Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.1 dated 2024-06-30 and 0.8.2 dated 2025-10-02
DESCRIPTION | 15 MD5 | 118 +- NAMESPACE | 264 ++-- NEWS | 7 R/AIC.R | 328 ++--- R/accessors.R | 418 +++---- R/fastLasso.R | 100 - R/initialSubsets.R | 100 - R/nci60.R | 188 +-- R/perry.R | 314 ++--- R/plot.R | 1780 +++++++++++++++---------------- R/print.R | 374 +++--- R/regFun.R | 114 - R/robustHD-package.R | 58 - R/seqModel.R | 212 +-- R/setupCoefPlot.R | 570 ++++----- R/setupCritPlot.R | 478 ++++---- R/standardize.R | 260 ++-- R/test.R | 62 - R/tsBlocks.R | 180 +-- R/utils.R | 512 ++++---- R/weights.R | 124 +- build/partial.rdb |binary data/TopGear.RData |binary data/nci60.RData |binary man/AIC.seqModel.Rd | 216 +-- man/coef.seqModel.Rd | 230 ++-- man/coefPlot.Rd | 264 ++-- man/corHuber.Rd | 228 +-- man/critPlot.Rd | 246 ++-- man/diagnosticPlot.Rd | 400 +++--- man/fitted.seqModel.Rd | 222 +-- man/getScale.Rd | 138 +- man/grplars.Rd | 544 ++++----- man/lambda0.Rd | 230 ++-- man/nci60.Rd | 176 +-- man/partialOrder.Rd | 84 - man/perry.seqModel.Rd | 286 ++-- man/plot.seqModel.Rd | 190 +-- man/predict.seqModel.Rd | 242 ++-- man/residuals.seqModel.Rd | 238 ++-- man/rlars.Rd | 478 ++++---- man/robustHD-package.Rd | 68 - man/setupCoefPlot.Rd | 312 ++--- man/setupCritPlot.Rd | 296 ++--- man/setupDiagnosticPlot.Rd | 322 ++--- man/sparseLTS.Rd | 594 +++++----- man/standardize.Rd | 152 +- man/tsBlocks.Rd | 82 - man/tslars.Rd | 402 +++---- man/tslarsP.Rd | 458 +++---- man/weights.sparseLTS.Rd | 172 +- man/winsorize.Rd | 252 ++-- src/fastGrplars.cpp | 399 +++--- src/fastLars.cpp | 31 src/fastSparseLTS.cpp | 2 tests/testthat.R | 8 tests/testthat/test-fastLasso-highdim.R | 102 - tests/testthat/test-fastLasso-multiple.R | 132 +- tests/testthat/test-fastLasso-simple.R | 124 +- 60 files changed, 7451 insertions(+), 7445 deletions(-)
Title: (Robust) Canonical Correlation Analysis via Projection Pursuit
Description: Canonical correlation analysis and maximum correlation via
projection pursuit, as well as fast implementations of correlation
estimators, with a focus on robust and nonparametric methods.
Author: Andreas Alfons [aut, cre] ,
David Simcha [ctb] ) implementation of Kendall correlation)
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between ccaPP versions 0.3.4 dated 2024-09-04 and 0.3.5 dated 2025-10-02
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary data/diabetes.RData |binary inst/doc/ccaPP-intro.pdf |binary src/cca.cpp | 4 ++-- vignettes/maxCor.bib | 2 +- 9 files changed, 24 insertions(+), 18 deletions(-)
Title: Access the UNESCO Institute for Statistics API
Description: Retrieve data from the UNESCO Institute for Statistics (UIS) API
<https://api.uis.unesco.org/api/public/documentation/>. UIS provides public
access to more than 4,000 indicators focusing on education, science and
technology, culture, and communication.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between uisapi versions 0.1.0 dated 2025-03-06 and 0.1.1 dated 2025-10-02
DESCRIPTION | 10 ++--- MD5 | 8 ++-- NEWS.md | 4 ++ R/uis_get_indicators.R | 5 ++ README.md | 96 +++++++++++++++++++++++++++++++------------------ 5 files changed, 79 insertions(+), 44 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.8.0 dated 2024-01-09 and 0.8.4 dated 2025-10-02
tidyseurat-0.8.0/tidyseurat/build/tidyseurat.pdf |only tidyseurat-0.8.0/tidyseurat/tests/testthat/Rplots.pdf |only tidyseurat-0.8.4/tidyseurat/DESCRIPTION | 20 tidyseurat-0.8.4/tidyseurat/MD5 | 42 - tidyseurat-0.8.4/tidyseurat/NAMESPACE | 3 tidyseurat-0.8.4/tidyseurat/R/dplyr_methods.R | 2 tidyseurat-0.8.4/tidyseurat/R/methods.R | 4 tidyseurat-0.8.4/tidyseurat/R/print_method.R | 1 tidyseurat-0.8.4/tidyseurat/R/tidyr_methods.R | 2 tidyseurat-0.8.4/tidyseurat/R/utilities.R | 23 tidyseurat-0.8.4/tidyseurat/README.md | 8 tidyseurat-0.8.4/tidyseurat/build/stage23.rdb |binary tidyseurat-0.8.4/tidyseurat/build/vignette.rds |binary tidyseurat-0.8.4/tidyseurat/inst/doc/figures_article.R | 316 +++++------ tidyseurat-0.8.4/tidyseurat/inst/doc/figures_article.html | 189 +++---- tidyseurat-0.8.4/tidyseurat/inst/doc/introduction.R | 286 +++++----- tidyseurat-0.8.4/tidyseurat/inst/doc/introduction.html | 372 ++++++-------- tidyseurat-0.8.4/tidyseurat/man/as_tibble.Rd | 2 tidyseurat-0.8.4/tidyseurat/man/formatting.Rd | 2 tidyseurat-0.8.4/tidyseurat/man/fragments/intro.Rmd | 3 tidyseurat-0.8.4/tidyseurat/man/ggplot.Rd | 3 tidyseurat-0.8.4/tidyseurat/man/slice.Rd | 4 tidyseurat-0.8.4/tidyseurat/tests/testthat/test-methods.R | 5 23 files changed, 623 insertions(+), 664 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.4 dated 2025-08-20 and 4.5 dated 2025-10-02
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 3 R/Analyze.CondPoisson.R | 6 - R/Analyze.Multinomial.R | 214 +++++++++++++++++++++++++++------------- R/AnalyzeSetUp.CondPoisson.R | 4 R/AnalyzeSetUp.Multinomial.R | 15 +- man/Analyze.Multinomial.Rd | 128 +++++++++++++++-------- man/AnalyzeSetUp.Multinomial.Rd | 7 - man/Sequential-package.Rd | 14 ++ 10 files changed, 272 insertions(+), 147 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 0.3.1 dated 2025-08-19 and 0.3.2 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test_mbo_defaults.R | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: General Linear Mixed Models for Gene-Level Differential
Expression
Description: Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine <doi:10.1038/s41591-022-01789-0>.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Elisabetta Sciacca [aut] ,
Cankut Cubuk [ctb] ,
Anna Surace [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between glmmSeq versions 0.5.5 dated 2022-10-08 and 0.5.7 dated 2025-10-02
DESCRIPTION | 27 MD5 | 30 NAMESPACE | 3 NEWS.md | 9 R/AllClass.R | 6 R/glmmRefit.R | 2 R/glmmSeq.R | 17 R/lmmSeq.R | 12 README.md | 4 build/vignette.rds |binary inst/doc/glmmSeq.R | 132 +- inst/doc/glmmSeq.html | 2704 ++++++++++++++++++++++++++------------------------ inst/doc/glmmSeq.rmd | 4 man/glmmRefit.Rd | 2 man/lmmSeq.Rd | 2 vignettes/glmmSeq.rmd | 4 16 files changed, 1545 insertions(+), 1413 deletions(-)
Title: Accounting for Random Displacements of True GPS Coordinates of
Data
Description: The purpose is to account for the random displacements
(jittering) of true survey household cluster center coordinates in geostatistical
analyses of Demographic and Health Surveys program (DHS) data. Adjustment for
jittering can be implemented either in the spatial random effect, or in the
raster/distance based covariates, or in both. Detailed information about the methods
behind the package functionality can be found in our two papers.
Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2024) <doi:10.32614/RJ-2024-027>.
Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2023) <doi:10.1177/1471082X231219847>.
Author: Umut Altay [cre, aut],
John Paige [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Umut Altay <altayumut.ua@gmail.com>
Diff between GeoAdjust versions 2.0.0 dated 2023-09-15 and 2.0.1 dated 2025-10-02
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/plotPred.R | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: A Data Analysis GUI for R
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows [aut, cre]
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between Deducer versions 0.9-0 dated 2025-05-07 and 0.9-1 dated 2025-10-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- inst/java/deducer.jar |binary java/org/deducer.jar |binary 5 files changed, 9 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-14 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-24 0.4.1
2019-02-15 0.4.0
2018-12-17 0.3.0
2018-09-27 0.2.2
2018-09-16 0.2.1
Title: Continuous Time Mediation
Description: Calculates effect sizes, standard errors and confidence intervals
in continuous-time mediation models
(Deboeck and Preacher, 2015 <doi:10.1080/10705511.2014.973960>;
Ryan and Hamaker, 2021 <doi:10.1007/s11336-021-09767-0>).
