Title: Tools for Managing, Measuring and Visualizing Policy Portfolios
Description: Tools for simplifying the creation and management of data structures
suitable for dealing with policy portfolios, that is, two-dimensional spaces
of policy instruments and policy targets. The package also allows to generate measures of
portfolio characteristics and facilitates their visualization.
Author: Xavier Fernandez i Marin [aut, cre]
Maintainer: Xavier Fernandez i Marin <xavier.fim@gmail.com>
Diff between PolicyPortfolios versions 0.3 dated 2022-03-11 and 0.5 dated 2025-10-31
PolicyPortfolios-0.3/PolicyPortfolios/man/PolicyPortfolios.Rd |only PolicyPortfolios-0.5/PolicyPortfolios/DESCRIPTION | 12 PolicyPortfolios-0.5/PolicyPortfolios/MD5 | 60 - PolicyPortfolios-0.5/PolicyPortfolios/NEWS | 33 PolicyPortfolios-0.5/PolicyPortfolios/R/data.R | 44 PolicyPortfolios-0.5/PolicyPortfolios/R/functions.R | 4 PolicyPortfolios-0.5/PolicyPortfolios/R/globals.R | 1 PolicyPortfolios-0.5/PolicyPortfolios/R/help.R | 3 PolicyPortfolios-0.5/PolicyPortfolios/R/pp_clean.R | 436 ++++--- PolicyPortfolios-0.5/PolicyPortfolios/R/pp_measures.R | 43 PolicyPortfolios-0.5/PolicyPortfolios/R/pp_plot.R | 2 PolicyPortfolios-0.5/PolicyPortfolios/R/pp_similarity.R | 28 PolicyPortfolios-0.5/PolicyPortfolios/build/vignette.rds |binary PolicyPortfolios-0.5/PolicyPortfolios/data/P.education.rda |binary PolicyPortfolios-0.5/PolicyPortfolios/data/P.energy.rda |binary PolicyPortfolios-0.5/PolicyPortfolios/data/accupol.instruments.rda |only PolicyPortfolios-0.5/PolicyPortfolios/data/accupol.v1.rda |only PolicyPortfolios-0.5/PolicyPortfolios/data/consensus.instruments.rda |binary PolicyPortfolios-0.5/PolicyPortfolios/data/consensus.rda |binary PolicyPortfolios-0.5/PolicyPortfolios/data/consensus.targets.rda |binary PolicyPortfolios-0.5/PolicyPortfolios/inst/doc/using_PolicyPortfolios.R | 39 PolicyPortfolios-0.5/PolicyPortfolios/inst/doc/using_PolicyPortfolios.Rmd | 13 PolicyPortfolios-0.5/PolicyPortfolios/inst/doc/using_PolicyPortfolios.html | 557 ++++++---- PolicyPortfolios-0.5/PolicyPortfolios/man/PolicyPortfolios-package.Rd |only PolicyPortfolios-0.5/PolicyPortfolios/man/accupol.instruments.Rd |only PolicyPortfolios-0.5/PolicyPortfolios/man/accupol.v1.Rd |only PolicyPortfolios-0.5/PolicyPortfolios/man/consensus.Rd | 2 PolicyPortfolios-0.5/PolicyPortfolios/man/pp_clean.Rd | 5 PolicyPortfolios-0.5/PolicyPortfolios/man/pp_measures.Rd | 6 PolicyPortfolios-0.5/PolicyPortfolios/man/pp_similarity.Rd | 2 PolicyPortfolios-0.5/PolicyPortfolios/tests/testthat/test_diversity.R | 2 PolicyPortfolios-0.5/PolicyPortfolios/tests/testthat/test_pp_array.R | 2 PolicyPortfolios-0.5/PolicyPortfolios/tests/testthat/test_pp_measures.R | 2 PolicyPortfolios-0.5/PolicyPortfolios/vignettes/using_PolicyPortfolios.Rmd | 13 34 files changed, 799 insertions(+), 510 deletions(-)
More information about PolicyPortfolios at CRAN
Permanent link
Title: Working with Precision Teaching Values
Description: An implementation of an S3 class based on a double vector for storing and displaying precision teaching measures, representing a growing or a decaying (multiplicative) change between two frequencies. The main format method allows researchers to display measures (including data.frame) that respect the established conventions in the precision teaching community (i.e., prefixed multiplication or division symbol, displayed number <= 1). Basic multiplication and division methods are allowed and other useful functions are provided for creating, converting or inverting precision teaching measures. For more details, see Pennypacker, Gutierrez and Lindsley (2003, ISBN: 1-881317-13-7).
Author: Alexandre Gellen-Kamel [aut, cre, cph]
Maintainer: Alexandre Gellen-Kamel <kamel.ag@outlook.com>
Diff between ptvalue versions 0.1.0 dated 2025-08-29 and 0.2.0 dated 2025-10-31
ptvalue-0.1.0/ptvalue/man/abs_sign.Rd |only ptvalue-0.1.0/ptvalue/man/invert_sign.Rd |only ptvalue-0.2.0/ptvalue/DESCRIPTION | 10 - ptvalue-0.2.0/ptvalue/MD5 | 21 +- ptvalue-0.2.0/ptvalue/NAMESPACE | 4 ptvalue-0.2.0/ptvalue/NEWS.md | 29 ++- ptvalue-0.2.0/ptvalue/R/ptvalue.R | 192 +++++++++++++++----- ptvalue-0.2.0/ptvalue/README.md | 94 ++++++++- ptvalue-0.2.0/ptvalue/inst/CITATION | 4 ptvalue-0.2.0/ptvalue/man/convert_sign.Rd |only ptvalue-0.2.0/ptvalue/man/ptvalue.Rd | 46 +++- ptvalue-0.2.0/ptvalue/man/timesdiv.Rd | 22 +- ptvalue-0.2.0/ptvalue/tests/testthat/test-ptvalue.R | 115 +++++++++++ 13 files changed, 434 insertions(+), 103 deletions(-)
Title: Cross-Validated Post-Lasso
Description: Provides tools for cross-validated Lasso and Post-Lasso estimation.
Built on top of the 'glmnet' package by Friedman, Hastie and Tibshirani (2010) <doi:10.18637/jss.v033.i01>,
the main function plasso() extends the standard 'glmnet' output with coefficient paths
for Post-Lasso models, while cv.plasso() performs cross-validation for both Lasso
and Post-Lasso models and different ways to select the penalty parameter lambda as discussed in Knaus (2021) <doi:10.1111/rssa.12623>.
Author: Michael C. Knaus [aut, cre] ,
Stefan Glaisner [aut]
Maintainer: Michael C. Knaus <michael.knaus@uni-tuebingen.de>
This is a re-admission after prior archival of version 0.1.2 dated 2023-12-03
Diff between plasso versions 0.1.2 dated 2023-12-03 and 0.1.3 dated 2025-10-31
DESCRIPTION | 33 +++--- MD5 | 52 +++++----- NEWS.md | 5 build/vignette.rds |binary inst/doc/plasso.R | 14 +- inst/doc/plasso.Rmd | 4 inst/doc/plasso.html | 210 ++++++++++++++++++++--------------------- man/CV_core.Rd | 64 ++++++------ man/add_intercept.Rd | 36 +++---- man/coef.cv.plasso.Rd | 88 ++++++++--------- man/coef.plasso.Rd | 82 ++++++++-------- man/cv.plasso.Rd | 132 ++++++++++++------------- man/handle_weights.Rd | 40 +++---- man/norm_w_to_n.Rd | 40 +++---- man/plot.cv.plasso.Rd | 90 ++++++++--------- man/plot.plasso.Rd | 84 ++++++++-------- man/predict.cv.plasso.Rd | 130 ++++++++++++------------- man/predict.plasso.Rd | 102 +++++++++---------- man/print.cv.plasso.Rd | 44 ++++---- man/print.plasso.Rd | 42 ++++---- man/print.summary.cv.plasso.Rd | 42 ++++---- man/summary.cv.plasso.Rd | 74 +++++++------- man/summary.plasso.Rd | 38 +++---- man/toeplitz.Rd | 76 +++++++------- tests/testthat.R | 24 ++-- tests/testthat/test-predict.R | 12 -- vignettes/plasso.Rmd | 4 27 files changed, 779 insertions(+), 783 deletions(-)
Title: Creation of Mock Observational Medical Outcomes Partnership
Common Data Model
Description: Creates mock data for testing and package development for the
Observational Medical Outcomes Partnership common data model. The
package offers functions crafted with pipeline-friendly
implementation, enabling users to effortlessly include only the
necessary tables for their testing needs.
Author: Mike Du [aut, cre] ,
Marti Catala [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Mike Du <mike.du@ndorms.ox.ac.uk>
Diff between omock versions 0.5.0 dated 2025-09-01 and 0.6.0 dated 2025-10-31
omock-0.5.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.R |only omock-0.5.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.Rmd |only omock-0.5.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.html |only omock-0.5.0/omock/inst/doc/a02_Creating_synthetic_cohorts.R |only omock-0.5.0/omock/inst/doc/a02_Creating_synthetic_cohorts.Rmd |only omock-0.5.0/omock/inst/doc/a02_Creating_synthetic_cohorts.html |only omock-0.5.0/omock/inst/doc/a03_Creating_a_synthetic_vocabulary.R |only omock-0.5.0/omock/inst/doc/a03_Creating_a_synthetic_vocabulary.Rmd |only omock-0.5.0/omock/inst/doc/a03_Creating_a_synthetic_vocabulary.html |only omock-0.5.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.R |only omock-0.5.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.Rmd |only omock-0.5.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.html |only omock-0.5.0/omock/vignettes/a01_Creating_synthetic_clinical_tables.Rmd |only omock-0.5.0/omock/vignettes/a02_Creating_synthetic_cohorts.Rmd |only omock-0.5.0/omock/vignettes/a03_Creating_a_synthetic_vocabulary.Rmd |only omock-0.5.0/omock/vignettes/a04_Building_a_bespoke_mock_cdm.Rmd |only omock-0.6.0/omock/DESCRIPTION | 20 omock-0.6.0/omock/MD5 | 149 +++--- omock-0.6.0/omock/NAMESPACE | 37 + omock-0.6.0/omock/NEWS.md | 74 ++- omock-0.6.0/omock/R/changeCdmVersion.R |only omock-0.6.0/omock/R/checkInputs.R | 30 - omock-0.6.0/omock/R/checks.R | 55 +- omock-0.6.0/omock/R/mockCdmFromTables.R | 158 +++++- omock-0.6.0/omock/R/mockCdmReference.R | 9 omock-0.6.0/omock/R/mockCohort.R | 77 +-- omock-0.6.0/omock/R/mockConcept.R | 17 omock-0.6.0/omock/R/mockConditionOccurrence.R | 46 +- omock-0.6.0/omock/R/mockDatasets.R | 227 +++++----- omock-0.6.0/omock/R/mockDeath.R | 6 omock-0.6.0/omock/R/mockDrugExposure.R | 35 - omock-0.6.0/omock/R/mockMeasurement.R | 19 omock-0.6.0/omock/R/mockObservation.R | 36 - omock-0.6.0/omock/R/mockObservationPeriod.R | 78 +-- omock-0.6.0/omock/R/mockPerson.R | 8 omock-0.6.0/omock/R/mockProcedureOccurrence.R | 41 - omock-0.6.0/omock/R/mockVisitOccurrence.R | 113 ++++ omock-0.6.0/omock/R/mockVocabulary.R | 26 - omock-0.6.0/omock/R/mockVocabularySet.R | 32 - omock-0.6.0/omock/R/reexports-omopgenerics.R | 84 ++- omock-0.6.0/omock/R/sysdata.rda |binary omock-0.6.0/omock/README.md | 46 +- omock-0.6.0/omock/build/vignette.rds |binary omock-0.6.0/omock/data/mockDatasets.rda |binary omock-0.6.0/omock/inst/CITATION | 17 omock-0.6.0/omock/inst/doc/mock_from_tables.R |only omock-0.6.0/omock/inst/doc/mock_from_tables.Rmd |only omock-0.6.0/omock/inst/doc/mock_from_tables.html |only omock-0.6.0/omock/inst/doc/synthetic_clinical_tables.R |only omock-0.6.0/omock/inst/doc/synthetic_clinical_tables.Rmd |only omock-0.6.0/omock/inst/doc/synthetic_clinical_tables.html |only omock-0.6.0/omock/inst/doc/synthetic_cohorts.R |only omock-0.6.0/omock/inst/doc/synthetic_cohorts.Rmd |only omock-0.6.0/omock/inst/doc/synthetic_cohorts.html |only omock-0.6.0/omock/inst/doc/synthetic_datasets.R |only omock-0.6.0/omock/inst/doc/synthetic_datasets.Rmd |only omock-0.6.0/omock/inst/doc/synthetic_datasets.html |only omock-0.6.0/omock/inst/doc/synthetic_vocabulary.R |only omock-0.6.0/omock/inst/doc/synthetic_vocabulary.Rmd |only omock-0.6.0/omock/inst/doc/synthetic_vocabulary.html |only omock-0.6.0/omock/man/downloadMockDataset.Rd | 6 omock-0.6.0/omock/man/figures/logo.png |binary omock-0.6.0/omock/man/isMockDatasetDownloaded.Rd | 4 omock-0.6.0/omock/man/mockConcepts.Rd | 6 omock-0.6.0/omock/man/mockDatasets.Rd | 3 omock-0.6.0/omock/man/mockDatasetsFolder.Rd | 4 omock-0.6.0/omock/man/mockVisitOccurrence.Rd | 10 omock-0.6.0/omock/man/mockVocabularyTables.Rd | 3 omock-0.6.0/omock/man/omock-package.Rd | 2 omock-0.6.0/omock/man/reexports.Rd | 21 omock-0.6.0/omock/tests/testthat/test-changeCdmVersion.R |only omock-0.6.0/omock/tests/testthat/test-mockCdmFromTables.R | 111 ++++ omock-0.6.0/omock/tests/testthat/test-mockCdmReference.R | 7 omock-0.6.0/omock/tests/testthat/test-mockCohort.R | 17 omock-0.6.0/omock/tests/testthat/test-mockCondtitionOccurrence.R | 90 +++ omock-0.6.0/omock/tests/testthat/test-mockDatasets.R | 4 omock-0.6.0/omock/tests/testthat/test-mockDeath.R | 1 omock-0.6.0/omock/tests/testthat/test-mockDrugExposure.R | 29 + omock-0.6.0/omock/tests/testthat/test-mockMeasurement.R | 31 + omock-0.6.0/omock/tests/testthat/test-mockObservation.R | 28 + omock-0.6.0/omock/tests/testthat/test-mockObservationPeriod.R | 1 omock-0.6.0/omock/tests/testthat/test-mockPerson.R | 1 omock-0.6.0/omock/tests/testthat/test-mockProcedureOccurrence.R | 19 omock-0.6.0/omock/tests/testthat/test-mockVisitOccurrence.R |only omock-0.6.0/omock/tests/testthat/test-mockVocabularySet.R | 6 omock-0.6.0/omock/tests/testthat/test-mockVocabularyTables.R | 10 omock-0.6.0/omock/vignettes/a01_Creating_synthetic_clinical_tables.R |only omock-0.6.0/omock/vignettes/a01_Creating_synthetic_clinical_tables.html |only omock-0.6.0/omock/vignettes/a02_Creating_synthetic_cohorts.R |only omock-0.6.0/omock/vignettes/a02_Creating_synthetic_cohorts.html |only omock-0.6.0/omock/vignettes/a03_Creating_a_synthetic_vocabulary.R |only omock-0.6.0/omock/vignettes/a03_Creating_a_synthetic_vocabulary.html |only omock-0.6.0/omock/vignettes/a04_Building_a_bespoke_mock_cdm.R |only omock-0.6.0/omock/vignettes/a04_Building_a_bespoke_mock_cdm.html |only omock-0.6.0/omock/vignettes/mock_from_tables.Rmd |only omock-0.6.0/omock/vignettes/synthetic_clinical_tables.Rmd |only omock-0.6.0/omock/vignettes/synthetic_cohorts.Rmd |only omock-0.6.0/omock/vignettes/synthetic_datasets.Rmd |only omock-0.6.0/omock/vignettes/synthetic_vocabulary.Rmd |only 99 files changed, 1218 insertions(+), 636 deletions(-)
Title: Explicit Exploration Strategy for Evolutionary Algorithms
Description: Implements an explicit exploration strategy for evolutionary algorithms in order to have a more effective search in solving optimization problems. Along with this exploration search strategy, a set of four different Estimation of Distribution Algorithms (EDAs) are also implemented for solving optimization problems in continuous domains. The implemented explicit exploration strategy in this package is described in Salinas-Gutiérrez and Muñoz Zavala (2023) <doi:10.1016/j.asoc.2023.110230>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Pedro Abraham Montoya Calzada [aut, cph] ,
Angel Eduardo Munoz Zavala [aut, cph] ,
Alejandro Fausto Cortes Salinas [aut, cph],
Ilse Daniela Saldivar Olvera [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rsalinas@correo.uaa.mx>
Diff between EEEA versions 1.0.0 dated 2025-04-24 and 1.0.1 dated 2025-10-31
DESCRIPTION | 22 +++++++++++----------- MD5 | 20 ++++++++++---------- R/EDA.ecdf.R | 6 +++--- R/EDA.hist.R | 7 ++++--- R/EDA.norm.R | 6 +++--- R/EE.Hist.R | 1 + R/EE.ecdf.R | 2 +- R/EE.mnorm.R | 7 ++++++- R/EE.norm.R | 2 +- R/ExplicitExploration.R | 1 + build/partial.rdb |binary 11 files changed, 41 insertions(+), 33 deletions(-)
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data in Brazil.
Implements water quality indices including the Water Quality Index (WQI/IQA),
the Trophic State Index (TSI/IET) after Carlson (1977) <doi:10.4319/lo.1977.22.2.0361>
and Lamparelli (2004) <https://www.teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index (NSF WQI)
<doi:10.1007/s11157-023-09650-7>. The package also checks
compliance with Brazilian standard CONAMA Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
and generates reproducible reports for routine monitoring workflows.
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.7.2 dated 2025-10-22 and 0.7.3 dated 2025-10-31
DESCRIPTION | 6 +- MD5 | 19 ++++----- NEWS.md | 7 +++ R/iet.R | 54 +++++++++++++++++++++---- R/iet_lamparelli.R | 97 ++++++++++++++++++++++------------------------ R/iqa.R | 34 ++++++++++------ R/utils_sanitize.R |only README.md | 16 +++++++ man/iet_carlson.Rd | 27 +++++++++--- man/iet_lamparelli.Rd | 64 ++++++++---------------------- tests/testthat/test-iqa.R | 9 ++++ 11 files changed, 200 insertions(+), 133 deletions(-)
Title: Optimal Design and Statistical Power for Experimental Studies
Investigating Main, Mediation, and Moderation Effects
Description: Calculate the optimal sample size allocation that
uses the minimum resources to achieve targeted statistical
power in experiments.
Perform power analyses with and without accommodating
costs and budget. The designs cover single-level
and multilevel experiments detecting main, mediation,
and moderation effects (and some combinations).
The references for the proposed methods include:
(1) Shen, Z., & Kelcey, B. (2020).
Optimal sample allocation under unequal costs in
cluster-randomized trials.
Journal of Educational and Behavioral Statistics, 45(4): 446-474.
<doi:10.3102/1076998620912418>.
(2) Shen, Z., & Kelcey, B. (2022b). Optimal sample allocation for
three-level multisite cluster-randomized trials.
Journal of Research on Educational Effectiveness, 15 (1), 130-150.
<doi:10.1080/19345747.2021.1953200>.
(3) Shen, Z., & Kelcey, B. (2022a). Optimal sample allocation in
multisite randomized trials. The Journal of Experimental Education,
90(3), 693-711. <doi:10.108 [...truncated...]
Author: Zuchao Shen [aut, cre] ,
Benjamin Kelcey [aut]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between odr versions 1.6.3 dated 2025-08-20 and 1.7.3 dated 2025-10-31
DESCRIPTION | 8 - MD5 | 20 ++- NAMESPACE | 2 R/od.2m.111m.R |only R/plot.power.R | 256 +++++++++++++++++++++++++++++++++++++++++++- R/power.2m.111m.R |only inst/doc/odr.R | 16 +- inst/doc/odr.Rmd | 35 ++++-- inst/doc/odr.html | 294 ++++++++++++++++++++++++++------------------------- man/od.2m.111m.Rd |only man/plot.power.Rd | 20 +++ man/power.2m.111m.Rd |only vignettes/odr.Rmd | 35 ++++-- 13 files changed, 504 insertions(+), 182 deletions(-)
Title: Interactive Reliability Probability Plots
Description: Build interactive Reliability Probability Plots with 'plotly' by Carson Sievert (2020) <https://plotly.com/r/>, an interactive web-based graphing library.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaPlotR versions 0.4 dated 2025-10-15 and 0.4.1 dated 2025-10-31
DESCRIPTION | 8 ++-- MD5 | 22 +++++------ NEWS.md | 7 +++ R/plotly_contour.R | 3 - R/plotly_duane.R | 38 ++++++++++++++------ R/plotly_rga.R | 13 +++--- R/plotly_wblr.R | 85 ++++----------------------------------------- README.md | 15 +++---- man/ReliaPlotR-package.Rd | 2 - man/plotly_duane.Rd | 3 + man/plotly_wblr.Rd | 3 - tests/testthat/test-wblr.R | 10 +---- 12 files changed, 79 insertions(+), 130 deletions(-)
Title: Predictive Approaches in Psychology
Description: Recent years have seen an increased interest in novel methods
for analyzing quantitative data from experimental psychology. Currently, however, they lack an
established and accessible software framework. Many existing implementations provide no guidelines,
consisting of small code snippets, or sets of packages. In addition, the use of existing packages
often requires advanced programming experience. 'PredPsych' is a user-friendly toolbox based on
machine learning predictive algorithms. It comprises of multiple functionalities for multivariate
analyses of quantitative behavioral data based on machine learning models.
Author: Atesh Koul [aut, cre]
Maintainer: Atesh Koul <atesh.koul@gmail.com>
Diff between PredPsych versions 0.4 dated 2019-07-23 and 0.5 dated 2025-10-31
DESCRIPTION | 17 +- MD5 | 36 ++--- NAMESPACE | 51 +++---- R/ClassPerm.R | 5 R/ModelCluster.R | 2 R/PredPsych-package.r | 3 R/classifyFun.R | 13 + R/predictNewData.R | 2 man/ClassPerm.Rd | 235 +++++++++++++++++---------------- man/DTModel.Rd | 285 +++++++++++++++++++++-------------------- man/DimensionRed.Rd | 117 ++++++++-------- man/KinData.Rd | 110 ++++++++------- man/LinearDA.Rd | 249 ++++++++++++++++++----------------- man/ModelCluster.Rd | 106 +++++++-------- man/PredPsych.Rd | 46 +++--- man/classifyFun.Rd | 281 +++++++++++++++++++++------------------- man/fscore.Rd | 102 +++++++------- man/overallConfusionMetrics.Rd | 176 ++++++++++++------------- man/predictNewData.Rd | 60 ++++---- 19 files changed, 983 insertions(+), 913 deletions(-)
Title: Dynamic Models for Confidence and Response Time Distributions
Description: Provides density functions for the joint distribution of
choice, response time and confidence for discrete confidence judgments
as well as functions for parameter fitting, prediction and simulation
for various dynamical models of decision confidence. All models are
explained in detail by Hellmann et al. (2023;
Preprint available at <https://osf.io/9jfqr/>, published version: <doi:10.1037/rev0000411>). Implemented models are the dynaViTE model,
dynWEV model, the 2DSD model (Pleskac & Busemeyer, 2010, <doi:10.1037/a0019737>),
and various race models. C++ code for dynWEV and 2DSD is based on the
'rtdists' package by Henrik Singmann.
Author: Sebastian Hellmann [aut, cre] ,
Manuel Rausch [aut, fnd]
Maintainer: Sebastian Hellmann <sebastian.hellmann@tum.de>
Diff between dynConfiR versions 1.1.0 dated 2025-09-19 and 1.1.1 dated 2025-10-31
DESCRIPTION | 6 - MD5 | 64 ++++++++++---------- NEWS.md | 7 +- R/QuantitativeAnalysis.R | 33 ++++++++-- R/dDDConf.R | 18 ++--- R/dMTLNR.R | 18 ++--- R/ddynaViTE.R | 2 R/fitRTConf.R | 4 - R/fitRTConfModels.R | 4 - R/int_find_start_thetas_MTLNR_simulation.R | 2 R/int_find_start_thetas_dynWEV_simulation.R | 6 + R/int_fitting_2DSD.R | 21 +++--- R/int_fitting_DDConf.R | 4 - R/int_fitting_MTLNR.R | 87 +++++++++++----------------- R/int_fitting_RMs_simulate_start_thetas.R | 12 +-- R/int_fitting_dynWEV.R | 12 +-- R/likelihood_MTLNR.R | 41 ++++++++----- R/likelihood_RM.R | 2 R/likelihoods_WEV.R | 2 R/predictratingdist_MTLNR.R | 57 ++++++++++-------- R/simulateMTLNR.R | 48 +++++++++------ R/simulateRM.R | 2 R/simulateWEV.R | 2 inst/doc/dynConfiR.html | 2 man/LogLikMTLNR.Rd | 28 +++++---- man/QuantModelComparison.Rd | 3 man/dDDConf.Rd | 18 ++--- man/dynaViTE.Rd | 2 man/fitRTConf.Rd | 2 man/predictMTLNR.Rd | 34 ++++++---- man/simulateMTLNR.Rd | 37 ++++++----- man/simulateRM.Rd | 2 man/simulateWEV.Rd | 2 33 files changed, 322 insertions(+), 262 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.5.0 dated 2025-07-30 and 0.6.0 dated 2025-10-31
CohortConstructor-0.5.0/CohortConstructor/man/padObservationDoc.Rd |only CohortConstructor-0.6.0/CohortConstructor/DESCRIPTION | 28 CohortConstructor-0.6.0/CohortConstructor/MD5 | 316 +- CohortConstructor-0.6.0/CohortConstructor/NAMESPACE | 3 CohortConstructor-0.6.0/CohortConstructor/R/CohortConstructor-package.R | 1 CohortConstructor-0.6.0/CohortConstructor/R/addIndex.R | 24 CohortConstructor-0.6.0/CohortConstructor/R/benchmark.R | 63 CohortConstructor-0.6.0/CohortConstructor/R/collapseCohorts.R | 2 CohortConstructor-0.6.0/CohortConstructor/R/conceptCohort.R | 301 +- CohortConstructor-0.6.0/CohortConstructor/R/copyCohorts.R | 12 CohortConstructor-0.6.0/CohortConstructor/R/deathCohort.R | 10 CohortConstructor-0.6.0/CohortConstructor/R/demographicsCohort.R | 9 CohortConstructor-0.6.0/CohortConstructor/R/documentationHelper.R | 34 CohortConstructor-0.6.0/CohortConstructor/R/entryAtColumnDate.R | 59 CohortConstructor-0.6.0/CohortConstructor/R/exitAtColumnDate.R | 117 CohortConstructor-0.6.0/CohortConstructor/R/exitAtDate.R | 18 CohortConstructor-0.6.0/CohortConstructor/R/intersectCohorts.R | 53 CohortConstructor-0.6.0/CohortConstructor/R/matchCohorts.R | 4 CohortConstructor-0.6.0/CohortConstructor/R/measurementCohort.R | 376 +-- CohortConstructor-0.6.0/CohortConstructor/R/mockCohortConstructor.R | 123 - CohortConstructor-0.6.0/CohortConstructor/R/padCohortDate.R | 82 CohortConstructor-0.6.0/CohortConstructor/R/renameCohort.R | 31 CohortConstructor-0.6.0/CohortConstructor/R/requireCohortIntersect.R | 191 + CohortConstructor-0.6.0/CohortConstructor/R/requireConceptIntersect.R | 57 CohortConstructor-0.6.0/CohortConstructor/R/requireDateRange.R | 19 CohortConstructor-0.6.0/CohortConstructor/R/requireDemographics.R | 61 CohortConstructor-0.6.0/CohortConstructor/R/requireDuration.R |only CohortConstructor-0.6.0/CohortConstructor/R/requireIsEntry.R | 30 CohortConstructor-0.6.0/CohortConstructor/R/requireMinCohortCount.R | 7 CohortConstructor-0.6.0/CohortConstructor/R/requireTableIntersect.R | 14 CohortConstructor-0.6.0/CohortConstructor/R/sampleCohorts.R | 5 CohortConstructor-0.6.0/CohortConstructor/R/stratifyCohorts.R | 12 CohortConstructor-0.6.0/CohortConstructor/R/subsetCohorts.R | 15 CohortConstructor-0.6.0/CohortConstructor/R/sysdata.rda |binary CohortConstructor-0.6.0/CohortConstructor/R/test-helper.R |only CohortConstructor-0.6.0/CohortConstructor/R/trimDemographics.R | 68 CohortConstructor-0.6.0/CohortConstructor/R/unionCohorts.R | 32 CohortConstructor-0.6.0/CohortConstructor/R/utilities.R | 18 CohortConstructor-0.6.0/CohortConstructor/R/validateFunctions.R | 91 CohortConstructor-0.6.0/CohortConstructor/R/yearCohorts.R | 13 CohortConstructor-0.6.0/CohortConstructor/README.md | 64 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a01_building_base_cohorts.R | 95 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a01_building_base_cohorts.Rmd | 104 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a01_building_base_cohorts.html | 298 +- CohortConstructor-0.6.0/CohortConstructor/inst/doc/a02_cohort_table_requirements.R | 59 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a02_cohort_table_requirements.Rmd | 78 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a02_cohort_table_requirements.html | 684 +++++ CohortConstructor-0.6.0/CohortConstructor/inst/doc/a03_require_demographics.R | 22 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a03_require_demographics.Rmd | 23 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a03_require_demographics.html | 75 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a04_require_intersections.R | 79 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a04_require_intersections.Rmd | 88 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a04_require_intersections.html | 118 - CohortConstructor-0.6.0/CohortConstructor/inst/doc/a05_update_cohort_start_end.R | 22 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a05_update_cohort_start_end.Rmd | 26 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a05_update_cohort_start_end.html | 172 - CohortConstructor-0.6.0/CohortConstructor/inst/doc/a06_concatanate_cohorts.R | 30 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a06_concatanate_cohorts.Rmd | 33 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a06_concatanate_cohorts.html | 15 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a07_filter_cohorts.R | 40 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a07_filter_cohorts.Rmd | 43 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a07_filter_cohorts.html | 15 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a08_split_cohorts.R | 28 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a08_split_cohorts.Rmd | 31 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a08_split_cohorts.html | 43 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a09_combine_cohorts.R | 38 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a09_combine_cohorts.Rmd | 40 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a09_combine_cohorts.html | 24 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a10_match_cohorts.R | 16 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a10_match_cohorts.Rmd | 18 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a10_match_cohorts.html | 20 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a11_benchmark.R | 28 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a11_benchmark.Rmd | 30 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a11_benchmark.html | 11 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a12_behind_the_scenes.R | 28 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a12_behind_the_scenes.Rmd | 30 CohortConstructor-0.6.0/CohortConstructor/inst/doc/a12_behind_the_scenes.html | 20 CohortConstructor-0.6.0/CohortConstructor/man/CohortConstructor-package.Rd | 2 CohortConstructor-0.6.0/CohortConstructor/man/baseCohortDoc.Rd |only CohortConstructor-0.6.0/CohortConstructor/man/conceptCohort.Rd | 42 CohortConstructor-0.6.0/CohortConstructor/man/copyCohorts.Rd | 11 CohortConstructor-0.6.0/CohortConstructor/man/deathCohort.Rd | 5 CohortConstructor-0.6.0/CohortConstructor/man/demographicsCohort.Rd | 12 CohortConstructor-0.6.0/CohortConstructor/man/entryAtFirstDate.Rd | 29 CohortConstructor-0.6.0/CohortConstructor/man/entryAtLastDate.Rd | 30 CohortConstructor-0.6.0/CohortConstructor/man/exitAtDeath.Rd | 2 CohortConstructor-0.6.0/CohortConstructor/man/exitAtFirstDate.Rd | 24 CohortConstructor-0.6.0/CohortConstructor/man/exitAtLastDate.Rd | 24 CohortConstructor-0.6.0/CohortConstructor/man/exitAtObservationEnd.Rd | 13 CohortConstructor-0.6.0/CohortConstructor/man/intersectCohorts.Rd | 11 CohortConstructor-0.6.0/CohortConstructor/man/matchCohorts.Rd | 4 CohortConstructor-0.6.0/CohortConstructor/man/measurementCohort.Rd | 186 - CohortConstructor-0.6.0/CohortConstructor/man/mockCohortConstructor.Rd | 46 CohortConstructor-0.6.0/CohortConstructor/man/padCohortDate.Rd | 11 CohortConstructor-0.6.0/CohortConstructor/man/padCohortEnd.Rd | 11 CohortConstructor-0.6.0/CohortConstructor/man/padCohortStart.Rd | 11 CohortConstructor-0.6.0/CohortConstructor/man/renameCohort.Rd | 20 CohortConstructor-0.6.0/CohortConstructor/man/requireAge.Rd | 12 CohortConstructor-0.6.0/CohortConstructor/man/requireCohortIntersect.Rd | 27 CohortConstructor-0.6.0/CohortConstructor/man/requireConceptIntersect.Rd | 17 CohortConstructor-0.6.0/CohortConstructor/man/requireDemographics.Rd | 15 CohortConstructor-0.6.0/CohortConstructor/man/requireDuration.Rd |only CohortConstructor-0.6.0/CohortConstructor/man/requireFullContributionDoc.Rd |only CohortConstructor-0.6.0/CohortConstructor/man/requireFutureObservation.Rd | 12 CohortConstructor-0.6.0/CohortConstructor/man/requireInDateRange.Rd | 14 CohortConstructor-0.6.0/CohortConstructor/man/requireIntersectDoc.Rd | 2 CohortConstructor-0.6.0/CohortConstructor/man/requireIsEntry.Rd | 17 CohortConstructor-0.6.0/CohortConstructor/man/requireIsFirstEntry.Rd | 17 CohortConstructor-0.6.0/CohortConstructor/man/requireIsLastEntry.Rd | 16 CohortConstructor-0.6.0/CohortConstructor/man/requireMinCohortCount.Rd | 5 CohortConstructor-0.6.0/CohortConstructor/man/requirePriorObservation.Rd | 12 CohortConstructor-0.6.0/CohortConstructor/man/requireSex.Rd | 12 CohortConstructor-0.6.0/CohortConstructor/man/requireTableIntersect.Rd | 17 CohortConstructor-0.6.0/CohortConstructor/man/sampleCohorts.Rd | 5 CohortConstructor-0.6.0/CohortConstructor/man/stratifyCohorts.Rd | 13 CohortConstructor-0.6.0/CohortConstructor/man/subsetCohorts.Rd | 22 CohortConstructor-0.6.0/CohortConstructor/man/trimDemographics.Rd | 18 CohortConstructor-0.6.0/CohortConstructor/man/trimDuration.Rd |only CohortConstructor-0.6.0/CohortConstructor/man/trimToDateRange.Rd | 2 CohortConstructor-0.6.0/CohortConstructor/man/unionCohorts.Rd | 17 CohortConstructor-0.6.0/CohortConstructor/man/yearCohorts.Rd | 7 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/setup.R | 103 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-addIndex.R | 107 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-benchmark.R | 23 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-collapseCohorts.R | 294 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-conceptCohort.R | 1178 +++------- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-copyCohorts.R | 29 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-deathCohort.R | 252 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-demographicsCohort.R | 109 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-entryAtColumnDate.R | 141 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-exitAtColumnDate.R | 249 -- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-exitAtDate.R | 179 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-intersectCohorts.R | 664 ++--- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-matchCohorts.R | 231 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-measurementCohort.R | 799 ++---- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-padCohortDate.R | 190 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-renameCohort.R | 73 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireCohortIntersect.R | 540 ++-- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireConceptIntersect.R | 344 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireDateRange.R | 244 -- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireDemographics.R | 316 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireDuration.R |only CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireIsEntry.R | 338 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireMinCohortCount.R | 70 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-requireTableIntersect.R | 263 +- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-sampleCohorts.R | 133 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-stratifyCohorts.R | 106 CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-subsetCohorts.R | 143 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-trimDemographics.R | 118 - CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-unionCohorts.R | 536 +--- CohortConstructor-0.6.0/CohortConstructor/tests/testthat/test-yearCohorts.R | 105 CohortConstructor-0.6.0/CohortConstructor/vignettes/a01_building_base_cohorts.Rmd | 104 CohortConstructor-0.6.0/CohortConstructor/vignettes/a02_cohort_table_requirements.Rmd | 78 CohortConstructor-0.6.0/CohortConstructor/vignettes/a03_require_demographics.Rmd | 23 CohortConstructor-0.6.0/CohortConstructor/vignettes/a04_require_intersections.Rmd | 88 CohortConstructor-0.6.0/CohortConstructor/vignettes/a05_update_cohort_start_end.Rmd | 26 CohortConstructor-0.6.0/CohortConstructor/vignettes/a06_concatanate_cohorts.Rmd | 33 CohortConstructor-0.6.0/CohortConstructor/vignettes/a07_filter_cohorts.Rmd | 43 CohortConstructor-0.6.0/CohortConstructor/vignettes/a08_split_cohorts.Rmd | 31 CohortConstructor-0.6.0/CohortConstructor/vignettes/a09_combine_cohorts.Rmd | 40 CohortConstructor-0.6.0/CohortConstructor/vignettes/a10_match_cohorts.Rmd | 18 CohortConstructor-0.6.0/CohortConstructor/vignettes/a11_benchmark.Rmd | 30 CohortConstructor-0.6.0/CohortConstructor/vignettes/a12_behind_the_scenes.Rmd | 30 163 files changed, 6797 insertions(+), 7284 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Bayesian Cure Rate Modeling for Time-to-Event Data
Description: A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2024) <doi:10.1007/s11749-024-00942-w> and Papastamoulis and Milienos (2024b) <doi:10.48550/arXiv.2409.10221>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of distributions. In both cases, user-defined families of distributions are allowed under some specific requirements. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of th [...truncated...]
Author: Panagiotis Papastamoulis [aut, cre] ,
Fotios Milienos [aut]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between bayesCureRateModel versions 1.4 dated 2025-06-18 and 1.5 dated 2025-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bayesian_cure_rate_model.R | 2 +- build/partial.rdb |binary 4 files changed, 8 insertions(+), 8 deletions(-)
More information about bayesCureRateModel at CRAN
Permanent link
Title: Extra Appenders for 'lgr'
Description: Additional appenders for the logging package 'lgr' that
support logging to 'Elasticsearch', 'Dynatrace', 'AWSCloudWatchLog',
databases, 'syslog', email- and push notifications, and more.
Author: Stefan Fleck [aut, cre] ,
Jimmy Briggs [ctb, rev]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgrExtra versions 0.2.1 dated 2025-08-25 and 0.2.2 dated 2025-10-31
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 1 + NEWS.md | 5 +++++ R/DynatraceLayout.R | 11 +++++++++++ man/as_unix_epoch_ms.Rd |only tests/testthat/test_AppenderDynatrace.R | 4 ++-- tests/testthat/test_DynatraceLayout.R | 2 +- 8 files changed, 30 insertions(+), 12 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb],
PoYen Chuang [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.11 dated 2025-10-16 and 1.0.12 dated 2025-10-31
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 5 ++++- R/CommonFun.R | 25 ++++++++++++++++++++++--- R/FD_Fun.R | 5 +++++ R/MainFun.r | 36 +++++++++++++++++++++++++++--------- R/PD_Fun.R | 4 ++++ inst/doc/Introduction.pdf |binary 8 files changed, 72 insertions(+), 23 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) with the goal of maximizing between-group similarity or within-group heterogeneity. The anticlustering approach thereby reverses the logic of cluster analysis that strives for high within-group homogeneity and clear separation between groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The main function anticlustering() gives access to optimal and heuristic anticlustering methods described in Papenberg and Klau Klau (2021; <doi:10.1037/met0000301>), Brusco et al. (2020; <doi:10.1111/bmsp.12186>), Papenberg (2024; <doi:10.1111/bmsp.12315>), Papenberg, Wang, et al. (2025; <doi:10.1016/j.crmeth.2025.101137>), Papenberg, Breuer, et al. (2025; <doi:10.1017/psy.2025.10052>), and Yang et [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.10-1 dated 2025-03-26 and 0.8.12 dated 2025-10-31
DESCRIPTION | 15 MD5 | 81 - R/Optimal_Dispersion.R | 14 R/bicriterion_iterated_local_search_call.R | 26 R/brunel2025.R |only R/cannot_link_anticlustering.R | 22 R/categories_to_binary.R | 7 R/exact-anticlustering.R | 9 R/input-validation.R | 72 R/nn-centroid-clustering.R | 8 R/objective-kplus.R | 29 R/optimal_anticlustering.R | 30 R/wrapper-anticlustering.R | 183 +- R/wrapper-clustering.R | 9 R/wrapper-k-plus-anticlustering.R | 4 build/vignette.rds |binary data/brunel2025.rda |only inst/data_raw |only inst/doc/Anticlustering_in_2025.R |only inst/doc/Anticlustering_in_2025.Rmd |only inst/doc/Anticlustering_in_2025.html |only inst/doc/Best_practices.html | 106 - inst/doc/Categorical_vars.R | 67 inst/doc/Categorical_vars.Rmd | 111 - inst/doc/Categorical_vars.html | 618 ++------ inst/doc/Speeding_up_anticlustering.html | 772 +++------- inst/doc/stimulus-selection.html | 694 +++----- inst/tinytest/test-2pml.R | 28 inst/tinytest/test-NAs.R |only inst/tinytest/test-cannot-link.R | 13 inst/tinytest/test-errors-input.R | 14 inst/tinytest/test-factor-input.R |only inst/tinytest/test-high-level-functions.R | 3 inst/tinytest/test-ilp-solvers.R | 7 inst/tinytest/test-kplus-criterion.R | 21 inst/tinytest/test-must-link.R | 29 inst/tinytest/test-three-phase-search-dynamic-population-size.R | 10 man/anticlustering.Rd | 54 man/bicriterion_anticlustering.Rd | 24 man/brunel2025.Rd |only man/categories_to_binary.Rd | 5 man/optimal_anticlustering.Rd | 29 man/optimal_dispersion.Rd | 13 vignettes/Anticlustering_in_2025.Rmd |only vignettes/Categorical_vars.Rmd | 111 - 45 files changed, 1396 insertions(+), 1842 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.6.3 dated 2025-10-06 and 0.7.0 dated 2025-10-31
DESCRIPTION | 6 - MD5 | 64 ++++++++-------- NAMESPACE | 2 NEWS.md | 12 +++ R/MaestroPipeline.R | 73 ++++++++++++++++-- R/MaestroPipelineList.R | 5 + R/build_schedule_entry.R | 6 + R/invoke.R | 12 ++- R/roxy_maestro.R | 24 ++++++ R/run_schedule.R | 2 R/utils.R | 13 +++ build/vignette.rds |binary inst/doc/maestro-1-quick-start.html | 13 +-- inst/doc/maestro-2-motivation-concepts.html | 40 +--------- inst/doc/maestro-3-advanced-scheduling.html | 54 +++---------- inst/doc/maestro-4-directed-acyclic-graphs.R | 10 +- inst/doc/maestro-4-directed-acyclic-graphs.Rmd | 10 +- inst/doc/maestro-4-directed-acyclic-graphs.html | 84 ++++++++++----------- inst/doc/maestro-5-logging.html | 94 ++++++++---------------- inst/doc/maestro-6-deployment.html | 40 +--------- inst/doc/maestro-7-tag-reference.html | 50 ++++-------- inst/doc/maestro-7-tag-reference.qmd | 21 +++++ inst/doc/maestro-8-conditionals.R |only inst/doc/maestro-8-conditionals.Rmd |only inst/doc/maestro-8-conditionals.html |only man/MaestroPipeline.Rd | 5 + man/invoke.Rd | 13 +++ man/run_schedule.Rd | 2 tests/testthat/_snaps/conditionals.md |only tests/testthat/test-conditionals.R |only tests/testthat/test-invoke.R | 3 tests/testthat/test-roclets.R | 52 +++++++++++++ tests/testthat/test-run_schedule.R | 3 vignettes/maestro-4-directed-acyclic-graphs.Rmd | 10 +- vignettes/maestro-7-tag-reference.qmd | 21 +++++ vignettes/maestro-8-conditionals.Rmd |only 36 files changed, 426 insertions(+), 318 deletions(-)
Title: Generalized Measure of Correlation (GMC)
Description: Provides tools to compute the Generalized Measure of Correlation (GMC),
a dependence measure accounting for nonlinearity and asymmetry in the relationship
between variables. Based on the method proposed by Zheng, Shi, and Zhang (2012) <doi:10.1080/01621459.2012.710509>.
