Title: Graphical Elements of the University of Konstanz's Corporate
Design
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package <doi:10.5281/zenodo.7096191> provides color functions (by defining dedicated colors and color palettes, and commands for finding, changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text decoration functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other purposes or institutions.
Author: Hansjoerg Neth [aut, cre] ,
Nico Gradwohl [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between unikn versions 1.0.0 dated 2024-04-16 and 1.1.0 dated 2026-11-11
DESCRIPTION | 23 +- MD5 | 138 +++++++------ NAMESPACE | 30 ++ NEWS.md | 56 ++++- R/color_def_1.R | 11 + R/color_fun_1.R | 221 ++++++++++------------ R/color_fun_2.R | 94 +++++++++ R/plot_cube.R |only R/plot_demo.R | 109 ++++++++++ R/plot_kn.R | 8 R/plot_themes.R | 411 +++++++++++++++++++++++++++++++++++------ README.md | 148 +++++++++----- build/vignette.rds |binary inst/CITATION | 8 inst/doc/color_functions.R | 31 +-- inst/doc/color_functions.Rmd | 8 inst/doc/color_functions.html | 237 ++++++++++++----------- inst/doc/color_recipes.R | 102 +++++----- inst/doc/color_recipes.html | 33 +-- inst/doc/inst_colors.Rmd | 6 inst/doc/inst_colors.html | 30 +- inst/doc/text_decorations.R | 336 ++++++++++++++++----------------- inst/doc/text_decorations.html | 53 ++--- inst/pix/logo.png |only inst/pix/logo_unicol.png |binary inst/pix/logo_unicol_old.png |only man/Bordeaux.Rd | 7 man/Grau.Rd | 7 man/Karpfenblau.Rd | 7 man/Peach.Rd | 7 man/Petrol.Rd | 7 man/Pinky.Rd | 7 man/Seeblau.Rd | 7 man/Seegruen.Rd | 7 man/Signal.Rd | 7 man/ac.Rd | 17 - man/all_colors.Rd | 2 man/demopal.Rd | 17 - man/grepal.Rd | 17 - man/mark.Rd | 8 man/newpal.Rd | 17 - man/pal_bordeaux.Rd | 7 man/pal_grau.Rd | 7 man/pal_karpfenblau.Rd | 7 man/pal_peach.Rd | 7 man/pal_petrol.Rd | 7 man/pal_pinky.Rd | 7 man/pal_seeblau.Rd | 7 man/pal_seegruen.Rd | 7 man/pal_signal.Rd | 7 man/pal_unikn.Rd | 7 man/pal_unikn_dark.Rd | 7 man/pal_unikn_light.Rd | 7 man/pal_unikn_pair.Rd | 7 man/pal_unikn_ppt.Rd | 7 man/pal_unikn_pref.Rd | 7 man/pal_unikn_web.Rd | 7 man/plot_cube.Rd |only man/post.Rd | 8 man/seecol.Rd | 77 +++++-- man/shades_of.Rd | 17 - man/simcol.Rd | 17 - man/slide.Rd | 10 man/theme_bwkn.Rd |only man/theme_grau.Rd | 43 ++-- man/theme_minikn.Rd |only man/theme_unikn.Rd | 40 ++- man/uline.Rd | 8 man/url_unikn.Rd | 8 man/usecol.Rd | 17 - man/xbox.Rd | 10 vignettes/color_functions.Rmd | 8 vignettes/inst_colors.Rmd | 6 73 files changed, 1592 insertions(+), 1023 deletions(-)
Title: Globally-Applicable Area Disaggregated General Ecosystem Toolbox
V3
Description: A framework to assist creation of marine ecosystem models,
generating either 'R' or 'C++' code which can then be optimised using
the 'TMB' package and standard 'R' tools. Principally designed to
reproduce gadget2 models in 'TMB', but can be extended beyond
gadget2's capabilities.
Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.".
