |only src/cgraph.cpp | 4 src/cgraph.h | 1 src/distance_mat.cpp | 176 +++++++++++ src/distance_mat.h | 38 ++ src/distance_pair.cpp | 701 +++++++++++++++++++++++++++++++++++++++++++++ src/distance_pair.h | 43 ++ src/external_sort.h |only src/graph.cpp | 116 +++++++ src/graph.h | 25 + src/io_geom_graph.cpp |only src/io_geom_graph.h |only src/io_osm_graph.cpp |only src/io_osm_graph.h |only src/io_osm_graph_disk.cpp |only src/io_osm_graph_disk.h |only src/io_osm_tags.h |only src/io_osmpbf.cpp |only src/io_osmpbf.h |only src/io_shp.cpp |only src/io_shp.h |only src/simplify.cpp | 18 + src/test_external_sort.cpp |only src/traffic.cpp | 183 ++++++++--- src/wrapper.cpp | 387 ++++++++++++++++++++++++ tests |only 81 files changed, 3138 insertions(+), 232 deletions(-)
Title: Generate Citation File Format ('CFF') Metadata
Description: Citation File Format ('CFF') version 1.2.0
<doi:10.5281/zenodo.5171937> is a human- and machine-readable file
format for software citation metadata. Core utilities generate, read,
write and validate Citation File Format metadata for 'R' packages.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.4.2 dated 2026-08-24 and 1.4.3 dated 2026-11-10
DESCRIPTION | 9 MD5 | 186 ++++++++--------- NEWS.md | 178 +++++----------- R/as-bibentry.R | 14 - R/as-cff-person.R | 28 +- R/as-cff.R | 24 +- R/cff-create.R | 21 + R/cff-gha-update.R | 4 R/cff-git-hook.R | 18 - R/cff-modify.R | 4 R/cff-read-bib-text.R | 12 - R/cff-read.R | 72 +++--- R/cff-validate.R | 16 - R/cff-write-misc.R | 10 R/cff-write.R | 10 R/cff.R | 2 R/data.R | 3 R/deprecated.R | 19 + R/docs.R | 2 R/encoded-utf-to-latex.R | 5 R/methods.R | 4 R/utils-alerts.R | 33 ++- R/utils-bib.R | 52 ++-- R/utils-cff-read.R | 49 ++-- R/utils-cff-ref.R | 145 ++++++++++--- R/utils-create.R | 23 +- R/utils-persons.R | 24 +- R/utils-schema.R | 8 R/utils.R | 69 +++++- README.md | 177 +++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/WORDLIST | 8 inst/doc/bibtex-cff.html | 100 +++++---- inst/doc/bibtex-cff.qmd | 114 +++++----- inst/doc/cffr.R | 4 inst/doc/cffr.html | 18 - inst/doc/cffr.qmd | 16 - inst/doc/r-cff.R | 19 - inst/doc/r-cff.html | 53 ++-- inst/doc/r-cff.qmd | 70 ++++-- inst/examples/CITATION_biascorrector |only inst/extdata/cran_licenses.csv | 310 ++++++++++++++--------------- inst/extdata/crosswalk_tables.csv | 8 inst/schemaorg.json | 4 man/as_bibentry.Rd | 10 man/as_cff.Rd | 12 - man/as_cff_person.Rd | 22 -- man/cff_class.Rd | 22 +- man/cff_create.Rd | 19 + man/cff_gha_update.Rd | 6 man/cff_git_hook.Rd | 17 - man/cff_read.Rd | 25 +- man/cff_read_bib_text.Rd | 6 man/cff_schema.Rd | 6 man/cff_validate.Rd | 8 man/cff_write.Rd | 12 - man/cff_write_misc.Rd | 10 man/chunks/cffclass.Rmd | 20 + man/cran_to_spdx.Rd | 3 man/deprecated_cff_from_bib.Rd | 2 man/deprecated_cff_person.Rd | 4 man/deprecated_cff_to_bib.Rd | 5 man/deprecated_write.Rd | 5 man/encoded_utf_to_latex.Rd | 5 tests/testthat/_snaps/as-bibentry.md | 2 tests/testthat/_snaps/as-cff-reference.md | 6 tests/testthat/_snaps/as-cff.md | 8 tests/testthat/_snaps/cff-create.md | 2 tests/testthat/_snaps/cff-read-bib-text.md | 8 tests/testthat/_snaps/cff-read.md | 2 tests/testthat/_snaps/utils-create.md | 19 - tests/testthat/_snaps/utils.md |only tests/testthat/setup-available-packages.R | 1 tests/testthat/test-as-bibentry.R | 10 tests/testthat/test-as-cff-person.R | 2 tests/testthat/test-as-cff-reference.R | 5 tests/testthat/test-as-cff.R | 75 ++++++- tests/testthat/test-cff-create.R | 51 ++-- tests/testthat/test-cff-modify.R | 2 tests/testthat/test-cff-read-bib-text.R | 17 + tests/testthat/test-cff-read.R | 194 +++++++++++++++--- tests/testthat/test-cff-write.R | 2 tests/testthat/test-methods.R | 2 tests/testthat/test-utils-alerts.R | 25 ++ tests/testthat/test-utils-bib.R | 43 ++++ tests/testthat/test-utils-cff-create.R | 29 ++ tests/testthat/test-utils-cff-ref.R | 306 ++++++++++++++++++++++++++++ tests/testthat/test-utils-create.R | 139 ++++++++++--- tests/testthat/test-utils.R | 65 ++++++ vignettes/REFERENCES.bib | 6 vignettes/bibtex-cff.qmd | 114 +++++----- vignettes/cffr.qmd | 16 - vignettes/r-cff.qmd | 70 ++++-- 95 files changed, 2213 insertions(+), 1172 deletions(-)
Title: Bayesian Stability Analysis of Genotype by Environment
Interaction (GEI)
Description: Performs the general Bayesian estimation method of
linear-bilinear models for genotype x environment interaction of
Perez-Elizalde, Jarquin and Crossa (2012) <doi:10.1007/s13253-011-0063-9>:
the additive main effects and multiplicative interaction (AMMI) model
and the sites regression (SREG, GGE) model, with the data of an earlier
trial as the prior (conjugate normal and von Mises-Fisher priors weighted
by its replicates) or with vague priors; a compiled Gibbs sampler;
posterior summaries with highest posterior density intervals;
convergence diagnostics; biplots with highest posterior density regions;
DIC and WAIC; a plain-language interpretation of every result; and a
built-in 'shiny' application. For
Bayesian stability analysis in general (regression and variance models,
stability indices, probabilities of superior performance), see the
package 'bayesstability'.
Author: Muhammad Yaseen [aut, cre] ,
Diego Jarquin [aut, ctb],
Sergio Perez-Elizalde [aut, ctb],
Juan Burgueno [aut, ctb],
Jose Crossa [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between baystability versions 0.2.0 dated 2024-10-15 and 1.0.0 dated 2026-11-10
baystability-0.2.0/baystability/R/cultivo2008.R |only baystability-0.2.0/baystability/R/cultivo2009.R |only baystability-0.2.0/baystability/man/cultivo2009.Rd |only baystability-0.2.0/baystability/man/e_eff.Rd |only baystability-0.2.0/baystability/man/g_eff.Rd |only baystability-0.2.0/baystability/man/ge_ammi.Rd |only baystability-0.2.0/baystability/man/ge_eff.Rd |only baystability-0.2.0/baystability/man/ge_mean.Rd |only baystability-0.2.0/baystability/man/ge_model.Rd |only baystability-0.2.0/baystability/man/ge_var.Rd |only baystability-0.2.0/baystability/man/matrix_k.Rd |only baystability-0.2.0/baystability/man/orthnorm.Rd |only baystability-1.0.0/baystability/DESCRIPTION | 63 baystability-1.0.0/baystability/MD5 | 160 + baystability-1.0.0/baystability/NAMESPACE | 81 baystability-1.0.0/baystability/NEWS.md | 88 baystability-1.0.0/baystability/R/RcppExports.R |only baystability-1.0.0/baystability/R/app.R |only baystability-1.0.0/baystability/R/bayes_ammi.R | 1074 +++++------- baystability-1.0.0/baystability/R/bayes_gge.R |only baystability-1.0.0/baystability/R/baystability-package.R |only baystability-1.0.0/baystability/R/biplots.R |only baystability-1.0.0/baystability/R/bys_interpret.R |only baystability-1.0.0/baystability/R/common-notation.R |only baystability-1.0.0/baystability/R/common-objects.R |only baystability-1.0.0/baystability/R/common-plot.R |only baystability-1.0.0/baystability/R/common-reference.R |only baystability-1.0.0/baystability/R/common-validate.R |only baystability-1.0.0/baystability/R/core-data.R |only baystability-1.0.0/baystability/R/core-gibbs.R |only baystability-1.0.0/baystability/R/core-layout.R |only baystability-1.0.0/baystability/R/cultivo.R |only baystability-1.0.0/baystability/R/deprecated.R |only baystability-1.0.0/baystability/R/e_eff.R | 110 - baystability-1.0.0/baystability/R/g_eff.R | 110 - baystability-1.0.0/baystability/R/ge_ammi.R | 219 -- baystability-1.0.0/baystability/R/ge_eff.R | 142 - baystability-1.0.0/baystability/R/ge_mean.R | 124 - baystability-1.0.0/baystability/R/ge_model.R | 111 - baystability-1.0.0/baystability/R/ge_var.R | 125 - baystability-1.0.0/baystability/R/matrix_k.R | 68 baystability-1.0.0/baystability/R/model_choice.R |only baystability-1.0.0/baystability/R/orthnorm.R | 107 - baystability-1.0.0/baystability/R/references.R |only baystability-1.0.0/baystability/README.md | 237 +- baystability-1.0.0/baystability/build |only baystability-1.0.0/baystability/inst/CITATION | 82 baystability-1.0.0/baystability/inst/REFERENCES.bib |only baystability-1.0.0/baystability/inst/doc |only baystability-1.0.0/baystability/inst/extdata |only baystability-1.0.0/baystability/inst/notation |only baystability-1.0.0/baystability/man/bayes_ammi.Rd | 564 ++---- baystability-1.0.0/baystability/man/bayes_ammi_biplot.Rd |only baystability-1.0.0/baystability/man/bayes_gge.Rd |only baystability-1.0.0/baystability/man/baystability-package.Rd |only baystability-1.0.0/baystability/man/bys-deprecated.Rd |only baystability-1.0.0/baystability/man/bys-draws.Rd |only baystability-1.0.0/baystability/man/bys-methods.Rd |only baystability-1.0.0/baystability/man/bys_app.Rd |only baystability-1.0.0/baystability/man/bys_cite.Rd |only baystability-1.0.0/baystability/man/bys_compare.Rd |only baystability-1.0.0/baystability/man/bys_contrasts.Rd |only baystability-1.0.0/baystability/man/bys_interpret.Rd |only baystability-1.0.0/baystability/man/bys_ls_ammi.Rd |only baystability-1.0.0/baystability/man/bys_ls_env_effects.Rd |only baystability-1.0.0/baystability/man/bys_ls_ge_effects.Rd |only baystability-1.0.0/baystability/man/bys_ls_gen_effects.Rd |only baystability-1.0.0/baystability/man/bys_ls_means.Rd |only baystability-1.0.0/baystability/man/bys_ls_model.Rd |only baystability-1.0.0/baystability/man/bys_ls_var.Rd |only baystability-1.0.0/baystability/man/bys_notation.Rd |only baystability-1.0.0/baystability/man/bys_orthonormal.Rd |only baystability-1.0.0/baystability/man/bys_priors.Rd |only baystability-1.0.0/baystability/man/bys_reference.Rd |only baystability-1.0.0/baystability/man/bys_save.Rd |only baystability-1.0.0/baystability/man/bys_theme.Rd |only baystability-1.0.0/baystability/man/cultivo2008.Rd | 59 baystability-1.0.0/baystability/man/figures |only baystability-1.0.0/baystability/src |only baystability-1.0.0/baystability/tests |only baystability-1.0.0/baystability/vignettes |only 81 files changed, 1703 insertions(+), 1821 deletions(-)
Title: Bayesian Estimation of the Additive Main Effects and
Multiplicative Interaction Model
Description: Bayesian estimation of the additive main effects and
multiplicative interaction (AMMI) model of multi-environment trials by
the Gibbs sampler of Crossa, Perez-Elizalde, Jarquin, Cotes, Viele, Liu
and Cornelius (2011) <doi:10.2135/cropsci2010.06.0343>: posterior
distributions of the overall mean, genotype and environment effects,
