Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.2.4 dated 2024-12-17 and 0.2.5 dated 2025-02-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/aplot.R | 25 +++++++++++++++++-------- R/insertion.R | 1 + R/method-accessor.R | 39 +++++++++++++++++++++++++++------------ R/utilities.R | 38 ++++++++++++++++++++++++++++++++++++++ 8 files changed, 100 insertions(+), 31 deletions(-)
Title: Archaeological Time Series
Description: A toolkit for archaeological time series and time intervals.
This package provides a system of classes and methods to represent and
work with archaeological time series and time intervals. Dates are
represented as "rata die" and can be converted to (virtually) any
calendar defined by Reingold and Dershowitz (2018)
<doi:10.1017/9781107415058>. This packages offers a simple API that
can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] ,
Joe Roe [aut] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between aion versions 1.3.0 dated 2024-12-10 and 1.4.0 dated 2025-02-26
aion-1.3.0/aion/man/is.Rd |only aion-1.4.0/aion/DESCRIPTION | 40 ++++--- aion-1.4.0/aion/MD5 | 122 ++++++++++++----------- aion-1.4.0/aion/NAMESPACE | 8 + aion-1.4.0/aion/NEWS.md | 5 aion-1.4.0/aion/R/AllGenerics.R | 106 ++++++++++++------- aion-1.4.0/aion/R/aion-package.R | 8 - aion-1.4.0/aion/R/axis.R | 41 ------- aion-1.4.0/aion/R/calendar-gregorian.R | 12 -- aion-1.4.0/aion/R/calendar-julian.R | 12 -- aion-1.4.0/aion/R/calendar.R | 67 ++++++++++++ aion-1.4.0/aion/R/format.R |only aion-1.4.0/aion/R/graph.R |only aion-1.4.0/aion/R/overlap.R | 15 +- aion-1.4.0/aion/R/plot.R | 19 ++- aion-1.4.0/aion/R/show.R | 2 aion-1.4.0/aion/R/zzz.R | 3 aion-1.4.0/aion/README.md | 13 -- aion-1.4.0/aion/build/partial.rdb |binary aion-1.4.0/aion/build/vignette.rds |binary aion-1.4.0/aion/inst/CITATION | 4 aion-1.4.0/aion/inst/doc/aion.R | 10 - aion-1.4.0/aion/inst/doc/aion.Rmd | 12 +- aion-1.4.0/aion/inst/doc/aion.html | 16 +-- aion-1.4.0/aion/inst/doc/extending.Rmd | 4 aion-1.4.0/aion/inst/doc/extending.html | 6 - aion-1.4.0/aion/inst/examples/ex-graph.R |only aion-1.4.0/aion/inst/po/fr/LC_MESSAGES/R-aion.mo |binary aion-1.4.0/aion/inst/tinytest/test_arith.R | 2 aion-1.4.0/aion/inst/tinytest/test_calendar.R | 13 ++ aion-1.4.0/aion/inst/tinytest/test_convert.R | 2 aion-1.4.0/aion/inst/tinytest/test_fixed.R | 2 aion-1.4.0/aion/inst/tinytest/test_graph.R |only aion-1.4.0/aion/inst/tinytest/test_gregorian.R | 2 aion-1.4.0/aion/inst/tinytest/test_intervals.R | 3 aion-1.4.0/aion/inst/tinytest/test_julian.R | 2 aion-1.4.0/aion/inst/tinytest/test_plot.R | 3 aion-1.4.0/aion/inst/tinytest/test_series.R | 1 aion-1.4.0/aion/inst/tinytest/test_show.R | 3 aion-1.4.0/aion/inst/tinytest/test_subset.R | 2 aion-1.4.0/aion/inst/tinytest/test_time.R | 2 aion-1.4.0/aion/inst/tinytest/test_window.R | 2 aion-1.4.0/aion/inst/tinytest/test_zero.R | 3 aion-1.4.0/aion/man/aion-package.Rd | 12 -- aion-1.4.0/aion/man/as_graph.Rd |only aion-1.4.0/aion/man/calendar.Rd | 6 - aion-1.4.0/aion/man/calendar_get.Rd | 3 aion-1.4.0/aion/man/convert.Rd | 3 aion-1.4.0/aion/man/format.Rd | 4 aion-1.4.0/aion/man/get_calendar.Rd |only aion-1.4.0/aion/man/gregorian.Rd | 3 aion-1.4.0/aion/man/image.Rd | 2 aion-1.4.0/aion/man/is_calendar.Rd |only aion-1.4.0/aion/man/julian.Rd | 3 aion-1.4.0/aion/man/overlap.Rd | 14 +- aion-1.4.0/aion/man/plot.Rd | 4 aion-1.4.0/aion/man/pretty.Rd | 2 aion-1.4.0/aion/man/span.Rd | 1 aion-1.4.0/aion/man/start.Rd | 1 aion-1.4.0/aion/man/time.Rd | 1 aion-1.4.0/aion/man/window.Rd | 1 aion-1.4.0/aion/po/R-aion.pot | 24 +++- aion-1.4.0/aion/po/R-fr.po | 35 ++++-- aion-1.4.0/aion/vignettes/aion.Rmd | 12 +- aion-1.4.0/aion/vignettes/bibliography.bib | 16 ++- aion-1.4.0/aion/vignettes/extending.Rmd | 4 66 files changed, 417 insertions(+), 301 deletions(-)
Title: 'SAS' Interface
Description: Provides a 'SAS' interface, through
'SASPy'(<https://sassoftware.github.io/saspy/>) and
'reticulate'(<https://rstudio.github.io/reticulate/>). This package
helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS'
servers, retrieve execution results and log, and exchange datasets
between 'SAS' and 'R'. It also helps you to install 'SASPy' and
create a configuration file for the connection. Please review the
'SASPy' license file as instructed so that you comply with its
separate and independent license.
Author: Liming Li [aut, cre],
Daniel Sabanes Bove [aut],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Liming Li <clark.liming@gmail.com>
Diff between sasr versions 0.1.3 dated 2025-02-21 and 0.1.4 dated 2025-02-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 2 +- man/sasr-package.Rd | 2 +- tests/testthat/test-rmarkdown.R | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Correct Overloaded Peaks from GC-APCI-MS Data
Description: Analyzes and modifies metabolomics raw data (generated using
Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass Spectrometry)
to correct overloaded signals, i.e. ion intensities exceeding detector
saturation leading to a cut-off peak. Data in 'xcmsRaw' format are
accepted as input and 'mzXML' files can be processed alternatively.
Overloaded signals are detected automatically and modified using an Gaussian
or an Isotopic-Ratio approach. Quality control plots are generated and
corrected data are stored within the original 'xcmsRaw' or 'mzXML'
respectively to allow further processing.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between CorrectOverloadedPeaks versions 1.3.3 dated 2023-09-08 and 1.3.5 dated 2025-02-26
CorrectOverloadedPeaks-1.3.3/CorrectOverloadedPeaks/R/GroupByGaps.R |only CorrectOverloadedPeaks-1.3.3/CorrectOverloadedPeaks/R/is.FlatTopPeak.R |only CorrectOverloadedPeaks-1.3.3/CorrectOverloadedPeaks/man/verify_suggested.Rd |only CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/DESCRIPTION | 35 ++++-- CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/MD5 | 24 ++-- CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/NAMESPACE | 1 CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/R/cop_utils.R | 35 ++++++ CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/R/read.mzData.R | 56 ++++++++-- CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/README.md |only CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/build/partial.rdb |binary CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/build/vignette.rds |binary CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/inst/WORDLIST |only CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/inst/doc/CorrectOverloadedPeaks.R | 2 CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/inst/doc/CorrectOverloadedPeaks.html | 2 CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/man/read.mzData.Rd | 13 +- CorrectOverloadedPeaks-1.3.5/CorrectOverloadedPeaks/tests |only 16 files changed, 131 insertions(+), 37 deletions(-)
More information about CorrectOverloadedPeaks at CRAN
Permanent link
Title: Mechanistic Simulation of Species Range Dynamics
Description: Integrates population dynamics and dispersal into a mechanistic
virtual species simulator. The package can be used to study the effects of
environmental change on population growth and range shifts. It allows for
simple and straightforward definition of population dynamics (including
positive density dependence), extensive possibilities for defining dispersal
kernels, and the ability to generate virtual ecologist data. Learn more about
the 'rangr' at <https://docs.ropensci.org/rangr/>.
