Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
Heather Turner [ctb] ,
David Firth [ctb],
Daniel Sabanes Bove [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.9.0 dated 2026-01-21 and 0.9.1 dated 2026-02-09
DESCRIPTION | 15 MD5 | 275 - NAMESPACE | 256 - NEWS.md | 18 R/CrabSatellites.R | 126 R/Crossings.R | 150 R/color_table.R |only R/data.R | 6264 ++++++++++++++++++------------------ R/get_model.R |only R/glmlist.R | 146 R/labeling_points.R |only R/mosaic.glm.R | 718 ++-- R/mosaic3d.R | 15 R/seq_loglm.R | 30 R/split3d.R | 3 R/vcdExtra-package.R | 246 - R/woolf_test.R | 718 ++-- build/partial.rdb |only build/vignette.rds |binary data/Reinis.rda |only demo/00Index | 4 demo/Wong2-3.R | 10 demo/Wong3-1.R | 2 demo/mosaic3d-hec.R | 2 demo/ucb-glm.R | 53 demo/yaish-unidiff.R | 72 inst/WORDLIST | 546 +-- inst/doc/a1-creating.Rmd | 1552 ++++---- inst/doc/a1-creating.html | 9 inst/doc/a2-tests.Rmd | 796 ++-- inst/doc/a2-tests.html | 9 inst/doc/a3-loglinear.Rmd | 508 +- inst/doc/a3-loglinear.html | 9 inst/doc/a4-mosaics.Rmd | 878 ++--- inst/doc/a4-mosaics.html | 11 inst/doc/a5-demo-housing.Rmd | 742 ++-- inst/doc/a5-demo-housing.html | 9 inst/doc/a6-mobility.Rmd | 804 ++-- inst/doc/a6-mobility.html | 9 inst/doc/a7-continuous.Rmd | 440 +- inst/doc/a7-continuous.html | 11 inst/doc/datasets.Rmd | 288 - inst/doc/datasets.html | 11 inst/doc/tidyCats.Rmd | 21 inst/doc/tidyCats.html | 27 inst/extdata/tv.dat | 1650 ++++----- man/Abortion.Rd | 116 man/Accident.Rd | 236 - man/AirCrash.Rd | 136 man/Alligator.Rd | 126 man/Asbestos.Rd | 118 man/Bartlett.Rd | 126 man/Burt.Rd | 104 man/CMHtest.Rd | 444 +- man/Caesar.Rd | 170 man/Cancer.Rd | 78 man/Cormorants.Rd | 156 man/CrabSatellites.Rd | 124 man/Crossings.Rd | 116 man/CyclingDeaths.Rd | 120 man/DaytonSurvey.Rd | 150 man/Depends.Rd | 110 man/Detergent.Rd | 110 man/Donner.Rd | 240 - man/Draft1970.Rd | 136 man/Draft1970table.Rd | 182 - man/Dyke.Rd | 162 man/Fungicide.Rd | 122 man/GKgamma.Rd | 138 man/GSS.Rd | 86 man/Geissler.Rd | 142 man/Gilby.Rd | 112 man/Glass.Rd | 144 man/HLtest.Rd | 226 - man/HairEyePlace.Rd | 112 man/Hauser79.Rd | 314 - man/Heart.Rd | 78 man/Heckman.Rd | 148 man/HospVisits.Rd | 102 man/HouseTasks.Rd | 124 man/Hoyt.Rd | 230 - man/ICU.Rd | 226 - man/JobSat.Rd | 76 man/Kway.Rd | 218 - man/LRstats.Rd | 178 - man/Mammograms.Rd | 80 man/Mental.Rd | 106 man/Mice.Rd | 90 man/Mobility.Rd | 96 man/PhdPubs.Rd | 110 man/Reinis.Rd |only man/ShakeWords.Rd | 90 man/Summarise.Rd | 160 man/TV.Rd | 154 man/Titanicp.Rd | 104 man/Toxaemia.Rd | 138 man/Vietnam.Rd | 100 man/Vote1980.Rd | 94 man/WorkerSat.Rd | 76 man/Yamaguchi87.Rd | 214 - man/blogits.Rd | 148 man/collapse.table.Rd | 218 - man/color_table.Rd |only man/cutfac.Rd | 166 man/datasets.Rd | 156 man/expand.dft.Rd | 134 man/figures/logo-new.jpg |only man/figures/logo-old.png |only man/figures/logo.png |binary man/get_model.Rd |only man/glmlist.Rd | 272 - man/labeling_points.Rd |only man/logLik.loglm.Rd | 160 man/loglin-utilities.Rd | 241 - man/logseries.Rd | 200 - man/mcaplot.Rd | 200 - man/modFit.Rd | 104 man/mosaic.glm.Rd | 490 +- man/mosaic.glmlist.Rd | 332 - man/mosaic3d.Rd | 357 +- man/print.Kappa.Rd | 102 man/seq_loglm.Rd | 211 - man/seq_mosaic.Rd | 180 - man/split3d.Rd | 181 - man/update.xtabs.Rd | 94 man/vcdExtra-package.Rd | 240 - man/woolf_test.Rd | 2 man/zero.test.Rd | 148 tests/testthat.R | 24 tests/testthat/data/adcibc.csv | 464 +- tests/testthat/data/create_adcibc.R | 32 tests/testthat/test-CMHtest.R | 340 - vignettes/a1-creating.Rmd | 1552 ++++---- vignettes/a2-tests.Rmd | 796 ++-- vignettes/a3-loglinear.Rmd | 508 +- vignettes/a4-mosaics.Rmd | 878 ++--- vignettes/a5-demo-housing.Rmd | 742 ++-- vignettes/a6-mobility.Rmd | 804 ++-- vignettes/a7-continuous.Rmd | 440 +- vignettes/apa.csl | 1242 +++---- vignettes/datasets.Rmd | 288 - vignettes/tidyCats.Rmd | 21 vignettes/vcdExtra.bib | 4 vignettes/vignettes.bib | 90 144 files changed, 19048 insertions(+), 18614 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling
techniques or better understand data generating processes. The user
specifies a set of relationships between covariates, and generates
data based on these specifications. The final data sets can represent
data from randomized control trials, repeated measure (longitudinal)
designs, and cluster randomized trials. Missingness can be generated
using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] ,
Jacob Wujciak-Jens [aut]
Maintainer: Keith Goldfeld <keith.goldfeld@nyulangone.org>