singular values, genotype and environment scores (von Mises-Fisher
conditionals on the constrained spheres) and error variance; several
chains with burn-in and thinning; posterior summaries with highest
posterior density intervals; the convergence diagnostics of
Raftery-Lewis, Heidelberger-Welch and Gelman-Rubin; the AMMI biplot with
highest posterior density regions for inference on genotypes and
environments; least-squares AMMI; and a plain-language interpretation of
every result, computed from its numbers. Beyond the article: unbalanced
trials with missing plots and cells (data augmentation),
environment-specific error variances, the Bayesian GGE (site [...truncated...]
Author: Muhammad Yaseen [aut, cre] ,
Jose Crossa [aut, ctb],
Sergio Perez-Elizalde [aut, ctb],
Diego Jarquin [aut, ctb],
Jose Miguel Cotes [aut, ctb],
Kert Viele [aut, ctb],
Genzhou Liu [aut, ctb],
Paul L. Cornelius [aut, ctb],
Julian Garcia Abadillo Velasco [...truncated...]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between bayesammi versions 0.3.0 dated 2024-11-22 and 1.0.0 dated 2026-11-10
DESCRIPTION | 87 ++- MD5 | 237 +++++++++- NAMESPACE | 79 ++- NEWS.md | 134 +++++- R/Maiz.R | 68 +-- R/RcppExports.R |only R/app.R |only R/bam_interpret.R |only R/bayes_ammi.R | 1039 +++++++++++++++++++++++------------------------ R/bayes_stability.R |only R/bayesammi-package.R |only R/biplots.R | 521 ++++++++++------------- R/common-notation.R |only R/common-objects.R |only R/common-plot.R |only R/common-reference.R |only R/common-validate.R |only R/core-data.R |only R/core-gibbs.R |only R/core-layout.R |only R/decisions.R |only R/e_eff.R | 105 +--- R/g_eff.R | 106 +--- R/ge_ammi.R | 212 +++------ R/ge_eff.R | 140 +----- R/ge_mean.R | 120 +---- R/ge_model.R | 111 +---- R/ge_var.R | 122 +---- R/indices.R |only R/matrix_k.R | 64 +- R/model_choice.R |only R/orthnorm.R | 128 ++--- R/references.R |only README.md | 311 ++++++++++---- build |only inst/CITATION | 348 +++++++++++++++ inst/REFERENCES.bib |only inst/doc |only inst/extdata |only inst/notation |only man/Maiz.Rd | 63 +- man/bam-draws.Rd |only man/bam-methods.Rd |only man/bam_ammi_indices.Rd |only man/bam_app.Rd |only man/bam_cite.Rd |only man/bam_compare.Rd |only man/bam_indices.Rd |only man/bam_interpret.Rd |only man/bam_notation.Rd |only man/bam_ppc.Rd |only man/bam_predict.Rd |only man/bam_priors.Rd |only man/bam_ranks.Rd |only man/bam_reference.Rd |only man/bam_save.Rd |only man/bam_stab_priors.Rd |only man/bam_stability.Rd |only man/bam_superiority.Rd |only man/bam_theme.Rd |only man/bam_winners.Rd |only man/bayes_ammi.Rd | 480 ++++++++++----------- man/bayes_stability.Rd |only man/bayesammi-package.Rd |only man/biplots.Rd | 153 +++++- man/e_eff.Rd | 47 +- man/figures |only man/g_eff.Rd | 49 +- man/ge_ammi.Rd | 83 ++- man/ge_eff.Rd | 59 +- man/ge_mean.Rd | 53 +- man/ge_model.Rd | 64 +- man/ge_var.Rd | 53 +- man/matrix_k.Rd | 40 + man/orthnorm.Rd | 44 + src |only tests |only vignettes |only 78 files changed, 2856 insertions(+), 2264 deletions(-)
Title: Modelling Survey Data (E.g., DHS) with Adjustment for Location
Perturbations
Description: Bayesian spatial models for survey data, such as Demographic and Health Survey (DHS), with spatial cluster location displacement adjustments. The package implements models for (1) continuous, (2) binary, (3) count and (4) spatially varying models for continuous outcomes. For more details see Bakar et al. (2026) <doi:10.1093/jrsssa/qnag068>.
