Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to test
data, which includes both dichotomous and polytomous items, calibrate
pretest item parameters, estimate examinees' abilities, and examine
the IRT model-data fit on item-level in different ways as well as provide
useful functions related to IRT analyses such as IRT model-data fit
evaluation and differential item functioning analysis.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function was written by modifying the bisection() function
(Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve
scoring in the est_score() function was written by modifying the irt.eq.tse() func [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 0.2.1 dated 2024-08-24 and 1.0.0 dated 2025-07-16
DESCRIPTION | 20 MD5 | 180 +-- NAMESPACE | 6 NEWS.md | 33 R/LSAT6.R | 11 R/SimCAT_DC.R | 21 R/SimCAT_MX.R | 25 R/bisection.R | 68 - R/breakdown.R | 6 R/bring_output.R | 184 ++- R/cac_lee.R | 158 +-- R/cac_rud.R | 124 +- R/catsib.R | 418 ++++---- R/covirt.R | 127 +- R/crdif.R |only R/est_irt.R | 956 +++++++++++------- R/est_item.R | 283 +++-- R/est_mg.R | 963 +++++++++++------- R/est_score.R | 454 +++++--- R/gen_weight.R | 89 + R/getirt.R | 283 +++-- R/grdif.R | 424 ++++---- R/info.R | 155 +-- R/irtQ-package.R | 965 +++++++++++------- R/irtfit.R | 363 ++++--- R/irtmodel.R | 95 + R/llike_score.R | 98 - R/lwrc.R | 120 +- R/pcd2.R | 515 +++++++--- R/plot_info.R | 108 +- R/plot_irtfit.R | 214 ++-- R/plot_traceline.R | 263 +++-- R/print.R | 135 ++ R/rdif.R | 612 +++++++---- R/reval_mst.R | 216 ++-- R/run_flexmirt.R | 109 +- R/shape_df.R | 131 +- R/shape_df_fipc.R |only R/simMST.R | 58 - R/simdat.R | 214 ++-- R/summary.R | 30 R/sx2_fit.R | 184 ++- R/traceline.R | 86 + R/util.R | 43 R/write_flexmirt.R | 100 + README.md | 1993 +++++++++++++++++---------------------- man/LSAT6.Rd | 11 man/bind.fill.Rd | 41 man/bisection.Rd | 56 - man/bring.flexmirt.Rd | 161 +-- man/cac_lee.Rd | 140 +- man/cac_rud.Rd | 105 +- man/catsib.Rd | 421 +++++--- man/covirt.Rd | 137 +- man/crdif.Rd |only man/drm.Rd | 34 man/est_irt.Rd | 906 ++++++++++------- man/est_item.Rd | 334 +++--- man/est_mg.Rd | 967 +++++++++++------- man/est_score.Rd | 386 ++++--- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/figures/README-example-6.png |binary man/figures/README-example-7.png |binary man/gen.weight.Rd | 83 + man/getirt.Rd | 281 +++-- man/grdif.Rd | 443 ++++---- man/info.Rd | 149 +- man/irtQ-package.Rd | 931 +++++++++++------- man/irtfit.Rd | 330 +++--- man/llike_score.Rd | 116 +- man/lwrc.Rd | 121 +- man/pcd2.Rd | 279 +++-- man/plot.info.Rd | 87 - man/plot.irtfit.Rd | 189 ++- man/plot.traceline.Rd | 134 +- man/prm.Rd | 53 - man/rdif.Rd | 398 ++++--- man/reval_mst.Rd | 240 ++-- man/run_flexmirt.Rd | 104 +- man/shape_df.Rd | 131 +- man/shape_df_fipc.Rd |only man/simCAT_DC.Rd | 23 man/simCAT_MX.Rd | 27 man/simMST.Rd | 55 - man/simdat.Rd | 228 ++-- man/summary.Rd | 28 man/sx2_fit.Rd | 175 +-- man/traceline.Rd | 93 + man/write.flexmirt.Rd | 92 - 93 files changed, 11897 insertions(+), 8232 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: Provides a unified interface to interact with multiple Large Language Model (LLM) APIs. The package supports text generation, embeddings, parallelization, as well as tidyverse integration. Users can switch between different LLM providers seamlessly within R workflows, or call multiple models in parallel. The package enables creation of LLM agents for automated tasks and provides consistent error handling across all supported APIs. APIs include 'OpenAI' (see <https://platform.openai.com/docs> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), 'Gemini' (see <https://aistudio.google.com> for details), 'xAI' (see <https://docs.x.ai/> for details), and 'Voyage AI' (see <https://docs.voyageai.co [...truncated...]
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.4.2 dated 2025-06-26 and 0.5.0 dated 2025-07-16
LLMR-0.4.2/LLMR/R/Zagent.R |only LLMR-0.4.2/LLMR/man/Agent.Rd |only LLMR-0.4.2/LLMR/man/AgentAction.Rd |only LLMR-0.4.2/LLMR/man/LLMConversation.Rd |only LLMR-0.4.2/LLMR/vignettes/parallel_calls.Rmd |only LLMR-0.4.2/LLMR/vignettes/parallel_calls.html |only LLMR-0.5.0/LLMR/DESCRIPTION | 8 LLMR-0.5.0/LLMR/MD5 | 54 - LLMR-0.5.0/LLMR/NAMESPACE | 16 LLMR-0.5.0/LLMR/R/LLMR.R | 797 ++++++++++++++------- LLMR-0.5.0/LLMR/R/LLMR_tidy.R | 44 - LLMR-0.5.0/LLMR/R/LLM_chat_session.R |only LLMR-0.5.0/LLMR/R/LLM_parallel_utils.R | 294 ++++--- LLMR-0.5.0/LLMR/R/LLM_param_translate.R |only LLMR-0.5.0/LLMR/R/LLM_robust_utils.R | 7 LLMR-0.5.0/LLMR/R/globalVariables.R |only LLMR-0.5.0/LLMR/build/vignette.rds |binary LLMR-0.5.0/LLMR/inst/doc/demo.pdf |binary LLMR-0.5.0/LLMR/inst/doc/demo.pdf.asis | 2 LLMR-0.5.0/LLMR/man/build_factorial_experiments.Rd | 21 LLMR-0.5.0/LLMR/man/cache_llm_call.Rd | 10 LLMR-0.5.0/LLMR/man/call_llm.Rd | 116 ++- LLMR-0.5.0/LLMR/man/call_llm_broadcast.Rd | 33 LLMR-0.5.0/LLMR/man/call_llm_compare.Rd | 28 LLMR-0.5.0/LLMR/man/call_llm_par.Rd | 68 - LLMR-0.5.0/LLMR/man/call_llm_robust.Rd | 6 LLMR-0.5.0/LLMR/man/call_llm_sweep.Rd | 29 LLMR-0.5.0/LLMR/man/get_batched_embeddings.Rd | 13 LLMR-0.5.0/LLMR/man/llm_chat_session.Rd |only LLMR-0.5.0/LLMR/man/llm_config.Rd | 23 LLMR-0.5.0/LLMR/man/llm_fn.Rd | 31 LLMR-0.5.0/LLMR/man/llm_mutate.Rd | 13 LLMR-0.5.0/LLMR/vignettes/demo.pdf.asis | 2 33 files changed, 1095 insertions(+), 520 deletions(-)
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 1.1.1 dated 2024-06-03 and 1.2.0 dated 2025-07-16
DESCRIPTION | 6 MD5 | 24 +-- NEWS.md | 6 R/allocate_wave.R | 145 ++++++++++++++------ R/optimum_allocation.R | 222 +++++++++++++++++++++++++++---- R/summary.multiwave.R | 1 README.md | 24 +-- inst/doc/optimall-vignette.html | 2 man/allocate_wave.Rd | 6 man/optimum_allocation.Rd | 42 +++++ tests/testthat/test-allocate_wave.R | 88 ++++++++++++ tests/testthat/test-optimum_allocation.R | 129 ++++++++++++++++++ tests/testthat/test-summary.R | 11 - 13 files changed, 604 insertions(+), 102 deletions(-)
Title: National Emergency Medical Service Quality Alliance Measure
Calculations
Description: Designed to automate the calculation of Emergency Medical
Service (EMS) quality metrics, 'nemsqar' implements measures defined
by the National EMS Quality Alliance (NEMSQA). By providing reliable,
evidence-based quality assessments, the package supports EMS agencies,
healthcare providers, and researchers in evaluating and improving
patient outcomes. Users can find details on all approved NEMSQA
measures at <https://www.nemsqa.org/measures>. Full technical
specifications, including documentation and pseudocode used to develop
'nemsqar', are available on the NEMSQA website after creating a user
profile at <https://www.nemsqa.org>.
