Title: Global, Parameterwise and Joint Shrinkage Factor Estimation
Description: The predictive value of a statistical model can often be improved
by applying shrinkage methods. This can be achieved, e.g., by regularized
regression or empirical Bayes approaches. Various types of shrinkage factors can
also be estimated after a maximum likelihood. While global shrinkage modifies
all regression coefficients by the same factor, parameterwise shrinkage factors
differ between regression coefficients. With variables which are either highly
correlated or associated with regard to contents, such as several columns of a
design matrix describing a nonlinear effect, parameterwise shrinkage factors are
not interpretable and a compromise between global and parameterwise shrinkage,
termed 'joint shrinkage', is a useful extension. A computational shortcut to
resampling-based shrinkage factor estimation based on DFBETA residuals can be
applied. Global, parameterwise and joint shrinkage for models fitted by lm(),
glm(), coxph(), or mfp() is available.
The package is also available a [...truncated...]
Author: Daniela Dunkler [aut, cre],
Georg Heinze [aut]
Maintainer: Daniela Dunkler <daniela.dunkler@meduniwien.ac.at>
Diff between shrink versions 1.2.3 dated 2023-10-31 and 1.2.4 dated 2026-11-11
DESCRIPTION | 9 ++++--- MD5 | 18 +++++++------- NAMESPACE | 2 - R/shrink.R | 2 - R/zzz.R | 7 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++++ inst/doc/JSSexample.html | 57 +++++++++++++++++++++++------------------------ man/shrink-package.Rd | 10 ++++++++ 10 files changed, 65 insertions(+), 46 deletions(-)
Title: Generalised Additive Extreme Value Models
Description: Methods for fitting various extreme value distributions with parameters of
generalised additive model (GAM) form are provided. For details of distributions
see Coles, S.G. (2001) <doi:10.1007/978-1-4471-3675-0>, GAMs see Wood, S.N. (2017)
<doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. &
Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>. Details of how evgam works
and various examples are given in Youngman, B.D. (2022) <doi:10.18637/jss.v103.i03>.
Author: Ben Youngman [aut, cre]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between evgam versions 1.0.2 dated 2026-09-03 and 1.0.3 dated 2026-11-11
DESCRIPTION | 8 +- MD5 | 24 ++++--- NAMESPACE | 3 NEWS.md | 16 ++++ R/cvevgam.R |only R/evgam_sandwich.R |only R/exp.R | 38 +++++++++++ R/generic.R | 86 +++++++++++++++++++------ R/optim.R | 168 -------------------------------------------------- R/pp.R | 2 R/predict.R | 13 ++- R/setup_and_fit.R | 12 +++ man/cvevgam.Rd |only man/evgam.control.Rd | 68 +++++++++++++++----- man/evgam_sandwich.Rd |only 15 files changed, 215 insertions(+), 223 deletions(-)
Title: A Two-Stage Estimation Approach to Cox Regression Using M-Spline
Function
Description: Implements a two-stage estimation approach for Cox
regression using five-parameter M-spline functions to model the baseline hazard. It allows
for flexible hazard shapes and model selection based on log-likelihood criteria as described in
Teranishi et al.(2025).
In addition, the package provides functions for constructing and evaluating B-spline copulas
based on five M-spline or I-spline basis functions, allowing users to flexibly model and
compute bivariate dependence structures. Both the copula function and its density can be evaluated.
Furthermore, the package supports computation of dependence measures such as Kendall's tau and
Spearman's rho, derived analytically from the copula parameters.
Author: Ren Teranishi [aut, cre]
Maintainer: Ren Teranishi <ren.teranishi1227@gmail.com>
Diff between splineCox versions 0.0.8 dated 2026-01-26 and 0.0.9 dated 2026-11-11
DESCRIPTION | 6 - MD5 | 17 ++-- NEWS.md | 9 +- R/splinecopulaMLE.R | 24 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/splineCox-introduction.html | 143 ++++++++++++++++------------------- man/spline.copula.MLE.Rd | 13 ++- tests/initialization.R |only 10 files changed, 117 insertions(+), 97 deletions(-)
Title: Approximate Optimal Experimental Designs Using Generalised
Linear Mixed Models
Description: Optimal design analysis algorithms for any study design that can be represented or
modelled as a generalised linear mixed model including cluster randomised trials,
cohort studies, spatial and temporal epidemiological studies, and split-plot designs.
See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a
detailed manual on model specification. A detailed discussion of the methods in this
package can be found in Watson, Hemming, and Girling (2023) <doi:10.1177/09622802231202379>.
Author: Sam Watson [aut, cre],
Yi Pan [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrOptim versions 0.5.1 dated 2026-06-07 and 0.5.2 dated 2026-11-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/gd_search.cpp | 17 ++++++++++++++++- 4 files changed, 23 insertions(+), 8 deletions(-)
Title: Ecological Niche Modeling using Presence-Absence Data
Description: A set of tools to perform Ecological Niche Modeling with
presence-absence data. It includes algorithms for data partitioning,
model fitting, calibration, evaluation, selection, and prediction.
Other functions help to explore signals of ecological niche using univariate
and multivariate analyses, and model features such as variable response
curves and variable importance. Unique characteristics of this package are
the ability to exclude models with concave quadratic responses, and the
option to clamp model predictions to specific variables. These tools are
implemented following principles proposed in
Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>,
Cobos et al., (2019) <doi:10.7717/peerj.6281>,
and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
Author: Luis F. Arias-Giraldo [aut, cre] ,
Marlon E. Cobos [aut] ,
A. Townsend Peterson [ctb]
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Diff between enmpa versions 0.2.5 dated 2026-06-25 and 0.2.6 dated 2026-11-11
DESCRIPTION | 14 +++--- MD5 | 20 ++++----- NAMESPACE | 113 ++++++++++++++++++++++++++++------------------------ NEWS.md | 33 ++++++++++----- R/calibration_glm.R | 38 ++++++----------- R/jackknife.R | 2 R/plot_jk.R | 2 R/resp2var.R | 2 man/jackknife.Rd | 2 man/plot_jk.Rd | 2 man/resp2var.Rd | 2 11 files changed, 122 insertions(+), 108 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test; parametric post hoc methods such
as Tukey, Scheffe, Duncan, SNK, LSD, Games-Howell and Tamhane; and rank-based
post hoc methods such as Dunn, Conover-Iman, Nemenyi, Dwass-Steel-Critchlow-Fligner
and Bonferroni-corrected Mann-Whitney tests, with plots suited to each type of
procedure. Also includes the Jonckheere-Terpstra trend test, the Jarque-Bera test
with Glinskiy's (2024) correction, and a post hoc test planner that helps choose
the most suitable procedure. Designed for use in teaching, applied statistical
analysis, and reproducible research.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 2.4.0 dated 2026-10-26 and 2.4.1 dated 2026-11-11
DESCRIPTION | 6 +- MD5 | 8 +- R/JarqueBera_GTest.R | 126 +++++++++++++++++++++++++++--------------- inst/doc/Analitica-intro.html | 4 - man/JBGTest.Rd | 36 +++++++++--- 5 files changed, 119 insertions(+), 61 deletions(-)
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:
2025-09-15 0.1.1
2023-01-17 0.1.0
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:
2025-12-03 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:
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:
2025-01-23 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(-)
Title: Three-Step Estimation for Latent Class Analysis
Description: Bias-adjusted three-step estimation of latent class models with
covariates and distal outcomes. The latent class measurement model is
estimated first, with 'multilevLCA' (Lyrvall et al., 2025)
<doi:10.1080/00273171.2025.2473935>, and held fixed; observations are then
classified; and the classes are related to covariates and distal outcomes
with the maximum likelihood correction of Vermunt (2010)
<doi:10.1093/pan/mpq025> and Bakk, Tekle and Vermunt (2013)
<doi:10.1177/0081175012470644>, or the correction of Bolck, Croon and
Hagenaars (2004) <doi:10.1093/pan/mph001>. Standard errors account for the
uncertainty of the measurement model (Bakk, Oberski and Vermunt, 2014)
<doi:10.1093/pan/mpu003>. Includes class enumeration, modal and
proportional class assignment, covariate formulas, Gaussian, Poisson,
binomial, and multinomial distal outcomes, the two-step estimator of Bakk
and Kuha (2018) <doi:10.1007/s11336-017-9592-7>, measurement models
applied to ne [...truncated...]
Author: Sam Lee [aut, cre, cph] ,
Jay Goodliffe [aut, cph]
Maintainer: Sam Lee <samlee@arizona.edu>
Diff between tseLCA versions 2.1.1 dated 2026-10-31 and 2.1.2 dated 2026-11-10
DESCRIPTION | 6 MD5 | 20 NEWS.md | 910 +++++++++++++++++++-------------------- R/methods-tseLCA.R | 186 ++++++- R/three_step.R | 1 R/tse_structural.R | 2 inst/doc/tseLCA-workflow.html | 28 - man/summary.tseLCA_structural.Rd | 4 man/three_step.Rd | 1 man/tse_twostep.Rd | 2 tests/testthat/test-s3.R | 8 11 files changed, 643 insertions(+), 525 deletions(-)
Title: Treatment Effect Inference for Terminal and Non-Terminal Events
under Competing Risks
Description: Provides several confidence interval and testing procedures, based on either
semiparametric (using event-specific win ratios) or nonparametric measures,
including the ratio of integrated cumulative hazard (RICH) and the ratio of
integrated transformed cumulative hazard (RITCH), for treatment effect inference
with terminal and non-terminal events under competing risks. The semiparametric
results were developed in Yang et al. (2022 <doi:10.1002/sim.9266>), and the
nonparametric results were developed in Yang (2025 <doi:10.1002/sim.70205>).
For comparison, results for the win ratio (Finkelstein and Schoenfeld 1999
<doi:10.1002/(SICI)1097-0258(19990615)18:11%3C1341::AID-SIM129%3E3.0.CO;2-7>),
Pocock et al. 2012 <doi:10.1093/eurheartj/ehr352>, and Bebu and Lachin 2016
<doi:10.1093/biostatistics/kxv032>) are included. The package also supports
univariate survival analysis with a single event. In this package, effect size
estimates and confidence intervals are ob [...truncated...]
Author: Daewoo Pak [aut, cre],
Song Yang [aut]
Maintainer: Daewoo Pak <dpak@yonsei.ac.kr>
Diff between TxEffectsSurvival versions 1.0.2 dated 2026-01-09 and 1.0.3 dated 2026-11-10
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 7 ++++++ R/fn_wr0.R | 63 +++++++++++++++++++++++++----------------------------------- 4 files changed, 40 insertions(+), 42 deletions(-)
More information about TxEffectsSurvival at CRAN
Permanent link
Title: Parametric Modal Regression with Right Censoring
Description: Implements parametric modal regression for continuous positive
distributions of the exponential family and beyond (e.g., Log-Logistic,
Birnbaum-Saunders, Log-t) under right censoring. Provides functions to link the
conditional mode to a linear predictor using alternative parameterizations. Includes maximum
likelihood estimation via numerical optimization, asymptotic inference based on
the observed Fisher information matrix, and model diagnostics using randomized
quantile residuals. See Galarza and Lachos (2026) <doi:10.48550/arXiv.2603.07099>.
Author: Christian Galarza [aut, cre],
Victor Lachos [aut]
Maintainer: Christian Galarza <chedgala@espol.edu.ec>
Diff between ModalCens versions 0.3.0 dated 2026-10-16 and 0.3.1 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 17 +++++++++++++++++ R/modal_reg.R | 36 +++++++++++++++++++++++++++++++++--- 4 files changed, 56 insertions(+), 9 deletions(-)
Title: A Test Environment for Database Requests
Description: Testing and documenting code that communicates with remote
databases can be painful. Although the interaction with R is usually relatively
simple (e.g. data(frames) passed to and from a database), because they rely on
a separate service and the data there, testing them can be difficult to set up,
unsustainable in a continuous integration environment, or impossible without
replicating an entire production cluster. This package addresses that by
allowing you to make recordings from your database interactions and then play
them back while testing (or in other contexts) all without needing to spin up
or have access to the database your code would typically connect to.
Author: Jonathan Keane [aut, cre] ,
Mauricio Vargas [aut] ,
Helen Miller [rev] ,
Etienne Racine [rev]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between dittodb versions 0.1.11 dated 2026-02-24 and 0.1.12 dated 2026-11-10
DESCRIPTION | 6 MD5 | 24 +- NEWS.md | 9 R/capture-requests.R | 2 R/connection.R | 67 ++----- R/utils.R | 3 inst/WORDLIST | 40 +--- inst/doc/developing-dittodb.html | 4 inst/doc/dittodb.html | 11 - inst/doc/nycflights.html | 303 --------------------------------- tests/testthat/test-capture-requests.R | 23 +- tests/testthat/test-connection.R | 29 +++ tests/testthat/test-utils.R | 2 13 files changed, 126 insertions(+), 397 deletions(-)
Title: Error Detection in Science
Description: Test published summary statistics for consistency
(Brown and Heathers, 2017, <doi:10.1177/1948550616673876>;
Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>;
Heathers and Brown, 2019, <https://osf.io/5vb3u/>).
The package also provides infrastructure for implementing new
error detection techniques.
Author: Lukas Jung [aut, cre],
Aurelien Allard [ctb],
Nicolas Roman Posner [ctb]
Maintainer: Lukas Jung <jung-lukas@gmx.net>
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Title: 'ChatGPT' Plan Provider for 'ellmer'
Description: Connects 'ellmer' chats to a 'ChatGPT' subscription through
'OpenAI''s documented "Sign in with ChatGPT" flow for open-source,
locally hosted apps
<https://developers.openai.com/siwc/token-sharing-open-source>. Provides
a stable, explicitly bounded core of the public 'ellmer' (>= 0.5.1) Chat
object, including browser sign-in with dynamic client registration,
package-scoped credential storage, redacted diagnostics, multi-turn text,
streaming, structured-output, function-tool, asynchronous, cancellation,
cloning, metadata, multimodal chat, account-specific model discovery, and
reasoning-effort selection through the public 'Responses' API. Parallel
and batch helper functions are explicitly unsupported because 'ChatGPT'
plan usage is stream-only. This independent third-party integration is
not endorsed by 'OpenAI'.
Author: Simon Herrera [aut, cre, cph]
Maintainer: Simon Herrera <simxnherrera@gmail.com>
Diff between ellmercodex versions 0.2.0 dated 2026-10-16 and 0.2.1 dated 2026-11-10
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Title: White Noise Normalization for Mass Spectrometry Profiling Data
Description: Provides a decision-guided workflow for correcting technical
variability in chemical profiling data. Tests for white noise identify
measured features that need correction while preserving those that
already pass. The workflow combines robust outlier adjustment, adaptive
drift detection, change-point segmentation, batch correction, and
probabilistic quotient normalization in a single pipeline or as modular
steps. It supports parameter tuning using pooled quality-control samples
as well as operation for studies without pooled controls.
Author: Tanmay Tanna [aut, cre, cph]
Maintainer: Tanmay Tanna <tanmay@tanmaytanna.com>
Diff between winn versions 0.1.5 dated 2026-09-27 and 0.1.6 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 13 +++++++++++++ R/winn.R | 10 +++++----- README.md | 22 +++++++++++++--------- inst/doc/winn_tutorial.html | 8 ++++---- tests/testthat/test-spline-smoother-terms.R |only 7 files changed, 44 insertions(+), 26 deletions(-)
Title: Rich Inline Text for 'grid' Graphics and 'flextable'
Description: Renders rich inline text (bold, italic, code, links, images)
in grid graphics and 'ggplot2', from markdown or 'flextable' chunks.
Provides grobs, theme elements, and geometry layers for styled text rendering.
Only works with graphics devices that support 'systemfonts', such as
those provided by 'ragg', 'svglite', or 'ggiraph'. The 'cairo_pdf'
device is also supported when fonts are installed at the system level.
Author: David Gohel [aut, cre],
ArData [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between munch versions 0.0.2 dated 2026-04-16 and 0.0.3 dated 2026-11-10
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Title: Manually Plot Path Diagrams for Structural Equation Models
Description: Manually plot fully customisable path diagrams for structural equation
models (SEM). Map out node positions using simple coordinates and specify where on the
perimeter of each node paths begin and end. Extensive fine-tuning options allow the creation of
a path diagram exactly as envisioned, entirely within R.
Author: Sebastian Nagy [aut, cre, cph]
Maintainer: Sebastian Nagy <snagy8610@gmail.com>
Diff between diy.sem.plot versions 1.0.0 dated 2026-09-26 and 1.1.0 dated 2026-11-10
diy.sem.plot-1.0.0/diy.sem.plot/man/figures/README-example1-1.png |only diy.sem.plot-1.0.0/diy.sem.plot/tests/testthat/test-prettyPaths.R |only diy.sem.plot-1.1.0/diy.sem.plot/DESCRIPTION | 6 diy.sem.plot-1.1.0/diy.sem.plot/MD5 | 32 diy.sem.plot-1.1.0/diy.sem.plot/NAMESPACE | 2 diy.sem.plot-1.1.0/diy.sem.plot/NEWS.md | 31 diy.sem.plot-1.1.0/diy.sem.plot/R/diyPaths.R | 678 ++++- diy.sem.plot-1.1.0/diy.sem.plot/README.md | 241 +- diy.sem.plot-1.1.0/diy.sem.plot/inst/doc/diyPaths-vignette.R | 472 +--- diy.sem.plot-1.1.0/diy.sem.plot/inst/doc/diyPaths-vignette.Rmd | 588 ++--- diy.sem.plot-1.1.0/diy.sem.plot/inst/doc/diyPaths-vignette.html | 1136 +++++----- diy.sem.plot-1.1.0/diy.sem.plot/man/diyPaths.Rd | 169 - diy.sem.plot-1.1.0/diy.sem.plot/man/figures/README-unnamed-chunk-4-1.png |only diy.sem.plot-1.1.0/diy.sem.plot/man/node.Rd | 6 diy.sem.plot-1.1.0/diy.sem.plot/man/panel_note.Rd |only diy.sem.plot-1.1.0/diy.sem.plot/man/panel_title.Rd | 7 diy.sem.plot-1.1.0/diy.sem.plot/man/path.Rd | 13 diy.sem.plot-1.1.0/diy.sem.plot/man/template.Rd |only diy.sem.plot-1.1.0/diy.sem.plot/tests/testthat/test-diyPaths.R |only diy.sem.plot-1.1.0/diy.sem.plot/vignettes/diyPaths-vignette.Rmd | 588 ++--- 20 files changed, 2145 insertions(+), 1824 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse 'intraspecific' trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in 'Taudiere' and 'Violle' (2016) <doi:10.1111/ecog.01433>.
Author: Adrien Taudiere [aut, cre, cph] ,
Cyrille Violle [aut] ,
Francois Munoz [ctb]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between cati versions 0.99.6 dated 2026-03-31 and 0.99.7 dated 2026-11-10
DESCRIPTION | 8 MD5 | 29 - NEWS.md | 63 +++ R/allfunctions_cati.R | 634 ++++++++++++++++++-------------- build/partial.rdb |binary man/CVNND.Rd | 4 man/ComIndex.Rd | 33 - man/MinMaxMST.Rd | 4 man/Pval.Rd | 4 man/plotRandtest.Rd | 1 man/ses.Rd | 10 tests/testthat/test-ComIndex.R | 177 ++++++++ tests/testthat/test-Tstats.R | 130 ++++++ tests/testthat/test-diversity-metrics.R | 4 tests/testthat/test-plotRandtest.R |only tests/testthat/test-ses.R | 58 ++ 16 files changed, 834 insertions(+), 325 deletions(-)
Title: Zero-Inflated and Hurdle INAR(1) Models
Description: Provides tools for estimating Zero-Inflated INAR(1)
(ZI-INAR(1)) and Hurdle INAR(1) (H-INAR(1)) models using 'Stan'.
It allows users to simulate time series data for these models,
estimate parameters, and evaluate model fit using various criteria.
Functions include model estimation, simulation, and likelihood-based metrics.
The zero-inflated and hurdle INAR(1) methods are described by Yang et al.
(2025) <doi:10.1214/25-BJPS646>. Zero-inflated models also support
Conway-Maxwell-Poisson innovations.
Author: Fusheng Yang [aut, cre],
Victor Hugo Lachos Davila [aut],
Alokesh Manna [aut],
Dipak K. Dey [aut]
Maintainer: Fusheng Yang <fusheng.yang@uconn.edu>
Diff between ZIHINAR1 versions 0.3.0 dated 2026-11-10 and 0.3.1 dated 2026-11-10
DESCRIPTION | 6 MD5 | 14 - README.md | 327 ++++++++++++++++++++------------------ man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |binary man/figures/README-example1-3.png |binary man/figures/README-example1-4.png |binary man/figures/README-example1-5.png |binary 8 files changed, 187 insertions(+), 160 deletions(-)
Title: Datasets for Stat2
Description: Provides datasets for the textbook Stat2: Modeling
with Regression and ANOVA (second edition). Also includes
datasets from the first edition, Stat2: Building Models for
a World of Data, and functions for plotting diagnostic
graphics.
Author: Robin Lock [aut, cre],
Ann Cannon [aut],
Bradley Hartlaub [aut],
Allan Rossman [aut],
Jeffrey Witmer [aut]
Maintainer: Robin Lock <rlock@stlawu.edu>
This is a re-admission after prior archival of version 2.0.0 dated 2019-01-04
Diff between Stat2Data versions 2.0.0 dated 2019-01-04 and 2.0.1 dated 2026-11-10
DESCRIPTION | 40 ++++++++++++++++++++++++++++------------ MD5 | 14 +++++++------- NEWS.md | 4 +++- man/AutoPollution.Rd | 2 +- man/ThreeCars2017.Rd | 2 +- man/TukeyNonaddPlot.Rd | 9 +++++++-- man/emplogitplot1.Rd | 27 ++++++++++++++++++++++----- man/emplogitplot2.Rd | 27 ++++++++++++++++++++++----- 8 files changed, 91 insertions(+), 34 deletions(-)
Title: Fit Spatial Generalized Extreme Value Models
Description: Fit latent variable models with the GEV distribution as the data likelihood and the GEV parameters following latent Gaussian processes. The models in this package are built using the template model builder 'TMB' in R, which has the fast ability to integrate out the latent variables using Laplace approximation. This package allows the users to choose in the fit function which GEV parameter(s) is considered as a spatially varying random effect following a Gaussian process, so the users can fit spatial GEV models with different complexities to their dataset without having to write the models in 'TMB' by themselves. This package also offers methods to sample from both fixed and random effects posteriors as well as the posterior predictive distributions at different spatial locations. Methods for fitting this class of models are described in Chen, Ramezan, and Lysy (2024) <doi:10.1002/cjs.11829>.
Author: Meixi Chen [aut, cre],
Martin Lysy [aut],
Reza Ramezan [ctb]
Maintainer: Meixi Chen <meixi.chen@uwaterloo.ca>
Diff between SpatialGEV versions 1.0.1 dated 2024-06-09 and 1.0.2 dated 2026-11-10
SpatialGEV-1.0.1/SpatialGEV/inst/doc/SpatialGEV-vignette.Rmd |only SpatialGEV-1.0.1/SpatialGEV/inst/doc/SpatialGEV-vignette.html |only SpatialGEV-1.0.1/SpatialGEV/vignettes/SpatialGEV-vignette.Rmd |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim-1plot-y-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim1-plot-abs-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim1-plot-num-obs-per-loc-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim1-pos-plots-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim2-plot-ab-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/sim2-pred-plot-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/snow-display-grid-data-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/snow-display-raw-data-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/snow-return-plots-1.png |only SpatialGEV-1.0.1/SpatialGEV/vignettes/snow-return-plots-2.png |only SpatialGEV-1.0.2/SpatialGEV/DESCRIPTION | 17 - SpatialGEV-1.0.2/SpatialGEV/MD5 | 97 ++++--- SpatialGEV-1.0.2/SpatialGEV/NAMESPACE | 8 SpatialGEV-1.0.2/SpatialGEV/NEWS.md |only SpatialGEV-1.0.2/SpatialGEV/R/SpatialGEV-package.R | 5 SpatialGEV-1.0.2/SpatialGEV/R/data.R | 42 +++ SpatialGEV-1.0.2/SpatialGEV/R/grid_location.R | 29 +- SpatialGEV-1.0.2/SpatialGEV/R/matern_pc_prior.R | 3 SpatialGEV-1.0.2/SpatialGEV/R/sim_cond_normal.R | 9 SpatialGEV-1.0.2/SpatialGEV/R/spatialGEV_fit.R | 16 - SpatialGEV-1.0.2/SpatialGEV/R/spatialGEV_model.R | 78 +++++- SpatialGEV-1.0.2/SpatialGEV/R/spatialGEV_predict.R | 16 - SpatialGEV-1.0.2/SpatialGEV/R/spatialGEV_sample.R | 4 SpatialGEV-1.0.2/SpatialGEV/R/summary.R | 30 +- SpatialGEV-1.0.2/SpatialGEV/README.md | 129 ++++++---- SpatialGEV-1.0.2/SpatialGEV/build/partial.rdb |only SpatialGEV-1.0.2/SpatialGEV/build/vignette.rds |binary SpatialGEV-1.0.2/SpatialGEV/data/simulatedData3.RData |only SpatialGEV-1.0.2/SpatialGEV/data/simulatedData_withcov.RData |only SpatialGEV-1.0.2/SpatialGEV/inst/doc/SpatialGEV.Rmd |only SpatialGEV-1.0.2/SpatialGEV/inst/doc/SpatialGEV.html |only SpatialGEV-1.0.2/SpatialGEV/inst/doc/helper-functions.R |only SpatialGEV-1.0.2/SpatialGEV/inst/include/SpatialGEV/templates/make_templates.R | 2 SpatialGEV-1.0.2/SpatialGEV/inst/include/SpatialGEV/utils.hpp | 18 + SpatialGEV-1.0.2/SpatialGEV/man/SpatialGEV-package.Rd | 10 SpatialGEV-1.0.2/SpatialGEV/man/figures/README-sample-plot-1.png |only SpatialGEV-1.0.2/SpatialGEV/man/figures/README-show-data-1.png |binary SpatialGEV-1.0.2/SpatialGEV/man/figures/README-show-data-2.png |binary SpatialGEV-1.0.2/SpatialGEV/man/figures/README-show-data-3.png |binary SpatialGEV-1.0.2/SpatialGEV/man/simulatedData3.Rd |only SpatialGEV-1.0.2/SpatialGEV/man/simulatedData_withcov.Rd |only SpatialGEV-1.0.2/SpatialGEV/man/spatialGEV_fit.Rd | 12 SpatialGEV-1.0.2/SpatialGEV/src/TMB/model_ptp_spde.hpp | 4 SpatialGEV-1.0.2/SpatialGEV/tests/dontrun/test-spatialGEV_sample.R | 3 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/helper_rnll.R | 48 ++- SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_a_exp.R | 2 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_a_matern.R | 2 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_ab_exp.R | 2 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_ab_matern.R | 2 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_abs_exp.R | 2 SpatialGEV-1.0.2/SpatialGEV/tests/testthat/test-model_abs_matern.R | 2 SpatialGEV-1.0.2/SpatialGEV/vignettes/.install_extras |only SpatialGEV-1.0.2/SpatialGEV/vignettes/SpatialGEV.Rmd |only SpatialGEV-1.0.2/SpatialGEV/vignettes/SpatialGEV_figures |only SpatialGEV-1.0.2/SpatialGEV/vignettes/helper-functions.R |only SpatialGEV-1.0.2/SpatialGEV/vignettes/references.bib | 15 - SpatialGEV-1.0.2/SpatialGEV/vignettes/technometrics.csl |only 60 files changed, 421 insertions(+), 186 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.3.1 dated 2026-09-10 and 0.4.0 dated 2026-11-10
DESCRIPTION | 16 MD5 | 104 +++- NAMESPACE | 8 NEWS.md | 103 ++++ R/aaa-utils.R | 14 R/ellmer.R | 2 R/embed.R | 2 R/ingest.R | 266 +++++++++--- R/legacy.R | 8 R/markdown-chunk.R | 6 R/ragnar-package.R | 13 R/read-html.R | 427 ++++++++++++++++++-- R/read-markdown.R | 5 R/retrieve.R | 205 +++++---- R/store-v1.R | 1 R/store-v2.R | 79 +++ R/store.R | 244 +++++++++++ README.md | 82 +-- inst/doc/ragnar.Rmd | 2 inst/doc/ragnar.html | 4 man/embed_ollama.Rd | 2 man/ragnar_chunks_view.Rd | 2 man/ragnar_find_links.Rd | 63 ++ man/ragnar_register_tool_retrieve.Rd | 2 man/ragnar_retrieve.Rd | 5 man/ragnar_retrieve_bm25.Rd | 2 man/ragnar_retrieve_vss.Rd | 4 man/ragnar_retrieve_vss_and_bm25.Rd | 5 man/ragnar_store_atlas.Rd | 6 man/ragnar_store_audit.Rd |only man/ragnar_store_create.Rd | 25 + man/ragnar_store_ingest.Rd | 27 + man/ragnar_store_sync.Rd |only tests/testthat/_snaps/find-links.md |only tests/testthat/_snaps/legacy.md |only tests/testthat/_snaps/store.md | 2 tests/testthat/helper-link-site.R |only tests/testthat/helper-webfakes.R |only tests/testthat/setup-webfakes.R |only tests/testthat/test-chunk.R | 37 + tests/testthat/test-embed.R |only tests/testthat/test-find-links-metadata.R |only tests/testthat/test-find-links-problems.R |only tests/testthat/test-find-links-root.R |only tests/testthat/test-find-links-sitemap-duplicates.R |only tests/testthat/test-find-links-sitemap.R |only tests/testthat/test-find-links.R |only tests/testthat/test-ingest-freshness.R |only tests/testthat/test-ingest-incremental.R |only tests/testthat/test-ingest-index.R |only tests/testthat/test-ingest-n-workers.R |only tests/testthat/test-ingest-progress.R |only tests/testthat/test-ingest-summary.R |only tests/testthat/test-ingest-worker-errors.R |only tests/testthat/test-legacy.R |only tests/testthat/test-read-markdown.R | 4 tests/testthat/test-retrieve-memory.R |only tests/testthat/test-retrieve-metadata.R |only tests/testthat/test-retrieve-rowid.R |only tests/testthat/test-retrieve.R | 22 + tests/testthat/test-store-audit.R |only tests/testthat/test-store-sync.R |only tests/testthat/test-store-v2-freshness.R |only tests/testthat/test-store-v2.R | 41 + tests/testthat/test-windows-arm64.R |only tools/configure_deps.R | 54 +- tools/test-install-warm-cache.R |only vignettes/ragnar.Rmd | 2 68 files changed, 1546 insertions(+), 350 deletions(-)
Title: Stateful Matrix Client Helpers
Description: Stateful helpers for building 'Matrix' (<https://matrix.org>)
chat clients in R. Builds on the low-level 'mx.api' Client-Server API
bindings, adding local configuration persistence, room resolution,
sync cursor handling, sync-event extraction, invite acceptance, a
conservative Markdown-to-HTML converter for formatted messages, and
'Olm'/'Megolm' end-to-end encryption orchestration over the optional
'mx.crypto' package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.client versions 0.2.1 dated 2026-09-11 and 0.3.0 dated 2026-11-10
DESCRIPTION | 10 ++-- MD5 | 42 ++++++++++++-------- NAMESPACE | 4 + NEWS.md | 50 ++++++++++++++++++++++++ R/e2ee.R | 59 +++++++++++++++++++++++----- R/media-encrypted.R |only R/messages.R | 8 +++ R/olm-receive.R | 19 +++++++-- R/profile.R | 11 +++-- R/session.R | 6 ++ R/to-device.R |only R/transport.R | 7 ++- build/partial.rdb |binary inst/tinytest/test_encrypted_media.R |only inst/tinytest/test_olm_receive.R | 72 +++++++++++++++++++++++++++++++---- inst/tinytest/test_relogin.R | 38 ++++++++++++++++++ inst/tinytest/test_to_device.R |only man/mx_crypto_encrypt_to_device.Rd |only man/mx_crypto_process_sync.Rd | 11 +++-- man/mx_download_encrypted.Rd |only man/mx_send_encrypted.Rd | 6 ++ man/mx_send_media.Rd | 4 + man/mx_send_to_device_encrypted.Rd |only man/mx_set_displayname.Rd | 6 +- man/mx_upload_encrypted.Rd |only man/mx_with_relogin.Rd | 8 +++ 26 files changed, 303 insertions(+), 58 deletions(-)
Title: Information-Dense Centroid Metrics
Description: Traditional central tendency and dispersion measures such as the
mean and standard deviation can be misleading for multimodal or
outlier-contaminated data. This package implements information-theoretic
alternatives that weight observations by their local probability density,
focusing on the region containing the bulk of the data. The core functions
include ic_weights() for kernel density or histogram based entropy
weighting, ic_center() and ic_dispersion() for weighted location and
spread, ic_combined() for a single information density score between zero
and one, and ic_plot() for visualization.
Author: Ahmet Kutuk [aut, cre]
Maintainer: Ahmet Kutuk <ahmetkutuk@gmail.com>
Diff between infocentroid versions 0.1.0 dated 2026-11-08 and 0.1.1 dated 2026-11-10
DESCRIPTION | 6 +- LICENSE | 4 - MD5 | 34 +++++++-------- NAMESPACE | 26 ++++++------ R/globals.R | 12 ++--- R/ic_center.R | 32 +++++++------- R/ic_combined.R | 82 +++++++++++++++++++------------------- R/ic_dispersion.R | 28 ++++++------ R/ic_plot.R | 110 +++++++++++++++++++++++++-------------------------- R/ic_summary.R | 68 +++++++++++++++---------------- R/ic_weights.R | 76 +++++++++++++++++------------------ README.md | 9 ++-- man/ic_center.Rd | 54 ++++++++++++------------- man/ic_combined.Rd | 46 ++++++++++----------- man/ic_dispersion.Rd | 46 ++++++++++----------- man/ic_plot.Rd | 46 ++++++++++----------- man/ic_summary.Rd | 50 +++++++++++------------ man/ic_weights.Rd | 46 ++++++++++----------- 18 files changed, 388 insertions(+), 387 deletions(-)
Title: Bayesian Error Propagation and Forecast Uncertainty
Decomposition
Description: Provides a full pipeline from regularized or standard regression
models (elastic net, linear models, generalized linear models, random
forests) to informed Bayesian priors, or accepts an existing 'brms' fit
directly, for structured forecast uncertainty decomposition (parameter /
environmental / residual, plus group-level variance for new random-effect
levels and a temporal component under autocorrelation, alongside global
Sobol indices), forecast shelf life analysis (quantifying when a forecast
becomes uninformative, with Kaplan-Meier pooling across forecast origins),
null-model skill scoring, and calibration diagnostics. Designed for
ecological and genomic forecasting with climate or environmental
covariates. Methods build on Bürkner (2017) <doi:10.18637/jss.v080.i01>
for Bayesian regression via 'Stan', Friedman, Hastie, and Tibshirani
(2010) <doi:10.18637/jss.v033.i01> for elastic net regularization,
Wright and Ziegler (2017) <doi:10.18637/jss.v077.i01> for random f [...truncated...]
Author: Luis Javier Madrigal-Roca [aut, cre],
John Kelly [aut]
Maintainer: Luis Javier Madrigal-Roca <madrigalrocalj@yahoo.com>
Diff between ErrorTracer versions 1.4.2 dated 2026-11-05 and 1.4.3 dated 2026-11-10
DESCRIPTION | 10 +- MD5 | 47 +++++----- NEWS.md | 73 ++++++++++++++++ R/decompose.R | 12 +- R/fit.R | 43 ++++++++- R/plot.R | 14 +-- R/predict.R | 95 ++++++++++++++------- R/utils.R | 110 ++++++++++++++++++++++++- README.md | 4 inst/doc/introduction.html | 8 - inst/doc/worked_example.html | 8 - man/as_et_model.Rd | 2 man/decompose_uncertainty.Rd | 10 +- man/et_fit.Rd | 55 +++++++----- man/et_plot_decomposition.Rd | 4 man/et_predict.Rd | 20 ++-- tests/testthat/helper.R | 4 tests/testthat/test-autocor-family.R |only tests/testthat/test-decompose-autocor.R | 2 tests/testthat/test-decompose-families-truth.R | 2 tests/testthat/test-decompose-hierarchical.R | 12 +- tests/testthat/test-decompose.R | 8 - tests/testthat/test-draw-pairing.R | 4 tests/testthat/test-family-predictive.R | 4 tests/testthat/test-plot.R | 2 25 files changed, 412 insertions(+), 141 deletions(-)
Title: Double Constrained Correspondence Analysis for Trait-Environment
Analysis in Ecology
Description: Double constrained correspondence analysis (dc-CA) analyzes
(multi-)trait (multi-)environment ecological data by using the 'vegan'
package and native R code. Throughout the two step algorithm of ter Braak
et al. (2018) is used. This algorithm combines and extends community-
(sample-) and species-level analyses, i.e. the usual community weighted
means (CWM)-based regression analysis and the species-level analysis of
species-niche centroids (SNC)-based regression analysis. The two steps use
canonical correspondence analysis to regress the abundance data on to the
traits and (weighted) redundancy analysis to regress the CWM of the
orthonormalized traits on to the environmental predictors. The function
dc_CA() has an option to divide the abundance data of a site by the site
total, giving equal site weights. This division has the advantage that the
multivariate analysis corresponds with an unweighted (multi-trait)
community-level analysis, instead of being weighted. The first step of
the al [...truncated...]
Author: Cajo J.F ter Braak [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between douconca versions 1.2.6 dated 2026-09-09 and 1.2.6.1 dated 2026-11-10
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/ipfN2marginals.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/douconca.html | 2 +- inst/tinytest/test_anova.dcca.R | 17 +++-------------- inst/tinytest/test_anova.dccav.R | 30 ++++++++++-------------------- man/ipf2N2.Rd | 5 +++++ 10 files changed, 42 insertions(+), 49 deletions(-)
Title: Bunch-Gay-Welsch Statistical Estimation
Description: Performs statistical estimation and inference-related computations
by accessing and executing modified versions of 'Fortran' subroutines
originally published in the Association for Computing Machinery (ACM)
journal Transactions on Mathematical Software (TOMS) by Bunch, Gay and
Welsch (1993) <doi:10.1145/151271.151279>. The acronym 'BGW' (from the
authors' last names) will be used when making reference to technical
content (e.g., algorithm, methodology) that originally appeared in ACM TOMS.
A key feature of BGW is that it exploits the special structure of statistical
estimation problems within a trust-region-based optimization approach to
produce an estimation algorithm that is much more effective than the usual
practice of using optimization methods and codes originally developed for
general optimization. The 'bgw' package bundles 'R' wrapper (and related)
functions with modified 'Fortran' source code so that it can be compiled and
linked in the 'R' environment for fast execution [...truncated...]
Author: David S. Bunch [aut, cre] ,
David M. Gay [ctb],
Roy E. Welsch [ctb],
Stephane Hess [ctb],
David Palma [ctb]
Maintainer: David S. Bunch <dsbunch@ucdavis.edu>
Diff between bgw versions 0.1.4 dated 2026-02-04 and 0.1.5 dated 2026-11-10
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Title: Comprehensive Statistical Tools for Agricultural Research
Description: Analysis of variance for the experimental designs used in
agricultural research, with the correct error term for every stratum,
standard error of mean (SEm), standard error of difference (SEd),
critical difference (CD), coefficient of variation (CV) and letter
groupings: completely randomized design (CRD), randomized complete
block design (RCBD) with missing plots, Latin square, two- and
three-factor factorials, split-plot designs (including factorial main
or sub-plots), split-split-plot and strip-plot designs, and combined
analysis over environments. Also covers the augmented randomized
complete block design with adjusted means and genetic parameters
(Federer, 1961 <doi:10.2307/2527837>), alpha lattice designs with
intra-block or residual maximum likelihood (REML) analysis (Patterson
and Williams, 1976 <doi:10.1093/biomet/63.1.83>) and repeated measures
with Greenhouse-Geisser and Huynh-Feldt corrections and covariance
structure models. Mean comparisons (least significant [...truncated...]
Author: Lalit Kumar Rolaniya [aut, cre] ,
Ram Lal Jat [aut] ,
Monika Punia [aut] ,
Raja Ram Choudhary [aut],
Hemant Poonia [aut]
Maintainer: Lalit Kumar Rolaniya <lalitrolaniya@gmail.com>
Diff between aridagri versions 2.0.4 dated 2026-07-10 and 2.1.0 dated 2026-11-10
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Title: Flexible, Interactive 'shiny' Modules for Almost Any Plot
Description: Offers a core selection of interactivity-first 'shiny' modules for many
plot types meant to serve as flexible building blocks for applications and
as the base for more complex modules. These modules
allow for the rapid and convenient construction of 'shiny' apps with very few lines
of code and decouple plotting from the underlying data. These modules allow
for full plot aesthetic customization by the end user through UI inputs. Utility
functions for simple UI organization, automated UI tooltips, and additional
plot enhancements are also provided. Includes a multi-panel figure builder app
for arranging multiple modules together in a free-form layout.