Diff between simstudy versions 0.9.1 dated 2025-12-16 and 0.9.2 dated 2026-02-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/clustered.html | 2 +- inst/doc/longitudinal.html | 2 +- tests/testthat/test-generate_correlated_data.R | 8 ++++++-- 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Bayesian Estimation of Probit Unfolding Models for Binary
Preference Data
Description: Bayesian estimation and analysis methods for Probit Unfolding Models (PUMs), a novel class of scaling models designed for binary preference data. These models allow for both monotonic and non-monotonic response functions. The package supports Bayesian inference for both static and dynamic PUMs using Markov chain Monte Carlo (MCMC) algorithms with minimal or no tuning. Key functionalities include posterior sampling, hyperparameter selection, data preprocessing, model fit evaluation, and visualization. The methods are particularly suited to analyzing voting data, such as from the U.S. Congress or Supreme Court, but can also be applied in other contexts where non-monotonic responses are expected. For methodological details, see Shi et al. (2025) <doi:10.48550/arXiv.2504.00423>.
Author: Skylar Shi [aut, cre] ,
Abel Rodriguez [aut] ,
Rayleigh Lei [aut] ,
Jonathan Olmsted [cph]
Maintainer: Skylar Shi <dshi98@uw.edu>
This is a re-admission after prior archival of version 1.0.1 dated 2025-10-22
Diff between pumBayes versions 1.0.1 dated 2025-10-22 and 1.0.2 dated 2026-02-09
DESCRIPTION | 6 ++-- MD5 | 10 +++--- R/scotus.1937.2021.R | 1 README.md | 32 ++++++++++++++++++++- man/scotus.1937.2021.Rd | 1 src/three_utility_probit_helper_functions.cpp | 39 +++++++++++++------------- 6 files changed, 59 insertions(+), 30 deletions(-)
Title: Professional Comprehensive Omics Data Analysis
Description: Provides a comprehensive suite of tools for analyzing omics data. It includes
functionalities for alpha diversity analysis, beta diversity analysis, differential
abundance analysis, community assembly analysis, visualization of phylogenetic tree, and
functional enrichment analysis. With a progressive approach, the package offers a range of
analysis methods to explore and understand the complex communities. It is designed to
support researchers and practitioners in conducting in-depth and professional omics data
analysis.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <bfzede@gmail.com>
Diff between pctax versions 0.1.3 dated 2024-12-02 and 0.1.7 dated 2026-02-09
pctax-0.1.3/pctax/vignettes/pctax_cache/html/lib_edaa109a9155baa43419851f33b3cf81.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/lib_edaa109a9155baa43419851f33b3cf81.rdx |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/setup_8ae11416e5c5639c1c730c1286b53fc5.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/setup_8ae11416e5c5639c1c730c1286b53fc5.rdx |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_a4c6eae63fe4b35c079f4cfe25d48d88.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_a4c6eae63fe4b35c079f4cfe25d48d88.rdx |only pctax-0.1.7/pctax/DESCRIPTION | 41 pctax-0.1.7/pctax/MD5 | 73 pctax-0.1.7/pctax/NAMESPACE | 23 pctax-0.1.7/pctax/NEWS.md | 29 pctax-0.1.7/pctax/R/Rtaxonkit.R | 14 pctax-0.1.7/pctax/R/b_analyse.R | 91 pctax-0.1.7/pctax/R/diff_analyse.R | 117 + pctax-0.1.7/pctax/R/other_software.R | 963 +++++++++- pctax-0.1.7/pctax/R/pctax-package.R | 4 pctax-0.1.7/pctax/R/phylogenetic.R | 226 ++ pctax-0.1.7/pctax/R/stats.R |only pctax-0.1.7/pctax/build/vignette.rds |binary pctax-0.1.7/pctax/inst/doc/pctax.R | 6 pctax-0.1.7/pctax/inst/doc/pctax.html | 3 pctax-0.1.7/pctax/man/ALDEX.Rd | 12 pctax-0.1.7/pctax/man/RDA_plot.Rd | 7 pctax-0.1.7/pctax/man/ann_tree.Rd | 4 pctax-0.1.7/pctax/man/batch_mediate.Rd |only pctax-0.1.7/pctax/man/df2tree.Rd | 4 pctax-0.1.7/pctax/man/df2tree1.Rd | 8 pctax-0.1.7/pctax/man/drop_tips_update.Rd |only pctax-0.1.7/pctax/man/load_mpa_df.Rd |only pctax-0.1.7/pctax/man/multi_bar.Rd | 2 pctax-0.1.7/pctax/man/multi_conf.Rd |only pctax-0.1.7/pctax/man/myRDA.Rd | 1 pctax-0.1.7/pctax/man/pctax-package.Rd | 2 pctax-0.1.7/pctax/man/permanova.Rd | 3 pctax-0.1.7/pctax/man/plot.b_res.Rd | 6 pctax-0.1.7/pctax/man/plot_checkm2_res.Rd |only pctax-0.1.7/pctax/man/plot_contigs_quality.Rd |only pctax-0.1.7/pctax/man/plot_gtdb_tr.Rd |only pctax-0.1.7/pctax/man/plot_one_phage.Rd |only pctax-0.1.7/pctax/man/pre_assembly_stats.Rd |only pctax-0.1.7/pctax/man/pre_format_report.Rd |only pctax-0.1.7/pctax/man/pre_genomad.Rd |only