Author: Nicolas Foss [aut, cre],
Samuel Kordik [aut] ,
Alyssa Green [ctb],
Iowa Department of Health and Human Services [cph]
Maintainer: Nicolas Foss <nicolas.foss@hhs.iowa.gov>
Diff between nemsqar versions 1.1.0 dated 2025-03-13 and 1.1.1 dated 2025-07-16
DESCRIPTION | 47 MD5 | 34 NAMESPACE | 2 NEWS.md | 9 R/airway_01_population.R | 1143 ++++++----- R/import-standalone-purrr.R |only R/nemsqar-package.R | 20 R/summarize_measure.R | 45 R/trauma_03_population.R | 1846 ++++++++++------- R/trauma_04_population.R | 3329 +++++++++++++++++--------------- R/trauma_14_population.R | 3404 ++++++++++++++++++--------------- README.md | 55 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/figures/logo.png |only man/nemsqar-package.Rd | 2 man/summarize_measure.Rd | 2 19 files changed, 5672 insertions(+), 4450 deletions(-)
Title: Interactive Weibull Probability Plots
Description: Build interactive Weibull Probability
Plots with 'WeibullR' by David Silkworth and Jurgen Symynck (2022)
<https://CRAN.R-project.org/package=WeibullR>, an R package for
Weibull analysis, and 'plotly' by Carson Sievert (2020) <https://plotly-r.com>,
an interactive web-based graphing library.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between WeibullR.plotly versions 0.3 dated 2024-11-06 and 0.3.1 dated 2025-07-16
DESCRIPTION | 9 MD5 | 28 +- NAMESPACE | 4 NEWS.md | 5 R/plotly_contour.R | 212 ++++++++-------- R/plotly_duane.R | 2 R/plotly_rga.R | 7 R/plotly_wblr.R | 550 ++++++++++++++++++++++-------------------- README.md | 25 - inst/WORDLIST | 8 man/plotly_contour.Rd | 38 +- man/plotly_duane.Rd | 2 man/plotly_rga.Rd | 2 man/plotly_wblr.Rd | 2 tests/testthat/test-contour.R | 4 15 files changed, 497 insertions(+), 401 deletions(-)
More information about WeibullR.plotly at CRAN
Permanent link
Title: An Interactive Introduction to Life Data Analysis
Description: An interactive introduction to Life Data Analysis that depends on 'WeibullR'
by David Silkworth and Jurgen Symynck (2022) <https://CRAN.R-project.org/package=WeibullR>,
a R package for Weibull Analysis, and 'learnr' by Garrick Aden-Buie et al. (2023)
<https://CRAN.R-project.org/package=learnr>, a framework for building interactive learning
modules in R.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between WeibullR.learnr versions 0.2 dated 2024-11-04 and 0.2.1 dated 2025-07-16
DESCRIPTION | 11 MD5 | 22 - NEWS.md | 5 README.md | 4 inst/paper/paper.html | 109 +++----- inst/paper/paper.md | 20 - inst/tutorials/RAMRlearnr/RAMRlearnr.Rmd | 2 inst/tutorials/RAMRlearnr/RAMRlearnr.html | 88 +++--- inst/tutorials/TestRlearnr/TestRlearnr.Rmd | 91 +++---- inst/tutorials/TestRlearnr/TestRlearnr.html | 286 ++++++++++------------ inst/tutorials/WeibullRlearnr/WeibullRlearnr.Rmd | 2 inst/tutorials/WeibullRlearnr/WeibullRlearnr.html | 70 ++--- 12 files changed, 354 insertions(+), 356 deletions(-)
More information about WeibullR.learnr at CRAN
Permanent link
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.19.2 dated 2025-03-28 and 2.20.0 dated 2025-07-16
DESCRIPTION | 13 MD5 | 73 +-- NAMESPACE | 2 NEWS.md | 13 R/Design.R | 88 ++++ R/PBA.R | 29 + R/SimCheck.R | 31 + R/SimCollect.R | 20 - R/SimDesign.R | 2 R/SimExtract.R | 23 - R/SimSolve.R | 23 - R/reSummarise.R | 27 + R/runArraySimulation.R | 2 R/runSimulation.R | 30 - R/summary_functions.R | 13 R/util.R | 3 inst/doc/Catch_errors.html | 343 ++++++------------ inst/doc/Fixed_obj_fun.Rmd | 27 + inst/doc/Fixed_obj_fun.html | 261 ++++++------- inst/doc/HPC-computing.html | 737 ++++++++++----------------------------- inst/doc/MultipleAnalyses.R | 66 ++- inst/doc/MultipleAnalyses.Rmd | 31 + inst/doc/MultipleAnalyses.html | 327 ++++++----------- inst/doc/Parallel-computing.html | 315 +++++----------- inst/doc/Saving-results.html | 318 ++++++---------- inst/doc/SimDesign-intro.html | 461 +++++++----------------- man/SimCheck.Rd | 5 man/SimExtract.Rd | 11 man/SimSolve.Rd | 38 +- man/bias.Rd | 5 man/expandDesign.Rd | 5 man/expandReplications.Rd |only man/runArraySimulation.Rd | 2 man/runSimulation.Rd | 17 tests/tests/test-01-core.R | 25 + tests/tests/test-03-array.R | 30 + vignettes/Fixed_obj_fun.Rmd | 27 + vignettes/MultipleAnalyses.Rmd | 31 + 38 files changed, 1463 insertions(+), 2011 deletions(-)
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.9.3 dated 2025-05-29 and 1.9.4 dated 2025-07-16
mrbin-1.9.3/mrbin/inst/extdata/1/12 |only mrbin-1.9.3/mrbin/inst/extdata/2 |only mrbin-1.9.3/mrbin/inst/extdata/3 |only mrbin-1.9.3/mrbin/inst/extdata/data |only mrbin-1.9.4/mrbin/DESCRIPTION | 6 mrbin-1.9.4/mrbin/MD5 | 137 - mrbin-1.9.4/mrbin/NEWS.md | 9 mrbin-1.9.4/mrbin/R/mrbin.R | 1580 +++++++++++++++------ mrbin-1.9.4/mrbin/inst/doc/mrbin.R | 88 - mrbin-1.9.4/mrbin/inst/doc/mrbin.Rnw | 82 - mrbin-1.9.4/mrbin/inst/doc/mrbin.pdf |binary mrbin-1.9.4/mrbin/inst/extdata/1.mr1 |only mrbin-1.9.4/mrbin/inst/extdata/1.mr2 |only mrbin-1.9.4/mrbin/inst/extdata/1/10/pdata/10/1r |binary mrbin-1.9.4/mrbin/inst/extdata/1/10/pdata/10/proc | 14 mrbin-1.9.4/mrbin/inst/extdata/1/10/pdata/10/procs | 41 mrbin-1.9.4/mrbin/inst/extdata/1/10/pdata/10/title | 3 mrbin-1.9.4/mrbin/inst/extdata/2.mr1 |only mrbin-1.9.4/mrbin/inst/extdata/2.mr2 |only mrbin-1.9.4/mrbin/inst/extdata/3.mr1 |only mrbin-1.9.4/mrbin/inst/extdata/3.mr2 |only mrbin-1.9.4/mrbin/inst/extdata/TMP |only mrbin-1.9.4/mrbin/man/PQNScaling.Rd | 11 mrbin-1.9.4/mrbin/man/annotatemrbin.Rd | 35 mrbin-1.9.4/mrbin/man/atnv.Rd | 17 mrbin-1.9.4/mrbin/man/contMin.Rd | 8 mrbin-1.9.4/mrbin/man/contPlus.Rd | 4 mrbin-1.9.4/mrbin/man/cropNMR.Rd | 7 mrbin-1.9.4/mrbin/man/dilutionCorrection.Rd | 11 mrbin-1.9.4/mrbin/man/down.Rd | 8 mrbin-1.9.4/mrbin/man/editmetabolitesmrbin.Rd | 13 mrbin-1.9.4/mrbin/man/intMin.Rd | 7 mrbin-1.9.4/mrbin/man/intPlus.Rd | 7 mrbin-1.9.4/mrbin/man/left.Rd | 8 mrbin-1.9.4/mrbin/man/logTrafo.Rd | 9 mrbin-1.9.4/mrbin/man/metadatamrbin.Rd | 8 mrbin-1.9.4/mrbin/man/mrbin.Rd | 12 mrbin-1.9.4/mrbin/man/mrbinrun.Rd | 12 mrbin-1.9.4/mrbin/man/mrheatmap.Rd | 11 mrbin-1.9.4/mrbin/man/mrplot.Rd | 15 mrbin-1.9.4/mrbin/man/plotMultiNMR.Rd | 8 mrbin-1.9.4/mrbin/man/plotNMR.Rd | 8 mrbin-1.9.4/mrbin/man/plotPCA.Rd | 11 mrbin-1.9.4/mrbin/man/plotResults.Rd | 9 mrbin-1.9.4/mrbin/man/recreatemrbin.Rd | 1 mrbin-1.9.4/mrbin/man/removeNoise.Rd | 13 mrbin-1.9.4/mrbin/man/removeSpectrum.Rd | 14 mrbin-1.9.4/mrbin/man/resetEnv.Rd | 2 mrbin-1.9.4/mrbin/man/right.Rd | 8 mrbin-1.9.4/mrbin/man/setDilutionFactors.Rd | 8 mrbin-1.9.4/mrbin/man/setNoiseLevels.Rd | 8 mrbin-1.9.4/mrbin/man/setOffset.Rd | 1 mrbin-1.9.4/mrbin/man/setParam.Rd | 1 mrbin-1.9.4/mrbin/man/trimZeros.Rd | 10 mrbin-1.9.4/mrbin/man/unitVarianceScaling.Rd | 11 mrbin-1.9.4/mrbin/man/up.Rd | 8 mrbin-1.9.4/mrbin/man/zoom.Rd | 7 mrbin-1.9.4/mrbin/man/zoomIn.Rd | 7 mrbin-1.9.4/mrbin/man/zoomOut.Rd | 7 mrbin-1.9.4/mrbin/vignettes/mrbin.Rnw | 82 - 60 files changed, 1591 insertions(+), 796 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://www.coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between coursekata versions 0.18.1 dated 2024-12-12 and 0.19.0 dated 2025-07-16
coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-boxplot-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-dens-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-density-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-dhistogram-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-freqpoly-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-histogram-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-rug-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-rugx-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-violin-horizontal-mull-mod-y-on-x.svg |only coursekata-0.18.1/coursekata/tests/testthat/_snaps/gf_model-visual/gf-violin-mull-mod-y-on-x-2.svg |only coursekata-0.19.0/coursekata/DESCRIPTION | 16 +- coursekata-0.19.0/coursekata/MD5 | 47 +++--- coursekata-0.19.0/coursekata/NAMESPACE | 2 coursekata-0.19.0/coursekata/NEWS.md | 4 coursekata-0.19.0/coursekata/R/data.R | 2 coursekata-0.19.0/coursekata/R/gf_model.R | 2 coursekata-0.19.0/coursekata/R/gf_resid_gf_squaresid.R |only coursekata-0.19.0/coursekata/README.md | 11 + coursekata-0.19.0/coursekata/build/partial.rdb |binary coursekata-0.19.0/coursekata/man/coursekata-package.Rd | 2 coursekata-0.19.0/coursekata/man/fevdata.Rd | 2 coursekata-0.19.0/coursekata/man/figures/README-samp_dist_of_b1-1.png |binary coursekata-0.19.0/coursekata/man/figures/README-samp_dist_of_hp-1.png |binary coursekata-0.19.0/coursekata/man/gf_resid.Rd |only coursekata-0.19.0/coursekata/man/gf_squaresid.Rd |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-boxplot-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-dens-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-density-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-dhistogram-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-freqpoly-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-histogram-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-rug-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-rugx-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-violin-horizontal-null-mod-y-on-x.svg |only coursekata-0.19.0/coursekata/tests/testthat/_snaps/gf_model-visual/gf-violin-null-mod-y-on-x-2.svg |only coursekata-0.19.0/coursekata/tests/testthat/test-gf_model-visual.R | 72 ++++++++-- 36 files changed, 116 insertions(+), 44 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Provides tools for autoregressive conditional duration (ACD, Engle and Russell, 1998) models. Functions to create trade, price, or volume durations from transaction data, perform diurnal adjustments, fit various ACD models, and test them.