Author: Katarzyna Markowska [aut, cre],
Lechoslaw Kuczynski [aut],
Tad Dallas [rev],
Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between rangr versions 1.0.5 dated 2025-02-14 and 1.0.6 dated 2025-02-26
DESCRIPTION | 6 ++-- MD5 | 17 +++++++------- NEWS.md | 9 +++++++ R/sim.R | 2 - inst/doc/rangr.html | 2 - tests/testthat/fixtures/generate_test_data.R | 15 +++++++++--- tests/testthat/fixtures/test_ncells_in_circle_lon_lat.rds |binary tests/testthat/fixtures/test_sim_data_lon_lat_circle.rds |only tests/testthat/test-initialise.R | 6 ++-- tests/testthat/test-sim_results_to_rast.R | 8 ++++-- 10 files changed, 43 insertions(+), 22 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre],
D.L. Parkhurst [aut],
C.A.J. Appelo [aut],
with contributions from D. Gillespie for Chipmunk BASIC [aut],
S.D. Cohen [aut],
A.C. Hindmarsh [aut],
R. Serban [aut],
D. Shumaker [aut],
A.G. Taylor for CVODE/SUNDIALS [aut]
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.8.6 dated 2025-01-10 and 3.8.7 dated 2025-02-26
DESCRIPTION | 6 +-- MD5 | 51 +++++++++++++-------------- R/phreeqc.R | 15 +++++++ data/databases.rda |binary man/Amm.dat.Rd | 1 man/ColdChem.dat.Rd | 1 man/Kinec.v2.dat.Rd | 1 man/Kinec_v3.dat.Rd | 1 man/PHREEQC_ThermoddemV1.10_15Dec2020.dat.Rd | 1 man/Tipping_Hurley.dat.Rd | 1 man/core10.dat.Rd | 1 man/ex15.dat.Rd | 1 man/frezchem.dat.Rd | 1 man/iso.dat.Rd | 1 man/llnl.dat.Rd | 1 man/minteq.dat.Rd | 1 man/minteq.v4.dat.Rd | 1 man/phreeqc-package.Rd | 2 - man/phreeqc.dat.Rd | 1 man/phreeqc_rates.dat.Rd | 1 man/pitzer.dat.Rd | 1 man/sit.dat.Rd | 1 man/stimela.dat.Rd |only man/wateq4f.dat.Rd | 3 + src/IPhreeqc.h | 2 - src/Version.h | 8 ++-- src/phreeqcpp/GasComp.cpp | 16 ++++---- 27 files changed, 76 insertions(+), 44 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.55 dated 2025-02-19 and 0.56 dated 2025-02-26
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/latex.R | 2 +- tests/test-ci/sub |only tests/test-ci/test-latex.R | 6 ++++++ 5 files changed, 14 insertions(+), 7 deletions(-)
Title: Flexible Bayesian Model Selection and Model Averaging
Description: Implements the Mode Jumping Markov Chain Monte Carlo algorithm described in <doi:10.1016/j.csda.2018.05.020> and its Genetically Modified counterpart described in <doi:10.1613/jair.1.13047> as well as the sub-sampling versions described in <doi:10.1016/j.ijar.2022.08.018> for flexible Bayesian model selection and model averaging.
Author: Jon Lachmann [cre, aut],
Aliaksandr Hubin [aut]
Maintainer: Jon Lachmann <jon@lachmann.nu>
Diff between FBMS versions 1.0 dated 2023-12-21 and 1.1 dated 2025-02-26
FBMS-1.0/FBMS/README.md |only FBMS-1.1/FBMS/DESCRIPTION | 17 FBMS-1.1/FBMS/MD5 | 118 +-- FBMS-1.1/FBMS/NAMESPACE | 16 FBMS-1.1/FBMS/R/abalone-data.R |only FBMS-1.1/FBMS/R/alpha_generation.R | 34 FBMS-1.1/FBMS/R/arguments.R | 228 ++++++ FBMS-1.1/FBMS/R/diagnostics.R | 8 FBMS-1.1/FBMS/R/fbms.R | 120 ++- FBMS-1.1/FBMS/R/feature.R | 12 FBMS-1.1/FBMS/R/feature_generation.R | 8 FBMS-1.1/FBMS/R/functions.R | 4 FBMS-1.1/FBMS/R/gmjmcmc.R | 64 + FBMS-1.1/FBMS/R/gmjmcmc_support.R | 21 FBMS-1.1/FBMS/R/imports.R | 7 FBMS-1.1/FBMS/R/likelihoods.R | 71 +- FBMS-1.1/FBMS/R/local_optim.R | 18 FBMS-1.1/FBMS/R/mjmcmc.R | 71 -- FBMS-1.1/FBMS/R/nonlinear_functions.R | 2 FBMS-1.1/FBMS/R/parallel.R | 128 +++ FBMS-1.1/FBMS/R/predict.R | 171 ++++ FBMS-1.1/FBMS/R/proposals.R | 10 FBMS-1.1/FBMS/R/results.R | 369 ++++++---- FBMS-1.1/FBMS/R/sanger-data.R |only FBMS-1.1/FBMS/R/summary.R |only FBMS-1.1/FBMS/build/partial.rdb |binary FBMS-1.1/FBMS/build/vignette.rds |binary FBMS-1.1/FBMS/data/SangerData2.rda |only FBMS-1.1/FBMS/data/abalone.rda |only FBMS-1.1/FBMS/inst/doc/FBMS-guide.R | 6 FBMS-1.1/FBMS/inst/doc/FBMS-guide.Rmd | 2 FBMS-1.1/FBMS/inst/doc/FBMS-guide.html | 891 +++++++++++++++----------- FBMS-1.1/FBMS/man/SangerData2.Rd |only FBMS-1.1/FBMS/man/abalone.Rd |only FBMS-1.1/FBMS/man/diagn_plot.Rd | 4 FBMS-1.1/FBMS/man/fbms.Rd | 29 FBMS-1.1/FBMS/man/gaussian.loglik.alpha.Rd | 5 FBMS-1.1/FBMS/man/gen.params.gmjmcmc.Rd | 98 ++ FBMS-1.1/FBMS/man/gen.params.mjmcmc.Rd | 56 + FBMS-1.1/FBMS/man/gen.probs.gmjmcmc.Rd | 47 + FBMS-1.1/FBMS/man/gen.probs.mjmcmc.Rd | 16 FBMS-1.1/FBMS/man/get.best.model.Rd |only FBMS-1.1/FBMS/man/get.mpm.model.Rd |only FBMS-1.1/FBMS/man/gmjmcmc.Rd | 2 FBMS-1.1/FBMS/man/gmjmcmc.parallel.Rd | 25 FBMS-1.1/FBMS/man/log_prior.Rd |only FBMS-1.1/FBMS/man/logistic.loglik.Rd | 2 FBMS-1.1/FBMS/man/logistic.loglik.ala.Rd |only FBMS-1.1/FBMS/man/merge_results.Rd | 34 FBMS-1.1/FBMS/man/mjmcmc.Rd | 4 FBMS-1.1/FBMS/man/mjmcmc.parallel.Rd | 4 FBMS-1.1/FBMS/man/plot.gmjmcmc.Rd | 6 FBMS-1.1/FBMS/man/plot.gmjmcmc_merged.Rd | 8 FBMS-1.1/FBMS/man/predict.bgnlm_model.Rd |only FBMS-1.1/FBMS/man/predict.gmjmcmc.Rd | 16 FBMS-1.1/FBMS/man/predict.gmjmcmc_merged.Rd | 16 FBMS-1.1/FBMS/man/predict.gmjmcmc_parallel.Rd | 2 FBMS-1.1/FBMS/man/predict.mjmcmc.Rd | 2 FBMS-1.1/FBMS/man/predict.mjmcmc_parallel.Rd | 2 FBMS-1.1/FBMS/man/rmclapply.Rd |only FBMS-1.1/FBMS/man/string.population.Rd | 4 FBMS-1.1/FBMS/man/string.population.models.Rd | 4 FBMS-1.1/FBMS/man/summary.gmjmcmc.Rd | 19 FBMS-1.1/FBMS/man/summary.gmjmcmc_merged.Rd | 19 FBMS-1.1/FBMS/man/summary.mjmcmc.Rd | 13 FBMS-1.1/FBMS/man/summary.mjmcmc_parallel.Rd | 13 FBMS-1.1/FBMS/vignettes/FBMS-guide.Rmd | 2 67 files changed, 1966 insertions(+), 882 deletions(-)
Title: RT-QuIC Data Formatting and Analysis
Description: Designed for the curation and analysis of data generated from real-time quaking-induced conversion (RT-QuIC) assays first described by Atarashi et al. (2011) <doi:10.1038/nm.2294>. 'quicR' calculates useful metrics such as maxpoint ratio: Rowden et al. (2023) <doi:10.1099/vir.0.069906-0>; time-to-threshold: Shi et al. (2013) <doi:10.1186/2051-5960-1-44>; and maximum slope. Integration with the output from plate readers allows for seamless input of raw data into the R environment.