Author: Jared Andrews [aut, cre] ,
Jacob Martin [aut]
Maintainer: Jared Andrews <jared.andrews07@gmail.com>
Diff between VizModules versions 0.5.0 dated 2026-09-29 and 0.6.0 dated 2026-11-10
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VizModules-0.6.0/VizModules/man/INTERNAL_box_sort_levels.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_brackets_skipped_note.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_ensure_built.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_error_y_spec.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_extract_annotation_from_text.Rd | 3 VizModules-0.6.0/VizModules/man/INTERNAL_freq_sample_choices.Rd | 2 VizModules-0.6.0/VizModules/man/INTERNAL_freq_selected_vars.Rd | 2 VizModules-0.6.0/VizModules/man/INTERNAL_has_interval.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_has_js.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_heatmap_annotation_tracks.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_heatmap_resolve_data.Rd | 2 VizModules-0.6.0/VizModules/man/INTERNAL_heatmap_resolve_title.Rd | 17 VizModules-0.6.0/VizModules/man/INTERNAL_heatmap_slice_count.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_heatmap_tracks_annotation.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_multivar_long_df.Rd | 2 VizModules-0.6.0/VizModules/man/INTERNAL_rd_page.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_rd_params.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_rd_text.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_reference_axis_pairs.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_ribbon_rows.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_send_layout_only.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_settled_reactive.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_split_bar_range.Rd | 14 VizModules-0.6.0/VizModules/man/INTERNAL_structure_note.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_structure_notifier.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_style_input_ids.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_trajectory_paths.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_trajectory_rows.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_update_in_place.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_update_text_position_slider.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_webgl_threshold.Rd |only VizModules-0.6.0/VizModules/man/INTERNAL_widget_json.Rd |only VizModules-0.6.0/VizModules/man/add_marginal_plots.Rd |only VizModules-0.6.0/VizModules/man/add_size_legend.Rd |only VizModules-0.6.0/VizModules/man/adjusted_values.Rd |only VizModules-0.6.0/VizModules/man/adjustment_fn.Rd |only VizModules-0.6.0/VizModules/man/apply_axis_padding.Rd |only VizModules-0.6.0/VizModules/man/apply_highlight_styling.Rd |only VizModules-0.6.0/VizModules/man/apply_legend_inputs.Rd | 5 VizModules-0.6.0/VizModules/man/apply_legend_styling.Rd | 15 VizModules-0.6.0/VizModules/man/apply_level_order.Rd |only VizModules-0.6.0/VizModules/man/apply_subplot_axis_styling.Rd | 3 VizModules-0.6.0/VizModules/man/apply_tick_notation.Rd |only VizModules-0.6.0/VizModules/man/apply_uniform_styling.Rd |only VizModules-0.6.0/VizModules/man/as_plotted.Rd |only 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| 5 VizModules-0.6.0/VizModules/man/parse_highlight_values.Rd |only VizModules-0.6.0/VizModules/man/plotthis_AreaPlotInputsUI.Rd | 6 VizModules-0.6.0/VizModules/man/plotthis_BarPlotInputsUI.Rd | 7 VizModules-0.6.0/VizModules/man/plotthis_BoxPlotInputsUI.Rd | 12 VizModules-0.6.0/VizModules/man/plotthis_DensityPlotInputsUI.Rd | 6 VizModules-0.6.0/VizModules/man/plotthis_DotPlotInputsUI.Rd | 15 VizModules-0.6.0/VizModules/man/plotthis_HistogramInputsUI.Rd | 6 VizModules-0.6.0/VizModules/man/plotthis_SplitBarPlotInputsUI.Rd | 4 VizModules-0.6.0/VizModules/man/require_data_frame.Rd |only VizModules-0.6.0/VizModules/man/reset_colorscale_inputs.Rd |only VizModules-0.6.0/VizModules/man/reset_group_colors.Rd |only VizModules-0.6.0/VizModules/man/reset_lines_inputs.Rd | 3 VizModules-0.6.0/VizModules/man/reset_manual_edits.Rd |only VizModules-0.6.0/VizModules/man/reset_stats_inputs.Rd |only VizModules-0.6.0/VizModules/man/resolve_colorscale.Rd |only VizModules-0.6.0/VizModules/man/setup_auto_update_logic.Rd | 18 VizModules-0.6.0/VizModules/man/setup_level_order.Rd |only VizModules-0.6.0/VizModules/man/setup_manual_edits.Rd | 5 VizModules-0.6.0/VizModules/man/setup_reactive_defaults.Rd | 2 VizModules-0.6.0/VizModules/man/split_color_shape_legend.Rd |only VizModules-0.6.0/VizModules/man/stat_bracket_headroom.Rd |only VizModules-0.6.0/VizModules/man/subplot_spacing_defaults.Rd |only VizModules-0.6.0/VizModules/man/toggle_facet_title_inputs.Rd |only VizModules-0.6.0/VizModules/man/uniform_axes_inputs_ui.Rd | 17 VizModules-0.6.0/VizModules/man/uniform_colorscale_inputs_ui.Rd |only VizModules-0.6.0/VizModules/man/uniform_lines_inputs_ui.Rd | 6 VizModules-0.6.0/VizModules/man/uniform_plotly_inputs_ui.Rd | 2 VizModules-0.6.0/VizModules/man/uniform_stats_inputs_ui.Rd |only VizModules-0.6.0/VizModules/man/uniform_subplot_spacing_inputs_ui.Rd |only VizModules-0.6.0/VizModules/man/webgl_input.Rd |only 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VizModules-0.6.0/VizModules/tests/testthat/test-group_colors.R | 16 VizModules-0.6.0/VizModules/tests/testthat/test-heatmap.R | 135 VizModules-0.6.0/VizModules/tests/testthat/test-layout-updates.R |only VizModules-0.6.0/VizModules/tests/testthat/test-legend-sections.R |only VizModules-0.6.0/VizModules/tests/testthat/test-level_order.R |only VizModules-0.6.0/VizModules/tests/testthat/test-linePlot.R | 386 + VizModules-0.6.0/VizModules/tests/testthat/test-multiColorPicker.R | 12 VizModules-0.6.0/VizModules/tests/testthat/test-multiDynamicInput.R | 42 VizModules-0.6.0/VizModules/tests/testthat/test-parallelCoordinatesPlot.R | 19 VizModules-0.6.0/VizModules/tests/testthat/test-plot_marginals.R |only VizModules-0.6.0/VizModules/tests/testthat/test-plot_mods.R | 3470 +++++----- VizModules-0.6.0/VizModules/tests/testthat/test-plot_source_data.R | 31 VizModules-0.6.0/VizModules/tests/testthat/test-radarPlot.R | 11 VizModules-0.6.0/VizModules/tests/testthat/test-scatterPlot.R | 511 + VizModules-0.6.0/VizModules/tests/testthat/test-showcase.R | 2 VizModules-0.6.0/VizModules/tests/testthat/test-stat_helper.R | 12 VizModules-0.6.0/VizModules/tests/testthat/test-two-tier.R |only VizModules-0.6.0/VizModules/tests/testthat/test-ui_utils.R | 40 VizModules-0.6.0/VizModules/tests/testthat/test-webgl.R |only VizModules-0.6.0/VizModules/tests/testthat/test-yPlot.R | 115 VizModules-0.6.0/VizModules/vignettes/adding-a-new-module.Rmd | 1705 ++-- VizModules-0.6.0/VizModules/vignettes/custom-model-lines.Rmd | 4 VizModules-0.6.0/VizModules/vignettes/custom-modules.Rmd | 149 VizModules-0.6.0/VizModules/vignettes/custom-shiny-inputs.Rmd | 42 VizModules-0.6.0/VizModules/vignettes/defaults-and-hiding.Rmd | 3 278 files changed, 18049 insertions(+), 11771 deletions(-)
Title: Seamless AWS Cloud Bursting for Parallel R Workloads
Description: A 'future' backend that enables seamless execution of parallel R
workloads on 'Amazon Web Services' ('AWS', <https://aws.amazon.com>),
including 'EC2' and 'Fargate'. 'staRburst' handles environment
synchronization, data transfer, quota management, and worker orchestration
automatically, allowing users to scale from local execution to 100+ cloud
workers with a single line of code change.
Author: Scott Friedman [aut, cre]
Maintainer: Scott Friedman <help@starburst.ing>
Diff between starburst versions 0.3.11 dated 2026-11-06 and 0.3.12 dated 2026-11-10
starburst-0.3.11/starburst/man/register_cleanup.Rd |only starburst-0.3.12/starburst/DESCRIPTION | 8 starburst-0.3.12/starburst/MD5 | 90 ++--- starburst-0.3.12/starburst/NAMESPACE | 2 starburst-0.3.12/starburst/NEWS.md | 65 +++ starburst-0.3.12/starburst/R/StarburstBackend-class.R | 34 + starburst-0.3.12/starburst/R/aws-clients.R | 4 starburst-0.3.12/starburst/R/cost.R | 12 starburst-0.3.12/starburst/R/ec2-pool.R | 167 ++++++++- starburst-0.3.12/starburst/R/future-starburst.R | 180 +++++++++- starburst-0.3.12/starburst/R/images.R | 10 starburst-0.3.12/starburst/R/plan-starburst.R | 59 --- starburst-0.3.12/starburst/R/s3-io.R | 33 + starburst-0.3.12/starburst/R/session-api.R | 12 starburst-0.3.12/starburst/R/session-backend.R | 5 starburst-0.3.12/starburst/R/setup.R | 14 starburst-0.3.12/starburst/R/starburst-map.R | 10 starburst-0.3.12/starburst/R/task-registry.R | 45 +- starburst-0.3.12/starburst/README.md | 11 starburst-0.3.12/starburst/inst/doc/detached-sessions.Rmd | 3 starburst-0.3.12/starburst/inst/doc/detached-sessions.html | 5 starburst-0.3.12/starburst/inst/doc/performance.R | 14 starburst-0.3.12/starburst/inst/doc/performance.Rmd | 18 - starburst-0.3.12/starburst/inst/doc/performance.html | 20 - starburst-0.3.12/starburst/inst/templates/Dockerfile.template | 8 starburst-0.3.12/starburst/man/StarburstBackend.Rd | 4 starburst-0.3.12/starburst/man/backend_state.Rd |only starburst-0.3.12/starburst/man/cancel_pool_release.Rd |only starburst-0.3.12/starburst/man/cleanup_s3_files.Rd | 5 starburst-0.3.12/starburst/man/compute_env_hash.Rd | 2 starburst-0.3.12/starburst/man/delete_task_objects.Rd |only starburst-0.3.12/starburst/man/ecs_task_status.Rd |only starburst-0.3.12/starburst/man/get_task_status_cache.Rd |only starburst-0.3.12/starburst/man/hold_warm_pool.Rd |only starburst-0.3.12/starburst/man/initialize_detached_backend.Rd | 2 starburst-0.3.12/starburst/man/plan.starburst.Rd | 8 starburst-0.3.12/starburst/man/refresh_task_status.Rd |only starburst-0.3.12/starburst/man/release_warm_pool.Rd |only starburst-0.3.12/starburst/man/result_in_s3.Rd |only starburst-0.3.12/starburst/man/starburst_session.Rd | 6 starburst-0.3.12/starburst/man/stopWorkers.StarburstBackend.Rd |only starburst-0.3.12/starburst/man/stop_running_tasks.Rd | 8 starburst-0.3.12/starburst/man/stop_warm_pool.Rd | 3 starburst-0.3.12/starburst/man/task_failure.Rd |only starburst-0.3.12/starburst/tests/testthat/helper-roundtrip.R | 150 +++++++- starburst-0.3.12/starburst/tests/testthat/test-cost.R | 38 -- starburst-0.3.12/starburst/tests/testthat/test-docker.R | 9 starburst-0.3.12/starburst/tests/testthat/test-ec2-pool.R | 8 starburst-0.3.12/starburst/tests/testthat/test-future-backend.R | 27 + starburst-0.3.12/starburst/tests/testthat/test-roundtrip.R | 108 ++++++ starburst-0.3.12/starburst/vignettes/detached-sessions.Rmd | 3 starburst-0.3.12/starburst/vignettes/performance.Rmd | 18 - 52 files changed, 962 insertions(+), 266 deletions(-)
Title: Simulation-Based Sample Size Tools for Prediction Models
Description: Provides a flexible, simulation-based toolkit for exploring how
much data are needed to develop reliable prediction models. It works by
repeatedly generating data, fitting models, and evaluating performance
to show how sample size affects predictive accuracy, calibration, and
overfitting. The package supports continuous, binary, and time-to-event
outcomes and can be used with both regression-based modelling approaches
and machine-learning methods. It is designed to help researchers plan
studies, assess feasibility, and build more robust and generalisable
models. The methods are described in Olaniran et al. (2026)
<doi:10.1186/s12874-026-02935-9> and Shamsutdinova et al. (2026)
<doi:10.48550/arXiv.2602.23507>.
Author: Ewan Carr [aut, cre] ,
Gordon Forbes [aut] ,
Ridwan Olaniran [aut] ,
Diana Shamsutdinova [aut] ,
Daniel Stahl [aut] ,
Sarah Markham [aut] ,
Felix Zimmer [aut]
Maintainer: Ewan Carr <ewan.carr@kcl.ac.uk>
Diff between pmsims versions 1.0.0 dated 2026-09-17 and 1.1.0 dated 2026-11-10
pmsims-1.0.0/pmsims/man/survival_calib_slope_cox.Rd |only pmsims-1.1.0/pmsims/DESCRIPTION | 20 pmsims-1.1.0/pmsims/MD5 | 113 - pmsims-1.1.0/pmsims/NAMESPACE | 1 pmsims-1.1.0/pmsims/NEWS.md | 126 + pmsims-1.1.0/pmsims/R/binary_tuning.R | 12 pmsims-1.1.0/pmsims/R/calculate_metrics_perf.R | 2 pmsims-1.1.0/pmsims/R/calibration_fits.R |only pmsims-1.1.0/pmsims/R/continuous_tuning.R | 6 pmsims-1.1.0/pmsims/R/csse_internal.R | 30 pmsims-1.1.0/pmsims/R/curve_engine.R |only pmsims-1.1.0/pmsims/R/data.R | 8 pmsims-1.1.0/pmsims/R/data_generators.R | 346 +++- pmsims-1.1.0/pmsims/R/engines.R | 1016 ++++++------ pmsims-1.1.0/pmsims/R/input_validation.R | 16 pmsims-1.1.0/pmsims/R/metric_generators.R | 737 +++----- pmsims-1.1.0/pmsims/R/model_generators.R | 133 + pmsims-1.1.0/pmsims/R/plotting.R | 200 ++ pmsims-1.1.0/pmsims/R/print.R | 53 pmsims-1.1.0/pmsims/R/simulate_custom.R | 393 ++++ pmsims-1.1.0/pmsims/R/simulate_wrappers.R | 259 ++- pmsims-1.1.0/pmsims/R/simulation_core.R |only pmsims-1.1.0/pmsims/R/start_values.R | 527 +++--- pmsims-1.1.0/pmsims/R/survival_tuning.R | 30 pmsims-1.1.0/pmsims/README.md | 10 pmsims-1.1.0/pmsims/data/binary_example.rda |binary pmsims-1.1.0/pmsims/data/continuous_example.rda |binary pmsims-1.1.0/pmsims/data/custom_example.rda |binary pmsims-1.1.0/pmsims/data/survival_example.rda |binary pmsims-1.1.0/pmsims/inst/CITATION | 2 pmsims-1.1.0/pmsims/inst/doc/pmsims.R | 7 pmsims-1.1.0/pmsims/inst/doc/pmsims.Rmd | 508 +----- pmsims-1.1.0/pmsims/inst/doc/pmsims.html | 606 ++----- pmsims-1.1.0/pmsims/man/calculate_bisection.Rd | 14 pmsims-1.1.0/pmsims/man/calculate_curve.Rd |only pmsims-1.1.0/pmsims/man/calculate_mlpwr.Rd | 14 pmsims-1.1.0/pmsims/man/calculate_mlpwr_bs.Rd | 14 pmsims-1.1.0/pmsims/man/generate_binary_data.Rd | 6 pmsims-1.1.0/pmsims/man/generate_continuous_data.Rd | 6 pmsims-1.1.0/pmsims/man/generate_linear_predictor.Rd | 28 pmsims-1.1.0/pmsims/man/generate_predictors.Rd | 5 pmsims-1.1.0/pmsims/man/generate_survival_data.Rd | 6 pmsims-1.1.0/pmsims/man/plot.pmsims.Rd | 13 pmsims-1.1.0/pmsims/man/pmsims-package.Rd | 2 pmsims-1.1.0/pmsims/man/precomputed.Rd | 16 pmsims-1.1.0/pmsims/man/simulate_binary.Rd | 39 pmsims-1.1.0/pmsims/man/simulate_continuous.Rd | 37 pmsims-1.1.0/pmsims/man/simulate_custom.Rd | 88 - pmsims-1.1.0/pmsims/man/simulate_survival.Rd | 39 pmsims-1.1.0/pmsims/tests/testthat/fixtures |only pmsims-1.1.0/pmsims/tests/testthat/test-curve_engine.R |only pmsims-1.1.0/pmsims/tests/testthat/test-data_generators.R | 135 + pmsims-1.1.0/pmsims/tests/testthat/test-engines.R | 55 pmsims-1.1.0/pmsims/tests/testthat/test-fast_paths.R |only pmsims-1.1.0/pmsims/tests/testthat/test-metric_generators.R | 114 + pmsims-1.1.0/pmsims/tests/testthat/test-model_generators.R | 95 + pmsims-1.1.0/pmsims/tests/testthat/test-simulate_custom.R | 25 pmsims-1.1.0/pmsims/tests/testthat/test-simulate_wrappers.R | 163 + pmsims-1.1.0/pmsims/tests/testthat/test-simulation_core.R |only pmsims-1.1.0/pmsims/tests/testthat/test-start_values.R | 43 pmsims-1.1.0/pmsims/tests/testthat/test-truth.R |only pmsims-1.1.0/pmsims/vignettes/images/live_plot.mp4 |only pmsims-1.1.0/pmsims/vignettes/pmsims.Rmd | 508 +----- 63 files changed, 4039 insertions(+), 2587 deletions(-)
Title: Remote Sensing Metrics for Spatial Health Analysis
Description: Calculate and extract remote sensing metrics for spatial analysis in the field of health.
The package offers R users a quick and straightforward way to obtain areal or zonal statistics of key environmental indicators, covariates, and vector-borne disease data ideal for modeling infectious diseases within the framework of spatial epidemiology.
Author: Antony Barja [aut, cph] ,
Yomali Ferreyra [cre] ,
Diego Villa [ctb],
Gabriel Carrasco-Escobar [aut]
Maintainer: Yomali Ferreyra <yomali.ferreyra@upch.pe>
Diff between land4health versions 0.3.0 dated 2026-10-08 and 0.3.2 dated 2026-11-10
DESCRIPTION | 15 MD5 | 60 +- NEWS.md | 16 R/l4h_chirps.R | 754 ++++++++++++++++----------------- R/l4h_co_column.R | 402 ++++++++--------- R/l4h_era5land.R | 841 ++++++++++++++++++++++--------------- R/l4h_forest_loss.R | 388 ++++++++--------- R/l4h_human_built.R | 422 +++++++++--------- R/l4h_install.R | 572 ++++++++++++------------- R/l4h_malaria.R | 678 ++++++++++++++--------------- R/l4h_night_lights.R | 432 +++++++++---------- R/l4h_pm2_5.R | 434 +++++++++---------- R/l4h_rural_access_index.R | 420 +++++++++--------- R/l4h_sebal_modis.R | 566 ++++++++++++------------ R/l4h_surface_temp.R | 522 +++++++++++----------- R/l4h_terra_climate.R | 542 +++++++++++------------ R/l4h_travel_time.R | 376 ++++++++-------- R/l4h_urban_heat_index.R | 288 ++++++------ R/l4h_urban_rural_area.R | 350 +++++++-------- R/l4h_use_python.R | 198 ++++---- R/l4h_vegetation.R | 640 ++++++++++++++-------------- R/sysdata.rda |binary R/zzz.R | 2 README.md | 17 build/vignette.rds |binary inst/doc/land4health-setup.Rmd | 252 +++++------ inst/exdata/sources.csv | 2 man/l4h_era5land.Rd | 70 ++- man/land4health-package.Rd | 1 tests/testthat/test-l4h_era5land.R | 42 + vignettes/land4health-setup.Rmd | 252 +++++------ 31 files changed, 4940 insertions(+), 4614 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read and manipulate landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.1.1 dated 2026-07-05 and 4.1.2 dated 2026-11-10
DESCRIPTION | 8 +- MD5 | 34 +++++----- NAMESPACE | 154 +++++++++++++++++++++++++---------------------- NEWS.md | 12 +++ R/bilat.symmetry.r | 5 - R/extended.pgls.r | 8 +- R/geomorph.utils.r | 15 +++- R/morphol.disparity.r | 3 R/physignal.eigen.R | 4 - R/plotOutliers.r | 30 ++++----- R/read.ply.r | 4 - R/warpRefOutline.r | 4 - man/build.template.Rd | 28 ++++---- man/extended.pgls.Rd | 8 +- man/morphol.disparity.Rd | 3 man/plot.gm.prcomp.Rd | 5 - man/read.ply.Rd | 4 - man/warpRefOutline.Rd | 2 18 files changed, 184 insertions(+), 147 deletions(-)
Title: Neutral Versioned Form Definitions and Workbook Layouts
Description: Loads explicit YAML resources describing versioned forms,
fields, declarative constraints, reference requirements, and workbook
layouts. Checks model definitions against an installed YAML schema and
consistency rules, and provides value-like inspection APIs. Does not
validate submitted data or connect to external services.
Author: Tony Chemit [aut, cre, cph]
Maintainer: Tony Chemit <dev@tchemit.fr>
Diff between form.model versions 0.3.2 dated 2026-11-06 and 0.6.2 dated 2026-11-10
form.model-0.3.2/form.model/inst/examples/survey-form.yaml |only form.model-0.6.2/form.model/DESCRIPTION | 16 form.model-0.6.2/form.model/MD5 | 96 - form.model-0.6.2/form.model/NEWS.md | 33 form.model-0.6.2/form.model/R/check.R | 116 +- form.model-0.6.2/form.model/R/inspect.R | 76 - form.model-0.6.2/form.model/R/read.R | 25 form.model-0.6.2/form.model/R/values.R | 2 form.model-0.6.2/form.model/README.md | 132 -- form.model-0.6.2/form.model/build/vignette.rds |binary form.model-0.6.2/form.model/inst/doc/downstream-packages.R | 23 form.model-0.6.2/form.model/inst/doc/downstream-packages.Rmd | 28 form.model-0.6.2/form.model/inst/doc/downstream-packages.html | 560 +++++----- form.model-0.6.2/form.model/inst/doc/form.model.R | 84 + form.model-0.6.2/form.model/inst/doc/form.model.Rmd | 110 + form.model-0.6.2/form.model/inst/doc/form.model.html | 176 ++- form.model-0.6.2/form.model/inst/doc/model-authoring.R | 13 form.model-0.6.2/form.model/inst/doc/model-authoring.Rmd | 15 form.model-0.6.2/form.model/inst/doc/model-authoring.html | 109 + form.model-0.6.2/form.model/inst/doc/model-specification.Rmd | 66 + form.model-0.6.2/form.model/inst/doc/model-specification.html | 171 ++- form.model-0.6.2/form.model/inst/doc/terminology.Rmd |only form.model-0.6.2/form.model/inst/doc/terminology.html |only form.model-0.6.2/form.model/inst/examples/survey |only form.model-0.6.2/form.model/inst/schema/model-1.0.0.yaml | 80 + form.model-0.6.2/form.model/man/as_form_model.Rd | 6 form.model-0.6.2/form.model/man/check_form_model.Rd | 6 form.model-0.6.2/form.model/man/form.model-package.Rd | 4 form.model-0.6.2/form.model/man/form_definition.Rd | 9 form.model-0.6.2/form.model/man/form_field.Rd | 6 form.model-0.6.2/form.model/man/form_fields.Rd | 9 form.model-0.6.2/form.model/man/form_layout.Rd | 6 form.model-0.6.2/form.model/man/form_metadata.Rd | 6 form.model-0.6.2/form.model/man/form_references.Rd | 13 form.model-0.6.2/form.model/man/form_resource.Rd | 3 form.model-0.6.2/form.model/man/form_schema.Rd | 1 form.model-0.6.2/form.model/man/form_sheets.Rd | 12 form.model-0.6.2/form.model/man/form_value_matches_type.Rd | 2 form.model-0.6.2/form.model/man/load_form_model.Rd | 13 form.model-0.6.2/form.model/man/read_form_model.Rd | 6 form.model-0.6.2/form.model/man/select_form_model.Rd | 3 form.model-0.6.2/form.model/tests/testthat/helper-model.R | 2 form.model-0.6.2/form.model/tests/testthat/test-check.R | 22 form.model-0.6.2/form.model/tests/testthat/test-model.R | 45 form.model-0.6.2/form.model/tests/testthat/test-row-constraints.R |only form.model-0.6.2/form.model/tests/testthat/test-sequence.R |only form.model-0.6.2/form.model/vignettes/downstream-packages.Rmd | 28 form.model-0.6.2/form.model/vignettes/form.model.Rmd | 110 + form.model-0.6.2/form.model/vignettes/model-authoring.Rmd | 15 form.model-0.6.2/form.model/vignettes/model-specification.Rmd | 66 + form.model-0.6.2/form.model/vignettes/terminology.Rmd |only 51 files changed, 1597 insertions(+), 727 deletions(-)
Title: Differentially Private Principal Component Analysis and
Visualization
Description: Provides tools for differentially private principal component
analysis (PCA) and visualization. Includes private principal component
directions, scree and proportion of variance explained (PVE) estimates,
and two-dimensional private score histograms with synthetic sampled
points. Supports additive and sparse histogram mechanisms, group-wise
score visualizations, and optional non-private comparisons. An integrated
workflow produces loading plots, scree plots, score plots, variable plots,
and biplots from shared private PCA estimates. An interactive 'shiny'
application is also provided. Private direction estimation is based on
Kim and Jung (2025) <doi:10.1002/sam.70053>. Private scree estimation
draws on Dwork and Roth (2014) <doi:10.1561/0400000042>, Ramsay and
Spicker (2025) <doi:10.48550/arXiv.2501.14095>, and Yu, Ren and Zhou
(2024) <doi:10.3150/23-BEJ1706>. Private score frames use unbounded
quantile mechanisms from Durfee (2023) <doi:10.52202/075280-3394& [...truncated...]
Author: Yejin Jo [aut, cre],
Minwoo Kim [aut],
Sungkyu Jung [aut]
Maintainer: Yejin Jo <yejinjo0220@gmail.com>
Diff between dppca versions 0.1.0 dated 2026-06-04 and 1.0.0 dated 2026-11-10
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Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Kara Woo [aut, cre],
Toph Allen [aut],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Kara Woo <kara.woo@posit.co>
Diff between connectapi versions 0.12.1 dated 2026-04-29 and 0.13.0 dated 2026-11-10
connectapi-0.12.1/connectapi/R/ptype.R |only connectapi-0.13.0/connectapi/DESCRIPTION | 10 connectapi-0.13.0/connectapi/MD5 | 196 - connectapi-0.13.0/connectapi/NAMESPACE | 29 connectapi-0.13.0/connectapi/NEWS.md | 24 connectapi-0.13.0/connectapi/R/connect.R | 37 connectapi-0.13.0/connectapi/R/connectapi.R | 2 connectapi-0.13.0/connectapi/R/content.R | 51 connectapi-0.13.0/connectapi/R/get.R | 73 connectapi-0.13.0/connectapi/R/groups.R | 9 connectapi-0.13.0/connectapi/R/integrations.R | 5 connectapi-0.13.0/connectapi/R/lazy.R | 58 connectapi-0.13.0/connectapi/R/page.R | 26 connectapi-0.13.0/connectapi/R/parse.R | 237 - connectapi-0.13.0/connectapi/R/processes.R |only connectapi-0.13.0/connectapi/R/remote.R | 2 connectapi-0.13.0/connectapi/R/user.R | 1 connectapi-0.13.0/connectapi/R/utils.R | 2 connectapi-0.13.0/connectapi/R/variant.R | 9 connectapi-0.13.0/connectapi/build/vignette.rds |binary connectapi-0.13.0/connectapi/inst/doc/customize-http.html | 4 connectapi-0.13.0/connectapi/inst/doc/getting-started.html | 4 connectapi-0.13.0/connectapi/man/Bundle.Rd | 111 connectapi-0.13.0/connectapi/man/Content.Rd | 771 ++-- connectapi-0.13.0/connectapi/man/ContentTask.Rd | 235 - connectapi-0.13.0/connectapi/man/EnvironmentR6.Rd | 254 - connectapi-0.13.0/connectapi/man/PositConnect.Rd | 1921 +++++----- connectapi-0.13.0/connectapi/man/Task.Rd | 180 connectapi-0.13.0/connectapi/man/Vanity.Rd | 189 connectapi-0.13.0/connectapi/man/VariantR6.Rd | 455 +- connectapi-0.13.0/connectapi/man/VariantSchedule.Rd | 367 - connectapi-0.13.0/connectapi/man/VariantTask.Rd | 260 - connectapi-0.13.0/connectapi/man/audit_access_open.Rd | 8 connectapi-0.13.0/connectapi/man/audit_r_versions.Rd | 8 connectapi-0.13.0/connectapi/man/audit_runas.Rd | 8 connectapi-0.13.0/connectapi/man/bundle_dir.Rd | 12 connectapi-0.13.0/connectapi/man/bundle_path.Rd | 12 connectapi-0.13.0/connectapi/man/bundle_static.Rd | 12 connectapi-0.13.0/connectapi/man/connectapi-package.Rd | 13 connectapi-0.13.0/connectapi/man/content_delete.Rd | 52 connectapi-0.13.0/connectapi/man/content_item.Rd | 52 connectapi-0.13.0/connectapi/man/content_title.Rd | 52 connectapi-0.13.0/connectapi/man/content_update.Rd | 52 connectapi-0.13.0/connectapi/man/create_integration.Rd | 14 connectapi-0.13.0/connectapi/man/create_random_name.Rd | 52 connectapi-0.13.0/connectapi/man/dashboard_url.Rd | 52 connectapi-0.13.0/connectapi/man/delete_integration.Rd | 14 connectapi-0.13.0/connectapi/man/delete_runtime_cache.Rd | 4 connectapi-0.13.0/connectapi/man/delete_thumbnail.Rd | 60 connectapi-0.13.0/connectapi/man/delete_vanity_url.Rd | 52 connectapi-0.13.0/connectapi/man/deploy.Rd | 12 connectapi-0.13.0/connectapi/man/deploy_repo.Rd | 52 connectapi-0.13.0/connectapi/man/download_bundle.Rd | 12 connectapi-0.13.0/connectapi/man/environment.Rd | 52 connectapi-0.13.0/connectapi/man/get_associations.Rd | 66 connectapi-0.13.0/connectapi/man/get_bundles.Rd | 81 connectapi-0.13.0/connectapi/man/get_content_packages.Rd | 4 connectapi-0.13.0/connectapi/man/get_group_content.Rd | 6 connectapi-0.13.0/connectapi/man/get_group_members.Rd | 6 connectapi-0.13.0/connectapi/man/get_groups.Rd | 6 connectapi-0.13.0/connectapi/man/get_integration.Rd | 14 connectapi-0.13.0/connectapi/man/get_integrations.Rd | 14 connectapi-0.13.0/connectapi/man/get_jobs.Rd | 58 connectapi-0.13.0/connectapi/man/get_log.Rd | 58 connectapi-0.13.0/connectapi/man/get_packages.Rd | 4 connectapi-0.13.0/connectapi/man/get_processes.Rd |only connectapi-0.13.0/connectapi/man/get_procs.Rd | 35 connectapi-0.13.0/connectapi/man/get_runtime_caches.Rd | 4 connectapi-0.13.0/connectapi/man/get_thumbnail.Rd | 60 connectapi-0.13.0/connectapi/man/get_timezones.Rd | 6 connectapi-0.13.0/connectapi/man/get_vanity_url.Rd | 52 connectapi-0.13.0/connectapi/man/get_variant_schedule.Rd | 6 connectapi-0.13.0/connectapi/man/git.Rd | 54 connectapi-0.13.0/connectapi/man/has_thumbnail.Rd | 60 connectapi-0.13.0/connectapi/man/lock_content.Rd | 52 connectapi-0.13.0/connectapi/man/permissions.Rd | 54 connectapi-0.13.0/connectapi/man/poll_task.Rd | 12 connectapi-0.13.0/connectapi/man/search_content.Rd | 52 connectapi-0.13.0/connectapi/man/set_integrations.Rd | 66 connectapi-0.13.0/connectapi/man/set_run_as.Rd | 52 connectapi-0.13.0/connectapi/man/set_schedule.Rd | 6 connectapi-0.13.0/connectapi/man/set_thumbnail.Rd | 60 connectapi-0.13.0/connectapi/man/set_vanity_url.Rd | 52 connectapi-0.13.0/connectapi/man/swap_vanity_urls.Rd | 52 connectapi-0.13.0/connectapi/man/terminate_jobs.Rd | 58 connectapi-0.13.0/connectapi/man/update_integration.Rd | 14 connectapi-0.13.0/connectapi/man/vanity_is_available.Rd | 8 connectapi-0.13.0/connectapi/man/variant.Rd | 10 connectapi-0.13.0/connectapi/man/variant_render.Rd | 4 connectapi-0.13.0/connectapi/man/verify_content_name.Rd | 52 connectapi-0.13.0/connectapi/tests/integrated/helper.R | 25 connectapi-0.13.0/connectapi/tests/integrated/test-get.R | 51 connectapi-0.13.0/connectapi/tests/integrated/test-lazy.R | 35 connectapi-0.13.0/connectapi/tests/integrated/test-processes.R |only connectapi-0.13.0/connectapi/tests/testthat/2026.03.0 |only connectapi-0.13.0/connectapi/tests/testthat/setup.R | 12 connectapi-0.13.0/connectapi/tests/testthat/test-content.R | 55 connectapi-0.13.0/connectapi/tests/testthat/test-get.R | 45 connectapi-0.13.0/connectapi/tests/testthat/test-page.R | 152 connectapi-0.13.0/connectapi/tests/testthat/test-parse.R | 276 - connectapi-0.13.0/connectapi/tests/testthat/test-processes.R |only 101 files changed, 4144 insertions(+), 3884 deletions(-)
Title: Simplex Regression Models with Parametric or Fixed Mean Link
Functions
Description: Fits and analyzes simplex regression models with either
fixed or parametric mean link functions. Implements the simplex
probability density function, cumulative distribution function,
quantile function, random number generation, and variance evaluation.
Offers several fixed and parametric link functions for the mean
submodel, tools for residual analysis and diagnostic plotting,
hypothesis testing procedures, and influence measures such as Cook's
distance and leverage (hat values). Includes the Scout Score (SS)
criterion for model selection, enabling comprehensive inference and
diagnostic analysis within the simplex regression framework.
For more details see Barndorff-Nielsen and Jorgensen (1991)
<doi:10.1016/0047-259X(91)90008-P> and Justino and Cribari-Neto (2026)
<doi:10.1016/j.apm.2025.116713>.
Author: Maria Eduarda da Cruz Justino [aut, cre] ,
Francisco Cribari-Neto [ctb, ths]
Maintainer: Maria Eduarda da Cruz Justino <eueduardacruz@gmail.com>
Diff between SimplexRegression versions 0.1.6 dated 2026-08-21 and 0.1.7 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/simplexreg_dist.R | 24 +++++++++++++----------- R/simplexreg_fit.R | 18 ++++++------------ R/simplexreg_var.R | 21 +++++++-------------- inst/doc/relative-humidity.html | 4 ++-- man/variance.simplex.Rd | 4 ---- 8 files changed, 43 insertions(+), 53 deletions(-)
More information about SimplexRegression at CRAN
Permanent link
Title: 'Kaggle' Dataset Downloader 'API'
Description: Easily download datasets from Kaggle <https://www.kaggle.com/> directly into your R environment using 'RKaggle'. Streamline your data analysis workflows by importing datasets effortlessly and focusing on insights rather than manual data handling. Perfect for data enthusiasts and professionals looking to integrate Kaggle datasets into their R projects with minimal hassle.
Author: Benjamin Smith [aut, cre]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between RKaggle versions 0.1.1 dated 2025-05-08 and 0.1.2 dated 2026-11-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/get_dataset.R | 11 +++++++---- man/get_dataset.Rd | 2 +- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: National Institutes of Health Brain Development Cohorts Data Hub
Tools
Description: A suite of functions to work with data from the National Institutes
of Health Brain Development Cohorts Data Hub. The package provides tools to
create, clean, process, and filter datasets and associated metadata. These
utilities are intended to simplify reproducible data-preparation for
future research.
Author: Le Zhang [aut, cre] ,
Janosch Linkersdoerfer [aut]
Maintainer: Le Zhang <dairc.service@gmail.com>
Diff between NBDCtools versions 1.1.0 dated 2026-03-23 and 1.1.2 dated 2026-11-10
DESCRIPTION | 10 MD5 | 64 +- NEWS.md | 73 ++ R/NBDCtools-package.R | 3 R/dataset.R | 14 R/join.R | 198 +++++- R/transform.R | 8 R/utils.R | 10 R/zzz.R | 16 README.md | 18 build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/NBDCtools.R | 26 inst/doc/NBDCtools.Rmd | 2 inst/doc/NBDCtools.html | 974 +++++++++++++++++----------------- man/NBDCtools-package.Rd | 6 man/create_bids_sidecar_metadata.Rd | 2 man/create_dataset.Rd | 8 man/filter_empty_cols.Rd | 2 man/filter_empty_rows.Rd | 2 man/filter_events_abcd.Rd | 2 man/filter_id_events.Rd | 2 man/get_dd.Rd | 2 man/get_id_cols.Rd | 2 man/get_levels.Rd | 2 man/get_metadata.Rd | 2 man/get_releases.Rd | 2 man/get_sessions.Rd | 2 man/join_tabulated.Rd | 45 + man/read_dsv_formatted.Rd | 2 man/shadow_bind_data.Rd | 2 man/shadow_replace_binding_missing.Rd | 2 vignettes/NBDCtools.Rmd | 2 34 files changed, 898 insertions(+), 607 deletions(-)
Title: Random Fields on Metric Graphs
Description: Facilitates creation and manipulation of metric graphs, such as street or river networks. Further facilitates operations and visualizations of data on metric graphs, and the creation of a large class of random fields and stochastic partial differential equations on such spaces. These random fields can be used for simulation, prediction and inference. In particular, linear mixed effects models including random field components can be fitted to data based on computationally efficient sparse matrix representations. Interfaces to the R packages 'INLA' and 'inlabru' are also provided, which facilitate working with Bayesian statistical models on metric graphs. The main references for the methods are Bolin, Simas and Wallin (2024) <doi:10.3150/23-BEJ1647>, Bolin, Kovacs, Kumar and Simas (2023) <doi:10.1090/mcom/3929> and Bolin, Simas and Wallin (2023) <doi:10.48550/arXiv.2304.03190> and <doi:10.48550/arXiv.2304.10372>.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Jonas Wallin [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between MetricGraph versions 1.6.0 dated 2026-05-06 and 1.7.0 dated 2026-11-10
MetricGraph-1.6.0/MetricGraph/man/posterior_crossvalidation.Rd |only MetricGraph-1.6.0/MetricGraph/tests/testthat/test-metric-graph-components.R |only MetricGraph-1.7.0/MetricGraph/DESCRIPTION | 13 MetricGraph-1.7.0/MetricGraph/MD5 | 119 + MetricGraph-1.7.0/MetricGraph/NAMESPACE | 139 + MetricGraph-1.7.0/MetricGraph/NEWS.md | 107 + MetricGraph-1.7.0/MetricGraph/R/MetricGraph-package.R | 3 MetricGraph-1.7.0/MetricGraph/R/RcppExports.R | 95 + MetricGraph-1.7.0/MetricGraph/R/covariance_directional_ou.R |only MetricGraph-1.7.0/MetricGraph/R/graph_crossval.R | 411 +---- MetricGraph-1.7.0/MetricGraph/R/graph_crossval_full.R |only MetricGraph-1.7.0/MetricGraph/R/graph_inference.R | 742 ++++++---- MetricGraph-1.7.0/MetricGraph/R/graph_likelihoods.R | 591 ++++--- MetricGraph-1.7.0/MetricGraph/R/graph_likelihoods_v2.R |only MetricGraph-1.7.0/MetricGraph/R/graph_lme.R | 215 ++ MetricGraph-1.7.0/MetricGraph/R/graph_simulate.R |only MetricGraph-1.7.0/MetricGraph/R/graph_spde.R | 171 +- MetricGraph-1.7.0/MetricGraph/R/likelihood_directional_ou_covariance.R |only MetricGraph-1.7.0/MetricGraph/R/metric_graph.R | 669 +++++---- MetricGraph-1.7.0/MetricGraph/R/osm.R |only MetricGraph-1.7.0/MetricGraph/R/snap_lines.R | 41 MetricGraph-1.7.0/MetricGraph/R/spde_covariance.R | 27 MetricGraph-1.7.0/MetricGraph/R/spde_posteriors.R | 172 +- MetricGraph-1.7.0/MetricGraph/R/spde_precision.R | 378 +++-- MetricGraph-1.7.0/MetricGraph/R/spde_sampling.R | 35 MetricGraph-1.7.0/MetricGraph/R/util.R | 635 +++++--- MetricGraph-1.7.0/MetricGraph/R/weighted_stiffness.R |only MetricGraph-1.7.0/MetricGraph/build/vignette.rds |binary MetricGraph-1.7.0/MetricGraph/inst/CITATION | 4 MetricGraph-1.7.0/MetricGraph/inst/COPYRIGHTS | 2 MetricGraph-1.7.0/MetricGraph/inst/dev |only MetricGraph-1.7.0/MetricGraph/inst/doc/MetricGraph_pkg.html | 4 MetricGraph-1.7.0/MetricGraph/man/cross_validation.Rd | 27 MetricGraph-1.7.0/MetricGraph/man/directional_ou_covariance.Rd |only MetricGraph-1.7.0/MetricGraph/man/directional_ou_variance.Rd |only MetricGraph-1.7.0/MetricGraph/man/fetch_osm.Rd |only MetricGraph-1.7.0/MetricGraph/man/graph_spde.Rd | 9 MetricGraph-1.7.0/MetricGraph/man/metric_graph.Rd | 87 + MetricGraph-1.7.0/MetricGraph/man/metric_graph_from_osm.Rd |only MetricGraph-1.7.0/MetricGraph/man/posterior_crossvalidation.graph_lme.Rd |only MetricGraph-1.7.0/MetricGraph/man/simulate.metric_graph.Rd |only MetricGraph-1.7.0/MetricGraph/man/simulate_parallel.Rd |only MetricGraph-1.7.0/MetricGraph/man/weighted_stiffness.Rd |only MetricGraph-1.7.0/MetricGraph/src/CB.cpp | 4 MetricGraph-1.7.0/MetricGraph/src/CB_revisited.cpp | 6 MetricGraph-1.7.0/MetricGraph/src/RcppExports.cpp | 160 ++ MetricGraph-1.7.0/MetricGraph/src/aux_functions.cpp | 77 + MetricGraph-1.7.0/MetricGraph/src/crossval_full.cpp |only MetricGraph-1.7.0/MetricGraph/src/directional_edge_precision.cpp |only MetricGraph-1.7.0/MetricGraph/src/directional_ou_covariance.cpp |only MetricGraph-1.7.0/MetricGraph/src/edge_simulation.cpp |only MetricGraph-1.7.0/MetricGraph/src/metric_graph_helpers.cpp | 275 +++ MetricGraph-1.7.0/MetricGraph/tests/testthat/helper-directional-ou.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/helper-inla.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/helper-metric-graph.R | 9 MetricGraph-1.7.0/MetricGraph/tests/testthat/helper-subgraph-equivalence.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-cpp-helpers.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-cross-validation-routing.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-crossval-full.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-directional-ou-covariance.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-directional-ou-likelihood.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-directional-precision-cpp.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-disconnected-models.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-geodist-pte-duplicates.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-get-largest.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-graph-crossval-sampling.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-graph-simulate.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-observation-to-vertex.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-prune-vertices-perf.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-prune-vertices.R | 52 MetricGraph-1.7.0/MetricGraph/tests/testthat/test-sample_spde-nsim.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-single-edge-constraints.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-snap-points-to-lines.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test-weighted-stiffness.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test.alpha2.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test.alpha2.circular.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test.alpha2.constraints.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test.alpha2.profile.sign.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test.alpha2.sign.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_cgeneric.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_crossval.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_directional.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_exp.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_isoExp.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_obs_improvements.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_posterior_crossvalidation_generic.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_precomputed_likelihood.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_profile_likelihood.R |only MetricGraph-1.7.0/MetricGraph/tests/testthat/test_split_line.R |only 89 files changed, 3478 insertions(+), 1801 deletions(-)
Title: Run and Optimize Cross-Situational Word Learning Models
Description: A collection of cognitive models of cross-situational word
learning, together with methods and datasets for fitting and
cross-validating them against experimental and corpus data, and for
plotting the results.