Author: Xuejing Ding [aut, cre],
Zhengjun Zhang [aut]
Maintainer: Xuejing Ding <dingxuejing24@mails.ucas.ac.cn>
Diff between GMC versions 0.1.1 dated 2025-10-30 and 0.1.2 dated 2025-10-31
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between mclust versions 6.1.1 dated 2024-04-29 and 6.1.2 dated 2025-10-31
mclust-6.1.1/mclust/src/dmvnorm.f |only mclust-6.1.1/mclust/src/logsumexp.f |only mclust-6.1.1/mclust/src/mclustaddson.f |only mclust-6.1.2/mclust/DESCRIPTION | 23 +- mclust-6.1.2/mclust/MD5 | 49 ++-- mclust-6.1.2/mclust/NAMESPACE | 2 mclust-6.1.2/mclust/NEWS.md | 8 mclust-6.1.2/mclust/R/bootstrap.R | 131 ++++++++++- mclust-6.1.2/mclust/R/densityMclust.R | 16 + mclust-6.1.2/mclust/R/graphics.R | 3 mclust-6.1.2/mclust/R/mbahc.R | 50 ++-- mclust-6.1.2/mclust/R/mclust.R | 169 +++++++------- mclust-6.1.2/mclust/R/mclustda.R | 65 +++-- mclust-6.1.2/mclust/R/mclustssc.R | 40 ++- mclust-6.1.2/mclust/R/util.R | 45 +++ mclust-6.1.2/mclust/R/weights.R | 6 mclust-6.1.2/mclust/build/partial.rdb |binary mclust-6.1.2/mclust/build/vignette.rds |binary mclust-6.1.2/mclust/inst/doc/mclust.R | 6 mclust-6.1.2/mclust/inst/doc/mclust.Rmd | 8 mclust-6.1.2/mclust/inst/doc/mclust.html | 332 ++++++++++++++--------------- mclust-6.1.2/mclust/man/em.Rd | 2 mclust-6.1.2/mclust/man/mclust-internal.Rd | 1 mclust-6.1.2/mclust/man/simE.Rd | 2 mclust-6.1.2/mclust/src/init.c | 2 mclust-6.1.2/mclust/src/mclust2.f |only mclust-6.1.2/mclust/src/util.f |only mclust-6.1.2/mclust/vignettes/mclust.Rmd | 8 28 files changed, 609 insertions(+), 359 deletions(-)
Title: Solving Imbalanced Regression Tasks
Description: Imbalanced domain learning has almost exclusively focused on solving
classification tasks, where the objective is to predict cases labelled with a
rare class accurately. Such a well-defined approach for regression tasks lacked
due to two main factors. First, standard regression tasks assume that each value
is equally important to the user. Second, standard evaluation metrics focus on
assessing the performance of the model on the most common cases. This package
contains methods to tackle imbalanced domain learning problems in regression
tasks, where the objective is to predict extreme (rare) values.
The methods contained in this package are: 1) an automatic and non-parametric
method to obtain such relevance functions; 2) visualisation tools; 3) suite of
evaluation measures for optimisation/validation processes; 4) the squared-error
relevance area measure, an evaluation metric tailored for imbalanced regression tasks.
More information can be found in Ribeiro and Moniz (2020) <doi:10.1 [...truncated...]
Author: Nuno Moniz [aut],
Rita P. Ribeiro [cre, aut],
Miguel Margarido [ctb]
Maintainer: Rita P. Ribeiro <rpribeiro@fc.up.pt>
Diff between IRon versions 0.1.4 dated 2023-01-20 and 0.1.5 dated 2025-10-31
DESCRIPTION | 24 +++++++------- MD5 | 16 +++++---- NAMESPACE | 1 R/data.R | 2 - R/nonstdMetrics.R | 88 +++++++++++++++++++++++++++++++++++++++++++--------- man/NO2Emissions.Rd | 2 - man/ser.Rd | 3 - man/sera.Rd | 3 - tests |only 9 files changed, 99 insertions(+), 40 deletions(-)
Title: Indicators for the Analysis of Dispersion of Datasets with
Batched and Ordered Samples
Description: Provides methods for analyzing the dispersion of tabular datasets
with batched and ordered samples. Based on convex hull or integrated covariance
Mahalanobis, several indicators are implemented for inter and intra batch dispersion
analysis. It is designed to facilitate robust statistical assessment of data
variability, supporting applications in exploratory data analysis and quality
control, for such datasets as the one found in metabololomics studies.
For more details see Salanon (2024) <doi:10.1016/j.chemolab.2024.105148> and
Salanon (2025) <doi:10.1101/2025.08.01.668073>.
Author: Brice Mulot [aut],
Elfried Salanon [ctb],
Etienne Jules [aut, cre],
INRAE [cph]
Maintainer: Etienne Jules <etienne.jules@inrae.fr>
This is a re-admission after prior archival of version 0.1.1 dated 2025-10-16
Diff between dispersionIndicators versions 0.1.1 dated 2025-10-16 and 0.1.4 dated 2025-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 17 ++++++++++++++++- tests/testthat/test-convex_function.R | 32 +++++++++++++++++++++++++------- 4 files changed, 48 insertions(+), 15 deletions(-)
More information about dispersionIndicators at CRAN
Permanent link
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between robmixglm versions 1.2-4 dated 2024-09-27 and 1.2-5 dated 2025-10-31
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/RcppExports.R | 38 +++++++++++++++++++------------------- R/binomial.fit.robmixglm.R | 4 +--- R/fitnegbin.R | 2 +- R/gamma.fit.robmixglm.R | 3 +-- R/gaussian.fit.robmixglm.R | 3 +-- R/nbinom.fit.robmixglm.R | 3 ++- R/poisson.fit.robmixglm.R | 9 ++++++--- R/truncpoisson.fit.robmixglm.R | 4 +--- build/vignette.rds |binary inst/NEWS | 4 ++++ 12 files changed, 51 insertions(+), 49 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.7-0 dated 2025-10-19 and 1.7-1 dated 2025-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/R.R | 7 +++---- inst/NEWS.Rd | 9 +++++++++ 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Deep Learning with 'mlr3'
Description: Deep Learning library that extends the mlr3 framework by building
upon the 'torch' package. It allows to conveniently build, train,
and evaluate deep learning models without having to worry about low level
details. Custom architectures can be created using the graph language
defined in 'mlr3pipelines'.
Author: Sebastian Fischer [cre, aut] ,
Bernd Bischl [ctb] ,
Lukas Burk [ctb] ,
Martin Binder [aut],
Florian Pfisterer [ctb] ,
Carson Zhang [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3torch versions 0.3.1 dated 2025-08-26 and 0.3.2 dated 2025-10-31
DESCRIPTION | 14 - MD5 | 234 ++++++++++++++--------------- NEWS.md | 9 + R/PipeOpTorchActivation.R | 4 R/PipeOpTorchConv.R | 4 R/PipeOpTorchConvTranspose.R | 4 R/PipeOpTorchMaxPool.R | 2 R/TorchOptimizer.R | 6 R/cache.R | 2 R/learner_torch_methods.R | 3 R/zzz.R | 1 man/DataDescriptor.Rd | 2 man/TorchCallback.Rd | 2 man/TorchIngressToken.Rd | 2 man/TorchLoss.Rd | 2 man/TorchOptimizer.Rd | 2 man/as_data_descriptor.Rd | 2 man/as_lazy_tensor.Rd | 2 man/cross_entropy.Rd | 2 man/lazy_shape.Rd | 2 man/lazy_tensor.Rd | 2 man/materialize.Rd | 2 man/mlr3torch_callbacks.Rd | 2 man/mlr3torch_losses.Rd | 2 man/mlr3torch_optimizers.Rd | 2 man/mlr_backends_lazy.Rd | 2 man/mlr_callback_set.checkpoint.Rd | 2 man/mlr_callback_set.history.Rd | 2 man/mlr_callback_set.progress.Rd | 2 man/mlr_callback_set.unfreeze.Rd | 2 man/mlr_learners.ft_transformer.Rd | 2 man/mlr_learners.mlp.Rd | 2 man/mlr_learners.module.Rd | 2 man/mlr_learners.tab_resnet.Rd | 2 man/mlr_learners.torch_featureless.Rd | 2 man/mlr_learners_torch_model.Rd | 2 man/mlr_pipeops_module.Rd | 2 man/mlr_pipeops_nn_adaptive_avg_pool1d.Rd | 2 man/mlr_pipeops_nn_adaptive_avg_pool2d.Rd | 2 man/mlr_pipeops_nn_adaptive_avg_pool3d.Rd | 2 man/mlr_pipeops_nn_avg_pool1d.Rd | 2 man/mlr_pipeops_nn_avg_pool2d.Rd | 2 man/mlr_pipeops_nn_avg_pool3d.Rd | 2 man/mlr_pipeops_nn_batch_norm1d.Rd | 2 man/mlr_pipeops_nn_batch_norm2d.Rd | 2 man/mlr_pipeops_nn_batch_norm3d.Rd | 2 man/mlr_pipeops_nn_block.Rd | 2 man/mlr_pipeops_nn_celu.Rd | 2 man/mlr_pipeops_nn_conv1d.Rd | 6 man/mlr_pipeops_nn_conv2d.Rd | 6 man/mlr_pipeops_nn_conv3d.Rd | 6 man/mlr_pipeops_nn_conv_transpose1d.Rd | 7 man/mlr_pipeops_nn_conv_transpose2d.Rd | 7 man/mlr_pipeops_nn_conv_transpose3d.Rd | 7 man/mlr_pipeops_nn_dropout.Rd | 2 man/mlr_pipeops_nn_elu.Rd | 2 man/mlr_pipeops_nn_flatten.Rd | 2 man/mlr_pipeops_nn_fn.Rd | 2 man/mlr_pipeops_nn_ft_cls.Rd | 2 man/mlr_pipeops_nn_ft_transformer_block.Rd | 2 man/mlr_pipeops_nn_geglu.Rd | 2 man/mlr_pipeops_nn_gelu.Rd | 2 man/mlr_pipeops_nn_glu.Rd | 2 man/mlr_pipeops_nn_hardshrink.Rd | 2 man/mlr_pipeops_nn_hardsigmoid.Rd | 2 man/mlr_pipeops_nn_hardtanh.Rd | 2 man/mlr_pipeops_nn_head.Rd | 2 man/mlr_pipeops_nn_identity.Rd | 2 man/mlr_pipeops_nn_layer_norm.Rd | 2 man/mlr_pipeops_nn_leaky_relu.Rd | 4 man/mlr_pipeops_nn_linear.Rd | 2 man/mlr_pipeops_nn_log_sigmoid.Rd | 2 man/mlr_pipeops_nn_max_pool1d.Rd | 4 man/mlr_pipeops_nn_max_pool2d.Rd | 4 man/mlr_pipeops_nn_max_pool3d.Rd | 4 man/mlr_pipeops_nn_merge_cat.Rd | 2 man/mlr_pipeops_nn_merge_prod.Rd | 2 man/mlr_pipeops_nn_merge_sum.Rd | 2 man/mlr_pipeops_nn_prelu.Rd | 2 man/mlr_pipeops_nn_reglu.Rd | 2 man/mlr_pipeops_nn_relu.Rd | 2 man/mlr_pipeops_nn_relu6.Rd | 2 man/mlr_pipeops_nn_reshape.Rd | 2 man/mlr_pipeops_nn_rrelu.Rd | 2 man/mlr_pipeops_nn_selu.Rd | 2 man/mlr_pipeops_nn_sigmoid.Rd | 2 man/mlr_pipeops_nn_softmax.Rd | 2 man/mlr_pipeops_nn_softplus.Rd | 2 man/mlr_pipeops_nn_softshrink.Rd | 2 man/mlr_pipeops_nn_softsign.Rd | 2 man/mlr_pipeops_nn_squeeze.Rd | 2 man/mlr_pipeops_nn_tanh.Rd | 2 man/mlr_pipeops_nn_tanhshrink.Rd | 2 man/mlr_pipeops_nn_threshold.Rd | 4 man/mlr_pipeops_nn_tokenizer_categ.Rd | 2 man/mlr_pipeops_nn_tokenizer_num.Rd | 2 man/mlr_pipeops_nn_unsqueeze.Rd | 2 man/mlr_pipeops_preproc_torch.Rd | 2 man/mlr_pipeops_torch.Rd | 2 man/mlr_pipeops_torch_callbacks.Rd | 2 man/mlr_pipeops_torch_ingress_categ.Rd | 2 man/mlr_pipeops_torch_ingress_ltnsr.Rd | 2 man/mlr_pipeops_torch_ingress_num.Rd | 2 man/mlr_pipeops_torch_loss.Rd | 2 man/mlr_pipeops_torch_model_classif.Rd | 2 man/mlr_pipeops_torch_model_regr.Rd | 2 man/mlr_pipeops_torch_optimizer.Rd | 2 man/mlr_tasks_lazy_iris.Rd | 2 man/nn_geglu.Rd | 2 man/nn_graph.Rd | 2 man/nn_reglu.Rd | 2 man/pipeop_preproc_torch.Rd | 2 man/t_clbk.Rd | 2 man/t_loss.Rd | 4 man/t_opt.Rd | 4 man/task_dataset.Rd | 2 man/torch_callback.Rd | 2 tests/testthat/test_CallbackSetTB.R | 3 118 files changed, 275 insertions(+), 264 deletions(-)
Title: Algorithms and Tools for Tabular Statistics and Hierarchical
Computations
Description: Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.8.2 dated 2025-09-19 and 1.8.4 dated 2025-10-31
DESCRIPTION | 8 ++--- MD5 | 13 +++++--- NAMESPACE | 2 + NEWS.md | 7 ++++ R/SSBtoolsData.R | 76 ++++++++++++++++++++++++++++++++++++++++++++++++ R/diff_groups.R |only man/SSBtoolsData.Rd | 10 ++++++ man/data_diff_groups.Rd |only man/diff_groups.Rd |only 9 files changed, 107 insertions(+), 9 deletions(-)
Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data published in Thrun, M.C. et al.: "Analyzing the Fine Structure of Distributions" (2020), PLoS ONE, <DOI:10.1371/journal.pone.0238835>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot and geom_violin plot of ggplot2. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for tw [...truncated...]
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [aut, rev],
Onno Hansen-Goos [ctr, ctb],
Quirin Stier [ctb, rev] ,
Hamza Tayyab [ctr, ctb],
Luca Brinkmann [ctr, ctb],
Dirk Eddelbuettel [ctb],
Winston Chang [ctb],
Craig Varrichio [ctb],
Alfred Ultsch [dtc, [...truncated...]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DataVisualizations versions 1.3.5 dated 2025-08-24 and 1.4.0 dated 2025-10-31
DataVisualizations-1.3.5/DataVisualizations/R/Choroplethmap.R |only DataVisualizations-1.3.5/DataVisualizations/data/ChoroplethPostalCodesAndAGS_Germany.rda |only DataVisualizations-1.3.5/DataVisualizations/man/ChoroplethPostalCodesAndAGS_Germany.Rd |only DataVisualizations-1.3.5/DataVisualizations/man/Choroplethmap.Rd |only DataVisualizations-1.3.5/DataVisualizations/src/c_quantile.cpp |only DataVisualizations-1.4.0/DataVisualizations/DESCRIPTION | 18 DataVisualizations-1.4.0/DataVisualizations/MD5 | 53 DataVisualizations-1.4.0/DataVisualizations/NAMESPACE | 175 DataVisualizations-1.4.0/DataVisualizations/NEWS |only DataVisualizations-1.4.0/DataVisualizations/R/MDplot.R | 1011 +- DataVisualizations-1.4.0/DataVisualizations/R/MDstrips.R |only DataVisualizations-1.4.0/DataVisualizations/R/Multiplot.R | 2 DataVisualizations-1.4.0/DataVisualizations/R/OpposingViolinBiclassPlot.R |only DataVisualizations-1.4.0/DataVisualizations/R/PDEstrip.R |only DataVisualizations-1.4.0/DataVisualizations/R/ParetoDensityEstimation.R | 22 DataVisualizations-1.4.0/DataVisualizations/R/ParetoRadius.R | 84 DataVisualizations-1.4.0/DataVisualizations/R/ParetoRadius_fast.R | 50 DataVisualizations-1.4.0/DataVisualizations/R/RcppExports.R | 58 DataVisualizations-1.4.0/DataVisualizations/R/order_features_hlp.R |only DataVisualizations-1.4.0/DataVisualizations/R/stat_pde_density.R | 4 DataVisualizations-1.4.0/DataVisualizations/build/partial.rdb |binary DataVisualizations-1.4.0/DataVisualizations/build/vignette.rds |binary DataVisualizations-1.4.0/DataVisualizations/inst/NEWS | 9 DataVisualizations-1.4.0/DataVisualizations/inst/doc/DataVisualizations.R | 274 DataVisualizations-1.4.0/DataVisualizations/inst/doc/DataVisualizations.html | 3881 +++++----- DataVisualizations-1.4.0/DataVisualizations/man/MAplot.Rd | 166 DataVisualizations-1.4.0/DataVisualizations/man/MDplot.Rd | 7 DataVisualizations-1.4.0/DataVisualizations/man/MDstrips.Rd |only DataVisualizations-1.4.0/DataVisualizations/man/OpposingViolinBiclassPlot.Rd |only DataVisualizations-1.4.0/DataVisualizations/man/PDEstrip.Rd |only DataVisualizations-1.4.0/DataVisualizations/man/ParetoRadius_fast.Rd | 4 DataVisualizations-1.4.0/DataVisualizations/man/stat_pde_density.Rd | 192 DataVisualizations-1.4.0/DataVisualizations/src/RcppExports.cpp | 25 DataVisualizations-1.4.0/DataVisualizations/src/dist1d.cpp |only DataVisualizations-1.4.0/DataVisualizations/src/quantileDist1d.cpp |only 35 files changed, 2955 insertions(+), 3080 deletions(-)
More information about DataVisualizations at CRAN
Permanent link
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.15.0 dated 2025-05-18 and 1.16.0 dated 2025-10-31
DESCRIPTION | 6 MD5 | 72 +++++----- R/data.R | 49 ++++--- R/help.R | 10 + R/microtable.R | 35 +++-- R/trans_abund.R | 117 ++++++++++++++-- R/trans_alpha.R | 132 +++++++++++-------- R/trans_diff.R | 18 +- R/trans_env.R | 16 +- R/trans_func.R | 265 +++++++++++++++++++++++++++----------- R/trans_network.R | 17 +- R/trans_norm.R | 13 + R/trans_venn.R | 51 ++++--- inst/CITATION | 16 ++ man/Tax4Fun2_KEGG.Rd | 5 man/dataset.Rd | 7 - man/env_data_16S.Rd | 5 man/fungi_func_FUNGuild.Rd | 5 man/fungi_func_FungalTraits.Rd | 5 man/microeco.Rd | 10 + man/microtable.Rd | 26 ++- man/otu_table_16S.Rd | 5 man/otu_table_ITS.Rd | 5 man/phylo_tree_16S.Rd | 5 man/prok_func_FAPROTAX.Rd | 9 - man/prok_func_NJC19_list.Rd | 9 - man/sample_info_16S.Rd | 5 man/sample_info_ITS.Rd | 5 man/taxonomy_table_16S.Rd | 5 man/taxonomy_table_ITS.Rd | 5 man/trans_abund.Rd | 29 +++- man/trans_diff.Rd | 18 +- man/trans_env.Rd | 10 + man/trans_func.Rd | 283 +++++++++++++++++++++++++++++------------ man/trans_network.Rd | 3 man/trans_norm.Rd | 6 man/trans_venn.Rd | 14 +- 37 files changed, 906 insertions(+), 390 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.16.1 dated 2025-10-16 and 0.16.2 dated 2025-10-31
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NAMESPACE | 3 + NEWS.md | 2 + R/install.R | 84 ++++++++++++++++++++++++++++++++++++-------------- R/nn-loss.R | 2 - R/package.R | 14 +++++++- build/partial.rdb |binary man/nn_aum_loss.Rd | 2 - man/nn_kl_div_loss.Rd | 2 - 10 files changed, 94 insertions(+), 41 deletions(-)
Title: Music Notation Syntax, Manipulation, Analysis and Transcription
in R
Description: Provides a music notation syntax and a collection of music
programming functions for generating, manipulating, organizing, and analyzing
musical information in R. Music syntax can be entered directly in character
strings, for example to quickly transcribe short pieces of music. The
package contains functions for directly performing various mathematical,
logical and organizational operations and musical transformations on special
object classes that facilitate working with music data and notation. The
same music data can be organized in tidy data frames for a familiar and
powerful approach to the analysis of large amounts of structured music data.
Functions are available for mapping seamlessly between these formats and
their representations of musical information. The package also provides an
API to 'LilyPond' (<https://lilypond.org/>) for transcribing musical
representations in R into tablature ("tabs") and sheet music. 'LilyPond' is
open source music engraving software for gener [...truncated...]
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <rpkgs@pm.me>
Diff between tabr versions 0.5.3 dated 2025-07-03 and 0.5.4 dated 2025-10-31
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 6 +++--- build/vignette.rds |binary tests/testthat/test-music.R | 4 ++-- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.20 dated 2025-09-29 and 1.21 dated 2025-10-31
openxlsx2-1.20/openxlsx2/man/figures/lifecycle-archived.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-defunct.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-deprecated.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-experimental.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-maturing.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-questioning.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-retired.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-soft-deprecated.svg |only openxlsx2-1.20/openxlsx2/man/figures/lifecycle-stable.svg |only openxlsx2-1.21/openxlsx2/DESCRIPTION | 6 - openxlsx2-1.21/openxlsx2/MD5 | 31 +++------- openxlsx2-1.21/openxlsx2/NEWS.md | 10 +++ openxlsx2-1.21/openxlsx2/R/class-workbook-wrappers.R | 12 +++ openxlsx2-1.21/openxlsx2/R/helper-functions.R | 5 + openxlsx2-1.21/openxlsx2/R/wb_functions.R | 6 + openxlsx2-1.21/openxlsx2/inst/AUTHORS | 5 - openxlsx2-1.21/openxlsx2/man/wb_add_data_table.Rd | 4 - openxlsx2-1.21/openxlsx2/man/wb_add_formula.Rd | 8 ++ openxlsx2-1.21/openxlsx2/man/write_datatable.Rd | 4 - openxlsx2-1.21/openxlsx2/tests/testthat/test-date_time_conversion.R | 17 +++++ openxlsx2-1.21/openxlsx2/tests/testthat/test-helper-functions.R | 8 +- 21 files changed, 80 insertions(+), 36 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb],
Reinhold Kainhofer [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.8 dated 2025-01-25 and 4.2.8.1 dated 2025-10-31
DESCRIPTION | 13 +- MD5 | 16 +-- NEWS.md | 4 R/writeDataTable.R | 30 +++--- build/vignette.rds |binary inst/doc/Formatting.html | 4 inst/doc/Introduction.html | 180 +++++++++++++++++++------------------- man/writeDataTable.Rd | 4 tests/testthat/test-activeSheet.R | 2 9 files changed, 133 insertions(+), 120 deletions(-)
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.7-6 dated 2025-07-24 and 1.7-7 dated 2025-10-31
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/griddev.R | 6 ++++-- build/vignette.rds |binary inst/NEWS.Rd | 11 ++++++++++- inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary 8 files changed, 24 insertions(+), 13 deletions(-)
Title: Import and Analyse Ego-Centered Network Data
Description: Tools for importing, analyzing and visualizing ego-centered
network data. Supports several data formats, including the export formats of
'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the
intuitive visualization of ego-centered networks is provided. Also included
are procedures for creating and visualizing Clustered Graphs
(Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Author: Till Krenz [aut, cre],
Pavel N. Krivitsky [aut],
Raffaele Vacca [aut],
Michal Bojanowski [aut] ,
Markus Gamper [ctb],
Andreas Herz [aut],
Christopher McCarty [ctb]
Maintainer: Till Krenz <egor@tillt.net>
Diff between egor versions 1.24.2 dated 2024-02-02 and 1.25.10 dated 2025-10-31
DESCRIPTION | 19 - MD5 | 93 +++--- NAMESPACE | 2 NEWS.md | 4 R/as_egor.R | 19 - R/as_igraph_network.R |only R/clustered.graphs.R | 16 - R/conversions.R | 301 -------------------- R/density.R | 6 R/dplyr_methods.R | 466 +++++++++----------------------- R/ego.design.R | 36 +- R/ego_constraint.R | 2 R/egor-package.R | 2 R/egor.R | 84 +++-- R/ei.R | 2 R/gss2004.R | 2 R/plot_ego_gram.R | 6 R/plot_ego_graph.R | 48 ++- R/plot_egor.R | 1 R/read.egonet.R | 11 R/subset.egor.R | 10 R/zzz.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/check_and_release.R | 7 inst/doc/egor_allbus.Rmd | 2 inst/doc/egor_allbus.html | 15 - inst/doc/qualtrics.html | 21 - inst/doc/using_egor.html | 47 +-- man/as_igraph.Rd | 12 man/as_tibble.egor.Rd | 6 man/ego_density.Rd | 6 man/ego_design.Rd | 20 + man/egor-package.Rd | 3 man/egor.Rd | 33 +- man/gss2004.Rd | 2 man/plot_egor.Rd | 3 man/rowlist.Rd | 4 man/subset.egor.Rd | 4 tests/testthat/test-as_egor.R | 7 tests/testthat/test-as_igraph_network.R |only tests/testthat/test-clustered_graphs.R | 11 tests/testthat/test-conversions.R | 112 ------- tests/testthat/test-ego_design.R | 58 +++ tests/testthat/test-plot_egor.R | 72 ++++ tests/testthat/test-qualtrics.R | 2 tests/testthat/test-rotate.R | 4 tests/testthat/test-summary_egor.R |only vignettes/egor_allbus.Rmd | 2 49 files changed, 607 insertions(+), 984 deletions(-)
Title: Generator of Main Scientific References
Description: Generates a list, with a size defined by the user, containing the main scientific references and the frequency distribution of authors and journals in the list obtained.
The database is a dataframe with academic production metadata made available by bibliographic collections such as Scopus, Web of Science, etc.
The temporal evolution of scientific production on a given topic is presented and ordered lists of articles are constructed by number of citations and of authors and journals by level of productivity.
Massimo Aria, Corrado Cuccurullo. (2017) <doi:10.1016/j.joi.2017.08.007>.
Caibo Zhou, Wenyan Song. (2021) <doi:10.1016/j.jclepro.2021.126943>.
Author: Marcio Eustaquio [aut, cre]
Maintainer: Marcio Eustaquio <marcioeustaquio@id.uff.br>
Diff between bibliorefer versions 0.1.1 dated 2025-01-31 and 0.1.2 dated 2025-10-31
DESCRIPTION | 10 MD5 | 32 - R/ajust_pagin.R | 62 +- R/auxinf_autr.R | 126 ++--- R/crit_quant.R | 64 +-- R/example_database.R | 6 R/principal_lister.R | 148 +++---- R/produc_cientific.R | 52 +- R/tabel_gera.R | 62 +- inst/extdata/example_database.csv | 802 +++++++++++++++++++++++--------------- man/ajust_pagin.Rd | 2 man/auxinf_autr.Rd | 2 man/crit_quant.Rd | 2 man/example_database.Rd | 2 man/principal_lister.Rd | 4 man/produc_cientific.Rd | 2 man/tabel_gera.Rd | 2 17 files changed, 790 insertions(+), 590 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho [aut, cre]
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.11 dated 2025-01-14 and 1.12-1 dated 2025-10-31
asbio-1.11/asbio/R/selftest_ttest_R.R |only asbio-1.12-1/asbio/DESCRIPTION | 12 asbio-1.12-1/asbio/MD5 | 51 +- asbio-1.12-1/asbio/NAMESPACE | 1 asbio-1.12-1/asbio/R/anm.ExpDesign.r | 3 asbio-1.12-1/asbio/R/anm.LV.r | 3 asbio-1.12-1/asbio/R/anm.ci.r | 3 asbio-1.12-1/asbio/R/anm.coin.r | 3 asbio-1.12-1/asbio/R/anm.cont.pdf.r | 3 asbio-1.12-1/asbio/R/anm.die.r | 3 asbio-1.12-1/asbio/R/anm.popgrowth.r | 10 asbio-1.12-1/asbio/R/anm.samp.design.R | 3 asbio-1.12-1/asbio/R/anm.transM.r | 3 asbio-1.12-1/asbio/R/loglik.exp.plot.r | 3 asbio-1.12-1/asbio/R/r.dist.r | 3 asbio-1.12-1/asbio/R/samp.dist.mech.r | 4 asbio-1.12-1/asbio/R/samp.dist.r | 2 asbio-1.12-1/asbio/R/see.mnom.tck.r | 2 asbio-1.12-1/asbio/R/see.power.r | 20 asbio-1.12-1/asbio/R/selftest.regdiag.R | 622 +++++++++++----------------- asbio-1.12-1/asbio/R/selftestANOVAdesign.R | 13 asbio-1.12-1/asbio/R/selftest_ttest_tck.R | 4 asbio-1.12-1/asbio/build/vignette.rds |binary asbio-1.12-1/asbio/inst/doc/ranefCov.pdf |binary asbio-1.12-1/asbio/inst/doc/simpson.pdf |binary asbio-1.12-1/asbio/inst/doc/typeISS_key.pdf |binary asbio-1.12-1/asbio/man/world.emissions.Rd | 3 27 files changed, 343 insertions(+), 431 deletions(-)
Title: 'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications
Description: Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<something>() are the main plotting functions, and functions starting with extract_<something>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis> and a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>.
Author: Evelyn Jade [aut, cre, cph]
Maintainer: Evelyn Jade <evelynjade42@gmail.com>
Diff between ggDNAvis versions 0.3.0 dated 2025-10-01 and 0.3.2 dated 2025-10-31
DESCRIPTION | 6 +- MD5 | 30 +++++----- NEWS.md | 10 +++ R/visualise_many_sequences.R | 1 R/visualise_methylation.R | 1 R/visualise_single_sequence.R | 1 tests/testthat/reference_images/sone_2019_f1_1_expanded_test_02.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_04.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_08.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_10.jpg |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_12.PNG |binary tests/testthat/reference_images/visualise_many_sequences_test_09.png |binary tests/testthat/reference_images/visualise_methylation_test_03.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_02.png |binary tests/testthat/test_plot_images/visualise_many_sequences_test_09.png |binary tests/testthat/test_plot_images/visualise_methylation_test_03.png |binary 16 files changed, 31 insertions(+), 18 deletions(-)
Title: Efficient and Precise Single-Cell Reference Atlas Mapping
Description: Implements the Symphony single-cell reference building and query mapping algorithms and additional functions described in Kang et al <https://www.nature.com/articles/s41467-021-25957-x>.
Author: Joyce Kang [aut, cre] ,
Ilya Korsunsky [aut] ,
Soumya Raychaudhuri [aut]
Maintainer: Joyce Kang <joyce_kang@hms.harvard.edu>
Diff between symphony versions 0.1.1 dated 2023-01-16 and 0.1.2 dated 2025-10-30
symphony-0.1.1/symphony/man/symphony.Rd |only symphony-0.1.2/symphony/DESCRIPTION | 17 symphony-0.1.2/symphony/MD5 | 27 symphony-0.1.2/symphony/NAMESPACE | 2 symphony-0.1.2/symphony/NEWS.md |only symphony-0.1.2/symphony/R/RcppExports.R | 30 symphony-0.1.2/symphony/R/symphony-package.R | 11 symphony-0.1.2/symphony/README.md | 71 +- symphony-0.1.2/symphony/build/vignette.rds |binary symphony-0.1.2/symphony/inst/doc/quickstart_tutorial.R | 15 symphony-0.1.2/symphony/inst/doc/quickstart_tutorial.Rmd | 5 symphony-0.1.2/symphony/inst/doc/quickstart_tutorial.html | 428 +++++++------- symphony-0.1.2/symphony/man/symphony-package.Rd |only symphony-0.1.2/symphony/src/Makevars | 3 symphony-0.1.2/symphony/src/Makevars.win | 4 symphony-0.1.2/symphony/vignettes/quickstart_tutorial.Rmd | 5 16 files changed, 309 insertions(+), 309 deletions(-)
Title: Vis-NIR Spectral Analysis Wrapper
Description: Originally designed application in the context of
resource-limited plant research and breeding programs, 'waves'
provides an open-source solution to spectral data processing and model
development by bringing useful packages together into a streamlined
pipeline. This package is wrapper for functions related to the
analysis of point visible and near-infrared reflectance measurements.
It includes visualization, filtering, aggregation, preprocessing,
cross-validation set formation, model training, and prediction
functions to enable open-source association of spectral and reference
data. This package is documented in a peer-reviewed manuscript in the
Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized
cross-validation schemes are described in detail in Jarquín et al.
(2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from
Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Author: Jenna Hershberger [aut, cre] ,
Michael Gore [ths],
NSF BREAD IOS-1543958 [fnd]
Maintainer: Jenna Hershberger <jmh579@cornell.edu>
This is a re-admission after prior archival of version 0.2.5 dated 2023-12-12
Diff between waves versions 0.2.5 dated 2023-12-12 and 0.2.6 dated 2025-10-30
waves-0.2.5/waves/man/get_mode.Rd |only waves-0.2.6/waves/DESCRIPTION | 13 waves-0.2.6/waves/MD5 | 33 - waves-0.2.6/waves/NAMESPACE | 3 waves-0.2.6/waves/NEWS.md | 22 + waves-0.2.6/waves/R/filter_spectra.R | 6 waves-0.2.6/waves/R/plot_spectra.R | 2 waves-0.2.6/waves/R/rename.R | 2 waves-0.2.6/waves/R/save_model.R | 5 waves-0.2.6/waves/R/test_spectra.R | 191 +++------- waves-0.2.6/waves/R/train_spectra.R | 426 +++++++--------------- waves-0.2.6/waves/R/utils.R | 634 +++++++++++++++++++++++++++++++++- waves-0.2.6/waves/build/vignette.rds |binary waves-0.2.6/waves/inst/doc/waves.R | 27 - waves-0.2.6/waves/inst/doc/waves.Rmd | 19 - waves-0.2.6/waves/inst/doc/waves.html | 211 ++++++----- waves-0.2.6/waves/man/plot_spectra.Rd | 2 waves-0.2.6/waves/vignettes/waves.Rmd | 19 - 18 files changed, 1052 insertions(+), 563 deletions(-)
Title: Visualise the Path to a Stopping Point in Qualitative Interviews
Based on Novel Codes
Description: In semi-structured interviews that use the 'framework' method, it
is not always clear how refinements to interview questions affect the
decision of when to stop interviews. The trend of 'novel' and 'duplicate'
interview codes (novel codes are information that other interviewees have
not previously mentioned) provides insight into the richness of qualitative
information. This package provides tools to visualise when refinements occur
and how that affects the trends of novel and duplicate codes. These
visualisations, when used progressively as new interviews are finished, can
help the researcher to decide on a stopping point for their interviews. For
context, see Wong et al., (2023) <doi:10.1177/16094069231220773>.
Author: Kam Wong [aut, cph] ,
Desi Quintans [cre, aut, cph]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between novelqualcodes versions 0.13.1 dated 2024-02-08 and 0.13.5 dated 2025-10-30
DESCRIPTION | 16 +- MD5 | 44 +++---- NAMESPACE | 24 ++-- NEWS.md |only R/exp_import_field_notes.R | 103 +++++++++-------- R/exp_plot_novelty.R | 191 +++++++++++++++++--------------- R/exp_plot_richness.R | 219 +++++++++++++++++++------------------ R/prv_reshape_for_plots.R | 68 ++++++----- README.md | 4 build/partial.rdb |only build/vignette.rds |binary inst/doc/guided-tour.R | 64 +++++----- inst/doc/guided-tour.Rmd | 2 inst/doc/guided-tour.html | 37 +++--- man/create_field_notes_template.Rd | 88 +++++++------- man/import_coding_matrices.Rd | 96 ++++++++-------- man/import_field_notes.Rd | 76 ++++++------ man/novelqualcodes-package.Rd | 56 ++++----- man/plot_novelty.Rd | 154 +++++++++++++------------- man/plot_richness.Rd | 153 +++++++++++++------------ man/reshape_for_plots.Rd | 46 +++---- man/save_last_plot.Rd | 114 +++++++++---------- man/score_codes.Rd | 122 ++++++++++---------- vignettes/guided-tour.Rmd | 2 24 files changed, 869 insertions(+), 810 deletions(-)
More information about novelqualcodes at CRAN
Permanent link
Title: Longitudinal Gaussian Process Regression
Description: Interpretable nonparametric modeling of longitudinal data
using additive Gaussian process regression. Contains functionality
for inferring covariate effects and assessing covariate relevances.
Models are specified using a convenient formula syntax, and can include
shared, group-specific, non-stationary, heterogeneous and temporally
uncertain effects. Bayesian inference for model parameters is performed
using 'Stan'. The modeling approach and methods are described in detail in
Timonen et al. (2021) <doi:10.1093/bioinformatics/btab021>.
Author: Juho Timonen [aut, cre] ,
Andrew Johnson [ctb]
Maintainer: Juho Timonen <juho.timonen@iki.fi>
Diff between lgpr versions 1.2.4 dated 2023-09-24 and 1.2.5 dated 2025-10-30
DESCRIPTION | 11 MD5 | 40 R/aaa.R | 3 R/utils-create_model-prior.R | 2 README.md | 24 build/vignette.rds |binary inst/doc/math.R | 2 inst/doc/math.html | 472 ++- man/add_dis_age.Rd | 2 man/adjusted_c_hat.Rd | 2 man/lgpr-package.Rd | 8 man/new_x.Rd | 2 man/prior_to_num.Rd | 2 man/split.Rd | 2 src/RcppExports.cpp | 100 src/exports.stanfunctions.cpp | 3015 +++++++++----------- src/lgpr_types.h | 2 src/stanExports_lgp.h | 4283 +++++++++++++---------------- src/stanExports_lgp_latent.h | 5306 +++++++++++++++++------------------- src/stanExports_parameter_prior.h | 2947 +++++++++---------- tests/testthat/test_misc-invgamma.R | 6 21 files changed, 7764 insertions(+), 8467 deletions(-)
Title: Extracts Phylogenetic Island Community Data from Phylogenetic
Trees
Description: Extracts colonisation and branching times of island
species to be used for analysis in the R package 'DAISIE'. It uses
phylogenetic and endemicity data to extract the separate island colonists
and store them.
