Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.8.4 dated 2025-10-02 and 0.8.7 dated 2025-11-09
DESCRIPTION | 8 +-- MD5 | 40 ++++++++--------- NAMESPACE | 3 - R/methods.R | 30 ++++--------- R/methods_DEPRECATED.R | 6 +- README.md | 26 +++++------ build/stage23.rdb |binary inst/NEWS.rd | 6 ++ inst/doc/figures_article.html | 2 inst/doc/introduction.R | 2 inst/doc/introduction.html | 83 ++++++++++++++++++------------------- man/figures/pc_plot-1.png |binary man/figures/plot1-1.png |binary man/figures/plot2-1.png |binary man/figures/unnamed-chunk-15-1.png |binary man/fragments/intro.Rmd | 4 - man/join_features.Rd | 2 man/join_transcripts.Rd | 2 man/plotly.Rd | 2 man/tidy.Rd | 19 +++----- tests/testthat/test-methods.R | 8 +++ 21 files changed, 121 insertions(+), 122 deletions(-)
Title: Robust Sufficient Dimension Reduction
Description: A novel sufficient-dimension reduction method is robust against outliers using alpha-distance covariance and manifold-learning in dimensionality reduction problems. Please refer Hsin-Hsiung Huang, Feng Yu & Teng Zhang (2024) <doi:10.1080/10485252.2024.2313137> for the details.
Author: Sheau-Chiann Chen [aut, cre] ,
Shilin Zhao [aut],
Hsin-Hsiung Bill Huang [aut]
Maintainer: Sheau-Chiann Chen <sheau-chiann.chen.1@vumc.org>
Diff between rSDR versions 1.0.2.1 dated 2025-10-28 and 1.0.3.0 dated 2025-11-09
DESCRIPTION | 14 +- MD5 | 22 ++-- R/cost_fun_esting.R | 20 ++-- R/optimal_alpha_boot.R | 5 - R/optimal_alpha_cv.R | 2 R/rSDR.R | 38 +++++--- inst/doc/rSDR_vignette.R | 28 ++--- inst/doc/rSDR_vignette.Rmd | 37 +++---- inst/doc/rSDR_vignette.html | 208 +++++++++++++++++++++----------------------- man/optimal_alpha_boot.Rd | 3 man/optimal_alpha_cv.Rd | 2 vignettes/rSDR_vignette.Rmd | 37 +++---- 12 files changed, 211 insertions(+), 205 deletions(-)
Title: Network Representations of Attitudes
Description: A tool for computing network representations of attitudes,
extracted from tabular data such as sociological surveys. Development of
surveygraph software and training materials was initially funded by the
European Union under the ERC Proof-of-concept programme (ERC,
Attitude-Maps-4-All, project number: 101069264). Views and opinions expressed
are however those of the author(s) only and do not necessarily reflect those
of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible
for them.
Author: Samuel Unicomb [aut, cre],
Ana Jovancevic [aut],
Caoimhe O'Reilly [aut],
Alejandro Dinkelberg [aut],
Padraig MacCarron [aut],
David O'Sullivan [aut],
Paul Maher [aut],
Mike Quayle [aut]
Maintainer: Samuel Unicomb <samuelunicomb@gmail.com>
Diff between surveygraph versions 0.1.2 dated 2024-06-04 and 1.0.0 dated 2025-11-09
surveygraph-0.1.2/surveygraph/R/projection.R |only surveygraph-0.1.2/surveygraph/R/synthetic-data.R |only surveygraph-0.1.2/surveygraph/R/threshold-profile.R |only surveygraph-0.1.2/surveygraph/src/build_graphs.cc |only surveygraph-0.1.2/surveygraph/src/components.cc |only surveygraph-0.1.2/surveygraph/src/graph.h |only surveygraph-0.1.2/surveygraph/src/make_projection.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_agent_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_symbolic_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_threshold_profile.cc |only surveygraph-0.1.2/surveygraph/tests/README.md |only surveygraph-0.1.2/surveygraph/tests/testthat/test-projection.R |only surveygraph-0.1.2/surveygraph/tests/testthat/test-synthetic-data.R |only surveygraph-1.0.0/surveygraph/DESCRIPTION | 18 - surveygraph-1.0.0/surveygraph/MD5 | 54 +-- surveygraph-1.0.0/surveygraph/NAMESPACE | 5 surveygraph-1.0.0/surveygraph/NEWS.md | 4 surveygraph-1.0.0/surveygraph/R/data-preprocess.R |only surveygraph-1.0.0/surveygraph/R/make-projection.R |only surveygraph-1.0.0/surveygraph/R/make-synthetic-data.R |only surveygraph-1.0.0/surveygraph/R/make-threshold-profile.R |only surveygraph-1.0.0/surveygraph/R/surveygraph.R | 6 surveygraph-1.0.0/surveygraph/README.md | 33 + surveygraph-1.0.0/surveygraph/build |only surveygraph-1.0.0/surveygraph/inst/doc |only surveygraph-1.0.0/surveygraph/man/data_preprocess.Rd |only surveygraph-1.0.0/surveygraph/man/make_projection.Rd | 77 +++- surveygraph-1.0.0/surveygraph/man/make_synthetic_data.Rd | 20 - surveygraph-1.0.0/surveygraph/man/make_threshold_profile.Rd | 25 + surveygraph-1.0.0/surveygraph/man/surveygraph.Rd | 32 + surveygraph-1.0.0/surveygraph/src/edge.h |only surveygraph-1.0.0/surveygraph/src/init.cc | 70 +--- surveygraph-1.0.0/surveygraph/src/make_projection_pilot.cc |only surveygraph-1.0.0/surveygraph/src/make_threshold_profile_pilot.cc | 175 ++++++---- surveygraph-1.0.0/surveygraph/src/surveygraph.h | 110 +++--- surveygraph-1.0.0/surveygraph/src/surveygraph_edgelist.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_projection.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_threshold_profile.cc |only surveygraph-1.0.0/surveygraph/src/unionfind.h |only surveygraph-1.0.0/surveygraph/tests/testthat/test_make_projection_comparisons.R |only surveygraph-1.0.0/surveygraph/vignettes |only 41 files changed, 400 insertions(+), 229 deletions(-)
Title: Analysis and Manipulation of Data from Minecraft Bedrock Edition
Description: Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
Author: Reed Cartwright [aut, cre] ,
Rich FitzJohn [ctb],
Christian Stigen Larsen [ctb],
The LevelDB Authors [cph]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between rbedrock versions 0.4.1 dated 2025-08-24 and 0.4.2 dated 2025-11-09
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/finalized_state.R | 2 +- R/legacy-checksums.R | 2 +- data/biome_df.rda |binary data/vanilla_block_list.rda |binary data/vanilla_block_property_type_list.rda |binary data/vanilla_block_states_df.rda |binary man/FinalizedState.Rd | 2 +- tests/testthat/test_legacy-checksums.R | 2 +- 11 files changed, 23 insertions(+), 17 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak, area under the curve, wash in rate and wash out rate are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.3 dated 2025-05-26 and 1.1.0 dated 2025-11-09
DESCRIPTION | 10 +- MD5 | 32 ++++---- NAMESPACE | 3 NEWS.md | 4 + R/tic_analyse.R | 102 ++++++++++++++++----------- R/tic_auc.R | 22 ----- R/tic_wir.R |only R/tic_wor.R |only R/ttpeak.R | 24 ------ build/vignette.rds |binary inst/doc/tican-vignette.R | 76 ++++++++++++++++---- inst/doc/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- inst/doc/tican-vignette.html | 162 ++++++++++++++++++++++++------------------- man/tic_analyse.Rd | 35 +++------ man/tic_auc.Rd | 21 ----- man/tic_wir.Rd |only man/tic_wor.Rd |only man/ttpeak.Rd | 23 ------ vignettes/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- 19 files changed, 443 insertions(+), 281 deletions(-)