Begley, J., & Howell, D. (2004) <doi:10.17895/ices.pub.25349308> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Author: Jamie Lentin [aut, cre] ,
Bjarki Thor Elvarsson [aut] ,
William Butler [aut] ,
Marine and Freshwater Research Institute [cph]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between gadget3 versions 0.15-1 dated 2026-01-12 and 1.0-0 dated 2026-11-11
DESCRIPTION | 15 +++++---- MD5 | 28 +++++++++--------- NAMESPACE | 4 ++ NEWS.md | 5 +++ R/aab_env.R | 12 +++++-- R/action_grow.R | 8 +++-- R/env_dif.R | 2 - R/param_project.R | 4 +- R/quota.R | 3 + inst/doc/introduction-single-stock.html | 16 +++++----- inst/doc/model-structure.html | 44 +++++++++++++++------------- inst/doc/writing_actions.html | 4 +- tests/test-action_grow.R | 4 +- tests/test-stock_time.R | 48 +++++++++++++++---------------- vignettes/random-effect-recruitment.R |only vignettes/random-effect-recruitment.html |only 16 files changed, 112 insertions(+), 85 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues. Provides formula and matrix interfaces for count and
cumulative-link ordinal models, mean bias reduction, and fitting from data read in blocks of rows for supported
model classes.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph],
Noah Greifer [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.1.3 dated 2026-11-09 and 0.1.4 dated 2026-11-11
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ NEWS.md | 12 ++++++++ inst/doc/fastglm.html | 12 ++++---- inst/doc/firth-fastglm.html | 52 ++++++++++++++++++------------------- inst/include/ordinal_constrained.h | 3 ++ src/count_kernels.cpp | 4 +- src/fit_glm_dense.cpp | 2 - tests/testthat/test-sources.R | 1 9 files changed, 62 insertions(+), 46 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.8.0 dated 2026-03-25 and 1.8.1 dated 2026-11-11
DESCRIPTION | 12 - MD5 | 114 +++++------ NAMESPACE | 12 - NEWS.md | 4 R/accessors.R | 47 +++- R/epiweek-class.R | 11 - R/grates-package.R | 3 R/isoweek-class.R | 11 - R/month-class.R | 3 R/month-utils.R | 3 R/yearmonth-class.R | 3 R/yearweek-class.R | 46 ---- build/vignette.rds |binary inst/doc/grates.html | 42 ++-- man/grates-package.Rd | 5 man/grouped_date_accessors.Rd | 6 src |only tests/testthat/_snaps/plots/epiweek.png |binary tests/testthat/_snaps/plots/epiweek2025.png |binary tests/testthat/_snaps/plots/epiweek_breaks.png |binary tests/testthat/_snaps/plots/epiweek_breaks_dates.png |binary tests/testthat/_snaps/plots/epiweek_weeks.png |binary tests/testthat/_snaps/plots/isoweek.png |binary tests/testthat/_snaps/plots/isoweek2025.png |binary tests/testthat/_snaps/plots/isoweek_breaks.png |binary tests/testthat/_snaps/plots/isoweek_breaks_dates.png |binary tests/testthat/_snaps/plots/isoweek_weeks.png |binary tests/testthat/_snaps/plots/month.png |binary tests/testthat/_snaps/plots/month2.png |binary tests/testthat/_snaps/plots/month_breaks.png |binary tests/testthat/_snaps/plots/p_breaks.png |binary tests/testthat/_snaps/plots/p_breaks_centred.png |binary tests/testthat/_snaps/plots/p_one.png |binary tests/testthat/_snaps/plots/p_two.png |binary tests/testthat/_snaps/plots/twentyeight_days.png |binary tests/testthat/_snaps/plots/twentyeight_days_breaks.png |binary tests/testthat/_snaps/plots/two_weeks.png |binary tests/testthat/_snaps/plots/two_weeks_breaks.png |binary tests/testthat/_snaps/plots/year.png |binary tests/testthat/_snaps/plots/year2.png |binary tests/testthat/_snaps/plots/year2_breaks.png |binary tests/testthat/_snaps/plots/year_breaks.png |binary tests/testthat/_snaps/plots/yearmonth.png |binary tests/testthat/_snaps/plots/yearmonth2.png |binary tests/testthat/_snaps/plots/yearmonth_breaks.png |binary tests/testthat/_snaps/plots/yearquarter.png |binary tests/testthat/_snaps/plots/yearquarter2.png |binary tests/testthat/_snaps/plots/yearquarter2_breaks.png |binary tests/testthat/_snaps/plots/yearquarter_breaks.png |binary tests/testthat/_snaps/plots/yearweek2023.png |binary tests/testthat/_snaps/plots/yearweek_monday.png |binary tests/testthat/_snaps/plots/yearweek_monday_breaks.png |binary tests/testthat/_snaps/plots/yearweek_thursday.png |binary tests/testthat/_snaps/plots/yearweek_thursday_breaks.png |binary tests/testthat/_snaps/plots/yearweek_thursday_weeks_only.png |binary tests/testthat/test-epiweek.R | 22 +- tests/testthat/test-isoweek.R | 22 +- tests/testthat/test-yearweek.R | 48 ++-- 58 files changed, 212 insertions(+), 202 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] ,
Austin Dickey [ctb],
Matthias Grenie [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb],
Emik Lin [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.24 dated 2026-10-01 and 0.4.25 dated 2026-11-11
DESCRIPTION | 8 ++--- MD5 | 10 +++--- NEWS.md | 4 ++ R/fortify_stats_lm.R | 35 +++++++++++++++--------- man/autoplot.lm.Rd | 2 - tests/testthat/test-stats-lm.R | 59 ++++++++++++++++++++++++++++++++++++++--- 6 files changed, 93 insertions(+), 25 deletions(-)
Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that
cannot be directly estimated from the data). These tools can be used
to define objects for creating, simulating, or validating values for
such parameters.