Author: George Kachergis [aut, cre] ,
Mika Braginsky [aut] ,
Michael C. Frank [aut]
Maintainer: George Kachergis <george.kachergis@gmail.com>
Diff between XSLmodels versions 0.4.0 dated 2026-10-18 and 0.5.0 dated 2026-11-10
DESCRIPTION | 12 MD5 | 137 +++++++---- NAMESPACE | 3 NEWS.md | 73 ++++++ R/crossval.R | 35 ++ R/data.R | 110 ++++++++- R/evaluation.R | 230 ++++++++++++++++++ R/fitting.R | 166 ++++++++++++- R/helper.R | 238 +++++++++++++------ R/model-fazly.R | 4 R/model-kalman.R | 162 ++++++++++--- R/model-rescorla_wagner.R | 104 +++++++- R/model-tilles.R | 114 +++++++-- R/model-uncfam.R | 71 ----- R/model-uncfam_attention.R | 73 ------ R/model-uncfam_elimination.R | 67 ----- R/model-uncfam_gamma.R | 54 ---- R/model-uncfam_general.R |only R/model-unfam_sampling.R | 91 ------- R/plotting.R | 65 +++-- R/xslControl-class.R | 35 ++ R/xslData-class.R | 55 +++- R/xslMod-class.R | 47 ++- README.md | 1 build/partial.rdb |only build/vignette.rds |binary data/kachergis_priming.rda |only data/koehne2013.rda |only data/suanda2014.rda |only data/xsl_datasets.rda |binary data/xsl_holdout_datasets.rda |binary inst/doc/XSLmodels.R | 6 inst/doc/XSLmodels.Rmd | 36 ++ inst/doc/XSLmodels.html | 352 +++++++++++++++++------------ inst/doc/corpora.html | 12 inst/doc/custom-models.R |only inst/doc/custom-models.Rmd |only inst/doc/custom-models.html |only inst/doc/model-comparison.R |only inst/doc/model-comparison.Rmd |only inst/doc/model-comparison.html |only inst/doc/nested-comparisons.R |only inst/doc/nested-comparisons.Rmd |only inst/doc/nested-comparisons.html |only man/XSLmodels-package.Rd | 2 man/choice_probabilities.Rd |only man/cross_validated_group_fits.Rd | 13 - man/fazly.Rd | 4 man/get_crossvalidated_model_fit.Rd | 13 - man/get_group_model_fit.Rd | 14 + man/kachergis_priming.Rd |only man/kalman_filter.Rd | 94 ++++++- man/koehne2013.Rd |only man/mafc_test.Rd | 14 - man/predict_referent.Rd | 10 man/rescorla_wagner.Rd | 77 ++++++ man/show_models.Rd | 10 man/softmax_weights.Rd |only man/suanda2014.Rd |only man/uncfam_general.Rd |only man/update_params.Rd | 32 +- man/xslControl-class.Rd | 29 ++ man/xslData-class.Rd | 17 + man/xsl_datasets.Rd | 22 + man/xsl_fit.Rd | 51 +++- man/xsl_holdout_datasets.Rd | 13 - man/xsl_run.Rd | 17 + tests/testthat/fixtures |only tests/testthat/helper-tilles-literal.R |only tests/testthat/test-data.R | 86 +++++++ tests/testthat/test-error-driven-options.R |only tests/testthat/test-evaluation.R | 125 ++++++++++ tests/testthat/test-fitting.R | 30 ++ tests/testthat/test-invariants.R |only tests/testthat/test-likelihood.R |only tests/testthat/test-models.R | 148 +++++++++--- tests/testthat/test-multiblock.R |only tests/testthat/test-plotting.R |only tests/testthat/test-registry.R |only tests/testthat/test-rescorla_wagner.R |only tests/testthat/test-start-matrix.R | 5 tests/testthat/test-uncfam_general.R |only vignettes/XSLmodels.Rmd | 36 ++ vignettes/custom-models.Rmd |only vignettes/model-comparison.Rmd |only vignettes/nested-comparisons.Rmd |only 86 files changed, 2331 insertions(+), 884 deletions(-)
Title: A Shiny Dashboard Template Modular System with Chat Bot Support
Description: A template dashboard system with AI agent integrated.
Comes with default themes that can be customized.
Developers can upload modified templates on 'Github', and users can
easily download templates with 'RStudio' project wizard.
The key features of the default template include light and dark theme
switcher, resizing graphs, synchronizing inputs across sessions,
new notification system, fancy progress bars, and card-like flip
panels with back sides, as well as various of 'HTML' tool widgets.
Author: Zhengjia Wang [cph, aut, cre] ,
ColorlibHQ [cph] ,
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Ivan Sagalaev [ctb, cph] ,
Rene Haas [ctb, cph] ,
Zeno Rocha [ctb, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between shidashi versions 0.3.0 dated 2026-10-11 and 0.3.1 dated 2026-11-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/mcp-wrapper.R | 30 +++++++++++++++++++++++++++++- man/register_io.Rd | 5 ++++- 5 files changed, 44 insertions(+), 9 deletions(-)
Title: Geometric Methods for Nonparametric Regression and Density
Estimation
Description: Provides geometric methods for nonparametric regression and
density estimation on data represented as coordinate matrices or weighted
graphs.
Methods include local polynomial smoothing, model-averaged local polynomial
smoothing, local polynomial lifting trend filtering, synchronized local
polynomial lifting trend filtering, order-2 Gaussian and logistic trend filtering,
graph low-pass filtering, and
Hessian-energy regression. Methodological references include Gajer and
Ravel (2025) "Adaptive Geometric Regression for High-Dimensional Structured
Data" <doi:10.48550/arXiv.2511.03817>, Fan and Gijbels (1996,
ISBN:9780412983214), Wang et al. (2016) "Trend Filtering on Graphs"
<https://www.jmlr.org/papers/v17/15-147.html>, and Kim et al. (2009)
"Semi-Supervised Regression Using Hessian Energy"
<https://papers.nips.cc/paper/3741-semi-supervised-regression-using-hessian-energy-with-an-application-to-semi-supervised-dimensionality-reduction>.
Author: Pawel Gajer [aut, cre],
Gael Guennebaud [ctb] ,
Benoit Jacob [ctb] ,
Authors of Eigen [cph] ,
Yixuan Qiu [ctb, cph] ,
Contributors to Spectra [cph] ,
Sunil Arya [ctb, cph] ,
David M. Mount [ctb, cph] ,
University of Maryland [cph]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between geosmooth versions 0.1.0 dated 2026-09-12 and 0.2.0 dated 2026-11-10
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Title: Coarse Approximation Linear Function
Description: Contains greedy algorithms for coarse approximation linear functions.
Author: Stephanie Lane [aut],
John Ford [aut, cre],
Clark Jeffries [aut],
Diana Perkins [aut]
Maintainer: John Ford <JoRuFo@gmail.com>
Diff between CALF versions 1.0.17 dated 2022-03-07 and 1.2.0 dated 2026-11-10
DESCRIPTION | 28 MD5 | 11 NAMESPACE | 6 R/calf_internal.R | 741 +++++++++---------- R/calf_wrappers.R | 2057 +++++++++++++++++++++++++++--------------------------- man/cv.calf.Rd | 84 +- tests |only 7 files changed, 1470 insertions(+), 1457 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre] ,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.26 dated 2026-08-22 and 1.2.27 dated 2026-11-10
DESCRIPTION | 8 MD5 | 40 +-- R/wiki_utils.R | 6 README.md | 4 inst/doc/wiki_utils.Rmd | 3 inst/doc/wiki_utils.html | 508 ++++++++++++++++++++++++++--------------------- man/filext.Rd | 58 ++--- man/getFiles.Rd | 102 ++++----- man/getWikiFiles.Rd | 88 ++++---- man/httrGetJSON.Rd | 62 ++--- man/nametoWikiFrame.Rd | 74 +++--- man/nametoWikiHtml.Rd | 70 +++--- man/nametoWikiURL.Rd | 74 +++--- man/preName.Rd | 60 ++--- man/searchWiki.Rd | 96 ++++---- man/selectLang.Rd | 48 ++-- man/urltoFrame.Rd | 70 +++--- man/urltoHtml.Rd | 86 +++---- man/v_dfVIAF.Rd | 88 ++++---- man/validUrl.Rd | 56 ++--- vignettes/wiki_utils.Rmd | 3 21 files changed, 837 insertions(+), 767 deletions(-)
Title: Design and Analysis of Pilot Trials Assessing Recruitment
Feasibility
Description: Find optimal decisions rules for guiding progression decisions
following a pilot trial, assuming a hierarchical recruitment model. Estimate
the time until the main trial recruits to target, given the recruitment data
observed in the pilot.
Author: Duncan Wilson [aut, cre, cph]
Maintainer: Duncan Wilson <d.t.wilson@leeds.ac.uk>
Diff between fahb versions 1.0.1 dated 2026-09-25 and 1.0.2 dated 2026-11-10
fahb |only 1 file changed
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data
mining tasks such as clustering and classification. The development of
this package was supported in part by NSF IIS-0948893, NSF CMMI
1728612, and NIH R21HG005912. Hahsler et al (2017)
<doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Bolanos [ctb],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 2.0.6 dated 2026-07-27 and 2.0.7 dated 2026-11-10
stream-2.0.6/stream/inst/doc/stream.Rnw |only stream-2.0.6/stream/inst/doc/stream.pdf |only stream-2.0.6/stream/vignettes/stream.Rnw |only stream-2.0.7/stream/DESCRIPTION | 18 stream-2.0.7/stream/MD5 | 127 +- stream-2.0.7/stream/NAMESPACE | 94 - stream-2.0.7/stream/NEWS.md | 24 stream-2.0.7/stream/R/DSC_DBSCAN.R | 6 stream-2.0.7/stream/R/DSC_DBSTREAM.R | 7 stream-2.0.7/stream/R/DSC_EA.R | 2 stream-2.0.7/stream/R/DSC_Macro.R | 6 stream-2.0.7/stream/R/DSC_Reachability.R | 2 stream-2.0.7/stream/R/DSC_evoStream.R | 2 stream-2.0.7/stream/R/DSD_Cubes.R | 2 stream-2.0.7/stream/R/DSD_Gaussians.R | 15 stream-2.0.7/stream/R/DSD_MG.R | 42 stream-2.0.7/stream/R/DSD_ReadStream.R | 6 stream-2.0.7/stream/R/DSF_Convolve.R | 31 stream-2.0.7/stream/R/DSF_Downsample.R | 5 stream-2.0.7/stream/R/DSF_ExponentialMA.R | 5 stream-2.0.7/stream/R/DSF_FeaturesSelection.R | 10 stream-2.0.7/stream/R/DSF_Func.R | 14 stream-2.0.7/stream/R/DSF_Scale.R | 22 stream-2.0.7/stream/R/DSF_dplyr.R | 7 stream-2.0.7/stream/R/MGC.R | 172 +- stream-2.0.7/stream/R/evaluate.DSC.R | 45 stream-2.0.7/stream/R/evaluate.R | 11 stream-2.0.7/stream/README.md | 61 stream-2.0.7/stream/build/partial.rdb |binary stream-2.0.7/stream/build/vignette.rds |binary stream-2.0.7/stream/inst/doc/DBSTREAM.R |only stream-2.0.7/stream/inst/doc/DBSTREAM.Rmd |only stream-2.0.7/stream/inst/doc/DBSTREAM.html |only stream-2.0.7/stream/inst/doc/DSD_MG.R |only stream-2.0.7/stream/inst/doc/DSD_MG.Rmd |only stream-2.0.7/stream/inst/doc/DSD_MG.html |only stream-2.0.7/stream/inst/doc/evaluation_non-stationary.R |only stream-2.0.7/stream/inst/doc/evaluation_non-stationary.Rmd |only stream-2.0.7/stream/inst/doc/evaluation_non-stationary.html |only stream-2.0.7/stream/inst/doc/extending_stream.pdf |binary stream-2.0.7/stream/inst/doc/stream.R | 632 +--------- stream-2.0.7/stream/inst/doc/stream.Rmd |only stream-2.0.7/stream/inst/doc/stream.html |only stream-2.0.7/stream/inst/doc/stream_vignette.R |only stream-2.0.7/stream/inst/doc/stream_vignette.Rnw |only stream-2.0.7/stream/inst/doc/stream_vignette.pdf |only stream-2.0.7/stream/man/DSC_DBSCAN.Rd | 6 stream-2.0.7/stream/man/DSC_DBSTREAM.Rd | 6 stream-2.0.7/stream/man/DSC_EA.Rd | 2 stream-2.0.7/stream/man/DSC_Macro.Rd | 6 stream-2.0.7/stream/man/DSC_Reachability.Rd | 2 stream-2.0.7/stream/man/DSC_evoStream.Rd | 2 stream-2.0.7/stream/man/DSD_Cubes.Rd | 2 stream-2.0.7/stream/man/DSD_Gaussians.Rd | 15 stream-2.0.7/stream/man/DSD_MG.Rd | 42 stream-2.0.7/stream/man/DSD_ReadStream.Rd | 2 stream-2.0.7/stream/man/DSF_Convolve.Rd | 31 stream-2.0.7/stream/man/DSF_Downsample.Rd | 5 stream-2.0.7/stream/man/DSF_ExponentialMA.Rd | 5 stream-2.0.7/stream/man/DSF_FeatureSelection.Rd | 10 stream-2.0.7/stream/man/DSF_Func.Rd | 14 stream-2.0.7/stream/man/DSF_Scale.Rd | 22 stream-2.0.7/stream/man/DSF_dplyr.Rd | 7 stream-2.0.7/stream/man/MGC.Rd | 163 +- stream-2.0.7/stream/man/evaluate.Rd | 11 stream-2.0.7/stream/man/figures/README-DSOutlier_DBSTREAM-1.png |only stream-2.0.7/stream/man/figures/README-Dstream-1.png |only stream-2.0.7/stream/man/figures/README-stream-1.png |only stream-2.0.7/stream/man/stream-package.Rd | 1 stream-2.0.7/stream/src/BICO/kmeans.h | 52 stream-2.0.7/stream/src/DBSTREAM.cpp | 1 stream-2.0.7/stream/tests/testthat/test-DSF_transformations.R |only stream-2.0.7/stream/tests/testthat/test-evaluate_stream.R |only stream-2.0.7/stream/vignettes/DBSTREAM.Rmd |only stream-2.0.7/stream/vignettes/DSD_MG.Rmd |only stream-2.0.7/stream/vignettes/evaluation_non-stationary.Rmd |only stream-2.0.7/stream/vignettes/stream.Rmd |only stream-2.0.7/stream/vignettes/stream_vignette.Rnw |only 78 files changed, 766 insertions(+), 1009 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM).
Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli, Poisson or Gaussian emission laws on the edges). For Simple and Bipartite SBM, covariates can be given on the edges, or on the nodes to drive the block memberships, and the network may contain missing values. See Léger (2016) <doi:10.48550/arXiv.1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and 'Bar-Hen et al.' (2020) <doi:10.48550/arXiv.1807.10138>.
Author: Julien Chiquet [aut, cre] ,
Sophie Donnet [aut] ,
Pierre Barbillon [aut] ,
Louis Lacoste [aut],
Jean-Benoist Leger [ctb],
Julie Aubert [ctb] ,
grossBM team [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.4.7 dated 2024-09-16 and 1.0.0 dated 2026-11-10
sbm-0.4.7/sbm/inst/doc/Multipartite_EcologicalNetwork.Rmd |only sbm-0.4.7/sbm/inst/doc/MultiplexNetwork_principle.Rmd |only sbm-0.4.7/sbm/inst/doc/Multiplex_allianceNwar_case_study.Rmd |only sbm-0.4.7/sbm/inst/doc/SBM_fungus_tree_network.Rmd |only sbm-0.4.7/sbm/inst/visnetwork.Rmd |only sbm-0.4.7/sbm/vignettes/Multipartite_EcologicalNetwork.Rmd |only sbm-0.4.7/sbm/vignettes/MultiplexNetwork_principle.Rmd |only sbm-0.4.7/sbm/vignettes/Multiplex_allianceNwar_case_study.Rmd |only sbm-0.4.7/sbm/vignettes/Multiplex_allianceNwar_case_study.rds |only sbm-0.4.7/sbm/vignettes/SBM_fungus_tree_network.Rmd |only sbm-0.4.7/sbm/vignettes/resMultipartiteEcological.rda |only sbm-0.4.7/sbm/vignettes/resVignetteSimuMultiplex.rda |only sbm-1.0.0/sbm/DESCRIPTION | 47 sbm-1.0.0/sbm/MD5 | 169 sbm-1.0.0/sbm/NAMESPACE | 20 sbm-1.0.0/sbm/NEWS.md | 43 sbm-1.0.0/sbm/R/R6Class-BipartiteSBM.R | 100 sbm-1.0.0/sbm/R/R6Class-BipartiteSBM_fit.R | 157 sbm-1.0.0/sbm/R/R6Class-MultipartiteSBM.R | 13 sbm-1.0.0/sbm/R/R6Class-MultipartiteSBM_fit.R | 9 sbm-1.0.0/sbm/R/R6Class-MultiplexSBM_fit.R | 66 sbm-1.0.0/sbm/R/R6Class-SBM.R | 381 + sbm-1.0.0/sbm/R/R6Class-SimpleSBM.R | 85 sbm-1.0.0/sbm/R/R6Class-SimpleSBM_fit.R | 56 sbm-1.0.0/sbm/R/defineSBM.R | 5 sbm-1.0.0/sbm/R/estimate.R | 83 sbm-1.0.0/sbm/R/plotAlluvial.R | 40 sbm-1.0.0/sbm/R/plotMyGraphon.R |only sbm-1.0.0/sbm/R/plotMyMatrix.R | 4 sbm-1.0.0/sbm/R/plotMyMultipartiteMatrix.R | 5 sbm-1.0.0/sbm/R/plotMyMultiplexMatrix.R | 5 sbm-1.0.0/sbm/R/sample.R | 48 sbm-1.0.0/sbm/R/utils.R | 48 sbm-1.0.0/sbm/R/utils_plot.R | 838 ++-- sbm-1.0.0/sbm/README.md | 119 sbm-1.0.0/sbm/build/partial.rdb |binary sbm-1.0.0/sbm/build/vignette.rds |binary sbm-1.0.0/sbm/inst/WORDLIST | 55 sbm-1.0.0/sbm/inst/doc/Multipartite_EcologicalNetwork.R | 95 sbm-1.0.0/sbm/inst/doc/Multipartite_EcologicalNetwork.html | 749 +-- sbm-1.0.0/sbm/inst/doc/Multipartite_EcologicalNetwork.qmd |only sbm-1.0.0/sbm/inst/doc/MultiplexNetwork_principle.R | 99 sbm-1.0.0/sbm/inst/doc/MultiplexNetwork_principle.html | 911 +--- sbm-1.0.0/sbm/inst/doc/MultiplexNetwork_principle.qmd |only sbm-1.0.0/sbm/inst/doc/Multiplex_allianceNwar_case_study.R | 116 sbm-1.0.0/sbm/inst/doc/Multiplex_allianceNwar_case_study.html | 1206 +++--- sbm-1.0.0/sbm/inst/doc/Multiplex_allianceNwar_case_study.qmd |only sbm-1.0.0/sbm/inst/doc/SBM_fungus_tree_network.R | 171 sbm-1.0.0/sbm/inst/doc/SBM_fungus_tree_network.html | 1945 +++++++--- sbm-1.0.0/sbm/inst/doc/SBM_fungus_tree_network.qmd |only sbm-1.0.0/sbm/inst/doc/SBM_nodes_covariates.R |only sbm-1.0.0/sbm/inst/doc/SBM_nodes_covariates.html |only sbm-1.0.0/sbm/inst/doc/SBM_nodes_covariates.qmd |only sbm-1.0.0/sbm/inst/doc/SBM_principle.R |only sbm-1.0.0/sbm/inst/doc/SBM_principle.html |only sbm-1.0.0/sbm/inst/doc/SBM_principle.qmd |only sbm-1.0.0/sbm/man/BipartiteSBM.Rd | 307 - sbm-1.0.0/sbm/man/BipartiteSBM_fit.Rd | 235 - sbm-1.0.0/sbm/man/MultipartiteSBM.Rd | 202 - sbm-1.0.0/sbm/man/MultipartiteSBM_fit.Rd | 222 - sbm-1.0.0/sbm/man/MultiplexSBM_fit.Rd | 218 - sbm-1.0.0/sbm/man/SBM.Rd | 209 - sbm-1.0.0/sbm/man/SimpleSBM.Rd | 318 - sbm-1.0.0/sbm/man/SimpleSBM_fit.Rd | 238 - sbm-1.0.0/sbm/man/defineSBM.Rd | 2 sbm-1.0.0/sbm/man/estimateBipartiteSBM.Rd | 29 sbm-1.0.0/sbm/man/estimateMultipartiteSBM.Rd | 9 sbm-1.0.0/sbm/man/estimateMultiplexSBM.Rd | 17 sbm-1.0.0/sbm/man/estimateSimpleSBM.Rd | 27 sbm-1.0.0/sbm/man/figures |only sbm-1.0.0/sbm/man/plot.SBM.Rd | 62 sbm-1.0.0/sbm/man/plotAlluvial.Rd | 5 sbm-1.0.0/sbm/man/plotMyGraphon.Rd |only sbm-1.0.0/sbm/man/plotMyMatrix.Rd | 4 sbm-1.0.0/sbm/man/plotMyMultipartiteMatrix.Rd | 5 sbm-1.0.0/sbm/man/plotMyMultiplexMatrix.Rd | 5 sbm-1.0.0/sbm/man/sampleBipartiteSBM.Rd | 10 sbm-1.0.0/sbm/man/sampleSimpleSBM.Rd | 12 sbm-1.0.0/sbm/man/sbm-package.Rd | 6 sbm-1.0.0/sbm/tests/spelling.Rout.save |only sbm-1.0.0/sbm/tests/testthat/Rplots.pdf |binary sbm-1.0.0/sbm/tests/testthat/test-BipartiteSBM_fit.R | 144 sbm-1.0.0/sbm/tests/testthat/test-BipartiteSBM_fit_covariates.R | 53 sbm-1.0.0/sbm/tests/testthat/test-BipartiteSBM_fit_nodes_covariates.R |only sbm-1.0.0/sbm/tests/testthat/test-BipartiteSBM_sampler.R | 8 sbm-1.0.0/sbm/tests/testthat/test-MultipartiteSBM.R | 5 sbm-1.0.0/sbm/tests/testthat/test-MultiplexSBM_fit.R | 13 sbm-1.0.0/sbm/tests/testthat/test-SimpleSBM_fit.R | 563 ++ sbm-1.0.0/sbm/tests/testthat/test-SimpleSBM_fit_covariates.R | 45 sbm-1.0.0/sbm/tests/testthat/test-SimpleSBM_fit_nodes_covariates.R |only sbm-1.0.0/sbm/tests/testthat/test-backward-compatibility.R |only sbm-1.0.0/sbm/tests/testthat/test-defineNetwork.R | 35 sbm-1.0.0/sbm/tests/testthat/test-plots.R |only sbm-1.0.0/sbm/tests/testthat/test-predict-bernoulli-covariates.R |only sbm-1.0.0/sbm/vignettes/Multipartite_EcologicalNetwork.qmd |only sbm-1.0.0/sbm/vignettes/Multipartite_EcologicalNetwork_fits.rda |only sbm-1.0.0/sbm/vignettes/MultiplexNetwork_principle.qmd |only sbm-1.0.0/sbm/vignettes/MultiplexNetwork_principle_fits.rda |only sbm-1.0.0/sbm/vignettes/Multiplex_allianceNwar_case_study.qmd |only sbm-1.0.0/sbm/vignettes/Multiplex_allianceNwar_case_study_fits.rda |only sbm-1.0.0/sbm/vignettes/SBM_fungus_tree_network.qmd |only sbm-1.0.0/sbm/vignettes/SBM_fungus_tree_network_fits.rda |only sbm-1.0.0/sbm/vignettes/SBM_nodes_covariates.qmd |only sbm-1.0.0/sbm/vignettes/SBM_nodes_covariates_fits.rda |only sbm-1.0.0/sbm/vignettes/SBM_principle.qmd |only sbm-1.0.0/sbm/vignettes/Tree-Fungus.jpg |only sbm-1.0.0/sbm/vignettes/references.bib | 12 107 files changed, 6766 insertions(+), 3942 deletions(-)
Title: NASA's Global Ecosystem Dynamics Investigation (GEDI) Data
Visualization and Processing
Description: Provides an end-to-end workflow for NASA Global Ecosystem
Dynamics Investigation (GEDI) Level 1B, Level 2A, Level 2B, Level 3, Level
4A, and Level 4B data. Functions search NASA catalogues, download granules,
stream HDF5 products from Earthdata Cloud, and extract geolocations,
waveforms, elevation and relative-height metrics, canopy cover, plant area
profiles, and aboveground biomass. Methods quality-filter and spatially clip
HDF5, tabular, and raster products; calculate footprint and polygon
statistics; create gridded summaries; and visualize orbital tracks and
measurements. The package also simulates GEDI-like waveforms from airborne
laser-scanning point clouds and supports spatial sampling, predictive
modelling, ancillary-data extraction, and wall-to-wall upscaling with
optional Google Earth Engine workflows.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
This is a re-admission after prior archival of version 0.1.11 dated 2021-01-20
Diff between rGEDI versions 0.1.11 dated 2021-01-20 and 0.6.0 dated 2026-11-10
rGEDI-0.1.11/rGEDI/R/C_processExtractMetrics.R |only rGEDI-0.1.11/rGEDI/R/C_simulateFullWaveform.R |only rGEDI-0.1.11/rGEDI/R/libHandler.R |only rGEDI-0.1.11/rGEDI/R/zzz.R |only rGEDI-0.1.11/rGEDI/cleanup |only rGEDI-0.1.11/rGEDI/configure |only rGEDI-0.1.11/rGEDI/configure.ac |only rGEDI-0.1.11/rGEDI/inst/COPYRIGHTS |only rGEDI-0.1.11/rGEDI/inst/extdata/Amazon.zip |only rGEDI-0.1.11/rGEDI/inst/extdata/Savanna.zip |only rGEDI-0.1.11/rGEDI/inst/m4 |only rGEDI-0.1.11/rGEDI/man/gedi.level1bSim-class.Rd |only rGEDI-0.1.11/rGEDI/src |only rGEDI-0.1.11/rGEDI/tools/deps.R |only rGEDI-0.1.11/rGEDI/tools/winlibs.R |only rGEDI-0.6.0/rGEDI/DESCRIPTION | 76 rGEDI-0.6.0/rGEDI/MD5 | 376 +- rGEDI-0.6.0/rGEDI/NAMESPACE | 140 - rGEDI-0.6.0/rGEDI/NEWS.md |only rGEDI-0.6.0/rGEDI/R/argParse.R | 50 rGEDI-0.6.0/rGEDI/R/class.gedi.R | 377 +- rGEDI-0.6.0/rGEDI/R/clip.R |only rGEDI-0.6.0/rGEDI/R/clipLevel1B.R | 611 ++-- rGEDI-0.6.0/rGEDI/R/clipLevel1BGeo.R | 352 +- rGEDI-0.6.0/rGEDI/R/clipLevel2A.R | 389 +- rGEDI-0.6.0/rGEDI/R/clipLevel2AM.R | 322 +- rGEDI-0.6.0/rGEDI/R/clipLevel2B.R | 368 +- rGEDI-0.6.0/rGEDI/R/clipLevel2BPAIProfile.R | 300 +- rGEDI-0.6.0/rGEDI/R/clipLevel2BPAVDProfile.R | 301 +- rGEDI-0.6.0/rGEDI/R/clipLevel2BVPM.R | 360 +- rGEDI-0.6.0/rGEDI/R/clipTools.R | 487 ++- rGEDI-0.6.0/rGEDI/R/cloud.R |only rGEDI-0.6.0/rGEDI/R/gediDownload.R | 305 +- rGEDI-0.6.0/rGEDI/R/gedifinder.R | 301 +- rGEDI-0.6.0/rGEDI/R/gee.R |only rGEDI-0.6.0/rGEDI/R/getLevel1BGeo.R | 296 +- rGEDI-0.6.0/rGEDI/R/getLevel1BWF.R | 154 - rGEDI-0.6.0/rGEDI/R/getLevel2AM.R | 177 - rGEDI-0.6.0/rGEDI/R/getLevel2BPAIProfile.R | 165 - rGEDI-0.6.0/rGEDI/R/getLevel2BPAVDProfile.R | 165 - rGEDI-0.6.0/rGEDI/R/getLevel2BVPM.R | 276 +- rGEDI-0.6.0/rGEDI/R/gridStatsLevel2AM.R | 194 - rGEDI-0.6.0/rGEDI/R/gridStatsLevel2BVPM.R | 173 - rGEDI-0.6.0/rGEDI/R/lazy_applier.R |only rGEDI-0.6.0/rGEDI/R/level4A.R |only rGEDI-0.6.0/rGEDI/R/modeling.R |only rGEDI-0.6.0/rGEDI/R/orbitAnimation.R |only rGEDI-0.6.0/rGEDI/R/plotPAIProfile.R | 256 - rGEDI-0.6.0/rGEDI/R/plotPAVDProfile.R | 254 - rGEDI-0.6.0/rGEDI/R/plotWFMetrics.R | 210 - rGEDI-0.6.0/rGEDI/R/polyStatsLevel2AM.R | 161 - rGEDI-0.6.0/rGEDI/R/polyStatsLevel2BVPM.R | 140 - rGEDI-0.6.0/rGEDI/R/rGEDI-package.R | 7 rGEDI-0.6.0/rGEDI/R/rasterProducts.R |only rGEDI-0.6.0/rGEDI/R/readLevel1B.R | 65 rGEDI-0.6.0/rGEDI/R/readLevel2A.R | 65 rGEDI-0.6.0/rGEDI/R/readLevel2B.R | 61 rGEDI-0.6.0/rGEDI/R/sampling.R |only rGEDI-0.6.0/rGEDI/R/simulator.R |only rGEDI-0.6.0/rGEDI/README.md | 1324 ++++++---- rGEDI-0.6.0/rGEDI/build |only rGEDI-0.6.0/rGEDI/inst/extdata/orbit |only rGEDI-0.6.0/rGEDI/inst/extdata/stands_cerrado.qpj | 2 rGEDI-0.6.0/rGEDI/inst/scripts |only rGEDI-0.6.0/rGEDI/man/addEEImage.Rd |only rGEDI-0.6.0/rGEDI/man/aggregateLevel3.Rd |only rGEDI-0.6.0/rGEDI/man/aggregateLevel4B.Rd |only rGEDI-0.6.0/rGEDI/man/aspect.Rd |only rGEDI-0.6.0/rGEDI/man/build_ee_forest.Rd |only rGEDI-0.6.0/rGEDI/man/clip.Rd |only rGEDI-0.6.0/rGEDI/man/clipLevel1B.Rd | 128 rGEDI-0.6.0/rGEDI/man/clipLevel1BGeo.Rd | 140 - 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Title: Fit Hidden Markov Models using Template Model Builder
Description: Fitting hidden Markov models using automatic differentiation
and Laplace approximation, allowing for fast inference and flexible covariate
effects (including random effects and smoothing splines) on model parameters.
The package is described by Michelot (2025) <doi:10.18637/jss.v114.i05>.
Author: Theo Michelot [aut, cre],
Richard Glennie [aut],
Jan-Ole Fischer [ctb] ,
Duncan Cameron-Steinke [ctb] ,
Pauline Rocu [ctb] ,
Litty Mathew [ctb]
Maintainer: Theo Michelot <theo.michelot@dal.ca>
Diff between hmmTMB versions 1.1.2 dated 2025-11-05 and 2.0.0 dated 2026-11-10
DESCRIPTION | 37 MD5 | 84 - NAMESPACE | 96 - NEWS.md | 61 R/dist_def.R | 52 R/forecast.R |only R/hmm.R | 1581 +++++++++++++++---------- R/make_formulas.R | 5 R/make_mat.R | 144 +- R/markovchain.R | 39 R/observation.R | 37 R/spde.R |only R/update.R | 4 R/utility.R | 177 ++ README.md | 10 build/partial.rdb |only inst/case_studies/lions_kalahari.R |only inst/devel/forecast_example.ipynb |only inst/devel/test_forecast_dists.ipynb |only inst/doc/hmmTMB_list_of_online_resources.Rmd | 8 inst/doc/hmmTMB_list_of_online_resources.pdf |binary inst/examples/spde |only man/Dist.Rd | 551 ++++---- man/Forecast.Rd |only man/HMM.Rd | 1593 ++++++++++++++------------ man/MarkovChain.Rd | 981 ++++++++-------- man/Observation.Rd | 1070 +++++++++-------- man/check_smooths.Rd |only man/cov_grid_2d.Rd |only man/cov_names_in_data.Rd |only man/gam_shell.Rd |only man/hmmTMB-package.Rd | 13 man/hmmTMB_cols.Rd | 5 man/make_matrices.Rd | 20 man/rmvn_prec.Rd |only man/smooth.construct.spde.smooth.spec.Rd |only man/spde_extent.Rd |only man/spde_loc.Rd |only man/spde_mesh_1d.Rd |only src/Makefile | 13 src/Makefile.win | 10 src/dist.hpp | 2 src/dist_def.hpp | 36 src/hmmTMB.hpp | 85 - src/likelihood.hpp |only tests/testthat/test_banded.R |only tests/testthat/test_forecast_dists.R |only tests/testthat/test_forecast_multivariate.R |only tests/testthat/test_forecast_validation.R |only tests/testthat/test_hmm_misc.R | 13 tests/testthat/test_make_mat.R |only tests/testthat/test_plot_2d.R |only tests/testthat/test_spde.R |only tests/testthat/test_uncertainty.R |only vignettes/hmmTMB_list_of_online_resources.Rmd | 8 vignettes/refs.bib | 31 56 files changed, 4026 insertions(+), 2740 deletions(-)
Title: Download 'Eurostat' 'GISCO' Spatial Data
Description: Tools to download global and European spatial data from the
'Eurostat' 'GISCO' (Geographic Information System of the Commission)
data distribution <https://ec.europa.eu/eurostat/web/gisco>. The
package provides helpers for country boundaries, Nomenclature of
Territorial Units for Statistics ('NUTS') regions, administrative
units, statistical units, transport networks, basic service locations
and other 'GISCO' datasets. This package is neither affiliated with
nor endorsed by 'Eurostat'.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 1.3.0 dated 2026-10-01 and 1.3.1 dated 2026-11-10
DESCRIPTION | 10 +-- MD5 | 72 +++++++++++++-------------- NEWS.md | 9 +++ R/data.R | 5 + R/docs.R | 36 ------------- R/gisco-id-api.R | 39 ++++++-------- R/utils-country.R | 4 - R/utils.R | 2 README.md | 10 +-- build/stage23.rdb |binary build/vignette.rds |binary data/gisco_coastal_lines.rda |binary data/gisco_countries_2024.rda |binary data/gisco_countrycode.rda |binary data/gisco_db.rda |binary data/gisco_nuts_2024.rda |binary inst/doc/apis.html | 22 ++++---- inst/doc/apis.qmd | 20 +++---- inst/doc/giscoR.html | 4 - inst/schemaorg.json | 4 - man/figures/logo.png |binary man/gisco_countries_2024.Rd | 5 + man/gisco_db.Rd | 2 man/gisco_id_api.Rd | 41 +++++++-------- tests/testthat/_snaps/docs.md | 14 ----- tests/testthat/_snaps/gisco-get-cached-db.md | 2 tests/testthat/test-docs.R | 25 --------- tests/testthat/test-gisco-address-api.R | 25 +++++---- tests/testthat/test-gisco-get-cached-db.R | 9 +-- tests/testthat/test-gisco-get-communes.R | 7 +- tests/testthat/test-gisco-get-education.R | 10 ++- tests/testthat/test-gisco-get-lau.R | 7 +- tests/testthat/test-gisco-get-postal-codes.R | 7 +- tests/testthat/test-gisco-id-api.R | 14 +++-- tests/testthat/test-utils-url.R | 47 +++++++++-------- vignettes/apis.qmd | 20 +++---- vignettes/fig-giscor-1.png |binary 37 files changed, 211 insertions(+), 261 deletions(-)
More information about amazonasdatahub at CRAN
Permanent link
Title: Zero-Inflated and Hurdle INAR(1) Models
Description: Provides tools for estimating Zero-Inflated INAR(1)
(ZI-INAR(1)) and Hurdle INAR(1) (H-INAR(1)) models using 'Stan'.
It allows users to simulate time series data for these models,
estimate parameters, and evaluate model fit using various criteria.
Functions include model estimation, simulation, and likelihood-based metrics.
The zero-inflated and hurdle INAR(1) methods are described by Yang et al.
(2025) <doi:10.1214/25-BJPS646>. Zero-inflated models also support
Conway-Maxwell-Poisson innovations.
Author: Fusheng Yang [aut, cre],
Victor Hugo Lachos Davila [aut],
Alokesh Manna [aut],
Dipak K. Dey [aut]
Maintainer: Fusheng Yang <fusheng.yang@uconn.edu>
Diff between ZIHINAR1 versions 0.2.1 dated 2026-02-12 and 0.3.0 dated 2026-11-10
DESCRIPTION | 23 +++- MD5 | 43 ++++---- NAMESPACE | 56 ++++++---- R/data_simu.R | 75 +++++++++++--- R/get_est.R | 10 + R/get_mol_sel.R | 22 ++-- R/get_pred.R | 147 +++++++++++++++------------- R/get_stanfit.R | 69 +++++++++++-- R/mod_sel_criteria.R | 28 +++-- R/model_helpers.R |only R/stanfit_est.R | 24 ++-- build/partial.rdb |binary inst/stan/HNB-INAR1.stan | 206 ++++++++++++++++++++-------------------- inst/stan/HP-INAR1.stan | 192 ++++++++++++++++++------------------- inst/stan/ZICMP-INAR1-fast.stan |only inst/stan/ZICMP-INAR1.stan |only inst/stan/ZIGP-INAR1.stan | 10 - inst/stan/ZINB-INAR1.stan | 202 +++++++++++++++++++-------------------- inst/stan/ZIP-INAR1.stan | 188 ++++++++++++++++++------------------ man/data_simu.Rd | 24 +++- man/get_est.Rd | 2 man/get_mod_sel.Rd | 9 + man/get_pred.Rd | 2 man/get_stanfit.Rd | 33 ++++++ 24 files changed, 781 insertions(+), 584 deletions(-)
Title: Official Gridded Data from the German Census
Description: Provides fast and easy access to German census grid data
from the 2011 and 2022 censuses <https://www.zensus2022.de/>, including a
wide range of socio-economic indicators at multiple spatial resolutions
(100m, 1km, 10km). Enables efficient download, processing, and analysis
of large census datasets covering population, households, families,
dwellings, and buildings. Harmonized data structures allow direct
comparison with the 2011 census, supporting temporal and spatial analyses.
Facilitates conversion of data into common formats for spatial analysis and
mapping ('terra', 'sf', 'ggplot2').
Author: Jonas Lieth [cre, aut, cph]
Maintainer: Jonas Lieth <jslth@outlook.com>
Diff between z22 versions 1.1.4 dated 2026-01-23 and 1.2.0 dated 2026-11-10
DESCRIPTION | 10 +-- MD5 | 47 +++++++++-------- NEWS.md | 19 +++++++ R/categories.R | 52 +++++++++++-------- R/data.R | 66 ++++++++++++++++++------- R/decode.R | 5 + R/features.R | 2 R/pivot.R | 1 README.md | 6 +- inst/doc/z22.Rmd | 51 +++++++++++-------- inst/doc/z22.html | 64 +++++++++++++----------- man/categories.Rd | 79 +++++++++++++++--------------- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/vignette/100m_plot-1.png |binary man/figures/vignette/allcells_plot-1.png |binary man/figures/vignette/normalize_plot-1.png |binary man/figures/vignette/patchwork_plot-1.png |binary man/z22_data.Rd | 32 +++++++++--- man/z22_decode.Rd | 8 ++- man/z22_grid.Rd | 6 +- man/z22_pivot_longer.Rd | 2 tests/testthat/test-pkg.R | 43 ++++++++++++++++ tests/testthat/test-zzz_cats.R |only vignettes/z22.Rmd | 51 +++++++++++-------- vignettes/z22.Rmd.orig | 4 - 25 files changed, 351 insertions(+), 197 deletions(-)
Title: Tidy Analysis of Wikipedia
Description: Access 'Wikipedia' through the several 'MediaWiki' APIs
(<https://www.mediawiki.org/wiki/API>), as well as through the
'XTools' API (<https://www.mediawiki.org/wiki/XTools/API>). Ensure
your API calls are correct, and receive results in tidy tibbles.
Author: Michael Falk [aut, cre, cph]
Maintainer: Michael Falk <michaelgfalk@gmail.com>
Diff between wikkitidy versions 0.1.14 dated 2025-02-13 and 0.2.0 dated 2026-11-10
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Title: Orthogonalizing EM: Penalized Regression for Big Tall Data
Description: Solves penalized least squares problems for big tall data
using the orthogonalizing EM algorithm of Xiong et al. (2016)
<doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the
functions cv.oem() and xval.oem() are for cross validation, the latter being an
accelerated cross validation function for linear models. The big.oem() function
allows for out of memory fitting. A description of the underlying methods and
code interface is described in Huling and Chien (2022) <doi:10.18637/jss.v104.i06>.
Author: Bin Dai [aut],
Jared Huling [aut, cre] ,
Yixuan Qiu [ctb],
Gael Guennebaud [cph],
Jitse Niesen [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.12 dated 2024-07-31 and 2.1.0 dated 2026-11-10
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Title: Numerical Tools for University Calculus
Description: Independent reconstruction of numerical tools for teaching
university calculus. Provides finite difference derivative approximations
with numerical sensitivity diagnostics and local linear models. Optional
interactive graphics illustrate secants, tangents, differentials and
numerical Taylor polynomials of orders one and two. Includes finite limit
probes, critical-point and concavity analysis, and Newton iteration with
explicit numerical diagnostics. Provides signed Riemann sums, partition
refinement, fixed and adaptive quadrature with error diagnostics, and
optional interactive illustrations of numerical integration. Evaluates
accumulation functions and compares their numerical derivatives with
integrands while retaining quadrature and sensitivity diagnostics. Computes
geometric areas, graph lengths, revolution volumes and surface areas,
with separate interactive region and solid illustrations. Approximates
coordinate partials, gradients and line-restriction directional derivatives
wit [...truncated...]
Author: Julio Lizarazo Osorio [aut],
Julian Mauricio Fajardo [aut, cre]
Maintainer: Julian Mauricio Fajardo <julian.fajardo1908@gmail.com>
Diff between vectorialcalculus versions 1.0.5 dated 2026-01-19 and 2.0.0 dated 2026-11-10
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Title: Bayesian Rasch Analysis Using 'brms'
Description: Reproduces classic Rasch psychometric analysis features
using Bayesian item response theory models fitted with 'brms' following
Bürkner (2021) <doi:10.18637/jss.v100.i05> and Bürkner (2020) <doi:10.3390/jintelligence8010005>.
Supports dichotomous and polytomous Rasch models, and a hurdle
partial credit model. Features include posterior predictive item fit,
including infit and item-restscore associations conditional on the
total score, person fit, differential item functioning, local dependence
assessment via Q3 residual correlations, dimensionality assessment with
residual principal components analysis, person-item targeting plots,
item category probability curves, and reliability using relative
measurement uncertainty following Bignardi et al. (2025) <doi:10.31234/osf.io/h54k8_v1>.
Author: Magnus Johansson [aut, cre] ,
Giacomo Bignardi [ctb] ,
Kristoffer Magnusson [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRaschBayes versions 0.3.0 dated 2026-06-18 and 0.4.0 dated 2026-11-10
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More information about easyRaschBayes at CRAN
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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
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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
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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(-)
Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.5.8 dated 2026-07-12 and 1.5.9 dated 2026-11-09
DESCRIPTION | 10 MD5 | 30 - R/RcppExports.R | 40 +- R/data.R | 30 - README.md | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/nebula_example.Rmd | 2 inst/doc/nebula_example.html | 17 man/load_sample_seurat.Rd | 68 +-- src/RcppExports.cpp | 246 ++++++------- src/hlik.cpp |only src/optimization.cpp | 773 ------------------------------------------ src/preprocess.cpp |only tests/testthat.R | 14 tests/testthat/test-scToNeb.R | 700 +++++++++++++++++++------------------- vignettes/nebula_example.Rmd | 2 17 files changed, 582 insertions(+), 1359 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and
'SubCortexMesh' subcortical outputs for a given sample by
restructuring the data values into a single file. The single file can
then be used by the package for analyses independently from its base
dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.5.5 dated 2026-10-16 and 1.6.0 dated 2026-11-09
DESCRIPTION | 10 +- MD5 | 34 ++++---- NAMESPACE | 1 NEWS.md | 8 + R/SCMvextract.R | 14 ++- R/TFCE_vertex_analysis.R | 56 ++++++++++--- R/TFCE_vertex_analysis_mixed.R | 110 ++++++++++++++++++++++++--- R/other_functions.R | 3 inst/doc/VertexWiseR_Example_1.html | 11 +- inst/doc/VertexWiseR_Example_2.html | 52 ++++++------ inst/doc/VertexWiseR_Example_3.html | 54 +++++++++---- inst/doc/VertexWiseR_surface_extraction.html | 13 ++- man/SCMvextract.Rd | 4 man/TFCE_vertex_analysis.Rd | 9 +- man/TFCE_vertex_analysis_mixed.Rd | 18 +++- vignettes/VertexWiseR_Example_3.Rmd | 21 +++-- vignettes/VertexWiseR_surface_extraction.Rmd | 4 vignettes/references.bib | 10 ++ 18 files changed, 315 insertions(+), 117 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Description: Provides nonparametric procedures for the analysis of longitudinal data in factorial experiments. The package implements hypothesis tests on marginal distribution functions and unweighted relative marginal effects. It supports arbitrary crossed factorial designs with longitudinal or repeated-measures factors, missing observations, dependent replicates, rank- and pseudo-rank-based inference, Wald-type and ANOVA-type statistics, multiple contrast tests, and simultaneous confidence intervals.
