Title: Data Analysis Part of 'IOHprofiler'
Description: The data analysis module for the Iterative Optimization Heuristics
Profiler ('IOHprofiler'). This module provides statistical analysis methods for the
benchmark data generated by optimization heuristics, which can be visualized through a
web-based interface. The benchmark data is usually generated by the
experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports
the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Author: Hao Wang [aut] ,
Diederick Vermetten [cre, aut] ,
Carola Doerr [aut] ,
Thomas Baeck [aut]
Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>
Diff between IOHanalyzer versions 0.1.8.10 dated 2024-03-01 and 0.1.8.17 dated 2025-11-21
DESCRIPTION | 20 ++++++++--------- MD5 | 37 ++++++++++++++++----------------- NAMESPACE | 2 + R/DataSet.R | 13 +++++++++-- R/DataSetList.R | 3 +- R/IOHanalyzer.R | 3 +- R/plotDataSetList.R | 8 +++++-- R/readFiles.R | 10 ++++++-- R/stats.R | 8 ++++--- README.md | 27 +++++++++++------------- inst/shiny-server/server/upload.R | 4 +++ inst/shiny-server/ui.R | 10 ++++++++ inst/shiny-server/ui/BBOB_Analysis.R |only inst/shiny-server/ui/upload_box.R | 2 - man/IOHanalyzer.Rd | 2 - man/Plot.Stats.Significance_Graph.Rd | 2 + man/Plot.cumulative_difference_plot.Rd | 3 +- man/generate_data.CDP.Rd | 3 +- man/get_FV_overview.Rd | 2 - man/glicko2_ranking.Rd | 2 + 20 files changed, 102 insertions(+), 59 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 1.6.0 dated 2025-08-26 and 1.7.0 dated 2025-11-21
DESCRIPTION | 8 +-- MD5 | 33 ++++++++------ NEWS.md | 11 ++++ R/epiweek-scale.R | 13 ++++- R/isoweek-scale.R | 13 ++++- R/yearweek-scale.R | 11 ++++ build/vignette.rds |binary inst/doc/grates.html | 2 man/scale_x_grates_epiweek.Rd | 11 +++- man/scale_x_grates_isoweek.Rd | 11 +++- man/scale_x_grates_month.Rd | 2 man/scale_x_grates_period.Rd | 2 man/scale_x_grates_year.Rd | 2 man/scale_x_grates_yearquarter.Rd | 2 man/scale_x_grates_yearweek.Rd | 11 +++- tests/testthat/_snaps/plots/epiweek2025.png |only tests/testthat/_snaps/plots/isoweek2025.png |only tests/testthat/_snaps/plots/yearweek2023.png |only tests/testthat/test-plots.R | 60 +++++++++++++++++++++++++++ 19 files changed, 151 insertions(+), 41 deletions(-)
Title: Construct, Evaluate and Plot Value and Utility Functions
Description: Construct and plot objective hierarchies and associated value and utility functions.
Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables.
Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies.
Get numerical results of the evaluations in standard R data types for further processing.
Author: Peter Reichert [cre, aut],
Nele Schuwirth [aut]
Maintainer: Peter Reichert <peter.reichert@emeriti.eawag.ch>
Diff between utility versions 1.4.6 dated 2023-08-27 and 1.4.7 dated 2025-11-21
DESCRIPTION | 22 ++++- MD5 | 104 ++++++++++++++-------------- inst/NEWS | 7 + man/figures/aggregationadd.pdf |binary man/figures/aggregationaddmin.pdf |binary man/figures/aggregationaddmin.png |binary man/figures/aggregationaddpower.pdf | 6 - man/figures/aggregationaddpower.png |binary man/figures/aggregationaddsplitpower.pdf | 6 - man/figures/aggregationaddsplitpower.png |binary man/figures/aggregationbonusmalus.pdf | 6 - man/figures/aggregationbonusmalus.png |binary man/figures/aggregationgeo.pdf | 6 - man/figures/aggregationgeo.png |binary man/figures/aggregationharmo.pdf | 6 - man/figures/aggregationharmo.png |binary man/figures/aggregationmax.pdf | 6 - man/figures/aggregationmax.png |binary man/figures/aggregationmin.pdf |binary man/figures/aggregationmin.png |binary man/figures/aggregationmix.pdf | 6 - man/figures/aggregationmix.png |binary man/figures/aggregationmult.pdf | 6 - man/figures/aggregationmult.png |binary man/figures/aggregationrevaddpower.pdf | 6 - man/figures/aggregationrevaddpower.png |binary man/figures/aggregationrevaddsplitpower.pdf | 6 - man/figures/aggregationrevaddsplitpower.png |binary man/figures/aggregationrevgeo.pdf | 6 - man/figures/aggregationrevgeo.png |binary man/figures/aggregationrevharmo.pdf | 6 - man/figures/aggregationrevharmo.png |binary man/utility-package.Rd | 11 +- man/utility.aggregate.add.Rd | 2 man/utility.aggregate.addmin.Rd | 2 man/utility.aggregate.addpower.Rd | 2 man/utility.aggregate.addsplitpower.Rd | 2 man/utility.aggregate.bonusmalus.Rd | 2 man/utility.aggregate.cobbdouglas.Rd | 2 man/utility.aggregate.geo.Rd | 2 man/utility.aggregate.geooff.Rd | 2 man/utility.aggregate.harmo.Rd | 2 man/utility.aggregate.harmooff.Rd | 2 man/utility.aggregate.max.Rd | 2 man/utility.aggregate.min.Rd | 2 man/utility.aggregate.mix.Rd | 2 man/utility.aggregate.mult.Rd | 2 man/utility.aggregate.revaddpower.Rd | 2 man/utility.aggregate.revaddsplitpower.Rd | 2 man/utility.aggregate.revgeo.Rd | 2 man/utility.aggregate.revgeooff.Rd | 2 man/utility.aggregate.revharmo.Rd | 2 man/utility.aggregate.revharmooff.Rd | 2 53 files changed, 137 insertions(+), 119 deletions(-)
Title: Simulated Sampling Procedure for Community Ecology
Description: The Simulation-based Sampling Protocol (SSP) is an R package designed to estimate sampling effort in studies of ecological communities. It is based on the concept of pseudo-multivariate standard error (MultSE) (Anderson & Santana-Garcon, 2015, <doi:10.1111/ele.12385>) and the simulation of ecological data. The theoretical background is described in Guerra-Castro et al. (2020, <doi:10.1111/ecog.05284>).
Author: Edlin Guerra-Castro [aut, cre],
Maite Mascaro [aut],
Nuno Simoes [aut],
Juan Cruz-Motta [aut],
Juan Cajas [aut]
Maintainer: Edlin Guerra-Castro <edlinguerra@gmail.com>
Diff between SSP versions 1.0.2 dated 2025-04-24 and 1.1.0 dated 2025-11-21
DESCRIPTION | 10 +-- MD5 | 37 ++++++------- NEWS.md | 19 ++++++ R/datquality.R | 10 --- R/ioptimum.R | 16 ----- R/plot_ssp.R | 12 ---- R/sampsd.R | 9 --- R/simdata.R | 132 ++++++++++++++++++++++++++++-------------------- R/summary_ssp.R | 10 --- inst/doc/SSP-guide.R | 102 ++++++++++++++++++------------------- inst/doc/SSP-guide.Rmd | 19 ++++-- inst/doc/SSP-guide.html | 89 +++++++++++++++++++------------- man/datquality.Rd | 10 --- man/ioptimum.Rd | 16 ----- man/plot_ssp.Rd | 12 ---- man/sampsd.Rd | 9 --- man/simdata.Rd | 17 ++++-- man/summary_ssp.Rd | 10 --- vignettes/SSP-guide.Rmd | 19 ++++-- vignettes/fig2b.png |only 20 files changed, 284 insertions(+), 274 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.4-2 dated 2025-09-21 and 3.4-3 dated 2025-11-21
DESCRIPTION | 10 - MD5 | 26 +- NEWS | 13 + R/clusterinfo.R | 356 ++++++++++++++++++++++++---------------- R/rclusterBKBC.R | 37 ++-- build |only inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/default.expand.Rd | 2 man/macros/defns.Rd | 3 man/rGRFgauss.Rd |only man/rLGCP.Rd | 2 man/rmh.default.Rd | 30 +-- man/spatstat.random-internal.Rd | 14 - tests/Random.R | 29 +++ 15 files changed, 324 insertions(+), 200 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-22 dated 2025-09-01 and 1.1-23 dated 2025-11-21
DESCRIPTION | 12 ++++++------ MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/TA.plot.R | 6 +++--- R/misc-goodies.R | 9 +++++++++ R/pkgDesc.R | 4 +++- R/prettylab.R | 6 ++++++ build/partial.rdb |binary inst/NEWS.Rd | 20 ++++++++++++++++++++ man/formatN.Rd |only man/n.plot.Rd | 20 ++++++++++++++++---- man/pkgDesc.Rd | 14 +++++++++++++- 12 files changed, 88 insertions(+), 25 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.5 dated 2025-03-07 and 0.1.6 dated 2025-11-21
ChangeLog | 10 + DESCRIPTION | 10 - MD5 | 60 ++++---- NAMESPACE | 21 +- R/RcppExports.R | 8 + R/qx_functions.R | 4 R/starnames.R | 2 R/zstd_file_functions.R |only build/vignette.rds |binary data/starnames.rda |binary inst/doc/vignette.R | 56 +++---- inst/doc/vignette.html | 317 +++++++++++++++++++++++--------------------- man/qd_deserialize.Rd | 2 man/qd_read.Rd | 2 man/qd_save.Rd | 2 man/qd_serialize.Rd | 2 man/qs_deserialize.Rd | 2 man/qs_read.Rd | 2 man/qs_save.Rd | 2 man/qs_serialize.Rd | 2 man/starnames.Rd | 2 man/zstd_compress_file.Rd |only man/zstd_decompress_file.Rd |only src/RcppExports.cpp | 57 +++++-- src/ZSTD/zstd.c | 76 +++++----- src/io/io_common.h | 4 src/io/zstd_file.h |only src/qd_deserializer.h | 18 +- src/qd_serializer.h | 4 src/qx_file_headers.h | 2 src/qx_functions.cpp | 107 +++++++++----- src/zstd_file_functions.h |only tests/correctness_testing.R | 13 + tests/utility_testing.R |only 34 files changed, 454 insertions(+), 333 deletions(-)
Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language
('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a
list-based representation of 'EML' in R, so that 'EML' data can easily
be manipulated using standard 'R' tools. This makes this package an
effective backend for other 'R'-based tools working with 'EML.' By
abstracting away the complexity of 'XML' Schema, developers can
build around native 'R' list objects and not have to worry about satisfying
many of the additional constraints of set by the schema (such as element
ordering, which is handled automatically). Additionally, the 'JSON-LD'
representation enables the use of developer-friendly 'JSON' parsing and
serialization that may facilitate the use of 'EML' in contexts outside of 'R,'
as well as the informatics-friendly serializations such as 'RDF' and
'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph] ,
Matthew B. Jones [aut, cph] ,
Bryce Mecum [aut, cph]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between emld versions 0.5.1 dated 2020-09-27 and 0.5.2 dated 2025-11-21
DESCRIPTION | 18 +- MD5 | 25 +-- NAMESPACE | 2 NEWS.md | 10 + R/as_jsonlist.R | 5 R/as_xml.R | 2 R/emld-package.R |only README.md | 43 ++--- build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST | 38 +--- inst/doc/tutorial.R | 134 ++++++++-------- inst/doc/tutorial.html | 404 +++++++++++++++++++++++++++++-------------------- man/emld-package.Rd | 14 + 14 files changed, 400 insertions(+), 299 deletions(-)
Title: Multi-Response (Multivariate) Interpretable Machine Learning
Description: Builds and interprets multi-response machine learning models using 'tidymodels' syntax. Users can supply a tidy model, and 'mrIML' automates the process of fitting multiple response models to multivariate data and applying interpretable machine learning techniques across them. For more details see Fountain-Jones (2021) <doi:10.1111/1755-0998.13495> and Fountain-Jones et al. (2024) <doi:10.22541/au.172676147.77148600/v1>.
Author: Nick Fountain-Jones [aut, cre, cph] ,
Ryan Leadbetter [aut] ,
Gustavo Machado [aut] ,
Chris Kozakiewicz [aut],
Nick Clark [aut]
Maintainer: Nick Fountain-Jones <nick.fountainjones@utas.edu.au>
Diff between mrIML versions 2.1.0 dated 2025-07-28 and 2.2.0 dated 2025-11-20
DESCRIPTION | 6 MD5 | 40 ++- NEWS.md | 9 R/mrBootstrap.R | 58 ++--- R/mrCoOccurNet.R | 31 +-- R/mrCovar.R | 75 ++++--- R/mrFlashlight.R | 33 +-- R/mrIMLperformance.R | 36 +-- R/mrIMLpredicts.R | 197 +++++++++---------- R/mrInteractions.R | 60 +++-- R/mrPdPlotBootstrap.R | 64 +++--- R/mrPerformancePlot.R | 70 ++++-- R/mrVip.R | 8 R/utils.R | 371 +++++++++++++++++++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mrIML.html | 62 +++--- man/cbind.Rd |only man/mrIMLpredicts.Rd | 12 - man/readSnpsPed.Rd | 2 tests/testthat/test-mrBootstrap.R |only tests/testthat/test-mrIMLpredicts.R | 57 ++++- 22 files changed, 671 insertions(+), 520 deletions(-)
Title: Statistical Framework for in Vivo Drug Combination Studies
Description: A framework for evaluating drug combination effects in preclinical in vivo studies.
'SynergyLMM' provides functions to analyze longitudinal tumor growth experiments using mixed-effects models,
perform time-resolved analyses of synergy and antagonism, evaluate model diagnostics and performance,
and assess both post-hoc and a priori statistical power.
The calculation of drug combination synergy follows the statistical framework provided by Demidenko and Miller (2019, <doi:10.1371/journal.pone.0224137>).
The implementation and analysis of linear mixed-effect models is based on the methods described by Pinheiro and Bates (2000, <doi:10.1007/b98882>),
and Gałecki and Burzykowski (2013, <doi:10.1007/978-1-4614-3900-4>).
Author: Rafael Romero-Becerra [aut, cre] ,
Zhi Zhao [ctb],
Tero Aittokallio [ctb]
Maintainer: Rafael Romero-Becerra <r.r.becerra@medisin.uio.no>
Diff between SynergyLMM versions 1.1.1 dated 2025-08-22 and 1.1.2 dated 2025-11-20
SynergyLMM-1.1.1/SynergyLMM/man/figures/README-CooksD-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-CooksD_fitted-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-CooksD_fixef-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-bliss_syn-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-fit_model-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-fit_model_gomp-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-hsa_syn-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-logLikDisp-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-obs_vs_pred-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-pwrsamplesize-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-ra_syn-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-ranef_diag-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-resid_diagnostics-1.png |only SynergyLMM-1.1.1/SynergyLMM/man/figures/README-robustSE-1.png |only SynergyLMM-1.1.2/SynergyLMM/DESCRIPTION | 8 SynergyLMM-1.1.2/SynergyLMM/MD5 | 79 +-- SynergyLMM-1.1.2/SynergyLMM/NEWS.md | 10 SynergyLMM-1.1.2/SynergyLMM/R/APrioriPwr.R | 26 - SynergyLMM-1.1.2/SynergyLMM/R/CookDistance.R | 8 SynergyLMM-1.1.2/SynergyLMM/R/PostHocPwr.R | 6 SynergyLMM-1.1.2/SynergyLMM/R/PwrSampleSize.R | 18 SynergyLMM-1.1.2/SynergyLMM/R/PwrTime.R | 18 SynergyLMM-1.1.2/SynergyLMM/R/lmmModel_estimates.R | 13 SynergyLMM-1.1.2/SynergyLMM/R/lmmSynergy.R | 12 SynergyLMM-1.1.2/SynergyLMM/R/logLikSubjectDisplacements.R | 2 SynergyLMM-1.1.2/SynergyLMM/R/utils.R | 2 SynergyLMM-1.1.2/SynergyLMM/inst/CITATION |only SynergyLMM-1.1.2/SynergyLMM/inst/doc/SynergyLMM.R | 57 +- SynergyLMM-1.1.2/SynergyLMM/inst/doc/SynergyLMM.Rmd | 74 +-- SynergyLMM-1.1.2/SynergyLMM/inst/doc/SynergyLMM.html | 241 +++++----- SynergyLMM-1.1.2/SynergyLMM/man/APrioriPwr.Rd | 9 SynergyLMM-1.1.2/SynergyLMM/man/CookDistance.Rd | 8 SynergyLMM-1.1.2/SynergyLMM/man/PostHocPwr.Rd | 6 SynergyLMM-1.1.2/SynergyLMM/man/PwrSampleSize.Rd | 14 SynergyLMM-1.1.2/SynergyLMM/man/PwrTime.Rd | 14 SynergyLMM-1.1.2/SynergyLMM/man/figures/README-ObsvsPred-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-apriori_pwr_freq-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-apriori_pwr_size-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-apriori_pwr_time-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-apriori_pwr_var-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-bliss_robust-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-exp_model-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-hsa-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-ra-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-ranefDiagnostics-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-residDiagnostics-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-unnamed-chunk-7-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/figures/README-unnamed-chunk-8-1.png |only SynergyLMM-1.1.2/SynergyLMM/man/lmmModel_estimates.Rd | 5 SynergyLMM-1.1.2/SynergyLMM/man/lmmSynergy.Rd | 12 SynergyLMM-1.1.2/SynergyLMM/tests/testthat/test-lmmModel.R | 15 SynergyLMM-1.1.2/SynergyLMM/vignettes/Fig1_LMM_Graphical_Abstract.png |binary SynergyLMM-1.1.2/SynergyLMM/vignettes/Flowchart_v2.png |only SynergyLMM-1.1.2/SynergyLMM/vignettes/Gompertz_model.png |binary SynergyLMM-1.1.2/SynergyLMM/vignettes/SynergyLMM.Rmd | 74 +-- 55 files changed, 408 insertions(+), 323 deletions(-)
Title: Clinical Trial Simulation
Description: Provides some basic routines for simulating a
clinical trial. The primary intent is to provide some tools to
generate trial simulations for trials with time to event outcomes.
Piecewise exponential failure rates and piecewise constant
enrollment rates are the underlying mechanism used to simulate
a broad range of scenarios such as those presented in
Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>.
However, the basic generation of data is done using pipes to allow
maximum flexibility for users to meet different needs.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
John Blischak [aut],
Nan Xiao [ctb],
Yilong Zhang [aut],
Jianxiao Yang [ctb],
Lili Ling [ctb],
Xintong Li [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Yalin Zhu [ctb],
Heng Zhou [ctb],
Amin Sh [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between simtrial versions 1.0.1 dated 2025-09-11 and 1.0.2 dated 2025-11-20
DESCRIPTION | 8 MD5 | 53 NEWS.md | 12 R/get_analysis_date.R | 46 R/sim_gs_n.R | 28 inst/doc/arbitrary-hazard.html | 277 - inst/doc/discrepancy-between-simtrial-and-survival.html | 536 +- inst/doc/maxcombo.html | 3693 ++++++------- inst/doc/modest-wlrt.html | 494 + inst/doc/parallel.html | 542 +- inst/doc/rmst.R | 64 inst/doc/rmst.html | 817 --- inst/doc/routines.html | 4266 +++++++--------- inst/doc/sim_fixed_design_custom.html | 3904 ++++++-------- inst/doc/sim_fixed_design_simple.html | 2264 ++++---- inst/doc/sim_gs_design_simple.html | 1682 +++--- inst/doc/workflow.html | 69 man/early_zero.Rd | 2 man/get_analysis_date.Rd | 20 man/get_cut_date_by_event.Rd | 2 man/randomize_by_fixed_block.Rd | 2 man/sim_fixed_n.Rd | 2 man/sim_gs_n.Rd | 6 man/sim_pw_surv.Rd | 2 man/simtrial-package.Rd | 2 tests/testthat/test-developer-get_analysis_date.R |only tests/testthat/test-unvalidated-get_analysis_date.R | 16 tests/testthat/test-unvalidated-sim_gs_n.R | 6 28 files changed, 8996 insertions(+), 9819 deletions(-)
Title: Facilitate Exploration of touRR optimisatioN
Description: Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser
takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and
also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the
name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/articles/RJ-2021-105/index.html>.
Author: H. Sherry Zhang [aut, cre] ,
Dianne Cook [aut] ,
Ursula Laa [aut] ,
Nicolas Langrene [aut] ,
Patricia Menendez [aut]
Maintainer: H. Sherry Zhang <huizezhangsh@gmail.com>
Diff between ferrn versions 0.1.0 dated 2024-06-23 and 0.3.0 dated 2025-11-20
DESCRIPTION | 31 ++++++----- MD5 | 47 +++++++++++------ NAMESPACE | 6 ++ NEWS.md | 7 ++ R/calc-squintability.R | 93 ++++++++++++++++++++++++++-------- R/data-pipe-sine.R | 15 +++++ R/data.R | 3 + R/explore-space-tour.R | 2 R/huber-plot.R |only R/plot-projection.R | 76 +++++++++++++++++++++------ README.md | 19 ++++++ data/holes_2d_jellyfish.rda |only data/pipe1000_4d.rda |only data/pipe1000_6d.rda |only data/sine1000_4d.rda |only data/sine1000_6d.rda |only man/data.Rd | 5 + man/explore_space_tour.Rd | 2 man/ferrn-package.Rd | 5 + man/figures/README-pca-plot-1.png |binary man/figures/README-trace-plot-1.png |binary man/huber.Rd |only man/pipe-sine-boa.Rd | 23 ++++++++ man/projection.Rd | 34 +++++++++++- tests/testthat/_snaps |only tests/testthat/test-huber-plot.R |only tests/testthat/test-plot-projection.R |only 27 files changed, 295 insertions(+), 73 deletions(-)
Title: Analyzing the Survey of Consumer Finances
Description: Analyze public-use micro data from the Survey of Consumer Finances.
Provides tools to download prepared data files, construct replicate-weighted
multiply imputed survey designs, compute descriptive statistics and model
estimates, and produce plots and tables. Methods follow design-based inference
for complex surveys and pooling across multiple imputations. See the package
website and the code book for background.
Author: Joseph Cohen [aut, cre]
Maintainer: Joseph Cohen <joseph.cohen@qc.cuny.edu>
Diff between scf versions 1.0.4 dated 2025-10-22 and 1.0.5 dated 2025-11-20
scf-1.0.4/scf/R/SE.R |only scf-1.0.5/scf/DESCRIPTION | 6 scf-1.0.5/scf/MD5 | 142 +++++---- scf-1.0.5/scf/NAMESPACE | 11 scf-1.0.5/scf/NEWS | 11 scf-1.0.5/scf/R/scf_MIcombine.R | 58 ++-- scf-1.0.5/scf/R/scf_corr.R | 16 - scf-1.0.5/scf/R/scf_design.R | 34 +- scf-1.0.5/scf/R/scf_download.R | 23 + scf-1.0.5/scf/R/scf_freq.R | 33 +- scf-1.0.5/scf/R/scf_glm.R | 9 scf-1.0.5/scf/R/scf_implicates.R | 6 scf-1.0.5/scf/R/scf_imports.R | 1 scf-1.0.5/scf/R/scf_load.R | 8 scf-1.0.5/scf/R/scf_logit.R | 9 scf-1.0.5/scf/R/scf_mean.R | 151 ++++++---- scf-1.0.5/scf/R/scf_median.R | 43 +-- scf-1.0.5/scf/R/scf_model_methods.R |only scf-1.0.5/scf/R/scf_ols.R | 11 scf-1.0.5/scf/R/scf_percentile.R | 344 +++++++++++++++--------- scf-1.0.5/scf/R/scf_plot_bbar.R | 6 scf-1.0.5/scf/R/scf_plot_cbar.R | 6 scf-1.0.5/scf/R/scf_plot_dbar.R | 6 scf-1.0.5/scf/R/scf_plot_dist.R | 17 - scf-1.0.5/scf/R/scf_plot_hex.R | 6 scf-1.0.5/scf/R/scf_plot_hist.R | 6 scf-1.0.5/scf/R/scf_plot_smooth.R | 6 scf-1.0.5/scf/R/scf_prop_test.R | 6 scf-1.0.5/scf/R/scf_regtable.R | 91 +++--- scf-1.0.5/scf/R/scf_subset.R | 12 scf-1.0.5/scf/R/scf_ttest.R | 8 scf-1.0.5/scf/R/scf_update.R | 6 scf-1.0.5/scf/R/scf_update_by_implicate.R | 5 scf-1.0.5/scf/R/scf_xtab.R | 5 scf-1.0.5/scf/R/zzz.R | 1 scf-1.0.5/scf/README.md | 45 +-- scf-1.0.5/scf/inst/doc/SCF-guide.R | 19 - scf-1.0.5/scf/inst/doc/SCF-guide.Rmd | 22 - scf-1.0.5/scf/inst/doc/SCF-guide.html | 34 -- scf-1.0.5/scf/man/AIC.scf_model_result.Rd |only scf-1.0.5/scf/man/SE.Rd | 22 - scf-1.0.5/scf/man/coef.scf_model_result.Rd |only scf-1.0.5/scf/man/formula.scf_model_result.Rd |only scf-1.0.5/scf/man/predict.scf_model_result.Rd |only scf-1.0.5/scf/man/residuals.scf_model_result.Rd |only scf-1.0.5/scf/man/scf_MIcombine.Rd | 282 ++++++++++--------- scf-1.0.5/scf/man/scf_corr.Rd | 176 ++++++------ scf-1.0.5/scf/man/scf_design.Rd | 116 ++++---- scf-1.0.5/scf/man/scf_download.Rd | 140 +++++---- scf-1.0.5/scf/man/scf_freq.Rd | 153 +++++----- scf-1.0.5/scf/man/scf_glm.Rd | 6 scf-1.0.5/scf/man/scf_implicates.Rd | 100 +++--- scf-1.0.5/scf/man/scf_load.Rd | 130 ++++----- scf-1.0.5/scf/man/scf_logit.Rd | 168 +++++------ scf-1.0.5/scf/man/scf_mean.Rd | 120 ++++---- scf-1.0.5/scf/man/scf_median.Rd | 141 +++++---- scf-1.0.5/scf/man/scf_ols.Rd | 139 ++++----- scf-1.0.5/scf/man/scf_percentile.Rd | 182 ++++++------ scf-1.0.5/scf/man/scf_plot_bbar.Rd | 160 +++++------ scf-1.0.5/scf/man/scf_plot_cbar.Rd | 166 +++++------ scf-1.0.5/scf/man/scf_plot_dbar.Rd | 160 +++++------ scf-1.0.5/scf/man/scf_plot_dist.Rd | 159 +++++------ scf-1.0.5/scf/man/scf_plot_hex.Rd | 148 +++++----- scf-1.0.5/scf/man/scf_plot_hist.Rd | 148 +++++----- scf-1.0.5/scf/man/scf_plot_smooth.Rd | 156 +++++----- scf-1.0.5/scf/man/scf_prop_test.Rd | 154 +++++----- scf-1.0.5/scf/man/scf_regtable.Rd | 154 +++++----- scf-1.0.5/scf/man/scf_subset.Rd | 133 ++++----- scf-1.0.5/scf/man/scf_ttest.Rd | 142 +++++---- scf-1.0.5/scf/man/scf_update.Rd | 150 +++++----- scf-1.0.5/scf/man/scf_update_by_implicate.Rd | 139 ++++----- scf-1.0.5/scf/man/scf_xtab.Rd | 115 ++++---- scf-1.0.5/scf/man/vcov.scf_model_result.Rd |only scf-1.0.5/scf/tests/testthat/test-scf-package.R | 13 scf-1.0.5/scf/tests/testthat/test-scf_glm.R | 3 scf-1.0.5/scf/vignettes/SCF-guide.Rmd | 22 - 76 files changed, 2786 insertions(+), 2434 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.0.2 dated 2025-10-14 and 1.1.0 dated 2025-11-20
qol-1.0.2/qol/man/running_number.Rd |only qol-1.1.0/qol/DESCRIPTION | 7 qol-1.1.0/qol/MD5 | 75 +- qol-1.1.0/qol/NAMESPACE | 85 +- qol-1.1.0/qol/NEWS.md | 83 ++ qol-1.1.0/qol/R/any_table.R | 524 ++++++++++++----- qol-1.1.0/qol/R/apply_format.R | 17 qol-1.1.0/qol/R/build_master.R |only qol-1.1.0/qol/R/build_rstheme.R |only qol-1.1.0/qol/R/conversion.R | 2 qol-1.1.0/qol/R/create_format.R | 60 +- qol-1.1.0/qol/R/crosstabs.R | 35 - qol-1.1.0/qol/R/dummy_data.R | 4 qol-1.1.0/qol/R/excel_helpers.R | 98 +-- qol-1.1.0/qol/R/export_with_style.R | 13 qol-1.1.0/qol/R/frequencies.R | 73 +- qol-1.1.0/qol/R/globals.R | 3 qol-1.1.0/qol/R/if_else.R | 458 +++++++-------- qol-1.1.0/qol/R/internal.R | 280 ++++----- qol-1.1.0/qol/R/monitor.R | 474 +++++++-------- qol-1.1.0/qol/R/qol.R | 14 qol-1.1.0/qol/R/recode.R | 7 qol-1.1.0/qol/R/retain.R |only qol-1.1.0/qol/R/small_helpers.R | 117 +-- qol-1.1.0/qol/R/split_by.R | 288 ++++----- qol-1.1.0/qol/R/summarise_plus.R | 17 qol-1.1.0/qol/README.md | 97 +++ qol-1.1.0/qol/man/any_table.Rd | 627 ++++++++++----------- qol-1.1.0/qol/man/build_master.Rd |only qol-1.1.0/qol/man/build_rstheme.Rd |only qol-1.1.0/qol/man/combine_into_workbook.Rd |only qol-1.1.0/qol/man/figures/theme.png |only qol-1.1.0/qol/man/formats.Rd | 17 qol-1.1.0/qol/man/frequencies.Rd | 276 ++++----- qol-1.1.0/qol/man/qol-package.Rd | 248 ++++---- qol-1.1.0/qol/man/replace_except.Rd |only qol-1.1.0/qol/man/retain.Rd |only qol-1.1.0/qol/tests/testthat/test-any_table.R | 72 +- qol-1.1.0/qol/tests/testthat/test-build_master.R |only qol-1.1.0/qol/tests/testthat/test-build_rstheme.R |only qol-1.1.0/qol/tests/testthat/test-create_format.R | 15 qol-1.1.0/qol/tests/testthat/test-recode.R | 1 qol-1.1.0/qol/tests/testthat/test-retain.R |only qol-1.1.0/qol/tests/testthat/test-small_helpers.R | 69 +- qol-1.1.0/qol/tests/testthat/test-summarise_plus.R | 6 45 files changed, 2325 insertions(+), 1837 deletions(-)
Title: Flexible Bayesian Model Selection and Model Averaging
Description: Implements the Mode Jumping Markov Chain Monte Carlo algorithm described in <doi:10.1016/j.csda.2018.05.020> and its Genetically Modified counterpart described in <doi:10.1613/jair.1.13047> as well as the sub-sampling versions described in <doi:10.1016/j.ijar.2022.08.018> for flexible Bayesian model selection and model averaging.
Author: Jon Lachmann [cre, aut],
Aliaksandr Hubin [aut]
Maintainer: Jon Lachmann <jon@lachmann.nu>
Diff between FBMS versions 1.2 dated 2025-09-12 and 1.3 dated 2025-11-20
FBMS-1.2/FBMS/man/gaussian.loglik.alpha.Rd |only FBMS-1.2/FBMS/man/gaussian.loglik.g.Rd |only FBMS-1.2/FBMS/man/gaussian_tcch_log_likelihood.Rd |only FBMS-1.2/FBMS/man/glm.loglik.Rd |only FBMS-1.2/FBMS/man/glm.loglik.g.Rd |only FBMS-1.2/FBMS/man/glm.logpost.bas.Rd |only FBMS-1.2/FBMS/man/lm.logpost.bas.Rd |only FBMS-1.2/FBMS/man/logistic.loglik.ala.Rd |only FBMS-1.2/FBMS/man/logistic.loglik.alpha.Rd |only FBMS-1.3/FBMS/DESCRIPTION | 13 FBMS-1.3/FBMS/MD5 | 231 ++- FBMS-1.3/FBMS/NAMESPACE | 46 FBMS-1.3/FBMS/R/abalone-data.R | 2 FBMS-1.3/FBMS/R/alpha_generation.R | 8 FBMS-1.3/FBMS/R/arguments.R | 8 FBMS-1.3/FBMS/R/coefs.R |only FBMS-1.3/FBMS/R/diagnostics.R | 72 - FBMS-1.3/FBMS/R/exa-data.R | 4 FBMS-1.3/FBMS/R/fbms.R | 5 FBMS-1.3/FBMS/R/feature.R | 6 FBMS-1.3/FBMS/R/gmjmcmc.R | 5 FBMS-1.3/FBMS/R/gmjmcmc_support.R | 9 FBMS-1.3/FBMS/R/impute.R |only FBMS-1.3/FBMS/R/likelihoods.R | 181 --- FBMS-1.3/FBMS/R/mjmcmc.R | 6 FBMS-1.3/FBMS/R/nonlinear_functions.R | 61 - FBMS-1.3/FBMS/R/parallel.R | 6 FBMS-1.3/FBMS/R/predict.R | 319 ++++- FBMS-1.3/FBMS/R/print.R |only FBMS-1.3/FBMS/R/residuals.R |only FBMS-1.3/FBMS/R/results.R | 258 ++-- FBMS-1.3/FBMS/R/sanger-data.R | 4 FBMS-1.3/FBMS/R/summary.R | 9 FBMS-1.3/FBMS/build/partial.rdb |binary FBMS-1.3/FBMS/build/vignette.rds |binary FBMS-1.3/FBMS/inst/doc/FBMS-guide.R | 2 FBMS-1.3/FBMS/inst/doc/FBMS-guide.Rmd | 9 FBMS-1.3/FBMS/inst/doc/FBMS-guide.html | 1310 +++++++++++++--------- FBMS-1.3/FBMS/man/SangerData2.Rd | 2 FBMS-1.3/FBMS/man/abalone.Rd | 2 FBMS-1.3/FBMS/man/aggr.Rd |only FBMS-1.3/FBMS/man/aggr.fbms_predict.Rd |only FBMS-1.3/FBMS/man/arcsinh.Rd | 4 FBMS-1.3/FBMS/man/coef.bgnlm_model.Rd |only FBMS-1.3/FBMS/man/coef.gmjmcmc.Rd |only FBMS-1.3/FBMS/man/coef.gmjmcmc_merged.Rd |only FBMS-1.3/FBMS/man/coef.mjmcmc.Rd |only FBMS-1.3/FBMS/man/coef.mjmcmc_parallel.Rd |only FBMS-1.3/FBMS/man/compute_effects.Rd | 2 FBMS-1.3/FBMS/man/cos_deg.Rd | 4 FBMS-1.3/FBMS/man/diagn_plot.Rd | 29 FBMS-1.3/FBMS/man/erf.Rd | 4 FBMS-1.3/FBMS/man/exoplanet.Rd | 2 FBMS-1.3/FBMS/man/exp_dbl.Rd | 4 FBMS-1.3/FBMS/man/fbms.Rd | 3 FBMS-1.3/FBMS/man/fitted.fbms_predict.Rd |only FBMS-1.3/FBMS/man/gaussian.loglik.Rd | 4 FBMS-1.3/FBMS/man/gelu.Rd | 4 FBMS-1.3/FBMS/man/gen.params.gmjmcmc.Rd | 2 FBMS-1.3/FBMS/man/gen.params.mjmcmc.Rd | 4 FBMS-1.3/FBMS/man/gen.probs.gmjmcmc.Rd | 4 FBMS-1.3/FBMS/man/gen.probs.mjmcmc.Rd | 4 FBMS-1.3/FBMS/man/get.best.model.Rd | 31 FBMS-1.3/FBMS/man/gmjmcmc.Rd | 4 FBMS-1.3/FBMS/man/gmjmcmc.parallel.Rd | 4 FBMS-1.3/FBMS/man/hs.Rd | 4 FBMS-1.3/FBMS/man/impute_x.Rd |only FBMS-1.3/FBMS/man/impute_x_pred.Rd |only FBMS-1.3/FBMS/man/log_prior.Rd | 4 FBMS-1.3/FBMS/man/logistic.loglik.Rd | 5 FBMS-1.3/FBMS/man/marginal.probs.Rd | 4 FBMS-1.3/FBMS/man/merge_results.Rd | 17 FBMS-1.3/FBMS/man/mjmcmc.Rd | 4 FBMS-1.3/FBMS/man/mjmcmc.parallel.Rd | 4 FBMS-1.3/FBMS/man/model.string.Rd | 4 FBMS-1.3/FBMS/man/ngelu.Rd | 4 FBMS-1.3/FBMS/man/nhs.Rd | 4 FBMS-1.3/FBMS/man/not.Rd | 4 FBMS-1.3/FBMS/man/nrelu.Rd | 4 FBMS-1.3/FBMS/man/p0.Rd | 4 FBMS-1.3/FBMS/man/p05.Rd | 4 FBMS-1.3/FBMS/man/p0p0.Rd | 4 FBMS-1.3/FBMS/man/p0p05.Rd | 4 FBMS-1.3/FBMS/man/p0p1.Rd | 4 FBMS-1.3/FBMS/man/p0p2.Rd | 4 FBMS-1.3/FBMS/man/p0p3.Rd | 4 FBMS-1.3/FBMS/man/p0pm05.Rd | 4 FBMS-1.3/FBMS/man/p0pm1.Rd | 4 FBMS-1.3/FBMS/man/p0pm2.Rd | 4 FBMS-1.3/FBMS/man/p2.Rd | 4 FBMS-1.3/FBMS/man/p3.Rd | 4 FBMS-1.3/FBMS/man/plot.bgnlm_model.Rd |only FBMS-1.3/FBMS/man/plot.fbms_predict.Rd |only FBMS-1.3/FBMS/man/plot.gmjmcmc.Rd | 6 FBMS-1.3/FBMS/man/plot.gmjmcmc_merged.Rd | 4 FBMS-1.3/FBMS/man/plot.mjmcmc.Rd | 6 FBMS-1.3/FBMS/man/plot.mjmcmc_parallel.Rd | 4 FBMS-1.3/FBMS/man/pm05.Rd | 4 FBMS-1.3/FBMS/man/pm1.Rd | 4 FBMS-1.3/FBMS/man/pm2.Rd | 4 FBMS-1.3/FBMS/man/predict.bgnlm_model.Rd | 22 FBMS-1.3/FBMS/man/predict.gmjmcmc.Rd | 4 FBMS-1.3/FBMS/man/predict.gmjmcmc_merged.Rd | 4 FBMS-1.3/FBMS/man/predict.gmjmcmc_parallel.Rd | 4 FBMS-1.3/FBMS/man/predict.mjmcmc.Rd | 4 FBMS-1.3/FBMS/man/predict.mjmcmc_parallel.Rd | 4 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FBMS-1.3/FBMS/man/string.population.models.Rd | 4 FBMS-1.3/FBMS/man/summary.fbms_predict.Rd |only FBMS-1.3/FBMS/man/summary.gmjmcmc.Rd | 4 FBMS-1.3/FBMS/man/summary.gmjmcmc_merged.Rd | 4 FBMS-1.3/FBMS/man/summary.mjmcmc.Rd | 4 FBMS-1.3/FBMS/man/summary.mjmcmc_parallel.Rd | 4 FBMS-1.3/FBMS/man/troot.Rd | 4 FBMS-1.3/FBMS/vignettes/FBMS-guide.Rmd | 9 137 files changed, 1689 insertions(+), 1251 deletions(-)
Title: The Maraca Plot: Visualizing Hierarchical Composite Endpoints
Description: Supports visual interpretation of hierarchical composite
endpoints (HCEs). HCEs are complex constructs used as primary endpoints in
clinical trials, combining outcomes of different types into ordinal endpoints,
in which each patient contributes the most clinically important event (one and
only one) to the analysis. See Karpefors M et al. (2022)
<doi:10.1177/17407745221134949>.
Author: Martin Karpefors [aut] ,
Samvel B. Gasparyan [aut] ,
Stefano Borini [ctb],
Kevin Anderson [aut] ,
Monika Huhn [aut, cre]
Maintainer: Monika Huhn <monika.huhn@astrazeneca.com>
Diff between maraca versions 1.0.1 dated 2025-07-28 and 1.1.0 dated 2025-11-20
maraca-1.0.1/maraca/build/partial.rdb |only maraca-1.0.1/maraca/man/plot.hce.Rd |only maraca-1.1.0/maraca/DESCRIPTION | 16 maraca-1.1.0/maraca/MD5 | 83 ++-- maraca-1.1.0/maraca/NAMESPACE | 12 maraca-1.1.0/maraca/NEWS.md | 37 + maraca-1.1.0/maraca/R/aaa.R | 8 maraca-1.1.0/maraca/R/animation.R |only maraca-1.1.0/maraca/R/general.R | 2 maraca-1.1.0/maraca/R/internal.R | 27 - maraca-1.1.0/maraca/R/internal_animation.R |only maraca-1.1.0/maraca/R/internal_plot.R |only maraca-1.1.0/maraca/R/internal_validation.R | 69 ++- maraca-1.1.0/maraca/R/internal_winOdds.R | 6 maraca-1.1.0/maraca/R/maraca.R | 420 +++++---------------- maraca-1.1.0/maraca/R/mosaicPlot.R | 37 - maraca-1.1.0/maraca/R/themes.R | 2 maraca-1.1.0/maraca/R/winOddsPlots.R | 58 -- maraca-1.1.0/maraca/build/vignette.rds |binary maraca-1.1.0/maraca/inst/doc/animation.R |only maraca-1.1.0/maraca/inst/doc/animation.Rmd |only maraca-1.1.0/maraca/inst/doc/animation.html |only maraca-1.1.0/maraca/inst/doc/faq.R | 2 maraca-1.1.0/maraca/inst/doc/faq.Rmd | 2 maraca-1.1.0/maraca/inst/doc/faq.html | 449 ++++++++++++----------- maraca-1.1.0/maraca/inst/doc/maraca.R | 3 maraca-1.1.0/maraca/inst/doc/maraca.Rmd | 15 maraca-1.1.0/maraca/inst/doc/maraca.html | 394 ++++++++++++-------- maraca-1.1.0/maraca/inst/doc/mosaic.Rmd | 2 maraca-1.1.0/maraca/inst/doc/mosaic.html | 345 +++++++++-------- maraca-1.1.0/maraca/inst/doc/otherEndpoints.html | 407 +++++++++++--------- maraca-1.1.0/maraca/inst/doc/themes.html | 331 +++++++++------- maraca-1.1.0/maraca/inst/doc/validation.html | 449 ++++++++++++----------- maraca-1.1.0/maraca/inst/doc/winOdds.Rmd | 352 +++++++++--------- maraca-1.1.0/maraca/inst/doc/winOdds.html | 359 +++++++++--------- maraca-1.1.0/maraca/man/animate_plot.Rd |only maraca-1.1.0/maraca/man/component_plot.Rd | 16 maraca-1.1.0/maraca/man/cumulative_plot.Rd | 18 maraca-1.1.0/maraca/man/maraca.Rd | 26 - maraca-1.1.0/maraca/man/mosaic_plot.Rd | 18 maraca-1.1.0/maraca/man/plot.adhce.Rd |only maraca-1.1.0/maraca/man/plot.maraca.Rd | 6 maraca-1.1.0/maraca/man/plot_maraca.Rd | 6 maraca-1.1.0/maraca/vignettes/animation.Rmd |only maraca-1.1.0/maraca/vignettes/faq.Rmd | 2 maraca-1.1.0/maraca/vignettes/maraca.Rmd | 15 maraca-1.1.0/maraca/vignettes/mosaic.Rmd | 2 maraca-1.1.0/maraca/vignettes/winOdds.Rmd | 352 +++++++++--------- 48 files changed, 2275 insertions(+), 2073 deletions(-)
Title: A New Four-Arm Within-Study Comparison Data on Math and
Vocabulary Training
Description: This dataset was collected using a new four-arm within-study comparison design. The study aimed to examine the impact of a mathematics training intervention and a vocabulary study session on post-test scores in mathematics and vocabulary, respectively. The innovative four-arm within-study comparison design facilitates both experimental and quasi-experimental identification of average causal effects.
Author: Bryan Keller [aut, cph],
Sangbaek Park [aut, ctb],
Jingru Zhang [aut, cre]
Maintainer: Jingru Zhang <jzhang2637@wisc.edu>
Diff between WSCdata versions 0.1.1 dated 2025-10-23 and 0.1.2 dated 2025-11-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 +++- R/WSCdata.R | 14 ++++++++++++-- man/WSCdata.Rd | 12 ++++++++++-- 5 files changed, 32 insertions(+), 12 deletions(-)
Title: Resampling Algorithms for 'mlr3' Framework
Description: A supervised learning algorithm inputs a train set,
and outputs a prediction function, which can be used on a test set.
If each data point belongs to a subset
(such as geographic region, year, etc), then
how do we know if subsets are similar enough so that
we can get accurate predictions on one subset,
after training on Other subsets?
And how do we know if training on All subsets would improve
prediction accuracy, relative to training on the Same subset?
SOAK, Same/Other/All K-fold cross-validation, <doi:10.48550/arXiv.2410.08643>
can be used to answer these questions, by fixing a test subset,
training models on Same/Other/All subsets, and then
comparing test error rates (Same versus Other and Same versus All).
Also provides code for estimating how many train samples
are required to get accurate predictions on a test set.
Author: Toby Hocking [aut, cre] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Jakob Richter [ctb] ,
Patrick Schratz [ctb] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [ctb],
Florian Pfisterer [ctb] ,
Raphael Sonabend [ctb] , [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between mlr3resampling versions 2025.6.23 dated 2025-06-23 and 2025.11.19 dated 2025-11-20
DESCRIPTION | 13 MD5 | 69 NAMESPACE | 14 NEWS | 237 + R/Learners.R |only R/ResamplingBase.R | 58 R/ResamplingSameOtherCV.R | 240 - R/ResamplingSameOtherSizesCV.R | 362 +- R/ResamplingVariableSizeTrainCV.R | 186 - R/proj.R | 551 ++-- R/pvalue.R | 330 +- R/score.R | 84 R/zzz.R | 39 build/vignette.rds |binary inst/doc/Newer_resamplers.R | 1147 ++++----- inst/doc/Newer_resamplers.Rmd | 1802 +++++++------- inst/doc/Newer_resamplers.html | 3072 ++++++++++++------------ inst/doc/Older_resamplers.R | 2003 +++++++-------- inst/doc/Older_resamplers.Rmd | 2947 +++++++++++------------ inst/doc/Older_resamplers.html | 4432 +++++++++++++++++------------------ inst/slurm-afterok.tmpl | 100 man/AZtrees.Rd | 120 man/Learners.Rd |only man/ResamplingSameOtherCV.Rd | 374 +- man/ResamplingSameOtherSizesCV.Rd | 432 +-- man/ResamplingVariableSizeTrainCV.Rd | 310 +- man/proj_compute.Rd | 156 - man/proj_grid.Rd | 190 - man/proj_results.Rd | 190 - man/proj_submit.Rd | 168 - man/proj_test.Rd |only man/pvalue.Rd | 144 - man/score.Rd | 128 - tests/testthat.R | 4 tests/testthat/test-CRAN.R | 1546 +++++------- vignettes/Newer_resamplers.Rmd | 1802 +++++++------- vignettes/Older_resamplers.Rmd | 2947 +++++++++++------------ 37 files changed, 13399 insertions(+), 12798 deletions(-)
More information about mlr3resampling at CRAN
Permanent link
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.4.1 dated 2025-09-22 and 0.4.3 dated 2025-11-20
DESCRIPTION | 10 MD5 | 52 NAMESPACE | 1 NEWS.md | 15 R/mapboxgl.R | 20 R/maplibre.R | 23 R/quickview.R | 39 R/sources.R | 76 R/style_helpers.R | 8 R/themes.R |only inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.css | 2 inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.js | 8 inst/htmlwidgets/lib/turf/turf.min.js | 13 inst/htmlwidgets/mapboxgl.js | 789 +- inst/htmlwidgets/mapboxgl.yaml | 6 inst/htmlwidgets/mapboxgl_compare.js | 529 + inst/htmlwidgets/mapboxgl_compare.yaml | 6 inst/htmlwidgets/maplibregl.js | 835 +- inst/htmlwidgets/maplibregl.yaml | 4 inst/htmlwidgets/maplibregl_compare.js | 7784 +++++++++++------------ inst/htmlwidgets/maplibregl_compare.yaml | 2 inst/htmlwidgets/turf-operations.js | 29 man/add_pmtiles_source.Rd | 19 man/add_vector_source.Rd | 4 man/mapboxgl.Rd | 7 man/maplibre.Rd | 10 man/openfreemap_style.Rd | 2 man/palette_to_lut.Rd |only 28 files changed, 5754 insertions(+), 4539 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent class mixed models, mixed models for curvilinear outcomes, mixed models for multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
Author: Cecile Proust-Lima [aut, cre],
Viviane Philipps [aut],
Amadou Diakite [ctb],
Benoit Liquet [ctb],
Alan Genz [ctb] ,
John Burkardt [ctb]
Maintainer: Cecile Proust-Lima <cecile.proust-lima@u-bordeaux.fr>
Diff between lcmm versions 2.2.1 dated 2025-02-12 and 2.2.2 dated 2025-11-20
DESCRIPTION | 14 - MD5 | 78 +++++---- NAMESPACE | 5 NEWS.md | 9 + R/Contlcmm.R | 20 +- R/ItemInfo.R | 31 ++- R/Jointlcmm.R | 20 +- R/Ordlcmm.R | 12 - R/applyLink.R |only R/createVarianceMatrix.R |only R/hlme.R | 23 +- R/lcmm-package.R | 4 R/loglik.R | 10 - R/mpjlcmm.R | 31 ++- R/multlcmm.R | 22 +- R/predictCor.R |only R/predictL.Jointlcmm.R | 86 ++++++++++ R/predictL.lcmm.R | 105 +++++++++++-- R/predictL.multlcmm.R | 79 +++++++++- R/predictRE.R | 17 +- R/predictY.Jointlcmm.R | 68 ++++++++ R/predictY.hlme.R | 105 ++++++++----- R/predictY.lcmm.R | 33 ++-- R/predictY.multlcmm.R | 2 R/removeNA.R |only R/sampleParameters.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/lcmm.html | 347 ++++++++++++++++++++++++++------------------ man/createVarianceMatrix.Rd |only man/lcmm-package.Rd | 2 man/predictCor.Rd |only man/predictL.Rd | 32 +++- man/predictRE.Rd | 7 man/predictY.Rd | 41 +++-- man/sampleParameters.Rd |only src/Integ.f90 | 2 src/Jointhet.f90 | 10 - src/hetmixCont.f90 | 7 src/hetmixMult.f90 | 7 src/hetmixOrd.f90 | 2 src/hetmixlin.f90 | 11 - src/iteminfo.f90 | 5 src/mpjhet.f90 | 9 - 44 files changed, 895 insertions(+), 361 deletions(-)
Title: Binarization of One-Dimensional Data
Description: Provides methods for the binarization of one-dimensional data and some visualization functions.
Author: Stefan Mundus [aut],
Christoph Muessel [aut],
Florian Schmid [aut],
Ludwig Lausser [aut],
Tamara J. Blaette [aut],
Martin Hopfensitz [aut],
Paul Kaftan [ctb],
Hans A. Kestler [aut, cre]
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>
Diff between Binarize versions 1.3.1 dated 2023-04-04 and 1.3.2 dated 2025-11-20
DESCRIPTION | 46 ++++++++++++++++++++++++++++++++++++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/Vignette.pdf |binary src/binarizeBASCB.c | 32 ++++++++++++++++---------------- 5 files changed, 60 insertions(+), 26 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 1.0.0 dated 2025-11-17 and 1.0.1 dated 2025-11-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/autoplot.R | 3 ++- R/fit_growth_rate.R | 17 +++++++++++++++-- R/plot.R | 2 +- man/autoplot.Rd | 3 ++- man/plot.Rd | 2 +- tests/testthat/test-seasonal_onset.R | 25 +++++++++++++++++++++++++ 9 files changed, 63 insertions(+), 18 deletions(-)
Title: Continuous-Time Multivariate Analysis
Description: Implements a basis function or functional data analysis framework
for several techniques of multivariate analysis in continuous-time
setting. Specifically, we introduced continuous-time analogues of
several classical techniques of multivariate analysis, such as
principal component analysis, canonical correlation analysis,
Fisher linear discriminant analysis, K-means clustering, and so
on. Details are in Biplab Paul, Philip T. Reiss, Erjia Cui and Noemi Foa (2025)
"Continuous-time multivariate analysis" <doi: 10.1080/10618600.2024.2374570>.