Author: Max Kuhn [aut],
Hannah Frick [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between dials versions 1.4.4 dated 2026-06-22 and 1.4.5 dated 2026-11-11
DESCRIPTION | 12 ++-- MD5 | 48 +++++++++------- NAMESPACE | 105 ++++++++++++++++++++++------------- NEWS.md | 10 +++ R/aaa_ranges.R | 4 - R/encode_unit.R | 4 - R/grids.R | 4 - R/hybrid.R |only R/param_engine_catboost.R | 86 ++++++++++++++++++++++++++++ R/param_ordinal_link.R | 7 +- R/param_parallel_reg.R |only R/param_threshold_structure.R |only R/parameters.R | 2 build/vignette.rds |binary man/catboost_parameters.Rd | 60 +++++++++++++++++++- man/grid_hybrid.Rd |only man/grid_space_filling.Rd | 6 +- man/ordinal_link.Rd | 6 +- man/parallel_reg.Rd |only man/rmd/sfd_notes.Rmd | 6 +- man/rmd/sfd_notes.md | 2 man/threshold_structure.Rd |only tests/testthat/_snaps/aaa_ranges.md | 4 - tests/testthat/_snaps/encode_unit.md | 6 +- tests/testthat/_snaps/grids.md | 4 - tests/testthat/_snaps/hybrid.md |only tests/testthat/_snaps/parameters.md | 4 - tests/testthat/test-hybrid.R |only tests/testthat/test-params.R | 11 +++ 29 files changed, 294 insertions(+), 97 deletions(-)
Title: eXtended Empirical Mode Decomposition
Description: Signals are decomposed into oscillatory modes by empirical mode
decomposition and its ensemble, complementary ensemble, complete
ensemble, masked, bivariate and multivariate variants, by variational
mode decomposition and its multivariate and successive variants, and by
local mean decomposition, iterative filtering, time varying filter
empirical mode decomposition and the empirical wavelet transform; the
synchrosqueezed wavelet transform is also provided. Empirical mode
decomposition is due to Huang et al. (1998)
<doi:10.1098/rspa.1998.0193>, its ensemble variant to Wu and Huang (2009)
<doi:10.1142/S1793536909000047> and variational mode decomposition to
Dragomiretskiy and Zosso (2014) <doi:10.1109/TSP.2013.2288675>. The
modes can be described by their instantaneous amplitude and frequency and
their Hilbert spectrum, tested as intrinsic mode functions or against
white noise, selected by energy and compared through orthogonality, mode
splitting, reconstruction quality, [...truncated...]
Author: Alejandro Daniel Verri [aut, cre, cph, trl] ,
G. Rilling [ctb] ,
Marcelo A. Colominas [cph] ,
Pierre Masselot [ctb] ,
Vinicius Rezende Carvalho [ctb, cph] ,
Eduardo Mazoni [cph] ,
Jerome Gilles [ctb, cph] ,
Kathryn Heal [ctb] ,
Emanuele Papini [ctb, [...truncated...]
Maintainer: Alejandro Daniel Verri <averri@fi.uba.ar>
Diff between xemd versions 0.1.5 dated 2026-11-08 and 0.1.6 dated 2026-11-11
xemd-0.1.5/xemd/inst/build.R |only xemd-0.1.5/xemd/inst/cran-check.R |only xemd-0.1.5/xemd/inst/cran-submit.R |only xemd-0.1.5/xemd/inst/install.R |only xemd-0.1.5/xemd/inst/package.R |only xemd-0.1.5/xemd/inst/rhub-check.R |only xemd-0.1.5/xemd/inst/rhub.R |only xemd-0.1.6/xemd/DESCRIPTION | 14 +++++----- xemd-0.1.6/xemd/LICENSE.note |only xemd-0.1.6/xemd/MD5 | 40 +++++++++++++------------------ xemd-0.1.6/xemd/NEWS.md | 25 +++++++++++++++++++ xemd-0.1.6/xemd/R/decomposeTSL.R | 12 ++++++--- xemd-0.1.6/xemd/R/measureModesTSL.R | 2 - xemd-0.1.6/xemd/inst/CITATION | 2 - xemd-0.1.6/xemd/inst/NOTICE | 5 ++- xemd-0.1.6/xemd/inst/api/operations.json | 8 ++++-- xemd-0.1.6/xemd/inst/doc/seismic.html | 8 +++--- xemd-0.1.6/xemd/inst/doc/xemd.Rmd | 2 - xemd-0.1.6/xemd/inst/doc/xemd.html | 6 ++-- xemd-0.1.6/xemd/man/decomposeTSL.Rd | 7 +++++ xemd-0.1.6/xemd/man/measureModesTSL.Rd | 2 - xemd-0.1.6/xemd/tests/testAnalysis.R | 3 +- xemd-0.1.6/xemd/tests/testExtractions.R | 7 +++-- xemd-0.1.6/xemd/tests/testTSL.R | 2 - xemd-0.1.6/xemd/vignettes/xemd.Rmd | 2 - 25 files changed, 93 insertions(+), 54 deletions(-)
Title: T-Rex Selector: High-Dimensional Variable Selection and FDR
Control
Description: Variable selection for regression and classification in high-dimensional
settings with control of the false discovery rate (FDR) at a user-specified target level.
The implementations are primarily based on the T-Rex selector of Machkour, Muma and
Palomar (2025) <doi:10.1016/j.sigpro.2025.109894> and its dependency-aware extension for
correlated variables by Machkour, Muma and Palomar (2025) <doi:10.1016/j.sigpro.2025.109990>.
Since version 2.0.0 the package comes as R bindings to the 'TRexSelector' C++ library, which
replaces the pure-R implementation of the 1.x releases.
Author: Jasin Machkour [aut, cre],
Fabian Scheidt [aut],
Simon Tien [ctb],
Daniel P. Palomar [aut],
Michael Muma [aut]
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
Diff between TRexSelector versions 2.0.0 dated 2026-11-06 and 2.0.1 dated 2026-11-11
TRexSelector |only 1 file changed
Title: Kriging-Based Inversion for Deterministic and Noisy Computer
Experiments
Description: Criteria and algorithms for sequentially estimating level sets of a multivariate numerical function, possibly observed with noise. The methods are described in Chevalier, Picheny and Ginsbourger (2014) <doi:10.1016/j.csda.2013.03.008> and Azzimonti, Ginsbourger, Chevalier, Bect and Richet (2021) <doi:10.1080/00401706.2019.1693427>.