Title: Quantum Computing for Analyzing CD4 Lymphocytes and
Antiretroviral Therapy
Description: Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Author: Juan Pablo Acuna Gonzalez [aut, cre, cph]
Maintainer: Juan Pablo Acuna Gonzalez <22253567@uagro.mx>
Diff between qvirus versions 0.0.4 dated 2025-05-20 and 0.0.5 dated 2025-11-09
DESCRIPTION | 12 MD5 | 74 +-- NAMESPACE | 38 - NEWS.md | 54 ++ R/InteractionClassification.R | 90 ++-- R/cd_diff.R | 70 +-- R/cds_diff.R | 70 +-- R/data.R | 328 ++++++++-------- R/estimate_payoffs.R | 84 ++-- R/mse.InteractionClassification.R | 126 +++--- R/mse.payoffs.R | 116 ++--- R/nearest_payoff.R | 64 +-- R/payoffs_list.R | 112 ++--- R/phen_hiv.R | 132 +++--- R/run_bb84_simulation.R |only R/run_e91_simulation.R |only R/summary.InteractionClassification.R | 116 ++--- R/summary.payoffs.R | 94 ++-- R/vl_diff.R | 72 +-- R/vlog_diff.R | 76 +-- R/vlogs_diff.R | 82 ++-- README.md | 44 +- build/partial.rdb |binary man/run_bb84_simulation.Rd |only man/run_e91_simulation.Rd |only tests/testthat/test-InteractionClassification.R | 24 - tests/testthat/test-cd_diff.R | 14 tests/testthat/test-cds_diff.R | 12 tests/testthat/test-estimate_payoffs.R | 26 - tests/testthat/test-mse.InteractionClassification.R | 24 - tests/testthat/test-mse.payoffs.R | 26 - tests/testthat/test-nearest_payoff.R | 18 tests/testthat/test-payoffs_list.R | 18 tests/testthat/test-phen_hiv.R | 22 - tests/testthat/test-run_bb84_simulation.R |only tests/testthat/test-run_e91_simulation.R |only tests/testthat/test-summary.InteractionClassification.R | 24 - tests/testthat/test-summary.payoffs.R | 28 - tests/testthat/test-vl_diff.R | 16 tests/testthat/test-vlog_diff.R | 14 tests/testthat/test-vlogs_diff.R | 12 41 files changed, 1086 insertions(+), 1046 deletions(-)
Title: Structure Learning with Copula Graphical Model
Description: Statistical tool for learning the structure of direct associations among variables for
continuous data, discrete data and mixed discrete-continuous data. The package is based
on the copula graphical model in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>.
Author: Pariya Behrouzi [aut, cre]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between nutriNetwork versions 0.1.2 dated 2023-07-05 and 0.2.0 dated 2025-11-09
DESCRIPTION | 17 +++-- MD5 | 9 +-- R/selectnet.R | 156 ++++++++++++++++++++++++++--------------------------- inst |only man/plot.select.Rd | 21 +++---- man/selectnet.Rd | 32 +++++----- 6 files changed, 120 insertions(+), 115 deletions(-)
Title: Sampling from the von Mises-Fisher Distribution
Description: Provides fast sampling from von Mises-Fisher distribution using the method proposed by Andrew T.A Wood (1994) <doi:10.1080/03610919408813161>.
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between vMF versions 0.0.3 dated 2024-03-09 and 0.0.4 dated 2025-11-09
vMF-0.0.3/vMF/README.md |only vMF-0.0.4/vMF/DESCRIPTION | 16 ++++++------ vMF-0.0.4/vMF/MD5 | 20 +++++++-------- vMF-0.0.4/vMF/build/partial.rdb |binary vMF-0.0.4/vMF/build/vignette.rds |binary vMF-0.0.4/vMF/inst/doc/vMF.R | 52 +++++++++++++++++++-------------------- vMF-0.0.4/vMF/inst/doc/vMF.Rmd | 12 ++++----- vMF-0.0.4/vMF/inst/doc/vMF.pdf |binary vMF-0.0.4/vMF/man/vMF-package.Rd |only vMF-0.0.4/vMF/src/Makevars | 13 --------- vMF-0.0.4/vMF/src/Makevars.win | 9 ------ vMF-0.0.4/vMF/vignettes/vMF.Rmd | 12 ++++----- 12 files changed, 58 insertions(+), 76 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or
'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Mueller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyz [...truncated...]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.6.4 dated 2023-11-09 and 3.6.5 dated 2025-11-09
covr-3.6.4/covr/tests/testthat/test-tally_coverage.R |only covr-3.6.5/covr/DESCRIPTION | 18 covr-3.6.5/covr/MD5 | 159 +- covr-3.6.5/covr/NAMESPACE | 6 covr-3.6.5/covr/NEWS.md | 31 covr-3.6.5/covr/R/R6.R | 26 covr-3.6.5/covr/R/S7.R |only covr-3.6.5/covr/R/box.R |only covr-3.6.5/covr/R/cobertura.R | 6 covr-3.6.5/covr/R/codecov.R | 14 covr-3.6.5/covr/R/compiled.R | 47 covr-3.6.5/covr/R/coveralls.R | 6 covr-3.6.5/covr/R/covr.R | 71 - covr-3.6.5/covr/R/exclusions.R | 10 covr-3.6.5/covr/R/gitlab.R | 2 covr-3.6.5/covr/R/icc.R | 2 covr-3.6.5/covr/R/parse_data.R | 20 covr-3.6.5/covr/R/replace.R | 4 covr-3.6.5/covr/R/summary_functions.R | 30 covr-3.6.5/covr/R/trace_calls.R | 24 covr-3.6.5/covr/R/trace_tests.R | 146 +- covr-3.6.5/covr/R/utils.R | 11 covr-3.6.5/covr/README.md | 2 covr-3.6.5/covr/build/vignette.rds |binary covr-3.6.5/covr/inst/doc/how_it_works.R | 2 covr-3.6.5/covr/inst/doc/how_it_works.Rmd | 3 covr-3.6.5/covr/inst/doc/how_it_works.html | 25 covr-3.6.5/covr/man/covr.record_tests.Rd | 27 covr-3.6.5/covr/man/current_test_call_count.Rd |only covr-3.6.5/covr/man/current_test_index.Rd |only covr-3.6.5/covr/man/current_test_key.Rd |only covr-3.6.5/covr/man/gitlab.Rd | 2 covr-3.6.5/covr/src/reassign.c | 132 +- covr-3.6.5/covr/tests/testthat.R | 20 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple-header.h | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiledSubdir/src/lib/simple.c | 2 covr-3.6.5/covr/tests/testthat/TestS7 |only covr-3.6.5/covr/tests/testthat/Testbox |only covr-3.6.5/covr/tests/testthat/Testbox_R6 |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions_R6 |only covr-3.6.5/covr/tests/testthat/_snaps |only covr-3.6.5/covr/tests/testthat/test-Compiled.R | 30 covr-3.6.5/covr/tests/testthat/test-R6.R | 2 covr-3.6.5/covr/tests/testthat/test-RC.R | 1 covr-3.6.5/covr/tests/testthat/test-S4.R | 1 covr-3.6.5/covr/tests/testthat/test-S7.R |only covr-3.6.5/covr/tests/testthat/test-box-R6.R |only covr-3.6.5/covr/tests/testthat/test-box.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions-R6.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions.R |only covr-3.6.5/covr/tests/testthat/test-braceless.R | 2 covr-3.6.5/covr/tests/testthat/test-cobertura.R | 2 covr-3.6.5/covr/tests/testthat/test-codecov.R | 649 ++++------ covr-3.6.5/covr/tests/testthat/test-corner-cases.R | 2 covr-3.6.5/covr/tests/testthat/test-coveralls.R | 182 +- covr-3.6.5/covr/tests/testthat/test-covr.R | 3 covr-3.6.5/covr/tests/testthat/test-exclusions.R | 4 covr-3.6.5/covr/tests/testthat/test-file_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-functions.R | 1 covr-3.6.5/covr/tests/testthat/test-gcov.R | 105 - covr-3.6.5/covr/tests/testthat/test-gitlab.R | 2 covr-3.6.5/covr/tests/testthat/test-memoised.R | 1 covr-3.6.5/covr/tests/testthat/test-null.R | 2 covr-3.6.5/covr/tests/testthat/test-package_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-parallel.R | 5 covr-3.6.5/covr/tests/testthat/test-print.R | 18 covr-3.6.5/covr/tests/testthat/test-record_tests.R | 24 covr-3.6.5/covr/tests/testthat/test-report.R | 4 covr-3.6.5/covr/tests/testthat/test-sonarqube.R | 2 covr-3.6.5/covr/tests/testthat/test-summary.R | 4 covr-3.6.5/covr/tests/testthat/test-trace_calls.R | 1 covr-3.6.5/covr/tests/testthat/test-utils.R | 66 - covr-3.6.5/covr/tests/testthat/test-vectorized.R | 1 covr-3.6.5/covr/vignettes/how_it_works.Rmd | 3 79 files changed, 1163 insertions(+), 812 deletions(-)