Author: Biplab Paul [aut, cre],
Philip Tzvi Reiss [aut],
Noemi Foa [aut],
Dror Arbiv [aut]
Maintainer: Biplab Paul <paul.biplab497@gmail.com>
Diff between ctmva versions 1.4.0 dated 2024-02-06 and 1.5.0 dated 2025-11-20
ctmva-1.4.0/ctmva/R/ctmva-package.R |only ctmva-1.4.0/ctmva/man/ctmva-package.Rd |only ctmva-1.5.0/ctmva/DESCRIPTION | 26 +++-- ctmva-1.5.0/ctmva/MD5 | 36 ++++--- ctmva-1.5.0/ctmva/NAMESPACE | 67 +++++++------- ctmva-1.5.0/ctmva/R/ccor.R |only ctmva-1.5.0/ctmva/R/ccor_boot.R |only ctmva-1.5.0/ctmva/R/ccor_oneboot.R |only ctmva-1.5.0/ctmva/R/ccor_posim.R |only ctmva-1.5.0/ctmva/R/cor.ct.R | 12 +- ctmva-1.5.0/ctmva/R/kmeans.ct.R | 25 ++--- ctmva-1.5.0/ctmva/R/meanbasis.R | 2 ctmva-1.5.0/ctmva/R/plot.kmeans.ct.R | 142 +++++++++++++++---------------- ctmva-1.5.0/ctmva/R/plot.lda.ct.R | 6 - ctmva-1.5.0/ctmva/R/plot.silhouette.ct.R | 46 +++++----- ctmva-1.5.0/ctmva/R/standardize.ct.R | 38 ++++---- ctmva-1.5.0/ctmva/man/ccor.Rd |only ctmva-1.5.0/ctmva/man/ccor_boot.Rd |only ctmva-1.5.0/ctmva/man/ccor_oneboot.Rd |only ctmva-1.5.0/ctmva/man/ccor_posim.Rd |only ctmva-1.5.0/ctmva/man/cor.ct.Rd | 6 + ctmva-1.5.0/ctmva/man/kmeans.ct.Rd | 8 - ctmva-1.5.0/ctmva/man/lda.ct.Rd | 88 +++++++++---------- ctmva-1.5.0/ctmva/man/standardize.ct.Rd | 6 - 24 files changed, 264 insertions(+), 244 deletions(-)
Title: Seamless Access to World Bank World Development Indicators (WDI)
Description: Access and analyze the World Bank's World Development Indicators
(WDI) using the corresponding API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>.
WDI provides more than 24,000 country or region-level indicators for various
contexts. 'wbwdi' enables users to download, process and work with WDI
series across multiple countries, aggregates, and time periods.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between wbwdi versions 1.0.2 dated 2025-10-28 and 1.0.3 dated 2025-11-20
DESCRIPTION | 10 ++++---- MD5 | 32 +++++++++++++------------- NEWS.md | 6 +++++ R/wdi_get.R | 49 ++++++++++++++++++++++++----------------- README.md | 24 +++++++++++++++++--- man/wbwdi-package.Rd | 2 - man/wdi_get.Rd | 2 - man/wdi_get_entities.Rd | 2 - man/wdi_get_income_levels.Rd | 2 - man/wdi_get_indicators.Rd | 2 - man/wdi_get_languages.Rd | 2 - man/wdi_get_lending_types.Rd | 2 - man/wdi_get_regions.Rd | 2 - man/wdi_get_sources.Rd | 2 - man/wdi_get_topics.Rd | 2 - man/wdi_search.Rd | 2 - tests/testthat/tests-wdi_get.R | 27 ++++++++++++++++++++++ 17 files changed, 115 insertions(+), 55 deletions(-)
Title: Chat UI Component for 'shiny'
Description: Provides a scrolling chat interface with multiline input,
suitable for creating chatbot apps based on Large Language Models
(LLMs). Designed to work particularly well with the 'ellmer' R package
for calling LLMs.
Author: Joe Cheng [aut],
Carson Sievert [aut],
Garrick Aden-Buie [aut, cre] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between shinychat versions 0.2.0 dated 2025-05-16 and 0.3.0 dated 2025-11-20
DESCRIPTION | 25 - MD5 | 82 +++- NAMESPACE | 11 NEWS.md | 34 + R/chat.R | 199 +++++++++-- R/chat_app.R | 220 +++++++++--- R/chat_restore.R |only R/client_state.R |only R/contents_shinychat.R |only R/markdown-stream.R | 2 R/shinychat-package.R | 12 R/utils-ellmer.R |only R/utils-shiny.R | 4 R/utils.R | 5 R/zzz.R | 1 README.md | 33 + inst/lib/shiny/GIT_VERSION | 2 inst/lib/shiny/chat/chat.css | 2 inst/lib/shiny/chat/chat.css.map | 6 inst/lib/shiny/chat/chat.js | 214 ++++++------ inst/lib/shiny/chat/chat.js.map | 8 inst/lib/shiny/markdown-stream/markdown-stream.css | 2 inst/lib/shiny/markdown-stream/markdown-stream.css.map | 4 inst/lib/shiny/markdown-stream/markdown-stream.js | 293 ++++++++--------- inst/lib/shiny/markdown-stream/markdown-stream.js.map | 8 man/chat_app.Rd | 65 +++ man/chat_append.Rd | 14 man/chat_append_message.Rd | 7 man/chat_clear.Rd | 2 man/chat_restore.Rd |only man/chat_ui.Rd | 12 man/contents_shinychat.Rd |only man/figures/app.png |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/markdown_stream.Rd | 2 man/shinychat-package.Rd | 5 man/update_chat_user_input.Rd |only tests/testthat/_snaps/chat.md | 16 tests/testthat/_snaps/contents_shinychat.md |only tests/testthat/apps |only tests/testthat/helpers-contents_shinychat.R |only tests/testthat/test-contents_shinychat.R |only 45 files changed, 850 insertions(+), 440 deletions(-)
Title: Estimate the Cause of Recurrent Vivax Malaria using Genetic Data
Description: Plot malaria parasite genetic data on two or more episodes.
Compute per-person posterior probabilities that each
Plasmodium vivax (Pv) recurrence is a recrudescence, relapse,
or reinfection (3Rs) using per-person P. vivax genetic data on two or
more episodes and a statistical model described in
Taylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>.
Plot per-recurrence posterior probabilities.
Author: Aimee Taylor [aut, cre] ,
Yong See Foo [aut] ,
Tymoteusz Kwiecinski [com] ,
Duncan Murdoch [ctb] ,
Mans Magnusson [ctb] ,
Institut Pasteur [cph],
European Union, Project 101110393 [fnd]
Maintainer: Aimee Taylor <aimee.taylor@pasteur.fr>
Diff between Pv3Rs versions 0.0.2 dated 2025-07-31 and 1.0.0 dated 2025-11-20
Pv3Rs-0.0.2/Pv3Rs/LICENSE |only Pv3Rs-1.0.0/Pv3Rs/DESCRIPTION | 20 +- Pv3Rs-1.0.0/Pv3Rs/LICENSE.note |only Pv3Rs-1.0.0/Pv3Rs/MD5 | 45 +++--- Pv3Rs-1.0.0/Pv3Rs/NEWS.md | 27 +++ Pv3Rs-1.0.0/Pv3Rs/R/compute_posterior.R | 7 + Pv3Rs-1.0.0/Pv3Rs/R/data.R | 4 Pv3Rs-1.0.0/Pv3Rs/R/helpers.R | 58 -------- Pv3Rs-1.0.0/Pv3Rs/R/msg_progress_bar.R |only Pv3Rs-1.0.0/Pv3Rs/R/plot_RG.R | 4 Pv3Rs-1.0.0/Pv3Rs/R/plot_data.R | 15 +- Pv3Rs-1.0.0/Pv3Rs/R/plot_simplex.R | 20 ++ Pv3Rs-1.0.0/Pv3Rs/R/recombine_parent_ids.R | 2 Pv3Rs-1.0.0/Pv3Rs/README.md | 151 ++++++++++------------ Pv3Rs-1.0.0/Pv3Rs/build/partial.rdb |binary Pv3Rs-1.0.0/Pv3Rs/build/vignette.rds |binary Pv3Rs-1.0.0/Pv3Rs/inst/doc/demonstrate-usage.html | 9 - Pv3Rs-1.0.0/Pv3Rs/man/Pv3Rs-package.Rd | 6 Pv3Rs-1.0.0/Pv3Rs/man/compute_posterior.Rd | 7 + Pv3Rs-1.0.0/Pv3Rs/man/fs_VHX_BPD.Rd | 2 Pv3Rs-1.0.0/Pv3Rs/man/macros/macros.Rd | 9 + Pv3Rs-1.0.0/Pv3Rs/man/plot_RG.Rd | 5 Pv3Rs-1.0.0/Pv3Rs/man/plot_data.Rd | 15 +- Pv3Rs-1.0.0/Pv3Rs/man/plot_simplex.Rd | 12 + Pv3Rs-1.0.0/Pv3Rs/man/ys_VHX_BPD.Rd | 2 25 files changed, 224 insertions(+), 196 deletions(-)
Title: 'HPZone' API Interface
Description: Package that simplifies the use of the 'HPZone' API. Most of the annoying and labor-intensive parts of the interface are handled by wrapper functions. Note that the API and its details are not publicly available. Information can be found at <https://www.ggdghorkennisnet.nl/groep/726-platform-infectieziekte-epidemiologen/documenten/map/9609> for those with access.
Author: Aart Dijkstra [aut, cre, cph]
Maintainer: Aart Dijkstra <a.dijkstra@ggdnog.nl>
Diff between HPZoneAPI versions 1.0.0 dated 2025-10-28 and 1.1.0 dated 2025-11-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 11 ++++++++--- R/HPZone_convert_dates.R | 2 +- R/HPZone_request.R | 9 ++++++--- 5 files changed, 23 insertions(+), 15 deletions(-)
Title: Retrieve Genomic and Clinical Data from CBioPortal Including
TCGA Data
Description: The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see <https://www.cbioportal.org/> for more information).
Author: Damiano Fantini [aut, cre]
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between TCGAretriever versions 1.9.1 dated 2024-01-23 and 1.10.1 dated 2025-11-20
TCGAretriever-1.10.1/TCGAretriever/DESCRIPTION | 14 - TCGAretriever-1.10.1/TCGAretriever/MD5 | 38 +-- TCGAretriever-1.10.1/TCGAretriever/R/tcgaretriever_v_1_10_1.R |only TCGAretriever-1.10.1/TCGAretriever/build/vignette.rds |binary TCGAretriever-1.10.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.R | 18 - TCGAretriever-1.10.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.html | 107 ++++------ TCGAretriever-1.10.1/TCGAretriever/man/TCGAretriever-package.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/blcaOutputExamples.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/cb_query.Rd | 8 TCGAretriever-1.10.1/TCGAretriever/man/expand_cases.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/fetch_all_tcgadata.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_cancer_studies.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_cancer_types.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_case_lists.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_clinical_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_gene_identifiers.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_genetic_profiles.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_molecular_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_mutation_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/make_groups.Rd | 2 TCGAretriever-1.9.1/TCGAretriever/R/tcgaretriever_v_1_9e.R |only 21 files changed, 108 insertions(+), 103 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 3.6.0 dated 2025-09-22 and 3.7.0 dated 2025-11-20
DESCRIPTION | 14 - MD5 | 62 +++-- NAMESPACE | 6 NEWS.md | 6 R/fit_svs.R | 103 +++++++-- R/fit_svs_edited.R | 320 +++++++++++++++++++++++++++--- R/fmrs.R | 25 ++ R/mol_parameters.R | 38 +++ R/mrs_data_display.R | 71 ++++-- R/mrs_data_proc.R | 196 +++++++++++++++--- R/mrs_read_nifti.R | 30 +- R/utils.R | 113 ++++++++++ inst/doc/spant-intro.html | 94 ++++---- inst/doc/spant-metabolite-simulation.html | 11 - inst/doc/spant-preprocessing.html | 4 inst/rmd/dataset_summary_svs_qa.Rmd | 52 ++-- inst/rmd/dyn_svs_report.Rmd | 5 inst/rmd/svs_edited_report.Rmd | 172 +++++++++++++++- inst/rmd/svs_report.Rmd | 4 man/add_noise_spec_snr.Rd | 11 - man/assign_dyns.Rd |only man/fit_svs.Rd | 15 + man/fit_svs_edited.Rd | 13 + man/fit_svs_edited_group_results.Rd |only man/fit_svs_group_results.Rd | 16 + man/lb_renoise.Rd |only man/match_files.Rd |only man/match_lineshape.Rd | 15 + man/paths2df.Rd |only man/preproc_svs.Rd | 8 man/preproc_svs_dataset.Rd | 6 man/segment_t1_fsl.Rd | 5 man/sim_asy_pvoigt.Rd | 2 man/stackplot.mrs_data.Rd | 6 man/trim_paths.Rd |only 35 files changed, 1173 insertions(+), 250 deletions(-)
Title: Mediation Analysis Confidence Intervals
Description: Computes confidence intervals for nonlinear functions of model
parameters (e.g., product of k coefficients) in single-level and multilevel
structural equation models. Methods include the distribution of the product,
Monte Carlo simulation, and bootstrap methods. It also performs the Model-Based
Constrained Optimization (MBCO) procedure for hypothesis testing of indirect
effects.
References:
Tofighi, D., and MacKinnon, D. P. (2011). RMediation: An R package for mediation
analysis confidence intervals. Behavior Research Methods, 43, 692-700.
<doi:10.3758/s13428-011-0076-x>;
Tofighi, D., and Kelley, K. (2020). Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.
Psychological Methods, 25(4), 496-515. <doi:10.1037/met0000259>;
Tofighi, D. (2020). Bootstrap Model-Based Constrained Optimization Tests of
Indirect Effects. Frontiers in Psychology, 10, 2989.
<doi:10.3389/fpsyg.2019.02989>.
Author: Davood Tofighi [aut, cre]
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Diff between RMediation versions 1.2.2 dated 2023-05-11 and 1.3.0 dated 2025-11-20
DESCRIPTION | 60 +++++++---- LICENSE |only MD5 | 79 ++++++++------- NAMESPACE | 74 ++++++++++---- NEWS.md | 19 +++ R/RMediation.R |only R/ci.R | 222 ++++++++++++++++++++++++++++++++++--------- R/confintAsymp.R | 160 +++++++++++++++---------------- R/confintMC.R | 237 ++++++++++++++++++++++------------------------ R/mbco.R | 146 ++++++++++++++-------------- R/mbco_asymp.R | 7 - R/mbco_parametric.R | 20 ++- R/mbco_semi.R | 29 +++-- R/medci.R | 228 ++++++++++++++++++++++++++++---------------- R/medciAsymp.R | 14 +- R/medciMC.R | 22 ++-- R/medciMeeker.R | 23 ++-- R/memory_exp.R | 1 R/pMC.R | 100 +++++++++++++------ R/pprodnormal.R | 66 +++++------- R/pprodnormalMC.R | 33 +++--- R/pprodnormalMeeker.R | 37 +++---- R/qMC.R | 98 ++++++++++++------- R/qprodnormal.R | 85 ++++++---------- R/qprodnormalMC.R | 31 +++--- R/qprodnormalMeeker.R | 103 +++++++++---------- R/tidy_logLik.R |only README.md | 94 +++++++++++++++++- build/partial.rdb |binary inst/WORDLIST |only man/RMediation-package.Rd | 13 ++ man/ci.Rd | 28 +++-- man/figures |only man/mbco.Rd | 39 +++---- man/medci.Rd | 11 +- man/pMC.Rd | 9 - man/pprodnormal.Rd | 2 man/qMC.Rd | 9 - man/qprodnormal.Rd | 16 +-- man/reexports.Rd |only man/tidy_logLik.Rd |only tests |only 42 files changed, 1268 insertions(+), 847 deletions(-)
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Description: A comprehensive suite of tools for managing, processing, and
analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports
quality control, geospatial analysis, and preparation of IFCB data for
publication in databases like <https://www.gbif.org>,
<https://www.obis.org>, <https://emodnet.ec.europa.eu/en>,
<https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package
integrates with the MATLAB 'ifcb-analysis' tool, which is described in
Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides
features for working with raw, manually classified, and machine
learning–classified image datasets. Key functionalities include image
extraction, particle size distribution analysis, taxonomic data
handling, and biomass concentration calculations, essential for
plankton research.
Author: Anders Torstensson [aut, cre] ,
Kendra Hayashi [ctb] ,
Jamie Enslein [ctb],
Raphael Kudela [ctb] ,
Alle Lie [ctb] ,
Jayme Smith [ctb] ,
DTO-BioFlow [fnd] ,
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between iRfcb versions 0.5.2 dated 2025-09-03 and 0.6.0 dated 2025-11-20
DESCRIPTION | 11 LICENSE | 4 LICENSE.note | 64 MD5 | 414 ++-- NAMESPACE | 394 ++-- NEWS.md | 22 R/defunct.R | 56 R/iRfcb-package.R | 72 R/ifcb_adjust_classes.R | 96 - R/ifcb_annotate_batch.R | 350 +-- R/ifcb_convert_filenames.R | 140 - R/ifcb_correct_annotation.R | 224 +- R/ifcb_count_mat_annotations.R | 266 +- R/ifcb_create_class2use.R | 96 - R/ifcb_create_empty_manual_file.R | 142 - R/ifcb_create_manifest.R | 126 - R/ifcb_download_dashboard_data.R | 769 ++++---- R/ifcb_download_dashboard_metadata.R |only R/ifcb_download_test_data.R | 284 +-- R/ifcb_download_whoi_plankton.R | 352 +-- R/ifcb_extract_annotated_images.R | 324 +-- R/ifcb_extract_biovolumes.R | 676 +++---- R/ifcb_extract_classified_images.R | 278 +-- R/ifcb_extract_pngs.R | 340 +-- R/ifcb_get_ecotaxa_example.R | 80 R/ifcb_get_ferrybox_data.R | 390 ++-- R/ifcb_get_mat_names.R | 82 R/ifcb_get_mat_variable.R | 110 - R/ifcb_get_runtime.R | 156 - R/ifcb_get_shark_colnames.R | 76 R/ifcb_get_shark_example.R | 48 R/ifcb_get_trophic_type.R | 160 - R/ifcb_helper_functions.R | 1560 ++++++++--------- R/ifcb_is_diatom.R | 122 - R/ifcb_is_in_basin.R | 180 - R/ifcb_is_near_land.R | 462 ++--- R/ifcb_list_dashboard_bins.R |only R/ifcb_match_taxa_names.R | 214 +- R/ifcb_merge_manual.R | 406 ++-- R/ifcb_prepare_whoi_plankton.R | 590 +++--- R/ifcb_psd.R | 432 ++-- R/ifcb_psd_plot.R | 265 +- R/ifcb_py_install.R | 196 +- R/ifcb_read_features.R | 132 - R/ifcb_read_hdr_data.R | 202 +- R/ifcb_read_mat.R | 122 - R/ifcb_read_summary.R | 336 +-- R/ifcb_replace_mat_values.R | 148 - R/ifcb_run_image_gallery.R | 58 R/ifcb_summarize_biovolumes.R | 307 +-- R/ifcb_summarize_class_counts.R | 280 +-- R/ifcb_summarize_png_counts.R | 360 +-- R/ifcb_summarize_png_metadata.R | 175 - R/ifcb_volume_analyzed.R | 130 - R/ifcb_volume_analyzed_from_adc.R | 160 - R/ifcb_which_basin.R | 192 +- R/ifcb_zip_matlab.R | 586 +++--- R/ifcb_zip_pngs.R | 380 ++-- R/zzz.R | 144 - README.md | 217 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/WORDLIST | 508 +++-- inst/doc/a-general-tutorial.R | 304 +-- inst/doc/a-general-tutorial.Rmd | 500 ++--- inst/doc/a-general-tutorial.html | 1475 ++++++++-------- inst/doc/qc-tutorial.R | 435 ++-- inst/doc/qc-tutorial.Rmd | 615 +++--- inst/doc/qc-tutorial.html | 1338 +++++++------- inst/exdata/MATLAB-template.md | 232 +- inst/exdata/README-template.md | 36 inst/exdata/ecotaxa_table_minimum.tsv | 10 inst/exdata/ecotaxa_table_with_classification.tsv | 22 inst/exdata/ecotaxa_table_without_classification.tsv | 18 inst/exdata/example.txt | 6 inst/exdata/example_ferrybox.txt | 6 inst/exdata/example_table_ifcb.tsv | 12 inst/python/create_manual_mat.py | 78 inst/python/edit_manual_file.py | 32 inst/python/psd.py | 878 +++++---- inst/python/read_mat_file.py | 150 - inst/python/replace_value_in_classlist.py | 56 inst/python/requirements.txt | 6 inst/python/save_class2use_to_mat.py | 20 inst/python/start_mc_adjust_classes_user_training.py | 62 inst/shiny/ifcb_image_gallery/server.R | 290 +-- inst/shiny/ifcb_image_gallery/ui.R | 66 man/create_package_manifest.Rd | 50 man/defunct.Rd | 32 man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/iRfcb-package.Rd | 72 man/ifcb_adjust_classes.Rd | 94 - man/ifcb_annotate_batch.Rd | 176 - man/ifcb_convert_filenames.Rd | 84 man/ifcb_correct_annotation.Rd | 152 - man/ifcb_count_mat_annotations.Rd | 122 - man/ifcb_create_class2use.Rd | 86 man/ifcb_create_empty_manual_file.Rd | 126 - man/ifcb_create_manifest.Rd | 84 man/ifcb_download_dashboard_data.Rd | 191 +- man/ifcb_download_dashboard_metadata.Rd |only man/ifcb_download_test_data.Rd | 110 - man/ifcb_download_whoi_plankton.Rd | 94 - man/ifcb_extract_annotated_images.Rd | 192 +- man/ifcb_extract_biovolumes.Rd | 255 +- man/ifcb_extract_classified_images.Rd | 184 +- man/ifcb_extract_pngs.Rd | 144 - man/ifcb_get_ecotaxa_example.Rd | 76 man/ifcb_get_ferrybox_data.Rd | 108 - man/ifcb_get_mat_names.Rd | 86 man/ifcb_get_mat_variable.Rd | 114 - man/ifcb_get_runtime.Rd | 68 man/ifcb_get_shark_colnames.Rd | 62 man/ifcb_get_shark_example.Rd | 48 man/ifcb_get_trophic_type.Rd | 74 man/ifcb_is_diatom.Rd | 108 - man/ifcb_is_in_basin.Rd | 86 man/ifcb_is_near_land.Rd | 164 - man/ifcb_list_dashboard_bins.Rd |only man/ifcb_match_taxa_names.Rd | 116 - man/ifcb_merge_manual.Rd | 162 - man/ifcb_prepare_whoi_plankton.Rd | 234 +- man/ifcb_psd.Rd | 257 +- man/ifcb_psd_plot.Rd | 134 - man/ifcb_py_install.Rd | 106 - man/ifcb_read_features.Rd | 82 man/ifcb_read_hdr_data.Rd | 84 man/ifcb_read_mat.Rd | 78 man/ifcb_read_summary.Rd | 108 - man/ifcb_replace_mat_values.Rd | 106 - man/ifcb_run_image_gallery.Rd | 56 man/ifcb_summarize_biovolumes.Rd | 245 +- man/ifcb_summarize_class_counts.Rd | 110 - man/ifcb_summarize_png_counts.Rd | 128 - man/ifcb_summarize_png_metadata.Rd | 75 man/ifcb_volume_analyzed.Rd | 78 man/ifcb_volume_analyzed_from_adc.Rd | 80 man/ifcb_which_basin.Rd | 86 man/ifcb_zip_matlab.Rd | 190 +- man/ifcb_zip_pngs.Rd | 136 - man/process_ifcb_string.Rd | 70 man/read_hdr_file.Rd | 34 man/retrieve_worms_records.Rd | 74 man/split_large_zip.Rd | 56 man/summarize_TBclass.Rd | 48 man/vol2C_lgdiatom.Rd | 54 man/vol2C_nondiatom.Rd | 54 tests/spelling.R | 6 tests/testthat.R | 24 tests/testthat/helper.R | 251 +- tests/testthat/setup-venv.R | 39 tests/testthat/test-defunct.R | 14 tests/testthat/test-ifcb_adjust_classes.R | 96 - tests/testthat/test-ifcb_annotate_batch.R | 266 +- tests/testthat/test-ifcb_convert_filenames.R | 202 +- tests/testthat/test-ifcb_correct_annotation.R | 466 ++--- tests/testthat/test-ifcb_count_mat_annotations.R | 142 - tests/testthat/test-ifcb_create_class2use.R | 46 tests/testthat/test-ifcb_create_empty_manual_file.R | 136 - tests/testthat/test-ifcb_create_manifest.R | 202 +- tests/testthat/test-ifcb_download_dashboard_data.R | 322 +-- tests/testthat/test-ifcb_download_dashboard_metadata.R |only tests/testthat/test-ifcb_download_test_data.R | 89 tests/testthat/test-ifcb_download_whoi_plankton.R | 42 tests/testthat/test-ifcb_extract_annotated_images.R | 304 +-- tests/testthat/test-ifcb_extract_biovolumes.R | 430 ++-- tests/testthat/test-ifcb_extract_classified_images.R | 482 ++--- tests/testthat/test-ifcb_extract_pngs.R | 150 - tests/testthat/test-ifcb_get_ecotaxa_example.R | 76 tests/testthat/test-ifcb_get_ferrybox_data.R | 339 +-- tests/testthat/test-ifcb_get_mat_names.R | 80 tests/testthat/test-ifcb_get_mat_variable.R | 112 - tests/testthat/test-ifcb_get_runtime.R | 158 - tests/testthat/test-ifcb_get_shark_colnames.R | 74 tests/testthat/test-ifcb_get_shark_example.R | 58 tests/testthat/test-ifcb_get_trophic_type.R | 80 tests/testthat/test-ifcb_is_diatom.R | 92 - tests/testthat/test-ifcb_is_in_basin.R | 118 - tests/testthat/test-ifcb_is_near_land.R | 160 - tests/testthat/test-ifcb_list_dashboard_bins.R |only tests/testthat/test-ifcb_match_taxa_names.R | 64 tests/testthat/test-ifcb_merge_manual.R | 266 +- tests/testthat/test-ifcb_prepare_whoi_plankton.R | 294 +-- tests/testthat/test-ifcb_psd.R | 226 +- tests/testthat/test-ifcb_psd_plot.R | 178 + tests/testthat/test-ifcb_py_install.R | 116 - tests/testthat/test-ifcb_read_features.R | 108 - tests/testthat/test-ifcb_read_hdr_data.R | 150 - tests/testthat/test-ifcb_read_summary.R | 220 +- tests/testthat/test-ifcb_replace_mat_values.R | 280 +-- tests/testthat/test-ifcb_run_image_gallery.R | 34 tests/testthat/test-ifcb_summarize_biovolumes.R | 230 +- tests/testthat/test-ifcb_summarize_class_counts.R | 88 tests/testthat/test-ifcb_summarize_png_counts.R | 226 +- tests/testthat/test-ifcb_summarize_png_metadata.R | 126 - tests/testthat/test-ifcb_volume_analyzed.R | 94 - tests/testthat/test-ifcb_volume_analyzed_from_adc.R | 78 tests/testthat/test-ifcb_which_basin.R | 130 - tests/testthat/test-ifcb_zip_matlab.R | 206 +- tests/testthat/test-ifcb_zip_pngs.R | 146 - vignettes/a-general-tutorial.Rmd | 500 ++--- vignettes/qc-tutorial.Rmd | 615 +++--- 211 files changed, 19368 insertions(+), 18875 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short
cgeneric, to define a Gaussian Markov random (GMRF) model.
The cgeneric contain code to specify GMRF elements such as
the graph and the precision matrix, and also the initial and
prior for its parameters, useful for model inference.
It can be accessed from a C program and is the recommended
way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>).
The 'INLAtools' implement functions to evaluate
each one of the model specifications from R.
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
A very useful functionality is the Kronecker product method
that creates a new model from multiple cgeneric models.
It also works with the rgeneric, the R version of the
cgeneric intended to easy try implementation of new GMRF models.
The Kronecker between two cgeneric models was used in
Sterr [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.0.4 dated 2025-06-23 and 0.0.5 dated 2025-11-20
INLAtools-0.0.4/INLAtools/man/cgeneric.Rd |only INLAtools-0.0.4/INLAtools/man/rgeneric.Rd |only INLAtools-0.0.4/INLAtools/tests |only INLAtools-0.0.5/INLAtools/DESCRIPTION | 44 ++ INLAtools-0.0.5/INLAtools/MD5 | 48 +-- INLAtools-0.0.5/INLAtools/NAMESPACE | 21 + INLAtools-0.0.5/INLAtools/R/Matrix.R | 33 +- INLAtools-0.0.5/INLAtools/R/aaa_classes.R | 18 - INLAtools-0.0.5/INLAtools/R/aaa_methods.R | 35 +- INLAtools-0.0.5/INLAtools/R/cgeneric.R | 281 +++++++++++-------- INLAtools-0.0.5/INLAtools/R/cgeneric_generic0.R | 28 - INLAtools-0.0.5/INLAtools/R/cgeneric_kronecker.R | 281 ++++++++++++++----- INLAtools-0.0.5/INLAtools/R/cgeneric_utils.R | 85 +++-- INLAtools-0.0.5/INLAtools/R/rgeneric.R | 60 ++-- INLAtools-0.0.5/INLAtools/R/utils.R | 18 - INLAtools-0.0.5/INLAtools/demo |only INLAtools-0.0.5/INLAtools/man/cgeneric-class.Rd | 123 +++++--- INLAtools-0.0.5/INLAtools/man/cgeneric_generic0.Rd | 2 INLAtools-0.0.5/INLAtools/man/extraconstr.Rd | 10 INLAtools-0.0.5/INLAtools/man/is.zero.Rd | 14 INLAtools-0.0.5/INLAtools/man/multi_generic_model.Rd |only INLAtools-0.0.5/INLAtools/man/rgeneric-class.Rd | 64 +++- INLAtools-0.0.5/INLAtools/src/INLAtools.h | 8 INLAtools-0.0.5/INLAtools/src/cgeneric_generic0.c | 19 - INLAtools-0.0.5/INLAtools/src/cgeneric_get.c | 27 - INLAtools-0.0.5/INLAtools/src/cgeneric_kronecker.c | 127 +++++--- 26 files changed, 857 insertions(+), 489 deletions(-)
Title: Gini-Based Composite Indicators
Description: An implementation of Gini-based weighting approaches in constructing composite indicators, providing functionalities for normalization, aggregation, and ranking comparison.
Author: Viet Duong Nguyen [aut, cre] ,
Chiara Gigliarano [aut] ,
Mariateresa Ciommi [aut]
Maintainer: Viet Duong Nguyen <viet-duong.nguyen@outlook.com>
Diff between giniCI versions 0.1.0 dated 2025-02-13 and 0.1.3 dated 2025-11-20
DESCRIPTION | 21 +++++++++++++-------- MD5 | 28 +++++++++++++++------------- NEWS.md |only R/bli.R | 2 +- R/giniCI-package.R | 4 ++-- R/giniCI.R | 12 ++++++++---- R/normalize.R | 4 ++-- R/summary.rankComp.R | 4 ++-- README.md |only build/vignette.rds |binary inst/doc/giniCI.pdf |binary man/bli.Rd | 2 +- man/giniCI-package.Rd | 4 ++-- man/giniCI.Rd | 12 ++++++++---- man/normalize.Rd | 4 ++-- man/summary.rankComp.Rd | 4 ++-- 16 files changed, 58 insertions(+), 43 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages (notably 'ggplot2')
to help facilitate the plotting of data over long time intervals, including,
but not limited to, geological, evolutionary, and ecological data. The
primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to
assist with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 2.2.0 dated 2025-06-19 and 2.3.0 dated 2025-11-20
deeptime-2.2.0/deeptime/man/getScaleData.Rd |only deeptime-2.2.0/deeptime/tests/testthat/_snaps/gggeo_scale |only deeptime-2.2.0/deeptime/tests/testthat/_snaps/ggplot4/gggeo_scale |only deeptime-2.3.0/deeptime/DESCRIPTION | 8 deeptime-2.3.0/deeptime/MD5 | 167 ++-- deeptime-2.3.0/deeptime/NAMESPACE | 11 deeptime-2.3.0/deeptime/NEWS.md | 22 deeptime-2.3.0/deeptime/R/coord_geo.R | 46 - deeptime-2.3.0/deeptime/R/data.R | 25 deeptime-2.3.0/deeptime/R/get_scale_data.R | 14 deeptime-2.3.0/deeptime/R/gggeo_scale.R | 363 ---------- deeptime-2.3.0/deeptime/R/gggeo_scale_old.R | 4 deeptime-2.3.0/deeptime/R/patterns.R | 55 + deeptime-2.3.0/deeptime/R/scales.R | 2 deeptime-2.3.0/deeptime/R/zzz.R | 2 deeptime-2.3.0/deeptime/README.md | 6 deeptime-2.3.0/deeptime/build/vignette.rds |binary deeptime-2.3.0/deeptime/data/FGDC_names.rda |only deeptime-2.3.0/deeptime/inst/CITATION | 16 deeptime-2.3.0/deeptime/inst/doc/coord.Rmd | 2 deeptime-2.3.0/deeptime/inst/doc/coord.html | 16 deeptime-2.3.0/deeptime/inst/doc/coord_geo.html | 19 deeptime-2.3.0/deeptime/inst/doc/geo.R | 4 deeptime-2.3.0/deeptime/inst/doc/geo.Rmd | 7 deeptime-2.3.0/deeptime/inst/doc/geo.html | 81 +- deeptime-2.3.0/deeptime/inst/doc/ggarrange2.html | 23 deeptime-2.3.0/deeptime/inst/doc/phylogenies.R | 15 deeptime-2.3.0/deeptime/inst/doc/phylogenies.Rmd | 26 deeptime-2.3.0/deeptime/inst/doc/phylogenies.html | 61 + deeptime-2.3.0/deeptime/inst/doc/time.html | 23 deeptime-2.3.0/deeptime/inst/doc/traits.html | 11 deeptime-2.3.0/deeptime/man/coord_geo.Rd | 39 - 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deeptime-2.3.0/deeptime/tests/testthat/test-gggeo_scale.R | 35 deeptime-2.3.0/deeptime/tests/testthat/test-patterns.R | 10 deeptime-2.3.0/deeptime/vignettes/coord.Rmd | 2 deeptime-2.3.0/deeptime/vignettes/geo.Rmd | 7 deeptime-2.3.0/deeptime/vignettes/phylogenies-6.png |only deeptime-2.3.0/deeptime/vignettes/phylogenies.Rmd | 26 87 files changed, 848 insertions(+), 1062 deletions(-)
Title: Statistical Inference and Prediction of Annotations in
Phylogenetic Trees
Description: Implements a parsimonious evolutionary model to analyze and
predict gene-functional annotations in phylogenetic trees as described in Vega
Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on
computational efficiency, 'aphylo' makes it possible to estimate pooled
phylogenetic models, including thousands (hundreds) of annotations (trees) in
the same run. The package also provides the tools for visualization of
annotated phylogenies, calculation of posterior probabilities (prediction)
and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Author: George Vega Yon [aut, cre] ,
National Cancer Institute [fnd] ,
USC Biostatistics [cph]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.3-4 dated 2024-12-03
Diff between aphylo versions 0.3-4 dated 2024-12-03 and 0.3-5 dated 2025-11-20
DESCRIPTION | 11 MD5 | 28 build/vignette.rds |binary configure | 1402 +++++++++++++++++++++++++--------------- configure.ac | 10 inst/doc/example.R | 22 inst/doc/example.html | 28 man/figures/MCMC-1.png |binary man/figures/MCMC-2.png |binary man/figures/MLE-1.png |binary man/figures/Predict-1.png |binary man/figures/get-offspring-1.png |binary man/figures/get-offspring-2.png |binary src/Makevars.in | 2 src/Makevars.win | 4 15 files changed, 945 insertions(+), 562 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.4.1 dated 2025-11-06 and 1.4.2 dated 2025-11-20
DESCRIPTION | 14 +++++++------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 3 +++ NEWS | 14 ++++++++++---- R/do_possession_stats.R | 11 +++++++++-- R/get_four_factors_plot.R | 6 +++--- R/get_roster_age_profile.R | 29 ++++++++++++++++++++--------- R/get_shooting_plot.R | 5 ++++- R/get_sticker.R |only data/acb_age_profile_data_2526.RData |binary data/acb_sticker_data_2526.RData |only inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- inst/doc/BAwiR_sc.html | 4 ++-- man/acb_sticker_data_2526.Rd |only man/get_four_factors_plot.Rd | 2 +- man/get_shooting_plot.Rd | 3 +++ man/get_sticker.Rd |only 18 files changed, 83 insertions(+), 46 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.6-0 dated 2025-09-20 and 3.6-1 dated 2025-11-20
DESCRIPTION | 8 +- MD5 | 54 +++++++-------- NEWS | 32 +++++++++ R/diagram.R | 8 +- R/funxy.R | 2 R/hyperframe.R | 6 - R/hypersub.R | 2 R/layered.R | 6 - R/listof.R | 4 - R/marks.R | 2 R/morphology.R | 2 R/nnfun.R | 4 - R/owin2mask.R | 6 - R/pp3.R | 4 - R/psp.R | 2 R/quadratcount.R | 4 - R/solist.R | 12 +-- R/split.ppp.R | 2 R/symbolmap.R | 2 R/tess.R | 160 ++++++++++++++++++++++++++++++--------------- R/tessfun.R | 2 R/texture.R | 2 R/wingeom.R | 4 - inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/as.im.Rd | 9 ++ man/macros/defns.Rd | 3 man/owin2mask.Rd | 5 - 28 files changed, 228 insertions(+), 121 deletions(-)
Title: Number-Theoretic Functions
Description: Provides number-theoretic functions for factorization, prime
numbers, twin primes, primitive roots, modular logarithm and
inverses, extended GCD, Farey series and continued fractions.
Includes Legendre and Jacobi symbols, some divisor functions,
Euler's Phi function, etc.
Author: Hans Werner Borchers [aut],
Hans W. Borchers [cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.8-5 dated 2022-11-23 and 0.9-2 dated 2025-11-20
DESCRIPTION | 20 +++++--- MD5 | 20 +++++--- NAMESPACE | 6 +- NEWS | 16 ++++++ R/contFrac.R | 125 ++++++++++++++++++++++++++++++++++++++++------------- R/modNthroot.R |only R/polygonal.R |only R/progression.R |only build/partial.rdb |binary man/cf2num.Rd | 99 +++++++++++++++++++++++++++++++---------- man/divisors.Rd | 17 +++++++ man/modNthroot.Rd |only man/polygonal.Rd |only man/progression.Rd |only 14 files changed, 233 insertions(+), 70 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and only
adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019) <doi:10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre] ,
Guillem Rigaill [aut],
Nathalie Vialaneix [aut] ,
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.6.10 dated 2024-10-08 and 0.6.11 dated 2025-11-20
DESCRIPTION | 14 - MD5 | 28 +-- NEWS.md | 18 +- R/adjclust.R | 2 R/plotSim.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/hicClust.R | 24 +- inst/doc/hicClust.html | 288 +++++++++++++++++++++++--------- inst/doc/notesCHAC.R | 8 inst/doc/notesCHAC.html | 386 +++++++++++++++++++++++++++++-------------- inst/doc/snpClust.html | 285 +++++++++++++++++++------------ man/adjClust.Rd | 2 man/plotSim.Rd | 2 tests/testthat/test_modify.R | 10 - 15 files changed, 713 insertions(+), 356 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.20.0 dated 2025-09-17 and 0.21.0 dated 2025-11-20
adbcdrivermanager-0.20.0/adbcdrivermanager/src/c/vendor/portable-snippets/safe-math.h |only adbcdrivermanager-0.21.0/adbcdrivermanager/DESCRIPTION | 6 adbcdrivermanager-0.21.0/adbcdrivermanager/MD5 | 20 +- adbcdrivermanager-0.21.0/adbcdrivermanager/R/driver_void.R | 1 adbcdrivermanager-0.21.0/adbcdrivermanager/R/helpers.R | 9 - adbcdrivermanager-0.21.0/adbcdrivermanager/man/adbc_driver_load.Rd | 3 adbcdrivermanager-0.21.0/adbcdrivermanager/man/read_adbc.Rd | 7 adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/bind_stream.h | 6 adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/copy/reader.h | 40 +++- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/statement.cc | 18 +- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver_manager/adbc_driver_manager.cc | 89 +++++++--- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/vendor/portable-snippets/include |only 12 files changed, 147 insertions(+), 52 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: Group Sequential Design with Non-Constant Effect
Description: The goal of 'gsDesign2' is to enable fixed or group sequential
design under non-proportional hazards. To enable highly flexible enrollment,
time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise
constant enrollment, failure rates, and dropout rates for a stratified
population. This package includes three methods for designs:
average hazard ratio, weighted logrank tests in Yung and Liu (2019)
<doi:10.1111/biom.13196>, and MaxCombo tests.
Substantial flexibility on top of what is in the 'gsDesign' package
is intended for selecting boundaries.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
Yilong Zhang [aut],
John Blischak [aut],
Yihui Xie [aut],
Nan Xiao [aut],
Jianxiao Yang [aut],
Amin Shirazi [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Xin Tong Li [ctb],
Chenxiang Li [ctb],
[...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between gsDesign2 versions 1.1.6 dated 2025-09-11 and 1.1.7 dated 2025-11-19
DESCRIPTION | 10 MD5 | 114 NAMESPACE | 10 NEWS.md | 19 R/ahr.R | 6 R/as_gt.R | 70 R/as_rtf.R | 11 R/expected_event.R | 21 R/expected_time.R | 1 R/fixed_design_ahr.R | 16 R/fixed_design_fh.R | 24 R/fixed_design_lf.R | 25 R/fixed_design_maxcombo.R | 32 R/fixed_design_mb.R | 21 R/fixed_design_milestone.R | 22 R/fixed_design_rd.R | 20 R/fixed_design_rmst.R | 23 R/gs_bound_summary.R | 6 R/gs_design_ahr.R | 61 R/gs_design_combo.R | 20 R/gs_design_rd.R | 17 R/gs_design_wlr.R | 22 R/gs_power_ahr.R | 21 R/gs_power_combo.R | 20 R/gs_power_npe.R | 15 R/gs_power_rd.R | 22 R/gs_power_wlr.R | 21 R/gs_spending_bound.R | 7 R/gs_spending_combo.R | 3 R/gs_update_ahr.R | 9 R/print.R |only R/pw_info.R | 13 R/summary.R | 35 R/text_summary.R | 40 R/to_integer.R | 62 R/utils.R | 13 inst/doc/gsDesign2.html | 6157 ++++------ man/ahr.Rd | 2 man/as_gt.Rd | 8 man/as_rtf.Rd | 8 man/expected_event.Rd | 18 man/fixed_design.Rd | 6 man/gs_design_ahr.Rd | 24 man/gs_design_combo.Rd | 6 man/gs_design_wlr.Rd | 24 man/gs_power_ahr.Rd | 26 man/gs_power_combo.Rd | 6 man/gs_power_design_npe.Rd | 27 man/gs_power_wlr.Rd | 24 man/pw_info.Rd | 2 man/text_summary.Rd | 9 tests/testthat/_snaps/independent_as_gt.md | 84 tests/testthat/_snaps/independent_as_rtf/fixed_design_ahr_footnote.rtf | 2 tests/testthat/_snaps/independent_as_rtf/fixed_design_ahr_title.rtf | 2 tests/testthat/test-developer-as_gt.R |only tests/testthat/test-developer-pw_info.R | 15 tests/testthat/test-developer-to_integer.R | 18 tests/testthat/test-independent-ahr.R | 13 tests/testthat/test-independent-gs_power_ahr.R | 50 59 files changed, 3677 insertions(+), 3706 deletions(-)
Title: Precision Agriculture Computational Utilities
Description: Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.
Author: dos Santos Caio [aut, cre],
Miguez Fernando [aut]
Maintainer: dos Santos Caio <clsantos@iastate.edu>
Diff between pacu versions 0.1.72 dated 2025-09-26 and 0.1.74 dated 2025-11-19
pacu-0.1.72/pacu/inst/extdata/S2B_MSIL2A_20230630T165849_N0509_R069_T15TVG_20230630T213917.zip |only pacu-0.1.72/pacu/inst/extdata/S2B_MSIL2A_20230703T170859_N0509_R112_T15TVG_20230703T211843.zip |only pacu-0.1.74/pacu/DESCRIPTION | 6 +- pacu-0.1.74/pacu/MD5 | 28 +++++----- pacu-0.1.74/pacu/R/get_rgb.R | 28 +++++----- pacu-0.1.74/pacu/R/yield.R | 14 +++-- pacu-0.1.74/pacu/inst/doc/pacu.html | 4 - pacu-0.1.74/pacu/inst/doc/pacu_faq.html | 4 - pacu-0.1.74/pacu/inst/doc/pacu_sat.Rmd | 2 pacu-0.1.74/pacu/inst/doc/pacu_sat.html | 22 +++---- pacu-0.1.74/pacu/inst/doc/pacu_weather.html | 4 - pacu-0.1.74/pacu/inst/doc/pacu_ym.html | 4 - pacu-0.1.74/pacu/inst/extdata/S2B_MSIL2A_20230623T170849_N0510_R112_T15TVG_20240910T005418.zip |only pacu-0.1.74/pacu/inst/extdata/S2B_MSIL2A_20230630T165849_N0510_R069_T15TVG_20241003T133505.zip |only pacu-0.1.74/pacu/inst/extdata/ds-browse-object.rds |binary pacu-0.1.74/pacu/man/pa_get_rgb.Rd | 5 + pacu-0.1.74/pacu/vignettes/pacu_sat.Rmd | 2 17 files changed, 64 insertions(+), 59 deletions(-)
Title: Econdataverse 'IMF Data API' Client
Description: Provides user-friendly functions for programmatic access to macroeconomic data from the International Monetary Fund's 'SDMX 3.0 IMF Data API' <https://data.imf.org/en/Resource-Pages/IMF-API>.
Author: Teal Insights [cre, cph],
Christopher C. Smith [aut],
Christoph Scheuch [ctb]
Maintainer: Teal Insights <lte@tealinsights.com>
Diff between imfapi versions 0.1.1 dated 2025-10-30 and 0.1.2 dated 2025-11-19
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/imf_get_codelists.R | 2 ++ R/imf_get_dataflows.R | 2 ++ R/imf_get_datastructure.R | 2 ++ README.md | 16 ++++++++-------- man/imf_get_codelists.Rd | 2 ++ man/imf_get_dataflows.Rd | 2 ++ man/imf_get_datastructure.Rd | 2 ++ 10 files changed, 36 insertions(+), 20 deletions(-)
Title: Extension Types for Spatial Data for Use with 'Arrow'
Description: Provides extension types and conversions to between R-native
object types and 'Arrow' columnar types. This includes integration among
the 'arrow', 'nanoarrow', 'sf', and 'wk' packages such that spatial
metadata is preserved wherever possible. Extension type implementations
ensure first-class geometry data type support in the 'arrow' and 'nanoarrow'
packages.
Author: Dewey Dunnington [aut, cre] ,
Anthony North [ctb],
Apache Software Foundation [cph],
Ulf Adams [cph],
Daniel Lemire [cph],
Joao Paulo Magalhaes [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between geoarrow versions 0.4.0 dated 2025-09-21 and 0.4.1 dated 2025-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-pkg-sf.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Behavioral Insight Design: A Toolkit for Integrating Behavioral
Science in UI/UX Design
Description: Provides a framework and toolkit to guide R dashboard developers in
implementing the Behavioral Insight Design (BID) framework. The package offers
functions for documenting each of the five stages (Interpret, Notice,
Anticipate, Structure, and Validate), along with a comprehensive concept
dictionary. Works with both 'shiny' applications and 'Quarto' dashboards.
Author: Jeremy Winget [aut, cre]
Maintainer: Jeremy Winget <contact@jrwinget.com>
Diff between bidux versions 0.3.2 dated 2025-10-28 and 0.3.3 dated 2025-11-19
DESCRIPTION | 19 MD5 | 115 +- NAMESPACE | 1 NEWS.md | 24 R/bid_anticipate.R | 75 + R/bid_interpret.R | 10 R/bid_notice.R | 4 R/bid_quick_suggest.R |only R/bid_report.R | 3 R/bid_structure.R | 34 R/data_classes.R | 19 R/mappings.R | 2 R/structure_components.R | 14 R/structure_suggest.R | 179 ++++ R/suggest_rules.R | 5 R/telemetry_ingest.R | 240 ++++-- R/telemetry_notices.R | 100 +- R/utils_domain.R | 2 R/utils_validation.R | 8 README.md | 20 build/vignette.rds |binary inst/WORDLIST | 11 inst/doc/api-modernization.R | 4 inst/doc/api-modernization.Rmd | 6 inst/doc/api-modernization.html | 6 inst/doc/getting-started.R | 52 + inst/doc/getting-started.Rmd | 73 + inst/doc/getting-started.html | 447 ++++++----- inst/doc/practical-examples.R | 4 inst/doc/practical-examples.Rmd | 4 inst/doc/practical-examples.html | 4 inst/doc/quick-start.R |only inst/doc/quick-start.Rmd |only inst/doc/quick-start.html |only inst/doc/telemetry-integration.R | 78 +- inst/doc/telemetry-integration.Rmd | 78 +- inst/doc/telemetry-integration.html | 130 +-- inst/extdata/bid_concepts_data.csv | 6 man/assign_category.Rd |only man/assign_difficulty.Rd |only man/bid_ingest_telemetry.Rd | 39 - man/bid_quick_suggest.Rd |only man/bid_report.Rd | 3 man/bid_structure.Rd | 25 man/bid_suggest_components.Rd | 8 man/bid_telemetry.Rd | 29 man/bidux-package.Rd | 2 man/flatten_suggestions_to_tibble.Rd |only man/read_telemetry_data.Rd | 10 man/read_telemetry_sqlite.Rd | 6 man/structure_suggestions.Rd | 15 tests/testthat/test-bid_anticipate.R | 1031 ++++++++++++++++++++++++++ tests/testthat/test-bid_ingest_telemetry.R | 1114 +++++++++++++++++++++++++++++ tests/testthat/test-bid_interpret.R | 652 ++++++++++++++++ tests/testthat/test-bid_quick_suggest.R |only tests/testthat/test-data_concepts.R | 4 tests/testthat/test-structure_tibble.R |only tests/testthat/test-telemetry_ingest.R | 5 tests/testthat/test-utils.R | 9 vignettes/api-modernization.Rmd | 6 vignettes/getting-started.Rmd | 73 + vignettes/practical-examples.Rmd | 4 vignettes/quick-start.Rmd |only vignettes/telemetry-integration.Rmd | 78 +- 64 files changed, 4202 insertions(+), 688 deletions(-)
Title: Develop and Apply Two-Regression Algorithms
Description: Facilitates development and application of two-regression
algorithms for research-grade wearable devices. It provides an easy
way for users to access previously-developed algorithms, and also to
develop their own. Initial motivation came from Hibbing PR, LaMunion SR,
Kaplan AS, & Crouter SE (2018) <doi:10.1249/MSS.0000000000001532>.
However, other algorithms are now supported. Please see the associated
references in the package documentation for full details of the algorithms
that are supported.