Author: Clement Chevalier [aut],
Dario Azzimonti [aut, cre] ,
David Ginsbourger [aut] ,
Victor Picheny [aut] ,
Yann Richet [ctb]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between KrigInv versions 1.4.2 dated 2022-09-09 and 1.4.3 dated 2026-11-11
KrigInv |only 1 file changed
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 1.2.0 dated 2026-10-22 and 1.2.1 dated 2026-11-11
DESCRIPTION | 11 MD5 | 23 NEWS.md | 8 R/smap.R | 24 inst/doc/glycan-graph.html | 478 +++++++----------- inst/doc/glyrepr.html | 781 +++++++++++++----------------- inst/doc/smap.html | 638 +++++++++++------------- src/Makevars | 4 src/Makevars.win | 4 src/compact-core.h | 15 src/compact-iupac.cpp | 5 src/compact-syntax.h |only tests/testthat/test-native-locale.R |only tests/testthat/test-smap-key-collisions.R |only 14 files changed, 869 insertions(+), 1122 deletions(-)
Title: Multi-Purpose Core Subset Selection
Description: Core Hunter is a tool to sample diverse, representative subsets from large germplasm
collections, with minimum redundancy. Such so-called core collections have applications in plant
breeding and genetic resource management in general. Core Hunter can construct cores based on
genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many
provided evaluation measures depending on the precise purpose of the core (e.g. high diversity,
representativeness, or allelic richness). In addition, multiple measures can be simultaneously
optimized as part of a weighted index to bring the different perspectives closer together.
The Core Hunter library is implemented in Java 8 as an open source project (see
<http://www.corehunter.org>).
Author: Herman De Beukelaer [aut, cre],
Guy Davenport [aut],
Veerle Fack [ths]
Maintainer: Herman De Beukelaer <herman.debeukelaer@gmail.com>
Diff between corehunter versions 3.2.3 dated 2023-09-01 and 3.2.4 dated 2026-11-11
DESCRIPTION | 8 LICENSE | 4 MD5 | 86 NAMESPACE | 57 NEWS.md | 97 - R/analysis.R | 148 - R/corehunter-package.R | 130 - R/data.R | 2444 +++++++++++++-------------- R/execution.R | 1248 ++++++------- R/java.R | 186 +- R/zzz.R | 28 README.md | 134 - inst/extdata/distances.csv | 438 ++-- inst/extdata/genotypes-biparental.csv | 438 ++-- inst/extdata/genotypes-frequency.csv | 438 ++-- inst/extdata/genotypes.csv | 438 ++-- inst/extdata/phenotypes.csv | 440 ++-- inst/java/LICENSE | 402 ++-- inst/java/NOTICE | 100 - man/coreHunterData.Rd | 104 - man/corehunter-package.Rd | 162 - man/distances.Rd | 98 - man/evaluateCore.Rd | 82 man/exampleData.Rd | 66 man/genotypes.Rd | 280 +-- man/getAlleleFrequencies.Rd | 34 man/getNormalizationRanges.Rd | 242 +- man/objective.Rd | 242 +- man/phenotypes.Rd | 220 +- man/read.autodelim.Rd | 150 - man/sampleCore.Rd | 324 +-- man/setRange.Rd | 46 man/wrapData.Rd | 36 tests/test.R | 10 tests/testthat/data/distances-small.txt | 10 tests/testthat/data/genotypes-bi-small.csv | 10 tests/testthat/data/genotypes-freq-small.csv | 14 tests/testthat/data/genotypes-small.csv | 10 tests/testthat/data/phenotypes-single.csv | 22 tests/testthat/testAnalysis.R | 52 tests/testthat/testData.R | 1516 ++++++++-------- tests/testthat/testExecution.R | 510 ++--- tests/testthat/testJava.R | 106 - tests/testthat/testUtils.R | 312 +-- 44 files changed, 5965 insertions(+), 5957 deletions(-)
Title: Visualization and Polytomous Modeling of Survival and Competing
Risks
Description: A publication-ready toolkit for modern survival and competing risks
analysis with a minimal, formula-based interface. Both nonparametric
estimation and direct polytomous regression of cumulative incidence
functions (CIFs) are supported. The main functions 'cifcurve()', 'cifplot()',
and 'cifpanel()' estimate survival and CIF curves and produce high-quality
graphics with risk tables, censoring and competing-risk marks, and
multi-panel or inset layouts built on 'ggplot2' and 'ggsurvfit'. The modeling
function 'polyreg()' performs direct polytomous regression for coherent joint
modeling of all cause-specific CIFs to estimate risk ratios, odds ratios, or
subdistribution hazard ratios at user-specified time points. The function
'ciftest()' provides log-rank, Gray, robust score, augmented score, and
multiple-direction tests for survival and competing-risk outcomes. All core
functions adopt a formula-and-data syntax and return tidy and extensible
outputs that integrate smoothly with 'modelsumm [...truncated...]