Author: Gage Rowden [aut, cre]
Maintainer: Gage Rowden <gage.rowden1145@gmail.com>
Diff between quicR versions 1.0.2 dated 2024-11-15 and 2.1.0 dated 2025-02-26
DESCRIPTION | 11 - MD5 | 83 ++++---- NAMESPACE | 17 + NEWS.md | 68 +++++- R/BMG_format.R | 191 +++++++++---------- R/calculate_MPR.R | 74 +++---- R/calculate_MS.R | 85 ++++---- R/calculate_TtT.R | 122 ++++++------ R/calculate_metrics.R |only R/calculate_threshold.R |only R/convert_tables.R | 81 ++++---- R/get_meta.R | 95 ++++----- R/get_real.R | 176 +++++++---------- R/get_sample_locations.R |only R/get_wells.R | 86 ++++---- R/normalize_RFU.R | 127 +++++------- R/organize_tables.R | 133 ++++++------- R/plate_view.R | 269 ++++++++++++--------------- R/plot_metrics.R |only R/quicR.R |only R/separate_raw.R | 239 +++++++++++------------ R/transpose_real.R | 28 ++ README.md | 112 ++++++++--- inst/extdata/BMG_formatting/plate_layout.csv | 16 - inst/extdata/input_files/rt_data.csv | 194 +++++++++---------- inst/extdata/input_files/test2.xlsx |binary inst/extdata/input_files/test3.xlsx |binary inst/extdata/input_files/test4.xlsx |only man/BMG_format.Rd | 5 man/calculate_MPR.Rd | 16 - man/calculate_MS.Rd | 15 - man/calculate_TtT.Rd | 14 - man/calculate_metrics.Rd |only man/calculate_threshold.Rd |only man/convert_tables.Rd | 11 - man/figures |only man/get_meta.Rd | 7 man/get_real.Rd | 13 - man/get_sample_locations.Rd |only man/get_wells.Rd | 7 man/normalize_RFU.Rd | 12 - man/organize_tables.Rd | 7 man/plate_view.Rd | 38 +-- man/plot_metrics.Rd |only man/quicR-package.Rd |only man/transpose_real.Rd |only tests/testthat/input_files/test3.xlsx |binary tests/testthat/input_files/test4.xlsx |only tests/testthat/input_files/test_no_meta.xlsx |only tests/testthat/test_organize_tables.R | 16 + 50 files changed, 1225 insertions(+), 1143 deletions(-)
Title: OPTICS K-Xi Density-Based Clustering
Description: Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in nois [...truncated...]
Author: Thomas Charlon [aut, cre]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between opticskxi versions 1.1.0 dated 2024-12-09 and 1.2.0 dated 2025-02-26
opticskxi-1.1.0/opticskxi/R/0_imports.R |only opticskxi-1.1.0/opticskxi/R/framework.R |only opticskxi-1.1.0/opticskxi/R/m_psychwords.R |only opticskxi-1.1.0/opticskxi/R/psych_kxi_example.R |only opticskxi-1.1.0/opticskxi/data/m_psychwords.rda |only opticskxi-1.1.0/opticskxi/man/m_psychwords.Rd |only opticskxi-1.1.0/opticskxi/man/pipe-assign.Rd |only opticskxi-1.1.0/opticskxi/man/pipe-with.Rd |only opticskxi-1.1.0/opticskxi/man/print_table.Rd |only opticskxi-1.1.0/opticskxi/man/psych_kxi_ensemble_models.Rd |only opticskxi-1.1.0/opticskxi/man/psych_kxi_pipeline.Rd |only opticskxi-1.2.0/opticskxi/DESCRIPTION | 11 - opticskxi-1.2.0/opticskxi/MD5 | 71 +++++---- opticskxi-1.2.0/opticskxi/NAMESPACE | 11 + opticskxi-1.2.0/opticskxi/NEWS.md | 7 opticskxi-1.2.0/opticskxi/R/dimred.R | 23 ++- opticskxi-1.2.0/opticskxi/R/dist_matrix.R |only opticskxi-1.2.0/opticskxi/R/ensemble_models.R | 88 +++++++++++- opticskxi-1.2.0/opticskxi/R/ggpairs.R | 19 ++ opticskxi-1.2.0/opticskxi/R/m_psych_embeds.R |only opticskxi-1.2.0/opticskxi/R/opticskxi_pipeline.R |only opticskxi-1.2.0/opticskxi/R/package.R |only opticskxi-1.2.0/opticskxi/R/utils.R | 32 +++- opticskxi-1.2.0/opticskxi/build/vignette.rds |binary opticskxi-1.2.0/opticskxi/data/m_psych_embeds.rda |only opticskxi-1.2.0/opticskxi/inst/doc/ensemble_metrics.R |only opticskxi-1.2.0/opticskxi/inst/doc/ensemble_metrics.Rnw |only opticskxi-1.2.0/opticskxi/inst/doc/ensemble_metrics.pdf |only opticskxi-1.2.0/opticskxi/inst/doc/opticskxi.R | 9 - opticskxi-1.2.0/opticskxi/inst/doc/opticskxi.Rnw | 7 opticskxi-1.2.0/opticskxi/inst/doc/opticskxi.pdf |binary opticskxi-1.2.0/opticskxi/inst/scripts |only opticskxi-1.2.0/opticskxi/man/compound.Rd |only opticskxi-1.2.0/opticskxi/man/cosine_simi.Rd |only opticskxi-1.2.0/opticskxi/man/dist_matrix.Rd |only opticskxi-1.2.0/opticskxi/man/ensemble_metrics.Rd | 12 + opticskxi-1.2.0/opticskxi/man/ensemble_metrics_bootstrap.Rd |only opticskxi-1.2.0/opticskxi/man/ensemble_models.Rd | 50 ++++++ opticskxi-1.2.0/opticskxi/man/exposition.Rd |only opticskxi-1.2.0/opticskxi/man/get_best_kxi.Rd | 2 opticskxi-1.2.0/opticskxi/man/m_psych_embeds.Rd |only opticskxi-1.2.0/opticskxi/man/norm_inprod.Rd |only opticskxi-1.2.0/opticskxi/man/opticskxi_pipeline.Rd | 24 +++ opticskxi-1.2.0/opticskxi/man/pipe.Rd | 15 +- opticskxi-1.2.0/opticskxi/man/print_vignette_table.Rd |only opticskxi-1.2.0/opticskxi/man/stddev_mean.Rd |only opticskxi-1.2.0/opticskxi/tests/testthat/Rplots.pdf |only opticskxi-1.2.0/opticskxi/tests/testthat/test-ensemble.R |only opticskxi-1.2.0/opticskxi/tests/testthat/test-opticskxi.R | 34 +++- opticskxi-1.2.0/opticskxi/tests/testthat/test-psychkxi.R | 26 ++- opticskxi-1.2.0/opticskxi/vignettes/ensemble_metrics.Rnw |only opticskxi-1.2.0/opticskxi/vignettes/ensemble_metrics.bib |only opticskxi-1.2.0/opticskxi/vignettes/opticskxi.Rnw | 7 53 files changed, 344 insertions(+), 104 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.4 dated 2024-12-11 and 0.4.5 dated 2025-02-26
