Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 14. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood estimation" , Hammond (2021, <doi:10.2166/nh.2021.059>). "The FEH 2025 statistical method update", UK Centre for Ecology and Hydrology (2025). "Low flow es [...truncated...]
Author: Anthony Hammond [aut, cre]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 1.0.2 dated 2025-10-10 and 2.0.0 dated 2025-10-28
UKFE-1.0.2/UKFE/NEWS.md |only UKFE-1.0.2/UKFE/R/AMSP.R |only UKFE-1.0.2/UKFE/R/NRFAData.R |only UKFE-1.0.2/UKFE/R/QMEDData.R |only UKFE-1.0.2/UKFE/README.md |only UKFE-1.0.2/UKFE/build |only UKFE-1.0.2/UKFE/data/AMSP.rda |only UKFE-1.0.2/UKFE/data/NRFAData.rda |only UKFE-1.0.2/UKFE/data/QMEDData.rda |only UKFE-1.0.2/UKFE/inst |only UKFE-1.0.2/UKFE/man/AMSP.Rd |only UKFE-1.0.2/UKFE/man/GetDataSEPA_QH.Rd |only UKFE-1.0.2/UKFE/man/GetDataSEPA_Rain.Rd |only UKFE-1.0.2/UKFE/man/LSkewUrb.Rd |only UKFE-1.0.2/UKFE/man/NRFAData.Rd |only UKFE-1.0.2/UKFE/man/PoolSmall.Rd |only UKFE-1.0.2/UKFE/man/QMEDData.Rd |only UKFE-1.0.2/UKFE/man/WGaugLSkew.Rd |only UKFE-1.0.2/UKFE/man/WGaugLcv.Rd |only UKFE-1.0.2/UKFE/man/WeightsGLSkew.Rd |only UKFE-1.0.2/UKFE/man/WeightsGLcv.Rd |only UKFE-1.0.2/UKFE/man/WeightsUnLSkew.Rd |only UKFE-1.0.2/UKFE/man/WeightsUnLcv.Rd |only UKFE-1.0.2/UKFE/man/WungLSkew.Rd |only UKFE-1.0.2/UKFE/man/WungLcv.Rd |only UKFE-1.0.2/UKFE/tests |only UKFE-1.0.2/UKFE/vignettes |only UKFE-2.0.0/UKFE/DESCRIPTION | 25 UKFE-2.0.0/UKFE/MD5 | 168 UKFE-2.0.0/UKFE/NAMESPACE | 16 UKFE-2.0.0/UKFE/R/AMPF.R |only UKFE-2.0.0/UKFE/R/All.R |13735 ++++++++++++++------------------ UKFE-2.0.0/UKFE/R/FlowAnalysis.R | 621 - UKFE-2.0.0/UKFE/R/GISfuncs.R | 220 UKFE-2.0.0/UKFE/R/GetData.R | 1666 +-- UKFE-2.0.0/UKFE/R/PeakFlowData.R |only UKFE-2.0.0/UKFE/R/RainfallAnalysis.R | 256 UKFE-2.0.0/UKFE/R/ReFH.R |only UKFE-2.0.0/UKFE/R/ThamesPQ.R | 28 UKFE-2.0.0/UKFE/R/UKOutline.R | 22 UKFE-2.0.0/UKFE/data/AMPF.rda |only UKFE-2.0.0/UKFE/data/PeakFlowData.rda |only UKFE-2.0.0/UKFE/data/ThamesPQ.rda |binary UKFE-2.0.0/UKFE/data/UKOutline.rda |binary UKFE-2.0.0/UKFE/man/AMImport.Rd | 9 UKFE-2.0.0/UKFE/man/AMPF.Rd |only UKFE-2.0.0/UKFE/man/AddGauge.Rd | 14 UKFE-2.0.0/UKFE/man/BFI.Rd | 10 UKFE-2.0.0/UKFE/man/CDsXML.Rd | 10 UKFE-2.0.0/UKFE/man/CDsXML_Legacy.Rd |only UKFE-2.0.0/UKFE/man/DDF.Rd | 6 UKFE-2.0.0/UKFE/man/DDFImport.Rd | 4 UKFE-2.0.0/UKFE/man/DiagPlots.Rd | 8 UKFE-2.0.0/UKFE/man/DonAdj.Rd | 26 UKFE-2.0.0/UKFE/man/ERPlot.Rd | 8 UKFE-2.0.0/UKFE/man/EVPool.Rd | 13 UKFE-2.0.0/UKFE/man/FlowSplit.Rd | 6 UKFE-2.0.0/UKFE/man/GetCDs.Rd | 5 UKFE-2.0.0/UKFE/man/GetDataEA_QH.Rd | 2 UKFE-2.0.0/UKFE/man/GetDataNRFA.Rd | 8 UKFE-2.0.0/UKFE/man/GetDataSEPA.Rd |only UKFE-2.0.0/UKFE/man/HistoricMLE.Rd |only UKFE-2.0.0/UKFE/man/HydroPlot.Rd | 3 UKFE-2.0.0/UKFE/man/Kappa3GF.Rd | 6 UKFE-2.0.0/UKFE/man/LRatioChange.Rd | 4 UKFE-2.0.0/UKFE/man/LcvUrb.Rd | 20 UKFE-2.0.0/UKFE/man/LowFlows.Rd |only UKFE-2.0.0/UKFE/man/NonFloodAdjPool.Rd | 2 UKFE-2.0.0/UKFE/man/OptimPars.Rd | 2 UKFE-2.0.0/UKFE/man/POTextract.Rd | 2 UKFE-2.0.0/UKFE/man/PeakFlowData.Rd |only UKFE-2.0.0/UKFE/man/Pool.Rd | 48 UKFE-2.0.0/UKFE/man/PoolEst.Rd | 48 UKFE-2.0.0/UKFE/man/QMED.Rd | 52 UKFE-2.0.0/UKFE/man/QMEDDonEq.Rd | 40 UKFE-2.0.0/UKFE/man/QuickResults.Rd | 35 UKFE-2.0.0/UKFE/man/ReFH.Rd | 50 UKFE-2.0.0/UKFE/man/Seasonality.Rd |only UKFE-2.0.0/UKFE/man/TrendTest.Rd | 4 UKFE-2.0.0/UKFE/man/UAF.Rd | 24 UKFE-2.0.0/UKFE/man/UEF.Rd | 8 UKFE-2.0.0/UKFE/man/Uncertainty.Rd | 58 UKFE-2.0.0/UKFE/man/WeightedMoments.Rd |only UKFE-2.0.0/UKFE/man/WeightsLCV.Rd |only UKFE-2.0.0/UKFE/man/WeightsLSKEW.Rd |only UKFE-2.0.0/UKFE/man/Zdists.Rd | 6 86 files changed, 7935 insertions(+), 9363 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Craig Gower-Page [aut, cre],
Isaac Gravestock [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@novartis.com>
Diff between rbmi versions 1.5.1 dated 2025-10-14 and 1.5.2 dated 2025-10-28
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++++------- NEWS.md | 7 +++++ inst/doc/advanced.html | 2 - inst/doc/quickstart.html | 42 +++++++++++++++++----------------- tests/scripts |only tests/testthat/helper-misc.R | 17 ++++++++----- tests/testthat/setup.R | 35 ++++++++++++++++++---------- tests/testthat/test-mcmc.R | 1 tests/testthat/test-print.R | 1 tests/testthat/test-reproducibility.R | 1 11 files changed, 82 insertions(+), 52 deletions(-)
Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to
version, share, deploy, and monitor a trained model. Functions handle
both recording and checking the model's input data prototype, and
predicting from a remote API endpoint. The 'vetiver' package is
extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between vetiver versions 0.2.5 dated 2023-11-16 and 0.2.6 dated 2025-10-28
DESCRIPTION | 33 ++--- MD5 | 99 ++++++++--------- NAMESPACE | 24 ++++ NEWS.md | 8 + R/endpoint.R | 2 R/mlr3.R | 2 R/probably.R |only R/prototype.R | 2 R/recipe.R | 6 - R/rsconnect.R | 23 ++- R/sagemaker.R | 9 - R/vetiver-model.R | 6 - R/write-docker.R | 5 R/write-plumber.R | 6 - README.md | 12 +- build/vignette.rds |binary inst/doc/vetiver.R | 2 inst/doc/vetiver.Rmd | 2 inst/doc/vetiver.html | 24 ++-- man/api_spec.Rd | 2 man/handler_startup.Rd | 28 ++++ man/vetiver-package.Rd | 2 man/vetiver_api.Rd | 2 man/vetiver_compute_metrics.Rd | 2 man/vetiver_create_description.Rd | 28 ++++ man/vetiver_create_meta.Rd | 16 ++ man/vetiver_create_ptype.Rd | 18 ++- man/vetiver_create_rsconnect_bundle.Rd | 13 +- man/vetiver_deploy_rsconnect.Rd | 11 + man/vetiver_deploy_sagemaker.Rd | 2 man/vetiver_endpoint_sagemaker.Rd | 2 man/vetiver_pin_metrics.Rd | 2 man/vetiver_pin_write.Rd | 2 man/vetiver_plot_metrics.Rd | 2 man/vetiver_prepare_docker.Rd | 2 man/vetiver_sm_build.Rd | 3 man/vetiver_write_docker.Rd | 2 man/vetiver_write_plumber.Rd | 8 + tests/testthat/_snaps/monitor/default-metrics-plot.svg | 28 ++-- tests/testthat/_snaps/predict.md | 2 tests/testthat/_snaps/probably.md |only tests/testthat/_snaps/sagemaker.md | 1 tests/testthat/_snaps/type-convert.md | 2 tests/testthat/_snaps/write-docker.md | 6 + tests/testthat/_snaps/write-plumber.md | 21 +++ tests/testthat/test-keras.R | 46 +++++-- tests/testthat/test-luz.R | 12 +- tests/testthat/test-mlr3.R | 1 tests/testthat/test-probably.R |only tests/testthat/test-recipe.R | 2 tests/testthat/test-write-plumber.R | 13 ++ vignettes/vetiver.Rmd | 2 52 files changed, 374 insertions(+), 174 deletions(-)
Title: Standardization-Based Effect Estimation with Optional Prior
Covariance Adjustment
Description: The Prognostic Regression Offsets with Propagation of
ERrors (for Treatment Effect Estimation) package facilitates
direct adjustment for experiments and observational studies that
is compatible with a range of study designs and covariance
adjustment strategies. It uses explicit specification of clusters,
blocks and treatment allocations to furnish probability of
assignment-based weights targeting any of several average
treatment effect parameters, and for standard error calculations
reflecting these design parameters. For covariance adjustment of
its Hajek and (one-way) fixed effects estimates, it enables
offsetting the outcome against predictions from a dedicated
covariance model, with standard error calculations propagating
error as appropriate from the covariance model.