Author: Frank Konietschke [aut, cre],
Kimihiro Noguchi [ctb] ,
Mahbub Latif [ctb] ,
Karthinathan Thangavelu [ctb] ,
Yulia R. Gel [ctb] ,
Marek Sztuka [ctb] ,
Edgar Brunner [ctb]
Maintainer: Frank Konietschke <frank.konietschke@charite.de>
Diff between nparLD versions 2.3.3 dated 2026-10-14 and 2.3.4 dated 2026-11-09
DESCRIPTION | 9 MD5 | 61 - NAMESPACE | 3 R/Design.R | 56 + R/PairedData.R | 44 - R/Statistics.R | 401 +++++++--- R/Utility.R | 763 +++++++++++++++----- R/accessors.R | 97 +- R/data.R | 2 R/nparLD.R | 545 +++++++++----- R/shinyApp_nparLD.R |only data/shoulder.rda |binary inst/WORDLIST | 4 inst/doc/nparLD.R | 5 inst/doc/nparLD.Rmd | 1399 ++++++++++++++++++------------------- inst/doc/nparLD.html | 489 ++++++------ man/ATS.Rd | 4 man/MCTP.Rd | 2 man/WTS.Rd | 4 man/contrastMatrix.Rd | 2 man/covariance.Rd | 19 man/effects.nparld_fit.Rd | 2 man/factorInfo.Rd | 2 man/nparLD.Rd | 44 - man/nparLDApp.Rd |only man/permTest.Rd | 17 man/plot.nparld_mctp.Rd | 17 man/plot.nparld_permtest.Rd |only man/print.nparld_covarianceinfo.Rd | 4 man/shoulder.Rd | 2 tests/testthat/test-basic.R | 34 tests/testthat/test-examples.R | 22 vignettes/nparLD.Rmd | 1399 ++++++++++++++++++------------------- 33 files changed, 3243 insertions(+), 2209 deletions(-)
Title: Map Quantiles for Physical Activity from 'NHANES'
Description: Maps physical activity from the National Health and Nutrition
Examination Survey ('NHANES') study into population-based quantiles,
using the NHANES 2011-2014 step count and physical activity summaries
described in Koffman, Crainiceanu, and Muschelli (2025)
<doi:10.1249/MSS.0000000000003616>, with minute-level data from
Koffman and Muschelli (2025) <doi:10.13026/9n0r-tv02>.
Author: John Muschelli [aut, cre] ,
Lily Koffman [aut]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mapnhanespa versions 0.3.0 dated 2026-10-22 and 0.4.0 dated 2026-11-09
DESCRIPTION | 8 - MD5 | 40 +++--- NAMESPACE | 1 NEWS.md | 16 ++ R/data.R | 73 ++++++++++- R/map-quantiles.R | 105 ++++++++++++--- R/measure-map.R | 13 + R/wear-criteria.R |only README.md | 138 ++++++++++++++------ build/partial.rdb |only data/nhanes_measure_data_wear_criteria.rda |only inst/doc/mapnhanespa.R | 17 ++ inst/doc/mapnhanespa.Rmd | 39 +++++ inst/doc/mapnhanespa.html | 192 +++++++++++++++++++---------- man/map_nhanes_pa_quantiles.Rd | 18 ++ man/nhanes_measure_data.Rd | 16 ++ man/nhanes_measure_data_wear_criteria.Rd |only man/nhanes_pa_measure_cdf.Rd | 17 ++ man/nhanes_pa_quantile.Rd | 24 +++ man/nhanes_pa_wear_criteria.Rd |only man/precompute_nhanes_pa_cdfs.Rd | 16 ++ tests/testthat/test-map-quantiles.R | 4 tests/testthat/test-wear-criteria.R |only vignettes/mapnhanespa.Rmd | 39 +++++ 24 files changed, 614 insertions(+), 162 deletions(-)
Title: Project Scaffolding for R and 'Quarto'
Description: Creates structured R and 'Quarto' projects with a consistent directory layout: scripts in R/, analysis documents in analysis/, and web assets in www/. The primary entry point, init(), downloads the latest template from a companion 'GitHub' repository so that project structure evolves independently of package releases. Supports persistent author metadata and 'Quarto' brand configuration that carry across projects automatically.
Author: Kyle Grealis [aut, cre]
Maintainer: Kyle Grealis <kyleGrealis@proton.me>
Diff between froggeR versions 1.0.1 dated 2026-03-17 and 1.1.0 dated 2026-11-09
DESCRIPTION | 8 +-- MD5 | 24 ++++----- NEWS.md | 15 ++++++ R/write_variables.R | 4 - README.md | 16 ++++-- build/vignette.rds |binary inst/CITATION | 4 - inst/doc/every-file-in-its-place.Rmd | 22 ++++----- inst/doc/every-file-in-its-place.html | 54 +++++++++++----------- inst/doc/from-zero-to-project.Rmd | 48 ++++--------------- inst/doc/from-zero-to-project.html | 82 ++++++++++++---------------------- vignettes/every-file-in-its-place.Rmd | 22 ++++----- vignettes/from-zero-to-project.Rmd | 48 ++++--------------- 13 files changed, 146 insertions(+), 201 deletions(-)
Title: R Client for the ZENTRA Cloud V5 API
Description: Downloads environmental sensor data from the ZENTRA Cloud V5 API
(<https://api.zentracloud.io>) into tidy data frames. Provides device
discovery, reading retrieval with automatic pagination and rate-limit
handling, tidy long output with a wide-format helper, and an incremental
'sync' engine with pluggable local storage (RDS files, CSV files, or
return-only) so that new readings can be fetched on a schedule and
appended to a growing local record.
Author: Travis Bates [aut, cre],
METER Group, Inc. [cph, fnd]
Maintainer: Travis Bates <travis@metergroup.com>
Diff between zentraR versions 0.1.3 dated 2026-08-07 and 0.1.4 dated 2026-11-09
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 15 R/auth.R | 8 R/readings.R | 27 R/sync-parallel.R | 4 R/sync.R | 4 R/utils-time.R | 71 ++ README.md | 42 + build/vignette.rds |binary inst/doc/getting-started.R | 183 +++--- inst/doc/getting-started.Rmd | 11 inst/doc/getting-started.html | 1056 ++++++++++++++++++------------------ inst/doc/scheduling.R | 130 ++-- inst/doc/scheduling.html | 974 ++++++++++++++++----------------- inst/doc/working-with-data.R | 148 ++--- inst/doc/working-with-data.html | 962 ++++++++++++++++---------------- man/zc_get_readings.Rd | 20 man/zc_set_key.Rd | 8 tests/testthat/helper-live.R |only tests/testthat/test-api.R | 36 + tests/testthat/test-live-contract.R |only tests/testthat/test-time.R | 62 ++ vignettes/getting-started.Rmd | 11 24 files changed, 2034 insertions(+), 1788 deletions(-)
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] . All of its contents
are solely the responsibility of the authors and do not necessarily
represent t [...truncated...]
Maintainer: Nik Krieger <nikkrieger@gmail.com>
Diff between sociome versions 3.0.1 dated 2026-06-03 and 3.1.1 dated 2026-11-09
DESCRIPTION | 8 LICENSE | 2 MD5 | 86 - NEWS.md | 391 ++++--- R/calculate_adi.R | 1348 +++++++++++++-------------- R/census_api_key.R | 14 R/centers.R | 956 +++++++++---------- R/data_documentation.R | 304 +++--- R/dissimilarity.R | 294 ++--- R/get_adi.R | 576 +++++------ R/get_geoids.R | 244 ++-- R/get_tidycensus.R | 840 ++++++++-------- R/ref_area.R | 600 ++++++------ R/setup.R | 2 R/synthetic_population.R | 688 ++++++------- R/utils-pipe.R | 24 R/validation.R | 858 ++++++++--------- data/dataset_year_geography_availability.rda |binary man/acs_age_sex_race_ethnicity_vars.Rd | 64 - man/acs_vars.Rd | 102 +- man/append_dissimilarities.Rd | 178 +-- man/calculate_adi.Rd | 144 +- man/census_api_key.Rd | 16 man/dataset_year_geography_availability.Rd | 54 - man/decennial_age_sex_race_ethnicity_vars.Rd | 66 - man/decennial_vars.Rd | 54 - man/get_areas_near_coordinates.Rd | 322 +++--- man/get_geoids.Rd | 250 ++--- man/lon_lat_from_area.Rd | 122 +- man/pipe.Rd | 24 man/state_geoids.Rd | 48 man/synthetic_population.Rd | 360 +++---- tests/testthat.R | 24 tests/testthat/_snaps/get_adi.md | 36 tests/testthat/_snaps/get_geoids.md | 59 - tests/testthat/helper-setup.R | 2 tests/testthat/test-dissimilarity.R | 52 - tests/testthat/test-get_adi.R | 282 ++--- tests/testthat/test-get_geoids.R | 517 +++++----- tests/testthat/test-get_tidycensus.R | 14 tests/testthat/test-ref_area.R | 900 +++++++++--------- tests/testthat/test-synthetic_population.R | 94 - tests/testthat/test-validators.R | 244 ++-- tests/testthat/test_area_population.R | 114 +- 44 files changed, 5719 insertions(+), 5658 deletions(-)
Title: Local Large Language Models as Base-R Objects
Description: Load and run local large language models (through a vendored,
patched 'llama.cpp') from R and work with them as plain data frames and
matrices in base-R idiom. Provides model loading and tokenization (llm(),
llm_tokens()), text generation (llm_generate()), next-token distributions
(llm_logits()), embeddings (llm_embed()), and mechanistic
interpretability tools -- activation tracing (llm_trace()), activation
steering (llm_steer()), neuron ablation (llm_ablate()), and grouped statistical
probes (llm_probe()). Vision-language
models loaded with their projector take image input in generation and
embeddings. A checksum-verified downloader (llm_download()) fetches pinned
models.
Author: Alessandro Vadala [aut, cre, cph],
ggml authors [ctb, cph] ),
Authors of the bundled Rust and native dependencies [ctb, cph]
Maintainer: Alessandro Vadala <vadale93@gmail.com>
Diff between relm versions 0.6.2 dated 2026-11-02 and 0.6.3 dated 2026-11-09
DESCRIPTION | 6 MD5 | 36 - NEWS.md | 9 build/vignette.rds |binary inst/doc/anatomy-lab.R | 390 +++++++------- inst/doc/anatomy-lab.html | 860 ++++++++++++++++---------------- inst/doc/contrast-directions.R | 210 +++---- inst/doc/contrast-directions.html | 832 +++++++++++++++---------------- inst/doc/model-interventions.R | 170 +++--- inst/doc/model-interventions.html | 648 ++++++++++++------------ inst/doc/token-streaming.R | 114 ++-- inst/doc/token-streaming.html | 568 ++++++++++----------- inst/doc/topics-without-python.R | 384 +++++++------- inst/doc/topics-without-python.html | 896 +++++++++++++++++----------------- inst/doc/vision.R | 362 ++++++------- inst/doc/vision.html | 798 +++++++++++++++--------------- src/llama-sources.tar.xz |binary src/rust/rebirth-llm/src/async_job.rs | 10 tools/bundled-sources.json | 15 19 files changed, 3162 insertions(+), 3146 deletions(-)
Title: Core File Structures and Workflows for 'RAVE'
Description: Defines storage standard for Read, process, and analyze
intracranial electroencephalography and deep-brain stimulation in 'RAVE',
a reproducible framework for analysis and visualization of iEEG
by Magnotti, Wang, and Beauchamp, (2020,
<doi:10.1016/j.neuroimage.2020.117341>).
Supports brain imaging data structure (BIDS)
<https://bids.neuroimaging.io> and native file structure to
ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5),
European data format (EDF), BrainVision core data format (BVCDF), or
BlackRock Microsystem (NEV/NSx); process images in
Neuroimaging informatics technology initiative (NIfTI) and
'FreeSurfer' formats, providing brain imaging normalization to template
brain, facilitating 'threeBrain' package for comprehensive electrode
localization via 'YAEL' (your advanced electrode localizer) by Wang,
Magnotti, Zhang, and Beauchamp
(2023, <doi:10.1523/ENEURO.0328-23.2023>).
Author: Zhengjia Wang [aut, cre] ,
Xiang Zhang [aut],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravecore versions 0.1.1 dated 2026-04-02 and 1.0.0 dated 2026-11-09
DESCRIPTION | 18 MD5 | 160 +-- NAMESPACE | 16 NEWS.md | 56 + R/aaa-constants.R | 7 R/class002-project.R | 2 R/class004-epoch.R | 326 +++++- R/class005-subject.R | 243 ++++ R/class006-rawsubject.R | 2 R/class011-YAEL_native_process.R |only R/class011-YAEL_process.R | 343 +++++- R/class012-rave_brain.R | 14 R/class100-base_repository.R | 60 + R/import-h5_matlab_per_channel.R | 2 R/import-nev.R | 2 R/math-baseline_power.R | 17 R/utils-package.R | 1 R/utils-realign_trials.R |only R/utils-spikeinterface.R | 6 R/validator-condition_groups.R |only R/validator-nev.R | 22 R/validator-subject.R | 142 +- R/workflow-YBA_atlas.R |only R/workflow-dcm2niix.R | 29 R/workflow-freesurfer_macaque.R |only R/workflow-freesurfer_recon_all.R | 49 R/workflow-reg3d.R |only R/workflow-template_mapping.R | 13 R/workflow-volumetric_atlases.R | 76 - R/workflow-yael_brain_extract.R |only R/workflow-yael_native_helpers.R |only R/workflow-yael_preprocess.R | 75 + R/workflow-yael_preprocess_native.R |only build/partial.rdb |binary inst/reports/atlas-overlay.rmd |only inst/shell-templates/rave-reg3d-rigid.R |only inst/shell-templates/yael-preprocess-native.R |only inst/shell-templates/yael-preprocess.R | 24 inst/tech-details |only man/Auxiliary_electrode.Rd | 455 ++++----- man/LFP_electrode.Rd | 557 +++++------ man/LFP_reference.Rd | 503 +++++----- man/RAVEAbstarctElectrode.Rd | 441 ++++---- man/RAVEEpoch.Rd | 431 +++++--- man/RAVEPreprocessSettings.Rd | 488 +++++---- man/RAVEProject.Rd | 342 +++--- man/RAVESubject.Rd | 759 +++++++-------- man/RAVESubjectBaseRepository.Rd | 309 +++--- man/RAVESubjectEpochPhaseRepository.Rd | 190 +-- man/RAVESubjectEpochPowerRepository.Rd | 190 +-- man/RAVESubjectEpochRawVoltageRepository.Rd | 230 ++-- man/RAVESubjectEpochRepository.Rd | 345 +++--- man/RAVESubjectEpochTimeFreqBaseRepository.Rd | 239 ++-- man/RAVESubjectEpochTimeFreqCoefRepository.Rd | 192 +-- man/RAVESubjectEpochVoltageRepository.Rd | 228 ++-- man/RAVESubjectRecordingBlockPhaseRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockPowerRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockRawVoltageRepository.Rd | 231 ++-- man/RAVESubjectRecordingBlockRepository.Rd | 256 ++--- man/RAVESubjectRecordingBlockTimeFreqBaseRepository.Rd | 222 ++-- man/RAVESubjectRecordingBlockTimeFreqCoefRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockVoltageRepository.Rd | 223 ++-- man/Spike_electrode.Rd | 455 ++++----- man/YAELNativeProcess.Rd |only man/YAELProcess.Rd | 853 +++++++++-------- man/as_rave_project.Rd | 2 man/as_yael_process.Rd | 16 man/cmd_run_yael_preprocess.Rd | 24 man/cmd_run_yael_preprocess_native.Rd |only man/generate_atlas_YBA.Rd |only man/generate_atlases_from_template.Rd | 12 man/get_available_morph_to_template.Rd | 9 man/import-signals.Rd | 4 man/power_baseline.Rd | 12 man/rave_brain.Rd | 6 man/ravecore-constants.Rd | 13 man/ravecore-package.Rd | 4 man/realign_trials.Rd |only man/reg3d_rigid.Rd |only man/validate_condition_groupings.Rd |only man/validate_subject.Rd | 16 man/yael_brain_extract.Rd |only man/yael_macaque.Rd |only tests/testthat/helper-yael-native.R |only tests/testthat/test-atlas-surface.R |only tests/testthat/test-class004-epoch.R |only tests/testthat/test-class005-subject.R |only tests/testthat/test-class011-YAEL_native_process.R |only tests/testthat/test-class011-YAEL_process.R | 26 tests/testthat/test-class011-YAEL_talairach.R |only tests/testthat/test-namespace_call_signatures.R |only tests/testthat/test-validator-nev.R |only tests/testthat/test-workflow-dcm2niix.R |only tests/testthat/test-workflow-reg3d.R |only tests/testthat/test-workflow-yael_brain_extract.R |only tests/testthat/test-workflow-yael_preprocess_native.R |only tests/testthat/test-workflow-yael_readers_native.R |only tests/testthat/test-yael-engine-consistency.R |only 98 files changed, 6005 insertions(+), 4529 deletions(-)
Title: Mobility Oriented-Parity Metric
Description: A set of tools to perform multiple versions of the Mobility
Oriented-Parity metric. This multivariate analysis helps to characterize
levels of dissimilarity between a set of conditions of reference and another
set of conditions of interest. If predictive models are transferred to
conditions different from those over which models were calibrated (trained),
this metric helps to identify transfer conditions that differ
substantially from those of calibration. These tools are implemented
following principles proposed in Owens et al. (2013)
<doi:10.1016/j.ecolmodel.2013.04.011>, and expanded to obtain more detailed
results that aid in interpretation as in Cobos et al. (2024)
<doi:10.21425/fob.17.132916>.
Author: Marlon E. Cobos [aut, cre] ,
Hannah L. Owens [aut] ,
Jorge Soberon [aut] ,
A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between mop versions 0.1.4 dated 2026-04-22 and 0.1.5 dated 2026-11-09
DESCRIPTION | 14 ++-- MD5 | 28 ++++---- NAMESPACE | 10 +-- NEWS.md | 5 + R/methods.R | 2 R/mop_distance.R | 49 +++++++-------- README.md | 129 +++++++++++++++++++++-------------------- man/figures/README-load-1.png |binary man/figures/README-load-2.png |binary man/figures/README-plots-1.png |binary man/figures/README-plots-2.png |binary man/figures/README-plots-3.png |binary man/figures/README-plots-4.png |binary man/figures/README-plots-5.png |binary man/mop-package.Rd | 1 15 files changed, 125 insertions(+), 113 deletions(-)
Title: Fast Masked K-Nearest Neighbor Imputation
Description: Fast masked k-nearest neighbor imputation for mixed-type
tabular data. Distances are computed only on the variables jointly observed
by the receiver and the donor, and missing values are filled by local
regression (numeric) or weighted vote (categorical) over the nearest donors.
Returns completed data for single imputation or a list of completed data
sets for multiple imputation.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between missknn versions 1.1.2 dated 2026-08-21 and 1.2.0 dated 2026-11-09
missknn-1.1.2/missknn/R/complete.R |only missknn-1.1.2/missknn/R/print_summary.R |only missknn-1.1.2/missknn/man/complete.Rd |only missknn-1.2.0/missknn/DESCRIPTION | 15 missknn-1.2.0/missknn/MD5 | 107 missknn-1.2.0/missknn/NAMESPACE | 6 missknn-1.2.0/missknn/NEWS.md |only missknn-1.2.0/missknn/R/internal.R | 50 missknn-1.2.0/missknn/R/missknn.R | 51 missknn-1.2.0/missknn/README.md | 381 +- missknn-1.2.0/missknn/inst/CITATION |only missknn-1.2.0/missknn/inst/benchmark/benchmark_30.R | 7 missknn-1.2.0/missknn/inst/benchmark/benchmark_bigdata.R | 100 missknn-1.2.0/missknn/inst/benchmark/benchmark_bio.R | 5 missknn-1.2.0/missknn/inst/benchmark/benchmark_biobench.R |only missknn-1.2.0/missknn/inst/benchmark/benchmark_mixed.R | 9 missknn-1.2.0/missknn/inst/benchmark/benchmark_real.R | 70 missknn-1.2.0/missknn/inst/benchmark/benchmark_real_bign.R |only missknn-1.2.0/missknn/inst/benchmark/benchmark_speed_mixgb.R | 2 missknn-1.2.0/missknn/inst/benchmark/output/benchmark_report.md | 8 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_benchmark_report.md | 57 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_cells |only missknn-1.2.0/missknn/inst/benchmark/output/bigdata_mse_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/bigdata_results.csv | 30 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_runtime_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/bign_cells |only missknn-1.2.0/missknn/inst/benchmark/output/bio_data_benchmark_report.md | 24 missknn-1.2.0/missknn/inst/benchmark/output/bio_data_results.csv | 24 missknn-1.2.0/missknn/inst/benchmark/output/bio_data_speed_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/biobench |only missknn-1.2.0/missknn/inst/benchmark/output/coefficient_results.csv | 1296 +++++----- missknn-1.2.0/missknn/inst/benchmark/output/mixed_categorical_results.csv | 8 missknn-1.2.0/missknn/inst/benchmark/output/mixed_correlated_results.csv | 4 missknn-1.2.0/missknn/inst/benchmark/output/mixed_validation_report.md | 12 missknn-1.2.0/missknn/inst/benchmark/output/real_data_benchmark_report.md | 54 missknn-1.2.0/missknn/inst/benchmark/output/real_data_nrmse_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/real_data_results.csv | 32 missknn-1.2.0/missknn/inst/benchmark/output/real_data_speed_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/runtime_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/runtime_results.csv | 240 - missknn-1.2.0/missknn/inst/doc/missknn.R | 19 missknn-1.2.0/missknn/inst/doc/missknn.Rmd | 35 missknn-1.2.0/missknn/inst/doc/missknn.html | 55 missknn-1.2.0/missknn/man/missknn-package.Rd | 2 missknn-1.2.0/missknn/man/missknn.Rd | 43 missknn-1.2.0/missknn/tests/testthat/test-missknn.R | 115 missknn-1.2.0/missknn/vignettes/missknn.Rmd | 35 47 files changed, 1573 insertions(+), 1323 deletions(-)
Title: Balancing Confounder Distributions with Forest Energy Balancing
Description: Estimates average treatment effects using kernel energy balancing
with random forest similarity kernels. A multivariate random forest jointly
models covariates, outcome, and treatment to build a similarity kernel
between observations. This kernel is then used for energy balancing to create
weights that control for confounding. The method is described in
De and Huling (2025) <doi:10.48550/arXiv.2512.18069>.
Author: Jared Huling [aut, cre],
Simion De [aut]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between forestBalance versions 0.1.0 dated 2026-04-07 and 0.1.1 dated 2026-11-09
DESCRIPTION | 6 MD5 | 56 ++--- NEWS.md |only R/RcppExports.R | 4 R/forest_balance.R | 193 ++++++++++++++----- R/kernel_balance.R | 287 ++++++++++++++++++++++++----- R/summary.R | 5 inst/doc/augmented.Rmd | 24 +- inst/doc/augmented.html | 60 +++--- inst/doc/crossfitting.Rmd | 43 ++-- inst/doc/crossfitting.html | 113 +++++------ inst/doc/guide.Rmd | 61 +++--- inst/doc/guide.html | 85 ++++---- inst/doc/performance.Rmd | 71 +++---- inst/doc/performance.html | 134 ++++++------- man/forest_balance.Rd | 23 ++ man/kernel_balance.Rd | 13 + src/RcppExports.cpp | 9 src/cg_solve.cpp | 16 + tests/testthat/test-forest_balance.R | 37 +++ tests/testthat/test-kernel_balance.R | 70 +++++++ tests/testthat/test-production-guards.R |only vignettes/augmented.Rmd | 24 +- vignettes/crossfitting.Rmd | 43 ++-- vignettes/guide-sim-plot-1.png |binary vignettes/guide.Rmd | 61 +++--- vignettes/performance-breakdown-plot-1.png |binary vignettes/performance-timing-plot-1.png |binary vignettes/performance-tree-plot-1.png |binary vignettes/performance.Rmd | 71 +++---- 30 files changed, 987 insertions(+), 522 deletions(-)
Title: Nonparametric Sobol Estimator with Bootstrap Bandwidth
Description: Algorithm to estimate the Sobol indices using a non-parametric
fit of the regression curve. The bandwidth is estimated using bootstrap
to reduce the finite-sample bias. The package is based on the paper
Solís, M. (2021) <doi:10.1080/03610918.2019.1655575>.
Author: Maikol Solis [aut, cre]
Maintainer: Maikol Solis <maikol.solis@ucr.ac.cr>
Diff between sobolnp versions 0.1.0 dated 2019-04-29 and 0.2.0 dated 2026-11-09
sobolnp-0.1.0/sobolnp/man/plot.Rd |only sobolnp-0.1.0/sobolnp/man/print.Rd |only sobolnp-0.1.0/sobolnp/tests/tests.R |only sobolnp-0.2.0/sobolnp/DESCRIPTION | 26 + sobolnp-0.2.0/sobolnp/MD5 | 25 + sobolnp-0.2.0/sobolnp/NAMESPACE | 26 + sobolnp-0.2.0/sobolnp/NEWS.md | 37 ++ sobolnp-0.2.0/sobolnp/R/plot.sobolnp.R | 111 +++---- sobolnp-0.2.0/sobolnp/R/print.sobolnp.R | 35 +- sobolnp-0.2.0/sobolnp/R/sobolnp.R | 411 +++++++++++------------------ sobolnp-0.2.0/sobolnp/README.md |only sobolnp-0.2.0/sobolnp/build |only sobolnp-0.2.0/sobolnp/inst |only sobolnp-0.2.0/sobolnp/man/figures |only sobolnp-0.2.0/sobolnp/man/plot.sobolnp.Rd |only sobolnp-0.2.0/sobolnp/man/print.sobolnp.Rd |only sobolnp-0.2.0/sobolnp/man/sobolnp.Rd | 52 +++ sobolnp-0.2.0/sobolnp/tests/testthat |only sobolnp-0.2.0/sobolnp/tests/testthat.R |only 19 files changed, 349 insertions(+), 374 deletions(-)
Title: Statistical Inference on Lineup Fairness
Description: Computes statistical measures for laboratory and police lineups in
forensic psychology, including lineup bias, functional and effective size,
diagnosticity, confidence-accuracy curves, signal detection models, and
simulation tools. Optional face-similarity functions use numeric face
representations computed by Python's 'deepface' library; optional
lineup-memory model fitting uses a separately installed, pinned
'pyWitness' engine.
Author: Colin Tredoux [aut, cre] ,
Tamsyn Naylor [aut]
Maintainer: Colin Tredoux <colin.tredoux@uct.ac.za>
Diff between r4lineups versions 2.3.0 dated 2026-11-02 and 2.3.1 dated 2026-11-09
DESCRIPTION | 6 MD5 | 374 ++-- NEWS.md | 147 + R/anri_functions.R | 29 R/bayes_curves_functions.R | 121 + R/bias_effective_distributions.R | 18 R/cac_functions.R | 6 R/calibration_bayes.R | 12 R/calibration_functions.R | 139 + R/classify_choices.R | 22 R/data_standardization.R | 12 R/datacheck1.R | 8 R/datacheck2.R | 12 R/datacheck3.R | 12 R/diag_ratio_T.R | 4 R/diag_ratio_T_bayes.R | 9 R/diag_ratio_W.R | 4 R/eff_size_per_foils.R | 11 R/effsize_compare.R | 23 R/eig_functions.R | 8 R/embeddings.R | 4 R/esize_T_bayes.R | 5 R/esize_T_ci_n.R | 6 R/esize_m.R | 5 R/fullroc_functions.R | 55 R/func_size.R | 5 R/func_size_bayes.R | 11 R/func_size_report.R | 5 R/gen_lineup_prop.R | 9 R/homog_diag.R | 17 R/line73.R | 12 R/lineup_boot_allprop.R | 2 R/lineup_models_pywitness.R | 20 R/lineup_prop_tab.R | 12 R/make_roc.R | 7 R/max_sdt_fit.R | 16 R/mockdata.R | 1 R/model_comparison.R | 21 R/multid_functions.R | 10 R/nortje2012.R | 1 R/pauc_comparison.R | 33 R/ppv_range_functions.R | 17 R/ppv_range_plots.R | 15 R/rac_functions.R | 11 R/roc_functions.R | 6 R/sdt_compare.R | 26 R/sdt_glm.R | 7 R/sdt_summary_compare.R | 47 R/setup.R | 13 R/similarity.R | 8 R/simulate_lineup_data.R | 92 - R/utility_functions.R | 26 R/var_d.R | 4 R/visualization_faces.R | 8 R/winter_2ht_boot.R | 2 R/zroc_sdt.R | 32 inst/doc/Vignette.R | 8 inst/doc/Vignette.Rmd | 72 inst/doc/Vignette.html | 109 - inst/doc/bayesian_inference.R | 2 inst/doc/bayesian_inference.Rmd | 7 inst/doc/bayesian_inference.html | 27 inst/doc/calibration_decision_analysis.R | 13 inst/doc/calibration_decision_analysis.Rmd | 189 +- inst/doc/calibration_decision_analysis.html | 1208 +++++++-------- inst/doc/face_similarity.Rmd | 19 inst/doc/face_similarity.html | 25 inst/doc/fullroc_analysis.Rmd | 52 inst/doc/fullroc_analysis.html | 106 - inst/doc/information_error_rate_analysis.R | 2 inst/doc/information_error_rate_analysis.Rmd | 46 inst/doc/information_error_rate_analysis.html | 63 inst/doc/lineup_memory_models.Rmd | 12 inst/doc/lineup_memory_models.html | 17 inst/doc/model_comparison.R | 2 inst/doc/model_comparison.Rmd | 72 inst/doc/model_comparison.html | 151 + inst/doc/msdt_model.html | 4 inst/doc/multid_model.Rmd | 16 inst/doc/multid_model.html | 20 inst/doc/pauc_statistical_comparison.Rmd | 19 inst/doc/pauc_statistical_comparison.html | 37 inst/doc/rac_analysis.Rmd | 45 inst/doc/rac_analysis.html | 64 inst/doc/sdt_glm_analysis.R | 45 inst/doc/sdt_glm_analysis.Rmd | 95 - inst/doc/sdt_glm_analysis.html | 256 +-- inst/doc/sdt_summary_comparisons.Rmd | 25 inst/doc/sdt_summary_comparisons.html | 31 inst/doc/simulation_power_analysis.R | 6 inst/doc/simulation_power_analysis.Rmd | 88 - inst/doc/simulation_power_analysis.html | 123 + inst/doc/winter_2ht_model.Rmd | 50 inst/doc/winter_2ht_model.html | 67 inst/shiny/r4lineups_app/R/mod_bayes.R | 2 inst/shiny/r4lineups_app/R/mod_calibration.R | 6 inst/shiny/r4lineups_app/R/mod_roc.R | 2 man/available_detectors.Rd | 5 man/available_models.Rd | 2 man/bootstrap_anri.Rd | 8 man/calibration_bayes.Rd | 5 man/check_pywitness_deps.Rd | 3 man/classify_lineup_choices.Rd | 4 man/compare_anri.Rd | 5 man/compare_models.Rd | 11 man/compare_pauc.Rd | 20 man/compare_sdt_summary.Rd | 6 man/compute_anri.Rd | 11 man/compute_eig.Rd | 3 man/create_example_lineup_data.Rd | 10 man/datacheck1.Rd | 8 man/datacheck2.Rd | 12 man/datacheck3.Rd | 12 man/diag_ratio_T.Rd | 4 man/diag_ratio_W.Rd | 4 man/eff_size_per_foils.Rd | 6 man/esize_T_ci_n.Rd | 8 man/face_similarity.Rd | 4 man/fit_lineup_models.Rd | 3 man/fit_sdt_glm.Rd | 5 man/fit_sdt_roc.Rd | 6 man/get_embedding.Rd | 4 man/innocent_id_rate_nominal.Rd | 4 man/install_pywitness.Rd | 4 man/install_r4lineups_python.Rd | 4 man/line73.Rd | 12 man/lineup_boot_allprop.Rd | 2 man/lineup_prop_tab.Rd | 3 man/lineup_similarity.Rd | 4 man/make_bayes_curves.Rd | 48 man/make_cacdata.Rd | 6 man/make_calibration.Rd | 21 man/make_calibration_by_condition.Rd | 5 man/make_calibration_data.Rd | 48 man/make_eig_data.Rd | 5 man/make_fullroc.Rd | 4 man/make_fullroc_data.Rd | 18 man/make_multid.Rd | 6 man/make_racdata.Rd | 11 man/make_roc.Rd | 7 man/make_rocdata.Rd | 6 man/make_utility_curves.Rd | 6 man/make_utility_difference.Rd | 8 man/mockdata.Rd | 3 man/nortje2012.Rd | 3 man/plot_bayes_information_gain.Rd | 19 man/plot_effective_size_conf.Rd | 6 man/plot_embedding_space.Rd | 8 man/plot_error_rate_conf.Rd | 9 man/plot_fullroc.Rd | 6 man/ppv_range_by_confidence.Rd | 13 man/sdt_compare.Rd | 16 man/sdt_summary_from_counts.Rd | 12 man/simulate_lineup_data.Rd | 19 man/simulate_power_analysis.Rd | 53 man/validate_lineup_data.Rd | 2 man/var_diag_ratio.Rd | 4 tests/testthat/test-calibration-population.R |only tests/testthat/test-classify-choices.R | 6 tests/testthat/test-decision-rules.R | 3 tests/testthat/test-eig-ppv.R | 33 tests/testthat/test-export-contracts.R | 3 tests/testthat/test-fullroc.R | 19 tests/testthat/test-homog-diag-boundary.R |only tests/testthat/test-homog-diag-heterogeneity.R | 1 tests/testthat/test-innocent-suspect.R | 1 tests/testthat/test-max-sdt-fit.R | 8 tests/testthat/test-multid.R | 6 tests/testthat/test-pauc-comparison.R | 6 tests/testthat/test-published-bayes-bree.R |only tests/testthat/test-published-core-fairness.R |only tests/testthat/test-published-eig-ppv.R |only tests/testthat/test-published-process-sdt.R |only tests/testthat/test-published-roc-calibration-decision.R |only tests/testthat/test-sdt-none-correction.R |only tests/testthat/test-simulation.R | 7 tests/testthat/test-zroc-sdt.R | 1 vignettes/Vignette.Rmd | 72 vignettes/bayesian_inference.Rmd | 7 vignettes/calibration_decision_analysis.Rmd | 189 +- vignettes/face_similarity.Rmd | 19 vignettes/fullroc_analysis.Rmd | 52 vignettes/information_error_rate_analysis.Rmd | 46 vignettes/lineup_memory_models.Rmd | 12 vignettes/model_comparison.Rmd | 72 vignettes/multid_model.Rmd | 16 vignettes/pauc_statistical_comparison.Rmd | 19 vignettes/rac_analysis.Rmd | 45 vignettes/sdt_glm_analysis.Rmd | 95 - vignettes/sdt_summary_comparisons.Rmd | 25 vignettes/simulation_power_analysis.Rmd | 88 - vignettes/winter_2ht_model.Rmd | 50 192 files changed, 4021 insertions(+), 2205 deletions(-)
Title: Algorithm Portfolio Selection with Machine Learning
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
Author: Brais Gonzalez-Rodriguez [aut, cre] ,
Ignacio Gomez-Casares [aut] ,
Beatriz Pateiro-Lopez [aut] ,
Julio Gonzalez-Diaz [aut] ,
Maria Caseiro-Arias [ctb],
Antonio Farina-Elorza [ctb],
Manuel Timiraos-Lopez [ctb],
MICIU/AEI/10.13039/501100011033 [fnd]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>
Diff between ASML versions 1.1.0 dated 2025-09-29 and 1.1.1 dated 2026-11-09
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 6 +++++- NEWS.md |only R/ASML-package.R |only build |only man/ASML-package.Rd |only 6 files changed, 21 insertions(+), 7 deletions(-)
Title: Browse Microdata Catalogs Using 'NADA' REST API
Description: Provides a unified, programmatic interface for searching,
browsing, and retrieving metadata from data repositories that use the
National Data Archive ('NADA') software, such as the World Bank, 'FAO',
the International Household Survey Network ('IHSN'), 'UNHCR', the World
Health Organization, and the statistics offices of Kenya and Zambia.
Functions discover available data collections, country codes, and access
types, search by keyword, country, and year, and retrieve study metadata,
file lists, and variable-level data dictionaries.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between nadaverse versions 0.1.0 dated 2025-12-11 and 0.2.0 dated 2026-11-09
nadaverse-0.1.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/2606 |only nadaverse-0.2.0/nadaverse/DESCRIPTION | 33 nadaverse-0.2.0/nadaverse/MD5 | 115 nadaverse-0.2.0/nadaverse/NAMESPACE | 23 nadaverse-0.2.0/nadaverse/NEWS.md | 20 nadaverse-0.2.0/nadaverse/R/data_files.R | 25 nadaverse-0.2.0/nadaverse/R/http_helpers.R.R | 122 nadaverse-0.2.0/nadaverse/R/metadata_helpers.R | 88 nadaverse-0.2.0/nadaverse/R/nadaverse-package.R |only nadaverse-0.2.0/nadaverse/R/search_catalog.R | 47 nadaverse-0.2.0/nadaverse/README.md | 53 nadaverse-0.2.0/nadaverse/build |only nadaverse-0.2.0/nadaverse/inst/doc |only nadaverse-0.2.0/nadaverse/man/catalogs.Rd | 276 nadaverse-0.2.0/nadaverse/man/data_files.Rd | 163 nadaverse-0.2.0/nadaverse/man/nadaverse-package.Rd |only nadaverse-0.2.0/nadaverse/man/search_catalog.Rd | 288 nadaverse-0.2.0/nadaverse/man/set_user_agent.Rd |only nadaverse-0.2.0/nadaverse/tests/testthat/_collections/microdata.worldbank.org/collections.json | 420 nadaverse-0.2.0/nadaverse/tests/testthat/_country_codes/microdata.fao.org/country_codes.json | 2510 nadaverse-0.2.0/nadaverse/tests/testthat/_latest_entries/microdata.worldbank.org/latest-00819a.json | 48 nadaverse-0.2.0/nadaverse/tests/testthat/_metadata/microdata.worldbank.org/8098-b6ace8.json | 436 nadaverse-0.2.0/nadaverse/tests/testthat/_metadata/microdata.worldbank.org/ALB_2012_LSMS_v01_M_v01_A_PUF.json | 284 nadaverse-0.2.0/nadaverse/tests/testthat/_nc |only nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.fao.org/search-2bc657.json | 788 nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.fao.org/search-3ad53d.json | 70 nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.worldbank.org/search-13f018.json | 317 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/2905 |only nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/search-7315b4.json | 788 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.worldbank.org/ETH_2015_ESS_v03_M/data_files.json | 2052 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.worldbank.org/ETH_2015_ESS_v03_M/variables.json |25294 ---------- nadaverse-0.2.0/nadaverse/tests/testthat/_snaps/nadaverse.md | 115 nadaverse-0.2.0/nadaverse/tests/testthat/test-nadaverse.R | 336 nadaverse-0.2.0/nadaverse/vignettes |only 34 files changed, 5701 insertions(+), 29010 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between LaMa versions 3.0.0 dated 2026-10-28 and 3.1.0 dated 2026-11-09
DESCRIPTION | 8 - MD5 | 143 ++++++++++--------- NAMESPACE | 7 NEWS.md | 266 +++++++++++++++++++++--------------- R/data.R | 2 R/decoding_functions.R | 24 +-- R/distribution_functions.R | 4 R/forward_algorithms.R | 47 +++--- R/helper_functions.R | 27 +++ R/hsmm_functions_old.R | 40 ++--- R/lama.R | 69 +++++++++ R/mcreport.R | 38 ++++- R/model_matrix_functions.R | 4 R/penalty_functions.R | 36 ++-- R/qreml_functions.R | 267 +++++++++++++++++++++++++++++-------- R/residual_functions.R | 22 ++- R/stationary_functions.R | 22 +-- R/summary_functions.R | 15 +- R/tpm_functions.R | 179 +++++++++++++++++------- inst/doc/Continuous_time_HMMs.html | 4 inst/doc/Extensions.html | 2 inst/doc/HSMMs.html | 4 inst/doc/Intro_to_LaMa.html | 4 inst/doc/Longitudinal_data.html | 6 inst/doc/MMMPPs.html | 4 inst/doc/Penalised_splines.html | 83 +++++------ inst/doc/State_space_models.html | 4 man/MCreport.Rd | 17 +- man/coef.LaMaModel.Rd |only man/ddwell.Rd | 2 man/dgmrf2.Rd | 2 man/forward.Rd | 7 man/forward_hsmm.Rd | 10 - man/forward_ihsmm.Rd | 16 +- man/forward_p.Rd | 2 man/forward_phsmm.Rd | 12 - man/forward_s.Rd | 6 man/forward_sp.Rd | 8 - man/generator.Rd | 20 ++ man/generator_g.Rd | 6 man/grapes-sp-grapes.Rd | 6 man/nessi.Rd | 2 man/penalty.Rd | 2 man/penalty2.Rd | 4 man/penalty_uni.Rd | 6 man/pred_matrix.Rd | 2 man/process_hid_formulas.Rd | 2 man/pseudo_res.Rd | 6 man/qreml.Rd | 26 ++- man/residuals.LaMaModel.Rd |only man/sdreport_outer.Rd | 6 man/stateprobs_p.Rd | 12 - man/stationary.Rd | 6 man/stationary_ct.Rd | 4 man/stationary_p.Rd | 4 man/stationary_p_sparse.Rd | 4 man/stationary_sparse.Rd | 4 man/tpm.Rd | 4 man/tpm_ct.Rd | 32 ++++ man/tpm_g.Rd | 10 - man/tpm_g2.Rd | 16 +- man/tpm_hsmm.Rd | 4 man/tpm_hsmm2.Rd | 8 - man/tpm_ihsmm.Rd | 14 - man/tpm_p.Rd | 2 man/tpm_phsmm.Rd | 16 +- man/tpm_phsmm2.Rd | 18 +- man/tpm_thinned.Rd | 8 - man/vcov.LaMaModel.Rd |only man/viterbi_p.Rd | 12 - tests/testthat/test-lama.R | 81 +++++++++++ tests/testthat/test-residuals.R | 1 tests/testthat/test-tpm.R | 68 +++++++++ vignettes/refs.bib | 4 74 files changed, 1241 insertions(+), 592 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the
grammar of graphics. 'GGally' extends 'ggplot2' by adding several
functions to reduce the complexity of combining geometric objects with
transformed data. Some of these functions include a pairwise plot
matrix, a two group pairwise plot matrix, a parallel coordinates plot,
a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] ,
Di Cook [aut, ths] ,
Joseph Larmarange [aut] ,
Francois Briatte [aut],
Moritz Marbach [aut],
Edwin Thoen [aut],
Amos Elberg [aut],
Ott Toomet [ctb],
Jason Crowley [aut],
Heike Hofmann [ths] ,
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 2.4.0 dated 2025-08-23 and 2.5.0 dated 2026-11-09
GGally-2.4.0/GGally/R/ggaly_trends.R |only GGally-2.4.0/GGally/R/ggmatrix_legend.R |only GGally-2.4.0/GGally/R/ggpairs_add.R |only GGally-2.4.0/GGally/R/ggpairs_getput.R |only GGally-2.4.0/GGally/R/ggpairs_internal_plots.R |only GGally-2.4.0/GGally/tests/testthat/data |only GGally-2.5.0/GGally/DESCRIPTION | 32 GGally-2.5.0/GGally/MD5 | 356 ++++++- GGally-2.5.0/GGally/NAMESPACE | 146 +-- GGally-2.5.0/GGally/NEWS.md | 27 GGally-2.5.0/GGally/R/crosstalk.R |only GGally-2.5.0/GGally/R/gg-plots.R | 50 - GGally-2.5.0/GGally/R/ggally_trends.R |only GGally-2.5.0/GGally/R/ggcoef.R | 25 GGally-2.5.0/GGally/R/gglegend.R |only GGally-2.5.0/GGally/R/gglyph.R | 7 GGally-2.5.0/GGally/R/ggmatrix.R | 2 GGally-2.5.0/GGally/R/ggmatrix_add.R |only GGally-2.5.0/GGally/R/ggmatrix_getput.R |only GGally-2.5.0/GGally/R/ggmatrix_internal_plots.R |only GGally-2.5.0/GGally/R/ggmatrix_location.R |only GGally-2.5.0/GGally/R/ggmatrix_print.R | 4 GGally-2.5.0/GGally/R/ggnet.R | 237 ++--- GGally-2.5.0/GGally/R/ggnet2.R | 432 ++++----- GGally-2.5.0/GGally/R/ggnetworkmap.R | 10 GGally-2.5.0/GGally/R/ggnostic.R | 103 +- GGally-2.5.0/GGally/R/ggpairs.R | 90 -- GGally-2.5.0/GGally/R/ggsurv.R | 4 GGally-2.5.0/GGally/R/ggtable.R | 36 GGally-2.5.0/GGally/R/reexports.R | 4 GGally-2.5.0/GGally/R/utils.R | 8 GGally-2.5.0/GGally/R/wrap.R |only GGally-2.5.0/GGally/R/zzz.R | 16 GGally-2.5.0/GGally/README.md | 6 GGally-2.5.0/GGally/build/stage23.rdb |binary GGally-2.5.0/GGally/man/GGally-package.Rd | 1 GGally-2.5.0/GGally/man/add_ref_boxes.Rd | 2 GGally-2.5.0/GGally/man/add_ref_lines.Rd | 2 GGally-2.5.0/GGally/man/add_to_ggmatrix.Rd | 2 GGally-2.5.0/GGally/man/broomify.Rd | 8 GGally-2.5.0/GGally/man/getPlot.Rd | 2 GGally-2.5.0/GGally/man/ggally_autopoint.Rd | 26 GGally-2.5.0/GGally/man/ggally_blank.Rd | 2 GGally-2.5.0/GGally/man/ggally_count.Rd | 2 GGally-2.5.0/GGally/man/ggally_cross.Rd | 2 GGally-2.5.0/GGally/man/ggally_density.Rd | 20 GGally-2.5.0/GGally/man/ggally_nostic_cooksd.Rd | 10 GGally-2.5.0/GGally/man/ggally_nostic_hat.Rd | 14 GGally-2.5.0/GGally/man/ggally_nostic_line.Rd | 2 GGally-2.5.0/GGally/man/ggally_nostic_resid.Rd | 8 GGally-2.5.0/GGally/man/ggally_nostic_se_fit.Rd | 8 GGally-2.5.0/GGally/man/ggally_nostic_sigma.Rd | 12 GGally-2.5.0/GGally/man/ggally_nostic_std_resid.Rd | 8 GGally-2.5.0/GGally/man/ggally_trends.Rd | 4 GGally-2.5.0/GGally/man/ggcoef.Rd | 31 GGally-2.5.0/GGally/man/gglegend.Rd | 2 GGally-2.5.0/GGally/man/ggmatrix_location.Rd | 4 GGally-2.5.0/GGally/man/ggnet.Rd | 52 - GGally-2.5.0/GGally/man/ggnet2.Rd | 106 +- GGally-2.5.0/GGally/man/ggnetworkmap.Rd | 12 GGally-2.5.0/GGally/man/ggnostic.Rd | 69 - GGally-2.5.0/GGally/man/ggpairs.Rd | 56 - GGally-2.5.0/GGally/man/ggtable.Rd | 36 GGally-2.5.0/GGally/man/grab_legend.Rd | 2 GGally-2.5.0/GGally/man/is_ggmatrix.Rd | 2 GGally-2.5.0/GGally/man/print.ggmatrix.Rd | 3 GGally-2.5.0/GGally/man/putPlot.Rd | 2 GGally-2.5.0/GGally/man/reexports.Rd | 3 GGally-2.5.0/GGally/man/str.ggmatrix.Rd | 5 GGally-2.5.0/GGally/man/wrap.Rd | 2 GGally-2.5.0/GGally/tests/testthat/_snaps |only GGally-2.5.0/GGally/tests/testthat/helper-doppelganger.R | 84 + GGally-2.5.0/GGally/tests/testthat/test-crosstalk.R | 54 - GGally-2.5.0/GGally/tests/testthat/test-deprecated.R | 14 GGally-2.5.0/GGally/tests/testthat/test-find-combo.R |only GGally-2.5.0/GGally/tests/testthat/test-gg-plots.R | 21 GGally-2.5.0/GGally/tests/testthat/test-ggbivariate.R | 5 GGally-2.5.0/GGally/tests/testthat/test-ggcoef.R | 1 GGally-2.5.0/GGally/tests/testthat/test-ggcorr.R | 4 GGally-2.5.0/GGally/tests/testthat/test-gglyph.R | 28 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix.R | 57 - GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_add.R | 2 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_getput.R | 23 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_location.R | 70 - GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_progress.R |only GGally-2.5.0/GGally/tests/testthat/test-ggnet.R | 71 - GGally-2.5.0/GGally/tests/testthat/test-ggnet2.R | 126 +- GGally-2.5.0/GGally/tests/testthat/test-ggnetworkmap.R | 49 - GGally-2.5.0/GGally/tests/testthat/test-ggnostic.R | 10 GGally-2.5.0/GGally/tests/testthat/test-ggparcoord.R | 80 - GGally-2.5.0/GGally/tests/testthat/test-ggscatmat.R | 15 GGally-2.5.0/GGally/tests/testthat/test-ggsurv.R | 20 GGally-2.5.0/GGally/tests/testthat/test-ggtable.R | 1 GGally-2.5.0/GGally/tests/testthat/test-wrap.R | 14 GGally-2.5.0/GGally/tests/testthat/test-zzz_ggpairs.R | 540 +----------- GGally-2.5.0/GGally/tests/testthat/test-zzzz_ggmatrix.R |only 96 files changed, 1662 insertions(+), 1744 deletions(-)
Title: Objective Bayesian Distribution Fitting and AFT Regression
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation.