pctax-0.1.7/pctax/man/pre_gtdb_tk.Rd |only pctax-0.1.7/pctax/man/pre_tax_table.Rd | 5 pctax-0.1.7/pctax/man/print.virus_res.Rd |only pctax-0.1.7/pctax/man/stamp_plot.Rd |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/lib_7858f483600c014896211e60e0626680.rdb |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/lib_7858f483600c014896211e60e0626680.rdx |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/setup_35e25c351e84cb5efd95fe39f6eabc01.rdb |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/setup_35e25c351e84cb5efd95fe39f6eabc01.rdx |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_277d2e2f2b7b90d394584184e383ae77.rdb |only pctax-0.1.7/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_277d2e2f2b7b90d394584184e383ae77.rdx |only 51 files changed, 1475 insertions(+), 169 deletions(-)
Title: Network Analysis for Omics Data
Description: Comprehensive network analysis package.
Calculate correlation network fastly, accelerate lots of analysis by parallel computing.
Support for multi-omics data, search sub-nets fluently.
Handle bigger data, more than 10,000 nodes in each omics.
Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize.
Provide comprehensive topology indexes calculation, including ecological network stability.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <bfzede@gmail.com>
Diff between MetaNet versions 0.2.7 dated 2025-06-26 and 0.2.8 dated 2026-02-09
DESCRIPTION | 10 +++---- MD5 | 30 ++++++++++++---------- NAMESPACE | 1 R/1.calculate.R | 60 ++++++++++++++++++++++++++++++++++++++++++++- R/2-2.manipulate.R | 12 +++------ R/2-3.RMT.R | 15 ++++++++--- R/5.topological.R | 7 +++-- R/8.net_compare.R | 4 +-- R/MetaNet-package.R | 1 README.md | 55 ++++++++++------------------------------- build/vignette.rds |binary inst/doc/MetaNet.R | 6 ++-- inst/doc/MetaNet.html | 9 +++--- man/RMT_threshold.Rd | 3 ++ man/figures/MetaNet_GA.jpg |only man/net_par.Rd | 5 +++ man/plot_corr_heatmap.Rd |only 17 files changed, 133 insertions(+), 85 deletions(-)
Title: Grammar of Graphics and Plot Helpers for Time Series
Visualization
Description: Extends the capabilities of 'ggplot2' by providing grammatical
elements and plot helpers designed for visualizing temporal patterns. The
package implements a grammar of temporal graphics, which leverages calendar
structures to highlight changes over time. The package also provides plot
helper functions to quickly produce commonly used time series graphics,
including time plots, season plots, and seasonal sub-series plots.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Cynthia A. Huang [aut] ,
Matthew Kay [aut] ,
Rob Hyndman [aut] ,
Earo Wang [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggtime versions 0.1.0 dated 2025-06-10 and 0.2.0 dated 2026-02-09
ggtime-0.1.0/ggtime/R/cal_wrap.R |only ggtime-0.1.0/ggtime/R/coord-calendar.R |only ggtime-0.1.0/ggtime/R/seq-gen.R |only ggtime-0.1.0/ggtime/tests/testthat/Rplots.pdf |only ggtime-0.2.0/ggtime/DESCRIPTION | 28 ggtime-0.2.0/ggtime/MD5 | 51 ggtime-0.2.0/ggtime/NAMESPACE | 15 ggtime-0.2.0/ggtime/NEWS.md | 15 ggtime-0.2.0/ggtime/R/ggplot-dep.R |only ggtime-0.2.0/ggtime/R/ggtime-package.R | 3 ggtime-0.2.0/ggtime/R/plot-dable.R | 147 +- ggtime-0.2.0/ggtime/R/plot-fable.R |only ggtime-0.2.0/ggtime/R/plot-helpers.R | 706 +++++++---- ggtime-0.2.0/ggtime/R/plot-tsibble.R | 92 - ggtime-0.2.0/ggtime/R/utils.R | 202 ++- ggtime-0.2.0/ggtime/README.md | 55 ggtime-0.2.0/ggtime/man/autoplot.dcmp_ts.Rd | 1 ggtime-0.2.0/ggtime/man/autoplot.fbl_ts.Rd |only ggtime-0.2.0/ggtime/man/autoplot.tbl_cf.Rd |only ggtime-0.2.0/ggtime/man/autoplot.tbl_ts.Rd | 7 ggtime-0.2.0/ggtime/man/figures/README-seasonplot-1.png |binary ggtime-0.2.0/ggtime/man/figures/README-timeplot-1.png |binary ggtime-0.2.0/ggtime/man/figures/README-unnamed-chunk-2-1.png |only ggtime-0.2.0/ggtime/man/figures/logo.svg |only ggtime-0.2.0/ggtime/man/ggtime-package.Rd | 14 ggtime-0.2.0/ggtime/man/scale_cf_lag.Rd |only ggtime-0.2.0/ggtime/tests/testthat/_snaps |only ggtime-0.2.0/ggtime/tests/testthat/helper-vdiffr.R |only ggtime-0.2.0/ggtime/tests/testthat/test-plot-helpers.R | 41 29 files changed, 982 insertions(+), 395 deletions(-)
Title: Probabilities for Pedigrees Given DNA Data
Description: An interface to the core 'Familias' functions which are
programmed in C++. The implementation is described in Egeland, Mostad and Olaisen
(1997) <doi:10.1016/S1355-0306(97)72202-0> and Simonsson and Mostad
(2016) <doi:10.1016/j.fsigen.2016.04.005>.