Author: K. Shuvo Bakar [aut, cre] ,
Jahidur Rahman Khan [ctb] ,
Bernard Baffour [ctb]
Maintainer: K. Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between svyLocAdj versions 1.0.1 dated 2026-09-28 and 1.0.2 dated 2026-11-10
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- R/utility_fnc.R | 1 - README.md |only inst/ChangeLog | 6 ++++++ man/plot.svyLocAdj.Rd | 4 ---- man/summary.svyLocAdj.Rd | 3 --- 7 files changed, 16 insertions(+), 17 deletions(-)
Title: Context Engineering for Large Language Model Agents
Description: Context-engineering primitives for Artificial Intelligence (AI)
coding agents working in R. Assembles agent context from memory and
instruction files ('AGENTS.md', 'CLAUDE.md'), traces function call
blast radius across projects, generates project briefings, parses
source into Abstract Syntax Tree (AST) symbol indices, discovers
dependency graphs, and introspects installed packages.
Zero dependencies.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between saber versions 0.7.2 dated 2026-06-25 and 0.8.0 dated 2026-11-10
DESCRIPTION | 10 - MD5 | 95 +++++++++----- NAMESPACE | 14 ++ NEWS.md | 88 +++++++++++++ R/agent_context.R | 105 +++++++--------- R/blast.R | 37 ++++- R/briefing.R | 5 R/context_audit.R |only R/context_manifest.R |only R/context_select.R |only R/context_source.R |only R/doc_scan.R | 6 R/fn_graph.R | 8 - R/graph_svg.R | 7 - R/heartbeat.R |only R/md_sections.R |only R/pkg.R | 7 - R/pkg_graph.R | 6 R/projects.R | 30 +++- R/saber-package.R | 1 R/skill_manifest.R |only R/skill_metadata.R |only R/skill_paths.R |only R/skill_read.R |only R/src_symbols.R |only R/symbols.R | 9 - R/utils.R | 5 README.md | 148 +++++++++++++++++++++-- build |only inst/scripts/session-start.R | 79 +++++++++--- inst/skills |only inst/tinytest/test_agent_context.R | 64 +++++++++ inst/tinytest/test_agent_hygiene.R |only inst/tinytest/test_context_manifest.R |only inst/tinytest/test_heartbeat.R |only inst/tinytest/test_project_aliases.R |only inst/tinytest/test_session_start.R | 67 ++++++++++ inst/tinytest/test_session_start_compatibility.R |only inst/tinytest/test_skill_manifest.R |only inst/tinytest/test_src_symbols.R |only man/agent_context.Rd | 64 +++++---- man/blast_radius.Rd | 35 +++-- man/briefing.Rd | 16 +- man/context_audit.Rd |only man/context_manifest.Rd |only man/context_render.Rd |only man/default_src_exclude.Rd |only man/find_downstream.Rd | 7 - man/fn_graph.Rd | 16 +- man/git_commit_count_since.Rd |only man/git_log_since.Rd |only man/graph_svg.Rd | 20 +-- man/heartbeat.Rd |only man/pkg_exports.Rd | 6 man/pkg_graph.Rd | 14 +- man/projects.Rd | 10 - man/saber-package.Rd | 18 -- man/skill_manifest.Rd |only man/skill_read.Rd |only man/src_symbols.Rd |only man/symbols.Rd | 13 +- tests/tinytest.R | 8 + 62 files changed, 748 insertions(+), 270 deletions(-)
Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation. Calculations of propagated uncertainties are based on matrix calculus including covariance structure according to Arras 1998 <doi:10.3929/ethz-a-010113668> (first order), Wang & Iyer 2005 <doi:10.1088/0026-1394/42/5/011> (second order) and the Monte Carlo method of GUM Supplement 1 (2008) <doi:10.59161/JCGM101-2008>.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between propagate versions 1.2-0 dated 2026-07-27 and 1.3-0 dated 2026-11-10
propagate-1.2-0/propagate/README.md |only propagate-1.2-0/propagate/man/datasets.rd |only propagate-1.3-0/propagate/DESCRIPTION | 17 propagate-1.3-0/propagate/MD5 | 122 +++- propagate-1.3-0/propagate/NAMESPACE | 41 + propagate-1.3-0/propagate/NEWS | 44 + propagate-1.3-0/propagate/R/WelchSatter.R | 72 ++ propagate-1.3-0/propagate/R/bigcor.R | 3 propagate-1.3-0/propagate/R/conformity.R |only propagate-1.3-0/propagate/R/corDist.R |only propagate-1.3-0/propagate/R/distr-densities.R | 541 +++++++++++++++------ propagate-1.3-0/propagate/R/distr-samplers.R | 339 ++++--------- propagate-1.3-0/propagate/R/doGauge.R |only propagate-1.3-0/propagate/R/fitDistr.R | 237 ++++++++- propagate-1.3-0/propagate/R/interval.R | 91 ++- propagate-1.3-0/propagate/R/makeDat.R | 172 +++++- propagate-1.3-0/propagate/R/matrixStats.R | 2 propagate-1.3-0/propagate/R/mixCov.R | 59 -- propagate-1.3-0/propagate/R/numGrad.R | 2 propagate-1.3-0/propagate/R/numHess.R | 2 propagate-1.3-0/propagate/R/plot.propagate.R | 20 propagate-1.3-0/propagate/R/predictNLS.R | 245 +++++---- propagate-1.3-0/propagate/R/propagate.R | 411 +++++++++++++-- propagate-1.3-0/propagate/R/propagateMV.R |only propagate-1.3-0/propagate/R/report.R |only propagate-1.3-0/propagate/R/sobol.R | 146 +++-- propagate-1.3-0/propagate/R/statVec.R | 16 propagate-1.3-0/propagate/R/stochContr.R | 124 ++-- propagate-1.3-0/propagate/R/summary.propagate.R | 425 +++++++++++++--- propagate-1.3-0/propagate/R/utils.R | 163 ------ propagate-1.3-0/propagate/build/partial.rdb |binary propagate-1.3-0/propagate/build/vignette.rds |only propagate-1.3-0/propagate/data/H.1.rda |only propagate-1.3-0/propagate/data/H.5.rda |only propagate-1.3-0/propagate/data/H.6.rda |only propagate-1.3-0/propagate/data/QUAM.A4.rda |only propagate-1.3-0/propagate/data/QUAM.A5.rda |only propagate-1.3-0/propagate/data/S1.9.3.rda |only propagate-1.3-0/propagate/data/S1.9.5.rda |only propagate-1.3-0/propagate/data/S2.9.4.rda |only propagate-1.3-0/propagate/data/S2.9.5.rda |only propagate-1.3-0/propagate/data/TN.E11.rda |only propagate-1.3-0/propagate/data/TN.E2.rda |only propagate-1.3-0/propagate/demo |only propagate-1.3-0/propagate/inst |only propagate-1.3-0/propagate/man/WelchSatter.Rd | 114 +++- propagate-1.3-0/propagate/man/bigcor.Rd | 23 propagate-1.3-0/propagate/man/conformity.Rd |only propagate-1.3-0/propagate/man/cor2cov.Rd | 22 propagate-1.3-0/propagate/man/corDist.Rd |only propagate-1.3-0/propagate/man/datasets.Rd |only propagate-1.3-0/propagate/man/doGauge.Rd |only propagate-1.3-0/propagate/man/fitDistr.Rd | 204 +++++-- propagate-1.3-0/propagate/man/interval.Rd | 143 ++--- propagate-1.3-0/propagate/man/makeDat.Rd | 99 +++ propagate-1.3-0/propagate/man/makeDerivs.Rd | 19 propagate-1.3-0/propagate/man/matrixStats.Rd | 13 propagate-1.3-0/propagate/man/mixCov.Rd | 53 +- propagate-1.3-0/propagate/man/moments.Rd | 11 propagate-1.3-0/propagate/man/numDerivs.Rd | 19 propagate-1.3-0/propagate/man/plot.propagate.Rd | 15 propagate-1.3-0/propagate/man/predictNLS.Rd | 102 ++- propagate-1.3-0/propagate/man/propagate.Rd | 433 ++++++++-------- propagate-1.3-0/propagate/man/propagateMV.Rd |only propagate-1.3-0/propagate/man/rDistr.Rd | 90 ++- propagate-1.3-0/propagate/man/report.Rd |only propagate-1.3-0/propagate/man/sobol.Rd | 179 ++++-- propagate-1.3-0/propagate/man/statVec.Rd | 20 propagate-1.3-0/propagate/man/stochContr.Rd | 34 - propagate-1.3-0/propagate/man/summary.propagate.Rd | 230 ++++++-- propagate-1.3-0/propagate/vignettes |only 71 files changed, 3319 insertions(+), 1798 deletions(-)
Title: Matrix End-to-End Encryption Primitives
Description: 'Olm' and 'Megolm' encryption ratchet primitives for the
'Matrix' messaging protocol <https://matrix.org/>, wrapping the
'vodozemac' Rust crate. Provides device-key generation, one-time-key
management, 1:1 'Olm' sessions, and 'Megolm' group sessions. Pairs
with the 'mx.api' package, which handles 'Matrix' HTTP transport.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
The Matrix.org Foundation C.I.C. [ctb, cph] ,
Authors of the dependency Rust crates [ctb]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.crypto versions 0.2.2 dated 2026-09-11 and 0.3.0 dated 2026-11-10
DESCRIPTION | 8 +- MD5 | 109 ++++++++++++++++++------------------ NAMESPACE | 2 NEWS.md | 25 ++++++++ R/account.R | 21 ++++++ R/attachment.R |only R/cross-signing.R | 23 +++++++ R/megolm.R | 67 ++++++++++++++++++++++ R/olm.R | 59 +++++++++++++++++++ R/roxido.R | 2 R/sas.R | 36 +++++++++++ build/partial.rdb |binary inst/AUTHORS | 5 + inst/tinytest/test_attachment.R |only inst/tinytest/test_olm.R | 63 ++++++++++++++++++++ man/mxc_account_fallback_key.Rd | 5 + man/mxc_account_mark_published.Rd | 7 ++ man/mxc_account_pickle.Rd | 6 + man/mxc_account_unpickle.Rd | 7 ++ man/mxc_attachment_decrypt.Rd |only man/mxc_attachment_encrypt.Rd |only man/mxc_megolm_decrypt.Rd | 8 ++ man/mxc_megolm_encrypt.Rd | 6 + man/mxc_megolm_inbound_export.Rd | 7 ++ man/mxc_megolm_inbound_import.Rd | 7 ++ man/mxc_megolm_inbound_info.Rd | 5 + man/mxc_megolm_inbound_new.Rd | 6 + man/mxc_megolm_inbound_pickle.Rd | 7 ++ man/mxc_megolm_inbound_unpickle.Rd | 8 ++ man/mxc_megolm_outbound_info.Rd | 7 ++ man/mxc_megolm_outbound_new.Rd | 4 + man/mxc_megolm_outbound_pickle.Rd | 6 + man/mxc_megolm_outbound_unpickle.Rd | 8 ++ man/mxc_olm_create_inbound.Rd | 12 +++ man/mxc_olm_create_outbound.Rd | 8 ++ man/mxc_olm_decrypt.Rd | 13 ++++ man/mxc_olm_encrypt.Rd | 10 +++ man/mxc_olm_session_pickle.Rd | 10 +++ man/mxc_olm_session_unpickle.Rd | 12 +++ man/mxc_sas_bytes.Rd | 8 ++ man/mxc_sas_commitment.Rd | 4 + man/mxc_sas_establish.Rd | 6 + man/mxc_sas_mac.Rd | 