Author: Paul R. Hibbing [aut, cre],
Vincent T. van Hees [ctb]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2022-09-05
Diff between TwoRegression versions 1.0.0 dated 2022-09-05 and 1.1.1 dated 2025-11-19
TwoRegression-1.0.0/TwoRegression/LICENSE |only TwoRegression-1.0.0/TwoRegression/R/hibbing_smooth_old.R |only TwoRegression-1.0.0/TwoRegression/README.md |only TwoRegression-1.1.1/TwoRegression/DESCRIPTION | 14 TwoRegression-1.1.1/TwoRegression/MD5 | 71 TwoRegression-1.1.1/TwoRegression/NEWS.md | 16 TwoRegression-1.1.1/TwoRegression/R/TwoRegression.R | 8 TwoRegression-1.1.1/TwoRegression/R/hibbing_subwrapper__main.R | 11 TwoRegression-1.1.1/TwoRegression/R/plot_2rm__main.R | 43 TwoRegression-1.1.1/TwoRegression/R/plot_2rm_helpers.R | 2 TwoRegression-1.1.1/TwoRegression/R/predict_2rm.R | 10 TwoRegression-1.1.1/TwoRegression/build/vignette.rds |binary TwoRegression-1.1.1/TwoRegression/inst/CITATION | 7 TwoRegression-1.1.1/TwoRegression/inst/doc/TwoRegression.R | 6 TwoRegression-1.1.1/TwoRegression/inst/doc/TwoRegression.html | 907 +++++----- TwoRegression-1.1.1/TwoRegression/man/DualCP_LOSO.Rd | 156 - TwoRegression-1.1.1/TwoRegression/man/all_data.Rd | 84 TwoRegression-1.1.1/TwoRegression/man/count_data.Rd | 46 TwoRegression-1.1.1/TwoRegression/man/directions.Rd | 52 TwoRegression-1.1.1/TwoRegression/man/fit_2rm.Rd | 214 +- TwoRegression-1.1.1/TwoRegression/man/get_2rm_formula.Rd | 34 TwoRegression-1.1.1/TwoRegression/man/get_cut_point.Rd | 76 TwoRegression-1.1.1/TwoRegression/man/get_cv.Rd | 138 - TwoRegression-1.1.1/TwoRegression/man/get_lm_formula.Rd | 30 TwoRegression-1.1.1/TwoRegression/man/hibbing-helpers.Rd | 12 TwoRegression-1.1.1/TwoRegression/man/imu_to_check.Rd | 56 TwoRegression-1.1.1/TwoRegression/man/imu_to_collapse.Rd | 78 TwoRegression-1.1.1/TwoRegression/man/plot.TwoRegression.Rd | 280 +-- TwoRegression-1.1.1/TwoRegression/man/plotCP.Rd | 42 TwoRegression-1.1.1/TwoRegression/man/plot_sed.Rd | 76 TwoRegression-1.1.1/TwoRegression/man/plot_walkrun.Rd | 72 TwoRegression-1.1.1/TwoRegression/man/predict.TwoRegression.Rd | 170 - TwoRegression-1.1.1/TwoRegression/man/raw_for_cv.Rd | 42 TwoRegression-1.1.1/TwoRegression/man/raw_to_collapse.Rd | 44 TwoRegression-1.1.1/TwoRegression/man/summary.TwoRegression.Rd | 190 +- TwoRegression-1.1.1/TwoRegression/tests/testthat.R | 8 TwoRegression-1.1.1/TwoRegression/tests/testthat/_snaps/fit_2rm__main/2rm.rds |binary TwoRegression-1.1.1/TwoRegression/tests/testthat/_snaps/summary_2rm__main/summary2rm.rds |binary 38 files changed, 1503 insertions(+), 1492 deletions(-)
Title: Apply Sojourn Methods for Processing ActiGraph Accelerometer
Data
Description: Provides a simple way for utilizing Sojourn methods for
accelerometer processing, as detailed in Lyden K, Keadle S,
Staudenmayer J, & Freedson P (2014) <doi:10.1249/MSS.0b013e3182a42a2d>,
Ellingson LD, Schwabacher IJ, Kim Y, Welk GJ, & Cook DB (2016)
<doi:10.1249/MSS.0000000000000915>, and Hibbing PR, Ellingson LD,
Dixon PM, & Welk GJ (2018) <doi:10.1249/MSS.0000000000001486>.
Author: Paul R. Hibbing [aut, cre],
Kate Lyden [aut],
Isaac J. Schwabacher [aut]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2021-05-07
Diff between Sojourn versions 1.1.0 dated 2021-05-07 and 1.2.1 dated 2025-11-19
Sojourn-1.1.0/Sojourn/README.md |only Sojourn-1.2.1/Sojourn/DESCRIPTION | 8 ++++---- Sojourn-1.2.1/Sojourn/MD5 | 13 ++++++------- Sojourn-1.2.1/Sojourn/NEWS.md | 20 ++++++++++++++++++++ Sojourn-1.2.1/Sojourn/R/SIP_Functions.R | 2 ++ Sojourn-1.2.1/Sojourn/R/youth_input_demographic.R | 4 ++-- Sojourn-1.2.1/Sojourn/inst/CITATION | 19 +++++++++++-------- Sojourn-1.2.1/Sojourn/man/enhance_actigraph.Rd | 3 +++ 8 files changed, 48 insertions(+), 21 deletions(-)
Title: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and
Machine Learning Toolkit as Described in Burdukiewicz (2022)
<doi:10.21105/Joss.04407>
Description: Extracts features from amplification curve data of quantitative
Polymerase Chain Reactions (qPCR) according to Pabinger et al. 2014
<doi:10.1016/j.bdq.2014.08.002> for machine learning purposes. Helper
functions prepare the amplification curve data for processing as functional
data (e.g., Hausdorff distance) or enable the plotting of amplification
curve classes (negative, ambiguous, positive). The hookreg() and hookregNL()
functions of Burdukiewicz et al. (2018) <doi:10.1016/j.bdq.2018.08.001>
can be used to predict amplification curves with an hook effect-like
curvature. The pcrfit_single() function can be used to extract features
from an amplification curve.
Author: Stefan Roediger [aut] ,
Michal Burdukiewicz [aut] ,
Andrej-Nikolai Spiess [cre, aut] ,
Konstantin A. Blagodatskikh [aut] ,
Dominik Rafacz [ctb]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between PCRedux versions 1.2-0 dated 2025-06-13 and 1.2-1 dated 2025-11-19
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++----------- NEWS | 3 ++ build/vignette.rds |binary inst/doc/PCRedux.pdf |binary tests/testthat/test_encu.R | 4 +-- tests/testthat/test_head2tailratio.R | 28 ++++++++++++------------ tests/testthat/test_hookreg.R | 28 ++++++++++++------------ tests/testthat/test_hookregNL.R | 40 +++++++++++++++++------------------ tests/testthat/test_mblrr.R | 32 ++++++++++++++-------------- tests/testthat/test_pcrfit_single.R | 14 ++++++------ tests/testthat/test_performeR.R | 24 ++++++++++----------- tests/testthat/test_qPCR2fdata.R | 30 +++++++++++++------------- 13 files changed, 119 insertions(+), 116 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.20.0 dated 2025-09-16 and 0.21.0 dated 2025-11-19
adbcsqlite-0.20.0/adbcsqlite/src/c/vendor/portable-snippets/safe-math.h |only adbcsqlite-0.21.0/adbcsqlite/DESCRIPTION | 6 adbcsqlite-0.21.0/adbcsqlite/MD5 | 14 - adbcsqlite-0.21.0/adbcsqlite/src/c/driver/postgresql/bind_stream.h | 6 adbcsqlite-0.21.0/adbcsqlite/src/c/driver/postgresql/copy/reader.h | 40 +++- adbcsqlite-0.21.0/adbcsqlite/src/c/driver/postgresql/statement.cc | 18 +- adbcsqlite-0.21.0/adbcsqlite/src/c/driver_manager/adbc_driver_manager.cc | 89 +++++++--- adbcsqlite-0.21.0/adbcsqlite/src/c/vendor/portable-snippets/include |only adbcsqlite-0.21.0/adbcsqlite/tests/testthat/test-adbcsqlite-package.R | 19 ++ 9 files changed, 151 insertions(+), 41 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.20.0 dated 2025-09-16 and 0.21.0 dated 2025-11-19
adbcpostgresql-0.20.0/adbcpostgresql/src/c/vendor/portable-snippets/safe-math.h |only adbcpostgresql-0.21.0/adbcpostgresql/DESCRIPTION | 6 adbcpostgresql-0.21.0/adbcpostgresql/MD5 | 18 +- adbcpostgresql-0.21.0/adbcpostgresql/src/Makevars.in | 2 adbcpostgresql-0.21.0/adbcpostgresql/src/Makevars.ucrt | 2 adbcpostgresql-0.21.0/adbcpostgresql/src/Makevars.win | 2 adbcpostgresql-0.21.0/adbcpostgresql/src/c/driver/postgresql/bind_stream.h | 6 adbcpostgresql-0.21.0/adbcpostgresql/src/c/driver/postgresql/copy/reader.h | 40 +++- adbcpostgresql-0.21.0/adbcpostgresql/src/c/driver/postgresql/statement.cc | 18 +- adbcpostgresql-0.21.0/adbcpostgresql/src/c/driver_manager/adbc_driver_manager.cc | 89 +++++++--- adbcpostgresql-0.21.0/adbcpostgresql/src/c/vendor/portable-snippets/include |only 11 files changed, 137 insertions(+), 46 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Plotting 'ggplot2' Graphics in an 'XKCD' Style
Description: Provides custom geoms and themes to create charts and graphics in
the distinctive, hand-drawn 'XKCD' webcomic style using the 'ggplot2' framework.
The package utilizes custom layers for jittered lines, segments, circles, and
figures, and includes a theme that supports the necessary 'XKCD' font.
Author: Emilio Torres-Manzanera [aut],
Enrique Toledo [ctb, cre]
Maintainer: Enrique Toledo <enriquetoledo@gmail.com>
This is a re-admission after prior archival of version 0.0.6 dated 2018-07-11
Diff between xkcd versions 0.0.6 dated 2018-07-11 and 0.1.0 dated 2025-11-19
xkcd-0.0.6/xkcd/inst/doc/xkcd-intro.Rnw |only xkcd-0.0.6/xkcd/inst/doc/xkcd-intro.pdf |only xkcd-0.0.6/xkcd/vignettes/article-ref.bib |only xkcd-0.0.6/xkcd/vignettes/convincing.png |only xkcd-0.0.6/xkcd/vignettes/gr1.pdf |only xkcd-0.0.6/xkcd/vignettes/gr1.png |only xkcd-0.0.6/xkcd/vignettes/graxis.png |only xkcd-0.0.6/xkcd/vignettes/grbar.png |only xkcd-0.0.6/xkcd/vignettes/grcaritas.png |only xkcd-0.0.6/xkcd/vignettes/grhelp.png |only xkcd-0.0.6/xkcd/vignettes/grhomosapiens.png |only xkcd-0.0.6/xkcd/vignettes/grlatex.png |only xkcd-0.0.6/xkcd/vignettes/grmathematica.png |only xkcd-0.0.6/xkcd/vignettes/grmotherday.png |only xkcd-0.0.6/xkcd/vignettes/grnofonts.png |only xkcd-0.0.6/xkcd/vignettes/grpython.png |only xkcd-0.0.6/xkcd/vignettes/grrange.png |only xkcd-0.0.6/xkcd/vignettes/grsevan.png |only xkcd-0.0.6/xkcd/vignettes/grstickfigure.png |only xkcd-0.0.6/xkcd/vignettes/grtwo.png |only xkcd-0.0.6/xkcd/vignettes/jsslogo.jpg |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-008.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-011.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-012.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-015.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-016.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-017.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-018.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-021.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-022.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-CaritasSpain.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-angles.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-facetcity.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-facetvs.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-motherday.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro-twoman.png |only xkcd-0.0.6/xkcd/vignettes/xkcd-intro.Rnw |only xkcd-0.1.0/xkcd/DESCRIPTION | 39 xkcd-0.1.0/xkcd/LICENSE |only xkcd-0.1.0/xkcd/MD5 | 82 - xkcd-0.1.0/xkcd/NAMESPACE | 6 xkcd-0.1.0/xkcd/NEWS | 17 xkcd-0.1.0/xkcd/R/geom_xkcdpath.R |only xkcd-0.1.0/xkcd/R/theme_xkcd.R | 81 - xkcd-0.1.0/xkcd/R/xkcdaxis.R | 308 +---- xkcd-0.1.0/xkcd/R/xkcdline.R | 246 +--- xkcd-0.1.0/xkcd/R/xkcdman.R | 210 +-- xkcd-0.1.0/xkcd/R/xkcdrect.R | 181 +-- xkcd-0.1.0/xkcd/R/zzz.R | 42 xkcd-0.1.0/xkcd/README.md |only xkcd-0.1.0/xkcd/build/partial.rdb |binary xkcd-0.1.0/xkcd/build/vignette.rds |binary xkcd-0.1.0/xkcd/inst/_pkgdown.yml |only xkcd-0.1.0/xkcd/inst/doc/xkcd-intro.R | 1023 ++++++++---------- xkcd-0.1.0/xkcd/inst/doc/xkcd-intro.Rmd |only xkcd-0.1.0/xkcd/inst/doc/xkcd-intro.html |only xkcd-0.1.0/xkcd/man/geom_xkcdpath.Rd |only xkcd-0.1.0/xkcd/man/theme_xkcd.Rd | 11 xkcd-0.1.0/xkcd/man/xkcdaxis.Rd | 9 xkcd-0.1.0/xkcd/man/xkcdline.Rd | 55 xkcd-0.1.0/xkcd/man/xkcdman.Rd | 77 - xkcd-0.1.0/xkcd/man/xkcdrect.Rd | 52 xkcd-0.1.0/xkcd/vignettes/font_check.png |only xkcd-0.1.0/xkcd/vignettes/grfonts.png |binary xkcd-0.1.0/xkcd/vignettes/xkcd-intro.Rmd |only 65 files changed, 1051 insertions(+), 1388 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.5 dated 2025-07-25 and 0.8.6 dated 2025-11-19
DESCRIPTION | 14 +-- MD5 | 55 ++++++++------- NAMESPACE | 13 +++ NEWS.md | 5 + R/RcppExports.R | 6 + R/cache.R | 5 - R/config.R | 46 ++++++------ R/convert.R | 3 R/credential_providers.R | 66 ++++++++++++++++++ R/credentials.R | 6 + R/handlers_rest.R | 14 +-- R/handlers_stream.R | 81 ++++++++++++++++++++-- R/jsonutil.R | 101 ---------------------------- R/populate.R | 8 -- R/signer_bearer.R |only R/signer_v4.R | 15 ++++ R/tags.R | 34 +++------ R/util.R | 11 +++ man/paws_reset_cache.Rd | 1 src/RcppExports.cpp | 12 +++ src/json_builder.cpp |only src/json_escape.cpp | 2 src/json_escape.h |only src/utils.cpp | 50 +++++++++++++ src/utils.h |only tests/testthat/test_config.R | 12 +-- tests/testthat/test_credential_providers.R | 104 +++++++++++++++++++++++++++++ tests/testthat/test_credentials.R | 72 ++++++++++++++++++++ tests/testthat/test_handlers_stream.R | 4 - tests/testthat/test_jsonutil.R | 33 ++++++++- tests/testthat/test_signer_bearer.R |only 31 files changed, 563 insertions(+), 210 deletions(-)
Title: HIC diffeREntial Analysis Method
Description: Perform Hi-C data differential analysis based on pixel-level
differential analysis and a post hoc inference strategy to quantify
signal in clusters of pixels. Clusters of pixels are obtained through
a connectivity-constrained two-dimensional hierarchical clustering.
Author: Elise Jorge [aut, cre],
Sylvain Foissac [aut] ,
Toby Hocking [aut] ,
Pierre Neuvial [aut] ,
Nathalie Vialaneix [aut] ,
Gilles Blanchard [ctb],
Guillermo Durand [ctb] ,
Nicolas Enjalbert-Courrech [ctb],
Etienne Roquain [ctb]
Maintainer: Elise Jorge <elise.jorge@inrae.fr>
Diff between hicream versions 0.0.1 dated 2025-07-25 and 0.0.2 dated 2025-11-19
DESCRIPTION | 24 ++-- MD5 | 41 +++---- NEWS.md |only R/AggloClust2D.R | 58 ++++++++-- R/helpers.R | 59 +++++++++- R/loadData.R | 1 R/performTest.R | 1 R/postHoc.R | 21 +++ README.md | 232 ++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/A-Installation.Rmd | 3 inst/doc/A-Installation.html | 19 +-- inst/doc/B-Introduction.R | 25 ++-- inst/doc/B-Introduction.Rmd | 48 +++++--- inst/doc/B-Introduction.html | 192 ++++++++++++++++++++--------------- inst/python/2Dclust.py | 22 +--- man/AggloClust2D.Rd | 16 +- man/loadData.Rd | 1 man/performTest.Rd | 1 man/postHoc.Rd | 11 +- vignettes/A-Installation.Rmd | 3 vignettes/B-Introduction.Rmd | 48 +++++--- 22 files changed, 515 insertions(+), 311 deletions(-)
Title: Easily Convert GDP Data
Description: Convert GDP time series data from one unit to
another. All common GDP units are included, i.e. current and constant
local currency units, US$ via market exchange rates and international
dollars via purchasing power parities.
Author: Johannes Koch [aut, cre]
Maintainer: Johannes Koch <jokoch@pik-potsdam.de>
Diff between GDPuc versions 1.0.4 dated 2024-09-04 and 1.6.0 dated 2025-11-19
DESCRIPTION | 18 - MD5 | 86 +++---- NAMESPACE | 4 NEWS.md | 13 + R/GDPuc-package.R | 4 R/adapt_source.R | 87 +++++-- R/check_user_input.R | 89 ++++--- R/composite_conversions.R | 220 ++++++++---------- R/convertGDP.R | 133 ++++++++--- R/elemental_conversions.R | 95 +++++--- R/get_conversion_factors.R | 3 R/madrat.R |only R/print_source_info.R | 1 R/replace_regions_with_countries.R | 49 ++-- R/transform_user_input.R | 113 ++++++--- R/utils.R | 10 README.md | 9 build/vignette.rds |binary inst/doc/handle_NAs.R | 15 - inst/doc/handle_NAs.Rmd | 24 -- inst/doc/handle_NAs.html | 104 +++----- inst/doc/magpie.html | 2 inst/doc/source.R | 41 ++- inst/doc/source.Rmd | 82 ++++-- inst/doc/source.html | 295 +++++++++++++++---------- inst/doc/verbose.html | 2 inst/doc/warn.R | 2 inst/doc/warn.html | 2 inst/doc/with_regions.R | 16 + inst/doc/with_regions.Rmd | 34 ++ inst/doc/with_regions.html | 107 +++++---- man/GDPuc-package.Rd | 2 man/convertGDP.Rd | 80 +++++- man/print_source_info.Rd | 2 tests/testthat/setup-global_vars.R | 4 tests/testthat/test-01_check_user_input.R | 115 ++++++--- tests/testthat/test-02_transform_user_input.R | 34 ++ tests/testthat/test-03_elemental_conversions.R | 90 +++++-- tests/testthat/test-04_composite_conversions.R | 99 ++++---- tests/testthat/test-05_convertGDP.R | 116 +++++---- tests/testthat/test-06_replace_NAs.R | 72 +++++- tests/testthat/test-11_wrappers.R |only vignettes/handle_NAs.Rmd | 24 -- vignettes/source.Rmd | 82 ++++-- vignettes/with_regions.Rmd | 34 ++ 45 files changed, 1534 insertions(+), 880 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
Description: Many tools for making, modifying, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.6.5 dated 2025-10-24 and 1.7.0 dated 2025-11-19
DESCRIPTION | 8 MD5 | 55 - NAMESPACE | 3 NEWS.md | 57 + R/class_marks.R | 6 R/class_models.R | 1 R/class_networks.R | 7 R/make_generate.R | 14 R/manip_as.R | 30 - R/manip_nodes.R | 6 R/manip_split.R | 97 ++- R/manynet-glossary.R | 16 R/manynet-utils.R | 3 R/mark_net.R | 5 R/mark_nodes.R | 69 +- R/measure_diffusion.R | 6 R/measure_heterogeneity.R | 277 ++++++++- inst/tutorials/tutorial1/data.Rmd | 7 inst/tutorials/tutorial1/data.html | 812 +++++++++++++++------------- man/manip_changes.Rd | 3 man/mark_diff.Rd | 2 man/measure_diffusion_infection.Rd | 2 man/measure_diffusion_node.Rd | 4 man/measure_heterogeneity.Rd | 104 +++ tests/testthat/test-make_generate.R | 23 tests/testthat/test-make_play.R |only tests/testthat/test-manip_add.R | 5 tests/testthat/test-manip_as.R | 7 tests/testthat/test-measure_heterogeneity.R | 11 29 files changed, 1119 insertions(+), 521 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: Extends the Cox model to events with more than one causes. Also supports random and fixed effects, tied events, and time-varying variables. Model details are provided in Peng et al. (2018) <doi:10.1509/jmr.14.0643>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between CoxPlus versions 1.5.6 dated 2025-11-19 and 1.5.7 dated 2025-11-19
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <https://spark.apache.org/>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] ,
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut] ,
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] ,
Wil Davis [ctb],
Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr versions 1.9.2 dated 2025-10-05 and 1.9.3 dated 2025-11-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/install_spark.R | 2 +- R/ml_persistence.R | 40 ++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary inst/extdata/versions-next.json | 4 ++-- inst/extdata/versions.json | 2 +- 8 files changed, 51 insertions(+), 23 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman [aut, cre] ,
Hao Wu [aut],
Gary Churchill [ctb] ,
Saunak Sen [ctb] ,
Danny Arends [ctb] ,
Robert Corty [ctb],
Timothee Flutre [ctb],
Ritsert Jansen [ctb],
Pjotr Prins [ctb] ,
Lars Ronnegard [ctb],
Rohan Shah [ctb],
Laura Shannon [ctb],
[...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.70 dated 2024-08-21 and 1.72 dated 2025-11-19
DESCRIPTION | 21 +++++++++++---------- MD5 | 42 +++++++++++++++++++++--------------------- NEWS.md | 9 +++++++++ R/cim.R | 9 ++++++--- build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/INSTALL_ME.txt | 16 ++++++++-------- inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary man/cim.Rd | 9 ++++----- 22 files changed, 59 insertions(+), 47 deletions(-)
Title: Calculate and Track Dates and Medications During Pregnancy
Description: Provides functionality for calculating pregnancy-related dates and
tracking medications during pregnancy and fertility treatment. Calculates
due dates from various starting points including last menstrual period and
IVF (In Vitro Fertilisation) transfer dates, determines pregnancy progress
on any given date, and identifies when specific pregnancy weeks are
reached. Includes medication tracking capabilities for individuals
undergoing fertility treatment or during pregnancy, allowing users to
monitor remaining doses and quantities needed over specified time periods.
Designed for those tracking their own pregnancies or supporting partners
through the process, making use of options to personalise output messages.
For details on due date calculations, see
<https://www.acog.org/clinical/clinical-guidance/committee-opinion/articles/2017/05/methods-for-estimating-the-due-date>.
Author: Ella Kaye [aut, cre, cph]
Maintainer: Ella Kaye <ella.kaye@gmail.com>
Diff between pregnancy versions 0.1.1 dated 2025-09-14 and 0.2.0 dated 2025-11-19
DESCRIPTION | 6 MD5 | 27 ++-- NEWS.md | 8 + R/data.R | 10 + R/meds.R | 18 ++ README.md | 77 +++++++----- data/medications_simple.rda |only inst/doc/pregnancy.R | 34 +++-- inst/doc/pregnancy.Rmd | 53 +++++--- inst/doc/pregnancy.html | 230 ++++++++++++++++++++------------------ man/medications.Rd | 9 + man/pregnancy-package.Rd | 2 tests/testthat/_snaps/due_date.md |only tests/testthat/_snaps/utils.md |only tests/testthat/test-meds.R | 15 ++ vignettes/pregnancy.Rmd | 53 +++++--- 16 files changed, 332 insertions(+), 210 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.3.2 dated 2025-06-10 and 1.4.0 dated 2025-11-19
nhdplusTools-1.3.2/nhdplusTools/R/geoserver_tools.R |only nhdplusTools-1.3.2/nhdplusTools/man/query_usgs_geoserver.Rd |only nhdplusTools-1.4.0/nhdplusTools/DESCRIPTION | 8 nhdplusTools-1.4.0/nhdplusTools/MD5 | 84 nhdplusTools-1.4.0/nhdplusTools/NAMESPACE | 2 nhdplusTools-1.4.0/nhdplusTools/NEWS.md | 747 +- nhdplusTools-1.4.0/nhdplusTools/R/A_nhdplusTools.R | 46 nhdplusTools-1.4.0/nhdplusTools/R/arcrest_tools.R | 518 - nhdplusTools-1.4.0/nhdplusTools/R/discover_nhdplus.R | 12 nhdplusTools-1.4.0/nhdplusTools/R/downloading_tools.R | 749 +- nhdplusTools-1.4.0/nhdplusTools/R/get_geoconnex.R | 269 nhdplusTools-1.4.0/nhdplusTools/R/get_hydro.R | 40 nhdplusTools-1.4.0/nhdplusTools/R/get_nhdplus.R | 33 nhdplusTools-1.4.0/nhdplusTools/R/oafeat_tools.R |only nhdplusTools-1.4.0/nhdplusTools/R/subset_nhdplus.R | 33 nhdplusTools-1.4.0/nhdplusTools/build/partial.rdb |binary nhdplusTools-1.4.0/nhdplusTools/build/vignette.rds |binary nhdplusTools-1.4.0/nhdplusTools/inst/doc/get_3dhp_data.html | 96 nhdplusTools-1.4.0/nhdplusTools/inst/doc/get_data_overview.html | 3465 ---------- nhdplusTools-1.4.0/nhdplusTools/inst/doc/indexing.html | 5 nhdplusTools-1.4.0/nhdplusTools/inst/doc/nhdplusTools.Rmd | 2 nhdplusTools-1.4.0/nhdplusTools/inst/doc/nhdplusTools.html | 3090 -------- nhdplusTools-1.4.0/nhdplusTools/inst/doc/nhdplushr.html | 20 nhdplusTools-1.4.0/nhdplusTools/inst/doc/plot_nhdplus.R | 2 nhdplusTools-1.4.0/nhdplusTools/inst/doc/plot_nhdplus.Rmd | 502 - nhdplusTools-1.4.0/nhdplusTools/inst/doc/plot_nhdplus.html | 192 nhdplusTools-1.4.0/nhdplusTools/man/download_nhdplusv2.Rd | 2 nhdplusTools-1.4.0/nhdplusTools/man/get_gagesII.Rd | 4 nhdplusTools-1.4.0/nhdplusTools/man/get_huc.Rd | 6 nhdplusTools-1.4.0/nhdplusTools/man/get_nhdarea.Rd | 4 nhdplusTools-1.4.0/nhdplusTools/man/get_nhdplus.Rd | 138 nhdplusTools-1.4.0/nhdplusTools/man/get_nwis.Rd | 76 nhdplusTools-1.4.0/nhdplusTools/man/get_waterbodies.Rd | 4 nhdplusTools-1.4.0/nhdplusTools/man/query_usgs_oafeat.Rd |only nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_01_get_nldi.R | 594 - nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_02_subset.R | 436 - nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_02_subset_extras.R | 370 - nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_03_get_functions.R | 47 nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_arcrest.R | 43 nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_calc_network.R | 212 nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_get_nhdplus.R | 146 nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_get_nhdplushr.R | 468 - nhdplusTools-1.4.0/nhdplusTools/tests/testthat/test_get_path.R | 308 nhdplusTools-1.4.0/nhdplusTools/vignettes/nhdplusTools.Rmd | 2 nhdplusTools-1.4.0/nhdplusTools/vignettes/plot_nhdplus.Rmd | 502 - 45 files changed, 3566 insertions(+), 9711 deletions(-)
Title: Tools for Data Analysis in Experimental Agriculture
Description: Methods to analyse experimental agriculture data,
from data synthesis to model selection and visualisation.
The package is named after W.S. Gosset aka ‘Student’, a pioneer
of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
David Brown [aut] ,
Jonathan Steinke [aut] ,
Joost van Heerwaarden [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between gosset versions 1.4 dated 2024-12-05 and 1.5.1 dated 2025-11-19
DESCRIPTION | 24 ++--- MD5 | 26 +++-- NAMESPACE | 4 NEWS.md | 30 ++++++ R/preference_index.R |only R/rank_numeric.R | 11 ++ R/rank_tricot2.R |only inst/doc/vignette-1-trait-prioritization-and-crop-performance.Rmd | 11 +- inst/doc/vignette-1-trait-prioritization-and-crop-performance.html | 46 ++++------ man/preference_index.Rd |only man/rank_numeric.Rd | 1 man/rank_tricot.Rd | 1 man/rank_tricot2.Rd |only man/set_binomialfreq.Rd | 1 man/set_paircomp.Rd | 1 vignettes/vignette-1-trait-prioritization-and-crop-performance.Rmd | 11 +- 16 files changed, 109 insertions(+), 58 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>
Diff between cotram versions 0.5-3 dated 2025-10-08 and 0.6-0 dated 2025-11-19
DESCRIPTION | 16 ++++++++-------- MD5 | 20 +++++++++++++------- NAMESPACE | 5 +---- R/mcotram.R |only build/partial.rdb |binary build/vignette.rds |binary demo |only inst/NEWS.Rd | 10 +++++++++- inst/doc/cotram.pdf |binary man/mcotram.Rd |only tests/confband-Ex.Rout.save |only vignettes/defs.tex | 2 +- 12 files changed, 32 insertions(+), 21 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.1.2 dated 2025-10-14 and 1.1.3 dated 2025-11-19
DESCRIPTION | 8 MD5 | 264 +-- NAMESPACE | 2 NEWS.md | 43 R/Studio_Classifier_Create.R | 6 R/Studio_Error_Checks.R | 6 R/Studio_License.R | 1 R/Studio_ProgressModal.R | 1 R/Studio_Tabs_Classifier_Predict.R | 1 R/Studio_Tabs_DM_DataSetEditor.R | 2 R/Studio_Tabs_DM_TableEditor.R | 1 R/Studio_Tabs_Fill_Mask.R | 2 R/Studio_Tabs_Sustainability.R | 78 R/Studio_Tabs_Training.R | 43 R/Studio_TextEmbeddingModel_Create.R | 126 + R/def_DocumentationDesc.R | 7 R/def_ParameterDefinitions.R | 671 ++++++-- R/install_and_config.R | 24 R/obj_AIFEBaseModel.R | 2 R/obj_BaseModelBert.R | 4 R/obj_BaseModelCore.R | 158 + R/obj_BaseModelDebertaV2.R | 4 R/obj_BaseModelFunnel.R | 11 R/obj_BaseModelMPNet.R | 44 R/obj_BaseModelModernBert.R | 20 R/obj_BaseModelRoberta.R | 4 R/obj_ClassifiersBasedOnTextEmbeddings.R | 35 R/obj_DataManager.R | 12 R/obj_FeatureExtractor.R | 27 R/obj_LargeDataSetBase.R | 1 R/obj_ModelsBasedOnTextEmbeddings.R | 205 ++ R/obj_TEClassifierParallel.R | 17 R/obj_TEClassifierParallelPrototype.R | 16 R/obj_TEClassifierProtoNet.R | 2 R/obj_TEClassifierRegular.R | 2 R/obj_TEClassifierSequential.R | 17 R/obj_TEClassifierSequentialPrototype.R | 16 R/obj_TEClassifiersBasedOnProtoNet.R | 57 R/obj_TEClassifiersBasedOnRegular.R | 2 R/obj_TextEmbeddingModel.R | 5 R/obj_Tokenizer.R | 7 R/onLoad.R | 2 R/saving_and_loading.R | 4 R/utils_Studio.R | 1 R/utils_general.R | 1 R/utils_memory_cache.R | 60 R/utils_plot.R |only R/utils_test_that.R | 142 + R/utils_update_models.R | 3 README.md | 10 inst/doc/aifeducation.R | 2 inst/doc/aifeducation.Rmd | 2 inst/doc/aifeducation.html | 18 inst/python/pytorch_autoencoder.py | 33 inst/python/pytorch_classifier_models.py | 98 + inst/python/pytorch_cls_training_loops.py | 71 inst/python/pytorch_distance_fun.py |only inst/python/pytorch_layers.py | 179 +- inst/python/pytorch_stack_layers.py | 5 man/BaseModelBert.Rd | 20 man/BaseModelCore.Rd | 112 - man/BaseModelDebertaV2.Rd | 20 man/BaseModelFunnel.Rd | 40 man/BaseModelMPNet.Rd | 71 man/BaseModelModernBert.Rd | 26 man/BaseModelRoberta.Rd | 20 man/BaseModelsIndex.Rd | 1 man/ClassifiersBasedOnTextEmbeddings.Rd | 24 man/DataManagerClassifier.Rd | 12 man/DataSetsIndex.Rd | 1 man/EmbeddedText.Rd | 2 man/HuggingFaceTokenizer.Rd | 2 man/LargeDataSetForTextEmbeddings.Rd | 2 man/ModelsBasedOnTextEmbeddings.Rd | 21 man/TEClassifierParallel.Rd | 40 man/TEClassifierParallelPrototype.Rd | 44 man/TEClassifierProtoNet.Rd | 22 man/TEClassifierRegular.Rd | 20 man/TEClassifierSequential.Rd | 42 man/TEClassifierSequentialPrototype.Rd | 46 man/TEClassifiersBasedOnProtoNet.Rd | 46 man/TEClassifiersBasedOnRegular.Rd | 34 man/TEFeatureExtractor.Rd | 35 man/TextEmbeddingModel.Rd | 26 man/TokenizerBase.Rd | 8 man/TokenizerIndex.Rd | 1 man/WordPieceTokenizer.Rd | 6 man/calc_tokenizer_statistics.Rd | 2 man/check_adjust_n_samples_on_CI.Rd | 1 man/doc_formula.Rd |only man/generate_args_for_tests.Rd | 7 man/generate_embeddings.Rd | 1 man/generate_tensors.Rd | 1 man/get_TEClassifiers_class_names.Rd | 1 man/get_called_args.Rd | 1 man/get_current_args_for_print.Rd | 1 man/get_depr_obj_names.Rd | 1 man/get_fixed_test_tensor.Rd | 1 man/get_magnitude_values.Rd | 1 man/get_n_chunks.Rd | 2 man/get_param_def.Rd | 1 man/get_param_dict.Rd | 1 man/get_param_doc_desc.Rd | 1 man/get_test_data_for_classifiers.Rd | 1 man/inspect_tmp_dir.Rd |only man/install_py_modules.Rd | 10 man/monitor_test_time_on_CI.Rd |only man/random_bool_on_CI.Rd | 3 tests/testthat/test-00_01_generating_test_data.R | 9 tests/testthat/test-00_02_setup_Classifiers.R | 10 tests/testthat/test-01_01_install_and_config.R | 8 tests/testthat/test-01_02_Performance_Measures.R | 9 tests/testthat/test-01_03_R_utils.R | 109 + tests/testthat/test-01_04_R_and_Python_utils.R | 9 tests/testthat/test-01_05_KNNOR.R | 9 tests/testthat/test-01_06_logging.R | 9 tests/testthat/test-01_07_DataCollator.R | 9 tests/testthat/test-02_01_pytorch_loss_fcts.R | 9 tests/testthat/test-02_02_pytorch_layers.R | 202 +- tests/testthat/test-02_03_pytorch_stack_layers.R | 119 - tests/testthat/test-02_04_other_fcts.R |only tests/testthat/test-02_05_tokenizer.R | 18 tests/testthat/test-02_06_BaseModels.R | 50 tests/testthat/test-02_07_BaseModels_from_hf.R | 20 tests/testthat/test-03_01_LargeDataSetForTexts.R | 9 tests/testthat/test-03_02_LargeDataSetForTextEmbeddings.R | 9 tests/testthat/test-03_03_EmbeddedText.R | 9 tests/testthat/test-03_04_DataManager.R | 9 tests/testthat/test-03_05_FeatureExtractor.R | 9 tests/testthat/test-03_06_TextEmbeddingModels.R | 1111 +++++++------ tests/testthat/test-03_08_TEClassifiers_core.R | 1118 +++++--------- tests/testthat/test-03_09_TEClassifiersProtoNet_old.R | 40 tests/testthat/test-03_09_TEClassifiersPrototype.R | 500 ++---- tests/testthat/test-04_01_LoadOldModels.R | 9 tests/testthat/test-99_clean_tmp_directories.R | 9 vignettes/aifeducation.Rmd | 2 136 files changed, 4101 insertions(+), 2698 deletions(-)
Title: ANSI Control Sequence Aware String Functions
Description: Counterparts to R string manipulation functions that account for
the effects of ANSI text formatting control sequences.
Author: Brodie Gaslam [aut, cre],
Elliott Sales De Andrade [ctb],
R Core Team [cph] ,
Michael Chirico [ctb] ,
Unicode, Inc. [cph, dtc]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between fansi versions 1.0.6 dated 2023-12-07 and 1.0.7 dated 2025-11-19
fansi-1.0.6/fansi/src/rnchar.c |only fansi-1.0.7/fansi/DESCRIPTION | 24 +++-- fansi-1.0.7/fansi/MD5 | 75 ++++++++-------- fansi-1.0.7/fansi/NAMESPACE | 1 fansi-1.0.7/fansi/NEWS.md | 7 + fansi-1.0.7/fansi/R/fansi-package.R | 26 +---- fansi-1.0.7/fansi/R/misc.R | 12 ++ fansi-1.0.7/fansi/R/substr2.R | 18 +-- fansi-1.0.7/fansi/README.md | 9 + fansi-1.0.7/fansi/build/vignette.rds |binary fansi-1.0.7/fansi/inst/doc/sgr-in-rmd.R | 2 fansi-1.0.7/fansi/inst/doc/sgr-in-rmd.html | 5 - fansi-1.0.7/fansi/man/fansi.Rd | 37 ++++--- fansi-1.0.7/fansi/man/fansi_unicode_version.Rd |only fansi-1.0.7/fansi/man/nchar_ctl.Rd | 18 +-- fansi-1.0.7/fansi/man/nchar_sgr.Rd | 4 fansi-1.0.7/fansi/man/state_at_end.Rd | 10 +- fansi-1.0.7/fansi/man/strsplit_ctl.Rd | 10 +- fansi-1.0.7/fansi/man/strtrim_ctl.Rd | 2 fansi-1.0.7/fansi/man/strtrim_sgr.Rd | 2 fansi-1.0.7/fansi/man/strwrap_ctl.Rd | 14 +- fansi-1.0.7/fansi/man/substr_ctl.Rd | 18 +-- fansi-1.0.7/fansi/man/substr_sgr.Rd | 4 fansi-1.0.7/fansi/man/trimws_ctl.Rd | 12 +- fansi-1.0.7/fansi/src/fansi-ext.h | 2 fansi-1.0.7/fansi/src/fansi-struct.h | 2 fansi-1.0.7/fansi/src/fansi.h | 12 -- fansi-1.0.7/fansi/src/init.c | 1 fansi-1.0.7/fansi/src/read.c | 31 ++---- fansi-1.0.7/fansi/src/state.c | 5 - fansi-1.0.7/fansi/src/utf8.c | 4 fansi-1.0.7/fansi/src/width.c |only fansi-1.0.7/fansi/src/wrap.c | 2 fansi-1.0.7/fansi/src/write.c | 1 fansi-1.0.7/fansi/tests/run.R | 6 + fansi-1.0.7/fansi/tests/special/cps.R |only fansi-1.0.7/fansi/tests/special/cps.unitizer |only fansi-1.0.7/fansi/tests/special/emo-graph.R | 15 +++ fansi-1.0.7/fansi/tests/special/utf8.R | 15 +++ fansi-1.0.7/fansi/tests/unitizer/misc.R | 3 fansi-1.0.7/fansi/tests/unitizer/misc.unitizer/data.rds |binary 41 files changed, 223 insertions(+), 186 deletions(-)
Title: Reconstruction of Daily Data - Precipitation
Description: Applies quality control to daily precipitation observations;
reconstructs the original series by estimating precipitation in missing values; and
creates gridded datasets of daily precipitation.
Author: Roberto Serrano-Notivoli [aut, cre] ,
Adrian Huerta [aut] ,
Abel Centella [ctb]
Maintainer: Roberto Serrano-Notivoli <roberto.serrano@unizar.es>
Diff between reddPrec versions 3.0.1 dated 2025-09-10 and 3.0.2 dated 2025-11-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/eqc_Ts.R | 1 + R/hmg_Ts.R | 2 +- R/hmg_cleaning_trend_ar1.R | 7 ++++--- R/stand_qq.R | 2 +- 7 files changed, 18 insertions(+), 16 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.1.11 dated 2025-02-18 and 0.1.12 dated 2025-11-19
DESCRIPTION | 15 ++- MD5 | 129 ++++++++++++++++----------------- NEWS.md | 58 ++++++++------ R/LearnerClust.R | 1 R/LearnerClustAffinityPropagation.R | 27 +++--- R/LearnerClustAgnes.R | 11 +- R/LearnerClustBICO.R | 9 +- R/LearnerClustBIRCH.R | 11 +- R/LearnerClustCMeans.R | 9 +- R/LearnerClustCobweb.R | 1 R/LearnerClustDBSCAN.R | 9 +- R/LearnerClustDBSCANfpc.R | 11 +- R/LearnerClustDiana.R | 3 R/LearnerClustEM.R | 3 R/LearnerClustFanny.R | 5 - R/LearnerClustFarthestFirst.R | 1 R/LearnerClustFeatureless.R | 3 R/LearnerClustHDBSCAN.R | 6 + R/LearnerClustHclust.R | 6 + R/LearnerClustKKMeans.R | 9 +- R/LearnerClustKMeans.R | 6 - R/LearnerClustMclust.R | 1 R/LearnerClustMeanShift.R | 1 R/LearnerClustMiniBatchKMeans.R | 3 R/LearnerClustOPTICS.R | 7 + R/LearnerClustPAM.R | 9 +- R/LearnerClustSimpleKMeans.R | 33 ++++---- R/LearnerClustXMeans.R | 33 ++++---- R/MeasureClust.R | 15 +++ R/MeasureClustInternal.R | 2 R/as_prediction_clust.R | 4 - R/as_task_clust.R | 5 - R/bibentries.R | 6 + R/zzz.R | 12 ++- README.md | 16 +++- build/partial.rdb |binary man/LearnerClust.Rd | 2 man/TaskClust.Rd | 1 man/figures |only man/mlr_learners_clust.MBatchKMeans.Rd | 27 +++++- man/mlr_learners_clust.SimpleKMeans.Rd | 29 +++++-- man/mlr_learners_clust.agnes.Rd | 27 +++++- man/mlr_learners_clust.ap.Rd | 20 ++--- man/mlr_learners_clust.bico.Rd | 27 +++++- man/mlr_learners_clust.birch.Rd | 14 +-- man/mlr_learners_clust.cmeans.Rd | 27 +++++- man/mlr_learners_clust.cobweb.Rd | 27 +++++- man/mlr_learners_clust.dbscan.Rd | 16 ++-- man/mlr_learners_clust.dbscan_fpc.Rd | 16 ++-- man/mlr_learners_clust.diana.Rd | 27 +++++- man/mlr_learners_clust.em.Rd | 27 +++++- man/mlr_learners_clust.fanny.Rd | 27 +++++- man/mlr_learners_clust.featureless.Rd | 27 +++++- man/mlr_learners_clust.ff.Rd | 27 +++++- man/mlr_learners_clust.hclust.Rd | 29 +++++-- man/mlr_learners_clust.hdbscan.Rd | 28 +++++-- man/mlr_learners_clust.kkmeans.Rd | 27 +++++- man/mlr_learners_clust.kmeans.Rd | 29 +++++-- man/mlr_learners_clust.mclust.Rd | 29 +++++-- man/mlr_learners_clust.meanshift.Rd | 27 +++++- man/mlr_learners_clust.optics.Rd | 14 +-- man/mlr_learners_clust.pam.Rd | 29 +++++-- man/mlr_learners_clust.xmeans.Rd | 14 +-- tests/testthat/helper_expectations.R | 9 -- tests/testthat/helper_mlr3.R | 8 -- tests/testthat/test_TaskClust.R | 4 - 66 files changed, 706 insertions(+), 389 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.90 dated 2025-10-18 and 1.1.0 dated 2025-11-19
lme4breeding-1.0.90/lme4breeding/R/lmebreed.R |only lme4breeding-1.0.90/lme4breeding/R/plottingFuns.R |only lme4breeding-1.0.90/lme4breeding/data |only lme4breeding-1.0.90/lme4breeding/man/A.mat.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_augment.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_big.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_btdata.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_cornhybrids.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_cpdata.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_example.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_expdesigns.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_fulldiallel.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_gryphon.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_h2.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_halfdiallel.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_ige.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_legendre.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_mohring.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_polyploid.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_rice.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_sleepstudy.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_technow.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_wheat.Rd |only lme4breeding-1.0.90/lme4breeding/man/DT_yatesoats.Rd |only lme4breeding-1.0.90/lme4breeding/man/I.mat.Rd |only lme4breeding-1.0.90/lme4breeding/man/add.diallel.vars.Rd |only lme4breeding-1.0.90/lme4breeding/man/atcg1234.Rd |only lme4breeding-1.0.90/lme4breeding/man/bbasis.Rd |only lme4breeding-1.0.90/lme4breeding/man/build.HMM.Rd |only lme4breeding-1.0.90/lme4breeding/man/getCi.Rd |only lme4breeding-1.0.90/lme4breeding/man/impute.Rd |only lme4breeding-1.0.90/lme4breeding/man/leg.Rd |only lme4breeding-1.0.90/lme4breeding/man/lmebreed-class.Rd |only lme4breeding-1.0.90/lme4breeding/man/lmebreed.Rd |only lme4breeding-1.0.90/lme4breeding/man/overlay.Rd |only lme4breeding-1.0.90/lme4breeding/man/redmm.Rd |only lme4breeding-1.0.90/lme4breeding/man/rrm.Rd |only lme4breeding-1.0.90/lme4breeding/man/simage.Rd |only lme4breeding-1.0.90/lme4breeding/man/simage2.Rd |only lme4breeding-1.0.90/lme4breeding/man/tps.Rd |only lme4breeding-1.1.0/lme4breeding/ChangeLog | 9 lme4breeding-1.1.0/lme4breeding/DESCRIPTION | 12 lme4breeding-1.1.0/lme4breeding/MD5 | 117 lme4breeding-1.1.0/lme4breeding/NAMESPACE | 16 lme4breeding-1.1.0/lme4breeding/R/AllClass.R | 26 lme4breeding-1.1.0/lme4breeding/R/lmeb.R |only lme4breeding-1.1.0/lme4breeding/R/predict.R |only lme4breeding-1.1.0/lme4breeding/R/utils.R | 1446 ---------- lme4breeding-1.1.0/lme4breeding/README.md |only lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.gxe.R | 54 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.gxe.Rmd | 69 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.gxe.html | 560 ++- lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.qg.R | 83 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.qg.Rmd | 87 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.qg.html | 139 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.summaries.R | 8 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.summaries.Rmd | 8 lme4breeding-1.1.0/lme4breeding/inst/doc/lmebreed.summaries.html | 12 lme4breeding-1.1.0/lme4breeding/man/Dtable.Rd | 10 lme4breeding-1.1.0/lme4breeding/man/adjBeta.Rd | 6 lme4breeding-1.1.0/lme4breeding/man/balanceData.Rd | 5 lme4breeding-1.1.0/lme4breeding/man/condVarRotated.Rd |only lme4breeding-1.1.0/lme4breeding/man/getMME.Rd | 22 lme4breeding-1.1.0/lme4breeding/man/lme4breeding-package.Rd | 47 lme4breeding-1.1.0/lme4breeding/man/lmeb-class.Rd |only lme4breeding-1.1.0/lme4breeding/man/lmeb.Rd |only lme4breeding-1.1.0/lme4breeding/man/mkMmeIndex.Rd | 12 lme4breeding-1.1.0/lme4breeding/man/predict.lmeb.Rd |only lme4breeding-1.1.0/lme4breeding/man/smm.Rd | 4 lme4breeding-1.1.0/lme4breeding/man/umat.Rd | 6 lme4breeding-1.1.0/lme4breeding/vignettes/lmebreed.gxe.Rmd | 69 lme4breeding-1.1.0/lme4breeding/vignettes/lmebreed.qg.Rmd | 87 lme4breeding-1.1.0/lme4breeding/vignettes/lmebreed.summaries.Rmd | 8 73 files changed, 866 insertions(+), 2056 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash
digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32',
'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128'
algorithms) permitting easy comparison of R language objects, as well as functions
such as 'hmac()' to create hash-based message authentication code. Please note that
this package is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel [aut, cre] ,
Antoine Lucas [ctb] ,
Jarek Tuszynski [ctb],
Henrik Bengtsson [ctb] ,
Simon Urbanek [ctb] ,
Mario Frasca [ctb],
Bryan Lewis [ctb],
Murray Stokely [ctb],
Hannes Muehleisen [ctb] ,
Duncan Murdoch [ctb],
Jim Hester [ctb] , [...truncated...]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.38 dated 2025-11-12 and 0.6.39 dated 2025-11-19
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/vdigest.R | 6 ++---- src/SpookyV2.cpp | 2 +- 5 files changed, 25 insertions(+), 13 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.5.1-4 dated 2025-06-30 and 1.5.2-2 dated 2025-11-19
DESCRIPTION | 10 MD5 | 140 NEWS.md | 35 R/MLR.R | 18 R/NLR.R | 39 R/ORD.R | 31 R/ddfMLR.R | 256 - R/difNLR-package.R | 4 R/difNLR.R | 715 +- R/difORD.R | 522 -- R/private.R | 194 R/startNLR.R | 87 README.md | 4 build/partial.rdb |binary man/ddfMLR.Rd | 51 man/difNLR-package.Rd | 4 man/difNLR.Rd | 52 man/difORD.Rd | 53 tests/testthat/_snaps/ddfMLR.md | 443 + tests/testthat/_snaps/difNLR.md | 3551 -------------- tests/testthat/_snaps/difNLR/difnlr-fit1-plot3.svg | 78 tests/testthat/_snaps/difNLR/difnlr-fit1-plot4.svg | 4 tests/testthat/_snaps/difNLR/difnlr-fit7b-plot1.svg |only tests/testthat/_snaps/difNLR/difnlr-fit7c-plot1.svg |only tests/testthat/_snaps/difNLR/difnlr-fit7d-plot1.svg |only tests/testthat/_snaps/difORD.md | 498 + tests/testthat/_snaps/difORD/diford-rjournal-plot5.svg |only tests/testthat/_snaps/difORD/diford-rjournal-plot6.svg |only tests/testthat/_snaps/difORD/diford-rjournal-plot7.svg |only tests/testthat/fixtures/ddfMLR_RJournal_fit1.rds |binary tests/testthat/fixtures/ddfMLR_fit1.rds |binary tests/testthat/fixtures/ddfMLR_fit2.rds |binary tests/testthat/fixtures/ddfMLR_fit3.rds |binary tests/testthat/fixtures/ddfMLR_fit4.rds |binary tests/testthat/fixtures/ddfMLR_fit5.rds |binary tests/testthat/fixtures/ddfMLR_fit6a.rds |only tests/testthat/fixtures/ddfMLR_fit6b.rds |only tests/testthat/fixtures/ddfMLR_fit6c.rds |only tests/testthat/fixtures/ddfMLR_fit7.rds |only tests/testthat/fixtures/ddfMLR_fit8.rds |only tests/testthat/fixtures/difNLR_RJournal_fit1.rds |binary tests/testthat/fixtures/difNLR_RJournal_fit12b.rds |binary tests/testthat/fixtures/difNLR_fit1.rds |binary tests/testthat/fixtures/difNLR_fit10.rds |binary tests/testthat/fixtures/difNLR_fit11.rds |binary tests/testthat/fixtures/difNLR_fit13.rds |binary tests/testthat/fixtures/difNLR_fit14.rds |binary tests/testthat/fixtures/difNLR_fit1_fitted_item1.rds |only tests/testthat/fixtures/difNLR_fit1_fitted_summary.rds |only tests/testthat/fixtures/difNLR_fit1_predict_item1.rds |only tests/testthat/fixtures/difNLR_fit1_predict_item1_new.rds |only tests/testthat/fixtures/difNLR_fit1_predict_summary.rds |only tests/testthat/fixtures/difNLR_fit1_residuals_item1.rds |only tests/testthat/fixtures/difNLR_fit1_residuals_summary.rds |only tests/testthat/fixtures/difNLR_fit2.rds |binary tests/testthat/fixtures/difNLR_fit3.rds |binary tests/testthat/fixtures/difNLR_fit4.rds |binary tests/testthat/fixtures/difNLR_fit5.rds |binary tests/testthat/fixtures/difNLR_fit6.rds |binary tests/testthat/fixtures/difNLR_fit7a.rds |only tests/testthat/fixtures/difNLR_fit7b.rds |only tests/testthat/fixtures/difNLR_fit7c.rds |only tests/testthat/fixtures/difNLR_fit8.rds |binary tests/testthat/fixtures/difNLR_fit9.rds |binary tests/testthat/fixtures/difORD_RJournal_fit1.rds |binary tests/testthat/fixtures/difORD_RJournal_fit2.rds |binary tests/testthat/fixtures/difORD_fit1.rds |binary tests/testthat/fixtures/difORD_fit2.rds |binary tests/testthat/fixtures/difORD_fit3.rds |binary tests/testthat/fixtures/difORD_fit4.rds |binary tests/testthat/fixtures/difORD_fit5.rds |binary tests/testthat/fixtures/difORD_fit6a.rds |only tests/testthat/fixtures/difORD_fit6b.rds |only tests/testthat/fixtures/difORD_fit6c.rds |only tests/testthat/fixtures/difORD_fit7.rds |binary tests/testthat/fixtures/difORD_fit8.rds |only tests/testthat/fixtures/difORD_fit9.rds |only tests/testthat/test-ddfMLR.R | 111 tests/testthat/test-difNLR.R | 170 tests/testthat/test-difORD.R | 112 tests/testthat/test-estimNLR.R | 14 tests/testthat/test-formulaNLR.R | 3 tests/testthat/test-genNLR.R | 6 tests/testthat/test-startNLR.R | 6 84 files changed, 2696 insertions(+), 4515 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>
Diff between ChannelAttribution versions 2.2.3 dated 2025-11-17 and 2.2.4 dated 2025-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ChannelAttribution.R | 8 ++++---- man/ChannelAttribution-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Easily Build, Simulate, and Visualise Stock-and-Flow Models
Description: Stock-and-flow models are a computational method from the field of
system dynamics. They represent how systems change over time and are
mathematically equivalent to ordinary differential equations. 'sdbuildR'
(system dynamics builder) provides an intuitive interface for constructing
stock-and-flow models without requiring extensive domain knowledge. Models
can quickly be simulated and revised, supporting iterative development.