Author: Josh Errickson [cre, aut],
Josh Wasserman [aut],
Mark Fredrickson [ctb],
Adam Sales [ctb],
Xinhe Wang [ctb],
Ben Hansen [aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between propertee versions 1.0.1 dated 2025-08-26 and 1.0.3 dated 2025-10-28
DESCRIPTION | 6 +-- MD5 | 32 ++++++++-------- NEWS.md | 6 +++ R/SandwichLayer.R | 54 +++++++++++++++++----------- R/SandwichLayerVariance.R | 35 +++++++++++------- R/bread.R | 6 ++- R/lmitt.R | 14 +++++-- inst/doc/RDD.html | 9 ++-- inst/doc/intro-to-propertee.R | 4 +- inst/doc/intro-to-propertee.Rmd | 5 +- inst/doc/intro-to-propertee.html | 16 ++++---- inst/doc/non-binary-treatment.html | 9 ++-- man/lmitt.Rd | 14 +++++-- man/var_estimators.Rd | 5 +- tests/testthat/test.SandwichLayer.R | 39 ++++++++++++++++++++ tests/testthat/test.SandwichLayerVariance.R | 38 +++++++++++++++++++ vignettes/intro-to-propertee.Rmd | 5 +- 17 files changed, 205 insertions(+), 92 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>)
with or without multilevel or additive terms (Catalina, Bürkner, and
Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for
some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2025,
<doi:10.1007/s00180-024-01506-0>), and for many other regression models
(using the latent projection by Catalina, Bürkner, and Vehtari, 2021,
<doi:10.48550/arXiv.2109.04702>, which can also be applied to most of the
former models). The package is compatible with the 'rstanarm' and 'brms'
packages, but other reference models can also be used. See the vignettes and
the documentation for more information and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [aut],
Osvaldo Martin [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb],
Brian Sullivan [ctb], [...truncated...]
Maintainer: Osvaldo Martin <aloctavodia@gmail.com>
Diff between projpred versions 2.9.0 dated 2025-07-08 and 2.9.1 dated 2025-10-28
DESCRIPTION | 8 MD5 | 28 +- NEWS.md | 12 R/extend_family.R | 6 R/formula.R | 158 ++++++------ R/project.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/latent.R | 394 +++++++++++++++--------------- inst/doc/latent.html | 346 ++++++++++++--------------- inst/doc/projpred.R | 282 +++++++++++----------- inst/doc/projpred.html | 472 +++++++++++++++---------------------- man/extend_family.Rd | 6 tests/testthat/test_formula.R | 26 ++ tests/testthat/test_proj_predfun.R | 13 - 15 files changed, 848 insertions(+), 905 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for mo [...truncated...]
Author: Alireza Khodadadi-Jamayran [aut, cre] ,
Joseph Pucella [aut, ctb] ,
Hua Zhou [aut, ctb] ,
Nicole Doudican [aut, ctb] ,
John Carucci [aut, ctb] ,
Adriana Heguy [aut, ctb],
Boris Reizis [aut, ctb] ,
Aristotelis Tsirigos [aut, ctb]
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.6.7 dated 2024-01-29 and 1.7.0 dated 2025-10-28
DESCRIPTION | 32 ++-- MD5 | 22 +- R/F0018.R | 316 ++++------------------------------------- R/F0051.R | 2 R/F0053.R | 2 R/F0064.R | 8 + R/F0072.R | 13 + R/F0100.R | 3 man/bubble.gg.plot.Rd | 3 man/g2m.phase.Rd | 2 man/run.umap.Rd | 380 ++++++++------------------------------------------ man/s.phase.Rd | 2 12 files changed, 161 insertions(+), 624 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Description: Various utilities for the complex multivariate Gaussian distribution and complex Gaussian processes.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between cmvnorm versions 1.0-7 dated 2022-01-30 and 1.1-1 dated 2025-10-28
DESCRIPTION | 17 ++-- MD5 | 41 +++++----- NAMESPACE | 44 +++++++---- NEWS.md | 5 + R/cmvnorm.R | 40 ++++++++++ README.md | 156 ++++++++++++++++++----------------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/cmvnorm.R | 1 inst/doc/cmvnorm.Rnw | 85 ++++++++++------------ inst/doc/cmvnorm.pdf |binary man/Mvcnorm.Rd | 17 +--- man/cmvnorm-package.Rd | 9 +- man/corr_complex.Rd | 18 ++-- man/isHermitian.Rd | 14 +-- man/setreal.Rd | 1 man/var.Rd | 4 - man/wishart.Rd | 11 +- tests |only vignettes/cmvnorm.Rnw | 85 ++++++++++------------ vignettes/complex_gaussian.bib | 2 22 files changed, 287 insertions(+), 263 deletions(-)
Title: Download Data from the Reserve Bank of New Zealand Website
Description: Provides a convenient way of accessing data published by the Reserve Bank of New Zealand (RBNZ) on their website, <https://www.rbnz.govt.nz/statistics>. A range of financial and economic data is provided in spreadsheet format including exchange and interest rates, commercial lending statistics, Reserve Bank market operations, financial institution statistics, household financial data, New Zealand debt security information, and economic indicators. This package provides a method to download those spreadsheets and read them directly into R.
Author: Jasper Watson [aut, cre]
Maintainer: Jasper Watson <jasper.g.watson@gmail.com>
Diff between RBNZ versions 1.1.0 dated 2020-07-27 and 3.0.0 dated 2025-10-28