tectonicr-0.4.4/tectonicr/man/PoR_shmax.Rd |only tectonicr-0.4.5/tectonicr/DESCRIPTION | 8 tectonicr-0.4.5/tectonicr/MD5 | 190 - tectonicr-0.4.5/tectonicr/NAMESPACE | 13 tectonicr-0.4.5/tectonicr/NEWS.md | 293 - tectonicr-0.4.5/tectonicr/R/coordinates.R | 998 ++--- tectonicr-0.4.5/tectonicr/R/data_models.R | 244 - tectonicr-0.4.5/tectonicr/R/draw_eulerpole.R | 551 +- tectonicr-0.4.5/tectonicr/R/interpolation.R | 1863 +++++----- tectonicr-0.4.5/tectonicr/R/model_shmax.R | 1054 ++--- tectonicr-0.4.5/tectonicr/R/pb_distance.R | 440 +- tectonicr-0.4.5/tectonicr/R/plotting.R | 51 tectonicr-0.4.5/tectonicr/R/roll_statistics.R | 169 tectonicr-0.4.5/tectonicr/R/rotation.R | 11 tectonicr-0.4.5/tectonicr/R/stat_tests.R | 1616 ++++---- tectonicr-0.4.5/tectonicr/R/statistics.R | 76 tectonicr-0.4.5/tectonicr/R/tectonicr-package.R | 63 tectonicr-0.4.5/tectonicr/R/trigonometry_degrees.R | 4 tectonicr-0.4.5/tectonicr/R/various.R | 687 +-- tectonicr-0.4.5/tectonicr/README.md | 13 tectonicr-0.4.5/tectonicr/data/cpm_models.rda |binary tectonicr-0.4.5/tectonicr/inst/doc/A_tectonicr.R | 2 tectonicr-0.4.5/tectonicr/inst/doc/A_tectonicr.Rmd | 2 tectonicr-0.4.5/tectonicr/inst/doc/A_tectonicr.html | 6 tectonicr-0.4.5/tectonicr/inst/doc/B_datasets.R | 50 tectonicr-0.4.5/tectonicr/inst/doc/B_datasets.Rmd | 56 tectonicr-0.4.5/tectonicr/inst/doc/B_datasets.html | 138 tectonicr-0.4.5/tectonicr/inst/doc/C_stress_trajectories.R | 246 - tectonicr-0.4.5/tectonicr/inst/doc/C_stress_trajectories.Rmd | 56 tectonicr-0.4.5/tectonicr/inst/doc/C_stress_trajectories.html | 71 tectonicr-0.4.5/tectonicr/inst/doc/D_statistics.R | 8 tectonicr-0.4.5/tectonicr/inst/doc/D_statistics.Rmd | 10 tectonicr-0.4.5/tectonicr/inst/doc/D_statistics.html | 29 tectonicr-0.4.5/tectonicr/inst/doc/E_interpolation.R | 3 tectonicr-0.4.5/tectonicr/inst/doc/E_interpolation.Rmd | 305 - tectonicr-0.4.5/tectonicr/inst/doc/E_interpolation.html | 15 tectonicr-0.4.5/tectonicr/inst/doc/F_spatial.R | 19 tectonicr-0.4.5/tectonicr/inst/doc/F_spatial.Rmd | 20 tectonicr-0.4.5/tectonicr/inst/doc/F_spatial.html | 59 tectonicr-0.4.5/tectonicr/inst/recent_plate_motion.xlsx |only tectonicr-0.4.5/tectonicr/man/PoR2Geo_azimuth.Rd | 4 tectonicr-0.4.5/tectonicr/man/PoR_azi.Rd |only tectonicr-0.4.5/tectonicr/man/PoR_stress2grid.Rd | 2 tectonicr-0.4.5/tectonicr/man/Q4_to_euler.Rd | 1 tectonicr-0.4.5/tectonicr/man/circle_stats.Rd | 1 tectonicr-0.4.5/tectonicr/man/circular_mode.Rd | 13 tectonicr-0.4.5/tectonicr/man/circular_summary.Rd | 4 tectonicr-0.4.5/tectonicr/man/compact-grid.Rd | 2 tectonicr-0.4.5/tectonicr/man/conjugate_Q4.Rd | 1 tectonicr-0.4.5/tectonicr/man/cpm_models.Rd | 31 tectonicr-0.4.5/tectonicr/man/dispersion.Rd | 5 tectonicr-0.4.5/tectonicr/man/distance_binned_stats.Rd |only tectonicr-0.4.5/tectonicr/man/distance_from_pb.Rd | 6 tectonicr-0.4.5/tectonicr/man/distance_mod.Rd | 1 tectonicr-0.4.5/tectonicr/man/est.kappa.Rd | 1 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-archived.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-defunct.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-deprecated.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-experimental.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-maturing.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-questioning.svg | 22 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-soft-deprecated.svg |only tectonicr-0.4.5/tectonicr/man/figures/lifecycle-stable.svg | 30 tectonicr-0.4.5/tectonicr/man/figures/lifecycle-superseded.svg | 22 tectonicr-0.4.5/tectonicr/man/get_distance.Rd | 1 tectonicr-0.4.5/tectonicr/man/get_projected_pb_strike.Rd | 1 tectonicr-0.4.5/tectonicr/man/get_relrot.Rd | 1 tectonicr-0.4.5/tectonicr/man/is.Q4.Rd | 1 tectonicr-0.4.5/tectonicr/man/kernel_dispersion.Rd | 172 tectonicr-0.4.5/tectonicr/man/mean_SC.Rd | 2 tectonicr-0.4.5/tectonicr/man/normalize_Q4.Rd | 1 tectonicr-0.4.5/tectonicr/man/parse_wsm.Rd | 4 tectonicr-0.4.5/tectonicr/man/plot_density.Rd | 9 tectonicr-0.4.5/tectonicr/man/plot_points.Rd | 10 tectonicr-0.4.5/tectonicr/man/por_transformation.Rd |only tectonicr-0.4.5/tectonicr/man/por_transformation_df.Rd | 19 tectonicr-0.4.5/tectonicr/man/por_transformation_quat.Rd | 8 tectonicr-0.4.5/tectonicr/man/por_transformation_sf.Rd | 10 tectonicr-0.4.5/tectonicr/man/product_Q4.Rd | 1 tectonicr-0.4.5/tectonicr/man/quick_plot.Rd | 5 tectonicr-0.4.5/tectonicr/man/raster_transformation.Rd | 1 tectonicr-0.4.5/tectonicr/man/roll_circstats.Rd | 2 tectonicr-0.4.5/tectonicr/man/rolling_test.Rd | 10 tectonicr-0.4.5/tectonicr/man/rolling_test_dist.Rd | 30 tectonicr-0.4.5/tectonicr/man/rose.Rd | 6 tectonicr-0.4.5/tectonicr/man/rotation_Q4.Rd | 1 tectonicr-0.4.5/tectonicr/man/sample_median.Rd | 3 tectonicr-0.4.5/tectonicr/man/stress2grid.Rd | 6 tectonicr-0.4.5/tectonicr/man/superimposed_shmax_PB.Rd | 2 tectonicr-0.4.5/tectonicr/man/vonmises.Rd | 29 tectonicr-0.4.5/tectonicr/man/weighted_rayleigh.Rd | 6 tectonicr-0.4.5/tectonicr/tests/testthat/lifecylce.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-dispersion.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test_that.R | 417 +- tectonicr-0.4.5/tectonicr/vignettes/A_tectonicr.Rmd | 2 tectonicr-0.4.5/tectonicr/vignettes/B_datasets.Rmd | 56 tectonicr-0.4.5/tectonicr/vignettes/C_stress_trajectories.Rmd | 56 tectonicr-0.4.5/tectonicr/vignettes/D_statistics.Rmd | 10 tectonicr-0.4.5/tectonicr/vignettes/E_interpolation.Rmd | 305 - tectonicr-0.4.5/tectonicr/vignettes/F_spatial.Rmd | 20 100 files changed, 5698 insertions(+), 5204 deletions(-)
Title: Interface for the 'QuickJS' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript'
engine. The engine and all 'R' to 'JavaScript' interoperability is bundled
within the package, requiring no dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
QuickJS Authors [cph] ,
QuickJS-NG Authors [cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.5.2 dated 2025-02-22 and 1.6.0 dated 2025-02-26
DESCRIPTION | 6 MD5 | 71 NEWS.md | 4 inst/doc/working_with_js_types.html | 2 inst/include/cpp11/R.hpp | 2 inst/include/cpp11/named_arg.hpp | 2 inst/include/quickjs/cutils.h | 64 inst/include/quickjs/dirent_compat.h | 2 inst/include/quickjs/libregexp.h | 11 inst/include/quickjs/libunicode.h | 21 inst/include/quickjs/quickjs-libc.h | 8 inst/include/quickjs/quickjs-opcode.h | 6 inst/include/quickjs/quickjs.h | 206 + src/quickjs/CMakeLists.txt | 82 src/quickjs/LICENSE | 8 src/quickjs/api-test.c |only src/quickjs/cutils.c | 17 src/quickjs/cutils.h | 64 src/quickjs/dirent_compat.h | 2 src/quickjs/fuzz.c | 2 src/quickjs/libbf.c | 124 - src/quickjs/libregexp.c | 122 - src/quickjs/libregexp.h | 11 src/quickjs/libunicode.c | 36 src/quickjs/libunicode.h | 21 src/quickjs/qjs.c | 60 src/quickjs/qjsc.c | 23 src/quickjs/quickjs-libc.c | 176 - src/quickjs/quickjs-libc.h | 8 src/quickjs/quickjs-opcode.h | 6 src/quickjs/quickjs.c | 4027 ++++++++++++++++------------------ src/quickjs/quickjs.h | 206 + src/quickjs/run-test262.c | 188 - src/quickjs/test262.conf | 6 src/quickjs/test262_errors.txt | 1 src/quickjs/tests.conf | 1 src/quickjs/unicode_gen.c | 50 37 files changed, 2789 insertions(+), 2857 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.2.3 dated 2024-12-12 and 1.3.0 dated 2025-02-26