Author: Markus Belfrage [aut, cre]
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.4.3 dated 2024-02-20 and 1.1.0 dated 2025-07-16
ACDm-1.0.4.3/ACDm/inst/doc |only ACDm-1.0.4.3/ACDm/src/getdudtheta.c |only ACDm-1.0.4.3/ACDm/src/sim_ACDSpline.c |only ACDm-1.1.0/ACDm/DESCRIPTION | 26 ACDm-1.1.0/ACDm/MD5 | 108 +- ACDm-1.1.0/ACDm/NAMESPACE | 14 ACDm-1.1.0/ACDm/R/RcppExports.R |only ACDm-1.1.0/ACDm/R/acdFit.R | 725 +++++++++++++------ ACDm-1.1.0/ACDm/R/acdFitClassMethods.R | 23 ACDm-1.1.0/ACDm/R/acf_acd.R | 10 ACDm-1.1.0/ACDm/R/computeDurations.R | 128 ++- ACDm-1.1.0/ACDm/R/computeScore.R |only ACDm-1.1.0/ACDm/R/distributions.R | 10 ACDm-1.1.0/ACDm/R/diurnalAdj.R | 53 - ACDm-1.1.0/ACDm/R/getLL.R | 444 ++++++++--- ACDm-1.1.0/ACDm/R/internals.R | 400 ++++++---- ACDm-1.1.0/ACDm/R/plotLL.R | 116 ++- ACDm-1.1.0/ACDm/R/resiDensityAcd.R | 2 ACDm-1.1.0/ACDm/R/sim_ACD.R | 262 ++++-- ACDm-1.1.0/ACDm/data/adjDurData.RData |binary ACDm-1.1.0/ACDm/data/defaultSplineObj.RData |binary ACDm-1.1.0/ACDm/data/durData.RData |binary ACDm-1.1.0/ACDm/data/transData.RData |binary ACDm-1.1.0/ACDm/inst/NEWS.Rd | 14 ACDm-1.1.0/ACDm/man/acdFit-methods.Rd | 2 ACDm-1.1.0/ACDm/man/acdFit.Rd | 63 + ACDm-1.1.0/ACDm/man/acf_acd.Rd | 9 ACDm-1.1.0/ACDm/man/computeDurations.Rd | 4 ACDm-1.1.0/ACDm/man/diurnalAdj.Rd | 13 ACDm-1.1.0/ACDm/man/mixinvgauss.Rd | 10 ACDm-1.1.0/ACDm/man/mixqwe.Rd | 4 ACDm-1.1.0/ACDm/man/mixqww.Rd | 2 ACDm-1.1.0/ACDm/man/plotDescTrans.Rd | 1 ACDm-1.1.0/ACDm/man/plotHazard.Rd | 2 ACDm-1.1.0/ACDm/man/plotHistAcd.Rd | 1 ACDm-1.1.0/ACDm/man/plotLL.Rd | 14 ACDm-1.1.0/ACDm/man/plotRollMeanAcd.Rd | 1 ACDm-1.1.0/ACDm/man/plotScatterAcd.Rd | 3 ACDm-1.1.0/ACDm/man/qqplotAcd.Rd | 1 ACDm-1.1.0/ACDm/man/resiDensityAcd.Rd | 1 ACDm-1.1.0/ACDm/man/sim_ACD.Rd | 20 ACDm-1.1.0/ACDm/man/testRmACD.Rd | 7 ACDm-1.1.0/ACDm/man/testSTACD.Rd | 7 ACDm-1.1.0/ACDm/man/testTVACD.Rd | 3 ACDm-1.1.0/ACDm/src/ACD_tool_cpp.cpp |only ACDm-1.1.0/ACDm/src/Makevars | 2 ACDm-1.1.0/ACDm/src/Makevars.win |only ACDm-1.1.0/ACDm/src/RcppExports.cpp |only ACDm-1.1.0/ACDm/src/computeDurations.c | 6 ACDm-1.1.0/ACDm/src/computeScoreAACD.cpp |only ACDm-1.1.0/ACDm/src/getLL.c | 1058 +++++++++++++++++++++++++--- ACDm-1.1.0/ACDm/src/getScore.c | 2 ACDm-1.1.0/ACDm/src/sim_AACD.c |only ACDm-1.1.0/ACDm/src/sim_ABACD.c | 4 ACDm-1.1.0/ACDm/src/sim_ACDCALL.c | 6 ACDm-1.1.0/ACDm/src/sim_AMACD.c | 4 ACDm-1.1.0/ACDm/src/sim_BACD.c |only ACDm-1.1.0/ACDm/src/sim_BCACD.c |only ACDm-1.1.0/ACDm/src/sim_EXACD.c |only ACDm-1.1.0/ACDm/src/sim_LSNIACDCALL.c |only ACDm-1.1.0/ACDm/src/sim_SNIACDCALL.c |only ACDm-1.1.0/ACDm/src/sim_TACD.c |only ACDm-1.1.0/ACDm/src/sim_TAMACD.c |only ACDm-1.1.0/ACDm/src/wrapper.cpp |only 64 files changed, 2633 insertions(+), 952 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 0.6.0
Title: Perform a Relative Weights Analysis
Description: Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described
in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes
the total variance predicted in a regression model into weights that accurately reflect the proportional
contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios,
RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between rwa versions 0.0.3 dated 2020-11-24 and 0.1.0 dated 2025-07-16
DESCRIPTION | 25 ++++--- MD5 | 41 ++++++++++-- NAMESPACE | 13 ++++ NEWS.md | 32 +++++++++ R/bootstrap_rwa.R |only R/plot_rwa.R | 7 +- R/rwa.R | 152 +++++++++++++++++++++++++++++++++++++++-------- README.md | 38 ++++++++++- build |only inst |only man/extract_ci.Rd |only man/plot_rwa.Rd | 4 - man/run_rwa_bootstrap.Rd |only man/rwa.Rd | 87 ++++++++++++++++++++++---- tests |only vignettes |only 16 files changed, 335 insertions(+), 64 deletions(-)
Title: Explainable Ensemble Trees
Description: The Explainable Ensemble Trees 'e2tree' approach has been proposed by Aria et al. (2024) <doi:10.1007/s00180-022-01312-6>. It aims to explain and interpret decision tree ensemble models using a single tree-like structure. 'e2tree' is a new way of explaining an ensemble tree trained through 'randomForest' or 'xgboost' packages.
Author: Massimo Aria [aut, cre, cph] ,
Agostino Gnasso [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between e2tree versions 0.1.2 dated 2025-04-12 and 0.2.0 dated 2025-07-16
DESCRIPTION | 15 - MD5 | 53 +++--- NAMESPACE | 1 NEWS.md | 5 R/createDisMatrix.R | 115 ++++++++++--- R/e2tree.R | 47 ++++- R/eComparison.R | 13 - R/eStoppingRules.R | 13 + R/rpart2Tree.R | 92 ++++++---- R/zzz.R | 1 README.md | 256 +++++++++++++----------------- man/createDisMatrix.Rd | 61 +++++-- man/e2tree.Rd | 10 + man/figures/README-unnamed-chunk-10-1.png |only man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |only man/figures/README-unnamed-chunk-16-2.png |only man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-19-2.png |only man/figures/README-unnamed-chunk-19-3.png |only man/figures/README-unnamed-chunk-20-1.png |only man/figures/README-unnamed-chunk-20-2.png |only man/figures/README-unnamed-chunk-20-3.png |only man/figures/README-unnamed-chunk-21-1.png |only man/figures/README-unnamed-chunk-21-2.png |only man/figures/README-unnamed-chunk-21-3.png |only man/figures/e2tree_logo.png |only man/rpart2Tree.Rd | 10 + tests/testthat/Rplots.pdf |binary tests/testthat/test-createDisMatrix.R | 123 ++++++++++++++ tests/testthat/test-e2tree.R | 4 tests/testthat/test-rpart2Tree.R | 8 tests/testthat/testthat-problems.rds |only 34 files changed, 555 insertions(+), 272 deletions(-)
Title: Metabolism Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package focusing on the
metabolism therapeutic area.