RBNZ-1.1.0/RBNZ/R/getSDDS.R |only RBNZ-1.1.0/RBNZ/man/M13.Rd |only RBNZ-3.0.0/RBNZ/DESCRIPTION | 14 RBNZ-3.0.0/RBNZ/MD5 | 237 +++--- RBNZ-3.0.0/RBNZ/NEWS.md | 39 - RBNZ-3.0.0/RBNZ/R/RBNZ.R | 18 RBNZ-3.0.0/RBNZ/R/Utils.R | 137 ++- RBNZ-3.0.0/RBNZ/R/availableData.R | 209 +++-- RBNZ-3.0.0/RBNZ/R/getDownloadLink.R | 76 +- RBNZ-3.0.0/RBNZ/R/getSeries.R | 264 ++++--- RBNZ-3.0.0/RBNZ/R/readSeriesPage.R | 136 +-- RBNZ-3.0.0/RBNZ/R/readSpreadsheet.R | 233 ++---- RBNZ-3.0.0/RBNZ/R/seriesDescriptions.R | 1205 +++++++++++++++++--------------- RBNZ-3.0.0/RBNZ/R/seriesOptions.R | 248 +++--- RBNZ-3.0.0/RBNZ/R/specialParsing.R |only RBNZ-3.0.0/RBNZ/README.md | 50 + RBNZ-3.0.0/RBNZ/build/vignette.rds |binary RBNZ-3.0.0/RBNZ/inst/WORDLIST |only RBNZ-3.0.0/RBNZ/inst/doc/Overview.R | 21 RBNZ-3.0.0/RBNZ/inst/doc/Overview.Rmd | 52 + RBNZ-3.0.0/RBNZ/inst/doc/Overview.html | 342 ++++++--- RBNZ-3.0.0/RBNZ/man/B1.Rd | 4 RBNZ-3.0.0/RBNZ/man/B10.Rd | 2 RBNZ-3.0.0/RBNZ/man/B13.Rd | 16 RBNZ-3.0.0/RBNZ/man/B2.Rd | 4 RBNZ-3.0.0/RBNZ/man/B20.Rd | 2 RBNZ-3.0.0/RBNZ/man/B21.Rd | 2 RBNZ-3.0.0/RBNZ/man/B25.Rd | 2 RBNZ-3.0.0/RBNZ/man/B26.Rd | 2 RBNZ-3.0.0/RBNZ/man/B27.Rd | 2 RBNZ-3.0.0/RBNZ/man/B3.Rd | 2 RBNZ-3.0.0/RBNZ/man/B30.Rd |only RBNZ-3.0.0/RBNZ/man/B4.Rd | 2 RBNZ-3.0.0/RBNZ/man/B6.Rd | 2 RBNZ-3.0.0/RBNZ/man/B7.Rd |only RBNZ-3.0.0/RBNZ/man/C12.Rd | 2 RBNZ-3.0.0/RBNZ/man/C13.Rd | 2 RBNZ-3.0.0/RBNZ/man/C21.Rd | 2 RBNZ-3.0.0/RBNZ/man/C22.Rd | 2 RBNZ-3.0.0/RBNZ/man/C30.Rd | 10 RBNZ-3.0.0/RBNZ/man/C31.Rd | 2 RBNZ-3.0.0/RBNZ/man/C32.Rd | 2 RBNZ-3.0.0/RBNZ/man/C33.Rd |only RBNZ-3.0.0/RBNZ/man/C35.Rd | 2 RBNZ-3.0.0/RBNZ/man/C40.Rd | 2 RBNZ-3.0.0/RBNZ/man/C41.Rd | 2 RBNZ-3.0.0/RBNZ/man/C5.Rd | 2 RBNZ-3.0.0/RBNZ/man/C50.Rd | 2 RBNZ-3.0.0/RBNZ/man/C51.Rd | 2 RBNZ-3.0.0/RBNZ/man/C52.Rd | 2 RBNZ-3.0.0/RBNZ/man/C55.Rd | 2 RBNZ-3.0.0/RBNZ/man/C60.Rd | 4 RBNZ-3.0.0/RBNZ/man/C65.Rd | 2 RBNZ-3.0.0/RBNZ/man/C66.Rd | 2 RBNZ-3.0.0/RBNZ/man/C70.Rd |only RBNZ-3.0.0/RBNZ/man/C71.Rd |only RBNZ-3.0.0/RBNZ/man/D10.Rd | 6 RBNZ-3.0.0/RBNZ/man/D12.Rd | 2 RBNZ-3.0.0/RBNZ/man/D3.Rd | 2 RBNZ-3.0.0/RBNZ/man/D30.Rd | 2 RBNZ-3.0.0/RBNZ/man/D31.Rd | 2 RBNZ-3.0.0/RBNZ/man/D35.Rd | 2 RBNZ-3.0.0/RBNZ/man/D9.Rd | 5 RBNZ-3.0.0/RBNZ/man/E1.Rd | 2 RBNZ-3.0.0/RBNZ/man/E2.Rd | 2 RBNZ-3.0.0/RBNZ/man/F3.Rd | 2 RBNZ-3.0.0/RBNZ/man/F4.Rd | 2 RBNZ-3.0.0/RBNZ/man/F5.Rd | 2 RBNZ-3.0.0/RBNZ/man/H1.Rd |only RBNZ-3.0.0/RBNZ/man/H2.Rd |only RBNZ-3.0.0/RBNZ/man/H3.Rd |only RBNZ-3.0.0/RBNZ/man/J10.Rd | 2 RBNZ-3.0.0/RBNZ/man/J20.Rd | 2 RBNZ-3.0.0/RBNZ/man/L1.Rd | 2 RBNZ-3.0.0/RBNZ/man/L2.Rd | 2 RBNZ-3.0.0/RBNZ/man/L3.Rd | 2 RBNZ-3.0.0/RBNZ/man/M1.Rd | 2 RBNZ-3.0.0/RBNZ/man/M10.Rd | 2 RBNZ-3.0.0/RBNZ/man/M12.Rd | 2 RBNZ-3.0.0/RBNZ/man/M14.Rd | 2 RBNZ-3.0.0/RBNZ/man/M15.Rd |only RBNZ-3.0.0/RBNZ/man/M2.Rd | 2 RBNZ-3.0.0/RBNZ/man/M3.Rd | 2 RBNZ-3.0.0/RBNZ/man/M4.Rd | 2 RBNZ-3.0.0/RBNZ/man/M5.Rd | 2 RBNZ-3.0.0/RBNZ/man/M6.Rd | 2 RBNZ-3.0.0/RBNZ/man/M7.Rd | 2 RBNZ-3.0.0/RBNZ/man/M8.Rd | 2 RBNZ-3.0.0/RBNZ/man/M9.Rd | 2 RBNZ-3.0.0/RBNZ/man/R1.Rd | 2 RBNZ-3.0.0/RBNZ/man/R2.Rd | 2 RBNZ-3.0.0/RBNZ/man/R3.Rd | 2 RBNZ-3.0.0/RBNZ/man/RBNZ.Rd | 10 RBNZ-3.0.0/RBNZ/man/S10.Rd | 7 RBNZ-3.0.0/RBNZ/man/S20.Rd | 2 RBNZ-3.0.0/RBNZ/man/S21.Rd | 2 RBNZ-3.0.0/RBNZ/man/S30.Rd | 2 RBNZ-3.0.0/RBNZ/man/S31.Rd | 2 RBNZ-3.0.0/RBNZ/man/S32.Rd | 2 RBNZ-3.0.0/RBNZ/man/S33.Rd | 2 RBNZ-3.0.0/RBNZ/man/S34.Rd | 2 RBNZ-3.0.0/RBNZ/man/S35.Rd |only RBNZ-3.0.0/RBNZ/man/S36.Rd |only RBNZ-3.0.0/RBNZ/man/S37.Rd |only RBNZ-3.0.0/RBNZ/man/S40.Rd | 2 RBNZ-3.0.0/RBNZ/man/S41.Rd | 2 RBNZ-3.0.0/RBNZ/man/S50.Rd |only RBNZ-3.0.0/RBNZ/man/SDDS.Rd | 8 RBNZ-3.0.0/RBNZ/man/T1.Rd | 2 RBNZ-3.0.0/RBNZ/man/T11.Rd | 2 RBNZ-3.0.0/RBNZ/man/T21.Rd | 2 RBNZ-3.0.0/RBNZ/man/T31.Rd | 2 RBNZ-3.0.0/RBNZ/man/T4.Rd | 2 RBNZ-3.0.0/RBNZ/man/T40.Rd | 2 RBNZ-3.0.0/RBNZ/man/T41.Rd | 2 RBNZ-3.0.0/RBNZ/man/T42.Rd | 2 RBNZ-3.0.0/RBNZ/man/T43.Rd | 2 RBNZ-3.0.0/RBNZ/man/T44.Rd | 2 RBNZ-3.0.0/RBNZ/man/T45.Rd | 2 RBNZ-3.0.0/RBNZ/man/T46.Rd | 2 RBNZ-3.0.0/RBNZ/man/T47.Rd | 2 RBNZ-3.0.0/RBNZ/man/T48.Rd | 2 RBNZ-3.0.0/RBNZ/man/getDownloadLink.Rd | 2 RBNZ-3.0.0/RBNZ/man/getSeries.Rd | 35 RBNZ-3.0.0/RBNZ/man/getSeriesPageURL.Rd | 2 RBNZ-3.0.0/RBNZ/man/readSeriesPage.Rd | 16 RBNZ-3.0.0/RBNZ/man/readSpreadsheet.Rd | 10 RBNZ-3.0.0/RBNZ/vignettes/Overview.Rmd | 52 + 128 files changed, 2093 insertions(+), 1535 deletions(-)
Title: Prior Diagnostics and Sensitivity Analysis
Description: Provides functions for prior and likelihood sensitivity analysis in Bayesian models. Currently it implements methods to determine the sensitivity of the posterior to power-scaling perturbations of the prior and likelihood.
Author: Noa Kallioinen [aut, cre, cph],
Topi Paananen [aut],
Paul-Christian Buerkner [aut],
Aki Vehtari [aut],
Frank Weber [ctb]
Maintainer: Noa Kallioinen <noa.kallioinen@aalto.fi>
Diff between priorsense versions 1.1.1 dated 2025-08-22 and 1.2.0 dated 2025-10-28
priorsense-1.1.1/priorsense/R/cumulative_plot.R |only priorsense-1.2.0/priorsense/DESCRIPTION | 14 +- priorsense-1.2.0/priorsense/MD5 | 31 ++--- priorsense-1.2.0/priorsense/NAMESPACE | 1 priorsense-1.2.0/priorsense/NEWS.md | 6 priorsense-1.2.0/priorsense/R/plots.R | 73 +++++++++--- priorsense-1.2.0/priorsense/R/powerscale.R | 19 ++- priorsense-1.2.0/priorsense/R/powerscale_gradients.R | 6 priorsense-1.2.0/priorsense/R/powerscale_sequence.R | 13 ++ priorsense-1.2.0/priorsense/README.md | 2 priorsense-1.2.0/priorsense/inst/doc/powerscaling.html | 4 priorsense-1.2.0/priorsense/man/powerscale-gradients.Rd | 2 priorsense-1.2.0/priorsense/man/powerscale-overview.Rd | 6 priorsense-1.2.0/priorsense/man/powerscale_plots.Rd | 10 + priorsense-1.2.0/priorsense/tests/testthat/_snaps |only priorsense-1.2.0/priorsense/tests/testthat/test_plots.R | 8 - priorsense-1.2.0/priorsense/tests/testthat/test_variables.R |only 17 files changed, 144 insertions(+), 51 deletions(-)
More information about CspStandSegmentation at CRAN
Permanent link
Title: Detect Clinical Trial Sites Over- or Under-Reporting Clinical
Events
Description: Monitoring reporting rates of subject-level clinical events (e.g.
adverse events, protocol deviations) reported by clinical trial sites is an
important aspect of risk-based quality monitoring strategy. Sites that are
under-reporting or over-reporting events can be detected using bootstrap
simulations during which patients are redistributed between sites. Site-specific
distributions of event reporting rates are generated that are used to assign
probabilities to the observed reporting rates.
(Koneswarakantha 2024 <doi:10.1007/s43441-024-00631-8>).