Author: Joshua W. Lambert [aut, cre] ,
Luis Valente [aut] ,
Pedro Santos Neves [aut] ,
Lizzie Roeble [aut] ,
Theo Pannetier [aut]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Diff between DAISIEprep versions 1.0.0 dated 2024-12-17 and 1.0.1 dated 2025-10-30
DESCRIPTION | 24 ++--- MD5 | 26 +++-- NEWS.md | 25 +++++ README.md | 23 ++-- build/vignette.rds |binary inst/doc/DAISIE_FAQs.Rmd |only inst/doc/DAISIE_FAQs.html |only inst/doc/Forcing_nonendemic_singleton.html | 138 +++++++++++++++++++++++++---- inst/doc/Multi_tip_extraction.html | 78 ++++++++++++++-- inst/doc/Performance.html | 11 +- inst/doc/Sensitivity.html | 11 +- inst/doc/Tutorial.html | 90 +++++++++++++++--- man/DAISIEprep-package.Rd | 2 tests/testthat/test-plot_phylod.R | 37 ++++++- vignettes/DAISIE_FAQs.Rmd |only vignettes/Figure1.png |only 16 files changed, 370 insertions(+), 95 deletions(-)
Title: Analysis and Visualization of Basketball Data
Description: Contains data and code to accompany the book
P. Zuccolotto and M. Manisera (2020) Basketball Data Science. Applications with R. CRC Press. ISBN 9781138600799.
Author: Marco Sandri [aut, cre] ,
Paola Zuccolotto [aut] ,
Marica Manisera [aut]
Maintainer: Marco Sandri <basketballanalyzer.help@unibs.it>
Diff between BasketballAnalyzeR versions 0.8.0 dated 2025-04-17 and 0.8.1 dated 2025-10-30
BasketballAnalyzeR-0.8.0/BasketballAnalyzeR/R/scoredifference.R |only BasketballAnalyzeR-0.8.0/BasketballAnalyzeR/man/scoredifference.Rd |only BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/DESCRIPTION | 18 ++-- BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/MD5 | 22 ++--- BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/NAMESPACE | 1 BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/barline.R | 2 BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/drawNBAcourt.R | 44 +++++----- BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/expectedpts.R | 4 BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/plot.inequality.R | 6 - BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/plot.simplereg.R | 4 BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/scoringprob.R | 4 BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/R/shotchart.R | 36 +++++--- BasketballAnalyzeR-0.8.1/BasketballAnalyzeR/build/stage23.rdb |binary 13 files changed, 75 insertions(+), 66 deletions(-)
More information about BasketballAnalyzeR at CRAN
Permanent link
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.6.0 dated 2025-09-19 and 0.7.0 dated 2025-10-30
altdoc-0.6.0/altdoc/tests/testthat/DESCRIPTION |only altdoc-0.6.0/altdoc/tests/testthat/_snaps/rd2qmd.md |only altdoc-0.7.0/altdoc/DESCRIPTION | 14 altdoc-0.7.0/altdoc/LICENSE | 4 altdoc-0.7.0/altdoc/MD5 | 137 - altdoc-0.7.0/altdoc/NAMESPACE | 12 altdoc-0.7.0/altdoc/NEWS.md | 23 altdoc-0.7.0/altdoc/R/render_docs.R | 3 altdoc-0.7.0/altdoc/R/settings_mkdocs.R | 27 altdoc-0.7.0/altdoc/R/setup_docs.R | 3 altdoc-0.7.0/altdoc/R/utils.R | 80 altdoc-0.7.0/altdoc/README.md | 488 ++-- altdoc-0.7.0/altdoc/build/vignette.rds |binary altdoc-0.7.0/altdoc/inst/doc/get-started.R | 6 altdoc-0.7.0/altdoc/inst/doc/get-started.Rmd | 10 altdoc-0.7.0/altdoc/inst/doc/get-started.html | 1136 +++++----- altdoc-0.7.0/altdoc/inst/docsify/docsify.html | 90 altdoc-0.7.0/altdoc/inst/docsify/docsify.md | 18 altdoc-0.7.0/altdoc/inst/docute/docute.html | 104 altdoc-0.7.0/altdoc/inst/gha/altdoc.yaml | 146 - altdoc-0.7.0/altdoc/inst/mkdocs/mkdocs.yml | 80 altdoc-0.7.0/altdoc/inst/preamble/preamble_man_qmd.yml | 12 altdoc-0.7.0/altdoc/inst/preamble/preamble_vignettes_qmd.yml | 12 altdoc-0.7.0/altdoc/inst/preamble/preamble_vignettes_rmd.yml | 8 altdoc-0.7.0/altdoc/inst/quarto_website/quarto_website.yml | 84 altdoc-0.7.0/altdoc/man/preview_docs.Rd | 62 altdoc-0.7.0/altdoc/man/render_docs.Rd | 4 altdoc-0.7.0/altdoc/man/setup_docs.Rd | 168 - altdoc-0.7.0/altdoc/man/setup_github_actions.Rd | 50 altdoc-0.7.0/altdoc/tests/testthat.R | 8 altdoc-0.7.0/altdoc/tests/testthat/_snaps/docsify/render_docs |only altdoc-0.7.0/altdoc/tests/testthat/_snaps/docsify/render_docs.md | 102 altdoc-0.7.0/altdoc/tests/testthat/_snaps/docute/render_docs |only altdoc-0.7.0/altdoc/tests/testthat/_snaps/mkdocs/render_docs |only altdoc-0.7.0/altdoc/tests/testthat/_snaps/mkdocs/render_docs.md | 498 ++-- altdoc-0.7.0/altdoc/tests/testthat/_snaps/rd2qmd |only altdoc-0.7.0/altdoc/tests/testthat/_snaps/render_docs.md |only altdoc-0.7.0/altdoc/tests/testthat/examples/examples-man/between.Rd | 36 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-man/between.md | 80 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-man/is-internal.Rd | 36 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-man/should-fail.Rd | 34 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-qmd/with-preamble.qmd | 26 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-qmd/without-preamble.qmd | 16 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-vignettes/several-outputs.Rmd | 48 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-vignettes/with-figure.Rmd | 50 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-yaml/basic.Rmd | 20 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-yaml/options.Rmd | 28 altdoc-0.7.0/altdoc/tests/testthat/examples/examples-yaml/several-outputs.Rmd | 32 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/NEWS.md | 18 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/README.Rmd | 82 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/README.md | 72 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/man/examplesIf_false.Rd | 44 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/man/examplesIf_true.Rd | 44 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/man/hello_base.Rd | 74 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/man/hello_r6.Rd | 178 - altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.altdoc/vignettes/test.Rmd | 42 altdoc-0.7.0/altdoc/tests/testthat/examples/testpkg.lifecycle/DESCRIPTION | 3 altdoc-0.7.0/altdoc/tests/testthat/test-check_md_structure.R | 1 altdoc-0.7.0/altdoc/tests/testthat/test-rd2qmd.R | 2 altdoc-0.7.0/altdoc/tests/testthat/test-render_docs.R | 190 + altdoc-0.7.0/altdoc/tests/testthat/test-setup_docs.R | 35 altdoc-0.7.0/altdoc/vignettes/customize.qmd | 546 ++-- altdoc-0.7.0/altdoc/vignettes/deploy.qmd | 176 - altdoc-0.7.0/altdoc/vignettes/get-started.Rmd | 10 64 files changed, 2785 insertions(+), 2527 deletions(-)
Title: Useful Functions for Harmonized W4M Tool Development
Description: Provides a set of utility function to prevent the spread of
utility scripts in W4M (Workflow4Metabolomics) tools, and centralize
them in a single package.
To note, some are meant to be replaced by the use of dedicated packages in the future, like
the parse_args() function: it is here only to prepare the ground for
more global changes in W4M scripts and tools.
This package is used by part of the W4M Galaxy modules, some of them
being available on the community-maintained GitHub repository for
Metabolomics' Galaxy tools <https://github.com/workflow4metabolomics/tools-metabolomics>.
See Delporte et al (2025) <doi:10.1002/cpz1.70095> for more details.
Author: Lain Pavot [aut],
Melanie Petera [aut, cre],
Helge Hecht [ctb]
Maintainer: Melanie Petera <melanie.petera@inrae.fr>
This is a re-admission after prior archival of version 1.0.0 dated 2023-09-08
Diff between W4MRUtils versions 1.0.0 dated 2023-09-08 and 1.2.1 dated 2025-10-30
DESCRIPTION | 33 MD5 | 193 - NAMESPACE | 117 - NEWS.md |only R/Filtering_datasets.R |only R/RcheckLibrary.R | 486 ++-- R/dataframe_helpers.R | 228 - R/galaxy.R | 1103 ++++----- R/intensity_checks.R |only R/logging.R | 1103 ++++----- R/miniTools.R | 1145 ++++------ R/optparse_helper.R | 591 ++--- R/utils.R | 1010 ++++---- README.md | 54 build/vignette.rds |binary inst/doc/W4MRUtils.R | 4 inst/doc/W4MRUtils.Rmd | 373 +-- inst/doc/W4MRUtils.html | 399 ++- inst/doc/logging.R | 2 inst/doc/logging.Rmd | 258 +- inst/doc/logging.html | 258 +- inst/doc/parse_arguments.R | 2 inst/doc/parse_arguments.Rmd | 164 - inst/doc/parse_arguments.html | 282 +- inst/extdata/example_df_read_table.csv | 10 man/Filtering_datasets.Rd |only man/W4MLogger.Rd | 126 - man/W4MLogger_-sub-info-warning-error-debug-verbose-close-brace.Rd | 70 man/W4MLogger_.message__.Rd | 66 man/W4MLogger_add_out_paths.Rd | 18 man/W4MLogger_finalize.Rd | 52 man/W4MLogger_set_debug.Rd | 32 man/W4MLogger_set_error.Rd | 32 man/W4MLogger_set_info.Rd | 32 man/W4MLogger_set_out_paths.Rd | 18 man/W4MLogger_set_verbose.Rd | 32 man/W4MLogger_set_warning.Rd | 32 man/check_err.Rd | 42 man/check_one_character.Rd | 138 - man/check_one_complex.Rd | 138 - man/check_one_integer.Rd | 138 - man/check_one_logical.Rd | 138 - man/check_one_numeric.Rd | 138 - man/check_param_type_n_length.Rd | 343 +- man/check_parameter_length.Rd | 325 +- man/check_parameter_type.Rd | 325 +- man/collapse.Rd | 51 man/collapse_lines.Rd | 51 man/convert_parameters.Rd | 80 man/df_force_numeric.Rd | 60 man/df_is.Rd | 72 man/df_read_table.Rd | 82 man/generic_filter.Rd |only man/get_base_dir.Rd | 36 man/get_logger.Rd | 117 - man/get_r_env.Rd | 42 man/import2.Rd | 128 - man/import3.Rd | 144 - man/in_galaxy_env.Rd | 30 man/intens_check.Rd |only man/intensity_checks.Rd |only man/match2.Rd | 52 man/match3.Rd | 50 man/metab_merge.Rd |only man/mini_tools.Rd | 33 man/optparse_character.Rd | 86 man/optparse_flag.Rd | 94 man/optparse_integer.Rd | 86 man/optparse_list.Rd | 144 - man/optparse_numeric.Rd | 86 man/optparse_parameters.Rd | 166 - man/parse_args.Rd | 152 - man/printf.Rd | 59 man/printfp.Rd | 94 man/printp.Rd | 59 man/reproduce_id.Rd | 104 man/run_galaxy_function.Rd | 73 man/run_galaxy_processing.Rd | 378 +-- man/show_galaxy_footer.Rd | 105 man/show_galaxy_header.Rd | 135 - man/show_sys.Rd | 41 man/shy_lib.Rd | 56 man/source_local.Rd | 106 man/stock_id.Rd | 116 - man/stopaste.Rd | 84 man/stopaste0.Rd | 80 man/stopf.Rd | 67 man/unmangle_galaxy_param.Rd | 54 man/unmangle_galaxy_string.Rd | 50 tests/testthat.R | 24 tests/testthat/Rplots.pdf |only tests/testthat/test-Filtering_datasets.R |only tests/testthat/test-RcheckLibrary.R | 516 ++-- tests/testthat/test-dataframe_helpers.R | 254 +- tests/testthat/test-galaxy.R | 256 +- tests/testthat/test-intensity_checks.R |only tests/testthat/test-logging.R | 408 +-- tests/testthat/test-miniTools.R | 754 +++--- tests/testthat/test-optparse-helpers.R | 170 - tests/testthat/test-utils.R | 242 +- vignettes/W4MRUtils.Rmd | 373 +-- vignettes/logging.Rmd | 258 +- vignettes/parse_arguments.Rmd | 164 - 103 files changed, 8310 insertions(+), 8662 deletions(-)
Title: Tools for the Analysis of Ecosystem Metabolism
Description: A collection of tools for the calculation of freewater metabolism
from in situ time series of dissolved oxygen, water temperature, and,
optionally, additional environmental variables. LakeMetabolizer implements
5 different metabolism models with diverse statistical underpinnings:
bookkeeping, ordinary least squares, maximum likelihood, Kalman filter,
and Bayesian. Each of these 5 metabolism models can be combined with
1 of 7 models for computing the coefficient of gas exchange across the
air–water interface (k). LakeMetabolizer also features a variety of
supporting functions that compute conversions and implement calculations
commonly applied to raw data prior to estimating metabolism (e.g., oxygen
saturation and optical conversion models).
Author: Luke Winslow [aut],
Jacob Zwart [cre, aut] ,
Ryan Batt [aut],
Jessica Corman [aut],
Hilary Dugan [aut],
Paul Hanson [aut],
Aline Jaimes [aut],
Jordan Read [aut],
Richard Woolway [aut]
Maintainer: Jacob Zwart <jayzlimno@gmail.com>
Diff between LakeMetabolizer versions 1.5.5 dated 2022-11-15 and 1.5.6 dated 2025-10-30
DESCRIPTION | 14 MD5 | 171 NEWS.md | 43 R/LakeMetabolizer-package.R |only R/addNAs.R | 140 R/byeShort.R | 44 R/calc.lw.net.R | 582 - R/calc.zeng.R | 478 R/date2doy.R | 16 R/getSchmidt.R | 106 R/helper.functions.R | 910 - R/k.cole.R | 52 R/k.crusius.R | 84 R/k.heiskanen.R | 306 R/k.macIntyre.R | 348 R/k.read.R | 2 R/k.read.soloviev.R | 424 R/k.vachon.R | 68 R/k600.2.kGAS.R | 124 R/load.all.data.R | 150 R/load.meta.R | 104 R/metab.bayesian.R | 2 R/metab.bookkeep.R | 244 R/metab.kalman.R | 710 - R/metab.mle.R | 456 R/metab.ols.R | 220 R/o2.at.sat.R | 320 R/par.to.sw.R | 122 R/sun.rise.set.R | 216 R/sw.to.par.R | 118 R/temp.kalman.R | 248 R/wind.scale.R | 128 demo/00Index | 6 inst/CITATION | 42 inst/extdata/mendota.doobs |20156 ++++++++++++++++++------------------ inst/extdata/mendota.meta | 16 inst/extdata/mendota.par |20162 ++++++++++++++++++------------------- inst/extdata/mendota.rh |16820 +++++++++++++++--------------- inst/extdata/mendota.wnd |20158 ++++++++++++++++++------------------ inst/extdata/mendota.wtr |19872 ++++++++++++++++++------------------ inst/extdata/sparkling.airT | 2594 ++-- inst/extdata/sparkling.doobs | 2594 ++-- inst/extdata/sparkling.meta | 16 inst/extdata/sparkling.par | 2594 ++-- inst/extdata/sparkling.rh | 2594 ++-- inst/extdata/sparkling.wnd | 2594 ++-- inst/extdata/sparkling.wtr | 2594 ++-- inst/extdata/troutbog.airT | 2594 ++-- inst/extdata/troutbog.doobs | 2594 ++-- inst/extdata/troutbog.meta | 16 inst/extdata/troutbog.par | 2594 ++-- inst/extdata/troutbog.rh | 2594 ++-- inst/extdata/troutbog.wnd | 2594 ++-- inst/extdata/troutbog.wtr | 2566 ++-- inst/jags/bayes.mod.allk.JAGS | 36 inst/jags/bayes.mod.bothk.JAGS | 42 inst/jags/bayes.mod.nok.JAGS | 32 man/calc.lw.net.Rd | 172 man/calc.zeng.Rd | 110 man/get.Ts.Rd | 56 man/get.vars.Rd | 54 man/getSchmidt.Rd | 72 man/has.vars.Rd | 54 man/is.day.Rd | 54 man/is.night.Rd | 54 man/k.read.Rd | 266 man/k.read.base.Rd | 290 man/k600.2.kGAS.Rd | 106 man/load.all.data.Rd | 68 man/load.meta.Rd | 54 man/metab.Rd | 218 man/metab.bayesian.Rd | 170 man/metab.bookkeep.Rd | 142 man/metab.kalman.Rd | 218 man/metab.mle.Rd | 220 man/metab.ols.Rd | 134 man/o2.at.sat.Rd | 218 man/par.to.sw.Rd | 98 man/rmv.vars.Rd | 62 man/sun.rise.set.Rd | 68 man/sw.to.par.Rd | 102 man/temp.kalman.Rd | 74 man/var.indx.Rd | 56 man/watts.in.Rd | 120 man/wind.scale.Rd | 104 tests/testthat.R | 8 tests/testthat/test_sun.rise.set.R | 44 87 files changed, 69452 insertions(+), 69438 deletions(-)
More information about LakeMetabolizer at CRAN
Permanent link
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control, by A. Luciani (2022) <doi:10.13140/RG.2.2.31160.83202>.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
This is a re-admission after prior archival of version 4.1.0 dated 2025-10-20
Diff between bimets versions 4.1.0 dated 2025-10-20 and 4.1.1 dated 2025-10-30
bimets-4.1.0/bimets/vignettes/Thumbs.db |only bimets-4.1.1/bimets/DESCRIPTION | 8 - bimets-4.1.1/bimets/MD5 | 45 ++++---- bimets-4.1.1/bimets/NEWS.md | 6 + bimets-4.1.1/bimets/R/bimets_model_functions.R | 11 -- bimets-4.1.1/bimets/R/bimets_ts_functions.R | 127 ++++++++++++------------- bimets-4.1.1/bimets/README.md | 14 +- bimets-4.1.1/bimets/inst/doc/bimets.R | 17 ++- bimets-4.1.1/bimets/inst/doc/bimets.Rnw | 12 +- bimets-4.1.1/bimets/inst/doc/bimets.pdf |binary bimets-4.1.1/bimets/inst/doc/frb2bimets.R | 11 +- bimets-4.1.1/bimets/inst/doc/frb2bimets.Rnw | 9 + bimets-4.1.1/bimets/inst/doc/frb2bimets.pdf |binary bimets-4.1.1/bimets/man/BIMETS2CSV.Rd | 14 +- bimets-4.1.1/bimets/man/CSV2BIMETS.Rd | 13 +- bimets-4.1.1/bimets/man/MDL.Rd | 8 - bimets-4.1.1/bimets/man/RENORM.Rd | 2 bimets-4.1.1/bimets/man/SIMULATE.Rd | 4 bimets-4.1.1/bimets/man/STOCHSIMULATE.Rd | 2 bimets-4.1.1/bimets/man/bimets-package.Rd | 17 +-- bimets-4.1.1/bimets/man/bimetsDataset.Rd | 1 bimets-4.1.1/bimets/man/idxOver.Rd | 2 bimets-4.1.1/bimets/vignettes/bimets.Rnw | 12 +- bimets-4.1.1/bimets/vignettes/frb2bimets.Rnw | 9 + 24 files changed, 186 insertions(+), 158 deletions(-)
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.0.0 dated 2025-10-13 and 2.0.2 dated 2025-10-30
nuggets-2.0.0/nuggets/R/dichotomize.R |only nuggets-2.0.0/nuggets/man/dichotomize.Rd |only nuggets-2.0.2/nuggets/DESCRIPTION | 10 nuggets-2.0.2/nuggets/MD5 | 34 nuggets-2.0.2/nuggets/NAMESPACE | 3 nuggets-2.0.2/nuggets/NEWS.md | 12 nuggets-2.0.2/nuggets/R/association_matrix.R |only nuggets-2.0.2/nuggets/R/explore-associations.R | 2 nuggets-2.0.2/nuggets/R/nuggets-package.R | 1 nuggets-2.0.2/nuggets/R/testers.R | 20 nuggets-2.0.2/nuggets/build/vignette.rds |binary nuggets-2.0.2/nuggets/inst/doc/data-preparation.R |only nuggets-2.0.2/nuggets/inst/doc/data-preparation.Rmd |only nuggets-2.0.2/nuggets/inst/doc/data-preparation.html |only nuggets-2.0.2/nuggets/inst/doc/nuggets.R | 143 -- nuggets-2.0.2/nuggets/inst/doc/nuggets.Rmd | 595 ++---------- nuggets-2.0.2/nuggets/inst/doc/nuggets.html | 878 ++++++------------ nuggets-2.0.2/nuggets/man/association_matrix.Rd |only nuggets-2.0.2/nuggets/src/Makevars | 7 nuggets-2.0.2/nuggets/src/dig/CombinatorialProgress.h | 3 nuggets-2.0.2/nuggets/vignettes/data-preparation.Rmd |only nuggets-2.0.2/nuggets/vignettes/nuggets.Rmd | 595 ++---------- 22 files changed, 702 insertions(+), 1601 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.53 dated 2025-08-18 and 0.54 dated 2025-10-30
DESCRIPTION | 8 +++--- MD5 | 30 ++++++++++++------------ R/record.R | 51 ++++++++++++++++++++++++++++++++++++++++-- inst/doc/xfun.Rmd | 12 ++++----- inst/doc/xfun.html | 22 +++++++++--------- man/download_cache.Rd | 2 - man/github_releases.Rd | 2 - man/mime_type.Rd | 2 - man/news2md.Rd | 2 - man/record.Rd | 7 +++++ man/rest_api.Rd | 2 - man/retry.Rd | 2 - man/session_info.Rd | 2 - man/system3.Rd | 2 - tests/test-cran/test-record.R | 16 +++++++++++++ vignettes/xfun.Rmd | 12 ++++----- 16 files changed, 122 insertions(+), 52 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.3.4 dated 2023-10-19 and 1.3.5 dated 2025-10-30
FCPS-1.3.4/FCPS/R/DBscan.R |only FCPS-1.3.4/FCPS/man/DBscan.Rd |only FCPS-1.3.5/FCPS/DESCRIPTION | 31 FCPS-1.3.5/FCPS/MD5 | 40 FCPS-1.3.5/FCPS/NAMESPACE | 20 FCPS-1.3.5/FCPS/R/ClusterAMI.R |only FCPS-1.3.5/FCPS/R/ClusterCreateClassification.R | 19 FCPS-1.3.5/FCPS/R/ClusterNMI.R |only FCPS-1.3.5/FCPS/R/ClusterRedefine.R | 90 FCPS-1.3.5/FCPS/R/DBSCAN.R |only FCPS-1.3.5/FCPS/R/DatabionicSwarmClustering.R | 42 FCPS-1.3.5/FCPS/R/SubspaceClustering.R | 144 FCPS-1.3.5/FCPS/build/partial.rdb |binary FCPS-1.3.5/FCPS/build/vignette.rds |binary FCPS-1.3.5/FCPS/inst/doc/FCPS.R | 208 FCPS-1.3.5/FCPS/inst/doc/FCPS.html | 5057 ++++++++++----------- FCPS-1.3.5/FCPS/man/ClusterAMI.Rd |only FCPS-1.3.5/FCPS/man/ClusterARI.Rd | 2 FCPS-1.3.5/FCPS/man/ClusterCreateClassification.Rd | 114 FCPS-1.3.5/FCPS/man/ClusterNMI.Rd |only FCPS-1.3.5/FCPS/man/ClusterRedefine.Rd | 118 FCPS-1.3.5/FCPS/man/ClusterShannonInfo.Rd | 12 FCPS-1.3.5/FCPS/man/DBSCAN.Rd |only FCPS-1.3.5/FCPS/man/DatabionicSwarmClustering.Rd | 13 FCPS-1.3.5/FCPS/man/SubspaceClustering.Rd | 134 25 files changed, 3048 insertions(+), 2996 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between SLOPE versions 1.0.1 dated 2025-07-02 and 1.1.0 dated 2025-10-30
SLOPE-1.0.1/SLOPE/src/slope/clusters.h |only SLOPE-1.0.1/SLOPE/src/slope/constants.h |only SLOPE-1.0.1/SLOPE/src/slope/cv.h |only SLOPE-1.0.1/SLOPE/src/slope/diagnostics.h |only SLOPE-1.0.1/SLOPE/src/slope/estimate_alpha.h |only SLOPE-1.0.1/SLOPE/src/slope/folds.h |only SLOPE-1.0.1/SLOPE/src/slope/jit_normalization.h |only SLOPE-1.0.1/SLOPE/src/slope/logger.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/logistic.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/loss.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/multinomial.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/poisson.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/quadratic.h |only SLOPE-1.0.1/SLOPE/src/slope/losses/setup_loss.h |only SLOPE-1.0.1/SLOPE/src/slope/math.h |only SLOPE-1.0.1/SLOPE/src/slope/normalize.h |only SLOPE-1.0.1/SLOPE/src/slope/ols.h |only SLOPE-1.0.1/SLOPE/src/slope/regularization_sequence.h |only SLOPE-1.0.1/SLOPE/src/slope/score.h |only SLOPE-1.0.1/SLOPE/src/slope/screening.h |only SLOPE-1.0.1/SLOPE/src/slope/slope.h |only SLOPE-1.0.1/SLOPE/src/slope/slope_fit.h |only SLOPE-1.0.1/SLOPE/src/slope/slope_path.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/hybrid.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/hybrid_cd.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/pgd.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/setup_solver.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/slope_threshold.h |only SLOPE-1.0.1/SLOPE/src/slope/solvers/solver.h |only SLOPE-1.0.1/SLOPE/src/slope/sorted_l1_norm.h |only SLOPE-1.0.1/SLOPE/src/slope/threads.h |only SLOPE-1.0.1/SLOPE/src/slope/timer.h |only SLOPE-1.0.1/SLOPE/src/slope/utils.h |only SLOPE-1.1.0/SLOPE/DESCRIPTION | 6 SLOPE-1.1.0/SLOPE/MD5 | 146 ++++++++-------- SLOPE-1.1.0/SLOPE/NEWS.md | 7 SLOPE-1.1.0/SLOPE/R/data.R | 33 +++ SLOPE-1.1.0/SLOPE/README.md | 5 SLOPE-1.1.0/SLOPE/build/partial.rdb |only SLOPE-1.1.0/SLOPE/data/glioma.rda |only SLOPE-1.1.0/SLOPE/inst/WORDLIST | 21 ++ SLOPE-1.1.0/SLOPE/inst/doc/introduction.html | 13 - SLOPE-1.1.0/SLOPE/inst/doc/solvers.html | 13 - SLOPE-1.1.0/SLOPE/inst/include |only SLOPE-1.1.0/SLOPE/man/glioma.Rd |only SLOPE-1.1.0/SLOPE/man/student.Rd | 7 SLOPE-1.1.0/SLOPE/src/Makevars | 2 SLOPE-1.1.0/SLOPE/src/slope/clusters.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/cv.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/folds.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/kkt_check.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/kkt_check.h | 6 SLOPE-1.1.0/SLOPE/src/slope/logger.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/losses/logistic.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/losses/loss.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/losses/multinomial.cpp | 8 SLOPE-1.1.0/SLOPE/src/slope/losses/poisson.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/losses/quadratic.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/losses/setup_loss.cpp | 10 - SLOPE-1.1.0/SLOPE/src/slope/math.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/normalize.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/qnorm.cpp | 1 SLOPE-1.1.0/SLOPE/src/slope/qnorm.h | 13 - SLOPE-1.1.0/SLOPE/src/slope/regularization_sequence.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/score.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/screening.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/slope.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/solvers/hybrid.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/solvers/hybrid_cd.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/solvers/pgd.cpp | 6 SLOPE-1.1.0/SLOPE/src/slope/solvers/setup_solver.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/solvers/slope_threshold.cpp | 4 SLOPE-1.1.0/SLOPE/src/slope/sorted_l1_norm.cpp | 8 SLOPE-1.1.0/SLOPE/src/slope/timer.cpp | 2 SLOPE-1.1.0/SLOPE/src/slope/utils.cpp | 2 SLOPE-1.1.0/SLOPE/tests/testthat/test-binomial.R | 22 ++ 76 files changed, 231 insertions(+), 176 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards, Poisson, and Fine-Gray competing risks regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.3.0 dated 2025-06-05 and 1.4.3 dated 2025-10-30
Colossus-1.3.0/Colossus/inst/doc/Alt_Distrib_Starts.R |only Colossus-1.3.0/Colossus/inst/doc/Alt_Distrib_Starts.Rmd |only Colossus-1.3.0/Colossus/inst/doc/Alt_Distrib_Starts.html |only Colossus-1.3.0/Colossus/man/Check_Dupe_Columns.Rd |only Colossus-1.3.0/Colossus/man/Check_Trunc.Rd |only Colossus-1.3.0/Colossus/man/Check_Verbose.Rd |only Colossus-1.3.0/Colossus/man/Convert_Model_Eq.Rd |only Colossus-1.3.0/Colossus/man/Correct_Formula_Order.Rd |only Colossus-1.3.0/Colossus/man/CoxCurveSolver.Rd |only Colossus-1.3.0/Colossus/man/Cox_Relative_Risk.Rd |only Colossus-1.3.0/Colossus/man/Def_Control.Rd |only Colossus-1.3.0/Colossus/man/Def_Control_Guess.Rd |only Colossus-1.3.0/Colossus/man/Def_model_control.Rd |only Colossus-1.3.0/Colossus/man/Def_modelform_fix.Rd |only Colossus-1.3.0/Colossus/man/Gather_Guesses_CPP.Rd |only Colossus-1.3.0/Colossus/man/GetCensWeight.Rd |only Colossus-1.3.0/Colossus/man/Interpret_Output.Rd |only Colossus-1.3.0/Colossus/man/PoissonCurveSolver.Rd |only Colossus-1.3.0/Colossus/man/Rcomp_version.Rd |only Colossus-1.3.0/Colossus/man/Rcpp_version.Rd |only Colossus-1.3.0/Colossus/man/RunCoxNull.Rd |only Colossus-1.3.0/Colossus/man/RunCoxPlots.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Basic.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_CR.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Guesses_CPP.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Omnibus_Multidose.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Single.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Strata.Rd |only Colossus-1.3.0/Colossus/man/RunCoxRegression_Tier_Guesses.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonEventAssignment.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonEventAssignment_bound.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Guesses_CPP.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Joint_Omnibus.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Residual.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Single.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Strata.Rd |only Colossus-1.3.0/Colossus/man/RunPoissonRegression_Tier_Guesses.Rd |only Colossus-1.3.0/Colossus/man/factorize_par.Rd |only Colossus-1.3.0/Colossus/man/gcc_version.Rd |only Colossus-1.3.0/Colossus/man/get_os.Rd |only Colossus-1.3.0/Colossus/man/interact_them.Rd |only Colossus-1.3.0/Colossus/tests/testthat/test-Guess.R |only Colossus-1.3.0/Colossus/tests/testthat/test-Simplify.R |only Colossus-1.3.0/Colossus/vignettes/Alt_Distrib_Starts.Rmd |only Colossus-1.4.3/Colossus/DESCRIPTION | 26 Colossus-1.4.3/Colossus/MD5 | 324 Colossus-1.4.3/Colossus/NAMESPACE | 72 Colossus-1.4.3/Colossus/NEWS.md | 25 Colossus-1.4.3/Colossus/R/BasicRun.R |only Colossus-1.4.3/Colossus/R/CaseControl_Regression.R | 158 Colossus-1.4.3/Colossus/R/Cox_Regression.R | 1098 - Colossus-1.4.3/Colossus/R/LogitRegression.R |only Colossus-1.4.3/Colossus/R/ObjValidate.R |only Colossus-1.4.3/Colossus/R/PlotTypes.R | 346 Colossus-1.4.3/Colossus/R/Poisson_Regression.R | 1074 - Colossus-1.4.3/Colossus/R/RcppExports.R | 623 Colossus-1.4.3/Colossus/R/SurvTypes.R |only Colossus-1.4.3/Colossus/R/Utility.R | 2008 -- Colossus-1.4.3/Colossus/R/utils-roxygen.R | 28 Colossus-1.4.3/Colossus/R/zzz.R |only Colossus-1.4.3/Colossus/README.md | 30 Colossus-1.4.3/Colossus/build/vignette.rds |binary Colossus-1.4.3/Colossus/inst/CITATION | 2 Colossus-1.4.3/Colossus/inst/WORDLIST | 22 Colossus-1.4.3/Colossus/inst/doc/Alt_Run_Opt.R | 98 Colossus-1.4.3/Colossus/inst/doc/Alt_Run_Opt.Rmd | 122 Colossus-1.4.3/Colossus/inst/doc/Alt_Run_Opt.html | 585 Colossus-1.4.3/Colossus/inst/doc/Control_Options.Rmd | 72 Colossus-1.4.3/Colossus/inst/doc/Control_Options.html | 323 Colossus-1.4.3/Colossus/inst/doc/Dose_Formula_Inputs.R | 13 Colossus-1.4.3/Colossus/inst/doc/Dose_Formula_Inputs.Rmd | 16 Colossus-1.4.3/Colossus/inst/doc/Dose_Formula_Inputs.html | 198 Colossus-1.4.3/Colossus/inst/doc/Equation_Expression.R | 11 Colossus-1.4.3/Colossus/inst/doc/Equation_Expression.Rmd | 61 Colossus-1.4.3/Colossus/inst/doc/Equation_Expression.html | 406 Colossus-1.4.3/Colossus/inst/doc/Excess_and_Predicted_Cases.R | 20 Colossus-1.4.3/Colossus/inst/doc/Excess_and_Predicted_Cases.Rmd | 18 Colossus-1.4.3/Colossus/inst/doc/Excess_and_Predicted_Cases.html | 195 Colossus-1.4.3/Colossus/inst/doc/Grad_Hess.R | 14 Colossus-1.4.3/Colossus/inst/doc/Grad_Hess.Rmd | 14 Colossus-1.4.3/Colossus/inst/doc/Grad_Hess.html | 493 Colossus-1.4.3/Colossus/inst/doc/Logistic.R |only Colossus-1.4.3/Colossus/inst/doc/Logistic.Rmd |only Colossus-1.4.3/Colossus/inst/doc/Logistic.html |only Colossus-1.4.3/Colossus/inst/doc/Matched_Case_Control.R | 58 Colossus-1.4.3/Colossus/inst/doc/Matched_Case_Control.Rmd | 63 Colossus-1.4.3/Colossus/inst/doc/Matched_Case_Control.html | 457 Colossus-1.4.3/Colossus/inst/doc/Multi_Realization.R | 13 Colossus-1.4.3/Colossus/inst/doc/Multi_Realization.Rmd | 19 Colossus-1.4.3/Colossus/inst/doc/Multi_Realization.html | 213 Colossus-1.4.3/Colossus/inst/doc/Plotting_And_Analysis.R | 46 Colossus-1.4.3/Colossus/inst/doc/Plotting_And_Analysis.Rmd | 46 Colossus-1.4.3/Colossus/inst/doc/Plotting_And_Analysis.html | 516 Colossus-1.4.3/Colossus/inst/doc/SMR_Analysis.R | 31 Colossus-1.4.3/Colossus/inst/doc/SMR_Analysis.Rmd | 31 Colossus-1.4.3/Colossus/inst/doc/SMR_Analysis.html | 293 Colossus-1.4.3/Colossus/inst/doc/Script_Comparison_Epicure.R | 41 Colossus-1.4.3/Colossus/inst/doc/Script_Comparison_Epicure.Rmd | 51 Colossus-1.4.3/Colossus/inst/doc/Script_Comparison_Epicure.html | 253 Colossus-1.4.3/Colossus/inst/doc/Starting-Description.R | 42 Colossus-1.4.3/Colossus/inst/doc/Starting-Description.Rmd | 54 Colossus-1.4.3/Colossus/inst/doc/Starting-Description.html | 624 Colossus-1.4.3/Colossus/inst/doc/Time_Dep_Cov.R | 5 Colossus-1.4.3/Colossus/inst/doc/Time_Dep_Cov.Rmd | 5 Colossus-1.4.3/Colossus/inst/doc/Time_Dep_Cov.html | 395 Colossus-1.4.3/Colossus/inst/doc/Wald_and_Log_Bound.R | 152 Colossus-1.4.3/Colossus/inst/doc/Wald_and_Log_Bound.Rmd | 152 Colossus-1.4.3/Colossus/inst/doc/Wald_and_Log_Bound.html | 827 - Colossus-1.4.3/Colossus/inst/doc/count_time_tables.html | 600 Colossus-1.4.3/Colossus/man/CaseControlRun.Rd |only Colossus-1.4.3/Colossus/man/Check_Iters.Rd |only Colossus-1.4.3/Colossus/man/ColossusCoxSurv.Rd |only Colossus-1.4.3/Colossus/man/ColossusLogitSurv.Rd |only Colossus-1.4.3/Colossus/man/ColossusPoisSurv.Rd |only Colossus-1.4.3/Colossus/man/CoxRun.Rd |only Colossus-1.4.3/Colossus/man/CoxRunMulti.Rd |only Colossus-1.4.3/Colossus/man/Date_Shift.Rd | 15 Colossus-1.4.3/Colossus/man/EventAssignment.Rd |only Colossus-1.4.3/Colossus/man/EventAssignment.default.Rd |only Colossus-1.4.3/Colossus/man/EventAssignment.poisres.Rd |only Colossus-1.4.3/Colossus/man/Event_Count_Gen.Rd | 15 Colossus-1.4.3/Colossus/man/Event_Time_Gen.Rd | 15 Colossus-1.4.3/Colossus/man/Joint_Multiple_Events.Rd | 15 Colossus-1.4.3/Colossus/man/LikelihoodBound.Rd |only Colossus-1.4.3/Colossus/man/LikelihoodBound.coxres.Rd |only Colossus-1.4.3/Colossus/man/LikelihoodBound.default.Rd |only Colossus-1.4.3/Colossus/man/LikelihoodBound.poisres.Rd |only Colossus-1.4.3/Colossus/man/LogisticRun.Rd |only Colossus-1.4.3/Colossus/man/OMP_Check.Rd | 2 Colossus-1.4.3/Colossus/man/PoisRun.Rd |only Colossus-1.4.3/Colossus/man/PoisRunJoint.Rd |only Colossus-1.4.3/Colossus/man/PoisRunMulti.Rd |only Colossus-1.4.3/Colossus/man/RelativeRisk.Rd |only Colossus-1.4.3/Colossus/man/RelativeRisk.coxres.Rd |only Colossus-1.4.3/Colossus/man/RelativeRisk.default.Rd |only Colossus-1.4.3/Colossus/man/Replace_Missing.Rd | 15 Colossus-1.4.3/Colossus/man/Residual.Rd |only Colossus-1.4.3/Colossus/man/Residual.default.Rd |only Colossus-1.4.3/Colossus/man/Residual.poisres.Rd |only Colossus-1.4.3/Colossus/man/RunCaseControlRegression_Omnibus.Rd | 24 Colossus-1.4.3/Colossus/man/RunCoxRegression_Omnibus.Rd | 20 Colossus-1.4.3/Colossus/man/RunLogisticRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunPoissonRegression_Omnibus.Rd | 29 Colossus-1.4.3/Colossus/man/System_Version.Rd | 7 Colossus-1.4.3/Colossus/man/Time_Since.Rd | 15 Colossus-1.4.3/Colossus/man/apply_norm.Rd |only Colossus-1.4.3/Colossus/man/factorize.Rd | 15 Colossus-1.4.3/Colossus/man/gen_time_dep.Rd | 19 Colossus-1.4.3/Colossus/man/get_form.Rd |only Colossus-1.4.3/Colossus/man/get_form_joint.Rd |only Colossus-1.4.3/Colossus/man/plot.coxres.Rd |only Colossus-1.4.3/Colossus/man/print.caseconres.Rd |only Colossus-1.4.3/Colossus/man/print.coxres.Rd |only Colossus-1.4.3/Colossus/man/print.coxresbound.Rd |only Colossus-1.4.3/Colossus/man/print.logitres.Rd |only Colossus-1.4.3/Colossus/man/print.poisres.Rd |only Colossus-1.4.3/Colossus/man/print.poisresbound.Rd |only Colossus-1.4.3/Colossus/src/Calc_Repeated.cpp | 1844 +- Colossus-1.4.3/Colossus/src/Calc_Repeated.h | 46 Colossus-1.4.3/Colossus/src/Colossus_types.h | 24 Colossus-1.4.3/Colossus/src/Main_Bound.cpp |only Colossus-1.4.3/Colossus/src/Main_Bound.h |only Colossus-1.4.3/Colossus/src/Main_Functions.cpp | 6786 ++-------- Colossus-1.4.3/Colossus/src/Main_Functions.h | 43 Colossus-1.4.3/Colossus/src/Main_Multi.cpp |only Colossus-1.4.3/Colossus/src/Main_Multi.h |only Colossus-1.4.3/Colossus/src/Omnibus_Pieces.cpp | 939 - Colossus-1.4.3/Colossus/src/Omnibus_Pieces.h | 48 Colossus-1.4.3/Colossus/src/Plot_Extensions.cpp | 377 Colossus-1.4.3/Colossus/src/Plot_Extensions.h | 34 Colossus-1.4.3/Colossus/src/R_Interface.cpp | 666 Colossus-1.4.3/Colossus/src/R_Interface.h | 55 Colossus-1.4.3/Colossus/src/RcppExports.cpp | 2731 ---- Colossus-1.4.3/Colossus/src/Step_Calc.cpp | 867 - Colossus-1.4.3/Colossus/src/Step_Calc.h | 37 Colossus-1.4.3/Colossus/src/Step_Grad.cpp |only Colossus-1.4.3/Colossus/src/Step_Grad.h |only Colossus-1.4.3/Colossus/src/Step_Newton.cpp |only Colossus-1.4.3/Colossus/src/Step_Newton.h |only Colossus-1.4.3/Colossus/src/Subterms_Risk.cpp | 448 Colossus-1.4.3/Colossus/src/Subterms_Risk.h | 31 Colossus-1.4.3/Colossus/tests/testthat/sholom.csv |only Colossus-1.4.3/Colossus/tests/testthat/test-Assigned.R | 331 Colossus-1.4.3/Colossus/tests/testthat/test-CaseControl.R | 452 Colossus-1.4.3/Colossus/tests/testthat/test-Cox_Plot.R | 197 Colossus-1.4.3/Colossus/tests/testthat/test-Cox_Regression.R | 211 Colossus-1.4.3/Colossus/tests/testthat/test-Formula.R |only Colossus-1.4.3/Colossus/tests/testthat/test-Gradient.R | 140 Colossus-1.4.3/Colossus/tests/testthat/test-Joint.R | 290 Colossus-1.4.3/Colossus/tests/testthat/test-Logbound.R | 311 Colossus-1.4.3/Colossus/tests/testthat/test-Logit.R |only Colossus-1.4.3/Colossus/tests/testthat/test-Multidose.R | 351 Colossus-1.4.3/Colossus/tests/testthat/test-Norm.R |only Colossus-1.4.3/Colossus/tests/testthat/test-Omnibus.R | 385 Colossus-1.4.3/Colossus/tests/testthat/test-Poisson_Regression.R | 23 Colossus-1.4.3/Colossus/tests/testthat/test-Poisson_Residual.R | 49 Colossus-1.4.3/Colossus/tests/testthat/test-Utility.R | 1376 -- Colossus-1.4.3/Colossus/vignettes/Alt_Run_Opt.Rmd | 122 Colossus-1.4.3/Colossus/vignettes/Control_Options.Rmd | 72 Colossus-1.4.3/Colossus/vignettes/Dose_Formula_Inputs.Rmd | 16 Colossus-1.4.3/Colossus/vignettes/Equation_Expression.Rmd | 61 Colossus-1.4.3/Colossus/vignettes/Excess_and_Predicted_Cases.Rmd | 18 Colossus-1.4.3/Colossus/vignettes/Grad_Hess.Rmd | 14 Colossus-1.4.3/Colossus/vignettes/Logistic.Rmd |only Colossus-1.4.3/Colossus/vignettes/Matched_Case_Control.Rmd | 63 Colossus-1.4.3/Colossus/vignettes/Multi_Realization.Rmd | 19 Colossus-1.4.3/Colossus/vignettes/Plotting_And_Analysis.Rmd | 46 Colossus-1.4.3/Colossus/vignettes/SMR_Analysis.Rmd | 31 Colossus-1.4.3/Colossus/vignettes/Script_Comparison_Epicure.Rmd | 51 Colossus-1.4.3/Colossus/vignettes/Starting-Description.Rmd | 54 Colossus-1.4.3/Colossus/vignettes/Time_Dep_Cov.Rmd | 5 Colossus-1.4.3/Colossus/vignettes/Wald_and_Log_Bound.Rmd | 152 214 files changed, 11255 insertions(+), 22249 deletions(-)
Title: Bayesian Model Selection Approach for Parsimonious Gaussian
Mixture Models
Description: Model-based clustering using Bayesian parsimonious Gaussian mixture models.