Author: Shiro Tanaka [aut, cre, cph] ,
Shigetaka Kobari [ctb],
Chisato Honda [ctb]
Maintainer: Shiro Tanaka <gestimation@gmail.com>
Diff between cifmodeling versions 1.0.0 dated 2026-06-30 and 1.2.3 dated 2026-11-11
DESCRIPTION | 17 LICENSE | 4 MD5 | 220 +- NAMESPACE | 28 NEWS.md | 405 +++- R/Event.R | 7 R/RcppExports.R | 40 R/binregRatioLOP.R | 1212 ++++++------ R/calculateKM.R |only R/censoring-km.R |only R/cif-stat-arguments.R | 9 R/cifcurve-calculateCI.R | 110 - R/cifcurve-inference.R |only R/cifcurve-reporting.R |only R/cifcurve.R | 1754 +++++++++--------- R/cifpanel.R | 30 R/cifplot.R | 56 R/cifsimulate.R |only R/ciftest-mdir.R |only R/ciftest-phase2.R |only R/ciftest.R | 2356 +++++++++++++++++++++++++ R/extract_time_to_event.R | 18 R/functions-utility.R | 346 ++- R/functions-warning.R | 208 +- R/helper-cifpanel.R | 10 R/helper-cifplot.R | 107 - R/helper-polyreg.R | 25 R/ipcw.R |only R/output-interop.R |only R/output-style.R |only R/polyreg-IPCW-estimating-equations.R | 253 -- R/polyreg-calculate-ipcw.R | 69 R/polyreg-calculate-potential-CIFs.R | 154 + R/polyreg-initial-values.R | 100 - R/polyreg-methods.R | 108 + R/polyreg-outputs.R | 72 R/polyreg-reporting.R |only R/polyreg.R | 178 + README.md | 73 build/cifmodeling.pdf |only build/stage23.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/v1_overview.R | 4 inst/doc/v1_overview.Rmd | 13 inst/doc/v1_overview.html | 35 inst/doc/v2_polyreg.Rmd | 8 inst/doc/v2_polyreg.html | 43 inst/doc/v3_formulas.R |only inst/doc/v3_formulas.Rmd | 204 +- inst/doc/v3_formulas.html | 481 ++++- inst/doc/v4_examples.Rmd | 6 inst/doc/v4_examples.html | 42 inst/doc/v5_gallery.html | 20 inst/doc/v6_information.Rmd | 5 inst/doc/v6_information.html | 16 inst/doc/v7_arguments.R |only inst/doc/v7_arguments.Rmd | 58 inst/doc/v7_arguments.html | 275 ++ inst/doc/v8_reporting_cif.R |only inst/doc/v8_reporting_cif.Rmd |only inst/doc/v8_reporting_cif.html |only inst/doc/v9_reporting_polyreg.R |only inst/doc/v9_reporting_polyreg.Rmd |only inst/doc/v9_reporting_polyreg.html |only man/as_ggplot.Rd |only man/as_modelsummary.Rd |only man/as_prediction_data.Rd |only man/build_closed_form_augmentation.Rd |only man/build_fg_score_iid.Rd |only man/build_iterated_score_iid.Rd |only man/calculateKM.Rd |only man/calculate_gray.Rd |only man/censoring_km_score_correction.Rd |only man/cif-stat-arguments.Rd | 9 man/cifcurve.Rd | 89 man/cifmodeling-package.Rd | 2 man/cifpanel.Rd | 9 man/cifplot.Rd | 16 man/ciftest.Rd |only man/ciftest_iteration_setup.Rd |only man/ciftest_mdir.Rd |only man/diabetes.complications.Rd | 11 man/estimate_censoring_km.Rd |only man/estimate_working_aj.Rd |only man/extract_time_to_event.Rd | 4 man/polyreg-methods.Rd | 50 man/polyreg.Rd | 35 man/predict_censoring_km.Rd |only man/predict_working_aj.Rd |only man/prostate.Rd | 4 src/RcppExports.cpp | 243 ++ src/calculateAJ_Rcpp.cpp | 242 +- src/calculateKM.cpp | 34 src/ciftest_kernels.cpp |only tests/testthat.R | 24 tests/testthat/fixtures |only tests/testthat/helper-gray-reference.R |only tests/testthat/test-calculateCI.R | 2237 ++++++++++++----------- tests/testthat/test-calculateKM.R | 81 tests/testthat/test-cif-shared-input.R |only tests/testthat/test-cifcurve-inference.R |only tests/testthat/test-cifcurve-weight-presence.R |only tests/testthat/test-cifpanel.R | 49 tests/testthat/test-cifplot.R | 38 tests/testthat/test-cifsimulate.R |only tests/testthat/test-ciftest-event-strata.R |only tests/testthat/test-ciftest-phase2.R |only tests/testthat/test-ciftest.R | 502 +++++ tests/testthat/test-ipcw.R |only tests/testthat/test-output-interop.R |only tests/testthat/test-polyreg.R | 78 tests/testthat/test-potential-risk.R | 3 tests/testthat/test-release-regressions.R |only tests/testthat/test-reporting-cifcurve.R |only tests/testthat/test-reporting-ciftest.R |only tests/testthat/test-reporting-polyreg.R |only vignettes/fig/function-example04-1-1-1.png |binary vignettes/fig/function-example04-2-1-1.png |binary vignettes/fig/function-gallery-1-01-1.png |binary vignettes/fig/function-gallery-1-02-1.png |binary vignettes/fig/function-gallery-2-02-1.png |binary vignettes/fig/function-gallery-2-03-1.png |binary vignettes/fig/function-gallery-2-04-1.png |binary vignettes/fig/function-gallery-3-01-1.png |binary vignettes/fig/function-gallery-4-01-1.png |binary vignettes/fig/function-gallery-4-02-1.png |binary vignettes/fig/function-gallery-7-01-1.png |binary vignettes/fig/function-gallery-7-02-1.png |binary vignettes/fig/overview-example01-1-1.png |binary vignettes/v1_overview.Rmd | 13 vignettes/v2_polyreg.Rmd | 8 vignettes/v3_formulas.Rmd | 204 +- vignettes/v4_examples.Rmd | 6 vignettes/v6_information.Rmd | 5 vignettes/v7_arguments.Rmd | 58 vignettes/v8_reporting_cif.Rmd |only vignettes/v9_reporting_polyreg.Rmd |only 138 files changed, 9108 insertions(+), 4125 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-11 0.3.5
2017-12-05 0.3.4
2017-09-12 0.3.3
2017-08-28 0.3.2
2017-07-10 0.3.1
2017-06-28 0.3.0
2017-01-03 0.2.0
2016-11-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-13 1.0.1
2023-10-11 1.0.0
2023-08-23 0.5.0
2023-06-13 0.4.2
2022-06-20 0.4.1
2022-02-10 0.4.0
2021-01-30 0.3.0
2020-11-02 0.2.0
2020-09-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-03 1.2.2
2024-11-01 1.2.1
2024-07-26 1.1.1
2024-07-18 1.1.0
2024-03-07 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-15 0.1.1
2023-01-17 0.1.0
Title: Semi-Supervised Ensemble Learning
Description: Weighted-ensemble regression over base learners supported by
'caret' (Kuhn (2008) <doi:10.18637/jss.v028.i05>), with cross-validated
hyperparameter selection, out-of-fold diagnostics, and signed residual-
offset estimates. Multi-response problems use iterative input-space
expansion related to Spyromitros-Xioufis et al. (2016)
<doi:10.1007/s10994-016-5546-z>, with Jacobi or 'Gauss-Seidel' sweeps,
package-defined companion gates and per-response iteration stitching.
