Title: Dataset and Variable Picker and Merge Module for 'teal'
Applications
Description: Allows users to interactively select datasets, variables, and
values within 'teal' applications using a 'tidyselect'-style
interface. Selected picks can be merged and transformed into
analysis-ready data within 'teal' modules.
Author: Dawid Kaledkowski [aut] ,
Andre Verissimo [aut] ,
Marcin Kosinski [aut],
Lluis Revilla Sancho [aut] ,
Oriol Senan [aut] ,
Dony Unardi [rev, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.picks versions 0.3.0 dated 2026-07-30 and 0.3.1 dated 2026-10-09
DESCRIPTION | 23 - MD5 | 70 ++-- NAMESPACE | 3 NEWS.md | 16 + R/as_picks.R | 5 R/helpers.R | 75 +++++ R/module_merge.R | 6 R/module_picks.R | 67 +++- R/picks.R | 38 +- R/resolver.R | 34 +- R/teal.picks.R | 1 R/tm_merge.R | 2 R/zzz.R | 10 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/teal-picks-in-teal.html | 4 inst/doc/teal-picks-standalone-shiny.html | 4 man/as.picks.Rd | 7 man/dot-determine_choices.Rd | 2 man/ensure_picks_datasets.Rd |only man/picks_datanames.Rd |only man/picks_module.Rd | 20 + tests/testthat.R | 2 tests/testthat/helper-shinytest2_options.R | 2 tests/testthat/test-as_picks.R | 58 ++-- tests/testthat/test-assertion.R | 34 +- tests/testthat/test-badge_dropdown.R | 2 tests/testthat/test-helper-shinytest2.R | 8 tests/testthat/test-helpers.R | 108 +++++-- tests/testthat/test-interaction.R | 10 tests/testthat/test-module_merge.R | 228 +++++++++++---- tests/testthat/test-module_picks.R | 239 ++++++++-------- tests/testthat/test-picks.R | 372 +++++++++++++++----------- tests/testthat/test-print.R | 40 +- tests/testthat/test-shinytest2-module_picks.R |only tests/testthat/test-tidyselect_helpers.R | 90 +++--- tests/testthat/test-tm_merge.R | 54 +-- tests/testthat/test-zzz.R |only 38 files changed, 1012 insertions(+), 623 deletions(-)
Title: Create Datasets with Hidden Images in Residual Plots
Description: Implements the "Residual (Sur)Realism" algorithm described by
Stefanski (2007) <doi:10.1198/000313007X190079> to generate datasets
that reveal hidden images or messages in their residual plots. It offers
both predefined datasets and tools to embed custom text or images
into residual structures. Allowing users to create intriguing visual
demonstrations for teaching model diagnostics.
Author: James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <james.balamuta@gmail.com>
Diff between surreal versions 0.0.2 dated 2026-01-11 and 0.0.3 dated 2026-10-09
DESCRIPTION | 10 MD5 | 64 +++- NAMESPACE | 9 NEWS.md | 50 +++ R/data-documentation.R | 2 R/surreal-app.R | 6 R/surreal-decoys.R |only R/surreal-image.R | 269 +++++++++++------ R/surreal-path.R |only R/surreal-text.R | 82 ++++- R/surreal-trace.R |only R/surreal.R | 158 +++++++--- README.md | 39 ++ build/partial.rdb |binary inst/surreal-app/R |only inst/surreal-app/app.R | 608 +++++++++++++++++++++------------------ man/figures/app-surreal.png |only man/jackolantern_surreal_data.Rd | 2 man/plot.surreal_path.Rd |only man/plot.surreal_trace.Rd |only man/surreal_app.Rd | 6 man/surreal_decoys.Rd |only man/surreal_image.Rd | 1 man/surreal_image_points.Rd |only man/surreal_path.Rd |only man/surreal_text.Rd | 7 man/surreal_text_points.Rd |only man/surreal_trace.Rd |only tests |only 29 files changed, 876 insertions(+), 437 deletions(-)
Title: Vignettes for Analyzing Data using 'OlinkAnalyze'
Description: Exemplifying analysis of large-scale protein
data from the 'Olink platform', primarily relative protein expression
data that has been exported from
'Olink NPX Software', as well as QUANT data from 'Olink'.
QUANT data is log-transformed. Materials focus on reading data,
demonstrating data wrangling and quality control analysis,
performing statistical analysis and generating
figures to visualize the results of the statistical analysis.
The goal of this package is to guide users extract biological insights
from large-scale protein data run on the 'Olink platform'.
More information on 'Olink' data can be found at <https://olink.com/>.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyzeVignettes versions 1.0.1 dated 2026-06-08 and 1.1.0 dated 2026-10-09
DESCRIPTION | 10 MD5 | 34 NEWS.md | 7 build/vignette.rds |binary inst/doc/bridging_cross-product.R | 1342 ++++---- inst/doc/bridging_cross-product.html | 5329 +++++++++++++++++------------------ inst/doc/bridging_introduction.R | 1412 ++++----- inst/doc/bridging_introduction.Rmd | 16 inst/doc/bridging_introduction.html | 4863 +++++++++++++++---------------- inst/doc/lod.R | 654 ++-- inst/doc/lod.Rmd | 4 inst/doc/lod.html | 3658 ++++++++++++------------ inst/doc/outlier_exclusion.R | 938 +++--- inst/doc/outlier_exclusion.html | 1973 ++++++------ inst/doc/plate_randomizer.R | 292 - inst/doc/plate_randomizer.html | 2209 +++++++------- vignettes/bridging_introduction.Rmd | 16 vignettes/lod.Rmd | 4 18 files changed, 11393 insertions(+), 11368 deletions(-)
More information about OlinkAnalyzeVignettes at CRAN
Permanent link
Title: Circular Analyses Helper Functions
Description: Light-weight functions for computing descriptive statistics in different circular spaces (e.g., 2pi, 180, or 360 degrees), to handle angle-dependent biases, pad circular data, and more. Specifically aimed for psychologists and neuroscientists analyzing circular data. Basic methods are based on Jammalamadaka and SenGupta (2001) <doi:10.1142/4031>, removal of cardinal biases is based on the approach introduced in van Bergen, Ma, Pratte, & Jehee (2015) <doi:10.1038/nn.4150> and Chetverikov and Jehee (2023) <doi:10.1038/s41467-023-43251-w>.
Author: Andrey Chetverikov [aut, cre] ,
Eline Van Geert [ctb]
Maintainer: Andrey Chetverikov <andrey.chetverikov@uib.no>
Diff between circhelp versions 1.1 dated 2024-07-04 and 1.4.0 dated 2026-10-09
DESCRIPTION | 25 MD5 | 68 NAMESPACE | 129 NEWS.md | 69 R/circhelp-package.R | 50 R/data.R | 6 R/functions.R | 2986 ++++++++++------- README.md | 182 - build/circhelp.pdf |only build/stage23.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/cardinal_biases.R | 66 inst/doc/cardinal_biases.Rmd | 271 - inst/doc/cardinal_biases.html | 135 inst/doc/serial_dependence_with_density_asymmetry.R |only inst/doc/serial_dependence_with_density_asymmetry.Rmd |only inst/doc/serial_dependence_with_density_asymmetry.html |only man/Bae_Luck_2018_data.Rd | 6 man/angle_diff_rad.Rd | 7 man/circ_corr.Rd | 7 man/circ_lin_corr.Rd | 3 man/circ_loess.Rd | 1 man/circ_mean_rad.Rd | 7 man/circ_sd_rad.Rd | 7 man/circhelp-package.Rd | 5 man/density_asymmetry.Rd |only man/density_asymmetry_discrete.Rd |only man/get_boundary_preds.Rd | 17 man/pad_circ.Rd | 2 man/remove_cardinal_biases.Rd | 16 man/smoothed_circ_sd.Rd |only man/vm_kappa_to_circ_sd.Rd | 4 man/weighted_circ_mean.Rd | 6 man/weighted_sem.Rd | 2 tests/testthat.R | 2 tests/testthat/test-density-asymmetry.R |only tests/testthat/test-functions.R | 157 vignettes/cardinal_biases.Rmd | 271 - vignettes/serial_dependence_with_density_asymmetry.Rmd |only 40 files changed, 2776 insertions(+), 1731 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'ewtp', 'rewtp', 'ewtpr', 'rewtpr', 'max', 'wtr', 'rwtr', 'pwt', and 'rpwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<doi:10.1002/sim.10045>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 1.0.0 dated 2026-09-11 and 1.0.1 dated 2026-10-09
DESCRIPTION | 6 +-- MD5 | 10 ++--- R/bootstrap.R | 12 ++++++ R/ewt.R | 73 +++++++++++++++++++++++++++++++---------- R/rmt.R | 6 ++- inst/doc/wintime_vignette.html | 20 +++++------ 6 files changed, 89 insertions(+), 38 deletions(-)
Title: Sample Size Estimation for Bio-Equivalence Trials Through
Simulation
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach
that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in
hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints.
Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability,
and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error
rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for
equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987)
<doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022)
<doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>.
Comprehensive documentation and vignettes guid [...truncated...]