Author: Bjoern Koneswarakantha [aut, cre, cph] ,
F. Hoffmann-La Roche Ltd [cph]
Maintainer: Bjoern Koneswarakantha <bjoern.koneswarakantha@roche.com>
Diff between simaerep versions 0.7.0 dated 2025-04-09 and 1.0.0 dated 2025-10-28
simaerep-0.7.0/simaerep/man/get_config.Rd |only simaerep-0.7.0/simaerep/man/get_ecd_values.Rd |only simaerep-0.7.0/simaerep/man/get_pat_pool_config.Rd |only simaerep-0.7.0/simaerep/man/get_portf_perf.Rd |only simaerep-0.7.0/simaerep/man/sim_scenario.Rd |only simaerep-0.7.0/simaerep/man/sim_studies.Rd |only simaerep-0.7.0/simaerep/man/sim_ur.Rd |only simaerep-0.7.0/simaerep/man/sim_ur_scenarios.Rd |only simaerep-0.7.0/simaerep/man/simaerep_inframe.Rd |only simaerep-0.7.0/simaerep/tests/testthat/_snaps/eval_sites.md |only simaerep-0.7.0/simaerep/tests/testthat/_snaps/validation/study-025.svg |only simaerep-0.7.0/simaerep/tests/testthat/_snaps/validation/study-050.svg |only simaerep-0.7.0/simaerep/tests/testthat/_snaps/validation/study-075.svg |only simaerep-0.7.0/simaerep/tests/testthat/_snaps/validation/study-100.svg |only simaerep-0.7.0/simaerep/tests/testthat/test_sim_studies.R |only simaerep-1.0.0/simaerep/DESCRIPTION | 28 simaerep-1.0.0/simaerep/MD5 | 153 - simaerep-1.0.0/simaerep/NAMESPACE | 37 simaerep-1.0.0/simaerep/NEWS.md | 17 simaerep-1.0.0/simaerep/R/0_imports.R | 7 simaerep-1.0.0/simaerep/R/S3_orivisit.R | 142 - simaerep-1.0.0/simaerep/R/S3_simaerep.R | 734 ++++-- simaerep-1.0.0/simaerep/R/inframe.R | 81 simaerep-1.0.0/simaerep/R/simaerep.R | 816 +++---- simaerep-1.0.0/simaerep/R/simaerep_plot.R | 403 +-- simaerep-1.0.0/simaerep/R/simulate_test_data.R | 1099 ++-------- simaerep-1.0.0/simaerep/R/zzz_test_helper.R |only simaerep-1.0.0/simaerep/README.md | 162 - simaerep-1.0.0/simaerep/inst/WORDLIST | 35 simaerep-1.0.0/simaerep/man/aggr_duplicated_visits.Rd | 1 simaerep-1.0.0/simaerep/man/check_df_visit.Rd | 19 simaerep-1.0.0/simaerep/man/eval_sites.Rd | 43 simaerep-1.0.0/simaerep/man/exp_implicit_missing_visits.Rd | 1 simaerep-1.0.0/simaerep/man/figures/README-unnamed-chunk-2-1.png |binary simaerep-1.0.0/simaerep/man/figures/README-unnamed-chunk-3-1.png |binary simaerep-1.0.0/simaerep/man/get_cum_mean_event_dev.Rd |only simaerep-1.0.0/simaerep/man/get_df_visit_test.Rd |only simaerep-1.0.0/simaerep/man/get_df_visit_test_mapped.Rd |only simaerep-1.0.0/simaerep/man/get_portf_config.Rd |only simaerep-1.0.0/simaerep/man/get_portf_event_rates.Rd |only simaerep-1.0.0/simaerep/man/get_site_mean_ae_dev.Rd | 3 simaerep-1.0.0/simaerep/man/get_visit_med75.Rd | 3 simaerep-1.0.0/simaerep/man/is_orivisit.Rd | 1 simaerep-1.0.0/simaerep/man/is_simaerep.Rd | 1 simaerep-1.0.0/simaerep/man/max_rank.Rd | 5 simaerep-1.0.0/simaerep/man/orivisit.Rd | 33 simaerep-1.0.0/simaerep/man/p_adjust_bh_inframe.Rd | 2 simaerep-1.0.0/simaerep/man/pat_aggr.Rd | 1 simaerep-1.0.0/simaerep/man/pat_pool.Rd | 17 simaerep-1.0.0/simaerep/man/plot.simaerep.Rd | 16 simaerep-1.0.0/simaerep/man/plot_sim_examples.Rd | 1 simaerep-1.0.0/simaerep/man/plot_study.Rd | 36 simaerep-1.0.0/simaerep/man/plot_visit_med75.Rd | 22 simaerep-1.0.0/simaerep/man/poiss_test_site_ae_vs_study_ae.Rd | 7 simaerep-1.0.0/simaerep/man/prep_for_sim.Rd | 21 simaerep-1.0.0/simaerep/man/print.orivisit.Rd |only simaerep-1.0.0/simaerep/man/print.simaerep.Rd |only simaerep-1.0.0/simaerep/man/prob_lower_site_ae_vs_study_ae.Rd | 18 simaerep-1.0.0/simaerep/man/remap_col_names.Rd |only simaerep-1.0.0/simaerep/man/sim_after_prep.Rd | 23 simaerep-1.0.0/simaerep/man/sim_inframe.Rd | 20 simaerep-1.0.0/simaerep/man/sim_out.Rd |only simaerep-1.0.0/simaerep/man/sim_pat.Rd |only simaerep-1.0.0/simaerep/man/sim_sites.Rd | 24 simaerep-1.0.0/simaerep/man/sim_test_data_events.Rd | 16 simaerep-1.0.0/simaerep/man/sim_test_data_patient.Rd | 13 simaerep-1.0.0/simaerep/man/sim_test_data_portfolio.Rd | 53 simaerep-1.0.0/simaerep/man/sim_test_data_study.Rd | 67 simaerep-1.0.0/simaerep/man/simaerep.Rd | 159 - simaerep-1.0.0/simaerep/man/site_aggr.Rd | 30 simaerep-1.0.0/simaerep/tests/testthat/_snaps/S3_orivisit.md | 23 simaerep-1.0.0/simaerep/tests/testthat/_snaps/S3_simaerep.md | 100 simaerep-1.0.0/simaerep/tests/testthat/_snaps/event_names.md |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-025-or.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-025-ur.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-050-or.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-050-ur.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-075-or.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-075-ur.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-100-or.svg |only simaerep-1.0.0/simaerep/tests/testthat/_snaps/validation/study-100-ur.svg |only simaerep-1.0.0/simaerep/tests/testthat/test_S3_orivisit.R | 38 simaerep-1.0.0/simaerep/tests/testthat/test_S3_simaerep.R | 176 + simaerep-1.0.0/simaerep/tests/testthat/test_check_df_visit.R | 25 simaerep-1.0.0/simaerep/tests/testthat/test_column_naming.R |only simaerep-1.0.0/simaerep/tests/testthat/test_data.R | 303 -- simaerep-1.0.0/simaerep/tests/testthat/test_eval_sites.R | 30 simaerep-1.0.0/simaerep/tests/testthat/test_event_names.R | 176 - simaerep-1.0.0/simaerep/tests/testthat/test_get_portf_perf.R | 84 simaerep-1.0.0/simaerep/tests/testthat/test_inframe.R | 172 - simaerep-1.0.0/simaerep/tests/testthat/test_over_reporting.R | 75 simaerep-1.0.0/simaerep/tests/testthat/test_plot.R | 77 simaerep-1.0.0/simaerep/tests/testthat/test_regression.R |only simaerep-1.0.0/simaerep/tests/testthat/test_sim_sites.R | 30 simaerep-1.0.0/simaerep/tests/testthat/test_site_aggr.R | 43 simaerep-1.0.0/simaerep/tests/testthat/test_validation.R | 136 - 96 files changed, 2772 insertions(+), 3086 deletions(-)
Title: Regularized Estimation in Mixed Effects Model
Description: Implementation of an algorithm in two steps to estimate parameters of a model whose latent dynamics are inferred through latent processes, jointly regularized. This package uses 'Monolix' software (<https://monolixsuite.slp-software.com/>), which provide robust statistical method for non-linear mixed effects modeling. 'Monolix' must have been installed prior to use.
Author: Auriane Gabaut [aut, cre],
Ariane Bercu [aut],
Melanie Prague [aut],
Cecile Proust-Lima [aut]
Maintainer: Auriane Gabaut <auriane.gabaut@inria.fr>
Diff between REMixed versions 0.1.0 dated 2025-06-27 and 1.1.0 dated 2025-10-28
DESCRIPTION | 8 +- MD5 | 28 ++++--- NEWS.md |only R/REMixed-package.R | 2 R/cv.remix.R | 18 +++- R/gh_LL.R | 92 +++++++++++++++++-------- R/plot.R | 11 ++- R/remix.R | 2 R/searpas.R | 178 ++++++++++++++++++++++++++++++++++++++++++------- build |only inst/doc |only man/REMixed-package.Rd | 2 man/cv.remix.Rd | 4 - man/gh.LL.Rd | 7 + man/remix.Rd | 2 vignettes |only 16 files changed, 273 insertions(+), 81 deletions(-)
Title: Reverse Engineers Regular Expression Patterns for R Objects
Description: Reverse engineer a regular expression pattern for the characters
contained in an R object. Individual characters can be categorised into
digits, letters, punctuation or spaces and encoded into run-lengths. This
can be used to summarise the structure of a dataset or identify non-standard
entries. Many non-character inputs such as numeric vectors and data frames
are supported.
Author: Jasper Watson [aut, cre]
Maintainer: Jasper Watson <jasper.g.watson@gmail.com>
Diff between inverseRegex versions 0.1.1 dated 2022-10-23 and 0.2.0 dated 2025-10-28
inverseRegex-0.1.1/inverseRegex/R/nonCharacter.R |only inverseRegex-0.1.1/inverseRegex/inst/doc/overview.R |only inverseRegex-0.1.1/inverseRegex/inst/doc/overview.Rmd |only inverseRegex-0.1.1/inverseRegex/inst/doc/overview.html |only inverseRegex-0.1.1/inverseRegex/vignettes/overview.Rmd |only inverseRegex-0.2.0/inverseRegex/DESCRIPTION | 9 inverseRegex-0.2.0/inverseRegex/MD5 | 28 inverseRegex-0.2.0/inverseRegex/NEWS.md | 9 inverseRegex-0.2.0/inverseRegex/R/inverseRegex.R | 426 +++++++--- inverseRegex-0.2.0/inverseRegex/R/occurrencesLessThan.R | 117 +- inverseRegex-0.2.0/inverseRegex/README.md | 2 inverseRegex-0.2.0/inverseRegex/build/vignette.rds |binary inverseRegex-0.2.0/inverseRegex/inst/WORDLIST |only inverseRegex-0.2.0/inverseRegex/inst/doc/Overview.R |only inverseRegex-0.2.0/inverseRegex/inst/doc/Overview.Rmd |only inverseRegex-0.2.0/inverseRegex/inst/doc/Overview.html |only inverseRegex-0.2.0/inverseRegex/man/inverseRegex.Rd | 69 - inverseRegex-0.2.0/inverseRegex/tests/testthat/test.inverseRegex.R | 297 +++--- inverseRegex-0.2.0/inverseRegex/tests/testthat/test.occurrencesLessThan.R | 58 - inverseRegex-0.2.0/inverseRegex/vignettes/Overview.Rmd |only 20 files changed, 631 insertions(+), 384 deletions(-)
Title: Cancer RADAR Project Tool
Description: Cancer RADAR is a project which aim is to develop an
infrastructure that allows quantifying the risk of cancer by migration
background across Europe. This package contains a set of functions
cancer registries partners should use to reshape 5 year-age group
cancer incidence data into a set of summary statistics (see Boyle &
Parkin (1991, ISBN:978-92-832-1195-2)) in lines with Cancer RADAR data
protections rules.