Author: Anders Askeland [aut, cre] ,
Andrii Yurovskyi [aut] ,
Kathrin Flunkert [aut],
Edoardo Mancini [aut] ,
Shunsuke Goto [aut],
Siddhesh Pujari [aut] ,
Sonali Das [aut],
Olga Starostecka [aut],
Vang Le-Quy [aut] ,
Keita Takahashi [aut]
Maintainer: Anders Askeland <iakd@novonordisk.com>
Diff between admiralmetabolic versions 0.1.0 dated 2025-01-20 and 0.2.0 dated 2025-07-16
admiralmetabolic-0.1.0/admiralmetabolic/data/dm_metabolic.rda |only admiralmetabolic-0.1.0/admiralmetabolic/data/qs_metabolic.rda |only admiralmetabolic-0.1.0/admiralmetabolic/data/vs_metabolic.rda |only admiralmetabolic-0.1.0/admiralmetabolic/man/dm_metabolic.Rd |only admiralmetabolic-0.1.0/admiralmetabolic/man/qs_metabolic.Rd |only admiralmetabolic-0.1.0/admiralmetabolic/man/vs_metabolic.Rd |only admiralmetabolic-0.2.0/admiralmetabolic/DESCRIPTION | 55 admiralmetabolic-0.2.0/admiralmetabolic/MD5 | 86 admiralmetabolic-0.2.0/admiralmetabolic/NAMESPACE | 280 - admiralmetabolic-0.2.0/admiralmetabolic/NEWS.md | 73 admiralmetabolic-0.2.0/admiralmetabolic/R/admiralmetabolic-package.R | 60 admiralmetabolic-0.2.0/admiralmetabolic/R/data.R | 43 admiralmetabolic-0.2.0/admiralmetabolic/R/derive_advs_params.R | 1312 ++--- admiralmetabolic-0.2.0/admiralmetabolic/R/global.R | 288 - admiralmetabolic-0.2.0/admiralmetabolic/README.md | 155 admiralmetabolic-0.2.0/admiralmetabolic/build/vignette.rds |binary admiralmetabolic-0.2.0/admiralmetabolic/data/admiralmetabolic_adsl.rda |only admiralmetabolic-0.2.0/admiralmetabolic/data/admiralmetabolic_advs.rda |only admiralmetabolic-0.2.0/admiralmetabolic/inst/WORDLIST | 124 admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adcoeq.R | 265 - admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adcoeq.Rmd | 456 - admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adcoeq.html | 1862 +++---- admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adlb.R |only admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adlb.Rmd |only admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/adlb.html |only admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/admiralmetabolic.R | 36 admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/admiralmetabolic.Rmd | 124 admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/admiralmetabolic.html | 816 +-- admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/advs.R | 444 - admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/advs.Rmd | 804 +-- admiralmetabolic-0.2.0/admiralmetabolic/inst/doc/advs.html | 2486 +++++----- admiralmetabolic-0.2.0/admiralmetabolic/inst/templates/ad_adcoeq.R | 527 +- admiralmetabolic-0.2.0/admiralmetabolic/inst/templates/ad_adlb.R |only admiralmetabolic-0.2.0/admiralmetabolic/inst/templates/ad_adsl_metabolic.R |only admiralmetabolic-0.2.0/admiralmetabolic/inst/templates/ad_advs.R | 609 +- admiralmetabolic-0.2.0/admiralmetabolic/man/admiralmetabolic-package.Rd | 85 admiralmetabolic-0.2.0/admiralmetabolic/man/admiralmetabolic_adsl.Rd |only admiralmetabolic-0.2.0/admiralmetabolic/man/admiralmetabolic_advs.Rd |only admiralmetabolic-0.2.0/admiralmetabolic/man/derive_param_ratio.Rd | 286 - admiralmetabolic-0.2.0/admiralmetabolic/man/derive_param_waisthgt.Rd | 446 - admiralmetabolic-0.2.0/admiralmetabolic/man/derive_param_waisthip.Rd | 364 - admiralmetabolic-0.2.0/admiralmetabolic/man/roxygen/meta.R | 28 admiralmetabolic-0.2.0/admiralmetabolic/man/unit-conversion.Rd | 42 admiralmetabolic-0.2.0/admiralmetabolic/tests/testthat.R | 8 admiralmetabolic-0.2.0/admiralmetabolic/tests/testthat/test-derive_param_ratio.R | 494 - admiralmetabolic-0.2.0/admiralmetabolic/tests/testthat/test-derive_param_waisthgt.R | 312 - admiralmetabolic-0.2.0/admiralmetabolic/tests/testthat/test-derive_param_waisthip.R | 226 admiralmetabolic-0.2.0/admiralmetabolic/tests/testthat/test-get_conv_factor.R | 38 admiralmetabolic-0.2.0/admiralmetabolic/vignettes/adcoeq.Rmd | 456 - admiralmetabolic-0.2.0/admiralmetabolic/vignettes/adlb.Rmd |only admiralmetabolic-0.2.0/admiralmetabolic/vignettes/admiralmetabolic.Rmd | 124 admiralmetabolic-0.2.0/admiralmetabolic/vignettes/advs.Rmd | 804 +-- 52 files changed, 7337 insertions(+), 7281 deletions(-)
More information about admiralmetabolic at CRAN
Permanent link
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP
<doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors'
package in the 'Monolix' installation, as described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>.
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
Chart Data instead of exporting it from the 'Monolix' gui.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [aut] ,
Seid Hamzic [aut],
Benjamin Gui [...truncated...]
Maintainer: Aleksandr Pogodaev <alex.pogodaev@novartis.com>
Diff between ggPMX versions 1.2.11 dated 2023-11-30 and 1.3.0 dated 2025-07-16
ggPMX-1.2.11/ggPMX/inst/testdata/extdata/for_testing |only ggPMX-1.3.0/ggPMX/DESCRIPTION | 31 ggPMX-1.3.0/ggPMX/MD5 | 201 ++-- ggPMX-1.3.0/ggPMX/NAMESPACE | 4 ggPMX-1.3.0/ggPMX/NEWS.md | 15 ggPMX-1.3.0/ggPMX/R/assertions.R | 12 ggPMX-1.3.0/ggPMX/R/classInt.R | 2 ggPMX-1.3.0/ggPMX/R/ggPMX-options.R | 3 ggPMX-1.3.0/ggPMX/R/ggforce-facet-paginate.R | 3 ggPMX-1.3.0/ggPMX/R/gpar.R | 15 ggPMX-1.3.0/ggPMX/R/nlmixr.R | 7 ggPMX-1.3.0/ggPMX/R/plot-base.R | 14 ggPMX-1.3.0/ggPMX/R/plot-density.R | 1 ggPMX-1.3.0/ggPMX/R/plot-eta-cov.R | 2 ggPMX-1.3.0/ggPMX/R/plot-eta-pairs.R | 6 ggPMX-1.3.0/ggPMX/R/plot-themes.R | 1 ggPMX-1.3.0/ggPMX/R/plot-vpc.R | 51 - ggPMX-1.3.0/ggPMX/R/pmx-add-plot.R | 2 ggPMX-1.3.0/ggPMX/R/pmx-all-plots.R | 11 ggPMX-1.3.0/ggPMX/R/pmx-filter.R | 4 ggPMX-1.3.0/ggPMX/R/pmx-plots-eta-cov.R | 5 ggPMX-1.3.0/ggPMX/R/pmx-plots-individual.R | 7 ggPMX-1.3.0/ggPMX/R/pmx-plots-saem-convergence.R |only ggPMX-1.3.0/ggPMX/R/pmx-report.R | 2 ggPMX-1.3.0/ggPMX/R/pmxClass.R | 55 - ggPMX-1.3.0/ggPMX/build/vignette.rds |binary ggPMX-1.3.0/ggPMX/inst/doc/ggPMX-guide.R | 294 ++--- ggPMX-1.3.0/ggPMX/inst/doc/ggPMX-guide.Rmd | 1 ggPMX-1.3.0/ggPMX/inst/doc/ggPMX-guide.pdf |binary ggPMX-1.3.0/ggPMX/inst/examples/eta_cov.R | 6 ggPMX-1.3.0/ggPMX/inst/init/gpar.yaml | 1 ggPMX-1.3.0/ggPMX/inst/init/standing.ppmx | 37 ggPMX-1.3.0/ggPMX/inst/templates/mlx/standing.ipmx | 6 ggPMX-1.3.0/ggPMX/inst/testdata/theophylline/Monolix/ChartsData |only ggPMX-1.3.0/ggPMX/man/distrib.Rd | 5 ggPMX-1.3.0/ggPMX/man/eta_cov.Rd | 5 ggPMX-1.3.0/ggPMX/man/eta_cov_plot.Rd | 15 ggPMX-1.3.0/ggPMX/man/eta_pairs.Rd | 5 ggPMX-1.3.0/ggPMX/man/eval_sym_parent_env.Rd | 7 ggPMX-1.3.0/ggPMX/man/getPmxOption.Rd | 3 ggPMX-1.3.0/ggPMX/man/get_cats.Rd | 2 ggPMX-1.3.0/ggPMX/man/get_conts.Rd | 2 ggPMX-1.3.0/ggPMX/man/get_covariates.Rd | 2 ggPMX-1.3.0/ggPMX/man/get_data.Rd | 2 ggPMX-1.3.0/ggPMX/man/get_occ.Rd | 2 ggPMX-1.3.0/ggPMX/man/get_strats.Rd | 2 ggPMX-1.3.0/ggPMX/man/ggPMX.Rd | 8 ggPMX-1.3.0/ggPMX/man/gtable_remove_grobs.Rd | 3 ggPMX-1.3.0/ggPMX/man/individual.Rd | 5 ggPMX-1.3.0/ggPMX/man/n_pages.Rd | 2 ggPMX-1.3.0/ggPMX/man/plot_names.Rd | 2 ggPMX-1.3.0/ggPMX/man/plot_pmx.Rd | 1 ggPMX-1.3.0/ggPMX/man/plot_pmx.distrib.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.eta_cov.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.eta_pairs.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.individual.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.pmx_dens.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.pmx_gpar.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.pmx_param_history.Rd |only ggPMX-1.3.0/ggPMX/man/plot_pmx.pmx_qq.Rd | 5 ggPMX-1.3.0/ggPMX/man/plot_pmx.residual.Rd | 5 ggPMX-1.3.0/ggPMX/man/plots.Rd | 2 ggPMX-1.3.0/ggPMX/man/pmxOptions.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_dens.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_plot.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_plot_cats.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_plot_saem_convergence.Rd |only ggPMX-1.3.0/ggPMX/man/pmx_plot_vpc.Rd | 4 ggPMX-1.3.0/ggPMX/man/pmx_register_plot.Rd | 4 ggPMX-1.3.0/ggPMX/man/pmx_theme.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_update.Rd | 2 ggPMX-1.3.0/ggPMX/man/pmx_vpc.Rd | 3 ggPMX-1.3.0/ggPMX/man/pmx_vpc_bin.Rd | 7 ggPMX-1.3.0/ggPMX/man/pmx_vpc_ci.Rd | 7 ggPMX-1.3.0/ggPMX/man/pmx_vpc_obs.Rd | 7 ggPMX-1.3.0/ggPMX/man/pmx_vpc_pi.Rd | 9 ggPMX-1.3.0/ggPMX/man/pmx_vpc_rug.Rd | 7 ggPMX-1.3.0/ggPMX/man/read_mlx_saem_conv.Rd |only ggPMX-1.3.0/ggPMX/man/set_data.Rd | 2 ggPMX-1.3.0/ggPMX/man/set_plot.Rd | 5 ggPMX-1.3.0/ggPMX/tests/testthat/helper-skip.R | 2 ggPMX-1.3.0/ggPMX/tests/testthat/test-2023table.R | 4 ggPMX-1.3.0/ggPMX/tests/testthat/test-classInt.R | 4 ggPMX-1.3.0/ggPMX/tests/testthat/test-config.R | 32 ggPMX-1.3.0/ggPMX/tests/testthat/test-gpar.R | 22 ggPMX-1.3.0/ggPMX/tests/testthat/test-nlmixr.R | 23 ggPMX-1.3.0/ggPMX/tests/testthat/test-nonmem_reader.R | 19 ggPMX-1.3.0/ggPMX/tests/testthat/test-param_table.R | 5 ggPMX-1.3.0/ggPMX/tests/testthat/test-plot-density.R | 19 ggPMX-1.3.0/ggPMX/tests/testthat/test-plot-individual.R | 76 - ggPMX-1.3.0/ggPMX/tests/testthat/test-plot-residual.R | 25 ggPMX-1.3.0/ggPMX/tests/testthat/test-plot.R | 2 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-all-plots.R | 68 - ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-plot-vpc.R | 20 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-plots-distribution.R | 2 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-plots-saem-convergence.R |only ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-plots-scatter.R | 46 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-post_load.R | 1 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx-report.R | 497 ++-------- ggPMX-1.3.0/ggPMX/tests/testthat/test-pmxClass.R | 28 ggPMX-1.3.0/ggPMX/tests/testthat/test-pmx_nlmixr.R | 33 ggPMX-1.3.0/ggPMX/tests/testthat/test-simBlq-npde.R |only ggPMX-1.3.0/ggPMX/tests/testthat/test-utils.R | 33 ggPMX-1.3.0/ggPMX/tests/testthat/test-vdiff.R | 20 ggPMX-1.3.0/ggPMX/vignettes/ggPMX-guide.Rmd | 1 105 files changed, 1032 insertions(+), 936 deletions(-)
Title: Clean and Standardize Epidemiological Data
Description: Cleaning and standardizing tabular data package, tailored
specifically for curating epidemiological data. It streamlines various
data cleaning tasks that are typically expected when working with
datasets in epidemiology. It returns the processed data in the same
format, and generates a comprehensive report detailing the outcomes of
each cleaning task.