Author: Thomas Debray [aut, cre],
Tim Friede [ctb],
Johanna Munoz [ctb],
Dewi Amaliah [ctb],
Wei Wei [ctb],
Marian Mitroiu [ctb],
Scott McDonald [ctb],
Biogen Inc [cph, fnd] ,
Smart Data Analysis and Statistics B.V. [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>
Diff between SimTOST versions 1.0.1 dated 2025-02-18 and 1.1.0 dated 2026-10-09
SimTOST-1.0.1/SimTOST/R/helper.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_crossover.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_crossover.Rmd |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_crossover.html |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel.Rmd |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel.html |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A1E.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A1E.Rmd |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A1E.html |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A3E.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A3E.Rmd |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_2A3E.html |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_3A1E.R |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_3A1E.Rmd |only SimTOST-1.0.1/SimTOST/inst/doc/sampleSize_parallel_3A1E.html |only 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SimTOST-1.1.0/SimTOST/R/confint.simss.R |only SimTOST-1.1.0/SimTOST/R/count.R |only SimTOST-1.1.0/SimTOST/R/count_joint.R |only SimTOST-1.1.0/SimTOST/R/count_methods.R |only SimTOST-1.1.0/SimTOST/R/diagnostic_plots.R |only SimTOST-1.1.0/SimTOST/R/distribution_plots.R |only SimTOST-1.1.0/SimTOST/R/get_par.R | 190 SimTOST-1.1.0/SimTOST/R/helper.r |only SimTOST-1.1.0/SimTOST/R/plot.sims.R | 314 + SimTOST-1.1.0/SimTOST/R/plot_helpers.R |only SimTOST-1.1.0/SimTOST/R/power.R |only SimTOST-1.1.0/SimTOST/R/print.simss_mielke.R |only SimTOST-1.1.0/SimTOST/R/run_simulations.R |only SimTOST-1.1.0/SimTOST/R/sampleSize_Mielke.R | 520 +- SimTOST-1.1.0/SimTOST/R/sim_data.R |only SimTOST-1.1.0/SimTOST/R/simpower_methods.R |only SimTOST-1.1.0/SimTOST/R/summary.simss.R |only SimTOST-1.1.0/SimTOST/R/type1Error.R |only SimTOST-1.1.0/SimTOST/R/type1Error_joint_methods.R |only SimTOST-1.1.0/SimTOST/R/type1Error_methods.R |only SimTOST-1.1.0/SimTOST/R/update_methods.R |only SimTOST-1.1.0/SimTOST/R/utils.R | 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SimTOST-1.1.0/SimTOST/man/test_par_rom.Rd | 168 SimTOST-1.1.0/SimTOST/man/type1Error.Rd |only SimTOST-1.1.0/SimTOST/man/uniroot.integer.mod.Rd | 104 SimTOST-1.1.0/SimTOST/man/update.countpower.Rd |only SimTOST-1.1.0/SimTOST/man/update.countss.Rd |only SimTOST-1.1.0/SimTOST/man/update.simpower.Rd |only SimTOST-1.1.0/SimTOST/man/update.simss.Rd |only SimTOST-1.1.0/SimTOST/src/Makevars | 2 SimTOST-1.1.0/SimTOST/src/Makevars.win | 2 SimTOST-1.1.0/SimTOST/src/RcppExports.cpp | 121 SimTOST-1.1.0/SimTOST/src/module.cpp | 629 +++ SimTOST-1.1.0/SimTOST/tests/testthat.R | 24 SimTOST-1.1.0/SimTOST/tests/testthat/test-check_equivalence.R | 127 SimTOST-1.1.0/SimTOST/tests/testthat/test-count-crossover.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-count-methods.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-count-simulation-inputs.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-derive_varcov_list.R | 51 SimTOST-1.1.0/SimTOST/tests/testthat/test-diagnostic-plots.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-distribution-parameters.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-endpoint-resolution.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-error_armnames.R | 62 SimTOST-1.1.0/SimTOST/tests/testthat/test-error_length_mu_sd.R | 62 SimTOST-1.1.0/SimTOST/tests/testthat/test-error_log_dom.R | 62 SimTOST-1.1.0/SimTOST/tests/testthat/test-error_logf_rom_2x2.R | 62 SimTOST-1.1.0/SimTOST/tests/testthat/test-error_no_mu.R | 68 SimTOST-1.1.0/SimTOST/tests/testthat/test-error_no_sigma.R | 56 SimTOST-1.1.0/SimTOST/tests/testthat/test-mielke-adjustment.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-power_cal.R | 330 - SimTOST-1.1.0/SimTOST/tests/testthat/test-run_simulations_2x2_dom.R | 98 SimTOST-1.1.0/SimTOST/tests/testthat/test-run_simulations_par_dom.R | 112 SimTOST-1.1.0/SimTOST/tests/testthat/test-same_results.R | 106 SimTOST-1.1.0/SimTOST/tests/testthat/test-test_2x2_dom.R | 76 SimTOST-1.1.0/SimTOST/tests/testthat/test-test_par_dom.R | 198 - SimTOST-1.1.0/SimTOST/tests/testthat/test-test_studies.R | 310 - SimTOST-1.1.0/SimTOST/tests/testthat/test-type1Error.R |only SimTOST-1.1.0/SimTOST/tests/testthat/test-update-methods.R |only SimTOST-1.1.0/SimTOST/vignettes/continuous_crossover.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/continuous_parallel.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/continuous_parallel_2A1E.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/continuous_parallel_2A3E.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/continuous_parallel_3A1E.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/continuous_parallel_3A3E.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/count.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/count_parallel_3A3E.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/intropkg.Rmd | 466 +- SimTOST-1.1.0/SimTOST/vignettes/methodological_assumptions.Rmd |only SimTOST-1.1.0/SimTOST/vignettes/references.bib | 576 +- SimTOST-1.1.0/SimTOST/vignettes/workflow.Rmd |only 194 files changed, 8412 insertions(+), 5737 deletions(-)
Title: A Collection of Proteome Panels and Metadata
Description: It aggregates protein panel data and metadata for protein quantitative
trait locus (pQTL) analysis using 'pQTLtools' (<https://jinghuazhao.github.io/pQTLtools/>).
The package includes data from affinity-based panels such as 'Olink' (<https://olink.com/>)
and 'SomaScan' (<https://somalogic.com/>), as well as mass spectrometry-based panels from
'CellCarta' (<https://cellcarta.com/>), 'Seer' (<https://seer.bio/>) and 'SWATH-MS'
(<doi:10.15252/msb.20178126>). The metadata encompasses updated annotations
and publication details.
Author: Jing Hua Zhao [aut, cre] ,
Uwe Ligges [ctb],
Benjamin Altmann [ctb],
Brian Ripley [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between pQTLdata versions 0.6 dated 2026-03-09 and 0.7 dated 2026-10-09
DESCRIPTION | 14 ++--- MD5 | 71 +++++++++++++++------------- NEWS.md | 9 +++ R/caprion.R | 44 +++++++++++------ build/partial.rdb |binary build/vignette.rds |binary data/Olink_Explore_1536.rda |binary data/Olink_Explore_3072.rda |binary data/Olink_Explore_HT.rda |binary data/Olink_Target_96.rda |binary data/Olink_qPCR.rda |binary data/SomaScan11k.rda |binary data/SomaScan160410.rda |binary data/SomaScanV4.1.rda |binary data/caprion.rda |binary data/inf1.rda |binary data/scallop_inf1.rda |binary data/seer1980.rda |binary data/swath_ms.rda |binary inst/UniProt |only inst/doc/pQTLdata.html | 108 ++++++++++++++++++++++---------------------- inst/scripts/caprion.py |only inst/scripts/caprion2.R |only inst/scripts/cran.sh | 49 ++++++------------- inst/scripts/hg19Tables.R | 2 man/Olink_Explore_1536.Rd | 2 man/Olink_Explore_3072.Rd | 2 man/Olink_Explore_HT.Rd | 2 man/Olink_Target_96.Rd | 2 man/Olink_qPCR.Rd | 2 man/SomaScan11k.Rd | 2 man/SomaScan160410.Rd | 2 man/SomaScanV4.1.Rd | 2 man/caprion.Rd | 48 ++++++++++++------- man/inf1.Rd | 2 man/scallop_inf1.Rd | 2 man/seer1980.Rd | 2 man/swath_ms.Rd | 2 38 files changed, 194 insertions(+), 175 deletions(-)
Title: Estimation, Simulation and Reliability of Drifting Markov Models
Description: Performs the drifting Markov models (DMM) which are
non-homogeneous Markov models designed for modeling the heterogeneities of
sequences in a more flexible way than homogeneous Markov chains or even
hidden Markov models. In this context, we developed an R package dedicated to
the estimation, simulation and the exact computation of associated reliability
of drifting Markov models. The implemented methods are described in
Vergne, N. (2008), <doi:10.2202/1544-6115.1326> and
Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .
Author: Nicolas Vergne [aut, cre] ,
Corentin Lothode [aut] ,
Alexandre Seiller [aut],
Victor Mataigne [ctb],
Arnaud Lefebvre [ctb],
Annthomy Gilles [ctb],
Vlad Stefan Barbu [aut]
Maintainer: Nicolas Vergne <nicolas.vergne@univ-rouen.fr>
Diff between drimmR versions 1.0.3 dated 2026-02-12 and 1.0.4 dated 2026-10-09
DESCRIPTION | 9 +++++---- MD5 | 23 +++++++++++++++-------- NAMESPACE | 3 +-- NEWS.md | 12 ++++++++++++ R/allgenerics.R | 2 +- R/dmm.R | 13 ++++++++----- R/metrics.R | 12 ++++++++---- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/drimmR-package.Rd | 18 ++++++++++++++++++ vignettes |only 12 files changed, 68 insertions(+), 24 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
Selvaraj Shanmugam [ctb],
Renfei Mao [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.7 dated 2026-09-28 and 0.0.8 dated 2026-10-09
DESCRIPTION | 12 ++++++--- MD5 | 72 +++++++++++++++++++++++++++--------------------------- NEWS.md | 8 +++++- R/adae.R | 2 - R/adaecomp.R | 2 - R/adaeocmq.R | 2 - R/adagocmq.R | 2 - R/adcm.R | 2 - R/addili.R | 2 - R/addisp.R | 2 - R/adeg.R | 2 - R/adex.R | 2 - R/adexsum.R | 2 - R/adishum.R | 2 - R/adlb.R | 2 - R/adpc.R | 2 - R/adsl.R | 2 - R/adslcomp.R | 2 - R/adttesaf.R | 2 - R/advs.R | 2 - data/adae.rda |binary data/adaecomp.rda |binary data/adaeocmq.rda |binary data/adcm.rda |binary data/addili.rda |binary data/addisp.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adishum.rda |binary data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adslcomp.rda |binary data/adttesaf.rda |binary data/advs.rda |binary man/adlb.Rd | 2 - 37 files changed, 70 insertions(+), 58 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03167>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 1.1.1 dated 2026-08-25 and 1.1.2 dated 2026-10-09
DESCRIPTION | 32 +-- MD5 | 154 ++++++++--------- NAMESPACE | 18 +- NEWS.md | 8 R/0-utils.R | 5 R/combine-plots.R | 2 R/data.R | 29 +-- R/extract-stats.R | 28 ++- R/ggbarstats.R | 19 +- R/ggbetweenstats-helpers.R | 12 - R/ggbetweenstats.R | 49 +++-- R/ggcoefstats.R | 62 ++++--- R/ggcorrmat.R | 44 +++- R/ggdotplotstats.R | 25 +- R/gghistostats-helpers.R | 22 -- R/gghistostats.R | 25 +- R/ggpiestats.R | 61 ++++-- R/ggscatterstats.R | 22 +- R/ggstatsplot-package.R | 2 R/ggwithinstats.R | 12 + R/theme-ggstatsplot.R | 2 README.md | 74 ++++---- inst/doc/additional.Rmd | 66 +------ inst/doc/additional.html | 48 +---- inst/doc/ggstatsplot.Rmd | 12 + inst/doc/ggstatsplot.html | 22 +- man/Titanic_full.Rd | 4 man/bugs_long.Rd | 16 - man/combine_plots.Rd | 2 man/dot-grouped_list.Rd | 5 man/extract_stats.Rd | 29 ++- man/figures/README-customplot-1.png |binary man/figures/README-ggcorrmat1-1.png |binary man/figures/README-ggwithinstats2-1.png |binary man/ggbarstats.Rd | 69 ++++--- man/ggbetweenstats.Rd | 35 ++- man/ggcoefstats.Rd | 76 ++++---- man/ggcorrmat.Rd | 40 ++-- man/ggdotplotstats.Rd | 36 ++-- man/gghistostats.Rd | 26 +- man/ggpiestats.Rd | 65 ++++--- man/ggscatterstats.Rd | 22 +- man/ggstatsplot-package.Rd | 2 man/ggwithinstats.Rd | 35 ++- man/grouped_ggbarstats.Rd | 62 ++++--- man/grouped_ggbetweenstats.Rd | 39 ++-- man/grouped_ggcorrmat.Rd | 44 +++- man/grouped_ggdotplotstats.Rd | 43 +++- man/grouped_gghistostats.Rd | 39 ++-- man/grouped_ggpiestats.Rd | 54 +++--- man/grouped_ggscatterstats.Rd | 27 ++- man/grouped_ggwithinstats.Rd | 39 ++-- man/iris_long.Rd | 8 man/movies_long.Rd | 8 man/rmd-fragments/ggcoefstats_graphics.Rmd | 2 man/rmd-fragments/ggdotplotstats_graphics.Rmd | 4 man/theme_ggstatsplot.Rd | 2 tests/testthat.R | 3 tests/testthat/test-ggbetweenstats.R | 15 + tests/testthat/test-ggwithinstats.R | 16 + vignettes/additional.Rmd | 66 +------ vignettes/ggstatsplot.Rmd | 12 + vignettes/paper.bib | 21 -- vignettes/web_only/faq.Rmd | 229 +++++++++++++++++++------- vignettes/web_only/ggbarstats.Rmd | 62 +++++-- vignettes/web_only/ggbetweenstats.Rmd | 85 ++++++--- vignettes/web_only/ggcoefstats.Rmd | 80 +++++---- vignettes/web_only/ggcorrmat.Rmd | 59 ++++-- vignettes/web_only/ggdotplotstats.Rmd | 48 ++++- vignettes/web_only/gghistostats.Rmd | 67 ++++--- vignettes/web_only/ggpiestats.Rmd | 63 +++++-- vignettes/web_only/ggscatterstats.Rmd | 71 ++++---- vignettes/web_only/ggwithinstats.Rmd | 158 +++++++++++------ vignettes/web_only/interpretation.Rmd | 34 ++- vignettes/web_only/pairwise.Rmd | 67 ++++--- vignettes/web_only/paper.bib | 18 -- vignettes/web_only/principles.Rmd | 74 ++++---- vignettes/web_only/purrr_examples.Rmd | 126 ++++++-------- 78 files changed, 1832 insertions(+), 1230 deletions(-)
Title: Demonstration of Disease Freedom (DDF)
Description: Implements the formulae required to calculate freedom
from disease according to Cameron and Baldock (1998)
<doi:10.1016/S0167-5877(97)00081-0>. These are the
methods used at the Swedish national veterinary institute (SVA) to
evaluate the performance of our nation animal disease
surveillance programmes.