'sdbuildR' simulates models in 'R' and 'Julia', where 'Julia' offers unit
support and large-scale ensemble simulations. Additionally, 'sdbuildR' can
import models created in 'Insight Maker' (<https://insightmaker.com/>).
Author: Kyra Caitlin Evers [aut, cre, cph]
Maintainer: Kyra Caitlin Evers <kyra.c.evers@gmail.com>
Diff between sdbuildR versions 1.0.7 dated 2025-11-03 and 1.0.8 dated 2025-11-19
DESCRIPTION | 6 - MD5 | 48 ++++---- NAMESPACE | 1 NEWS.md | 9 + R/assemble_script_julia.R | 69 ++++++----- R/assemble_script_r.R | 88 +++++++------- R/build_xmile.R | 32 +++-- R/custom_func.R | 37 +++++- R/helpers.R | 14 -- R/insightmaker_conv.R | 2 R/insightmaker_conv_eqn.R | 2 R/julia_conv_eqn.R | 54 +++++---- R/julia_setup.R | 3 R/simulate.R | 168 ++++++++++++++++++++++++---- R/units.R | 3 R/visualise.R | 11 + README.md | 4 inst/Project.toml | 54 ++++----- man/logistic.Rd | 32 ++++- tests/testthat/test-assemble_script_julia.R | 13 +- tests/testthat/test-assemble_script_r.R | 12 +- tests/testthat/test-build.R | 16 +- tests/testthat/test-custom_func.R | 10 + tests/testthat/test-ensemble.R | 3 tests/testthat/test-insightmaker_to_sfm.R | 13 +- 25 files changed, 459 insertions(+), 245 deletions(-)
Title: UNHCR Refugee Population Statistics Database
Description: The Refugee Population Statistics Database published by
The Office of The United Nations High Commissioner for Refugees (UNHCR)
contains information about forcibly displaced populations
spanning more than 70 years of statistical activities.
It covers displaced populations such as refugees, asylum-seekers and
internally displaced people, including their demographics.
Stateless people are also included, most of who have never been displaced.
The database also reflects the different types of solutions
for displaced populations such as repatriation or resettlement.
More information on the data and methodology can be found on
the UNHCR Refugee Data Finder <https://www.unhcr.org/refugee-statistics/>.
Author: Hisham Galal [aut],
Ahmadou Dicko [aut],
Janis Kreuder [cre],
UNHCR [cph]
Maintainer: Janis Kreuder <kreuder@unhcr.org>
Diff between refugees versions 2024.12.0 dated 2025-06-14 and 2025.06.0 dated 2025-11-19
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ data/asylum_applications.rda |binary data/asylum_decisions.rda |binary data/countries.rda |binary data/demographics.rda |binary data/flows.rda |binary data/idmc.rda |binary data/population.rda |binary data/solutions.rda |binary data/unrwa.rda |binary man/refugees-package.Rd | 8 ++++---- 13 files changed, 35 insertions(+), 25 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.5.1 dated 2025-06-19 and 1.0.0 dated 2025-11-19
OmopSketch-0.5.1/OmopSketch/R/summariseTableQuality.R |only OmopSketch-0.5.1/OmopSketch/R/tableQuality.R |only OmopSketch-0.5.1/OmopSketch/man/interval.Rd |only OmopSketch-0.5.1/OmopSketch/tests/testthat/test-plotInObservation.R |only OmopSketch-0.5.1/OmopSketch/tests/testthat/test-summariseInObservation.R |only OmopSketch-0.5.1/OmopSketch/tests/testthat/test-summariseRecordCount.R |only OmopSketch-0.5.1/OmopSketch/tests/testthat/test-summariseTableQuality.R |only OmopSketch-1.0.0/OmopSketch/DESCRIPTION | 26 OmopSketch-1.0.0/OmopSketch/MD5 | 231 OmopSketch-1.0.0/OmopSketch/NAMESPACE | 8 OmopSketch-1.0.0/OmopSketch/NEWS.md | 37 OmopSketch-1.0.0/OmopSketch/R/OmopSketch-package.R | 1 OmopSketch-1.0.0/OmopSketch/R/checks.R | 32 OmopSketch-1.0.0/OmopSketch/R/databaseCharacteristics.R | 162 OmopSketch-1.0.0/OmopSketch/R/documentationHelper.R | 74 OmopSketch-1.0.0/OmopSketch/R/mockOmopSketch.R | 107 OmopSketch-1.0.0/OmopSketch/R/plotConceptSetCounts.R | 32 OmopSketch-1.0.0/OmopSketch/R/plotInObservation.R | 108 OmopSketch-1.0.0/OmopSketch/R/plotObservationPeriod.R | 69 OmopSketch-1.0.0/OmopSketch/R/plotPerson.R |only OmopSketch-1.0.0/OmopSketch/R/plotRecordCount.R | 109 OmopSketch-1.0.0/OmopSketch/R/plotTrend.R |only OmopSketch-1.0.0/OmopSketch/R/shinyCharacteristics.R | 290 OmopSketch-1.0.0/OmopSketch/R/sqlTranslations.R |only OmopSketch-1.0.0/OmopSketch/R/summariseClinicalRecords.R | 617 OmopSketch-1.0.0/OmopSketch/R/summariseConceptCounts.R | 15 OmopSketch-1.0.0/OmopSketch/R/summariseConceptIdCounts.R | 107 OmopSketch-1.0.0/OmopSketch/R/summariseConceptSetCounts.R | 31 OmopSketch-1.0.0/OmopSketch/R/summariseInObservation.R | 388 OmopSketch-1.0.0/OmopSketch/R/summariseInternal.R | 96 OmopSketch-1.0.0/OmopSketch/R/summariseMissingData.R | 77 OmopSketch-1.0.0/OmopSketch/R/summariseObservationPeriod.R | 220 OmopSketch-1.0.0/OmopSketch/R/summariseOmopSnapshot.R | 206 OmopSketch-1.0.0/OmopSketch/R/summarisePerson.R |only 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OmopSketch-1.0.0/OmopSketch/inst/doc/database_characteristics.html | 220 OmopSketch-1.0.0/OmopSketch/inst/doc/missing_data.R | 133 OmopSketch-1.0.0/OmopSketch/inst/doc/missing_data.Rmd | 123 OmopSketch-1.0.0/OmopSketch/inst/doc/missing_data.html |90483 ++++++---- OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_clinical_tables_records.R | 167 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_clinical_tables_records.Rmd | 233 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_clinical_tables_records.html | 2701 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_concept_id_counts.R | 78 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_concept_id_counts.Rmd | 89 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_concept_id_counts.html | 700 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_observation_period.R | 172 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_observation_period.Rmd | 257 OmopSketch-1.0.0/OmopSketch/inst/doc/summarise_observation_period.html | 1523 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OmopSketch-1.0.0/OmopSketch/tests/testthat/test-summariseObservationPeriod.R | 254 OmopSketch-1.0.0/OmopSketch/tests/testthat/test-summariseOmopSnapshot.R | 29 OmopSketch-1.0.0/OmopSketch/tests/testthat/test-summarisePerson.R |only OmopSketch-1.0.0/OmopSketch/tests/testthat/test-summariseTrend.R |only OmopSketch-1.0.0/OmopSketch/vignettes/database_characteristics.Rmd | 138 OmopSketch-1.0.0/OmopSketch/vignettes/missing_data.Rmd | 123 OmopSketch-1.0.0/OmopSketch/vignettes/summarise_clinical_tables_records.Rmd | 233 OmopSketch-1.0.0/OmopSketch/vignettes/summarise_concept_id_counts.Rmd | 89 OmopSketch-1.0.0/OmopSketch/vignettes/summarise_observation_period.Rmd | 257 OmopSketch-1.0.0/OmopSketch/vignettes/summarise_person.Rmd |only OmopSketch-1.0.0/OmopSketch/vignettes/summarise_trend.Rmd |only 136 files changed, 66509 insertions(+), 38128 deletions(-)
Title: Inferential Methods for Multimodal and Other Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate
conditional uniform graph and quadratic assignment procedure testing,
and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.5.3 dated 2025-10-27 and 1.5.6 dated 2025-11-19
DESCRIPTION | 10 MD5 | 35 - NAMESPACE | 7 NEWS.md | 30 + R/class_makes.R | 14 R/class_models.R | 134 ++++ R/measure_over.R | 7 R/migraph-package.R | 2 R/model_predict.R |only inst/tutorials/tutorial7/diffusion.Rmd | 146 ++--- inst/tutorials/tutorial7/diffusion.html | 856 ++++++++++++++---------------- inst/tutorials/tutorial8/diversity.Rmd | 107 ++- inst/tutorials/tutorial8/diversity.html | 893 +++++++++++++++++++++++--------- inst/tutorials/tutorial9 |only man/predict.Rd |only tests/testthat/test-measure_over.R | 2 tests/testthat/test-model_regression.R | 2 tests/testthat/test-model_tests.R | 9 18 files changed, 1428 insertions(+), 826 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.0.4 dated 2025-07-02 and 1.0.5 dated 2025-11-19
DESCRIPTION | 21 MD5 | 138 NAMESPACE | 2 NEWS.md | 13 R/addDrugUtilisation.R | 24 R/addIntersect.R | 4 R/benchmarkDrugUtilisation.R | 29 R/cohortUtilities.R | 18 R/dailyDose.R | 35 R/documentationHelpers.R | 30 R/erafyCohort.R | 1 R/mockDrugUtilisation.R | 76 R/pattern.R | 18 R/plots.R | 113 R/reexports.R | 4 R/require.R | 6 R/summariseDrugRestart.R | 18 R/summariseIntersect.R | 4 R/summariseProportionOfPatientsCovered.R | 12 R/tables.R | 37 README.md | 36 inst/doc/create_cohorts.R | 174 inst/doc/create_cohorts.Rmd | 242 inst/doc/create_cohorts.html | 813 inst/doc/drug_utilisation.R | 66 inst/doc/drug_utilisation.Rmd | 24 inst/doc/drug_utilisation.html |13570 ++++++------- man/addIndication.Rd | 4 man/benchmarkDrugUtilisation.Rd | 7 man/erafyCohort.Rd | 1 man/mockDrugUtilisation.Rd | 25 man/plotDoc.Rd | 12 man/plotDrugRestart.Rd | 19 man/plotDrugUtilisation.Rd | 12 man/plotIndication.Rd | 21 man/plotProportionOfPatientsCovered.Rd | 11 man/plotTreatment.Rd | 19 man/reexports.Rd | 3 man/summariseIndication.Rd | 4 man/tableDoc.Rd | 23 man/tableDoseCoverage.Rd | 26 man/tableDrugRestart.Rd | 26 man/tableDrugUtilisation.Rd | 26 man/tableIndication.Rd | 26 man/tableProportionOfPatientsCovered.Rd | 26 man/tableTreatment.Rd | 26 tests/testthat/setup.R | 82 tests/testthat/test-addDrugUtilisation.R | 33 tests/testthat/test-benchmarkDrugUtilisation.R | 8 tests/testthat/test-dailyDose.R | 27 tests/testthat/test-erafyCohort.R | 9 tests/testthat/test-generateDrugUtilisationCohortSet.R | 34 tests/testthat/test-generatedAtcCohortSet.R | 5 tests/testthat/test-generatedIngredientCohortSet.R | 28 tests/testthat/test-indication.R | 71 tests/testthat/test-patterns.R | 11 tests/testthat/test-plotProportionOfPatientsCovered.R | 20 tests/testthat/test-plotTreatment.R | 16 tests/testthat/test-plots.R | 25 tests/testthat/test-require.R | 69 tests/testthat/test-summariseDrugRestart.R | 14 tests/testthat/test-summariseDrugUtilisation.R | 7 tests/testthat/test-summariseProportionOfPatientsCovered.R | 40 tests/testthat/test-summariseTreatment.R | 13 tests/testthat/test-tables.R | 54 vignettes/create_cohorts.Rmd | 242 vignettes/daily_dose_calculation.html |only vignettes/drug_restart.html |only vignettes/drug_utilisation.Rmd | 24 vignettes/indication.html |only vignettes/mock_data.html |only vignettes/summarise_treatments.html |only vignettes/treatment_discontinuation.html |only 73 files changed, 8947 insertions(+), 7730 deletions(-)
More information about DrugUtilisation at CRAN
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Title: Automatic Plotting of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 0.4.1 dated 2025-09-11 and 0.5.0 dated 2025-11-19
autograph-0.4.1/autograph/R/plot_graphr.R |only autograph-0.4.1/autograph/R/plot_graphs.R |only autograph-0.4.1/autograph/R/plot_grapht.R |only autograph-0.4.1/autograph/tests/testthat/test-plot_graphr.R |only autograph-0.5.0/autograph/DESCRIPTION | 14 - autograph-0.5.0/autograph/MD5 | 60 +++--- autograph-0.5.0/autograph/NAMESPACE | 5 autograph-0.5.0/autograph/NEWS.md | 38 +++ autograph-0.5.0/autograph/R/autograph-package.R | 5 autograph-0.5.0/autograph/R/autograph_utilities.R | 25 -- autograph-0.5.0/autograph/R/data_precooked.R | 14 + autograph-0.5.0/autograph/R/graph_edges.R |only autograph-0.5.0/autograph/R/graph_labels.R |only autograph-0.5.0/autograph/R/graph_layout.R |only autograph-0.5.0/autograph/R/graph_nodes.R |only autograph-0.5.0/autograph/R/graphr.R |only autograph-0.5.0/autograph/R/graphs.R |only autograph-0.5.0/autograph/R/grapht.R |only autograph-0.5.0/autograph/R/plot_convergence.R | 15 - autograph-0.5.0/autograph/R/plot_diagnostics.R |only autograph-0.5.0/autograph/R/plot_manynet.R | 16 + autograph-0.5.0/autograph/R/plot_migraph.R | 8 autograph-0.5.0/autograph/R/theme_palettes.R | 54 +++++ autograph-0.5.0/autograph/R/theme_set.R | 97 ++++------ autograph-0.5.0/autograph/R/zzz.R | 12 - autograph-0.5.0/autograph/README.md | 13 - autograph-0.5.0/autograph/data/goldfish_changepoints.rda |only autograph-0.5.0/autograph/data/goldfish_outliers.rda |only autograph-0.5.0/autograph/inst/tutorials/tutorial2/visualisation.Rmd | 13 + autograph-0.5.0/autograph/inst/tutorials/tutorial2/visualisation.html | 75 +++++-- autograph-0.5.0/autograph/man/ag_call.Rd | 21 ++ autograph-0.5.0/autograph/man/figures/README-theme-opts-1.png |only autograph-0.5.0/autograph/man/figures/README-theme-opts-2.png |only autograph-0.5.0/autograph/man/made_earlier.Rd | 10 + autograph-0.5.0/autograph/man/plot_adequacy.Rd |only autograph-0.5.0/autograph/man/plot_graphr.Rd | 4 autograph-0.5.0/autograph/man/plot_graphs.Rd | 2 autograph-0.5.0/autograph/man/plot_grapht.Rd | 4 autograph-0.5.0/autograph/man/theme_set.Rd | 13 + autograph-0.5.0/autograph/tests/testthat/test-graphr.R |only 40 files changed, 360 insertions(+), 158 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models. There is also a function for partial and semipartial
correlations and a function for conducting Cohen's
set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.2.7 dated 2025-09-26 and 0.2.8 dated 2025-11-19
DESCRIPTION | 11 +- MD5 | 24 ++-- NAMESPACE | 7 - R/COUNT_REGRESSION.R | 202 +++++++++++++++++++++++++------------ R/LOGISTIC_REGRESSION.R | 242 ++++++++++++++++++++++++++++----------------- R/OLS_REGRESSION.R | 124 +++++++++++++++++------ R/PARTIAL_COR.R | 12 +- R/SET_CORRELATION.R | 86 +++++++-------- R/utilities_boc.R | 34 ++++++ man/COUNT_REGRESSION.Rd | 34 +++++- man/LOGISTIC_REGRESSION.Rd | 27 +++++ man/OLS_REGRESSION.Rd | 12 +- man/PARTIAL_COR.Rd | 52 +++++++++ 13 files changed, 600 insertions(+), 267 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.5.4 dated 2024-11-20 and 1.5.5 dated 2025-11-19
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- R/BetaCorrBin.R | 8 ++++---- build/partial.rdb |binary man/dBetaCorrBin.Rd | 4 ++-- man/pBetaCorrBin.Rd | 4 ++-- 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.3.3 dated 2025-05-19 and 1.3.4 dated 2025-11-19
DESCRIPTION | 6 ++--- MD5 | 8 +++---- build/partial.rdb |binary inst/REFERENCES.bib | 4 +-- inst/doc/Intro_to_EgoCor.html | 47 +++++++++++++++++++++--------------------- 5 files changed, 33 insertions(+), 32 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Isaac Gravestock [aut, cre] ,
Li Su [aut],
Roonak Rezvani [aut] ,
Julia Moesch [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.4.5 dated 2025-06-13 and 0.0.4.8 dated 2025-11-19
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 10 + inst/doc/Getting-Started.Rmd | 2 inst/doc/Getting-Started.html | 193 ++++++++++++++++----------------- inst/doc/new-interface.html | 8 - tests/testthat/test-data_preparation.R | 8 - vignettes/Getting-Started.Rmd | 2 8 files changed, 124 insertions(+), 121 deletions(-)
More information about TrialEmulation at CRAN
Permanent link
Title: Visualization of Spline Effects in GAM and GLM Models
Description: Creates 'ggplot2'-based visualizations of smooth effects from GAM (Generalized Additive Models)
fitted with 'mgcv' and spline effects from GLM (Generalized Linear Models). Supports interaction terms
and provides hazard ratio plots with histograms for survival analysis.
Wood (2017, ISBN:9781498728331) provides comprehensive methodology for generalized additive models.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between splineplot versions 0.2.0 dated 2025-10-24 and 0.2.1 dated 2025-11-19
DESCRIPTION | 7 +++-- MD5 | 10 +++---- NEWS.md | 9 ++++++ R/splineplot.R | 14 +++++++++- README.md | 10 +++---- inst/doc/getting-started.html | 56 +++++++++++++++++++++--------------------- 6 files changed, 63 insertions(+), 43 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: 'HDF5' (Hierarchical Data Format 5) is a high-performance
library and file format for storing and managing large, complex
data. This package provides the static libraries and headers for
the 'HDF5' 'C' library (release 1.14.6). It is intended for R
package developers to use in the 'LinkingTo' field, which
eliminates the need for users to install system-level 'HDF5'
dependencies. This build is compiled with thread-safety enabled
and supports dynamic loading of external compression filters.
'HDF5' is developed by 'The HDF Group' <https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
The HDF Group [cph] ,
Jean-loup Mark [cph] ,
Gailly Adler [cph]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
This is a re-admission after prior archival of version 1.14.6.7 dated 2025-11-17
Diff between hdf5lib versions 1.14.6.7 dated 2025-11-17 and 1.14.6.8 dated 2025-11-19
DESCRIPTION | 7 ++++--- MD5 | 15 ++++++++------- NEWS.md | 8 ++++++++ R/flags.r | 35 ++++++++++++++++++++++++++--------- README.md | 27 +++++++++++++-------------- configure | 25 ++++++++++++++++++------- configure.win | 10 +++++----- man/figures |only man/ld_flags.Rd | 2 +- 9 files changed, 83 insertions(+), 46 deletions(-)
Title: Bindings to 'GDAL'
Description: API bindings to the Geospatial Data Abstraction Library ('GDAL',
<https://gdal.org>). Implements the 'GDAL' Raster and Vector Data Models.
Bindings are implemented with 'Rcpp' modules. Exposed C++ classes and
stand-alone functions wrap much of the 'GDAL' API and provide additional
functionality. Calling signatures resemble the native C, C++ and Python APIs
provided by the 'GDAL' project. Class 'GDALRaster' encapsulates a
'GDALDataset' and its raster band objects. Class 'GDALVector' encapsulates
an 'OGRLayer' and the 'GDALDataset' that contains it. Initial bindings are
provided to the unified 'gdal' command line interface added in 'GDAL' 3.11.
C++ stand-alone functions provide bindings to most 'GDAL' "traditional"
raster and vector utilities, including 'OGR' facilities for vector
geoprocessing, several algorithms, as well as the Geometry API ('GEOS' via
'GDAL' headers), the Spatial Reference Systems API, and methods for
coordinate transformation. Bindings to the Virtual Systems In [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [ctb],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <jctoney@gmail.com>
Diff between gdalraster versions 2.2.1 dated 2025-08-29 and 2.3.0 dated 2025-11-19
DESCRIPTION | 10 MD5 | 174 ++--- NAMESPACE | 1 NEWS.md | 53 + R/RcppExports.R | 395 ++++++++++- R/cmb_table.R | 9 R/display.R | 52 + R/gdal_cli.R | 203 +++-- R/gdal_helpers.R | 84 ++ R/gdal_mdim.R |only R/gdalalg.R | 43 + R/gdalraster.R | 142 +++- R/gdalraster_proc.R | 99 ++ R/geom.R | 465 +++++++++++-- R/ogr_manage.R | 2 README.md | 32 build/vignette.rds |binary configure | 248 +++++++ configure.ac | 35 - inst/COPYRIGHTS | 3 inst/doc/gdal-config-quick-ref.Rmd | 2 inst/doc/gdal-config-quick-ref.html | 5 inst/doc/raster-api-tutorial.html | 23 inst/doc/raster-attribute-tables.html | 111 +-- inst/extdata/byte.nc |only man/CmbTable-class.Rd | 9 man/GDALAlg-class.Rd | 45 + man/GDALRaster-class.Rd | 143 +++- man/bbox_to_wkt.Rd | 1 man/combine.Rd | 4 man/g_factory.Rd | 63 + man/g_query.Rd | 11 man/g_unary_op.Rd | 121 ++- man/g_util.Rd | 31 man/g_wk2wk.Rd | 6 man/gdal_cli.Rd | 45 + man/gdal_get_driver_md.Rd |only man/gdalraster-package.Rd | 15 man/make_chunk_index.Rd |only man/mdim_as_classic.Rd |only man/mdim_info.Rd |only man/mdim_translate.Rd |only man/ogr2ogr.Rd | 3 man/ogrinfo.Rd | 2 man/pixel_extract.Rd | 2 man/plot_geom.Rd |only man/polygonize.Rd | 7 man/rasterToVRT.Rd | 22 man/vsi_get_file_metadata.Rd | 2 man/vsi_stat.Rd | 48 + src/RcppExports.cpp | 222 ++++++ src/cmb_table.cpp | 97 +- src/cmb_table.h | 26 src/gdal_dt.cpp | 6 src/gdal_dt.h | 9 src/gdal_exp.cpp | 682 +++++++++++++------- src/gdal_mdim.cpp |only src/gdal_vsi.cpp | 229 ++++-- src/gdal_vsi.h | 12 src/gdalalg.cpp | 984 +++++++++++++++++++++------- src/gdalalg.h | 35 - src/gdalraster.cpp | 1120 +++++++++++++++++++++------------ src/gdalraster.h | 154 ++-- src/gdalraster_types.h | 6 src/gdalvector.cpp | 494 +++++++------- src/gdalvector.h | 106 +-- src/geom_api.cpp | 618 ++++++++++++++---- src/geom_api.h | 30 src/ogr_util.cpp | 965 +++++++++++++++------------- src/ogr_util.h | 151 ---- src/progress_r.cpp | 1 src/rcpp_util.cpp | 31 src/rcpp_util.h | 30 src/running_stats.cpp | 37 - src/running_stats.h | 9 src/srs_api.cpp | 51 - src/srs_api.h | 6 src/transform.cpp | 105 +-- src/transform.h | 8 src/vsifile.cpp | 55 - src/vsifile.h | 14 tests/testthat/test-GDALAlg-class.R | 286 ++++++++ tests/testthat/test-GDALRaster-class.R | 288 ++++++++ tests/testthat/test-GDALVector-class.R | 12 tests/testthat/test-display.R | 8 tests/testthat/test-gdal_cli.R | 8 tests/testthat/test-gdal_exp.R | 11 tests/testthat/test-gdal_helpers.R | 12 tests/testthat/test-gdal_mdim.R |only tests/testthat/test-gdal_vsi.R | 10 tests/testthat/test-gdalraster_proc.R | 92 ++ tests/testthat/test-geom.R | 137 ++++ vignettes/gdal-config-quick-ref.Rmd | 2 93 files changed, 7057 insertions(+), 2873 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: Extends the Cox model to events with more than one causes. Also supports random and fixed effects, tied events, and time-varying variables. Model details are provided in Peng et al. (2018) <doi:10.1509/jmr.14.0643>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <pengjing@live.com>
Diff between CoxPlus versions 1.1.1 dated 2015-10-24 and 1.5.6 dated 2025-11-19
DESCRIPTION | 21 +- MD5 | 20 +- NAMESPACE | 4 R/CoxPlus.R |only R/cumHazard.R | 37 ++--- R/fastCox.R | 68 ++++++--- inst |only man/CoxPlus.Rd | 48 ------ man/fastCox.Rd |only src/Makevars | 9 - src/Makevars.win | 1 src/RcppExports.cpp |only src/coxReg.cpp | 375 ++++++++++++++++++++++++++++++---------------------- 13 files changed, 327 insertions(+), 256 deletions(-)
Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.10.1 dated 2025-11-17 and 0.10.2 dated 2025-11-19
DESCRIPTION | 6 +-- MD5 | 34 +++++++++--------- NEWS.md | 14 +++++++ R/util.R | 58 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/vig01_intro.Rmd | 52 ++++++++++++++-------------- inst/doc/vig01_intro.html | 55 +++++++++++++++--------------- tests/testthat/test-util.R | 11 ++---- vignettes/articles/vig02_math.Rmd | 4 +- vignettes/articles/vig03_priors.Rmd | 4 +- vignettes/articles/vig04_svd.Rmd | 4 +- vignettes/articles/vig05_bdef.Rmd | 4 +- vignettes/articles/vig06_mortality.Rmd | 4 +- vignettes/articles/vig07_simulation.Rmd | 4 +- vignettes/articles/vig08_workflow.Rmd | 4 +- vignettes/articles/vig09_covariates.Rmd | 4 +- vignettes/articles/vig10_datamod.Rmd | 4 +- vignettes/vig01_intro.Rmd | 52 ++++++++++++++-------------- 18 files changed, 168 insertions(+), 150 deletions(-)
Title: Computes Adaptable Radial Axes Mappings
Description: Computes low-dimensional point representations of high-dimensional numerical data according to the data visualization method Adaptable Radial Axes described in: Manuel Rubio-Sánchez, Alberto Sanchez, and Dirk J. Lehmann (2017) "Adaptable radial axes plots for improved multivariate data visualization" <doi:10.1111/cgf.13196>.
Author: Manuel Rubio-Sanchez [aut, cre, cph] ,
Dirk J. Lehmann [ctb] ,
Miguel Angel Munoz Mohedano [ctb] ,
Alberto Sanchez Campos [ctb] ,
Cristina Soguero-Ruiz [ctb]
Maintainer: Manuel Rubio-Sanchez <manuel.rubio@urjc.es>
Diff between aramappings versions 0.1.0 dated 2025-11-18 and 0.1.1 dated 2025-11-19
aramappings-0.1.0/aramappings/man/figures/readme_autompg_unconstrained_l2.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_exact_l1_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_exact_l2_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_exact_linf_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_ordered_l1_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_ordered_l2_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_ordered_linf_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_unconstrained_l1_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_unconstrained_l2_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_autompg_unconstrained_linf_bb.svg |only aramappings-0.1.0/aramappings/man/figures/vignette_cereals_ara_bb.svg |only aramappings-0.1.1/aramappings/DESCRIPTION | 6 - aramappings-0.1.1/aramappings/MD5 | 34 ++++------ aramappings-0.1.1/aramappings/NEWS.md | 8 ++ aramappings-0.1.1/aramappings/README.md | 6 - aramappings-0.1.1/aramappings/inst/doc/intro_to_aramappings.R | 12 +-- aramappings-0.1.1/aramappings/inst/doc/intro_to_aramappings.Rmd | 12 +-- aramappings-0.1.1/aramappings/inst/doc/intro_to_aramappings.html | 22 +++--- aramappings-0.1.1/aramappings/man/figures/readme_autompg_unconstrained_l2.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_autompg_exact_l1_bb.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_autompg_exact_l2_bb.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_autompg_ordered_l2_bb.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_autompg_unconstrained_l1_bb.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_autompg_unconstrained_l2_bb.jpg |only aramappings-0.1.1/aramappings/man/figures/vignette_cereals_ara_bb.jpg |only aramappings-0.1.1/aramappings/tests/testthat/test-ara_unconstrained_l1.R | 2 aramappings-0.1.1/aramappings/vignettes/intro_to_aramappings.Rmd | 12 +-- 27 files changed, 59 insertions(+), 55 deletions(-)
Title: Association Among Disease Counts and Socio-Environmental Factors
Description: Estimation of association between disease or death counts (e.g. COVID-19) and socio-environmental risk factors using a zero-inflated Bayesian spatiotemporal model. Non-spatiotemporal models and/or models without zero-inflation are also included for comparison. Functions to produce corresponding maps are also included. See Chakraborty et al. (2022) <doi:10.1007/s13253-022-00487-1> for more details on the method.
Author: Suman Majumder [cre, aut, cph],
Yoon-Bae Jun [aut, cph],
Sounak Chakraborty [ctb],
Chae-Young Lim [ctb],
Tanujit Dey [ctb]
Maintainer: Suman Majumder <smajumd2@gmail.com>
Diff between BSTZINB versions 2.0.0 dated 2025-01-30 and 2.0.1 dated 2025-11-19
DESCRIPTION | 10 MD5 | 35 +- NAMESPACE | 4 NEWS.md | 6 R/BNB.R | 1 R/BSTNB.R | 1 R/BSTZINB.R | 5 R/BZINB.R | 2 R/aux_func.R | 48 +- R/methods.R |only R/synth_dat_IA.R |only data/synth_dat_IA.rda |only inst/doc/BSTZINB_vignette.R | 21 - inst/doc/BSTZINB_vignette.Rmd | 21 - inst/doc/BSTZINB_vignette.html | 672 ++++++++++++++++++++--------------------- man/compute_NB_DIC.Rd | 8 man/compute_ZINB_DIC.Rd | 8 man/print.DCMB.Rd |only man/print.summ.DCMB.Rd |only man/summary.DCMB.Rd |only man/synth_dat_IA.Rd |only vignettes/BSTZINB_vignette.Rmd | 21 - 22 files changed, 462 insertions(+), 401 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.57 dated 2025-04-15 and 0.58 dated 2025-11-19
DESCRIPTION | 16 +++++++++------- MD5 | 10 +++++----- R/latex.R | 6 ++++++ man/check_installed.Rd | 2 +- man/tlmgr.Rd | 2 +- tests/test-cran/test-latex.R | 1 + 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support Summary and Analysis of
Extension Program Evaluation in R, and An R
Companion for the Handbook of Biological Statistics.
Vignettes are available at <https://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 2.5.0 dated 2025-02-13 and 2.5.1 dated 2025-11-19
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NEWS.md | 12 ++++++++++++ R/correlation.r | 3 +-- R/mangiaficoD.r | 42 +++++++++++++++++++++++++++++++----------- R/multiMangiaficoD.r | 22 ++++++++++++++++++---- R/nagelkerke.r | 2 +- inst/CITATION | 4 ++-- man/correlation.Rd | 2 +- man/mangiaficoD.Rd | 24 +++++++++++++++++------- man/multiMangiaficoD.Rd | 11 ++++++++++- 11 files changed, 110 insertions(+), 46 deletions(-)
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu [aut, cre]
Maintainer: Chong Gu <chong@purdue.edu>
Diff between gss versions 2.2-9 dated 2025-04-13 and 2.2-10 dated 2025-11-19
ChangeLog | 8 +++++++- DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/family.R | 3 ++- src/dchdc0.f |only 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A large C/C++-based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust, and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R, fast
functions for data transformation and common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data. It
seamlessly supports base R objects/cla [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
Alina Cherkas [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999- [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.1.4 dated 2025-10-24 and 2.1.5 dated 2025-11-19
DESCRIPTION | 8 +++---- MD5 | 30 ++++++++++++++-------------- NEWS.md | 4 +++ R/collap.R | 31 +++++++++++++++-------------- inst/doc/collapse_and_sf.html | 5 ++-- inst/doc/collapse_documentation.html | 4 +-- inst/doc/collapse_for_tidyverse_users.html | 9 ++++---- inst/doc/collapse_object_handling.html | 9 ++++---- inst/doc/developing_with_collapse.html | 5 ++-- man/pivot.Rd | 2 - src/ffirst.c | 3 -- src/flast.c | 3 -- src/fmean.c | 2 - src/fmode.c | 4 +-- src/fndistinct.c | 2 - src/fsum.c | 2 - 16 files changed, 66 insertions(+), 57 deletions(-)
Title: Summarise and Visualise Characteristics of Patients in the OMOP
CDM
Description: Summarise and visualise the characteristics of patients in data
mapped to the Observational Medical Outcomes Partnership (OMOP) common data
model (CDM).
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [ctb] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between CohortCharacteristics versions 1.0.2 dated 2025-10-23 and 1.1.0 dated 2025-11-19
DESCRIPTION | 12 MD5 | 90 NEWS.md | 16 R/documentationHelpers.R | 10 R/plot.R | 15 R/plotCharacteristics.R | 7 R/plotCohortAttrition.R | 4 R/plotCohortCount.R | 6 R/plotCohortOverlap.R | 5 R/plotCohortTiming.R | 6 R/plotComparedLargeScaleCharacteristics.R | 6 R/plotLargeScaleCharacteristics.R | 6 R/summariseCharacteristics.R | 96 R/summariseLargeScaleCharacteristics.R | 72 R/table.R | 8 R/tableCharacteristics.R | 5 R/tableCohortAttrition.R | 2 R/tableCohortCount.R | 2 R/tableCohortOverlap.R | 2 R/tableCohortTiming.R | 2 R/tableLargeScaleCharacteristics.R | 7 inst/doc/summarise_characteristics.Rmd | 3 inst/doc/summarise_characteristics.html | 3325 ++++++++------- inst/doc/summarise_cohort_overlap.html | 582 +- inst/doc/summarise_cohort_timing.html | 674 +-- inst/doc/summarise_large_scale_characteristics.html | 543 +- man/plotCharacteristics.Rd | 7 man/plotCohortCount.Rd | 14 man/plotCohortOverlap.Rd | 7 man/plotCohortTiming.Rd | 9 man/plotComparedLargeScaleCharacteristics.Rd | 9 man/plotDoc.Rd | 6 man/plotLargeScaleCharacteristics.Rd | 9 man/summariseCharacteristics.Rd | 10 man/tableCharacteristics.Rd | 7 man/tableCohortAttrition.Rd | 7 man/tableCohortCount.Rd | 7 man/tableCohortOverlap.Rd | 7 man/tableCohortTiming.Rd | 7 man/tableDoc.Rd | 6 man/tableTopLargeScaleCharacteristics.Rd | 13 tests/testthat/test-plotCharacteristics.R | 24 tests/testthat/test-summariseCharacteristics.R | 37 tests/testthat/test-summariseCohortCodelist.R | 3 tests/testthat/test-summariseLargeScaleCharacteristics.R | 23 vignettes/summarise_characteristics.Rmd | 3 46 files changed, 3212 insertions(+), 2509 deletions(-)
More information about CohortCharacteristics at CRAN
Permanent link
Title: Bridge Sampling for Marginal Likelihoods and Bayes Factors
Description: Provides functions for estimating marginal likelihoods, Bayes
factors, posterior model probabilities, and normalizing constants in general,
via different versions of bridge sampling (Meng & Wong, 1996,
<https://www3.stat.sinica.edu.tw/statistica/j6n4/j6n43/j6n43.htm>).
Gronau, Singmann, & Wagenmakers (2020) <doi:10.18637/jss.v092.i10>.
Author: Quentin F. Gronau [aut, cre] ,
Henrik Singmann [aut] ,
Jonathan J. Forster [ctb],
Eric-Jan Wagenmakers [ths],
The JASP Team [ctb],
Jiqiang Guo [ctb],
Jonah Gabry [ctb],
Ben Goodrich [ctb],
Kees Mulder [ctb],
Perry de Valpine [ctb],
Aki Vehtari [ctb], [...truncated...]
Maintainer: Quentin F. Gronau <Quentin.F.Gronau@gmail.com>
Diff between bridgesampling versions 1.1-2 dated 2021-04-16 and 1.2-1 dated 2025-11-19
bridgesampling-1.1-2/bridgesampling/NEWS |only bridgesampling-1.2-1/bridgesampling/DESCRIPTION | 27 bridgesampling-1.2-1/bridgesampling/MD5 | 143 bridgesampling-1.2-1/bridgesampling/NAMESPACE | 101 bridgesampling-1.2-1/bridgesampling/NEWS.md |only bridgesampling-1.2-1/bridgesampling/R/bf.R | 406 +- bridgesampling-1.2-1/bridgesampling/R/bridge_methods.R | 332 +- bridgesampling-1.2-1/bridgesampling/R/bridge_sampler.R | 1629 +++++----- bridgesampling-1.2-1/bridgesampling/R/bridge_sampler_internals.R | 661 ++-- bridgesampling-1.2-1/bridgesampling/R/bridge_sampler_normal.R | 482 +- bridgesampling-1.2-1/bridgesampling/R/bridge_sampler_tools.R | 95 bridgesampling-1.2-1/bridgesampling/R/bridge_sampler_warp3.R | 694 ++-- bridgesampling-1.2-1/bridgesampling/R/error_measures.R | 176 - bridgesampling-1.2-1/bridgesampling/R/ier-data.R | 32 bridgesampling-1.2-1/bridgesampling/R/logml.R | 57 bridgesampling-1.2-1/bridgesampling/R/post_prob.R | 305 + bridgesampling-1.2-1/bridgesampling/R/turtles-data.R | 64 bridgesampling-1.2-1/bridgesampling/build/partial.rdb |binary bridgesampling-1.2-1/bridgesampling/build/vignette.rds |binary bridgesampling-1.2-1/bridgesampling/inst/doc/bridgesampling_example_jags.R | 348 +- bridgesampling-1.2-1/bridgesampling/inst/doc/bridgesampling_example_jags.Rmd | 452 +- bridgesampling-1.2-1/bridgesampling/inst/doc/bridgesampling_example_jags.html | 753 ++-- bridgesampling-1.2-1/bridgesampling/inst/doc/bridgesampling_example_nimble.R | 228 - 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More information about bridgesampling at CRAN
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Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to
agriculture. Example graphics and analyses are included. Data come
from small-plot trials, multi-environment trials, uniformity trials,
yield monitors, and more.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.25 dated 2025-10-08 and 1.26 dated 2025-11-19
DESCRIPTION | 6 - MD5 | 32 +++++---- NEWS.md | 8 ++ build/vignette.rds |binary data/kirk.potato.uniformity.txt |only data/wehner.cucumber.uniformity.txt |only inst/doc/agridat_uniformity_data.Rmd | 109 ++++++++++++++++++++++++++++++---- inst/doc/agridat_uniformity_data.html | 82 ++++++++++++++++++++++--- man/agridat.Rd | 2 man/crossa.wheat.Rd | 6 - man/gorski.oats.uniformity.Rd | 2 man/kirk.potato.Rd | 1 man/kirk.potato.uniformity.Rd |only man/kotowski.potato.uniformity.Rd | 3 man/larsen.timothy.uniformity.Rd | 4 - man/ridout.appleshoots.Rd | 3 man/stroup.splitplot.Rd | 2 man/wehner.cucumber.uniformity.Rd |only vignettes/agridat_uniformity_data.Rmd | 109 ++++++++++++++++++++++++++++++---- 19 files changed, 308 insertions(+), 61 deletions(-)
Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
approximate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.6.2 dated 2025-08-24 and 0.6.3 dated 2025-11-18
DESCRIPTION | 8 MD5 | 34 +-- NEWS.md | 4 R/prop_allocation.R | 3 R/sps_iterator.R | 15 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/sps.R | 5 inst/doc/sps.html | 170 +++++++++++++++++-- inst/doc/sps.qmd | 5 inst/doc/take-all.R | 1 inst/doc/take-all.html | 328 ++++++++++++++++++++++++++++++++++--- inst/doc/take-all.qmd | 6 man/prop_allocation.Rd | 3 man/sps_iterator.Rd | 11 - tests/testthat/test-sps_iterator.R | 9 + vignettes/sps.qmd | 5 vignettes/take-all.qmd | 6 18 files changed, 536 insertions(+), 77 deletions(-)
Title: Improved Random Number Generator Seeding
Description: A procedure for seeding R's built in random number
generators using a variable-length sequence of values.
Accumulates input entropy into a 256-bit hash digest or "ironseed"
and is able to generate a variable-length sequence of output seeds
from an ironseed.
Author: Reed Cartwright [aut, cre] ,
National Science Foundation DBI-1929850 [fnd]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between ironseed versions 0.2.0 dated 2025-08-20 and 0.3.0 dated 2025-11-18
DESCRIPTION | 8 - MD5 | 34 +++--- NAMESPACE | 1 NEWS.md | 45 +++++++- R/ironseed.R | 84 ++++++++-------- R/set_seed.R | 6 - R/stream.R | 2 README.md | 53 +++++----- build/partial.rdb |binary inst/tinytest/test_ironseed-values.R | 100 +++++++++---------- inst/tinytest/test_ironseed.R | 173 +++++++++++++++++----------------- inst/tinytest/test_set-seed.R | 10 - inst/tinytest/test_stream.R | 8 - inst/tinytest/test_with.R | 46 ++++----- man/figures/README-analysis_256-1.png |binary man/figures/README-analysis_32-1.png |binary man/ironseed.Rd | 37 ++----- src/ironseed.c | 41 +++++--- 18 files changed, 350 insertions(+), 298 deletions(-)
Title: Fast, Robust, and High-Quality Synthetic Data Generation with a
Tuneable Privacy-Utility Trade-Off
Description: Synthesize numeric, categorical, mixed and time series data. Data
circumstances including mixed (or zero-inflated) distributions and missing
data patterns are reproduced in the synthetic data. A single parameter allows
balancing between high-quality synthetic data that represents correlations of
the original data and lower quality but more privacy safe synthetic data
without correlations. Tuning can be done per variable or for the whole
dataset.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between synthesizer versions 0.5.0 dated 2025-07-10 and 0.6.0 dated 2025-11-18
DESCRIPTION | 6 MD5 | 28 +- NAMESPACE | 40 +-- NEWS | 57 ++-- R/synthesizer.R | 496 +++++++++++++++++++-------------------- R/synthesizer_package.R | 14 - build/vignette.rds |binary inst/doc/introduction.R | 98 +++---- inst/doc/introduction.html | 495 +++++++++++++++++++++----------------- inst/doc/introduction.md | 340 +++++++++++++------------- inst/tinytest/test_clustering.R | 74 ++--- inst/tinytest/test_synthesizer.R | 192 +++++++-------- tests/tinytest.R | 10 vignettes/introduction.md | 340 +++++++++++++------------- vignettes/style.css | 88 +++--- 15 files changed, 1166 insertions(+), 1112 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Arthur Bazolli [ctb],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.3.0 dated 2025-10-08 and 0.4.0 dated 2025-11-18
geocodebr-0.3.0/geocodebr/R/RcppExports.R |only geocodebr-0.3.0/geocodebr/R/geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/R/trata_empates_geocode.R |only geocodebr-0.3.0/geocodebr/R/trata_empates_geocode_duckdb2.R |only geocodebr-0.3.0/geocodebr/src |only geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode_duckdb.R |only geocodebr-0.4.0/geocodebr/DESCRIPTION | 13 geocodebr-0.4.0/geocodebr/MD5 | 92 +- geocodebr-0.4.0/geocodebr/NAMESPACE | 2 geocodebr-0.4.0/geocodebr/NEWS.md | 41 geocodebr-0.4.0/geocodebr/R/busca_por_cep.R | 26 geocodebr-0.4.0/geocodebr/R/create_geocodebr_db.R | 7 geocodebr-0.4.0/geocodebr/R/geocode.R | 181 +++- geocodebr-0.4.0/geocodebr/R/geocode_reverso.R | 65 - geocodebr-0.4.0/geocodebr/R/geocodebr-package.R | 2 geocodebr-0.4.0/geocodebr/R/match_cases.R | 39 geocodebr-0.4.0/geocodebr/R/match_cases_probabilistic.R | 74 - geocodebr-0.4.0/geocodebr/R/match_weighted_cases.R | 103 +- geocodebr-0.4.0/geocodebr/R/match_weighted_cases_probabilistic.R | 151 +-- geocodebr-0.4.0/geocodebr/R/trata_empates_geocode_duckdb.R | 413 +++++----- geocodebr-0.4.0/geocodebr/R/utils.R | 106 ++ geocodebr-0.4.0/geocodebr/build/vignette.rds |binary geocodebr-0.4.0/geocodebr/inst/doc/geocode.R | 52 - geocodebr-0.4.0/geocodebr/inst/doc/geocode.html | 46 + geocodebr-0.4.0/geocodebr/inst/doc/geocode_reverso.R | 38 geocodebr-0.4.0/geocodebr/inst/doc/geocode_reverso.html | 56 - geocodebr-0.4.0/geocodebr/inst/doc/geocodebr.R | 116 +- geocodebr-0.4.0/geocodebr/inst/doc/geocodebr.html | 23 geocodebr-0.4.0/geocodebr/man/apaga_data_release_antigo.Rd | 34 geocodebr-0.4.0/geocodebr/man/busca_por_cep.Rd | 7 geocodebr-0.4.0/geocodebr/man/create_index.Rd | 24 geocodebr-0.4.0/geocodebr/man/deletar_pasta_cache.Rd | 2 geocodebr-0.4.0/geocodebr/man/download_cnefe.Rd | 2 geocodebr-0.4.0/geocodebr/man/figures/logo.svg | 412 ++++----- geocodebr-0.4.0/geocodebr/man/geocode.Rd | 7 geocodebr-0.4.0/geocodebr/man/geocode_reverso.Rd | 2 geocodebr-0.4.0/geocodebr/man/roxygen/templates/h3_res.R | 5 geocodebr-0.4.0/geocodebr/man/update_input_db.Rd | 44 - geocodebr-0.4.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 69 + geocodebr-0.4.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 57 - geocodebr-0.4.0/geocodebr/tests/tests_rafa/test_rafa.R | 4 geocodebr-0.4.0/geocodebr/tests/tests_rafa/timer_performance.R |only geocodebr-0.4.0/geocodebr/tests/testthat/_snaps/cache.md | 60 - geocodebr-0.4.0/geocodebr/tests/testthat/_snaps/definir_campos.md | 16 geocodebr-0.4.0/geocodebr/tests/testthat/_snaps/download_cnefe.md | 18 geocodebr-0.4.0/geocodebr/tests/testthat/_snaps/error.md | 18 geocodebr-0.4.0/geocodebr/tests/testthat/_snaps/message.md | 14 geocodebr-0.4.0/geocodebr/tests/testthat/test-busca_por_cep.R | 5 geocodebr-0.4.0/geocodebr/tests/testthat/test-download_cnefe.R | 2 geocodebr-0.4.0/geocodebr/tests/testthat/test-geocode.R | 14 50 files changed, 1441 insertions(+), 1021 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.13 dated 2025-10-07 and 1.0.14 dated 2025-11-18
modsem-1.0.13/modsem/vignettes/set_eval_false.bash |only modsem-1.0.13/modsem/vignettes/set_eval_true.bash |only modsem-1.0.14/modsem/DESCRIPTION | 10 modsem-1.0.14/modsem/MD5 | 193 +- modsem-1.0.14/modsem/NAMESPACE | 2 modsem-1.0.14/modsem/R/RcppExports.R | 12 modsem-1.0.14/modsem/R/bootstrap.R | 56 modsem-1.0.14/modsem/R/calc_se_da.R | 209 +- modsem-1.0.14/modsem/R/check_model_da.R | 26 modsem-1.0.14/modsem/R/construct_matrices_da.R | 27 modsem-1.0.14/modsem/R/cov_model.R | 6 modsem-1.0.14/modsem/R/equations_lms.R | 647 +++++--- modsem-1.0.14/modsem/R/equations_qml.R | 159 + modsem-1.0.14/modsem/R/est_h0.R | 9 modsem-1.0.14/modsem/R/est_lms.R | 50 modsem-1.0.14/modsem/R/est_qml.R | 2 modsem-1.0.14/modsem/R/fit_modsem_da.R | 228 ++ modsem-1.0.14/modsem/R/generics_lavaan.R | 2 modsem-1.0.14/modsem/R/generics_modsem_da.R | 425 +++-- modsem-1.0.14/modsem/R/generics_modsem_pi.R | 14 modsem-1.0.14/modsem/R/inspect_da.R | 289 ++- modsem-1.0.14/modsem/R/labelled_params_da.R | 23 modsem-1.0.14/modsem/R/lavaan_labels.R | 26 modsem-1.0.14/modsem/R/method_settings_da.R | 16 modsem-1.0.14/modsem/R/model_da.R | 320 ++- modsem-1.0.14/modsem/R/model_parameters_da.R | 346 ++-- modsem-1.0.14/modsem/R/modsem_da.R | 143 + modsem-1.0.14/modsem/R/modsem_pi.R | 18 modsem-1.0.14/modsem/R/multiple_imputation_da.R | 2 modsem-1.0.14/modsem/R/optimize_da.R | 459 +++-- modsem-1.0.14/modsem/R/parser.R | 44 modsem-1.0.14/modsem/R/plot_interaction.R | 91 + modsem-1.0.14/modsem/R/reliablity_single_item.R | 130 + modsem-1.0.14/modsem/R/scale_correction_ordered.R | 134 - modsem-1.0.14/modsem/R/simple_slopes.R | 60 modsem-1.0.14/modsem/R/simulate_partable.R | 35 modsem-1.0.14/modsem/R/standardized_solution.R | 189 +- modsem-1.0.14/modsem/R/standardized_solution_da.R | 8 modsem-1.0.14/modsem/R/standardized_solution_pi.R | 247 +-- modsem-1.0.14/modsem/R/tokenizer.R | 7 modsem-1.0.14/modsem/R/twostep.R | 6 modsem-1.0.14/modsem/R/utils.R | 99 + modsem-1.0.14/modsem/R/utils_da.R | 407 ++++- modsem-1.0.14/modsem/R/utils_pi.R | 29 modsem-1.0.14/modsem/R/var_interactions.R | 41 modsem-1.0.14/modsem/README.md | 7 modsem-1.0.14/modsem/build/partial.rdb |binary modsem-1.0.14/modsem/build/vignette.rds |binary modsem-1.0.14/modsem/inst/CITATION | 8 modsem-1.0.14/modsem/inst/doc/customize_plot_interactions.R |only modsem-1.0.14/modsem/inst/doc/customize_plot_interactions.Rmd |only modsem-1.0.14/modsem/inst/doc/customize_plot_interactions.html |only modsem-1.0.14/modsem/inst/doc/customizing.html | 435 ++++- modsem-1.0.14/modsem/inst/doc/estimation_lms.html | 423 ++++- modsem-1.0.14/modsem/inst/doc/fit_measures_da.html | 382 +++- modsem-1.0.14/modsem/inst/doc/higher_order_interactions.html | 519 ++++-- modsem-1.0.14/modsem/inst/doc/interaction_two_etas.html | 433 ++++- modsem-1.0.14/modsem/inst/doc/lavaan.html | 345 +++- modsem-1.0.14/modsem/inst/doc/lms_qml.Rmd | 2 modsem-1.0.14/modsem/inst/doc/lms_qml.html | 430 ++++- modsem-1.0.14/modsem/inst/doc/meanstructure_lms_qml.html | 382 +++- modsem-1.0.14/modsem/inst/doc/methods.html | 377 +++- modsem-1.0.14/modsem/inst/doc/missing_lms_qml.html | 379 +++- modsem-1.0.14/modsem/inst/doc/modsem.html | 515 ++++-- modsem-1.0.14/modsem/inst/doc/observed_lms_qml.html | 808 ++++++---- modsem-1.0.14/modsem/inst/doc/plot_interactions.html | 674 +++++--- modsem-1.0.14/modsem/inst/doc/quadratic.html | 399 +++- modsem-1.0.14/modsem/inst/doc/relcorr_items.html | 394 +++- modsem-1.0.14/modsem/inst/doc/simple_slopes.html | 430 ++++- modsem-1.0.14/modsem/man/fit_modsem_da.Rd | 11 modsem-1.0.14/modsem/man/modsem_da.Rd | 21 modsem-1.0.14/modsem/man/modsem_inspect.Rd | 4 modsem-1.0.14/modsem/man/plot_interaction.Rd | 3 modsem-1.0.14/modsem/man/plot_jn.Rd | 3 modsem-1.0.14/modsem/man/plot_surface.Rd | 4 modsem-1.0.14/modsem/man/relcorr_single_item.Rd | 8 modsem-1.0.14/modsem/src/RcppExports.cpp | 35 modsem-1.0.14/modsem/src/equations_lms.cpp | 125 - modsem-1.0.14/modsem/src/mvnorm.cpp | 84 - modsem-1.0.14/modsem/src/mvnorm.h | 25 modsem-1.0.14/modsem/tests/testthat/mplusResults.inp |only modsem-1.0.14/modsem/tests/testthat/mplusResults.out |only modsem-1.0.14/modsem/tests/testthat/mplusResults_1902fe5a594fdff027c6f333f1b42374.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_1d99a51710dbe72680bd2167846dfc39.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_2f55eb38256759e6ebc9b0699ecf1d13.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_3d0f8823f6af05dbc789d0ed60a54090.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_6507283a847451aff127c84c87ebd81b.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_6bb11f99c9f63d831155403fa8debc11.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_ad18af3b9c89a45fac7dc52df3607909.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_c0d691516a85482200cebd668c136807.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_d4fd46d7e74eb5a0b73e2cb1369c4b51.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_d7630a570fe7052efa569a29540ef19e.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_e8725a6185cbe0286c28c26f935f24e2.dat |only modsem-1.0.14/modsem/tests/testthat/test_cluster.R | 6 modsem-1.0.14/modsem/tests/testthat/test_grad_lms.R | 6 modsem-1.0.14/modsem/tests/testthat/test_lav_models.R | 13 modsem-1.0.14/modsem/tests/testthat/test_linear_da.R | 15 modsem-1.0.14/modsem/tests/testthat/test_lms.R | 16 modsem-1.0.14/modsem/tests/testthat/test_missing.R | 9 modsem-1.0.14/modsem/tests/testthat/test_mplus.R | 2 modsem-1.0.14/modsem/tests/testthat/test_multigroup.R | 39 modsem-1.0.14/modsem/tests/testthat/test_orthogonal_da.R | 4 modsem-1.0.14/modsem/tests/testthat/test_ovchecks_da.R | 2 modsem-1.0.14/modsem/tests/testthat/test_overlapping_inds.R |only modsem-1.0.14/modsem/tests/testthat/test_sampling_weights_da.R |only modsem-1.0.14/modsem/tests/testthat/test_simple_slopes.R | 3 modsem-1.0.14/modsem/vignettes/customize_plot_interactions.Rmd |only modsem-1.0.14/modsem/vignettes/lms_qml.Rmd | 2 108 files changed, 9366 insertions(+), 3662 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.12.0 dated 2025-08-20 and 0.13.0 dated 2025-11-18
DESCRIPTION | 6 +- MD5 | 16 ++--- NEWS.md | 4 + README.md | 31 ++++------ inst/doc/vapour.html | 24 ++++---- inst/include/gdalarrowstream/gdalvectorstream.h | 17 +++-- inst/include/gdallibrary/gdallibrary.h | 71 +++++++++++++++--------- man/figures/README-lod-1.png |binary src/00_raster_block_io.cpp | 9 +-- 9 files changed, 99 insertions(+), 79 deletions(-)
Title: Optimal Subset Selection for Transformation Models
Description: Greedy optimal subset selection for transformation models
(Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess
algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to
models from packages 'tram' and 'cotram'. Application to shift-scale
transformation models are described in Siegfried et al. (2024,
<doi:10.1080/00031305.2023.2203177>).