MCMC (Markov chain Monte Carlo) are used for parameter estimation. The RJMCMC (Reversible-jump Markov chain Monte Carlo) is used for model selection.
GREEN et al. (1995) <doi:10.1093/biomet/82.4.711>.
Author: Yaoxiang Li [aut, cre],
Xiang Lu [aut],
Tanzy Love [aut]
Maintainer: Yaoxiang Li <yl814@georgetown.edu>
Diff between bpgmm versions 1.0.9 dated 2022-06-01 and 1.1.1 dated 2025-10-30
bpgmm-1.0.9/bpgmm/man/EvaluateProposalPsy.Rd |only bpgmm-1.0.9/bpgmm/man/MstepRJMCMCupdate.Rd |only bpgmm-1.0.9/bpgmm/man/VstepRJMCMCupdate.Rd |only bpgmm-1.0.9/bpgmm/man/calculateRatio.Rd |only bpgmm-1.0.9/bpgmm/man/calculateVarList.Rd |only bpgmm-1.0.9/bpgmm/man/changeConstraintFormat.Rd |only bpgmm-1.0.9/bpgmm/man/clearCurrentThetaYlist.Rd |only bpgmm-1.0.9/bpgmm/man/combineClusterPara.Rd |only bpgmm-1.0.9/bpgmm/man/evaluatePrior.Rd |only bpgmm-1.0.9/bpgmm/man/evaluatePriorLambda.Rd |only bpgmm-1.0.9/bpgmm/man/evaluatePriorPsi.Rd |only bpgmm-1.0.9/bpgmm/man/getIndThetaY.Rd |only bpgmm-1.0.9/bpgmm/man/getRemovedIndThetaY.Rd |only bpgmm-1.0.9/bpgmm/man/getThetaYWithEmpty.Rd |only bpgmm-1.0.9/bpgmm/man/getZmat.Rd |only bpgmm-1.0.9/bpgmm/man/getmode.Rd |only bpgmm-1.0.9/bpgmm/man/likelihood.Rd |only bpgmm-1.0.9/bpgmm/man/listToStrVec.Rd |only bpgmm-1.0.9/bpgmm/man/sumerizeZ.Rd |only bpgmm-1.0.9/bpgmm/man/toNEthetaYlist.Rd |only bpgmm-1.0.9/bpgmm/man/updatePostThetaY.Rd |only bpgmm-1.0.9/bpgmm/man/updatePostZ.Rd |only bpgmm-1.1.1/bpgmm/DESCRIPTION | 21 bpgmm-1.1.1/bpgmm/MD5 | 87 - bpgmm-1.1.1/bpgmm/NAMESPACE | 14 bpgmm-1.1.1/bpgmm/R/PGMMmain.R | 316 ++---- bpgmm-1.1.1/bpgmm/R/RcppExports.R | 62 - bpgmm-1.1.1/bpgmm/R/bpgmm-package.R | 6 bpgmm-1.1.1/bpgmm/R/hyperParamClass.R | 78 - bpgmm-1.1.1/bpgmm/R/paramClass.R | 166 +-- bpgmm-1.1.1/bpgmm/R/pgmmMstep.R | 788 +++++++--------- bpgmm-1.1.1/bpgmm/R/pgmmStay.R | 529 ++--------- bpgmm-1.1.1/bpgmm/R/pgmmVstep.R | 423 +++----- bpgmm-1.1.1/bpgmm/R/pkgData.R | 82 - bpgmm-1.1.1/bpgmm/R/posteriorZ.R | 157 --- bpgmm-1.1.1/bpgmm/R/prior.R | 872 +++++++----------- bpgmm-1.1.1/bpgmm/R/proposalLambda.R | 953 +++++++------------- bpgmm-1.1.1/bpgmm/R/proposalPsi.R | 1083 ++++++++--------------- bpgmm-1.1.1/bpgmm/R/sourceR.R | 88 - bpgmm-1.1.1/bpgmm/R/summerizeRes.R | 93 - bpgmm-1.1.1/bpgmm/R/updatePostThetaY.R | 225 +--- bpgmm-1.1.1/bpgmm/R/utils.R | 869 +++--------------- bpgmm-1.1.1/bpgmm/R/zzz.R | 14 bpgmm-1.1.1/bpgmm/man/CalculateProposalLambda.Rd | 143 --- bpgmm-1.1.1/bpgmm/man/CalculateProposalPsy.Rd | 140 -- bpgmm-1.1.1/bpgmm/man/EvaluateProposalLambda.Rd | 151 --- bpgmm-1.1.1/bpgmm/man/Hparam-class.Rd | 3 bpgmm-1.1.1/bpgmm/man/generatePriorLambda.Rd | 27 bpgmm-1.1.1/bpgmm/man/generatePriorPsi.Rd | 17 bpgmm-1.1.1/bpgmm/man/generatePriorThetaY.Rd | 22 bpgmm-1.1.1/bpgmm/man/pgmmRJMCMC.Rd | 55 - bpgmm-1.1.1/bpgmm/man/stayMCMCupdate.Rd | 92 - bpgmm-1.1.1/bpgmm/man/summerizePgmmRJMCMC.Rd | 36 bpgmm-1.1.1/bpgmm/man/toEthetaYlist.Rd | 75 - bpgmm-1.1.1/bpgmm/src/Makevars | 16 bpgmm-1.1.1/bpgmm/src/Makevars.win |only 56 files changed, 2469 insertions(+), 5234 deletions(-)
Title: Meteorological Data Processing
Description: Set of tools aimed at processing meteorological data, converting hourly recorded data to daily, monthly and annual data.
Author: Wagner Martins dos Santos [aut, cre] ,
Hoi Leong Lee [aut],
Edimir Xavier Leal Ferraz [aut] ,
Abelardo Antonio de Assuncao Montenegro [aut],
Lady Daiane Costa de Sousa Martins [aut] ,
Alan Cezar Bezerra [aut],
Ênio Farias de Franca e Silva [aut],
Thi [...truncated...]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
Diff between DataMetProcess versions 1.0.6 dated 2025-08-23 and 1.0.7 dated 2025-10-30
DESCRIPTION | 10 ++--- MD5 | 8 ++-- R/adjustDate.R | 58 ++++++++++++++++------------------ build/vignette.rds |binary inst/doc/DataMetProcess-vignette.html | 7 ++-- 5 files changed, 41 insertions(+), 42 deletions(-)
More information about DataMetProcess at CRAN
Permanent link
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.8.0 dated 2025-07-30 and 0.9.0 dated 2025-10-30
connectapi-0.8.0/connectapi/R/utils-ci.R |only connectapi-0.8.0/connectapi/inst/ci |only connectapi-0.8.0/connectapi/man/as.data.frame.connect_list_integrations.Rd |only connectapi-0.8.0/connectapi/man/as_tibble.connect_list_integrations.Rd |only connectapi-0.8.0/connectapi/tests/integrated/test-ldap.R |only connectapi-0.9.0/connectapi/DESCRIPTION | 10 connectapi-0.9.0/connectapi/MD5 | 182 +-- connectapi-0.9.0/connectapi/NAMESPACE | 19 connectapi-0.9.0/connectapi/NEWS.md | 17 connectapi-0.9.0/connectapi/R/connect.R | 14 connectapi-0.9.0/connectapi/R/content.R | 388 +++++-- connectapi-0.9.0/connectapi/R/deploy.R | 26 connectapi-0.9.0/connectapi/R/git.R | 35 connectapi-0.9.0/connectapi/R/integrations.R | 533 +++++++++- connectapi-0.9.0/connectapi/R/page.R | 6 connectapi-0.9.0/connectapi/R/promote.R | 2 connectapi-0.9.0/connectapi/R/schedule.R | 20 connectapi-0.9.0/connectapi/R/tags.R | 4 connectapi-0.9.0/connectapi/R/variant.R | 63 - connectapi-0.9.0/connectapi/README.md | 4 connectapi-0.9.0/connectapi/build/vignette.rds |binary connectapi-0.9.0/connectapi/inst/doc/customize-http.html | 4 connectapi-0.9.0/connectapi/inst/doc/getting-started.html | 4 connectapi-0.9.0/connectapi/man/Content.Rd | 71 - connectapi-0.9.0/connectapi/man/ContentTask.Rd | 4 connectapi-0.9.0/connectapi/man/EnvironmentR6.Rd | 4 connectapi-0.9.0/connectapi/man/PositConnect.Rd | 11 connectapi-0.9.0/connectapi/man/Task.Rd | 11 connectapi-0.9.0/connectapi/man/Vanity.Rd | 4 connectapi-0.9.0/connectapi/man/VariantR6.Rd | 18 connectapi-0.9.0/connectapi/man/VariantSchedule.Rd | 5 connectapi-0.9.0/connectapi/man/VariantTask.Rd | 5 connectapi-0.9.0/connectapi/man/as.data.frame.connect_content_list.Rd |only connectapi-0.9.0/connectapi/man/as.data.frame.connect_integration_list.Rd |only connectapi-0.9.0/connectapi/man/as_integration.Rd |only connectapi-0.9.0/connectapi/man/as_tibble.connect_content_list.Rd |only connectapi-0.9.0/connectapi/man/as_tibble.connect_integration_list.Rd |only connectapi-0.9.0/connectapi/man/bundle_dir.Rd | 2 connectapi-0.9.0/connectapi/man/bundle_path.Rd | 2 connectapi-0.9.0/connectapi/man/bundle_static.Rd | 2 connectapi-0.9.0/connectapi/man/connect.Rd | 2 connectapi-0.9.0/connectapi/man/content_delete.Rd | 4 connectapi-0.9.0/connectapi/man/content_item.Rd | 4 connectapi-0.9.0/connectapi/man/content_title.Rd | 4 connectapi-0.9.0/connectapi/man/content_update.Rd | 4 connectapi-0.9.0/connectapi/man/create_integration.Rd |only connectapi-0.9.0/connectapi/man/create_random_name.Rd | 4 connectapi-0.9.0/connectapi/man/dashboard_url.Rd | 4 connectapi-0.9.0/connectapi/man/delete_integration.Rd |only connectapi-0.9.0/connectapi/man/delete_thumbnail.Rd | 4 connectapi-0.9.0/connectapi/man/delete_vanity_url.Rd | 4 connectapi-0.9.0/connectapi/man/deploy.Rd | 2 connectapi-0.9.0/connectapi/man/deploy_repo.Rd | 4 connectapi-0.9.0/connectapi/man/environment.Rd | 4 connectapi-0.9.0/connectapi/man/get_associations.Rd |only connectapi-0.9.0/connectapi/man/get_bundles.Rd | 8 connectapi-0.9.0/connectapi/man/get_image.Rd | 4 connectapi-0.9.0/connectapi/man/get_integration.Rd |only connectapi-0.9.0/connectapi/man/get_integrations.Rd | 84 - connectapi-0.9.0/connectapi/man/get_job.Rd | 4 connectapi-0.9.0/connectapi/man/get_jobs.Rd | 4 connectapi-0.9.0/connectapi/man/get_log.Rd | 4 connectapi-0.9.0/connectapi/man/get_thumbnail.Rd | 4 connectapi-0.9.0/connectapi/man/get_vanity_url.Rd | 4 connectapi-0.9.0/connectapi/man/git.Rd | 4 connectapi-0.9.0/connectapi/man/has_thumbnail.Rd | 4 connectapi-0.9.0/connectapi/man/lock_content.Rd |only connectapi-0.9.0/connectapi/man/permissions.Rd | 4 connectapi-0.9.0/connectapi/man/search_content.Rd |only connectapi-0.9.0/connectapi/man/set_image.Rd | 4 connectapi-0.9.0/connectapi/man/set_integrations.Rd |only connectapi-0.9.0/connectapi/man/set_run_as.Rd | 4 connectapi-0.9.0/connectapi/man/set_thumbnail.Rd | 4 connectapi-0.9.0/connectapi/man/set_vanity_url.Rd | 4 connectapi-0.9.0/connectapi/man/swap_vanity_url.Rd | 4 connectapi-0.9.0/connectapi/man/swap_vanity_urls.Rd | 4 connectapi-0.9.0/connectapi/man/terminate_jobs.Rd | 4 connectapi-0.9.0/connectapi/man/update_integration.Rd |only connectapi-0.9.0/connectapi/man/verify_content_name.Rd | 4 connectapi-0.9.0/connectapi/tests/integrated/helper.R | 4 connectapi-0.9.0/connectapi/tests/integrated/test-content.R | 50 connectapi-0.9.0/connectapi/tests/integrated/test-deploy.R | 20 connectapi-0.9.0/connectapi/tests/integrated/test-get.R | 4 connectapi-0.9.0/connectapi/tests/integrated/test-git.R | 12 connectapi-0.9.0/connectapi/tests/integrated/test-run-as.R | 8 connectapi-0.9.0/connectapi/tests/testthat.R | 16 connectapi-0.9.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/c3426b0b/README.md | 4 connectapi-0.9.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/c3426b0b/repository.R |only connectapi-0.9.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/f2f37341/repository.json |only connectapi-0.9.0/connectapi/tests/testthat/2024.12.0/__api__/v1/content |only connectapi-0.9.0/connectapi/tests/testthat/2024.12.0/__api__/v1/oauth/integrations |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/content |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations-7ae937-POST.R |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations-aef9b2-POST.json |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations.json |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations/0000001.json |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations/0000002.json |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations/60586f1c-DELETE.204 |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations/60586f1c-b90ada-PATCH.R |only connectapi-0.9.0/connectapi/tests/testthat/2025.07.0/__api__/v1/oauth/integrations/60586f1c-c0720f-PATCH.json |only connectapi-0.9.0/connectapi/tests/testthat/2025.09.0 |only connectapi-0.9.0/connectapi/tests/testthat/test-content.R | 196 +++ connectapi-0.9.0/connectapi/tests/testthat/test-git.R | 35 connectapi-0.9.0/connectapi/tests/testthat/test-integrations.R | 245 ++++ connectapi-0.9.0/connectapi/tests/testthat/test-page.R |only 105 files changed, 1759 insertions(+), 509 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.81 dated 2025-07-14 and 2.4.82 dated 2025-10-30
BCEA-2.4.81/BCEA/R/make.report.R |only BCEA-2.4.81/BCEA/inst/jags |only BCEA-2.4.81/BCEA/inst/rmarkdown |only BCEA-2.4.81/BCEA/man/make.report.Rd |only BCEA-2.4.81/BCEA/man/openPDF.Rd |only BCEA-2.4.82/BCEA/DESCRIPTION | 25 +- BCEA-2.4.82/BCEA/MD5 | 84 +++---- BCEA-2.4.82/BCEA/NAMESPACE | 13 - BCEA-2.4.82/BCEA/NEWS.md | 38 +++ BCEA-2.4.82/BCEA/R/BCEA-deprecated.R | 9 BCEA-2.4.82/BCEA/R/CEriskav.R | 3 BCEA-2.4.82/BCEA/R/CEriskav_plot_graph.R | 155 ++++++++------ BCEA-2.4.82/BCEA/R/CreateInputs.R | 14 + BCEA-2.4.82/BCEA/R/bcea.R | 12 - BCEA-2.4.82/BCEA/R/bcea.default.R | 92 +++++--- BCEA-2.4.82/BCEA/R/ceac.plot.R | 14 - BCEA-2.4.82/BCEA/R/ceac_plot_graph.R | 2 BCEA-2.4.82/BCEA/R/ceplane_plot_graph.R | 301 ++++++++++++++-------------- BCEA-2.4.82/BCEA/R/compute_xxx.R | 1 BCEA-2.4.82/BCEA/R/contour.R | 6 BCEA-2.4.82/BCEA/R/contour_graph.R | 2 BCEA-2.4.82/BCEA/R/evppi.R | 4 BCEA-2.4.82/BCEA/R/evppi_plot_ggplot.R | 37 ++- BCEA-2.4.82/BCEA/R/info.rank.R | 1 BCEA-2.4.82/BCEA/R/info_rank_graph.R | 9 BCEA-2.4.82/BCEA/R/line_labels.R | 2 BCEA-2.4.82/BCEA/R/misc_helpers.R | 10 BCEA-2.4.82/BCEA/R/new_bcea.R | 143 +++++++------ BCEA-2.4.82/BCEA/R/prep_delta_ce.R | 45 ++-- BCEA-2.4.82/BCEA/R/struct.psa.R | 3 BCEA-2.4.82/BCEA/R/zzz.R | 2 BCEA-2.4.82/BCEA/build/partial.rdb |binary BCEA-2.4.82/BCEA/man/BCEA-deprecated.Rd | 9 BCEA-2.4.82/BCEA/man/CEriskav_assign.Rd | 3 BCEA-2.4.82/BCEA/man/bcea.Rd | 22 -- BCEA-2.4.82/BCEA/man/ceac.plot.Rd | 14 - BCEA-2.4.82/BCEA/man/contour.Rd | 6 BCEA-2.4.82/BCEA/man/createInputs.Rd | 14 + BCEA-2.4.82/BCEA/man/evppi.Rd | 8 BCEA-2.4.82/BCEA/man/quiet.Rd | 2 BCEA-2.4.82/BCEA/tests/testthat/test-bcea.R | 30 +- 41 files changed, 637 insertions(+), 498 deletions(-)
Title: Deep Neural Networks for Survival Analysis Using 'torch'
Description: Provides deep learning models for right-censored survival data using the 'torch' backend.
Supports multiple loss functions, including Cox partial likelihood, L2-penalized Cox, time-dependent Cox,
and accelerated failure time (AFT) loss. Offers a formula-based interface, built-in support for cross-validation,
hyperparameter tuning, survival curve plotting, and evaluation metrics such as the C-index, Brier score,
and integrated Brier score. For methodological details, see Kvamme et al. (2019) <https://www.jmlr.org/papers/v20/18-424.html>.
Author: Imad EL BADISY [aut, cre]
Maintainer: Imad EL BADISY <elbadisyimad@gmail.com>
Diff between survdnn versions 0.6.0 dated 2025-07-22 and 0.6.3 dated 2025-10-30
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++--------------------- NEWS.md | 53 ++++++++++++++++++++++++++++++++++------ R/evaluation.R | 6 ++++ R/gridsearch_survdnn.R | 5 --- R/losses.R | 1 R/metrics.R | 6 ++++ R/plot.survdnn.R | 2 + R/predict.survdnn.R | 2 + R/print.survdnn.R | 2 + R/summary.survdnn.R | 2 + R/survdnn.R | 4 +++ R/zzz.R | 25 ++++++++----------- README.md | 56 +++++++++++++++++++++++++++---------------- man/brier.Rd | 2 + man/build_dnn.Rd | 2 + man/cindex_survmat.Rd | 2 + man/cv_survdnn.Rd | 2 + man/evaluate_survdnn.Rd | 2 + man/gridsearch_survdnn.Rd | 5 --- man/ibs_survmat.Rd | 2 + man/plot.survdnn.Rd | 2 + man/predict.survdnn.Rd | 2 + man/print.survdnn.Rd | 2 + man/summarize_cv_survdnn.Rd | 2 + man/summary.survdnn.Rd | 2 + man/survdnn.Rd | 2 + tests/testthat/test-losses.R | 12 ++++++--- 28 files changed, 180 insertions(+), 87 deletions(-)
Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2022) <doi:10.48550/arXiv.2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.5 dated 2024-09-06 and 1.6.0 dated 2025-10-30
polle-1.5/polle/tests/testthat/test-policy_data_functions.R |only polle-1.5/polle/tests/testthat/test-policy_eval_subgroup.R |only polle-1.5/polle/tests/testthat/test-policy_learn_blip.R |only polle-1.5/polle/tests/testthat/test-policy_learn_drql.R |only polle-1.5/polle/tests/testthat/test-policy_learn_earl.R |only polle-1.5/polle/tests/testthat/test-policy_learn_owl.R |only polle-1.5/polle/tests/testthat/test-policy_learn_ptl.R |only polle-1.5/polle/tests/testthat/test-policy_learn_ql.R |only polle-1.5/polle/tests/testthat/test-policy_learn_rwl.R |only polle-1.6.0/polle/DESCRIPTION | 22 polle-1.6.0/polle/MD5 | 158 +- polle-1.6.0/polle/NAMESPACE | 16 polle-1.6.0/polle/NEWS.md | 9 polle-1.6.0/polle/R/Q_function.R | 93 - polle-1.6.0/polle/R/blip.R | 296 +++- polle-1.6.0/polle/R/c_function.R |only polle-1.6.0/polle/R/c_models.R |only polle-1.6.0/polle/R/drql.R | 17 polle-1.6.0/polle/R/earl.R | 3 polle-1.6.0/polle/R/estimate_target.R | 525 ++++++-- polle-1.6.0/polle/R/fit_functions.R | 123 + polle-1.6.0/polle/R/g_function.R | 104 - polle-1.6.0/polle/R/g_models.R | 202 +-- polle-1.6.0/polle/R/helper_functions.R | 62 polle-1.6.0/polle/R/history_functions.R | 26 polle-1.6.0/polle/R/m_function.R |only polle-1.6.0/polle/R/model_designs.R |only polle-1.6.0/polle/R/nuisance_functions.R | 16 polle-1.6.0/polle/R/owl.R | 10 polle-1.6.0/polle/R/policy_data.R | 482 ++++--- polle-1.6.0/polle/R/policy_data_functions.R | 339 +++-- polle-1.6.0/polle/R/policy_def.R | 50 polle-1.6.0/polle/R/policy_eval.R | 585 ++++++-- polle-1.6.0/polle/R/policy_eval_functions.R | 35 polle-1.6.0/polle/R/policy_eval_online.R |only polle-1.6.0/polle/R/policy_learn.R | 15 polle-1.6.0/polle/R/polle-package.R | 4 polle-1.6.0/polle/R/ptl.R | 14 polle-1.6.0/polle/R/q_models.R | 64 polle-1.6.0/polle/R/rql.R | 3 polle-1.6.0/polle/R/rwl.R | 3 polle-1.6.0/polle/R/simulation.R | 9 polle-1.6.0/polle/build/partial.rdb |binary polle-1.6.0/polle/build/vignette.rds |binary polle-1.6.0/polle/inst/doc/optimal_subgroup.html | 39 polle-1.6.0/polle/inst/doc/policy_data.R | 1 polle-1.6.0/polle/inst/doc/policy_data.Rmd | 1 polle-1.6.0/polle/inst/doc/policy_data.html | 480 +++---- polle-1.6.0/polle/inst/doc/policy_eval.R | 22 polle-1.6.0/polle/inst/doc/policy_eval.html | 86 - polle-1.6.0/polle/inst/doc/policy_learn.html | 249 +-- polle-1.6.0/polle/inst/doc/right_censoring.R |only polle-1.6.0/polle/inst/doc/right_censoring.Rmd |only polle-1.6.0/polle/inst/doc/right_censoring.html |only polle-1.6.0/polle/man/c_model.Rd |only polle-1.6.0/polle/man/control_blip.Rd | 5 polle-1.6.0/polle/man/figures |only polle-1.6.0/polle/man/fit_c_functions.Rd |only polle-1.6.0/polle/man/g_model.Rd | 2 polle-1.6.0/polle/man/get_event.Rd |only polle-1.6.0/polle/man/get_history.Rd | 4 polle-1.6.0/polle/man/get_id_stage.Rd | 6 polle-1.6.0/polle/man/plot.policy_data.Rd | 5 polle-1.6.0/polle/man/policy_data.Rd | 6 polle-1.6.0/polle/man/policy_eval.Rd | 37 polle-1.6.0/polle/man/policy_eval_online.Rd |only polle-1.6.0/polle/man/policy_learn.Rd | 8 polle-1.6.0/polle/man/polle-package.Rd | 2 polle-1.6.0/polle/man/predict.nuisance_functions.Rd | 8 polle-1.6.0/polle/man/q_model.Rd | 2 polle-1.6.0/polle/man/sim_two_stage.Rd | 2 polle-1.6.0/polle/tests/test-all.R | 2 polle-1.6.0/polle/tests/testthat/test-c_cox.R |only polle-1.6.0/polle/tests/testthat/test-fit_c_functions.R |only polle-1.6.0/polle/tests/testthat/test-fit_functions.R | 159 ++ polle-1.6.0/polle/tests/testthat/test-fit_m_function.R |only polle-1.6.0/polle/tests/testthat/test-g_models.R | 141 +- polle-1.6.0/polle/tests/testthat/test-model_designs.R |only polle-1.6.0/polle/tests/testthat/test-policy_data-functions.R |only polle-1.6.0/polle/tests/testthat/test-policy_data-right-censoring.R |only polle-1.6.0/polle/tests/testthat/test-policy_data.R | 281 ++-- polle-1.6.0/polle/tests/testthat/test-policy_def.R | 10 polle-1.6.0/polle/tests/testthat/test-policy_eval-censoring.R |only polle-1.6.0/polle/tests/testthat/test-policy_eval-subgroup.R |only polle-1.6.0/polle/tests/testthat/test-policy_eval.R | 655 +++++++++- polle-1.6.0/polle/tests/testthat/test-policy_eval_online.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-blip-censoring.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-blip.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-drql.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-earl.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-owl.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-ptl.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-ql.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn-rwl.R |only polle-1.6.0/polle/tests/testthat/test-policy_learn.R | 121 + polle-1.6.0/polle/tests/testthat/test-q_glmnet.R | 70 + polle-1.6.0/polle/tests/testthat/test-q_models.R | 56 polle-1.6.0/polle/vignettes/policy_data.Rmd | 1 polle-1.6.0/polle/vignettes/ref.bib | 15 polle-1.6.0/polle/vignettes/right_censoring.Rmd |only 100 files changed, 4056 insertions(+), 1705 deletions(-)
Title: Higher Level 'API' for 'torch'
Description: A high level interface for 'torch' providing utilities to reduce the
the amount of code needed for common tasks, abstract away torch details and
make the same code work on both the 'CPU' and 'GPU'. It's flexible enough to
support expressing a large range of models. It's heavily inspired by 'fastai' by
Howard et al. (2020) <doi:10.48550/arXiv.2002.04688>, 'Keras' by Chollet et al. (2015) and
'PyTorch Lightning' by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.
Author: Daniel Falbel [aut, cre, cph],
Christophe Regouby [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between luz versions 0.5.0 dated 2025-07-29 and 0.5.1 dated 2025-10-30
DESCRIPTION | 6 +- MD5 | 12 ++--- NEWS.md | 4 + R/module.R | 8 ++- inst/doc/get-started.R | 88 +++++++++++++++++++++---------------------- inst/doc/get-started.html | 40 +++++++++++-------- tests/testthat/test-module.R | 28 +++++++++++++ 7 files changed, 113 insertions(+), 73 deletions(-)
Title: Alternative and Fast ROC Analysis
Description: Alternative and fast algorithms for the analysis of receiver operating
characteristics curves (ROC curves) as described in Thomas et al. (2017)
<doi:10.1186/s41512-017-0017-y> and Thomas et al. (2023) <doi:10.1016/j.ajogmf.2023.101110>.
Author: Gregoire Thomas [aut, cre] ,
Robin Tuytten [ctb] ,
Jef Moerman [ctb],
Xavier Robin [cph] ,
Stefan Siegert [cph]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between alternativeROC versions 1.0.1 dated 2025-08-19 and 1.0.3 dated 2025-10-30
DESCRIPTION | 10 +-- MD5 | 14 ++--- NEWS | 11 ++++ R/rocperf.R | 96 ++++++++++++++++++++++++++--------- R/rocsesp.R | 7 +- man/rocperf.Rd | 19 +++++-- tests/testthat/test_rocperf.R | 110 ++++++++++++++++++++--------------------- tests/testthat/test_rocperfZ.R |only tests/testthat/test_rocsesp.R |only 9 files changed, 171 insertions(+), 96 deletions(-)
More information about alternativeROC at CRAN
Permanent link
Title: Procedures Related to the Zadeh's Extension Principle for Fuzzy
Data
Description: Procedures for calculation, plotting, animation, and approximation of the outputs for fuzzy numbers (see A.I. Ban, L. Coroianu, P. Grzegorzewski "Fuzzy Numbers: Approximations, Ranking and Applications" (2015)) based on the Zadeh's Extension Principle (see de Barros, L.C., Bassanezi, R.C., Lodwick, W.A. (2017) <doi:10.1007/978-3-662-53324-6_2>).
Author: Maciej Romaniuk [cre, aut] ),
Abbas Parchami [aut] ),
Przemyslaw Grzegorzewski [aut] )
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between ZEP versions 0.2.3 dated 2025-09-24 and 0.3.1 dated 2025-10-30
ZEP-0.2.3/ZEP/R/AnimateZFunction.R |only ZEP-0.2.3/ZEP/R/ApplyZFunction.R |only ZEP-0.2.3/ZEP/R/PlotZFunction.R |only ZEP-0.2.3/ZEP/man/AnimateZFunction.Rd |only ZEP-0.2.3/ZEP/man/ApplyZFunction.Rd |only ZEP-0.2.3/ZEP/man/PlotZFunction.Rd |only ZEP-0.2.3/ZEP/tests/testthat/_snaps/ApplyZFunction.md |only ZEP-0.2.3/ZEP/tests/testthat/test-AnimateZFunction.R |only ZEP-0.2.3/ZEP/tests/testthat/test-ApplyZFunction.R |only ZEP-0.2.3/ZEP/tests/testthat/test-PlotZFunction.R |only ZEP-0.3.1/ZEP/DESCRIPTION | 12 - ZEP-0.3.1/ZEP/MD5 | 36 +-- ZEP-0.3.1/ZEP/NAMESPACE | 6 ZEP-0.3.1/ZEP/R/AnimateListZEP.R |only ZEP-0.3.1/ZEP/R/AnimateZEP.R | 204 ++++-------------- ZEP-0.3.1/ZEP/R/ApplyZEP.R |only ZEP-0.3.1/ZEP/R/FuzzyApproximation.R | 4 ZEP-0.3.1/ZEP/R/PlotZEP.R |only ZEP-0.3.1/ZEP/R/approximationMehodsInside.R | 2 ZEP-0.3.1/ZEP/man/AnimateListZEP.Rd |only ZEP-0.3.1/ZEP/man/AnimateZEP.Rd | 54 ++-- ZEP-0.3.1/ZEP/man/ApplyZEP.Rd |only ZEP-0.3.1/ZEP/man/FuzzyApproximation.Rd | 2 ZEP-0.3.1/ZEP/man/PlotZEP.Rd |only ZEP-0.3.1/ZEP/tests/testthat/_snaps/ApplyZEP.md |only ZEP-0.3.1/ZEP/tests/testthat/test-AnimateListZEP.R |only ZEP-0.3.1/ZEP/tests/testthat/test-AnimateZEP.R | 18 - ZEP-0.3.1/ZEP/tests/testthat/test-ApplyZEP.R |only ZEP-0.3.1/ZEP/tests/testthat/test-PlotZEP.R |only 29 files changed, 120 insertions(+), 218 deletions(-)
Title: Analysis of Oceanographic Argo Floats
Description: Supports the analysis of oceanographic data recorded by Argo autonomous drifting profiling floats. Functions are provided to (a) download and cache data files, (b) subset data in various ways, (c) handle quality-control flags and (d) plot the results according to oceanographic conventions. A shiny app is provided for easy exploration of datasets. The package is designed to work well with the 'oce' package, providing a wide range of processing capabilities that are particular to oceanographic analysis. See Kelley, Harbin, and Richards (2021) <doi:10.3389/fmars.2021.635922> for more on the scientific context and applications.
Author: Dan Kelley [aut, cre, cph] ,
Jaimie Harbin [aut] ,
Dewey Dunnington [ctb] ,
Clark Richards [ctb]
Maintainer: Dan Kelley <dan.kelley@dal.ca>
Diff between argoFloats versions 1.0.7 dated 2023-10-17 and 1.0.9 dated 2025-10-30
DESCRIPTION | 19 MD5 | 100 - R/AllClass.R | 394 ++--- R/adjusted.R | 139 +- R/debug.R | 97 - R/defaults.R | 27 R/download.R | 65 R/extdata.R | 13 R/get.R | 473 +++--- R/mapApp.R | 51 R/merge.R | 132 + R/misc.R | 8 R/plot.R | 790 ++++++----- R/plot_TS.R | 203 +- R/qc.R | 128 - R/read.R | 214 +-- R/show.R | 61 R/subset.R | 956 +++++++------ R/summary.R | 51 README.md | 32 build/partial.rdb |binary build/vignette.rds |binary inst/doc/argoFloats.R | 134 - inst/doc/argoFloats.html | 15 inst/doc/qc.R | 158 +- inst/doc/qc.html | 17 inst/shiny/mapApp/app.R | 2131 ++++++++++++++++--------------- man/D4900785_048.nc.Rd | 2 man/R3901602_163.nc.Rd | 2 man/SD5903586_001.nc.Rd | 6 man/SR2902204_131.nc.Rd | 2 man/applyQC.Rd | 16 man/argoFloats.Rd | 2 man/argoFloatsDebug.Rd | 8 man/figures/README-unnamed-chunk-6-1.png |binary man/getIndex.Rd | 16 man/hexToBits.Rd | 4 man/index.Rd | 2 man/indexBgc.Rd | 6 man/indexDeep.Rd | 6 man/indexSynthetic.Rd | 6 man/merge-argoFloats-method.Rd | 6 man/plot-argoFloats-method.Rd | 76 - man/readProfiles.Rd | 24 man/showQCTests.Rd | 2 man/sub-sub-argoFloats-method.Rd | 8 man/subset-argoFloats-method.Rd | 180 ++ man/useAdjusted.Rd | 8 tests/testthat/test_download.R | 271 +-- tests/testthat/test_merge.R | 39 tests/testthat/test_subset.R | 269 ++- 51 files changed, 4074 insertions(+), 3295 deletions(-)
Title: Causal Inference with Super Learner and Deep Neural Networks
Description: Functions for deep learning estimation of Conditional Average Treatment Effects (CATEs)
from meta-learner models and Population Average Treatment Effects on the Treated (PATT) in settings with
treatment noncompliance using reticulate, TensorFlow and Keras3. Functions in the package also implements
the conformal prediction framework that enables computation and illustration of conformal prediction (CP)
intervals for estimated individual treatment effects (ITEs) from meta-learner models. Additional
functions in the package permit users to estimate the meta-learner CATEs and the PATT in settings with
treatment noncompliance using weighted ensemble learning via the super learner approach and R neural networks.
Author: Nguyen K. Huynh [aut, cre] ,
Bumba Mukherjee [aut] ,
Yang Yang [aut]
Maintainer: Nguyen K. Huynh <khoinguyen.huynh@r.hit-u.ac.jp>
Diff between DeepLearningCausal versions 0.0.106 dated 2025-06-11 and 0.0.107 dated 2025-10-30
DeepLearningCausal-0.0.106/DeepLearningCausal/R/global.R |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/metalearner_deepneural.Rd |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/pattc_deepneural.Rd |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/plot.metalearner_deepneural.Rd |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/plot.pattc_deepneural.Rd |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/print.metalearner_deepneural.Rd |only DeepLearningCausal-0.0.106/DeepLearningCausal/man/print.pattc_deepneural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/DESCRIPTION | 65 DeepLearningCausal-0.0.107/DeepLearningCausal/MD5 | 81 DeepLearningCausal-0.0.107/DeepLearningCausal/NAMESPACE | 27 DeepLearningCausal-0.0.107/DeepLearningCausal/R/deep_meta_learners.R |only DeepLearningCausal-0.0.107/DeepLearningCausal/R/meta_learners.R | 1271 ++++++---- DeepLearningCausal-0.0.107/DeepLearningCausal/R/neural_meta_learners.R | 126 DeepLearningCausal-0.0.107/DeepLearningCausal/R/patt_deep.R |only DeepLearningCausal-0.0.107/DeepLearningCausal/R/patt_ensemble.R | 62 DeepLearningCausal-0.0.107/DeepLearningCausal/R/patt_neural.R | 138 - DeepLearningCausal-0.0.107/DeepLearningCausal/R/plots.R | 457 ++- DeepLearningCausal-0.0.107/DeepLearningCausal/R/py_setup.R |only DeepLearningCausal-0.0.107/DeepLearningCausal/R/utils.R | 72 DeepLearningCausal-0.0.107/DeepLearningCausal/R/zzz.R |only DeepLearningCausal-0.0.107/DeepLearningCausal/data/exp_data.rda |binary DeepLearningCausal-0.0.107/DeepLearningCausal/data/exp_data_full.rda |binary DeepLearningCausal-0.0.107/DeepLearningCausal/data/pop_data.rda |binary DeepLearningCausal-0.0.107/DeepLearningCausal/data/pop_data_full.rda |binary DeepLearningCausal-0.0.107/DeepLearningCausal/man/build_model.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/check_cran_deps.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/check_python_modules.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/complier_mod.Rd | 69 DeepLearningCausal-0.0.107/DeepLearningCausal/man/conformal_plot.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/deep_complier_mod.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/deep_predict.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/deep_response_model.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/hte_plot.Rd | 19 DeepLearningCausal-0.0.107/DeepLearningCausal/man/metalearner_deeplearning.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/metalearner_ensemble.Rd | 59 DeepLearningCausal-0.0.107/DeepLearningCausal/man/metalearner_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/neuralnet_complier_mod.Rd | 3 DeepLearningCausal-0.0.107/DeepLearningCausal/man/neuralnet_pattc_counterfactuals.Rd | 4 DeepLearningCausal-0.0.107/DeepLearningCausal/man/neuralnet_response_model.Rd | 9 DeepLearningCausal-0.0.107/DeepLearningCausal/man/pattc_counterfactuals.Rd | 66 DeepLearningCausal-0.0.107/DeepLearningCausal/man/pattc_deeplearning.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/pattc_deeplearning_counterfactuals.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/pattc_ensemble.Rd | 197 - DeepLearningCausal-0.0.107/DeepLearningCausal/man/pattc_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/plot.metalearner_ensemble.Rd | 2 DeepLearningCausal-0.0.107/DeepLearningCausal/man/plot.metalearner_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/plot.pattc_deeplearning.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/plot.pattc_ensemble.Rd | 2 DeepLearningCausal-0.0.107/DeepLearningCausal/man/plot.pattc_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/popcall.Rd | 2 DeepLearningCausal-0.0.107/DeepLearningCausal/man/print.metalearner_deeplearning.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/print.metalearner_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/print.pattc_deeplearning.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/print.pattc_neural.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/python_ready.Rd |only DeepLearningCausal-0.0.107/DeepLearningCausal/man/response_model.Rd | 4 DeepLearningCausal-0.0.107/DeepLearningCausal/tests |only 57 files changed, 1749 insertions(+), 986 deletions(-)
More information about DeepLearningCausal at CRAN
Permanent link
Title: Optimal Categorisation of Continuous Variables in Prediction
Models
Description: Allows the user to categorise a continuous predictor variable in a logistic or a Cox proportional hazards regression setting, by maximising the discriminative ability of the model. I Barrio, I Arostegui, MX Rodriguez-Alvarez, JM Quintana (2015) <doi:10.1177/0962280215601873>. I Barrio, MX Rodriguez-Alvarez, L Meira-Machado, C Esteban, I Arostegui (2017) <https://www.idescat.cat/sort/sort411/41.1.3.barrio-etal.pdf>.