Author: Thomas Rosendal [aut, cre] ,
Petter Hopp [ctb]
Maintainer: Thomas Rosendal <trosendal@gmail.com>
Diff between freedom versions 1.0.1 dated 2020-09-08 and 1.1.1 dated 2026-10-09
DESCRIPTION | 22 +-- MD5 | 52 ++++--- NAMESPACE | 3 NEWS.md | 27 +++ R/data_gen.R | 73 +++++----- R/distribution.R | 9 - R/freedom-package.R |only R/herd_se.R | 101 ++++++++++---- R/risk.R | 25 ++- R/temporal_discounting.R | 13 + README.md | 5 build/vignette.rds |binary inst/doc/simple_prob_freedom.R | 6 inst/doc/simple_prob_freedom.html | 266 +++++++++++++++++-------------------- man/hse.Rd | 21 ++ man/hse_finite.Rd | 20 ++ man/rpert.Rd | 1 man/sysse.Rd | 10 - tests/EPHI.R |only tests/adjusted_risk.R |only tests/gen_data.R | 34 ++-- tests/hse.R |only tests/hse_finite.R |only tests/hse_infinite.R |only tests/multi_risk_herd_and_animal.R | 68 +++++---- tests/multirisk_test.R | 4 tests/pert.R |only tests/risk.R | 25 ++- tests/sample_data.R |only tests/sysse.R |only tests/sysse_finite.R |only tests/temporal_discounting.R |only tests/valid_proportion.R |only 33 files changed, 473 insertions(+), 312 deletions(-)
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells. It also predicts the direction (up or down) of the response of each gene from the WT expression, and reads all knockouts of a network from a single heat kernel, which makes transcriptome-wide knockout screens practical.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Qian Xu [aut, ctb],
Yongjian Yang [aut, ctb],
Yanan Tian [aut, ctb],
Robert Chapkin [aut, ctb],
Jianhua Huang [aut, ctb],
James J. Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldKnk versions 1.1 dated 2026-09-02 and 2.0.0 dated 2026-10-09
DESCRIPTION | 12 +- MD5 | 29 ++++-- NAMESPACE | 13 ++ NEWS.md |only R/dRegulation.R | 74 ++++++++++++++- R/heatKernel.R |only R/perturbationMap.R |only R/plotKO.R | 22 +++- R/restoreSeed.R |only R/scTenifoldKnk.R | 216 ++++++++++++++++++++++++++++++--------------- man/dRegulation.Rd | 37 ++++++- man/heatKernel.Rd |only man/hkManifoldAlignment.Rd |only man/knockoutDirection.Rd |only man/perturbationMap.Rd |only man/plotKO.Rd | 3 man/scTenifoldKnk.Rd | 50 ++++++++-- tests |only 18 files changed, 345 insertions(+), 111 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides a
high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<doi:10.48550/arXiv.1902.08318> paper for more details about 'simdjson'. This
package parses 'JSON' from string, file, or remote URLs under a variety of
settings.
Author: Dirk Eddelbuettel [aut, cre] ,
Brendan Knapp [aut] ,
Daniel Lemire [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.15 dated 2026-01-14 and 0.1.16 dated 2026-10-09
ChangeLog | 118 DESCRIPTION | 10 MD5 | 67 R/RcppExports.R | 22 R/exported-utils.R | 5 R/fload.R | 2 R/fparse.R | 63 R/utils.R | 15 build/partial.rdb |binary inst/NEWS.Rd | 15 inst/include/RcppSimdJson/common.hpp | 118 inst/include/RcppSimdJson/deserialize.hpp | 112 inst/include/RcppSimdJson/deserialize/Type_Doctor.hpp | 15 inst/include/RcppSimdJson/deserialize/dataframe.hpp | 402 inst/include/RcppSimdJson/deserialize/matrix.hpp | 21 inst/include/RcppSimdJson/deserialize/scalar.hpp | 22 inst/include/RcppSimdJson/deserialize/simplify.hpp | 26 inst/include/RcppSimdJson/deserialize/vector.hpp | 35 inst/include/RcppSimdJson_RcppExports.h | 2 inst/include/simdjson.cpp |31756 +++- inst/include/simdjson.h |141442 ++++++++++++++---- inst/tinytest/test_fparse_fload.R | 1 inst/tinytest/test_misc.R | 8 inst/tinytest/test_query.R | 16 man/fparse.Rd | 3 man/parseExample.Rd | 10 man/release_json_memory.Rd |only man/simdjson-utilities.Rd | 3 src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 14 src/deserialize.cpp | 4 src/exported-utils.cpp | 22 src/internal-utils.cpp | 4 src/simdjson_example.cpp | 4 35 files changed, 144121 insertions(+), 30242 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre] ,
Tom Willis [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 1.1.0 dated 2026-09-17 and 1.2.0 dated 2026-10-09
DESCRIPTION | 20 ++-- MD5 | 57 ++++++----- NAMESPACE | 18 --- NEWS.md | 8 + R/eqtl_plot.R | 4 R/eqtl_plotly.R |only R/genetrack_ly.R | 30 ++++-- R/gg_scatter.R | 11 +- R/link_LD.R | 2 R/link_eqtl.R | 16 ++- R/locus_plotly.R | 82 ++++++++++++---- R/overlay_plotly.R |only R/scatter_plotly.R | 9 - R/zoom.R | 218 +++++++++++++++++++++++++++++++++++---------- R/zoom_funcs.R | 17 +++ inst/doc/locuszoomr.R | 38 +++---- inst/doc/locuszoomr.Rmd | 42 ++++---- inst/doc/locuszoomr.html | 62 ++++++------ inst/doc/zoom_browser.R | 9 + inst/doc/zoom_browser.Rmd | 26 ++++- inst/doc/zoom_browser.html | 27 ++++- man/eqtl_plotly.Rd |only man/genetrack_ly.Rd | 6 + man/link_LD.Rd | 2 man/link_eqtl.Rd | 17 ++- man/locus_plotly.Rd | 31 ++++-- man/overlay_plotly.Rd |only man/zoom.Rd | 9 + vignettes/locuszoomr.Rmd | 42 ++++---- vignettes/zoom2.png |binary vignettes/zoom_browser.Rmd | 26 ++++- vignettes/zoom_eqtl.png |only 32 files changed, 548 insertions(+), 281 deletions(-)
Title: Explore and Analyse General Transit Feed Specification (GTFS)
Files with a Focus on Urban Mobility
Description: A bundle of methods to
harmonize GTFS and OSM data, enabling the integration and exploration
of different layers of transit data, starting with the planned
operations (GTFS), but also the infrastructure topology (OSM) and
real-time information (GTFS-RT).
Author: Goncalo F. Matos [aut, cre] ,
Rosa Felix [aut] ,
Miguel Relvas Pires [ctb]
Maintainer: Goncalo F. Matos <goncaloafmatos@tecnico.pt>
Diff between GTFShift versions 1.0.0 dated 2026-09-27 and 1.1.0 dated 2026-10-09
DESCRIPTION | 6 +- MD5 | 44 +++++++++-------- NAMESPACE | 6 ++ NEWS.md |only R/get_trip_speed_profile.R |only R/osm_utils.R | 26 ++++++++++ R/query_osm_bus_lanes.R | 14 +++-- R/query_osm_centerlines.R | 2 R/query_osm_shapes_match_routes.R | 1 R/query_osm_shapes_to_routes.R | 1 R/rt_extend_prioritisation.R | 4 + README.md | 15 ++++-- inst/WORDLIST | 1 inst/doc/GTFShift.R | 5 +- inst/doc/GTFShift.Rmd | 13 ++++- inst/doc/GTFShift.html | 16 +++--- man/get_trip_speed_profile.Rd |only man/osm_bus_lanes.Rd | 6 +- man/osm_centerlines.Rd | 2 man/rt_collect_protobuf.Rd | 1 man/rt_extend_prioritisation.Rd | 2 tests/testthat/test-get_trip_speed_profile.R |only tests/testthat/test-osm_utils.R | 34 +++++++++++++ tests/testthat/test-rt_extend_prioritisation.R | 62 ++++++++++++++++++++++++- vignettes/GTFShift.Rmd | 13 ++++- 25 files changed, 221 insertions(+), 53 deletions(-)
Title: Fuzzy and Non-Fuzzy Classifiers
Description: It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
Author: Jodavid Ferreira [aut, cre] ,
Ronei Moraes [ctb] ,
Liliane Machado [ctb] ,
Arthur Ricardo [ctb],
Isaac Araujo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Diff between FuzzyClass versions 0.1.7 dated 2025-09-03 and 0.2.0 dated 2026-10-09
DESCRIPTION | 16 MD5 | 103 +- NAMESPACE | 40 - NEWS.md | 20 R/DWFuzzyGammaNaiveBayes.R | 76 - R/DoubleWeightedFuzzyHiperGeometricNaiveBayes.R | 193 +--- R/ExpNBFuzzyParam.R | 127 --- R/FuzzyBayesRule.R | 54 - R/FuzzyBetaNaiveBayes.R | 66 - R/FuzzyBinomialNaiveBayes.R | 101 +- R/FuzzyExponentialNaiveBayes.R | 75 - R/FuzzyGammaNaiveBayes.R | 75 - R/FuzzyGaussianNaiveBayes.R | 97 +- R/FuzzyGeoNaiveBayes.R | 191 +--- R/FuzzyHiperGeometricNaiveBayes.R | 180 +--- R/FuzzyNaiveBayes.R | 271 ++---- R/FuzzyPoissonNaiveBayes.R | 82 -- R/FuzzyRuleBasedSystem.R | 53 - R/FuzzyTrapeNaiveBayes.R | 149 +-- R/FuzzyTriangNaiveBayes.R | 98 -- R/GauNBFuzzyParam.R | 123 --- R/PoiNBFuzzyParam.R | 135 --- R/functions.R | 935 +++++++++++++++--------- R/getMembershipsTrapezoidal.R | 1 README.md | 440 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/FuzzyClass.Rmd | 2 inst/doc/FuzzyClass.html | 6 inst/doc/index.Rmd | 2 inst/doc/index.html | 6 man/DWFuzzyGammaNaiveBayes.Rd | 2 man/DWFuzzyHipergeometricNaiveBayes.Rd | 2 man/ExpNBFuzzyParam.Rd | 18 man/FuzzyBayesRule.Rd | 2 man/FuzzyBetaNaiveBayes.Rd | 2 man/FuzzyBinomialNaiveBayes.Rd | 2 man/FuzzyClass-package.Rd | 8 man/FuzzyExponentialNaiveBayes.Rd | 2 man/FuzzyGammaNaiveBayes.Rd | 2 man/FuzzyGaussianNaiveBayes.Rd | 2 man/FuzzyGeoNaiveBayes.Rd | 2 man/FuzzyHipergeometricNaiveBayes.Rd | 2 man/FuzzyPoissonNaiveBayes.Rd | 2 man/FuzzyTrapezoidalNaiveBayes.Rd | 2 man/FuzzyTriangularNaiveBayes.Rd | 2 man/GauNBFuzzyParam.Rd | 18 man/PoiNBFuzzyParam.Rd | 18 man/figures/logo.png |binary man/figures/logo.svg |only tests/test_type.R | 72 + vignettes/FuzzyClass.Rmd | 2 vignettes/index.Rmd | 2 53 files changed, 1767 insertions(+), 2114 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.4.1 dated 2026-09-18 and 1.4.2 dated 2026-10-09
DESCRIPTION | 6 MD5 | 8 NEWS.md | 5 R/meteo_shortening_imgw.R | 9 inst/doc/getstarted.html | 732 +++++++++++++++++++++++++++++++++------------- 5 files changed, 548 insertions(+), 212 deletions(-)
Title: Unify Dimensionality Reduction Results
Description: Dimensionality reduction is widely used in many domains for
analyzing and visualizing high-dimensional data. 'tidydr' provides uniform
output and is compatible with multiple methods, including 'prcomp',
'cmdscale', 'Rtsne', 'umap' and 'metaMDS'. Any function returning a numeric
matrix can also be used. The unified result can be visualized directly with
'ggplot2', and several methods can be run and compared in a single call.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidydr versions 0.0.6 dated 2025-07-25 and 0.0.7 dated 2026-10-09
DESCRIPTION | 25 + MD5 | 68 ++--- NAMESPACE | 136 +++++----- NEWS.md | 175 +++++++++---- R/available_methods.R | 108 ++++---- R/dr-compare.R |only R/dr.R | 236 +++++++++++++---- R/element_line2.R | 110 ++++---- R/method-autoplot.R | 267 ++++++++++++-------- R/method-dr-extract.R | 292 ++++++++++++--------- R/method-drawDetails.R | 30 +- R/method-fortify.R | 117 ++++++-- R/silinfo.R | 432 ++++++++++++++++++++++++++++---- R/theme.R | 84 +++--- R/tidydr-package.R | 6 R/utilities.R | 34 +- README.md | 73 +++++ build/vignette.rds |binary inst/doc/tidydr.R | 97 +++++-- inst/doc/tidydr.Rmd | 237 ++++++++++++----- inst/doc/tidydr.html | 624 ++++++++++++++++++++++++++++------------------- man/available_methods.Rd | 46 +-- man/dr-extract.Rd | 59 ++-- man/dr.Rd | 77 +++-- man/dr_compare.Rd |only man/element_line2.Rd | 104 +++---- man/nk.Rd | 43 +++ man/reexports.Rd | 34 +- man/silinfo_widths.Rd |only man/theme_dr.Rd | 56 ++-- man/theme_noaxis.Rd | 40 +-- man/tidydr-package.Rd | 8 tests |only vignettes/tidydr.Rmd | 237 ++++++++++++----- 34 files changed, 2528 insertions(+), 1327 deletions(-)
Title: Stratigraphic Plug Alignment for Integrating Plug-Based and XRF
Data
Description: Implements the Stratigraphic Plug Alignment (SPA) procedure for
integrating sparsely sampled plug-based measurements (e.g., total organic
carbon, porosity, mineralogy) with high-resolution X-ray fluorescence
(XRF) geochemical data. SPA uses linear interpolation via the base
approx() function with constrained extrapolation (rule = 1) to preserve
stratigraphic order and avoid estimation beyond observed depths. The
method aligns all datasets to a common depth grid, enabling high-resolution
multivariate analysis and stratigraphic interpretation of core-based
datasets such as those from the Utica and Point Pleasant formations.