Author: Lucas Kook [aut, cre] ,
Sandra Siegfried [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramvs versions 0.0-7 dated 2025-01-31 and 0.0-8 dated 2025-11-18
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- build/partial.rdb |only build/vignette.rds |binary inst/doc/tramvs.R | 2 +- inst/doc/tramvs.Rnw | 2 +- inst/doc/tramvs.pdf |binary man/abess_tram.Rd | 6 +++++- tests/testthat/test-continuous.R | 4 ++-- tests/testthat/test-survival.R | 14 ++++++++------ tests/testthat/test-weibull.R | 2 +- vignettes/defs.tex | 2 +- vignettes/tramvs.Rnw | 2 +- 13 files changed, 36 insertions(+), 29 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), models for
binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
linear models, and continuous outcome logistic regression. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlrMBO'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2016) <doi:10.48550/arXiv.1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramnet versions 0.0-9 dated 2025-10-08 and 0.0-10 dated 2025-11-18
tramnet-0.0-10/tramnet/DESCRIPTION | 7 +++---- tramnet-0.0-10/tramnet/MD5 | 11 +++++------ tramnet-0.0-10/tramnet/build/vignette.rds |binary tramnet-0.0-10/tramnet/inst/doc/tramnet.Rnw | 2 +- tramnet-0.0-10/tramnet/inst/doc/tramnet.pdf |binary tramnet-0.0-10/tramnet/vignettes/tramnet.Rnw | 2 +- tramnet-0.0-9/tramnet/inst/NEWS.Rd |only 7 files changed, 10 insertions(+), 12 deletions(-)
Title: Synthetic Microdata Generator
Description: This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
Author: Juhee Lee [aut, cre],
Hang J. Kim [aut],
Young-Min Kim [aut],
Jared Murray [aut]
Maintainer: Juhee Lee <ljh988488@gmail.com>
Diff between synMicrodata versions 2.1.1 dated 2025-09-04 and 2.1.2 dated 2025-11-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/R_functions.R | 19 ++++++++++++++++--- man/multipleSyn.Rd | 14 ++++++++++++-- man/readData.Rd | 37 +++++++++++++++++++++++++++++++++++-- 5 files changed, 71 insertions(+), 15 deletions(-)
Title: Faster Raster and Spatial Vector Processing Using 'GRASS'
Description: Processing of large-in-memory/large-on disk rasters and spatial
vectors using 'GRASS' <https://grass.osgeo.org/>. Most functions in the
'terra' package are recreated. Processing of medium-sized and smaller
spatial objects will nearly always be faster using 'terra' or 'sf', but
for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster.
To use most of the functions, you must have the stand-alone version (not
the 'OSGeoW4' installer version) of 'GRASS' 8.0 or higher.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between fasterRaster versions 8.4.1.0 dated 2025-06-19 and 8.4.1.1 dated 2025-11-18
DESCRIPTION | 10 - MD5 | 80 ++++++------ NEWS.md | 16 ++ R/04_arithmetic.r | 12 + R/addons.r | 11 + R/backdoor.r | 16 ++ R/fast.r | 9 + R/fastData.r | 28 ++-- R/fasterRaster.r | 10 - R/fillNAs.r | 2 R/fragmentation.r | 34 ++--- R/geomorphons.r | 16 +- R/ls.r | 71 ++++------ R/mask.r | 3 R/rbind.r | 19 ++ R/ruggedness.r | 2 R/scale.r | 247 ++++++++++++++++++++++++++++++-------- R/sun.r | 6 README.md | 4 data/madCoast0.rda |binary data/madCoast4.rda |binary data/madDypsis.rda |binary data/madRivers.rda |binary inst/doc/GRasters.html | 4 inst/doc/fasterRaster.html | 76 ++++++----- inst/doc/faster_fasterRaster.html | 4 inst/doc/hidden_functions.html | 4 inst/doc/projects_mapsets.html | 4 inst/doc/regions.html | 4 inst/doc/three_d_objects.html | 4 inst/pkgdown.yml | 4 man/Arithmetic.Rd | 2 man/dot-backdoor.Rd | 4 man/fastData.Rd | 4 man/fasterRaster.Rd | 10 - man/figures/logo.png |binary man/fragmentation.Rd | 4 man/hist.Rd | 2 man/ruggedness.Rd | 2 man/scale.Rd | 12 + man/sun.Rd | 7 - 41 files changed, 483 insertions(+), 264 deletions(-)
Title: Base-Rate Item Evaluation and Typicality Scoring Using Large
Language Models
Description: Download typicality rating datasets, generate new stereotype-based typicality ratings using large language models via the Inference Providers API (<https://huggingface.co/docs/inference-providers>), and evaluate them against human-annotated validation data. Also includes functions to extract stereotype strength and base-rate items from typicality matrices. For more details see Beucler et al. (2025) <doi:10.31234/osf.io/eqrfu_v1>.
Author: Jeremie Beucler [aut, cre]
Maintainer: Jeremie Beucler <jeremie.beucler@gmail.com>
Diff between baserater versions 0.1.1 dated 2025-11-11 and 0.1.2 dated 2025-11-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ README.md | 17 ++++++----------- inst/CITATION | 8 ++++---- inst/doc/Introduction-to-the-baserater-package.Rmd | 4 ++-- inst/doc/Introduction-to-the-baserater-package.html | 6 +++--- vignettes/Introduction-to-the-baserater-package.Rmd | 4 ++-- 8 files changed, 33 insertions(+), 32 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-8 dated 2025-10-08 and 0.3-9 dated 2025-11-18
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/tbm_supplement.pdf |binary tests/bodyfat.R | 2 +- tests/bodyfat.Rout.save |only vignettes/defs.tex | 2 +- 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Robust Regression and Estimation Through Maximum Mean
Discrepancy Minimization
Description: The functions in this package compute robust estimators by minimizing a kernel-based distance known as MMD (Maximum Mean Discrepancy) between the sample and a statistical model. Recent works proved that these estimators enjoy a universal consistency property, and are extremely robust to outliers. Various optimization algorithms are implemented: stochastic gradient is available for most models, but the package also allows gradient descent in a few models for which an exact formula is available for the gradient. In terms of distribution fit, a large number of continuous and discrete distributions are available: Gaussian, exponential, uniform, gamma, Poisson, geometric, etc. In terms of regression, the models available are: linear, logistic, gamma, beta and Poisson.
Alquier, P. and Gerber, M. (2024) <doi:10.1093/biomet/asad031>
Cherief-Abdellatif, B.-E. and Alquier, P. (2022) <doi:10.3150/21-BEJ1338>.
Author: Pierre Alquier [aut, cre] ,
Mathieu Gerber [aut]
Maintainer: Pierre Alquier <pierre.alquier.stat@gmail.com>
Diff between regMMD versions 0.0.3 dated 2025-10-16 and 0.1.0 dated 2025-11-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/summaryMMDest.R | 2 +- build/partial.rdb |binary inst/REFERENCES.bib | 7 +++++++ man/mmd_est.Rd | 2 ++ man/mmd_reg.Rd | 2 ++ 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<https://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
S [...truncated...]
Author: Georgina Anderson [aut, cre],
Sebastian Fox [ctb],
Matthew Francis [ctb],
Emma Clegg [ctb],
Annabel Westermann [ctb],
Joshua Woolner [ctb],
Charlotte Fellows [ctb],
Olivia Box Power [ctb],
Paul Fryers [rev],
Department of Health and Social Care [cph]
Maintainer: Georgina Anderson <georgina.anderson@dhsc.gov.uk>
Diff between PHEindicatormethods versions 2.1.0 dated 2024-12-12 and 2.1.1 dated 2025-11-18
DESCRIPTION | 22 - MD5 | 18 NEWS.md | 7 R/DSR.R | 2 README.md | 11 inst/doc/DSR-vignette.html | 96 ++--- inst/doc/Introduction_to_PHEindicatormethods.html | 422 +++++++++++----------- inst/doc/WorkedExamples_phe_sii.html | 192 +++++----- man/PHEindicatormethods-package.Rd | 7 man/calculate_dsr.Rd | 2 10 files changed, 405 insertions(+), 374 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Indicators for the Analysis of Dispersion of Datasets with
Batched and Ordered Samples
Description: Provides methods for analyzing the dispersion of tabular datasets
with batched and ordered samples. Based on convex hull or integrated covariance
Mahalanobis, several indicators are implemented for inter and intra batch dispersion
analysis. It is designed to facilitate robust statistical assessment of data
variability, supporting applications in exploratory data analysis and quality
control, for such datasets as the one found in metabololomics studies.
For more details see Salanon (2024) <doi:10.1016/j.chemolab.2024.105148> and
Salanon (2025) <doi:10.1101/2025.08.01.668073>.
Author: Brice Mulot [aut],
Elfried Salanon [ctb],
Etienne Jules [aut, cre],
INRAE [cph]
Maintainer: Etienne Jules <etienne.jules@inrae.fr>
Diff between dispersionIndicators versions 0.1.4 dated 2025-10-31 and 0.1.5 dated 2025-11-18
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- NEWS.md | 5 ++++- 3 files changed, 11 insertions(+), 6 deletions(-)
More information about dispersionIndicators at CRAN
Permanent link
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.6.1 dated 2025-11-04 and 1.6.2 dated 2025-11-18
DESCRIPTION | 8 +++++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/bundlePython.R | 3 +++ inst/resources/environment.py | 13 ++++++++++--- inst/resources/pyproject.py | 20 +++++++++++++------- tests/testthat/test-bundlePython.R | 13 +++++++++++++ tests/testthat/test-http.R | 2 ++ 8 files changed, 61 insertions(+), 20 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.0 dated 2025-11-07 and 1.0.1 dated 2025-11-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/algebra.cpp | 2 +- tests/testthat/test-gmp.R | 13 ++++++++----- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.8 dated 2025-09-17 and 7.9 dated 2025-11-18
DESCRIPTION | 9 +++--- MD5 | 33 ++++++++++++------------ R/aeqdist.etest.R | 8 +++--- R/alfa.R | 2 - R/alfa.reg.R | 2 - R/alfa.reg2.R | 57 +++++++++++++++++++++++++++++++++++++++++-- R/alfareg.tune.R | 4 +-- R/eqdist.etest.R | 40 ++++++++++++++++++++++++++++-- R/scls.R | 4 +-- R/scls.betest.R | 4 +-- R/scls.indeptest.R | 4 +-- R/scrq.R | 4 +-- R/tflr.R | 8 +++--- R/tflr.irls.R |only man/Compositional-package.Rd | 6 ++-- man/alfa.reg.Rd | 2 - man/alfareg.tune.Rd | 10 +++---- man/tflr.Rd | 15 ++++++++++- 18 files changed, 159 insertions(+), 53 deletions(-)
Title: Partial Least Squares for Cox Models with Big Matrices
Description: Provides Partial least squares Regression and various regular, sparse
or kernel, techniques for fitting Cox models for big data. Provides a Partial
Least Squares (PLS) algorithm adapted to Cox proportional hazards models that
works with 'bigmemory' matrices without loading the entire dataset in memory.
Also implements a gradient-descent based solver for Cox proportional hazards
models that works directly on 'bigmemory' matrices.
Bertrand and Maumy (2023) <https://hal.science/hal-05352069>, and
<https://hal.science/hal-05352061> highlighted
fitting and cross-validating PLS-based Cox models to censored big data.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between bigPLScox versions 0.6.0 dated 2025-11-11 and 0.8.1 dated 2025-11-18
bigPLScox-0.6.0/bigPLScox/R/big_pls_cox.R.R |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/benchmark-20251031.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/benchmark_bigPLScox-20251031-031744.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/cox-benchmark-20251031-010008.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/cox-benchmark-20251031-010540.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/cox-benchmark-20251031-031709.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/cox_pls-benchmark-bigmemory-20251031-031721.csv |only bigPLScox-0.6.0/bigPLScox/inst/benchmarks/results/cox_pls-benchmark-dense-20251031-031721.csv |only bigPLScox-0.6.0/bigPLScox/inst/doc/bigPLScox-overview.R |only bigPLScox-0.6.0/bigPLScox/inst/doc/bigPLScox-overview.Rmd |only bigPLScox-0.6.0/bigPLScox/inst/doc/bigPLScox-overview.html |only bigPLScox-0.6.0/bigPLScox/vignettes/bigPLScox-overview.Rmd |only bigPLScox-0.8.1/bigPLScox/DESCRIPTION | 12 bigPLScox-0.8.1/bigPLScox/MD5 | 116 - bigPLScox-0.8.1/bigPLScox/NAMESPACE | 15 bigPLScox-0.8.1/bigPLScox/NEWS.md | 47 bigPLScox-0.8.1/bigPLScox/R/RcppExports.R | 24 bigPLScox-0.8.1/bigPLScox/R/align_bigpls_cox.R |only bigPLScox-0.8.1/bigPLScox/R/bigPLScox-package.R | 3 bigPLScox-0.8.1/bigPLScox/R/bigSurvSGD.na.omit.R | 1 bigPLScox-0.8.1/bigPLScox/R/big_fast.R |only bigPLScox-0.8.1/bigPLScox/R/big_pls_cox.R |only bigPLScox-0.8.1/bigPLScox/R/big_pls_cox_gd.R | 157 + bigPLScox-0.8.1/bigPLScox/R/big_pls_cox_gd_diagnostics.R |only bigPLScox-0.8.1/bigPLScox/R/big_pls_cox_transform.R |only bigPLScox-0.8.1/bigPLScox/R/cv.coxDKsgplsDR.R | 2 bigPLScox-0.8.1/bigPLScox/R/plot-big_pls_cox.R |only bigPLScox-0.8.1/bigPLScox/R/plot.big_pls_cox_gd.R |only bigPLScox-0.8.1/bigPLScox/R/predict-big_pls.R | 48 bigPLScox-0.8.1/bigPLScox/R/predict-big_pls_gd.R |only bigPLScox-0.8.1/bigPLScox/R/predict.pls.cox.R | 2 bigPLScox-0.8.1/bigPLScox/R/summary-big_pls_cox.R |only bigPLScox-0.8.1/bigPLScox/README.md | 390 ++-- bigPLScox-0.8.1/bigPLScox/build/vignette.rds |binary bigPLScox-0.8.1/bigPLScox/inst/benchmarks/benchmark_bigPLScox.R | 2 bigPLScox-0.8.1/bigPLScox/inst/benchmarks/results/benchmark_bigPLScox-20251115-171009.csv |only bigPLScox-0.8.1/bigPLScox/inst/benchmarks/results/cox-benchmark-20251115-170850.csv |only bigPLScox-0.8.1/bigPLScox/inst/benchmarks/results/cox_pls-benchmark-bigmemory-20251115-170918.csv |only bigPLScox-0.8.1/bigPLScox/inst/benchmarks/results/cox_pls-benchmark-dense-20251115-170918.csv |only bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox-benchmarking.R | 77 bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox-benchmarking.Rmd | 169 -- bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox-benchmarking.html | 248 +- bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox.R | 226 +- bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox.Rmd | 349 ++-- bigPLScox-0.8.1/bigPLScox/inst/doc/bigPLScox.html | 733 ++++++-- bigPLScox-0.8.1/bigPLScox/inst/doc/getting-started.R | 139 + bigPLScox-0.8.1/bigPLScox/inst/doc/getting-started.Rmd | 267 ++- bigPLScox-0.8.1/bigPLScox/inst/doc/getting-started.html | 580 +++++- bigPLScox-0.8.1/bigPLScox/man/align_big_plscox.Rd |only bigPLScox-0.8.1/bigPLScox/man/big_pls_cox.Rd | 2 bigPLScox-0.8.1/bigPLScox/man/big_pls_cox_fast.Rd |only bigPLScox-0.8.1/bigPLScox/man/big_pls_cox_gd.Rd | 95 - 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bigPLScox-0.8.1/bigPLScox/src/big_pls_cox_fast_big.cpp |only bigPLScox-0.8.1/bigPLScox/src/big_pls_cox_fast_dense.cpp |only bigPLScox-0.8.1/bigPLScox/src/big_pls_cox_gd.cpp | 832 ++++++---- bigPLScox-0.8.1/bigPLScox/src/big_pls_cox_transform.cpp |only bigPLScox-0.8.1/bigPLScox/src/cox_score_residuals_fast.cpp |only bigPLScox-0.8.1/bigPLScox/src/fast_common.h |only bigPLScox-0.8.1/bigPLScox/tests/testthat/test-big_pls_cox_gd.R | 56 bigPLScox-0.8.1/bigPLScox/tests/testthat/test-deviance-residuals.R | 20 bigPLScox-0.8.1/bigPLScox/tests/testthat/test-gd-diagnostics.R |only bigPLScox-0.8.1/bigPLScox/tests/testthat/test-gd-optimizers.R |only bigPLScox-0.8.1/bigPLScox/vignettes/bigPLScox-benchmarking.Rmd | 169 -- bigPLScox-0.8.1/bigPLScox/vignettes/bigPLScox.Rmd | 349 ++-- bigPLScox-0.8.1/bigPLScox/vignettes/getting-started.Rmd | 267 ++- 82 files changed, 3773 insertions(+), 1822 deletions(-)
Title: Hydro-Meteorological Catchments Datasets for the 'airGR'
Packages
Description: Sample of hydro-meteorological datasets extracted from the 'CAMELS-FR' French database <doi:10.57745/WH7FJR>.
It provides metadata and catchment-scale aggregated hydro-meteorological time series on a pool of French catchments for use by the 'airGR' packages.
Author: Olivier Delaigue [aut, cre] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut] ,
Benoît Genot [ctb],
Guilherme Mendoza Guimaraes [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRdatasets versions 0.2.1 dated 2023-07-12 and 0.2.2 dated 2025-11-18
DESCRIPTION | 24 ++++++++------ MD5 | 52 ++++++++++++++++---------------- NEWS.md | 30 ++++++++++++++++-- README.md | 8 +++- build/partial.rdb |binary data/A273011002.rda |binary data/A605102001.rda |binary data/B222001001.rda |binary data/E540031001.rda |binary data/E645651001.rda |binary data/F439000101.rda |binary data/H010002001.rda |binary data/H120101001.rda |binary data/H622101001.rda |binary data/J171171001.rda |binary data/J421191001.rda |binary data/K134181001.rda |binary data/K265401001.rda |binary data/K731261001.rda |binary data/V123521001.rda |binary data/X031001001.rda |binary data/X045401001.rda |binary data/Y643401001.rda |binary data/Y862000101.rda |binary inst/CITATION | 5 +-- man/airGRdatasets-package.Rd | 25 +++++++++------ man/lumped_daily.Rd | 69 +++++++++++++++++++++++++++++++------------ 27 files changed, 139 insertions(+), 74 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <diego.pedregal@uclm.es>
This is a re-admission after prior archival of version 5.1.4 dated 2025-10-22
Diff between UComp versions 5.1.4 dated 2025-10-22 and 5.1.5 dated 2025-11-18
UComp-5.1.4/UComp/man/fitted.Rd |only UComp-5.1.4/UComp/man/plot.ARIMA.Rd |only UComp-5.1.4/UComp/man/plot.Rd |only UComp-5.1.4/UComp/man/print.Rd |only UComp-5.1.4/UComp/man/residuals.Rd |only UComp-5.1.4/UComp/man/summary.ARIMA.Rd |only UComp-5.1.4/UComp/man/summary.ETS.Rd |only UComp-5.1.4/UComp/man/summary.TETS.Rd |only UComp-5.1.5/UComp/ChangeLog | 3 UComp-5.1.5/UComp/DESCRIPTION | 16 - UComp-5.1.5/UComp/MD5 | 175 +++++------ UComp-5.1.5/UComp/NAMESPACE | 3 UComp-5.1.5/UComp/R/ARIMAS3functions.R | 19 + UComp-5.1.5/UComp/R/ARIMAestim.R | 11 UComp-5.1.5/UComp/R/ARIMAmodel.R | 67 +++- UComp-5.1.5/UComp/R/ARIMAvalidate.R | 2 UComp-5.1.5/UComp/R/ETSS3functions.R | 29 + UComp-5.1.5/UComp/R/ETScomponents.R | 5 UComp-5.1.5/UComp/R/ETSestim.R | 2 UComp-5.1.5/UComp/R/ETSmodel.R | 103 ++++++ UComp-5.1.5/UComp/R/ETSvalidate.R | 4 UComp-5.1.5/UComp/R/TETSS3functions.R | 25 + UComp-5.1.5/UComp/R/TETScomponents.R | 5 UComp-5.1.5/UComp/R/TETSestim.R | 2 UComp-5.1.5/UComp/R/TETSmodel.R | 104 +++++- UComp-5.1.5/UComp/R/TETSvalidate.R | 4 UComp-5.1.5/UComp/R/UCS3functions.R | 85 +++-- UComp-5.1.5/UComp/R/UCestim.R | 37 +- UComp-5.1.5/UComp/R/UCmodel.R | 56 +++ UComp-5.1.5/UComp/R/data.R | 28 + UComp-5.1.5/UComp/R/tools.R | 476 +++++++++++++++++--------------- UComp-5.1.5/UComp/man/AIC.UComp.Rd | 5 UComp-5.1.5/UComp/man/ARIMA.Rd | 18 + UComp-5.1.5/UComp/man/ARIMAestim.Rd | 12 UComp-5.1.5/UComp/man/ARIMAforecast.Rd | 4 UComp-5.1.5/UComp/man/ARIMAsetup.Rd | 18 + UComp-5.1.5/UComp/man/ARIMAvalidate.Rd | 2 UComp-5.1.5/UComp/man/Accuracy.Rd | 2 UComp-5.1.5/UComp/man/BIC.UComp.Rd | 5 UComp-5.1.5/UComp/man/ETS.Rd | 25 + UComp-5.1.5/UComp/man/ETScomponents.Rd | 5 UComp-5.1.5/UComp/man/ETSestim.Rd | 2 UComp-5.1.5/UComp/man/ETSforecast.Rd | 8 UComp-5.1.5/UComp/man/ETSsetup.Rd | 25 + UComp-5.1.5/UComp/man/ETSvalidate.Rd | 2 UComp-5.1.5/UComp/man/OECDgdp.Rd | 5 UComp-5.1.5/UComp/man/TETS.Rd | 25 + UComp-5.1.5/UComp/man/TETScomponents.Rd | 5 UComp-5.1.5/UComp/man/TETSestim.Rd | 2 UComp-5.1.5/UComp/man/TETSforecast.Rd | 8 UComp-5.1.5/UComp/man/TETSsetup.Rd | 25 + UComp-5.1.5/UComp/man/TETSvalidate.Rd | 2 UComp-5.1.5/UComp/man/UC.Rd | 2 UComp-5.1.5/UComp/man/UCcommand.Rd |only UComp-5.1.5/UComp/man/UCcomponents.Rd | 2 UComp-5.1.5/UComp/man/UCdisturb.Rd | 2 UComp-5.1.5/UComp/man/UCestim.Rd | 2 UComp-5.1.5/UComp/man/UCfilter.Rd | 2 UComp-5.1.5/UComp/man/UCforecast.Rd | 4 UComp-5.1.5/UComp/man/UChp.Rd | 2 UComp-5.1.5/UComp/man/UCsetup.Rd | 4 UComp-5.1.5/UComp/man/UCsmooth.Rd | 2 UComp-5.1.5/UComp/man/UCvalidate.Rd | 2 UComp-5.1.5/UComp/man/USgdp.Rd | 5 UComp-5.1.5/UComp/man/airpas.Rd | 5 UComp-5.1.5/UComp/man/arma2tsi.Rd | 3 UComp-5.1.5/UComp/man/auxInvBoxCox.Rd | 3 UComp-5.1.5/UComp/man/box.cox.Rd | 5 UComp-5.1.5/UComp/man/ch4.Rd | 5 UComp-5.1.5/UComp/man/colMedians.Rd | 2 UComp-5.1.5/UComp/man/cusum.Rd | 3 UComp-5.1.5/UComp/man/extract.Rd | 2 UComp-5.1.5/UComp/man/gaussTest.Rd | 3 UComp-5.1.5/UComp/man/gdp.Rd | 5 UComp-5.1.5/UComp/man/getp0.Rd | 2 UComp-5.1.5/UComp/man/ident.Rd | 2 UComp-5.1.5/UComp/man/inv.box.cox.Rd | 5 UComp-5.1.5/UComp/man/invBoxCox.Rd | 3 UComp-5.1.5/UComp/man/ipi.Rd | 5 UComp-5.1.5/UComp/man/plotAcfPacf.Rd | 3 UComp-5.1.5/UComp/man/plotSlide.Rd | 2 UComp-5.1.5/UComp/man/predict.UComp.Rd | 4 UComp-5.1.5/UComp/man/rowMedians.Rd | 2 UComp-5.1.5/UComp/man/sales.Rd | 5 UComp-5.1.5/UComp/man/size.Rd | 6 UComp-5.1.5/UComp/man/slide.Rd | 2 UComp-5.1.5/UComp/man/slideAux.Rd | 5 UComp-5.1.5/UComp/man/sumStats.Rd | 2 UComp-5.1.5/UComp/man/tests.Rd | 3 UComp-5.1.5/UComp/man/tsDisplay.Rd | 3 UComp-5.1.5/UComp/man/zplane.Rd | 3 UComp-5.1.5/UComp/src/ARIMAmodel.h | 87 +++-- UComp-5.1.5/UComp/src/UCompC.cpp | 266 ----------------- 93 files changed, 1112 insertions(+), 829 deletions(-)
Title: Identification of Dysregulated MiRNAs Based on MiRNA-MiRNA
Interaction Network
Description: A systematic biology tool was developed to identify dysregulated miRNAs via a miRNA-miRNA interaction network. 'IDMIR' first constructed a weighted miRNA interaction network through integrating miRNA-target interaction information, molecular function data from Gene Ontology (GO) database and gene transcriptomic data in specific-disease context, and then, it used a network propagation algorithm on the network to identify significantly dysregulated miRNAs.
Author: Junwei Han [aut, cre, cph],
Xilong Zhao [aut],
Jiashuo Wu [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between IDMIR versions 0.1.0 dated 2023-11-09 and 0.1.1 dated 2025-11-18
DESCRIPTION | 10 +- MD5 | 12 +-- R/IdentifyMiRNA.R | 6 - build/vignette.rds |binary data/MirnaData.rda |binary inst/doc/IDMIR.R | 14 ++-- inst/doc/IDMIR.html | 180 +++++++++++++++++++++++++--------------------------- 7 files changed, 109 insertions(+), 113 deletions(-)
Title: A Cross Between a 2D Density Plot and a Scatter Plot
Description: A cross between a 2D density plot and a scatter plot,
implemented as a 'ggplot2' geom. Points in the scatter plot are
colored by the number of neighboring points. This is useful to
visualize the 2D-distribution of points in case of overplotting.
Author: Lukas P. M. Kremer [aut, cre] ,
Simon Anders [ctb]
Maintainer: Lukas P. M. Kremer <L-Kremer@web.de>
Diff between ggpointdensity versions 0.2.0 dated 2025-05-16 and 0.2.1 dated 2025-11-18
DESCRIPTION | 8 +-- MD5 | 38 +++++++++------- NAMESPACE | 2 NEWS.md |only R/geom_pointdensity.R | 8 +-- R/ggpointdensity-package.R | 1 README.md | 63 +++++++++++++++++++++++----- man/figures/make_demo_plots.qmd | 55 +++++++++++++++++++++++- man/figures/pointdensity.png |binary man/figures/pointdensity_adj.png |binary man/figures/pointdensity_custom.png |binary man/figures/pointdensity_facet.png |binary man/figures/pointdensity_facet_relative.png |only man/figures/pointdensity_logo.png |binary man/figures/pointdensity_methods.png |only man/figures/pointdensity_relative.png |only man/figures/pointdensity_shape.png |binary man/figures/pointdensity_xyadj.png |binary man/figures/pointdensity_zoom.png |binary man/figures/scatter_dens_bin2d.png |binary man/geom_pointdensity.Rd | 40 +++++++++-------- man/stat_pointdensity.Rd | 38 +++++++++------- 22 files changed, 181 insertions(+), 72 deletions(-)
More information about ggpointdensity at CRAN
Permanent link
Title: Convert and Impute Dates to ISO Standard ("International
Organization for Standardization")
Description: Provides functions to convert and impute date values to the ISO 8601
standard format. The package automatically recognizes date patterns within a
data frame and transforms them into consistent ISO-formatted dates. It also
supports imputing missing month or day components in partial date strings
using user-defined rules. Only one date format can be applied within a single
data frame column.
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Diff between datetoiso versions 1.0.0 dated 2025-11-12 and 1.1.1 dated 2025-11-18
datetoiso-1.0.0/datetoiso/man/prepare_date.Rd |only datetoiso-1.1.1/datetoiso/DESCRIPTION | 6 datetoiso-1.1.1/datetoiso/MD5 | 35 datetoiso-1.1.1/datetoiso/NAMESPACE | 1 datetoiso-1.1.1/datetoiso/NEWS.md | 86 - datetoiso-1.1.1/datetoiso/R/date_to_iso.R | 112 + datetoiso-1.1.1/datetoiso/R/impute_date.R | 378 +++- datetoiso-1.1.1/datetoiso/R/viso.R | 2 datetoiso-1.1.1/datetoiso/README.md | 2 datetoiso-1.1.1/datetoiso/man/check_day_correctly_entered_dmy.Rd |only datetoiso-1.1.1/datetoiso/man/check_day_correctly_entered_ymd.Rd |only datetoiso-1.1.1/datetoiso/man/check_if_month_year_entered.Rd |only datetoiso-1.1.1/datetoiso/man/check_if_only_year_entered.Rd |only datetoiso-1.1.1/datetoiso/man/check_if_year_month_day_entered.Rd |only datetoiso-1.1.1/datetoiso/man/check_if_year_month_entered.Rd |only datetoiso-1.1.1/datetoiso/man/clean_date.Rd |only datetoiso-1.1.1/datetoiso/man/find_unknow_date.Rd | 40 datetoiso-1.1.1/datetoiso/man/impute_date.Rd | 144 - datetoiso-1.1.1/datetoiso/man/impute_date_dmy.Rd | 138 - datetoiso-1.1.1/datetoiso/man/impute_date_ymd.Rd | 138 - datetoiso-1.1.1/datetoiso/man/remove_no_date_characters.Rd | 62 datetoiso-1.1.1/datetoiso/tests/testthat/test-date_to_iso.R |only datetoiso-1.1.1/datetoiso/tests/testthat/test-impute_date.R | 807 +++++++++- 23 files changed, 1545 insertions(+), 406 deletions(-)
Title: Interface with Google Cloud Document AI API
Description: R interface for the Google Cloud Services 'Document AI API'
<https://cloud.google.com/document-ai> with additional tools for
output file parsing and text reconstruction. 'Document AI' is a
powerful server-based OCR service that extracts text and tables from
images and PDF files with high accuracy. 'daiR' gives R users
programmatic access to this service and additional tools to handle
and visualize the output. See the package website <https://dair.info/>
for more information and examples.
Author: Thomas Hegghammer [aut, cre]
Maintainer: Thomas Hegghammer <hegghammer@gmail.com>
Diff between daiR versions 1.0.1 dated 2024-11-13 and 1.2.0 dated 2025-11-18
DESCRIPTION | 11 MD5 | 92 - NAMESPACE | 2 NEWS.md | 27 R/auth.R | 17 R/draw.R | 212 ++ R/extract.R | 181 +- R/manipulate.R | 331 ++-- R/processors.R | 455 +++--- R/send_to_dai.R | 99 - R/utils.R | 14 R/xml.R | 900 +++++++---- R/zzz.R | 5 build/vignette.rds |binary inst/doc/complex_file_and_folder_management.R | 64 inst/doc/complex_file_and_folder_management.html | 5 inst/doc/configuration.R | 8 inst/doc/configuration.html | 5 inst/doc/gcs_storage.R | 64 inst/doc/gcs_storage.html | 5 inst/doc/quickstart.R | 44 inst/doc/quickstart.html | 5 inst/doc/reconstructing_text.R | 110 - inst/doc/reconstructing_text.html | 5 inst/doc/tables.R | 54 inst/doc/tables.Rmd | 4 inst/doc/tables.html | 7 inst/doc/usage.R | 90 - inst/doc/usage.Rmd | 2 inst/doc/usage.html | 7 man/create_processor.Rd | 2 man/get_ids_by_type.Rd |only man/get_processor_info.Rd | 2 man/get_processors.Rd | 2 man/get_versions_by_type.Rd |only man/list_processor_types.Rd | 2 man/make_hocr.Rd | 8 tests/testthat/test_auth.R | 220 ++ tests/testthat/test_draw.R | 1744 ++++++++++------------- tests/testthat/test_extract.R | 418 ++++- tests/testthat/test_manipulate.R | 1190 ++++++++++----- tests/testthat/test_processors.R | 754 ++++++--- tests/testthat/test_send_to_dai.R | 831 ++++++++++ tests/testthat/test_utils.R | 464 +++++- tests/testthat/test_xml.R | 585 +++++++ tests/testthat/test_zzz.R | 2 vignettes/tables.Rmd | 4 vignettes/usage.Rmd | 2 48 files changed, 6149 insertions(+), 2906 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.2-5 dated 2025-10-08 and 1.3-0 dated 2025-11-18
tram-1.2-5/tram/cleanup |only tram-1.3-0/tram/DESCRIPTION | 27 - tram-1.3-0/tram/MD5 | 113 ++-- tram-1.3-0/tram/NAMESPACE | 2 tram-1.3-0/tram/R/Compris.R | 6 tram-1.3-0/tram/R/methods.R | 30 - tram-1.3-0/tram/R/mmlt.R | 16 tram-1.3-0/tram/R/mtram.R | 8 tram-1.3-0/tram/R/tram.R | 77 ++- tram-1.3-0/tram/build/partial.rdb |binary tram-1.3-0/tram/build/vignette.rds |binary tram-1.3-0/tram/demo/NAMI.Rout.save |only tram-1.3-0/tram/demo/SCI_ePolr.Rout.save |only tram-1.3-0/tram/demo/hcc.Rout.save |only tram-1.3-0/tram/demo/mtram.Rout.save |only tram-1.3-0/tram/demo/npb.Rout.save |only tram-1.3-0/tram/demo/npn.Rout.save |only tram-1.3-0/tram/demo/stram.R | 51 +- tram-1.3-0/tram/demo/stram.Rout.save |only tram-1.3-0/tram/demo/survtram.R | 22 tram-1.3-0/tram/demo/survtram.Rout.save |only tram-1.3-0/tram/demo/tram.Rout.save |only tram-1.3-0/tram/demo/undernutrition.R | 10 tram-1.3-0/tram/demo/undernutrition.Rout.save |only tram-1.3-0/tram/inst/NEWS.Rd | 22 tram-1.3-0/tram/inst/doc/NAMI.R | 91 ++- tram-1.3-0/tram/inst/doc/NAMI.Rnw | 328 ++++++++++---- tram-1.3-0/tram/inst/doc/NAMI.pdf |binary tram-1.3-0/tram/inst/doc/mtram.R | 19 tram-1.3-0/tram/inst/doc/mtram.Rnw | 21 tram-1.3-0/tram/inst/doc/mtram.pdf |binary tram-1.3-0/tram/inst/doc/survtram.R | 183 +++----- tram-1.3-0/tram/inst/doc/survtram.Rnw | 457 +++++++++----------- tram-1.3-0/tram/inst/doc/survtram.pdf |binary tram-1.3-0/tram/inst/doc/tram.R | 3 tram-1.3-0/tram/inst/doc/tram.Rnw | 3 tram-1.3-0/tram/inst/doc/tram.pdf |binary tram-1.3-0/tram/inst/simulations/sim2d.Rout.save |only tram-1.3-0/tram/inst/simulations/sim5d.Rout.save |only tram-1.3-0/tram/man/Compris.Rd | 46 -- tram-1.3-0/tram/man/Coxph.Rd | 12 tram-1.3-0/tram/man/mmlt.Rd | 9 tram-1.3-0/tram/man/mtram.Rd | 2 tram-1.3-0/tram/man/tram-methods.Rd | 2 tram-1.3-0/tram/man/tram.Rd | 41 + tram-1.3-0/tram/tests/Coxph-Ex.Rout.save |only tram-1.3-0/tram/tests/Polr-Ex.R |only tram-1.3-0/tram/tests/Polr-Ex.Rout.save |only tram-1.3-0/tram/tests/Survreg-Ex.R | 9 tram-1.3-0/tram/tests/Survreg-Ex.Rout.save |only tram-1.3-0/tram/tests/bugfixes.R | 41 + tram-1.3-0/tram/tests/intercepts-Ex.Rout.save |only tram-1.3-0/tram/tests/mmlt-Ex.R | 2 tram-1.3-0/tram/tests/mmlt-Ex.Rout.save |only tram-1.3-0/tram/tests/mtram-Ex.Rout.save |only tram-1.3-0/tram/tests/stram-Ex.R | 4 tram-1.3-0/tram/tests/stram-Ex.Rout.save |only tram-1.3-0/tram/vignettes/COXME-margsurv-plot-1.pdf |binary tram-1.3-0/tram/vignettes/HTECOX-DFS-plot-1.pdf |binary tram-1.3-0/tram/vignettes/NAMI.Rnw | 328 ++++++++++---- tram-1.3-0/tram/vignettes/TVAR-DFS-plot-1.pdf |binary tram-1.3-0/tram/vignettes/TVAR-iDFS-plot-1.pdf |binary tram-1.3-0/tram/vignettes/defs.tex | 2 tram-1.3-0/tram/vignettes/mlt.bib | 47 ++ tram-1.3-0/tram/vignettes/mtram.Rnw | 21 tram-1.3-0/tram/vignettes/survtram.Rnw | 457 +++++++++----------- tram-1.3-0/tram/vignettes/survtram.bib | 1 tram-1.3-0/tram/vignettes/tram.Rnw | 3 68 files changed, 1497 insertions(+), 1019 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in
R. The framework is unopinionated when it comes to how HTTP requests
and WebSocket messages are handled and supports all levels of app
complexity; from serving static content to full-blown dynamic
web-apps. Fiery does not hold your hand as much as e.g. the shiny
package does, but instead sets you free to create your web app the way
you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.4.0 dated 2025-11-10 and 1.4.1 dated 2025-11-18
DESCRIPTION | 10 ++--- MD5 | 20 +++++----- NAMESPACE | 1 NEWS.md | 4 ++ R/Fire.R | 7 ++- R/loggers.R | 8 ++++ R/request_store.R | 6 +-- man/loggers.Rd | 3 + tests/testthat/_snaps/Fire.md | 68 +++++++++++++++++----------------- tests/testthat/_snaps/HandlerStack.md | 44 +++++++++++----------- tests/testthat/helper.R | 1 11 files changed, 95 insertions(+), 77 deletions(-)
Title: Pedigree Inference from SNPs
Description: Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 3.0.3 dated 2025-08-19 and 3.1.3 dated 2025-11-18
DESCRIPTION | 10 - MD5 | 75 ++++--- NAMESPACE | 130 ++++++------- NEWS.md | 17 + R/CalcBYprobs.R | 4 R/CalcMaxMismatch.R | 11 - R/CalcOHLLR.R | 29 ++ R/CalcPairLL.R | 23 +- R/CalcParentProbs.R | 3 R/CheckLifeHist.R | 9 R/CountPairOH.R |only R/DuplicateCheck.R | 20 +- R/GetMaybeRel.R | 4 R/MkAgePrior.R | 7 R/PedPolish.R | 32 +-- R/PedToNum.R | 11 - R/PlotPropAssigned.R |only R/Prepare.R | 31 +-- R/SeqListSummary.R | 30 +-- R/Sequoia_F90wrappers.R | 8 R/Sequoia_Main.R | 61 +++--- inst/doc/quick_start_example1.html | 14 - inst/doc/vignette-age.pdf |binary inst/doc/vignette-main.pdf |binary inst/doc/vignette_mtDNA.pdf |binary man/CalcMaxMismatch.Rd | 11 - man/CalcOHLLR.Rd | 19 + man/CalcPairLL.Rd | 17 + man/CountOH.Rd |only man/DuplicateCheck.Rd | 4 man/GetMaybeRel.Rd | 9 man/LLtoProb.Rd | 3 man/MakeAgePrior.Rd | 5 man/PedPolish.Rd | 4 man/PlotPropAssigned.Rd |only man/SeqParSib.Rd | 2 man/SummarySeq.Rd | 17 + man/sequoia.Rd | 51 +++-- src/Sequoia.f90 | 365 +++++++++++++++++++------------------ src/countpairOH.f90 |only src/init.c | 48 +++- 41 files changed, 620 insertions(+), 464 deletions(-)
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [ctb] ,
Martin R. Smith [ctb] ,
David L. Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.5.0 dated 2024-09-04 and 1.6.0 dated 2025-11-18
DESCRIPTION | 35 ++- MD5 | 100 +++++----- NAMESPACE | 7 NEWS.md | 8 R/add_phylopic_base.r | 4 R/add_phylopic_tree.R |only R/geom_phylopic.R | 14 + R/get_phylopic.R | 51 +++-- R/pick_phylopic.R | 3 R/resolve_phylopic.R | 19 - R/rphylopic-package.R | 1 README.md | 4 build/vignette.rds |binary inst/doc/a-getting-started.Rmd | 12 - inst/doc/a-getting-started.html | 19 + inst/doc/b-advanced-ggplot.Rmd | 4 inst/doc/b-advanced-ggplot.html | 33 +-- inst/doc/c-advanced-base.Rmd | 18 + inst/doc/c-advanced-base.html | 48 ++-- man/add_phylopic_tree.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/get_phylopic.Rd | 14 + tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_phylopic/phylopic-in-background.svg | 4 tests/testthat/_snaps/add_phylopic/phylopic-png-in-background.svg | 4 tests/testthat/_snaps/add_phylopic_tree |only tests/testthat/_snaps/geom_phylopic/geom-phylopic-with-alt-height-and-width.svg | 28 +- tests/testthat/_snaps/geom_phylopic/geom-phylopic-with-no-dims.svg | 28 +- tests/testthat/_snaps/geom_phylopic/geom-phylopic-with-png.svg | 28 +- tests/testthat/_snaps/geom_phylopic/geom-phylopic-with-width.svg | 56 ++--- tests/testthat/_snaps/geom_phylopic/geom-phylopic.svg | 56 ++--- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-img.svg | 28 +- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-larger-glyphs.svg | 28 +- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-uuid.svg | 28 +- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph.svg | 28 +- tests/testthat/test-add_phylopic_tree.R |only tests/testthat/test-geom_phylopic.R | 2 tests/testthat/test-get_phylopic.R | 8 vignettes/a-getting-started.Rmd | 12 - vignettes/b-advanced-ggplot.Rmd | 4 vignettes/base-penguin-plot-1-1.png |binary vignettes/base-penguin-plot-2-1.png |binary vignettes/base-penguin-plot-3-1.png |binary vignettes/base-penguin-plot-4-1.png |binary vignettes/base-penguin-plot-5-1.png |binary vignettes/base-phylo-plot-1-1.png |binary vignettes/base-phylo-plot-2-1.png |binary vignettes/base-phylo-plot-3-1.png |binary vignettes/base-phylo-plot-4-1.png |binary vignettes/c-advanced-base.Rmd | 18 + vignettes/source |only 54 files changed, 430 insertions(+), 324 deletions(-)
Title: A Simple Router for HTTP and WebSocket Requests
Description: In order to make sure that web request ends up in the correct
handler function a router is often used. 'routr' is a package implementing a
simple but powerful routing functionality for R based servers. It is a fully
functional 'fiery' plugin, but can also be used with other 'httpuv' based
servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between routr versions 1.0.0 dated 2025-08-21 and 1.1.0 dated 2025-11-18
DESCRIPTION | 12 - MD5 | 66 ++++--- NEWS.md | 18 ++ R/aaa.R | 38 ++++ R/asset_route.R | 98 ++++++++--- R/openapi_route.R | 78 +++++++-- R/otel.R |only R/redirector.R | 13 + R/report_route.R | 232 ++++++++++++++++++++++------ R/resource_route.R | 163 +++++++++++-------- R/route.R | 154 ++++++++++++++---- R/routestack.R | 115 ++++++++++--- R/shared_secret_route.R | 20 +- R/sizelimit_route.R | 2 R/tidy_api.R | 6 man/AssetRoute.Rd | 4 man/Route-class.Rd | 9 - man/RouteStack.Rd | 26 +++ man/report_info.Rd | 5 man/report_route.Rd | 38 +++- man/route_add.Rd | 2 man/route_merge.Rd | 2 man/route_stack.Rd | 2 tests/testthat/_snaps/report_route.md | 2 tests/testthat/fixtures/reports/python.qmd |only tests/testthat/fixtures/reports/test.qmd | 4 tests/testthat/fixtures/sample_openapi.yaml | 4 tests/testthat/test-asset_route.R | 30 +++ tests/testthat/test-openapi_route.R | 6 tests/testthat/test-report_route.R | 79 +++++++-- tests/testthat/test-resource_route.R | 10 - tests/testthat/test-route.R | 55 +++++- tests/testthat/test-routestack.R | 86 +++++----- tests/testthat/test-shared_secret_route.R | 24 +- tests/testthat/test-sizelimit_route.R | 20 +- 35 files changed, 1032 insertions(+), 391 deletions(-)
Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database.
<https://api.neotomadb.org/api-docs/>.