Author: Irantzu Barrio [aut, cre],
Maria Xose Rodriguez-Alvarez [aut],
Inmaculada Arostegui [ctb],
Diana Marcela Perez [ctb]
Maintainer: Irantzu Barrio <irantzu.barrio@ehu.eus>
Diff between CatPredi versions 1.3 dated 2022-01-10 and 1.4 dated 2025-10-30
DESCRIPTION | 17 ++- MD5 | 54 ++++++------ NAMESPACE | 6 + R/backaddfor.R |only R/backaddfor.cind.R |only R/calculate.CPE.R | 53 +++++------ R/catpredi.R | 40 ++++++-- R/catpredi.survival.R | 64 +++++++++++--- R/comp.cutpoints.survival.R | 173 +++++++++++++++++++------------------- R/compare.AUC.ht.R |only R/controlcatpredi.R | 15 +-- R/controlcatpredi.survival.R | 16 +-- R/cpe.opt.corrected.R | 78 ++++++++--------- R/k.points.max.cind.R | 49 +++++----- R/plot.catpredi.R | 44 +++++++-- R/plot.catpredi.survival.R | 22 ++-- R/print.catpredi.R | 107 ++++++++++++----------- R/print.catpredi.survival.R | 179 ++++++++++++++++++++-------------------- R/select.cutpoint.cpe.R | 60 ++++++------- man/CatPredi-package.Rd | 62 +++++++------ man/catpredi.Rd | 26 ++++- man/catpredi.survival.Rd | 169 ++++++++++++++++++------------------- man/comp.cutpoints.Rd | 148 ++++++++++++++++----------------- man/comp.cutpoints.survival.Rd | 146 ++++++++++++++++---------------- man/compare.AUC.ht.Rd |only man/controlcatpredi.Rd | 83 +++++++++--------- man/controlcatpredi.survival.Rd | 4 man/plot.catpredi.Rd | 12 +- man/plot.catpredi.survival.Rd | 112 ++++++++++++------------- man/summary.catpredi.Rd | 132 ++++++++++++++--------------- 30 files changed, 988 insertions(+), 883 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.0.2 dated 2025-08-19 and 1.1.0 dated 2025-10-30
clinpubr-1.0.2/clinpubr/R/answer_check.r |only clinpubr-1.0.2/clinpubr/R/baseline_table.r |only clinpubr-1.0.2/clinpubr/R/calculate_index.r |only clinpubr-1.0.2/clinpubr/R/check_nonnum.r |only clinpubr-1.0.2/clinpubr/R/classif_model_compare.r |only clinpubr-1.0.2/clinpubr/R/combine_files.r |only clinpubr-1.0.2/clinpubr/R/cut_by.r |only clinpubr-1.0.2/clinpubr/R/extract_num.r |only clinpubr-1.0.2/clinpubr/R/get_valid.r |only clinpubr-1.0.2/clinpubr/R/get_valid_subset.r |only clinpubr-1.0.2/clinpubr/R/importance_plot.r |only clinpubr-1.0.2/clinpubr/R/initial_cleaning.r |only clinpubr-1.0.2/clinpubr/R/interactions.r |only clinpubr-1.0.2/clinpubr/R/mark_outlier.r |only clinpubr-1.0.2/clinpubr/R/misc.r |only clinpubr-1.0.2/clinpubr/R/multichoice.r |only clinpubr-1.0.2/clinpubr/R/rcs_plot.r |only clinpubr-1.0.2/clinpubr/R/regressions.r |only clinpubr-1.0.2/clinpubr/R/subgroup_forest.r |only clinpubr-1.0.2/clinpubr/R/subject_standardize.r |only clinpubr-1.0.2/clinpubr/R/to_date.r |only clinpubr-1.0.2/clinpubr/R/unit_standardize.r |only clinpubr-1.0.2/clinpubr/tests/testthat/subject_view.csv |only clinpubr-1.0.2/clinpubr/tests/testthat/test-calculate_index.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-check_nonnum.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-classif_model_compare.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-get_valid.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-get_valid_subset.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-interactions.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-multichoice.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-rcs_plot.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-regressions.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-subject_standardize.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-to_date.r |only clinpubr-1.0.2/clinpubr/tests/testthat/test-unit_standardize.r |only clinpubr-1.1.0/clinpubr/DESCRIPTION | 27 clinpubr-1.1.0/clinpubr/MD5 | 252 +-- clinpubr-1.1.0/clinpubr/NAMESPACE | 4 clinpubr-1.1.0/clinpubr/NEWS.md | 18 clinpubr-1.1.0/clinpubr/R/answer_check.R |only clinpubr-1.1.0/clinpubr/R/baseline_table.R |only clinpubr-1.1.0/clinpubr/R/calculate_index.R |only clinpubr-1.1.0/clinpubr/R/check_nonnum.R |only clinpubr-1.1.0/clinpubr/R/classif_model_compare.R |only clinpubr-1.1.0/clinpubr/R/combine_files.R |only clinpubr-1.1.0/clinpubr/R/cut_by.R |only clinpubr-1.1.0/clinpubr/R/exclusion_count.R |only clinpubr-1.1.0/clinpubr/R/extract_num.R |only clinpubr-1.1.0/clinpubr/R/get_valid.R |only clinpubr-1.1.0/clinpubr/R/get_valid_subset.R |only clinpubr-1.1.0/clinpubr/R/importance_plot.R |only clinpubr-1.1.0/clinpubr/R/initial_cleaning.R |only clinpubr-1.1.0/clinpubr/R/interactions.R |only clinpubr-1.1.0/clinpubr/R/mark_outlier.R |only clinpubr-1.1.0/clinpubr/R/misc.R |only clinpubr-1.1.0/clinpubr/R/multichoice.R |only clinpubr-1.1.0/clinpubr/R/predictor_effect_plot.R |only clinpubr-1.1.0/clinpubr/R/rcs_plot.R |only clinpubr-1.1.0/clinpubr/R/regressions.R |only clinpubr-1.1.0/clinpubr/R/subgroup_forest.R |only clinpubr-1.1.0/clinpubr/R/subject_standardize.R |only clinpubr-1.1.0/clinpubr/R/to_date.R |only clinpubr-1.1.0/clinpubr/R/unit_standardize.R |only clinpubr-1.1.0/clinpubr/R/utils.R | 11 clinpubr-1.1.0/clinpubr/README.md | 81 - clinpubr-1.1.0/clinpubr/man/add_lists.Rd | 2 clinpubr-1.1.0/clinpubr/man/answer_check.Rd | 2 clinpubr-1.1.0/clinpubr/man/baseline_table.Rd | 2 clinpubr-1.1.0/clinpubr/man/break_at.Rd | 2 clinpubr-1.1.0/clinpubr/man/calculate_index.Rd | 2 clinpubr-1.1.0/clinpubr/man/check_nonnum.Rd | 2 clinpubr-1.1.0/clinpubr/man/classif_model_compare.Rd | 6 clinpubr-1.1.0/clinpubr/man/combine_files.Rd | 2 clinpubr-1.1.0/clinpubr/man/combine_multichoice.Rd | 90 - clinpubr-1.1.0/clinpubr/man/common_prefix.Rd | 40 clinpubr-1.1.0/clinpubr/man/cut_by.Rd | 2 clinpubr-1.1.0/clinpubr/man/df_view_nonnum.Rd | 2 clinpubr-1.1.0/clinpubr/man/exclusion_count.Rd |only clinpubr-1.1.0/clinpubr/man/extract_num.Rd | 2 clinpubr-1.1.0/clinpubr/man/figures/README-example_3.3-1.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.4-1.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.4-2.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.5-1.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.5-2.png |only clinpubr-1.1.0/clinpubr/man/figures/README-example_3.6-1.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.7-1.png |binary clinpubr-1.1.0/clinpubr/man/figures/README-example_3.7-2.png |only clinpubr-1.1.0/clinpubr/man/figures/README-example_3.7-3.png |only clinpubr-1.1.0/clinpubr/man/figures/README-example_3.8-1.png |only clinpubr-1.1.0/clinpubr/man/fill_with_last.Rd | 2 clinpubr-1.1.0/clinpubr/man/filter_rcs_predictors.Rd | 2 clinpubr-1.1.0/clinpubr/man/first_mode.Rd | 2 clinpubr-1.1.0/clinpubr/man/format_pval.Rd | 2 clinpubr-1.1.0/clinpubr/man/formula_add_covs.Rd | 2 clinpubr-1.1.0/clinpubr/man/get_samples.Rd | 2 clinpubr-1.1.0/clinpubr/man/get_valid.Rd | 2 clinpubr-1.1.0/clinpubr/man/get_valid_subset.Rd | 2 clinpubr-1.1.0/clinpubr/man/get_var_types.Rd | 2 clinpubr-1.1.0/clinpubr/man/importance_plot.Rd | 2 clinpubr-1.1.0/clinpubr/man/indicate_duplicates.Rd | 58 clinpubr-1.1.0/clinpubr/man/interaction_p_value.Rd | 10 clinpubr-1.1.0/clinpubr/man/interaction_plot.Rd | 10 clinpubr-1.1.0/clinpubr/man/interaction_scan.Rd | 10 clinpubr-1.1.0/clinpubr/man/mad_outlier.Rd | 2 clinpubr-1.1.0/clinpubr/man/max_missing_rates.Rd | 2 clinpubr-1.1.0/clinpubr/man/merge_ordered_vectors.Rd | 2 clinpubr-1.1.0/clinpubr/man/na2false.Rd | 2 clinpubr-1.1.0/clinpubr/man/na_max.Rd |only clinpubr-1.1.0/clinpubr/man/predictor_effect_plot.Rd |only clinpubr-1.1.0/clinpubr/man/qq_show.Rd | 2 clinpubr-1.1.0/clinpubr/man/rcs_plot.Rd | 59 clinpubr-1.1.0/clinpubr/man/regression_basic_results.Rd | 12 clinpubr-1.1.0/clinpubr/man/regression_fit.Rd | 10 clinpubr-1.1.0/clinpubr/man/regression_forest.Rd | 10 clinpubr-1.1.0/clinpubr/man/regression_scan.Rd | 10 clinpubr-1.1.0/clinpubr/man/replace_elements.Rd | 2 clinpubr-1.1.0/clinpubr/man/split_multichoice.Rd | 2 clinpubr-1.1.0/clinpubr/man/str_match_replace.Rd | 2 clinpubr-1.1.0/clinpubr/man/subgroup_forest.Rd | 13 clinpubr-1.1.0/clinpubr/man/subject_view.Rd | 2 clinpubr-1.1.0/clinpubr/man/test_normality.Rd | 74 - clinpubr-1.1.0/clinpubr/man/to_date.Rd | 2 clinpubr-1.1.0/clinpubr/man/unit_standardize.Rd | 2 clinpubr-1.1.0/clinpubr/man/unit_view.Rd | 2 clinpubr-1.1.0/clinpubr/man/unmake_names.Rd | 2 clinpubr-1.1.0/clinpubr/man/value_initial_cleaning.Rd | 2 clinpubr-1.1.0/clinpubr/man/vec2code.Rd | 2 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/classif_model_compare.md | 8 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/classif_model_compare/calibration-plot.svg | 44 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/classif_model_compare/dca-plot.svg | 44 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/classif_model_compare/pr-plot.svg |only clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/classif_model_compare/roc-plot.svg | 44 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/importance_plot/test-plot-png.svg | 80 - clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/interactions.md | 7 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/interactions/cox-interaction-plot.svg | 36 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/interactions/logistic-interaction-plot.svg | 32 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/misc/qq-plot.svg | 26 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/predictor_effect_plot |only clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot.md | 7 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/cox-model-rcs-plot-y-0-5-to-2-5.svg | 16 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/cox-model-rcs-plot.svg | 48 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/linear-model-rcs-plot.svg | 38 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot-5-knots.svg | 14 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot-no-group.svg | 14 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot-ref-60.svg | 14 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot-ref-mean.svg | 14 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot-y-log10-transformed.svg | 26 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/rcs_plot/logistic-model-rcs-plot.svg | 36 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/regressions.md | 18 clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/regressions/cox-kmplot-median.svg | 658 ++++----- clinpubr-1.1.0/clinpubr/tests/testthat/_snaps/regressions/cox-kmplot-quartile.svg | 690 +++++----- clinpubr-1.1.0/clinpubr/tests/testthat/test-calculate_index.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-check_nonnum.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-classif_model_compare.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-exclusion_count.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-get_valid.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-get_valid_subset.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-interactions.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-misc.R | 8 clinpubr-1.1.0/clinpubr/tests/testthat/test-multichoice.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-predictor_effect_plot.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-rcs_plot.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-regressions.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-subject_standardize.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-to_date.R |only clinpubr-1.1.0/clinpubr/tests/testthat/test-unit_standardize.R |only 166 files changed, 1491 insertions(+), 1306 deletions(-)
Title: A Tidy Implementation of Heatmap
Description: This is a tidy implementation for heatmap. At the
moment it is based on the (great) package 'ComplexHeatmap'. The goal
of this package is to interface a tidy data frame with this powerful
tool. Some of the advantages are: Row and/or columns colour
annotations are easy to integrate just specifying one parameter
(column names). Custom grouping of rows is easy to specify providing
a grouped tbl. For example: df %>% group_by(...). Labels size
adjusted by row and column total number. Default use of Brewer and
Viridis palettes.
Author: Stefano Mangiola [aut, cre],
Anthony Papenfuss [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyHeatmap versions 1.12.3 dated 2025-10-26 and 1.13.1 dated 2025-10-30
DESCRIPTION | 6 MD5 | 42 ++- R/classes.R | 6 R/functions.R | 19 + R/methods.R | 21 + R/tidyHeatmap-package.R |only build/stage23.rdb |binary inst/NEWS.rd | 18 - inst/doc/introduction.R | 101 ++++++++ inst/doc/introduction.Rmd | 111 +++++++++ inst/doc/introduction.html | 362 +++++++++++++++++++----------- man/layer_text-method.Rd | 6 man/tidyHeatmap-package.Rd |only tests/testthat/_snaps/color-functionality |only tests/testthat/test-color-functionality.R |only vignettes/introduction.Rmd | 111 +++++++++ 16 files changed, 641 insertions(+), 162 deletions(-)
Title: Targeted Inference
Description: Various methods for targeted and semiparametric inference including
augmented inverse probability weighted (AIPW) estimators for missing data and
causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>),
variable importance and conditional average treatment effects (CATE)
(van der Laan (2006) <doi:10.2202/1557-4679.1008>),
estimators for risk differences and relative risks (Richardson et al. (2017)
<doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized
linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [aut],
Andreas Nordland [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between targeted versions 0.5 dated 2024-02-22 and 0.6 dated 2025-10-30
targeted-0.5/targeted/R/NB-methods.R |only targeted-0.5/targeted/R/NB.R |only targeted-0.5/targeted/R/NB2.R |only targeted-0.5/targeted/R/SL.R |only targeted-0.5/targeted/R/ml_model.R |only targeted-0.5/targeted/R/predict.NB.R |only targeted-0.5/targeted/R/procform.R |only targeted-0.5/targeted/inst/doc/ate.R |only targeted-0.5/targeted/inst/doc/ate.Rmd |only targeted-0.5/targeted/inst/doc/ate.html |only targeted-0.5/targeted/inst/doc/ode.R |only targeted-0.5/targeted/inst/doc/ode.Rmd |only targeted-0.5/targeted/inst/doc/ode.html |only targeted-0.5/targeted/inst/include/target |only targeted-0.5/targeted/inst/misc/ode.Rmd |only targeted-0.5/targeted/man/NB-class.Rd |only targeted-0.5/targeted/man/NB.Rd |only targeted-0.5/targeted/man/Scoring.Rd |only targeted-0.5/targeted/man/cv.Rd |only targeted-0.5/targeted/man/figures/logo.svg |only targeted-0.5/targeted/man/predict.NB.Rd |only targeted-0.5/targeted/src/cumres.cpp |only targeted-0.5/targeted/src/glm.cpp |only targeted-0.5/targeted/src/kalman.cpp |only targeted-0.5/targeted/src/mlogit.cpp |only targeted-0.5/targeted/src/nb.cpp |only targeted-0.5/targeted/src/nondom.cpp |only targeted-0.5/targeted/src/odesolver.cpp |only targeted-0.5/targeted/src/pava.cpp |only targeted-0.5/targeted/src/target.cpp |only targeted-0.5/targeted/src/utils.cpp |only targeted-0.5/targeted/tests/test-all.R |only targeted-0.5/targeted/tests/testthat |only targeted-0.5/targeted/vignettes/ate.Rmd |only targeted-0.5/targeted/vignettes/ode.Rmd |only targeted-0.6/targeted/DESCRIPTION | 29 targeted-0.6/targeted/MD5 | 299 ++-- targeted-0.6/targeted/NAMESPACE | 87 + targeted-0.6/targeted/NEWS.md | 84 + targeted-0.6/targeted/R/RATE.R | 259 +-- targeted-0.6/targeted/R/RcppExports.R | 8 targeted-0.6/targeted/R/aipw.R | 75 - targeted-0.6/targeted/R/alean.R | 122 - targeted-0.6/targeted/R/ate.R | 516 +++--- targeted-0.6/targeted/R/calibration.R | 296 ++-- targeted-0.6/targeted/R/cate.R | 1036 +++++++------- targeted-0.6/targeted/R/cate_link.R |only targeted-0.6/targeted/R/cumhaz.R | 206 ++ targeted-0.6/targeted/R/cv.R | 266 ++- targeted-0.6/targeted/R/deprecate.R |only targeted-0.6/targeted/R/design.R | 304 +++- targeted-0.6/targeted/R/expand.list.R | 74 - targeted-0.6/targeted/R/intsurv.R | 135 + targeted-0.6/targeted/R/learner.R |only targeted-0.6/targeted/R/learner_expand_grid.R |only targeted-0.6/targeted/R/learner_gam.R |only targeted-0.6/targeted/R/learner_glm.R |only targeted-0.6/targeted/R/learner_glmnet.R |only targeted-0.6/targeted/R/learner_grf.R |only targeted-0.6/targeted/R/learner_hal.R |only targeted-0.6/targeted/R/learner_isoreg.R |only targeted-0.6/targeted/R/learner_mars.R |only targeted-0.6/targeted/R/learner_naivebayes.R |only targeted-0.6/targeted/R/learner_sl.R |only targeted-0.6/targeted/R/learner_stratify.R |only targeted-0.6/targeted/R/learner_svm.R |only targeted-0.6/targeted/R/learner_wrappers.R |only targeted-0.6/targeted/R/learner_xgboost.R |only targeted-0.6/targeted/R/naivebayes.R |only targeted-0.6/targeted/R/nondom.R | 44 targeted-0.6/targeted/R/ode.R | 176 +- targeted-0.6/targeted/R/pava.R | 66 targeted-0.6/targeted/R/predict.density.R | 16 targeted-0.6/targeted/R/riskreg.R | 338 ++-- targeted-0.6/targeted/R/riskreg_cens.R | 275 +-- targeted-0.6/targeted/R/scoring.R | 103 - targeted-0.6/targeted/R/softmax.R | 19 targeted-0.6/targeted/R/superlearner.R |only targeted-0.6/targeted/R/targeted-methods.R | 86 - targeted-0.6/targeted/R/targeted-package.R | 133 + targeted-0.6/targeted/R/test_intersection_sw.R |only targeted-0.6/targeted/R/truncatedscore.R |only targeted-0.6/targeted/R/utils.R | 85 - targeted-0.6/targeted/README.md | 399 +++-- targeted-0.6/targeted/build/partial.rdb |binary targeted-0.6/targeted/build/vignette.rds |binary targeted-0.6/targeted/data |only targeted-0.6/targeted/demo/targeted.R | 2 targeted-0.6/targeted/inst/README.Rmd |only targeted-0.6/targeted/inst/doc/predictionclass.R |only targeted-0.6/targeted/inst/doc/predictionclass.Rmd |only targeted-0.6/targeted/inst/doc/predictionclass.html |only targeted-0.6/targeted/inst/doc/riskregression.R | 14 targeted-0.6/targeted/inst/doc/riskregression.Rmd | 14 targeted-0.6/targeted/inst/doc/riskregression.html | 649 +------- targeted-0.6/targeted/inst/include/targeted_RcppExports.h | 42 targeted-0.6/targeted/inst/misc/dp.R | 2 targeted-0.6/targeted/inst/misc/logohex1.png |only targeted-0.6/targeted/inst/misc/multiclasspred.Rmd | 27 targeted-0.6/targeted/inst/misc/proto.R | 58 targeted-0.6/targeted/inst/slowtest |only targeted-0.6/targeted/inst/slowtest.R |only targeted-0.6/targeted/inst/tinytest |only targeted-0.6/targeted/man/ML.Rd | 18 targeted-0.6/targeted/man/RATE.Rd | 12 targeted-0.6/targeted/man/RATE.surv.Rd | 40 targeted-0.6/targeted/man/SL.Rd | 16 targeted-0.6/targeted/man/aipw.Rd | 20 targeted-0.6/targeted/man/alean.Rd | 31 targeted-0.6/targeted/man/ate.Rd | 55 targeted-0.6/targeted/man/calibration-class.Rd | 15 targeted-0.6/targeted/man/calibration.Rd | 14 targeted-0.6/targeted/man/cate.Rd | 134 + targeted-0.6/targeted/man/cate_link.Rd | 2 targeted-0.6/targeted/man/constructor_shared.Rd |only targeted-0.6/targeted/man/cross_validated-class.Rd | 2 targeted-0.6/targeted/man/crr.Rd | 12 targeted-0.6/targeted/man/cumhaz.Rd |only targeted-0.6/targeted/man/cv.default.Rd |only targeted-0.6/targeted/man/cv.learner_sl.Rd |only targeted-0.6/targeted/man/deprecate_arg_warn.Rd |only targeted-0.6/targeted/man/deprecated_argument_names.Rd |only targeted-0.6/targeted/man/design.Rd | 33 targeted-0.6/targeted/man/estimate_truncatedscore.Rd |only targeted-0.6/targeted/man/expand.list.Rd | 8 targeted-0.6/targeted/man/figures/README-lrplot-1.png |only targeted-0.6/targeted/man/figures/README-lrsl_plot-1.png |only targeted-0.6/targeted/man/figures/README-simplot-1.png |only targeted-0.6/targeted/man/figures/logo.png |only targeted-0.6/targeted/man/figures/logohex2.png |only targeted-0.6/targeted/man/figures/target.pdf |only targeted-0.6/targeted/man/figures/target.svg |only targeted-0.6/targeted/man/figures/targeted.svg |only targeted-0.6/targeted/man/int_surv.Rd |only targeted-0.6/targeted/man/learner.Rd |only targeted-0.6/targeted/man/learner_expand_grid.Rd |only targeted-0.6/targeted/man/learner_gam.Rd |only targeted-0.6/targeted/man/learner_glm.Rd |only targeted-0.6/targeted/man/learner_glmnet_cv.Rd |only targeted-0.6/targeted/man/learner_grf.Rd |only targeted-0.6/targeted/man/learner_hal.Rd |only targeted-0.6/targeted/man/learner_isoreg.Rd |only targeted-0.6/targeted/man/learner_mars.Rd |only targeted-0.6/targeted/man/learner_naivebayes.Rd |only targeted-0.6/targeted/man/learner_sl.Rd |only targeted-0.6/targeted/man/learner_stratify.Rd |only targeted-0.6/targeted/man/learner_svm.Rd |only targeted-0.6/targeted/man/learner_xgboost.Rd |only targeted-0.6/targeted/man/ml_model.Rd | 246 --- targeted-0.6/targeted/man/naivebayes-class.Rd |only targeted-0.6/targeted/man/naivebayes.Rd |only targeted-0.6/targeted/man/nondom.Rd | 6 targeted-0.6/targeted/man/predict.naivebayes.Rd |only targeted-0.6/targeted/man/predict.superlearner.Rd |only targeted-0.6/targeted/man/reexports.Rd |only targeted-0.6/targeted/man/riskreg.Rd | 78 - targeted-0.6/targeted/man/riskreg_cens.Rd | 13 targeted-0.6/targeted/man/score.superlearner.Rd |only targeted-0.6/targeted/man/scoring.Rd |only targeted-0.6/targeted/man/solve_ode.Rd | 3 targeted-0.6/targeted/man/specify_ode.Rd | 23 targeted-0.6/targeted/man/stratify.Rd |only targeted-0.6/targeted/man/superlearner.Rd |only targeted-0.6/targeted/man/targeted-class.Rd | 15 targeted-0.6/targeted/man/targeted-package.Rd | 21 targeted-0.6/targeted/man/terms.design.Rd |only targeted-0.6/targeted/man/test_intersection_sw.Rd |only targeted-0.6/targeted/man/truncatedscore.Rd |only targeted-0.6/targeted/man/weights.superlearner.Rd |only targeted-0.6/targeted/src/Makevars | 25 targeted-0.6/targeted/src/RcppExports.cpp | 79 + targeted-0.6/targeted/src/target |only targeted-0.6/targeted/src/utils_interface.cpp | 28 targeted-0.6/targeted/tests/tinytest.R |only targeted-0.6/targeted/vignettes/predictionclass.Rmd |only targeted-0.6/targeted/vignettes/riskregression.Rmd | 14 176 files changed, 4113 insertions(+), 3194 deletions(-)
Title: Econdataverse 'IMF Data API' Client
Description: Provides user-friendly functions for programmatic access to macroeconomic data from the International Monetary Fund's 'SDMX 3.0 IMF Data API' <https://data.imf.org/en/Resource-Pages/IMF-API>.
Author: Teal Insights [cre, cph],
Christopher C. Smith [aut],
Christoph Scheuch [ctb]
Maintainer: Teal Insights <lte@tealinsights.com>
Diff between imfapi versions 0.1.0 dated 2025-10-25 and 0.1.1 dated 2025-10-30
DESCRIPTION | 16 - MD5 | 14 - NEWS.md | 4 R/imf_get.R | 57 ++++- README.md | 16 - man/imf_get.Rd | 2 tests/testthat/test-imf_get.R | 387 +++++++++++++++++++++++++++++++++- tests/testthat/test-perform_request.R | 4 8 files changed, 475 insertions(+), 25 deletions(-)
Title: Data Analysis using Bootstrap-Coupled Estimation
Description: Data Analysis using Bootstrap-Coupled ESTimation. Estimation
statistics is a simple framework that avoids the pitfalls of
significance testing. It uses familiar statistical concepts: means,
mean differences, and error bars. More importantly, it focuses on the
effect size of one's experiment/intervention, as opposed to a false
dichotomy engendered by P values. An estimation plot has two key
features: 1. It presents all datapoints as a swarmplot, which orders
each point to display the underlying distribution. 2. It presents the
effect size as a bootstrap 95% confidence interval on a separate but
aligned axes. Estimation plots are introduced in Ho et al., Nature
Methods 2019, 1548-7105. <doi:10.1038/s41592-019-0470-3>. The
free-to-view PDF is located at
<https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlR [...truncated...]
Author: Joses W. Ho [aut] ,
Kah Seng Lian [aut],
Ana Rosa Castillo [aut],
Zhuoyu Wang [aut],
Jun Yang Liao [aut],
Felicia Low [aut],
Tayfun Tumkaya [aut] ,
Jonathan Anns [ctb] ,
Yishan Mai [cre, ctb] ,
Sangyu Xu [ctb] ,
Zinan Lu [ctb],
Hyungwon Choi [ctb] ,
[...truncated...]
Maintainer: Yishan Mai <maiyishan@u.duke.nus.edu>
Diff between dabestr versions 2025.3.14 dated 2025-02-26 and 2025.3.15 dated 2025-10-30
DESCRIPTION | 29 MD5 | 59 - NEWS.md | 3 build/vignette.rds |binary inst/doc/plot_aesthetics.R | 32 inst/doc/plot_aesthetics.html | 19 inst/doc/sample_datasets.R | 18 inst/doc/sample_datasets.html | 1 inst/doc/tutorial_basics.R | 26 inst/doc/tutorial_basics.html | 395 ++++------ inst/doc/tutorial_deltadelta.R | 50 - inst/doc/tutorial_deltadelta.html | 171 +--- inst/doc/tutorial_minimeta.R | 18 inst/doc/tutorial_minimeta.Rmd | 2 inst/doc/tutorial_minimeta.html | 143 +-- inst/doc/tutorial_proportion_plots.R | 40 - inst/doc/tutorial_proportion_plots.html | 169 +--- inst/doc/tutorial_repeated_measures.R | 46 - inst/doc/tutorial_repeated_measures.html | 39 tests/testthat/_snaps/001_plotter/deltadelta-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/minimeta-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/multigroup-baseline-colour-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/multigroup-baseline-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/multigroup-sequential-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff-colour.new.svg |only tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/proportion-baseline-flow-false-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/proportion-baseline-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-false.new.svg |only tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-true.new.svg |only tests/testthat/_snaps/001_plotter/proportion-sequential-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-false.new.svg |only tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-true.new.svg |only tests/testthat/_snaps/001_plotter/proportion-unpaired-multigroup-mean-diff.new.svg |only tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-false.new.svg |only tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-true.new.svg |only tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-false.new.svg |only tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-true.new.svg |only tests/testthat/test_002_plot_components.R | 4 vignettes/tutorial_minimeta.Rmd | 2 40 files changed, 527 insertions(+), 739 deletions(-)
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Description: Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and
PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically
access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types.
Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between PubChemR versions 2.1.5 dated 2025-08-29 and 2.1.6 dated 2025-10-30
PubChemR-2.1.5/PubChemR/build |only PubChemR-2.1.5/PubChemR/inst/doc |only PubChemR-2.1.5/PubChemR/vignettes |only PubChemR-2.1.6/PubChemR/DESCRIPTION | 14 ++++++-------- PubChemR-2.1.6/PubChemR/MD5 | 16 ++-------------- PubChemR-2.1.6/PubChemR/inst/CITATION |only 6 files changed, 8 insertions(+), 22 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.8.1 dated 2025-01-12 and 1.8.2 dated 2025-10-30
lava-1.8.1/lava/data/serotonin2.rda |only lava-1.8.1/lava/man/closed.testing.Rd |only lava-1.8.1/lava/man/serotonin2.Rd |only lava-1.8.1/lava/man/sim.Rd |only lava-1.8.2/lava/DESCRIPTION | 8 lava-1.8.2/lava/INDEX | 8 lava-1.8.2/lava/MD5 | 56 +-- lava-1.8.2/lava/NAMESPACE | 7 lava-1.8.2/lava/NEWS.md | 5 lava-1.8.2/lava/R/compare.R | 2 lava-1.8.2/lava/R/contr.R | 2 lava-1.8.2/lava/R/lava-package.R | 36 +- lava-1.8.2/lava/R/multipletesting.R | 167 +++++++--- lava-1.8.2/lava/R/sim.default.R | 7 lava-1.8.2/lava/R/sim.lvm.R | 39 +- lava-1.8.2/lava/README.md | 5 lava-1.8.2/lava/build/partial.rdb |binary lava-1.8.2/lava/build/vignette.rds |binary lava-1.8.2/lava/data/deprdiag.csv |only lava-1.8.2/lava/inst/doc/correlation.html | 102 +++--- lava-1.8.2/lava/inst/doc/influencefunction.R | 4 lava-1.8.2/lava/inst/doc/influencefunction.Rmd | 296 +++++++++---------- lava-1.8.2/lava/inst/doc/influencefunction.html | 143 ++++----- lava-1.8.2/lava/inst/doc/nonlinear.html | 66 ++-- lava-1.8.2/lava/man/closed_testing.Rd |only lava-1.8.2/lava/man/compare.Rd | 1 lava-1.8.2/lava/man/contr.Rd | 2 lava-1.8.2/lava/man/deprdiag.Rd |only lava-1.8.2/lava/man/figures/logohex.png |only lava-1.8.2/lava/man/hubble.Rd | 4 lava-1.8.2/lava/man/sim.default.Rd | 3 lava-1.8.2/lava/man/sim.lvm.Rd |only lava-1.8.2/lava/tests/testthat/test-closed_testing.R |only lava-1.8.2/lava/vignettes/influencefunction.Rmd | 296 +++++++++---------- 34 files changed, 659 insertions(+), 600 deletions(-)
Title: A Comprehensive Collection of Health and Human Motion Datasets
Description: Provides a broad collection of datasets focused on health, biomechanics, and human motion.
It includes clinical, physiological, and kinematic information from diverse sources,
covering aspects such as surgery outcomes, vital signs, rheumatoid arthritis, osteoarthritis,
accelerometry, gait analysis, motion sensing, and biomechanics experiments.
Designed for researchers, analysts, and students, the package facilitates exploration
and analysis of data related to health monitoring, physical activity, and rehabilitation.
Author: Oscar Alejandro Sialer Gallo [aut, cre]
Maintainer: Oscar Alejandro Sialer Gallo <alejandro.sialer.gallo@gmail.com>
Diff between healthmotionR versions 0.1.0 dated 2025-10-06 and 0.2.0 dated 2025-10-30
DESCRIPTION | 27 +++++--- MD5 | 70 +++++++++++----------- NAMESPACE | 1 NEWS.md |only R/data-documentation.R | 2 R/healthmotionR-packages.R | 2 R/view_datasets_healthmotionR.R |only inst/CITATION | 14 ++-- inst/doc/healthmotionR_vignette.html | 7 +- man/view_datasets_healthmotionR.Rd |only tests/testthat/test-AtrialFibrillation_list.R | 2 tests/testthat/test-BasicMotions_list.R | 2 tests/testthat/test-FingerMovements_char.R | 2 tests/testthat/test-HandMovementDir_char.R | 2 tests/testthat/test-Heartbeat_char.R | 2 tests/testthat/test-KinData_df.R | 2 tests/testthat/test-StandWalkJump_list.R | 2 tests/testthat/test-Stepping_df.R | 2 tests/testthat/test-acceldata2_list.R | 2 tests/testthat/test-acceldata_list.R | 2 tests/testthat/test-accelimp_list.R | 2 tests/testthat/test-admiral_vs_tbl_df.R | 2 tests/testthat/test-angle_walk_array.R | 2 tests/testthat/test-body_metrics_df.R | 2 tests/testthat/test-infant_walking_df.R | 2 tests/testthat/test-knee_speed_tbl_df.R | 2 tests/testthat/test-meniscal_list.R | 2 tests/testthat/test-motion_sense_list.R | 2 tests/testthat/test-motionpaths_list.R | 2 tests/testthat/test-osteoarthritis_df.R | 2 tests/testthat/test-rheuma_df.R | 2 tests/testthat/test-run_biomech_tbl_df.R | 2 tests/testthat/test-surgerydat_df.R | 2 tests/testthat/test-view_datasets_healthmotionR.R |only tests/testthat/test-vs_peds_tbl_df.R | 2 tests/testthat/test-walk_biomech_tbl_df.R | 2 tests/testthat/test-walking_df.R | 2 tests/testthat/test-z_labels_monitoring_df.R | 2 38 files changed, 96 insertions(+), 81 deletions(-)
Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame
Description: An S3 class 'groupedHyperframe' that
inherits from hyper data frame. Batch
processes on point-pattern hyper column.
Aggregation of function-value-table hyper
column(s) and numeric hyper column(s) over a
nested grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.3.0 dated 2025-10-14 and 0.3.1 dated 2025-10-30
groupedHyperframe-0.3.0/groupedHyperframe/R/split_kmeans.R |only groupedHyperframe-0.3.0/groupedHyperframe/man/aggregate.groupedHyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/cli_defunct_.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/kmeans.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/log_ppp.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/split_kmeans.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/vignette_methods.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/DESCRIPTION | 19 groupedHyperframe-0.3.1/groupedHyperframe/MD5 | 67 groupedHyperframe-0.3.1/groupedHyperframe/NAMESPACE | 55 groupedHyperframe-0.3.1/groupedHyperframe/R/Defunct.R | 70 groupedHyperframe-0.3.1/groupedHyperframe/R/aggregate.R | 63 groupedHyperframe-0.3.1/groupedHyperframe/R/append_marks.R | 1 groupedHyperframe-0.3.1/groupedHyperframe/R/as.groupedHyperframe.R | 20 groupedHyperframe-0.3.1/groupedHyperframe/R/data_doc.R | 5 groupedHyperframe-0.3.1/groupedHyperframe/R/interpolation.fv.R | 2 groupedHyperframe-0.3.1/groupedHyperframe/R/kmeans.R | 85 groupedHyperframe-0.3.1/groupedHyperframe/R/kmeans_S3.R |only groupedHyperframe-0.3.1/groupedHyperframe/R/loess.fv.R |only groupedHyperframe-0.3.1/groupedHyperframe/R/op_hyperframe.R | 931 ++++------ groupedHyperframe-0.3.1/groupedHyperframe/R/ppp_S3.R | 110 - groupedHyperframe-0.3.1/groupedHyperframe/R/rmax.R | 7 groupedHyperframe-0.3.1/groupedHyperframe/R/vignette.R | 92 groupedHyperframe-0.3.1/groupedHyperframe/R/vtrapz.R | 77 groupedHyperframe-0.3.1/groupedHyperframe/data/bib.rda |only groupedHyperframe-0.3.1/groupedHyperframe/inst/doc/groupedHyperframe.R | 56 groupedHyperframe-0.3.1/groupedHyperframe/inst/doc/groupedHyperframe.html | 125 - groupedHyperframe-0.3.1/groupedHyperframe/inst/doc/groupedHyperframe.qmd | 272 +- groupedHyperframe-0.3.1/groupedHyperframe/inst/extR |only groupedHyperframe-0.3.1/groupedHyperframe/man/Math.ppp.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/aggregate.hyperframe.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/as.groupedHyperframe.Rd | 3 groupedHyperframe-0.3.1/groupedHyperframe/man/batch.Rd | 5 groupedHyperframe-0.3.1/groupedHyperframe/man/bib.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/cli_.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/groupedHyperframe-package.Rd | 4 groupedHyperframe-0.3.1/groupedHyperframe/man/kmeans_etc.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/loess.fv.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/methods2kable.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/plot.pppkm.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/print.pppkm.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/split.hyperframekm.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/split.pppkm.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/split.pppkmlist.Rd |only groupedHyperframe-0.3.1/groupedHyperframe/man/visualize_vtrapz.Rd | 10 groupedHyperframe-0.3.1/groupedHyperframe/vignettes/groupedHyperframe.qmd | 272 +- 46 files changed, 1108 insertions(+), 1243 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Generate UpSet Plots of VP and HP Based on the ASV Concept
Description: Using matrix layout to visualize the unique, common, or individual contribution of each predictor (or matrix of predictors) towards explained variation on different models. These contributions were derived from variation partitioning (VP) and hierarchical partitioning (HP), applying the algorithm of "Lai et al. (2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution, 13: 782-788 <doi:10.1111/2041-210X.13800>".
Author: Jiangshan Lai [aut, cre] ,
Yao Liu [aut],
Bangken Ying [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between upset.hp versions 0.0.4 dated 2025-07-20 and 0.0.5 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- R/zzz.r | 9 ++++++++- inst |only 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Sweave Drivers with Extra Tricks Up their Sleeve
Description: Weave and tangle drivers for Sweave extending the
standard drivers. RweaveExtraLatex and RtangleExtra provide options
to completely ignore code chunks on weaving, tangling, or both.
Chunks ignored on weaving are not parsed, yet are written out
verbatim on tangling. Chunks ignored on tangling may be evaluated as
usual on weaving, but are completely left out of the tangled
scripts. The driver RtangleExtra also provides options to control
the separation between code chunks in the tangled script, and to
specify the extension of the file name (or remove it entirely) when
splitting is selected.