Title: Econometrics of Network Data
Description: Simulating and estimating peer effect models and network formation models. The class of peer effect models includes linear-in-means models (Lee, 2004; <doi:10.1111/j.1468-0262.2004.00558.x>), Tobit models (Xu and Lee, 2015; <doi:10.1016/j.jeconom.2015.05.004>), and discrete numerical data models (Houndetoungan, 2025; <doi:10.48550/arXiv.2405.17290>). The network formation models include pair-wise regressions with degree heterogeneity (Graham, 2017; <doi:10.3982/ECTA12679>) and exponential random graph models (Mele, 2017; <doi:10.3982/ECTA10400>).
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between CDatanet versions 2.2.1 dated 2025-01-07 and 2.2.2 dated 2025-11-09
DESCRIPTION | 18 MD5 | 40 + NAMESPACE | 9 NEWS.md | 14 R/CDatanet.R | 2 R/RcppExports.R | 52 ++ R/auxfunc.R | 1 R/cdnet.R | 214 +++++----- R/homophily.fe.R | 58 ++ R/homophily.re.R | 15 R/meffects.R |only R/sart.R | 144 +++---- build/partial.rdb |binary man/CDatanet-package.Rd | 4 man/meffects.Rd |only man/simcdnet.Rd | 6 man/simsart.Rd | 16 src/RcppExports.cpp | 261 +++++++++++- src/cdnet.cpp | 987 ++++++++++++++++++++++++++++++++---------------- src/homophily.cpp | 2 src/sartcomplet.cpp | 82 +-- src/sartincomplet.cpp | 421 +++++++++++++++----- 22 files changed, 1638 insertions(+), 708 deletions(-)
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
Author: Lissandro Costa de Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Diff between adcontabil versions 1.1.0 dated 2025-11-08 and 1.1.8 dated 2025-11-09
DESCRIPTION | 6 +- MD5 | 12 ++-- R/AV_AH.R | 136 ++++++++++++++++++++++++++++++------------------- R/indicadores.R | 31 +++++++++++ R/padronizar_balanco.R | 8 +- man/calcular_AV_AH.Rd | 38 ++++++------- man/indicadores.Rd | 32 +++++++++++ 7 files changed, 178 insertions(+), 85 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like, and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra functions for st [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.5.3 dated 2025-10-10 and 0.1.6.1 dated 2025-11-09
broadcast-0.1.5.3/broadcast/R/internal_cast.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bycolumn.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bylayer.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-byrow.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/class/test-class.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/internal/test-orthogonal.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-bc_dim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-ndim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-rep_dim.R |only broadcast-0.1.5.3/broadcast/src/C_bindhelper_vdims.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_equal.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_orthogonal.c |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_dec.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_str.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcFact_int.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_normalize_dims.cpp |only broadcast-0.1.6.1/broadcast/DESCRIPTION | 9 broadcast-0.1.6.1/broadcast/MD5 | 297 +- broadcast-0.1.6.1/broadcast/NAMESPACE | 10 broadcast-0.1.6.1/broadcast/NEWS.md | 20 broadcast-0.1.6.1/broadcast/R/RcppExports.R | 220 +- broadcast-0.1.6.1/broadcast/R/aaa00_broadcast_help.R | 7 broadcast-0.1.6.1/broadcast/R/aaa02_broadcast_casting.R | 10 broadcast-0.1.6.1/broadcast/R/aaa03_broadcast_bind.R | 20 broadcast-0.1.6.1/broadcast/R/aaa04_broadcast_linearalgebra.R | 2 broadcast-0.1.6.1/broadcast/R/acast.R | 45 broadcast-0.1.6.1/broadcast/R/bc_b.R | 16 broadcast-0.1.6.1/broadcast/R/bc_bit.R | 16 broadcast-0.1.6.1/broadcast/R/bc_cplx.R | 16 broadcast-0.1.6.1/broadcast/R/bc_d.R | 49 broadcast-0.1.6.1/broadcast/R/bc_i.R | 40 broadcast-0.1.6.1/broadcast/R/bc_ifelse.R | 16 broadcast-0.1.6.1/broadcast/R/bc_list.R | 15 broadcast-0.1.6.1/broadcast/R/bc_raw.R | 8 broadcast-0.1.6.1/broadcast/R/bc_str.R | 30 broadcast-0.1.6.1/broadcast/R/bc_strrep.R |only broadcast-0.1.6.1/broadcast/R/bcapply.R | 12 broadcast-0.1.6.1/broadcast/R/bind_array.R | 18 broadcast-0.1.6.1/broadcast/R/broadcastWrappers.R | 55 broadcast-0.1.6.1/broadcast/R/broadcaster.R | 85 broadcast-0.1.6.1/broadcast/R/cast_dim2hier.R | 6 broadcast-0.1.6.1/broadcast/R/cast_hier2dim.R | 30 broadcast-0.1.6.1/broadcast/R/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/R/dropnests.R | 2 broadcast-0.1.6.1/broadcast/R/hier2dim.R | 110 - broadcast-0.1.6.1/broadcast/R/internal_acast.R |only broadcast-0.1.6.1/broadcast/R/internal_acast_names.R |only broadcast-0.1.6.1/broadcast/R/internal_binary.R | 104 - broadcast-0.1.6.1/broadcast/R/internal_binary_names.R | 18 broadcast-0.1.6.1/broadcast/R/internal_bind.R | 123 - broadcast-0.1.6.1/broadcast/R/internal_bind_names.R | 4 broadcast-0.1.6.1/broadcast/R/internal_functions.R | 8 broadcast-0.1.6.1/broadcast/R/internal_hiercast.R |only broadcast-0.1.6.1/broadcast/R/internal_opfuns.R | 2 broadcast-0.1.6.1/broadcast/R/internal_typefuns.R | 38 broadcast-0.1.6.1/broadcast/R/linear_algebra_stats.R | 3 broadcast-0.1.6.1/broadcast/R/meta_functions.R | 142 + broadcast-0.1.6.1/broadcast/R/ndim.R | 2 broadcast-0.1.6.1/broadcast/R/overload_ops_math.R | 6 broadcast-0.1.6.1/broadcast/R/overload_relops.R | 8 broadcast-0.1.6.1/broadcast/R/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/examples/bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/examples/bind_array.R | 8 broadcast-0.1.6.1/broadcast/inst/examples/broadcaster.R | 32 broadcast-0.1.6.1/broadcast/inst/examples/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/inst/examples/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-backtransform.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bycolumn_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bylayer_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-byrow_namedR.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-crashtest.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-edgecases.