DESCRIPTION | 19 - MD5 | 94 +++-- NAMESPACE | 4 NEWS.md | 18 + R/addCategories.R | 5 R/addCohortIntersect.R | 12 R/addConceptIntersect.R | 202 +++++++++++- R/addDemographics.R | 2 R/addDemographicsQuery.R | 73 +--- R/addIntersect.R | 393 ++++++++++++------------- R/addTableIntersect.R | 25 + R/benchmarkPatientProfiles.R |only R/checks.R | 33 -- R/filterCohortId.R |only R/filterInObservation.R |only R/mockPatientProfiles.R | 16 - R/summariseResult.R | 192 ++++++++---- R/sysdata.rda |binary README.md | 257 ++++++++-------- inst/doc/cohort-intersect.html | 98 +++--- inst/doc/concept-intersect.R | 16 - inst/doc/concept-intersect.Rmd | 17 - inst/doc/concept-intersect.html | 104 +++--- inst/doc/demographics.html | 248 +++++++-------- inst/doc/summarise.R | 8 inst/doc/summarise.Rmd | 9 inst/doc/summarise.html | 221 ++++++-------- inst/doc/table-intersect.R | 14 inst/doc/table-intersect.Rmd | 15 inst/doc/table-intersect.html | 98 +++--- man/addCategories.Rd | 3 man/addConceptIntersectField.Rd |only man/addTableIntersectCount.Rd | 4 man/addTableIntersectDate.Rd | 4 man/addTableIntersectDays.Rd | 4 man/addTableIntersectField.Rd | 9 man/addTableIntersectFlag.Rd | 4 man/benchmarkPatientProfiles.Rd |only man/filterCohortId.Rd |only man/filterInObservation.Rd |only man/summariseResult.Rd | 6 tests/manual/test-sqltest.R | 8 tests/testthat/setup.R | 7 tests/testthat/test-addCohortIntersect.R | 119 +++++++ tests/testthat/test-addConceptIntersect.R | 80 ++++- tests/testthat/test-addDemographics.R | 2 tests/testthat/test-benchmarkPatientProfiles.R |only tests/testthat/test-filterCohortId.R |only tests/testthat/test-filterInObservation.R |only tests/testthat/test-summariseResult.R | 256 +++++++++++----- vignettes/concept-intersect.Rmd | 17 - vignettes/summarise.Rmd | 9 vignettes/table-intersect.Rmd | 15 53 files changed, 1603 insertions(+), 1137 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Automated Reproducibility Checks for R Markdown Documents
Description: Provide reproducible R chunks in R Markdown document that automatically check computational results for reproducibility. This is achieved by creating json files storing metadata about computational results. A comprehensive tutorial to the package is available as preprint by Brandmaier & Peikert (2024, <doi:10.31234/osf.io/3zjvf>).
Author: Andreas M. Brandmaier [aut, cre],
Aaron Peikert [ctb]
Maintainer: Andreas M. Brandmaier <andreas.brandmaier@medicalschool-berlin.de>
Diff between reproducibleRchunks versions 1.0.2 dated 2025-01-29 and 1.0.3 dated 2025-02-26
reproducibleRchunks-1.0.2/reproducibleRchunks/inst/examples/deleteme |only reproducibleRchunks-1.0.3/reproducibleRchunks/DESCRIPTION | 8 +- reproducibleRchunks-1.0.3/reproducibleRchunks/MD5 | 30 ++++--- reproducibleRchunks-1.0.3/reproducibleRchunks/NAMESPACE | 1 reproducibleRchunks-1.0.3/reproducibleRchunks/NEWS.md | 7 + reproducibleRchunks-1.0.3/reproducibleRchunks/R/add_to_repror_summary.R | 7 + reproducibleRchunks-1.0.3/reproducibleRchunks/R/get_reproducibility_summary.R | 14 ++- reproducibleRchunks-1.0.3/reproducibleRchunks/R/isReproducible.R |only reproducibleRchunks-1.0.3/reproducibleRchunks/R/reproducibleR.R | 10 +- reproducibleRchunks-1.0.3/reproducibleRchunks/R/save_repro_data.R | 3 reproducibleRchunks-1.0.3/reproducibleRchunks/R/zzz.R | 40 +++++----- reproducibleRchunks-1.0.3/reproducibleRchunks/inst/examples/env |only reproducibleRchunks-1.0.3/reproducibleRchunks/inst/examples/override |only reproducibleRchunks-1.0.3/reproducibleRchunks/inst/examples/simple_demo/test.html | 14 +++ reproducibleRchunks-1.0.3/reproducibleRchunks/man/get_num_reproducibility_errors.Rd | 5 + reproducibleRchunks-1.0.3/reproducibleRchunks/man/get_reproducibility_summary.Rd | 5 + reproducibleRchunks-1.0.3/reproducibleRchunks/man/isReproducible.Rd |only 17 files changed, 96 insertions(+), 48 deletions(-)
More information about reproducibleRchunks at CRAN
Permanent link
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.4.0 dated 2024-09-02 and 0.4.1 dated 2025-02-26
DESCRIPTION | 6 +- MD5 | 40 +++++++++++---- NEWS.md | 33 +++++++------ R/ipea_palette.R | 2 R/theme_ipea.R | 108 +++++++++++++++++++------------------------ README.md | 6 +- build/vignette.rds |binary inst/doc/cookbook.R |only inst/doc/cookbook.Rmd |only inst/doc/cookbook.html |only inst/doc/intro_ipeaplot.R | 3 - inst/doc/intro_ipeaplot.Rmd | 3 - inst/doc/intro_ipeaplot.html | 8 +-- vignettes/cookbook.Rmd |only vignettes/intro_ipeaplot.Rmd | 3 - vignettes/prints_ipeaplot |only vignettes/prints_original |only 17 files changed, 113 insertions(+), 99 deletions(-)
More information about OhdsiReportGenerator at CRAN
Permanent link
Title: A Toolkit for Behavioral Scientists
Description: A collection of functions for analyzing data typically collected
or used by behavioral scientists. Examples of the functions include
a function that compares groups in a factorial experimental design,
a function that conducts two-way analysis of variance (ANOVA),
and a function that cleans a data set generated by Qualtrics surveys.
Some of the functions will require installing additional package(s).
Such packages and other references are cited within the section
describing the relevant functions. Many functions in this package
rely heavily on these two popular R packages:
Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>.
Wickham et al. (2021) <https://CRAN.R-project.org/package=ggplot2>.