Author: Petter Mostad [aut],
Thore Egeland [aut],
Franco Marsico [aut, cre],
Ivar Simonsson [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between Familias versions 2.6.3 dated 2025-05-12 and 2.6.4 dated 2026-02-09
DESCRIPTION | 17 MD5 | 36 - NAMESPACE | 20 NEWS.md | 18 R/FamiliasLocus.R | 1246 +++++++++++++++++++++---------------------- R/FamiliasPedigree.R | 62 +- R/FamiliasPosterior.R | 506 ++++++++--------- R/FamiliasPrior.R | 272 ++++----- R/plot.FamiliasPedigree.R | 64 +- README.md | 66 +- man/Familias-package.Rd | 148 ++--- man/FamiliasLocus.Rd | 382 ++++++------- man/FamiliasPedigree.Rd | 162 ++--- man/FamiliasPosterior.Rd | 458 +++++++-------- man/FamiliasPrior.Rd | 176 +++--- man/NorwegianFrequencies.Rd | 78 +- man/plot.FamiliasPedigree.Rd | 102 +-- src/GroupOfPersons.cpp | 23 src/table.cpp | 20 19 files changed, 1936 insertions(+), 1920 deletions(-)
Title: Panel Generalized Linear Models
Description: Estimation of panel models for glm-like models:
this includes binomial models (logit and probit), count models (poisson and negbin)
and ordered models (logit and probit), as described in:
Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7,
Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and
Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between pglm versions 0.2-3 dated 2021-07-19 and 0.2-4 dated 2026-02-09
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ data/Fairness.rda |binary data/HealthIns.rda |binary data/PatentsRD.rda |binary data/PatentsRDUS.rda |binary data/UnionWage.rda |binary man/HealthIns.Rd | 2 +- man/PatentsRD.Rd | 4 ++-- man/PatentsRDUS.Rd | 4 ++-- 11 files changed, 23 insertions(+), 19 deletions(-)
Title: Unconstrained Numerical Optimization Algorithms
Description: Optimization algorithms implemented in R, including
conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the
limited memory BFGS (L-BFGS) methods. Most internal parameters can be set
through the call interface. The solvers hold up quite well for
higher-dimensional problems.
Author: James Melville [aut, cre]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between mize versions 0.2.4 dated 2020-08-30 and 0.2.5 dated 2026-02-09
DESCRIPTION | 9 MD5 | 24 NEWS.md | 9 R/rasmussen.R | 6 build/vignette.rds |binary inst/doc/convergence.html | 547 +++++++++------- inst/doc/mize.Rmd | 8 inst/doc/mize.html | 1225 ++++++++++++++++++++++++------------ inst/doc/mmds.html | 503 ++++++++------ inst/doc/stateful.html | 694 ++++++++++++-------- tests/testthat/test_minfunc_wolfe.R | 14 tests/testthat/test_rasmussen_cg.R | 4 vignettes/mize.Rmd | 8 13 files changed, 1911 insertions(+), 1140 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.7.2 dated 2025-11-03 and 1.8.0 dated 2026-02-09
nanonext-1.7.2/nanonext/inst/CITATION |only nanonext-1.7.2/nanonext/src/mbedtls-362.tar.xz |only nanonext-1.7.2/nanonext/src/nng-111.tar.xz |only nanonext-1.8.0/nanonext/DESCRIPTION | 30 nanonext-1.8.0/nanonext/MD5 | 484 ++++++++ nanonext-1.8.0/nanonext/NAMESPACE | 17 nanonext-1.8.0/nanonext/NEWS.md | 24 nanonext-1.8.0/nanonext/R/aio.R | 17 nanonext-1.8.0/nanonext/R/context.R | 1 nanonext-1.8.0/nanonext/R/dispatcher.R |only nanonext-1.8.0/nanonext/R/ncurl.R | 84 - nanonext-1.8.0/nanonext/R/server.R |only nanonext-1.8.0/nanonext/R/tls.R | 23 nanonext-1.8.0/nanonext/README.md | 289 +---- nanonext-1.8.0/nanonext/build/vignette.rds |binary nanonext-1.8.0/nanonext/cleanup | 2 nanonext-1.8.0/nanonext/cleanup.win | 2 nanonext-1.8.0/nanonext/configure | 241 +--- nanonext-1.8.0/nanonext/configure.ucrt | 22 nanonext-1.8.0/nanonext/configure.win | 30 nanonext-1.8.0/nanonext/inst/doc/nanonext.Rmd | 820 ++++---------- nanonext-1.8.0/nanonext/inst/doc/nanonext.html | 881 +++++++--------- nanonext-1.8.0/nanonext/inst/doc/v01-messaging.Rmd |only nanonext-1.8.0/nanonext/inst/doc/v01-messaging.html |only nanonext-1.8.0/nanonext/inst/doc/v02-protocols.Rmd |only nanonext-1.8.0/nanonext/inst/doc/v02-protocols.html |only nanonext-1.8.0/nanonext/inst/doc/v03-configuration.Rmd |only nanonext-1.8.0/nanonext/inst/doc/v03-configuration.html |only nanonext-1.8.0/nanonext/inst/doc/v04-web.Rmd |only nanonext-1.8.0/nanonext/inst/doc/v04-web.html |only nanonext-1.8.0/nanonext/man/close.Rd | 7 nanonext-1.8.0/nanonext/man/dot-context.Rd | 1 nanonext-1.8.0/nanonext/man/dot-dispatcher.Rd |only nanonext-1.8.0/nanonext/man/format_sse.Rd |only nanonext-1.8.0/nanonext/man/handler.Rd |only nanonext-1.8.0/nanonext/man/handler_directory.Rd |only nanonext-1.8.0/nanonext/man/handler_file.Rd |only nanonext-1.8.0/nanonext/man/handler_inline.Rd |only nanonext-1.8.0/nanonext/man/handler_redirect.Rd |only nanonext-1.8.0/nanonext/man/handler_stream.Rd |only nanonext-1.8.0/nanonext/man/handler_ws.Rd |only nanonext-1.8.0/nanonext/man/http_server.Rd |only nanonext-1.8.0/nanonext/man/ncurl.Rd | 35 nanonext-1.8.0/nanonext/man/ncurl_aio.Rd | 30 nanonext-1.8.0/nanonext/man/ncurl_session.Rd | 30 nanonext-1.8.0/nanonext/man/race_aio.Rd |only nanonext-1.8.0/nanonext/man/tls_config.Rd | 26 nanonext-1.8.0/nanonext/src/Makevars.in | 19 nanonext-1.8.0/nanonext/src/Makevars.ucrt | 19 nanonext-1.8.0/nanonext/src/Makevars.win | 19 nanonext-1.8.0/nanonext/src/aio.c | 208 ++- nanonext-1.8.0/nanonext/src/comms.c | 121 +- nanonext-1.8.0/nanonext/src/core.c | 38 nanonext-1.8.0/nanonext/src/dispatcher.c |only nanonext-1.8.0/nanonext/src/init.c | 16 nanonext-1.8.0/nanonext/src/mbedtls |only nanonext-1.8.0/nanonext/src/nanonext.h | 143 ++ nanonext-1.8.0/nanonext/src/ncurl.c | 128 +- nanonext-1.8.0/nanonext/src/nng |only nanonext-1.8.0/nanonext/src/nng_structs.h |only nanonext-1.8.0/nanonext/src/proto.c | 10 nanonext-1.8.0/nanonext/src/server.c |only nanonext-1.8.0/nanonext/src/sync.c | 6 nanonext-1.8.0/nanonext/src/thread.c | 4 nanonext-1.8.0/nanonext/src/tls.c | 14 nanonext-1.8.0/nanonext/src/utils.c | 6 nanonext-1.8.0/nanonext/tests/tests.R | 722 ++++++++++++- nanonext-1.8.0/nanonext/vignettes/nanonext.Rmd | 820 ++++---------- nanonext-1.8.0/nanonext/vignettes/v01-messaging.Rmd |only nanonext-1.8.0/nanonext/vignettes/v02-protocols.Rmd |only nanonext-1.8.0/nanonext/vignettes/v03-configuration.Rmd |only nanonext-1.8.0/nanonext/vignettes/v04-web.Rmd |only 72 files changed, 3151 insertions(+), 2238 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-7 dated 2025-04-02 and 0.22-9 dated 2026-02-09
ChangeLog | 26 ++++ DESCRIPTION | 11 + MD5 | 165 +++++++++++++++-------------- R/axis.R | 171 ------------------------------- R/panels.R | 4 R/splom.R | 3 inst/doc/grid.pdf |binary inst/po/de/LC_MESSAGES/R-lattice.mo |binary inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary inst/po/fr/LC_MESSAGES/R-lattice.mo |binary inst/po/pl/LC_MESSAGES/R-lattice.mo |binary man/Lattice.Rd | 2 man/Rows.Rd | 2 man/USMortality.Rd | 2 man/axis.default.Rd | 2 man/banking.Rd | 2 man/barchart.table.Rd | 2 man/barley.Rd | 2 man/cloud.Rd | 2 man/draw.colorkey.Rd | 2 man/draw.key.Rd | 2 man/environmental.Rd | 2 man/ethanol.Rd | 2 man/figures |only man/histogram.Rd | 2 man/interaction.Rd | 2 man/lattice.options.Rd | 2 man/latticeParseFormula.Rd | 2 man/level.colors.Rd | 2 man/levelplot.Rd | 2 man/llines.Rd | 2 man/lset.Rd | 2 man/make.groups.Rd | 2 man/melanoma.Rd | 4 man/oneway.Rd | 2 man/packet.panel.default.Rd | 2 man/panel.axis.Rd | 2 man/panel.barchart.Rd | 2 man/panel.bwplot.Rd | 2 man/panel.cloud.Rd | 2 man/panel.densityplot.Rd | 2 man/panel.dotplot.Rd | 2 man/panel.functions.Rd | 2 man/panel.histogram.Rd | 2 man/panel.levelplot.Rd | 2 man/panel.loess.Rd | 2 man/panel.number.Rd | 2 man/panel.pairs.Rd | 