A package-defined pseudo-label stage promotes prediction rows by a
cross-model and cross-dataset range ratio and accepts rounds with an
out-of-fold squared-correlation gauge.
Author: Alejandro Verri Kozlowski [aut, cre, cph]
Maintainer: Alejandro Verri Kozlowski <averri@fi.uba.ar>
Diff between ssel versions 0.5.1 dated 2026-10-25 and 0.5.2 dated 2026-11-11
ssel-0.5.1/ssel/LICENSE |only ssel-0.5.1/ssel/R/log.R |only ssel-0.5.1/ssel/inst/build.R |only ssel-0.5.1/ssel/inst/cran-check.R |only ssel-0.5.1/ssel/inst/cran-submit.R |only ssel-0.5.1/ssel/inst/install.R |only ssel-0.5.1/ssel/inst/package.R |only ssel-0.5.1/ssel/inst/rhub-check.R |only ssel-0.5.1/ssel/inst/rhub.R |only ssel-0.5.1/ssel/tests/testthat/test-log.R |only ssel-0.5.2/ssel/DESCRIPTION | 14 - ssel-0.5.2/ssel/LICENSE.note |only ssel-0.5.2/ssel/MD5 | 105 ++++----- ssel-0.5.2/ssel/NAMESPACE | 9 ssel-0.5.2/ssel/NEWS.md | 63 +++++ ssel-0.5.2/ssel/R/aggregateResponses.R | 32 +- ssel-0.5.2/ssel/R/auditOverfit.R | 12 - ssel-0.5.2/ssel/R/auditQuantiles.R | 32 +- ssel-0.5.2/ssel/R/buildDataset.R | 30 +- ssel-0.5.2/ssel/R/chain.R | 108 +++++---- ssel-0.5.2/ssel/R/conditions.R |only ssel-0.5.2/ssel/R/describeModule.R |only ssel-0.5.2/ssel/R/model.R | 36 +-- ssel-0.5.2/ssel/R/oofEnsemble.R | 5 ssel-0.5.2/ssel/R/postProcess.R | 4 ssel-0.5.2/ssel/R/predictModel.R | 14 - ssel-0.5.2/ssel/R/semiSupervisedPipeline.R | 11 ssel-0.5.2/ssel/R/ssel-package.R | 58 ++--- ssel-0.5.2/ssel/R/trainRegressionModel.R | 126 +++++++---- ssel-0.5.2/ssel/R/utils.R | 10 ssel-0.5.2/ssel/README.md | 10 ssel-0.5.2/ssel/inst/CITATION | 2 ssel-0.5.2/ssel/inst/WORDLIST | 2 ssel-0.5.2/ssel/inst/doc/cli.Rmd | 57 +++- ssel-0.5.2/ssel/inst/doc/cli.html | 60 +++-- ssel-0.5.2/ssel/inst/doc/semi-supervised.R | 7 ssel-0.5.2/ssel/inst/doc/semi-supervised.Rmd | 7 ssel-0.5.2/ssel/inst/doc/semi-supervised.html | 47 +--- ssel-0.5.2/ssel/inst/doc/ssel-quickstart.html | 68 +++-- ssel-0.5.2/ssel/man/aggregateResponses.Rd | 5 ssel-0.5.2/ssel/man/auditOverfit.Rd | 20 - ssel-0.5.2/ssel/man/auditQuantiles.Rd | 6 ssel-0.5.2/ssel/man/buildDataset.Rd | 11 ssel-0.5.2/ssel/man/chainPipeline.Rd | 7 ssel-0.5.2/ssel/man/describeModule.Rd |only ssel-0.5.2/ssel/man/modelPipeline.Rd | 34 +- ssel-0.5.2/ssel/man/predictModel.Rd | 3 ssel-0.5.2/ssel/man/semiSupervisedPipeline.Rd | 7 ssel-0.5.2/ssel/man/trainModel.Rd | 13 - ssel-0.5.2/ssel/man/trainRegressionModel.Rd | 4 ssel-0.5.2/ssel/tests/testthat/test-apiFacts.R | 5 ssel-0.5.2/ssel/tests/testthat/test-auditDiagnostics.R | 12 + ssel-0.5.2/ssel/tests/testthat/test-bounds.R | 2 ssel-0.5.2/ssel/tests/testthat/test-collation.R | 25 +- ssel-0.5.2/ssel/tests/testthat/test-conditions.R |only ssel-0.5.2/ssel/tests/testthat/test-describeModule.R |only ssel-0.5.2/ssel/tests/testthat/test-ensembleValidation.R |only ssel-0.5.2/ssel/tests/testthat/test-semiSupervisedPipeline.R | 6 ssel-0.5.2/ssel/tests/testthat/test-trainRegressionModel.R | 2 ssel-0.5.2/ssel/tests/testthat/test-wipeGuard.R | 8 ssel-0.5.2/ssel/vignettes/cli.Rmd | 57 +++- ssel-0.5.2/ssel/vignettes/semi-supervised.Rmd | 7 62 files changed, 661 insertions(+), 502 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Generate stimuli and analyze data of reverse correlation image
classification experiments (psychophysical tasks aimed at visualizing
cognitive mental representations of faces). For the method see Dotsch and
Todorov (2012) <doi:10.1177/1948550611430272>; for a practical primer see
Brinkman, Todorov and Dotsch (2017) <doi:10.1080/10463283.2017.1381469>.