Author: Vincent Goulet [cre, aut] ,
R Core Team [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between RweaveExtra versions 1.2-1 dated 2025-08-18 and 1.3-0 dated 2025-10-29
RweaveExtra-1.2-1/RweaveExtra/inst/examples/auto |only RweaveExtra-1.2-1/RweaveExtra/man/RweaveExtraUtils.Rd |only RweaveExtra-1.3-0/RweaveExtra/DESCRIPTION | 16 +- RweaveExtra-1.3-0/RweaveExtra/MD5 | 26 ++-- RweaveExtra-1.3-0/RweaveExtra/R/RweaveExtra.R | 28 ++--- RweaveExtra-1.3-0/RweaveExtra/build/partial.rdb |binary RweaveExtra-1.3-0/RweaveExtra/inst/NEWS.Rd | 20 +++ RweaveExtra-1.3-0/RweaveExtra/inst/examples/example-extra.Rnw | 16 +- RweaveExtra-1.3-0/RweaveExtra/inst/po/en@quot/LC_MESSAGES/R-RweaveExtra.mo |binary RweaveExtra-1.3-0/RweaveExtra/inst/po/fr/LC_MESSAGES/R-RweaveExtra.mo |binary RweaveExtra-1.3-0/RweaveExtra/man/RtangleExtra.Rd | 56 ++++++---- RweaveExtra-1.3-0/RweaveExtra/man/RweaveExtra-package.Rd | 2 RweaveExtra-1.3-0/RweaveExtra/man/RweaveExtraLatex.Rd | 45 +++++--- RweaveExtra-1.3-0/RweaveExtra/po/R-RweaveExtra.pot | 4 RweaveExtra-1.3-0/RweaveExtra/po/R-fr.po | 4 15 files changed, 137 insertions(+), 80 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Ben Wilson [aut, cre],
Matei Zaharia [aut],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Ben Wilson <benjamin.wilson@databricks.com>
Diff between mlflow versions 3.4.0 dated 2025-09-24 and 3.5.1 dated 2025-10-29
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.4 dated 2025-10-01 and 1.2.5 dated 2025-10-29
DESCRIPTION | 6 MD5 | 20 +- NAMESPACE | 1 NEWS.md | 8 + R/imgw_read.R | 8 + R/meteo_imgw_daily.R | 4 R/ogimet_daily.R | 14 +- R/ogimet_hourly.R | 14 +- README.md | 2 inst/doc/getstarted.html | 329 ++++++++--------------------------------------- man/climate-package.Rd | 1 11 files changed, 117 insertions(+), 290 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.13 dated 2024-12-05 and 2.2.14 dated 2025-10-29
DESCRIPTION | 11 - MD5 | 18 +- R/RcppExports.R | 28 +++- R/mix.R | 15 ++ demo/mixedmodel.R | 45 +++--- demo/multivariates.R | 14 -- man/bWGR.Rd | 5 man/mvr.Rd | 20 ++ src/RcppEigen20230423.cpp | 315 ++++++++++++++++++++++++++++++++++++++++++++-- src/RcppExports.cpp | 87 +++++++++++- 10 files changed, 488 insertions(+), 70 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.5 dated 2025-10-01 and 1.0.6 dated 2025-10-29
DESCRIPTION | 13 +-- MD5 | 26 +++++-- NAMESPACE | 7 + R/CPEmbedding.R |only R/GridSearch.R | 31 ++++++-- R/MapperCorrelation.R |only R/Plotter.R | 120 ++++++++++++++++++++++++---------- README.md | 33 ++++++--- man/CPEmbedding.Rd |only man/GridSearch.Rd | 8 +- man/MapperCorrelation.Rd |only man/MapperPlotter.Rd | 11 ++- man/figures/Cover.png |only man/figures/Iris.png |only man/figures/IrisMapper.png |only man/figures/MNISTMapper.png |only man/figures/MapperOutput.png |only man/figures/stride_extension_new.png |only man/figures/stride_extension_old.png |only man/figures/stride_extension_old2.png |only 20 files changed, 184 insertions(+), 65 deletions(-)
Title: A Comprehensive Interface for Accessing the Protein Data Bank
Description: Streamlines the interaction with the 'RCSB' Protein Data Bank ('PDB') <https://www.rcsb.org/>. This interface offers an intuitive and
powerful tool for searching and retrieving a diverse range of data types from the 'PDB'. It includes advanced functionalities like
BLAST and sequence motif queries. Built upon the existing XML-based API of the 'PDB', it simplifies the creation of custom requests,
thereby enhancing usability and flexibility for researchers.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between rPDBapi versions 2.1.1 dated 2024-10-19 and 2.1.2 dated 2025-10-29
DESCRIPTION | 12 +++++++----- MD5 | 3 ++- inst |only 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 0.1.1 dated 2025-09-08 and 0.2.0 dated 2025-10-29
DESCRIPTION | 12 +- MD5 | 53 ++++---- NAMESPACE | 1 NEWS.md | 27 ++++ R/aaa.R | 16 -- R/client.R | 175 ++++++++++++++++++----------- R/mcptools-package.R | 3 R/server.R | 240 ++++++++++++++++++++++++++++++++++++---- R/session.R | 26 ++-- R/tools.R | 77 ++++++------ R/utils.R | 14 ++ README.md | 2 build/vignette.rds |binary inst/doc/server.Rmd | 4 inst/doc/server.html | 11 + inst/example-config-remote.json |only inst/example-ellmer-tools.R | 45 ++----- man/client.Rd | 33 +++++ man/figures/logo.png |binary man/server.Rd | 63 +++++++++- tests/testthat/_snaps/client.md | 9 + tests/testthat/_snaps/tools.md | 5 tests/testthat/test-client.R | 21 +++ tests/testthat/test-server.R | 42 ++++++- tests/testthat/test-session.R | 6 - tests/testthat/test-tools.R | 9 + tests/testthat/test-utils.R | 2 vignettes/server.Rmd | 4 28 files changed, 658 insertions(+), 242 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Candace Savonen [aut, cre]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between rsynthbio versions 3.0.0 dated 2025-10-15 and 3.0.2 dated 2025-10-29
rsynthbio-3.0.0/rsynthbio/man/transform_result_to_frames.Rd |only rsynthbio-3.0.2/rsynthbio/DESCRIPTION | 8 rsynthbio-3.0.2/rsynthbio/MD5 | 42 rsynthbio-3.0.2/rsynthbio/NAMESPACE | 2 rsynthbio-3.0.2/rsynthbio/NEWS.md | 2 rsynthbio-3.0.2/rsynthbio/R/call_model_api.R | 357 ++--- rsynthbio-3.0.2/rsynthbio/R/data-handlers.R | 46 rsynthbio-3.0.2/rsynthbio/R/utils.R | 15 rsynthbio-3.0.2/rsynthbio/README.md | 88 + rsynthbio-3.0.2/rsynthbio/build/vignette.rds |binary rsynthbio-3.0.2/rsynthbio/inst/doc/getting-started.R | 75 - rsynthbio-3.0.2/rsynthbio/inst/doc/getting-started.Rmd | 176 +- rsynthbio-3.0.2/rsynthbio/inst/doc/getting-started.html | 285 ++-- rsynthbio-3.0.2/rsynthbio/man/MODEL_MODES.Rd |only rsynthbio-3.0.2/rsynthbio/man/extract_expression_data.Rd | 7 rsynthbio-3.0.2/rsynthbio/man/get_valid_modes.Rd | 10 rsynthbio-3.0.2/rsynthbio/man/get_valid_query.Rd | 20 rsynthbio-3.0.2/rsynthbio/man/predict_query.Rd | 19 rsynthbio-3.0.2/rsynthbio/tests/testthat/helper-mocks.R | 16 rsynthbio-3.0.2/rsynthbio/tests/testthat/test-call_model_api.R | 272 +++- rsynthbio-3.0.2/rsynthbio/tests/testthat/test-data-handlers.R | 55 rsynthbio-3.0.2/rsynthbio/tests/testthat/test-live-api.R | 655 +++++++++- rsynthbio-3.0.2/rsynthbio/vignettes/getting-started.Rmd | 176 +- 23 files changed, 1747 insertions(+), 579 deletions(-)
Title: Fast Machine Learning Model Training and Evaluation
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing
comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning.
It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.6.2 dated 2025-07-24 and 0.7.0 dated 2025-10-29
fastml-0.6.2/fastml/data |only fastml-0.7.0/fastml/DESCRIPTION | 32 fastml-0.7.0/fastml/MD5 | 103 fastml-0.7.0/fastml/NAMESPACE | 58 fastml-0.7.0/fastml/R/counterfactual_explain.R |only fastml-0.7.0/fastml/R/engine_helpers.R | 210 + fastml-0.7.0/fastml/R/evaluate_models.R | 100 fastml-0.7.0/fastml/R/explain_ale.R |only fastml-0.7.0/fastml/R/explain_dalex.R |only fastml-0.7.0/fastml/R/explain_lime.R |only fastml-0.7.0/fastml/R/fastexplain.R | 269 - fastml-0.7.0/fastml/R/fastexplore.R | 5 fastml-0.7.0/fastml/R/fastml.R | 543 ++- fastml-0.7.0/fastml/R/flexsurv_utils.R |only fastml-0.7.0/fastml/R/interaction_strength.R |only fastml-0.7.0/fastml/R/model_selection_helpers.R | 3 fastml-0.7.0/fastml/R/native_survival_utils.R |only fastml-0.7.0/fastml/R/params_helpers.R | 20 fastml-0.7.0/fastml/R/piecewise_exp_utils.R |only fastml-0.7.0/fastml/R/plot.fastml.R | 107 fastml-0.7.0/fastml/R/plot_ice.R |only fastml-0.7.0/fastml/R/predict.fastml.R | 87 fastml-0.7.0/fastml/R/process_model.R | 1200 +++++++ fastml-0.7.0/fastml/R/process_model_helpers.R |only fastml-0.7.0/fastml/R/spec_linear.R | 10 fastml-0.7.0/fastml/R/spec_survival.R |only fastml-0.7.0/fastml/R/spec_tree.R | 133 fastml-0.7.0/fastml/R/summary.fastml.R | 1619 +++++++++- fastml-0.7.0/fastml/R/surrogate_tree.R |only fastml-0.7.0/fastml/R/survival_utils.R |only fastml-0.7.0/fastml/R/train_models.R | 875 +++++ fastml-0.7.0/fastml/R/xgboost_survival.R |only fastml-0.7.0/fastml/README.md | 28 fastml-0.7.0/fastml/man/align_survival_curve.Rd |only fastml-0.7.0/fastml/man/assign_risk_group.Rd |only fastml-0.7.0/fastml/man/availableMethods.Rd | 13 fastml-0.7.0/fastml/man/build_survfit_matrix.Rd |only fastml-0.7.0/fastml/man/clamp01.Rd |only fastml-0.7.0/fastml/man/compute_ibrier.Rd |only fastml-0.7.0/fastml/man/compute_rmst_difference.Rd |only fastml-0.7.0/fastml/man/compute_survreg_matrix.Rd |only fastml-0.7.0/fastml/man/compute_tau_limit.Rd |only fastml-0.7.0/fastml/man/compute_uno_c_index.Rd |only fastml-0.7.0/fastml/man/convert_survival_predictions.Rd |only fastml-0.7.0/fastml/man/counterfactual_explain.Rd |only fastml-0.7.0/fastml/man/create_censor_eval.Rd |only fastml-0.7.0/fastml/man/determine_round_digits.Rd |only fastml-0.7.0/fastml/man/evaluate_models.Rd | 44 fastml-0.7.0/fastml/man/explain_ale.Rd |only fastml-0.7.0/fastml/man/explain_dalex.Rd |only fastml-0.7.0/fastml/man/explain_lime.Rd |only fastml-0.7.0/fastml/man/extract_survreg_components.Rd |only fastml-0.7.0/fastml/man/fastexplain.Rd | 14 fastml-0.7.0/fastml/man/fastml.Rd | 47 fastml-0.7.0/fastml/man/fastml_normalize_survival_status.Rd |only fastml-0.7.0/fastml/man/figures |only fastml-0.7.0/fastml/man/get_default_engine.Rd | 6 fastml-0.7.0/fastml/man/get_default_params.Rd | 4 fastml-0.7.0/fastml/man/get_default_tune_params.Rd | 2 fastml-0.7.0/fastml/man/get_surv_info.Rd |only fastml-0.7.0/fastml/man/interaction_strength.Rd |only fastml-0.7.0/fastml/man/map_brier_values.Rd |only fastml-0.7.0/fastml/man/plot_ice.Rd |only fastml-0.7.0/fastml/man/predict.fastml.Rd | 14 fastml-0.7.0/fastml/man/predict_risk.Rd |only fastml-0.7.0/fastml/man/predict_survival.Rd |only fastml-0.7.0/fastml/man/process_model.Rd | 42 fastml-0.7.0/fastml/man/summary.fastml.Rd | 12 fastml-0.7.0/fastml/man/surrogate_tree.Rd |only fastml-0.7.0/fastml/man/train_models.Rd | 9 fastml-0.7.0/fastml/tests/testthat/test-fastexplain.R |only fastml-0.7.0/fastml/tests/testthat/test-fastml.R | 146 fastml-0.7.0/fastml/tests/testthat/test-flexsurv-utils.R |only fastml-0.7.0/fastml/tests/testthat/test-piecewise-exp-utils.R |only fastml-0.7.0/fastml/tests/testthat/test-survival.R |only 75 files changed, 4978 insertions(+), 777 deletions(-)
Title: R Source Packages Manager
Description: Manage a collection/library of R source packages. Discover, document, load, test
source packages. Enable to use those packages as if they were actually installed. Quickly reload
only what is needed on source code change. Run tests and checks in parallel.
Author: Karl Forner [aut, cre, cph]
Maintainer: Karl Forner <karl.forner@gmail.com>
Diff between srcpkgs versions 0.1 dated 2024-05-15 and 0.2 dated 2025-10-29
DESCRIPTION | 12 MD5 | 198 ++++++++++------ NAMESPACE | 29 ++ NEWS.md | 9 R/0_params.R | 4 R/1_imports.R |only R/examples.R |only R/find_srcpkgs.R | 24 + R/graph.R | 4 R/hack_r_loaders.R | 8 R/pkg_check.R |only R/pkg_has_changed.R | 7 R/pkg_load.R | 23 + R/pkg_roxygenise.R | 8 R/pkg_test.R |only R/pkg_unload.R | 7 R/pkg_utils.R | 55 +++- R/pkgs_check.R |only R/pkgs_deps.R |only R/pkgs_install.R |only R/pkgs_test.R |only R/plan.R | 5 R/project_root.R | 9 R/reset.R | 13 - R/srcpkg.R | 15 - R/srcpkgs.R | 43 ++- R/text_table.R |only R/utils.R | 14 + R/zzz.R | 7 README.md | 57 +++- build/vignette.rds |binary inst/doc/demo.R | 15 + inst/doc/demo.Rmd | 6 inst/doc/demo.html | 266 ++++++++-------------- inst/doc/getting_started.R | 2 inst/doc/getting_started.html | 1 inst/doc/testing_and_checking.R |only inst/doc/testing_and_checking.Rmd |only inst/doc/testing_and_checking.html |only inst/extdata |only man/find_srcpkgs.Rd | 4 man/get_srcpkgs.Rd | 12 man/hack_r_loaders.Rd | 2 man/params.Rd | 6 man/pkg_check.Rd |only man/pkg_create.Rd | 5 man/pkg_list_attached.Rd |only man/pkg_load.Rd | 27 -- man/pkg_roxygenise.Rd | 9 man/pkg_test.Rd |only man/pkg_unload.Rd | 7 man/pkgs_check.Rd |only man/pkgs_deps.Rd |only man/pkgs_install.Rd |only man/pkgs_test.Rd |only man/reset.Rd | 7 man/settings.Rd | 5 man/setup_and_get_dummy_srcpkg.Rd |only man/srcpkgs-package.Rd | 1 man/srcpkgs.Rd |only man/unhack_r_loaders.Rd | 5 tests/testthat.R | 2 tests/testthat/_snaps |only tests/testthat/helper-examples.R | 41 ++- tests/testthat/helper-functions.R | 193 ++++++++++++++- tests/testthat/setup.R | 10 tests/testthat/test-examples.R |only tests/testthat/test-find_srcpkgs.R | 24 + tests/testthat/test-graph.R | 6 tests/testthat/test-hack_r_loaders.R | 19 - tests/testthat/test-pkg_check.R |only tests/testthat/test-pkg_has_changed.R | 2 tests/testthat/test-pkg_load.R | 47 ++- tests/testthat/test-pkg_meta.R | 4 tests/testthat/test-pkg_test.R |only tests/testthat/test-pkg_unload.R | 6 tests/testthat/test-pkgs_check.R |only tests/testthat/test-pkgs_deps.R |only tests/testthat/test-pkgs_install.R |only tests/testthat/test-pkgs_test.R |only tests/testthat/test-plan.R | 3 tests/testthat/test-project_root.R | 23 + tests/testthat/test-reset.R | 1 tests/testthat/test-srcpkg.R | 23 - tests/testthat/test-srcpkgs.R | 42 +++ tests/testthat/test-utils.R | 18 + tests/testthat/test-zzz.R | 5 vignettes/demo.Rmd | 6 vignettes/pkgs_test.png |only vignettes/srcpkgs_lotr_demo/aragorn/DESCRIPTION | 7 vignettes/srcpkgs_lotr_demo/aragorn/NAMESPACE |only vignettes/srcpkgs_lotr_demo/aragorn/man |only vignettes/srcpkgs_lotr_demo/bilbo/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/bilbo/NAMESPACE |only vignettes/srcpkgs_lotr_demo/bilbo/man |only vignettes/srcpkgs_lotr_demo/elrond/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/elrond/NAMESPACE |only vignettes/srcpkgs_lotr_demo/elrond/man |only vignettes/srcpkgs_lotr_demo/elves/DESCRIPTION | 7 vignettes/srcpkgs_lotr_demo/elves/NAMESPACE |only vignettes/srcpkgs_lotr_demo/elves/man |only vignettes/srcpkgs_lotr_demo/frodo/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/frodo/NAMESPACE |only vignettes/srcpkgs_lotr_demo/frodo/man |only vignettes/srcpkgs_lotr_demo/galadriel/DESCRIPTION | 3 vignettes/srcpkgs_lotr_demo/galadriel/NAMESPACE |only vignettes/srcpkgs_lotr_demo/galadriel/man |only vignettes/srcpkgs_lotr_demo/gandalf/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/gandalf/NAMESPACE |only vignettes/srcpkgs_lotr_demo/gandalf/man |only vignettes/srcpkgs_lotr_demo/gimli/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/gimli/NAMESPACE |only vignettes/srcpkgs_lotr_demo/gimli/man |only vignettes/srcpkgs_lotr_demo/hobbits/DESCRIPTION | 6 vignettes/srcpkgs_lotr_demo/hobbits/NAMESPACE |only vignettes/srcpkgs_lotr_demo/hobbits/R/main.R | 1 vignettes/srcpkgs_lotr_demo/hobbits/man |only vignettes/srcpkgs_lotr_demo/legolas/DESCRIPTION | 3 vignettes/srcpkgs_lotr_demo/legolas/NAMESPACE |only vignettes/srcpkgs_lotr_demo/legolas/man |only vignettes/srcpkgs_lotr_demo/lotr/DESCRIPTION | 8 vignettes/srcpkgs_lotr_demo/lotr/NAMESPACE |only vignettes/srcpkgs_lotr_demo/lotr/man |only vignettes/testing_and_checking.Rmd |only 124 files changed, 1008 insertions(+), 463 deletions(-)
Title: Data Structures and Functions for Working with Forest Data
Description: Provides generic data structures and algorithms for use with forest
mensuration data in a consistent framework. The functions and objects
included are a collection of broadly applicable tools. More specialized
applications should be implemented in separate packages that build on this
foundation. Documentation about 'ForestElementsR' is provided by three
vignettes included in this package. For an introduction to the field of
forest mensuration, refer to the textbooks by Kershaw et al. (2017)
<doi:10.1002/9781118902028>, and van Laar and Akca (2007)
<doi:10.1007/978-1-4020-5991-9>.
Author: Peter Biber [aut, cre, cph] ,
Astor Torano Caicoya [aut] ,
Torben Hilmers [ctb]
Maintainer: Peter Biber <p.biber@tum.de>
Diff between ForestElementsR versions 2.1.0 dated 2025-02-07 and 2.2.0 dated 2025-10-29
DESCRIPTION | 20 +++--- MD5 | 40 ++++++------- NAMESPACE | 4 + NEWS.md | 14 ++++ R/fe_yield_table_methods.R | 76 +++++++++++++++++++++++-- R/get_center.R |only README.md | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/forestelementsr_package.Rmd | 48 +++++++-------- inst/doc/forestelementsr_package.html | 103 ++++++++++++++++------------------ inst/doc/tree_species_codings.Rmd | 32 +++++----- inst/doc/tree_species_codings.html | 46 +++++++-------- inst/doc/yield_tables.R | 6 - inst/doc/yield_tables.Rmd | 22 +++---- inst/doc/yield_tables.html | 44 +++++++------- man/get_center.Rd |only man/ytable_age_slice.Rd | 4 - man/ytable_max_slice.Rd | 3 vignettes/forestelementsr_package.Rmd | 48 +++++++-------- vignettes/tree_species_codings.Rmd | 32 +++++----- vignettes/yield_tables.Rmd | 22 +++---- 22 files changed, 326 insertions(+), 242 deletions(-)
More information about ForestElementsR at CRAN
Permanent link
Title: Analysis of Ecological Dynamic Regimes
Description: A toolbox for implementing the Ecological Dynamic Regime framework
(Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>) to characterize and
compare groups of ecological trajectories in multidimensional spaces defined
by state variables. The package includes the RETRA-EDR algorithm to identify
representative trajectories, functions to generate, summarize, and visualize
representative trajectories, and several metrics to quantify the distribution
and heterogeneity of trajectories in an ecological dynamic regime and quantify
the dissimilarity between two or more ecological dynamic regimes. The package
also includes a set of functions to assess ecological resilience based on
ecological dynamic regimes (Sánchez-Pinillos et al., 2024 <doi:10.1016/j.biocon.2023.110409>).
Author: Martina Sanchez-Pinillos [aut, cre, cph]
Maintainer: Martina Sanchez-Pinillos <martina.sanchez.pinillos@gmail.com>
Diff between ecoregime versions 0.2.1 dated 2025-05-01 and 0.3.0 dated 2025-10-29
DESCRIPTION | 14 - MD5 | 40 +-- NEWS.md | 16 + R/plot.R | 19 + R/plot_edr.R | 10 R/retra_edr.R | 3 R/state_to_trajectory.R | 109 ++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/EDR_framework.R | 25 -- inst/doc/EDR_framework.Rmd | 27 -- inst/doc/EDR_framework.html | 44 +--- inst/doc/Resilience.html | 25 +- man/state_to_trajectory.Rd | 34 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test-deviation_metrics.R | 314 +++++------------------------- tests/testthat/test-plot.R | 18 + tests/testthat/test-plot_edr.R | 36 ++- tests/testthat/test-retra_edr.R | 29 ++ tests/testthat/test-state_to_trajectory.R | 88 ++------ vignettes/EDR_framework.Rmd | 27 -- 21 files changed, 332 insertions(+), 546 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 21.0.0.1 dated 2025-08-18 and 22.0.0 dated 2025-10-29
arrow-21.0.0.1/arrow/tools/cpp/cmake_modules/aws-c-common-1208.patch |only arrow-21.0.0.1/arrow/tools/cpp/cmake_modules/snappy.diff |only arrow-22.0.0/arrow/DESCRIPTION | 14 arrow-22.0.0/arrow/MD5 | 795 ++-- arrow-22.0.0/arrow/NEWS.md | 18 arrow-22.0.0/arrow/R/dataset-write.R | 8 arrow-22.0.0/arrow/R/dplyr-funcs-augmented.R | 8 arrow-22.0.0/arrow/R/dplyr-funcs-datetime.R | 32 arrow-22.0.0/arrow/R/dplyr-funcs-doc.R | 7 arrow-22.0.0/arrow/R/dplyr-funcs-string.R | 7 arrow-22.0.0/arrow/R/dplyr-funcs-type.R | 4 arrow-22.0.0/arrow/R/dplyr-summarize.R | 8 arrow-22.0.0/arrow/R/dplyr.R | 8 arrow-22.0.0/arrow/R/duckdb.R | 20 arrow-22.0.0/arrow/R/python.R | 12 arrow-22.0.0/arrow/R/type.R | 4 arrow-22.0.0/arrow/R/udf.R | 6 arrow-22.0.0/arrow/README.md | 3 arrow-22.0.0/arrow/configure | 2 arrow-22.0.0/arrow/configure.win | 14 arrow-22.0.0/arrow/man/CsvFileFormat.Rd | 2 arrow-22.0.0/arrow/man/FileFormat.Rd | 2 arrow-22.0.0/arrow/man/JsonFileFormat.Rd | 2 arrow-22.0.0/arrow/man/ParquetFileReader.Rd | 2 arrow-22.0.0/arrow/man/Scanner.Rd | 2 arrow-22.0.0/arrow/man/acero.Rd | 7 arrow-22.0.0/arrow/man/add_filename.Rd | 8 arrow-22.0.0/arrow/man/arrow-package.Rd | 1 arrow-22.0.0/arrow/man/as_record_batch_reader.Rd | 2 arrow-22.0.0/arrow/man/cast.Rd | 4 arrow-22.0.0/arrow/man/copy_files.Rd | 2 arrow-22.0.0/arrow/man/csv_convert_options.Rd | 2 arrow-22.0.0/arrow/man/csv_parse_options.Rd | 2 arrow-22.0.0/arrow/man/csv_read_options.Rd | 2 arrow-22.0.0/arrow/man/data-type.Rd | 6 arrow-22.0.0/arrow/man/gs_bucket.Rd | 2 arrow-22.0.0/arrow/man/hive_partition.Rd | 2 arrow-22.0.0/arrow/man/load_flight_server.Rd | 2 arrow-22.0.0/arrow/man/open_dataset.Rd | 2 arrow-22.0.0/arrow/man/open_delim_dataset.Rd | 2 arrow-22.0.0/arrow/man/read_json_arrow.Rd | 2 arrow-22.0.0/arrow/man/read_parquet.Rd | 2 arrow-22.0.0/arrow/man/register_scalar_function.Rd | 8 arrow-22.0.0/arrow/man/s3_bucket.Rd | 4 arrow-22.0.0/arrow/man/show_exec_plan.Rd | 10 arrow-22.0.0/arrow/man/to_arrow.Rd | 14 arrow-22.0.0/arrow/man/to_duckdb.Rd | 10 arrow-22.0.0/arrow/man/write_dataset.Rd | 10 arrow-22.0.0/arrow/man/write_parquet.Rd | 2 arrow-22.0.0/arrow/src/altrep.cpp | 2 arrow-22.0.0/arrow/tests/testthat/_snaps/dataset-dplyr.md | 2 arrow-22.0.0/arrow/tests/testthat/_snaps/dplyr-across.md | 2 arrow-22.0.0/arrow/tests/testthat/_snaps/dplyr-funcs-datetime.md | 4 arrow-22.0.0/arrow/tests/testthat/_snaps/dplyr-glimpse.md | 9 arrow-22.0.0/arrow/tests/testthat/_snaps/dplyr-mutate.md | 4 arrow-22.0.0/arrow/tests/testthat/_snaps/dplyr-summarize.md | 8 arrow-22.0.0/arrow/tests/testthat/helper-filesystems.R | 22 arrow-22.0.0/arrow/tests/testthat/test-RecordBatch.R | 32 arrow-22.0.0/arrow/tests/testthat/test-Table.R | 10 arrow-22.0.0/arrow/tests/testthat/test-compute-sort.R | 4 arrow-22.0.0/arrow/tests/testthat/test-csv.R | 2 arrow-22.0.0/arrow/tests/testthat/test-dataset-csv.R | 156 arrow-22.0.0/arrow/tests/testthat/test-dataset-dplyr.R | 184 - arrow-22.0.0/arrow/tests/testthat/test-dataset-json.R | 16 arrow-22.0.0/arrow/tests/testthat/test-dataset-uri.R | 40 arrow-22.0.0/arrow/tests/testthat/test-dataset-write.R | 230 - arrow-22.0.0/arrow/tests/testthat/test-dataset.R | 450 +- arrow-22.0.0/arrow/tests/testthat/test-dplyr-across.R | 8 arrow-22.0.0/arrow/tests/testthat/test-dplyr-arrange.R | 154 arrow-22.0.0/arrow/tests/testthat/test-dplyr-collapse.R | 132 arrow-22.0.0/arrow/tests/testthat/test-dplyr-count.R | 62 arrow-22.0.0/arrow/tests/testthat/test-dplyr-distinct.R | 104 arrow-22.0.0/arrow/tests/testthat/test-dplyr-filter.R | 274 - arrow-22.0.0/arrow/tests/testthat/test-dplyr-funcs-conditional.R | 166 arrow-22.0.0/arrow/tests/testthat/test-dplyr-funcs-datetime.R | 1128 +++--- arrow-22.0.0/arrow/tests/testthat/test-dplyr-funcs-math.R | 172 - arrow-22.0.0/arrow/tests/testthat/test-dplyr-funcs-string.R | 685 ++-- arrow-22.0.0/arrow/tests/testthat/test-dplyr-funcs-type.R | 266 - arrow-22.0.0/arrow/tests/testthat/test-dplyr-glimpse.R | 28 arrow-22.0.0/arrow/tests/testthat/test-dplyr-group-by.R | 226 - arrow-22.0.0/arrow/tests/testthat/test-dplyr-join.R | 164 arrow-22.0.0/arrow/tests/testthat/test-dplyr-mutate.R | 376 +- arrow-22.0.0/arrow/tests/testthat/test-dplyr-query.R | 450 +- arrow-22.0.0/arrow/tests/testthat/test-dplyr-select.R | 112 arrow-22.0.0/arrow/tests/testthat/test-dplyr-slice.R | 74 arrow-22.0.0/arrow/tests/testthat/test-dplyr-summarize.R | 656 +-- arrow-22.0.0/arrow/tests/testthat/test-dplyr-union.R | 24 arrow-22.0.0/arrow/tests/testthat/test-duckdb.R | 120 arrow-22.0.0/arrow/tests/testthat/test-extension.R | 10 arrow-22.0.0/arrow/tests/testthat/test-metadata.R | 36 arrow-22.0.0/arrow/tests/testthat/test-parquet.R | 2 arrow-22.0.0/arrow/tests/testthat/test-python.R | 14 arrow-22.0.0/arrow/tests/testthat/test-query-engine.R | 2 arrow-22.0.0/arrow/tests/testthat/test-udf.R | 42 arrow-22.0.0/arrow/tools/checksums |only arrow-22.0.0/arrow/tools/cpp/CMakeLists.txt | 20 arrow-22.0.0/arrow/tools/cpp/CMakePresets.json | 63 arrow-22.0.0/arrow/tools/cpp/build-support/run-test.sh | 1 arrow-22.0.0/arrow/tools/cpp/build-support/update-flatbuffers.sh | 4 arrow-22.0.0/arrow/tools/cpp/cmake_modules/BuildUtils.cmake | 3 arrow-22.0.0/arrow/tools/cpp/cmake_modules/DefineOptions.cmake | 27 arrow-22.0.0/arrow/tools/cpp/cmake_modules/SetupCxxFlags.cmake | 12 arrow-22.0.0/arrow/tools/cpp/cmake_modules/ThirdpartyToolchain.cmake | 204 - arrow-22.0.0/arrow/tools/cpp/cmake_modules/mimalloc-1138.patch |only arrow-22.0.0/arrow/tools/cpp/cmake_modules/orc-2345.patch |only arrow-22.0.0/arrow/tools/cpp/cmake_modules/orc-2357.patch |only arrow-22.0.0/arrow/tools/cpp/meson.build | 45 arrow-22.0.0/arrow/tools/cpp/meson.options | 70 arrow-22.0.0/arrow/tools/cpp/src/arrow/ArrowConfig.cmake.in | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/CMakeLists.txt | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/aggregate_internal.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/asof_join_node.cc | 24 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/backpressure_handler.h | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/concurrent_queue_internal.h | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/exec_plan.cc | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/exec_plan_internal.h |only arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/fetch_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/filter_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/hash_join_node.cc | 33 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/meson.build | 9 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/options.h | 17 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/order_by_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/pivot_longer_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/project_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/sink_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/sorted_merge_node.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/source_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/acero/union_node.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/adapters/tensorflow/meson.build | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/builder_binary.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/builder_nested.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/builder_nested.h | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/builder_primitive.h | 103 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/data.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/diff.cc | 134 arrow-22.0.0/arrow/tools/cpp/src/arrow/array/statistics.h | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/buffer.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/buffer_builder.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/c/bridge.cc | 14 arrow-22.0.0/arrow/tools/cpp/src/arrow/chunked_array.cc | 19 arrow-22.0.0/arrow/tools/cpp/src/arrow/compare.cc | 30 arrow-22.0.0/arrow/tools/cpp/src/arrow/compare.h | 34 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/CMakeLists.txt | 17 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_aggregate.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_aggregate.h | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_scalar.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_scalar.h | 62 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_vector.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/api_vector.h | 32 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/cast.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/cast.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/expression.cc | 95 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/function.cc | 7 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/function.h | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/initialize.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernel.cc | 59 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernel.h | 33 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_basic.cc | 9 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_mode.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_pivot.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_quantile.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_tdigest.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_var_std.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/hash_aggregate.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/hash_aggregate_numeric.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/hash_aggregate_pivot.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/ree_util_internal.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_arithmetic.cc | 28 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_boolean.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_cast_dictionary.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_cast_numeric.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_cast_string.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_cast_temporal.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_compare.cc | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_if_else.cc | 26 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_nested.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_random.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_round.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_set_lookup.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_string_ascii.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_string_utf8.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_temporal_binary.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_temporal_unary.cc | 63 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_validity.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/temporal_internal.cc |only arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/temporal_internal.h | 102 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/test_util_internal.cc | 26 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/test_util_internal.h | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_array_sort.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_cumulative_ops.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_hash.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_nested.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_pairwise.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_rank.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_replace.cc | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_run_end_encode.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_select_k.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_selection.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_sort.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_statistics.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_swizzle.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/registry.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/row/compare_internal_avx2.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/test_env.cc | 9 arrow-22.0.0/arrow/tools/cpp/src/arrow/compute/util_avx2.cc | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/csv/meson.build | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/csv/options.h | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/csv/writer.cc | 126 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/CMakeLists.txt | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/dataset_writer.cc | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/discovery.cc | 28 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/file_base.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/file_csv.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/file_parquet.cc | 15 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/scanner.cc | 21 arrow-22.0.0/arrow/tools/cpp/src/arrow/dataset/scanner.h | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/expression_internal.cc | 28 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/extension_set.cc | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/extension_set.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/relation_internal.cc | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/serde.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/test_plan_builder.cc | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/engine/substrait/type_internal.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/extension/fixed_shape_tensor.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/extension/tensor_internal.h | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/filesystem.cc | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/filesystem_library.h | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs_internal.cc | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs_internal.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/hdfs.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/meson.build | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/s3_internal.h | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/filesystem/test_util.cc | 20 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/CMakeLists.txt | 45 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/client.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/client.h | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/meson.build | 29 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/serialization_internal.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/serialization_internal.h | 141 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/server.cc | 121 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/server_tracing_middleware.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/server_tracing_middleware.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/CMakeLists.txt | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/client.cc | 38 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/example/sqlite_tables_schema_batch_reader.cc | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/protocol_internal.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/server.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/sql/server_session_middleware.h | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/test_definitions.cc | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/test_util.cc | 15 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/test_util.h | 20 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/customize_grpc.h | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/serialization_internal.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/transport_server.cc | 131 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/types.cc | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/flight/types.h | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/integration/meson.build | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/io/CMakeLists.txt | 14 arrow-22.0.0/arrow/tools/cpp/src/arrow/io/hdfs_internal.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/CMakeLists.txt | 7 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/meson.build | 14 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/message.cc | 68 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/reader.cc | 156 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/test_common.cc | 32 arrow-22.0.0/arrow/tools/cpp/src/arrow/ipc/writer.cc | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/json/meson.build | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/meson.build | 167 arrow-22.0.0/arrow/tools/cpp/src/arrow/record_batch.cc | 109 arrow-22.0.0/arrow/tools/cpp/src/arrow/record_batch.h | 20 arrow-22.0.0/arrow/tools/cpp/src/arrow/result.h | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/scalar.h | 19 arrow-22.0.0/arrow/tools/cpp/src/arrow/sparse_tensor.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/sparse_tensor.h | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/stl.h | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/table.cc | 48 arrow-22.0.0/arrow/tools/cpp/src/arrow/table.h | 22 arrow-22.0.0/arrow/tools/cpp/src/arrow/tensor.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/tensor/csx_converter.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/testing/process.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/testing/random.cc | 168 - arrow-22.0.0/arrow/tools/cpp/src/arrow/testing/random.h | 30 arrow-22.0.0/arrow/tools/cpp/src/arrow/testing/util.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/testing/util.h | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/type.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/arrow/type_fwd.h | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/type_traits.h | 5 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/CMakeLists.txt | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bit_run_reader.h | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bit_stream_utils_internal.h | 192 - arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bit_util.h | 123 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bitmap_ops.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bitmap_reader.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking.cc | 20 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking64_default_internal.h | 8 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_avx2.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_avx2_internal.h | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_avx512.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_avx512_internal.h | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_benchmark.cc |only arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_internal.h | 19 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_neon.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/bpacking_neon_internal.h | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/byte_stream_split_internal.cc |only arrow-22.0.0/arrow/tools/cpp/src/arrow/util/byte_stream_split_internal.h | 415 -- arrow-22.0.0/arrow/tools/cpp/src/arrow/util/byte_stream_split_internal_avx2.cc |only arrow-22.0.0/arrow/tools/cpp/src/arrow/util/compression_zlib.cc | 18 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/cpu_info.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/date_internal.h |only arrow-22.0.0/arrow/tools/cpp/src/arrow/util/dispatch_internal.h | 3 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/float16.h | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/io_util.cc | 36 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/io_util.h | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/macros.h | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/math_internal.h | 16 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/memory.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/meson.build | 7 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/rle_encoding_internal.h | 1380 +++++--- arrow-22.0.0/arrow/tools/cpp/src/arrow/util/secure_string.h | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/small_vector.h | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/span.h | 6 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/thread_pool.cc | 24 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/thread_pool.h | 29 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/tracing.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/tracing_internal.h | 1 arrow-22.0.0/arrow/tools/cpp/src/arrow/util/visibility.h | 13 arrow-22.0.0/arrow/tools/cpp/src/arrow/vendored/xxhash/README.md | 2 arrow-22.0.0/arrow/tools/cpp/src/arrow/vendored/xxhash/xxhash.c | 7 arrow-22.0.0/arrow/tools/cpp/src/arrow/vendored/xxhash/xxhash.h | 1676 +++++++--- arrow-22.0.0/arrow/tools/cpp/src/parquet/api/meson.build |only arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/CMakeLists.txt | 2 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/generate_fuzz_corpus.cc | 252 + arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/meson.build |only arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/reader.cc | 9 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/reader_internal.cc | 146 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/schema.cc | 42 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/schema_internal.cc | 28 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/schema_internal.h | 8 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/test_util.h | 121 arrow-22.0.0/arrow/tools/cpp/src/parquet/arrow/writer.cc | 54 arrow-22.0.0/arrow/tools/cpp/src/parquet/column_reader.cc | 41 arrow-22.0.0/arrow/tools/cpp/src/parquet/column_reader.h | 5 arrow-22.0.0/arrow/tools/cpp/src/parquet/column_writer.cc | 92 arrow-22.0.0/arrow/tools/cpp/src/parquet/column_writer.h | 4 arrow-22.0.0/arrow/tools/cpp/src/parquet/decoder.cc | 34 arrow-22.0.0/arrow/tools/cpp/src/parquet/encoder.cc | 11 arrow-22.0.0/arrow/tools/cpp/src/parquet/encoding_benchmark.cc | 94 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/crypto_factory.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/encryption.cc | 112 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/encryption.h | 93 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal_nossl.cc | 4 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/file_key_unwrapper.cc | 8 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/file_key_unwrapper.h | 6 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/file_key_wrapper.cc | 10 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/file_key_wrapper.h | 2 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_decryptor.cc | 50 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_decryptor.h | 20 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.cc | 29 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.h | 7 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/key_encryption_key.h | 7 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/key_toolkit.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/key_toolkit.h | 12 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/key_toolkit_internal.cc | 21 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/key_toolkit_internal.h | 9 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/kms_client.h | 14 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/local_wrap_kms_client.cc | 19 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/local_wrap_kms_client.h | 13 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/meson.build |only arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/test_encryption_util.cc | 18 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/test_encryption_util.h | 16 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/test_in_memory_kms.cc | 29 arrow-22.0.0/arrow/tools/cpp/src/parquet/encryption/test_in_memory_kms.h | 31 arrow-22.0.0/arrow/tools/cpp/src/parquet/file_reader.cc | 11 arrow-22.0.0/arrow/tools/cpp/src/parquet/geospatial/meson.build |only arrow-22.0.0/arrow/tools/cpp/src/parquet/level_comparison.cc | 9 arrow-22.0.0/arrow/tools/cpp/src/parquet/level_comparison_avx2.cc | 2 arrow-22.0.0/arrow/tools/cpp/src/parquet/level_comparison_avx2_internal.h |only arrow-22.0.0/arrow/tools/cpp/src/parquet/level_conversion.cc | 12 arrow-22.0.0/arrow/tools/cpp/src/parquet/level_conversion_bmi2.cc | 3 arrow-22.0.0/arrow/tools/cpp/src/parquet/level_conversion_bmi2_internal.h |only arrow-22.0.0/arrow/tools/cpp/src/parquet/meson.build |only arrow-22.0.0/arrow/tools/cpp/src/parquet/metadata.cc | 41 arrow-22.0.0/arrow/tools/cpp/src/parquet/printer.cc | 59 arrow-22.0.0/arrow/tools/cpp/src/parquet/properties.h | 50 arrow-22.0.0/arrow/tools/cpp/src/parquet/statistics.cc | 64 arrow-22.0.0/arrow/tools/cpp/src/parquet/statistics.h | 61 arrow-22.0.0/arrow/tools/cpp/src/parquet/stream_writer.cc | 16 arrow-22.0.0/arrow/tools/cpp/src/parquet/stream_writer.h | 11 arrow-22.0.0/arrow/tools/cpp/src/parquet/symbols.map | 2 arrow-22.0.0/arrow/tools/cpp/src/parquet/thrift_internal.h | 12 arrow-22.0.0/arrow/tools/cpp/src/parquet/types.cc | 190 - arrow-22.0.0/arrow/tools/cpp/src/parquet/types.h | 16 arrow-22.0.0/arrow/tools/cpp/subprojects/google-benchmark.wrap | 10 arrow-22.0.0/arrow/tools/cpp/subprojects/openssl.wrap |only arrow-22.0.0/arrow/tools/cpp/subprojects/packagefiles |only arrow-22.0.0/arrow/tools/cpp/subprojects/rapidjson.wrap | 15 arrow-22.0.0/arrow/tools/cpp/subprojects/re2.wrap |only arrow-22.0.0/arrow/tools/cpp/subprojects/thrift.wrap |only arrow-22.0.0/arrow/tools/cpp/thirdparty/versions.txt | 16 arrow-22.0.0/arrow/tools/cpp/tools/parquet/meson.build |only arrow-22.0.0/arrow/tools/cpp/valgrind.supp | 19 arrow-22.0.0/arrow/tools/cpp/vcpkg.json | 3 arrow-22.0.0/arrow/tools/dotenv | 22 arrow-22.0.0/arrow/tools/nixlibs.R | 67 arrow-22.0.0/arrow/tools/test-nixlibs.R | 11 arrow-22.0.0/arrow/tools/update-checksums.R | 11 407 files changed, 10561 insertions(+), 7166 deletions(-)
Title: Streamline Building Panel Data from Panel Study of Income
Dynamics ('PSID') Raw Files
Description: Streamline the management, creation, and formatting of panel data from the Panel Study of Income Dynamics ('PSID') <https://psidonline.isr.umich.edu> using this user-friendly tool. Simply define variable names and input code book details directly from the 'PSID' official website, and this toolbox will efficiently facilitate the data preparation process, transforming raw 'PSID' files into a well-organized format ready for further analysis.
Author: Shuyi Qiu [aut, cre]
Maintainer: Shuyi Qiu <shuyi.qiu@duke.edu>
Diff between psidread versions 1.0.5 dated 2025-07-15 and 1.0.6 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/psid_str.R | 6 +++--- build/vignette.rds |binary inst/doc/my-vignette.R | 36 ++++++++++++++++++------------------ inst/doc/my-vignette.html | 8 ++++---- 7 files changed, 39 insertions(+), 35 deletions(-)
Title: Patient Reported Outcomes Regression Analysis
Description: It offers a wide variety of techniques, such as graphics, recoding, or regression models, for a comprehensive analysis of patient-reported outcomes (PRO). Especially novel is the broad range of regression models based on the beta-binomial distribution useful for analyzing binomial data with over-dispersion in cross-sectional, longitudinal, or multidimensional response studies (see Najera-Zuloaga J., Lee D.-J. and Arostegui I. (2019) <doi:10.1002/bimj.201700251>).