Author: Nienke Alberts [aut],
Damien Georges [aut, cre] ,
Stefano Rosso [aut],
Iacopo Baussano [aut]
Maintainer: Damien Georges <georgesd@iarc.who.int>
Diff between cancerradarr versions 1.3.1 dated 2025-07-18 and 2.0.0 dated 2025-10-28
cancerradarr-1.3.1/cancerradarr/R/flexible_cancer_aggregation.R |only cancerradarr-1.3.1/cancerradarr/R/utils-pipe.R |only cancerradarr-1.3.1/cancerradarr/man/pipe.Rd |only cancerradarr-2.0.0/cancerradarr/DESCRIPTION | 49 cancerradarr-2.0.0/cancerradarr/MD5 | 96 cancerradarr-2.0.0/cancerradarr/NAMESPACE | 3 cancerradarr-2.0.0/cancerradarr/R/age_standardized_incidence_rates.R | 21 cancerradarr-2.0.0/cancerradarr/R/ageg_overlap_utils.R | 128 cancerradarr-2.0.0/cancerradarr/R/aggregated_ageg_name.R | 18 cancerradarr-2.0.0/cancerradarr/R/chop_vector.R | 8 cancerradarr-2.0.0/cancerradarr/R/create_canradar_summary_file.R | 1745 ++++++++-- cancerradarr-2.0.0/cancerradarr/R/create_registry_input_file.R | 126 cancerradarr-2.0.0/cancerradarr/R/create_static_report.R | 18 cancerradarr-2.0.0/cancerradarr/R/custom_ageg_aggregation.R | 260 - cancerradarr-2.0.0/cancerradarr/R/data.R | 18 cancerradarr-2.0.0/cancerradarr/R/incidence_rates.R | 18 cancerradarr-2.0.0/cancerradarr/R/incidence_rates_difference.R | 13 cancerradarr-2.0.0/cancerradarr/R/incidence_rates_ratio.R | 14 cancerradarr-2.0.0/cancerradarr/R/indirect_proportional_incidence_ratio.R | 9 cancerradarr-2.0.0/cancerradarr/R/indirect_standardized_incidence_ratio.R | 20 cancerradarr-2.0.0/cancerradarr/R/open_canradar_dictionary.R | 18 cancerradarr-2.0.0/cancerradarr/R/proportional_rates.R | 14 cancerradarr-2.0.0/cancerradarr/R/read_cancerradar_output_01.R | 165 cancerradarr-2.0.0/cancerradarr/R/read_cancerradar_output_02.R | 123 cancerradarr-2.0.0/cancerradarr/R/read_cancerradar_output_03.R |only cancerradarr-2.0.0/cancerradarr/R/run_dynamic_report.R | 18 cancerradarr-2.0.0/cancerradarr/R/standardized_incidence_rate_difference.R | 21 cancerradarr-2.0.0/cancerradarr/R/standardized_incidence_rate_ratio.R | 26 cancerradarr-2.0.0/cancerradarr/README.md | 34 cancerradarr-2.0.0/cancerradarr/build/vignette.rds |binary cancerradarr-2.0.0/cancerradarr/inst/doc/getting-started.R | 5 cancerradarr-2.0.0/cancerradarr/inst/doc/getting-started.html | 68 cancerradarr-2.0.0/cancerradarr/inst/doc/getting-started.qmd | 9 cancerradarr-2.0.0/cancerradarr/inst/extdata/CancerRADAR_protocol.pdf |only cancerradarr-2.0.0/cancerradarr/inst/extdata/dynamic_report.Rmd | 18 cancerradarr-2.0.0/cancerradarr/inst/extdata/ex_cancerRADAR_output.xlsx |binary cancerradarr-2.0.0/cancerradarr/man/age_standardized_incidence_rates.Rd | 6 cancerradarr-2.0.0/cancerradarr/man/create_canradar_summary_file.Rd | 5 cancerradarr-2.0.0/cancerradarr/man/custom_ageg_aggregation.Rd | 11 cancerradarr-2.0.0/cancerradarr/man/incidence_rates.Rd | 8 cancerradarr-2.0.0/cancerradarr/man/incidence_rates_difference.Rd | 6 cancerradarr-2.0.0/cancerradarr/man/incidence_rates_ratio.Rd | 6 cancerradarr-2.0.0/cancerradarr/man/indirect_standardized_incidence_ratio.Rd | 13 cancerradarr-2.0.0/cancerradarr/man/open_canradar_dictionary.Rd | 2 cancerradarr-2.0.0/cancerradarr/man/read_cancerradar_output_03.Rd |only cancerradarr-2.0.0/cancerradarr/man/standardized_incidence_rate_difference.Rd | 7 cancerradarr-2.0.0/cancerradarr/man/standardized_incidence_rate_ratio.Rd | 7 cancerradarr-2.0.0/cancerradarr/tests/testthat/test-ageg_overlap_utils.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test-chop_vector.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test-create_static_report.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test-read_cancerradar_output_01.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test-read_cancerradar_output_02.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test-run_dynamic_report.R |only cancerradarr-2.0.0/cancerradarr/tests/testthat/test_cancerradarr.R | 60 cancerradarr-2.0.0/cancerradarr/vignettes/getting-started.qmd | 9 55 files changed, 2381 insertions(+), 842 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.9 dated 2025-01-08 and 0.8.10 dated 2025-10-28
breathtestcore-0.8.10/breathtestcore/DESCRIPTION | 10 +++--- breathtestcore-0.8.10/breathtestcore/MD5 | 11 +++---- breathtestcore-0.8.10/breathtestcore/R/cleanup_data.R | 2 - breathtestcore-0.8.10/breathtestcore/build/vignette.rds |binary breathtestcore-0.8.10/breathtestcore/inst/doc/data_formats.html | 15 +++++----- breathtestcore-0.8.10/breathtestcore/inst/doc/methods_and_concepts.html | 7 ++-- breathtestcore-0.8.9/breathtestcore/tests/testthat/testthat-problems.rds |only 7 files changed, 23 insertions(+), 22 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Collection and Analysis of Otolith Shape Data
Description: Studies otolith shape variation among fish populations.
Otoliths are calcified structures found in the inner ear of teleost fish and their shape has
been known to vary among several fish populations and stocks, making them very useful in taxonomy,
species identification and to study geographic variations. The package extends previously described
software used for otolith shape analysis by allowing the user to automatically extract closed
contour outlines from a large number of images, perform smoothing to eliminate pixel noise described in Haines and Crampton (2000) <doi:10.1111/1475-4983.00148>,
choose from conducting either a Fourier or wavelet see Gençay et al (2001) <doi:10.1016/S0378-4371(00)00463-5> transform to the outlines and visualize
the mean shape. The output of the package are independent Fourier or wavelet coefficients
which can be directly imported into a wide range of statistical packages in R. The package
might prove useful in studies of any two dimensional [...truncated...]
Author: Lisa Anne Libungan [aut, cre],
Snaebjorn Palsson [aut, ths]
Maintainer: Lisa Anne Libungan <lisa.libungan@gmail.com>
Diff between shapeR versions 1.0-1 dated 2022-11-21 and 1.0-2 dated 2025-10-28
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- R/shapeR.R | 22 +++++++++++++--------- man/cluster.plot.Rd | 2 +- man/detect.outline.Rd | 2 +- man/generateShapeCoefficients.Rd | 8 ++++---- man/plotWaveletShape.Rd | 2 +- man/shapeR-package.Rd |only man/shapeR.Rd | 2 +- 9 files changed, 34 insertions(+), 29 deletions(-)
Title: Economics and Pricing Tools
Description: Functions to aid in micro and macro economic analysis and handling of price and
currency data. Includes extraction of relevant inflation and exchange rate data from World Bank
API, data cleaning/parsing, and standardisation. Inflation adjustment
calculations as found in Principles of Macroeconomics by Gregory Mankiw et al (2014). Current
and historical end of day exchange rates for 171 currencies from the European Central Bank
Statistical Data Warehouse (2020).
Author: Steve Condylios [aut, cre],
Bruno Mioto [ctb],
Bryan Shalloway [ctb]
Maintainer: Steve Condylios <steve.condylios@gmail.com>
Diff between priceR versions 1.0.2 dated 2024-08-17 and 1.0.3 dated 2025-10-28
priceR-1.0.2/priceR/tests/working |only priceR-1.0.3/priceR/DESCRIPTION | 16 +++--- priceR-1.0.3/priceR/MD5 | 7 +- priceR-1.0.3/priceR/R/extract_salary.R | 2 priceR-1.0.3/priceR/README.md | 84 ++++++++++++++++----------------- 5 files changed, 54 insertions(+), 55 deletions(-)
Title: Generating Features for a Cohort
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Author: Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Jenna Reps [aut],
Anthony Sena [aut],
Ger Inberg [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between FeatureExtraction versions 3.11.0 dated 2025-09-01 and 3.12.0 dated 2025-10-28
FeatureExtraction-3.11.0/FeatureExtraction/inst/java/featureExtraction-3.11.0.jar |only FeatureExtraction-3.12.0/FeatureExtraction/DESCRIPTION | 8 +- FeatureExtraction-3.12.0/FeatureExtraction/MD5 | 22 +++---- FeatureExtraction-3.12.0/FeatureExtraction/NEWS.md | 5 + FeatureExtraction-3.12.0/FeatureExtraction/R/Normalization.R | 2 FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.pdf |binary FeatureExtraction-3.12.0/FeatureExtraction/inst/java/featureExtraction-3.12.0.jar |only FeatureExtraction-3.12.0/FeatureExtraction/tests/testthat/test-tidyCovariates.R | 30 ++++++++++ 13 files changed, 51 insertions(+), 16 deletions(-)
More information about FeatureExtraction at CRAN
Permanent link
Title: Collaborative Graphical Lasso - Multi-Omics Network
Reconstruction
Description: Reconstruct networks from multi-omics data sets with the
collaborative graphical lasso (coglasso) algorithm described in Albanese, A.,
Kohlen, W., and Behrouzi, P. (2024) <doi:10.48550/arXiv.2403.18602>. Use the main wrapper
function `bs()` to build and select a multi-omics network.