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-errors.R | 62 broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-simple.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_b/test-bc_b.R | 1026 +--------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_cplx/test-bc_cplx_math.R | 352 --- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-binaryerrors.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_list/test-bc_list.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_d_math.R | 662 ------ broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_math.R | 791 ------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_rel.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-1d.R | 38 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-array.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-between.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-ortho.R | 39 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-vector.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-zerolen.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-errors.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array_internal.R | 30 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-partialdimnames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_3_row/test-rbind_bc.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim-nonames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim_names.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-errors.R | 4 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-nonames.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-broadcaster_set.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-mbroadcasters.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/count/count_tests.R | 6 broadcast-0.1.6.1/broadcast/inst/tinytest/helper |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-conformable.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimmode.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimnames_fit.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-mini.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx.R | 362 --- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx_by_other.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_d.R | 535 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/shallow2atomic |only broadcast-0.1.6.1/broadcast/inst/tinytest/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/test-S4error-callerenv.R | 3 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary1d.R | 27 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_attr_broadcaster.R | 28 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_errors.R | 109 - broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_zerolen.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/test-ellipsis.R | 17 broadcast-0.1.6.1/broadcast/man/aaa00_broadcast_help.Rd | 9 broadcast-0.1.6.1/broadcast/man/aaa01_broadcast_operators.Rd | 32 broadcast-0.1.6.1/broadcast/man/aaa02_broadcast_casting.Rd | 10 broadcast-0.1.6.1/broadcast/man/acast.Rd | 31 broadcast-0.1.6.1/broadcast/man/bc_ifelse.Rd | 4 broadcast-0.1.6.1/broadcast/man/bc_strrep.Rd |only broadcast-0.1.6.1/broadcast/man/bcapply.Rd | 2 broadcast-0.1.6.1/broadcast/man/bind_array.Rd | 27 broadcast-0.1.6.1/broadcast/man/broadcaster.Rd | 69 broadcast-0.1.6.1/broadcast/man/cast_dim2hier.Rd | 2 broadcast-0.1.6.1/broadcast/man/cast_hier2dim.Rd | 8 broadcast-0.1.6.1/broadcast/man/cast_shallow2atomic.Rd |only broadcast-0.1.6.1/broadcast/man/hier2dim.Rd | 5 broadcast-0.1.6.1/broadcast/man/linear_algebra_stats.Rd | 2 broadcast-0.1.6.1/broadcast/man/ndim.Rd | 2 broadcast-0.1.6.1/broadcast/man/vector2array.Rd |only broadcast-0.1.6.1/broadcast/src/C_any_nonarray.c |only broadcast-0.1.6.1/broadcast/src/C_arraysize_overflow.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_get_alongdims.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_need_coerce.c |only broadcast-0.1.6.1/broadcast/src/C_check_conf_dim.c | 51 broadcast-0.1.6.1/broadcast/src/C_determine_dimmode.c |only broadcast-0.1.6.1/broadcast/src/C_dims_allge.c |only broadcast-0.1.6.1/broadcast/src/C_make_dcp.c | 9 broadcast-0.1.6.1/broadcast/src/C_sd_lc.c | 34 broadcast-0.1.6.1/broadcast/src/C_unlisthelper_maxlen.c |only broadcast-0.1.6.1/broadcast/src/RcppExports.cpp | 687 +++++- broadcast-0.1.6.1/broadcast/src/broadcast.h | 808 +++---- broadcast-0.1.6.1/broadcast/src/rcpp_bcD_dec.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_int.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_str.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_b.cpp | 43 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_cplx.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_int.cpp | 31 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_str.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bc_b.cpp | 184 + broadcast-0.1.6.1/broadcast/src/rcpp_bc_bind.cpp | 62 broadcast-0.1.6.1/broadcast/src/rcpp_bc_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bc_cplx.cpp | 44 broadcast-0.1.6.1/broadcast/src/rcpp_bc_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_ifelse.cpp | 38 broadcast-0.1.6.1/broadcast/src/rcpp_bc_int.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_list.cpp | 29 broadcast-0.1.6.1/broadcast/src/rcpp_bc_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_str.cpp | 32 broadcast-0.1.6.1/broadcast/src/rcpp_bc_strrep.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcapply.cpp | 21 broadcast-0.1.6.1/broadcast/src/rcpp_bindhelpers.cpp | 81 broadcast-0.1.6.1/broadcast/src/rcpp_cast_shallow2atomic.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_set_attr.cpp | 44 broadcast-0.1.6.1/broadcast/tests/tinytest.R | 12 173 files changed, 3769 insertions(+), 6105 deletions(-)
Title: Assessing Normality of Stationary Process
Description: Despite that several tests for normality in stationary processes have been proposed in the literature, consistent implementations of these tests in programming languages are limited. Seven normality test are implemented. The asymptotic Lobato & Velasco's, asymptotic Epps, Psaradakis and Vávra, Lobato & Velasco's and Epps sieve bootstrap approximations, El bouch et al., and the random projections tests for univariate stationary process. Some other diagnostics such as, unit root test for stationarity, seasonal tests for seasonality, and arch effect test for volatility; are also performed. Additionally, the El bouch test performs normality tests for bivariate time series. The package also offers residual diagnostic for linear time series models developed in several packages.