A separate interface fits independently right-censored observations using
the registered complete-data priors, observed-data likelihood sampling or
data augmentation, with sufficient posterior-propriety checks. Optional
post-processing provides WAIC, PSIS-LOO, and DIC for observed-data likelihoods.
Formula-based accelerated failure time regression is available for nine
lifetime families with complete or right-censored dat [...truncated...]
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.6.0 dated 2026-10-19 and 0.8.0 dated 2026-11-09
DESCRIPTION | 14 ++- MD5 | 31 +++++++- NAMESPACE | 15 ++++ NEWS.md | 69 +++++++++++++++++++ R/aft-families.R |only R/aft-gg.R |only R/aft-loglik-factory.R |only R/aft-precision.R |only R/aft-sampling.R |only R/aft-standard-fit.R |only R/criteria.R | 128 +++++++++++++++++++++++++++--------- R/fitAFTBayes-methods.R |only R/fitAFTBayes.R |only README.md | 56 ++++++++++++++- inst/doc/aft-models-theory.txt |only inst/doc/gg-aft-theory.txt |only inst/examples/tutorial_aft_gg.R |only inst/examples/tutorial_aft_models.R |only man/criteria.Rd | 21 +++++ man/fitAFTBayes-methods.Rd |only man/fitAFTBayes.Rd |only man/fitAFTBayes_models.Rd |only tests/tests_aft.R |only tests/tests_aft_models.R |only tests/tests_aft_sampling.R |only tests/tests_loo_roundoff.R |only 26 files changed, 289 insertions(+), 45 deletions(-)
Title: Comprehensive, User-Friendly Toolkit for Probing Interactions
Description: A suite of functions for conducting and interpreting analysis
of statistical interaction in regression models that was formerly part of the
'jtools' package. Functionality includes visualization of two- and three-way
interactions among continuous and/or categorical variables as well as
calculation of "simple slopes" and Johnson-Neyman intervals (see e.g.,
Bauer & Curran, 2005 <doi:10.1207/s15327906mbr4003_5>). These
capabilities are implemented for generalized linear models in addition to the
standard linear regression context.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <jacob.long@sc.edu>
Diff between interactions versions 1.2.0 dated 2024-07-29 and 1.3.0 dated 2026-11-09
DESCRIPTION | 13 MD5 | 179 NAMESPACE | 7 NEWS.md | 29 R/cat_plot.R | 73 R/contrast_jn.R |only R/int_utils.R | 170 R/interact_plot.R | 70 R/johnson_neyman.R | 33 R/panel_slopes.R |only R/simple_slopes.R | 121 R/slopes_refit.R |only R/utils.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/categorical.html | 27 inst/doc/interactions.html | 171 man/cat_plot.Rd | 25 man/interact_plot.Rd | 25 man/johnson_neyman.Rd | 24 man/sim_slopes.Rd | 70 tests/testthat/_snaps/cat_plot/p0bar.svg | 102 tests/testthat/_snaps/cat_plot/p0bari.svg | 102 tests/testthat/_snaps/cat_plot/p0barpp.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p0pt.svg | 102 tests/testthat/_snaps/cat_plot/p0pti.svg | 102 tests/testthat/_snaps/cat_plot/p0ptpp.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p0ptps.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p3bar.svg | 202 tests/testthat/_snaps/cat_plot/p3bari.svg | 202 tests/testthat/_snaps/cat_plot/p3barpp.svg | 656 tests/testthat/_snaps/cat_plot/p3barps.svg | 656 tests/testthat/_snaps/cat_plot/p3line.svg | 202 tests/testthat/_snaps/cat_plot/p3linei.svg | 202 tests/testthat/_snaps/cat_plot/p3linelty.svg | 680 tests/testthat/_snaps/cat_plot/p3linepp.svg | 680 tests/testthat/_snaps/cat_plot/p3lineps.svg | 680 tests/testthat/_snaps/cat_plot/p3pt.svg | 190 tests/testthat/_snaps/cat_plot/p3pti.svg | 190 tests/testthat/_snaps/cat_plot/p3ptpp.svg | 668 tests/testthat/_snaps/cat_plot/p3ptps.svg | 668 tests/testthat/_snaps/cat_plot/pcatbfit.svg | 54 tests/testthat/_snaps/cat_plot/pglmcatoff.svg | 54 tests/testthat/_snaps/cat_plot/plmbar-interact-plot.svg | 166 tests/testthat/_snaps/cat_plot/plmbar.svg | 326 tests/testthat/_snaps/cat_plot/plmbari.svg | 326 tests/testthat/_snaps/cat_plot/plmbarpp.svg | 4326 ++--- tests/testthat/_snaps/cat_plot/plme4cat.svg | 66 tests/testthat/_snaps/cat_plot/plmline.svg | 346 tests/testthat/_snaps/cat_plot/plmlinei-interact-plot.svg | 346 tests/testthat/_snaps/cat_plot/plmlinei.svg | 346 tests/testthat/_snaps/cat_plot/plmlinelt.svg | 4346 ++--- tests/testthat/_snaps/cat_plot/plmlinepp.svg | 4346 ++--- tests/testthat/_snaps/cat_plot/plmlineps.svg | 8588 +++++----- tests/testthat/_snaps/cat_plot/plmpt.svg | 326 tests/testthat/_snaps/cat_plot/plmpti.svg | 326 tests/testthat/_snaps/cat_plot/plmptpp.svg | 4326 ++--- tests/testthat/_snaps/cat_plot/plmptps-interact-plot.svg | 8568 ++++----- tests/testthat/_snaps/cat_plot/plmptps.svg | 8568 ++++----- tests/testthat/_snaps/cat_plot/psvycat.svg | 54 tests/testthat/_snaps/interact_plot/pbfcat.svg | 54 tests/testthat/_snaps/interact_plot/pbfcont.svg | 72 tests/testthat/_snaps/interact_plot/pglmoff.svg | 72 tests/testthat/_snaps/interact_plot/pglmrob.svg | 72 tests/testthat/_snaps/interact_plot/plm0.svg | 162 tests/testthat/_snaps/interact_plot/plm1.svg | 170 tests/testthat/_snaps/interact_plot/plma.svg | 170 tests/testthat/_snaps/interact_plot/plme4-interact-plot-to-cat-plot.svg | 74 tests/testthat/_snaps/interact_plot/plme4.svg | 62 tests/testthat/_snaps/interact_plot/plme4i.svg | 64 tests/testthat/_snaps/interact_plot/plmlabelsc.svg | 170 tests/testthat/_snaps/interact_plot/plmlabelsc2.svg | 170 tests/testthat/_snaps/interact_plot/plmlabelscpred-interact-plot-to-cat-plot.svg | 78 tests/testthat/_snaps/interact_plot/plmlabelscpred.svg | 60 tests/testthat/_snaps/interact_plot/plmlabelscs.svg | 170 tests/testthat/_snaps/interact_plot/plmlinearchnp.svg | 136 tests/testthat/_snaps/interact_plot/plmlinearchp.svg | 300 tests/testthat/_snaps/interact_plot/plmm.svg | 162 tests/testthat/_snaps/interact_plot/plmnfchar.svg | 72 tests/testthat/_snaps/interact_plot/plmrob.svg | 170 tests/testthat/_snaps/interact_plot/plmrugb.svg | 332 tests/testthat/_snaps/interact_plot/plmruglb.svg | 432 tests/testthat/_snaps/interact_plot/plmtercs.svg | 154 tests/testthat/_snaps/interact_plot/plmtf.svg | 64 tests/testthat/_snaps/interact_plot/plmw.svg | 154 tests/testthat/_snaps/interact_plot/prsacont.svg | 96 tests/testthat/_snaps/interact_plot/psvy1.svg | 140 tests/testthat/_snaps/interact_plot/psvya.svg | 140 tests/testthat/test-contrast-slopes.R |only tests/testthat/test-panelr-plots.R |only tests/testthat/test-panelr-slopes.R |only tests/testthat/test-slopes-refits.R |only tests/testthat/test_cat_plot.R | 10 tests/testthat/test_interact_plot.R | 54 94 files changed, 35053 insertions(+), 34421 deletions(-)
Title: Decision-Theoretic Causal Diagnostics via Experiment Deficiency
Description: Implements a deficiency-theoretic framework for causal inference,
grounded in the classical theory of statistical experiment comparison,
as described in Akdemir (2026) <doi:10.5281/zenodo.18367346>. Provides
theorem-backed bounds together with computable proxy diagnostics for
information loss from confounding, selection bias, and distributional
shift. Supports continuous, binary, count, survival, and competing risks
outcomes. Key features include propensity-score total-variation deficiency
proxies, negative control diagnostics, policy regret bounds, and
sensitivity analysis via confounding frontiers.
Author: Deniz Akdemir [aut, cre]
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between causaldef versions 0.2.1 dated 2026-08-23 and 0.3.0 dated 2026-11-09
DESCRIPTION | 8 MD5 | 108 +-- NEWS.md | 35 + R/api.R | 16 R/causaldef-package.R | 2 R/confounding_frontier.R | 8 R/data_auditor.R | 2 R/methods-plot.R | 10 R/methods-print.R | 10 R/negative_controls.R | 2 R/policy_bounds.R | 73 +- R/theorem_bounds.R | 90 ++- README.md | 10 build/vignette.rds |binary inst/CITATION | 6 inst/doc/advanced_analysis.Rmd | 2 inst/doc/advanced_analysis.html | 551 +++++++----------- inst/doc/causaldef_methodology.R | 50 - inst/doc/causaldef_methodology.Rmd | 14 inst/doc/causaldef_methodology.html | 675 +++++++++------------- inst/doc/classical_benchmarks.html | 484 +++++++--------- inst/doc/complete_workflow.R | 138 ++-- inst/doc/complete_workflow.Rmd | 6 inst/doc/complete_workflow.html | 1035 +++++++++++++++-------------------- inst/doc/data_auditing.html | 582 ++++++++----------- inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 580 ++++++++----------- inst/doc/negative_controls.Rmd | 2 inst/doc/negative_controls.html | 477 ++++++---------- inst/doc/policy_and_transport.Rmd | 5 inst/doc/policy_and_transport.html | 520 +++++++---------- inst/doc/policy_learning.R | 9 inst/doc/policy_learning.Rmd | 44 - inst/doc/policy_learning.html | 643 ++++++++++----------- inst/doc/sensitivity_analysis.Rmd | 23 inst/doc/sensitivity_analysis.html | 600 +++++++++----------- inst/doc/survival_analysis.R | 16 inst/doc/survival_analysis.html | 614 +++++++++----------- man/audit_data.Rd | 2 man/causaldef-package.Rd | 2 man/confounding_frontier.Rd | 8 man/nc_diagnostic.Rd | 2 man/policy_regret_bound.Rd | 55 + man/policy_regret_bound_vc.Rd | 29 man/rkhs_rate_bound.Rd | 20 tests/testthat/test-policy_bounds.R | 42 + tests/testthat/test-theorem_bounds.R | 27 vignettes/advanced_analysis.Rmd | 2 vignettes/causaldef_methodology.Rmd | 14 vignettes/complete_workflow.Rmd | 6 vignettes/introduction.Rmd | 4 vignettes/negative_controls.Rmd | 2 vignettes/policy_and_transport.Rmd | 5 vignettes/policy_learning.Rmd | 44 - vignettes/sensitivity_analysis.Rmd | 23 55 files changed, 3605 insertions(+), 4136 deletions(-)
Title: Vehicle Routing Problem Solver Built on 'PyVRP'
Description: A 'tidyverse'-style interface to high-performance vehicle routing
problem (VRP) solving. Vendors the C++ core of the 'PyVRP' solver
(<https://github.com/PyVRP/PyVRP>) and rewires it through 'cpp11', with no
'Python' runtime dependency. Supports the capacitated VRP, time windows,
multiple depots, heterogeneous fleets, prize-collecting and multi-trip
variants, driven by an iterated local search metaheuristic.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
Niels Wouda [ctb, cph] ,
Thibaut Vidal [cph] ,
ORTEC [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between vrpr versions 0.2.2 dated 2026-10-06 and 0.2.3 dated 2026-11-09
DESCRIPTION | 6 MD5 | 26 ++-- NEWS.md | 16 ++ R/problem_data.R | 80 +++++++++++- R/solve.R | 34 +++++ README.md | 19 ++ inst/doc/vrpr.R | 21 +++ inst/doc/vrpr.Rmd | 53 ++++++++ inst/doc/vrpr.html | 236 ++++++++++++++++++++++++------------- man/vrp_problem_data.Rd | 35 ++++- man/vrp_solve.Rd | 32 ++++- tests/testthat/test-problem-data.R | 30 ++++ tests/testthat/test-solve.R | 33 +++++ vignettes/vrpr.Rmd | 53 ++++++++ 14 files changed, 569 insertions(+), 105 deletions(-)
Title: Tests and Checks Characteristics of R Objects
Description: Allows users to test characteristics of common R objects.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between tester versions 0.3.0 dated 2025-09-22 and 0.3.1 dated 2026-11-09
DESCRIPTION | 12 ++++----- MD5 | 50 +++++++++++++++++++------------------- NEWS.md | 4 +++ R/is-dataframe.r | 6 ++++ R/is-matrix.r | 6 ++++ R/is-scalar.r | 5 +++ R/is-tabular.r | 5 +++ R/is-triangular.r | 4 +++ R/is-vector.r | 6 ++++ R/list-of-vectors.r | 5 +++ R/list-with-vectors.r | 4 +++ R/true-false.r | 6 ++++ build/vignette.rds |binary inst/doc/tester_introduction.Rnw | 2 - inst/doc/tester_introduction.pdf |binary man/is_TRUE.Rd | 7 +++++ man/is_dataframe.Rd | 7 +++++ man/is_matrix.Rd | 7 +++++ man/is_scalar.Rd | 6 ++++ man/is_tabular.Rd | 6 ++++ man/is_triangular_matrix.Rd | 5 +++ man/is_vector.Rd | 7 +++++ man/list_of_vectors.Rd | 6 ++++ man/list_with_vectors.Rd | 5 +++ tests/testthat/test-Rd.R | 15 +++++++---- vignettes/tester_introduction.Rnw | 2 - 26 files changed, 150 insertions(+), 38 deletions(-)
Title: Partial Least Squares Regression for Cox Models and Related
Techniques
Description: Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings <doi:10.1093/bioinformatics/btu660>, Bastien, P., Bertrand, F., Meyer N., Maumy-Bertrand, M. (2015), Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Bioinformatics, 31(3):397-404. Cross validation criteria were studied in <doi:10.48550/arXiv.1810.02962>, Bertrand, F., Bastien, Ph. and Maumy-Bertrand, M. (2018), Cross validating extensions of kernel, sparse or regular partial least squares regression models to censored data.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsRcox versions 1.8.2 dated 2026-03-24 and 1.8.3 dated 2026-11-09
DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 46 +- NEWS.md |only R/internal-plsRcox.R | 3 R/plsRcox-package.R | 10 README.md | 485 ++++++++++++++++++++++------ build/partial.rdb |binary man/figures/README-cvcoxDKsplsDR-1.png |binary man/figures/README-cvcoxsplsDR-1.png |binary man/figures/README-cvplsRcox-1.png |binary man/figures/README-devianceresiduals-1.png |binary man/figures/README-devianceresiduals2-1.png |binary man/figures/README-devianceresiduals3-1.png |binary 14 files changed, 436 insertions(+), 143 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Fits n-dimensional data by means of orthogonal nonlinear least-squares using Levenberg-Marquardt minimization, with a solver that exploits the block structure of the problem as 'ODRPACK' does, so that its cost grows linearly with the number of observations, and provides functionality for fit diagnostics and plotting. Delivers the same results as the 'ODRPACK' Fortran implementation described in Boggs et al. (1989) <doi:10.1145/76909.76913>, but is implemented in pure R.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between onls versions 0.2 dated 2026-09-21 and 0.3 dated 2026-11-09
onls-0.2/onls/R/NIST.R |only onls-0.2/onls/man/NIST.Rd |only onls-0.3/onls/DESCRIPTION | 15 onls-0.3/onls/MD5 | 50 onls-0.3/onls/NAMESPACE | 21 onls-0.3/onls/NEWS | 39 onls-0.3/onls/R/S3_functions.R | 526 +--- onls-0.3/onls/R/doGauge.R |only onls-0.3/onls/R/fit_functions.R | 216 - onls-0.3/onls/R/inference.R |only onls-0.3/onls/R/onls.R | 605 +++- onls-0.3/onls/build/partial.rdb |binary onls-0.3/onls/build/vignette.rds |binary onls-0.3/onls/demo |only onls-0.3/onls/inst/doc/onls-vignette.R | 706 ++--- onls-0.3/onls/inst/doc/onls-vignette.Rmd | 160 - onls-0.3/onls/inst/doc/onls-vignette.html | 3912 +++++++++++++++--------------- onls-0.3/onls/man/anova.onls.Rd |only onls-0.3/onls/man/check_o.Rd | 58 onls-0.3/onls/man/confint.onls.Rd | 45 onls-0.3/onls/man/doGauge.Rd |only onls-0.3/onls/man/logLik_o.Rd | 53 onls-0.3/onls/man/onls.Rd | 295 -- onls-0.3/onls/man/plot.onls.Rd | 16 onls-0.3/onls/man/predict.onls.Rd |only onls-0.3/onls/man/print.onls.Rd | 2 onls-0.3/onls/man/profile.onls.Rd |only onls-0.3/onls/man/summary.onls.Rd | 12 onls-0.3/onls/man/x0.Rd | 8 onls-0.3/onls/vignettes/onls-vignette.Rmd | 160 - 30 files changed, 3534 insertions(+), 3365 deletions(-)
Title: Testing for Population Trends Using Low-Cost Ecological Count
Data
Description: A Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>, and the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Madleina Caduff [aut],
Andreas Fueglistaler [aut, cre],
Daniel Wegmann [aut],
Liam Singer [aut],
Raphael Eckel [ctb],
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Daniel Lemire [cph] ,
Joao Paulo Magalhaes [cph] ,
Rene Brun [cph] ),
Fons Rademakers [c [...truncated...]
Maintainer: Andreas Fueglistaler <andreas.fueglistaler@unifr.ch>
Diff between birp versions 0.9.1 dated 2026-11-02 and 0.9.2 dated 2026-11-09
DESCRIPTION | 8 +- MD5 | 12 ++-- NEWS.md | 3 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/birp-introduction.html | 114 ++++++++++++++++++++-------------------- src/Makevars.in | 28 ++++++++- 7 files changed, 95 insertions(+), 70 deletions(-)
Title: The Skellam Distribution: Densities, Sampling, Estimation and
Regression
Description: Density, distribution function, quantile function and random
generation for the Skellam distribution, the distribution of the
difference of two independent Poisson variables (Skellam, 1946), with
saddlepoint approximations, maximum likelihood estimation, and a
regression model in which both rates depend on covariates. The
distribution functions remain accurate for very large rates and far
into the tails, on the natural and the log scale.
Author: Jerry W. Lewis [aut],
Patrick E. Brown [aut],
Michail Tsagris [aut],
Montasser Ghachem [aut, cre],
Oguz Ersan [aut]
Maintainer: Montasser Ghachem <mg@pinstimation.com>
Diff between skellam versions 0.2.4 dated 2025-04-07 and 0.2.5 dated 2026-11-09
skellam-0.2.4/skellam/tests/skellam.R |only skellam-0.2.5/skellam/DESCRIPTION | 38 +- skellam-0.2.5/skellam/MD5 | 53 +-- skellam-0.2.5/skellam/NAMESPACE | 20 - skellam-0.2.5/skellam/NEWS.md | 45 ++ skellam-0.2.5/skellam/R/bessel.R |only skellam-0.2.5/skellam/R/dskellam.r | 249 +++++++------- skellam-0.2.5/skellam/R/dskellam.sp.r | 35 +- skellam-0.2.5/skellam/R/pskellam.r | 189 +++++++++- skellam-0.2.5/skellam/R/pskellam.sp.r | 17 skellam-0.2.5/skellam/R/qskellam.r | 97 +++-- skellam-0.2.5/skellam/R/rskellam.r | 19 - skellam-0.2.5/skellam/R/skellam.mle.R | 88 +++-- skellam-0.2.5/skellam/R/skellam.reg.R | 122 +++++-- skellam-0.2.5/skellam/R/utils.R |only skellam-0.2.5/skellam/README.md | 210 ++++-------- skellam-0.2.5/skellam/build/vignette.rds |binary skellam-0.2.5/skellam/inst/CITATION | 31 - skellam-0.2.5/skellam/inst/doc/validate_skellam.R | 140 ++++---- skellam-0.2.5/skellam/inst/doc/validate_skellam.Rmd | 231 ++++++------- skellam-0.2.5/skellam/inst/doc/validate_skellam.html | 331 ++++++++++--------- skellam-0.2.5/skellam/man/skellam.Rd | 277 ++++++++------- skellam-0.2.5/skellam/man/skellam.mle.Rd | 159 ++++----- skellam-0.2.5/skellam/man/skellam.reg.Rd | 144 ++++---- skellam-0.2.5/skellam/tests/testthat |only skellam-0.2.5/skellam/tests/testthat.R |only skellam-0.2.5/skellam/vignettes/validate_skellam.Rmd | 231 ++++++------- 27 files changed, 1570 insertions(+), 1156 deletions(-)
Title: 1d Goodness of Fit Tests
Description: Routines that allow the user to run a large number of goodness-of-fit tests.
It allows for data to be continuous or discrete. It includes routines to estimate
the power of the tests and display them as a power graph.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between Rgof versions 4.0.1 dated 2026-10-05 and 4.1.0 dated 2026-11-09
Rgof-4.0.1/Rgof/man/Cpporder.Rd |only Rgof-4.0.1/Rgof/man/TS_cont.Rd |only Rgof-4.0.1/Rgof/man/TS_disc.Rd |only Rgof-4.0.1/Rgof/man/TSw_cont.Rd |only Rgof-4.0.1/Rgof/man/TSw_disc.Rd |only Rgof-4.0.1/Rgof/man/bincounter.Rd |only Rgof-4.0.1/Rgof/man/calcTS.Rd |only Rgof-4.0.1/Rgof/man/check.functions.Rd |only Rgof-4.0.1/Rgof/man/chi_power_cont.Rd |only Rgof-4.0.1/Rgof/man/chi_power_disc.Rd |only Rgof-4.0.1/Rgof/man/chi_test_cont.Rd |only Rgof-4.0.1/Rgof/man/chi_test_disc.Rd |only Rgof-4.0.1/Rgof/man/gof_adj_C1.Rd |only Rgof-4.0.1/Rgof/man/gof_adj_C2.Rd |only Rgof-4.0.1/Rgof/man/gof_power_C.Rd |only Rgof-4.0.1/Rgof/man/gof_test_C.Rd |only Rgof-4.0.1/Rgof/man/makeTSextra.Rd |only Rgof-4.0.1/Rgof/man/make_bins_cont.Rd |only Rgof-4.0.1/Rgof/man/make_bins_disc.Rd |only Rgof-4.0.1/Rgof/man/makemaxProcessor.Rd |only Rgof-4.0.1/Rgof/man/maketypeTS.Rd |only Rgof-4.0.1/Rgof/man/power_newtest.Rd |only Rgof-4.0.1/Rgof/man/signif_digits.Rd |only Rgof-4.0.1/Rgof/man/validate_integer_scalar.Rd |only Rgof-4.0.1/Rgof/man/wbincounter.Rd |only Rgof-4.1.0/Rgof/DESCRIPTION | 9 Rgof-4.1.0/Rgof/MD5 | 130 Rgof-4.1.0/Rgof/NAMESPACE | 9 Rgof-4.1.0/Rgof/NEWS.md | 6 Rgof-4.1.0/Rgof/R/RcppExports.R | 25 Rgof-4.1.0/Rgof/R/case.studies.R | 2721 +++++------ Rgof-4.1.0/Rgof/R/check.functions.R | 1 Rgof-4.1.0/Rgof/R/chi_power_cont.R | 1 Rgof-4.1.0/Rgof/R/chi_power_disc.R | 1 Rgof-4.1.0/Rgof/R/chi_test_cont.R | 83 Rgof-4.1.0/Rgof/R/chi_test_disc.R | 140 Rgof-4.1.0/Rgof/R/data.R | 86 Rgof-4.1.0/Rgof/R/gof_power.R | 814 +-- Rgof-4.1.0/Rgof/R/gof_test.R | 704 +- Rgof-4.1.0/Rgof/R/gof_test_adjusted_pvalue.R | 363 - Rgof-4.1.0/Rgof/R/helper_functions.R | 18 Rgof-4.1.0/Rgof/R/hybrid_power.R |only Rgof-4.1.0/Rgof/R/hybrid_test.R |only Rgof-4.1.0/Rgof/R/make_bins_cont.R | 60 Rgof-4.1.0/Rgof/R/make_bins_disc.R | 1 Rgof-4.1.0/Rgof/R/myTS.R | 5 Rgof-4.1.0/Rgof/R/plot_power.R | 92 Rgof-4.1.0/Rgof/R/power_newtest.R | 1 Rgof-4.1.0/Rgof/R/run.studies.R | 270 - Rgof-4.1.0/Rgof/R/signif_digits.R | 1 Rgof-4.1.0/Rgof/R/test_methods.R | 117 Rgof-4.1.0/Rgof/data/power_study.rda |binary Rgof-4.1.0/Rgof/data/power_study_hybrid.rda |only Rgof-4.1.0/Rgof/data/power_study_hybrid_nMC5.rda |only Rgof-4.1.0/Rgof/inst/doc/Rgof.R | 85 Rgof-4.1.0/Rgof/inst/doc/Rgof.Rmd | 113 Rgof-4.1.0/Rgof/inst/doc/Rgof.html | 664 +- Rgof-4.1.0/Rgof/man/gof_power.Rd | 17 Rgof-4.1.0/Rgof/man/gof_test.Rd | 9 Rgof-4.1.0/Rgof/man/gof_test_adjusted_pvalue.Rd | 13 Rgof-4.1.0/Rgof/man/hybrid_power.Rd |only Rgof-4.1.0/Rgof/man/hybrid_test.Rd |only Rgof-4.1.0/Rgof/man/plot_power.Rd | 10 Rgof-4.1.0/Rgof/man/power_study.Rd | 4 Rgof-4.1.0/Rgof/man/power_study_hybrid.Rd |only Rgof-4.1.0/Rgof/man/power_study_hybrid_nMC5.Rd |only Rgof-4.1.0/Rgof/man/run.studies.Rd | 32 Rgof-4.1.0/Rgof/man/summary.Rgof_power_values.Rd |only Rgof-4.1.0/Rgof/src/Cpporder.cpp | 1 Rgof-4.1.0/Rgof/src/TS_cont.cpp | 92 Rgof-4.1.0/Rgof/src/TS_disc.cpp | 235 Rgof-4.1.0/Rgof/src/TSw_cont.cpp | 22 Rgof-4.1.0/Rgof/src/TSw_disc.cpp | 29 Rgof-4.1.0/Rgof/src/bincounter.cpp | 1 Rgof-4.1.0/Rgof/src/calcTS.cpp | 1 Rgof-4.1.0/Rgof/src/gof_adj_C.cpp | 12 Rgof-4.1.0/Rgof/src/gof_power_C.cpp | 1 Rgof-4.1.0/Rgof/src/gof_test_C.cpp | 6 Rgof-4.1.0/Rgof/src/wbincounter.cpp | 1 Rgof-4.1.0/Rgof/tests/testthat/test-gof-power-ci.R | 34 Rgof-4.1.0/Rgof/tests/testthat/test-hybrid.R |only Rgof-4.1.0/Rgof/tests/testthat/test-statistics-definitions.R |only Rgof-4.1.0/Rgof/vignettes/Rgof.Rmd | 113 Rgof-4.1.0/Rgof/vignettes/Rgof.bib | 36 84 files changed, 3983 insertions(+), 3206 deletions(-)
Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Description: Imputes missing species trait data for comparative analyses
by combining three sources of information: phylogenetic similarity
(closely related species share similar traits), cross-trait
correlations (observed traits inform missing ones), and optional
environmental covariates (climate, habitat, geography). Handles
continuous measurements, counts, binary variables, ordered categories,
unordered categories, bounded proportions, zero-inflated counts, and
compositional multi-proportion data in a single call. The default
method is a phylogenetic baseline calibrated on held-out data; an
optional graph neural network prediction is blended in through a
per-trait gate that retains a baseline fallback. Covariates can inform
the network and selected baseline paths. Provides conformal
prediction intervals for continuous, count, ordinal, and proportion
traits and an experimental analysis-aware multiple-imputation workflow
for one missing continuous covariate in Gaussian linear, binomial-logit,
and [...truncated...]
Author: Shinichi Nakagawa [aut, cre, cph],
Daniel Noble [ctb]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between pigauto versions 0.11.0 dated 2026-10-18 and 0.11.1 dated 2026-11-09
pigauto-0.11.0/pigauto/tests/testthat/fixtures/gbif_plants_300.rds |only pigauto-0.11.0/pigauto/tests/testthat/fixtures/worldclim_plants_300.rds |only pigauto-0.11.1/pigauto/DESCRIPTION | 25 pigauto-0.11.1/pigauto/MD5 | 267 +- pigauto-0.11.1/pigauto/NAMESPACE | 2 pigauto-0.11.1/pigauto/NEWS.md | 108 pigauto-0.11.1/pigauto/R/active_impute.R | 211 + pigauto-0.11.1/pigauto/R/bm_internal.R | 79 pigauto-0.11.1/pigauto/R/build_phylo_graph.R | 49 pigauto-0.11.1/pigauto/R/check_pigauto.R | 70 pigauto-0.11.1/pigauto/R/cross_validate.R | 56 pigauto-0.11.1/pigauto/R/data.R | 38 pigauto-0.11.1/pigauto/R/evaluate.R | 65 pigauto-0.11.1/pigauto/R/evaluate_imputation.R | 50 pigauto-0.11.1/pigauto/R/fit_baseline.R | 290 +- pigauto-0.11.1/pigauto/R/fit_pigauto.R | 277 +- pigauto-0.11.1/pigauto/R/gbif_centroids.R | 77 pigauto-0.11.1/pigauto/R/impute.R | 431 +-- pigauto-0.11.1/pigauto/R/mask_missing.R | 49 pigauto-0.11.1/pigauto/R/multi_impute.R | 383 ++- pigauto-0.11.1/pigauto/R/multi_impute_analysis.R | 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pigauto-0.11.1/pigauto/tests/testthat/test-community-surface.R | 69 pigauto-0.11.1/pigauto/tests/testthat/test-coverage-workflow.R |only pigauto-0.11.1/pigauto/tests/testthat/test-cran-audit-defaults.R | 6 pigauto-0.11.1/pigauto/tests/testthat/test-docs-phytools-warning.R | 11 pigauto-0.11.1/pigauto/tests/testthat/test-draws-auto.R | 2 pigauto-0.11.1/pigauto/tests/testthat/test-evaluation-gnn.R |only pigauto-0.11.1/pigauto/tests/testthat/test-evaluation-mode.R |only pigauto-0.11.1/pigauto/tests/testthat/test-gbif-centroids.R | 109 pigauto-0.11.1/pigauto/tests/testthat/test-gnn-off.R | 49 pigauto-0.11.1/pigauto/tests/testthat/test-honesty-warnings.R | 95 pigauto-0.11.1/pigauto/tests/testthat/test-issue-input-clarity.R |only pigauto-0.11.1/pigauto/tests/testthat/test-issue-visuals.R |only pigauto-0.11.1/pigauto/tests/testthat/test-joint-lambda.R | 6 pigauto-0.11.1/pigauto/tests/testthat/test-lambda-covariates.R | 77 pigauto-0.11.1/pigauto/tests/testthat/test-lambda-default.R | 13 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Title: Programmatic Access to the European Central Bank's Data Portal
Description: Provides an interface to the European Central Bank's Data
Portal API, allowing for programmatic retrieval of a vast quantity
of statistical data.
Author: Eric Persson [aut, cre],
Franz X. Mohr [ctb]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ecb versions 0.4.3 dated 2025-03-19 and 0.4.4 dated 2026-11-09
DESCRIPTION | 10 +- MD5 | 28 ++++---- NEWS.md |only R/main.R | 118 +++++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/ecb_edp.R | 104 ++++++++++++++++-------------- inst/doc/ecb_edp.Rmd | 19 ++++- inst/doc/ecb_edp.html | 141 ++++++++++++++++++------------------------ man/convert_dates.Rd | 11 ++- man/get_data.Rd | 7 +- man/get_dataflows.Rd | 5 + man/get_description.Rd | 9 ++ man/get_dimensions.Rd | 8 +- tests/testthat/tests.R | 69 +++++++++++++++++--- vignettes/ecb_edp.Rmd | 19 ++++- vignettes/phillips_plot-1.png |only 16 files changed, 343 insertions(+), 205 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control
of Research Outputs.
Author: Jim Smith [aut, ctb] ,
Maha Albashir [cre, ctb],
Richard John Preen [aut, ctb]
Maintainer: Maha Albashir <Maha.Albashir@uwe.ac.uk>
Diff between acro versions 1.0.0 dated 2026-09-09 and 1.1.1 dated 2026-11-09
acro-1.0.0/acro/man/create_factors.Rd |only acro-1.0.0/acro/man/is_excluded.Rd |only acro-1.0.0/acro/man/is_invalid.Rd |only acro-1.0.0/acro/man/to_pandas_categorical.Rd |only acro-1.0.0/acro/tests/testthat/Rplots.pdf |only acro-1.1.1/acro/DESCRIPTION | 20 acro-1.1.1/acro/LICENSE | 4 acro-1.1.1/acro/MD5 | 175 - acro-1.1.1/acro/NAMESPACE | 57 acro-1.1.1/acro/NEWS.md | 6 acro-1.1.1/acro/R/acro-package.R | 10 acro-1.1.1/acro/R/acro_init.R | 2 acro-1.1.1/acro/R/acro_regression.R | 192 + acro-1.1.1/acro/R/acro_tables.R | 910 ++++---- acro-1.1.1/acro/R/lung.R | 44 acro-1.1.1/acro/R/nursery_data.R | 48 acro-1.1.1/acro/R/output_commands.R | 302 +- acro-1.1.1/acro/R/utils.R | 277 +- acro-1.1.1/acro/R/zzz.R | 9 acro-1.1.1/acro/README.md | 130 - acro-1.1.1/acro/build/vignette.rds |binary acro-1.1.1/acro/inst/AI_POLICY.md | 168 - acro-1.1.1/acro/inst/INSTALL.md | 286 +- acro-1.1.1/acro/inst/Images/UK_Research_and_Innovation_logo.svg | 376 +-- acro-1.1.1/acro/inst/WORDLIST | 99 acro-1.1.1/acro/inst/doc/example-notebook.R | 18 acro-1.1.1/acro/inst/doc/example-notebook.Rmd | 38 acro-1.1.1/acro/inst/doc/example-notebook.html | 724 +++---- acro-1.1.1/acro/inst/doc/examples.Rmd | 98 acro-1.1.1/acro/inst/doc/examples.html | 794 +++---- acro-1.1.1/acro/inst/doc/installation.Rmd | 124 - acro-1.1.1/acro/inst/doc/installation.html | 810 +++---- acro-1.1.1/acro/inst/doc/supports.Rmd | 211 +- acro-1.1.1/acro/inst/doc/supports.html | 746 +++---- acro-1.1.1/acro/inst/doc/welcome.html | 850 ++++---- acro-1.1.1/acro/inst/index.md | 98 acro-1.1.1/acro/inst/notebooks/acro_demo_2026.R | 623 +++++- acro-1.1.1/acro/inst/notebooks/acro_demo_2026.Rmd | 1024 +++++----- acro-1.1.1/acro/inst/notebooks/acro_in_tidyverse_demo.Rmd | 182 - acro-1.1.1/acro/inst/notebooks/example-notebook-old.Rmd | 392 +-- acro-1.1.1/acro/man/acro_add_comments.Rd | 38 acro-1.1.1/acro/man/acro_add_exception.Rd | 38 acro-1.1.1/acro/man/acro_coxph.Rd |only acro-1.1.1/acro/man/acro_crosstab.Rd | 98 acro-1.1.1/acro/man/acro_custom_output.Rd | 38 acro-1.1.1/acro/man/acro_disable_rounding.Rd | 28 acro-1.1.1/acro/man/acro_disable_suppression.Rd | 28 acro-1.1.1/acro/man/acro_enable_rounding.Rd | 34 acro-1.1.1/acro/man/acro_enable_suppression.Rd | 28 acro-1.1.1/acro/man/acro_finalise.Rd | 38 acro-1.1.1/acro/man/acro_glm.Rd | 42 acro-1.1.1/acro/man/acro_hist.Rd | 68 acro-1.1.1/acro/man/acro_init.Rd | 78 acro-1.1.1/acro/man/acro_lm.Rd | 38 acro-1.1.1/acro/man/acro_pie.Rd | 92 acro-1.1.1/acro/man/acro_pivot_table.Rd | 62 acro-1.1.1/acro/man/acro_print_outputs.Rd | 28 acro-1.1.1/acro/man/acro_remove_output.Rd | 34 acro-1.1.1/acro/man/acro_rename_output.Rd | 38 acro-1.1.1/acro/man/acro_summarise.Rd | 46 acro-1.1.1/acro/man/acro_surv_func.Rd | 46 acro-1.1.1/acro/man/acro_table.Rd | 74 acro-1.1.1/acro/man/lung.Rd | 62 acro-1.1.1/acro/man/nursery_data.Rd | 70 acro-1.1.1/acro/tests/spelling.R | 12 acro-1.1.1/acro/tests/testthat.R | 24 acro-1.1.1/acro/tests/testthat/test-acro_add_comments.R | 44 acro-1.1.1/acro/tests/testthat/test-acro_add_exception.R | 40 acro-1.1.1/acro/tests/testthat/test-acro_coxph.R |only acro-1.1.1/acro/tests/testthat/test-acro_crosstab.R | 148 - acro-1.1.1/acro/tests/testthat/test-acro_custom_output.R | 32 acro-1.1.1/acro/tests/testthat/test-acro_disable_suppression.R | 28 acro-1.1.1/acro/tests/testthat/test-acro_enable_suppression.R | 28 acro-1.1.1/acro/tests/testthat/test-acro_finalise.R | 30 acro-1.1.1/acro/tests/testthat/test-acro_glm.R | 86 acro-1.1.1/acro/tests/testthat/test-acro_hist.R | 188 - acro-1.1.1/acro/tests/testthat/test-acro_init.R | 16 acro-1.1.1/acro/tests/testthat/test-acro_lm.R | 52 acro-1.1.1/acro/tests/testthat/test-acro_pie.R | 114 - acro-1.1.1/acro/tests/testthat/test-acro_pivot_table.R | 70 acro-1.1.1/acro/tests/testthat/test-acro_print_outputs.R | 26 acro-1.1.1/acro/tests/testthat/test-acro_remove_output.R | 34 acro-1.1.1/acro/tests/testthat/test-acro_rename_output.R | 34 acro-1.1.1/acro/tests/testthat/test-acro_rounding.R | 52 acro-1.1.1/acro/tests/testthat/test-acro_summarise.R | 598 ++--- acro-1.1.1/acro/tests/testthat/test-acro_surv_func.R | 46 acro-1.1.1/acro/tests/testthat/test-acro_table.R | 612 ++--- acro-1.1.1/acro/tests/testthat/test-install_acro.R | 22 acro-1.1.1/acro/vignettes/example-notebook.Rmd | 38 acro-1.1.1/acro/vignettes/examples.Rmd | 98 acro-1.1.1/acro/vignettes/installation.Rmd | 124 - acro-1.1.1/acro/vignettes/supports.Rmd | 211 +- 92 files changed, 7201 insertions(+), 6599 deletions(-)
Title: Facilitate Citation of R Packages
Description: Facilitates the citation of R packages used in analysis
projects. Scans project for packages used, gets their citations, and
produces a document with citations in the preferred bibliography
format, ready to be pasted into reports or manuscripts. Alternatively,
'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.