Author: Ron Dotsch [aut, cre]
Maintainer: Ron Dotsch <rdotsch@gmail.com>
Diff between rcicr versions 1.5.0 dated 2026-09-27 and 1.6.1 dated 2026-11-11
DESCRIPTION | 12 MD5 | 165 +++--- NAMESPACE | 8 NEWS.md | 85 +++ R/autoscale.R | 83 ++- R/batch-ci.R |only R/batchComputeInfoVal2IFC.R |only R/batchGenerateCI.R | 81 --- R/batchGenerateCI2IFC.R | 80 --- R/checkStimulusPNGs2IFC.R |only R/ci-compute.R | 69 +- R/ci-inputs.R | 60 ++ R/computeCumulativeCICorrelation.R | 80 --- R/computeInfoVal2IFC.R | 185 +++---- R/generateCI.R | 156 +++--- R/generateCI2IFC.R | 3 R/generateCINoise.R | 2 R/generateGabor.R | 9 R/generateNoiseImage.R | 33 - R/generateNoisePattern.R | 32 - R/generateReferenceDistribution.R | 145 +++-- R/generateSinusoid.R | 5 R/generateStimuli2IFC.R | 335 ++++++------- R/parallel.R | 12 R/plotZmap.R | 48 - R/random-stream.R |only R/rcicr-package.R | 6 R/rdata.R | 31 - R/reference-base.R | 311 +++++++++--- R/reference-stimuli.R |only R/simulateNoiseIntensities.R | 12 R/stimulus-lock.R | 111 ++++ R/zmap-compute.R | 19 R/zzz.R | 26 + README.md | 81 --- build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.html | 2 inst/doc/recipes.R |only inst/doc/recipes.Rmd |only inst/doc/recipes.html |only inst/doc/reverse-correlation-walkthrough.Rmd | 2 inst/doc/reverse-correlation-walkthrough.html | 16 inst/doc/stored-data.R |only inst/doc/stored-data.Rmd |only inst/doc/stored-data.html |only man/autoscale.Rd | 9 man/batchComputeInfoVal2IFC.Rd |only man/batchGenerateCI.Rd | 10 man/batchGenerateCI2IFC.Rd | 10 man/checkStimulusPNGs2IFC.Rd |only man/computeCumulativeCICorrelation.Rd | 2 man/computeInfoVal2IFC.Rd | 57 ++ man/generateCI.Rd | 9 man/generateCI2IFC.Rd | 5 man/generateReferenceDistribution2IFC.Rd | 83 ++- man/generateStimuli2IFC.Rd | 11 man/plotZmap.Rd | 3 man/rcicr-package.Rd | 6 tests/testthat/fixtures/noise-pattern-matlab-reference.rds |only tests/testthat/helper-fixtures.R | 21 tests/testthat/test-autoscale.R | 50 + tests/testthat/test-batch-ci.R |only tests/testthat/test-batch-tibble.R | 3 tests/testthat/test-batchComputeInfoVal2IFC.R |only tests/testthat/test-blas-mode.R |only tests/testthat/test-blas-product-check.R |only tests/testthat/test-check-stimulus-pngs-2ifc.R |only tests/testthat/test-computeCumulativeCICorrelation.R | 13 tests/testthat/test-computeInfoVal2IFC.R | 12 tests/testthat/test-correctness-oracles.R |only tests/testthat/test-first-few.R |only tests/testthat/test-fixed-bugs.R | 78 +++ tests/testthat/test-generateCI.R | 27 + tests/testthat/test-generateGabor.R | 7 tests/testthat/test-generateNoisePattern.R | 23 tests/testthat/test-generateReferenceDistribution2IFC.R | 24 tests/testthat/test-generateStimuli2IFC.R |only tests/testthat/test-gram-reference.R |only tests/testthat/test-independent-reference.R | 9 tests/testthat/test-legacy-rdata.R | 12 tests/testthat/test-masked-infoval.R |only tests/testthat/test-multi-base-stimuli.R | 9 tests/testthat/test-noise-without-matlab.R |only tests/testthat/test-parallel-backend.R | 4 tests/testthat/test-pixel-range.R |only tests/testthat/test-reference-checks.R |only tests/testthat/test-reference-from-saved-noise.R | 56 +- tests/testthat/test-reference-stimuli.R |only tests/testthat/test-resolve-reference-output.R |only tests/testthat/test-response-validation.R |only tests/testthat/test-rng-kind.R |only tests/testthat/test-scaling-metadata.R |only tests/testthat/test-seedless-reference.R | 8 tests/testthat/test-stimulus-lock.R | 4 tests/testthat/test-stimulus-png-collision.R |only tests/testthat/test-trial-validation.R | 1 tests/testthat/test-untested-paths.R |only tests/testthat/test-worker-memory.R |only vignettes/recipes.Rmd |only vignettes/reverse-correlation-walkthrough.Rmd | 2 vignettes/stored-data.Rmd |only 102 files changed, 1791 insertions(+), 1082 deletions(-)