Author: Asael Alonzo Matamoros [aut, cre],
Alicia Nieto-Reyes [aut],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb],
Trapletti A. [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between nortsTest versions 1.1.2 dated 2024-01-25 and 1.1.3 dated 2025-11-09
DESCRIPTION | 10 ++--- MD5 | 17 +++++---- NEWS.md | 15 ++++++++ R/autoplot.R | 4 +- R/epps_test.R | 21 +++++++++--- R/nortsTest-package.R | 60 +++++++++++++++------------------- README.md | 2 - man/autoplot.ts.Rd | 4 +- man/nortsTest-package.Rd | 78 ++++++++++++++++++++++++++++----------------- tests/testthat/test-epps.r |only 10 files changed, 126 insertions(+), 85 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Supports Gaussian and binomial responses. Also implements the randomized permutation whole-model test for SVEM with Gaussian responses (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Some parts of the package code were drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 2.3.1 dated 2025-10-13 and 2.5.4 dated 2025-11-09
SVEMnet-2.3.1/SVEMnet/R/predict_with_ci.R |only SVEMnet-2.3.1/SVEMnet/R/svem_significance_test.R |only SVEMnet-2.3.1/SVEMnet/man/predict_with_ci.Rd |only SVEMnet-2.3.1/SVEMnet/man/svem_significance_test.Rd |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_c2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_cvglm.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_and_objective.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_26AUG25.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_second_script_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_28AUG25_script.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV_par_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_identity.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_mixture_v2.R |only SVEMnet-2.5.4/SVEMnet/DESCRIPTION | 19 SVEMnet-2.5.4/SVEMnet/MD5 | 109 - SVEMnet-2.5.4/SVEMnet/NAMESPACE | 13 SVEMnet-2.5.4/SVEMnet/NEWS | 3 SVEMnet-2.5.4/SVEMnet/R/SVEMnet-package.R | 29 SVEMnet-2.5.4/SVEMnet/R/SVEMnet.R | 539 ++++- SVEMnet-2.5.4/SVEMnet/R/bigexp.R | 702 +++++-- SVEMnet-2.5.4/SVEMnet/R/coef.R | 178 + SVEMnet-2.5.4/SVEMnet/R/glmnet_with_cv.R | 386 +++ SVEMnet-2.5.4/SVEMnet/R/globals.R | 2 SVEMnet-2.5.4/SVEMnet/R/lipid_screen.R | 111 - SVEMnet-2.5.4/SVEMnet/R/plot.svemnet.R | 270 ++ SVEMnet-2.5.4/SVEMnet/R/plot.svemtest.R | 60 SVEMnet-2.5.4/SVEMnet/R/predict.cv.R | 155 + SVEMnet-2.5.4/SVEMnet/R/predict.svem_lasso.R | 405 ++-- SVEMnet-2.5.4/SVEMnet/R/svem_optimize_random.R | 987 +++++++--- SVEMnet-2.5.4/SVEMnet/R/svem_random_table_multi.R | 101 - SVEMnet-2.5.4/SVEMnet/R/svem_significance_test_parallel.R | 249 +- SVEMnet-2.5.4/SVEMnet/data/lipid_screen.rda |binary SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.R | 89 SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.html | 430 +--- SVEMnet-2.5.4/SVEMnet/man/SVEMnet-package.Rd | 34 SVEMnet-2.5.4/SVEMnet/man/SVEMnet.Rd | 171 + SVEMnet-2.5.4/SVEMnet/man/bigexp_formula.Rd | 31 SVEMnet-2.5.4/SVEMnet/man/bigexp_model_matrix.Rd | 30 SVEMnet-2.5.4/SVEMnet/man/bigexp_prepare.Rd | 63 SVEMnet-2.5.4/SVEMnet/man/bigexp_terms.Rd | 138 + SVEMnet-2.5.4/SVEMnet/man/bigexp_train.Rd | 54 SVEMnet-2.5.4/SVEMnet/man/coef.svem_model.Rd | 66 SVEMnet-2.5.4/SVEMnet/man/glmnet_with_cv.Rd | 277 ++ SVEMnet-2.5.4/SVEMnet/man/lipid_screen.Rd | 141 + SVEMnet-2.5.4/SVEMnet/man/plot.svem_binomial.Rd |only SVEMnet-2.5.4/SVEMnet/man/plot.svem_model.Rd | 49 SVEMnet-2.5.4/SVEMnet/man/plot.svem_significance_test.Rd | 21 SVEMnet-2.5.4/SVEMnet/man/predict.svem_model.Rd | 194 + SVEMnet-2.5.4/SVEMnet/man/predict_cv.Rd | 90 SVEMnet-2.5.4/SVEMnet/man/print.bigexp_spec.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_nonzero.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_optimize_random.Rd | 384 ++- SVEMnet-2.5.4/SVEMnet/man/svem_random_table_multi.Rd | 81 SVEMnet-2.5.4/SVEMnet/man/svem_significance_test_parallel.Rd | 170 + SVEMnet-2.5.4/SVEMnet/man/with_bigexp_contrasts.Rd | 31 SVEMnet-2.5.4/SVEMnet/tests/testthat/test-fit-and-predict.R | 369 +++ SVEMnet-2.5.4/SVEMnet/tests/testthat/test-optimize-random.R | 109 - SVEMnet-2.5.4/SVEMnet/tests/testthat/test-significance-tests.R | 4 SVEMnet-2.5.4/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/vignettes/binary_sim_05NOV25.R |only 67 files changed, 5403 insertions(+), 2257 deletions(-)
Title: Uniformity Tests on the Circle, Sphere, and Hypersphere
Description: Implementation of uniformity tests on the circle and
(hyper)sphere. The main function of the package is unif_test(), which
conveniently collects more than 35 tests for assessing uniformity on
S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are
implemented in the unif_stat() function, which allows computing several
statistics for different samples within a single call, thus facilitating
Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows
parallelizing them in a simple way. The asymptotic null distributions of
the statistics are available through the function unif_stat_distr(). The
core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package.