See R Core Team (2025)
<https://stat.ethz.ch/R-manual/R-devel/library/stats/html/stats-package.html>
and Omodolor (2025)
<http://rave.ohiolink.edu/etdc/view?acc_num=case175262671767524>
for methodological background and geological context.
Author: Hope E. Omodolor [aut] ,
Jeffrey M. Yarus [aut],
Roger H. French [cre]
Maintainer: Roger H. French <rxf131@case.edu>
Diff between spaAlign versions 0.0.6 dated 2026-01-07 and 0.0.7 dated 2026-10-09
DESCRIPTION | 25 ++-- MD5 | 16 +- NAMESPACE | 6 NEWS.md |only R/spa_align.R | 242 ++++++++++++++++++++-------------------- README.md |only man/figures |only man/spa_align.Rd | 136 +++++++++++----------- tests/testthat.R | 24 +-- tests/testthat/test-spa_align.R | 56 ++++----- 10 files changed, 258 insertions(+), 247 deletions(-)
Title: Reproducible Risk-Weighted Asset Calculations
Description: Provides transparent, deterministic and auditable calculations
of risk-weighted assets, own-funds requirements, interest-rate risk in the
banking book and related capital metrics. It supports canonical in-memory
tables and versioned spreadsheet datasets, strict validation, synthetic
reference profiles, bitemporal snapshots, calculation controls and
traceable regulatory source metadata. Methods are parameterised against
the European Parliament and Council (2013) Capital Requirements
Regulation <https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32013R0575> and its
amending Regulation (EU) 2024/1623
<https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32024R1623>. A granular analyst API exposes
individual formulae, domain views, controls, schemas and auditable
parameter overrides. The implementation is intended for
analytical, educational and model-validation use and does not constitute
legal or supervisory advice.
Author: Dimitrios Geromichalos [cre],
RiskDataScience GmbH [aut, cph]
Maintainer: Dimitrios Geromichalos <riskdatascience@web.de>
Diff between riskweightedassets versions 1.1.1 dated 2026-09-24 and 1.2.4 dated 2026-10-09
DESCRIPTION | 10 +- MD5 | 120 ++++++++++++++++++------------ NAMESPACE | 20 +++-- NEWS.md | 52 +++++++++++-- R/analyst_api.R | 7 + R/api.R | 5 + R/booleans.R |only R/contracts.R | 8 +- R/engine_credit.R | 39 ++++++++- R/engine_irrbb_icaap.R | 64 +++++++++------- R/excel_io.R | 6 + R/formula_api.R | 7 + R/formulas.R | 8 +- R/irb_contract.R |only R/pipeline.R | 5 - R/snapshot_time.R |only R/supporting_factors.R |only R/synthetic.R | 1 README.md | 21 ++++- build/vignette.rds |binary inst/CITATION | 2 inst/config/crr3_eu_2026_v1.yaml | 6 + inst/doc/complete-function-reference.R | 52 +++++++------ inst/doc/complete-function-reference.Rmd | 43 ++++++++++ inst/doc/complete-function-reference.html | 99 ++++++++++++++++++------ inst/doc/data-and-history.R | 6 - inst/doc/default-flags.Rmd |only inst/doc/default-flags.html |only inst/doc/getting-started.R | 16 ++-- inst/doc/irb-defaults.R |only inst/doc/irb-defaults.Rmd |only inst/doc/irb-defaults.html |only inst/doc/methodology-and-controls.R | 8 +- inst/doc/supporting-factors.R |only inst/doc/supporting-factors.Rmd |only inst/doc/supporting-factors.html |only man/analyze_credit_risk.Rd | 2 man/apply_credit_supporting_factors.Rd |only man/calculate_dataset.Rd | 2 man/calculate_tables.Rd | 7 + man/compare_calculation_views.Rd | 2 man/create_workspace.Rd | 2 man/failed_controls.Rd | 2 man/generate_synthetic_dataset.Rd | 2 man/infrastructure_supporting_factor.Rd |only man/irb_asset_correlation.Rd | 7 + man/irb_risk_weighted_assets.Rd |only man/official_snapshot.Rd | 9 ++ man/rwa_controls.Rd | 2 man/rwa_metric.Rd | 2 man/rwa_metrics.Rd | 2 man/rwa_result_table.Rd | 2 man/rwa_result_tables.Rd | 2 man/rwa_summary.Rd | 2 man/rwa_table_names.Rd | 2 man/rwa_validation.Rd | 2 man/sme_supporting_factor.Rd |only man/validate_dataset.Rd | 2 tests/testthat.R | 4 - tests/testthat/fixtures |only tests/testthat/helper-fixtures.R |only tests/testthat/helper-irrbb-reference.R |only tests/testthat/test-contracts-synthetic.R | 7 + tests/testthat/test-default-flags.R |only tests/testthat/test-e2e.R | 5 - tests/testthat/test-fixture-isolation.R |only tests/testthat/test-irb-default.R |only tests/testthat/test-irrbb-runtime.R |only tests/testthat/test-public-analyst-api.R | 16 +++- tests/testthat/test-snapshot-time.R |only tests/testthat/test-supporting-factors.R |only vignettes/complete-function-reference.Rmd | 43 ++++++++++ vignettes/default-flags.Rmd |only vignettes/irb-defaults.Rmd |only vignettes/supporting-factors.Rmd |only 75 files changed, 528 insertions(+), 205 deletions(-)
More information about riskweightedassets at CRAN
Permanent link
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Hugues Pecout [ctb] ,
Ronan Ysebaert [ctb] ,
Elina Marveaux [ctb] ,
Ian Fellows [cph] ,
Danielle Navarro [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 1.2.2 dated 2026-09-02 and 1.3.0 dated 2026-10-09
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++++-------------- NEWS.md | 8 +++++ R/deprecated.R | 2 - R/mf_annotation.R | 6 +++ R/mf_export.R | 4 +- R/mf_map.R | 31 +++++++++++--------- R/mf_map_utils.R | 7 +++- R/mf_prop_choro.R | 15 ++++++--- R/mf_prop_typo.R | 30 ++++++++++++------- R/mf_symb_choro.R | 16 ++++++---- R/mf_theme.R | 23 +++++++------- README.md | 21 +++++++------ inst/doc/mapsf.R | 16 +++++----- inst/doc/mapsf.Rmd | 36 +++++++++++------------ inst/doc/mapsf.html | 68 +++++++++++++++++++++----------------------- inst/tinytest/test_map_pc.R | 14 ++++----- inst/tinytest/test_map_pt.R | 4 +- inst/tinytest/test_map_sc.R | 2 - inst/tinytest/test_theme.R | 6 +-- man/mapsf-deprecated.Rd | 2 - man/mf_map.Rd | 27 +++++++++++------ vignettes/mapsf.Rmd | 36 +++++++++++------------ 23 files changed, 237 insertions(+), 187 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene
set collections. A 'GSON' object stores which genes belong to which gene
set, together with gene set and gene names, the identifier types in use,
species, versions and source metadata. A collection can be built from data
frames, read from and written to the 'gson' JavaScript Object Notation
(JSON) format and the 'GMT' format, subset by gene set, merged across
sources, validated, and resolved to the web addresses of the databases it
comes from, so that a collection gathered by one package can be analysed
by another.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.2.1 dated 2026-08-04 and 0.2.2 dated 2026-10-09
DESCRIPTION | 24 MD5 | 61 NAMESPACE | 69 NEWS.md | 54 R/00-AllClasses.R | 109 - R/GMT.R | 127 - R/IO.R | 235 +- R/gson-package.R | 6 R/gson.R | 74 R/gsonList.R | 20 R/methods.R | 66 R/print.R | 81 R/union.R |only R/utilities.r | 98 - R/validate.R | 108 + README.md | 455 ++++- inst/extdata/wikipathways-20220310-gmt-Homo_sapiens.gmt | 1448 ++++++++-------- man/GSON-class.Rd | 86 man/IO.Rd | 58 man/extract.GSON.Rd | 24 man/gson-package.Rd | 10 man/gson.Rd | 119 - man/gsonList.Rd | 34 man/gson_union.Rd |only man/gson_url.Rd |only man/read-gmt.Rd | 68 man/show-methods.Rd | 42 man/validate_gson.Rd | 7 tests/testthat/test-constructors.R | 75 tests/testthat/test-io.R | 161 + tests/testthat/test-methods.R | 78 tests/testthat/test-union.R |only tests/testthat/test-url.R |only tests/testthat/test-validate.R | 113 + 34 files changed, 2573 insertions(+), 1337 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Provides a collection of 'ggplot2' extensions and utilities
for creating geometric layers, applying themes, working with legends,
and modifying plot objects.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.2.1 dated 2026-07-02 and 0.2.2 dated 2026-10-09
ggfun-0.2.1/ggfun/R/geom-volpoint.R |only ggfun-0.2.1/ggfun/man/geom_volpoint.Rd |only ggfun-0.2.1/ggfun/man/volplot.Rd |only ggfun-0.2.2/ggfun/DESCRIPTION | 8 ggfun-0.2.2/ggfun/MD5 | 119 +- ggfun-0.2.2/ggfun/NAMESPACE | 242 ++--- ggfun-0.2.2/ggfun/NEWS.md | 225 ++-- ggfun-0.2.2/ggfun/R/axis.R | 122 +- ggfun-0.2.2/ggfun/R/facet_set.R | 118 +- ggfun-0.2.2/ggfun/R/geom-bezier.R |only ggfun-0.2.2/ggfun/R/geom-hist.r | 150 +-- ggfun-0.2.2/ggfun/R/geom-scatter-rect.R | 180 +-- ggfun-0.2.2/ggfun/R/geom-xspline.R | 268 ++--- ggfun-0.2.2/ggfun/R/geom_cake.R | 224 ++-- ggfun-0.2.2/ggfun/R/geom_segment_c.R | 198 ++-- ggfun-0.2.2/ggfun/R/geom_triangle.R | 152 +-- ggfun-0.2.2/ggfun/R/get-legend.r | 46 ggfun-0.2.2/ggfun/R/ggelement.R | 289 +++--- ggfun-0.2.2/ggfun/R/ggfun-package.R | 6 ggfun-0.2.2/ggfun/R/gglegend.R | 96 +- ggfun-0.2.2/ggfun/R/keybox.R | 76 - ggfun-0.2.2/ggfun/R/method-ggplot-add.R | 386 +++----- ggfun-0.2.2/ggfun/R/method-identify.R | 128 +- ggfun-0.2.2/ggfun/R/operator.R | 226 ++-- ggfun-0.2.2/ggfun/R/reexport.R | 10 ggfun-0.2.2/ggfun/R/set_font.R | 133 +- ggfun-0.2.2/ggfun/R/theme.R | 334 +++---- ggfun-0.2.2/ggfun/R/treedata-function.R | 148 +-- ggfun-0.2.2/ggfun/R/utilities.R | 400 ++++---- ggfun-0.2.2/ggfun/R/zzz.R | 10 ggfun-0.2.2/ggfun/README.md | 4 ggfun-0.2.2/ggfun/build/vignette.rds |binary ggfun-0.2.2/ggfun/inst/doc/ggfun.R | 462 ++++----- ggfun-0.2.2/ggfun/inst/doc/ggfun.html | 1081 +++++++++++------------ ggfun-0.2.2/ggfun/inst/doc/ggfun.qmd | 13 ggfun-0.2.2/ggfun/inst/prototype/geom_rtile.r | 94 +- ggfun-0.2.2/ggfun/man/attacher.Rd | 46 ggfun-0.2.2/ggfun/man/element_blinds.Rd | 84 - ggfun-0.2.2/ggfun/man/element_roundrect.Rd | 106 +- ggfun-0.2.2/ggfun/man/facet_set.Rd | 42 ggfun-0.2.2/ggfun/man/geom_bezier.Rd |only ggfun-0.2.2/ggfun/man/geom_cake.Rd | 60 - ggfun-0.2.2/ggfun/man/geom_segment_c.Rd | 136 +- ggfun-0.2.2/ggfun/man/geom_triangle.Rd | 56 - ggfun-0.2.2/ggfun/man/geom_xspline.Rd | 308 +++--- ggfun-0.2.2/ggfun/man/get_aes_var.Rd | 44 ggfun-0.2.2/ggfun/man/ggbreak2ggplot.Rd | 40 ggfun-0.2.2/ggfun/man/ggfun-package.Rd | 58 - ggfun-0.2.2/ggfun/man/gglegend.Rd | 74 - ggfun-0.2.2/ggfun/man/ggrange.Rd | 70 - ggfun-0.2.2/ggfun/man/identify.Rd | 48 - ggfun-0.2.2/ggfun/man/is-ggbreak.Rd | 40 ggfun-0.2.2/ggfun/man/is.ggtree.Rd | 40 ggfun-0.2.2/ggfun/man/keybox.Rd | 58 - ggfun-0.2.2/ggfun/man/reexports.Rd | 38 ggfun-0.2.2/ggfun/man/set_font.Rd | 84 + ggfun-0.2.2/ggfun/man/theme_blinds.Rd | 90 - ggfun-0.2.2/ggfun/man/theme_nothing.Rd | 44 ggfun-0.2.2/ggfun/man/theme_stamp.Rd | 36 ggfun-0.2.2/ggfun/man/theme_transparent.Rd | 40 ggfun-0.2.2/ggfun/tests/testthat/test-operator.R | 22 ggfun-0.2.2/ggfun/tests/testthat/test-set-font.R | 130 ++ ggfun-0.2.2/ggfun/vignettes/ggfun.qmd | 13 63 files changed, 3980 insertions(+), 3775 deletions(-)