Author: Alessio Albanese [aut, cre, cph] ,
Pariya Behrouzi [aut]
Maintainer: Alessio Albanese <alessio.albanese@wur.nl>
Diff between coglasso versions 1.0.2 dated 2024-04-03 and 1.1.0 dated 2025-10-28
coglasso-1.0.2/coglasso/R/StARS_coglasso.R |only coglasso-1.0.2/coglasso/tests/testthat/test-StARS_coglasso.R |only coglasso-1.1.0/coglasso/DESCRIPTION | 23 coglasso-1.1.0/coglasso/MD5 | 81 ++ coglasso-1.1.0/coglasso/NAMESPACE | 17 coglasso-1.1.0/coglasso/NEWS.md | 137 ++++- coglasso-1.1.0/coglasso/R/RcppExports.R | 8 coglasso-1.1.0/coglasso/R/XStARS.R |only coglasso-1.1.0/coglasso/R/bs.R |only coglasso-1.1.0/coglasso/R/coglasso-package.R | 29 - coglasso-1.1.0/coglasso/R/coglasso.R | 272 ++++++++-- coglasso-1.1.0/coglasso/R/plot.R |only coglasso-1.1.0/coglasso/R/select_coglasso.R |only coglasso-1.1.0/coglasso/R/utils.R |only coglasso-1.1.0/coglasso/README.md | 62 +- coglasso-1.1.0/coglasso/build/partial.rdb |binary coglasso-1.1.0/coglasso/build/vignette.rds |binary coglasso-1.1.0/coglasso/inst/CITATION | 2 coglasso-1.1.0/coglasso/inst/doc/coglasso.R | 41 - coglasso-1.1.0/coglasso/inst/doc/coglasso.Rmd | 64 -- coglasso-1.1.0/coglasso/inst/doc/coglasso.html | 176 +++--- coglasso-1.1.0/coglasso/inst/doc/manuscript.R | 104 +-- coglasso-1.1.0/coglasso/inst/doc/manuscript.Rmd | 30 - coglasso-1.1.0/coglasso/inst/doc/manuscript.html | 50 - coglasso-1.1.0/coglasso/man/bs.Rd |only coglasso-1.1.0/coglasso/man/coglasso-package.Rd | 5 coglasso-1.1.0/coglasso/man/coglasso.Rd | 55 +- coglasso-1.1.0/coglasso/man/figures |only coglasso-1.1.0/coglasso/man/get_network.Rd |only coglasso-1.1.0/coglasso/man/get_pcor.Rd |only coglasso-1.1.0/coglasso/man/plot.select_coglasso.Rd |only coglasso-1.1.0/coglasso/man/select_coglasso.Rd |only coglasso-1.1.0/coglasso/man/stars_coglasso.Rd | 101 --- coglasso-1.1.0/coglasso/man/xestars.Rd |only coglasso-1.1.0/coglasso/man/xstars.Rd |only coglasso-1.1.0/coglasso/src/RcppExports.cpp | 26 coglasso-1.1.0/coglasso/src/coglasso.cpp | 38 - coglasso-1.1.0/coglasso/src/coglassoD.cpp |only coglasso-1.1.0/coglasso/tests/testthat/_snaps |only coglasso-1.1.0/coglasso/tests/testthat/test-XStARS.R |only coglasso-1.1.0/coglasso/tests/testthat/test-bs.R |only coglasso-1.1.0/coglasso/tests/testthat/test-coglasso.R | 66 +- coglasso-1.1.0/coglasso/tests/testthat/test-plot.R |only coglasso-1.1.0/coglasso/tests/testthat/test-select_coglasso.R |only coglasso-1.1.0/coglasso/tests/testthat/test-utils.R |only coglasso-1.1.0/coglasso/vignettes/coglasso.Rmd | 64 -- coglasso-1.1.0/coglasso/vignettes/manuscript.Rmd | 30 - 47 files changed, 844 insertions(+), 637 deletions(-)
Title: Reinforcement Learning Tools for Two-Alternative Forced Choice
Tasks
Description: Tools for building Rescorla-Wagner Models for Two-Alternative
Forced Choice tasks, commonly employed in psychological research.
Most concepts and ideas within this R package are referenced from
Sutton and Barto (2018) <ISBN:9780262039246>.
The package allows for the intuitive definition of RL models using simple
if-else statements and three basic models built into this R package are
referenced from
Niv et al. (2012)<doi:10.1523/JNEUROSCI.5498-10.2012>.
Our approach to constructing and evaluating these computational models
is informed by the guidelines proposed in
Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Example datasets included with the package are sourced from the work of
Mason et al. (2024) <doi:10.3758/s13423-023-02415-x>.
Author: YuKi [aut, cre]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between binaryRL versions 0.9.7 dated 2025-08-19 and 0.9.8 dated 2025-10-28
DESCRIPTION | 6 MD5 | 34 ++-- R/8_output.R | 39 ++-- R/process_optimize_para.R | 34 ++-- R/process_recovery_data.R | 359 +++++++++++++++++++++++++++++++++++++--------- R/process_simulate_list.R | 91 ++++++----- R/step1_run_m.R | 6 R/step2_rcv_d.R | 236 +++++++++++++++++++++++------- R/step3_fit_p.R | 170 ++++++++++----------- R/step4_rpl_e.R | 9 - R/tool_update_priors.R | 2 man/fit_p.Rd | 178 +++++++++++----------- man/optimize_para.Rd | 92 ++++++----- man/rcv_d.Rd | 213 ++++++++++++++++++++------- man/recovery_data.Rd | 176 +++++++++++++++------- man/rpl_e.Rd | 9 - man/run_m.Rd | 6 man/simulate_list.Rd | 82 ++++------ 18 files changed, 1134 insertions(+), 608 deletions(-)
Title: Search and Get Data from the I14Y Interoperability Platform of
Switzerland
Description: Search and download Swiss data and metadata from the I14Y
interoperability platform of Switzerland using its public APIs
<https://www.i14y.admin.ch/api/index.html>.
Author: Felix Luginbuhl [aut, cre, cph] ,
Felix Lorenz [ctr]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between I14Y versions 0.1.6 dated 2025-09-24 and 0.1.7 dated 2025-10-28
I14Y-0.1.6/I14Y/R/i14y_get_data_service.R |only I14Y-0.1.6/I14Y/man/i14y_get_data_service.Rd |only I14Y-0.1.6/I14Y/tests/testthat/test-i14y_get_data_service.R |only I14Y-0.1.7/I14Y/DESCRIPTION | 6 +- I14Y-0.1.7/I14Y/MD5 | 11 +-- I14Y-0.1.7/I14Y/NAMESPACE | 1 I14Y-0.1.7/I14Y/NEWS.md | 3 + I14Y-0.1.7/I14Y/README.md | 34 ------------ 8 files changed, 10 insertions(+), 45 deletions(-)
Title: Generate Samples from Multivariate Truncated Normal
Distributions
Description: Efficient sampling from high-dimensional truncated Gaussian
distributions, or multivariate truncated normal (MTN). Techniques include
zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and
Marc A. Suchard (2024) <doi:10.1080/01621459.2024.2395587>, and harmonic Monte in Ari Pakman
and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.
Author: Zhenyu Zhang [aut, cre],
Andrew Chin [aut],
Akihiko Nishimura [aut],
Marc A. Suchard [aut],
John W. Ratcliff et al. [cph, ctb]
Maintainer: Zhenyu Zhang <zhangzhenyusa@gmail.com>
Diff between hdtg versions 0.2.2 dated 2025-10-25 and 0.2.3 dated 2025-10-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/aligned_allocator.h | 11 ++++++++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Simulation and Plots for Fossil and Taxonomy Data
Description: Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph],
Ugnė Stolz [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.4.1 dated 2024-10-02 and 2.4.2 dated 2025-10-28
DESCRIPTION | 8 MD5 | 58 NEWS.md | 10 R/FossilSim.R | 102 - R/SAtree.R | 34 R/conversions.R | 26 R/fossils.R | 30 R/plot.fossils.R | 12 R/sim.tip.sampling.R | 4 R/subsampling.R | 2 README.md | 11 build/vignette.rds |binary inst/doc/SAtree.R | 42 inst/doc/SAtree.html | 950 +++++++------- inst/doc/fossils.R | 582 ++++---- inst/doc/fossils.html | 1979 +++++++++++++++--------------- inst/doc/intro.R | 62 inst/doc/intro.html | 993 +++++++-------- inst/doc/paleotree.R | 44 inst/doc/paleotree.html | 1224 +++++++++--------- inst/doc/simfbd.R | 48 inst/doc/simfbd.html | 932 +++++++------- inst/doc/taxonomy.R | 112 - inst/doc/taxonomy.html | 1309 +++++++++---------- man/SAtree.from.fossils.Rd | 17 man/beast.fbd.format.Rd | 18 man/fossils.Rd | 4 man/plot.fossils.Rd | 3 man/prune.fossils.Rd | 5 man/reconstructed.tree.fossils.objects.Rd | 12 30 files changed, 4362 insertions(+), 4271 deletions(-)
Title: Harness ArcGIS Data Services
Description: Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or
'ArcGIS Platform' to read, write, publish, or manage vector and raster
data via ArcGIS location services REST API endpoints
<https://developers.arcgis.com/rest/>.
Author: Josiah Parry [aut, cre] ,
Eli Pousson [ctb] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Antony Barja [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgislayers versions 0.5.1 dated 2025-10-22 and 0.5.2 dated 2025-10-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/arc-select.R | 10 +++++----- R/get-estimates.R | 4 ++++ R/sf-methods.R | 4 ++-- man/get_layer_estimates.Rd | 4 ++++ 6 files changed, 24 insertions(+), 16 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-03 1.0.1
2024-11-14 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-22 1.1.1
Title: Seamless Access to World Bank World Development Indicators (WDI)
Description: Access and analyze the World Bank’s World Development Indicators
(WDI) using the corresponding API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>.
WDI provides more than 24,000 country or region-level indicators for various
contexts. 'wbwdi' enables users to download, process and work with WDI
series across multiple countries, aggregates, and time periods.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between wbwdi versions 1.0.1 dated 2025-03-25 and 1.0.2 dated 2025-10-28
DESCRIPTION | 10 MD5 | 50 ++-- NEWS.md | 9 R/perform_request.R | 93 ++++++--- R/wdi_get.R | 130 ++++++++---- R/wdi_get_entities.R | 103 +++++----- R/wdi_get_income_levels.R | 19 - R/wdi_get_indicators.R | 65 +++--- R/wdi_get_languages.R | 16 - R/wdi_get_lending_types.R | 19 - R/wdi_get_regions.R | 23 +- R/wdi_get_sources.R | 33 +-- R/wdi_get_topics.R | 13 - R/wdi_search.R | 30 +- README.md | 64 +++--- build/vignette.rds |binary tests/testthat/tests-perform_request.R | 272 ++++++++++++++++++++------- tests/testthat/tests-wdi_get.R | 85 ++++++-- tests/testthat/tests-wdi_get_entities.R | 78 +++++-- tests/testthat/tests-wdi_get_income_levels.R | 8 tests/testthat/tests-wdi_get_indicators.R | 28 +- tests/testthat/tests-wdi_get_lending_types.R | 24 +- tests/testthat/tests-wdi_get_regions.R | 16 + tests/testthat/tests-wdi_get_sources.R | 35 --- tests/testthat/tests-wdi_get_topics.R | 6 tests/testthat/tests-wdi_search.R | 8 26 files changed, 793 insertions(+), 444 deletions(-)
Title: Self-Controlled Case Series
Description: Execute the self-controlled case series (SCCS) design using observational
data in the OMOP Common Data Model. Extracts all necessary data from the database and
transforms it to the format required for SCCS. Age and season can be modeled
using splines assuming constant hazard within calendar months. Event-dependent
censoring of the observation period can be corrected for. Many exposures can be
included at once (MSCCS), with regularization on all coefficients except for the
exposure of interest. Includes diagnostics for all major assumptions of the SCCS.