2 man/panel.parallel.Rd | 2 man/panel.qqmath.Rd | 2 man/panel.qqmathline.Rd | 2 man/panel.smoothScatter.Rd | 2 man/panel.spline.Rd | 2 man/panel.stripplot.Rd | 2 man/panel.superpose.Rd | 2 man/panel.violin.Rd | 2 man/panel.xyplot.Rd | 2 man/prepanel.default.Rd | 2 man/prepanel.functions.Rd | 2 man/print.trellis.Rd | 2 man/qq.Rd | 2 man/qqmath.Rd | 2 man/rfs.Rd | 2 man/shingles.Rd | 2 man/simpleKey.Rd | 2 man/simpleTheme.Rd | 2 man/singer.Rd | 2 man/splom.Rd | 2 man/standard.theme.Rd | 2 man/strip.default.Rd | 2 man/tmd.Rd | 2 man/trellis.device.Rd | 2 man/trellis.object.Rd | 2 man/trellis.par.get.Rd | 2 man/update.trellis.Rd | 2 man/utilities.3d.Rd | 2 man/xyplot.Rd | 2 man/xyplot.ts.Rd | 2 po/R-de.po | 8 - po/R-fr.po | 8 - po/R-it.po | 5 po/R-ko.po | 5 po/R-lattice.pot | 7 - po/R-pl.po | 12 +- 84 files changed, 207 insertions(+), 352 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut] ,
Christian Kleiber [aut] ,
Achim Zeileis [aut, cre] ,
Nikolas Kuschnig [ctb] ,
R Core Team [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ivreg versions 0.6-5 dated 2025-01-19 and 0.6-6 dated 2026-02-09
DESCRIPTION | 18 - MD5 | 37 +- NAMESPACE | 1 NEWS.md | 29 ++ R/ivreg.R | 12 R/ivreg.fit.R | 61 ++-- R/ivregDiagnostics.R | 3 R/ivregMethods.R | 14 - R/summary.ivreg.R | 10 build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.html | 49 +-- inst/doc/ivreg.R | 8 inst/doc/ivreg.html | 342 ++++++++++---------------- man/ivreg.Rd | 12 man/ivreg.fit.Rd | 2 man/ivregDiagnostics.Rd | 2 man/ivregMethods.Rd | 8 tests/testthat/test-alias.R |only tests/testthat/test-case-deletion.R | 13 tests/testthat/test-stage1.R | 4 20 files changed, 316 insertions(+), 309 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.5.1 dated 2025-10-15 and 1.6 dated 2026-02-09
DESCRIPTION | 8 MD5 | 302 ++-- NAMESPACE | 158 +- NEWS.md | 20 R/data.R | 90 - R/gd.R | 176 +- R/gd_optunidisc.R | 172 +- R/gdverse-package.R | 8 R/geodetector.R | 1190 +++++++++--------- R/globals.R | 30 R/gozh.R | 463 +++---- R/idsa.R | 386 +++--- R/lesh.R | 378 ++--- R/loess_optscale.R | 78 - R/opgd.R | 264 ++-- R/pid_idsa.R | 426 +++--- R/psd_pseudop.R | 286 ++-- R/psd_spade.R | 402 +++--- R/r_interact_py.R | 14 R/rgd.R | 292 ++-- R/rid.R | 168 +- R/robustdisc.R | 92 - R/rpartdisc.R | 62 R/sesu_gozh.R | 378 ++--- R/sesu_opgd.R | 374 ++--- R/spade.R | 320 ++--- R/spd_lesh.R | 228 +-- R/srs_geodetecor.R | 742 +++++------ R/srsgd.R | 192 +-- R/utils.R | 182 +- R/zzz.R | 21 README.md | 4 build/vignette.rds |binary inst/CITATION | 25 inst/doc/gd.Rmd | 862 ++++++------- inst/doc/idsa.Rmd | 2 inst/doc/idsa.html | 2 inst/doc/opgd.Rmd | 432 +++--- inst/doc/opgd.html | 4 inst/doc/rgdrid.Rmd | 166 +- inst/doc/rgdrid.html | 12 inst/doc/sesu.Rmd | 1278 ++++++++++---------- inst/doc/sesu.html | 2 inst/doc/shegd.Rmd | 394 +++--- inst/doc/shegd.html | 42 inst/extdata/Depression.csv | 2146 +++++++++++++++++----------------- inst/python/cpd_disc.py | 106 - man/F_informationloss.Rd | 60 man/NTDs.Rd | 34 man/all2int.Rd | 44 man/cpsd_disc.Rd | 150 +- man/cpsd_spade.Rd | 88 - man/ecological_detector.Rd | 74 - man/factor_detector.Rd | 76 - man/figures/opgd/opgd_plot-1.png |binary man/figures/rgdrid/rgd_id-1.png |binary man/figures/rgdrid/rid_plot-1.png |binary man/gd.Rd | 92 - man/gd_optunidisc.Rd | 112 - man/gen_permutations.Rd | 46 man/geodetector.Rd | 122 - man/gozh.Rd | 102 - man/gozh_detector.Rd | 108 - man/idsa.Rd | 176 +- man/interaction_detector.Rd | 79 - man/lesh.Rd | 96 - man/loess_optscale.Rd | 94 - man/ndvi.Rd | 40 man/opgd.Rd | 144 +- man/pid_idsa.Rd | 74 - man/pipe.Rd | 30 man/plot.ecological_detector.Rd | 44 man/plot.factor_detector.Rd | 62 man/plot.gd_result.Rd | 44 man/plot.gozh_result.Rd | 44 man/plot.idsa_result.Rd | 44 man/plot.interaction_detector.Rd | 48 