Title: Simulation and Data Analysis for Plant Breeders
Description: Provides tools for simulation of plant breeding programs
as described, for example, by Melchinger and Frisch
(2023) <doi:10.1007/s00122-023-04446-3>, prediction of
segregation variance (Osthushenrich, Frisch and Herzog
(2017) <doi:10.1371/journal.pone.0188839>), genomic
prediction (Hofheinz and Frisch (2014)
<doi:10.1534/g3.113.010025>), linkage disequilibrium
based haplotype construction, and planning of marker
assisted back crossing programs. It provides an integrated
framework for simulation and analysis of plant breeding
programs.
Author: Matthias Frisch [aut, cre],
Hans Peter Maurer [ctb],
Philipp Heilmann [ctb]
Maintainer: Matthias Frisch <matthias.frisch@uni-giessen.de>
Diff between SelectionTools versions 26.4 dated 2026-09-21 and 26.5 dated 2026-10-09
SelectionTools-26.4/SelectionTools/inst/doc/v-simmd.Rmd |only SelectionTools-26.4/SelectionTools/man/evaluate.genotype2.Rd |only SelectionTools-26.4/SelectionTools/vignettes/v-simmd.Rmd |only SelectionTools-26.5/SelectionTools/DESCRIPTION | 8 SelectionTools-26.5/SelectionTools/MD5 | 142 SelectionTools-26.5/SelectionTools/NAMESPACE | 3 SelectionTools-26.5/SelectionTools/R/SelectionTools01.R | 87 SelectionTools-26.5/SelectionTools/R/SelectionTools02.R | 19 SelectionTools-26.5/SelectionTools/R/SelectionTools03.R | 31 SelectionTools-26.5/SelectionTools/R/SelectionTools04.R | 99 SelectionTools-26.5/SelectionTools/R/SelectionTools05.R | 4 SelectionTools-26.5/SelectionTools/build/vignette.rds |binary SelectionTools-26.5/SelectionTools/data/masbc.input.rda |only SelectionTools-26.5/SelectionTools/inst/doc/v-cross.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-hapld.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.R |only SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.Rnw |only SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.pdf |only SelectionTools-26.5/SelectionTools/inst/doc/v-phase.R | 172 SelectionTools-26.5/SelectionTools/inst/doc/v-phase.Rnw | 1135 - 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SelectionTools-26.5/SelectionTools/vignettes/v-simmd.Rnw |only 82 files changed, 9944 insertions(+), 4903 deletions(-)
More information about SelectionTools at CRAN
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Title: Univariate GARCH Models
Description: Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsgarch versions 1.0.4 dated 2026-05-23 and 1.0.5 dated 2026-10-09
tsgarch-1.0.4/tsgarch/man/plot.Rd |only tsgarch-1.0.4/tsgarch/tests/longtests/test-backtest.R |only tsgarch-1.0.4/tsgarch/tests/longtests/test-prediction.R |only tsgarch-1.0.4/tsgarch/tests/longtests/test-profile.R |only tsgarch-1.0.5/tsgarch/DESCRIPTION | 6 tsgarch-1.0.5/tsgarch/MD5 | 124 ++- tsgarch-1.0.5/tsgarch/NAMESPACE | 9 tsgarch-1.0.5/tsgarch/NEWS.md | 191 +++++ tsgarch-1.0.5/tsgarch/R/RcppExports.R | 28 tsgarch-1.0.5/tsgarch/R/arma.R |only tsgarch-1.0.5/tsgarch/R/backtest.R | 52 + tsgarch-1.0.5/tsgarch/R/constraints.R | 12 tsgarch-1.0.5/tsgarch/R/equations.R | 51 + tsgarch-1.0.5/tsgarch/R/estimate.R | 110 +++ tsgarch-1.0.5/tsgarch/R/extractors.R | 55 + tsgarch-1.0.5/tsgarch/R/filter.R | 109 ++- tsgarch-1.0.5/tsgarch/R/initialization.R | 45 - tsgarch-1.0.5/tsgarch/R/methods.R | 236 ++++++ tsgarch-1.0.5/tsgarch/R/plot-arma.R |only tsgarch-1.0.5/tsgarch/R/predict.R | 207 +++++- tsgarch-1.0.5/tsgarch/R/print.R | 17 tsgarch-1.0.5/tsgarch/R/profile.R | 15 tsgarch-1.0.5/tsgarch/R/simulate.R | 372 ++++++++--- tsgarch-1.0.5/tsgarch/R/specification.R | 78 ++ tsgarch-1.0.5/tsgarch/R/tsgarch-package.R | 2 tsgarch-1.0.5/tsgarch/R/utilities.R | 70 +- tsgarch-1.0.5/tsgarch/build/partial.rdb |binary tsgarch-1.0.5/tsgarch/build/vignette.rds |binary tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.R |only tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.Rmd |only tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.html |only tsgarch-1.0.5/tsgarch/inst/doc/benchmark.html | 42 - tsgarch-1.0.5/tsgarch/inst/doc/demonstration.html | 50 - tsgarch-1.0.5/tsgarch/inst/doc/garch_models.Rmd | 258 +++++++ tsgarch-1.0.5/tsgarch/inst/doc/garch_models.pdf |binary tsgarch-1.0.5/tsgarch/man/arma_coefficients.Rd |only tsgarch-1.0.5/tsgarch/man/arma_inverse_roots.Rd |only tsgarch-1.0.5/tsgarch/man/arma_irf.Rd |only tsgarch-1.0.5/tsgarch/man/arma_near_cancellation.Rd |only tsgarch-1.0.5/tsgarch/man/fitted.Rd | 15 tsgarch-1.0.5/tsgarch/man/garch_modelspec.Rd | 40 + tsgarch-1.0.5/tsgarch/man/plot.tsgarch.estimate.Rd | 94 ++ tsgarch-1.0.5/tsgarch/man/plot.tsgarch.newsimpact.Rd |only tsgarch-1.0.5/tsgarch/man/predict.Rd | 6 tsgarch-1.0.5/tsgarch/man/residuals.Rd | 16 tsgarch-1.0.5/tsgarch/man/simulate.Rd | 13 tsgarch-1.0.5/tsgarch/man/tsfilter.Rd | 5 tsgarch-1.0.5/tsgarch/man/tsgarch-package.Rd | 2 tsgarch-1.0.5/tsgarch/src/RcppExports.cpp | 73 +- tsgarch-1.0.5/tsgarch/src/TMB/aparchfun.hpp | 96 ++ tsgarch-1.0.5/tsgarch/src/TMB/cgarchfun.hpp | 93 ++ tsgarch-1.0.5/tsgarch/src/TMB/durbinlevinson.h |only tsgarch-1.0.5/tsgarch/src/TMB/egarchfun.hpp | 104 ++- tsgarch-1.0.5/tsgarch/src/TMB/fgarchfun.hpp | 96 ++ tsgarch-1.0.5/tsgarch/src/TMB/garchextra.h | 21 tsgarch-1.0.5/tsgarch/src/TMB/garchfun.hpp | 91 ++ tsgarch-1.0.5/tsgarch/src/TMB/gjrgarchfun.hpp | 102 ++- tsgarch-1.0.5/tsgarch/src/TMB/tsgarch_TMBExports.cpp | 1 tsgarch-1.0.5/tsgarch/src/simulation.cpp | 109 ++- tsgarch-1.0.5/tsgarch/tests/longtests/testthat |only tsgarch-1.0.5/tsgarch/tests/longtests/testthat.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-arma-diagnostics.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-arma.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-armax-dynamics.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-armax.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-estimation.R | 22 tsgarch-1.0.5/tsgarch/tests/testthat/test-filtering.R | 32 tsgarch-1.0.5/tsgarch/tests/testthat/test-simulation.R | 137 +++- tsgarch-1.0.5/tsgarch/vignettes/arma_garch.Rmd |only tsgarch-1.0.5/tsgarch/vignettes/garch_models.Rmd | 258 +++++++ 70 files changed, 3108 insertions(+), 457 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 2.1.1 dated 2026-08-24 and 2.1.2 dated 2026-10-09
DESCRIPTION | 23 +-- MD5 | 117 ++++++++-------- NAMESPACE | 16 +- NEWS.md | 38 +++++ R/add-expression-col.R | 42 +++-- R/centrality-description.R | 5 R/contingency-table.R | 107 ++------------- R/data.R | 23 +-- R/helpers-easystats.R | 10 + R/long-to-wide-converter.R | 36 ++--- R/meta-analysis.R | 77 +++++----- R/one-sample-test.R | 3 R/oneway-anova.R | 52 ++----- R/pairwise-comparisons.R | 37 +---- R/pairwise-contingency-table.R | 1 R/switch-functions.R | 13 + R/tidy-model-expressions.R | 10 - R/two-sample-test.R | 130 +++--------------- README.md | 93 ++++++++++--- inst/doc/statsExpressions.R | 4 inst/doc/statsExpressions.Rmd | 11 - inst/doc/statsExpressions.html | 15 +- inst/doc/stats_details.Rmd | 34 ++-- inst/doc/stats_details.html | 206 ++++++++++++++++++++++++++--- man/add_expression_col.Rd | 48 ++++-- man/bugs_long.Rd | 12 - man/centrality_description.Rd | 45 +++++- man/contingency_table.Rd | 95 +++++++++++-- man/corr_test.Rd | 67 +++++++-- man/examples/examples-contingency-table.R |only man/examples/examples-two-sample-test.R |only man/extract_stats_type.Rd | 12 + man/figures/README-anova_parametric2-1.png |binary man/figures/README-anova_rob1-1.png |binary man/figures/README-centrality-1.png |binary man/figures/README-corr-1.png |binary man/figures/README-custom_expr-1.png |binary man/figures/README-gof-1.png |binary man/figures/README-metaanalysis-1.png |binary man/figures/README-t_one-1.png |binary man/figures/README-t_two-1.png |binary man/figures/README-t_two_paired1-1.png |binary man/iris_long.Rd | 6 man/long_to_wide_converter.Rd | 36 ++--- man/meta_analysis.Rd | 98 ++++++++++--- man/movies_long.Rd | 5 man/one_sample_test.Rd | 67 +++++++-- man/oneway_anova.Rd | 91 +++++++++--- man/pairwise_comparisons.Rd | 96 +++++++++---- man/pairwise_contingency_table.Rd | 64 +++++++-- man/rmd-fragments/contingency_table.Rmd | 9 + man/rmd-fragments/functionality.Rmd | 3 man/rmd-fragments/return.Rmd | 67 +++++++-- man/rmd-fragments/return_centrality.Rmd |only man/rmd-fragments/summary_intro.Rmd |only man/tidy_model_expressions.Rd | 11 + man/tidy_model_parameters.Rd | 10 + man/two_sample_test.Rd | 92 +++++++++--- vignettes/statsExpressions.Rmd | 11 - vignettes/stats_details.Rmd | 34 ++-- vignettes/web_only/dataframe_outputs.Rmd | 177 ------------------------ vignettes/web_only/return_value_schema.Rmd |only 62 files changed, 1365 insertions(+), 894 deletions(-)