Author: Jin Kim [aut, cre]
Maintainer: Jin Kim <jinkim@aya.yale.edu>
Diff between kim versions 0.5.431 dated 2024-10-01 and 0.6.1 dated 2025-02-26
DESCRIPTION | 10 - MD5 | 42 ++++---- NEWS.md | 6 + R/chi_squared_test.R | 117 ++++++++++++++++++++++ R/chi_squared_test_pairwise.R | 90 +++++++++++++++++ R/compare_groups.R | 36 +++++-- R/factorial_anova_2_way.R | 69 +++++++------ R/floodlight_2_by_continuous.R | 16 +-- R/histogram.R | 2 R/scatterplot.R | 7 + R/simple_slopes_analysis.R | 168 ++++++++++++++++++++++----------- R/simple_slopes_analysis_logistic.R | 92 +++++++++--------- R/t_test_pairwise.R | 97 ++++++++++++++----- inst/CITATION | 8 - man/chi_squared_test.Rd | 35 ++++++ man/chi_squared_test_pairwise.Rd | 35 ++++++ man/compare_groups.Rd | 34 +++++- man/factorial_anova_2_way.Rd | 2 man/scatterplot.Rd | 4 man/simple_slopes_analysis.Rd | 15 ++ man/simple_slopes_analysis_logistic.Rd | 8 - man/t_test_pairwise.Rd | 51 +++++++--- 22 files changed, 716 insertions(+), 228 deletions(-)
Title: Historical, Relational, and Tail Anomaly-Detection Algorithms
Description: The presence of outliers in a dataset can substantially bias the
results of statistical analyses. To correct for outliers, micro edits are
manually performed on all records. A set of constraints and decision rules
is typically used to aid the editing process. However, straightforward
decision rules might overlook anomalies arising from disruption of linear
relationships. Computationally efficient methods are provided to
identify historical, tail, and relational anomalies at the data-entry
level (Sartore et al., 2024; <doi:10.6339/24-JDS1136>). A score statistic
is developed for each anomaly type, using a distribution-free approach
motivated by the Bienaymé-Chebyshev's inequality, and fuzzy logic is used
to detect cellwise outliers resulting from different types of anomalies.
Each data entry is individually scored and individual scores are combined
into a final score to determine anomalous entries. In contrast to fuzzy
logic, Bayesian bootstrap and a Bayesian test based on empiric [...truncated...]
Author: Luca Sartore [aut] ,
Luca Sartore [cre] ,
Lu Chen [aut] ,
Justin van Wart [aut],
Andrew Dau [aut] ,
Valbona Bejleri [aut]
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between HRTnomaly versions 25.2.18 dated 2025-02-20 and 25.2.25 dated 2025-02-26
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- README.md | 10 +++++----- inst/INSTALL.md | 4 ++-- man/HRTnomaly-package.Rd | 1 + man/bayesHRT.Rd | 1 + man/bayeswise.Rd | 1 + man/bootHRT.Rd | 1 + man/cellwise.Rd | 1 + man/class_check.Rd | 1 + man/dif.Rd | 1 + man/fuzzyHRT.Rd | 1 + man/gif.Rd | 1 + man/print.checkwise.Rd | 1 + man/toy.Rd | 1 + src/cellwise.c | 19 +++++++++++++++++-- src/fuzzyHRT.c | 26 +++++++++++--------------- 18 files changed, 88 insertions(+), 45 deletions(-)
Title: Data Analysis using Bootstrap-Coupled Estimation
Description: Data Analysis using Bootstrap-Coupled ESTimation. Estimation
statistics is a simple framework that avoids the pitfalls of
significance testing. It uses familiar statistical concepts: means,
mean differences, and error bars. More importantly, it focuses on the
effect size of one's experiment/intervention, as opposed to a false
dichotomy engendered by P values. An estimation plot has two key
features: 1. It presents all datapoints as a swarmplot, which orders
each point to display the underlying distribution. 2. It presents the
effect size as a bootstrap 95% confidence interval on a separate but
aligned axes. Estimation plots are introduced in Ho et al., Nature
Methods 2019, 1548-7105. <doi:10.1038/s41592-019-0470-3>. The
free-to-view PDF is located at
<https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlR [...truncated...]
Author: Joses W. Ho [aut] ,
Kah Seng Lian [aut],
Ana Rosa Castillo [aut],
Zhuoyu Wang [aut],
Jun Yang Liao [aut],
Felicia Low [aut],
Tayfun Tumkaya [aut] ,
Jonathan Anns [ctb] ,
Yishan Mai [cre, ctb] ,
Sangyu Xu [ctb] ,
Hyungwon Choi [ctb] ,
Adam Claridge-Ch [...truncated...]
Maintainer: Yishan Mai <maiyishan@u.duke.nus.edu>
Diff between dabestr versions 2023.9.12 dated 2023-10-13 and 2025.3.14 dated 2025-02-26
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Title: Efficient Estimation of Bid-Ask Spreads from Open, High, Low,
and Close Prices
Description: Implements the efficient estimator of bid-ask spreads from open, high, low, and close prices
described in Ardia, Guidotti, & Kroencke (JFE, 2024) <doi:10.1016/j.jfineco.2024.103916>.
It also provides an implementation of the estimators described in
Roll (JF, 1984) <doi:10.1111/j.1540-6261.1984.tb03897.x>,
Corwin & Schultz (JF, 2012) <doi:10.1111/j.1540-6261.2012.01729.x>,
and Abdi & Ranaldo (RFS, 2017) <doi:10.1093/rfs/hhx084>.
Author: Emanuele Guidotti [aut, cre] ,
David Ardia [ctb] ,
Tim Kroencke [ctb]
Maintainer: Emanuele Guidotti <emanuele.guidotti@usi.ch>
Diff between bidask versions 2.0.6 dated 2024-08-18 and 2.1.4 dated 2025-02-26
DESCRIPTION | 24 +- LICENSE |only MD5 | 58 +++-- NAMESPACE | 5 R/ar.R | 29 +- R/cs.R | 42 ++-- R/edge.R | 453 ++++++++++++++++++++++++++++++++------------- R/ohlc.R | 103 +++++----- R/roll.R | 38 +-- R/sim.R | 51 ++--- R/spread.R | 108 ++++++---- R/utils.R | 55 +++-- README.md | 89 +++++++- inst/doc/bidask.R | 35 ++- inst/doc/bidask.Rmd | 90 +++++--- inst/doc/bidask.html | 242 +++++++++++------------- man/AR.Rd | 2 man/CS.Rd | 2 man/EDGE.Rd | 17 - man/OHLC.Rd | 2 man/ROLL.Rd | 2 man/bidask-package.Rd | 2 man/edge_expanding.Rd |only man/edge_rolling.Rd |only man/rfun.Rd |only man/rmean.Rd | 2 man/rsum.Rd | 6 man/sim.Rd | 19 + man/spread.Rd | 58 +++-- tests/testthat.R | 1 tests/testthat/test-edge.R | 151 ++++++++++++--- vignettes/bidask.Rmd | 90 +++++--- 32 files changed, 1129 insertions(+), 647 deletions(-)
Title: Ranking using Probabilistic Models and Treatment Choice Criteria
Description: Implementation of a novel frequentist approach to produce clinically relevant treatment hierarchies in network meta-analysis. The method is based on treatment choice criteria (TCC) and probabilistic ranking models, as described by Evrenoglou et al. (2024) <DOI:10.48550/arXiv.2406.10612>. The TCC are defined using a rule based on the minimal clinically important difference. Using the defined TCC, the study-level data (i.e., treatment effects and standard errors) are first transformed into a preference format, indicating either a treatment preference (e.g., treatment A > treatment B) or a tie (treatment A = treatment B). The preference data are then synthesized using a probabilistic ranking model, which estimates the latent ability parameter of each treatment and produces the final treatment hierarchy. This parameter represents each treatment’s ability to outperform all the other competing treatments in the network. Consequently, larger ability estimates indicate higher position [...truncated...]