man/plot.lesh_result.Rd | 100 - man/plot.opgd_result.Rd | 44 man/plot.rgd_result.Rd | 58 man/plot.rid_result.Rd | 48 man/plot.risk_detector.Rd | 44 man/plot.sesu_gozh.Rd | 44 man/plot.sesu_opgd.Rd | 44 man/plot.spade_result.Rd | 60 man/plot.srs_ecological_detector.Rd | 44 man/plot.srs_factor_detector.Rd | 48 man/plot.srs_interaction_detector.Rd | 48 man/plot.srsgd_result.Rd | 44 man/print.ecological_detector.Rd | 44 man/print.factor_detector.Rd | 44 man/print.gd_result.Rd | 44 man/print.gozh_result.Rd | 44 man/print.idsa_result.Rd | 44 man/print.interaction_detector.Rd | 44 man/print.lesh_result.Rd | 44 man/print.opgd_result.Rd | 44 man/print.rgd_result.Rd | 44 man/print.rid_result.Rd | 44 man/print.risk_detector.Rd | 44 man/print.sesu_gozh.Rd | 44 man/print.sesu_opgd.Rd | 44 man/print.spade_result.Rd | 46 man/print.srs_ecological_detector.Rd | 44 man/print.srs_factor_detector.Rd | 44 man/print.srs_interaction_detector.Rd | 44 man/print.srsgd_result.Rd | 44 man/psd_iev.Rd | 80 - man/psd_pseudop.Rd | 92 - man/psd_spade.Rd | 80 - man/psmd_pseudop.Rd | 128 +- man/psmd_spade.Rd | 122 - man/rgd.Rd | 140 +- man/rid.Rd | 136 +- man/risk_detector.Rd | 58 man/robust_disc.Rd | 82 - man/rpart_disc.Rd | 72 - man/sesu_gozh.Rd | 178 +- man/sesu_opgd.Rd | 180 +- man/sim.Rd | 40 man/spade.Rd | 142 +- man/spd_lesh.Rd | 102 - man/srs_ecological_detector.Rd | 88 - man/srs_factor_detector.Rd | 78 - man/srs_geodetector.Rd | 92 - man/srs_interaction_detector.Rd | 92 - man/srs_table.Rd | 34 man/srs_wt.Rd | 34 man/srsgd.Rd | 112 - man/weight_assign.Rd | 52 src/RcppExports.cpp | 27 src/roughset.cpp | 117 - tests/testthat.R | 24 tests/testthat/test-data_type.R | 16 tests/testthat/test-geodetector.R | 14 tests/testthat/test-multicores.R | 18 tests/testthat/test-psd_spade.R | 12 tests/testthat/test-srs_geodetecor.R | 18 vignettes/consistency.Rmd.orig | 76 - vignettes/gd.Rmd | 862 ++++++------- vignettes/gd.Rmd.orig | 414 +++--- vignettes/idsa.Rmd | 2 vignettes/idsa.Rmd.orig | 108 - vignettes/opgd.Rmd | 432 +++--- vignettes/opgd.Rmd.orig | 162 +- vignettes/rgdrid.Rmd | 166 +- vignettes/rgdrid.Rmd.orig | 102 - vignettes/sesu.Rmd | 1278 ++++++++++---------- vignettes/sesu.Rmd.orig | 156 +- vignettes/shegd.Rmd | 394 +++--- vignettes/shegd.Rmd.orig | 192 +-- vignettes/spade.Rmd.orig | 218 +-- 152 files changed, 11999 insertions(+), 11949 deletions(-)
Title: Font Metrics and Font Management Utilities for R Graphics
Description: Compute text metrics (width, ascent, descent) using 'Cairo'
and 'FreeType', independently of the active graphic device. Font
lookup is delegated to 'systemfonts'. Additional utilities let users
register 'Google Fonts' or bundled 'Liberation' fonts, check font
availability, and assemble 'htmlDependency' objects so that fonts are
correctly embedded in 'Shiny' applications, 'R Markdown' documents,
and 'htmlwidgets' outputs such as 'ggiraph'.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.4.4 dated 2025-10-06 and 0.5.0 dated 2026-02-09
gdtools-0.4.4/gdtools/inst/include |only gdtools-0.4.4/gdtools/man/str_extents.Rd |only gdtools-0.4.4/gdtools/src/gdtools.cpp |only gdtools-0.4.4/gdtools/tests/testthat/test-str_extents.R |only gdtools-0.5.0/gdtools/DESCRIPTION | 22 - gdtools-0.5.0/gdtools/MD5 | 93 +++--- gdtools-0.5.0/gdtools/NAMESPACE | 8 gdtools-0.5.0/gdtools/NEWS.md | 31 ++ gdtools-0.5.0/gdtools/R/RcppExports.R | 20 - gdtools-0.5.0/gdtools/R/font-caching.R | 38 +- gdtools-0.5.0/gdtools/R/font_family_exists.R | 34 +- gdtools-0.5.0/gdtools/R/font_set.R |only gdtools-0.5.0/gdtools/R/fontconfig.R | 13 gdtools-0.5.0/gdtools/R/fonts.R | 44 ++- gdtools-0.5.0/gdtools/R/gdtools.R | 11 gdtools-0.5.0/gdtools/R/liberation.R | 85 ++++- gdtools-0.5.0/gdtools/R/str-metrics.R | 159 ++++++----- gdtools-0.5.0/gdtools/R/sysdata.rda |binary gdtools-0.5.0/gdtools/README.md | 185 +++++++++---- gdtools-0.5.0/gdtools/man/addGFontHtmlDependency.Rd | 2 gdtools-0.5.0/gdtools/man/dummy_setup.Rd | 9 gdtools-0.5.0/gdtools/man/font_family_exists.Rd | 12 gdtools-0.5.0/gdtools/man/font_google.Rd |only gdtools-0.5.0/gdtools/man/font_liberation.Rd |only gdtools-0.5.0/gdtools/man/font_set.Rd |only gdtools-0.5.0/gdtools/man/font_set_auto.Rd |only gdtools-0.5.0/gdtools/man/font_set_liberation.Rd |only gdtools-0.5.0/gdtools/man/fonts_cache_dir.Rd | 2 gdtools-0.5.0/gdtools/man/liberationmonoHtmlDependency.Rd | 2 gdtools-0.5.0/gdtools/man/liberationsansHtmlDependency.Rd | 2 gdtools-0.5.0/gdtools/man/liberationserifHtmlDependency.Rd | 2 gdtools-0.5.0/gdtools/man/m_str_extents.Rd | 23 + gdtools-0.5.0/gdtools/man/match_family.Rd | 5 gdtools-0.5.0/gdtools/man/register_gfont.Rd | 2 gdtools-0.5.0/gdtools/man/register_liberationmono.Rd | 14 gdtools-0.5.0/gdtools/man/register_liberationsans.Rd | 14 gdtools-0.5.0/gdtools/man/register_liberationserif.Rd | 14 gdtools-0.5.0/gdtools/man/str_metrics.Rd | 26 + gdtools-0.5.0/gdtools/man/strings_sizes.Rd | 22 + gdtools-0.5.0/gdtools/man/sys_fonts.Rd | 7 gdtools-0.5.0/gdtools/man/version_cairo.Rd | 12 gdtools-0.5.0/gdtools/src/CairoContext.cpp | 37 -- gdtools-0.5.0/gdtools/src/Makevars.in | 2 gdtools-0.5.0/gdtools/src/Makevars.win | 4 gdtools-0.5.0/gdtools/src/RcppExports.cpp | 162 ----------- gdtools-0.5.0/gdtools/src/font_metrics.cpp | 62 ++-- gdtools-0.5.0/gdtools/src/gdtools_types.h |only gdtools-0.5.0/gdtools/tests/testthat/helper-fontconfig.R | 8 gdtools-0.5.0/gdtools/tests/testthat/test-font-set.R |only gdtools-0.5.0/gdtools/tests/testthat/test-fonts.R | 33 ++ gdtools-0.5.0/gdtools/tests/testthat/test-str_metrics.R | 54 +++ gdtools-0.5.0/gdtools/tests/testthat/test-utils.R | 13 52 files changed, 772 insertions(+), 516 deletions(-)
Title: Evidence Accumulation Models
Description: Simulation-based evidence accumulation models for analyzing responses
and reaction times in single- and multi-response tasks. The package includes
simulation engines for five representative models: the Diffusion Decision
Model (DDM), Leaky Competing Accumulator (LCA), Linear Ballistic Accumulator
(LBA), Racing Diffusion Model (RDM), and Levy Flight Model (LFM), and
extends these frameworks to multi-response settings. The package supports
user-defined functions for item-level parameterization and the incorporation
of covariates, enabling flexible customization and the development of new
model variants based on existing architectures. Inference is performed using
simulation-based methods, including Approximate Bayesian Computation (ABC)
and Amortized Bayesian Inference (ABI), which allow parameter estimation
without requiring tractable likelihood functions. In addition to core
inference tools, the package provides modules for parameter recovery,
posterior predictive checks, and model com [...truncated...]
Author: Guangyu Zhu [aut] ,
Guang Yang [aut, cre]
Maintainer: Guang Yang <guang.spike.yang@gmail.com>
Diff between eam versions 1.0.1 dated 2026-01-17 and 1.1.0 dated 2026-02-09
eam-1.0.1/eam/README.md |only eam-1.1.0/eam/DESCRIPTION | 10 ++-- eam-1.1.0/eam/MD5 | 22 ++++++---- eam-1.1.0/eam/NAMESPACE | 1 eam-1.1.0/eam/NEWS.md |only eam-1.1.0/eam/R/abi_input.R |only eam-1.1.0/eam/R/plot_posterior_parameters.R | 54 ++++++++++++++++++------- eam-1.1.0/eam/R/plot_rt.R | 16 +++++-- eam-1.1.0/eam/R/simulation.R | 8 ++- eam-1.1.0/eam/R/summarise_by.R | 5 +- eam-1.1.0/eam/man/build_abi_input.Rd |only eam-1.1.0/eam/man/build_abi_input.Z.Rd |only eam-1.1.0/eam/man/build_abi_input.theta.Rd |only eam-1.1.0/eam/man/plot_posterior_parameters.Rd | 11 ++++- eam-1.1.0/eam/man/plot_rt.Rd | 6 ++ 15 files changed, 94 insertions(+), 39 deletions(-)