Author: Martijn Schuemie [aut, cre],
Patrick Ryan [aut],
Trevor Shaddox [aut],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SelfControlledCaseSeries versions 6.1.0 dated 2025-09-03 and 6.1.1 dated 2025-10-28
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NEWS.md | 8 ++++++++ R/Diagnostics.R | 34 ++++++++++++++++++++++++++++++++-- R/Export.R | 2 +- inst/doc/MultipleAnalyses.pdf |binary inst/doc/ResultsSchema.pdf |binary inst/doc/SingleStudies.pdf |binary tests/testthat/test-helperFunctions.R |only 9 files changed, 54 insertions(+), 15 deletions(-)
More information about SelfControlledCaseSeries at CRAN
Permanent link
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.5.1 dated 2025-08-28 and 1.6.0 dated 2025-10-28
rsconnect-1.5.1/rsconnect/R/client-cloud.R |only rsconnect-1.5.1/rsconnect/tests/testthat/test-client-cloud.R |only rsconnect-1.6.0/rsconnect/DESCRIPTION | 8 rsconnect-1.6.0/rsconnect/MD5 | 200 +++--- rsconnect-1.6.0/rsconnect/NAMESPACE | 2 rsconnect-1.6.0/rsconnect/NEWS.md | 30 rsconnect-1.6.0/rsconnect/R/account-find.R | 4 rsconnect-1.6.0/rsconnect/R/accounts.R | 220 ++++++ rsconnect-1.6.0/rsconnect/R/appDependencies.R | 2 rsconnect-1.6.0/rsconnect/R/appMetadata.R | 69 +- rsconnect-1.6.0/rsconnect/R/applications.R | 77 ++ rsconnect-1.6.0/rsconnect/R/auth.R | 25 rsconnect-1.6.0/rsconnect/R/bundleFiles.R | 14 rsconnect-1.6.0/rsconnect/R/bundlePackagePackrat.R | 2 rsconnect-1.6.0/rsconnect/R/bundlePackageRenv.R | 3 rsconnect-1.6.0/rsconnect/R/bundlePython.R | 4 rsconnect-1.6.0/rsconnect/R/client-cloudAuth.R |only rsconnect-1.6.0/rsconnect/R/client-connect.R | 5 rsconnect-1.6.0/rsconnect/R/client-connectCloud.R |only rsconnect-1.6.0/rsconnect/R/client-connectCloudLogs.R |only rsconnect-1.6.0/rsconnect/R/client-shinyapps.R | 11 rsconnect-1.6.0/rsconnect/R/client.R | 8 rsconnect-1.6.0/rsconnect/R/configureApp.R | 12 rsconnect-1.6.0/rsconnect/R/cookies.R | 18 rsconnect-1.6.0/rsconnect/R/deployAPI.R | 3 rsconnect-1.6.0/rsconnect/R/deployApp.R | 330 +++++++--- rsconnect-1.6.0/rsconnect/R/deployDoc.R | 2 rsconnect-1.6.0/rsconnect/R/deploySite.R | 3 rsconnect-1.6.0/rsconnect/R/deployTFModel.R | 3 rsconnect-1.6.0/rsconnect/R/deploymentTarget.R | 54 - rsconnect-1.6.0/rsconnect/R/deployments.R | 7 rsconnect-1.6.0/rsconnect/R/envvars.R | 4 rsconnect-1.6.0/rsconnect/R/http.R | 7 rsconnect-1.6.0/rsconnect/R/ide.R | 8 rsconnect-1.6.0/rsconnect/R/lint-framework.R | 6 rsconnect-1.6.0/rsconnect/R/lint.R | 6 rsconnect-1.6.0/rsconnect/R/purgeApp.R | 3 rsconnect-1.6.0/rsconnect/R/restartApp.R | 3 rsconnect-1.6.0/rsconnect/R/rpubs.R | 3 rsconnect-1.6.0/rsconnect/R/servers.R | 97 ++ rsconnect-1.6.0/rsconnect/R/tasks.R | 17 rsconnect-1.6.0/rsconnect/R/terminateApp.R | 3 rsconnect-1.6.0/rsconnect/R/usage.R | 12 rsconnect-1.6.0/rsconnect/R/utm.R |only rsconnect-1.6.0/rsconnect/R/writeManifest.R | 2 rsconnect-1.6.0/rsconnect/R/zzz.R |only rsconnect-1.6.0/rsconnect/README.md | 25 rsconnect-1.6.0/rsconnect/build/vignette.rds |binary rsconnect-1.6.0/rsconnect/inst/cert/api.connect.posit.cloud.pem |only rsconnect-1.6.0/rsconnect/man/accountUsage.Rd | 2 rsconnect-1.6.0/rsconnect/man/accounts.Rd | 3 rsconnect-1.6.0/rsconnect/man/addAuthorizedUser.Rd | 2 rsconnect-1.6.0/rsconnect/man/addLinter.Rd | 2 rsconnect-1.6.0/rsconnect/man/addServer.Rd | 2 rsconnect-1.6.0/rsconnect/man/appDependencies.Rd | 2 rsconnect-1.6.0/rsconnect/man/applications.Rd | 2 rsconnect-1.6.0/rsconnect/man/configureApp.Rd | 2 rsconnect-1.6.0/rsconnect/man/connectApiUser.Rd | 3 rsconnect-1.6.0/rsconnect/man/connectCloudUser.Rd |only rsconnect-1.6.0/rsconnect/man/connectSPCSUser.Rd | 2 rsconnect-1.6.0/rsconnect/man/deployAPI.Rd | 2 rsconnect-1.6.0/rsconnect/man/deployApp.Rd | 23 rsconnect-1.6.0/rsconnect/man/deployDoc.Rd | 2 rsconnect-1.6.0/rsconnect/man/deploySite.Rd | 2 rsconnect-1.6.0/rsconnect/man/deployTFModel.Rd | 2 rsconnect-1.6.0/rsconnect/man/deployments.Rd | 2 rsconnect-1.6.0/rsconnect/man/forgetDeployment.Rd | 2 rsconnect-1.6.0/rsconnect/man/lint.Rd | 2 rsconnect-1.6.0/rsconnect/man/linter.Rd | 2 rsconnect-1.6.0/rsconnect/man/listAccountEnvVars.Rd | 2 rsconnect-1.6.0/rsconnect/man/listDeploymentFiles.Rd | 2 rsconnect-1.6.0/rsconnect/man/makeLinterMessage.Rd | 2 rsconnect-1.6.0/rsconnect/man/purgeApp.Rd | 2 rsconnect-1.6.0/rsconnect/man/removeAuthorizedUser.Rd | 2 rsconnect-1.6.0/rsconnect/man/resendInvitation.Rd | 2 rsconnect-1.6.0/rsconnect/man/restartApp.Rd | 2 rsconnect-1.6.0/rsconnect/man/rpubsUpload.Rd | 2 rsconnect-1.6.0/rsconnect/man/servers.Rd | 8 rsconnect-1.6.0/rsconnect/man/setAccountInfo.Rd | 9 rsconnect-1.6.0/rsconnect/man/setProperty.Rd | 2 rsconnect-1.6.0/rsconnect/man/showInvited.Rd | 2 rsconnect-1.6.0/rsconnect/man/showLogs.Rd | 27 rsconnect-1.6.0/rsconnect/man/showMetrics.Rd | 3 rsconnect-1.6.0/rsconnect/man/showProperties.Rd | 2 rsconnect-1.6.0/rsconnect/man/showUsage.Rd | 2 rsconnect-1.6.0/rsconnect/man/showUsers.Rd | 2 rsconnect-1.6.0/rsconnect/man/syncAppMetadata.Rd | 2 rsconnect-1.6.0/rsconnect/man/taskLog.Rd | 4 rsconnect-1.6.0/rsconnect/man/tasks.Rd | 4 rsconnect-1.6.0/rsconnect/man/terminateApp.Rd | 2 rsconnect-1.6.0/rsconnect/man/unsetProperty.Rd | 2 rsconnect-1.6.0/rsconnect/man/writeManifest.Rd | 2 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/account-find.md | 2 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/bundleFiles.md | 4 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/deployApp.md | 27 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/deploymentTarget.md | 2 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/deployments-find.md | 2 rsconnect-1.6.0/rsconnect/tests/testthat/_snaps/servers.md | 29 rsconnect-1.6.0/rsconnect/tests/testthat/test-appMetadata.R | 110 ++- rsconnect-1.6.0/rsconnect/tests/testthat/test-client-connectCloud.R |only rsconnect-1.6.0/rsconnect/tests/testthat/test-client.R | 12 rsconnect-1.6.0/rsconnect/tests/testthat/test-cookies.R | 66 +- rsconnect-1.6.0/rsconnect/tests/testthat/test-deployApp.R | 15 rsconnect-1.6.0/rsconnect/tests/testthat/test-http.R | 4 rsconnect-1.6.0/rsconnect/tests/testthat/test-ide.R | 1 rsconnect-1.6.0/rsconnect/tests/testthat/test-servers.R | 43 - 106 files changed, 1315 insertions(+), 464 deletions(-)
Title: Machinery for Processing Random Effect Formulas
Description: Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.