Author: Theodoros Evrenoglou [aut, cre]
,
Guido Schwarzer [aut]
Maintainer: Theodoros Evrenoglou <theodoros.evrenoglou@uniklinik-freiburg.de>
Diff between mtrank versions 0.1-0 dated 2025-01-31 and 0.1-1 dated 2025-02-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/antidepressants.R | 9 ++++++--- R/mtrank.R | 34 +++++++++++++++++++++++++++------- R/tcc.R | 12 ++++++------ inst/doc/mtrank-tutorial.pdf |binary man/antidepressants.Rd | 9 ++++++--- man/mtrank.Rd | 34 +++++++++++++++++++++++++++------- 9 files changed, 93 insertions(+), 38 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.6 dated 2024-09-03 and 0.6.7 dated 2025-02-26
DESCRIPTION | 10 - MD5 | 54 +++--- NEWS.md | 16 + R/gdoc2qmd.R | 17 +- R/plot_smr.R | 68 ++++++-- R/tarpuy_plex.R | 97 +++++++++--- R/utils.R | 19 ++ R/yupana_analysis.R | 3 R/yupana_export.R | 57 ++----- R/yupana_import.R | 22 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/apps.html | 26 +-- inst/doc/heritability.html | 4 inst/doc/rticles.R | 32 +-- inst/doc/rticles.html | 28 +-- inst/doc/tarpuy.html | 4 inst/doc/yupana.html | 12 - inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy-test.dcf | 4 inst/tarpuy/server.R | 11 - inst/tarpuy/ui.R | 72 +++++--- inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 2 man/include_pdf.Rd | 42 ++--- man/plot_diagnostic.Rd | 66 ++++---- man/plot_smr.Rd | 12 - man/tarpuy_plex.Rd | 23 +- man/yupana_export.Rd | 4 man/yupana_import.Rd | 2 28 files changed, 425 insertions(+), 282 deletions(-)
Title: Data Simulation for Life Science and Breeding
Description: Data simulator including genotype, phenotype, pedigree,
selection and reproduction in R. It simulates most of reproduction process
of animals or plants and provides data for GS (Genomic Selection),
GWAS (Genome-Wide Association Study), and Breeding.
For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>.
For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.
Author: Dong Yin [aut],
Xuanning Zhang [aut],
Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Xiaohui Yuan [aut],
Xiang Zhou [aut],
Xinyun Li [aut],
Shuhong Zhao [aut],
Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xll198708@gmail.com>
Diff between simer versions 0.9.0.6 dated 2025-01-30 and 1.0.0 dated 2025-02-26
DESCRIPTION | 8 - MD5 | 154 ++++++++++++++++---------------- NAMESPACE | 178 ++++++++++++++++++------------------- R/simer.Data.R | 14 +- R/simer.Genotype.r | 22 +++- R/simer.Parameter.r | 22 ++-- R/simer.Phenotype.r | 24 ----- R/simer.Reproduces.r | 8 + R/simer.Selects.r | 8 - R/simer.r | 5 - README.md | 187 +++++++++++++++++++++++---------------- man/GxG.network.Rd | 66 ++++++------- man/IndPerGen.Rd | 90 +++++++++---------- man/annotation.Rd | 114 ++++++++++++------------ man/bigt.Rd | 78 ++++++++-------- man/build.cov.Rd | 76 ++++++++-------- man/cal.eff.Rd | 108 +++++++++++----------- man/checkEnv.Rd | 66 ++++++------- man/format_time.Rd | 56 +++++------ man/generate.map.Rd | 78 ++++++++-------- man/generate.pop.Rd | 68 +++++++------- man/geno.cvt1.Rd | 78 ++++++++-------- man/geno.cvt2.Rd | 78 ++++++++-------- man/genotype.Rd | 92 +++++++++---------- man/getfam.Rd | 72 +++++++-------- man/load_if_installed.Rd | 50 +++++----- man/logging.initialize.Rd | 52 +++++------ man/logging.log.Rd | 88 +++++++++--------- man/logging.print.Rd | 68 +++++++------- man/make_line.Rd | 66 ++++++------- man/mate.2waycro.Rd | 126 +++++++++++++------------- man/mate.3waycro.Rd | 126 +++++++++++++------------- man/mate.4waycro.Rd | 126 +++++++++++++------------- man/mate.Rd | 94 +++++++++---------- man/mate.assort.Rd | 122 ++++++++++++------------- man/mate.backcro.Rd | 126 +++++++++++++------------- man/mate.clone.Rd | 122 ++++++++++++------------- man/mate.dh.Rd | 122 ++++++++++++------------- man/mate.disassort.Rd | 122 ++++++++++++------------- man/mate.randexself.Rd | 122 ++++++++++++------------- man/mate.randmate.Rd | 122 ++++++++++++------------- man/mate.selfpol.Rd | 122 ++++++++++++------------- man/mate.userped.Rd | 115 ++++++++++++------------ man/mkl_env.Rd | 54 +++++------ man/param.annot.Rd | 108 +++++++++++----------- man/param.geno.Rd | 78 ++++++++-------- man/param.global.Rd | 88 +++++++++--------- man/param.pheno.Rd | 100 ++++++++++----------- man/param.reprod.Rd | 72 +++++++-------- man/param.sel.Rd | 84 ++++++++--------- man/param.simer.Rd | 76 ++++++++-------- man/paste_label.Rd | 62 ++++++------- man/phenotype.Rd | 208 ++++++++++++++++++++++---------------------- man/pop.geno.Rd | 42 ++++---- man/pop.map.Rd | 42 ++++---- man/print_accomplished.Rd | 54 +++++------ man/print_bar.Rd | 114 ++++++++++++------------ man/print_info.Rd | 140 ++++++++++++++--------------- man/remove_bigmatrix.Rd | 86 +++++++++--------- man/reproduces.Rd | 123 +++++++++++++------------- man/rule_wrap.Rd | 62 ++++++------- man/selects.Rd | 118 ++++++++++++------------ man/simer.Data.Bfile2MVP.Rd | 108 +++++++++++----------- man/simer.Data.Env.Rd | 118 ++++++++++++------------ man/simer.Data.Geno.Rd | 158 ++++++++++++++++----------------- man/simer.Data.Impute.Rd | 112 +++++++++++------------ man/simer.Data.Json.Rd | 128 +++++++++++++-------------- man/simer.Data.MVP2Bfile.Rd | 110 +++++++++++------------ man/simer.Data.MVP2MVP.Rd | 90 +++++++++---------- man/simer.Data.Map.Rd | 98 ++++++++++---------- man/simer.Data.Ped.Rd | 152 ++++++++++++++++---------------- man/simer.Data.Pheno.Rd | 122 ++++++++++++------------- man/simer.Data.Rd | 96 ++++++++++---------- man/simer.Data.SELIND.Rd | 102 ++++++++++----------- man/simer.Data.cHIBLUP.Rd | 114 ++++++++++++------------ man/simer.Rd | 82 ++++++++--------- man/simer.Version.Rd | 58 ++++++------ man/write.file.Rd | 68 +++++++------- 78 files changed, 3550 insertions(+), 3518 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 1.1.0 dated 2025-02-20 and 1.1.1 dated 2025-02-26
DESCRIPTION | 6 - MD5 | 40 ++++---- NEWS.md | 9 + R/args_validation.R | 6 - R/descr.R | 11 +- R/dfSummary.R | 14 ++ R/freq.R | 10 +- R/helpers.R | 15 ++- R/parse_call.R | 8 + R/tb.R | 3 inst/doc/introduction.R | 57 +++++------ inst/doc/introduction.Rmd | 53 +++++------ inst/doc/introduction.html | 216 ++++++--------------------------------------- inst/doc/rmarkdown.R | 12 +- inst/doc/rmarkdown.Rmd | 17 +-- inst/doc/rmarkdown.html | 58 ++++++------ man/descr.Rd | 2 man/tb.Rd | 3 man/zap_attr.Rd | 4 vignettes/introduction.Rmd | 53 +++++------ vignettes/rmarkdown.Rmd | 17 +-- 21 files changed, 248 insertions(+), 366 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb],
Roger Bivand [ctb] ,
Andrew Brown [ctb],
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-21 dated 2025-02-10 and 1.8-29 dated 2025-02-26
DESCRIPTION | 8 - MD5 | 68 ++++++------- NAMESPACE | 2 NEWS.md | 25 ++++ R/RcppExports.R | 12 +- R/extent.R | 1 R/gdal.R | 16 +-- R/generics.R | 5 R/options.R | 1 R/plot_vector.R | 11 -- R/sample.R | 255 ++++++++++++++++++++++++++++++++++++------------- R/time.R | 1 man/contour.Rd | 2 man/deepcopy.Rd | 23 +--- man/gdal.Rd | 5 man/merge.Rd | 2 man/panel.Rd | 2 man/rast.Rd | 2 man/roll.Rd | 14 +- man/rotate.Rd | 4 man/sample.Rd | 22 ++-- man/sapp.Rd | 2 src/RcppExports.cpp | 29 ++++- src/RcppFunctions.cpp | 35 +++++- src/focal.cpp | 6 - src/geos_methods.cpp | 14 ++ src/geos_spat.h | 7 - src/raster_methods.cpp | 4 src/read_gdal.cpp | 10 - src/read_ogr.cpp | 22 ++-- src/spatRaster.cpp | 2 src/spatRaster.h | 2 src/spatVector.cpp | 28 ++++- src/spatVector.h | 1 src/write_ogr.cpp | 26 ++++ 35 files changed, 457 insertions(+), 212 deletions(-)
Title: 1d Water Level Interpolation along the Rivers Elbe and Rhine
Description: An S4 class and several functions which utilize internally stored
datasets and gauging data enable 1d water level interpolation. The S4 class
(WaterLevelDataFrame) structures the computation and visualisation
of 1d water level information along the German federal waterways Elbe and
Rhine. 'hyd1d' delivers 1d water level data - extracted from the 'FLYS'
database - and validated gauging data - extracted from the hydrological
database 'WISKI7' - package-internally. For computations near real time
gauging data are queried externally from the 'PEGELONLINE REST API'
<https://pegelonline.wsv.de/webservice/dokuRestapi>.