Author: Dominguez Vidana Socorro [aut, cre] ,
Simon Goring [aut]
Maintainer: Dominguez Vidana Socorro <dominguezvid@wisc.edu>
Diff between neotoma2 versions 1.0.7 dated 2025-07-14 and 1.0.8 dated 2025-11-18
neotoma2-1.0.7/neotoma2/R/fix_nulls.r |only neotoma2-1.0.7/neotoma2/R/get0_params.R |only neotoma2-1.0.7/neotoma2/R/getids.R |only neotoma2-1.0.7/neotoma2/R/neotoma-methods.R |only neotoma2-1.0.7/neotoma2/R/pingNeotoma.R |only neotoma2-1.0.7/neotoma2/R/set_contacts.R |only neotoma2-1.0.7/neotoma2/R/set_publications.R |only neotoma2-1.0.7/neotoma2/man/add_chronology-collunit-chronology-data.frame-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-authors-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-chronologies-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-chronology-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-collunit-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-collunits-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-contact-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-contacts-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-dataset-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-datasets-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-publication-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-publications-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-site-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-sites-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-taxa-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.data.frame-taxon-method.Rd |only neotoma2-1.0.7/neotoma2/man/as.list-sites-method.Rd |only neotoma2-1.0.7/neotoma2/man/author-class.Rd |only neotoma2-1.0.7/neotoma2/man/authors-class.Rd |only neotoma2-1.0.7/neotoma2/man/build_specimen.Rd |only neotoma2-1.0.7/neotoma2/man/c-chronologies-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-collunits-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-contact-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-contacts-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-datasets-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-missingOrNULL-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-publications-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-samples-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-sites-method.Rd |only neotoma2-1.0.7/neotoma2/man/c-taxa-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-chronologies-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-chronology-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-collunit-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-collunits-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-contact-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-contacts-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-dataset-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-datasets-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-publication-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-sample-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-samples-method.Rd |only neotoma2-1.0.7/neotoma2/man/cash-set-chronology-method.Rd |only 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neotoma2-1.0.7/neotoma2/man/collunits-site-method.Rd |only neotoma2-1.0.7/neotoma2/man/contact-class.Rd |only neotoma2-1.0.7/neotoma2/man/contacts-class.Rd |only neotoma2-1.0.7/neotoma2/man/dataset-class.Rd |only neotoma2-1.0.7/neotoma2/man/datasets-class.Rd |only neotoma2-1.0.7/neotoma2/man/datasets-collunit-method.Rd |only neotoma2-1.0.7/neotoma2/man/datasets-site-method.Rd |only neotoma2-1.0.7/neotoma2/man/datasets-sites-method.Rd |only neotoma2-1.0.7/neotoma2/man/doi-publication-method.Rd |only neotoma2-1.0.7/neotoma2/man/doi-site-method.Rd |only neotoma2-1.0.7/neotoma2/man/filter.sites.Rd |only neotoma2-1.0.7/neotoma2/man/get_contacts.default.Rd |only neotoma2-1.0.7/neotoma2/man/get_contacts.numeric.Rd |only neotoma2-1.0.7/neotoma2/man/get_datasets.default.Rd |only neotoma2-1.0.7/neotoma2/man/get_datasets.numeric.Rd |only neotoma2-1.0.7/neotoma2/man/get_datasets.site.Rd |only neotoma2-1.0.7/neotoma2/man/get_datasets.sites.Rd |only 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neotoma2-1.0.7/neotoma2/man/write.csv-chronologies-method.Rd |only neotoma2-1.0.7/neotoma2/man/write.csv-collunits-method.Rd |only neotoma2-1.0.7/neotoma2/man/write.csv-datasets-method.Rd |only neotoma2-1.0.7/neotoma2/man/write.csv-sites-method.Rd |only neotoma2-1.0.7/neotoma2/man/write.csv-taxa-method.Rd |only neotoma2-1.0.7/neotoma2/tests/testthat/test-get_contacts.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-get_manual.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-get_table.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-parse_location.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-ping.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-set_server.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test-toJSON.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_check_contacts.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_download.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_generaltests.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_methods.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_setsample.R |only neotoma2-1.0.7/neotoma2/tests/testthat/test_setsite.r |only neotoma2-1.0.8/neotoma2/DESCRIPTION | 22 neotoma2-1.0.8/neotoma2/MD5 | 507 ++---- neotoma2-1.0.8/neotoma2/NAMESPACE | 88 - neotoma2-1.0.8/neotoma2/NEWS.md | 76 neotoma2-1.0.8/neotoma2/R/01_classDefinitions.R | 788 +++++----- neotoma2-1.0.8/neotoma2/R/02_genericDefinitions.R | 81 - neotoma2-1.0.8/neotoma2/R/build_chron.R | 55 neotoma2-1.0.8/neotoma2/R/build_collunit.R | 35 neotoma2-1.0.8/neotoma2/R/build_dataset.R | 42 neotoma2-1.0.8/neotoma2/R/build_sample.R | 58 neotoma2-1.0.8/neotoma2/R/build_site.R | 22 neotoma2-1.0.8/neotoma2/R/build_specimen.R | 63 neotoma2-1.0.8/neotoma2/R/build_speleothem.R |only neotoma2-1.0.8/neotoma2/R/check_contacts.R | 13 neotoma2-1.0.8/neotoma2/R/chroncontrols.R | 54 neotoma2-1.0.8/neotoma2/R/chronology-methods.R | 135 - neotoma2-1.0.8/neotoma2/R/clean.R | 158 -- neotoma2-1.0.8/neotoma2/R/cleanNULL.R | 13 neotoma2-1.0.8/neotoma2/R/collunits-methods.R | 276 +-- neotoma2-1.0.8/neotoma2/R/contact-methods.R | 142 - neotoma2-1.0.8/neotoma2/R/dataset-methods.R | 141 - neotoma2-1.0.8/neotoma2/R/filter.R | 148 - neotoma2-1.0.8/neotoma2/R/get_contacts.R | 167 +- neotoma2-1.0.8/neotoma2/R/get_datasets.R | 162 +- neotoma2-1.0.8/neotoma2/R/get_documentation.R |only neotoma2-1.0.8/neotoma2/R/get_downloads.R | 97 - neotoma2-1.0.8/neotoma2/R/get_manual.R | 10 neotoma2-1.0.8/neotoma2/R/get_params.R |only neotoma2-1.0.8/neotoma2/R/get_publications.R | 265 +-- neotoma2-1.0.8/neotoma2/R/get_sites.R | 131 - neotoma2-1.0.8/neotoma2/R/get_specimens.R | 321 +--- neotoma2-1.0.8/neotoma2/R/get_speleothems.R |only neotoma2-1.0.8/neotoma2/R/get_stats.R | 95 - neotoma2-1.0.8/neotoma2/R/get_table.R | 33 neotoma2-1.0.8/neotoma2/R/get_taxa.R | 86 - neotoma2-1.0.8/neotoma2/R/get_taxon.R | 182 +- neotoma2-1.0.8/neotoma2/R/getids.r |only neotoma2-1.0.8/neotoma2/R/group_data.R | 55 neotoma2-1.0.8/neotoma2/R/parseLocation.R | 46 neotoma2-1.0.8/neotoma2/R/parseURL.R | 229 +- neotoma2-1.0.8/neotoma2/R/parse_site.R | 118 - neotoma2-1.0.8/neotoma2/R/parse_speleothem.R |only neotoma2-1.0.8/neotoma2/R/pingNeotoma.r |only neotoma2-1.0.8/neotoma2/R/plotLeaflet.R | 60 neotoma2-1.0.8/neotoma2/R/pubAuthors.R | 13 neotoma2-1.0.8/neotoma2/R/publication-methods.R | 125 - neotoma2-1.0.8/neotoma2/R/samples-methods.R | 76 neotoma2-1.0.8/neotoma2/R/samples.R | 295 +-- neotoma2-1.0.8/neotoma2/R/set_chronology.R | 17 neotoma2-1.0.8/neotoma2/R/set_collunit.R | 29 neotoma2-1.0.8/neotoma2/R/set_contact.R |only neotoma2-1.0.8/neotoma2/R/set_dataset.R | 16 neotoma2-1.0.8/neotoma2/R/set_publication.R |only neotoma2-1.0.8/neotoma2/R/set_sample.R | 19 neotoma2-1.0.8/neotoma2/R/set_server.R | 27 neotoma2-1.0.8/neotoma2/R/set_site.R | 37 neotoma2-1.0.8/neotoma2/R/set_speleothem.R |only neotoma2-1.0.8/neotoma2/R/site-methods.R | 593 +++---- neotoma2-1.0.8/neotoma2/R/speleothem-methods.R |only neotoma2-1.0.8/neotoma2/R/speleothemdetails.R |only neotoma2-1.0.8/neotoma2/R/speleothems.R |only neotoma2-1.0.8/neotoma2/R/subset-methods.R | 66 neotoma2-1.0.8/neotoma2/R/taxa.R | 198 +- neotoma2-1.0.8/neotoma2/R/taxon-methods.R | 193 -- neotoma2-1.0.8/neotoma2/R/testNull.R | 8 neotoma2-1.0.8/neotoma2/R/toWide.R | 134 - neotoma2-1.0.8/neotoma2/R/use_na.R | 40 neotoma2-1.0.8/neotoma2/R/utils-pipe.R | 2 neotoma2-1.0.8/neotoma2/README.md | 2 neotoma2-1.0.8/neotoma2/build/vignette.rds |binary neotoma2-1.0.8/neotoma2/inst/CITATION | 2 neotoma2-1.0.8/neotoma2/inst/doc/neotoma2-package.R | 1 neotoma2-1.0.8/neotoma2/inst/doc/neotoma2-package.Rmd | 1 neotoma2-1.0.8/neotoma2/inst/doc/neotoma2-package.html | 19 neotoma2-1.0.8/neotoma2/man/add_chronology.Rd | 32 neotoma2-1.0.8/neotoma2/man/as.data.frame.Rd |only neotoma2-1.0.8/neotoma2/man/author_classes.Rd |only neotoma2-1.0.8/neotoma2/man/c.Rd |only neotoma2-1.0.8/neotoma2/man/cash-set.Rd |only neotoma2-1.0.8/neotoma2/man/cash.Rd |only neotoma2-1.0.8/neotoma2/man/check_contacts.Rd | 8 neotoma2-1.0.8/neotoma2/man/chroncontrols-sites-method.Rd | 3 neotoma2-1.0.8/neotoma2/man/chronologies-collunit-method.Rd | 6 neotoma2-1.0.8/neotoma2/man/chronologies.Rd | 11 neotoma2-1.0.8/neotoma2/man/chronologies_classes.Rd |only neotoma2-1.0.8/neotoma2/man/cite_data-sites-method.Rd | 4 neotoma2-1.0.8/neotoma2/man/cite_data.Rd | 8 neotoma2-1.0.8/neotoma2/man/clean.Rd |only neotoma2-1.0.8/neotoma2/man/collunits.Rd | 5 neotoma2-1.0.8/neotoma2/man/collunits_classes.Rd |only neotoma2-1.0.8/neotoma2/man/contacts_classes.Rd |only neotoma2-1.0.8/neotoma2/man/datasets-collunits-method.Rd | 8 neotoma2-1.0.8/neotoma2/man/datasets.Rd | 11 neotoma2-1.0.8/neotoma2/man/datasets_classes.Rd |only neotoma2-1.0.8/neotoma2/man/doi-sites-method.Rd | 4 neotoma2-1.0.8/neotoma2/man/doi.Rd | 9 neotoma2-1.0.8/neotoma2/man/filter.Rd | 46 neotoma2-1.0.8/neotoma2/man/get_contacts.Rd | 13 neotoma2-1.0.8/neotoma2/man/get_datasets.Rd | 36 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neotoma2-1.0.8/neotoma2/man/speleothems-sites-method.Rd |only neotoma2-1.0.8/neotoma2/man/speleothems.Rd |only neotoma2-1.0.8/neotoma2/man/speleothems_classes.Rd |only neotoma2-1.0.8/neotoma2/man/sub-sub.Rd |only neotoma2-1.0.8/neotoma2/man/sub-subset.Rd |only neotoma2-1.0.8/neotoma2/man/sub.Rd |only neotoma2-1.0.8/neotoma2/man/subset.Rd |only neotoma2-1.0.8/neotoma2/man/taxa-sites-method.Rd | 14 neotoma2-1.0.8/neotoma2/man/taxa.Rd | 11 neotoma2-1.0.8/neotoma2/man/taxa_classes.Rd |only neotoma2-1.0.8/neotoma2/man/toWide.Rd | 53 neotoma2-1.0.8/neotoma2/tests/testthat/all_aliases.csv |only neotoma2-1.0.8/neotoma2/tests/testthat/test_add_chronology.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_c.R | 16 neotoma2-1.0.8/neotoma2/tests/testthat/test_chroncontrols.R | 88 - neotoma2-1.0.8/neotoma2/tests/testthat/test_chronologies.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_cite_data.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_clean.R | 19 neotoma2-1.0.8/neotoma2/tests/testthat/test_collunits.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_coordinates.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_datasets.R | 132 - neotoma2-1.0.8/neotoma2/tests/testthat/test_doi.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_examples.R | 45 neotoma2-1.0.8/neotoma2/tests/testthat/test_filter.R | 281 +-- neotoma2-1.0.8/neotoma2/tests/testthat/test_get_contacts.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_datasets.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_documentation.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_downloads.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_manual.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_publications.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_sites.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_speleothems.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_stats.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_table.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_taxa.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_get_taxon.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_getids.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_length.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_parse_location.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_pingNeotoma.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_plot.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_plotLeaflet.r | 25 neotoma2-1.0.8/neotoma2/tests/testthat/test_samples.R | 78 neotoma2-1.0.8/neotoma2/tests/testthat/test_set_chronology.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_collunit.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_contact.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_dataset.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_default.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_publication.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_sample.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_server.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_site.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_set_speleothem.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_sites.R | 12 neotoma2-1.0.8/neotoma2/tests/testthat/test_specimens.R | 14 neotoma2-1.0.8/neotoma2/tests/testthat/test_speleothems.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_summary.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_taxa.R |only neotoma2-1.0.8/neotoma2/tests/testthat/test_toWide.R | 62 neotoma2-1.0.8/neotoma2/vignettes/neotoma2-package.Rmd | 1 395 files changed, 3960 insertions(+), 4307 deletions(-)
Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed
Data
Description: Semi-parametric approach for sparse canonical correlation analysis
which can handle mixed data types: continuous, binary and truncated continuous.
Bridge functions are provided to connect Kendall's tau to latent correlation
under the Gaussian copula model. The methods are described in
Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and
Yoon, Mueller and Gaynanova (2021) <doi:10.1080/10618600.2021.1882468>.
Author: Grace Yoon [aut] ,
Mingze Huang [ctb] ,
Irina Gaynanova [aut, cre]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between mixedCCA versions 1.6.2 dated 2022-09-09 and 1.6.3 dated 2025-11-18
DESCRIPTION | 21 +++++++++++---------- MD5 | 24 ++++++++++++------------ R/GenerateData.R | 22 +++++++++++----------- R/KendallCCA.R | 38 +++++++++++++++++++------------------- R/estimateR.R | 16 ++++++++-------- man/GenerateData.Rd | 22 +++++++++++----------- man/estimateR.Rd | 16 ++++++++-------- man/find_w12bic.Rd | 14 +++++++------- man/mixedCCA.Rd | 12 ++++++------ man/myrcc.Rd | 6 +++--- man/standardCCA.Rd | 6 +++--- src/Makevars | 6 ++---- src/Makevars.win | 7 ++----- 13 files changed, 103 insertions(+), 107 deletions(-)
Title: Simulate Evapotranspiration and Soil Moisture with the SVAT
Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation
atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran.
The model simulates daily transpiration, interception, soil and snow evaporation,
streamflow and soil water fluxes through a soil profile covered with vegetation,
as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003)
<doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions
for model set up, execution and parallelization provides easy access to plot-level SVAT
simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre] ,
Volodymyr Trotsiuk [aut] ,
Klaus Hammel [aut],
Martin Kennel [aut],
Anthony Federer [aut],
Tobias Hohenbrink [aut] ,
Gisbert Hetkamp [aut],
Michael Koehler [aut] ,
Robert Nuske [ctb] ,
Bavarian State Institute of Fores [...truncated...]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>
Diff between LWFBrook90R versions 0.6.2 dated 2025-04-29 and 0.6.3 dated 2025-11-18
LWFBrook90R-0.6.2/LWFBrook90R/man/param_to_rlwfbrook90.Rd |only LWFBrook90R-0.6.3/LWFBrook90R/DESCRIPTION | 22 LWFBrook90R-0.6.3/LWFBrook90R/MD5 | 74 +-- LWFBrook90R-0.6.3/LWFBrook90R/NAMESPACE | 1 LWFBrook90R-0.6.3/LWFBrook90R/NEWS.md | 40 + LWFBrook90R-0.6.3/LWFBrook90R/R/MakeSeasLAI.R | 72 ++ LWFBrook90R-0.6.3/LWFBrook90R/R/MakeStand.R | 3 LWFBrook90R-0.6.3/LWFBrook90R/R/approx_standprop.R | 2 LWFBrook90R-0.6.3/LWFBrook90R/R/extract_layer_output.R | 4 LWFBrook90R-0.6.3/LWFBrook90R/R/param_to_rbrook90.R | 244 ++++++---- LWFBrook90R-0.6.3/LWFBrook90R/R/pedotransfer_functions.R | 12 LWFBrook90R-0.6.3/LWFBrook90R/R/plantb90.R | 29 - LWFBrook90R-0.6.3/LWFBrook90R/R/plantcoupmodel.R | 17 LWFBrook90R-0.6.3/LWFBrook90R/R/r_lwfbrook90.R | 105 ++-- LWFBrook90R-0.6.3/LWFBrook90R/R/runLWFB90.R | 79 ++- LWFBrook90R-0.6.3/LWFBrook90R/R/setparms_LWFB90.R | 4 LWFBrook90R-0.6.3/LWFBrook90R/R/standprop_yrly_to_param.R | 20 LWFBrook90R-0.6.3/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.R | 24 LWFBrook90R-0.6.3/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.Rmd | 24 LWFBrook90R-0.6.3/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.html | 39 - LWFBrook90R-0.6.3/LWFBrook90R/inst/examples/make_seasLAI-help.R | 40 + LWFBrook90R-0.6.3/LWFBrook90R/inst/examples/pedotransfer_functions-help.R | 2 LWFBrook90R-0.6.3/LWFBrook90R/man/LWFBrook90R-package.Rd | 1 LWFBrook90R-0.6.3/LWFBrook90R/man/approx_standprop.Rd | 2 LWFBrook90R-0.6.3/LWFBrook90R/man/extract_layer_output.Rd | 4 LWFBrook90R-0.6.3/LWFBrook90R/man/make_seasLAI.Rd | 58 +- LWFBrook90R-0.6.3/LWFBrook90R/man/parms_to_rbrook90.Rd |only LWFBrook90R-0.6.3/LWFBrook90R/man/plant_b90.Rd | 35 + LWFBrook90R-0.6.3/LWFBrook90R/man/plant_coupmodel.Rd | 15 LWFBrook90R-0.6.3/LWFBrook90R/man/ptfs.Rd | 14 LWFBrook90R-0.6.3/LWFBrook90R/man/r_lwfbrook90.Rd | 49 -- LWFBrook90R-0.6.3/LWFBrook90R/man/set_paramLWFB90.Rd | 3 LWFBrook90R-0.6.3/LWFBrook90R/man/standprop_yearly_to_param.Rd | 2 LWFBrook90R-0.6.3/LWFBrook90R/src/PFILE.h | 4 LWFBrook90R-0.6.3/LWFBrook90R/src/md_brook90.f95 | 82 +-- LWFBrook90R-0.6.3/LWFBrook90R/src/md_typedefs.f95 | 87 +++ LWFBrook90R-0.6.3/LWFBrook90R/src/skeleton.c | 10 LWFBrook90R-0.6.3/LWFBrook90R/tests/testthat/test-runLWFB90.R | 30 + LWFBrook90R-0.6.3/LWFBrook90R/vignettes/LWFBrook90R-2-Options_Param.Rmd | 24 39 files changed, 788 insertions(+), 489 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] ,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.3.0 dated 2025-02-13 and 0.3.1 dated 2025-11-18
DESCRIPTION | 14 MD5 | 110 NEWS.md | 6 R/afstemningsomraader.R | 8 R/base_api.R | 19 R/get_data.R | 4 R/status_check.R | 45 build/vignette.rds |binary inst/doc/dawaR.html | 14 inst/doc/status.html | 21 tests/fixtures/afstemningsomraader_autocomplete_returns_the_right_answer_1.yml | 40 tests/fixtures/afstemningsomraader_autocomplete_returns_the_right_answer_2.yml | 24 tests/fixtures/afstemningsomraader_autocomplete_returns_the_right_answer_3.yml | 36 tests/fixtures/afstemningsomraader_autocomplete_returns_the_right_answer_4.yml | 324 tests/fixtures/autocomplete_returns_the_right_answer_afstemningsomraader_aebel.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_afstemningsomraader_broender.yml | 324 tests/fixtures/autocomplete_returns_the_right_answer_afstemningsomraader_dok.yml | 40 tests/fixtures/autocomplete_returns_the_right_answer_afstemningsomraader_roeddi.yml | 36 tests/fixtures/autocomplete_returns_the_right_answer_kommuner_aebel.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_kommuner_broender.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_kommuner_dok.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_kommuner_roeddi.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_politikredse_aebel.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_politikredse_broender.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_politikredse_dok.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_politikredse_roeddi.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_regioner_aebel.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_regioner_broender.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_regioner_dok.yml | 24 tests/fixtures/autocomplete_returns_the_right_answer_regioner_roeddi.yml | 24 tests/fixtures/get_data_kommuner_snapshot.yml | 204 tests/fixtures/get_data_politikredse_snapshot.yml | 82 tests/fixtures/get_data_regioner_snapshot.yml | 46 tests/fixtures/regioner_api_default.yml | 46 tests/fixtures/regioner_api_no_cache.yml | 46 tests/fixtures/regioner_get_data.yml | 46 tests/fixtures/regioner_get_data_list.yml | 46 tests/fixtures/regioner_get_data_no_list.yml | 46 tests/fixtures/reverse_geocode_afstemningsomraader.yml | 32 tests/fixtures/reverse_geocode_politikredse.yml | 30 tests/fixtures/reverse_geocode_regioner_1.yml | 24 tests/fixtures/reverse_geocode_regioner_2.yml | 24 tests/fixtures/voting_reverse_geocode_returns_information_in_different_formats_1.yml | 60 tests/fixtures/voting_reverse_geocode_returns_information_in_different_formats_2.yml | 60 tests/fixtures/voting_reverse_geocode_returns_information_in_different_formats_3.yml | 60 tests/testthat/_snaps/afstemningsomraader.md | 16 tests/testthat/_snaps/autocomplete.md | 342 tests/testthat/_snaps/base_api.md | 44 tests/testthat/_snaps/get_data.md |23130 +++++----- tests/testthat/_snaps/get_map_data-kommuner.md | 50 tests/testthat/_snaps/get_map_data-politikredse.md | 140 tests/testthat/_snaps/get_map_data-regioner.md | 60 tests/testthat/_snaps/get_map_data-vote.md | 310 tests/testthat/_snaps/reverse.md | 14 tests/testthat/_snaps/status_check.md | 8 tests/testthat/test-status_check.R | 5 56 files changed, 13093 insertions(+), 13255 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.13 dated 2025-06-19 and 0.6.14 dated 2025-11-18
DESCRIPTION | 12 +- MD5 | 96 +++++++++++-------- NEWS.md | 9 + build/vignette.rds |binary inst/WORDLIST | 8 + inst/doc/advanced_usage.html | 7 - inst/doc/ard_how_to.html | 7 - inst/doc/baseline.html | 7 - inst/doc/clinical_trials.html | 7 - inst/doc/col_counts.html | 7 - inst/doc/custom_appearance.html | 7 - inst/doc/example_analysis_coxreg.html | 7 - inst/doc/exploratory_analysis.html | 9 - inst/doc/format_precedence.html | 7 - inst/doc/guided_intermediate.R |only inst/doc/guided_intermediate.Rmd |only inst/doc/guided_intermediate.html |only inst/doc/guided_intermediate_afun_reqs.R |only inst/doc/guided_intermediate_afun_reqs.Rmd |only inst/doc/guided_intermediate_afun_reqs.html |only inst/doc/guided_intermediate_split_reqs.R |only inst/doc/guided_intermediate_split_reqs.Rmd |only inst/doc/guided_intermediate_split_reqs.html |only inst/doc/guided_intermediate_translating_shells.R |only inst/doc/guided_intermediate_translating_shells.Rmd |only inst/doc/guided_intermediate_translating_shells.html |only inst/doc/introspecting_tables.html | 7 - inst/doc/manual_table_construction.html | 7 - inst/doc/pathing.html | 7 - inst/doc/rtables.html | 9 - inst/doc/sorting_pruning.html | 11 +- inst/doc/split_functions.html | 7 - inst/doc/subsetting_tables.html | 7 - inst/doc/tabulation_concepts.html | 3 inst/doc/tabulation_dplyr.html | 7 - inst/doc/title_footer.html | 7 - man/add_overall_level.Rd | 2 man/analyze_colvars.Rd | 2 man/append_topleft.Rd | 2 man/cell_values.Rd | 2 man/gfc.Rd | 2 man/int_methods.Rd | 2 man/matrix_form-VTableTree-method.Rd | 2 man/row_paths_summary.Rd | 2 man/split_cols_by.Rd | 2 man/split_cols_by_multivar.Rd | 2 man/split_rows_by.Rd | 2 man/table_shell.Rd | 2 man/table_structure.Rd | 2 man/tostring.Rd | 2 man/varcuts.Rd | 2 tests/testthat/test-lyt-tabulation.R | 11 -- tests/testthat/test-make-afun.R | 2 vignettes/guided_intermediate.Rmd |only vignettes/guided_intermediate_afun_reqs.Rmd |only vignettes/guided_intermediate_split_reqs.Rmd |only vignettes/guided_intermediate_translating_shells.Rmd |only 57 files changed, 178 insertions(+), 127 deletions(-)
Title: Precision Based Sample Size Calculation
Description: Bland (2009) <doi:10.1136/bmj.b3985> recommended to
base study sizes on the width of the confidence interval rather the power of
a statistical test. The goal of 'presize' is to provide functions for such
precision based sample size calculations. For a given sample size, the
functions will return the precision (width of the confidence interval), and
vice versa.
Author: Armando Lenz [aut],
Alan G. Haynes [cre, aut],
Andreas Limacher [aut],
Odile Stalder [ctb],
Marie Roumet [ctb]
Maintainer: Alan G. Haynes <alan.haynes@unibe.ch>
Diff between presize versions 0.3.7 dated 2023-02-27 and 0.3.9 dated 2025-11-18
presize-0.3.7/presize/inst/shinyApp/rsconnect |only presize-0.3.7/presize/man/figures/sticker.png |only presize-0.3.9/presize/DESCRIPTION | 21 presize-0.3.9/presize/MD5 | 20 presize-0.3.9/presize/NEWS.md | 8 presize-0.3.9/presize/R/shinyApp.R | 2 presize-0.3.9/presize/build/partial.rdb |binary presize-0.3.9/presize/build/vignette.rds |binary presize-0.3.9/presize/inst/doc/presize.R | 4 presize-0.3.9/presize/inst/doc/presize.html | 584 ++++++++++++------------ presize-0.3.9/presize/man/launch_presize_app.Rd | 2 presize-0.3.9/presize/man/presize-package.Rd | 10 12 files changed, 346 insertions(+), 305 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph] ,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.1.2 dated 2024-07-24 and 1.1.3 dated 2025-11-18
DESCRIPTION | 12 MD5 | 62 +-- NAMESPACE | 2 R/encoding.R | 292 +++++++++++++++++- R/methods.R | 378 ++++++++++++++++++----- R/modelInputs.R | 5 R/utils.R | 43 +- README.md | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_usage.R | 16 inst/doc/basic_usage.html | 61 +-- inst/doc/benchmark.R | 76 ++-- inst/doc/benchmark.html | 3 inst/doc/convergence.R | 612 +++++++++++++++++++------------------- inst/doc/convergence.html | 1 inst/doc/data_formatting.R | 43 ++ inst/doc/data_formatting.Rmd | 77 ++++ inst/doc/data_formatting.html | 176 ++++++++++ inst/doc/interactions.html | 71 ++-- inst/doc/mnl_models.html | 74 ++-- inst/doc/mnl_models_weighted.html | 116 +++---- inst/doc/mxl_models.R | 80 ++-- inst/doc/mxl_models.html | 24 - inst/doc/predict.R | 28 - inst/doc/predict.html | 22 - inst/doc/summarizing_results.R | 4 inst/doc/summarizing_results.html | 278 ++++++++--------- inst/doc/utility_models.html | 3 man/miscmethods.logitr.Rd | 3 man/validate_data.Rd |only tests/testthat/test_validation.R |only vignettes/data_formatting.Rmd | 77 ++++ 33 files changed, 1769 insertions(+), 880 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness.
Supports generalized linear models, Weibull accelerated failure time (AFT) models,
quadratic programming problems, and customizable arbitrary correlation structures.
Options for fitting in parallel are provided. The method builds upon the framework described
by Ezhov et al. (2018) <doi:10.1515/jag-2017-0029> using Lagrangian multipliers
to fit cubic splines. For more information on correlation structure estimation,
see Searle et al. (2009) <ISBN:978-0470009598>. For quadratic programming and
constrained optimization in general, see Nocedal & Wright (2006) <doi:10.1007/978-0-387-40065-5>.
For a comprehensive background on smoothing splines, see Wahba (1990)
<doi:10.1137/1.9781611970128> and Wood (2006) <ISBN:978-1584884743>
[...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 0.2.0 dated 2025-04-24 and 0.3.0 dated 2025-11-18
DESCRIPTION | 9 +- MD5 | 15 ++-- NEWS.md |only R/lgspline-details.R | 167 ++++++++++++++++++++++++++++++++++++++++++++++++++- R/lgspline.R | 8 +- inst/WORDLIST | 119 +++++++++++++++++++----------------- man/Details.Rd | 167 ++++++++++++++++++++++++++++++++++++++++++++++++++- man/lgspline.Rd | 8 +- man/lgspline.fit.Rd | 4 - 9 files changed, 420 insertions(+), 77 deletions(-)
Title: Simulation and Resampling Methods for Epistemic Fuzzy Data
Description: Random simulations of fuzzy numbers are still a challenging problem. The aim of this package is to provide the respective
procedures to simulate fuzzy random variables, especially in the case of the piecewise linear fuzzy numbers (PLFNs,
see Coroianua et al. (2013) <doi:10.1016/j.fss.2013.02.005> for the further details).
Additionally, the special resampling algorithms known as the epistemic bootstrap are provided (see Grzegorzewski and Romaniuk
(2022) <doi:10.34768/amcs-2022-0021>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-031-08974-9_39>,
Romaniuk et al. (2024) <doi:10.32614/RJ-2024-016>)
together with the functions to apply statistical tests and estimate various characteristics based on the epistemic bootstrap.
The package also includes real-life datasets of epistemic fuzzy triangular and trapezoidal numbers.
The fuzzy numbers used in this package are consistent with the 'FuzzyNumbers' package.
Author: Maciej Romaniuk [cre, aut] ,
Przemyslaw Grzegorzewski [aut] ,
Abbas Parchami [aut] ,
Luis Carvalho [ctb, cph]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzySimRes versions 0.4.7 dated 2025-07-28 and 0.4.8 dated 2025-11-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SimulateFuzzyNumber.R | 6 +++--- build/vignette.rds |binary 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Interactive Volcano Plot
Description: Generate interactive volcano plots for exploring gene expression data. Built with 'ggplot2', the plots are rendered interactive using 'ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ivolcano versions 0.0.1 dated 2025-09-11 and 0.0.2 dated 2025-11-17
DESCRIPTION | 12 +-- MD5 | 9 +- R/ivolcano.R | 9 +- README.md |only build/vignette.rds |binary inst/doc/ivolcano.html | 191 +++++++++++++++++++++++++++++++++++++------------ 6 files changed, 161 insertions(+), 60 deletions(-)
Title: Collection of Data Structures
Description: A collection of functions to generate a large variety of
structures in high dimensions. These data structures are useful for
testing, validating, and improving algorithms used in dimensionality
reduction, clustering, machine learning, and visualization.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between cardinalR versions 0.2.6 dated 2025-09-21 and 1.0.1 dated 2025-11-17
cardinalR-0.2.6/cardinalR/inst/cardinalr01clustering.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr02branching.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr03circulars.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr04grid.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr05trian.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr06sph.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr07scurve.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr08nonlinear.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr09linear.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr10mobius.Rmd |only cardinalR-0.2.6/cardinalR/inst/cardinalr11highd.Rmd |only cardinalR-0.2.6/cardinalR/inst/clustering.Rmd |only cardinalR-0.2.6/cardinalR/inst/doc/main_function.R |only cardinalR-0.2.6/cardinalR/inst/doc/main_function.Rmd |only cardinalR-0.2.6/cardinalR/inst/doc/main_function.html |only cardinalR-0.2.6/cardinalR/inst/doc/quollr1sample.R |only cardinalR-0.2.6/cardinalR/inst/doc/quollr1sample.Rmd |only cardinalR-0.2.6/cardinalR/inst/doc/quollr1sample.html |only cardinalR-0.2.6/cardinalR/man/gen_cubehole.Rd |only cardinalR-0.2.6/cardinalR/tests/testthat/_snaps/branching.new.md |only cardinalR-0.2.6/cardinalR/vignettes/main_function.Rmd |only cardinalR-0.2.6/cardinalR/vignettes/quollr1sample.Rmd |only cardinalR-1.0.1/cardinalR/DESCRIPTION | 8 cardinalR-1.0.1/cardinalR/MD5 | 221 +-- cardinalR-1.0.1/cardinalR/NAMESPACE | 4 cardinalR-1.0.1/cardinalR/NEWS.md | 2 cardinalR-1.0.1/cardinalR/R/branching.R | 322 ----- cardinalR-1.0.1/cardinalR/R/cone.R | 4 cardinalR-1.0.1/cardinalR/R/cube.R | 61 - cardinalR-1.0.1/cardinalR/R/mobius.R | 43 cardinalR-1.0.1/cardinalR/R/multi_clusts.R | 192 ++- cardinalR-1.0.1/cardinalR/R/odd_shapes.R | 214 +-- cardinalR-1.0.1/cardinalR/R/polynomial.R | 88 - cardinalR-1.0.1/cardinalR/R/scurve.R | 106 - cardinalR-1.0.1/cardinalR/R/sphere.R | 128 -- cardinalR-1.0.1/cardinalR/R/swiss_roll.R | 43 cardinalR-1.0.1/cardinalR/R/three_clusters.R | 140 +- cardinalR-1.0.1/cardinalR/R/trefoil.R | 93 - cardinalR-1.0.1/cardinalR/R/trigonometric.R | 275 ---- cardinalR-1.0.1/cardinalR/R/util.R | 67 + cardinalR-1.0.1/cardinalR/build/vignette.rds |binary cardinalR-1.0.1/cardinalR/inst/doc/cardinalR01main_function.R |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR01main_function.Rmd |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR01main_function.html |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR02examples.R |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR02examples.Rmd |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR02examples.html |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR03additionalfun.R |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR03additionalfun.Rmd |only cardinalR-1.0.1/cardinalR/inst/doc/cardinalR03additionalfun.html |only cardinalR-1.0.1/cardinalR/man/gen_clusteredspheres.Rd | 12 cardinalR-1.0.1/cardinalR/man/gen_conicspiral.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_crescent.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_cubic.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_curvybranches.Rd | 14 cardinalR-1.0.1/cardinalR/man/gen_curvycylinder.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_expbranches.Rd | 13 cardinalR-1.0.1/cardinalR/man/gen_helicalspiral.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_hemisphere.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_hole.Rd |only cardinalR-1.0.1/cardinalR/man/gen_hollowsphere.Rd |only cardinalR-1.0.1/cardinalR/man/gen_linearbranches.Rd | 15 cardinalR-1.0.1/cardinalR/man/gen_mobius.Rd | 12 cardinalR-1.0.1/cardinalR/man/gen_multicluster.Rd | 85 - cardinalR-1.0.1/cardinalR/man/gen_nonlinear.Rd | 17 cardinalR-1.0.1/cardinalR/man/gen_orgcurvybranches.Rd | 19 cardinalR-1.0.1/cardinalR/man/gen_orglinearbranches.Rd | 18 cardinalR-1.0.1/cardinalR/man/gen_quadratic.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_scurve.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_scurvehole.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_sphericalspiral.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_swissroll.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_trefoil3d.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_trefoil4d.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_unifcubehole.Rd |only cardinalR-1.0.1/cardinalR/man/gen_unifsphere.Rd | 10 cardinalR-1.0.1/cardinalR/man/gen_wavydims3.Rd | 4 cardinalR-1.0.1/cardinalR/man/make_onegrid.Rd | 7 cardinalR-1.0.1/cardinalR/man/make_shape_para.Rd | 8 cardinalR-1.0.1/cardinalR/man/make_three_clust_01.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_02.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_03.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_04.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_05.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_06.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_07.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_08.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_09.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_10.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_11.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_12.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_13.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_14.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_15.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_16.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_17.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_18.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_19.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_three_clust_20.Rd | 6 cardinalR-1.0.1/cardinalR/man/make_twogrid_overlap.Rd | 10 cardinalR-1.0.1/cardinalR/man/make_twogrid_shift.Rd | 10 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/branching.md | 96 - cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/cone.md | 2 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/cube.md | 170 +- cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/mobius.md | 32 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/multicluster.md | 48 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/polynomial.md | 58 - cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/pyramid.md | 34 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/scurve.md | 63 - cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/sphere.md | 572 +++++++++- cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/swiss_roll.md | 29 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/trefoil.md | 31 cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/trigonometric.md | 64 - cardinalR-1.0.1/cardinalR/tests/testthat/_snaps/util.md | 555 +++++++++ cardinalR-1.0.1/cardinalR/tests/testthat/test-branching.R | 24 cardinalR-1.0.1/cardinalR/tests/testthat/test-cone.R | 10 cardinalR-1.0.1/cardinalR/tests/testthat/test-cube.R | 14 cardinalR-1.0.1/cardinalR/tests/testthat/test-mobius.R | 5 cardinalR-1.0.1/cardinalR/tests/testthat/test-multicluster.R | 67 - cardinalR-1.0.1/cardinalR/tests/testthat/test-polynomial.R | 10 cardinalR-1.0.1/cardinalR/tests/testthat/test-pyramid.R | 42 cardinalR-1.0.1/cardinalR/tests/testthat/test-scurve.R | 10 cardinalR-1.0.1/cardinalR/tests/testthat/test-sphere.R | 21 cardinalR-1.0.1/cardinalR/tests/testthat/test-swiss_roll.R | 5 cardinalR-1.0.1/cardinalR/tests/testthat/test-trefoil.R | 14 cardinalR-1.0.1/cardinalR/tests/testthat/test-trigonometric.R | 40 cardinalR-1.0.1/cardinalR/tests/testthat/test-util.R | 12 cardinalR-1.0.1/cardinalR/vignettes/cardinalR01main_function.Rmd |only cardinalR-1.0.1/cardinalR/vignettes/cardinalR02examples.Rmd |only cardinalR-1.0.1/cardinalR/vignettes/cardinalR03additionalfun.Rmd |only 130 files changed, 2263 insertions(+), 2280 deletions(-)
Title: Spatial Dynamic Panel Data Modeling
Description: Spatial model calculation for static and dynamic panel data models, weights matrix creation and Bayesian model comparison.
Bayesian model comparison methods were described by 'LeSage' (2014) <doi:10.1016/j.spasta.2014.02.002>.
The 'Lee'-'Yu' transformation approach is described in 'Yu', 'De Jong' and 'Lee' (2008) <doi:10.1016/j.jeconom.2008.08.002>, 'Lee' and 'Yu' (2010) <doi:10.1016/j.jeconom.2009.08.001> and 'Lee' and 'Yu' (2010) <doi:10.1017/S0266466609100099>.
Author: Rozeta Simonovska [aut, cre]
Maintainer: Rozeta Simonovska <simonovska.r@gmail.com>
Diff between SDPDmod versions 0.0.6 dated 2025-04-11 and 0.0.7 dated 2025-11-17
DESCRIPTION | 8 +-- MD5 | 38 ++++++++-------- NEWS.md | 4 + R/SDPDm.R | 60 ++++++++----------------- R/SharedBMat.R | 3 - R/coef.SDPDm.R | 2 R/logdet.R | 10 ---- R/mOrdNbr.R | 3 - R/rownor.R | 3 - build/vignette.rds |binary inst/doc/spatial_matrices.html | 5 +- inst/doc/spatial_model.R | 4 - inst/doc/spatial_model.Rmd | 4 - inst/doc/spatial_model.html | 97 ++++++++++++++++++++--------------------- man/SDPDm.Rd | 56 +++++++---------------- man/SharedBMat.Rd | 3 - man/coef.SDPDm.Rd | 2 man/mOrdNbr.Rd | 3 - man/rownor.Rd | 3 - vignettes/spatial_model.Rmd | 4 - 20 files changed, 129 insertions(+), 183 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.6.2 dated 2025-10-15 and 0.6.3 dated 2025-11-17
DESCRIPTION | 6 ++-- MD5 | 15 ++++++++---- NAMESPACE | 1 R/cov_vol.R |only R/data.R | 20 ++++++++++++++++ data/cov_vol_data.rda |only inst/doc/get_started.html | 24 +++++++++---------- inst/doc/user_cases.html | 52 +++++++++++++++++++++--------------------- man/cov_vol.Rd |only man/cov_vol_data.Rd |only tests/testthat/test-cov_vol.R |only 11 files changed, 72 insertions(+), 46 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] ,
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Luis De Araujo [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.59.0 dated 2025-10-21 and 4.60.0 dated 2025-11-17
DESCRIPTION | 8 ++--- MD5 | 51 +++++++++++++++++----------------- NAMESPACE | 1 R/build_run_modify.R | 14 ++++----- R/financial_functions.R | 60 ++++++++++++++++++++++++++++++++++++++++ R/umxDoC.R | 12 ++++---- R/umxPower.R | 4 +- R/umx_build_high_level_models.R | 4 +- R/umx_build_umxACEv.R | 2 - R/umx_build_umxSimplex.R | 2 - build/partial.rdb |binary inst/WORDLIST | 26 +++++++++-------- man/fin_CAGR.Rd |only man/power.ACE.test.Rd | 2 - man/umxACE.Rd | 6 ++-- man/umxACEcov.Rd | 2 - man/umxACEv.Rd | 2 - man/umxCP.Rd | 2 - man/umxDiffMZ.Rd | 6 ++-- man/umxDiscTwin.Rd | 4 +- man/umxDoC.Rd | 2 - man/umxEFA.Rd | 2 - man/umxGxE.Rd | 2 - man/umxIP.Rd | 2 - man/umxPower.Rd | 2 - man/umxSimplex.Rd | 2 - man/umxTwoStage.Rd | 2 - 27 files changed, 143 insertions(+), 79 deletions(-)
Title: The Most Comprehensive R Package for Turkish Election Results
Description: Includes the results of general, local, and presidential elections held in Turkey between 1995 and 2024, broken down by provinces and overall national results. It facilitates easy processing of this data and the creation of visual representations based on these election results.
Author: Ozancan Ozdemir [aut, cre]
Maintainer: Ozancan Ozdemir <ozancanozdemir@gmail.com>
Diff between turkeyelections versions 0.1.3 dated 2025-11-13 and 0.1.4 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
More information about turkeyelections at CRAN
Permanent link
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data in Brazil. Implements water quality indices including the Water Quality Index (WQI/IQA), the Trophic State Index (TSI/IET) after Carlson (1977) <doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004) <https://www.teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>, and the National Sanitation Foundation Water Quality Index (NSF WQI) <doi:10.1007/s11157-023-09650-7>. The package also checks compliance with Brazilian standard CONAMA Resolution 357/2005 <https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download> and generates reproducible reports for routine monitoring workflows.
The example dataset (`wq_demo`) is now a real subset from monitoring data (BURANHEM river, 2020-2024, 4 points, 20 rows, 14 columns including extra `rio`, `lat`, `lon`). All core examples and vignettes use this realistic sample, improving reproducibility an [...truncated...]
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.7.3 dated 2025-10-31 and 0.8.0 dated 2025-11-17
DESCRIPTION | 17 - MD5 | 72 ++++--- NAMESPACE | 18 + NEWS.md | 7 R/analysis_text.R | 4 R/conama.R | 16 + R/data_wq_demo.R | 18 + R/iet.R | 176 +++++++++++++----- R/iet_lamparelli.R | 162 ++++++++++++---- R/io_clean.R | 310 ++++++++++++++++++++++++++++---- R/iqa.R | 131 ++++++++----- R/plot_map.R | 230 +++++++++++++---------- R/utils_sanitize.R | 100 ++++++++++ R/wq_buranhem.R |only README.md | 39 ++-- build/vignette.rds |binary data/wq_demo.rda |binary inst/doc/tikatuwq-methods.R |only inst/doc/tikatuwq-methods.Rmd |only inst/doc/tikatuwq-methods.html |only inst/doc/tikatuwq-workflow.R |only inst/doc/tikatuwq-workflow.Rmd |only inst/doc/tikatuwq-workflow.html |only inst/doc/tikatuwq.html | 103 +++------- inst/extdata/wq_demo_README.txt | 8 man/classify_iqa.Rd |only man/classify_tsi_carlson.Rd |only man/classify_tsi_lamparelli.Rd |only man/clean_units.Rd | 24 +- man/fix_coords.Rd |only man/iet_carlson.Rd | 91 +++++---- man/iet_lamparelli.Rd | 67 ++++-- man/iqa.Rd | 81 ++++---- man/plot_map.Rd | 65 ++++-- man/read_wq.Rd | 56 +++-- man/validate_wq.Rd | 16 + man/wq_demo.Rd | 28 +- tests/testthat/test-clean_units.R |only tests/testthat/test-conama_text.R |only tests/testthat/test-fix_coords.R |only tests/testthat/test-generate_analysis.R |only tests/testthat/test-nd-ld-policy.R |only tests/testthat/test-plot_functions.R |only tests/testthat/test-plot_map.R | 39 ++-- tests/testthat/test-render_report.R |only vignettes/tikatuwq-methods.Rmd |only vignettes/tikatuwq-workflow.Rmd |only 47 files changed, 1312 insertions(+), 566 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 10.0.0 dated 2025-11-13 and 10.1.0 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ inst/doc/SimInf.pdf |binary src/solvers/SimInf_solver.c | 11 +++++++---- src/solvers/SimInf_solver_aem.c | 15 ++++++++++----- src/solvers/SimInf_solver_mssm.c | 12 ++++++++---- src/solvers/SimInf_solver_ssm.c | 12 ++++++++---- 8 files changed, 51 insertions(+), 27 deletions(-)
Title: Aid Querying 'nomis' and 'Office for National Statistics Open
Geography' APIs
Description: Facilitates extraction of geospatial data from the 'Office for National Statistics Open Geography' and 'nomis' Application Programming Interfaces (APIs). Simplifies process of querying 'nomis' datasets <https://www.nomisweb.co.uk/> and extracting desired datasets in dataframe format. Extracts area shapefiles at chosen resolution from 'Office for National Statistics Open Geography' <https://geoportal.statistics.gov.uk/>.
Author: Michael Stocks [aut, cre],
Andrew Christy [aut],
James Macpherson [aut],
Hadyn Jenkins [aut],
Crown Copyright
[cph]
Maintainer: Michael Stocks <sgapi.orhub@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2025-05-08
Diff between sgapi versions 1.1.0 dated 2025-05-08 and 1.1.1 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-list_boundaries.R | 24 ++++++++++++------------ 3 files changed, 17 insertions(+), 17 deletions(-)
Title: Privacy-Preserving Distributed Algorithms
Description: A collection of privacy-preserving distributed algorithms (PDAs) for conducting federated statistical learning across multiple data sites. The PDA framework includes models for various tasks such as regression, trial emulation, causal inference, design-specific analysis, and clustering. The PDA algorithms run on a lead site and only require summary statistics from collaborating sites, with one or few iterations. The package can be used together with the online data transfer system (<https://pda-ota.pdamethods.org/>) for safe and convenient collaboration. For more information, please visit our software websites: <https://github.com/Penncil/pda>, and <https://pdamethods.org/>.
Author: Chongliang Luo [cre],
Rui Duan [aut],
Mackenzie Edmondson [aut],
Jiayi Tong [aut],
Xiaokang Liu [aut],
Kenneth Locke [aut],
Jie Hu [aut],
Bingyu Zhang [aut],
Yicheng Shen [aut],
Yudong Wang [aut],
Yiwen Lu [aut],
Lu Li [aut],
Yong Chen [aut],
Penn Co [...truncated...]
Maintainer: Chongliang Luo <luocl3009@gmail.com>
Diff between pda versions 1.2.8 dated 2025-03-10 and 1.3.0 dated 2025-11-17
DESCRIPTION | 40 MD5 | 109 +- NAMESPACE | 11 NEWS.md | 63 - R/COLA.R |only R/DLM.R | 10 R/DPQL.R | 14 R/DisC2o.R |only R/LATTE.R |only R/ODACH_CC.R |only R/ODACT.R |only R/RcppExports.R | 98 +- R/case_cohort.R |only R/data.R | 618 +++++++++++-- R/dlmm.R | 59 + R/latte-misc.R |only R/odact-misc.R |only R/pda.R | 1864 ++++++++++++++++++++++++----------------- R/zzz.R |only build/partial.rdb |binary data/COLA_covid.rda |only data/LATTE_ADRD.rda |only data/long_covid.rda |only data/nominal_data_hetero.RData |only data/odach_cc.rda |only data/ordinal_data.RData |only demo/00Index | 5 demo/COLA.R |only demo/DLM.R | 25 demo/DPQL.R | 74 - demo/DisC2o.R |only demo/LATTE.R |only demo/ODAC.R | 1 demo/ODACAT.R | 1 demo/ODACH.R | 1 demo/ODACH_CC.R |only demo/ODACT.R |only demo/ODAH.R | 94 -- demo/ODAL.R | 19 demo/dGEM.R | 3 man/COLA.estimate.Rd |only man/COLA.initialize.Rd |only man/COLA_covid.Rd |only man/DisC2o.AIPWestimate.Rd |only man/DisC2o.OMderive.Rd |only man/DisC2o.OMestimate.Rd |only man/DisC2o.OMinitialize.Rd |only man/DisC2o.PSderive.Rd |only man/DisC2o.PSestimate.Rd |only man/DisC2o.PSinitialize.Rd |only man/DisC2o.synthesize.Rd |only man/LATTE.estimate.Rd |only man/LATTE.initialize.Rd |only man/LATTE_ADRD.Rd |only man/ODACAT_nominal.Rd | 14 man/ODACAT_ordinal.Rd | 2 man/ODACH_CC.derive.Rd |only man/ODACH_CC.estimate.Rd |only man/ODACH_CC.initialize.Rd |only man/ODACH_CC.synthesize.Rd |only man/ODACT.derive.Rd |only man/ODACT.estimate.Rd |only man/ODACT.initialize.Rd |only man/ODACT.synthesize.Rd |only man/cola_glmm.Rd |only man/estimatePool.Rd |only man/generate_CSU_site.Rd |only man/getCloudConfig.Rd | 4 man/long_covid.Rd |only man/make_patterns.Rd |only man/nominal_data_hetero.Rd |only man/odach_cc.Rd |only man/ordinal_data.Rd |only man/pda.Rd | 111 -- man/pdaCatalog.Rd |only man/pdaPut.Rd | 8 man/pdaSync.Rd | 8 man/run_pooled_analysis.Rd |only src/DisC2o.cpp |only src/RcppExports.cpp | 143 +++ src/odact.cpp |only src/rcpp_coxph.h | 4 src/rcpp_odach_cc.cpp |only 83 files changed, 2138 insertions(+), 1265 deletions(-)
Title: Joint Estimation of Latent Groups and Group-Specific
Coefficients in (Time-Varying) Panel Data Models
Description: Latent group structures are a common challenge in panel data analysis. Disregarding group-level heterogeneity can introduce bias. Conversely, estimating individual coefficients for each cross-sectional unit is inefficient and may lead to high uncertainty.
This package addresses the issue of unobservable group structures by implementing the pairwise adaptive group fused Lasso (PAGFL) by Mehrabani (2023) <doi:10.1016/j.jeconom.2022.12.002>. PAGFL identifies latent group structures and group-specific coefficients in a single step.
On top of that, we extend the PAGFL to time-varying coefficient functions (FUSE-TIME), following Haimerl et al. (2025) <doi:10.48550/arXiv.2503.23165>.
Author: Paul Haimerl [aut, cre] ,
Stephan Smeekes [ctb] ,
Ines Wilms [ctb] ,
Ali Mehrabani [ctb]
Maintainer: Paul Haimerl <paul.haimerl@econ.au.dk>
Diff between PAGFL versions 1.1.3 dated 2025-02-20 and 1.1.4 dated 2025-11-17
PAGFL-1.1.3/PAGFL/R/Checks.R |only PAGFL-1.1.3/PAGFL/R/Sim.R |only PAGFL-1.1.3/PAGFL/R/pagfl_tv.R |only PAGFL-1.1.3/PAGFL/man/tv_pagfl.Rd |only PAGFL-1.1.3/PAGFL/tests/testthat/fixtures/tv_pagfl_resid.rds |only PAGFL-1.1.3/PAGFL/tests/testthat/fixtures/tv_pagfl_sim.rds |only PAGFL-1.1.3/PAGFL/tests/testthat/fixtures/tv_pagfl_sim_2.rds |only PAGFL-1.1.4/PAGFL/DESCRIPTION | 21 PAGFL-1.1.4/PAGFL/MD5 | 77 - PAGFL-1.1.4/PAGFL/NAMESPACE | 17 PAGFL-1.1.4/PAGFL/NEWS.md | 15 PAGFL-1.1.4/PAGFL/R/RcppExports.R | 4 PAGFL-1.1.4/PAGFL/R/checks.R |only PAGFL-1.1.4/PAGFL/R/fuse_time.R |only PAGFL-1.1.4/PAGFL/R/grouped_plm.R | 41 PAGFL-1.1.4/PAGFL/R/grouped_tv_plm.R | 60 - PAGFL-1.1.4/PAGFL/R/helper.R | 110 +- PAGFL-1.1.4/PAGFL/R/pagfl.R | 45 PAGFL-1.1.4/PAGFL/R/s3_methods.R | 2 PAGFL-1.1.4/PAGFL/R/s3_methods_grouped_tv_plm.R | 4 PAGFL-1.1.4/PAGFL/R/s3_methods_tv.R | 72 - PAGFL-1.1.4/PAGFL/R/sim.R |only PAGFL-1.1.4/PAGFL/R/sim_tv.R | 26 PAGFL-1.1.4/PAGFL/README.md | 167 +-- PAGFL-1.1.4/PAGFL/build/partial.rdb |binary PAGFL-1.1.4/PAGFL/man/figures/README-unnamed-chunk-5-1.png |binary PAGFL-1.1.4/PAGFL/man/figures/README-unnamed-chunk-8-1.png |binary PAGFL-1.1.4/PAGFL/man/figures/README-unnamed-chunk-9-1.png |binary PAGFL-1.1.4/PAGFL/man/figures/icon.png |only PAGFL-1.1.4/PAGFL/man/fuse_time.Rd |only PAGFL-1.1.4/PAGFL/man/grouped_plm.Rd | 35 PAGFL-1.1.4/PAGFL/man/grouped_tv_plm.Rd | 252 ++--- PAGFL-1.1.4/PAGFL/man/pagfl.Rd | 39 PAGFL-1.1.4/PAGFL/man/sim_DGP.Rd | 28 PAGFL-1.1.4/PAGFL/man/sim_tv_DGP.Rd | 26 PAGFL-1.1.4/PAGFL/src/PAGFL-package.cpp | 10 PAGFL-1.1.4/PAGFL/src/RcppExports.cpp | 10 PAGFL-1.1.4/PAGFL/tests/testthat/_snaps/methods.md | 26 PAGFL-1.1.4/PAGFL/tests/testthat/fixtures/fuse_time_resid.rds |only PAGFL-1.1.4/PAGFL/tests/testthat/fixtures/fuse_time_sim.rds |only PAGFL-1.1.4/PAGFL/tests/testthat/fixtures/fuse_time_sim_2.rds |only PAGFL-1.1.4/PAGFL/tests/testthat/fixtures/test_helper.R | 8 PAGFL-1.1.4/PAGFL/tests/testthat/test-inputs.R | 36 PAGFL-1.1.4/PAGFL/tests/testthat/test-methods.R | 452 +++++----- PAGFL-1.1.4/PAGFL/tests/testthat/test-oracle.R | 276 +++--- PAGFL-1.1.4/PAGFL/tests/testthat/test-pagfl_results.R | 230 ++--- PAGFL-1.1.4/PAGFL/tests/testthat/test-sim.R | 26 47 files changed, 1105 insertions(+), 1010 deletions(-)
Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame
and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsindf versions 0.4.10 dated 2025-05-26 and 0.4.11 dated 2025-11-17
DESCRIPTION | 16 +++++------ MD5 | 46 +++++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 15 ++++++++++ R/collapse.R | 2 - R/excel.R |only R/expand.R | 4 +- R/utilities.R | 36 ++++--------------------- README.md | 10 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 ++-- inst/WORDLIST | 3 +- inst/doc/iris_pca.html | 14 +++++----- inst/doc/matsindf.Rmd | 6 ++-- inst/doc/matsindf.html | 15 +++++----- inst/doc/midf_apply_primer.Rmd | 2 - inst/doc/midf_apply_primer.html | 15 +++++----- man/check_worksheet_name_violations.Rd |only man/collapse_to_matrices.Rd | 2 - man/expand_to_tidy.Rd | 4 +- man/write_mats_to_excel.Rd |only tests/testthat/test-excel.R |only tests/testthat/test-expand.R | 3 +- vignettes/matsindf.Rmd | 6 ++-- vignettes/midf_apply_primer.Rmd | 2 - 26 files changed, 107 insertions(+), 102 deletions(-)
Title: Lightweight One-Line Resolving Microbial Ecology Program
Description: Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Author: Ningqi Wang [aut, cre, cph],
Yaozhong Zhang [aut],
Gaofei Jiang [aut]
Maintainer: Ningqi Wang <2434066068@qq.com>
Diff between LorMe versions 2.0.0 dated 2025-11-16 and 2.0.1 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/LorMe_pipeline.R | 1 + data/Facet_group.rda |binary data/Three_group.rda |binary data/Two_group.rda |binary man/LorMe_pipeline.Rd | 1 + 7 files changed, 11 insertions(+), 9 deletions(-)
Title: High-Dimensional Mediation Analysis
Description: Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Hou L, Liu L, HIMA: An R Package for High-Dimensional Mediation Analysis. Journal of Data Science. (2025). <doi:10.6339/25-JDS1192>.