Author: Francisco Rodriguez-Sanchez [aut, cre, cph] ,
Connor P. Jackson [aut] ,
Shaurita D. Hutchins [ctb],
James M. Clawson [ctb]
Maintainer: Francisco Rodriguez-Sanchez <f.rodriguez.sanc@gmail.com>
Diff between grateful versions 0.3.0 dated 2025-09-04 and 0.3.1 dated 2026-11-09
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++-------------- NEWS.md | 9 ++++++ R/cite_packages.R | 2 - R/create_rmd.R | 2 - R/get_citations.R | 3 +- R/render_citations.R | 4 +- R/scan_packages.R | 3 +- R/utils_citations.R | 7 ++++ R/write_citation_paragraph.R | 17 ++++++++--- README.md | 53 ++++++++++++++++++++++-------------- man/cite_packages.Rd | 4 +- man/get_citations.Rd | 2 - man/get_csl.Rd | 2 - man/get_pkgs_info.Rd | 2 - man/grateful-package.Rd | 1 man/nocite_references.Rd | 2 - man/scan_packages.Rd | 2 - tests/testthat/test-cite_packages.R | 47 ++++++++++++++++++++++++++++++- tests/testthat/test-get_citations.R | 10 ++++++ tests/testthat/test-scan_packages.R | 7 ++-- 21 files changed, 159 insertions(+), 68 deletions(-)
Title: Read 'SAS' Data in Chunks and Convert to 'Parquet'
Description: Reads 'SAS' 'sas7bdat' files through a persistent native reader.
Processes configurable chunks without reopening the input or restarting
the parser between chunks. Supports uncompressed, run-length encoded,
and Ross Data Compression data through the bundled 'ReadStat' library.
Also streams native decoded batches directly to 'Parquet' through the
'Arrow' C Data Interface and the optional 'arrow' package, without
constructing R data frames.
Author: Jianyun Wu [aut, cre],
Evan Miller [aut, cph]
Maintainer: Jianyun Wu <jianyun.fred.wu@hotmail.com>
Diff between anotherSAS7bdat versions 0.0.7 dated 2026-10-21 and 0.0.9 dated 2026-11-09
anotherSAS7bdat-0.0.7/anotherSAS7bdat/R/anotherSAS7bdat-package.R |only anotherSAS7bdat-0.0.7/anotherSAS7bdat/man/anotherSAS7bdat-package.Rd |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/DESCRIPTION | 12 anotherSAS7bdat-0.0.9/anotherSAS7bdat/MD5 | 31 anotherSAS7bdat-0.0.9/anotherSAS7bdat/NEWS.md |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/AnotherSAS7bdat-package.R |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/RcppExports.R | 54 - anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/parquet.R | 380 +++---- anotherSAS7bdat-0.0.9/anotherSAS7bdat/README.md | 11 anotherSAS7bdat-0.0.9/anotherSAS7bdat/configure | 2 anotherSAS7bdat-0.0.9/anotherSAS7bdat/inst/LICENSE.ReadStat | 38 anotherSAS7bdat-0.0.9/anotherSAS7bdat/man/AnotherSAS7bdat-package.Rd |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/man/sas7bdat_to_parquet.Rd | 234 ++-- anotherSAS7bdat-0.0.9/anotherSAS7bdat/src/reader.cpp | 57 - anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-adaptive-buffers.R | 12 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-parquet.R | 506 +++++----- anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-read-ahead.R | 21 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-reader.R | 2 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-time-conversion.R | 6 19 files changed, 760 insertions(+), 606 deletions(-)
More information about anotherSAS7bdat at CRAN
Permanent link
Title: Grouped and Nested Data Pipelines Built on 'data.table'
Description: A toolkit for grouped and nested data pipelines built on
'data.table': import many Excel / CSV files (including multi-row
headers) into one table, reshape and nest data by trait and group, run
reproducible (stratified) k-fold cross-validation inside every group,
summarise groups with report-ready descriptive statistics, and write
each piece back to its own file or sheet. Developed for animal
breeding, where it prepares phenotypic files for 'ASReml-R', 'HIBLUP'
or 'DMU', but useful for any multi-group, multi-variable analysis.
Author: Guo Meng [aut, cre],
Guo Meng [cph]
Maintainer: Guo Meng <tony2015116@163.com>
Diff between mintyr versions 0.2.0 dated 2026-10-05 and 0.2.1 dated 2026-11-09
mintyr-0.2.0/mintyr/man/figures/cheatsheet.svg |only mintyr-0.2.1/mintyr/DESCRIPTION | 6 - mintyr-0.2.1/mintyr/MD5 | 37 +++--- mintyr-0.2.1/mintyr/NAMESPACE | 2 mintyr-0.2.1/mintyr/NEWS.md | 28 ++++ mintyr-0.2.1/mintyr/R/import_csv.R | 34 +++++ mintyr-0.2.1/mintyr/R/import_xlsx.R | 99 ++++++++++++++--- mintyr-0.2.1/mintyr/R/resolve_cols.R | 78 +++++++++++++ mintyr-0.2.1/mintyr/README.md | 9 + mintyr-0.2.1/mintyr/inst/doc/import-and-export.R | 16 ++ mintyr-0.2.1/mintyr/inst/doc/import-and-export.Rmd | 16 ++ mintyr-0.2.1/mintyr/inst/doc/import-and-export.html | 81 +++++++++---- mintyr-0.2.1/mintyr/inst/doc/mintyr.html | 2 mintyr-0.2.1/mintyr/inst/doc/utilities.html | 2 mintyr-0.2.1/mintyr/man/import_csv.Rd | 11 + mintyr-0.2.1/mintyr/man/import_xlsx.Rd | 48 ++++++++ mintyr-0.2.1/mintyr/tests/testthat/test-import_csv.R | 26 ++++ mintyr-0.2.1/mintyr/tests/testthat/test-import_xlsx.R | 73 ++++++++++++ mintyr-0.2.1/mintyr/tests/testthat/test-resolve_cols.R | 20 +++ mintyr-0.2.1/mintyr/vignettes/import-and-export.Rmd | 16 ++ 20 files changed, 534 insertions(+), 70 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 0.1.2 dated 2026-08-27 and 0.1.3 dated 2026-11-09
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Title: Latent and Stochastic Block Model Estimation by a 'V-EM'
Algorithm
Description: Latent and Stochastic Block Model estimation by a Variational EM algorithm.
Various probability distribution are provided (Bernoulli,
Poisson...), with or without covariates. See Leger (2016)
<doi:10.48550/arXiv.1602.07587>.
Author: Jean-Benoist Leger [aut] ,
Julien Chiquet [aut, cre] ,
Pierre Barbillon [aut] ,
Louis Lacoste [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between blockmodels versions 1.1.5 dated 2021-12-01 and 1.2.1 dated 2026-11-09
DESCRIPTION | 35 +- MD5 | 107 ++++-- NEWS.md |only R/membership_LBM.R | 199 +++++++----- R/membership_SBM.R | 48 ++ R/membership_SBM_sym.R | 48 ++ R/misc.R | 62 +++ R/model.R | 21 - R/multivariate_model.R | 55 +++ R/parallel_lapply.R | 2 R/scalar_model.R | 78 +++- R/scalar_model_with_covariates.R | 5 R/zbernoulli_covariates.R | 26 - R/zbernoulli_covariates_fast.R | 26 - R/zgaussian_covariates.R | 2 R/zpoisson_covariates.R | 2 README.md |only inst |only man/BM_bernoulli.Rd | 7 man/BM_bernoulli_covariates.Rd | 9 man/BM_bernoulli_covariates_fast.Rd | 9 man/BM_bernoulli_multiplex.Rd | 7 man/BM_gaussian.Rd | 7 man/BM_gaussian_covariates.Rd | 9 man/BM_gaussian_multivariate.Rd | 7 man/BM_gaussian_multivariate_independent.Rd | 7 man/BM_gaussian_multivariate_independent_homoscedastic.Rd | 7 man/BM_poisson.Rd | 7 man/BM_poisson_covariates.Rd | 9 src/Makevars | 7 src/Makevars.win | 2 src/conf.h | 5 src/dispatcher.cc | 4 src/dispatcher.h | 1 src/memberships/lbm.h | 230 +++++++++----- src/memberships/sbm.h | 83 ++++- src/misc_functions.h | 58 +++ src/models/bernoulli.h | 65 +-- src/models/bernoulli_covariates.h | 9 src/models/bernoulli_covariates_fast.h | 15 src/models/gaussian.h | 49 ++ src/models/gaussian_covariates.h | 68 ++-- src/models/naive_bernoulli.h | 6 src/models/poisson.h | 15 src/models/poisson_covariates.h | 9 src/nodes_covariates.h |only tests/testthat |only tests/testthat.R |only 48 files changed, 1015 insertions(+), 412 deletions(-)
Title: Import Surface Meteorological Data from NOAA
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Global Historical Climate
Network (GHCN) and Integrated Surface Database (ISD).
Author: David Carslaw [aut, cre] ,
Jack Davison [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 1.1.0 dated 2026-05-18 and 1.2.0 dated 2026-11-09
DESCRIPTION | 10 MD5 | 52 - NAMESPACE | 6 NEWS.md | 56 + R/deprecated.R | 27 R/import_ghcn_daily.R | 27 R/import_ghcn_hourly.R | 175 ++- R/import_ghcn_monthly.R | 32 R/import_ghcn_stations.R | 1063 +++++++++++---------- R/import_isd_hourly.R | 2127 ++++++++++++++++++++++---------------------- R/import_isd_lite.R | 36 R/import_isd_stations.R | 15 R/utils.R | 273 +---- R/weatherCodes.R | 24 R/write_adms.R | 8 R/write_met.R | 15 inst |only man/deprecated-isd.Rd | 6 man/import_ghcn_daily.Rd | 2 man/import_ghcn_hourly.Rd | 2 man/import_ghcn_monthly.Rd | 2 man/import_ghcn_stations.Rd | 4 man/import_isd_hourly.Rd | 8 man/import_isd_lite.Rd | 26 man/import_isd_stations.Rd | 17 man/weatherCodes.Rd | 2 man/worldmet-package.Rd | 2 tests |only 28 files changed, 2032 insertions(+), 1985 deletions(-)
Title: Water-Energy-Food-Nutrient-Carbon Nexus Analysis for Agronomic
Systems
Description: Provides functions for analysing
Water-Energy-Food-Nutrient-Carbon (WEFNC) nexus interactions in
agricultural production systems. Includes functions for
computing water use efficiency (WUE), water productivity (WP),
and water footprint (WF) including green, blue, and grey
components following the methodology of Hoekstra et al. (2011,
ISBN:9781849712798). Includes energy budgeting tools for energy
use efficiency (EUE), energy return on investment (EROI), net
energy (NE), and energy productivity (EP). Computes nutrient
use efficiency (NUE) metrics including agronomic efficiency
(AE), physiological efficiency (PE), recovery efficiency (RE),
and partial factor productivity (PFP) as defined by Dobermann
(2007) <https://digitalcommons.unl.edu/agronomyfacpub/316/> and
Congreves et al. (2021) <doi:10.3389/fpls.2021.637108>.
Estimates carbon footprint (CF), greenhouse gas (GHG)
emissions, soil organic carbon (SOC) stocks, and global warming
potential (GWP) using Intergovernmental Pa [...truncated...]
Author: Lalit Kumar Rolaniya [aut, cre] ,
Hemant Poonia [aut] ,
Ram Lal Jat [aut] ,
Monika Punia [aut] ,
Raja Ram Choudhary [aut]
Maintainer: Lalit Kumar Rolaniya <lalitrolaniya@gmail.com>
Diff between wefnexus versions 1.0.0 dated 2026-03-10 and 1.1.0 dated 2026-11-09
DESCRIPTION | 84 +++-- MD5 | 181 ++++++----- NAMESPACE | 18 + NEWS.md | 131 ++++++++ R/analysis.R |only R/anova.R |only R/carbon.R | 253 +++++++++++----- R/classes.R | 5 R/data.R | 32 ++ R/energy.R | 60 ++- R/energy_budget.R |only R/food.R | 56 ++- R/nexus.R | 254 +++++++++++++--- R/nexus_advanced.R | 232 +++++++++----- R/nutrient.R | 85 +++-- R/plots.R |only R/robustness.R |only R/utils.R | 3 R/water.R | 55 ++- R/wefnexus-package.R | 12 R/weights.R |only README.md | 244 +++++++++++++-- build/partial.rdb |binary build/vignette.rds |binary data/arid_pulse_trial.rda |only data/energy_coefficients.rda |only inst/CITATION | 5 inst/doc/wefnexus-intro.R | 93 +++++ inst/doc/wefnexus-intro.Rmd | 176 +++++++++++ inst/doc/wefnexus-intro.html | 515 ++++++++++++++++++++++----------- man/agronomic_efficiency.Rd | 5 man/arid_pulse_trial.Rd |only man/caloric_yield.Rd | 9 man/carbon_efficiency.Rd | 9 man/carbon_footprint.Rd | 36 +- man/carbon_sequestration_rate.Rd | 10 man/carbon_sustainability_index.Rd | 9 man/crop_water_productivity.Rd | 9 man/crop_water_stress_index.Rd | 19 - man/crop_yield_index.Rd | 12 man/depleted_fraction.Rd | 9 man/energy_budget.Rd |only man/energy_coefficients.Rd |only man/energy_input.Rd | 5 man/energy_intensity.Rd | 9 man/energy_output.Rd | 5 man/energy_productivity.Rd | 9 man/energy_profitability.Rd | 14 man/energy_use_efficiency.Rd | 9 man/eroi.Rd | 7 man/figures/README-anova.png |only man/figures/README-radar.png |only man/figures/README-ranks.png |only man/food_productivity_index.Rd | 14 man/ghg_emission.Rd | 66 +++- man/global_warming_potential.Rd | 15 man/harvest_index.Rd | 9 man/human_energy_profitability.Rd | 9 man/internal_utilization_efficiency.Rd | 9 man/irrigation_efficiency.Rd | 5 man/land_equivalent_ratio.Rd | 5 man/net_energy.Rd | 9 man/nexus_analysis.Rd |only man/nexus_anova.Rd |only man/nexus_heatmap.Rd | 3 man/nexus_heatmap_gg.Rd | 8 man/nexus_index.Rd | 5 man/nexus_radar.Rd | 3 man/nexus_radar_gg.Rd | 24 + man/nexus_rank_compare.Rd |only man/nexus_sensitivity.Rd | 5 man/nexus_summary.Rd | 74 +++- man/nexus_sustainability_score.Rd | 9 man/nexus_topsis.Rd |only man/nexus_tradeoff.Rd | 19 - man/nexus_weights.Rd |only man/nutrient_balance.Rd | 14 man/nutrient_harvest_index.Rd | 9 man/nutrient_use_efficiency.Rd | 25 + man/partial_factor_productivity.Rd | 9 man/physiological_efficiency.Rd | 5 man/plot.energy_budget.Rd |only man/plot.nexus_analysis.Rd |only man/plot.nexus_anova.Rd |only man/plot.rank_compare.Rd |only man/plot.topsis_result.Rd |only man/plot.tradeoff_matrix.Rd |only man/plot_tradeoff.Rd |only man/print.energy_budget.Rd |only man/print.nexus_analysis.Rd |only man/print.nexus_anova.Rd |only man/print.rank_compare.Rd |only man/print.tradeoff_matrix.Rd |only man/production_efficiency_index.Rd | 13 man/protein_yield.Rd | 9 man/recovery_efficiency.Rd | 5 man/soil_carbon_stock.Rd | 18 - man/specific_energy.Rd | 17 - man/system_productivity_index.Rd | 10 man/water_footprint.Rd | 9 man/water_productivity.Rd | 5 man/water_use_efficiency.Rd | 9 man/wefnexus-package.Rd | 18 + tests/testthat/test-additional.R | 6 tests/testthat/test-all-modules.R | 14 tests/testthat/test-plots-robustness.R |only tests/testthat/test-v110.R |only vignettes/wefnexus-intro.Rmd | 176 +++++++++++ 108 files changed, 2577 insertions(+), 764 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.7 dated 2026-01-20 and 2.3.0 dated 2026-11-09
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 11 +++++++++++ R/set_priors.R | 11 +++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BayesMallows.html | 26 ++++++++++++-------------- inst/doc/SMC-Mallows.html | 7 +++---- inst/doc/parallel_chains.html | 3 +-- man/set_priors.Rd | 11 +++++++---- src/distances.cpp | 2 +- src/parameters_class.cpp | 17 +++++++---------- src/rank_proposal.cpp | 27 +++++++++++++++++++-------- tests/testthat/test-bernoulli_error_model.R |only tests/testthat/test-mcmc_correctness.R | 16 ++++++++-------- 15 files changed, 93 insertions(+), 71 deletions(-)
Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets, doing
intersection, union, complementary sets, power sets, cartesian product
and other set operations in a "tidy" way. These set operations are
available for both classical sets and fuzzy sets. Import sets from
several formats or from other several data structures.
Author: Lluis Revilla Sancho [aut, cre, cph] ,
Zebulun Arendsee [rev],
Jennifer Chang [rev]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between BaseSet versions 1.0.0 dated 2025-02-17 and 1.0.1 dated 2026-11-09
DESCRIPTION | 12 MD5 | 346 ++++++++++----------- NAMESPACE | 56 +-- NEWS.md | 9 R/AllClasses.R | 14 R/AllGenerics.R | 247 +++++++-------- R/GMT.R | 50 +-- R/GeneSetCollection.R | 128 +++---- R/activate.R | 52 +-- R/add.R | 214 ++++++------- R/add_column.R | 34 +- R/add_relation.R | 54 +-- R/adjacency.R | 43 +- R/arrange.R | 65 +--- R/c.R | 54 +-- R/cardinality.R | 30 - R/cartesian.R | 108 +++--- R/complement.R | 171 +++++----- R/data_frame.R | 82 ++--- R/deactivate.R | 6 R/droplevels.R | 70 ++-- R/elements.R | 46 +- R/extract.R | 552 +++++++++++++++++----------------- R/filter.R | 89 ++--- R/group.R | 48 +- R/group_by.R | 18 - R/head.R | 7 R/incidence.R | 36 +- R/independent.R | 19 - R/intersection.R | 110 +++--- R/length.R | 413 ++++++++++++------------- R/list.R | 37 +- R/move_to.R | 62 +-- R/mutate.R | 83 ++--- R/names.R | 325 ++++++++++---------- R/naming.R | 96 +++-- R/nested.R | 4 R/obo.R | 233 +++++++------- R/operations.R | 9 R/power_set.R | 94 ++--- R/print.R | 12 R/pull.R | 44 +- R/relations.R | 50 +-- R/remove.R | 68 ++-- R/remove_column.R | 22 - R/rename.R | 52 +-- R/select.R | 65 +--- R/set.R | 46 +- R/size.R | 37 +- R/subtract.R | 113 +++--- R/tidy-set.R | 281 ++++++++--------- R/union.R | 54 +-- R/union_closed.R | 70 ++-- R/utils.R | 14 R/validity.R | 43 +- R/zzz.R | 32 - README.md | 50 +-- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/BaseSet.R | 74 ++-- inst/doc/BaseSet.Rmd | 78 ++-- inst/doc/BaseSet.html | 163 +++++----- inst/doc/advanced.R | 260 ++++++++-------- inst/doc/advanced.Rmd | 266 ++++++++-------- inst/doc/advanced.html | 389 ++++++++++++----------- inst/doc/fuzzy.R | 94 +++-- inst/doc/fuzzy.Rmd | 100 +++--- inst/doc/fuzzy.html | 148 ++++----- man/BaseSet-package.Rd | 5 man/TidySet-class.Rd | 80 ++-- man/activate.Rd | 78 ++-- man/add_column.Rd | 82 ++--- man/add_elements.Rd | 6 man/add_relation.Rd | 78 ++-- man/add_relations.Rd | 6 man/add_sets.Rd | 6 man/arrange_.Rd | 78 ++-- man/cartesian.Rd | 78 ++-- man/complement.Rd | 86 ++--- man/complement_element.Rd | 96 ++--- man/complement_set.Rd | 96 ++--- man/element_size.Rd | 82 ++--- man/elements.Rd | 84 ++--- man/filter_.Rd | 78 ++-- man/getGAF.Rd | 10 man/getGMT.Rd | 6 man/getOBO.Rd | 6 man/group.Rd | 78 ++-- man/group_by_.Rd | 78 ++-- man/incidence.Rd | 78 ++-- man/intersection.Rd | 88 ++--- man/is.fuzzy.Rd | 78 ++-- man/is_nested.Rd | 78 ++-- man/move_to.Rd | 78 ++-- man/mutate_.Rd | 78 ++-- man/nElements.Rd | 84 ++--- man/nRelations.Rd | 84 ++--- man/nSets.Rd | 84 ++--- man/name_elements-set.Rd | 90 ++--- man/name_elements.Rd | 12 man/name_sets-set.Rd | 90 ++--- man/name_sets.Rd | 90 ++--- man/power_set.Rd | 78 ++-- man/pull_.Rd | 78 ++-- man/reexports.Rd | 2 man/relations.Rd | 84 ++--- man/remove_column.Rd | 82 ++--- man/remove_element.Rd | 84 ++--- man/remove_relation.Rd | 84 ++--- man/remove_set.Rd | 84 ++--- man/rename_elements.Rd | 94 ++--- man/rename_set.Rd | 94 ++--- man/select_.Rd | 78 ++-- man/set_size.Rd | 82 ++--- man/set_symbols.Rd | 5 man/sets.Rd | 84 ++--- man/subtract.Rd | 100 +++--- man/union.Rd | 88 ++--- tests/spelling.R | 9 tests/testthat.R | 6 tests/testthat/test-GMT.R | 12 tests/testthat/test-activate.R | 28 - tests/testthat/test-add_column.R | 20 - tests/testthat/test-add_relation.R | 40 +- tests/testthat/test-add_relations.R | 86 ++--- tests/testthat/test-adjacency.R | 42 +- tests/testthat/test-arrange.R | 56 +-- tests/testthat/test-c.R | 24 - tests/testthat/test-cardinality.R | 16 tests/testthat/test-cartesian.R | 20 - tests/testthat/test-complement.R | 158 ++++----- tests/testthat/test-data_frame.R | 32 - tests/testthat/test-df2TS.R | 38 +- tests/testthat/test-droplevels.R | 30 - tests/testthat/test-element_size.R | 62 +-- tests/testthat/test-elements.R | 30 - tests/testthat/test-extract.R | 118 +++---- tests/testthat/test-filter.R | 52 +-- tests/testthat/test-group.R | 36 +- tests/testthat/test-group_by.R | 28 - tests/testthat/test-head.R | 22 - tests/testthat/test-incidence.R | 12 tests/testthat/test-independent.R | 12 tests/testthat/test-intersection.R | 176 +++++----- tests/testthat/test-length.R | 116 +++---- tests/testthat/test-move_to.R | 18 - tests/testthat/test-mutate.R | 108 +++--- tests/testthat/test-name.R | 120 +++---- tests/testthat/test-naming.R | 32 - tests/testthat/test-nested.R | 10 tests/testthat/test-obo.R | 21 - tests/testthat/test-operations.R | 10 tests/testthat/test-power_set.R | 48 +- tests/testthat/test-print.R | 8 tests/testthat/test-pull.R | 110 +++--- tests/testthat/test-relations.R | 48 +- tests/testthat/test-remove_column.R | 22 - tests/testthat/test-remove_element.R | 16 tests/testthat/test-remove_relation.R | 34 +- tests/testthat/test-remove_set.R | 16 tests/testthat/test-rename.R | 36 +- tests/testthat/test-select.R | 52 +-- tests/testthat/test-setAs.R | 44 +- tests/testthat/test-set_size.R | 112 +++--- tests/testthat/test-sets.R | 30 - tests/testthat/test-size.R | 32 - tests/testthat/test-subtract.R | 44 +- tests/testthat/test-tidy.R | 86 ++--- tests/testthat/test-tidyset.R | 440 +++++++++++++-------------- tests/testthat/test-union.R | 218 ++++++------- tests/testthat/test-union_closed.R | 21 - vignettes/BaseSet.Rmd | 78 ++-- vignettes/advanced.Rmd | 266 ++++++++-------- vignettes/fuzzy.Rmd | 100 +++--- 174 files changed, 6928 insertions(+), 6696 deletions(-)
Title: Modified and Fully Modified Hodrick-Prescott Filters
Description: Decomposes macroeconomic time series into trend and cycle with
the Hodrick-Prescott (HP) filter and two data-driven versions of it. The
modified HP filter of McDermott (1997), assessed by Choudhary, Hanif and
Iqbal (2014) <doi:10.1080/00036846.2014.894631>, chooses the smoothing
parameter of every series by generalised cross-validation (as described
in Coe and McDermott (1997) <doi:10.2307/3867497>). The fully modified HP
filter of Hanif, Iqbal and Choudhary (2017, State Bank of Pakistan
Working Paper 88) also reduces the end-point bias of the HP filter: it
raises the smoothing parameter at the first and last observations, with
linear or quadratic weights chosen to minimise the loss of Bloechl (2014,
University of Munich Discussion Paper 2014-1). Every filter is a banded
linear solve, so the searches are fast; batch processing of many series,
comparisons of the filters, the filter weights, gain functions and
end-point loss, simulation of trend-plus-cycle series and the powe [...truncated...]
Author: Muhammad Yaseen [aut, cre, cph] ,
Javed Iqbal [ctb] ,
M. Nadim Hanif [ctb, cph] ,
M. Ali Choudhary [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between mhpfilter versions 0.1.0 dated 2026-02-13 and 1.0.0 dated 2026-11-09
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Title: Divisia Monetary Aggregates Index
Description: Builds monetary aggregates from their components by the methods
of index number theory. The Divisia index of Barnett (1980)
<doi:10.1016/0304-4076(80)90070-6> weights every component (currency,
demand deposits, savings and time deposits, ...) by its share in the
expenditure on monetary services, priced by its user cost (Barnett 1978)
<doi:10.1016/0165-1765(78)90051-4>. Also gives the Fisher ideal index, a
variant with simple growth rates, the simple-sum aggregate, the currency
equivalent index of Rotemberg, Driscoll and Poterba (1995), the dual
user-cost price index and the Divisia second moments of Barnett and
Serletis (1990) <doi:10.1016/0304-4076(90)90104-2>; benchmark rates
given or taken from the components (upper envelope); 'ggplot2'
graphics, a plain-language interpretation of every result and a built-in
'shiny' application.
Author: Muhammad Yaseen [aut, cre, cph] ,
Ahmad Nadeem [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between dmai versions 0.5.0 dated 2024-03-23 and 1.0.0 dated 2026-11-09
dmai-0.5.0/dmai/R/dmaiIntro-package.R |only dmai-0.5.0/dmai/man/dmaiIntro.Rd |only dmai-1.0.0/dmai/DESCRIPTION | 52 ++-- dmai-1.0.0/dmai/MD5 | 107 +++++++- dmai-1.0.0/dmai/NAMESPACE | 46 ++- dmai-1.0.0/dmai/NEWS.md | 91 ++++++- dmai-1.0.0/dmai/R/analyses.R |only dmai-1.0.0/dmai/R/app.R |only dmai-1.0.0/dmai/R/common-notation.R |only dmai-1.0.0/dmai/R/common-objects.R |only dmai-1.0.0/dmai/R/common-plot.R |only dmai-1.0.0/dmai/R/common-reference.R |only dmai-1.0.0/dmai/R/common-validate.R |only dmai-1.0.0/dmai/R/core.R |only dmai-1.0.0/dmai/R/data.R |only dmai-1.0.0/dmai/R/dmai-package.R |only dmai-1.0.0/dmai/R/dmai.R | 355 ++++++++++++++-------------- dmai-1.0.0/dmai/R/interpret.R |only dmai-1.0.0/dmai/R/plots.R |only dmai-1.0.0/dmai/R/references.R |only dmai-1.0.0/dmai/README.md | 183 +++++++++++++- dmai-1.0.0/dmai/build |only dmai-1.0.0/dmai/data |only dmai-1.0.0/dmai/inst |only dmai-1.0.0/dmai/man/autoplot.dmai_result.Rd |only dmai-1.0.0/dmai/man/cpi_ch19.Rd |only dmai-1.0.0/dmai/man/dmai-methods.Rd |only dmai-1.0.0/dmai/man/dmai-package.Rd |only dmai-1.0.0/dmai/man/dmai.Rd | 243 ++++++++++++------- dmai-1.0.0/dmai/man/dmai_app.Rd |only dmai-1.0.0/dmai/man/dmai_cite.Rd |only dmai-1.0.0/dmai/man/dmai_compare.Rd |only dmai-1.0.0/dmai/man/dmai_interpret.Rd |only dmai-1.0.0/dmai/man/dmai_moments.Rd |only dmai-1.0.0/dmai/man/dmai_notation.Rd |only dmai-1.0.0/dmai/man/dmai_reference.Rd |only dmai-1.0.0/dmai/man/dmai_save.Rd |only dmai-1.0.0/dmai/man/dmai_theme.Rd |only dmai-1.0.0/dmai/man/dmai_user_cost.Rd |only dmai-1.0.0/dmai/man/money_sim.Rd |only dmai-1.0.0/dmai/tests |only dmai-1.0.0/dmai/vignettes |only 42 files changed, 754 insertions(+), 323 deletions(-)
Title: Boxplots for Directional Data
Description: Functions for drawing boxplots for data on (the boundary of) a unit circle (i.e., circular and axial data), from Buttarazzi D., Pandolfo G., Porzio G.C. (2018) <doi:10.1111/biom.12889>. The package allows producing also circular violin plots, and includes methods to calculate robust measures of dispersion for circular data.
Author: Davide Buttarazzi [aut, cre]
Maintainer: Davide Buttarazzi <davidebuttarazzi90@gmail.com>
Diff between bpDir versions 0.1.2 dated 2021-04-08 and 0.2.6 dated 2026-11-09
DESCRIPTION | 18 MD5 | 52 + NAMESPACE | 60 + R/AxialBoxplot.R | 1598 ++++++++++++++++++------------------- R/CircMAD.R |only R/CircularBoxplot.R | 1233 ++++++++++++++-------------- R/CircularLMS.R |only R/CircularLTS.R |only R/CircularMAD.R |only R/CircularTukeyDepth.R | 106 +- R/CircularViolinPlot.R |only R/EstimateKappa.R |only R/EstimateKappaKo.R |only R/EstimateSigma.R |only R/add_geom.R |only R/angular_distance.R |only R/arc_ribbon_df.R |only R/as_circular_rad.R |only R/build_geom.R |only R/compute_SF_VM.R |only R/compute_SF_WN.R |only R/generate_results_grid_sigma.R |only R/generate_vonmises_grid.R |only R/global.R |only R/make_beans.R |only R/make_notch_cutout_df.R |only R/make_region_polygons.R |only R/pol2cart_circle.R |only R/to_plot_coords.R |only data |only man/AxialBoxplot.Rd | 188 ++-- man/CircularBoxplot.Rd | 194 ++-- man/CircularLMS.Rd |only man/CircularLTS.Rd |only man/CircularMAD.Rd |only man/CircularViolinPlot.Rd |only man/EstimateKappa.Rd |only man/EstimateKappaKo.Rd |only man/EstimateSigma.Rd |only man/Spring.Rd |only man/Summer.Rd |only man/e_healthy.Rd |only man/e_parkinson.Rd |only man/generate_results_grid_sigma.Rd |only man/generate_vonmises_grid.Rd |only 45 files changed, 1775 insertions(+), 1674 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
obtained in the 1990s by the research group around Cornelia Dowling
through querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 3.0-0 dated 2026-09-01 and 3.0-1 dated 2026-11-09
Changelog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/kmassessbayesian.R | 9 +++++---- R/kmassessmultiplicative.R | 9 +++++---- R/kmsrvalidate.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 5 ++--- 9 files changed, 34 insertions(+), 28 deletions(-)
Title: Tidy Tools for Actuarial Mathematics and Life Contingencies
Description: Provides tidyverse-aligned tools for actuarial mathematics
and life contingencies, including life tables, survival probabilities,
actuarial present values of cash flows, life annuities, life insurance,
premiums, reserves, multiple-life calculations, Monte Carlo simulation,
collective risk models, insurance coverage, tail risk measures, and
deterministic cash-flow diagrams. The package emphasizes clear
actuarial notation, reproducible workflows, and pipe-friendly tools for
actuarial education and applied actuarial analysis.
Author: Julian Fajardo [aut, cre]
Maintainer: Julian Fajardo <julian.fajardo1908@gmail.com>
Diff between tidyactuarial versions 0.2.0 dated 2026-10-25 and 0.2.1 dated 2026-11-08
DESCRIPTION | 8 MD5 | 349 - NAMESPACE | 238 NEWS.md | 23 R/a_angle.R | 816 +-- R/accumulation_factor.R | 984 ++-- R/aggregate-distribution.R | 4476 +++++++++--------- R/aggregate-moments.R | 1646 +++--- R/amort_schedule.R | 832 +-- R/amort_schedule_general.R | 1016 ++-- R/annuity_arith.R | 804 +-- R/annuity_geom.R | 930 +-- R/annuity_multi.R | 511 +- R/annuity_x.R | 1538 +++--- R/annuity_xy.R | 1490 +++--- R/bond_book_value.R | 942 +-- R/bond_callable_price.R | 732 +- R/bond_cash_flow.R | 294 - R/bond_convexity.R | 388 - R/bond_duration.R | 430 - R/bond_price.R | 274 - R/bond_ytm.R | 466 - R/collective-risk-spec.R | 876 +-- R/contract_components.R | 626 +- R/convexity_cash_flow.R | 596 +- R/data-mortality-regions.R |only R/data-pet-lifetables.R |only R/discount_factor.R | 302 - R/discount_factor_spot.R | 362 - R/discretize-severity.R | 2408 ++++----- R/distribution-convolution.R | 1274 ++--- R/distribution_moments.R | 804 +-- R/duration_cash_flow.R | 554 +- R/e_xy.R | 524 +- R/empirical-severity.R | 558 +- R/future_value.R | 418 - R/fv_flow.R | 518 +- R/inmunize_duration.R | 612 +- R/inmunize_duration_convexity.R | 658 +- R/insurance_variable_k.R | 818 +-- R/insurance_x.R | 1384 ++--- R/insurance_xj.R | 706 +- R/insurance_xy.R | 1182 ++-- R/interest_equivalents.R | 276 - R/irr_flow.R | 500 +- R/irr_flow_multi.R | 754 +-- R/life_contract.R | 646 +- R/mc-utils.R | 992 ++-- R/mc_annuity.R | 1826 +++---- R/mc_insurance.R | 1286 ++--- R/mc_loss.R | 1094 ++-- R/mc_multilife_status.R | 684 +- R/mc_premium.R | 1240 ++--- R/mc_reserve.R | 2568 +++++----- R/plot_inmunization_gap.R | 516 +- R/portfolio_convexity.R | 844 +-- R/portfolio_duration.R | 846 +-- R/premium_gross.R | 1128 ++-- R/premium_x.R | 1656 +++--- R/premium_xy.R | 1640 +++--- R/present_value.R | 422 - R/pv_flow.R | 444 - R/reserve_x.R | 2034 ++++---- R/reserve_xy.R | 1230 ++--- R/s_angle.R | 692 +- R/simulate_life_mc.R | 2478 +++++----- R/simulate_lifetimes.R | 924 +-- R/sinking_fund_schedule.R | 666 +- R/solve_value_v3.R | 1444 ++--- R/standardize_interest.R | 556 +- R/t_pxy.R | 382 - R/to_payment_basis.R | 838 +-- R/value_at_risk.R | 82 README.md | 77 build/vignette.rds |binary data/mortality_regions.rda |only data/pet_lifetables.rda |only inst/COPYRIGHTS |only inst/doc/working-with-datasets.R |only inst/doc/working-with-datasets.Rmd |only inst/doc/working-with-datasets.html |only man/a_angle.Rd | 350 - man/accumulation_factor.Rd | 348 - man/add_insurance.Rd | 150 man/add_premium_schedule.Rd | 138 man/amort_schedule.Rd | 352 - man/amort_schedule_general.Rd | 374 - man/annuity_arith.Rd | 322 - man/annuity_geom.Rd | 386 - man/annuity_multi.Rd | 371 - man/annuity_x.Rd | 482 - man/annuity_xy.Rd | 458 - man/apv_life_flow.Rd | 276 - man/bond_book_value.Rd | 360 - man/bond_callable_price.Rd | 382 - man/bond_cash_flows.Rd | 112 man/bond_convexity.Rd | 300 - man/bond_duration.Rd | 322 - man/bond_price.Rd | 276 - man/bond_ytm.Rd | 262 - man/bonds_sample.Rd | 144 man/cash_flows_sample.Rd | 140 man/commutation_table.Rd | 160 man/convexity_cash_flow.Rd | 254 - man/discount_factor.Rd | 352 - man/discount_factor_spot.Rd | 218 man/dot-mc_annuity_payment_times_annual.Rd | 56 man/dot-mc_annuity_payment_times_fractional.Rd | 76 man/dot-mc_assert_character_scalar.Rd | 40 man/dot-mc_assert_column.Rd | 44 man/dot-mc_assert_numeric_column.Rd | 44 man/dot-mc_assert_numeric_scalar.Rd | 76 man/dot-mc_assert_positive_integer.Rd | 40 man/dot-mc_discount_factor.Rd | 72 man/dot-mc_effective_rate.Rd | 96 man/dot-mc_payment_times.Rd | 46 man/duration_cash_flow.Rd | 230 man/e_x.Rd | 170 man/e_xy.Rd | 63 man/forward_rate.Rd | 356 - man/future_value.Rd | 234 man/fv_flow.Rd | 316 - man/immunize_duration.Rd | 310 - man/immunize_duration_convexity.Rd | 334 - man/insurance_variable_k.Rd | 430 - man/insurance_x.Rd | 402 - man/insurance_xj.Rd | 340 - man/insurance_xy.Rd | 418 - man/interest_equivalents.Rd | 192 man/irr_flow.Rd | 256 - man/irr_flow_multi.Rd | 284 - man/life_contract.Rd | 258 - man/loans_sample.Rd | 140 man/lt_tau.Rd | 82 man/mc_annuity.Rd | 590 +- man/mc_insurance.Rd | 574 +- man/mc_loss.Rd | 366 - man/mc_multilife_status.Rd | 232 man/mc_premium.Rd | 360 - man/mc_reserve.Rd | 486 - man/md_table.Rd | 152 man/mortality_colombia_tables.Rd | 150 man/mortality_law_table.Rd | 454 - man/mortality_regions.Rd |only man/mortality_world_sample_2015_2023.Rd | 120 man/mortality_world_sample_2023.Rd | 116 man/multiple_decrement_sample.Rd | 136 man/pet_lifetables.Rd |only man/plot_cash_flow.Rd | 368 - man/plot_immunization_gap.Rd | 226 man/plot_km.Rd | 172 man/portfolio_convexity.Rd | 290 - man/portfolio_duration.Rd | 292 - man/premium_gross.Rd | 418 - man/premium_x.Rd | 476 - man/premium_xy.Rd | 452 - man/present_value.Rd | 236 man/pv_flow.Rd | 284 - man/reserve_x.Rd | 458 - man/reserve_xy.Rd | 284 - man/s_angle.Rd | 342 - man/simulate_annuity_x.Rd | 286 - man/simulate_insurance_x.Rd | 210 man/simulate_lifetime.Rd | 262 - man/simulate_lifetimes.Rd | 230 man/sinking_fund_schedule.Rd | 300 - man/soa08lt.Rd | 138 man/solve_value.Rd | 412 - man/standardize_interest.Rd | 202 man/summary_mc.Rd | 254 - man/t_Ex.Rd | 290 - man/t_px.Rd | 136 man/t_pxy.Rd | 244 man/t_qxj.Rd | 142 man/yield_curve.Rd | 300 - tests/testthat/test-annuity-multi-status-horizon.R |only tests/testthat/test-e-xy-two-tables.R |only tests/testthat/test-frequency-spec.R | 5162 ++++++++++----------- tests/testthat/test-mc_annuity-v2.R | 432 - tests/testthat/test-mortality-regions.R |only tests/testthat/test-pet-lifetables.R |only tests/testthat/test-simulate_lifetime-v2.R | 654 +- vignettes/working-with-datasets.Rmd |only 183 files changed, 47856 insertions(+), 47658 deletions(-)
Title: Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Description: A wrapper around the LIBLINEAR C/C++ library for machine
learning (available at
<https://www.csie.ntu.edu.tw/~cjlin/liblinear/>). LIBLINEAR is
a simple library for solving large-scale regularized linear
classification and regression. It currently supports
L2-regularized classification (such as logistic regression,
L2-loss linear SVM and L1-loss linear SVM) as well as
L1-regularized classification (such as L2-loss linear SVM and
logistic regression), L2-regularized support vector
regression (with L1- or L2-loss), and one-class support vector
machines for outlier/novelty detection. The main features of
LiblineaR include multi-class classification (one-vs-the rest,
and Crammer & Singer method), cross validation for model
selection, probability estimates (logistic regression only) or
weights for unbalanced data. The estimation of the models is
particularly fast as compared to other libraries.