Author: Karim Mane [aut, cre] ,
Thibaut Jombart [ctb] .),
Abdoelnaser Degoot [aut] ,
Bankole Ahadzie [aut],
Nuredin Mohammed [aut],
Bubacarr Bah [aut] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [rev] ,
James M. Azam [rev] ,
Joshua W. Lambert [rev, ctb] ,
Chr [...truncated...]
Maintainer: Karim Mane <karim.mane@lshtm.ac.uk>
Diff between cleanepi versions 1.1.0 dated 2025-03-04 and 1.1.1 dated 2025-07-16
DESCRIPTION | 36 MD5 | 117 NAMESPACE | 1 NEWS.md | 46 R/check_date_sequence.R | 43 R/clean_data.R | 17 R/clean_data_helpers.R | 73 R/column_name_standardization.R | 14 R/convert_to_numeric.R | 14 R/correct_misspelled_values.R |only R/date_standardization_helpers.R | 86 R/dev-utils.R | 6 R/dictionary_based_cleaning.R | 12 R/find_and_remove_duplicates.R | 62 R/guess_dates.R | 6 R/print_report.R | 106 R/remove_constants.R | 45 R/replace_missing_values.R | 16 R/standardize_date.R | 38 R/standardize_subject_ids.R | 188 - R/utils-potools.R | 2 R/utils.R | 12 README.md | 22 inst/WORDLIST | 12 inst/doc/cleanepi.R | 269 + inst/doc/cleanepi.Rmd | 947 ++++-- inst/doc/cleanepi.html | 1657 +++++++----- inst/doc/design_principle.Rmd | 483 ++- inst/doc/design_principle.html | 2 inst/po/fr/LC_MESSAGES/R-cleanepi.mo |binary inst/rmarkdown/templates/printing-rmd/skeleton/skeleton.Rmd | 40 man/add_to_report.Rd | 2 man/check_date_sequence.Rd | 12 man/check_subject_ids.Rd | 23 man/clean_data.Rd | 17 man/clean_using_dictionary.Rd | 3 man/cleanepi-package.Rd | 2 man/convert_to_numeric.Rd | 12 man/correct_misspelled_values.Rd |only man/correct_subject_ids.Rd | 17 man/find_duplicates.Rd | 13 man/get_appropriate_format.Rd |only man/perform_remove_constants.Rd | 6 man/print_report.Rd | 35 man/remove_constants.Rd | 27 man/remove_duplicates.Rd | 19 man/replace_missing_values.Rd | 14 man/scan_data.Rd | 12 man/scan_in_character.Rd | 4 man/standardize_column_names.Rd | 6 man/standardize_dates.Rd | 18 man/unnest_report.Rd |only po/R-cleanepi.pot | 301 +- po/R-fr.po | 360 +- tests/spelling.R | 2 tests/testthat/test-check_date_sequence.R | 8 tests/testthat/test-correct_misspelled_values.R |only tests/testthat/test-find_and_remove_duplicates.R | 80 tests/testthat/test-remove_constants.R | 27 tests/testthat/test-standardize_subject_ids.R | 29 vignettes/cleanepi.Rmd | 947 ++++-- vignettes/design_principle.Rmd | 483 ++- 62 files changed, 4494 insertions(+), 2357 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
Author: Jure Demsar [cre, aut],
Grega Repovs [aut],
Erik Strumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] ,
Rasmus Baath [cph]
Maintainer: Jure Demsar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.2.12 dated 2023-09-29 and 1.2.13 dated 2025-07-16
bayes4psy-1.2.12/bayes4psy/src/Makevars.win |only bayes4psy-1.2.13/bayes4psy/DESCRIPTION | 6 bayes4psy-1.2.13/bayes4psy/MD5 | 37 bayes4psy-1.2.13/bayes4psy/NEWS.md | 4 bayes4psy-1.2.13/bayes4psy/build/vignette.rds |binary bayes4psy-1.2.13/bayes4psy/data/stroop_extended.rda |binary bayes4psy-1.2.13/bayes4psy/inst/doc/adaptation_level.R | 14 bayes4psy-1.2.13/bayes4psy/inst/doc/adaptation_level.html | 237 - bayes4psy-1.2.13/bayes4psy/inst/doc/afterimages.R | 12 bayes4psy-1.2.13/bayes4psy/inst/doc/afterimages.html | 519 +- bayes4psy-1.2.13/bayes4psy/inst/doc/flanker.R | 32 bayes4psy-1.2.13/bayes4psy/inst/doc/flanker.html | 433 +- bayes4psy-1.2.13/bayes4psy/inst/doc/stroop.R | 16 bayes4psy-1.2.13/bayes4psy/inst/doc/stroop.html | 297 - bayes4psy-1.2.13/bayes4psy/src/Makevars | 2 bayes4psy-1.2.13/bayes4psy/src/stanExports_color.h | 2290 ++++++------- bayes4psy-1.2.13/bayes4psy/src/stanExports_linear.h | 1627 ++++----- bayes4psy-1.2.13/bayes4psy/src/stanExports_reaction_time.h | 1756 ++++----- bayes4psy-1.2.13/bayes4psy/src/stanExports_success_rate.h | 945 ++--- bayes4psy-1.2.13/bayes4psy/src/stanExports_ttest.h | 925 ++--- 20 files changed, 4483 insertions(+), 4669 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet,
NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Author: Eduard Szoecs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmueller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
Joao Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Ethan Bass [ctb],
Tamas Stirling [ctb, cre [...truncated...]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.3.0 dated 2023-06-09 and 1.3.1 dated 2025-07-16
webchem-1.3.0/webchem/man/webchem.Rd |only webchem-1.3.1/webchem/DESCRIPTION | 12 - webchem-1.3.1/webchem/MD5 | 57 +++--- webchem-1.3.1/webchem/NEWS.md | 9 webchem-1.3.1/webchem/R/extractors.R | 6 webchem-1.3.1/webchem/R/jagst.R |only webchem-1.3.1/webchem/R/lc50.R |only webchem-1.3.1/webchem/R/opsin.R | 2 webchem-1.3.1/webchem/R/ping.R | 2 webchem-1.3.1/webchem/R/pubchem.R | 131 ++++++++++---- webchem-1.3.1/webchem/R/srs.R | 6 webchem-1.3.1/webchem/R/utils.R | 64 ++++-- webchem-1.3.1/webchem/R/webchem-package.R | 43 ---- webchem-1.3.1/webchem/R/zzz.R |only webchem-1.3.1/webchem/build/partial.rdb |binary webchem-1.3.1/webchem/build/vignette.rds |binary webchem-1.3.1/webchem/inst/doc/webchem.html | 4 webchem-1.3.1/webchem/man/get_cid.Rd | 20 +- webchem-1.3.1/webchem/man/is.inchikey.Rd | 5 webchem-1.3.1/webchem/man/is.inchikey_cs.Rd | 5 webchem-1.3.1/webchem/man/jagst.Rd | 4 webchem-1.3.1/webchem/man/lc50.Rd | 2 webchem-1.3.1/webchem/man/opsin_query.Rd | 2 webchem-1.3.1/webchem/man/pc_prop.Rd | 13 - webchem-1.3.1/webchem/man/webchem-package.Rd |only webchem-1.3.1/webchem/tests/fixtures/is_inchikey_cs_1.yml |only webchem-1.3.1/webchem/tests/fixtures/is_inchikey_cs_2.yml |only webchem-1.3.1/webchem/tests/testthat/test-chebi.R | 2 webchem-1.3.1/webchem/tests/testthat/test-chembl.R | 2 webchem-1.3.1/webchem/tests/testthat/test-pubchem.R | 31 ++- webchem-1.3.1/webchem/tests/testthat/test-srs.R | 2 webchem-1.3.1/webchem/tests/testthat/test-utils.R | 12 - webchem-1.3.1/webchem/tests/testthat/test-wikidata.R | 2 33 files changed, 268 insertions(+), 170 deletions(-)
Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library.
Watch files, or directories recursively, for changes in the
background. Log activity, or run an R function every time a change
event occurs.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between watcher versions 0.1.3 dated 2025-04-09 and 0.1.4 dated 2025-07-16
DESCRIPTION | 48 ++++++++++++++++++++++---------------------- MD5 | 19 +++++++++-------- NEWS.md | 4 +++ R/watch.R | 1 README.md | 10 ++++----- configure | 27 +++++++++++++++--------- configure.win | 3 -- man/watcher-package.Rd | 4 +-- src/watcher.c | 31 +++++++++++++++++----------- tests/testthat/_snaps |only tests/testthat/test-watch.R | 11 ++++++++-- 11 files changed, 91 insertions(+), 67 deletions(-)
Title: Site Occupancy Modeling for Environmental DNA Metabarcoding
Description: Fits community site occupancy models to environmental DNA
metabarcoding data collected using spatially-replicated survey design.
Model fitting results can be used to evaluate and compare the effectiveness
of species detection to find an efficient survey design.
Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>,
Fukaya and Hasebe (2025) <doi:10.1002/1438-390X.12219>.