Author: Yinan Zheng [aut, cre] ,
Haixiang Zhang [aut],
Lifang Hou [aut],
Lei Liu [aut, cph]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
Diff between HIMA versions 2.3.2 dated 2025-06-11 and 2.3.3 dated 2025-11-17
DESCRIPTION | 20 +- MD5 | 62 +++---- NAMESPACE | 4 NEWS.md | 4 R/HIMA-package.R | 39 ++-- R/hima.R | 280 ++++++++++++++++++++++----------- R/hima_classic.R | 18 -- R/hima_data.R | 35 ++++ R/hima_dblasso.R | 25 +- R/hima_efficient.R | 10 - R/hima_microbiome.R | 24 ++ R/hima_quantile.R | 41 ++++ R/hima_survival.R | 5 R/hima_survival_long.R |only R/utils.R | 47 ++++- README.md | 30 +-- data/BinaryOutcome.rda |binary data/ContinuousOutcome.rda |binary data/MicrobiomeData.rda |binary data/QuantileData.rda |binary data/SurvivalData.rda |binary data/SurvivalLongData.rda |only inst/CITATION | 55 +++++- inst/doc/hima-vignette.R | 19 ++ inst/doc/hima-vignette.Rmd | 31 +++ inst/doc/hima-vignette.html | 118 +++++++++---- inst/scripts/Example_data_generation.R | 221 ++++++++++++++++++++------ man/HIMA-package.Rd | 21 +- man/SurvivalLongData.Rd |only man/hima.Rd | 71 ++++++-- man/hima_classic.Rd | 2 man/hima_survival.Rd | 2 man/hima_survival_long.Rd |only vignettes/hima-vignette.Rmd | 31 +++ 34 files changed, 864 insertions(+), 351 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: 'HDF5' (Hierarchical Data Format 5) is a high-performance
library and file format for storing and managing large, complex
data. This package provides the static libraries and headers for
the 'HDF5' 'C' library (release 1.14.6). It is intended for R
package developers to use in the 'LinkingTo' field, which
eliminates the need for users to install system-level 'HDF5'
dependencies. This build is compiled with thread-safety enabled
and supports dynamic loading of external compression filters.
'HDF5' is developed by 'The HDF Group' <https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
The HDF Group [cph] ,
Jean-loup Mark [cph] ,
Gailly Adler [cph]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
This is a re-admission after prior archival of version 1.14.6.4 dated 2025-11-10
Diff between hdf5lib versions 1.14.6.4 dated 2025-11-10 and 1.14.6.7 dated 2025-11-17
hdf5lib-1.14.6.4/hdf5lib/inst/LICENSE.note |only hdf5lib-1.14.6.4/hdf5lib/inst/licenses |only hdf5lib-1.14.6.7/hdf5lib/DESCRIPTION | 22 +++---- hdf5lib-1.14.6.7/hdf5lib/MD5 | 16 ++--- hdf5lib-1.14.6.7/hdf5lib/NEWS.md | 18 ++++++ hdf5lib-1.14.6.7/hdf5lib/README.md | 84 +++++++++++++---------------- hdf5lib-1.14.6.7/hdf5lib/configure | 6 +- hdf5lib-1.14.6.7/hdf5lib/configure.win | 6 +- hdf5lib-1.14.6.7/hdf5lib/inst/COPYRIGHTS |only hdf5lib-1.14.6.7/hdf5lib/src/hdf5.tar.gz |binary 10 files changed, 82 insertions(+), 70 deletions(-)
Title: Data Package for the 2016 United States Federal Elections
Description: Easily analyze relational data from the United States 2016 federal
election cycle as reported by the Federal Election Commission.
This package contains data about candidates, committees, and a
variety of different financial expenditures. Data is from <https://www.fec.gov/data/browse-data/?tab=bulk-data>.
Author: Marium Tapal [aut, cre] ,
Rana Gahwagy [aut],
Irene Ryan [aut],
Benjamin S. Baumer [aut]
Maintainer: Marium Tapal <mariumtapal@gmail.com>
Diff between fec16 versions 0.1.5 dated 2025-09-01 and 0.1.6 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fec16-package.R | 2 +- build/vignette.rds |binary inst/doc/fec_vignette.html | 5 +++-- man/fec16.Rd | 2 +- 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Data and Code for Empirical Research in Accounting
Description: Handy functions and data to support the course book 'Empirical Research in Accounting: Tools and Methods' (1st ed.). Chapman and Hall/CRC. <doi:10.1201/9781003456230> and <https://iangow.github.io/far_book/>.
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>
Diff between farr versions 0.3.2 dated 2025-09-01 and 1.0.0 dated 2025-11-17
DESCRIPTION | 13 +++--- MD5 | 80 +++++++++++++++++++++--------------------- NEWS.md | 10 ++++- R/data.R | 24 ++++++------ R/get_annc_dates.R | 3 - R/get_event_cum_rets.R | 2 - R/get_event_cum_rets_mth.R | 3 - R/get_event_dates.R | 3 - R/get_event_rets.R | 1 R/get_me_breakpoints.R | 12 ++++-- R/get_test_scores.R | 2 - R/get_trading_dates.R | 2 - R/roc.R | 2 - R/rusboost.R | 2 + R/system_time.R | 2 - R/truncate.R | 4 +- R/winsorize.R | 4 +- build/partial.rdb |binary data/gvkey_ciks.rda |binary man/aaer_dates.Rd | 2 - man/auc.Rd | 2 - man/by_tag_year.Rd | 2 - man/cmsw_2018.Rd | 2 - man/fhk_pilot.Rd | 3 - man/get_annc_dates.Rd | 3 - man/get_event_cum_rets.Rd | 2 - man/get_event_cum_rets_mth.Rd | 3 - man/get_event_dates.Rd | 3 - man/get_event_rets.Rd | 1 man/get_me_breakpoints.Rd | 7 ++- man/get_test_scores.Rd | 2 - man/get_trading_dates.Rd | 2 - man/gvkey_ciks.Rd | 2 - man/llz_2018.Rd | 4 +- man/rusboost.Rd | 2 - man/sho_r3000.Rd | 2 - man/sho_tickers.Rd | 2 - man/system_time.Rd | 2 - man/truncate.Rd | 4 +- man/undisclosed_names.Rd | 6 +-- man/winsorize.Rd | 4 +- 41 files changed, 118 insertions(+), 113 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.1 dated 2025-10-16 and 1.4.2 dated 2025-11-17
DESCRIPTION | 6 MD5 | 60 +-- NEWS.md | 7 R/version.R | 2 src/altrepdataframe_relation.cpp | 1 src/altrepdataframe_relation.dd | 665 +++++++++++++++++++++++++++++++++- src/connection.cpp | 4 src/connection.dd | 666 +++++++++++++++++++++++++++++++++- src/convert.cpp | 1 src/convert.dd | 661 +++++++++++++++++++++++++++++++++ src/database.cpp | 9 src/database.dd | 668 ++++++++++++++++++++++++++++++++++ src/duckdb.tar.xz |binary src/register.cpp | 15 src/register.dd | 700 +++++++++++++++++++++++++++++++++++ src/relational.cpp | 39 - src/relational.dd | 709 ++++++++++++++++++++++++++++++++++++ src/reltoaltrep.cpp | 21 - src/reltoaltrep.dd | 761 ++++++++++++++++++++++++++++++++++++++ src/rfuns.cpp | 55 +- src/rfuns.dd | 654 +++++++++++++++++++++++++++++++++ src/scan.cpp | 3 src/scan.dd | 664 +++++++++++++++++++++++++++++++++ src/statement.cpp | 2 src/statement.dd | 762 ++++++++++++++++++++++++++++++++++++++- src/transform.cpp | 4 src/transform.dd | 663 +++++++++++++++++++++++++++++++++ src/types.cpp | 7 src/types.dd | 663 +++++++++++++++++++++++++++++++++ src/utils.cpp | 6 src/utils.dd | 671 ++++++++++++++++++++++++++++++++++ 31 files changed, 9006 insertions(+), 143 deletions(-)
Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational
Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database.
Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or
SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Author: Anthony Sena [aut, cre],
Jamie Gilbert [aut],
Gowtham Rao [aut],
Freddy Avila Cruz [aut],
Martijn Schuemie [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between CohortGenerator versions 1.0.0 dated 2025-11-12 and 1.0.1 dated 2025-11-17
DESCRIPTION | 12 ++++---- MD5 | 34 +++++++++++------------ NEWS.md | 6 ++++ R/CohortConstruction.R | 2 - R/CohortSample.R | 2 - R/NegativeControlCohorts.R | 32 ++++++++++----------- R/RunCohortGeneration.R | 2 - R/TemplateUnion.R | 4 +- README.md | 1 inst/doc/CreatingCohortSubsetDefinitions.html | 4 +- inst/doc/GeneratingCohorts.pdf |binary inst/doc/SamplingCohorts.pdf |binary inst/doc/UsingTemplateCohorts.html | 4 +- tests/testthat/setup.R | 2 - tests/testthat/test-CohortConstructionAndStats.R | 20 +++++++++++++ tests/testthat/test-CohortSample.R | 22 ++++++++++++++ tests/testthat/test-NegativeControlCohorts.R | 26 +++++++++++++++++ tests/testthat/test-RunCohortGeneration.R | 29 +++++++++++++++++++ 18 files changed, 152 insertions(+), 50 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Automatic Database Normalisation for Data Frames
Description: Automatic normalisation of a data frame to third normal form, with
the intention of easing the process of data cleaning. (Usage to design your
actual database for you is not advised.)
Originally inspired by the 'AutoNormalize' library for 'Python' by 'Alteryx'
(<https://github.com/alteryx/autonormalize>), with various changes and
improvements. Automatic discovery of functional or approximate dependencies,
normalisation based on those, and plotting of the resulting "database" via
'Graphviz', with options to exclude some attributes at discovery time, or
remove discovered dependencies at normalisation time.
Author: Mark Webster [aut, cre]
Maintainer: Mark Webster <markwebster204@yahoo.co.uk>
Diff between autodb versions 3.1.0 dated 2025-09-18 and 3.2.4 dated 2025-11-17
DESCRIPTION | 10 MD5 | 67 NAMESPACE | 6 NEWS.md | 24 R/database.r | 25 R/database_schema.r | 13 R/partition_handler.r | 2 R/plot.r | 653 ++++-- R/reference.r | 36 R/synthesise.r | 2 build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/autodb.R | 606 ----- inst/doc/autodb.Rmd | 1089 +--------- inst/doc/autodb.html | 2967 +++------------------------- inst/doc/limits.R |only inst/doc/limits.Rmd |only inst/doc/limits.html |only inst/doc/nudge.R |only inst/doc/nudge.Rmd |only inst/doc/nudge.html |only inst/doc/null.R |only inst/doc/null.Rmd |only inst/doc/null.html |only inst/doc/plans.R |only inst/doc/plans.Rmd |only inst/doc/plans.html |only man/d2.Rd | 7 man/d2.database.Rd |only man/d2.database_schema.Rd |only man/d2.relation.Rd |only tests/testthat/helper.r | 19 tests/testthat/setup.r | 5 tests/testthat/test-database.r | 26 tests/testthat/test-database_schema.r | 24 tests/testthat/test-functional_dependency.r | 11 tests/testthat/test-plot.r | 831 +++++++ tests/testthat/test-relation.r | 11 tests/testthat/test-relation_schema.r | 13 vignettes/autodb.Rmd | 1089 +--------- vignettes/limits.Rmd |only vignettes/nudge.Rmd |only vignettes/null.Rmd |only vignettes/plans.Rmd |only 44 files changed, 2200 insertions(+), 5345 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 0.3.0 dated 2025-04-09 and 1.0.0 dated 2025-11-17
aedseo-0.3.0/aedseo/man/aedseo.Rd |only aedseo-0.3.0/aedseo/man/tsd.Rd |only aedseo-1.0.0/aedseo/DESCRIPTION | 19 aedseo-1.0.0/aedseo/MD5 | 122 ++--- aedseo-1.0.0/aedseo/NAMESPACE | 3 aedseo-1.0.0/aedseo/NEWS.md | 226 +++++----- aedseo-1.0.0/aedseo/R/0_documentation.R | 80 +-- aedseo-1.0.0/aedseo/R/autoplot.R | 68 ++- aedseo-1.0.0/aedseo/R/combined_seasonal_output.R | 165 ++++++- aedseo-1.0.0/aedseo/R/consecutive_growth_warnings.R | 5 aedseo-1.0.0/aedseo/R/estimate_disease_threshold.R |only aedseo-1.0.0/aedseo/R/fit_growth_rate.R | 86 ++- aedseo-1.0.0/aedseo/R/fit_percentiles.R | 32 + aedseo-1.0.0/aedseo/R/generate_seasonal_data.R | 20 aedseo-1.0.0/aedseo/R/historical_summary.R | 34 + aedseo-1.0.0/aedseo/R/predict.R | 24 - aedseo-1.0.0/aedseo/R/seasonal_burden_levels.R | 46 +- aedseo-1.0.0/aedseo/R/seasonal_onset.R | 173 ++++--- aedseo-1.0.0/aedseo/R/summary.R | 99 ++-- aedseo-1.0.0/aedseo/R/to_time_series.R | 123 +++-- aedseo-1.0.0/aedseo/README.md | 16 aedseo-1.0.0/aedseo/build/vignette.rds |binary aedseo-1.0.0/aedseo/inst/doc/aedseo.R | 57 ++ aedseo-1.0.0/aedseo/inst/doc/aedseo.Rmd | 127 ++++- aedseo-1.0.0/aedseo/inst/doc/aedseo.html | 161 ++++--- aedseo-1.0.0/aedseo/inst/doc/burden_levels.R | 20 aedseo-1.0.0/aedseo/inst/doc/burden_levels.Rmd | 23 - aedseo-1.0.0/aedseo/inst/doc/burden_levels.html | 19 aedseo-1.0.0/aedseo/inst/doc/generate_seasonal_wave.R | 18 aedseo-1.0.0/aedseo/inst/doc/generate_seasonal_wave.Rmd | 18 aedseo-1.0.0/aedseo/inst/doc/generate_seasonal_wave.html | 36 - aedseo-1.0.0/aedseo/inst/doc/multiple_waves.R |only aedseo-1.0.0/aedseo/inst/doc/multiple_waves.Rmd |only aedseo-1.0.0/aedseo/inst/doc/multiple_waves.html |only aedseo-1.0.0/aedseo/inst/doc/seasonal_onset.R | 14 aedseo-1.0.0/aedseo/inst/doc/seasonal_onset.Rmd | 41 + aedseo-1.0.0/aedseo/inst/doc/seasonal_onset.html | 76 +-- aedseo-1.0.0/aedseo/man/aedseo-package.Rd | 1 aedseo-1.0.0/aedseo/man/autoplot.Rd | 9 aedseo-1.0.0/aedseo/man/combined_seasonal_output.Rd | 80 ++- aedseo-1.0.0/aedseo/man/consecutive_growth_warnings.Rd | 3 aedseo-1.0.0/aedseo/man/estimate_disease_threshold.Rd |only aedseo-1.0.0/aedseo/man/fit_growth_rate.Rd | 18 aedseo-1.0.0/aedseo/man/fit_percentiles.Rd | 11 aedseo-1.0.0/aedseo/man/generate_seasonal_data.Rd | 10 aedseo-1.0.0/aedseo/man/historical_summary.Rd | 1 aedseo-1.0.0/aedseo/man/predict.tsd_onset.Rd | 12 aedseo-1.0.0/aedseo/man/seasonal_burden_levels.Rd | 30 - aedseo-1.0.0/aedseo/man/seasonal_onset.Rd | 67 +- aedseo-1.0.0/aedseo/man/summary.tsd_onset.Rd | 1 aedseo-1.0.0/aedseo/man/to_time_series.Rd | 76 ++- aedseo-1.0.0/aedseo/tests/testthat/test-combined_seasonal_output.R | 134 +++++ aedseo-1.0.0/aedseo/tests/testthat/test-estimate_disease_threshold.R |only aedseo-1.0.0/aedseo/tests/testthat/test-fit_growth_rate.R | 4 aedseo-1.0.0/aedseo/tests/testthat/test-fit_percentiles.R | 10 aedseo-1.0.0/aedseo/tests/testthat/test-generate_seasonal_data.R | 46 +- aedseo-1.0.0/aedseo/tests/testthat/test-historical_summary.R | 54 ++ aedseo-1.0.0/aedseo/tests/testthat/test-plot.R |only aedseo-1.0.0/aedseo/tests/testthat/test-predict.R | 18 aedseo-1.0.0/aedseo/tests/testthat/test-seasonal_burden_levels.R | 83 +++ aedseo-1.0.0/aedseo/tests/testthat/test-seasonal_onset.R | 119 ++++- aedseo-1.0.0/aedseo/tests/testthat/test-to_time_series.R | 101 ++-- aedseo-1.0.0/aedseo/vignettes/aedseo.Rmd | 127 ++++- aedseo-1.0.0/aedseo/vignettes/burden_levels.Rmd | 23 - aedseo-1.0.0/aedseo/vignettes/generate_seasonal_wave.Rmd | 18 aedseo-1.0.0/aedseo/vignettes/multiple_waves.Rmd |only aedseo-1.0.0/aedseo/vignettes/seasonal_onset.Rmd | 41 + 67 files changed, 2069 insertions(+), 979 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.2.1 dated 2025-03-20 and 1.2.2 dated 2025-11-17
DESCRIPTION | 16 - MD5 | 24 +- NEWS.md | 18 ++ R/endpoints.R | 324 ++++++++++++++++++++++---------------- R/epidatacall.R | 54 ++++-- R/model.R | 45 ++--- README.md | 4 inst/doc/signal-discovery.html | 4 man/covidcast_epidata.Rd | 4 man/fetch_args_list.Rd | 7 man/parse_api_week.Rd | 4 tests/testthat/test-epidatacall.R | 9 - tests/testthat/test-model.R | 6 13 files changed, 315 insertions(+), 204 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.1.5 dated 2025-09-11 and 1.1.6 dated 2025-11-17
sleev-1.1.5/sleev/tests/testthat.R |only sleev-1.1.6/sleev/DESCRIPTION | 7 sleev-1.1.6/sleev/MD5 | 13 - sleev-1.1.6/sleev/NAMESPACE | 8 sleev-1.1.6/sleev/R/logistic2ph.R | 132 ++++++++++++---- sleev-1.1.6/sleev/build/vignette.rds |binary sleev-1.1.6/sleev/inst/doc/sleev_vignette_file.pdf |binary sleev-1.1.6/sleev/tests/testthat/helper-001-functions.R |only sleev-1.1.6/sleev/tests/testthat/test-001-logistic2ph.R |only 9 files changed, 123 insertions(+), 37 deletions(-)
Title: 'tidyverse' Methods for 'Earth Engine'
Description: Provides 'tidyverse' methods for wrangling
and analyzing 'Earth Engine' <https://earthengine.google.com/> data. These methods help the user with filtering,
joining and summarising 'Earth Engine' image collections.
Author: Zack Arno [aut, cre, cph],
Josh Erickson [aut, cph]
Maintainer: Zack Arno <zackarno@gmail.com>
Diff between tidyrgee versions 0.1.0 dated 2022-09-15 and 0.1.1 dated 2025-11-17
DESCRIPTION | 12 LICENSE | 4 MD5 | 117 +-- NAMESPACE | 169 ++--- NEWS.md | 7 R/add_date_to_bandname.R | 106 +-- R/as_ee.R | 58 - R/as_tidyee.R | 160 ++-- R/bgd_msna.R | 56 - R/bind.R | 84 +- R/clip.R | 328 ++++----- R/ee_extract_tidy.R | 626 +++++++++--------- R/ee_temporal_composites.R | 958 ++++++++++++++--------------- R/filter-helpers.R | 138 ++-- R/filter.R | 144 ++-- R/filter_bounds.R | 262 +++---- R/group_by.R | 104 +-- R/group_split.R | 184 ++--- R/inner_join.R | 156 ++-- R/mutate.R | 74 +- R/print.R | 64 - R/select.R | 132 +-- R/set_idx.R | 136 ++-- R/slice.R | 122 +-- R/summarise.R | 306 ++++----- R/ungroup.R | 34 - R/utils.R | 498 +++++++-------- README.md | 772 +++++++++++------------ inst/WORDLIST | 108 +-- man/add_date_to_bandname.Rd | 34 - man/as_ee.Rd | 62 - man/as_tidyee.Rd | 64 - man/bgd_msna.Rd | 74 +- man/bind_ics.Rd | 62 - man/clip.Rd | 156 ++-- man/create_tidyee.Rd | 38 - man/ee_composite.Rd | 50 - man/ee_extract_tidy.Rd | 150 ++-- man/ee_month_composite.Rd | 60 - man/ee_month_filter.Rd | 42 - man/ee_year_composite.Rd | 60 - man/ee_year_filter.Rd | 42 - man/ee_year_month_composite.Rd | 68 +- man/ee_year_month_filter.Rd | 46 - man/filter.Rd | 78 +- man/filter_bounds.Rd | 130 +-- man/group_by.Rd | 82 +- man/group_split.Rd | 82 +- man/ic_list_to_ic.Rd |only man/inner_join.Rd | 42 - man/mutate.Rd | 56 - man/print.tidyee.Rd | 38 - man/select.Rd | 74 +- man/slice.Rd | 78 +- man/summarise.Rd | 92 +- man/ungroup.Rd | 38 - tests/testthat.R | 128 +-- tests/testthat/test-filter.R | 422 ++++++------ tests/testthat/test-summarise.R | 124 +-- tests/testthat/test-year_month_composite.R | 66 - 60 files changed, 4237 insertions(+), 4220 deletions(-)
Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn
maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between TH.data versions 1.1-4 dated 2025-09-02 and 1.1-5 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/geyser.rda |binary data/mammoexp.rda |binary inst/doc/blood_loss_report.R | 7 ------- inst/doc/blood_loss_report.Rnw | 30 ++++++++++++++++++------------ inst/doc/blood_loss_report.pdf |binary inst/rda/aquabirds.rda |only vignettes/blood_loss_report.Rnw | 30 ++++++++++++++++++------------ 11 files changed, 50 insertions(+), 44 deletions(-)
Title: Causal Mediation Analysis Using Weighting Approach
Description: We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity analysis strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.
Author: Xu Qin [aut, cre],
Guanglei Hong [aut],
Fan Yang [aut]
Maintainer: Xu Qin <xuqin@uchicago.edu>
Diff between rmpw versions 0.0.5 dated 2024-03-05 and 0.0.6 dated 2025-11-17
DESCRIPTION | 24 ++++++--- MD5 | 6 +- R/rmpw.R | 139 ++++++++++++++++++++---------------------------------- build/partial.rdb |binary 4 files changed, 75 insertions(+), 94 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>
Diff between ChannelAttribution versions 2.2.2 dated 2025-11-02 and 2.2.3 dated 2025-11-17
DESCRIPTION | 8 +++--- MD5 | 6 ++--- R/ChannelAttribution.R | 45 +++++++++++++++++++++++++++++--------- man/ChannelAttribution-package.Rd | 4 +-- 4 files changed, 44 insertions(+), 19 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Multilevel Propensity Score Analysis
Description: Conducts and visualizes propensity score analysis for
multilevel, or clustered data. Bryer & Pruzek (2011)
<doi:10.1080/00273171.2011.636693>.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between multilevelPSA versions 1.3.0 dated 2025-04-04 and 1.3.1 dated 2025-11-17
multilevelPSA-1.3.0/multilevelPSA/R/psrange.r |only multilevelPSA-1.3.1/multilevelPSA/DESCRIPTION | 12 ++-- multilevelPSA-1.3.1/multilevelPSA/MD5 | 24 +++++--- multilevelPSA-1.3.1/multilevelPSA/NEWS.md | 7 ++ multilevelPSA-1.3.1/multilevelPSA/R/plot.balance.R | 2 multilevelPSA-1.3.1/multilevelPSA/R/psrange.R |only multilevelPSA-1.3.1/multilevelPSA/build/vignette.rds |binary multilevelPSA-1.3.1/multilevelPSA/inst/doc/multilevelPSA.html | 27 ++++++++-- multilevelPSA-1.3.1/multilevelPSA/inst/doc/shrinking_fitted_values.R |only multilevelPSA-1.3.1/multilevelPSA/inst/doc/shrinking_fitted_values.Rmd |only multilevelPSA-1.3.1/multilevelPSA/inst/doc/shrinking_fitted_values.html |only multilevelPSA-1.3.1/multilevelPSA/man/plot.psrange.Rd | 7 +- multilevelPSA-1.3.1/multilevelPSA/man/print.psrange.Rd | 2 multilevelPSA-1.3.1/multilevelPSA/man/psrange.Rd | 2 multilevelPSA-1.3.1/multilevelPSA/man/summary.psrange.Rd | 2 multilevelPSA-1.3.1/multilevelPSA/vignettes/shrinking_fitted_values.Rmd |only 16 files changed, 59 insertions(+), 26 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.5 dated 2025-08-25 and 1.0.6 dated 2025-11-17
DESCRIPTION | 10 MD5 | 223 - NEWS.md | 93 R/approach_regression_separate.R | 2 R/approach_vaeac.R | 10 R/asymmetric_and_causal_Shapley.R | 2 R/check_convergence.R | 2 R/cli.R | 8 R/compute_estimates.R | 4 R/compute_vS.R | 4 R/explain.R | 4 R/explain_forecast.R | 2 R/finalize_explanation.R | 2 R/get_results.R | 10 R/model.R | 2 R/plot.R | 150 R/prepare_next_iteration.R | 2 R/print.R | 2 R/save_results.R | 2 R/setup.R | 10 R/shapley_setup.R | 4 R/summary.R | 13 R/timing.R | 2 inst/doc/asymmetric_causal.Rmd | 969 ++--- inst/doc/asymmetric_causal.html | 1534 ++++--- inst/doc/general_usage.Rmd | 1247 +++--- inst/doc/general_usage.html | 1206 +++--- inst/doc/regression.Rmd | 1896 ++++----- inst/doc/regression.html | 1919 +++++----- inst/doc/vaeac.Rmd | 602 +-- inst/doc/vaeac.html | 619 +-- man/additional_regression_setup.Rd | 4 man/append_vS_list.Rd | 4 man/check_convergence.Rd | 4 man/cli_compute_vS.Rd | 4 man/cli_iter.Rd | 4 man/cli_startup.Rd | 4 man/compute_estimates.Rd | 4 man/compute_shapley.Rd | 4 man/compute_time.Rd | 4 man/compute_vS.Rd | 4 man/explain.Rd | 2 man/explain_forecast.Rd | 2 man/finalize_explanation.Rd | 4 man/format_round.Rd | 44 man/get_extra_comp_args_default.Rd | 4 man/get_output_args_default.Rd | 4 man/get_results.Rd | 11 man/get_supported_approaches.Rd | 4 man/get_supported_models.Rd | 4 man/plot.shapr.Rd | 21 man/plot_MSEv_eval_crit.Rd | 4 man/plot_SV_several_approaches.Rd | 21 man/prepare_data_causal.Rd | 2 man/prepare_next_iteration.Rd | 4 man/print.shapr.Rd | 4 man/print_iter.Rd | 4 man/regression.train_model.Rd | 2 man/round_manual.Rd | 44 man/save_results.Rd | 4 man/setup.Rd | 4 man/shapley_setup.Rd | 4 man/summary.shapr.Rd | 4 man/testing_cleanup.Rd | 4 man/vaeac_get_evaluation_criteria.Rd | 4 man/vaeac_get_extra_para_default.Rd | 2 man/vaeac_impute_missing_entries.Rd | 4 man/vaeac_train_model.Rd | 2 man/vaeac_train_model_continue.Rd | 2 man/weight_matrix.Rd | 4 vignettes/asymmetric_causal.Rmd | 969 ++--- vignettes/figure_asymmetric_causal/explanation_asym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_mar_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/group_cor-1.webp |binary vignettes/figure_asymmetric_causal/group_gaussian_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_SV-2.webp |only vignettes/figure_asymmetric_causal/n_coalitions_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/scatter_plots-1.webp |binary vignettes/figure_asymmetric_causal/setup_2-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_1-1.webp |binary vignettes/figure_general_usage/combined-1-1.webp |binary vignettes/figure_general_usage/custom-1.webp |binary vignettes/figure_general_usage/custom-2.webp |binary vignettes/figure_general_usage/factor-1.webp |binary vignettes/figure_general_usage/group-1.webp |binary vignettes/figure_general_usage/plot-beeswarm-1.webp |binary vignettes/figure_general_usage/plot-scatter-1.webp |binary vignettes/figure_general_usage/plot-waterfall-1.webp |binary vignettes/figure_general_usage/setup-2-1.webp |binary vignettes/figure_regression/MSEv-sum-1.webp |binary vignettes/figure_regression/MSEv-sum-2-1.webp |binary vignettes/figure_regression/SV-sum-1.webp |binary vignettes/figure_regression/SV-sum-2.webp |binary vignettes/figure_regression/SV-sum-3.webp |binary vignettes/figure_regression/dt-cv-plot-1.webp |binary vignettes/figure_regression/mixed-plot-1.webp |binary vignettes/figure_regression/mixed-plot-2-1.webp |binary vignettes/figure_regression/mixed-plot-3-1.webp |binary vignettes/figure_regression/mixed-plot-4-1.webp |binary vignettes/figure_regression/ppr-plot-1.webp |binary vignettes/figure_regression/surrogate-plot-1.webp |binary vignettes/figure_vaeac/continue-training-2.webp |binary vignettes/figure_vaeac/continue-training-5.webp |binary vignettes/figure_vaeac/first-vaeac-plots-1.webp |binary vignettes/figure_vaeac/vaeac-grouping-of-features-1.webp |binary vignettes/figure_vaeac/vaeac-mixed-data-2.webp |binary vignettes/figure_vaeac/vaeac-mixed-data-3.webp |binary vignettes/general_usage.Rmd | 1247 +++--- vignettes/regression.Rmd | 1896 ++++----- vignettes/vaeac.Rmd | 602 +-- 113 files changed, 7831 insertions(+), 7701 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. [...truncated...]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund versions 0.1-37 dated 2024-09-20 and 0.1-38 dated 2025-11-17
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 2 R/fgam.R | 4 R/pffr-methods.R | 14 +- R/pffr-robust.R | 277 +++++++++++++++++++++++++++----------------------- R/pffr.R | 142 ++++++++++++------------- R/pfr.R | 4 R/plot.pfr.R | 5 man/coefboot.pffr.Rd | 2 man/pfr_plot.gam.Rd | 33 ----- man/residuals.pffr.Rd | 8 + 12 files changed, 259 insertions(+), 264 deletions(-)
Title: Evolutionary Algorithm
Description: Runs an evolutionary algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> .
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.6 dated 2025-07-30 and 1.0.7 dated 2025-11-17
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Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 2.2 dated 2025-10-18 and 2.3 dated 2025-11-17
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 4 +--- R/ABregres.R | 2 +- R/ABrf2.R | 13 ++++++++++--- R/Aregres.R | 2 +- R/TauUabove.R | 16 ++++++++++++++-- R/TauUbelow.R | 18 +++++++++++++++++- 8 files changed, 56 insertions(+), 23 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and scientific computing. Includes functions for parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.2.0 dated 2025-10-05 and 0.3.1 dated 2025-11-17
DESCRIPTION | 11 + MD5 | 28 ++-- NEWS.md | 44 +++++++ R/add_pkg_file.R | 175 ++++++++++++++++++++++++++++- R/computation.R | 11 + R/figlet.R | 2 R/log_message.R | 122 ++++++++++++++++++++ R/parallelize_fun.R | 88 +++++++++++--- R/thisutils-package.R | 4 R/utils.R | 51 +++----- man/capitalize.Rd | 1 man/figlet.Rd | 2 man/log_message.Rd | 14 ++ src/matrix_to_table.cpp | 282 ++++++++++++++++++++++-------------------------- src/table_to_matrix.cpp | 2 15 files changed, 600 insertions(+), 237 deletions(-)
Title: Exploratory Web Apps for Analyzing Clinical Trials Data
Description: A 'shiny' based interactive exploration framework for
analyzing clinical trials data. 'teal' currently provides a dynamic
filtering facility and different data viewers. 'teal' 'shiny'
applications are built using standard 'shiny' modules.
Author: Dawid Kaledkowski [aut, cre] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Vedha Viyash [aut],
Marcin Kosinski [aut],
Adrian Waddell [aut],
Dony Unardi [rev],
Nina Qi [rev],
Nikolas Burkoff [aut],
M [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal versions 1.0.0 dated 2025-08-20 and 1.1.0 dated 2025-11-17
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teal-1.1.0/teal/inst/doc/adding-support-for-reporting.html | 1413 -- teal-1.1.0/teal/inst/doc/bootstrap-themes-in-teal.R | 110 teal-1.1.0/teal/inst/doc/bootstrap-themes-in-teal.Rmd | 432 teal-1.1.0/teal/inst/doc/bootstrap-themes-in-teal.html | 1158 - teal-1.1.0/teal/inst/doc/creating-custom-modules.R | 243 teal-1.1.0/teal/inst/doc/creating-custom-modules.Rmd | 588 teal-1.1.0/teal/inst/doc/creating-custom-modules.html | 1448 +- teal-1.1.0/teal/inst/doc/data-as-shiny-module.R | 314 teal-1.1.0/teal/inst/doc/data-as-shiny-module.Rmd | 450 teal-1.1.0/teal/inst/doc/data-as-shiny-module.html | 1048 - teal-1.1.0/teal/inst/doc/filter-panel.R | 156 teal-1.1.0/teal/inst/doc/filter-panel.Rmd | 264 teal-1.1.0/teal/inst/doc/filter-panel.html | 974 - teal-1.1.0/teal/inst/doc/getting-started-with-teal.R | 64 teal-1.1.0/teal/inst/doc/getting-started-with-teal.Rmd | 332 teal-1.1.0/teal/inst/doc/getting-started-with-teal.html | 1122 - teal-1.1.0/teal/inst/doc/including-data-in-teal-applications.R | 234 teal-1.1.0/teal/inst/doc/including-data-in-teal-applications.Rmd | 534 teal-1.1.0/teal/inst/doc/including-data-in-teal-applications.html | 1336 +- teal-1.1.0/teal/inst/doc/teal-as-a-shiny-module.R | 86 teal-1.1.0/teal/inst/doc/teal-as-a-shiny-module.Rmd | 144 teal-1.1.0/teal/inst/doc/teal-as-a-shiny-module.html | 852 - 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Title: Benchmark for Publication Bias Correction Methods
Description: Implements a unified interface for benchmarking meta-analytic
publication bias correction methods through simulation studies (see
Bartoš et al., 2025, <doi:10.48550/arXiv.2510.19489>). It provides
1) predefined data-generating mechanisms from the literature, 2) functions
for running meta-analytic methods on simulated data, 3) pre-simulated
datasets and pre-computed results for reproducible benchmarks, 4) tools for
visualizing and comparing method performance.
Author: Frantisek Bartos [aut, cre] ,
Samuel Pawel [aut] ,
Bjoern S. Siepe [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between PublicationBiasBenchmark versions 0.1.0 dated 2025-11-05 and 0.1.1 dated 2025-11-17
DESCRIPTION | 8 +- MD5 | 64 +++++++++--------- NEWS.md | 7 +- R/dgm-Carter2019.R | 6 - R/download.R | 22 ++---- R/measures_compute.R | 4 - R/measures_pairwise.R | 8 -- R/method.R | 8 ++ R/upload.R | 4 - R/utilities.R | 20 ++++- README.md | 27 +++++++- build/partial.rdb |binary inst/CITATION | 4 - man/PublicationBiasBenchmark-package.Rd | 2 man/create_empty_result.Rd | 42 ++++++------ man/download_dgm.Rd | 4 - man/method.AK.Rd | 108 ++++++++++++++++---------------- man/method.EK.Rd | 90 +++++++++++++------------- man/method.FMA.Rd | 90 +++++++++++++------------- man/method.PEESE.Rd | 80 +++++++++++------------ man/method.PET.Rd | 80 +++++++++++------------ man/method.PETPEESE.Rd | 98 ++++++++++++++--------------- man/method.RMA.Rd | 98 ++++++++++++++--------------- man/method.WAAPWLS.Rd | 82 ++++++++++++------------ man/method.WILS.Rd | 100 ++++++++++++++--------------- man/method.WLS.Rd | 78 +++++++++++------------ man/method.pcurve.Rd | 98 ++++++++++++++--------------- man/method.puniform.Rd | 96 ++++++++++++++-------------- man/method.trimfill.Rd | 92 +++++++++++++-------------- man/method_extra_columns.Rd | 78 ++++++++++++----------- man/method_settings.Rd | 58 ++++++++--------- man/retrieve_dgm_dataset.Rd | 2 man/validate_dgm_setting.Rd | 72 ++++++++++----------- 33 files changed, 832 insertions(+), 798 deletions(-)
More information about PublicationBiasBenchmark at CRAN
Permanent link
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.4.4 dated 2025-03-02 and 1.5.1 dated 2025-11-17
DESCRIPTION | 11 MD5 | 70 - NEWS.md | 184 +- R/BS_Geometric_Asian_Greeks.R | 560 ++++---- R/BS_Malliavin_Asian_Greeks.R | 534 ++++---- R/Binomial_American_Greeks.R | 15 R/Greeks_UI.R | 1098 ++++++++--------- R/Malliavin_European_Greeks.R | 4 R/Malliavin_Geometric_Asian_Greeks.R | 442 +++--- R/RcppExports.R | 94 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/using_greeks.R | 12 inst/doc/using_greeks.Rmd | 192 +- inst/doc/using_greeks.html | 674 +++++----- man/BS_Geometric_Asian_Greeks.Rd | 154 +- man/BS_Implied_Volatility.Rd | 154 +- man/Binomial_American_Greeks.Rd | 173 +- man/Greeks.Rd | 410 +++--- man/Greeks_UI.Rd | 48 man/Implied_Volatility.Rd | 172 +- man/Malliavin_Asian_Greeks.Rd | 248 +-- man/Malliavin_European_Greeks.Rd | 184 +- man/Malliavin_Geometric_Asian_Greeks.Rd | 248 +-- man/pipe.Rd | 40 src/Makevars | 1 tests/testthat/test-BS_European_Greeks.R | 218 +-- tests/testthat/test-BS_Geometric_Asian_Greeks.R | 167 +- tests/testthat/test-BS_Malliavin_Asian_Greeks.R | 304 ++-- tests/testthat/test-Binomial_American_Greeks.R | 440 +++--- tests/testthat/test-Greeks.R | 64 tests/testthat/test-Implied_Volatility.R | 191 +- tests/testthat/test-Malliavin_Asian_Greeks.R | 444 +++--- tests/testthat/test-Malliavin_European_Greeks.R | 154 +- tests/testthat/test-Malliavin_Geometric_Asian_Greeks.R | 292 ++-- vignettes/using_greeks.Rmd | 192 +- 36 files changed, 4087 insertions(+), 4101 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.11.1 dated 2025-06-26 and 1.11.3 dated 2025-11-17
DESCRIPTION | 8 MD5 | 62 ++--- NEWS.md | 7 R/display_DVH.R | 1 R/display_dV_dx.R | 1 R/espadon_hidden.R | 2 R/get_volume_from_bin.R | 1 R/get_volume_from_roi.R | 1 R/histo_vol.R | 1 R/rt_chi_index.R | 1 R/rt_gamma_index.R | 1 R/rt_indices_from_roi.R | 1 R/sp_similarity_from_bin.R | 1 R/sp_similarity_from_mesh.R | 1 R/struct_clustering.R | 1 build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 473 ++++++++++++++++++++--------------------- inst/doc/espadon_overview.html | 47 ++-- man/display.DVH.Rd | 3 man/display.dV_dx.Rd | 3 man/get.volume.from.bin.Rd | 3 man/get.volume.from.roi.Rd | 3 man/histo.vol.Rd | 3 man/rt.chi.index.Rd | 3 man/rt.gamma.index.Rd | 3 man/rt.indices.from.roi.Rd | 3 man/sp.similarity.from.bin.Rd | 3 man/sp.similarity.from.mesh.Rd | 3 man/struct.clustering.Rd | 3 src/dicombrowser.cpp | 372 -------------------------------- 32 files changed, 316 insertions(+), 699 deletions(-)
Title: A 'shiny' App to Evaluate Diagnostic Tests Performance
Description: Evaluate diagnostic test performance using data from laboratory or diagnostic research. It supports both binary and continuous test variables. It allows users to compute key performance indicators and visualize Receiver Operating Characteristic (ROC) curves, determine optimal cut-off thresholds, display confusion matrix, and export publication-ready plot. It aims to facilitate the application of statistical methods in diagnostic test evaluation by healthcare professionals. The methodology used to compute the performance indicators follows the overview described by Habibzadeh (2025) <doi:10.11613/BM.2025.010101>. Thanks to 'shiny' package.
Author: Nassim AYAD [aut, cre]
Maintainer: Nassim AYAD <nassim.ayad.ph@gmail.com>
Diff between EvalTest versions 1.0.3 dated 2025-10-15 and 1.0.5 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 28 +++++++++++++++++++++------- README.md | 11 ++++++++--- inst/app/app.R | 7 ++----- inst/doc/introduction.Rmd | 30 +++++++++++++++--------------- inst/doc/introduction.html | 38 +++++++++++++++++++------------------- vignettes/introduction.Rmd | 30 +++++++++++++++--------------- 8 files changed, 90 insertions(+), 74 deletions(-)
Title: Implementation of LT-FH++
Description: Implementation of LT-FH++, an extension of
the liability threshold family history (LT-FH) model.
LT-FH++ uses a Gibbs sampler for sampling from the truncated
multivariate normal distribution and allows for
flexible family structures. LT-FH++ was first described in
Pedersen, Emil M., et al. (2022)
<doi:10.1016/j.ajhg.2022.01.009>
as an extension to LT-FH with more flexible family structures,
and again as the age-dependent liability threshold (ADuLT) model
Pedersen, Emil M., et al. (2023)
<https://www.nature.com/articles/s41467-023-41210-z>
as an alternative to traditional time-to-event genome-wide
association studies, where family history was not considered.
Author: Emil Michael Pedersen [aut, cre],
Florian Prive [aut, ths],
Bjarni Johann Vilhjalmsson [ths],
Esben Agerbo [ths],
Jette Steinbach [aut],
Lucas Rasmussen [ctb]
Maintainer: Emil Michael Pedersen <emp@ph.au.dk>
Diff between LTFHPlus versions 2.1.4 dated 2025-05-26 and 2.2.0 dated 2025-11-17
DESCRIPTION | 13 +-- MD5 | 20 +++- NAMESPACE | 33 ++++++++ NEWS.md | 10 ++ R/Labelling_and_plotting_functions.R |only R/prepare_LTFHPlus_input.R | 143 +++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/LTFHPlus-package.Rd | 1 man/Relation_per_proband_plot.Rd |only man/attach_attributes.Rd |only man/familywise_attach_attributes.Rd |only man/get_family_graphs.Rd |only man/get_generations.Rd |only man/get_relations.Rd |only man/label_relatives.Rd |only 15 files changed, 208 insertions(+), 12 deletions(-)
Title: A Simple Sky Illuminance Model
Description: A tool to calculate sky illuminance values (in lux) for both sun and moon. The
model is a translation of the Fortran code by Janiczek and DeYoung (1987)
<https://archive.org/details/DTIC_ADA182110>.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between skylight versions 1.3 dated 2025-09-24 and 1.4 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/skylight.R | 9 +++------ build/vignette.rds |binary inst/doc/skylight.html | 4 ++-- inst/doc/skylight_advanced.html | 4 ++-- man/skylight.Rd | 7 +++---- tests/testthat/test_skylight.R | 5 ----- 8 files changed, 20 insertions(+), 29 deletions(-)
Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal
clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings.
'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Tatiana Vargas [aut, cre],
Frederic Breant [ctb],
Victor Perrier [ctb],
Baptiste Seguinot [ctb],
Benoit Thieurmel [ctb],
Titouan Robert [ctb],
Jalal-Edine Zawam [ctb],
Etienne Sanchez [ctb],
Janus De Bondt [ctb],
Assil Mansouri [ctb],
Abdallah Mahoud [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresEditObject versions 0.9.2 dated 2025-09-24 and 0.9.3 dated 2025-11-17
DESCRIPTION | 8 MD5 | 66 - NAMESPACE | 1 NEWS.md | 22 R/createBindingConstraint.R | 91 + R/createCluster.R | 113 +- R/createClusterST.R | 119 ++ R/createStudy.R | 9 R/editBindingConstraint.R | 46 R/editClusterST.R | 45 R/scenarioBuilder.R | 190 +++- R/updateGeneralSettings.R | 53 + build/vignette.rds |binary inst/doc/Antares_new_features_v920.R | 4 inst/doc/Antares_new_features_v920.Rmd | 4 inst/doc/Antares_new_features_v920.html | 1229 +------------------------- inst/doc/Antares_new_features_v930.R |only inst/doc/Antares_new_features_v930.Rmd |only inst/doc/Antares_new_features_v930.html |only inst/doc/api-variant-management.html | 2 man/createBindingConstraint.Rd | 2 man/createCluster.Rd | 8 man/createClusterST.Rd | 49 - man/editBindingConstraint.Rd | 2 man/editClusterST.Rd | 45 man/scenario-builder.Rd | 7 tests/testthat/test-createBindingConstraint.R | 182 +++ tests/testthat/test-createCluster.R | 92 + tests/testthat/test-createClusterST.R | 218 ++++ tests/testthat/test-createStudy.R | 27 tests/testthat/test-editBindingConstraint.R | 49 - tests/testthat/test-editClusterST.R | 238 +++++ tests/testthat/test-scenarioBuilder.R | 119 ++ tests/testthat/test-updateGeneralSettings.R | 49 + vignettes/Antares_new_features_v920.Rmd | 4 vignettes/Antares_new_features_v930.Rmd |only 36 files changed, 1727 insertions(+), 1366 deletions(-)
More information about antaresEditObject at CRAN
Permanent link
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph] ,
Tilman M. Davies [aut, ctb, cph] ,
Martin L. Hazelton [aut, ctb, cph] ,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.1-4 dated 2025-07-12 and 3.1-5 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS | 14 ++++++++++++++ R/ewcdf.R | 6 +++--- R/unnormdensity.R | 6 +++++- inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/knots.ewcdf.Rd | 22 +++++++++++++++------- man/macros/defns.Rd | 5 ++++- man/spatstat.univar-internal.Rd | 2 -- man/unnormdensity.Rd | 3 +++ 12 files changed, 62 insertions(+), 30 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability
distribution for a single parameter from an expert or a group of
experts. The expert provides a small number of probability judgements,
corresponding to points on his or her cumulative distribution
function. A range of parametric distributions can then be fitted and
displayed, with feedback provided in the form of fitted probabilities
and percentiles. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about
population distributions; eliciting multivariate distributions using a
Gaussian copula; eliciting a Dirichlet distribution; eliciting
distributions for variance parameters in a random effects
meta-analysis model; survival extrapolation. R Shiny apps for most of the methods are
included.
Author: Jeremy Oakley [aut, cre]
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.12.0 dated 2025-03-01 and 1.12.1 dated 2025-11-17
SHELF-1.12.0/SHELF/tests/testthat/_snaps/plots/multiple-expert-plot.new.svg |only SHELF-1.12.1/SHELF/DESCRIPTION | 10 +-- SHELF-1.12.1/SHELF/MD5 | 29 ++++------ SHELF-1.12.1/SHELF/R/survivalModelExtrapolations.R | 14 +++- SHELF-1.12.1/SHELF/R/survivalScenario.R | 4 - SHELF-1.12.1/SHELF/inst/NEWS.md | 5 + SHELF-1.12.1/SHELF/inst/doc/Dirichlet-elicitation.html | 9 +-- SHELF-1.12.1/SHELF/inst/doc/SHELF-overview.html | 16 ++++- SHELF-1.12.1/SHELF/man/survivalModelExtrapolations.Rd | 4 + SHELF-1.12.1/SHELF/man/survivalScenario.Rd | 4 - SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/cdf-plot.svg | 20 +++--- SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/error-message-plot.svg | 1 SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/single-expert-histogram-plot.svg | 8 +- SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/single-expert-plot.svg | 8 +- SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/survival-extrapolations-plot.svg | 24 ++++---- SHELF-1.12.1/SHELF/tests/testthat/_snaps/plots/survival-scenario-plot.svg | 20 +++--- 16 files changed, 98 insertions(+), 78 deletions(-)
Title: Robust Time Series Filters
Description: Implementations for several robust procedures that allow for (online)
extraction of the signal of univariate or multivariate time series by
applying robust regression techniques to a moving time window are provided.
Included are univariate filtering procedures based on repeated-median
regression as well as hybrid and trimmed filters derived from it;
see Schettlinger et al. (2006) <doi:10.1515/BMT.2006.010>. The adaptive
online repeated median by Schettlinger et al. (2010) <doi:10.1002/acs.1105>
and the slope comparing adaptive repeated median by Borowski and Fried (2013)
<doi:10.1007/s11222-013-9391-7> choose the width of the moving time
window adaptively. Multivariate versions are also provided; see
Borowski et al. (2009) <doi:10.1080/03610910802514972> for a multivariate
online adaptive repeated median and Borowski (2012) <doi:10.17877/DE290R-14393>
for a multivariate slope comparing adaptive repeated median. Furthermore,
a repeated-median based filter w [...truncated...]