Author: Ben Bolker [aut, cre]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between reformulas versions 0.4.1 dated 2025-04-30 and 0.4.2 dated 2025-10-28
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++++----------- NAMESPACE | 6 ++---- NEWS.md | 9 ++++++++- R/mkReTrms.R | 27 +++++++++++++++++++++++++++ R/randint.R |only R/utils.R | 28 ++++++++++++++++++++++------ build/partial.rdb |binary inst/tinytest/test_extractForm.R |only inst/tinytest/test_from_lme4.R |only inst/tinytest/test_mkReTrms.R | 8 ++++++++ inst/tinytest/test_noSpecial.R | 4 ++++ inst/tinytest/test_randint.R |only man/expandGrpVar.Rd | 12 +++++++----- man/formfuns.Rd | 7 +++++++ man/mkReTrms.Rd | 28 ++++++++++++++++++++++++++++ man/randint.Rd |only 17 files changed, 132 insertions(+), 30 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.8.2 dated 2025-07-13 and 2.9.0 dated 2025-10-28
DESCRIPTION | 8 +- MD5 | 49 ++++++++--------- NAMESPACE | 2 NEWS.md | 20 +++++++ R/getMap.R | 11 ++- R/marker_allelematrix.R | 17 ++++-- R/marker_genomatrix.R | 14 +++-- R/marker_locusattributes.R | 62 ++++++++-------------- R/marker_print.R | 22 +++++-- R/marker_properties.R | 6 +- R/marker_utils.R | 82 +++++++++++++++++------------ R/mergePed.R | 54 +++++++++---------- R/ped_convert.R | 2 R/ped_founder-inbreeding.R | 25 ++++++-- R/ped_subgroups.R | 84 ++++++++++++++++++++++++++++++ R/ped_utils.R | 2 README.md | 6 +- inst/doc/pedtools.html | 9 +-- man/extractSingletons.Rd |only man/getAlleles.Rd | 13 +++- man/getGenotypes.Rd | 12 +++- man/getMap.Rd | 11 ++- man/harmoniseMarkers.Rd | 30 +++++++--- man/locusAttributes.Rd | 56 ++++++++------------ man/mergePed.Rd | 31 ++--------- tests/testthat/test-marker-allelematrix.R | 15 +++-- 26 files changed, 398 insertions(+), 245 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre] ,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 6.5.1 dated 2025-08-29 and 6.6.0 dated 2025-10-28
lefko3-6.5.1/lefko3/vignettes/Ch2.25-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch2.35-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch5.18-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch5.24-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch5.28-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch8.15-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch8.19-1.png |only lefko3-6.5.1/lefko3/vignettes/Ch8.23-1.png |only lefko3-6.6.0/lefko3/DESCRIPTION | 10 lefko3-6.6.0/lefko3/MD5 | 191 lefko3-6.6.0/lefko3/NAMESPACE | 7 lefko3-6.6.0/lefko3/NEWS.md | 42 lefko3-6.6.0/lefko3/R/RcppExports.R | 781 + lefko3-6.6.0/lefko3/R/datamanag.R | 706 - lefko3-6.6.0/lefko3/R/errorchecks.R | 346 lefko3-6.6.0/lefko3/R/matrixcreation.R | 730 + lefko3-6.6.0/lefko3/R/modelselection.R | 2725 ++--- lefko3-6.6.0/lefko3/R/popchar.R | 534 + lefko3-6.6.0/lefko3/R/popdyn.R | 872 + lefko3-6.6.0/lefko3/inst/doc/Chapter1.Rmd | 24 lefko3-6.6.0/lefko3/inst/doc/Chapter1.html | 182 lefko3-6.6.0/lefko3/inst/doc/Chapter2.Rmd | 61 lefko3-6.6.0/lefko3/inst/doc/Chapter2.html | 430 lefko3-6.6.0/lefko3/inst/doc/Chapter5.Rmd | 333 lefko3-6.6.0/lefko3/inst/doc/Chapter5.html | 934 + lefko3-6.6.0/lefko3/inst/doc/Chapter6.Rmd | 8 lefko3-6.6.0/lefko3/inst/doc/Chapter6.html | 21 lefko3-6.6.0/lefko3/inst/doc/Chapter8.Rmd | 438 lefko3-6.6.0/lefko3/inst/doc/Chapter8.html | 792 + lefko3-6.6.0/lefko3/inst/doc/Chapter9.html | 5 lefko3-6.6.0/lefko3/inst/include/basic_funcs/main_utils.h | 805 + lefko3-6.6.0/lefko3/man/add_lM.Rd | 15 lefko3-6.6.0/lefko3/man/add_stage.Rd | 14 lefko3-6.6.0/lefko3/man/aflefko2.Rd | 28 lefko3-6.6.0/lefko3/man/append_lP.Rd | 2 lefko3-6.6.0/lefko3/man/arlefko2.Rd | 18 lefko3-6.6.0/lefko3/man/bootstrap3.Rd |only lefko3-6.6.0/lefko3/man/delete_lM.Rd | 14 lefko3-6.6.0/lefko3/man/edit_lM.Rd | 31 lefko3-6.6.0/lefko3/man/elasticity3.Rd | 2 lefko3-6.6.0/lefko3/man/elasticity3.dgCMatrix.Rd | 2 lefko3-6.6.0/lefko3/man/elasticity3.lefkoMat.Rd | 2 lefko3-6.6.0/lefko3/man/elasticity3.lefkoMatList.Rd |only lefko3-6.6.0/lefko3/man/elasticity3.list.Rd | 2 lefko3-6.6.0/lefko3/man/elasticity3.matrix.Rd | 2 lefko3-6.6.0/lefko3/man/f_projection3.Rd | 25 lefko3-6.6.0/lefko3/man/flefko2.Rd | 28 lefko3-6.6.0/lefko3/man/flefko3.Rd | 20 lefko3-6.6.0/lefko3/man/fleslie.Rd | 34 lefko3-6.6.0/lefko3/man/lambda3.Rd | 11 lefko3-6.6.0/lefko3/man/lmean.Rd | 11 lefko3-6.6.0/lefko3/man/ltre3.Rd | 3 lefko3-6.6.0/lefko3/man/modelsearch.Rd | 28 lefko3-6.6.0/lefko3/man/mpm_create.Rd | 17 lefko3-6.6.0/lefko3/man/projection3.Rd | 31 lefko3-6.6.0/lefko3/man/repvalue3.lefkoMatList.Rd |only lefko3-6.6.0/lefko3/man/rlefko2.Rd | 18 lefko3-6.6.0/lefko3/man/rlefko3.Rd | 18 lefko3-6.6.0/lefko3/man/rleslie.Rd | 17 lefko3-6.6.0/lefko3/man/sensitivity3.dgCMatrix.Rd | 2 lefko3-6.6.0/lefko3/man/sensitivity3.lefkoMat.Rd | 2 lefko3-6.6.0/lefko3/man/sensitivity3.lefkoMatList.Rd |only lefko3-6.6.0/lefko3/man/sensitivity3.list.Rd | 2 lefko3-6.6.0/lefko3/man/sensitivity3.matrix.Rd | 2 lefko3-6.6.0/lefko3/man/slambda3.Rd | 20 lefko3-6.6.0/lefko3/man/stablestage3.dgCMatrix.Rd | 2 lefko3-6.6.0/lefko3/man/stablestage3.lefkoMat.Rd | 2 lefko3-6.6.0/lefko3/man/stablestage3.lefkoMatList.Rd |only lefko3-6.6.0/lefko3/man/stablestage3.matrix.Rd | 2 lefko3-6.6.0/lefko3/man/stage_weight.Rd |only lefko3-6.6.0/lefko3/man/subset_lM.Rd | 16 lefko3-6.6.0/lefko3/man/summary.lefkoMat.Rd | 2 lefko3-6.6.0/lefko3/man/summary.lefkoMatList.Rd |only lefko3-6.6.0/lefko3/man/summary_hfv.Rd | 38 lefko3-6.6.0/lefko3/src/DataManagement.cpp | 1292 ++ lefko3-6.6.0/lefko3/src/Makevars | 2 lefko3-6.6.0/lefko3/src/Makevars.win | 1 lefko3-6.6.0/lefko3/src/Mats2.cpp | 749 + lefko3-6.6.0/lefko3/src/MatsNProj.cpp | 6601 +++++++++----- lefko3-6.6.0/lefko3/src/PopChar.cpp | 437 lefko3-6.6.0/lefko3/src/PopDyn2.cpp | 909 + lefko3-6.6.0/lefko3/src/RcppExports.cpp | 51 lefko3-6.6.0/lefko3/vignettes/Ch2.26-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch2.27-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch2.36-1.png |binary 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lefko3-6.6.0/lefko3/vignettes/Chapter6.Rmd.orig | 8 lefko3-6.6.0/lefko3/vignettes/Chapter8.Rmd | 438 lefko3-6.6.0/lefko3/vignettes/Chapter8.Rmd.orig | 73 108 files changed, 16350 insertions(+), 6320 deletions(-)
Title: Predict Drug Functional Similarity to Drug Repurposing
Description: A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.
Author: Junwei Han [aut, cre, cph],
Ji Li [aut],
Jiashuo Wu [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between DrugSim2DR versions 0.1.1 dated 2023-08-10 and 0.1.2 dated 2025-10-28
DrugSim2DR-0.1.1/DrugSim2DR/R/plotDrugstructure.R |only DrugSim2DR-0.1.1/DrugSim2DR/data/datalist |only DrugSim2DR-0.1.1/DrugSim2DR/man/plotDrugstructure.Rd |only DrugSim2DR-0.1.2/DrugSim2DR/DESCRIPTION | 11 ++-- DrugSim2DR-0.1.2/DrugSim2DR/MD5 | 23 ++++----- DrugSim2DR-0.1.2/DrugSim2DR/NAMESPACE | 5 -- DrugSim2DR-0.1.2/DrugSim2DR/R/DrugReposition.R | 14 ++--- DrugSim2DR-0.1.2/DrugSim2DR/build/vignette.rds |binary DrugSim2DR-0.1.2/DrugSim2DR/inst/doc/DrugSim2DR.R | 35 +++++--------- DrugSim2DR-0.1.2/DrugSim2DR/inst/doc/DrugSim2DR.Rmd | 20 -------- DrugSim2DR-0.1.2/DrugSim2DR/inst/doc/DrugSim2DR.html | 47 +++++-------------- DrugSim2DR-0.1.2/DrugSim2DR/man/DrugReposition.Rd | 6 +- DrugSim2DR-0.1.2/DrugSim2DR/man/datasummary.Rd | 1 DrugSim2DR-0.1.2/DrugSim2DR/vignettes/DrugSim2DR.Rmd | 20 -------- 14 files changed, 55 insertions(+), 127 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.21 dated 2025-03-15 and 1.22 dated 2025-10-28
DESCRIPTION | 16 +++++++++------- MD5 | 8 ++++---- R/utils.R | 4 +++- man/hugo_installers.Rd | 2 +- tests/test-ci/test-themes.R | 1 - 5 files changed, 17 insertions(+), 14 deletions(-)