Author: Keiichi Fukaya [aut, cre],
Ken Kellner [cph] ,
Mika Takahashi [aut]
Maintainer: Keiichi Fukaya <fukayak99@gmail.com>
Diff between occumb versions 1.2.0 dated 2025-05-24 and 1.2.1 dated 2025-07-16
DESCRIPTION | 8 MD5 | 18 NEWS.md | 3 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/model_specification.Rmd | 2 inst/doc/model_specification.html | 332 +++++- inst/doc/occumb.html | 1809 +++++++++++++++++++++----------------- vignettes/model_specification.Rmd | 2 10 files changed, 1321 insertions(+), 855 deletions(-)
Title: Linear Programming Discriminant Analysis
Description: Classification method obtained through linear programming.
It is advantageous with respect to the classical developments when the distribution of the variables
involved is unknown or when the number of variables is much greater than the number of individuals.
Mathematical details behind the method are published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming".
<doi:10.1371/journal.pone.0270403>.
Author: Maria Jose Nueda [aut, cre]
Maintainer: Maria Jose Nueda <mj.nueda@ua.es>
Diff between lpda versions 1.2.0 dated 2025-03-26 and 1.2.1 dated 2025-07-16
DESCRIPTION | 6 +- MD5 | 40 ++++++++-------- NEWS.md | 9 ++- R/lpda.3D.R | 4 - R/plot.lpda.3D.R | 4 - R/plot.lpda.R | 58 +++++++++++++++--------- build/vignette.rds |binary inst/doc/lpdaUsersGuide.R | 4 - inst/doc/lpdaUsersGuide.Rmd | 26 ++++++---- inst/doc/lpdaUsersGuide.html | 53 +++++++++++---------- man/PCA.Rd | 2 man/lpda.3D.Rd | 2 man/plot.lpda.3D.Rd | 4 - man/plot.lpda.Rd | 17 +++++-- vignettes/figures/README-unnamed-chunk-10-1.png |binary vignettes/figures/README-unnamed-chunk-13-1.png |binary vignettes/figures/README-unnamed-chunk-20-1.png |binary vignettes/figures/README-unnamed-chunk-21-1.png |binary vignettes/figures/README-unnamed-chunk-21-2.png |binary vignettes/figures/README-unnamed-chunk-8-1.png |binary vignettes/lpdaUsersGuide.Rmd | 26 ++++++---- 21 files changed, 146 insertions(+), 109 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.1.1 dated 2025-04-25 and 1.2.0 dated 2025-07-16
IssueTrackeR-1.1.1/IssueTrackeR/R/filter_issues.R |only IssueTrackeR-1.1.1/IssueTrackeR/R/sort_issues.R |only IssueTrackeR-1.1.1/IssueTrackeR/man/contains.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/filter_issues.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/format_milestone.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/format_timestamp.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/logical_reducer.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/no_milestones.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/simple_sort.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/sort.IssuesTB.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/man/vgrepl.Rd |only IssueTrackeR-1.1.1/IssueTrackeR/tests/testthat/test-logical_reducer.R |only IssueTrackeR-1.1.1/IssueTrackeR/tests/testthat/test-no_milestones.R |only IssueTrackeR-1.1.1/IssueTrackeR/tests/testthat/test-simple_sort.R |only IssueTrackeR-1.1.1/IssueTrackeR/tests/testthat/test-vgrepl.R |only IssueTrackeR-1.2.0/IssueTrackeR/DESCRIPTION | 10 IssueTrackeR-1.2.0/IssueTrackeR/MD5 | 69 IssueTrackeR-1.2.0/IssueTrackeR/NAMESPACE | 36 IssueTrackeR-1.2.0/IssueTrackeR/NEWS.md | 130 - IssueTrackeR-1.2.0/IssueTrackeR/R/IssueTrackeR-package.R | 29 IssueTrackeR-1.2.0/IssueTrackeR/R/format.R | 7 IssueTrackeR-1.2.0/IssueTrackeR/R/print.R | 267 ++- IssueTrackeR-1.2.0/IssueTrackeR/R/summary.R |only IssueTrackeR-1.2.0/IssueTrackeR/R/update_database.R | 170 +- IssueTrackeR-1.2.0/IssueTrackeR/R/wrangling_dataset_issues.R | 771 +++++----- IssueTrackeR-1.2.0/IssueTrackeR/R/wrangling_dataset_labels.R | 30 IssueTrackeR-1.2.0/IssueTrackeR/R/wrangling_dataset_milestones.R | 45 IssueTrackeR-1.2.0/IssueTrackeR/R/wrangling_issues.R | 678 +++++--- IssueTrackeR-1.2.0/IssueTrackeR/R/zzz.R | 23 IssueTrackeR-1.2.0/IssueTrackeR/README.md | 24 IssueTrackeR-1.2.0/IssueTrackeR/inst/WORDLIST | 46 IssueTrackeR-1.2.0/IssueTrackeR/inst/data_issues |only IssueTrackeR-1.2.0/IssueTrackeR/man/append.Rd | 66 IssueTrackeR-1.2.0/IssueTrackeR/man/format_issues.Rd | 110 - IssueTrackeR-1.2.0/IssueTrackeR/man/get.Rd | 254 +-- IssueTrackeR-1.2.0/IssueTrackeR/man/new_issue.Rd | 173 +- IssueTrackeR-1.2.0/IssueTrackeR/man/new_issues.Rd | 183 +- IssueTrackeR-1.2.0/IssueTrackeR/man/print.Rd | 90 - IssueTrackeR-1.2.0/IssueTrackeR/man/sample.Rd |only IssueTrackeR-1.2.0/IssueTrackeR/man/summary.Rd |only IssueTrackeR-1.2.0/IssueTrackeR/man/write.Rd | 190 +- IssueTrackeR-1.2.0/IssueTrackeR/tests/testthat/helper.R | 12 IssueTrackeR-1.2.0/IssueTrackeR/tests/testthat/test-format_timestamp.R | 28 IssueTrackeR-1.2.0/IssueTrackeR/tests/testthat/test-get_issues.R | 80 - 44 files changed, 2087 insertions(+), 1434 deletions(-)
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and block-specific factors using a flexible multilevel factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) estimate factor-augmented quantile regressions; (iv) recover full predictive densities from these quantile forecasts; and (v) estimate the density when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.4.0 dated 2025-06-13 and 0.5.0 dated 2025-07-16
FARS-0.4.0/FARS/R/compute_gamma_atcsr.R |only FARS-0.4.0/FARS/R/density.R |only FARS-0.4.0/FARS/inst/doc/introduction.R |only FARS-0.4.0/FARS/inst/doc/introduction.Rmd |only FARS-0.4.0/FARS/inst/doc/introduction.html |only FARS-0.4.0/FARS/man/compute_gamma_atcsr.Rd |only FARS-0.4.0/FARS/man/density.Rd |only FARS-0.4.0/FARS/vignettes/introduction.Rmd |only FARS-0.5.0/FARS/DESCRIPTION | 9 - FARS-0.5.0/FARS/MD5 | 67 +++++----- FARS-0.5.0/FARS/NAMESPACE | 5 FARS-0.5.0/FARS/R/apply_identifications.R | 2 FARS-0.5.0/FARS/R/compute_density.R |only FARS-0.5.0/FARS/R/compute_fars.R | 11 + FARS-0.5.0/FARS/R/compute_gamma_FPR.R |only FARS-0.5.0/FARS/R/compute_stressed_factors.R | 1 FARS-0.5.0/FARS/R/compute_subsample.R | 5 FARS-0.5.0/FARS/R/create_scenario.R | 45 ++++-- FARS-0.5.0/FARS/R/l_density.R |only FARS-0.5.0/FARS/R/mldfm.R | 8 - FARS-0.5.0/FARS/R/mldfm_subsampling.R | 4 FARS-0.5.0/FARS/R/multiple_blocks.R | 1 FARS-0.5.0/FARS/R/nl_density.R | 50 +------ FARS-0.5.0/FARS/R/plot.fars.R | 12 + FARS-0.5.0/FARS/R/plot_residuals_mldfm.R | 20 +- FARS-0.5.0/FARS/R/print.fars.R | 2 FARS-0.5.0/FARS/R/print.fars_density.R | 3 FARS-0.5.0/FARS/R/print.mldfm.R | 6 FARS-0.5.0/FARS/R/quantile_risk.R | 5 FARS-0.5.0/FARS/R/single_block.R | 46 ++++-- FARS-0.5.0/FARS/R/summary.mldfm.R | 8 - FARS-0.5.0/FARS/README.md | 2 FARS-0.5.0/FARS/build/vignette.rds |binary FARS-0.5.0/FARS/inst/CITATION |only FARS-0.5.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.Rmd |only FARS-0.5.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.html |only FARS-0.5.0/FARS/man/compute_density.Rd |only FARS-0.5.0/FARS/man/compute_gamma_FPR.Rd |only FARS-0.5.0/FARS/man/create_scenario.Rd | 4 FARS-0.5.0/FARS/man/l_density.Rd |only FARS-0.5.0/FARS/man/nl_density.Rd | 35 ----- FARS-0.5.0/FARS/man/quantile_risk.Rd | 5 FARS-0.5.0/FARS/vignettes/Factor_Augmented_Regression_Scenarios_in_R.Rmd |only FARS-0.5.0/FARS/vignettes/pdf |only 44 files changed, 184 insertions(+), 172 deletions(-)
Title: Creation, Reading and Validation of 'mzqc' Files
Description: Reads, writes and validates 'mzQC' files. The 'mzQC' format is a
standardized file format for the exchange, transmission, and archiving of
quality metrics derived from biological mass spectrometry data, as defined
by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative)
Quality Control working group.
See <https://hupo-psi.github.io/mzQC/> for details.