Author: Roland Fried [aut, cre],
Karen Schettlinger [aut],
Matthias Borowski [aut],
Robin Nunkesser [ctb],
Thorsten Bernholt [ctb]
Maintainer: Roland Fried <fried@statistik.tu-dortmund.de>
Diff between robfilter versions 4.1.5 dated 2024-07-16 and 4.1.6 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- build/partial.rdb |binary src/backports.h |only src/robust.cpp | 5 +++-- 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.9.8 dated 2025-10-16 and 0.10.1 dated 2025-11-17
bage-0.10.1/bage/DESCRIPTION | 9 bage-0.10.1/bage/MD5 | 249 - bage-0.10.1/bage/NAMESPACE | 7 bage-0.10.1/bage/NEWS.md | 76 bage-0.10.1/bage/R/bage-package.R | 35 bage-0.10.1/bage/R/bage_mod-functions.R | 5 bage-0.10.1/bage/R/bage_mod-methods.R | 314 +- bage-0.10.1/bage/R/bage_prior-constructors.R | 80 bage-0.10.1/bage/R/bage_ssvd-constructors.R | 50 bage-0.10.1/bage/R/bage_ssvd-functions.R | 42 bage-0.10.1/bage/R/bage_ssvd-methods.R | 126 bage-0.10.1/bage/R/check-functions.R | 41 bage-0.10.1/bage/R/data.R |only bage-0.10.1/bage/R/datasets.R | 313 -- bage-0.10.1/bage/R/fit.R | 8 bage-0.10.1/bage/R/make-inputs.R | 99 bage-0.10.1/bage/R/make-outputs.R | 252 - bage-0.10.1/bage/R/mapping-matrices.R | 48 bage-0.10.1/bage/R/svds.R |only bage-0.10.1/bage/R/util.R | 110 bage-0.10.1/bage/README.md | 8 bage-0.10.1/bage/build/vignette.rds |binary bage-0.10.1/bage/data/CSA.rda |only bage-0.10.1/bage/data/HFD.rda |binary bage-0.10.1/bage/data/HIMD_P1.rda |only bage-0.10.1/bage/data/HIMD_P5.rda |only 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bage-0.10.1/bage/man/Known.Rd | 2 bage-0.10.1/bage/man/LFP.Rd | 31 bage-0.10.1/bage/man/Lin.Rd | 2 bage-0.10.1/bage/man/Lin_AR.Rd | 2 bage-0.10.1/bage/man/Lin_AR1.Rd | 2 bage-0.10.1/bage/man/N.Rd | 2 bage-0.10.1/bage/man/NFix.Rd | 2 bage-0.10.1/bage/man/RW.Rd | 2 bage-0.10.1/bage/man/RW2.Rd | 2 bage-0.10.1/bage/man/RW2_Infant.Rd | 2 bage-0.10.1/bage/man/RW2_Seas.Rd | 2 bage-0.10.1/bage/man/RW_Seas.Rd | 2 bage-0.10.1/bage/man/SVD.Rd | 18 bage-0.10.1/bage/man/SVD_AR.Rd | 25 bage-0.10.1/bage/man/Sp.Rd | 4 bage-0.10.1/bage/man/WMD_C.Rd |only bage-0.10.1/bage/man/augment.bage_mod.Rd | 11 bage-0.10.1/bage/man/bage-package.Rd | 33 bage-0.10.1/bage/man/components.bage_mod.Rd | 1 bage-0.10.1/bage/man/components.bage_ssvd.Rd | 31 bage-0.10.1/bage/man/data_wmd.Rd |only bage-0.10.1/bage/man/datasets.Rd |only bage-0.10.1/bage/man/dispersion.Rd |only bage-0.10.1/bage/man/figures/sticker |only bage-0.10.1/bage/man/fit.bage_mod.Rd | 45 bage-0.10.1/bage/man/generate.bage_ssvd.Rd | 33 bage-0.10.1/bage/man/isl_deaths.Rd | 7 bage-0.10.1/bage/man/kor_births.Rd | 7 bage-0.10.1/bage/man/nld_expenditure.Rd | 7 bage-0.10.1/bage/man/nzl_divorces.Rd | 7 bage-0.10.1/bage/man/nzl_households.Rd | 7 bage-0.10.1/bage/man/nzl_injuries.Rd | 7 bage-0.10.1/bage/man/print.bage_mod.Rd | 5 bage-0.10.1/bage/man/prt_deaths.Rd | 7 bage-0.10.1/bage/man/replicate_data.Rd | 1 bage-0.10.1/bage/man/set_datamod_noise.Rd | 3 bage-0.10.1/bage/man/ssvd.Rd |only bage-0.10.1/bage/man/svds.Rd |only bage-0.10.1/bage/man/swe_infant.Rd | 7 bage-0.10.1/bage/man/tidy.bage_mod.Rd | 1 bage-0.10.1/bage/man/usa_deaths.Rd | 7 bage-0.10.1/bage/src/bage.cpp | 2 bage-0.10.1/bage/tests/testthat/_snaps/bage_ssvd-methods.md | 71 bage-0.10.1/bage/tests/testthat/helper.R | 3 bage-0.10.1/bage/tests/testthat/manual-checks.R |only bage-0.10.1/bage/tests/testthat/test-bage_mod-methods.R | 218 + bage-0.10.1/bage/tests/testthat/test-bage_prior-constructors.R | 67 bage-0.10.1/bage/tests/testthat/test-bage_prior-methods.R | 11 bage-0.10.1/bage/tests/testthat/test-bage_ssvd-constructors.R | 19 bage-0.10.1/bage/tests/testthat/test-bage_ssvd-functions.R | 184 + bage-0.10.1/bage/tests/testthat/test-bage_ssvd-methods.R | 97 bage-0.10.1/bage/tests/testthat/test-check-functions.R | 40 bage-0.10.1/bage/tests/testthat/test-fit.R | 68 bage-0.10.1/bage/tests/testthat/test-make-inputs.R | 44 bage-0.10.1/bage/tests/testthat/test-make-outputs.R | 678 ++-- bage-0.10.1/bage/tests/testthat/test-mapping-matrices.R | 51 bage-0.10.1/bage/tests/testthat/test-util.R | 150 + bage-0.10.1/bage/vignettes/articles |only bage-0.10.1/bage/vignettes/vig01_intro.Rmd | 9 bage-0.9.8/bage/inst/doc/vig02_math.R |only bage-0.9.8/bage/inst/doc/vig02_math.Rmd |only bage-0.9.8/bage/inst/doc/vig02_math.html |only bage-0.9.8/bage/inst/doc/vig03_priors.R |only bage-0.9.8/bage/inst/doc/vig03_priors.Rmd |only bage-0.9.8/bage/inst/doc/vig03_priors.html |only bage-0.9.8/bage/inst/doc/vig04_svd.R |only bage-0.9.8/bage/inst/doc/vig04_svd.Rmd |only 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Title: Parse XML
Description: Bindings to 'libxml2' for working with XML data using a simple,
consistent interface based on 'XPath' expressions. Also supports XML schema
validation; for 'XSLT' transformations see the 'xslt' package.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Jeroen Ooms [aut, cre],
Posit Software, PBC [cph, fnd],
R Foundation [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between xml2 versions 1.4.1 dated 2025-10-27 and 1.5.0 dated 2025-11-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/init.R | 7 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/modification.html | 22 +++++++++++----------- src/xml2_init.c | 41 ++++++++++++++++++++++++++++++++++++++++- 8 files changed, 72 insertions(+), 22 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.67.0 dated 2025-07-29 and 1.68.0 dated 2025-11-17
DESCRIPTION | 8 - MD5 | 86 +++++++-------- NEWS.md | 54 ++++++++- R/backend_api-01-FutureBackend-class.R | 31 ++--- R/backend_api-11.ClusterFutureBackend-class.R | 9 + R/backend_api-11.SequentialFutureBackend-class.R | 11 -- R/backend_api-Future-class.R | 5 R/backend_api-UniprocessFuture-class.R | 6 - R/backend_api-evalFuture.R | 2 R/core_api-cancel.R | 6 - R/core_api-reset.R | 7 - R/core_api-resolved.R | 1 R/core_api-value.R | 36 +++--- R/protected_api-journal.R | 2 R/protected_api-resolve.R | 8 - R/protected_api-signalConditions.R | 6 - R/utils-basic.R | 7 + R/utils_api-capture_journals.R | 4 R/utils_api-makeClusterFuture.R | 11 +- R/utils_api-plan.R | 24 ++-- build/vignette.rds |binary inst/doc/future-1-overview.html | 87 ++++++++-------- inst/doc/future-1-overview.md.rsp | 83 +++++++-------- inst/doc/future-2-output.html | 4 inst/doc/future-2b-backend.html | 10 - inst/doc/future-2b-backend.md.rsp | 8 - inst/doc/future-3-topologies.html | 4 inst/doc/future-4-issues.html | 4 inst/doc/future-4-non-exportable-objects.html | 4 inst/doc/future-5-startup.html | 4 inst/doc/future-6-future-api-backend-specification.html | 2 inst/doc/future-7-for-package-developers.html | 4 inst/doc/future-8-how-future-is-validated.html | 2 inst/testme/_prologue/090.context.R | 2 inst/testme/test-cancel.R | 8 + inst/testme/test-mpi.R | 10 + inst/vignettes-static/future-1-overview.md.rsp.rsp | 2 man/cancel.Rd | 2 man/makeClusterFuture.Rd | 13 +- man/resolved.Rd | 1 man/result.Rd | 3 man/value.Rd | 6 - vignettes/future-1-overview.md.rsp | 83 +++++++-------- vignettes/future-2b-backend.md.rsp | 8 - 44 files changed, 375 insertions(+), 303 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using the 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre],
John Magnotti [ctb] ,
Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.3.1 dated 2025-04-03 and 0.3.2 dated 2025-11-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/r_expr_addons.html | 13 +++++++------ inst/doc/shiny_customized_widgets.html | 5 +++-- inst/doc/utility_functions.html | 7 ++++--- src/utils.cpp | 20 +++++++++++++------- 8 files changed, 43 insertions(+), 29 deletions(-)
Title: Lightweight One-Line Resolving Microbial Ecology Program
Description: Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Author: Ningqi Wang [aut, cre, cph],
Yaozhong Zhang [aut],
Gaofei Jiang [aut]
Maintainer: Ningqi Wang <2434066068@qq.com>
Diff between LorMe versions 1.2.1 dated 2025-03-14 and 2.0.0 dated 2025-11-16
LorMe-1.2.1/LorMe/man/LorMe.Rd |only LorMe-2.0.0/LorMe/DESCRIPTION | 18 +-- LorMe-2.0.0/LorMe/MD5 | 98 ++++++++++------ LorMe-2.0.0/LorMe/NAMESPACE | 24 ++++ LorMe-2.0.0/LorMe/R/0.LorMe_define.R |only LorMe-2.0.0/LorMe/R/Alpha_diversity_calculator.R | 2 LorMe-2.0.0/LorMe/R/Alpha_diversity_calculator2.R | 2 LorMe-2.0.0/LorMe/R/Deseq_analysis.R | 12 +- LorMe-2.0.0/LorMe/R/LorMe.R | 131 ++++++++++------------ LorMe-2.0.0/LorMe/R/LorMe_defaults.R |only LorMe-2.0.0/LorMe/R/LorMe_options.R |only LorMe-2.0.0/LorMe/R/LorMe_pipeline.R |only LorMe-2.0.0/LorMe/R/Module_abundance.R | 37 +++--- LorMe-2.0.0/LorMe/R/Module_composition.R | 2 LorMe-2.0.0/LorMe/R/NC_remove.R | 2 LorMe-2.0.0/LorMe/R/Trans_from_microeco.R |only LorMe-2.0.0/LorMe/R/Trans_from_phylo.R |only LorMe-2.0.0/LorMe/R/Trans_to_microeco.R |only LorMe-2.0.0/LorMe/R/Trans_to_phylo.R |only LorMe-2.0.0/LorMe/R/add_tree.R |only LorMe-2.0.0/LorMe/R/community_plot.R | 2 LorMe-2.0.0/LorMe/R/differential_bar.R | 6 - LorMe-2.0.0/LorMe/R/global_options.R |only LorMe-2.0.0/LorMe/R/indicator_analysis.R | 2 LorMe-2.0.0/LorMe/R/nc.R | 2 LorMe-2.0.0/LorMe/R/network_analysis.R | 8 - LorMe-2.0.0/LorMe/R/network_analysis2.R | 2 LorMe-2.0.0/LorMe/R/network_visual.R | 54 +++++++++ LorMe-2.0.0/LorMe/R/network_withdiff.R | 2 LorMe-2.0.0/LorMe/R/object_config.R | 59 +++++++-- LorMe-2.0.0/LorMe/R/safe_run.R |only LorMe-2.0.0/LorMe/R/structure_plot.R | 4 LorMe-2.0.0/LorMe/R/sub_tax_summary.R | 79 +++++++------ LorMe-2.0.0/LorMe/R/tax_summary.R | 15 +- LorMe-2.0.0/LorMe/data/Facet_group.rda |binary LorMe-2.0.0/LorMe/data/Three_group.rda |binary LorMe-2.0.0/LorMe/data/Two_group.rda |binary LorMe-2.0.0/LorMe/man/LorMe-class.Rd |only LorMe-2.0.0/LorMe/man/LorMe-package.Rd |only LorMe-2.0.0/LorMe/man/LorMe_defaults.Rd |only LorMe-2.0.0/LorMe/man/LorMe_options.Rd |only LorMe-2.0.0/LorMe/man/LorMe_pipeline.Rd |only LorMe-2.0.0/LorMe/man/Module_abundance.Rd | 32 +++-- LorMe-2.0.0/LorMe/man/Module_composition.Rd | 2 LorMe-2.0.0/LorMe/man/NC_remove.Rd | 2 LorMe-2.0.0/LorMe/man/Trans_from_microeco.Rd |only LorMe-2.0.0/LorMe/man/Trans_from_phylo.Rd |only LorMe-2.0.0/LorMe/man/Trans_to_microeco.Rd |only LorMe-2.0.0/LorMe/man/Trans_to_phylo.Rd |only LorMe-2.0.0/LorMe/man/add_tree.Rd |only LorMe-2.0.0/LorMe/man/cash-LorMe-method.Rd |only LorMe-2.0.0/LorMe/man/dot-DollarNames.LorMe.Rd |only LorMe-2.0.0/LorMe/man/dot-LorMe_opts.Rd |only LorMe-2.0.0/LorMe/man/dot-onLoad.Rd |only LorMe-2.0.0/LorMe/man/nc.Rd | 2 LorMe-2.0.0/LorMe/man/network_analysis.Rd | 2 LorMe-2.0.0/LorMe/man/network_analysis2.Rd | 2 LorMe-2.0.0/LorMe/man/network_visual.Rd | 2 LorMe-2.0.0/LorMe/man/network_withdiff.Rd | 2 LorMe-2.0.0/LorMe/man/object_config.Rd | 10 - LorMe-2.0.0/LorMe/man/safe_run.Rd |only LorMe-2.0.0/LorMe/man/show-LorMe-method.Rd |only LorMe-2.0.0/LorMe/man/sub_tax_summary.Rd | 12 -- LorMe-2.0.0/LorMe/man/tax_summary.Rd | 4 64 files changed, 401 insertions(+), 234 deletions(-)
Title: Data on Base and Recommended Packages for Current and Previous
Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.5.1.0 dated 2025-07-18 and 4.5.2.0 dated 2025-11-16
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 5 ++ README.md | 55 +++++++++++++++---------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary 8 files changed, 42 insertions(+), 38 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.5.3 dated 2024-10-17 and 2.5.4 dated 2025-11-16
mizer-2.5.3/mizer/vignettes/mizer.R |only mizer-2.5.3/mizer/vignettes/mizer.html |only mizer-2.5.4/mizer/DESCRIPTION | 23 mizer-2.5.4/mizer/MD5 | 184 ++-- mizer-2.5.4/mizer/NAMESPACE | 1 mizer-2.5.4/mizer/NEWS.md | 38 mizer-2.5.4/mizer/R/MizerParams-class.R | 30 mizer-2.5.4/mizer/R/animateSpectra.R | 38 mizer-2.5.4/mizer/R/calibrate.R | 3 mizer-2.5.4/mizer/R/helpers.R | 18 mizer-2.5.4/mizer/R/manipulate_species.R | 84 + mizer-2.5.4/mizer/R/match.R | 25 mizer-2.5.4/mizer/R/newMultispeciesParams.R | 1 mizer-2.5.4/mizer/R/newSingleSpeciesParams.R | 11 mizer-2.5.4/mizer/R/plots.R | 443 ++++++---- mizer-2.5.4/mizer/R/pred_kernel_funcs.R | 59 - mizer-2.5.4/mizer/R/project_methods.R | 222 ++--- mizer-2.5.4/mizer/R/rate_functions.R | 6 mizer-2.5.4/mizer/R/resource_dynamics.R | 18 mizer-2.5.4/mizer/R/resource_logistic.R | 6 mizer-2.5.4/mizer/R/resource_semichemostat.R | 10 mizer-2.5.4/mizer/R/setBevertonHolt.R | 49 - mizer-2.5.4/mizer/R/setColours.R | 2 mizer-2.5.4/mizer/R/setExtMort.R | 36 mizer-2.5.4/mizer/R/setFishing.R | 26 mizer-2.5.4/mizer/R/setReproduction.R | 114 +- mizer-2.5.4/mizer/R/setResource.R | 88 + mizer-2.5.4/mizer/R/species_params.R | 6 mizer-2.5.4/mizer/R/steadySingleSpecies.R | 16 mizer-2.5.4/mizer/R/summary_methods.R | 2 mizer-2.5.4/mizer/R/validSpeciesParams.R | 4 mizer-2.5.4/mizer/R/wrapper_functions.R | 139 +-- mizer-2.5.4/mizer/build/vignette.rds |binary mizer-2.5.4/mizer/inst/WORDLIST | 2 mizer-2.5.4/mizer/inst/doc/mizer_vignette.R | 6 mizer-2.5.4/mizer/man/completeSpeciesParams.Rd | 3 mizer-2.5.4/mizer/man/figures/Beverton-Holt-plot-1.png |binary mizer-2.5.4/mizer/man/getEReproAndGrowth.Rd | 14 mizer-2.5.4/mizer/man/getEncounter.Rd | 8 mizer-2.5.4/mizer/man/getFMort.Rd | 2 mizer-2.5.4/mizer/man/l2w.Rd | 6 mizer-2.5.4/mizer/man/lognormal_pred_kernel.Rd | 2 mizer-2.5.4/mizer/man/mizerEReproAndGrowth.Rd | 14 mizer-2.5.4/mizer/man/mizerEncounter.Rd | 8 mizer-2.5.4/mizer/man/mizerPredRate.Rd | 4 mizer-2.5.4/mizer/man/newMultispeciesParams.Rd | 49 - mizer-2.5.4/mizer/man/plotBiomass.Rd | 3 mizer-2.5.4/mizer/man/plotDataFrame.Rd | 8 mizer-2.5.4/mizer/man/plotDiet.Rd | 4 mizer-2.5.4/mizer/man/plotFMort.Rd | 2 mizer-2.5.4/mizer/man/plotFeedingLevel.Rd | 2 mizer-2.5.4/mizer/man/plotSpectra.Rd | 6 mizer-2.5.4/mizer/man/power_law_pred_kernel.Rd | 2 mizer-2.5.4/mizer/man/renameGear.Rd |only mizer-2.5.4/mizer/man/resource_constant.Rd | 9 mizer-2.5.4/mizer/man/resource_logistic.Rd | 9 mizer-2.5.4/mizer/man/resource_params.Rd | 14 mizer-2.5.4/mizer/man/resource_semichemostat.Rd | 11 mizer-2.5.4/mizer/man/setExtMort.Rd | 2 mizer-2.5.4/mizer/man/setParams.Rd | 3 mizer-2.5.4/mizer/man/setReproduction.Rd | 12 mizer-2.5.4/mizer/man/setResource.Rd | 75 + mizer-2.5.4/mizer/man/truncated_lognormal_pred_kernel.Rd | 2 mizer-2.5.4/mizer/man/validParams.Rd | 4 mizer-2.5.4/mizer/man/validSpeciesParams.Rd | 3 mizer-2.5.4/mizer/tests/testthat/Rplots.pdf |binary mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-diet.svg | 86 - mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-single-growth-curve.svg | 2 mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-spectra.svg | 48 - mizer-2.5.4/mizer/tests/testthat/helper.R | 20 mizer-2.5.4/mizer/tests/testthat/test-MizerParams-class.R | 12 mizer-2.5.4/mizer/tests/testthat/test-age_mat.R | 61 + mizer-2.5.4/mizer/tests/testthat/test-animateSpectra.R | 167 +++ mizer-2.5.4/mizer/tests/testthat/test-calc-selectivity.R |only mizer-2.5.4/mizer/tests/testthat/test-extension.R | 2 mizer-2.5.4/mizer/tests/testthat/test-helpers-plot.R |only mizer-2.5.4/mizer/tests/testthat/test-idxFinalT.R |only mizer-2.5.4/mizer/tests/testthat/test-io.R |only mizer-2.5.4/mizer/tests/testthat/test-manipulate_species.R | 47 + mizer-2.5.4/mizer/tests/testthat/test-match.R | 7 mizer-2.5.4/mizer/tests/testthat/test-newMultispeciesParams.R | 29 mizer-2.5.4/mizer/tests/testthat/test-newSingleSpeciesParams.R | 8 mizer-2.5.4/mizer/tests/testthat/test-plotBiomassObservedVsModel.R | 2 mizer-2.5.4/mizer/tests/testthat/test-plotYieldObservedVsModel.R | 2 mizer-2.5.4/mizer/tests/testthat/test-plots.R | 71 + mizer-2.5.4/mizer/tests/testthat/test-pred_kernel_funcs.R | 99 ++ mizer-2.5.4/mizer/tests/testthat/test-project_simple.R |only mizer-2.5.4/mizer/tests/testthat/test-reproduction.R | 18 mizer-2.5.4/mizer/tests/testthat/test-setColours.R | 2 mizer-2.5.4/mizer/tests/testthat/test-setReproduction.R | 24 mizer-2.5.4/mizer/tests/testthat/test-setResource.R | 54 + mizer-2.5.4/mizer/tests/testthat/test-species_params.R | 9 mizer-2.5.4/mizer/tests/testthat/test-steady.R | 73 + mizer-2.5.4/mizer/tests/testthat/test-steadySingleSpecies.R | 36 mizer-2.5.4/mizer/tests/testthat/test-summary_methods.R | 44 mizer-2.5.4/mizer/tests/testthat/test-wrapper_functions.R | 59 - mizer-2.5.4/mizer/vignettes/mizer_vignette.html | 6 97 files changed, 2023 insertions(+), 956 deletions(-)
Title: Test Helpers for 'httr2'
Description: Testing and documenting code that communicates with remote servers
can be painful. This package helps with writing tests for packages that
use 'httr2'. It enables testing all of the logic
on the R sides of the API without requiring access to the
remote service, and it also allows recording real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables writing vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre] ,
Jonathan Keane [ctb],
Maelle Salmon [ctb]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest2 versions 1.2.1 dated 2025-07-27 and 1.2.2 dated 2025-11-16
DESCRIPTION | 11 +++--- MD5 | 24 +++++++------- NAMESPACE | 1 NEWS.md | 4 ++ R/expect-request.R | 3 + inst/doc/faq.html | 1 inst/doc/httptest2.html | 1 inst/doc/redacting.html | 1 man/capture_requests.Rd | 2 - man/expect_request_header.Rd | 2 - tests/testthat/_snaps |only tests/testthat/test-expect-request-header.R | 21 ++++++++---- tests/testthat/test-expect-request.R | 47 +++++++++++----------------- 13 files changed, 65 insertions(+), 53 deletions(-)
Title: Tools for Create Emissions for Air Quality Models
Description: Processing tools to create emissions for use in numerical air
quality models. Emissions can be calculated both using emission factors
and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using
pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>.
Functions to process individual point emissions, line emissions and
area emissions of pollutants are available as well as methods to
incorporate alternative data for Spatial distribution of emissions
such as satellite images (Gavidia-Calderon et. al, 2018)
<doi:10.1016/j.atmosenv.2018.09.026> or openstreetmap data
(Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
Author: Daniel Schuch [aut, cre] ,
Sergio Ibarra-Espinosa [aut]
Maintainer: Daniel Schuch <underschuch@gmail.com>
Diff between EmissV versions 0.665.9.0 dated 2025-01-24 and 0.666.0.0 dated 2025-11-16
EmissV-0.665.9.0/EmissV/tests/testthat/Rplots.pdf |only EmissV-0.666.0.0/EmissV/DESCRIPTION | 14 EmissV-0.666.0.0/EmissV/LICENSE | 4 EmissV-0.666.0.0/EmissV/MD5 | 90 EmissV-0.666.0.0/EmissV/NAMESPACE | 46 EmissV-0.666.0.0/EmissV/NEWS.md | 259 - EmissV-0.666.0.0/EmissV/R/EmissV-package.R | 4 EmissV-0.666.0.0/EmissV/R/areaSouce.R | 137 EmissV-0.666.0.0/EmissV/R/emission.R | 499 +- EmissV-0.666.0.0/EmissV/R/emissionfactors.R | 130 EmissV-0.666.0.0/EmissV/R/gridinfo.R | 376 +- EmissV-0.666.0.0/EmissV/R/hourly.R |only EmissV-0.666.0.0/EmissV/R/lineSource.R | 568 +-- EmissV-0.666.0.0/EmissV/R/monthly.R |only EmissV-0.666.0.0/EmissV/R/plumerise.R | 350 +- EmissV-0.666.0.0/EmissV/R/pointSource.R | 200 - EmissV-0.666.0.0/EmissV/R/profile.R | 208 - EmissV-0.666.0.0/EmissV/R/rasterSource.R | 184 - EmissV-0.666.0.0/EmissV/R/read.R | 1743 +++++----- EmissV-0.666.0.0/EmissV/R/speciation.R | 94 EmissV-0.666.0.0/EmissV/R/species.R | 218 - EmissV-0.666.0.0/EmissV/R/totalEmission.R | 134 EmissV-0.666.0.0/EmissV/R/vehicles.R | 254 - EmissV-0.666.0.0/EmissV/build/partial.rdb |binary EmissV-0.666.0.0/EmissV/data/hourly.rda |only EmissV-0.666.0.0/EmissV/data/monthly.rda |only EmissV-0.666.0.0/EmissV/inst/CITATION | 56 EmissV-0.666.0.0/EmissV/man/EmissV-package.Rd | 60 EmissV-0.666.0.0/EmissV/man/areaSource.Rd | 90 EmissV-0.666.0.0/EmissV/man/emission.Rd | 163 EmissV-0.666.0.0/EmissV/man/figures/blue_logo.png |only EmissV-0.666.0.0/EmissV/man/gridInfo.Rd | 104 EmissV-0.666.0.0/EmissV/man/hourly.Rd |only EmissV-0.666.0.0/EmissV/man/lineSource.Rd | 144 EmissV-0.666.0.0/EmissV/man/monthly.Rd |only EmissV-0.666.0.0/EmissV/man/pointSource.Rd | 78 EmissV-0.666.0.0/EmissV/man/rasterSource.Rd | 80 EmissV-0.666.0.0/EmissV/man/read.Rd | 264 - EmissV-0.666.0.0/EmissV/tests/testthat.R | 8 EmissV-0.666.0.0/EmissV/tests/testthat/test-EmissionFactors.R | 26 EmissV-0.666.0.0/EmissV/tests/testthat/test-areaSource.R | 40 EmissV-0.666.0.0/EmissV/tests/testthat/test-emission.R | 130 EmissV-0.666.0.0/EmissV/tests/testthat/test-gridInfo.R | 12 EmissV-0.666.0.0/EmissV/tests/testthat/test-lineSource.R | 28 EmissV-0.666.0.0/EmissV/tests/testthat/test-pointSource.R | 70 EmissV-0.666.0.0/EmissV/tests/testthat/test-rasterSource.R | 22 EmissV-0.666.0.0/EmissV/tests/testthat/test-read.R | 12 EmissV-0.666.0.0/EmissV/tests/testthat/test-speciation.R | 46 EmissV-0.666.0.0/EmissV/tests/testthat/test-totalEmission.R | 28 EmissV-0.666.0.0/EmissV/tests/testthat/test-vehicles.R | 10 50 files changed, 3539 insertions(+), 3444 deletions(-)
Title: Bayesian Power Analysis Using 'brms' and 'INLA'
Description: Provides tools for Bayesian power analysis and assurance calculations using the statistical frameworks of 'brms' and 'INLA'. Includes simulation-based approaches, support for multiple decision rules (direction, threshold, ROPE), sequential designs, and visualisation helpers. Methods are based on Kruschke (2014, ISBN:9780124058880) "Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan", O'Hagan & Stevens (2001) <doi:10.1177/0272989X0102100307> "Bayesian Assessment of Sample Size for Clinical Trials of Cost-Effectiveness", Kruschke (2018) <doi:10.1177/2515245918771304> "Rejecting or Accepting Parameter Values in Bayesian Estimation", Rue et al. (2009) <doi:10.1111/j.1467-9868.2008.00700.x> "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations", and Bürkner (2017) <doi:10.18637/jss.v080.i01> "brms: An R Package for Bayesian Multilevel Models using Stan".
Author: Tony Myers [aut, cre]
Maintainer: Tony Myers <admyers@aol.com>
Diff between powerbrmsINLA versions 1.0.0 dated 2025-09-01 and 1.1.1 dated 2025-11-16
DESCRIPTION | 15 MD5 | 48 +- NAMESPACE | 6 NEWS.md |only R/added_plotting_functions.R | 121 +++-- R/decision-helpers.R |only R/engine-main.R | 366 +++++++----------- R/engine-sequential.R | 2 R/engine-two-stage.R | 2 R/globals.R | 6 R/plotting-bf.R | 346 +++++++++++------ R/plotting-power.R | 112 ++++- R/plotting-precision.R | 295 ++++++++++---- R/plotting-robustness.R | 8 R/utils-plotting.R |only R/wrapper-brms-inla-power.R |only README.md | 35 - man/add_decision_overlay.Rd |only man/brms_inla_power.Rd | 47 -- man/brms_inla_power_design.Rd |only man/brms_inla_power_parallel.Rd |only man/brms_inla_power_sequential.Rd | 2 man/brms_inla_power_two_stage.Rd | 2 man/decide_sample_size.Rd |only man/dot-plot_decision_assurance_curve_from_summary.Rd |only man/plot_bf_assurance_curve.Rd | 37 - man/plot_bf_assurance_curve_smooth.Rd |only man/plot_power_contour.Rd | 5 man/plot_power_heatmap.Rd | 2 man/plot_precision_fan_chart.Rd | 40 + 30 files changed, 870 insertions(+), 627 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.6 dated 2025-10-29 and 1.0.7 dated 2025-11-16
DESCRIPTION | 8 +++---- MD5 | 4 +-- R/MapperAlgo.R | 59 +++++++++++++++++++++++++++++---------------------------- 3 files changed, 37 insertions(+), 34 deletions(-)
Title: Bayesian Seemingly Unrelated Regression Models in
High-Dimensional Settings
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 2.3-0 dated 2025-03-27 and 2.3-1 dated 2025-11-16
DESCRIPTION | 7 MD5 | 26 +- NAMESPACE | 8 NEWS.md | 6 R/BayesSUR.R | 3 R/plotEstimator.R | 17 + R/plotNetwork.R | 376 +++++++++++++++++++++++---------------- README.md | 3 build/vignette.rds |binary data/exampleGDSC.rda |binary inst/doc/BayesSUR-RE.R | 442 +++++++++++++++++++++++----------------------- inst/doc/BayesSUR-RE.html | 5 man/plotNetwork.Rd | 37 ++- src/HRR_Chain.cpp | 8 14 files changed, 520 insertions(+), 418 deletions(-)
Title: Hydraulic Engineering Tools
Description: The 'hydReng' package provides a set of functions for hydraulic engineering tasks and natural hazard assessments. It includes basic hydraulics (wetted area, wetted perimeter, flow, flow velocity, flow depth, and maximum flow) for open channels with arbitrary geometry under uniform flow conditions. For structures such as circular pipes, weirs, and gates, the package includes calculations for pressure flow, backwater depth, and overflow over a weir crest. Additionally, it provides formulas for calculating bedload transport. The formulas used can be found in standard literature on hydraulics, such as Bollrich (2019, ISBN:978-3-410-29169-5) or Hager (2011, ISBN:978-3-642-77430-0).
Author: Galatioto Niccolo [cre, aut],
Buehlmann Marius [aut],
HOLINGER AG [cph, fnd]
Maintainer: Galatioto Niccolo <niccolo.galatioto@gmail.com>
Diff between hydReng versions 0.1.0 dated 2025-01-09 and 1.0.0 dated 2025-11-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++++++++-- NAMESPACE | 12 ++++++++++++ R/River_Engineering.R |only R/scour.R |only README.md |only man/block_size.Rd |only man/filterlayer.Rd |only man/scour_curve.Rd |only man/scour_groyne.Rd |only man/scour_horz.Rd |only man/scour_vert.Rd |only man/shear_str.Rd |only man/wt_sup.Rd |only tests/testthat/test-block_size.R |only tests/testthat/test-filterlayer.R |only tests/testthat/test-scour.R |only tests/testthat/test-shear_stress.R |only tests/testthat/test-wt_sup.R |only 19 files changed, 34 insertions(+), 6 deletions(-)
Title: Create Data Frames for Exchange and Reuse
Description: The 'dataset' package helps create semantically rich,
machine-readable, and interoperable datasets in R. It extends tidy
data frames with metadata that preserves meaning, improves
interoperability, and makes datasets easier to publish, exchange,
and reuse in line with ISO and W3C standards.
Author: Daniel Antal [aut, cre] ,
Marcelo Perlin [rev] ,
Anna Marta Mester [rev] ,
Mauro Lepore [rev]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Diff between dataset versions 0.4.0 dated 2025-08-26 and 0.4.1 dated 2025-11-16
dataset-0.4.0/dataset/man/vec_cast.double.haven_labelled_defined.Rd |only dataset-0.4.1/dataset/DESCRIPTION | 16 dataset-0.4.1/dataset/MD5 | 85 ++- dataset-0.4.1/dataset/NAMESPACE | 11 dataset-0.4.1/dataset/NEWS.md | 29 + dataset-0.4.1/dataset/R/as.Date.R |only dataset-0.4.1/dataset/R/as.POSIXct.R |only dataset-0.4.1/dataset/R/as.data.frame.R |only dataset-0.4.1/dataset/R/as_character.R | 75 +-- dataset-0.4.1/dataset/R/as_factor.R | 62 +- dataset-0.4.1/dataset/R/as_logical.R |only dataset-0.4.1/dataset/R/as_numeric.R | 111 +--- dataset-0.4.1/dataset/R/defined.R | 244 +++++++--- dataset-0.4.1/dataset/R/dublincore.R | 2 dataset-0.4.1/dataset/R/haven_labelled_defined.R |only dataset-0.4.1/dataset/README.md | 30 - dataset-0.4.1/dataset/inst/CITATION | 10 dataset-0.4.1/dataset/inst/WORDLIST | 4 dataset-0.4.1/dataset/inst/doc/bibrecord.html | 5 dataset-0.4.1/dataset/inst/doc/dataset_df.R | 10 dataset-0.4.1/dataset/inst/doc/dataset_df.Rmd | 54 +- dataset-0.4.1/dataset/inst/doc/dataset_df.html | 177 ++++--- dataset-0.4.1/dataset/inst/doc/defined.R | 19 dataset-0.4.1/dataset/inst/doc/defined.Rmd | 73 ++ dataset-0.4.1/dataset/inst/doc/defined.html | 89 +++ dataset-0.4.1/dataset/inst/doc/design.html | 19 dataset-0.4.1/dataset/inst/doc/introduction.R | 26 - dataset-0.4.1/dataset/inst/doc/introduction.Rmd | 38 + dataset-0.4.1/dataset/inst/doc/introduction.html | 83 ++- dataset-0.4.1/dataset/inst/doc/rdf.html | 26 - dataset-0.4.1/dataset/man/as.Date.haven_labelled_defined.Rd |only dataset-0.4.1/dataset/man/as.POSIXct.haven_labelled_defined.Rd |only dataset-0.4.1/dataset/man/as.data.frame.dataset_df.Rd |only dataset-0.4.1/dataset/man/as_character.Rd | 56 +- dataset-0.4.1/dataset/man/as_factor.Rd | 76 +-- dataset-0.4.1/dataset/man/as_logical.Rd |only dataset-0.4.1/dataset/man/as_numeric.Rd | 54 -- dataset-0.4.1/dataset/man/as_tibble.dataset_df.Rd |only dataset-0.4.1/dataset/man/defined.Rd | 91 ++- dataset-0.4.1/dataset/man/haven_labelled_defined.Rd |only dataset-0.4.1/dataset/man/print.haven_labelled_defined.Rd |only dataset-0.4.1/dataset/tests/testthat/test-as.Date.R |only dataset-0.4.1/dataset/tests/testthat/test-as.POSIXct.R |only dataset-0.4.1/dataset/tests/testthat/test-as.data.frame.R |only dataset-0.4.1/dataset/tests/testthat/test-as_character.R | 96 +++ dataset-0.4.1/dataset/tests/testthat/test-as_factor.R | 121 ++++ dataset-0.4.1/dataset/tests/testthat/test-as_logical.R |only dataset-0.4.1/dataset/tests/testthat/test-as_numeric.R | 194 +++++++ dataset-0.4.1/dataset/tests/testthat/test-defined.R | 47 + dataset-0.4.1/dataset/vignettes/dataset_df.Rmd | 54 +- dataset-0.4.1/dataset/vignettes/defined.Rmd | 73 ++ dataset-0.4.1/dataset/vignettes/introduction.Rmd | 38 + 52 files changed, 1657 insertions(+), 541 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.5.0 dated 2025-11-05 and 3.5.1 dated 2025-11-16
DESCRIPTION | 8 +++---- MD5 | 17 ++++++++-------- R/opal.R | 41 +++++++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/datashield-admin.html | 4 +-- inst/doc/opal-files.html | 4 +-- inst/doc/opal-projects.html | 4 +-- inst/doc/opal-rsession.html | 4 +-- man/dot-extractOpalCSRFToken.Rd |only man/opalr-package.Rd | 2 - 10 files changed, 52 insertions(+), 32 deletions(-)
Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.4.0 dated 2025-07-08 and 0.5.0 dated 2025-11-16
OmopViewer-0.4.0/OmopViewer/inst/logos/hds_logo_noline.svg |only OmopViewer-0.5.0/OmopViewer/DESCRIPTION | 10 OmopViewer-0.5.0/OmopViewer/MD5 | 53 - OmopViewer-0.5.0/OmopViewer/NAMESPACE | 1 OmopViewer-0.5.0/OmopViewer/NEWS.md |only OmopViewer-0.5.0/OmopViewer/R/appDynamic.R | 11 OmopViewer-0.5.0/OmopViewer/R/appStatic.R | 16 OmopViewer-0.5.0/OmopViewer/R/buttons.R | 44 - OmopViewer-0.5.0/OmopViewer/R/createServer.R | 26 OmopViewer-0.5.0/OmopViewer/R/createUi.R | 46 + OmopViewer-0.5.0/OmopViewer/R/defaultPanels.R | 24 OmopViewer-0.5.0/OmopViewer/R/sysdata.rda |binary OmopViewer-0.5.0/OmopViewer/R/theme.R | 87 ++ OmopViewer-0.5.0/OmopViewer/R/utilities.R | 8 OmopViewer-0.5.0/OmopViewer/data/omopViewerPanels.rda |binary OmopViewer-0.5.0/OmopViewer/data/omopViewerResults.rda |binary OmopViewer-0.5.0/OmopViewer/inst/brand |only OmopViewer-0.5.0/OmopViewer/inst/doc/dynamic_app.R | 2 OmopViewer-0.5.0/OmopViewer/inst/doc/edit_static_content.R | 4 OmopViewer-0.5.0/OmopViewer/inst/doc/edit_static_content.html | 6 OmopViewer-0.5.0/OmopViewer/inst/doc/export_static_app.R | 22 OmopViewer-0.5.0/OmopViewer/inst/doc/export_static_app.html | 332 +++++----- OmopViewer-0.5.0/OmopViewer/inst/functions.R | 5 OmopViewer-0.5.0/OmopViewer/man/exportStaticApp.Rd | 4 OmopViewer-0.5.0/OmopViewer/man/omopViewerThemes.Rd |only OmopViewer-0.5.0/OmopViewer/man/panelDetailsFromResult.Rd | 5 OmopViewer-0.5.0/OmopViewer/tests/testthat/test-appStatic.R | 34 - 27 files changed, 440 insertions(+), 300 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.1.5 dated 2025-03-24 and 2.2.0 dated 2025-11-16
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/pr.R | 2 +- build/vignette.rds |binary configure | 2 +- inst/doc/gert.html | 22 +++++++++++----------- src/Makevars.win | 6 +++++- tests/testthat/test-commit.R | 3 ++- tests/testthat/test-merge.R | 13 +++++++------ tools/winlibs.R | 6 +++--- 11 files changed, 49 insertions(+), 39 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.1 dated 2025-11-06 and 0.2.2 dated 2025-11-16
DESCRIPTION | 12 - MD5 | 130 +++++++++------ NAMESPACE | 38 ++++ NEWS.md | 359 ++++++++++++++++++++++-------------------- R/RcppExports.R | 15 + R/ipcw.R | 86 +++++----- R/ipe.R | 97 ++++++----- R/liferegr.R | 51 ----- R/logisregr.R | 49 ----- R/msm.R | 84 +++++---- R/phregr.R | 62 +------ R/plot.ipcw.R |only R/plot.ipe.R |only R/plot.msm.R |only R/plot.rpsftm.R |only R/plot.tsegest.R |only R/plot.tsesimp.R |only R/print.ipcw.R |only R/print.ipe.R |only R/print.liferegr.R | 28 +-- R/print.logisregr.R | 28 +-- R/print.msm.R |only R/print.phregr.R | 26 +-- R/print.rpsftm.R |only R/print.tsegest.R |only R/print.tsesimp.R |only R/residuals_liferegr.R | 23 +- R/residuals_phregr.R | 23 +- R/rpsftm.R | 114 +++++++------ R/survfit_phregr.R | 15 + R/trtswitch-package.R | 9 - R/tsegest.R | 135 +++++++++------ R/tsesimp.R | 83 +++++---- inst/doc/rpsftm.R | 2 inst/doc/rpsftm.Rmd | 2 inst/doc/rpsftm.html | 2 inst/doc/tsegest.R | 3 inst/doc/tsegest.Rmd | 6 inst/doc/tsegest.html | 18 +- man/ipcw.Rd | 32 --- man/ipe.Rd | 40 +--- man/liferegr.Rd | 16 - man/logisregr.Rd | 16 - man/lrtest.Rd | 8 man/msm.Rd | 30 --- man/phregr.Rd | 19 -- man/plot.ipcw.Rd |only man/plot.ipe.Rd |only man/plot.msm.Rd |only man/plot.rpsftm.Rd |only man/plot.tsegest.Rd |only man/plot.tsesimp.Rd |only man/print.ipcw.Rd |only man/print.ipe.Rd |only man/print.msm.Rd |only man/print.rpsftm.Rd |only man/print.tsegest.Rd |only man/print.tsesimp.Rd |only man/rpsftm.Rd | 56 ++---- man/tsegest.Rd | 66 +++---- man/tsesimp.Rd | 34 +-- src/RcppExports.cpp | 9 - src/ipcw.cpp | 172 ++++++++++++++++---- src/ipe.cpp | 158 ++++++++++++++---- src/msm.cpp | 146 +++++++++++++---- src/recensor_sim_rpsftm.cpp | 4 src/rpsftm.cpp | 216 +++++++++++++++++-------- src/survival_analysis.cpp | 66 ++++++- src/survival_analysis.h | 1 src/tsegest.cpp | 333 +++++++++++++++++++++++++------------- src/tsesimp.cpp | 231 ++++++++++++++++++++------- src/utilities.cpp | 61 +++++-- src/utilities.h | 4 tests/testthat.R | 16 - tests/testthat/test-rpsftm.R | 2 tests/testthat/test-tsegest.R | 3 vignettes/rpsftm.Rmd | 2 vignettes/tsegest.Rmd | 6 78 files changed, 1944 insertions(+), 1303 deletions(-)
Title: Functions to Efficiently Simulate and Evaluate NFL Seasons
Description: A set of functions to simulate National Football League
seasons including the sophisticated tie-breaking procedures.
Author: Sebastian Carl [cre, aut, cph],
Lee Sharpe [aut]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflseedR versions 2.0.1 dated 2025-08-18 and 2.0.2 dated 2025-11-16
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- R/nflseedR-package.R | 3 +++ R/standings_prettify.R | 4 ++-- R/summary_nflseedR.R | 2 +- R/utils.R | 3 +-- README.md | 7 +++---- man/nfl_standings_prettify.Rd | 4 ++-- man/summary.nflseedR_simulation.Rd | 2 +- 10 files changed, 31 insertions(+), 26 deletions(-)
Title: Add Standardized Regression Coefficients to Linear-Model-Objects
Description: Adds standardized regression coefficients to objects created by 'lm'. Also extends the S3 methods 'print', 'summary' and 'coef' with additional boolean argument 'standardized' and provides 'xtable'-support.
Author: Stefan Behrendt [aut, cre]
Maintainer: Stefan Behrendt <r@behrendt-stefan.de>
Diff between lm.beta versions 1.7-2 dated 2023-03-12 and 1.7-3 dated 2025-11-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ build/vignette.rds |binary inst/doc/comparison.R | 12 ++++++------ inst/doc/comparison.pdf |binary inst/doc/implementation.pdf |binary man/xtable.lm.beta.Rd | 18 +++++++++--------- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: Investigating the Functional Characteristics of Selected
Variants and Their Vicinity Genomic Region
Description: To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 0.2.6.0 dated 2023-01-12 and 1.4.0 dated 2025-11-16
SNPannotator-0.2.6.0/SNPannotator/R/CADD.R |only SNPannotator-0.2.6.0/SNPannotator/R/checkReturnedVariantData.R |only SNPannotator-0.2.6.0/SNPannotator/R/codes.R |only SNPannotator-0.2.6.0/SNPannotator/R/getGeneFile.R |only SNPannotator-0.2.6.0/SNPannotator/R/getVariantData.R |only SNPannotator-0.2.6.0/SNPannotator/R/returnVariantDatatable.R |only SNPannotator-0.2.6.0/SNPannotator/inst/extdata/cytoband_GRCh37.rds |only SNPannotator-0.2.6.0/SNPannotator/man/LDlist.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/annotate.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/listDatabases.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/pingServer.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/releaseVersion.Rd |only SNPannotator-1.4.0/SNPannotator/DESCRIPTION | 26 SNPannotator-1.4.0/SNPannotator/MD5 | 70 SNPannotator-1.4.0/SNPannotator/NAMESPACE | 42 SNPannotator-1.4.0/SNPannotator/R/aaa.R |only SNPannotator-1.4.0/SNPannotator/R/annotate_shiny.R |only SNPannotator-1.4.0/SNPannotator/R/cadd_functions.R |only SNPannotator-1.4.0/SNPannotator/R/configFile_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/data_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/demo.R |only SNPannotator-1.4.0/SNPannotator/R/ensembl_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/eqtl_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/eqtl_graph_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/fgrepo_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/getVariantLDs.R | 303 ++ SNPannotator-1.4.0/SNPannotator/R/gwascat_graph_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/inSilicoSeqPipeline.R | 104 - SNPannotator-1.4.0/SNPannotator/R/join_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/logger_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/misc_files.R |only SNPannotator-1.4.0/SNPannotator/R/parse_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/runPipelineOnlist.R | 1017 ++++++++-- SNPannotator-1.4.0/SNPannotator/R/stringDB_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/string_network.R |only SNPannotator-1.4.0/SNPannotator/R/zzz.R | 76 SNPannotator-1.4.0/SNPannotator/build |only SNPannotator-1.4.0/SNPannotator/inst/doc |only SNPannotator-1.4.0/SNPannotator/inst/extdata/cytoband_grch37.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/cytoband_grch38.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/demo_config.ini |only SNPannotator-1.4.0/SNPannotator/inst/extdata/demo_input.txt |only SNPannotator-1.4.0/SNPannotator/inst/extdata/gene_names_grch37.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/gene_names_grch38.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/inSilicoSeqConfig.ini |only SNPannotator-1.4.0/SNPannotator/inst/rmd/style.css | 18 SNPannotator-1.4.0/SNPannotator/inst/rmd/variantReport.Rmd | 582 +++-- SNPannotator-1.4.0/SNPannotator/man/EnsemblDatabases.Rd |only SNPannotator-1.4.0/SNPannotator/man/EnsemblReleases.Rd |only SNPannotator-1.4.0/SNPannotator/man/annotate_shiny.Rd |only SNPannotator-1.4.0/SNPannotator/man/demo_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/man/findGenomicPos.Rd |only SNPannotator-1.4.0/SNPannotator/man/findPairwiseLD.Rd |only SNPannotator-1.4.0/SNPannotator/man/findProxy.Rd |only SNPannotator-1.4.0/SNPannotator/man/findRSID.Rd |only SNPannotator-1.4.0/SNPannotator/man/getConfigFile.Rd |only SNPannotator-1.4.0/SNPannotator/man/mergeResultFiles.Rd |only SNPannotator-1.4.0/SNPannotator/man/pingEnsembl.Rd |only SNPannotator-1.4.0/SNPannotator/man/run_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/man/run_stringdb_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/vignettes |only 61 files changed, 1798 insertions(+), 440 deletions(-)
Title: Twang Causal Mediation Modeling via Weighting
Description: Provides functions for estimating natural direct and indirect effects for mediation analysis. It uses weighting where the weights are functions of estimates of the probability of exposure or treatment assignment (Hong, G (2010). <https://cepa.stanford.edu/sites/default/files/workshops/GH_JSM%20Proceedings%202010.pdf> Huber, M. (2014). <doi:10.1002/jae.2341>). Estimation of probabilities can use generalized boosting or logistic regression. Additional functions provide diagnostics of the model fit and weights. The vignette provides details and examples.
Author: Dan McCaffrey [aut, cre],
Katherine Castellano [aut],
Donna Coffman [aut],
Brian Vegetabile [aut],
Megan Schuler [aut],
Haoyu Zhou [aut]
Maintainer: Dan McCaffrey <dmccaffrey@ets.org>
Diff between twangMediation versions 1.2 dated 2022-08-16 and 1.2.1 dated 2025-11-16
twangMediation-1.2.1/twangMediation/DESCRIPTION | 17 twangMediation-1.2.1/twangMediation/MD5 | 78 twangMediation-1.2.1/twangMediation/NAMESPACE | 46 twangMediation-1.2.1/twangMediation/NEWS.md |only twangMediation-1.2.1/twangMediation/R/bal.table.mediation.R | 450 +--- twangMediation-1.2.1/twangMediation/R/data.R | 128 - twangMediation-1.2.1/twangMediation/R/desc.effects.R | 64 twangMediation-1.2.1/twangMediation/R/desc.effects.mediation.R | 277 +- twangMediation-1.2.1/twangMediation/R/diag.plot.color.R | 408 ++-- twangMediation-1.2.1/twangMediation/R/dx.wts.mediation.R | 396 ++-- twangMediation-1.2.1/twangMediation/R/makePlotDat.R | 276 +- twangMediation-1.2.1/twangMediation/R/plot.mediation.R | 681 ++++--- twangMediation-1.2.1/twangMediation/R/print.bal.table.mediation.R | 158 - twangMediation-1.2.1/twangMediation/R/print.mediation.R | 228 +- twangMediation-1.2.1/twangMediation/R/summary.mediation.R | 314 +-- twangMediation-1.2.1/twangMediation/R/twangMediation-package.R | 14 twangMediation-1.2.1/twangMediation/R/twang_functions.R | 316 +-- twangMediation-1.2.1/twangMediation/R/utils_mediation.R | 350 +-- twangMediation-1.2.1/twangMediation/R/wgtmed.R | 965 ++++------ twangMediation-1.2.1/twangMediation/build/partial.rdb |only twangMediation-1.2.1/twangMediation/build/vignette.rds |binary twangMediation-1.2.1/twangMediation/inst/doc/twangMediation.pdf |binary twangMediation-1.2.1/twangMediation/inst/doc/twangMediation.pdf.asis |only twangMediation-1.2.1/twangMediation/man/NSDUH_female.Rd | 114 - twangMediation-1.2.1/twangMediation/man/bal.table.mediation.Rd | 90 twangMediation-1.2.1/twangMediation/man/calculate_effects.Rd | 60 twangMediation-1.2.1/twangMediation/man/check_missing.Rd | 38 twangMediation-1.2.1/twangMediation/man/desc.effects.Rd | 86 twangMediation-1.2.1/twangMediation/man/desc.effects.mediation.Rd | 94 twangMediation-1.2.1/twangMediation/man/dx.wts.mediation.Rd | 178 - twangMediation-1.2.1/twangMediation/man/plot.mediation.Rd | 136 - twangMediation-1.2.1/twangMediation/man/print.bal.table.mediation.Rd | 82 twangMediation-1.2.1/twangMediation/man/print.mediation.Rd | 82 twangMediation-1.2.1/twangMediation/man/summary.mediation.Rd | 92 twangMediation-1.2.1/twangMediation/man/swapTxCtrl.Rd | 44 twangMediation-1.2.1/twangMediation/man/tMdat.Rd | 74 twangMediation-1.2.1/twangMediation/man/twangMediation-package.Rd | 50 twangMediation-1.2.1/twangMediation/man/weighted_mean.Rd | 56 twangMediation-1.2.1/twangMediation/man/wgtmed.Rd | 385 +-- twangMediation-1.2.1/twangMediation/vignettes/twangMediation.pdf.asis |only twangMediation-1.2/twangMediation/R/vignettename.R |only twangMediation-1.2/twangMediation/inst/doc/twangMediation.Rnw |only twangMediation-1.2/twangMediation/vignettes/twangMediation.Rnw |only twangMediation-1.2/twangMediation/vignettes/twangMediation_tutorial.pdf |only 44 files changed, 3320 insertions(+), 3507 deletions(-)
More information about twangMediation at CRAN
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Title: Extract and Summarise Data from Published Figures
Description: High-throughput, flexible and reproducible extraction of data from figures in primary research papers. metaDigitise() can extract data and / or automatically calculate summary statistics for users from box plots, bar plots (e.g., mean and errors), scatter plots and histograms.
Author: Joel Pick [aut],
Shinichi Nakagawa [aut],
Daniel Noble [aut, cre]
Maintainer: Daniel Noble <daniel.wa.noble@gmail.com>
Diff between metaDigitise versions 1.0.1 dated 2020-03-13 and 1.0.2 dated 2025-11-16
metaDigitise-1.0.1/metaDigitise/tests |only metaDigitise-1.0.2/metaDigitise/DESCRIPTION | 11 metaDigitise-1.0.2/metaDigitise/MD5 | 38 metaDigitise-1.0.2/metaDigitise/NEWS.md | 12 metaDigitise-1.0.2/metaDigitise/R/edit_metaDigitise.R | 4 metaDigitise-1.0.2/metaDigitise/R/metaDigitise.R | 2 metaDigitise-1.0.2/metaDigitise/README.md | 26 metaDigitise-1.0.2/metaDigitise/build/vignette.rds |binary metaDigitise-1.0.2/metaDigitise/inst/CITATION | 16 metaDigitise-1.0.2/metaDigitise/inst/doc/metaDigitise.html | 510 +++++++++-- metaDigitise-1.0.2/metaDigitise/man/MB_extract.Rd | 10 metaDigitise-1.0.2/metaDigitise/man/group_scatter_extract.Rd | 8 metaDigitise-1.0.2/metaDigitise/man/histogram_extract.Rd | 3 metaDigitise-1.0.2/metaDigitise/man/internal_redraw.Rd | 19 metaDigitise-1.0.2/metaDigitise/man/metaDigitise.Rd | 2 metaDigitise-1.0.2/metaDigitise/man/redraw_calibration.Rd | 10 16 files changed, 534 insertions(+), 137 deletions(-)