Author: Thibault Helleputte [cre, aut, cph],
Jerome Paul [aut] ,
Pierre Gramme [aut] ,
Chih-Jen Lin [cph] ; see LICENSE.note)
Maintainer: Thibault Helleputte <thibault.helleputte@dnalytics.com>
Diff between LiblineaR versions 2.50-1 dated 2026-11-08 and 2.50-2 dated 2026-11-08
DESCRIPTION | 8 +- MD5 | 28 ++++--- NEWS | 8 ++ inst/doc/LiblineaR-intro.html | 22 +++--- inst/doc/LiblineaR-validation-benchmark.html | 4 - tests/testthat/helper-golden-portability.R |only tests/testthat/test-golden-portability-policy.R |only tests/testthat/test-train-types-classification.R | 18 ++++ tests/testthat/test-vendor-golden-classification.R | 6 + tests/testthat/test-vendor-golden-classweight-epsilon-bias.R | 36 +++++---- tests/testthat/test-vendor-golden-degenerate.R | 8 +- tests/testthat/test-vendor-golden-dual-cap-stress.R | 36 +++------ tests/testthat/test-vendor-golden-oneclass-svm.R | 16 +++- tests/testthat/test-vendor-golden-predict.R | 40 +++++++---- tests/testthat/test-vendor-golden-svr-paramgrid.R | 11 +-- tests/testthat/test-vendor-golden-type11-epsilon.R | 27 +++---- 16 files changed, 157 insertions(+), 111 deletions(-)
Title: Read Stable Isotope Data Files
Description: Interface to the raw data and metadata stored in the file formats
commonly encountered in scientific disciplines that make use of
stable isotopes. Supports Isodat (.dxf, .cf, .did, .caf, .scn),
IonOS (.iarc), LyticOS (.larc), Callisto (.bch), and Qtegra
(.imexp) file formats. Provides a consistent data structure together
with tools to aggregate, convert signal units, filter, and visualize the
extracted data. The approach is described in Kopf et al. (2021)
<doi:10.21105/joss.02878>.
Author: Sebastian Kopf [aut, cre]
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>
Diff between isoreader2 versions 0.7.0 dated 2026-08-24 and 0.7.1 dated 2026-11-08
DESCRIPTION | 6 +-- MD5 | 42 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 30 ++++++++++++++++++ R/aggregate.R | 59 +++++++++++++++++++++++++++++++++++- R/extract.R | 2 - R/isoreader2-package.R | 13 +++++++ R/metadata.R | 11 ++++-- R/print.R | 23 +++++++++----- R/read_imexp.R | 6 ++- R/read_isodat.R | 62 ++++++++++++++++++++++++++++++++++---- R/read_liarc.R | 26 +++++++++------ R/read_sercon.R | 2 + README.md | 16 ++++----- inst/doc/functionality_guide.html | 56 +++++++++++++++++----------------- man/ir_aggregator.Rd | 11 ++++++ man/ir_check_isoextract.Rd | 2 - man/ir_metadata.Rd | 4 +- tests/testthat/test-aggregate.R | 51 +++++++++++++++++++++++++++++++ tests/testthat/test-metadata.R | 22 +++++++++++++ tests/testthat/test-read_isodat.R | 36 ++++++++++++++++++++++ tests/testthat/test-read_liarc.R | 29 +++++++++++++++++ 22 files changed, 413 insertions(+), 97 deletions(-)
Title: Gaussian Model Invariant by Permutation Symmetry
Description: Find the permutation symmetry group such that the covariance
matrix of the given data is approximately invariant under it.
Discovering such a permutation decreases the number of observations
needed to fit a Gaussian model, which is of great use when it is
smaller than the number of variables. Even if that is not the case,
the covariance matrix found with 'gips' approximates the actual
covariance with less statistical error. The methods implemented in
this package are described in Graczyk et al. (2022)
<doi:10.1214/22-AOS2174>. Documentation about 'gips' is
provided via its website at <https://przechoj.github.io/gips/> and
the paper by Chojecki, Morgen, Kołodziejek
(2025, <doi:10.18637/jss.v112.i07>).
Author: Adam Przemyslaw Chojecki [aut, cre] ,
Pawel Morgen [aut],
Bartosz Kolodziejek [aut]
Maintainer: Adam Przemyslaw Chojecki <adam.prze.choj@gmail.com>
Diff between gips versions 1.3.0 dated 2026-07-26 and 1.3.1 dated 2026-11-08
DESCRIPTION | 16 MD5 | 136 ++-- NAMESPACE | 10 NEWS.md | 42 + R/calculate_gamma_function.R | 2 R/estimate_probabilities.R | 156 ++++- R/find_MAP.R | 387 +++++++++---- R/get_structure_constants.R | 130 ++-- R/gips_constructors.R | 197 +++++- R/gips_methods.R | 430 ++++++++------ R/gips_perm_class.R | 70 +- R/gips_plot.R | 126 ++-- R/log_posteriori_of_gips.R | 75 +- R/prepare_orthogonal_matrix.R | 9 R/project_matrix.R | 97 +-- R/sysdata.rda |binary R/utils.R | 61 -- README.md | 51 + inst/WORDLIST | 13 inst/doc/Optimizers.R | 101 ++- inst/doc/Optimizers.Rmd | 163 +++-- inst/doc/Optimizers.html | 497 +++++++++------- inst/doc/Theory.R | 6 inst/doc/Theory.Rmd | 68 +- inst/doc/Theory.html | 170 +++-- inst/doc/gips.R | 31 - inst/doc/gips.Rmd | 46 + inst/doc/gips.html | 111 +-- man/AIC.gips.Rd | 9 man/as.character.gips.Rd | 6 man/as.character.gips_perm.Rd | 4 man/compare_posteriories_of_perms.Rd | 4 man/figures/README-example_mean_known1_1-1.png |binary man/figures/README-example_mean_known3_1-1.png |binary man/figures/README-example_mean_known6-1.png |binary man/figures/README-example_mean_unknown2-1.png |binary man/figures/README-example_mean_unknown4-1.png |binary man/find_MAP.Rd | 59 + man/forget_perms.Rd | 2 man/get_probabilities_from_gips.Rd | 22 man/get_structure_constants.Rd | 2 man/gips.Rd | 63 +- man/gips_perm.Rd | 4 man/logLik.gips.Rd | 44 - man/log_posteriori_of_gips.Rd | 21 man/plot.gips.Rd | 31 - man/prepare_orthogonal_matrix.Rd | 6 man/print.gips.Rd | 14 man/project_matrix.Rd | 95 +-- man/summary.gips.Rd | 79 +- src/project_matrix.cpp | 4 tests/spelling.R | 10 tests/testthat/Rplots.pdf |only tests/testthat/test-estimate_probabilities.R | 272 ++++++++- tests/testthat/test-find_MAP.R | 714 +++++++++++++++++++++++- tests/testthat/test-get_structure_constants.R | 100 +++ tests/testthat/test-gips_class.R | 285 ++++++++- tests/testthat/test-gips_mult.R | 65 ++ tests/testthat/test-gips_perm_class.R | 94 +++ tests/testthat/test-gips_plot.R | 195 ++++++ tests/testthat/test-input_validation.R |only tests/testthat/test-log_posteriori_of_gips.R | 137 ++++ tests/testthat/test-posterior-probabilities.R |only tests/testthat/test-prepare_orthogonal_matrix.R | 16 tests/testthat/test-probabilities-api.R |only tests/testthat/test-probabilities-history.R |only tests/testthat/test-probabilities-legacy.R |only tests/testthat/test-project_matrix.R | 48 + tests/testthat/test-utils.R | 69 +- vignettes/Optimizers.Rmd | 163 +++-- vignettes/Theory.Rmd | 68 +- vignettes/gips.Rmd | 46 + 72 files changed, 4431 insertions(+), 1521 deletions(-)
Title: A Unified Toolkit for Feature Selection
Description: Filter, wrapper, and embedded feature-selection methods behind a
consistent set of functions that share one calling convention and one
return type: univariate threshold filters, correlation and chi-squared
filters, information gain, the least absolute shrinkage and selection
operator (LASSO) and elastic net, Bayesian model comparison, Boruta,
recursive feature elimination, random forest importance, multivariate
adaptive regression splines, support vector machine recursive feature
elimination, stepwise selection, and principal component / singular
value decomposition helpers. The implemented methods follow
Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>,
Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>,
Friedman (1991) <doi:10.1214/aos/1176347963>,
Breiman (2001) <doi:10.1023/A:1010933404324>,
Guyon, Weston, Barnhill and Vapnik (2002) <doi:10.1023/A:1012487302797>,
Kursa and Rudnicki (2010) <doi:10.18637/jss.v036.i11>, and
Vehta [...truncated...]
Author: Justin Chase [aut, cre, cph]
Maintainer: Justin Chase <jchase.msu@gmail.com>
Diff between featR versions 0.1.0 dated 2026-09-14 and 0.2.0 dated 2026-11-08
DESCRIPTION | 24 MD5 | 139 ++-- NAMESPACE | 28 NEWS.md | 255 +++++++- R/featR-package.R | 168 ++--- R/fs-result.R | 221 +++++-- R/fs_bayes.R | 572 +++++++++++++----- R/fs_boruta.R | 194 +++--- R/fs_chi.R | 260 +++++--- R/fs_correlation.R | 271 ++++---- R/fs_elastic.R | 469 +++++++++++---- R/fs_infogain.R | 275 +++++--- R/fs_lasso.R | 461 +++++++++----- R/fs_mars.R | 437 ++++++++++---- R/fs_pca.R | 229 ++++--- R/fs_randomforest.R | 700 +++++++++++++++------- R/fs_recursivefeature.R | 835 ++++++++++++++++++++------ R/fs_stepwise.R | 270 ++++++-- R/fs_supervised.R | 309 +++++---- R/fs_svd.R | 194 +++--- R/fs_svm.R | 928 +++++++++++++++++++----------- R/fs_unsupervised.R | 189 ++---- R/utils-checks.R | 141 ++++ R/utils-data.R | 68 ++ R/utils-parallel.R | 76 ++ R/utils-seed.R | 10 R/utils-split.R | 6 README.md | 133 ++-- inst/WORDLIST | 87 +- inst/doc/featR.R | 43 - inst/doc/featR.Rmd | 241 +++---- inst/doc/featR.html | 365 +++++------ man/featR-package.Rd | 184 +++-- man/fs_bayes.Rd | 289 +++++---- man/fs_boruta.Rd | 164 +++-- man/fs_chi.Rd | 218 ++++--- man/fs_correlation.Rd | 252 ++++---- man/fs_elastic.Rd | 250 +++++--- man/fs_infogain.Rd | 213 ++++-- man/fs_lasso.Rd | 247 ++++--- man/fs_mars.Rd | 249 ++++---- man/fs_pca.Rd | 165 ++--- man/fs_randomforest.Rd | 434 ++++++++------ man/fs_recursivefeature.Rd | 344 +++++++---- man/fs_stepwise.Rd | 165 +++-- man/fs_supervised.Rd | 206 +++--- man/fs_svd.Rd | 154 ++-- man/fs_svm.Rd | 407 ++++++++----- man/fs_unsupervised.Rd | 197 +++--- man/print.fs_result.Rd | 26 man/selected.Rd | 12 man/summary.fs_result.Rd | 64 +- tests/testthat/test-fs-result.R |only tests/testthat/test-fs_bayes.R | 362 +++++++++++ tests/testthat/test-fs_boruta.R | 50 + tests/testthat/test-fs_chi.R | 131 ++++ tests/testthat/test-fs_correlation.R | 31 + tests/testthat/test-fs_elastic.R | 286 +++++++++ tests/testthat/test-fs_infogain.R | 114 +++ tests/testthat/test-fs_lasso.R | 203 ++++++ tests/testthat/test-fs_mars.R | 277 ++++++++ tests/testthat/test-fs_pca.R | 67 ++ tests/testthat/test-fs_randomforest.R | 386 ++++++++++++ tests/testthat/test-fs_recursivefeature.R | 561 +++++++++++++++++- tests/testthat/test-fs_stepwise.R | 110 +++ tests/testthat/test-fs_supervised.R | 117 +++ tests/testthat/test-fs_svd.R | 53 + tests/testthat/test-fs_svm.R | 461 ++++++++++++++ tests/testthat/test-fs_unsupervised.R | 9 tests/testthat/test-utils.R | 196 ++++++ vignettes/featR.Rmd | 241 +++---- 71 files changed, 11820 insertions(+), 4673 deletions(-)
Title: Detection and Attribution Analysis of Climate Change
Description: Detection and attribution analysis of climate change using errors-in-variables
regression. Implements the polynomial shrinkage framework under variance
heterogeneity proposed by Li and Li (2026)
<doi:10.48550/arXiv.2608.12496> and the latent factor framework proposed
by Li and Li (2026) <doi:10.48550/arXiv.2609.13488>. Estimates forcing
scaling factors and variance inflation coefficients for
forced simulations and control runs relative to observations. Selects
polynomial covariance weights or bias-corrected spiked precision weights by
minimizing estimated total asymptotic scaling factor variance, and provides
asymptotic confidence intervals and residual diagnostics. Also retains
earlier total least squares and estimating equation procedures
(Li et al., 2025, <doi:10.1175/JCLI-D-24-0193.1>;
Ma et al., 2023, <doi:10.1175/JCLI-D-22-0681.1>) for comparison and
reproducibility, together with covariance shrinkage estimators.
Author: Haoran Li [aut],
Yan Li [aut, cre],
Kun Chen [aut],
Jun Yan [aut]
Maintainer: Yan Li <yan.4.li@uconn.edu>
Diff between dacc versions 0.0-7 dated 2025-09-16 and 0.1.0 dated 2026-11-08
DESCRIPTION | 39 +- MD5 | 44 ++- NAMESPACE | 58 ++-- R/Covest.R | 528 ++++++++++++++++++++++++---------------- R/data.R | 90 +++--- R/fingerprint-internal.R |only R/fingerprint-latent-internal.R |only R/fingerprint.R | 452 ++++++++++++++++------------------ R/fingerprintLatent.R |only R/fingerprintLegacy.R |only R/fingerprintPoly.R |only R/fingerprintTLS.R | 4 R/fingerprintTS.R | 2 R/fpPrep.R | 402 +++++++++++++++--------------- R/plot.fingerprint.R |only build |only inst/WORDLIST | 6 man/Covest.Rd | 102 +++---- man/fingerprint.Rd | 299 +++++++++++++--------- man/fingerprintLatent.Rd |only man/fingerprintLegacy.Rd |only man/fingerprintPoly.Rd |only man/fpPrep.Rd | 98 +++---- man/globalDat.Rd | 60 ++-- man/plot.fingerprint.Rd |only man/simDat.Rd | 56 ++-- tests |only 27 files changed, 1220 insertions(+), 1020 deletions(-)
Title: Centered Isotonic Regression and Dose-Response Utilities
Description: Isotonic regression (IR) and its improvement: centered isotonic regression (CIR). CIR is recommended in particular with small samples. Also, interval estimates for both, and additional utilities such as plotting dose-response data. For dev version and change history, see GitHub assaforon/cir.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@gmail.com>
Diff between cir versions 2.5.1 dated 2025-02-01 and 2.5.2 dated 2026-11-08
DESCRIPTION | 10 - MD5 | 52 ++--- R/cir.R | 8 R/classes.r | 15 + R/invCIR.r | 4 R/methods.r | 74 ++++--- R/utilities.r | 4 build/vignette.rds |binary inst/doc/BenHamou03.R | 57 +++-- inst/doc/BenHamou03.html | 408 ++++++++++++++++++++++------------------- inst/doc/BenHamou03.rmd | 136 ++++++++----- inst/examples/classExamples.r | 16 + inst/examples/fwdCiExamples.r | 2 inst/examples/invCiExamples.r | 3 inst/examples/shrinkExamples.r | 2 man/DRshrink.Rd | 4 man/DRtrace.Rd | 27 ++ man/cirPAVA.Rd | 4 man/deltaInverse.Rd | 3 man/doseFind.Rd | 2 man/isotInterval.Rd | 2 man/morrisCI.Rd | 2 man/plot.DRtrace.Rd | 50 +++-- man/quickInverse.Rd | 2 man/quickIsotone.Rd | 4 man/wilsonCI.Rd | 2 vignettes/BenHamou03.rmd | 136 ++++++++----- 27 files changed, 594 insertions(+), 435 deletions(-)
Title: Bayesian Prior Elicitation, Diagnostics, and Regulatory
Reporting
Description: A toolkit for constructing, validating, and justifying Bayesian priors
in clinical trial settings. Implements expert elicitation via quantile
matching, the roulette method, and moment matching across six distribution
families, linear and logarithmic expert pooling, meta-analytic-predictive
(MAP) priors derived from historical trials, prior-data conflict
diagnostics including the Box p-value (computed from the exact prior
predictive distribution where one has a closed form), an exploratory
surprisal (S-value) companion to it, surprise index, information
divergence, and Mahalanobis distance, sensitivity analyses with tornado
and influence heatmap plots, sceptical, robust, and power priors, and
automated prior justification reports. Includes a fully modular 'Shiny'
application for interactive use.
Methods based on O'Hagan et al. (2006, ISBN:9780470029886),
Box (1980) <doi:10.2307/2982063>,
Greenland (2023) <doi:10.1111/sjos.12625>,
Oakley and O'Hagan (2010) <https://tonyoha [...truncated...]
Author: Ndoh Penn [aut, cre]
Maintainer: Ndoh Penn <ndohpenn9@gmail.com>
Diff between bayprior versions 0.5.0 dated 2026-10-20 and 0.6.0 dated 2026-11-08
DESCRIPTION | 6 MD5 | 138 +- NAMESPACE | 1 NEWS.md | 284 ++++++ R/aggregation.R | 72 + R/app_server.R | 4 R/app_ui.R | 3 R/conflict_sensitivity.R | 365 +++++-- R/elicitation.R | 5 R/export_script.R |only R/globals.R | 2 R/likelihood_helpers.R |only R/map_prior.R | 92 + R/methods.R | 4 R/mod_conflict.R | 48 - R/mod_map_prior.R | 17 R/mod_pooling.R | 8 R/mod_report.R | 237 +++-- R/mod_robust_priors.R | 105 +- R/mod_roulette.R | 3 R/mod_sensitivity.R | 286 ++++-- R/mod_session.R |only R/mod_welcome.R | 4 R/plotting.R | 120 ++ R/prior_distribution.R |only R/prior_report.R | 23 R/robust_priors.R | 277 ++--- R/sensitivity_design.R |only R/session_io.R |only R/validation_utils.R | 108 +- R/zzz_patches.R | 5 README.md | 2 inst/WORDLIST | 5 inst/app/www/bp-live.css | 2 inst/app/www/bp-live.html | 24 inst/app/www/custom.css | 78 + inst/doc/bayprior-introduction.html | 16 inst/doc/conflict-diagnostics.R | 20 inst/doc/conflict-diagnostics.Rmd | 47 - inst/doc/conflict-diagnostics.html | 84 + inst/doc/prior-elicitation.html | 6 inst/doc/regulatory-reporting.html | 4 inst/doc/robust-priors.R | 13 inst/doc/robust-priors.Rmd | 44 inst/doc/robust-priors.html | 466 +++++----- inst/doc/sensitivity-analysis.R | 20 inst/doc/sensitivity-analysis.Rmd | 54 + inst/doc/sensitivity-analysis.html | 85 + inst/doc/using-with-rstanarm-brms.html | 12 inst/quarto/templates/prior_report/prior_report.qmd | 161 +++ man/aggregate_experts.Rd | 15 man/calibrate_power_prior.Rd | 23 man/map_prior.Rd | 32 man/prior_conflict.Rd | 28 man/robust_prior.Rd | 31 man/sensitivity_cri.Rd | 7 man/sensitivity_grid.Rd | 12 tests/testthat/_snaps/plots-snapshots/plot-bayprior-mixture-linear.svg | 4 tests/testthat/_snaps/plots-snapshots/plot-power-prior-calib.svg | 24 tests/testthat/_snaps/plots-snapshots/plot-robust-prior.svg | 59 - tests/testthat/_snaps/plots-snapshots/plot-sensitivity-heatmap.svg | 32 tests/testthat/test-aggregation.R | 42 tests/testthat/test-conflict.R | 181 +++ tests/testthat/test-export-script.R |only tests/testthat/test-likelihood-helpers.R |only tests/testthat/test-map-prior.R | 41 tests/testthat/test-plots-snapshots.R | 4 tests/testthat/test-robust.R | 46 tests/testthat/test-sensitivity-design.R |only tests/testthat/test-sensitivity.R | 111 +- tests/testthat/test-session-io.R |only tests/testthat/test-validation.R | 56 - vignettes/conflict-diagnostics.Rmd | 47 - vignettes/robust-priors.Rmd | 44 vignettes/sensitivity-analysis.Rmd | 54 + 75 files changed, 3058 insertions(+), 1195 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb] ,
Wendie Yang [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.3.7 dated 2026-09-03 and 0.3.8 dated 2026-11-08
DESCRIPTION | 17 MD5 | 138 +++-- NEWS.md | 60 ++ R/cond_indirect.R | 5 R/do_mc.R | 43 + R/get_indirect_effect.R | 29 + R/index_mome.R | 170 +++++- R/lavaan_helpers.R | 16 R/lm_helpers.R | 27 + R/mc2est_lavaan.R | 20 R/mc2est_lm.R |only R/mod_levels.R | 3 R/plot_effect_vs_w.R | 127 ++++- R/print_cond_indirect_effect.R | 25 R/pseudo_jn.r | 41 + R/q_auxiliary_helpers.R |only R/q_functions_helpers_lavaan.R | 18 R/q_functions_interface.R |only R/q_mediation.R | 141 +++++ README.md | 79 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/do_boot.Rmd | 4 inst/doc/do_boot.html | 6 inst/doc/do_mc.Rmd | 4 inst/doc/do_mc.html | 6 inst/doc/do_mc_lavaan_mi.Rmd | 21 inst/doc/do_mc_lavaan_mi.html | 303 ++++++------ inst/doc/manymome.Rmd | 18 inst/doc/manymome.html | 124 ++-- inst/doc/med_lav.Rmd | 2 inst/doc/med_lav.html | 4 inst/doc/med_lm.Rmd | 2 inst/doc/med_lm.html | 4 inst/doc/mod_levels.html | 6 inst/doc/mome_lm.Rmd | 7 inst/doc/mome_lm.html | 83 +-- man/index_of_mome.Rd | 56 +- man/manymome-package.Rd | 1 man/plot_effect_vs_w.Rd | 46 + man/pseudo_johnson_neyman.Rd | 37 + man/q_mediation.Rd | 97 +++ tests/testthat/test_compare_boot_mc_lm.R |only tests/testthat/test_cond_indirect_effects_lm_mc.R |only tests/testthat/test_cond_indirect_lm_mc.R |only tests/testthat/test_do_mc_lm.R |only tests/testthat/test_gen_mc_est_lm.R |only tests/testthat/test_get_vcov_lm.R |only tests/testthat/test_index_mome_n_prods.R |only tests/testthat/test_index_mome_q_fct.R |only tests/testthat/test_jn_fill_wlevels.R |only tests/testthat/test_jn_q_fct.R |only tests/testthat/test_jn_q_fct_fill_wlevels.R |only tests/testthat/test_mc2est_lm.R |only tests/testthat/test_mod_only_plot_vs_w.R | 5 tests/testthat/test_plot_indirect_vs_w.R | 2 tests/testthat/test_q_auxiliary_minimal.R |only vignettes/articles/med_mg.Rmd | 14 vignettes/articles/mo_lm.Rmd | 15 vignettes/articles/mo_lm_2x1w.Rmd | 10 vignettes/articles/mo_lm_2x2w.Rmd | 10 vignettes/articles/mo_lm_cat_2w.Rmd | 19 vignettes/articles/mo_lm_cat_num_2w.Rmd | 11 vignettes/articles/mo_sam.Rmd | 8 vignettes/articles/mome_sam.Rmd | 34 - vignettes/articles/q_mediation.Rmd | 14 vignettes/articles/q_mediation_sem_indicators_arbitrary.Rmd | 2 vignettes/articles/q_mediation_sem_indicators_parallel.Rmd | 2 vignettes/articles/q_mediation_sem_indicators_serial.Rmd | 2 vignettes/articles/q_mediation_sem_indicators_simple.Rmd | 2 vignettes/do_boot.Rmd | 4 vignettes/do_mc.Rmd | 4 vignettes/do_mc_lavaan_mi.Rmd | 21 vignettes/manymome.Rmd | 18 vignettes/manymome.Rmd.original | 10 vignettes/med_lav.Rmd | 2 vignettes/med_lm.Rmd | 2 vignettes/mome_lm.Rmd | 7 78 files changed, 1460 insertions(+), 548 deletions(-)
Title: Joint Quantile and Expected Shortfall Regression
Description: Simultaneous modeling of the quantile and the expected shortfall of a response variable given
a set of covariates, see Dimitriadis and Bayer (2019) <doi:10.1214/19-EJS1560>.
Author: Sebastian Bayer [aut, cre],
Timo Dimitriadis [aut]
Maintainer: Sebastian Bayer <sebastian.bayer@famba.org>
Diff between esreg versions 0.6.2 dated 2023-05-13 and 0.6.3 dated 2026-11-08
DESCRIPTION | 18 ++++++++++-------- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 15 ++++++--------- src/target_functions.cpp | 2 +- 5 files changed, 24 insertions(+), 22 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 26.0.0 dated 2026-10-24 and 26.0.1 dated 2026-11-08
arrow-26.0.0/arrow/tools/checksums/r-libarrow-darwin-arm64-26.0.0.zip.sha512 |only arrow-26.0.0/arrow/tools/checksums/r-libarrow-darwin-x86_64-26.0.0.zip.sha512 |only arrow-26.0.0/arrow/tools/checksums/r-libarrow-linux-arm64-26.0.0.zip.sha512 |only arrow-26.0.0/arrow/tools/checksums/r-libarrow-linux-x86_64-26.0.0.zip.sha512 |only arrow-26.0.0/arrow/tools/checksums/r-libarrow-windows-x86_64-26.0.0.zip.sha512 |only arrow-26.0.0/arrow/tools/cpp/cmake_modules/thrift-3187.patch |only arrow-26.0.1/arrow/DESCRIPTION | 8 arrow-26.0.1/arrow/MD5 | 56 ++-- arrow-26.0.1/arrow/NEWS.md | 2 arrow-26.0.1/arrow/README.md | 1 arrow-26.0.1/arrow/configure.win | 3 arrow-26.0.1/arrow/tools/checksums/r-libarrow-darwin-arm64-26.0.1.zip.sha512 |only arrow-26.0.1/arrow/tools/checksums/r-libarrow-darwin-x86_64-26.0.1.zip.sha512 |only arrow-26.0.1/arrow/tools/checksums/r-libarrow-linux-arm64-26.0.1.zip.sha512 |only arrow-26.0.1/arrow/tools/checksums/r-libarrow-linux-x86_64-26.0.1.zip.sha512 |only arrow-26.0.1/arrow/tools/checksums/r-libarrow-windows-x86_64-26.0.1.zip.sha512 |only arrow-26.0.1/arrow/tools/cpp/CMakeLists.txt | 2 arrow-26.0.1/arrow/tools/cpp/CMakeLists.txt-e |only arrow-26.0.1/arrow/tools/cpp/cmake_modules/SetupCxxFlags.cmake | 18 - arrow-26.0.1/arrow/tools/cpp/cmake_modules/ThirdpartyToolchain.cmake | 85 +----- arrow-26.0.1/arrow/tools/cpp/meson.build | 2 arrow-26.0.1/arrow/tools/cpp/src/arrow/compute/kernels/vector_selection.cc | 6 arrow-26.0.1/arrow/tools/cpp/src/arrow/ipc/reader.cc | 15 + arrow-26.0.1/arrow/tools/cpp/src/parquet/arrow/reader_writer_benchmark.cc | 42 +++ arrow-26.0.1/arrow/tools/cpp/src/parquet/chunker_internal.cc | 140 ++++++---- arrow-26.0.1/arrow/tools/cpp/src/parquet/chunker_internal.h | 9 arrow-26.0.1/arrow/tools/cpp/src/parquet/column_writer.cc | 69 ++-- arrow-26.0.1/arrow/tools/cpp/src/parquet/column_writer.h | 14 + arrow-26.0.1/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.cc | 4 arrow-26.0.1/arrow/tools/cpp/src/parquet/file_writer.cc | 36 +- arrow-26.0.1/arrow/tools/cpp/src/parquet/metadata.cc | 26 - arrow-26.0.1/arrow/tools/cpp/src/parquet/thrift_internal.h | 2 arrow-26.0.1/arrow/tools/cpp/thirdparty/versions.txt | 8 arrow-26.0.1/arrow/tools/cpp/vcpkg.json | 4 arrow-26.0.1/arrow/tools/dotenv | 2 35 files changed, 328 insertions(+), 226 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.6 dated 2026-08-28 and 0.3.7 dated 2026-11-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 1 - NEWS.md | 15 ++++++--------- R/BOW.R | 31 +++++++++++++++++++++++-------- R/prediction.R | 4 +++- inst/WORDLIST | 2 ++ man/predict_sentiment.Rd | 4 +++- 8 files changed, 47 insertions(+), 30 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: R Wrapper for the 'funz-fz' Parametric Simulation Framework
Description: Provides R bindings to the 'funz-fz' Python package using
'reticulate'. The 'fz' framework wraps arbitrary simulation codes to run
parameter sweeps, design-of-experiments studies, and iterative
algorithm-driven analyses by substituting variable placeholders in text
input files and collecting outputs into data frames. Calculators can run
locally (shell), over SSH, or on 'SLURM' clusters.
See <https://github.com/Funz/fz> for the underlying framework.
Author: Yann Richet [aut, cre]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between fz versions 1.2.0 dated 2026-09-04 and 2.0.0 dated 2026-11-08
DESCRIPTION | 10 ++-- MD5 | 22 +++++---- NEWS.md | 52 +++++++++++++++++++++ R/core-functions.R | 26 +++++++--- R/install.R | 24 ++++++++-- R/zzz.R | 90 +++++++++++++++++++++++++++++++++++++- README.md | 2 man/fz_available.Rd | 13 +++++ man/fz_install.Rd | 12 +++-- man/fzd.Rd | 12 +++-- man/fzr.Rd | 14 +++-- tests/testthat/test-funz-fz-2.R |only tests/testthat/test-python-sync.R |only 13 files changed, 236 insertions(+), 41 deletions(-)
Title: Data-Derived Graph Construction Utilities
Description: Constructs data-derived graphs from numerical observations using
mutual, shared-neighbor, intersection, geodesic, radius, adaptive-radius,
minimum-spanning-tree completion, Fermat-distance, and optional iterated
adaptive neighborhood methods. Provides graph conversion, pruning,
diagnostics, spectral embedding, endpoint detection, and path utilities,
including intrinsic Euclidean distances on the max-normalized compositional
simplex. Includes reproducible synthetic geometries, point sampling, and an
optional interactive graph explorer. The graph constructions include methods
described by Jarvis and Patrick (1973) <doi:10.1109/T-C.1973.223640>,
Brito et al. (1997)
<doi:10.1016/S0167-7152(96)00213-1>, Berry and Sauer (2019)
<doi:10.3934/fods.2019001>, and Gower and Ross (1969)
<doi:10.2307/2346439>.
Author: Pawel Gajer [aut, cre],
Sunil Arya [ctb] ,
David M. Mount [ctb] ,
University of Maryland [cph] ,
Yixuan Qiu [ctb, cph] ,
Anna Araslanova [ctb, cph] ,
Gael Guennebaud [ctb, cph] ,
Jitse Niesen [ctb, cph] ,
Netherlands eScience Center [ctb, cph] ,
Dani [...truncated...]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between dgraphs versions 0.4.0 dated 2026-11-07 and 0.4.1 dated 2026-11-08
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++----------- NEWS.md | 9 +++++++-- README.md | 17 +++++++++-------- inst/build-provenance.json | 19 ++++++++++--------- inst/doc/fermat-density-curvature.html | 2 +- src/SEXP_cpp_conversion_utils.cpp | 4 +++- src/geodesic_stats_r.cpp | 10 ++++++++-- src/graph_endpoint_geometry_rcpp.cpp | 14 ++++++++------ src/iknn_graphs.cpp | 4 +++- src/mst_completion_graphs_r.cpp | 8 ++++++-- src/set_wgraph.cpp | 16 ++++++++++------ tests/testthat/test-native-empty-vectors.R |only 13 files changed, 80 insertions(+), 52 deletions(-)
Title: Modeling Spatially Varying Coefficients
Description: Implements a maximum likelihood estimation (MLE) method for
estimation and prediction of Gaussian process-based spatially varying
coefficient (SVC) models (Dambon et al. (2021a)
<doi:10.1016/j.spasta.2020.100470>). Covariance tapering (Furrer et
al. (2006) <doi:10.1198/106186006X132178>) can be applied such that
the method scales to large data. Further, it implements a joint
variable selection of the fixed and random effects (Dambon et al.
(2021b) <doi:10.1080/13658816.2022.2097684>). The package and its
capabilities are described in (Dambon et al. (2021c)
<doi:10.48550/arXiv.2106.02364>).
Author: Jakob A. Dambon [aut, cre] ,
Fabio Sigrist [ctb] ,
Reinhard Furrer [ctb]
Maintainer: Jakob A. Dambon <varycoef@dambon.me>
Diff between varycoef versions 0.3.6 dated 2025-05-04 and 0.4.1 dated 2026-11-08
DESCRIPTION | 18 +- MD5 | 40 ++-- NAMESPACE | 15 - NEWS.md |only R/SVC_mle.R | 63 ++++++- R/SVC_selection.R | 225 +++++++++++++++++----------- R/objective_functions.R | 2 R/predict-SVC_mle.R | 74 +++++++-- R/utils.R | 101 ++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.R | 10 - inst/doc/Introduction.html | 140 ++++++++--------- man/SVC_mle.Rd | 13 - man/SVC_mle_control.Rd | 4 man/SVC_selection_control.Rd | 35 ++-- man/predict.SVC_mle.Rd | 11 - tests/testthat/test_SVC_mle.R | 116 ++++++++++++++ tests/testthat/test_SVC_selection.R | 100 +++++++++++- tests/testthat/test_optional_dependencies.R |only tests/testthat/test_predict-SVC_mle.R | 77 ++++++++- tests/testthat/test_utils.R | 37 ++++ 22 files changed, 814 insertions(+), 267 deletions(-)
Title: Truncated Gaussian Regression Models
Description: Estimation of regression models for truncated Gaussian variables by maximum likelihood.
Author: Yves Croissant [aut, cre] ,
Achim Zeileis [aut]
Maintainer: Yves Croissant <y.croissant@univ-lyon2.fr>
Diff between truncreg versions 0.2-5 dated 2018-08-18 and 0.3-0 dated 2026-11-08
truncreg-0.2-5/truncreg/NEWS |only truncreg-0.3-0/truncreg/DESCRIPTION | 33 +++++++++++++++----------------- truncreg-0.3-0/truncreg/MD5 | 11 +++++----- truncreg-0.3-0/truncreg/NAMESPACE | 15 +++++++++----- truncreg-0.3-0/truncreg/NEWS.md |only truncreg-0.3-0/truncreg/R/truncreg.R | 19 ++++++++++++++---- truncreg-0.3-0/truncreg/README.md |only truncreg-0.3-0/truncreg/man/truncreg.Rd | 9 +++++++- 8 files changed, 55 insertions(+), 32 deletions(-)
Title: Supervised Variational Autoencoder Regression via 'reticulate'
Description: Supervised latent-variable regression for high-dimensional predictors
such as soil reflectance spectra. The model uses an encoder-decoder neural
network with a stochastic Gaussian latent representation regularized by a
Kullback-Leibler term, and a supervised prediction head trained jointly with
the reconstruction objective (Kingma and Welling (2014)
<doi:10.48550/arXiv.1312.6114>). Predictors and response are standardised
inside the model, so new data are scaled like the training data. The
implementation interfaces R with a 'Python' deep-learning backend ('Keras'
and 'TensorFlow') and provides utilities for installation, training with
early stopping, tuning, prediction, latent embeddings, and saving models.
Author: Hugo Rodrigues [aut, cre]
Maintainer: Hugo Rodrigues <rodrigues.machado.hugo@gmail.com>
Diff between soilVAE versions 0.1.10 dated 2026-08-22 and 0.2.0 dated 2026-11-08
soilVAE-0.1.10/soilVAE/R/datsoilspc.R |only soilVAE-0.1.10/soilVAE/R/exports.R |only soilVAE-0.1.10/soilVAE/R/tune_vae.R |only soilVAE-0.1.10/soilVAE/data |only soilVAE-0.1.10/soilVAE/inst/COPYRIGHTS |only soilVAE-0.1.10/soilVAE/inst/doc/index.Rmd |only soilVAE-0.1.10/soilVAE/inst/doc/index.html |only soilVAE-0.1.10/soilVAE/man/datsoilspc.Rd |only soilVAE-0.1.10/soilVAE/man/figures/readme-Splits-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-absorbance_plot-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-plotting_splits_VAE-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-pls_cv-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-pls_pred-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-preprocess_plot-1.png |only soilVAE-0.1.10/soilVAE/man/figures/readme-spectrum_plot-1.png |only soilVAE-0.1.10/soilVAE/man/figures/soilVAE-og.png |only soilVAE-0.1.10/soilVAE/vignettes/index.Rmd |only soilVAE-0.1.10/soilVAE/vignettes/references.bib |only soilVAE-0.2.0/soilVAE/DESCRIPTION | 40 soilVAE-0.2.0/soilVAE/LICENSE | 2 soilVAE-0.2.0/soilVAE/MD5 | 92 - soilVAE-0.2.0/soilVAE/NAMESPACE | 5 soilVAE-0.2.0/soilVAE/NEWS.md | 75 soilVAE-0.2.0/soilVAE/R/py_setup.R | 19 soilVAE-0.2.0/soilVAE/R/soilVAE-package.R | 28 soilVAE-0.2.0/soilVAE/R/tune_vae_train_val.R | 70 soilVAE-0.2.0/soilVAE/R/utils-tf.R | 149 + soilVAE-0.2.0/soilVAE/R/vae_build.R | 94 - soilVAE-0.2.0/soilVAE/R/vae_configure.R | 28 soilVAE-0.2.0/soilVAE/R/vae_fit.R | 194 +- soilVAE-0.2.0/soilVAE/R/vae_install.R |only soilVAE-0.2.0/soilVAE/R/vae_predict.R | 101 - soilVAE-0.2.0/soilVAE/R/zzz.R |only soilVAE-0.2.0/soilVAE/README.md | 872 +--------- soilVAE-0.2.0/soilVAE/build/partial.rdb |only soilVAE-0.2.0/soilVAE/build/vignette.rds |binary soilVAE-0.2.0/soilVAE/inst/CITATION | 2 soilVAE-0.2.0/soilVAE/inst/doc/soilVAE-workflow.R | 322 --- soilVAE-0.2.0/soilVAE/inst/doc/soilVAE-workflow.Rmd | 353 +--- soilVAE-0.2.0/soilVAE/inst/doc/soilVAE-workflow.html | 424 +--- soilVAE-0.2.0/soilVAE/inst/python/requirements.txt | 2 soilVAE-0.2.0/soilVAE/inst/python/vae.py | 275 ++- soilVAE-0.2.0/soilVAE/man/figures/Badge_soilVAE_2.png |binary soilVAE-0.2.0/soilVAE/man/figures/readme-scatter-1.png |only soilVAE-0.2.0/soilVAE/man/soilVAE-package.Rd | 38 soilVAE-0.2.0/soilVAE/man/tune_vae_train_val.Rd | 35 soilVAE-0.2.0/soilVAE/man/vae_available.Rd |only soilVAE-0.2.0/soilVAE/man/vae_build.Rd | 57 soilVAE-0.2.0/soilVAE/man/vae_configure.Rd | 22 soilVAE-0.2.0/soilVAE/man/vae_encode.Rd | 22 soilVAE-0.2.0/soilVAE/man/vae_fit.Rd | 76 soilVAE-0.2.0/soilVAE/man/vae_history.Rd |only soilVAE-0.2.0/soilVAE/man/vae_install.Rd |only soilVAE-0.2.0/soilVAE/man/vae_predict.Rd | 27 soilVAE-0.2.0/soilVAE/man/vae_save.Rd |only soilVAE-0.2.0/soilVAE/tests |only soilVAE-0.2.0/soilVAE/vignettes/soilVAE-workflow.Rmd | 353 +--- 57 files changed, 1649 insertions(+), 2128 deletions(-)
Title: Quadratic Root for any Quadratic Equation
Description: It will assist the user to find simple quadratic roots from any quadratic equation.
Author: Pankaj Das [aut, cre]
Maintainer: Pankaj Das <pankaj.iasri@gmail.com>
Diff between QuadRoot versions 0.2.1 dated 2023-09-10 and 0.3.0 dated 2026-11-08
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/QuadRoot.R | 2 +- inst/doc/QuadRoot.html | 1 + 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Post-Translational Modification Enrichment, Integration, and
Matching Analysis
Description: Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2025) <doi:10.1002/pmic.202400238>.
Author: Mohieddin Jafari [aut],
Payman Nickchi [aut, cre]
Maintainer: Payman Nickchi <payman.nickchi@gmail.com>
Diff between PEIMAN2 versions 1.1.0 dated 2026-06-17 and 1.2.0 dated 2026-11-08
DESCRIPTION | 6 MD5 | 32 +- R/data.R | 152 ++++++------ R/database.R | 428 +++++++++++++++++------------------ R/peiman.R | 312 ++++++++++++------------- R/psea2mass.R | 164 ++++++------- R/runEnrichment.R | 212 ++++++++--------- R/runPSEA.R | 2 R/sea2mass.R | 106 ++++---- R/utility.R | 274 +++++++++++----------- README.md | 494 +++++++++++++++++++++++------------------ inst/doc/PEIMAN2-vignette.html | 240 +++++++++---------- man/exmplData2.Rd | 2 man/load_peiman_database.Rd | 70 ++--- man/load_ptmlist.Rd | 70 ++--- man/peiman.Rd | 86 +++---- man/update_peiman_database.Rd | 84 +++--- 17 files changed, 1401 insertions(+), 1333 deletions(-)
Title: Thread-Speed Async and Parallel R over Shared Memory
Description: Parallel computation and data exchange between R processes on
the same machine: lock-free channels, work-stealing task pools, and a
parallel map over 'POSIX' shared memory (Linux, macOS) or 'Win32' file
mappings (Windows), with the hot path entirely in user space.
Communication is cheap enough that work can be divided as finely as
with threads. Vectors and data frames transfer zero-copy, received as
'ALTREP' views over the shared pages, and 'Apache Arrow' tables and
record batches travel as a single frame with zero-copy conversion in
both directions. Receives and task results integrate with 'later' and
'promises' for non-blocking, event-driven applications such as
'shiny'. Channels, pools, and maps interoperate with 'pymizu', so a
peer or worker can equally be a Python process. It complements
'mirai', and its payloads interoperate with 'mori' shared objects.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd],
Pierre L'Ecuyer [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between mizu versions 0.1.0 dated 2026-11-04 and 0.1.1 dated 2026-11-08
DESCRIPTION | 10 ++++----- MD5 | 16 +++++++------- NEWS.md | 39 +++++++++++------------------------ src/arrow.c | 2 - src/codec.c | 2 - src/interop.c | 44 ++++++++++++++++++++-------------------- tests/testthat/helper-interop.R | 11 ++++++++++ tests/testthat/test-interop.R | 18 ++++++++++++++++ tests/testthat/test-map.R | 29 +++----------------------- 9 files changed, 84 insertions(+), 87 deletions(-)
Title: Data Cleaner for Anthropometric Measurements
Description: Flags implausible anthropometric (weight, height, and head circumference) measurements in longitudinal pediatric and adult datasets, such as those from electronic health records. Identifies other measurements that should often be excluded from analyses. The main function is cleangrowth(). Implements a modified version of the algorithm described in Daymont et al. (2017) <doi:10.1093/jamia/ocx037>.
Author: Carrie Daymont [cre, aut, cph],
Robert W Grundmeier [aut],
Jeffrey Miller [aut],
Diego Campos [aut],
Dan Chudnov [aut],
Hannah De los Santos [aut],
David Freedman [aut],
Wen Hu [aut],
Chris Penney [aut],
Jesse Anderson [ctb],
Matt Boyas [ctb],
Lusha [...truncated...]