More information about statsExpressions at CRAN
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Title: Convenient Plotting for the Modified Rankin Scale and Other
Ordinal Outcome Data
Description: Provides convenient tools for visualising ordinal outcome data following conventions within stroke research literature. It currently supports the "Grotta Bar" approach pioneered by The National Institute of Neurological Disorders and Stroke rt-PA Stroke Study Group (1995) <doi:10.1056/NEJM199512143332401> and Probability-Probability plots for visualising Desirability of Outcome Ranking (DOOR) scales with large numbers of categories proposed by Johns et al. (2026) <doi:10.1177/17474930261475853>.
Author: Hannah Johns [aut, cre] ,
Andreas Gammelgaard Damsbo [aut] ,
Florian van Leeuwen [aut]
Maintainer: Hannah Johns <dr.hannah.johns@gmail.com>
Diff between rankinPlot versions 1.1.0 dated 2023-01-30 and 1.2.0 dated 2026-10-09
DESCRIPTION | 30 +- MD5 | 22 +- NAMESPACE | 2 NEWS.md | 9 R/data.R | 20 + R/grottaBar.R | 556 ++++++++++++++++++++++++++++++++++++++--------------- R/pp_plot.R |only README.md | 9 data/alteplase.rda |binary data/remapcap.rda |only man/alteplase.Rd | 64 +++--- man/grottaBar.Rd | 206 ++++++++++++------- man/pp_plot.Rd |only man/remapcap.Rd |only 14 files changed, 648 insertions(+), 270 deletions(-)
Title: Estimation of Optimal Size for a Holdout Set for Updating a
Predictive Score
Description: Predictive scores must be updated with care, because actions taken on the basis of existing risk scores causes bias in risk estimates from the updated score. A holdout set is a straightforward way to manage this problem: a proportion of the population is 'held-out' from computation of the previous risk score. This package provides tools to estimate a size for this holdout set and associated errors. Comprehensive vignettes are included. Please see: Haidar-Wehbe S, Emerson SR, Aslett LJM, Liley J (2022) <doi:10.48550/arXiv.2202.06374> (in Annals of Applied Statistics) for details of methods.
Author: Sami Haidar-Wehbe [aut],
Sam Emerson [aut] ,
Louis Aslett [aut] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between OptHoldoutSize versions 0.1.0.2 dated 2026-04-07 and 0.1.0.3 dated 2026-10-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/ASPRE_example.Rmd | 2 +- inst/doc/ASPRE_example.pdf |binary inst/doc/comparison_of_algorithms.pdf |binary inst/doc/simulated_example.pdf |binary vignettes/ASPRE_example.Rmd | 2 +- 8 files changed, 16 insertions(+), 12 deletions(-)
More information about OptHoldoutSize at CRAN
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Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
This is a re-admission after prior archival of version 1.9.9.1 dated 2026-09-10
Diff between haplo.stats versions 1.9.9.1 dated 2026-09-10 and 1.9.9.1 dated 2026-10-09
0 files changed
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from
R. Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane
support, quality of life functions to make 'Databricks' simpler to
use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.14 dated 2026-07-24 and 0.2.15 dated 2026-10-09
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Title: OMOP CDM DDL and Documentation Generator
Description: Generates the scripts required to create an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database and associated documentation for supported database platforms. Leverages the 'SqlRender' package to convert the Data Definition Language (DDL) script written in parameterized Structured Query Language (SQL) to the other supported dialects.
Author: Clair Blacketer [aut, cre]
Maintainer: Clair Blacketer <mblacke@its.jnj.com>
Diff between CommonDataModel versions 1.0.1 dated 2024-10-01 and 1.1.0 dated 2026-10-09
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CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_indices.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_primary_keys.sql | 52 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sql_server/OMOPCDM_sql_server_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sql_server/OMOPCDM_sql_server_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite/OMOPCDM_sqlite_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite/OMOPCDM_sqlite_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite_extended/OMOPCDM_sqlite_extended_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite_extended/OMOPCDM_sqlite_extended_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/synapse/OMOPCDM_synapse_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/synapse/OMOPCDM_synapse_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql | 41 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/iris |only CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_ddl.sql | 169 - 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CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_ddl.sql | 54 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_constraints.sql | 4 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_ddl.sql | 212 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_indices.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_primary_keys.sql | 55 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.5 |only CommonDataModel-1.1.0/CommonDataModel/inst/sql/sql_server/OMOP_CDM_indices_v5.5.sql |only CommonDataModel-1.1.0/CommonDataModel/man/CommonDataModel-package.Rd |only CommonDataModel-1.1.0/CommonDataModel/tests/testthat/setup.R | 82 CommonDataModel-1.1.0/CommonDataModel/tests/testthat/test-executeDdl.R | 2 119 files changed, 2725 insertions(+), 3389 deletions(-)
More information about CommonDataModel at CRAN
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Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 1.1.0 dated 2026-01-23 and 1.2.0 dated 2026-10-09
DESCRIPTION | 8 MD5 | 99 +++--- NEWS.md | 17 + R/0_documentation.R | 40 ++ R/autoplot.R | 193 ++++++++----- R/combined_seasonal_output.R | 61 +++- R/consecutive_growth_warnings.R | 1 R/estimate_disease_threshold.R | 146 +++++++-- R/fit_growth_rate.R | 55 ++- R/fit_percentiles.R | 63 ++-- R/generate_seasonal_data.R | 82 +++++ R/historical_summary.R | 5 R/seasonal_burden_levels.R | 35 +- R/seasonal_onset.R | 145 +++++++-- R/summary.R | 118 ++------ R/to_time_series.R | 149 ++++++++-- README.md | 24 + build/vignette.rds |binary inst/CITATION |only inst/doc/aedseo.R | 124 +++++++- inst/doc/aedseo.Rmd | 205 ++++++++++++- inst/doc/aedseo.html | 338 ++++++++++++++++++++--- inst/doc/burden_levels.R | 9 inst/doc/burden_levels.Rmd | 20 - inst/doc/burden_levels.html | 48 +-- inst/doc/generate_seasonal_wave.html | 21 - inst/doc/multiple_waves.html | 7 inst/doc/seasonal_onset.Rmd | 6 inst/doc/seasonal_onset.html | 22 + man/aedseo-package.Rd | 1 man/autoplot.Rd | 11 man/combined_seasonal_output.Rd | 23 - man/estimate_disease_threshold.Rd | 47 ++- man/fit_growth_rate.Rd | 28 + man/fit_percentiles.Rd | 18 - man/generate_seasonal_data.Rd | 21 + man/seasonal_burden_levels.Rd | 16 - man/seasonal_onset.Rd | 20 - man/to_time_series.Rd | 29 + tests/testthat/test-combined_seasonal_output.R | 114 +++++++ tests/testthat/test-estimate_disease_threshold.R | 88 +++++ tests/testthat/test-fit_growth_rate.R | 28 + tests/testthat/test-fit_percentiles.R | 23 + tests/testthat/test-generate_seasonal_data.R | 126 ++++++++ tests/testthat/test-plot.R | 79 +++++ tests/testthat/test-seasonal_onset.R | 230 +++++++++++++++ tests/testthat/test-summary.R | 45 +++ tests/testthat/test-to_time_series.R | 57 +++ vignettes/aedseo.Rmd | 205 ++++++++++++- vignettes/burden_levels.Rmd | 20 - vignettes/seasonal_onset.Rmd | 6 51 files changed, 2696 insertions(+), 580 deletions(-)
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre] ,
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [aut] ,
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jenni [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.12 dated 2026-09-29 and 0.9.13 dated 2026-10-09