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.6 dated 2025-02-21 and 1.0.7 dated 2025-10-02
DESCRIPTION | 25 ++-- MD5 | 178 ++++++++++++++--------------- NEWS.md | 6 R/cTMed-boot-beta-dot.R | 11 - R/cTMed-boot-beta-std-dot.R | 41 ++---- R/cTMed-boot-beta-std.R | 4 R/cTMed-boot-beta.R | 4 R/cTMed-boot-central-dot.R | 11 - R/cTMed-boot-ci-dot.R | 106 ++++++++--------- R/cTMed-boot-indirect-central.R | 4 R/cTMed-boot-med-dot.R | 11 - R/cTMed-boot-med-std-dot.R | 59 ++++----- R/cTMed-boot-med-std.R | 8 - R/cTMed-boot-med.R | 8 - R/cTMed-boot-total-central.R | 4 R/cTMed-delta-beta-dot.R | 28 +--- R/cTMed-delta-beta-std-dot.R | 28 +--- R/cTMed-delta-beta-std.R | 2 R/cTMed-delta-beta.R | 2 R/cTMed-delta-central-dot.R | 30 ++-- R/cTMed-delta-ci-dot.R | 90 +++++++------- R/cTMed-delta-indirect-central.R | 2 R/cTMed-delta-med-dot.R | 34 ++--- R/cTMed-delta-med-std-dot.R | 34 ++--- R/cTMed-delta-med-std.R | 6 R/cTMed-delta-med.R | 6 R/cTMed-delta-total-central.R | 2 R/cTMed-direct-std.R | 6 R/cTMed-direct.R | 6 R/cTMed-indirect-central.R | 2 R/cTMed-indirect-std.R | 6 R/cTMed-indirect.R | 6 R/cTMed-mc-beta-dot.R | 41 ++---- R/cTMed-mc-beta-std-dot.R | 71 ++++------- R/cTMed-mc-beta-std.R | 2 R/cTMed-mc-beta.R | 2 R/cTMed-mc-central-dot.R | 41 ++---- R/cTMed-mc-ci-dot.R | 64 +++++----- R/cTMed-mc-indirect-central.R | 2 R/cTMed-mc-med-dot.R | 41 ++---- R/cTMed-mc-med-std-dot.R | 89 ++++++-------- R/cTMed-mc-med-std.R | 6 R/cTMed-mc-med.R | 6 R/cTMed-mc-phi-sigma.R | 24 +-- R/cTMed-mc-phi.R | 24 +-- R/cTMed-mc-total-central.R | 2 R/cTMed-med-std.R | 6 R/cTMed-med.R | 6 R/cTMed-methods-ctmedboot.R | 42 ++---- R/cTMed-methods-ctmeddelta.R | 38 ++---- R/cTMed-methods-ctmedmc.R | 38 ++---- R/cTMed-methods-ctmedmcphi.R | 2 R/cTMed-methods-ctmedmed.R | 69 +++++------ R/cTMed-methods-ctmedposteriorphi.R | 10 - R/cTMed-methods-ctmedtraj.R | 18 -- R/cTMed-plot-beta-ci-dot.R | 1 R/cTMed-plot-central-ci-dot.R | 1 R/cTMed-plot-central-dot.R | 1 R/cTMed-plot-med-ci-dot.R | 1 R/cTMed-plot-med-dot.R | 1 R/cTMed-plot-trajectory-dot.R | 1 R/cTMed-posterior-beta-dot.R | 13 -- R/cTMed-posterior-beta.R | 2 R/cTMed-posterior-central-dot.R | 44 ++----- R/cTMed-posterior-indirect-central.R | 2 R/cTMed-posterior-med-dot.R | 44 ++----- R/cTMed-posterior-med.R | 6 R/cTMed-posterior-total-central.R | 2 R/cTMed-total-central.R | 2 R/cTMed-total-std.R | 2 R/cTMed-total.R | 2 R/cTMed-trajectory.R | 2 R/wald-ci-wald-dot.R | 4 R/wald-probs-of-alpha-dot.R | 10 - build/partial.rdb |binary inst/CITATION | 2 man/BootBeta.Rd | 2 man/BootBetaStd.Rd | 2 man/BootIndirectCentral.Rd | 2 man/BootMed.Rd | 2 man/BootMedStd.Rd | 2 man/BootTotalCentral.Rd | 2 man/cTMed-package.Rd | 2 src/source.cpp | 16 +- tests/testthat/test-cTMed-boot-beta-std.R | 20 --- tests/testthat/test-cTMed-boot-med-std.R | 16 -- tests/testthat/test-cTMed-delta-beta-std.R | 4 tests/testthat/test-cTMed-mc-beta-std.R | 4 tests/testthat/test-cTMed-mc-phi-sigma.R | 8 - tests/testthat/test-cTMed-total-std.R | 8 - 90 files changed, 709 insertions(+), 938 deletions(-)