Author: Josu Najera-Zuloaga [aut, cre],
Dae-Jin Lee [aut],
Inmaculada Arostegui [aut]
Maintainer: Josu Najera-Zuloaga <josu.najera@ehu.eus>
Diff between PROreg versions 1.3.1 dated 2025-08-21 and 1.3.2 dated 2025-10-29
DESCRIPTION | 6 +- MD5 | 6 +- R/SF36rec.R | 152 ++++++++++++++++++++++++++++----------------------------- man/SF36rec.Rd | 150 +++++++++++++++++++++++++++----------------------------- 4 files changed, 155 insertions(+), 159 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 0.1.0 dated 2025-10-23 and 0.1.1 dated 2025-10-29
DESCRIPTION | 9 - MD5 | 14 +- src/dimensionalityReduction.cpp | 5 src/latticeOfIdeals.h | 2 src/matrice.h | 121 ------------------- src/poset.cpp | 8 - src/rwrapper.cpp | 243 ++++++++++++++++++++-------------------- src/separation.cpp | 56 ++++----- 8 files changed, 170 insertions(+), 288 deletions(-)
More information about poseticDataAnalysis at CRAN
Permanent link
Title: Find Range of Cronbach Alpha with a Dataset Including Missing
Data
Description: Provides functions to calculate the minimum and maximum possible
values of Cronbach's alpha when item-level missing data are present.
Cronbach's alpha (Cronbach, 1951 <doi:10.1007/BF02310555>) is one of the most widely used
measures of internal consistency in the social, behavioral, and medical sciences
(Bland & Altman, 1997 <doi:10.1136/bmj.314.7080.572>; Tavakol & Dennick, 2011
<doi:10.5116/ijme.4dfb.8dfd>). However, conventional implementations assume
complete data, and listwise deletion is often applied when missingness occurs,
which can lead to biased or overly optimistic reliability estimates (Enders, 2003
<doi:10.1037/1082-989X.8.3.322>). This package implements computational strategies
including enumeration, Monte Carlo sampling, and optimization algorithms
(e.g., Genetic Algorithm, Differential Evolution, Sequential Least Squares
Programming) to obtain sharp lower and upper bounds of Cronbach's alpha under
arbitrary missing data patterns. The ap [...truncated...]
Author: Feng Ji [aut],
Biying Zhou [aut, cre]
Maintainer: Biying Zhou <biying.zhou@psu.edu>
Diff between missalpha versions 0.1.0 dated 2025-09-09 and 0.2.0 dated 2025-10-29
DESCRIPTION | 8 - MD5 | 24 ++-- R/compute_alpha_max.R | 8 - R/compute_alpha_min.R | 6 - R/compute_cronbach_alpha.R | 3 R/cronbachs_alpha.R | 4 R/examine_alpha_bound.R | 212 ++++++++++++++++++++++---------------------- R/sigma_x_value.R | 2 R/sigma_y_value.R | 2 man/compute_alpha_max.Rd | 4 man/compute_alpha_min.Rd | 4 man/examine_alpha_bound.Rd | 4 tests/testthat/test_alpha.R | 8 + 13 files changed, 146 insertions(+), 143 deletions(-)
Title: Predict Carbon Emissions for UK SMEs
Description: Predict Scope 1, 2 and 3 carbon emissions for UK Small and Medium-sized Enterprises (SMEs), using Standard Industrial Classification (SIC) codes and annual turnover data, as well as Scope 1 carbon emissions for UK farms. The 'carbonpredict' package provides single and batch prediction, plotting, and workflow tools for carbon accounting and reporting. The package utilises pre-trained models, leveraging rich classified transaction data to accurately predict Scope 1, 2 and 3 carbon emissions for UK SMEs as well as identifying emissions hotspots. It also provides Scope 1 carbon emissions predictions for UK farms of types: Cereals ex. rice, Dairy, Mixed farming, Sheep and goats, Cattle & buffaloes, Poultry, Animal production and Support for crop production. The methodology used to produce the estimates in this package is fully detailed in the following peer-reviewed publication in the Journal of Industrial Ecology: Phillpotts, A., Owen. A., Norman, J., Trendl, A., Gathergood, J., Jobst [...truncated...]
Author: Hamza Suleman [aut, cre, cph],
Alec Phillpotts [ctb, aut],
Jasmine Wells [ctb, aut],
David Leake [ctb, aut]
Maintainer: Hamza Suleman <Hamza.Suleman@lloydsbanking.com>
Diff between carbonpredict versions 1.0.0 dated 2025-10-14 and 2.0.0 dated 2025-10-29
DESCRIPTION | 12 ++- MD5 | 27 +++++--- NAMESPACE | 1 R/batch_predict_emissions.R | 22 ++++-- R/farms_scope1.R |only README.md | 48 +++++++++++---- inst/extdata/farm_examples.csv |only inst/intdata/farms_validation_data.csv |only inst/intdata/sme_validation_data.csv |only inst/models/Farms_Scope_1_Model.rds |only man/batch_predict_emissions.Rd | 2 man/farms_scope1.Rd |only man/sme_scope3_hotspots.Rd | 40 ++++++------ tests/testthat/test-batch_predict_emissions.R | 82 +++++++++++++++++++++++--- tests/testthat/test-farms_scope1.R |only tests/testthat/test-sme_scope1.R | 2 tests/testthat/test-sme_scope2.R | 2 tests/testthat/test-sme_scope3.R | 2 18 files changed, 173 insertions(+), 67 deletions(-)
Title: Read, Manipulate and Visualise Magnetic Resonance Images
Description: Functions for working with magnetic resonance images. Reading and
writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH);
interactive and non-interactive visualisation; flexible image manipulation;
metadata and sparse image handling.
Author: Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between tractor.base versions 3.4.5.1 dated 2025-09-02 and 3.5.0 dated 2025-10-29
tractor.base-3.4.5.1/tractor.base/R/json.R |only tractor.base-3.4.5.1/tractor.base/man/files.Rd |only tractor.base-3.5.0/tractor.base/DESCRIPTION | 12 tractor.base-3.5.0/tractor.base/MD5 | 45 - tractor.base-3.5.0/tractor.base/NAMESPACE | 17 tractor.base-3.5.0/tractor.base/R/00_constants.R | 8 tractor.base-3.5.0/tractor.base/R/05_serialise.R | 145 +++- tractor.base-3.5.0/tractor.base/R/07_files.R |only tractor.base-3.5.0/tractor.base/R/08_sparse.R | 12 tractor.base-3.5.0/tractor.base/R/10_mri_image.R | 4 tractor.base-3.5.0/tractor.base/R/20_scheme.R |only tractor.base-3.5.0/tractor.base/R/files.R | 318 +++------- tractor.base-3.5.0/tractor.base/R/misc.R | 16 tractor.base-3.5.0/tractor.base/R/viewer.R | 4 tractor.base-3.5.0/tractor.base/R/zzz.R | 2 tractor.base-3.5.0/tractor.base/inst/tinytest/test-05-nifti.R | 1 tractor.base-3.5.0/tractor.base/inst/tinytest/test-10-mgh.R | 18 tractor.base-3.5.0/tractor.base/inst/tinytest/test-12-files.R |only tractor.base-3.5.0/tractor.base/inst/tinytest/test-40-misc.R | 17 tractor.base-3.5.0/tractor.base/man/DiffusionScheme-class.Rd |only tractor.base-3.5.0/tractor.base/man/FileMap-class.Rd |only tractor.base-3.5.0/tractor.base/man/FileSet-class.Rd |only tractor.base-3.5.0/tractor.base/man/ImageFileSet-class.Rd |only tractor.base-3.5.0/tractor.base/man/Optional.Rd |only tractor.base-3.5.0/tractor.base/man/asDiffusionScheme.Rd |only tractor.base-3.5.0/tractor.base/man/fillShells.Rd |only tractor.base-3.5.0/tractor.base/man/identifyImageFileNames.Rd |only tractor.base-3.5.0/tractor.base/man/imageFiles.Rd |only tractor.base-3.5.0/tractor.base/man/loso.Rd |only tractor.base-3.5.0/tractor.base/man/readDiffusionScheme.Rd |only tractor.base-3.5.0/tractor.base/man/readImageFile.Rd |only tractor.base-3.5.0/tractor.base/man/serialisation.Rd | 18 32 files changed, 303 insertions(+), 334 deletions(-)
Title: Network Meta-Analysis of Multiple Diagnostic Tests
Description: Provides statistical methods for network meta-analysis
of 1–5 diagnostic tests to simultaneously compare multiple tests within a
missing data framework, including:
- Bayesian hierarchical model for network meta-analysis of multiple
diagnostic tests
(Ma, Lian, Chu, Ibrahim, and Chen (2018) <doi:10.1093/biostatistics/kxx025>)
- Bayesian Hierarchical Summary Receiver Operating Characteristic Model
for Network Meta-Analysis of Diagnostic Tests
(Lian, Hodges, and Chu (2019) <doi:10.1080/01621459.2018.1476239>).
Author: Xing Xing [aut, cre] ,
Boyang Lu [aut],
Lifeng Lin [aut],
Qinshu Lian [aut],
James S. Hodges [aut],
Yong Chen [aut],
Haitao Chu [aut]
Maintainer: Xing Xing <xxing8@jh.edu>
Diff between NMADTA versions 0.1.0 dated 2025-10-14 and 0.1.1 dated 2025-10-29
NMADTA-0.1.0/NMADTA/R/forestplot.R |only NMADTA-0.1.0/NMADTA/R/hierarchical.plot.R |only NMADTA-0.1.0/NMADTA/R/hsroc.plot.R |only NMADTA-0.1.0/NMADTA/R/sroc.R |only NMADTA-0.1.0/NMADTA/inst/extdata |only NMADTA-0.1.0/NMADTA/man/hierarchical.plot.Rd |only NMADTA-0.1.0/NMADTA/man/hsroc.plot.Rd |only NMADTA-0.1.1/NMADTA/DESCRIPTION | 43 NMADTA-0.1.1/NMADTA/MD5 | 63 NMADTA-0.1.1/NMADTA/NAMESPACE | 32 NMADTA-0.1.1/NMADTA/R/contour_hierarchical.R | 79 - NMADTA-0.1.1/NMADTA/R/contour_hsroc.R | 94 - NMADTA-0.1.1/NMADTA/R/dat.kang.R |only NMADTA-0.1.1/NMADTA/R/density_hierarchical.R | 85 - NMADTA-0.1.1/NMADTA/R/density_hsroc.R | 93 - NMADTA-0.1.1/NMADTA/R/forestplot.hierarchical.R | 105 - NMADTA-0.1.1/NMADTA/R/forestplot.hsroc.R |only NMADTA-0.1.1/NMADTA/R/nmadt.hierarchical.MNAR.R | 53 NMADTA-0.1.1/NMADTA/R/nmadt.hierarchical.R | 44 NMADTA-0.1.1/NMADTA/R/nmadt.hsroc.MNAR.R | 28 NMADTA-0.1.1/NMADTA/R/nmadt.hsroc.R | 33 NMADTA-0.1.1/NMADTA/R/plot.nmadt.R |only NMADTA-0.1.1/NMADTA/R/print.nmadt.R |only NMADTA-0.1.1/NMADTA/R/sroc.hierarchical.R | 760 +++++----- NMADTA-0.1.1/NMADTA/R/sroc.hsroc.R |only NMADTA-0.1.1/NMADTA/R/summary.nmadt.R |only NMADTA-0.1.1/NMADTA/R/zzz-imports.R |only NMADTA-0.1.1/NMADTA/build/partial.rdb |binary NMADTA-0.1.1/NMADTA/data |only NMADTA-0.1.1/NMADTA/inst/REFERENCES.bib | 12 NMADTA-0.1.1/NMADTA/man/dat.kang.Rd |only NMADTA-0.1.1/NMADTA/man/nmadt.hierarchical.MNAR.Rd | 20 NMADTA-0.1.1/NMADTA/man/nmadt.hierarchical.Rd | 22 NMADTA-0.1.1/NMADTA/man/nmadt.hsroc.MNAR.Rd | 8 NMADTA-0.1.1/NMADTA/man/nmadt.hsroc.Rd | 8 NMADTA-0.1.1/NMADTA/man/plot.nmadt.Rd |only NMADTA-0.1.1/NMADTA/man/print.nmadt.Rd |only NMADTA-0.1.1/NMADTA/man/summary.nmadt.Rd |only NMADTA-0.1.1/NMADTA/tests/testthat/test-nmadt.hierarchical.MNAR.R | 4 NMADTA-0.1.1/NMADTA/tests/testthat/test-nmadt.hierarchical.R | 4 NMADTA-0.1.1/NMADTA/tests/testthat/test-nmadt.hsroc.MNAR.R | 4 NMADTA-0.1.1/NMADTA/tests/testthat/test-nmadt.hsroc.R | 4 42 files changed, 1005 insertions(+), 593 deletions(-)
Title: Modular Breeding Program Simulator
Description: Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. Associated publication: Pook et al. (2020) <doi:10.1534/g3.120.401193>.
Author: Torsten Pook [aut, cre] ,
Johannes Geibel [ctb] ,
Azadeh Hassanpour [ctb] ,
Tobias Niehoff [ctb]
Maintainer: Torsten Pook <torsten.pook@wur.nl>
Diff between MoBPS versions 1.6.64 dated 2021-11-09 and 1.13.1 dated 2025-10-29
MoBPS-1.13.1/MoBPS/DESCRIPTION | 34 MoBPS-1.13.1/MoBPS/MD5 | 505 MoBPS-1.13.1/MoBPS/NAMESPACE | 75 MoBPS-1.13.1/MoBPS/R/OGC.R | 135 MoBPS-1.13.1/MoBPS/R/add.array.R | 11 MoBPS-1.13.1/MoBPS/R/add.combi.R | 10 MoBPS-1.13.1/MoBPS/R/add.diag.R | 4 MoBPS-1.13.1/MoBPS/R/add.diversity.R |only MoBPS-1.13.1/MoBPS/R/add.fixed.effects.R |only MoBPS-1.13.1/MoBPS/R/add.founder.kinship.R | 9 MoBPS-1.13.1/MoBPS/R/analyze.bv.R | 28 MoBPS-1.13.1/MoBPS/R/analyze.population.R | 6 MoBPS-1.13.1/MoBPS/R/bitwise.storing.R | 6 MoBPS-1.13.1/MoBPS/R/breeding.diploid.R |14090 ++++++++++----- MoBPS-1.13.1/MoBPS/R/breeding.intern.R | 455 MoBPS-1.13.1/MoBPS/R/breeding.intern1.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern2.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern3.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern4.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern5.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern6.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern7.R |only MoBPS-1.13.1/MoBPS/R/breeding.intern8.R |only MoBPS-1.13.1/MoBPS/R/bv.development.R | 4 MoBPS-1.13.1/MoBPS/R/bv.development.box.R | 6 MoBPS-1.13.1/MoBPS/R/bv.standardization.R | 148 MoBPS-1.13.1/MoBPS/R/calculate.bv.R | 369 MoBPS-1.13.1/MoBPS/R/check.parents.R | 44 MoBPS-1.13.1/MoBPS/R/clean.up.R | 8 MoBPS-1.13.1/MoBPS/R/codeOriginsR.R | 4 MoBPS-1.13.1/MoBPS/R/combine.traits.R | 4 MoBPS-1.13.1/MoBPS/R/compute.costs.R | 14 MoBPS-1.13.1/MoBPS/R/compute.costs.cohorts.R | 14 MoBPS-1.13.1/MoBPS/R/compute.snps.R | 14 MoBPS-1.13.1/MoBPS/R/creating.diploid.R | 4443 +++- MoBPS-1.13.1/MoBPS/R/creating.phenotypic.transform.R | 79 MoBPS-1.13.1/MoBPS/R/creating.trait.R | 855 MoBPS-1.13.1/MoBPS/R/demiraculix.R | 6 MoBPS-1.13.1/MoBPS/R/derive.loop.elements.R | 6 MoBPS-1.13.1/MoBPS/R/diag.mobps.R | 6 MoBPS-1.13.1/MoBPS/R/edges.fromto.R | 4 MoBPS-1.13.1/MoBPS/R/edit.animal.R | 6 MoBPS-1.13.1/MoBPS/R/effect.estimate.add.R | 4 MoBPS-1.13.1/MoBPS/R/effective.size.R | 4 MoBPS-1.13.1/MoBPS/R/epi.R | 4 MoBPS-1.13.1/MoBPS/R/example.dataset.R | 18 MoBPS-1.13.1/MoBPS/R/exist.cohort.R |only MoBPS-1.13.1/MoBPS/R/find.chromo.R | 4 MoBPS-1.13.1/MoBPS/R/find.snpbefore.R | 6 MoBPS-1.13.1/MoBPS/R/founder.simulation.R | 93 MoBPS-1.13.1/MoBPS/R/generation.individual.R | 4 MoBPS-1.13.1/MoBPS/R/get.admixture.R | 80 MoBPS-1.13.1/MoBPS/R/get.age.point.R | 13 MoBPS-1.13.1/MoBPS/R/get.allele.freq.R |only MoBPS-1.13.1/MoBPS/R/get.bv.R | 15 MoBPS-1.13.1/MoBPS/R/get.bve.R | 15 MoBPS-1.13.1/MoBPS/R/get.class.R | 13 MoBPS-1.13.1/MoBPS/R/get.cohorts.R | 4 MoBPS-1.13.1/MoBPS/R/get.cohorts.individual.R |only MoBPS-1.13.1/MoBPS/R/get.computing.time.R |only MoBPS-1.13.1/MoBPS/R/get.creating.type.R | 13 MoBPS-1.13.1/MoBPS/R/get.culling.time.R |only MoBPS-1.13.1/MoBPS/R/get.culling.type.R |only MoBPS-1.13.1/MoBPS/R/get.cullingtime.R | 11 MoBPS-1.13.1/MoBPS/R/get.database.R | 302 MoBPS-1.13.1/MoBPS/R/get.death.point.R | 13 MoBPS-1.13.1/MoBPS/R/get.dendrogram.R | 19 MoBPS-1.13.1/MoBPS/R/get.dendrogram.heatmap.R | 17 MoBPS-1.13.1/MoBPS/R/get.dendrogram.trait.R | 9 MoBPS-1.13.1/MoBPS/R/get.distance.R | 14 MoBPS-1.13.1/MoBPS/R/get.effect.freq.R | 9 MoBPS-1.13.1/MoBPS/R/get.effective.size.R | 9 MoBPS-1.13.1/MoBPS/R/get.fixed.effects.p.R |only MoBPS-1.13.1/MoBPS/R/get.gen.effect.R |only MoBPS-1.13.1/MoBPS/R/get.geno.R | 65 MoBPS-1.13.1/MoBPS/R/get.geno.time.R |only MoBPS-1.13.1/MoBPS/R/get.genotyped.R | 53 MoBPS-1.13.1/MoBPS/R/get.genotyped.snp.R | 37 MoBPS-1.13.1/MoBPS/R/get.haplo.R | 71 MoBPS-1.13.1/MoBPS/R/get.id.R | 14 MoBPS-1.13.1/MoBPS/R/get.index.R |only MoBPS-1.13.1/MoBPS/R/get.infos.R | 17 MoBPS-1.13.1/MoBPS/R/get.is.first.R |only MoBPS-1.13.1/MoBPS/R/get.is.last.R |only MoBPS-1.13.1/MoBPS/R/get.litter.R |only MoBPS-1.13.1/MoBPS/R/get.litter.effect.R |only MoBPS-1.13.1/MoBPS/R/get.maf.R |only MoBPS-1.13.1/MoBPS/R/get.map.R | 21 MoBPS-1.13.1/MoBPS/R/get.ngen.R |only MoBPS-1.13.1/MoBPS/R/get.nindi.R |only MoBPS-1.13.1/MoBPS/R/get.npheno.R | 15 MoBPS-1.13.1/MoBPS/R/get.pca.R | 59 MoBPS-1.13.1/MoBPS/R/get.pedigree.R | 740 MoBPS-1.13.1/MoBPS/R/get.pedigree.visual.R |only MoBPS-1.13.1/MoBPS/R/get.pedmap.R | 32 MoBPS-1.13.1/MoBPS/R/get.pen.R |only MoBPS-1.13.1/MoBPS/R/get.pheno.R | 13 MoBPS-1.13.1/MoBPS/R/get.pheno.off.R | 14 MoBPS-1.13.1/MoBPS/R/get.pheno.off.count.R | 17 MoBPS-1.13.1/MoBPS/R/get.pheno.single.R |only MoBPS-1.13.1/MoBPS/R/get.pheno.time.R |only MoBPS-1.13.1/MoBPS/R/get.phylogenetic.tree.R | 20 MoBPS-1.13.1/MoBPS/R/get.plink.R |only MoBPS-1.13.1/MoBPS/R/get.pool.R |only MoBPS-1.13.1/MoBPS/R/get.pool.founder.R |only MoBPS-1.13.1/MoBPS/R/get.qtl.R | 11 MoBPS-1.13.1/MoBPS/R/get.recombi.R | 11 MoBPS-1.13.1/MoBPS/R/get.reliabilities.R | 13 MoBPS-1.13.1/MoBPS/R/get.selectionbve.R | 13 MoBPS-1.13.1/MoBPS/R/get.selectionindex.R | 11 MoBPS-1.13.1/MoBPS/R/get.sex.R |only MoBPS-1.13.1/MoBPS/R/get.size.R |only MoBPS-1.13.1/MoBPS/R/get.snapshot.R |only MoBPS-1.13.1/MoBPS/R/get.snapshot.single.R |only MoBPS-1.13.1/MoBPS/R/get.time.point.R | 15 MoBPS-1.13.1/MoBPS/R/get.trafo.p.R |only MoBPS-1.13.1/MoBPS/R/get.trafo.p.single.R |only MoBPS-1.13.1/MoBPS/R/get.uhat.R |only MoBPS-1.13.1/MoBPS/R/get.variance.R |only MoBPS-1.13.1/MoBPS/R/get.variance.components.R |only MoBPS-1.13.1/MoBPS/R/get.vcf.R | 78 MoBPS-1.13.1/MoBPS/R/group.diff.R | 23 MoBPS-1.13.1/MoBPS/R/inbreeding.emp.R |only MoBPS-1.13.1/MoBPS/R/inbreeding.exp.R |only MoBPS-1.13.1/MoBPS/R/insert.bve.R | 121 MoBPS-1.13.1/MoBPS/R/insert.pheno.single.R |only MoBPS-1.13.1/MoBPS/R/json.simulation.R | 375 MoBPS-1.13.1/MoBPS/R/kinship.development.R | 6 MoBPS-1.13.1/MoBPS/R/kinship.emp.R | 167 MoBPS-1.13.1/MoBPS/R/kinship.exp.store.R | 141 MoBPS-1.13.1/MoBPS/R/ld.decay.R | 52 MoBPS-1.13.1/MoBPS/R/matrix.posdef.R |only MoBPS-1.13.1/MoBPS/R/merge.trait.R |only MoBPS-1.13.1/MoBPS/R/merging.cohorts.R |only MoBPS-1.13.1/MoBPS/R/miesenberger.index.R | 10 MoBPS-1.13.1/MoBPS/R/miraculix.R | 8 MoBPS-1.13.1/MoBPS/R/mutation.intro.R | 50 MoBPS-1.13.1/MoBPS/R/new.base.generation.R | 101 MoBPS-1.13.1/MoBPS/R/ogc.mobps.R |only MoBPS-1.13.1/MoBPS/R/optimize.cores.R |only MoBPS-1.13.1/MoBPS/R/pedigree.simulation.R | 239 MoBPS-1.13.1/MoBPS/R/pedmap.to.phasedbeaglevcf.R | 4 MoBPS-1.13.1/MoBPS/R/plot.population.R | 6 MoBPS-1.13.1/MoBPS/R/recalculate.bv.R |only MoBPS-1.13.1/MoBPS/R/recalculate.manual.R |only MoBPS-1.13.1/MoBPS/R/recombination.function.haldane.R |only MoBPS-1.13.1/MoBPS/R/rename.cohort.R |only MoBPS-1.13.1/MoBPS/R/rowMedian.R |only MoBPS-1.13.1/MoBPS/R/scaling.relationship.R |only MoBPS-1.13.1/MoBPS/R/set.age.point.R |only MoBPS-1.13.1/MoBPS/R/set.class.R | 15 MoBPS-1.13.1/MoBPS/R/set.default.R | 4 MoBPS-1.13.1/MoBPS/R/set.mean.pool.R |only MoBPS-1.13.1/MoBPS/R/set.time.point.R |only MoBPS-1.13.1/MoBPS/R/sortd.R | 4 MoBPS-1.13.1/MoBPS/R/ssGBLUP.R | 4 MoBPS-1.13.1/MoBPS/R/startup.R | 74 MoBPS-1.13.1/MoBPS/R/summary.population.R | 22 MoBPS-1.13.1/MoBPS/R/vlist.R | 4 MoBPS-1.13.1/MoBPS/R/write.pedigree.mixblup.R |only MoBPS-1.13.1/MoBPS/data/ex_pop.RData |binary MoBPS-1.13.1/MoBPS/man/add.combi.Rd | 60 MoBPS-1.13.1/MoBPS/man/add.diversity.Rd |only MoBPS-1.13.1/MoBPS/man/add.fixed.effects.Rd |only MoBPS-1.13.1/MoBPS/man/add.founder.kinship.Rd | 2 MoBPS-1.13.1/MoBPS/man/analyze.bv.Rd | 5 MoBPS-1.13.1/MoBPS/man/analyze.population.Rd | 2 MoBPS-1.13.1/MoBPS/man/bit.snps.Rd | 2 MoBPS-1.13.1/MoBPS/man/breeding.diploid.Rd | 1240 - MoBPS-1.13.1/MoBPS/man/breeding.intern.Rd | 14 MoBPS-1.13.1/MoBPS/man/breeding.intern1.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern2.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern3.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern4.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern5.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern6.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern7.Rd |only MoBPS-1.13.1/MoBPS/man/breeding.intern8.Rd |only MoBPS-1.13.1/MoBPS/man/bv.development.box.Rd | 2 MoBPS-1.13.1/MoBPS/man/bv.standardization.Rd | 23 MoBPS-1.13.1/MoBPS/man/cattle_chip.Rd | 2 MoBPS-1.13.1/MoBPS/man/check.parents.Rd | 15 MoBPS-1.13.1/MoBPS/man/chicken_chip.Rd | 2 MoBPS-1.13.1/MoBPS/man/combine.traits.Rd | 72 MoBPS-1.13.1/MoBPS/man/computing.costs.Rd |only MoBPS-1.13.1/MoBPS/man/computing.costs.cohorts.Rd |only MoBPS-1.13.1/MoBPS/man/computing.snps.Rd |only MoBPS-1.13.1/MoBPS/man/computing.snps_single.Rd |only MoBPS-1.13.1/MoBPS/man/creating.diploid.Rd | 354 MoBPS-1.13.1/MoBPS/man/creating.phenotypic.transform.Rd | 34 MoBPS-1.13.1/MoBPS/man/creating.trait.Rd | 159 MoBPS-1.13.1/MoBPS/man/demiraculix.Rd | 44 MoBPS-1.13.1/MoBPS/man/diag.mobps.Rd | 40 MoBPS-1.13.1/MoBPS/man/effective.size.Rd | 42 MoBPS-1.13.1/MoBPS/man/ex_json.Rd | 2 MoBPS-1.13.1/MoBPS/man/ex_pop.Rd | 2 MoBPS-1.13.1/MoBPS/man/exist.cohort.Rd |only MoBPS-1.13.1/MoBPS/man/find.snpbefore.Rd | 2 MoBPS-1.13.1/MoBPS/man/founder.simulation.Rd | 287 MoBPS-1.13.1/MoBPS/man/get.admixture.Rd | 99 MoBPS-1.13.1/MoBPS/man/get.age.point.Rd | 9 MoBPS-1.13.1/MoBPS/man/get.allele.freq.Rd |only MoBPS-1.13.1/MoBPS/man/get.bv.Rd | 13 MoBPS-1.13.1/MoBPS/man/get.bve.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.class.Rd | 9 MoBPS-1.13.1/MoBPS/man/get.cohorts.individual.Rd |only MoBPS-1.13.1/MoBPS/man/get.computing.time.Rd |only MoBPS-1.13.1/MoBPS/man/get.creating.type.Rd | 9 MoBPS-1.13.1/MoBPS/man/get.culling.time.Rd |only MoBPS-1.13.1/MoBPS/man/get.culling.type.Rd |only MoBPS-1.13.1/MoBPS/man/get.cullingtime.Rd | 5 MoBPS-1.13.1/MoBPS/man/get.database.Rd | 37 MoBPS-1.13.1/MoBPS/man/get.death.point.Rd | 9 MoBPS-1.13.1/MoBPS/man/get.dendrogram.Rd | 85 MoBPS-1.13.1/MoBPS/man/get.dendrogram.heatmap.Rd | 101 MoBPS-1.13.1/MoBPS/man/get.dendrogram.trait.Rd | 89 MoBPS-1.13.1/MoBPS/man/get.distance.Rd | 124 MoBPS-1.13.1/MoBPS/man/get.effect.freq.Rd | 73 MoBPS-1.13.1/MoBPS/man/get.effective.size.Rd | 62 MoBPS-1.13.1/MoBPS/man/get.fixed.effects.p.Rd |only MoBPS-1.13.1/MoBPS/man/get.geno.Rd | 19 MoBPS-1.13.1/MoBPS/man/get.geno.time.Rd |only MoBPS-1.13.1/MoBPS/man/get.genotyped.Rd | 10 MoBPS-1.13.1/MoBPS/man/get.genotyped.snp.Rd | 82 MoBPS-1.13.1/MoBPS/man/get.haplo.Rd | 19 MoBPS-1.13.1/MoBPS/man/get.id.Rd | 16 MoBPS-1.13.1/MoBPS/man/get.index.Rd |only MoBPS-1.13.1/MoBPS/man/get.infos.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.is.first.Rd |only MoBPS-1.13.1/MoBPS/man/get.is.last.Rd |only MoBPS-1.13.1/MoBPS/man/get.litter.Rd |only MoBPS-1.13.1/MoBPS/man/get.litter.effect.Rd |only MoBPS-1.13.1/MoBPS/man/get.maf.Rd |only MoBPS-1.13.1/MoBPS/man/get.map.Rd | 4 MoBPS-1.13.1/MoBPS/man/get.ngen.Rd |only MoBPS-1.13.1/MoBPS/man/get.nindi.Rd |only MoBPS-1.13.1/MoBPS/man/get.npheno.Rd | 79 MoBPS-1.13.1/MoBPS/man/get.ntrait.Rd |only MoBPS-1.13.1/MoBPS/man/get.pca.Rd | 10 MoBPS-1.13.1/MoBPS/man/get.pedigree.Rd | 18 MoBPS-1.13.1/MoBPS/man/get.pedigree.visual.Rd |only MoBPS-1.13.1/MoBPS/man/get.pedigree2.Rd | 10 MoBPS-1.13.1/MoBPS/man/get.pedigree3.Rd | 11 MoBPS-1.13.1/MoBPS/man/get.pedigree_old.Rd |only MoBPS-1.13.1/MoBPS/man/get.pedmap.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.pen.Rd |only MoBPS-1.13.1/MoBPS/man/get.pen.effect.Rd |only MoBPS-1.13.1/MoBPS/man/get.pheno.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.pheno.off.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.pheno.off.count.Rd | 13 MoBPS-1.13.1/MoBPS/man/get.pheno.single.Rd |only MoBPS-1.13.1/MoBPS/man/get.pheno.time.Rd |only MoBPS-1.13.1/MoBPS/man/get.phylogenetic.tree.Rd | 91 MoBPS-1.13.1/MoBPS/man/get.plink.Rd |only MoBPS-1.13.1/MoBPS/man/get.pool.Rd |only MoBPS-1.13.1/MoBPS/man/get.pool.founder.Rd |only MoBPS-1.13.1/MoBPS/man/get.qtl.Rd | 42 MoBPS-1.13.1/MoBPS/man/get.qtl.effects.Rd | 42 MoBPS-1.13.1/MoBPS/man/get.qtl.variance.Rd | 62 MoBPS-1.13.1/MoBPS/man/get.recombi.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.reliability.Rd |only MoBPS-1.13.1/MoBPS/man/get.selectionbve.Rd | 9 MoBPS-1.13.1/MoBPS/man/get.selectionindex.Rd | 7 MoBPS-1.13.1/MoBPS/man/get.sex.Rd |only MoBPS-1.13.1/MoBPS/man/get.size.Rd |only MoBPS-1.13.1/MoBPS/man/get.snapshot.Rd |only MoBPS-1.13.1/MoBPS/man/get.snapshot.single.Rd |only MoBPS-1.13.1/MoBPS/man/get.time.point.Rd | 11 MoBPS-1.13.1/MoBPS/man/get.trafo.p.Rd |only MoBPS-1.13.1/MoBPS/man/get.trafo.p.single.Rd |only MoBPS-1.13.1/MoBPS/man/get.trait.name.Rd |only MoBPS-1.13.1/MoBPS/man/get.uhat.Rd |only MoBPS-1.13.1/MoBPS/man/get.variance.Rd |only MoBPS-1.13.1/MoBPS/man/get.variance.components.Rd |only MoBPS-1.13.1/MoBPS/man/get.vcf.Rd | 13 MoBPS-1.13.1/MoBPS/man/group.diff.Rd | 82 MoBPS-1.13.1/MoBPS/man/inbreeding.emp.Rd |only MoBPS-1.13.1/MoBPS/man/inbreeding.exp.Rd |only MoBPS-1.13.1/MoBPS/man/insert.bv.Rd |only MoBPS-1.13.1/MoBPS/man/insert.bve.Rd | 2 MoBPS-1.13.1/MoBPS/man/insert.pheno.Rd |only MoBPS-1.13.1/MoBPS/man/insert.pheno.single.Rd |only MoBPS-1.13.1/MoBPS/man/json.simulation.Rd | 13 MoBPS-1.13.1/MoBPS/man/kinship.development.Rd | 2 MoBPS-1.13.1/MoBPS/man/kinship.emp.Rd | 13 MoBPS-1.13.1/MoBPS/man/kinship.emp.fast.Rd | 13 MoBPS-1.13.1/MoBPS/man/kinship.emp.fast.between.Rd |only MoBPS-1.13.1/MoBPS/man/kinship.exp.Rd | 106 MoBPS-1.13.1/MoBPS/man/ld.decay.Rd | 14 MoBPS-1.13.1/MoBPS/man/maize_chip.Rd | 2 MoBPS-1.13.1/MoBPS/man/matrix.posdef.Rd |only MoBPS-1.13.1/MoBPS/man/merging.cohorts.Rd |only MoBPS-1.13.1/MoBPS/man/merging.trait.Rd |only MoBPS-1.13.1/MoBPS/man/miesenberger.index.Rd | 6 MoBPS-1.13.1/MoBPS/man/miraculix.Rd | 44 MoBPS-1.13.1/MoBPS/man/mutation.intro.Rd | 22 MoBPS-1.13.1/MoBPS/man/new.base.generation.Rd | 13 MoBPS-1.13.1/MoBPS/man/ogc.mobps.Rd |only MoBPS-1.13.1/MoBPS/man/optimize.cores.Rd |only MoBPS-1.13.1/MoBPS/man/pedigree.matrix.Rd |only MoBPS-1.13.1/MoBPS/man/pedigree.simulation.Rd | 498 MoBPS-1.13.1/MoBPS/man/pig_chip.Rd | 2 MoBPS-1.13.1/MoBPS/man/plot.population.Rd | 2 MoBPS-1.13.1/MoBPS/man/recalculate.bv.Rd |only MoBPS-1.13.1/MoBPS/man/recalculate.manual.Rd |only MoBPS-1.13.1/MoBPS/man/recombination.function.haldane.Rd |only MoBPS-1.13.1/MoBPS/man/renaming.cohort.Rd |only MoBPS-1.13.1/MoBPS/man/rowMedian.Rd |only MoBPS-1.13.1/MoBPS/man/scaling.relationship.Rd |only MoBPS-1.13.1/MoBPS/man/set.age.point.Rd |only MoBPS-1.13.1/MoBPS/man/set.class.Rd | 4 MoBPS-1.13.1/MoBPS/man/set.default.Rd | 70 MoBPS-1.13.1/MoBPS/man/set.mean.pool.Rd |only MoBPS-1.13.1/MoBPS/man/set.time.point.Rd |only MoBPS-1.13.1/MoBPS/man/sheep_chip.Rd | 2 MoBPS-1.13.1/MoBPS/man/summary.population.Rd | 2 MoBPS-1.13.1/MoBPS/man/write.pedigree.Rd |only MoBPS-1.6.64/MoBPS/R/get.individual.loc.R |only MoBPS-1.6.64/MoBPS/man/compute.costs.Rd |only MoBPS-1.6.64/MoBPS/man/compute.costs.cohorts.Rd |only MoBPS-1.6.64/MoBPS/man/compute.snps.Rd |only MoBPS-1.6.64/MoBPS/man/compute.snps_single.Rd |only MoBPS-1.6.64/MoBPS/man/get.individual.loc.Rd |only MoBPS-1.6.64/MoBPS/man/get.reliabilities.Rd |only 324 files changed, 19876 insertions(+), 9642 deletions(-)
Title: Official Gridded Data from the German Census 2022
Description: Provides fast and easy access to German census grid data
from the 2011 and 2022 censuses <https://www.zensus2022.de/>, including a
wide range of socio-economic indicators at multiple spatial resolutions
(100m, 1km, 10km). Enables efficient download, processing, and analysis
of large census datasets covering population, households, families,
dwellings, and buildings. Harmonized data structures allow direct
comparison with the 2011 census, supporting temporal and spatial analyses.
Facilitates conversion of data into common formats for spatial analysis and
mapping ('terra', 'sf', 'ggplot2').
Author: Jonas Lieth [cre, aut, cph]
Maintainer: Jonas Lieth <jonas.lieth@gesis.org>
Diff between z22 versions 1.0.0 dated 2025-05-19 and 1.1.0 dated 2025-10-29
DESCRIPTION | 6 - MD5 | 40 +++---- NEWS.md | 17 +++ R/data.R | 115 ++++++++++++++-------- R/inspire.R | 149 +++++++++++++++++++---------- R/pivot.R | 8 - README.md | 16 +-- inst/doc/z22.Rmd | 30 +++-- inst/doc/z22.html | 41 ++++--- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/vignette/allcells_plot-1.png |binary man/figures/vignette/multiplot-1.png |binary man/figures/vignette/normalize_plot-1.png |binary man/figures/vignette/patchwork_plot-1.png |binary man/figures/vignette/unnamed-chunk-5-1.png |binary man/inspire.Rd | 40 ++++--- man/z22_data.Rd | 23 ++-- man/z22_grid.Rd | 30 +---- tests/testthat/test-pkg.R | 46 ++++++-- vignettes/z22.Rmd | 30 +++-- vignettes/z22.Rmd.orig | 14 +- 21 files changed, 369 insertions(+), 236 deletions(-)
Title: Read Data from Relational Database Management Systems and Health
Information Systems
Description: Import Data from Relational Database Management Systems
(RDBMS) and Health Information Systems ('HIS'). The current version of the
package supports importing data from RDBMS including 'MS SQL', 'MySQL',
'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and
'SORMAS'.
Author: Karim Mane [aut] ,
Emmanuel Kabuga [aut] ,
Bubacarr Bah [aut, cre] ,
Bankole Ahadzie [ctb],
Nuredin Mohammed [ctb],
Abdoelnaser Degoot [ctb],
Hugo Gruson [rev] ,
Pratik Gupte [rev] ,
Andree Valle-Campos [rev] ,
London School of Hygiene and Tropical M [...truncated...]
Maintainer: Bubacarr Bah <Bubacarr.Bah1@lshtm.ac.uk>
Diff between readepi versions 1.0.2 dated 2025-10-27 and 1.0.3 dated 2025-10-29
DESCRIPTION | 22 +++++++++++----------- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ README.md | 22 ++++++++++++++++++++++ inst/CITATION | 12 ++++++++---- inst/doc/design_principle.html | 4 ++-- inst/doc/readepi.html | 2 +- 7 files changed, 56 insertions(+), 24 deletions(-)
Title: Risk Calculator for Cardiovascular Disease in Japan
Description: A calculation tool to obtain the 5-year or 10-year risk of cardiovascular disease from various risk models.
Author: Hiroshi Okumiyama [aut, cre],
Ryosuke Fujii [aut]
Maintainer: Hiroshi Okumiyama <xzxz2019@iCloud.com>
Diff between Jcvrisk versions 0.1.2 dated 2025-04-25 and 0.1.3 dated 2025-10-29
Jcvrisk-0.1.2/Jcvrisk/man/01_Hisayama.Rd |only Jcvrisk-0.1.2/Jcvrisk/man/02_SuitawECG.Rd |only Jcvrisk-0.1.2/Jcvrisk/man/03_SuitawoECG.Rd |only Jcvrisk-0.1.2/Jcvrisk/man/04_EPOCH_CHD.Rd |only Jcvrisk-0.1.2/Jcvrisk/man/05_EPOCH_Stroke.Rd |only Jcvrisk-0.1.2/Jcvrisk/man/06_EPOCH_CVD.Rd |only Jcvrisk-0.1.3/Jcvrisk/DESCRIPTION | 27 ++++++------ Jcvrisk-0.1.3/Jcvrisk/LICENSE | 2 Jcvrisk-0.1.3/Jcvrisk/MD5 | 48 ++++++++++++++-------- Jcvrisk-0.1.3/Jcvrisk/NAMESPACE | 14 +++++- Jcvrisk-0.1.3/Jcvrisk/NEWS.md | 16 +++++++ Jcvrisk-0.1.3/Jcvrisk/R/01_Hisayama.R | 8 +-- Jcvrisk-0.1.3/Jcvrisk/R/02_suita_wECG.R | 39 ++++++++--------- Jcvrisk-0.1.3/Jcvrisk/R/03_suita_woECG.R | 39 ++++++++--------- Jcvrisk-0.1.3/Jcvrisk/R/04_EPOCH_CHD.R | 23 +++++----- Jcvrisk-0.1.3/Jcvrisk/R/05_EPOCH_Stroke.R | 15 +++--- Jcvrisk-0.1.3/Jcvrisk/R/06_EPOCH_CVD.R | 19 ++++---- Jcvrisk-0.1.3/Jcvrisk/R/07_JALS_Stroke_wECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/08_JALS_Stroke_woECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/09_JALS_AMI_wECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/10_JALS_AMI_woECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/11_JALS_Com_wECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/12_JALS_Com_woECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/13_JALS_CVD_wECG.R |only Jcvrisk-0.1.3/Jcvrisk/R/14_JALS_CVD_woECG.R |only Jcvrisk-0.1.3/Jcvrisk/man/01_hisayama.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/02_suita_wecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/03_suita_woecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/04_epoch_chd.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/05_epoch_stroke.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/06_epoch_cvd.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/07_Jjals_stroke_wecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/08_jals_stroke_woecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/09_jals_ami_wecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/10_jals_ami_woecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/11_jals_co_wecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/12_jals_co_woecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/13_jals_cvd_wecg.Rd |only Jcvrisk-0.1.3/Jcvrisk/man/14_jals_cvd_woecg.Rd |only 39 files changed, 145 insertions(+), 105 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.10.0 dated 2025-08-19 and 4.10.1 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/format2.R | 5 +++-- inst/app/global.R | 5 ++++- inst/app/server.R | 28 ++++++++++++++-------------- inst/doc/compareGroups_vignette.html | 4 ++-- man/compareGroups-package.Rd | 4 ++-- man/figures/var1age.pdf |binary man/figures/var1sex.pdf |binary 10 files changed, 42 insertions(+), 34 deletions(-)
Title: Covariate-Adjusted Adaptive Randomization via
Mahalanobis-Distance
Description: In randomized controlled trial (RCT), balancing covariate is often one of the most important concern. CARM package provides functions to balance the covariates and generate allocation sequence by covariate-adjusted Adaptive Randomization via Mahalanobis-distance (ARM) for RCT. About what ARM is and how it works please see Y. Qin, Y. Li, W. Ma, H. Yang, and F. Hu (2024). "Adaptive randomization via Mahalanobis distance" Statistica Sinica. <doi:10.5705/ss.202020.0440>. In addition, the package is also suitable for the randomization process of multi-arm trials. For details, please see Yang H, Qin Y, Wang F, et al. (2023). "Balancing covariates in multi-arm trials via adaptive randomization" Computational Statistics & Data Analysis.<doi:10.1016/j.csda.2022.107642>.