tern-0.9.12/tern/man/h_miettinen_nurminen_var_est.Rd |only tern-0.9.13/tern/DESCRIPTION | 10 tern-0.9.13/tern/MD5 | 46 tern-0.9.13/tern/NAMESPACE | 44 tern-0.9.13/tern/NEWS.md | 16 tern-0.9.13/tern/R/prop_diff.R | 897 ++++--- tern-0.9.13/tern/R/prop_diff_test.R | 6 tern-0.9.13/tern/R/summarize_ancova.R | 5 tern-0.9.13/tern/R/utils.R | 38 tern-0.9.13/tern/build/partial.rdb |binary tern-0.9.13/tern/inst/doc/mantel_fleiss_criterion.html | 17 tern-0.9.13/tern/inst/doc/uncond_exact_prop_diff_ci.html | 2 tern-0.9.13/tern/man/escape_regex.Rd |only tern-0.9.13/tern/man/h_cmh_sato_var.Rd |only tern-0.9.13/tern/man/h_miettinen_nurminen_stratified_ci.Rd |only tern-0.9.13/tern/man/h_miettinen_nurminen_var.Rd |only tern-0.9.13/tern/man/h_prop_cmh.Rd |only tern-0.9.13/tern/man/h_prop_diff.Rd | 39 tern-0.9.13/tern/man/tern-package.Rd | 1 tern-0.9.13/tern/man/uniroot_catch_na.Rd |only tern-0.9.13/tern/tests/testthat/_snaps/prop_diff.md | 1242 +++++++++- tern-0.9.13/tern/tests/testthat/_snaps/summarize_ancova.md | 18 tern-0.9.13/tern/tests/testthat/_snaps/test_proportion_diff.md | 8 tern-0.9.13/tern/tests/testthat/helper-prop_diff.R |only tern-0.9.13/tern/tests/testthat/test-prop_diff.R | 271 +- tern-0.9.13/tern/tests/testthat/test-summarize_ancova.R | 31 tern-0.9.13/tern/tests/testthat/test-test_proportion_diff.R | 2 tern-0.9.13/tern/tests/testthat/test-utils.R | 15 28 files changed, 2238 insertions(+), 470 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://ec.europa.eu/eurostat/web/user-guides/data-browser/api-data-access/api-detailed-guidelines/sdmx2-1>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.25.0 dated 2026-03-30 and 0.30.0 dated 2026-10-09
DESCRIPTION | 14 - MD5 | 48 +++--- NEWS.md | 15 + R/create_filter_table.R | 2 R/extract_data.R | 32 +--- R/extract_dsd.R | 32 ++-- R/filter_raw_data.R | 2 R/get_compressed_sdmx.R | 12 - R/get_eurostat_bulk.R | 96 ++++++------ R/get_eurostat_codelist.R | 8 - R/get_eurostat_data.R | 315 +++++++++++++++++++++-------------------- R/get_eurostat_dsd.R | 16 +- R/get_eurostat_raw.R | 128 ++++++++-------- R/get_eurostat_toc.R | 56 +++---- R/load_cfg.R | 22 ++ README.md | 34 +--- inst/tinytest/test_restatapi.R | 148 ++++++++++++------- man/dot-restatapi_env.Rd | 5 man/extract_data.Rd | 14 - man/extract_dsd.Rd | 14 - man/get_eurostat_bulk.Rd | 34 ++-- man/get_eurostat_data.Rd | 90 ++++++----- man/get_eurostat_raw.Rd | 24 +-- man/get_eurostat_toc.Rd | 2 man/load_cfg.Rd | 3 25 files changed, 618 insertions(+), 548 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://help.openalex.org/>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 3.1.0 dated 2026-07-02 and 3.1.1 dated 2026-10-09
openalexR-3.1.0/openalexR/man/oa_email.Rd |only openalexR-3.1.1/openalexR/DESCRIPTION | 10 openalexR-3.1.1/openalexR/MD5 | 45 +- openalexR-3.1.1/openalexR/NAMESPACE | 1 openalexR-3.1.1/openalexR/NEWS.md | 50 ++ openalexR-3.1.1/openalexR/R/coro.R | 10 openalexR-3.1.1/openalexR/R/oa2df.R | 15 openalexR-3.1.1/openalexR/R/oa_fetch.R | 159 +++++-- openalexR-3.1.1/openalexR/R/oa_snowball.R | 2 openalexR-3.1.1/openalexR/R/simplify.R | 97 ++++ openalexR-3.1.1/openalexR/R/utils.R | 96 +++- openalexR-3.1.1/openalexR/README.md | 84 +--- openalexR-3.1.1/openalexR/data/oa2df_coverage.rda |binary openalexR-3.1.1/openalexR/man/oa_fetch.Rd | 9 openalexR-3.1.1/openalexR/man/oa_generate.Rd | 2 openalexR-3.1.1/openalexR/man/oa_request.Rd | 7 openalexR-3.1.1/openalexR/man/oa_snowball.Rd | 7 openalexR-3.1.1/openalexR/man/openalexR-package.Rd | 2 openalexR-3.1.1/openalexR/man/show_authors.Rd | 3 openalexR-3.1.1/openalexR/man/show_works.Rd | 5 openalexR-3.1.1/openalexR/tests/testthat/test-oa2df.R | 44 ++ openalexR-3.1.1/openalexR/tests/testthat/test-oa_fetch.R | 245 +++++++++++- openalexR-3.1.1/openalexR/tests/testthat/test-oa_snowball.R | 4 openalexR-3.1.1/openalexR/tests/testthat/test-simplify.R | 105 +++++ 24 files changed, 813 insertions(+), 189 deletions(-)
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.4 dated 2026-10-06 and 0.0.6 dated 2026-10-09
ICESat2VegR-0.0.4/ICESat2VegR/inst/proj |only ICESat2VegR-0.0.6/ICESat2VegR/DESCRIPTION | 6 ICESat2VegR-0.0.6/ICESat2VegR/MD5 | 33 ICESat2VegR-0.0.6/ICESat2VegR/R/zzz.R | 27 ICESat2VegR-0.0.6/ICESat2VegR/cleanup.ucrt | 32 ICESat2VegR-0.0.6/ICESat2VegR/configure.win |12284 +++++----- ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.in | 15 ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.ucrt | 15 ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.ucrt.in | 19 ICESat2VegR-0.0.6/ICESat2VegR/src/gdal_bindings.h | 12 ICESat2VegR-0.0.6/ICESat2VegR/tests/testthat/test-gdal-proj.R |only 11 files changed, 6178 insertions(+), 6265 deletions(-)
Title: Group Response Adaptive Randomization for Clinical Trials
Description: Implements group response-adaptive randomization procedures, which include standard (non-group) response-adaptive randomization methods as special cases. The package also handles delayed and missing responses, which broadens its use in real-world trials. It offers functions for simulating a variety of response-adaptive randomization procedures, to help guide the choice of design for a clinical trial, including the doubly adaptive biased coin design and the multi-arm efficient randomized adaptive design (ERADE), k-arm optimal target allocations, group sequential monitoring, and a function that computes allocation probabilities for an ongoing trial. For details of the methods and algorithms, see the following references:
Wei, L. J. (1979) <doi:10.1214/aos/1176344614>;
Wei, L. J. and Durham, S. (1978) <doi:10.1080/01621459.1978.10480109>;
Durham, S. D., Flournoy, N. and Li, W. (1998) <doi:10.2307/3315771>;
Ivanova, A., Rosenberger, W. F., Durham, S. D. and Flournoy, N. ( [...truncated...]
Author: Guannan Zhai [aut, cre],
Feifang Hu [aut, ths]
Maintainer: Guannan Zhai <guannanzhai1996@gmail.com>
Diff between grouprar versions 0.1.0 dated 2024-03-04 and 0.2.0 dated 2026-10-09
grouprar-0.1.0/grouprar/man/DBCD_bin.Rd |only grouprar-0.2.0/grouprar/DESCRIPTION | 45 grouprar-0.2.0/grouprar/MD5 | 55 grouprar-0.2.0/grouprar/NAMESPACE | 9 grouprar-0.2.0/grouprar/NEWS.md |only grouprar-0.2.0/grouprar/R/groupRAR_complement.R | 416 +++--- grouprar-0.2.0/grouprar/R/groupRAR_functions.R | 1264 ++++++++++----------- grouprar-0.2.0/grouprar/R/groupRAR_tools.R |only grouprar-0.2.0/grouprar/build |only grouprar-0.2.0/grouprar/inst |only grouprar-0.2.0/grouprar/man/Bai.Hu.Shen.Urn.Rd | 82 - grouprar-0.2.0/grouprar/man/BirthDeathUrn.Rd | 75 - grouprar-0.2.0/grouprar/man/CRDesign.Rd | 65 - grouprar-0.2.0/grouprar/man/DBCD_Bin.Rd |only grouprar-0.2.0/grouprar/man/DBCD_Cont.Rd | 113 + grouprar-0.2.0/grouprar/man/DLRule.Rd | 68 - grouprar-0.2.0/grouprar/man/GDLRule.Rd | 72 - grouprar-0.2.0/grouprar/man/Group.DBCD_Bin.Rd | 143 +- grouprar-0.2.0/grouprar/man/Group.DBCD_Cont.Rd | 107 + grouprar-0.2.0/grouprar/man/Group.dyldDBCD_Bin.Rd | 141 +- grouprar-0.2.0/grouprar/man/Group.dyldDBCD_Cont.Rd | 118 + grouprar-0.2.0/grouprar/man/PolyaUrn.Rd | 74 - grouprar-0.2.0/grouprar/man/RPWRule.Rd | 68 - grouprar-0.2.0/grouprar/man/WeiUrn.Rd | 75 - grouprar-0.2.0/grouprar/man/dyldDBCD_Bin.Rd | 119 + grouprar-0.2.0/grouprar/man/dyldDBCD_Cont.Rd | 115 + grouprar-0.2.0/grouprar/man/grouprar_package.Rd | 77 - grouprar-0.2.0/grouprar/man/nextAlloc.Rd |only grouprar-0.2.0/grouprar/man/print.grouprar.Rd |only grouprar-0.2.0/grouprar/man/sqMonitor.Rd |only grouprar-0.2.0/grouprar/tests |only 31 files changed, 1847 insertions(+), 1454 deletions(-)
Title: Interactive Plotting for Funnel, Sigma, and Statistical Process
Control Charts
Description: Generate interactive funnel plots, multi-indicator sigma charts,
and statistical process control ('SPC') charts. Chart calculation and plotting
use JavaScript, allowing dynamic charts without a Shiny server. For more details
see Spiegelhalter (2004) <doi:10.1002/sim.1970> and Pfadt & Wheeler (1995)
<doi:10.1901/jaba.1995.28-349>.
Author: Andrew R. Johnson [aut, cre] ,
Healthcare Quality Intelligence Unit [aut]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between controlcharts versions 0.0.19 dated 2026-08-04 and 0.0.23 dated 2026-10-09
DESCRIPTION | 20 MD5 | 58 NAMESPACE | 4 R/aaa.R | 2 R/funnel.R | 42 R/misc.R |only R/print.R | 11 R/spc.R | 75 - R/util.R | 269 +++- R/zzz.R | 3 inst/doc/aesthetic_options.html | 32 inst/doc/chart_types.html | 158 +- inst/doc/getting_started.html | 4 inst/doc/outlier_detection.html | 40 inst/htmlwidgets/funnel.yaml | 3 inst/htmlwidgets/lib/MISC |only inst/htmlwidgets/lib/PBIFUN/PBIFUN.js | 1409 ++++++++++++------------ inst/htmlwidgets/lib/PBISPC/PBISPC.js | 475 +++++--- inst/htmlwidgets/lib/UTILS/commonUtils.js | 143 +- inst/htmlwidgets/lib/UTILS/headlessUtils.js | 40 inst/htmlwidgets/lib/UTILS/interactiveUtils.css |only inst/htmlwidgets/lib/UTILS/interactiveUtils.js | 126 ++ inst/htmlwidgets/misc.js |only inst/htmlwidgets/misc.yaml |only inst/htmlwidgets/spc.yaml | 3 man/funnel.Rd | 11 man/misc-shiny.Rd |only man/misc.Rd |only man/misc_default_settings.Rd |only man/spc.Rd | 17 tests/testthat/test-export-html.R |only tests/testthat/test-knit-print.R |only tests/testthat/test-misc-html.R |only tests/testthat/test-misc.R |only tests/testthat/test-spc-indicators.R |only tests/testthat/test-tooltips.R |only vignettes/articles/interactive_charts.Rmd | 7 37 files changed, 1815 insertions(+), 1137 deletions(-)
Title: Bimodal GEV Distribution with Location Parameter
Description: Density, distribution function, quantile function random generation and estimation of bimodal GEV distribution given in Otiniano et al. (2023) <doi:10.1007/s10651-023-00566-7>. This new generalization of the well-known GEV (Generalized Extreme Value) distribution is useful for modeling heterogeneous bimodal data from different areas.