The package also provides several novel datasets and gives the replicability
for the data applications/simulations in García-Portugués et al. (2021)
<doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023)
<doi:10.3150/21-BEJ1454>, Fernández-de-Marcos and
García-Portugués (2024) <d [...truncated...]
Author: Eduardo Garcia-Portugues [aut, cre] ,
Thomas Verdebout [aut] ,
Alberto Fernandez-de-Marcos [ctb],
Paula Navarro [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between sphunif versions 1.4.2 dated 2025-08-18 and 1.4.3 dated 2025-11-09
DESCRIPTION | 10 - MD5 | 78 +++++++------- NEWS.md | 8 + R/Pn.R | 2 R/Sobolev.R | 29 +++-- R/cir_distr.R | 2 R/cir_stat.R | 5 R/data.R | 14 +- R/harmonics.R | 12 +- R/locdev.R | 2 R/sph_distr.R | 1 R/sph_stat.R | 2 R/sphunif-package.R | 20 +-- R/unif_stat.R | 2 R/unif_stat_distr.R | 57 ++++++---- R/unif_test.R | 6 - inst/WORDLIST | 2 inst/doc/sphunif.R | 4 inst/doc/sphunif.Rmd | 21 ++- inst/doc/sphunif.html | 181 ++++++++++++++++++---------------- man/Pn.Rd | 2 man/Sobolev.Rd | 3 man/Sobolev_coefs.Rd | 4 man/avail_tests.Rd | 2 man/cir_stat.Rd | 5 man/cir_stat_distr.Rd | 5 man/comets.Rd | 2 man/craters.Rd | 12 +- man/harmonics.Rd | 12 +- man/locdev.Rd | 2 man/sph_stat.Rd | 2 man/sphunif-package.Rd | 20 +-- man/unif_stat.Rd | 2 man/unif_stat_distr.Rd | 5 man/unif_test.Rd | 4 tests/testthat/test_Sobolev.R | 15 ++ tests/testthat/test_unif_stat.R | 4 tests/testthat/test_unif_stat_distr.R | 66 ++++++++++++ vignettes/sphunif.Rmd | 21 ++- vignettes/sphunif.bib | 15 +- 40 files changed, 398 insertions(+), 263 deletions(-)
Title: Longitudinal Surrogate Marker Analysis
Description: Assess the proportion of treatment effect explained by a longitudinal surrogate marker as described in Agniel D and Parast L (2021) <doi:10.1111/biom.13310>; and estimate the treatment effect on a longitudinal surrogate marker as described in Wang et al. (2025) <doi:10.1093/biomtc/ujaf104>. A tutorial for this package can be found at <https://www.laylaparast.com/longsurr>.
Author: Layla Parast [aut, cre],
Denis Agniel [aut],
Xuan Wang [aut]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between longsurr versions 1.0 dated 2022-09-29 and 1.1 dated 2025-11-09
DESCRIPTION | 16 - MD5 | 12 - NAMESPACE | 8 R/longsurr.functions.R | 416 ++++++++++++++++++++++++++++++++++++++++++++- data/data_sjm.RData |only man/data_sjm.Rd |only man/resam.Rd |only man/resam_nonlinear.Rd |only man/sjm_linear_estimate.Rd |only man/sjm_nl_estimate.Rd |only 10 files changed, 436 insertions(+), 16 deletions(-)
Title: Meta-Analysis of Quantiles and Functions of Quantiles
Description: Implements a novel density-based approach for estimating unknown parameters, distribution visualisations and meta-analyses of quantiles and ther functions.
A detailed vignettes with example datasets and code to prepare data and analyses is available at <https://bookdown.org/a2delivera/metaquant/>.
The methods are described in the pre-print by De Livera, Prendergast and Kumaranathunga (2024, <doi:10.48550/arXiv.2411.10971>).
Author: Udara Kumaranathunga [aut, cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Udara Kumaranathunga <U.Kumaranathunga@latrobe.edu.au>
Diff between metaquant versions 0.1.2 dated 2025-08-21 and 0.1.3 dated 2025-11-09
metaquant-0.1.2/metaquant/build |only metaquant-0.1.2/metaquant/man/est.density.five.Rd |only metaquant-0.1.2/metaquant/man/est.density.minq2max.Rd |only metaquant-0.1.2/metaquant/man/est.density.q1q2q3.Rd |only metaquant-0.1.3/metaquant/DESCRIPTION | 20 - metaquant-0.1.3/metaquant/MD5 | 29 - metaquant-0.1.3/metaquant/NAMESPACE | 11 metaquant-0.1.3/metaquant/R/est.mean.R | 99 ++--- metaquant-0.1.3/metaquant/R/est.sd.R | 26 - metaquant-0.1.3/metaquant/R/helper.functions.R | 308 +++++++++++++++++- metaquant-0.1.3/metaquant/R/metaquant.R |only metaquant-0.1.3/metaquant/R/plotdist.R | 201 ----------- metaquant-0.1.3/metaquant/man/est.gld.five.Rd |only metaquant-0.1.3/metaquant/man/est.mean.Rd | 18 - metaquant-0.1.3/metaquant/man/est.q.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.r.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.sd.Rd | 8 metaquant-0.1.3/metaquant/man/est.sld.minq2max.Rd |only metaquant-0.1.3/metaquant/man/est.sld.q1q2q3.Rd |only metaquant-0.1.3/metaquant/man/metaquant.Rd |only metaquant-0.1.3/metaquant/man/plotdist.Rd | 10 21 files changed, 413 insertions(+), 317 deletions(-)
Title: Neat Data for Presentation
Description: Utilities for unambiguous, neat and legible
representation of data (date, time stamp, numbers, percentages and strings)
for presentation of analysis , aiming for elegance and consistency.
The purpose of this package is to format data, that is better
for presentation and any automation jobs that reports numbers.
Author: Shivaprakash Suresh [aut, cre, cph]
Maintainer: Shivaprakash Suresh <dswithai@gmail.com>
This is a re-admission after prior archival of version 0.2.0 dated 2023-03-23
Diff between neatR versions 0.2.0 dated 2023-03-23 and 0.2.1 dated 2025-11-09
DESCRIPTION | 8 - MD5 | 28 ++--- R/src.R | 248 +++++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/neat-data.R | 54 +++++----- inst/doc/neat-data.Rmd | 70 ++++++------- inst/doc/neat-data.html | 213 ++++++++++++++++++++--------------------- man/ndate.Rd | 10 - man/nday.Rd | 8 - man/nnumber.Rd | 8 - man/npercent.Rd | 23 ++-- man/nstring.Rd | 20 +-- man/ntimestamp.Rd | 28 ++--- tests/testthat/tests.R | 32 +++--- vignettes/neat-data.Rmd | 70 ++++++------- 15 files changed, 432 insertions(+), 388 deletions(-)
Title: Access Infectious and Epidemiological Data via 'disease.sh API'
Description: Provides functions to access real-time infectious disease data from the 'disease.sh API',
including COVID-19 global, US states, continent, and country statistics, vaccination coverage,
influenza-like illness data from the Centers for Disease Control and Prevention (CDC), and more.