Title: Learn-as-You-Go Adaptive Trial Optimization
Description: Optimizes interventions for adaptive "Learn-As-you-GO" (LAGO)
trials, in which the intervention package is updated between stages using
accumulating data. Given data from completed stages, lago_optimization()
fits the outcome model (via 'stats' generalized linear models or, for
clustered designs, cluster-robust variance) and computes the cost-optimal
recommended intervention for the next stage that is expected to reach a
target mean outcome and/or a desired statistical power. get_confidence_set()
constructs confidence sets for the optimal intervention, and visualize_cost()
and lago_report() summarize the cost surface and results. Methods are
described in Nevo, Lok and Spiegelman (2021) <doi:10.1214/20-aos1978> and
Bing, Spiegelman, Nevo and Lok (2025) <doi:10.1093/biomtc/ujaf061>.
Author: Ante Bing [aut, cre],
Minh Bui [aut],
Jingyu Cui [aut],
Mike Bostock [cph]
Maintainer: Ante Bing <abing@bu.edu>
Diff between LAGOtrials versions 1.1.1 dated 2026-11-04 and 1.2.0 dated 2026-11-11
DESCRIPTION | 9 ++-- MD5 | 39 +++++++++++--------- NAMESPACE | 1 NEWS.md | 8 ++++ R/get_recommended_interventions.R | 39 ++++++++++++-------- R/lago_app.R |only R/lago_app_helpers.R |only R/visualize_cost.R | 4 +- README.md | 37 ++++++++++++------ inst/WORDLIST | 2 + man/lago_app.Rd |only tests/testthat/test-covariate-treatment-contrasts.R | 4 +- tests/testthat/test-hunt-fixes.R | 8 ++-- tests/testthat/test-hunt4-fixes.R | 2 - tests/testthat/test-hunt5-fixes.R | 10 ++--- tests/testthat/test-lago-app.R |only tests/testthat/test-links-and-covariates.R | 4 +- tests/testthat/test-minimize-and-bounds.R | 4 +- tests/testthat/test-model-rows.R | 6 ++- tests/testthat/test-power-missing-outcome.R | 6 +-- tests/testthat/test-sensitivity.R | 4 +- tests/testthat/test-solver-bounds.R |only tests/testthat/test-sweep-fit-cache.R | 4 +- 23 files changed, 119 insertions(+), 72 deletions(-)
Title: Curated Datasets and Tools for Epidemiological Data Analysis
Description: Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, 'DIVINE' makes the process more efficient, transparent, and reproducible.
Author: Natalia Pallares [aut, cre],
Joao Carmezim [aut],
Pau Satorra [aut],
Lucia Blanc [aut],
Cristian Tebe [aut]
Maintainer: Natalia Pallares <napallares@recerca.clinic.cat>
Diff between DIVINE versions 0.1.2 dated 2026-03-30 and 0.1.3 dated 2026-11-11
DESCRIPTION | 8 MD5 | 77 +-- NAMESPACE | 28 - NEWS.md | 44 +- R/analytics.R | 6 R/comorbidities.R | 6 R/complications.R | 6 R/concomitant_medication.R | 6 R/demographic.R | 6 R/end_followup.R | 10 R/icu.R | 12 R/inhosp_antibiotics.R | 6 R/inhosp_antivirals.R | 6 R/inhosp_other_treatments.R | 6 R/multi_plot.R | 816 ++++++++++++++++++++--------------------- R/scores.R | 6 R/symptoms.R | 6 R/vaccine.R | 6 R/vital_signs.R | 6 README.md | 242 ++++++------ build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 30 + inst/doc/DIVINE.Rmd | 676 ++++++++++++++++----------------- man/analytics.Rd | 6 man/comorbidities.Rd | 6 man/complications.Rd | 6 man/concomitant_medication.Rd | 6 man/demographic.Rd | 6 man/end_followup.Rd | 10 man/icu.Rd | 74 +-- man/impute_missing.Rd | 152 +++---- man/inhosp_antibiotics.Rd | 6 man/inhosp_antivirals.Rd | 6 man/inhosp_other_treatments.Rd | 6 man/scores.Rd | 6 man/symptoms.Rd | 6 man/vaccine.Rd | 6 man/vital_signs.Rd | 6 vignettes/DIVINE.Rmd | 676 ++++++++++++++++----------------- 40 files changed, 1581 insertions(+), 1418 deletions(-)