Author: Thiago do Rego Sousa [aut, cre],
Yasmin Lirio [aut],
Cira Etheowalda Guevara Otiniano [aut]
Maintainer: Thiago do Rego Sousa <thiagodoregosousa@gmail.com>
Diff between bgev versions 0.2 dated 2025-11-05 and 0.3 dated 2026-10-09
bgev-0.2/bgev/R/bgev_functions.R |only bgev-0.2/bgev/man/bgev-package.Rd |only bgev-0.2/bgev/man/bgev.mle.Rd |only bgev-0.2/bgev/man/bgev.support.Rd |only bgev-0.2/bgev/man/distCheck.Rd |only bgev-0.2/bgev/man/likbgev.Rd |only bgev-0.3/bgev/DESCRIPTION | 34 ++++-- bgev-0.3/bgev/MD5 | 39 +++++-- bgev-0.3/bgev/NAMESPACE | 22 +++- bgev-0.3/bgev/NEWS.md |only bgev-0.3/bgev/R/bgev_distribution.R |only bgev-0.3/bgev/R/bgev_domain.R |only bgev-0.3/bgev/R/bgev_estimation.R |only bgev-0.3/bgev/R/dist_check.R | 123 ++++++++++++++---------- bgev-0.3/bgev/README.md |only bgev-0.3/bgev/build/partial.rdb |binary bgev-0.3/bgev/build/vignette.rds |only bgev-0.3/bgev/inst |only bgev-0.3/bgev/man/bgev.Rd |only bgev-0.3/bgev/man/bgev_log_likelihood.Rd |only bgev-0.3/bgev/man/bgev_mle.Rd |only bgev-0.3/bgev/man/bgev_profile_likelihood.Rd |only bgev-0.3/bgev/man/bgev_start_using_quantiles.Rd |only bgev-0.3/bgev/man/bgev_support.Rd |only bgev-0.3/bgev/man/bgev_valid_params.Rd |only bgev-0.3/bgev/man/dist_check.Rd |only bgev-0.3/bgev/tests |only bgev-0.3/bgev/vignettes |only 28 files changed, 144 insertions(+), 74 deletions(-)
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre] ,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
This is a re-admission after prior archival of version 2.1.7 dated 2026-07-24
Diff between baRulho versions 2.1.7 dated 2026-07-24 and 2.2.0 dated 2026-10-09
DESCRIPTION | 7 MD5 | 134 +-- NEWS.md | 16 R/add_noise.R | 83 +- R/align_test_files.R | 57 + R/attenuation.R | 42 - R/auto_realign.R | 68 + R/baRulho-package.R | 17 R/blur_ratio.R | 59 + R/detection_distance.R | 80 +- R/envelope_correlation.R | 46 + R/excess_attenuation.R | 76 +- R/find_markers.R | 82 ++ R/internal_functions.R | 72 +- R/manual_realign.R | 131 +++ R/master_est-data.R | 15 R/master_sound_file.R | 81 +- R/noise_profile.R | 91 ++ R/plot_aligned_sounds.R | 115 ++- R/plot_blur_ratio.R | 97 ++ R/plot_degradation.R | 130 ++- R/set_reference_sounds.R | 92 ++ R/signal_to_noise_ratio.R | 103 ++ R/spcc.R | 44 + R/spectrum_blur_ratio.R | 69 + R/spectrum_correlation.R | 50 + R/spot_ambient_noise.R | 61 + R/synth_sounds.R | 119 ++- R/tail_to_signal_ratio.R | 97 ++ R/template_params.R | 81 +- R/test_sounds_est-data.R | 14 README.md | 121 ++- build/vignette.rds |binary data/master_est.rda |binary data/test_sounds_est.rda |binary inst/doc/align_test_sounds.R | 1 inst/doc/align_test_sounds.Rmd | 17 inst/doc/align_test_sounds.html | 522 ++++---------- inst/doc/quantify_degradation.Rmd | 25 inst/doc/quantify_degradation.html | 1293 +++++++++++++++---------------------- man/add_noise.Rd | 109 ++- man/align_test_files.Rd | 85 +- man/attenuation.Rd | 38 - man/auto_realign.Rd | 102 ++ man/baRulho-package.Rd | 24 man/blur_ratio.Rd | 133 ++- man/detection_distance.Rd | 165 +++- man/envelope_correlation.Rd | 122 ++- man/excess_attenuation.Rd | 119 ++- man/find_markers.Rd | 108 ++- man/manual_realign.Rd | 195 ++++- man/master_est.Rd | 14 man/master_sound_file.Rd | 102 ++ man/noise_profile.Rd | 126 ++- man/plot_aligned_sounds.Rd | 187 +++-- man/plot_blur_ratio.Rd | 187 +++-- man/plot_degradation.Rd | 234 ++++-- man/set_reference_sounds.Rd | 126 ++- man/signal_to_noise_ratio.Rd | 169 +++- man/spcc.Rd | 119 ++- man/spectrum_blur_ratio.Rd | 138 ++- man/spectrum_correlation.Rd | 126 ++- man/spot_ambient_noise.Rd | 85 +- man/synth_sounds.Rd | 136 ++- man/tail_to_signal_ratio.Rd | 139 ++- man/test_sounds_est.Rd | 14 vignettes/align_test_sounds.Rmd | 17 vignettes/quantify_degradation.Rmd | 25 68 files changed, 4793 insertions(+), 2559 deletions(-)
Title: Infrastructure for Interacting with GPUs
Description: Compiling, managing, and dispatching functions to GPUs. Will compile tooling for successfully detected frameworks, currently limited to: 'OpenCL' (<https://www.khronos.org/opencl/resources>), 'CUDA' (<https://docs.nvidia.com/cuda/>), and 'Metal' (<https://developer.apple.com/documentation/metal>).
Author: Nicholas Cooley [aut, cre]
Maintainer: Nicholas Cooley <npcooley@gmail.com>
Diff between ardea versions 0.0.9 dated 2026-10-08 and 0.1.1 dated 2026-10-09
DESCRIPTION | 6 - MD5 | 21 ++-- NAMESPACE | 3 R/utils.R | 39 ++++++++ build/vignette.rds |binary inst/doc/introduction_to_ardea.R | 81 ++++++++++-------- inst/doc/introduction_to_ardea.Rmd | 85 ++++++++++--------- inst/doc/introduction_to_ardea.html | 161 +++++++++++++++++++----------------- man/metal_compiler_is_available.Rd |only man/metal_make_program.Rd | 8 + man/simple_wrapper.Rd | 12 ++ vignettes/introduction_to_ardea.Rmd | 85 ++++++++++--------- 12 files changed, 296 insertions(+), 205 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-13 2.1.1
2025-09-07 2.0.1
2025-04-10 1.0.3
Title: R Interface for the 'STATcube' REST API and Open Government Data
Description: Import data from the 'STATcube' REST API or from the open data
portal of Statistics Austria. This package includes a client for API
requests as well as parsing utilities for data which originates from
'STATcube'. Documentation about 'STATcubeR' is provided by several vignettes
included in the package as well as on the public 'pkgdown' page at
<https://statistikat.github.io/STATcubeR/>.
Author: Bernhard Meindl [ctb, cre],
Alexander Kowarik [ctb] ,
Gregor de Cillia [aut]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Diff between STATcubeR versions 1.0.0 dated 2024-11-29 and 1.0.1 dated 2026-10-09
DESCRIPTION | 15 +- MD5 | 80 +++++------ NAMESPACE | 10 + NEWS.md | 21 +++ R/browse.R | 2 R/error.R | 7 - R/od_cache.R | 2 R/od_list.R | 197 ++++++++++++++++++++++------ R/od_resource.R | 21 ++- R/od_revisions.R | 4 R/od_table.R | 4 R/od_table_save.R | 2 R/od_utils.R | 58 ++++++++ R/other_endpoints.R | 10 + R/recoder.R | 2 R/sc_data.R | 8 - R/schema.R | 5 R/schema_db.R | 8 - R/table.R | 57 ++++++++ R/table_custom.R | 43 +++--- R/table_saved.R | 4 R/tabulate.R | 8 - inst/json_examples/accomodation.json | 12 - man/od_cache.Rd | 2 man/od_catalogue.Rd | 2 man/od_list.Rd | 11 + man/od_resource.Rd | 8 + man/od_revisions.Rd | 2 man/od_server_reachable.Rd |only man/od_table.Rd | 2 man/od_table_class.Rd | 86 ++++++------ man/od_table_save.Rd | 2 man/other_endpoints.Rd | 2 man/sc_data.Rd | 218 +++++++++++++------------------ man/sc_last_error.Rd | 2 man/sc_recoder.Rd | 243 +++++++++++++++++------------------ man/sc_schema.Rd | 10 - man/sc_server_reachable.Rd |only man/sc_table.Rd | 2 man/sc_table_class.Rd | 177 ++++++++++++------------- man/sc_table_custom.Rd | 40 +++-- man/sc_tabulate.Rd | 9 - 42 files changed, 851 insertions(+), 547 deletions(-)
Title: Gene Analysis Toolkit
Description: Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>
Diff between genekitr versions 1.2.8 dated 2024-09-06 and 1.3.0 dated 2026-10-09
ChangeLog | 25 DESCRIPTION | 23 MD5 | 70 - NAMESPACE | 226 ++-- R/asEnrichdat.R | 2 R/expoSheet.R | 123 +- R/genGSEA.R | 39 R/genInfo.R | 14 R/genORA.R | 2 R/getPubmed.R | 272 ++--- R/importCP.R | 448 ++++---- R/importPanther.R | 139 +- R/importShinygo.R | 70 - R/ploTheme.R | 8 R/plotEnrich.R | 2063 +++++++++++++++++++-------------------- R/plotEnrichAdv.R | 14 R/plotGSEA.R | 1174 +++++++++++----------- R/plotVenn.R | 22 R/plotVolcano.R | 250 ++-- R/transID.R | 9 R/transProbe.R | 52 R/utilities.R | 54 - R/zzz.R | 2 README.md | 2 data/biocOrg_name.rda |binary data/deg.rda |binary data/ensOrg_name.rda |binary data/geneList.rda |binary data/hsapiens_probe_platform.rda |binary data/keggOrg_name.rda |binary data/msig_category.rda |binary data/msig_org.rda |binary man/genGSEA.Rd | 3 man/plotEnrich.Rd | 2 man/plotVenn.Rd | 7 man/plotVolcano.Rd | 6 36 files changed, 2604 insertions(+), 2517 deletions(-)
Title: Suess and Laws Corrections for Marine Stable Carbon Isotope Data
Description: Generates region-specific Suess and Laws corrections for
stable carbon isotope data from marine organisms collected between 1850 and 2025. Version
0.1.7 of 'SuessR' contains four built-in regions: the Bering Sea ('Bering Sea'), the
Aleutian archipelago ('Aleutian Islands'), the Gulf of Alaska ('Gulf of Alaska'), and the
subpolar North Atlantic ('Subpolar North Atlantic'). Users can supply their own environmental
data for regions currently not built into the package to generate corrections for those regions.
Author: Casey Clark [cre, aut],
Mattias Cape [aut],
Mark Shapley [aut],
Franz Mueter [aut],
Bruce Finney [aut],
Nicole Misarti [aut]
Maintainer: Casey Clark <casey.t.clark@gmail.com>
Diff between SuessR versions 0.1.6 dated 2025-02-20 and 0.1.7 dated 2026-10-09
DESCRIPTION | 12 ++++++------ LICENSE | 2 +- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/SuessR_Package.R | 6 +++--- R/SuessR_Reference_Data.R | 4 ++-- data/SuessR_Reference_Data.RData |binary man/SuessR.Rd | 2 +- man/SuessR.custom.Rd | 4 ++-- man/SuessR.reference.data.Rd | 4 ++-- 10 files changed, 31 insertions(+), 26 deletions(-)