Author: Arnd Weber [aut, cre] ,
Marcus Hatz [aut],
Wolfgang Stuermer [ctb],
Wilfried Wiechmann [ctb],
Benjamin Eberhardt [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hyd1d versions 0.5.2 dated 2024-07-06 and 0.5.3 dated 2025-02-26
DESCRIPTION | 10 MD5 | 20 - NEWS.md | 7 README.md | 11 build/partial.rdb |binary build/vignette.rds |binary inst/doc/hyd1d.R | 8 inst/doc/hyd1d.html | 728 ++++++++++++++++++++++---------------------- inst/doc/vignette_DE.R | 20 - inst/doc/vignette_DE.html | 754 +++++++++++++++++++++++----------------------- man/getPegelonlineW.Rd | 4 11 files changed, 789 insertions(+), 773 deletions(-)
Title: Exporting 'flextable' to 'xlsx' Files
Description: Exports 'flextable' objects to 'xlsx' files,
utilizing functionalities provided by 'flextable' and 'openxlsx2'.
Author: Tobias Heidler [aut, cre, cph]
Maintainer: Tobias Heidler <tobias.heidler@googlemail.com>
Diff between flexlsx versions 0.3.2 dated 2025-02-25 and 0.3.4 dated 2025-02-26
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 4 ++++ R/wb_apply_content.R | 32 ++++++++++---------------------- tests/testthat/test-RcppExports.R |only 5 files changed, 21 insertions(+), 28 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 18.1.0.1 dated 2025-01-08 and 19.0.1 dated 2025-02-26
arrow-18.1.0.1/arrow/tools/checksums/darwin-arm64-openssl-1.1/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/darwin-arm64-openssl-3.0/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/darwin-x86_64-openssl-1.1/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/darwin-x86_64-openssl-3.0/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/linux-openssl-1.0/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/linux-openssl-1.1/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/linux-openssl-3.0/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/windows/arrow-18.1.0.zip.sha512 |only arrow-18.1.0.1/arrow/tools/checksums/windows/arrow-18.1.0.zip.sha512-e |only arrow-18.1.0.1/arrow/tools/cpp/src/arrow/result_internal.h |only arrow-18.1.0.1/arrow/tools/cpp/src/generated/parquet_constants.cpp |only arrow-18.1.0.1/arrow/tools/cpp/src/generated/parquet_constants.h |only 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arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/accumulation_queue.h | 1 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/asof_join_node.cc | 40 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/concurrent_queue_internal.h | 20 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/doc/key_map.md | 2 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/hash_join_benchmark.cc | 121 ++ arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/options.h | 9 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/partition_util.h | 5 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/sorted_merge_node.cc | 6 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/source_node.cc | 5 arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/swiss_join.cc | 467 ++++------ arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/swiss_join_avx2.cc | 339 ++++++- arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/swiss_join_internal.h | 151 ++- arrow-19.0.1/arrow/tools/cpp/src/arrow/acero/test_util_internal.cc | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/adapters/orc/adapter.cc | 16 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arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/key_map_internal.cc | 30 arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/key_map_internal.h | 25 arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/key_map_internal_avx2.cc | 55 - arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/light_array_internal.h | 8 arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/row/grouper.cc | 3 arrow-19.0.1/arrow/tools/cpp/src/arrow/compute/row/row_encoder_internal.h | 2 arrow-19.0.1/arrow/tools/cpp/src/arrow/csv/writer.cc | 34 arrow-19.0.1/arrow/tools/cpp/src/arrow/dataset/ArrowDatasetConfig.cmake.in | 8 arrow-19.0.1/arrow/tools/cpp/src/arrow/dataset/CMakeLists.txt | 2 arrow-19.0.1/arrow/tools/cpp/src/arrow/dataset/scanner.cc | 11 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/expression_internal.cc | 38 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/expression_internal.h | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/extended_expression_internal.h | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/extension_set.cc | 11 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/plan_internal.h | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/relation_internal.h | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/serde.cc | 2 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/test_plan_builder.cc | 6 arrow-19.0.1/arrow/tools/cpp/src/arrow/engine/substrait/util_internal.h | 4 arrow-19.0.1/arrow/tools/cpp/src/arrow/extension_type.h | 2 arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/azurefs.cc | 89 + arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/azurefs.h | 14 arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/filesystem.cc | 36 arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/gcsfs.cc | 7 arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/gcsfs.h | 3 arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/s3_internal.h | 87 + arrow-19.0.1/arrow/tools/cpp/src/arrow/filesystem/s3_test_cert_internal.h |only 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Title: Time-to-Event Dose-Finding Design for Multiple Toxicity Grades
Description: In some phase I trials, the design goal is to find the dose associated with a certain target toxicity rate or the dose with a certain weighted sum of rates of various toxicity grades. 'TITEgBOIN' provides the set up and calculations needed to run a dose-finding trial using bayesian optimal interval (BOIN) (Yuan et al. (2016) <doi:10.1158/1078-0432.CCR-16-0592>), generalized bayesian optimal interval (gBOIN) (Mu et al. (2019) <doi:10.1111/rssc.12263>), time-to-event bayesian optimal interval (TITEBOIN) (Lin et al. (2020) <doi:10.1093/biostatistics/kxz007>) and time-to-event generalized bayesian optimal interval (TITEgBOIN) (Takeda et al. (2022) <doi:10.1002/pst.2182>) designs. 'TITEgBOIN' can conduct tasks: run simulations and get operating characteristics; determine the dose for the next cohort; select maximum tolerated dose (MTD). These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose limiting toxicity (DLT) [...truncated...]
Author: Jing Zhu [cre, aut],
Jun Zhang [aut],
Kentaro Takeda [aut]
Maintainer: Jing Zhu <zhujing716@gmail.com>
Diff between TITEgBOIN versions 0.3.0 dated 2023-12-01 and 0.4.0 dated 2025-02-26
DESCRIPTION | 8 MD5 | 16 - NAMESPACE | 17 - R/get_oc_TITE_QuasiBOIN.R | 385 ++++++++++++++++++++++++++-------- R/next_TITE_QuasiBOIN.R | 126 ++++++++--- R/select_mtd_TITE_QuasiBOIN.R | 69 ++++-- man/get_oc_TITE_QuasiBOIN.Rd | 433 +++++++++++++++++++-------------------- man/next_TITE_QuasiBOIN.Rd | 289 ++++++++++++-------------- man/select_mtd_TITE_QuasiBOIN.Rd | 173 +++++++-------- 9 files changed, 899 insertions(+), 617 deletions(-)
Title: A Collection of Modified R Functions to Make Basic Coding More
Convenient
Description: A collection of recycled and modified R functions to aid in file manipulation, data exploration, wrangling, optimization, and object manipulation. Other functions aid in convenient data visualization, loop progression, software packaging, and installation.
Author: Paul Little [aut, cre]
Maintainer: Paul Little <pllittle321@gmail.com>
Diff between smarter versions 1.0.0 dated 2025-01-29 and 1.0.1 dated 2025-02-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/basic.R | 10 +++++----- R/latex.R | 36 +++++++++++++++++------------------- R/make_menu.R | 8 ++++---- R/plots.R | 16 ++++++++-------- 6 files changed, 43 insertions(+), 45 deletions(-)