Author: Chris Bielow [aut, cre] ,
David Jimenez-Morales [rev, ctb] ,
Jeremi Maciejewski [ctb]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between rmzqc versions 0.6.0 dated 2025-06-03 and 0.7.0 dated 2025-07-16
rmzqc-0.6.0/rmzqc/man/MzQCDateTime-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCanalysisSoftware-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCbaseQuality-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCcontrolledVocabulary-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCcvParameter-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCinputFile-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCmetadata-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCmzQC-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCqualityMetric-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCrunQuality-class.Rd |only rmzqc-0.6.0/rmzqc/man/MzQCsetQuality-class.Rd |only rmzqc-0.6.0/rmzqc/tests/testthat/_snaps |only rmzqc-0.7.0/rmzqc/DESCRIPTION | 16 rmzqc-0.7.0/rmzqc/MD5 | 50 rmzqc-0.7.0/rmzqc/NEWS.md | 8 rmzqc-0.7.0/rmzqc/R/conversion.R | 2 rmzqc-0.7.0/rmzqc/R/mzQC.R | 2334 ++++++------ rmzqc-0.7.0/rmzqc/inst/doc/basic_guide.html | 12 rmzqc-0.7.0/rmzqc/inst/doc/using_a_custom_cv.html | 122 rmzqc-0.7.0/rmzqc/inst/doc/validation_guide.html | 4 rmzqc-0.7.0/rmzqc/inst/schema/mzqc_schema.json | 4 rmzqc-0.7.0/rmzqc/man/MzQCDateTime.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCanalysisSoftware.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCbaseQuality.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCcontrolledVocabulary.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCcvParameter.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCinputFile.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCmetadata.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCmzQC.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCqualityMetric.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCrunQuality.Rd |only rmzqc-0.7.0/rmzqc/man/MzQCsetQuality.Rd |only rmzqc-0.7.0/rmzqc/man/isValidMzQC.Rd | 2 rmzqc-0.7.0/rmzqc/man/rmzqc-package.Rd | 1 rmzqc-0.7.0/rmzqc/tests/testthat/output_snaps |only rmzqc-0.7.0/rmzqc/tests/testthat/test-mzQC.R | 14 rmzqc-0.7.0/rmzqc/tests/testthat/test_improved_validation.R | 16 rmzqc-0.7.0/rmzqc/tests/testthat/test_io.R | 10 38 files changed, 1482 insertions(+), 1113 deletions(-)
Title: Unifying Multiple Biplot Visualisations into a Single Display
Description: Aligning multiple visualisations by utilising generalised orthogonal Procrustes analysis (GPA) before combining coordinates into a single biplot display as described in Nienkemper-Swanepoel, le Roux and Lubbe (2023)<doi:10.1080/03610918.2021.1914089>. This is mainly suitable to combine visualisations constructed from multiple imputations, however, it can be generalised to combine variations of visualisations from the same datasets (i.e. resamples).
Author: Johane Nienkemper-Swanepoel [aut, cre, cph]
Maintainer: Johane Nienkemper-Swanepoel <nienkemperj@sun.ac.za>
Diff between GPAbin versions 1.0.6 dated 2025-06-14 and 1.1.0 dated 2025-07-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/Procrustes.R | 10 +++++----- R/plotting.R | 2 +- README.md | 3 +-- 6 files changed, 17 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-13 1.0.1
2023-04-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-22 0.3.2
2023-01-06 0.3.1
2020-11-29 0.3
2020-10-10 0.2.5
2020-01-10 0.2.3
2019-05-31 0.2.1
2019-05-08 0.2
2019-01-28 0.1.2
2019-01-08 0.1.1
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 3.0.4 dated 2025-02-14 and 4.0.0 dated 2025-07-16
rxode2-3.0.4/rxode2/man/dot-linCmtSensB.Rd |only rxode2-3.0.4/rxode2/src/approx.c |only rxode2-3.0.4/rxode2/src/handle_evid.c |only rxode2-3.0.4/rxode2/src/lincmt.c |only rxode2-3.0.4/rxode2/src/lincmtB.cpp |only rxode2-3.0.4/rxode2/src/lincmtB1.h |only rxode2-3.0.4/rxode2/src/needSortDefines.h |only rxode2-3.0.4/rxode2/src/utilc.c |only rxode2-3.0.4/rxode2/tests/testthat/si.qs |only rxode2-3.0.4/rxode2/tests/testthat/test-npde-mac.R |only rxode2-4.0.0/rxode2/DESCRIPTION | 13 rxode2-4.0.0/rxode2/MD5 | 333 - rxode2-4.0.0/rxode2/NAMESPACE | 8 rxode2-4.0.0/rxode2/NEWS.md | 64 rxode2-4.0.0/rxode2/R/RcppExports.R | 61 rxode2-4.0.0/rxode2/R/asFunction.R | 11 rxode2-4.0.0/rxode2/R/build.R | 2 rxode2-4.0.0/rxode2/R/confint.R | 2 rxode2-4.0.0/rxode2/R/d.R | 168 rxode2-4.0.0/rxode2/R/dfIni.R | 241 - rxode2-4.0.0/rxode2/R/err-foceiBase.R | 50 rxode2-4.0.0/rxode2/R/err.R | 96 rxode2-4.0.0/rxode2/R/etTran.R | 18 rxode2-4.0.0/rxode2/R/intern.R | 6 rxode2-4.0.0/rxode2/R/linCmt.R |only rxode2-4.0.0/rxode2/R/mu.R | 25 rxode2-4.0.0/rxode2/R/parseFuns.R | 81 rxode2-4.0.0/rxode2/R/piping-ini.R | 70 rxode2-4.0.0/rxode2/R/piping.R | 57 rxode2-4.0.0/rxode2/R/rxJacobian.R | 14 rxode2-4.0.0/rxode2/R/rxLinCmt.R | 6 rxode2-4.0.0/rxode2/R/rxSymInv.R | 2 rxode2-4.0.0/rxode2/R/rxUiGet.R | 20 rxode2-4.0.0/rxode2/R/rxode-options.R | 3 rxode2-4.0.0/rxode2/R/rxode2.R | 5 rxode2-4.0.0/rxode2/R/rxode2_md5.R | 2 rxode2-4.0.0/rxode2/R/rxsolve.R | 296 + rxode2-4.0.0/rxode2/R/symengine.R | 505 ++ rxode2-4.0.0/rxode2/R/tran.R | 7 rxode2-4.0.0/rxode2/R/ui-fix.R | 105 rxode2-4.0.0/rxode2/R/utils.R | 102 rxode2-4.0.0/rxode2/README.md | 169 rxode2-4.0.0/rxode2/build/buildLinCmt.R |only rxode2-4.0.0/rxode2/build/linCmtTest.R |only rxode2-4.0.0/rxode2/build/linCmtTest.sh |only rxode2-4.0.0/rxode2/build/partial.rdb |binary rxode2-4.0.0/rxode2/build/test.R |only rxode2-4.0.0/rxode2/build/vignette.rds |binary rxode2-4.0.0/rxode2/data/rxReservedKeywords.rda |binary rxode2-4.0.0/rxode2/data/rxResidualError.rda |binary rxode2-4.0.0/rxode2/data/rxSyntaxFunctions.rda |binary rxode2-4.0.0/rxode2/inst/doc/rxode2-syntax.html | 712 +-- rxode2-4.0.0/rxode2/inst/include/needSortDefines.h |only rxode2-4.0.0/rxode2/inst/include/rxode2.h | 5 rxode2-4.0.0/rxode2/inst/include/rxode2_as.h | 26 rxode2-4.0.0/rxode2/inst/include/rxode2_control.h | 60 rxode2-4.0.0/rxode2/inst/include/rxode2_model_shared.c | 3 rxode2-4.0.0/rxode2/inst/include/rxode2_model_shared.h | 159 rxode2-4.0.0/rxode2/inst/include/rxode2dataErr.h |only rxode2-4.0.0/rxode2/inst/include/rxode2parse.h | 2 rxode2-4.0.0/rxode2/inst/include/rxode2parseGetTime.h | 113 rxode2-4.0.0/rxode2/inst/include/rxode2parseHandleEvid.h | 309 - rxode2-4.0.0/rxode2/inst/include/rxode2parseSbuf.h | 6 rxode2-4.0.0/rxode2/inst/include/rxode2parseStruct.h | 102 rxode2-4.0.0/rxode2/inst/include/rxode2parseVer.h | 4 rxode2-4.0.0/rxode2/inst/include/rxode2parse_control.h | 66 rxode2-4.0.0/rxode2/inst/include/sbuf.c | 8 rxode2-4.0.0/rxode2/man/dot-rxLinCmt.Rd |only rxode2-4.0.0/rxode2/man/dot-rxLinNcmt.Rd |only rxode2-4.0.0/rxode2/man/dot-solComp2.Rd |only rxode2-4.0.0/rxode2/man/dot-solComp3.Rd |only rxode2-4.0.0/rxode2/man/figures/README-intro-central-1.png |binary rxode2-4.0.0/rxode2/man/figures/README-intro-effect-1.png |binary rxode2-4.0.0/rxode2/man/print.rxModelVars.Rd | 2 rxode2-4.0.0/rxode2/man/rxFixRes.Rd |only rxode2-4.0.0/rxode2/man/rxFun.Rd | 2 rxode2-4.0.0/rxode2/man/rxGetLin.Rd | 6 rxode2-4.0.0/rxode2/man/rxSolve.Rd | 158 rxode2-4.0.0/rxode2/man/rxStateOde.Rd |only rxode2-4.0.0/rxode2/man/rxUiDeparse.Rd | 4 rxode2-4.0.0/rxode2/man/rxode2.Rd | 83 rxode2-4.0.0/rxode2/man/rxode2parse.Rd | 2 rxode2-4.0.0/rxode2/src/RcppExports.cpp | 80 rxode2-4.0.0/rxode2/src/approx.cpp |only rxode2-4.0.0/rxode2/src/boost.cpp | 6 rxode2-4.0.0/rxode2/src/cbindThetaOmega.cpp | 6 rxode2-4.0.0/rxode2/src/checkmate_stub.c | 12 rxode2-4.0.0/rxode2/src/codegen.c | 171 rxode2-4.0.0/rxode2/src/codegen.h | 41 rxode2-4.0.0/rxode2/src/codegen2.h | 1 rxode2-4.0.0/rxode2/src/cvPost.cpp | 2 rxode2-4.0.0/rxode2/src/dop853.c | 6 rxode2-4.0.0/rxode2/src/et.cpp | 287 + rxode2-4.0.0/rxode2/src/etTran.cpp | 499 ++ rxode2-4.0.0/rxode2/src/expandGrid.cpp | 6 rxode2-4.0.0/rxode2/src/expm.cpp | 6 rxode2-4.0.0/rxode2/src/extraDosing.h |only rxode2-4.0.0/rxode2/src/forder.cpp | 6 rxode2-4.0.0/rxode2/src/genModelVars.c | 221 - rxode2-4.0.0/rxode2/src/genModelVars.h | 160 rxode2-4.0.0/rxode2/src/getOption.c | 8 rxode2-4.0.0/rxode2/src/handle_evid.cpp |only rxode2-4.0.0/rxode2/src/init.c | 82 rxode2-4.0.0/rxode2/src/intdy.c | 6 rxode2-4.0.0/rxode2/src/itostr.c | 12 rxode2-4.0.0/rxode2/src/linCmt.cpp |only rxode2-4.0.0/rxode2/src/linCmt.h |only rxode2-4.0.0/rxode2/src/linCmtDiffConstant.h |only rxode2-4.0.0/rxode2/src/lsoda.c | 6 rxode2-4.0.0/rxode2/src/macros2micros.cpp |only rxode2-4.0.0/rxode2/src/macros2micros.h |only rxode2-4.0.0/rxode2/src/par_solve.cpp | 1867 ++++++++-- rxode2-4.0.0/rxode2/src/par_solve.h | 148 rxode2-4.0.0/rxode2/src/parseAssignStr.h | 6 rxode2-4.0.0/rxode2/src/parseCmtProperties.h | 16 rxode2-4.0.0/rxode2/src/parseFuns.h | 5 rxode2-4.0.0/rxode2/src/parseFunsLinCmt.h | 444 -- rxode2-4.0.0/rxode2/src/parseIdentifier.h | 7 rxode2-4.0.0/rxode2/src/parseLevels.h | 6 rxode2-4.0.0/rxode2/src/parseLinCmt.c | 184 rxode2-4.0.0/rxode2/src/parseLinCmt.h | 49 rxode2-4.0.0/rxode2/src/parseLinCmtApplyCmts.h |only rxode2-4.0.0/rxode2/src/parseStatements.h | 3 rxode2-4.0.0/rxode2/src/parseVars.h | 1 rxode2-4.0.0/rxode2/src/print_node.c | 3 rxode2-4.0.0/rxode2/src/print_node.h | 24 rxode2-4.0.0/rxode2/src/prja.c | 6 rxode2-4.0.0/rxode2/src/rx2api.c | 7 rxode2-4.0.0/rxode2/src/rxData.cpp | 727 --- rxode2-4.0.0/rxode2/src/rxData.h | 1 rxode2-4.0.0/rxode2/src/rxDerived.cpp |only rxode2-4.0.0/rxode2/src/rxInv.cpp | 6 rxode2-4.0.0/rxode2/src/rxThreadData.h | 1 rxode2-4.0.0/rxode2/src/rxode2_df.cpp | 53 rxode2-4.0.0/rxode2/src/rxthreefry.cpp | 5 rxode2-4.0.0/rxode2/src/sbuf.c | 8 rxode2-4.0.0/rxode2/src/seed.cpp | 6 rxode2-4.0.0/rxode2/src/solComp.cpp |only rxode2-4.0.0/rxode2/src/solComp.h |only rxode2-4.0.0/rxode2/src/threadSafeConstants.h |only rxode2-4.0.0/rxode2/src/tran.c | 29 rxode2-4.0.0/rxode2/src/tran.h | 7 rxode2-4.0.0/rxode2/src/utilc.cpp |only rxode2-4.0.0/rxode2/src/utilcpp.cpp | 6 rxode2-4.0.0/rxode2/tests/testthat.R | 2 rxode2-4.0.0/rxode2/tests/testthat/lincmt-solve-focei-sol.qs |only rxode2-4.0.0/rxode2/tests/testthat/test-activation.R | 2 rxode2-4.0.0/rxode2/tests/testthat/test-alag.R | 6 rxode2-4.0.0/rxode2/tests/testthat/test-as-ini.R | 27 rxode2-4.0.0/rxode2/tests/testthat/test-assert.R | 434 +- rxode2-4.0.0/rxode2/tests/testthat/test-bioavailibility.R | 16 rxode2-4.0.0/rxode2/tests/testthat/test-cmt-order.R | 39 rxode2-4.0.0/rxode2/tests/testthat/test-convertId.R | 4 rxode2-4.0.0/rxode2/tests/testthat/test-cov.R | 4 rxode2-4.0.0/rxode2/tests/testthat/test-derived.R | 4 rxode2-4.0.0/rxode2/tests/testthat/test-dollar-names.R | 73 rxode2-4.0.0/rxode2/tests/testthat/test-dsl.R | 792 ++++ rxode2-4.0.0/rxode2/tests/testthat/test-dur-0.R |only rxode2-4.0.0/rxode2/tests/testthat/test-et.R | 96 rxode2-4.0.0/rxode2/tests/testthat/test-etTrans.R | 16 rxode2-4.0.0/rxode2/tests/testthat/test-hmax.R | 14 rxode2-4.0.0/rxode2/tests/testthat/test-ignore-state.R | 56 rxode2-4.0.0/rxode2/tests/testthat/test-lhs-param.R | 43 rxode2-4.0.0/rxode2/tests/testthat/test-lincmt-solve.R | 726 ++- rxode2-4.0.0/rxode2/tests/testthat/test-missing-evid.R | 2 rxode2-4.0.0/rxode2/tests/testthat/test-model-rate.R | 6 rxode2-4.0.0/rxode2/tests/testthat/test-nmtest.R | 562 ++- rxode2-4.0.0/rxode2/tests/testthat/test-parsing.R | 21 rxode2-4.0.0/rxode2/tests/testthat/test-resample.R | 1 rxode2-4.0.0/rxode2/tests/testthat/test-rxFix.R | 34 rxode2-4.0.0/rxode2/tests/testthat/test-rxUiDeparse.R | 5 rxode2-4.0.0/rxode2/tests/testthat/test-solComp.R |only rxode2-4.0.0/rxode2/tests/testthat/test-steady-state.R | 10 rxode2-4.0.0/rxode2/tests/testthat/test-ui-assign-model-parts.R | 584 +-- rxode2-4.0.0/rxode2/tests/testthat/test-ui-bad.R | 25 rxode2-4.0.0/rxode2/tests/testthat/test-ui-dv.R |only rxode2-4.0.0/rxode2/tests/testthat/test-ui-err-bad-linCmt.R | 48 rxode2-4.0.0/rxode2/tests/testthat/test-ui-err.R | 65 rxode2-4.0.0/rxode2/tests/testthat/test-ui-expit.R | 56 rxode2-4.0.0/rxode2/tests/testthat/test-ui-ini-str.R | 90 rxode2-4.0.0/rxode2/tests/testthat/test-ui-lhs.R | 100 rxode2-4.0.0/rxode2/tests/testthat/test-ui-log-vs-backtransformed.R | 70 rxode2-4.0.0/rxode2/tests/testthat/test-ui-modelExtract.R | 278 - rxode2-4.0.0/rxode2/tests/testthat/test-ui-modelName.R | 54 rxode2-4.0.0/rxode2/tests/testthat/test-ui-mv.R | 5 rxode2-4.0.0/rxode2/tests/testthat/test-ui-piping.R | 106 rxode2-4.0.0/rxode2/tests/testthat/test-ui-props.R | 522 +- rxode2-4.0.0/rxode2/tests/testthat/test-ui-single-theta.R | 122 188 files changed, 9412 insertions(+), 5331 deletions(-)
Title: Methods in Structural Reliability
Description: Various reliability analysis methods for rare event inference (computing failure probability and quantile from model/function outputs).
Author: Bertrand Iooss [aut, cre],
Clement Walter [aut],
Gilles defaux [aut],
Vincent Moutoussamy [aut]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between mistral versions 2.2.2 dated 2024-01-17 and 2.2.3 dated 2025-07-16
DESCRIPTION | 15 MD5 | 16 NAMESPACE | 5 NEWS | 4 build/vignette.rds |binary inst/doc/mistral-vignette.R | 2 inst/doc/mistral-vignette.html | 7759 ----------------------------------------- man/MonteCarlo.Rd | 281 - man/mistral-package.Rd | 4 9 files changed, 335 insertions(+), 7751 deletions(-)
Title: Enable the Use of 'metacore' to Help Create and Check Dataset
Description: Uses the metadata information stored in 'metacore' objects to
check and build metadata associated columns.
Author: Liam Hobby [aut, cre],
Christina Fillmore [aut] ,
Bill Denney [aut],
Mike Stackhouse [aut] ,
Jana Stoilova [aut],
Tamara Senior [aut],
GlaxoSmithKline LLC [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
Atorus Research LLC [cph, fnd]
Maintainer: Liam Hobby <liam.f.hobby@gsk.com>
Diff between metatools versions 0.1.6 dated 2024-07-23 and 0.2.0 dated 2025-07-16
DESCRIPTION | 67 +- LICENSE | 4 MD5 | 100 ++-- NAMESPACE | 185 ++++---- NEWS.md | 65 +- R/build.R | 674 +++++++++++++++++------------ R/checks.R | 756 +++++++++++++++++---------------- R/codelists.R | 575 ++++++++++++++----------- R/labels.R | 268 ++++++----- R/metatools-package.R |only R/sort.R | 167 ++++--- R/supp.R | 653 ++++++++++++++-------------- R/utils.R | 83 ++- R/zzz.R | 93 ++-- README.md | 296 ++++++------ inst/WORDLIST | 52 +- inst/extdata/adsl.xpt |binary inst/extdata/dm.xpt |binary man/add_labels.Rd | 54 +- man/add_variables.Rd | 77 +-- man/build_from_derived.Rd | 132 +++-- man/build_qnam.Rd | 54 +- man/check_ct_col.Rd | 82 +-- man/check_ct_data.Rd | 100 ++-- man/check_unique_keys.Rd | 74 +-- man/check_variables.Rd | 81 ++- man/combine_supp.Rd | 48 +- man/convert_var_to_fct.Rd | 80 +-- man/create_cat_var.Rd | 105 ++-- man/create_subgrps.Rd | 55 +- man/create_var_from_codelist.Rd | 150 ++++-- man/drop_unspec_vars.Rd | 74 +-- man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/get_bad_ct.Rd | 84 +-- man/make_supp_qual.Rd | 69 +-- man/metatools-package.Rd |only man/metatools_example.Rd | 38 - man/order_cols.Rd | 70 +-- man/pipe.Rd | 40 - man/remove_labels.Rd | 46 +- man/set_variable_labels.Rd | 70 +-- man/sort_by_key.Rd | 70 +-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-build.R | 321 ++++++++------ tests/testthat/test-checks.R | 252 +++++------ tests/testthat/test-codelist.R | 361 +++++++++++---- tests/testthat/test-labels.R | 263 +++++------ tests/testthat/test-sort.R | 62 +- tests/testthat/test-supp.R | 522 +++++++++++----------- tests/testthat/test-utils.R | 41 - 54 files changed, 4131 insertions(+), 3396 deletions(-)