Maintainer: Carrie Daymont <cdaymont@pennstatehealth.psu.edu>
Diff between growthcleanr versions 2.2.3 dated 2026-05-09 and 3.0.0 dated 2026-11-08
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Title: Graph Drawing with Intelligent Placement (GRIP)
Description: Implements GRIP multiscale graph layout with a unified choice
between hop-count and geometry-aware edge-length graph metrics in 2D and
3D. Provides layout scoring, candidate
comparison, multiscale trace diagnostics, synthetic graph families,
and advanced experimental geodesic-KK utilities for weighted-layout
evaluation and polish. Based on Gajer and Kobourov (2002)
<doi:10.7155/jgaa.00052> and Gajer, Goodrich and Kobourov (2004)
<doi:10.1016/j.comgeo.2004.03.014>. Includes derived graph datasets from
the SuiteSparse Matrix Collection, with source attribution and
transformation metadata.
Author: Pawel Gajer [aut, cre],
Jonathan Zheng [ctb, cph] ,
Daniel Hangan [ctb] ,
The scikit-learn developers [cph]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between grip versions 0.2.0 dated 2026-08-31 and 0.3.0 dated 2026-11-08
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Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'Typst', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint', R 'Grid Graphics' and
'patchwork'. 'R Markdown', 'Quarto' and the package 'officer' can be
used to produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.10.3 dated 2026-10-14 and 0.10.4 dated 2026-11-08
flextable-0.10.3/flextable/man/args_selectors_with_all.Rd |only flextable-0.10.3/flextable/man/args_selectors_without_all.Rd |only flextable-0.10.3/flextable/man/args_x_i_j.Rd |only flextable-0.10.3/flextable/man/args_x_i_part.Rd |only flextable-0.10.3/flextable/man/args_x_i_part_no_all.Rd |only flextable-0.10.3/flextable/man/args_x_j.Rd |only flextable-0.10.3/flextable/man/args_x_j_part.Rd |only flextable-0.10.3/flextable/man/args_x_j_part_no_all.Rd |only flextable-0.10.3/flextable/man/args_x_only.Rd |only flextable-0.10.3/flextable/man/args_x_part.Rd |only flextable-0.10.3/flextable/man/args_x_part_no_all.Rd |only flextable-0.10.4/flextable/DESCRIPTION | 22 - flextable-0.10.4/flextable/MD5 | 116 +++---- flextable-0.10.4/flextable/NAMESPACE | 3 flextable-0.10.4/flextable/NEWS.md | 70 ++++ flextable-0.10.4/flextable/R/05_content.R | 4 flextable-0.10.4/flextable/R/append_chunk.R | 4 flextable-0.10.4/flextable/R/as_flextable_rtables.R | 10 flextable-0.10.4/flextable/R/augment_rows.R | 20 - flextable-0.10.4/flextable/R/border_fix.R | 2 flextable-0.10.4/flextable/R/borders.R | 14 flextable-0.10.4/flextable/R/chunk_images.R | 65 ++-- flextable-0.10.4/flextable/R/compose.R | 4 flextable-0.10.4/flextable/R/defaults.R | 11 flextable-0.10.4/flextable/R/doc-selectors.R | 139 --------- flextable-0.10.4/flextable/R/empty.R | 2 flextable-0.10.4/flextable/R/flextable.R | 2 flextable-0.10.4/flextable/R/flextable_sizes.R | 21 - flextable-0.10.4/flextable/R/footnote.R | 2 flextable-0.10.4/flextable/R/formatters.R | 4 flextable-0.10.4/flextable/R/grid_funs.R | 89 +++-- flextable-0.10.4/flextable/R/grid_grobs.R | 151 +++------- flextable-0.10.4/flextable/R/html_str.R | 6 flextable-0.10.4/flextable/R/image_cache.R |only flextable-0.10.4/flextable/R/latex_chunks.R | 29 + flextable-0.10.4/flextable/R/latex_str.R | 55 +++ flextable-0.10.4/flextable/R/layout_lines.R |only flextable-0.10.4/flextable/R/merge_flextable.R | 10 flextable-0.10.4/flextable/R/nrowcol.R | 4 flextable-0.10.4/flextable/R/paginate.R | 2 flextable-0.10.4/flextable/R/patchwork.R | 74 ++++ flextable-0.10.4/flextable/R/printers.R | 30 - flextable-0.10.4/flextable/R/read_structure.R | 6 flextable-0.10.4/flextable/R/runs_as_functions.R | 61 +++- flextable-0.10.4/flextable/R/splitters.R | 6 flextable-0.10.4/flextable/R/styles.R | 46 +-- flextable-0.10.4/flextable/R/table-properties.R | 22 + flextable-0.10.4/flextable/R/themes.R | 20 - flextable-0.10.4/flextable/R/typst_str.R | 4 flextable-0.10.4/flextable/man/as_equation.Rd | 4 flextable-0.10.4/flextable/man/as_flextable.TableTree.Rd | 6 flextable-0.10.4/flextable/man/as_image.Rd | 40 +- flextable-0.10.4/flextable/man/image_raster.Rd |only flextable-0.10.4/flextable/man/layout_lines.Rd |only flextable-0.10.4/flextable/man/padding.Rd | 12 flextable-0.10.4/flextable/man/set_flextable_defaults.Rd | 8 flextable-0.10.4/flextable/man/set_table_properties.Rd | 4 flextable-0.10.4/flextable/man/wrap_flextable.Rd | 37 ++ flextable-0.10.4/flextable/tests/testthat/test-deterministic-css.R | 11 flextable-0.10.4/flextable/tests/testthat/test-docx-images.R | 22 + flextable-0.10.4/flextable/tests/testthat/test-gen_grob.R | 129 ++++++++ flextable-0.10.4/flextable/tests/testthat/test-image-cache.R |only flextable-0.10.4/flextable/tests/testthat/test-latex.R | 98 ++++++ flextable-0.10.4/flextable/tests/testthat/test-layout-lines.R |only flextable-0.10.4/flextable/tests/testthat/test-patchwork.R | 37 ++ flextable-0.10.4/flextable/tests/testthat/test-rtables.R |only flextable-0.10.4/flextable/tests/testthat/test-text.R | 47 +++ flextable-0.10.4/flextable/tests/testthat/test-typst.R | 3 68 files changed, 1043 insertions(+), 545 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 0.5.0 dated 2026-09-04 and 0.5.1 dated 2026-11-08
DESCRIPTION | 15 MD5 | 450 +++---- NAMESPACE | 3 NEWS.md | 32 R/batch-chat.R | 4 R/chat-structured.R | 21 R/chat-tools.R | 20 R/chat.R | 828 ++++++++----- R/content-image.R | 5 R/content.R | 8 R/ellmer-package.R | 2 R/httr2.R | 7 R/live.R | 8 R/otel.R | 594 ++++++++- R/parallel-chat.R | 18 R/params.R | 6 R/prices.R | 8 R/provider-aws-api.R | 13 R/provider-aws.R | 40 R/provider-azure.R | 3 R/provider-claude.R | 49 R/provider-cloudflare.R | 21 R/provider-databricks.R | 29 R/provider-deepseek.R | 7 R/provider-google-interactions.R |only R/provider-google-tools.R | 4 R/provider-google-upload.R | 12 R/provider-google.R | 225 ++- R/provider-groq.R | 3 R/provider-huggingface.R | 7 R/provider-lmstudio.R | 3 R/provider-mistral.R | 3 R/provider-ollama.R | 3 R/provider-openai-compatible.R | 50 R/provider-openai.R | 59 R/provider-openrouter.R | 205 +++ R/provider-perplexity.R | 3 R/provider-portkey.R | 13 R/provider-posit.R | 55 R/provider-snowflake.R | 4 R/provider-vllm.R | 19 R/provider.R | 79 + R/sysdata.rda |binary R/tokens.R | 9 R/turns.R | 16 R/types.R | 2 R/utils.R | 2 R/zzz.R | 18 README.md | 59 build/vignette.rds |binary inst/_vcr/Chat.yml | 51 inst/_vcr/chat_anthropic.yml | 56 inst/_vcr/chat_openai.yml | 152 +- inst/_vcr/parallel_chat.yml | 504 ++++--- inst/_vcr/tool.yml | 108 - inst/doc/ellmer.R | 2 inst/doc/ellmer.Rmd | 6 inst/doc/ellmer.html | 20 inst/doc/otel.R |only inst/doc/otel.Rmd |only inst/doc/otel.html |only inst/doc/programming.R | 14 inst/doc/programming.Rmd | 16 inst/doc/programming.html | 329 ++--- inst/doc/prompt-design.Rmd | 8 inst/doc/prompt-design.html | 572 ++++---- inst/doc/streaming-async.Rmd | 4 inst/doc/streaming-async.html | 4 inst/doc/structured-data.html | 122 - inst/doc/tool-calling.R | 8 inst/doc/tool-calling.Rmd | 14 inst/doc/tool-calling.html | 82 - man/Content.Rd | 7 man/Turn.Rd | 12 man/Type.Rd | 2 man/batch_chat.Rd | 4 man/chat_anthropic.Rd | 2 man/chat_aws_bedrock.Rd | 12 man/chat_deepseek.Rd | 2 man/chat_google_gemini.Rd | 30 man/chat_huggingface.Rd | 6 man/chat_openai.Rd | 2 man/chat_openai_compatible.Rd | 4 man/chat_openrouter.Rd | 44 man/chat_portkey.Rd | 6 man/chat_posit.Rd | 2 man/chat_snowflake.Rd | 2 man/chat_vllm.Rd | 6 man/content_image_url.Rd | 3 man/google_tool_web_fetch.Rd | 2 man/google_tool_web_search.Rd | 2 man/has_credentials.Rd | 2 man/models_update_prices.Rd | 8 man/parallel_chat.Rd | 11 man/token_usage.Rd | 10 tests/testthat/_snaps/chat-tools-content.md | 11 tests/testthat/_snaps/otel.md |only tests/testthat/_snaps/parallel-chat.md | 11 tests/testthat/_snaps/prices-data.md |only tests/testthat/_snaps/provider-aws.md | 2 tests/testthat/_snaps/provider-azure.md | 4 tests/testthat/_snaps/provider-claude.md | 2 tests/testthat/_snaps/provider-databricks.md | 4 tests/testthat/_snaps/provider-deepseek.md | 2 tests/testthat/_snaps/provider-google-interactions.md |only tests/testthat/_snaps/provider-google-upload.md | 6 tests/testthat/_snaps/provider-google.md | 14 tests/testthat/_snaps/provider-openai.md | 2 tests/testthat/_snaps/provider-openrouter.md | 19 tests/testthat/_snaps/provider-snowflake.md | 2 tests/testthat/_snaps/provider.md | 2 tests/testthat/_snaps/utils-S7.md | 5 tests/testthat/_vcr/anthropic-basic.yml | 36 tests/testthat/_vcr/anthropic-count-tokens.yml | 130 -- tests/testthat/_vcr/anthropic-documents.yml | 33 tests/testthat/_vcr/anthropic-files.yml | 110 - tests/testthat/_vcr/anthropic-images.yml | 110 - tests/testthat/_vcr/anthropic-list-models.yml | 43 tests/testthat/_vcr/anthropic-pdfs.yml | 127 + tests/testthat/_vcr/anthropic-standard-params.yml | 36 tests/testthat/_vcr/anthropic-structured-data.yml | 66 - tests/testthat/_vcr/anthropic-tool-image.yml | 222 +-- tests/testthat/_vcr/anthropic-tool.yml | 149 +- tests/testthat/_vcr/anthropic-upload-file.yml | 172 +- tests/testthat/_vcr/anthropic-web-fetch.yml | 642 +++++----- tests/testthat/_vcr/anthropic-web-search.yml | 246 ++- tests/testthat/_vcr/anthropic-whitespace.yml | 70 - tests/testthat/_vcr/chat-duration.yml | 33 tests/testthat/_vcr/chat-tools-callbacks.yml | 70 - tests/testthat/_vcr/chat-tools-dangling.yml | 156 +- tests/testthat/_vcr/chat-tools-failure.yml | 88 - tests/testthat/_vcr/chat-tools-on-request.yml | 94 - tests/testthat/_vcr/chat-tools-parallel.yml | 133 +- tests/testthat/_vcr/chat-tools-reject-callback.yml | 291 +++- tests/testthat/_vcr/chat-tools-reject-tool-function.yml | 133 +- tests/testthat/_vcr/chat-tools-sequential.yml | 115 - tests/testthat/_vcr/google-count-tokens.yml | 103 - tests/testthat/_vcr/google-files.yml | 231 +-- tests/testthat/_vcr/google-image-gen.yml | 57 tests/testthat/_vcr/google-image.yml | 98 - tests/testthat/_vcr/google-thinking-level.yml | 76 - tests/testthat/_vcr/google-tool.yml | 244 --- tests/testthat/_vcr/google-upload.yml | 211 --- tests/testthat/_vcr/google-web-fetch.yml | 338 ----- tests/testthat/_vcr/google-web-search.yml | 677 ++++++++-- tests/testthat/_vcr/openai-count-tokens.yml | 127 + tests/testthat/_vcr/openai-files.yml | 233 +-- tests/testthat/_vcr/openai-image.yml | 94 - tests/testthat/_vcr/openai-pdf.yml | 145 +- tests/testthat/_vcr/openai-tool.yml | 241 ++- tests/testthat/_vcr/openai-v2-document.yml | 35 tests/testthat/_vcr/openai-v2-image.yml | 136 +- tests/testthat/_vcr/openai-v2-pdf.yml | 121 - tests/testthat/_vcr/openai-v2-service-tier.yml | 65 - tests/testthat/_vcr/openai-v2-tool-image.yml | 186 +- tests/testthat/_vcr/openai-v2-tool.yml | 144 +- tests/testthat/_vcr/openai-v2-web-search.yml | 223 +-- tests/testthat/_vcr/openrouter-list-models.yml |only tests/testthat/_vcr/parallel-basic.yml | 62 tests/testthat/_vcr/parallel-data.yml | 66 - 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vignettes/_vcr/prompt-design-code-explicit.yml | 38 vignettes/_vcr/prompt-design-code-new-feature.yml | 38 vignettes/_vcr/prompt-design-code-r-minimal.yml | 39 vignettes/_vcr/prompt-design-code-r.yml | 76 - vignettes/_vcr/prompt-design-code-styles.yml | 92 - vignettes/_vcr/prompt-design-code-teacher.yml | 71 - vignettes/_vcr/prompt-design-data-examples.yml | 61 vignettes/_vcr/prompt-design-data-loose.yml | 61 vignettes/_vcr/prompt-design-data-structured.yml | 64 - vignettes/_vcr/prompt-design-data-unstructured-input.yml | 61 vignettes/_vcr/structured-data-basics-image.yml | 56 vignettes/_vcr/structured-data-basics-text.yml | 45 vignettes/_vcr/structured-data-dataframe-wrong.yml | 57 vignettes/_vcr/structured-data-dataframe.yml | 59 vignettes/_vcr/structured-data-examples-classification.yml | 57 vignettes/_vcr/structured-data-examples-image.yml | 58 vignettes/_vcr/structured-data-examples-named-entity.yml | 59 vignettes/_vcr/structured-data-examples-sentiment.yml | 60 vignettes/_vcr/structured-data-examples-summarisation.yml | 66 - vignettes/_vcr/structured-data-examples-unknown-keys.yml | 33 vignettes/_vcr/structured-data-parallel-missing-2.yml | 226 +-- vignettes/_vcr/structured-data-parallel-missing.yml | 232 ++- vignettes/_vcr/structured-data-parallel.yml | 293 ++-- vignettes/_vcr/tool-calling-inputs-outputs.yml | 98 - vignettes/_vcr/tool-calling-no-tool.yml | 61 vignettes/_vcr/tool-calling-with-tool.yml | 143 +- vignettes/ellmer.Rmd | 6 vignettes/otel.Rmd |only vignettes/programming.Rmd | 16 vignettes/prompt-design.Rmd | 8 vignettes/streaming-async.Rmd | 4 vignettes/tool-calling.Rmd | 14 232 files changed, 11023 insertions(+), 7347 deletions(-)
Title: Drugs Databases Parser
Description: Parses drug and gene databases from their downloaded files:
the 'DrugBank' XML database <https://go.drugbank.com/>, the 'OnSIDES' and
'TWOSIDES' adverse drug event databases, Human Phenotype Ontology ('HPO')
gene-phenotype associations, the 'HGNC' gene nomenclature files, Health
Canada's Drug Product Database ('DPD') data extract, and the 'openFDA'
'Drugs@FDA' and 'NDC' directory downloads. The parsed
tables are returned in an 'R' object called 'dvobject', which records the
source release, licence and file hashes.
Author: Mohammed Ali [aut, cre],
Ali Ezzat [aut],
Hao Zhu [rev],
Emma Mendelsohn [rev],
Interstellar [cph, fnd]
Maintainer: Mohammed Ali <mohammed.ali@interstellar-egypt.com>
Diff between dbparser versions 2.2.1 dated 2026-01-08 and 2.3.0 dated 2026-11-08
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502 dbparser-2.3.0/dbparser/R/dbparser-package.R | 78 dbparser-2.3.0/dbparser/R/drug_atc_codes_node_parser.R | 108 dbparser-2.3.0/dbparser/R/drug_classfication_node_parser.R | 118 dbparser-2.3.0/dbparser/R/drug_common_utilities.R | 214 dbparser-2.3.0/dbparser/R/drug_main_node_parser.R | 150 dbparser-2.3.0/dbparser/R/drug_manufacturer_node_parser.R | 98 dbparser-2.3.0/dbparser/R/drug_parsers.R | 1120 - dbparser-2.3.0/dbparser/R/drug_pathway_node_parsers.R | 222 dbparser-2.3.0/dbparser/R/drug_pharmacology_parser.R | 172 dbparser-2.3.0/dbparser/R/drug_price_node_parser.R | 92 dbparser-2.3.0/dbparser/R/drug_reaction_node_parser.R | 184 dbparser-2.3.0/dbparser/R/drug_sequence_node_parser.R | 96 dbparser-2.3.0/dbparser/R/drug_synonym_node_parser.R | 90 dbparser-2.3.0/dbparser/R/drugbank_parser.R | 1220 - dbparser-2.3.0/dbparser/R/dvobject_metadata.R | 438 dbparser-2.3.0/dbparser/R/health_canada_dpd_parser.R |only dbparser-2.3.0/dbparser/R/hgnc_parser.R |only 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Title: Join World Bank Data, Country Codes and Maps on the ISO Spine
Description: A complete toolkit for getting country data onto honest maps.
Country names rarely line up across data sources ("US", "U.S.", "United
States", "United States of America" are one country, but a naive join
treats them as four), so 'countryatlas' makes ISO codes the universal
join key, and matches names in many languages. It joins indicators from
the World Bank, Our World in Data, the European Union's statistical
office and any statistical data and metadata exchange service to bundled
Natural Earth borders and the 'countrycode' Rosetta stone, recording
each value's source, unit and release, and can pin a World Bank release
so a result reproduces; treats country-year panels as first class, with
dated income groups, regions and group memberships, lags keyed on the
year and aggregates that report their coverage; adds analysis helpers
(per-capita, inequality, convergence, distribution dynamics, rates, and
spatial statistics with multiple-testing control); and draws a full
vocabulary of equal- [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between countryatlas versions 3.0.0 dated 2026-10-01 and 4.0.0 dated 2026-11-08
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countryatlas-4.0.0/countryatlas/man/countryatlas-package.Rd | 34 countryatlas-4.0.0/countryatlas/man/coverage_map.Rd | 12 countryatlas-4.0.0/countryatlas/man/dispute_policy.Rd | 21 countryatlas-4.0.0/countryatlas/man/distance_between.Rd | 11 countryatlas-4.0.0/countryatlas/man/dorling_map.Rd | 15 countryatlas-4.0.0/countryatlas/man/eb_morans_i.Rd |only countryatlas-4.0.0/countryatlas/man/facet_map.Rd | 29 countryatlas-4.0.0/countryatlas/man/fetch_indicator.Rd | 16 countryatlas-4.0.0/countryatlas/man/fetch_sdmx.Rd |only countryatlas-4.0.0/countryatlas/man/figures/README-map-1.png |only countryatlas-4.0.0/countryatlas/man/figures/lifecycle-deprecated.svg |only countryatlas-4.0.0/countryatlas/man/figures/lifecycle-experimental.svg |only countryatlas-4.0.0/countryatlas/man/figures/lifecycle-stable.svg |only countryatlas-4.0.0/countryatlas/man/figures/lifecycle-superseded.svg |only countryatlas-4.0.0/countryatlas/man/flow_map.Rd | 35 countryatlas-4.0.0/countryatlas/man/gearys_c.Rd | 7 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countryatlas-4.0.0/countryatlas/man/morans_i.Rd | 34 countryatlas-4.0.0/countryatlas/man/od_map.Rd | 4 countryatlas-4.0.0/countryatlas/man/project_lonlat.Rd |only countryatlas-4.0.0/countryatlas/man/projection_compare.Rd | 6 countryatlas-4.0.0/countryatlas/man/rank_countries.Rd | 9 countryatlas-4.0.0/countryatlas/man/rank_mobility.Rd |only countryatlas-4.0.0/countryatlas/man/rate_funnel.Rd |only countryatlas-4.0.0/countryatlas/man/repair_country_names.Rd | 10 countryatlas-4.0.0/countryatlas/man/simplify_geometry.Rd | 2 countryatlas-4.0.0/countryatlas/man/smooth_rates.Rd | 31 countryatlas-4.0.0/countryatlas/man/source_adapters.Rd | 55 countryatlas-4.0.0/countryatlas/man/source_info.Rd |only countryatlas-4.0.0/countryatlas/man/spatial_lag.Rd | 7 countryatlas-4.0.0/countryatlas/man/spatial_markov.Rd |only countryatlas-4.0.0/countryatlas/man/spike_map.Rd | 27 countryatlas-4.0.0/countryatlas/man/spin_globe.Rd | 11 countryatlas-4.0.0/countryatlas/man/ternary_map.Rd |only 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countryatlas-4.0.0/countryatlas/tests/testthat/helper-http.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-analysis.R | 1260 +++++++++- countryatlas-4.0.0/countryatlas/tests/testthat/test-arg-validation.R | 224 + countryatlas-4.0.0/countryatlas/tests/testthat/test-cache.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-citation.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-classifications.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-classify.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-countryatlas-package.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-data-integrity.R | 351 +- countryatlas-4.0.0/countryatlas/tests/testthat/test-data.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-degenerate-input.R | 55 countryatlas-4.0.0/countryatlas/tests/testthat/test-diagnostics.R | 200 + countryatlas-4.0.0/countryatlas/tests/testthat/test-disputes.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-dynamics.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-fetch-assembly.R | 63 countryatlas-4.0.0/countryatlas/tests/testthat/test-geometry.R | 987 +++++++ countryatlas-4.0.0/countryatlas/tests/testthat/test-ggsql.R | 202 + countryatlas-4.0.0/countryatlas/tests/testthat/test-helper-invariants.R | 11 countryatlas-4.0.0/countryatlas/tests/testthat/test-historical.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-honest-maps.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-http.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-join.R | 406 +++ countryatlas-4.0.0/countryatlas/tests/testthat/test-labels.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-live-contracts.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-locale.R | 56 countryatlas-4.0.0/countryatlas/tests/testthat/test-map-cartograms.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-core.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-globe.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-interactive.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-panels.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-projection.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-symbols.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-map-ternary.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-networks.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-numeric-anchors.R | 61 countryatlas-4.0.0/countryatlas/tests/testthat/test-overrides.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-parallel.R | 5 countryatlas-4.0.0/countryatlas/tests/testthat/test-projections.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-provenance.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-rates-spatial.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-rates.R |only 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countryatlas-4.0.0/countryatlas/tests/testthat/test-visual-regression.R | 163 + countryatlas-4.0.0/countryatlas/tests/testthat/test-world_data.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-worldbank.R |only countryatlas-4.0.0/countryatlas/tests/testthat/test-worldviews.R |only countryatlas-4.0.0/countryatlas/vignettes/beyond-the-choropleth.Rmd | 68 countryatlas-4.0.0/countryatlas/vignettes/countryatlas-and-ggsql.Rmd | 96 countryatlas-4.0.0/countryatlas/vignettes/countryatlas.Rmd | 22 countryatlas-4.0.0/countryatlas/vignettes/data-you-can-trace.Rmd |only countryatlas-4.0.0/countryatlas/vignettes/getting-started.Rmd | 10 countryatlas-4.0.0/countryatlas/vignettes/honest-maps.Rmd | 38 countryatlas-4.0.0/countryatlas/vignettes/joining-your-own-data.Rmd | 6 countryatlas-4.0.0/countryatlas/vignettes/panels.Rmd |only countryatlas-4.0.0/countryatlas/vignettes/sf-and-projections.Rmd | 17 293 files changed, 11391 insertions(+), 3141 deletions(-)
Title: Power and Sample Size Calculations for Bayes Factor Analysis
Description: Implements z-test, t-test, normal moment prior, and binomial test Bayes factors based on summary statistics, along with functionality to perform corresponding power and sample size calculations for fixed and sequential designs as described in Pawel and Held (2025) <doi:10.1080/00031305.2025.2467919>, Pawel and Held (2026) <doi:10.48550/ARXIV.2601.02851>, and Kelter and Pawel (2026) <doi:10.48550/arXiv.2502.02914>.
Author: Samuel Pawel [aut, cre] ,
Frantisek Bartos [aut]
Maintainer: Samuel Pawel <samuel.pawel@uzh.ch>
Diff between bfpwr versions 0.1.6 dated 2025-09-02 and 0.3 dated 2026-11-08
DESCRIPTION | 28 MD5 | 170 +++- NAMESPACE | 13 NEWS.md | 36 R/bf01.R | 92 ++ R/binbf01.R | 2 R/dirbf01.R |only R/helpers.R | 33 R/nbf01.R | 24 R/nbf01seq.R |only R/nbinbf01.R | 7 R/nmbf01.R | 88 ++ R/nnmbf01.R | 36 R/ntbf01.R | 92 ++ R/ntbf01seq.R |only R/numerical-defaults.R |only R/numerical-helpers.R |only R/pbf01.R | 67 + R/pbf01seq.R |only R/pbinbf01.R | 265 +++++-- R/pbinbf01seq.R |only R/pnmbf01.R | 45 + R/powerbf01.R | 137 ++- R/powerbf01seq.R |only R/powerbinbf01.R | 9 R/powerbinbf01seq.R |only R/powernmbf01.R | 12 R/powertbf01.R | 65 + R/powertbf01seq.R |only R/ptbf01.R | 336 ++++++-- R/ptbf01seq.R |only R/seqdesign.R |only R/seqhelpers.R |only R/seqsearch.R |only R/tbf01.R | 336 +++++++- R/tcrit-helpers.R |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 8 inst/doc/using-bfpwr.R | 31 inst/doc/using-bfpwr.Rnw | 51 + inst/doc/using-bfpwr.pdf |binary inst/tinytest/helper-extended-tests.R |only inst/tinytest/helper-test-precision.R |only inst/tinytest/test-bayesfactor-reference.R |only inst/tinytest/test-bf01.R | 26 inst/tinytest/test-dirbf01.R |only inst/tinytest/test-fixed-accuracy.R |only inst/tinytest/test-h0-search-and-empty-stopping-regions.R |only inst/tinytest/test-moment-boundary-range.R |only inst/tinytest/test-moment-one-sided-sequential.R |only inst/tinytest/test-moment-one-sided.R |only inst/tinytest/test-moment-positional-tol.R |only inst/tinytest/test-moment-power-scaling.R |only inst/tinytest/test-moment-scale-extremes.R |only inst/tinytest/test-moment-sequential-quadrature.R |only inst/tinytest/test-moment-standardization-extremes.R |only inst/tinytest/test-moment-tiny-q.R |only inst/tinytest/test-nbf01.R | 7 inst/tinytest/test-nbf01seq-adversarial.R |only inst/tinytest/test-nbf01seq.R |only inst/tinytest/test-nmbf01.R | 11 inst/tinytest/test-normal-narrow-prior.R |only inst/tinytest/test-ntbf01.R |only inst/tinytest/test-ntbf01seq-adversarial.R |only inst/tinytest/test-ntbf01seq.R |only inst/tinytest/test-numerical-helpers.R |only inst/tinytest/test-numerical-options.R |only inst/tinytest/test-paper-binomial-values.R |only inst/tinytest/test-paper-fixed-formulas.R |only inst/tinytest/test-paper-sequential-regions.R |only inst/tinytest/test-pbf01seq.R |only inst/tinytest/test-pbinbf01.R | 83 ++ inst/tinytest/test-pbinbf01seq.R |only inst/tinytest/test-performance-regressions.R |only inst/tinytest/test-ptbf01.R | 269 +++++++ inst/tinytest/test-ptbf01seq.R |only inst/tinytest/test-sequential-control-matching.R |only inst/tinytest/test-sequential-default-integration.R |only inst/tinytest/test-sequential-plot-integration.R |only inst/tinytest/test-sequential-setup-equivalence.R |only inst/tinytest/test-sequential-setup-reuse.R |only inst/tinytest/test-sequential-tail-cutoff.R |only inst/tinytest/test-tbf01.R | 525 ++++++++++++++ inst/tinytest/test-z-one-sided-sequential.R |only inst/tinytest/test-z-one-sided.R |only man/bf01.Rd | 21 man/bfpwrOptions.Rd |only man/binbf01.Rd | 2 man/dirbf01.Rd |only man/nbf01.Rd | 19 man/nbf01seq.Rd |only man/nbinbf01.Rd | 5 man/nmbf01.Rd | 21 man/nnmbf01.Rd | 26 man/ntbf01.Rd | 46 + man/ntbf01seq.Rd |only man/pbf01.Rd | 27 man/pbf01seq.Rd |only man/pbinbf01.Rd | 4 man/pbinbf01seq.Rd |only man/plot.bfseqdesign.Rd |only man/plot.power.bftest.Rd | 2 man/pnmbf01.Rd | 27 man/powerbf01.Rd | 28 man/powerbf01seq.Rd |only man/powerbinbf01.Rd | 8 man/powerbinbf01seq.Rd |only man/powernmbf01.Rd | 25 man/powertbf01.Rd | 54 + man/powertbf01seq.Rd |only man/print.bfseqdesign.Rd |only man/print.power.bftest.Rd | 2 man/print.power.bftestseq.Rd |only man/ptbf01.Rd | 43 - man/ptbf01seq.Rd |only man/tbf01.Rd | 23 vignettes/bibliography.bib | 3 vignettes/using-bfpwr.Rnw | 51 + 119 files changed, 2930 insertions(+), 411 deletions(-)
Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative)
related inputs and outputs. Converts data files to and from DDI, SPSS,
Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between DDIwR versions 0.22 dated 2026-10-08 and 0.23 dated 2026-11-08
DDIwR-0.22/DDIwR/R/metadataDialog.R |only DDIwR-0.22/DDIwR/R/metadataProjection.R |only DDIwR-0.22/DDIwR/R/metadataSession.R |only DDIwR-0.22/DDIwR/R/metadataSnapshot.R |only DDIwR-0.22/DDIwR/R/metadataSweepImport.R |only DDIwR-0.22/DDIwR/man/metadataSweepCapture.Rd |only DDIwR-0.22/DDIwR/man/metadataSweepImport.Rd |only DDIwR-0.22/DDIwR/src/readstat/spss/readstat_sav_parse_mr_name.rl |only DDIwR-0.23/DDIwR/DESCRIPTION | 6 DDIwR-0.23/DDIwR/MD5 | 202 - DDIwR-0.23/DDIwR/NAMESPACE | 12 DDIwR-0.23/DDIwR/R/DDIwR_package.R | 6 DDIwR-0.23/DDIwR/R/clearMetadata.R |only DDIwR-0.23/DDIwR/R/convert.R | 558 ++- DDIwR-0.23/DDIwR/R/exportCodebook.R | 95 DDIwR-0.23/DDIwR/R/inspectFile.R |only DDIwR-0.23/DDIwR/R/internals.R | 30 DDIwR-0.23/DDIwR/R/metadata.R |only DDIwR-0.23/DDIwR/R/readstat_internal.R | 778 ++++ DDIwR-0.23/DDIwR/R/recodeCharcat.R | 24 DDIwR-0.23/DDIwR/R/recodeMissings.R | 14 DDIwR-0.23/DDIwR/R/sasCatalog.R |only DDIwR-0.23/DDIwR/R/setupfile.R | 218 - DDIwR-0.23/DDIwR/R/updateCodebook.R | 121 DDIwR-0.23/DDIwR/R/validateCodebookXML.R |only DDIwR-0.23/DDIwR/R/vendorMetadata.R |only DDIwR-0.23/DDIwR/inst/ChangeLog | 28 DDIwR-0.23/DDIwR/inst/schemas |only DDIwR-0.23/DDIwR/man/DDIwR_internal.Rd | 6 DDIwR-0.23/DDIwR/man/DDIwR_package.Rd | 4 DDIwR-0.23/DDIwR/man/clearFormats.Rd |only DDIwR-0.23/DDIwR/man/convert.Rd | 386 +- DDIwR-0.23/DDIwR/man/exportCodebook.Rd | 13 DDIwR-0.23/DDIwR/man/inspectFile.Rd |only DDIwR-0.23/DDIwR/man/recodeCharcat.Rd | 7 DDIwR-0.23/DDIwR/man/recodeMissings.Rd | 10 DDIwR-0.23/DDIwR/man/setupfile.Rd | 73 DDIwR-0.23/DDIwR/man/updateCodebook.Rd | 9 DDIwR-0.23/DDIwR/man/vendorMetadata.Rd |only DDIwR-0.23/DDIwR/src/declared_types.c | 20 DDIwR-0.23/DDIwR/src/declared_types.h | 1 DDIwR-0.23/DDIwR/src/init.c | 4 DDIwR-0.23/DDIwR/src/readstat/readstat.h | 93 DDIwR-0.23/DDIwR/src/readstat/readstat_convert.c | 13 DDIwR-0.23/DDIwR/src/readstat/readstat_convert.h | 2 DDIwR-0.23/DDIwR/src/readstat/readstat_error.c | 18 DDIwR-0.23/DDIwR/src/readstat/readstat_metadata.c | 8 DDIwR-0.23/DDIwR/src/readstat/readstat_parser.c | 6 DDIwR-0.23/DDIwR/src/readstat/readstat_value.c | 4 DDIwR-0.23/DDIwR/src/readstat/readstat_variable.c | 7 DDIwR-0.23/DDIwR/src/readstat/readstat_writer.c | 281 + DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas.c | 211 - DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas.h | 36 DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas7bcat_read.c | 202 - DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas7bcat_write.c | 610 ++- DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas7bdat_read.c | 464 ++ DDIwR-0.23/DDIwR/src/readstat/sas/readstat_sas7bdat_write.c | 1759 +++++++--- DDIwR-0.23/DDIwR/src/readstat/sas/readstat_xport_read.c | 157 DDIwR-0.23/DDIwR/src/readstat/sas/readstat_xport_write.c | 91 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por.c | 433 ++ DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por.h | 9 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por_parse.c | 197 - DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por_parse.h | 7 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por_parse.rl | 101 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por_read.c | 109 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_por_write.c | 274 + DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav.c | 10 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav.h | 6 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_parse.c | 1400 +++---- DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_parse.rl | 10 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_parse_mr_name.c | 750 +--- DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_parse_mr_name.h | 2 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_read.c | 530 ++- DDIwR-0.23/DDIwR/src/readstat/spss/readstat_sav_write.c | 565 ++- DDIwR-0.23/DDIwR/src/readstat/spss/readstat_spss.c | 7 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_zsav_compress.c | 118 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_zsav_compress.h | 4 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_zsav_read.c | 5 DDIwR-0.23/DDIwR/src/readstat/spss/readstat_zsav_write.c | 7 DDIwR-0.23/DDIwR/src/readstat/stata/readstat_dta.c | 64 DDIwR-0.23/DDIwR/src/readstat/stata/readstat_dta.h | 5 DDIwR-0.23/DDIwR/src/readstat/stata/readstat_dta_read.c | 280 + DDIwR-0.23/DDIwR/src/readstat/stata/readstat_dta_write.c | 622 ++- DDIwR-0.23/DDIwR/src/readstat/txt/commands_util.c | 25 DDIwR-0.23/DDIwR/src/readstat/txt/commands_util.h | 8 DDIwR-0.23/DDIwR/src/readstat/txt/readstat_sas_commands_read.c | 173 DDIwR-0.23/DDIwR/src/readstat/txt/readstat_sas_commands_read.rl | 11 DDIwR-0.23/DDIwR/src/readstat/txt/readstat_spss_commands_read.c | 165 DDIwR-0.23/DDIwR/src/readstat/txt/readstat_spss_commands_read.rl | 11 DDIwR-0.23/DDIwR/src/readstat_reader.c | 317 + DDIwR-0.23/DDIwR/src/readstat_writer.c | 762 ++++ DDIwR-0.23/DDIwR/src/recode_native.c | 4 DDIwR-0.23/DDIwR/src/sc_parallel_read.c | 170 DDIwR-0.23/DDIwR/src/spss_attributes.h |only DDIwR-0.23/DDIwR/src/stata_characteristics.h |only DDIwR-0.23/DDIwR/src/vendor_metadata.h |only DDIwR-0.23/DDIwR/src/xmlvars.c | 13 97 files changed, 9939 insertions(+), 3822 deletions(-)
Title: Functions for Declared Missing Values
Description: A zero dependency package containing functions to declare labels
and missing values, coupled with associated functions to create (weighted)
tables of frequencies and various other summary measures.
Some of the base functions have been rewritten to make use of the specific
information about the missing values, most importantly to distinguish
between empty and declared NA values.
Some functions have similar functionality with the corresponding ones from
packages "haven" and "labelled". The aim is to ensure as much compatibility
as possible with these packages, while offering an alternative in the
objects of class "declared".
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.27 dated 2026-08-21 and 0.28 dated 2026-11-08
DESCRIPTION | 6 +-- MD5 | 22 ++++++------- R/declared_package.R | 4 +- R/internals.R | 4 ++ R/print.R | 2 - R/wmean.R | 4 +- R/wtable.R | 26 +++++++++++++++ build/vignette.rds |binary inst/ChangeLog | 8 ++++ man/declared_package.Rd | 4 +- src/declared.c | 72 +++++++++++++++++++++++++++++++++++++++----- src/registerDynamicSymbol.c | 23 ++++++++++++-- 12 files changed, 144 insertions(+), 31 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for Bayesian meta-analysis, including model estimation,
prior specification, model comparison, prediction, summaries, visualizations,
and diagnostics. The package fits single and model-averaged meta-analytic,
meta-regression, multilevel and multivariate, publication bias adjusted, and generalized linear
mixed models. The model-averaged meta-analytic models combine competing models
based on their predictive performance, weight inference by posterior model probabilities,
and test model components using Bayes factors (e.g., effect vs. no effect;
Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>; Bartoš et al., 2025, <doi:10.1037/met0000737>).
Users can specify flexible prior distributions for effect sizes, heterogeneity,
publication bias (including selection models and PET-PEESE), and moderators.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 4.0.0 dated 2026-05-07 and 4.1.1 dated 2026-11-08
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RoBMA-4.1.1/RoBMA/vignettes/v34-bma-norm-medicine.Rmd | 49 RoBMA-4.1.1/RoBMA/vignettes/v35-bma-glmm-medicine.Rmd | 305 RoBMA-4.1.1/RoBMA/vignettes/v36-zplot.Rmd | 70 RoBMA-4.1.1/RoBMA/vignettes/vignette-cache.R | 7 507 files changed, 44017 insertions(+), 34433 deletions(-)
Title: Temporal Parametric Hazard Modeling
Description: Provides native R implementations of the multiphase parametric
hazard model of Blackstone, Naftel, and Turner (1986)
<doi:10.1080/01621459.1986.10478314> with a focus on behavioral parity,
transparent numerics, and reproducible validation against reference
outputs from the original 'C'/'SAS' 'HAZARD' program, originally developed at
the University of Alabama at Birmingham (UAB). The 'SAS'/'C' code and this R
package are currently developed and maintained at The Cleveland Clinic
Foundation, and the R code was wholly developed at The Cleveland Clinic
Foundation. The generalized temporal
decomposition family extends to longitudinal mixed-effects settings
(Rajeswaran et al. 2018 <doi:10.1177/0962280215623583>). The package is
intentionally implemented in pure R first; performance-critical paths may
later be accelerated with 'Rcpp' without changing the public interface.
Author: John Ehrlinger [aut, cre, cph],
R Core Team [cph] ),
Makoto Matsumoto [cph] ),
Takuji Nishimura [cph] )
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between TemporalHazard versions 1.1.0 dated 2026-06-12 and 1.3.0 dated 2026-11-08
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| 357 TemporalHazard-1.3.0/TemporalHazard/man/hzr_theta_names.Rd |only TemporalHazard-1.3.0/TemporalHazard/man/hzr_translate_sas.Rd |only TemporalHazard-1.3.0/TemporalHazard/man/omc.Rd | 6 TemporalHazard-1.3.0/TemporalHazard/man/predict.hazard.Rd | 131 TemporalHazard-1.3.0/TemporalHazard/man/predict.hzr_outhaz.Rd |only TemporalHazard-1.3.0/TemporalHazard/man/print.hazard.Rd | 5 TemporalHazard-1.3.0/TemporalHazard/man/print.hzr_deciles.Rd | 12 TemporalHazard-1.3.0/TemporalHazard/man/print.hzr_gof.Rd | 4 TemporalHazard-1.3.0/TemporalHazard/man/print.hzr_sas_job.Rd |only TemporalHazard-1.3.0/TemporalHazard/man/print.summary.hazard.Rd | 10 TemporalHazard-1.3.0/TemporalHazard/man/stepwise_trace.Rd | 8 TemporalHazard-1.3.0/TemporalHazard/man/summary.hazard.Rd | 12 TemporalHazard-1.3.0/TemporalHazard/man/tga.Rd | 1 TemporalHazard-1.3.0/TemporalHazard/man/uslife2023.Rd |only TemporalHazard-1.3.0/TemporalHazard/man/valves.Rd | 3 TemporalHazard-1.3.0/TemporalHazard/man/vcov.hazard.Rd | 14 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TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stepwise-scope-honoured.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stepwise-scope-list.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stepwise-step.R | 29 TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stepwise-vector-interface.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stepwise-wald-below-base.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-stuck-start-single-dist.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-thalf-derivative-step.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-theta-check.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-theta-length-single.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-theta-names.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-time-lower-entry.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-time-varying-coefficients.R | 6 TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-time-zero-rows.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-translate-sas.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-unbounded-phase.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-unfitted-warning-scope.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-unverified-convergence-single-dist.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-vector-surv-status.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-vignette-fit-step.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-wald.R | 25 TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weak-direction-unexamined.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weak-direction.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weak-single-parameter.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weibull-hessian.R | 39 TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weibull-log-scale.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weibull-unrepresentable-scale.R |only TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-weights.R | 23 TemporalHazard-1.3.0/TemporalHazard/tests/testthat/test-zero-time-rows.R |only TemporalHazard-1.3.0/TemporalHazard/vignettes/ar-architecture.qmd | 99 TemporalHazard-1.3.0/TemporalHazard/vignettes/clinical-analysis-walkthrough.qmd | 193 TemporalHazard-1.3.0/TemporalHazard/vignettes/fitting-hazard-models.qmd | 199 TemporalHazard-1.3.0/TemporalHazard/vignettes/getting-started.qmd | 83 TemporalHazard-1.3.0/TemporalHazard/vignettes/inference-diagnostics.qmd | 109 TemporalHazard-1.3.0/TemporalHazard/vignettes/mf-mathematical-foundations.qmd | 75 TemporalHazard-1.3.0/TemporalHazard/vignettes/prediction-visualization.qmd | 96 TemporalHazard-1.3.0/TemporalHazard/vignettes/sas-to-r-migration.qmd | 577 364 files changed, 29011 insertions(+), 4670 deletions(-)
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