Also includes curated datasets on a variety of infectious diseases such as influenza, measles, dengue,
Ebola, tuberculosis, meningitis, AIDS, and others. The package supports epidemiological research
and data analysis by combining API access with high-quality historical and survey datasets on infectious diseases.
For more details on the 'disease.sh API', see <https://disease.sh/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between infectiousR versions 0.1.0 dated 2025-06-16 and 0.1.1 dated 2025-11-09
DESCRIPTION | 19 +- MD5 | 132 +++++++++--------- NAMESPACE | 2 NEWS.md |only R/data-documentation.R | 2 R/get_covid_stats_by_continent.R | 71 ++++++--- R/get_covid_stats_by_country.R | 73 +++++++-- R/get_covid_stats_by_country_name.R | 76 ++++++++-- R/get_covid_stats_for_state.R | 80 ++++++++-- R/get_global_covid_stats.R | 89 ++++++++---- R/get_influenza_cdc_ili.R | 103 +++++++++++--- R/get_us_states_covid_stats.R | 90 ++++++++---- R/infectiousR-package.R | 2 R/utils.R | 2 R/view_datasets_infectiousR.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/infectiousR_vignette.html | 5 man/get_covid_stats_by_continent.Rd | 13 + man/get_covid_stats_by_country.Rd | 13 + man/get_covid_stats_by_country_name.Rd | 13 + man/get_covid_stats_for_state.Rd | 9 - man/get_global_covid_stats.Rd | 18 +- man/get_influenza_cdc_ili.Rd | 12 + man/get_us_states_covid_stats.Rd | 10 - tests/testthat/test-active_hepatitis_df.R | 2 tests/testthat/test-aids_azt_df.R | 2 tests/testthat/test-bcg_vaccine_df.R | 2 tests/testthat/test-campy_infections_ts.R | 2 tests/testthat/test-china_dengue_tbl_df.R | 2 tests/testthat/test-contagious_diseases_df.R | 2 tests/testthat/test-covid_mortality_df.R | 2 tests/testthat/test-covid_new_york_df.R | 2 tests/testthat/test-covid_severity_df.R | 2 tests/testthat/test-diphtheria_philly_df.R | 2 tests/testthat/test-ebola_cases_df.R | 2 tests/testthat/test-ebola_sleone_df.R | 2 tests/testthat/test-ebola_survey_tbl_df.R | 2 tests/testthat/test-ecoli_infections_df.R | 2 tests/testthat/test-ehec_infections_df.R | 2 tests/testthat/test-flu_enrich_df.R | 2 tests/testthat/test-fungal_infections_df.R | 2 tests/testthat/test-get_covid_stats_by_continent.R |only tests/testthat/test-get_covid_stats_by_country.R |only tests/testthat/test-get_covid_stats_by_country_name.R |only tests/testthat/test-get_covid_stats_for_state.R |only tests/testthat/test-get_global_covid_stats.R |only tests/testthat/test-get_influenza_cdc_ili.R |only tests/testthat/test-get_us_states_covid_stats.R |only tests/testthat/test-gonorrhea_ma_df.R | 2 tests/testthat/test-hepatitisA_df.R | 2 tests/testthat/test-india_dengue_tbl_df.R | 2 tests/testthat/test-influenza_ice_df.R | 2 tests/testthat/test-influenza_infections_df.R | 2 tests/testthat/test-influenza_pneumonia_ts.R | 2 tests/testthat/test-influenza_vax_survey_df.R | 2 tests/testthat/test-korea_dengue_tbl_df.R | 2 tests/testthat/test-malaria_mice_df.R | 2 tests/testthat/test-measles_infections_df.R | 2 tests/testthat/test-measles_survey_df.R | 2 tests/testthat/test-meningitis_df.R | 2 tests/testthat/test-rubella_austria_df.R | 2 tests/testthat/test-rubella_peru_df.R | 2 tests/testthat/test-sars_canada_df.R | 2 tests/testthat/test-smallpox_nigeria_df.R | 2 tests/testthat/test-spanish_flu_df.R | 2 tests/testthat/test-streptomycin_tbl_df.R | 2 tests/testthat/test-us_covid_cases_df.R | 2 tests/testthat/test-view_datasets_infectiousR.R | 2 tests/testthat/test-zika_girardot_df.R | 2 tests/testthat/test-zika_sanandres_df.R | 2 71 files changed, 621 insertions(+), 295 deletions(-)
Title: Fast, Vectorized Hashmap
Description: A fast, vectorized hashmap that is built on top of 'C++' std::unordered_map <https://en.cppreference.com/w/cpp/container/unordered_map.html>.
The map can hold any 'R' object as key / value as long as it is serializable and supports
vectorized insertion, lookup, and deletion.
Author: Sven Glinz [aut, cre]
Maintainer: Sven Glinz <svenglinz@proton.me>
Diff between hashmapR versions 1.0.0 dated 2025-11-07 and 1.0.1 dated 2025-11-09
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- README.md | 6 ++++++ src/hashmap.cpp | 10 +++++----- src/init.c | 35 +++++++++++++++++------------------ tests/testthat/test_map.R | 3 ++- 6 files changed, 40 insertions(+), 35 deletions(-)
Title: Bayesian Hierarchical Modeling for Label-Free Proteomics
Description: Statistical decision in proteomics data using a hierarchical
Bayesian model. There are two regression models for describing the
mean-variance trend, a gamma regression or a latent gamma mixture
regression. The regression model is then used as an Empirical Bayes
estimator for the prior on the variance in a peptide. Further, it assumes
that each measurement has an uncertainty (increased variance) associated
with it that is also inferred. Finally, it tries to estimate the posterior
distribution (by Hamiltonian Monte Carlo) for the differences in means for
each peptide in the data. Once the posterior is inferred, it integrates the
tails to estimate the probability of error from which a statistical decision
can be made.
See Berg and Popescu for details (<doi:10.1016/j.mcpro.2023.100658>).