7 ++ man/mxc_sas_new.Rd | 4 + man/mxc_sas_public.Rd | 4 + man/mxc_sas_verify_mac.Rd | 10 +++ man/mxc_signing_key_new.Rd | 4 + man/mxc_signing_key_pickle.Rd | 6 + man/mxc_signing_key_public.Rd | 5 + man/mxc_signing_key_sign.Rd | 6 + man/mxc_signing_key_unpickle.Rd | 7 ++ man/mxc_verify_device_keys.Rd | 12 +++ man/mxc_verify_one_time_key.Rd | 12 +++ src/rust/Cargo.lock | 12 +++ src/rust/Cargo.toml | 3 src/rust/src/attachment.rs |only src/rust/src/lib.rs | 20 ++++++ src/rust/vendor.tar.xz |binary 58 files changed, 658 insertions(+), 61 deletions(-)
Title: Minimal Matrix Client-Server API
Description: A minimal-dependency client for the 'Matrix' Client-Server
HTTP API <https://spec.matrix.org/>, suitable for talking to a
'Synapse' <https://element-hq.github.io/synapse/> or 'Conduit'
<https://conduit.rs/> homeserver. Covers login, room management,
message send and history, media upload or download, and the
transport endpoints needed to coordinate end-to-end encryption
(device-key and one-time-key publication, key query and claim,
to-device events). Encryption itself is out of scope;
pair with a separate crypto package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.api versions 0.3.1 dated 2026-09-10 and 0.4.0 dated 2026-11-10
mx.api |only 1 file changed
Title: Fourier ARDL Methods: Quantile, Nonlinear, Multi-Threshold &
Unit Root Tests
Description: Implementation of ARDL methods for cointegration analysis with
structural breaks and asymmetric effects. Includes: (1) Fourier Quantile
ARDL (FQARDL), quantile regression with Fourier approximation following
the quantile ARDL of Cho, Kim and Shin (2015)
<doi:10.1016/j.jeconom.2015.05.003>; (2) Fourier Nonlinear ARDL (FNARDL),
asymmetric cointegration with partial sum decomposition following Shin,
Yu and Greenwood-Nimmo (2014) <doi:10.1007/978-1-4899-8008-3_9>;
(3) a deprecated Multi-Threshold NARDL (MTNARDL) function; (4) Fourier
unit root tests, ADF and KPSS tests with Fourier terms following Enders
and Lee (2012) <doi:10.1016/j.econlet.2012.04.081> and Becker, Enders and
Lee (2006) <doi:10.1111/j.1467-9892.2006.00478.x>. Features automatic lag
and frequency selection, Wald bounds statistics with the tables of
Pesaran, Shin and Smith (2001) <doi:10.1002/jae.616> (no verdict with
Fourier terms, for which the tables are not valid), recursive bootstrap
bound [...truncated...]
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between fqardl versions 1.1.0 dated 2026-10-10 and 1.1.1 dated 2026-11-10
DESCRIPTION | 8 MD5 | 24 +- NAMESPACE | 1 NEWS.md | 10 + R/fnardl.R | 293 +++++++++++++++++++++++++------- R/plots_nardl.R | 78 +++----- man/compute_asymmetric_multipliers.Rd | 9 man/dynamic_multipliers.Rd |only man/plot_cumulative_multipliers.Rd | 9 man/plot_dynamic_multipliers.Rd | 9 man/test_asymmetry.Rd | 40 +++- tests/testthat/test-bootstrap-1.1.0.R | 2 tests/testthat/test-fnardl.R | 15 + tests/testthat/test-nardl-paper-1.1.1.R |only 14 files changed, 358 insertions(+), 140 deletions(-)