Author: Philip Berg [aut, cre]
Maintainer: Philip Berg <pberg@live.se>
Diff between baldur versions 0.0.3 dated 2023-09-18 and 0.0.4 dated 2025-11-09
baldur-0.0.3/baldur/inst/doc/baldur_yeast_tutorial.Rmd |only baldur-0.0.3/baldur/inst/doc/baldur_yeast_tutorial.html |only baldur-0.0.3/baldur/vignettes/baldur_yeast_tutorial.Rmd |only baldur-0.0.4/baldur/DESCRIPTION | 16 baldur-0.0.4/baldur/MD5 | 88 baldur-0.0.4/baldur/NEWS.md | 9 baldur-0.0.4/baldur/R/baldur-package.R | 87 baldur-0.0.4/baldur/R/calculate_mean_sd_trends.R | 16 baldur-0.0.4/baldur/R/fit_lgmr.R | 2 baldur-0.0.4/baldur/R/psrn.R | 258 +- baldur-0.0.4/baldur/R/sample_posterior.R | 901 +++---- baldur-0.0.4/baldur/README.md | 177 + baldur-0.0.4/baldur/build/partial.rdb |binary baldur-0.0.4/baldur/build/vignette.rds |binary baldur-0.0.4/baldur/inst/CITATION |only baldur-0.0.4/baldur/inst/doc/Baldur_Yeast_Tutorial.Rmd |only baldur-0.0.4/baldur/inst/doc/Baldur_Yeast_Tutorial.html |only baldur-0.0.4/baldur/inst/doc/baldur_ups_tutorial.Rmd | 414 +-- baldur-0.0.4/baldur/inst/doc/baldur_ups_tutorial.html | 131 - baldur-0.0.4/baldur/inst/stan/empirical_bayes.stan | 104 baldur-0.0.4/baldur/inst/stan/lgmr_model.stan | 134 - baldur-0.0.4/baldur/inst/stan/weakly_informative.stan | 98 baldur-0.0.4/baldur/man/baldur-package.Rd | 66 baldur-0.0.4/baldur/man/calculate_mean_sd_trends.Rd | 74 baldur-0.0.4/baldur/man/fit_lgmr.Rd | 2 baldur-0.0.4/baldur/man/infer_data_and_decision_model.Rd | 20 baldur-0.0.4/baldur/src/stanExports_empirical_bayes.cc | 34 baldur-0.0.4/baldur/src/stanExports_empirical_bayes.h | 1292 +++++------ baldur-0.0.4/baldur/src/stanExports_lgmr_model.cc | 34 baldur-0.0.4/baldur/src/stanExports_lgmr_model.h | 1138 ++++----- baldur-0.0.4/baldur/src/stanExports_weakly_informative.cc | 34 baldur-0.0.4/baldur/src/stanExports_weakly_informative.h | 1210 +++++----- baldur-0.0.4/baldur/vignettes/Baldur_Yeast_Tutorial.Rmd |only baldur-0.0.4/baldur/vignettes/baldur_ups_tutorial.Rmd | 414 +-- baldur-0.0.4/baldur/vignettes/baldur_ups_tutorial.Rmd.orig | 36 baldur-0.0.4/baldur/vignettes/baldur_yeast_tutorial.Rmd.orig | 13 baldur-0.0.4/baldur/vignettes/compile_vignettes.R |only baldur-0.0.4/baldur/vignettes/plotting_lgmr-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr_yeast-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa_yeast-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc_yeast-2.png |binary 49 files changed, 3426 insertions(+), 3376 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.7.5 dated 2025-10-28 and 0.8.0 dated 2025-11-09
glyrepr-0.7.5/glyrepr/R/composition-utils.R |only glyrepr-0.7.5/glyrepr/man/normalize_substituents.Rd |only glyrepr-0.8.0/glyrepr/DESCRIPTION | 10 glyrepr-0.8.0/glyrepr/MD5 | 46 +- glyrepr-0.8.0/glyrepr/NAMESPACE | 2 glyrepr-0.8.0/glyrepr/NEWS.md | 22 + glyrepr-0.8.0/glyrepr/R/composition.R | 170 +++++--- glyrepr-0.8.0/glyrepr/R/count-mono.R |only glyrepr-0.8.0/glyrepr/R/get-structure-level.R |only glyrepr-0.8.0/glyrepr/R/linkage.R | 40 + glyrepr-0.8.0/glyrepr/R/substituent.R | 3 glyrepr-0.8.0/glyrepr/README.md | 2 glyrepr-0.8.0/glyrepr/inst/doc/glycan-graph.html | 6 glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.R | 12 glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.Rmd | 42 ++ glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.html | 201 +++++----- glyrepr-0.8.0/glyrepr/inst/doc/smap.html | 8 glyrepr-0.8.0/glyrepr/man/as_glycan_composition.Rd | 18 glyrepr-0.8.0/glyrepr/man/count_mono.Rd | 16 glyrepr-0.8.0/glyrepr/man/get_structure_level.Rd |only glyrepr-0.8.0/glyrepr/man/glyrepr-package.Rd | 2 glyrepr-0.8.0/glyrepr/man/has_linkages.Rd | 22 - glyrepr-0.8.0/glyrepr/tests/testthat/test-composition.R | 48 +- glyrepr-0.8.0/glyrepr/tests/testthat/test-count-mono.R | 5 glyrepr-0.8.0/glyrepr/tests/testthat/test-get-structure-level.R |only glyrepr-0.8.0/glyrepr/tests/testthat/test-linkage.R | 7 glyrepr-0.8.0/glyrepr/vignettes/glyrepr.Rmd | 42 ++ 27 files changed, 495 insertions(+), 229 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-03 1.0.1
2023-12-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-24 2.2.8
2023-07-16 2.2.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-26 0.1.0
Title: Fuzzy Rank Tests and Confidence Intervals
Description: Does fuzzy tests and confidence intervals (following Geyer
and Meeden, Statistical Science, 2005, <doi:10.1214/088342305000000340>)
for sign test and Wilcoxon signed rank and rank sum tests.
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between fuzzyRankTests versions 0.4 dated 2021-08-14 and 0.5 dated 2025-11-09
fuzzyRankTests-0.4/fuzzyRankTests/.Rinstignore |only fuzzyRankTests-0.4/fuzzyRankTests/inst/doc/design.tex |only fuzzyRankTests-0.5/fuzzyRankTests/ChangeLog | 3 fuzzyRankTests-0.5/fuzzyRankTests/DESCRIPTION | 18 +- fuzzyRankTests-0.5/fuzzyRankTests/MD5 | 42 +++--- fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.ranksum.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.ranksum.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.sign.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.sign.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.signrank.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.signrank.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/plot.fuzzyrankci.R | 4 fuzzyRankTests-0.5/fuzzyRankTests/build |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/design.Rnw |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/design.pdf |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.R |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.Rnw |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.pdf |only fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.ranksum.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.sign.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.signrank.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/tests/ranksum.R | 10 - fuzzyRankTests-0.5/fuzzyRankTests/tests/ranksum.Rout.save | 38 +---- fuzzyRankTests-0.5/fuzzyRankTests/tests/signrank.R | 12 - fuzzyRankTests-0.5/fuzzyRankTests/tests/signrank.Rout.save | 72 ++--------- fuzzyRankTests-0.5/fuzzyRankTests/vignettes |only 26 files changed, 119 insertions(+), 152 deletions(-)
More information about fuzzyRankTests at CRAN
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