Author: Fanglu Chen [aut, cre],
Haoyu Yang [aut],
Yichen Qin [aut],
Yang Li [aut]
Maintainer: Fanglu Chen <chenfanglu1031@qq.com>
Diff between CARM versions 1.1.0 dated 2023-06-07 and 2.0.0 dated 2025-10-29
DESCRIPTION | 25 +++++++++++++------------ MD5 | 19 ++++++++++++------- NAMESPACE | 1 + R/ARM.R | 3 ++- R/covariate.R |only R/inner_function.R | 37 +++++++++++++++++++++++++++++++++++++ R/package.R | 24 ++++++++++++------------ R/stratum_ARM.R |only data |only man/ARM.Rd | 2 +- man/CARM-package.Rd | 21 +++++++++++++++++---- man/covariate.Rd |only man/stratum_ARM.Rd |only 13 files changed, 95 insertions(+), 37 deletions(-)
Title: Location and Scale Invariant Power Transformations
Description: Location- and scale-invariant Box-Cox and Yeo-Johnson power transformations
allow for transforming variables with distributions distant from 0 to
normality. Transformers are implemented as S4 objects. These allow for
transforming new instances to normality after optimising fitting parameters
on other data. A test for central normality allows for rejecting
transformations that fail to produce a suitably normal distribution,
independent of sample number.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Diff between power.transform versions 1.0.1 dated 2025-04-12 and 1.0.2 dated 2025-10-29
power.transform-1.0.1/power.transform/man/cn.test.Rd |only power.transform-1.0.1/power.transform/man/ecn.test.Rd |only power.transform-1.0.2/power.transform/DESCRIPTION | 14 power.transform-1.0.2/power.transform/MD5 | 28 power.transform-1.0.2/power.transform/NAMESPACE | 61 power.transform-1.0.2/power.transform/NEWS.md | 12 power.transform-1.0.2/power.transform/R/FindParameters.R | 626 +-- power.transform-1.0.2/power.transform/R/GoodnessOfFit.R | 557 ++- power.transform-1.0.2/power.transform/R/ParameterEstimators.R | 996 +++--- power.transform-1.0.2/power.transform/R/Utilities.R | 557 +-- power.transform-1.0.2/power.transform/R/aaa.R |only power.transform-1.0.2/power.transform/R/sysdata.rda |binary power.transform-1.0.2/power.transform/man/assess_transformation.Rd | 12 power.transform-1.0.2/power.transform/man/ecn_test.Rd |only power.transform-1.0.2/power.transform/man/get_residuals.Rd | 4 power.transform-1.0.2/power.transform/tests/testthat/test-goodness-of-fit.R | 16 power.transform-1.0.2/power.transform/tests/testthat/test-transformation.R | 1630 +++++----- 17 files changed, 2349 insertions(+), 2164 deletions(-)
More information about power.transform at CRAN
Permanent link
Title: High-Performance Geocoding using 'photon'
Description: Features unstructured, structured and reverse geocoding using the
'photon' geocoding API <https://photon.komoot.io/>.
Facilitates the setup of local 'photon' instances to enable offline
geocoding.
Author: Jonas Lieth [aut, cre, cph]
Maintainer: Jonas Lieth <jonas.lieth@gesis.org>
Diff between photon versions 0.3.5 dated 2025-02-24 and 0.7.4 dated 2025-10-29
DESCRIPTION | 9 +- MD5 | 61 +++++++------- NAMESPACE | 1 NEWS.md | 25 ++++++ R/download-db.R | 41 +++++++--- R/download-photon.R | 23 +++-- R/geocode.R | 2 R/new_photon.R | 70 ++++++++++++++--- R/photon-package.R | 2 R/photon_local.R | 134 ++++++++++++++++++++------------ R/photon_remote.R | 4 R/purge.R | 2 R/query_photon.R | 2 R/reverse.R | 15 +++ R/run_photon.R | 50 ++++++++---- R/structured.R | 6 - R/utils.R | 9 -- build/vignette.rds |binary inst/doc/photon.R | 128 +++++++++++++++++++++++++------ inst/doc/photon.Rmd | 135 ++++++++++++++++++++++++++------- inst/doc/photon.html | 171 ++++++++++++++++++++++++++++++------------ man/download_photon.Rd | 18 ++-- man/download_searchindex.Rd | 38 ++++++--- man/new_photon.Rd | 33 +++++--- man/photon_local.Rd | 108 ++++++++++++++++---------- man/purge_java.Rd | 2 man/reverse.Rd | 2 man/with_photon.Rd |only tests/testthat/test-geocode.R | 7 - tests/testthat/test-setup.R | 158 ++++++++++++++++++++++++-------------- tests/testthat/test-utils.R | 10 +- vignettes/photon.Rmd | 135 ++++++++++++++++++++++++++------- 32 files changed, 992 insertions(+), 409 deletions(-)
Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Description: A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user,
which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class.
Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.
Author: Alem Gusinac [aut, cre] ,
Thomas Ederveen [aut] ,
Annemarie Boleij [aut, fnd]
Maintainer: Alem Gusinac <alem.gusinac@gmail.com>
Diff between OmicFlow versions 1.3.2 dated 2025-09-20 and 1.4.0 dated 2025-10-29
OmicFlow-1.3.2/OmicFlow/inst/extdata/mock_taxa.rds |only OmicFlow-1.3.2/OmicFlow/tests/testthat/test-autoflow.R |only OmicFlow-1.4.0/OmicFlow/DESCRIPTION | 19 OmicFlow-1.4.0/OmicFlow/LICENSE | 4 OmicFlow-1.4.0/OmicFlow/MD5 | 132 OmicFlow-1.4.0/OmicFlow/NAMESPACE | 134 OmicFlow-1.4.0/OmicFlow/R/OmicFlow-package.R | 2 OmicFlow-1.4.0/OmicFlow/R/RcppExports.R |only OmicFlow-1.4.0/OmicFlow/R/bray.R |only OmicFlow-1.4.0/OmicFlow/R/canberra.R |only OmicFlow-1.4.0/OmicFlow/R/colormap.R | 98 OmicFlow-1.4.0/OmicFlow/R/composition_plot.R | 310 OmicFlow-1.4.0/OmicFlow/R/cosine.R |only OmicFlow-1.4.0/OmicFlow/R/diversity.R | 185 OmicFlow-1.4.0/OmicFlow/R/diversity_plot.R | 286 OmicFlow-1.4.0/OmicFlow/R/foldchange.R | 385 - OmicFlow-1.4.0/OmicFlow/R/hill_taxa.R | 164 OmicFlow-1.4.0/OmicFlow/R/jaccard.R |only OmicFlow-1.4.0/OmicFlow/R/jsd.R |only OmicFlow-1.4.0/OmicFlow/R/manhattan.R |only OmicFlow-1.4.0/OmicFlow/R/metagenomics-class.R | 961 +- OmicFlow-1.4.0/OmicFlow/R/omics-class.R | 3258 +++++----- OmicFlow-1.4.0/OmicFlow/R/ordination_plot.R | 224 OmicFlow-1.4.0/OmicFlow/R/pairwise_adonis.R | 217 OmicFlow-1.4.0/OmicFlow/R/pairwise_anosim.R | 185 OmicFlow-1.4.0/OmicFlow/R/plot_pairwise_stats.R | 220 OmicFlow-1.4.0/OmicFlow/R/proteomics-class.R | 306 OmicFlow-1.4.0/OmicFlow/R/unifrac.R |only OmicFlow-1.4.0/OmicFlow/R/utils.R | 262 OmicFlow-1.4.0/OmicFlow/R/volcano_plot.R | 334 - OmicFlow-1.4.0/OmicFlow/exec/autoFlow.R | 177 OmicFlow-1.4.0/OmicFlow/inst/extdata/counts.tsv | 486 - OmicFlow-1.4.0/OmicFlow/inst/extdata/features.tsv | 486 - OmicFlow-1.4.0/OmicFlow/inst/extdata/metadata.tsv | 10 OmicFlow-1.4.0/OmicFlow/inst/extdata/tree.newick |only OmicFlow-1.4.0/OmicFlow/inst/report.Rmd | 474 - OmicFlow-1.4.0/OmicFlow/inst/styles.css | 74 OmicFlow-1.4.0/OmicFlow/man/bray.Rd |only OmicFlow-1.4.0/OmicFlow/man/canberra.Rd |only OmicFlow-1.4.0/OmicFlow/man/composition_plot.Rd | 176 OmicFlow-1.4.0/OmicFlow/man/cosine.Rd |only OmicFlow-1.4.0/OmicFlow/man/diversity.Rd | 4 OmicFlow-1.4.0/OmicFlow/man/diversity_plot.Rd | 164 OmicFlow-1.4.0/OmicFlow/man/jaccard.Rd |only OmicFlow-1.4.0/OmicFlow/man/jsd.Rd |only OmicFlow-1.4.0/OmicFlow/man/manhattan.Rd |only OmicFlow-1.4.0/OmicFlow/man/metagenomics.Rd | 659 +- OmicFlow-1.4.0/OmicFlow/man/omics.Rd | 1993 +++--- OmicFlow-1.4.0/OmicFlow/man/ordination_plot.Rd | 122 OmicFlow-1.4.0/OmicFlow/man/pairwise_adonis.Rd | 121 OmicFlow-1.4.0/OmicFlow/man/pairwise_anosim.Rd | 115 OmicFlow-1.4.0/OmicFlow/man/proteomics.Rd | 511 - OmicFlow-1.4.0/OmicFlow/man/unifrac.Rd |only OmicFlow-1.4.0/OmicFlow/man/volcano_plot.Rd | 166 OmicFlow-1.4.0/OmicFlow/src |only OmicFlow-1.4.0/OmicFlow/tests/testthat.R | 28 OmicFlow-1.4.0/OmicFlow/tests/testthat/_snaps |only OmicFlow-1.4.0/OmicFlow/tests/testthat/input/metagenomics/rooted_tree.newick | 2 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-alpha_diversity.R | 76 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-composition.R | 32 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-dfe.R | 37 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-distances.R |only OmicFlow-1.4.0/OmicFlow/tests/testthat/test-hill.R | 28 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-metagenomics.R | 32 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-ordination.R | 38 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-subsetting.R | 34 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-transformations.R | 34 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-utils.R | 62 OmicFlow-1.4.0/OmicFlow/tests/testthat/test-write_biom.R | 42 69 files changed, 7326 insertions(+), 6543 deletions(-)
Title: Lightweight Framework for Orchestrating Multi-Agent Large
Language Models
Description: Provides tools for creating agents with persistent state using
R6 classes <https://cran.r-project.org/package=R6> and the 'ellmer'
package <https://cran.r-project.org/package=ellmer>. Tracks prompts,
messages, and agent metadata for reproducible, multi-turn large language
model sessions.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between mini007 versions 0.1.0 dated 2025-09-05 and 0.2.0 dated 2025-10-29
mini007-0.1.0/mini007/R/main.R |only mini007-0.2.0/mini007/DESCRIPTION | 10 mini007-0.2.0/mini007/MD5 | 13 mini007-0.2.0/mini007/NEWS.md | 23 + mini007-0.2.0/mini007/R/Agent.R |only mini007-0.2.0/mini007/R/LeadAgent.R |only mini007-0.2.0/mini007/README.md | 426 +++++++++++++++---- mini007-0.2.0/mini007/man/Agent.Rd | 716 ++++++++++++++++++++++++++++++++- mini007-0.2.0/mini007/man/LeadAgent.Rd | 166 ++++++- 9 files changed, 1237 insertions(+), 117 deletions(-)
Title: Assessment of Agreement using the Total Deviation Index
Description: The total deviation index (TDI) is an unscaled statistical measure used to evaluate the deviation between paired quantitative measurements when assessing the extent of agreement between different raters. It describes a boundary such that a large specified proportion of the differences in paired measurements are within the boundary (Lin, 2000) <https://pubmed.ncbi.nlm.nih.gov/10641028/>.
This R package implements some methodologies existing in the literature for TDI estimation and inference in the case of two raters.
Author: Anna Felip-Badia [aut, cre] ,
Sara Perez-Jaume [aut] ,
Josep L Carrasco [aut]
Maintainer: Anna Felip-Badia <annafelipibadia@gmail.com>
Diff between TDIagree versions 0.1.2 dated 2025-06-18 and 0.2.0 dated 2025-10-29
DESCRIPTION | 11 - MD5 | 20 +-- NAMESPACE | 8 + R/TDI.Perez_Jaume_and_Carrasco.R | 15 +- R/TDI.R | 36 +++-- R/TDIagree.R | 36 ++--- R/descriptive.plots.R |only R/plot.tdi.R | 13 + R/print.tdi.R | 258 +++++++++++++++++++++++++++++++-------- man/TDI.Rd | 8 - man/TDIagree-package.Rd | 2 man/descriptive.plots.Rd |only 12 files changed, 298 insertions(+), 109 deletions(-)
Title: Suite of Functions to Help Get Plot Elements Exactly Where You
Want Them
Description: Provides a selection of tools that make it easier to place elements onto a (base R) plot exactly where you want them. It allows users to identify points and distances on a plot in terms of inches, pixels, margin lines, data units, and proportions of the plotting space, all in a manner more simple than manipulating par().
Author: Jasper Watson [aut, cre]
Maintainer: Jasper Watson <jasper.g.watson@gmail.com>
Diff between precisePlacement versions 0.1.0 dated 2021-06-15 and 0.2.0 dated 2025-10-29
DESCRIPTION | 9 MD5 | 76 ++--- NAMESPACE | 2 NEWS.md | 7 R/AnnotatePlot.R | 99 +++---- R/convertUnits.R | 353 ++++++++++++------------- R/getBoundaries.R | 136 ++++----- R/getRange.R | 208 +++++++-------- R/lineLocations.R | 26 - R/omiForSubFigure.R | 86 +++--- R/precisePlacement.R | 14 - R/relativeUnitConversions.R | 266 +++++++++---------- R/repelAxisLabels.R |only R/showMarginLines.R | 68 ++-- R/showOuterMarginLines.R | 62 ++-- R/stringSizes.R |only README.md | 6 build/vignette.rds |binary inst/WORDLIST |only inst/doc/Overview.R | 93 ++++++ inst/doc/Overview.Rmd | 91 ++++++ inst/doc/Overview.html | 602 ++++++++++++++++++++++++++++---------------- man/convertUnits.Rd | 14 - man/getBoundaries.Rd | 2 man/getDataPerInch.Rd | 2 man/getDataPerLine.Rd | 2 man/getDataPerPixel.Rd | 2 man/getInchesPerDatum.Rd | 2 man/getInchesPerLine.Rd | 6 man/getInchesPerPixel.Rd | 2 man/getLinesPerDatum.Rd | 2 man/getLinesPerInch.Rd | 6 man/getLinesPerPixel.Rd | 2 man/getPixelsPerDatum.Rd | 2 man/getPixelsPerInch.Rd | 2 man/getPixelsPerLine.Rd | 2 man/getRange.Rd | 2 man/omiForSubFigure.Rd | 8 man/precisePlacement.Rd | 8 man/repelAxisLabels.Rd |only vignettes/Overview.Rmd | 91 ++++++ 41 files changed, 1399 insertions(+), 962 deletions(-)
More information about precisePlacement at CRAN
Permanent link
Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with
package 'leaflet'. These charts can be used to represent at same time multiple
variables on a single map.
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Benoit Thieurmel [aut],
Francois Guillem [aut],
RTE [cph]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between leaflet.minicharts versions 0.6.2 dated 2021-05-11 and 0.6.3 dated 2025-10-29
DESCRIPTION | 18 LICENSE | 2 MD5 | 58 NEWS | 5 R/data-doc.R | 2 R/minicharts_deps.R | 36 R/popup_args.R | 58 R/prepare_js_args.R | 346 - R/preprocess_args.R | 72 R/sync_with.R | 86 R/zzz.R | 18 README.md | 3 build/vignette.rds |binary inst/doc/introduction.R | 214 inst/doc/introduction.Rmd | 368 - inst/doc/introduction.html | 5128 +++++++++++++++++++++-- inst/font-awesome-4.7.0/css/font-awesome.min.css | 8 inst/minicharts.css | 304 - man/addFlows.Rd | 284 - man/addMinicharts.Rd | 450 +- man/d3.schemeCategory10.Rd | 46 man/eco2mix.Rd | 74 man/popupArgs.Rd | 92 man/syncWith.Rd | 92 tests/testthat.R | 8 tests/testthat/test-flows.R | 64 tests/testthat/test-minicharts.R | 264 - tests/testthat/test-prepare_js_args.R | 406 - tests/testthat/test-preprocess_args.R | 80 vignettes/introduction.Rmd | 368 - 30 files changed, 6696 insertions(+), 2258 deletions(-)
More information about leaflet.minicharts at CRAN
Permanent link
Title: Bayesian Lasso Regression and Tools for the Lasso Distribution
Description: Implements Bayesian Lasso regression using efficient Gibbs sampling
algorithms, including modified versions of the Hans and Park–Casella (PC) samplers.
Includes functions for working with the Lasso distribution, such as its density,
cumulative distribution, quantile, and random generation functions, along with moment
calculations. Also includes a function to compute the Mills ratio. Designed for sparse
linear models and suitable for high-dimensional regression problems.
Author: John Ormerod [aut, cph] ,
Mohammad Javad Davoudabadi [aut, cre, cph] ,
Garth Tarr [aut, cph] ,
Samuel Mueller [aut, cph] ,
Jonathon Tidswell [aut, cph]
Maintainer: Mohammad Javad Davoudabadi <mohammad.davoudabadi@sydney.edu.au>
Diff between BayesianLasso versions 0.3.5 dated 2025-07-28 and 0.3.6 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md | 2 ++ README.md | 8 ++++---- inst/doc/BayesianLasso.html | 5 +++-- man/figures/logo.png |only src/lasso_distribution.cpp | 16 ++++++++-------- 7 files changed, 27 insertions(+), 23 deletions(-)
Title: Evaluation of Presence-Absence Models
Description: Collection of functions to evaluate presence-absence models. It
comprises functions to adjust discrimination statistics for the
representativeness effect through case-weighting, along with functions for
visualizing the outcomes. Originally outlined in:
Jiménez-Valverde (2022) The uniform AUC: dealing with the
representativeness effect in presence-absence models. Methods Ecol. Evol,
13, 1224-1236.
Author: Alberto Jimenez-Valverde [aut, cre]
Maintainer: Alberto Jimenez-Valverde <alberto.jimenez.valverde@gmail.com>
Diff between vandalico versions 0.1.0 dated 2024-09-06 and 0.2.0 dated 2025-10-29
DESCRIPTION | 20 ++++++++++++-------- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 +++ NEWS.md | 14 ++++++++++++-- R/AUCuniform.2.R |only R/AUCuniform.R | 30 ++++++++++++++---------------- R/AUCuniform_trap.R | 45 +++++++++++++++++++++------------------------ R/CALplot.R | 11 +++++------ R/HSgraph.R | 18 ++++++++---------- man/AUCuniform.2.Rd |only man/AUCuniform.Rd | 6 +++--- man/CALplot.Rd | 4 ++-- man/HSgraph.Rd | 4 ++-- 13 files changed, 94 insertions(+), 83 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.3.0 dated 2025-04-23 and 5.3.1 dated 2025-10-29
DESCRIPTION | 55 ++--- MD5 | 85 +++---- NAMESPACE | 8 NEWS.md | 29 ++ R/clustering.R | 254 +++++++++++++++-------- R/convenience.R | 3 R/differential_expression.R | 29 +- R/dimensional_reduction.R | 86 ++++++- R/integration.R | 108 ++++------ R/mixscape.R | 58 ++--- R/objects.R | 40 +-- R/preprocessing.R | 83 ++++--- R/preprocessing5.R | 14 - R/sketching.R | 104 +++++++-- R/utilities.R | 66 ++++-- R/visualization.R | 324 +++++++++++++++++------------- R/zzz.R | 4 build/Seurat.pdf |binary build/stage23.rdb |binary man/AddModuleScore.Rd | 2 man/BuildNicheAssay.Rd | 9 man/ColorDimSplit.Rd | 4 man/DEenrichRPlot.Rd | 2 man/DimPlot.Rd | 8 man/FeaturePlot.Rd | 6 man/FindClusters.Rd | 11 + man/MixscapeHeatmap.Rd | 2 man/MixscapeLDA.Rd | 2 man/PrepLDA.Rd | 2 man/PrepSCTFindMarkers.Rd | 2 man/ReadAkoya.Rd | 2 man/ReadNanostring.Rd | 2 man/ReadVitessce.Rd | 2 man/ReadVizgen.Rd | 2 man/RunICA.Rd | 2 man/RunLeiden.Rd | 17 + man/RunUMAP.Rd | 9 man/STARmap-class.Rd | 2 man/Seurat-package.Rd | 2 man/SlideSeq-class.Rd | 2 man/roxygen/templates/section-progressr.R | 2 tests/testthat/test_dimplot.R |only tests/testthat/test_find_clusters.R | 2 tests/testthat/test_integration.R | 2 44 files changed, 912 insertions(+), 536 deletions(-)
Title: Toolbox for Regression Discontinuity Design ('RDD')
Description: Set of functions for Regression Discontinuity Design ('RDD'), for
data visualisation, estimation and testing.
Author: Matthieu Stigler [aut, cre] ,
Bastiaan Quast [aut]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
This is a re-admission after prior archival of version 2.0.1 dated 2025-07-02
Diff between rddtools versions 2.0.1 dated 2025-07-02 and 2.0.2 dated 2025-10-29
DESCRIPTION | 21 ++++++++++++++------- MD5 | 19 +++++++++++-------- NAMESPACE | 9 ++++++++- NEWS.md | 7 ++++++- R/dens_test.R | 17 ++++++++++------- R/rdd_pkg_old_DCdensity.R |only R/rdd_pkg_old_kernelwts.R |only build/partial.rdb |only inst/devtools_internal_tests.R | 7 ++++++- inst/doc/morocco.html | 17 ++++++++++++----- inst/doc/rddtools.html | 9 +++++---- man/dens_test.Rd | 19 +++++++++++++------ 12 files changed, 85 insertions(+), 40 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.5.0 dated 2025-08-27 and 3.5.1 dated 2025-10-29
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/Cluster.R | 4 ++-- inst/doc/Logging.pdf |binary inst/doc/Parallel.pdf |binary man/makeCluster.Rd | 2 +- 7 files changed, 21 insertions(+), 14 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.5.1 dated 2025-05-15 and 0.5.2 dated 2025-10-29
DESCRIPTION | 8 MD5 | 18 R/FuzzyImputation.R | 22 R/FuzzyNumbersToMatrix.R | 4 man/FuzzyImputation.Rd | 9 tests/testthat/_snaps/FuzzyImputation.md | 148 +- tests/testthat/_snaps/FuzzyNumbersToMatrix.md | 16 tests/testthat/_snaps/MethodsComparison.md | 1578 +++++++++++++------------- tests/testthat/test-FuzzyImputation.R | 6 tests/testthat/test-MethodsComparison.R | 4 10 files changed, 936 insertions(+), 877 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
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] ,
Thibaut Jombart [ctb] .),
Abdoelnaser Degoot [aut] ,
Bankole Ahadzie [aut],
Nuredin Mohammed [aut],
Bubacarr Bah [aut, cre] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [rev] ,
James M. Azam [rev] ,
Joshua W. Lambert [rev, ctb] ,
Chr [...truncated...]
Maintainer: Bubacarr Bah <Bubacarr.Bah1@lshtm.ac.uk>
Diff between cleanepi versions 1.1.1 dated 2025-07-16 and 1.1.2 dated 2025-10-29
DESCRIPTION | 21 MD5 | 45 - NEWS.md | 24 R/correct_misspelled_values.R | 25 R/find_and_remove_duplicates.R | 12 R/print_report.R | 133 ++- R/replace_missing_values.R | 9 R/standardize_subject_ids.R | 32 R/utils.R | 11 README.md | 424 ------------ inst/WORDLIST | 3 inst/doc/cleanepi.html | 4 inst/extdata/logo.svg |only inst/po/fr/LC_MESSAGES/R-cleanepi.mo |binary inst/rmarkdown/templates/printing-rmd/skeleton/skeleton.Rmd | 12 man/cleanepi-package.Rd | 6 man/find_duplicates.Rd | 9 man/print_report.Rd | 99 +- man/replace_missing_values.Rd | 3 man/unnest_report.Rd | 2 po/R-cleanepi.pot | 87 +- po/R-fr.po | 102 +- tests/testthat/test-correct_misspelled_values.R | 16 tests/testthat/test-replace_missing_values.R | 9 24 files changed, 413 insertions(+), 675 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means. See Walvoort et al. (2010)
<doi:10.1016/j.cageo.2010.04.005> for details.
Author: Dennis Walvoort [aut, cre, cph] ,
Dick Brus [aut, cph] ,
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.4-5 dated 2025-10-14 and 0.4-6 dated 2025-10-29
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- inst/NEWS.Rd | 6 ++++ man/estimate-methods.Rd | 60 +++++++++++++++++++++++++----------------------- man/spsample-methods.Rd | 47 ++++++++++++++++++++----------------- man/stratify-methods.Rd | 28 ++++++++++++---------- 6 files changed, 87 insertions(+), 72 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.16 dated 2025-10-27 and 0.0.17 dated 2025-10-29
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/zzz.R | 2 +- build/partial.rdb |binary inst/CITATION | 19 +++++++++++++++---- inst/doc/choice-of-SEL-weights.html | 4 ++-- inst/doc/non-parametric-rcpp.html | 29 ++++++++++++++--------------- tests/testthat/test-ExEL1.R | 2 +- tests/testthat/test-ExEL2.R | 2 +- 10 files changed, 50 insertions(+), 36 deletions(-)
Title: Non-Local Prior Based Iterative Variable Selection Tool for
Genome-Wide Association Studies
Description: Performs variable selection with data from Genome-wide association studies (GWAS), or other high-dimensional data with continuous, binary or survival outcomes, combining in an iterative framework the computational efficiency of the structured screen-and-select variable selection strategy based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors (see Sanyal et al., 2019 <DOI:10.1093/bioinformatics/bty472>).
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>
This is a re-admission after prior archival of version 2.3 dated 2024-10-20
Diff between GWASinlps versions 2.3 dated 2024-10-20 and 2.4 dated 2025-10-29
DESCRIPTION | 13 +++---- MD5 | 16 ++++---- NAMESPACE | 1 NEWS | 4 ++ NEWS.md | 4 ++ R/GWASinlps.R | 84 ++++++++++++++++++++++++++--------------------- man/GWASinlps-package.Rd | 4 +- man/GWASinlps.Rd | 10 ++--- man/nlps.Rd | 8 ++-- 9 files changed, 81 insertions(+), 63 deletions(-)
Title: Chi-Square and G-Square Test of Independence, Power and Residual
Analysis, Measures of Categorical Association
Description: Provides the facility to perform the chi-square and G-square test of independence, calculates the retrospective power of the traditional chi-square test, compute permutation and Monte Carlo p-value, and provides measures of association for tables of any size such as Phi, Phi corrected, odds ratio with 95 percent CI and p-value, Yule' Q and Y, adjusted contingency coefficient, Cramer's V, V corrected, V standardised, bias-corrected V, W, Cohen's w, Goodman-Kruskal's lambda, and tau. It also calculates standardised, moment-corrected standardised, and adjusted standardised residuals, and their significance, as well as the Quetelet Index, IJ association factor, and adjusted standardised counts. It also computes the chi-square-maximising version of the input table. Different outputs are returned in nicely formatted tables.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between chisquare versions 1.1.1 dated 2024-10-27 and 1.2 dated 2025-10-29
DESCRIPTION | 6 MD5 | 18 NAMESPACE | 1 NEWS.md | 39 R/chisquare.r | 1756 ++++++++++++++++++++++++++------- R/compute_median_polish_residuals.R |only R/gk_tau_se.R |only R/multiple_ORs.R | 1 README.md | 5 man/chisquare.Rd | 732 ++++++++++--- man/compute_gk_tau_se.Rd |only man/compute_median_polish_residuals.Rd |only 12 files changed, 2018 insertions(+), 540 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.5 dated 2025-10-02 and 4.5.1 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Analyze.Multinomial.R | 30 ++++++++++++++++++++---------- man/Sequential-package.Rd | 9 ++++++--- 4 files changed, 33 insertions(+), 20 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.11.3 dated 2025-09-11 and 2.11.4 dated 2025-10-29
DESCRIPTION | 6 MD5 | 270 +- NEWS.md | 7 R/exportUserRoleAssignments.R | 22 R/importUserRoleAssignments.R | 74 R/logging.R | 24 R/redcapConnection.R | 1156 +++++----- R/redcapDataStructure.R | 17 inst/doc/redcapAPI-best-practices.pdf |binary inst/doc/redcapAPI-casting-data.pdf |binary inst/doc/redcapAPI-data-validation.pdf |binary inst/doc/redcapAPI-faq.pdf |binary inst/doc/redcapAPI-getting-started-connecting.pdf |binary inst/doc/redcapAPI-missing-data-detection.pdf |binary inst/doc/redcapAPI-offline-connection.pdf |binary inst/extdata/offlineConnectionFiles/TestRedcapAPI_UserRoleAssignments.csv | 4 man/redcapConnection.Rd | 12 tests/testthat/test-001-packageSetup.R | 68 tests/testthat/test-002-projectSetup.R | 6 tests/testthat/test-020-redcapConnection-ArgumentValidation.R | 70 tests/testthat/test-021-redcapConnection-caching.R | 160 - tests/testthat/test-022-offlineConnection-ArgumentValidation.R | 40 tests/testthat/test-022-offlineConnection-Functionality.R | 346 +- tests/testthat/test-024-unlockREDCap-ArgumentValidation.R | 2 tests/testthat/test-024-unlockREDCap.R | 2 tests/testthat/test-050-makeApiCall.R | 2 tests/testthat/test-051-stringCleanup.R | 62 tests/testthat/test-052-unitsFieldAnnotation.R | 11 tests/testthat/test-053-fieldValidationAndCasting.R | 988 ++++---- tests/testthat/test-054-fieldChoiceMapping.R | 78 tests/testthat/test-055-filterEmptyRow.R | 68 tests/testthat/test-056-redcapError.R | 22 tests/testthat/test-057-vectorToApiBodyList.R | 17 tests/testthat/test-058-writeDataForImport.R | 26 tests/testthat/test-059-isZeroCodedCheckField.R | 80 tests/testthat/test-060-reviewInvalidRecords.R | 42 tests/testthat/test-061-regularExpressions.R | 32 tests/testthat/test-100-projectInfo-ArgumentValidation.R | 144 - tests/testthat/test-100-projectInfo-functionality.R | 35 tests/testthat/test-101-userMethods-ArgumentValidation.R | 140 - tests/testthat/test-101-userMethods-Functionality.R | 112 tests/testthat/test-102-userRoleMethods-ArgumentValidation.R | 98 tests/testthat/test-102-userRoleMethods-Functionality.R | 74 tests/testthat/test-103-userRoleAssignmentMethods-ArgumentValidation.R | 114 tests/testthat/test-103-userRoleAssignmentMethods-Functionality.R | 66 tests/testthat/test-104-dagMethods-ArgumentValidation.R | 98 tests/testthat/test-104-dagMethods-Functionality.R | 62 tests/testthat/test-105-dagAssignment-ArgumentValidation.R | 82 tests/testthat/test-105-dagAssignment-Functionality.R | 60 tests/testthat/test-106-armsMethods-ArgumentValidation.R | 82 tests/testthat/test-106-armsMethods-Functionality.R | 228 - tests/testthat/test-107-eventsMethods-ArgumentValidation.R | 111 tests/testthat/test-107-eventsMethods-Functionality.R | 186 - tests/testthat/test-108-metadataMethods-ArgumentValidation.R | 300 +- tests/testthat/test-108-metadataMethods-Functionality.R | 38 tests/testthat/test-109-instrumentMethods-ArgumentValidation.R | 247 +- tests/testthat/test-109-instrumentMethods-Functionality.R | 2 tests/testthat/test-110-repeatingInstruments-ArgumentValidation.R | 32 tests/testthat/test-110-repeatingInstruments-Functionality.R | 116 - tests/testthat/test-111-switchDag-ArgumentValidation.R | 24 tests/testthat/test-111-switchDag-Functionality.R | 6 tests/testthat/test-150-importDeleteRecords-ArgumentValidation.R | 274 +- tests/testthat/test-150-importDeleteRecords-Functionality.R | 232 -- tests/testthat/test-151-exportRecords-ArgumentValidation.R | 6 tests/testthat/test-151-exportRecords-Functionality.R | 6 tests/testthat/test-152-exportRecordsWithDags.R | 6 tests/testthat/test-153-exportRecordsWithEvents.R | 6 tests/testthat/test-154-exportRecordsWithSurveys.R | 2 tests/testthat/test-155-exportRecordsWithRepeatingInstruments.R | 6 tests/testthat/test-180-exportRecordsOffline-ArgumentValidation.R | 6 tests/testthat/test-180-exportRecordsOffline-Functionality.R | 6 tests/testthat/test-190-exportReports-ArgumentValidation.R | 8 tests/testthat/test-190-exportReports-Functionality.R | 8 tests/testthat/test-200-exportTypedRecords-ArgumentValidation.R | 6 tests/testthat/test-200-exportTypedRecords-Functionality.R | 334 +- tests/testthat/test-201-exportTypedRecords-withDAGs.R | 42 tests/testthat/test-202-exportTypedRecords-withEvents.R | 32 tests/testthat/test-203-exportTypedRecords-withSurveys.R | 2 tests/testthat/test-204-exportTypedRecords-withRepeatingInstruments.R | 54 tests/testthat/test-205-exportTypedRecords-offline-ArgumentValidation.R | 70 tests/testthat/test-205-exportTypedRecords-offline-Functionality.R | 156 - tests/testthat/test-206-exportBulkRecords.R | 6 tests/testthat/test-210-exportSAS.R | 2 tests/testthat/test-240-exportTypedReports-ArgumentValidation.R | 18 tests/testthat/test-240-exportTypedReports-Functionality.R | 74 tests/testthat/test-250-recastRecords.R | 2 tests/testthat/test-251-castForImport.R | 682 ++--- tests/testthat/test-252-guessCast.R | 16 tests/testthat/test-253-guessDate.R | 4 tests/testthat/test-254-mChoiceCast.R | 21 tests/testthat/test-255-splitForms.R | 90 tests/testthat/test-256-dropRepeatingNA.R | 68 tests/testthat/test-300-reconstituteFileFromExport.R | 121 - tests/testthat/test-301-fileMethods-ArgumentValidation.R | 322 +- tests/testthat/test-301-fileMethods-Functionality.R | 144 - tests/testthat/test-302-createFileRepository-ArgumentValidation.R | 124 - tests/testthat/test-302-createFileRepository-Functionality.R | 6 tests/testthat/test-303-fileRepository-SingleFileMethods-ArgumentValidation.R | 161 - tests/testthat/test-303-fileRepository-SingleFileMethods-Functionality.R | 108 tests/testthat/test-304-fileRepository-BulkFileMethods-ArgumentValidation.R | 160 - tests/testthat/test-304-fileRepository-BulkFileMethods-Functionality.R | 116 - tests/testthat/test-305-exportFileRepositoryListing.R | 68 tests/testthat/test-306-fileRepositoryPath.R | 64 tests/testthat/test-350-exportNextRecordName-ArgumentValidation.R | 26 tests/testthat/test-350-exportNextRecordName-Functionality.R | 10 tests/testthat/test-351-exportVersion.R | 28 tests/testthat/test-352-savePurgeRestoreProject-ArgumentValidation.R | 250 +- tests/testthat/test-352-savePurgeRestoreProject-Functionality.R | 2 tests/testthat/test-353-allocationTable-ArgumentValidation.R | 259 +- tests/testthat/test-353-allocationTable-Functionality.R | 14 tests/testthat/test-354-getProjectIdFields.R | 26 tests/testthat/test-355-invalid.R | 14 tests/testthat/test-356-missingSummary.R | 102 tests/testthat/test-357-prepUserImportData.R | 42 tests/testthat/test-358-renameRecord-ArgumentValidation.R | 34 tests/testthat/test-358-renameRecord-Functionality.R | 42 tests/testthat/test-359-exportProjectXml-ArgumentValidation.R | 136 - tests/testthat/test-359-exportProjectXml-Functionality.R | 64 tests/testthat/test-360-createRedcapProject-ArgumentValidation.R | 150 - tests/testthat/test-361-userStructureVersion.R | 18 tests/testthat/test-400-exportSurveyParticipants-ArgumentValidation.R | 44 tests/testthat/test-400-exportSurveyParticipants-Functionality.R | 4 tests/testthat/test-401-exportSurveyLink-ArgumentValidation.R | 108 tests/testthat/test-401-exportSurveyLink-Functionality.R | 4 tests/testthat/test-402-exportSurveyQueueLink-ArgumentValidation.R | 54 tests/testthat/test-402-exportSurveyQueueLink-Functionality.R | 4 tests/testthat/test-403-exportSurveyReturnCode-ArgumentValidation.R | 108 tests/testthat/test-403-exportSurveyReturnCode-Functionality.R | 4 tests/testthat/test-800-exportLogging-Functionality.R | 120 - tests/testthat/test-800-exportLogging-argumentValidation.R | 74 tests/testthat/test-801-changedRecords.R | 2 tests/testthat/test-900-checkbox_suffixes.R | 42 tests/testthat/test-901-fieldToVar.R | 26 tests/testthat/test-902-fieldToVar-mChoice.R | 16 tests/testthat/test-903-validateImport_methods.R | 1 tests/testthat/test-904-exportDataQuality.R | 12 136 files changed, 5715 insertions(+), 5935 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.4.3 dated 2025-10-01 and 1.4.4 dated 2025-10-29
DESCRIPTION | 6 - MD5 | 22 ++-- NEWS.md | 12 ++ R/addConceptIntersect.R | 10 + R/addDemographics.R | 40 ++++++- R/addDemographicsQuery.R | 19 +++ R/addIntersect.R | 4 inst/doc/cohort-intersect.html | 68 ++++++------- inst/doc/concept-intersect.html | 96 +++++++++--------- inst/doc/demographics.html | 208 ++++++++++++++++++++-------------------- inst/doc/summarise.html | 152 ++++++++++++++--------------- inst/doc/table-intersect.html | 92 ++++++++--------- 12 files changed, 398 insertions(+), 331 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: 'Shiny' Modules for General Tasks
Description: 'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between formods versions 0.2.1 dated 2025-06-12 and 0.2.2 dated 2025-10-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/FG_Server.R | 6 ++---- build/vignette.rds |binary inst/doc/included_modules.html | 2 +- inst/doc/making_modules.html | 4 ++-- 6 files changed, 13 insertions(+), 15 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cph],
Julia Piaskowski [cre, aut],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Julia Piaskowski <julia.piask@gmail.com>
Diff between emmeans versions 1.11.2-8 dated 2025-08-27 and 2.0.0 dated 2025-10-29
emmeans-1.11.2-8/emmeans/data/autonoise.RData |only emmeans-1.11.2-8/emmeans/vignettes/rvlstyle.html |only emmeans-2.0.0/emmeans/DESCRIPTION | 29 +- emmeans-2.0.0/emmeans/MD5 | 99 ++++----- emmeans-2.0.0/emmeans/NAMESPACE | 7 emmeans-2.0.0/emmeans/NEWS.md | 22 ++ emmeans-2.0.0/emmeans/R/MCMC-support.R | 9 emmeans-2.0.0/emmeans/R/emm-contr.R | 2 emmeans-2.0.0/emmeans/R/emmGrid-methods.R | 30 ++ emmeans-2.0.0/emmeans/R/emmip.R | 145 +++++++++++-- emmeans-2.0.0/emmeans/R/multiv.R | 2 emmeans-2.0.0/emmeans/R/ordinal-support.R | 1 emmeans-2.0.0/emmeans/R/plot.emm.R | 98 ++++++--- emmeans-2.0.0/emmeans/R/pwpp.R | 17 - emmeans-2.0.0/emmeans/R/qdrg.R | 156 ++++++++------- emmeans-2.0.0/emmeans/R/summary.R | 11 - emmeans-2.0.0/emmeans/R/zzz.R | 13 - emmeans-2.0.0/emmeans/README.md | 25 -- emmeans-2.0.0/emmeans/build/vignette.rds |binary emmeans-2.0.0/emmeans/data/auto.noise.RData |only emmeans-2.0.0/emmeans/inst/doc/AQuickStart.html | 4 emmeans-2.0.0/emmeans/inst/doc/FAQs.html | 8 emmeans-2.0.0/emmeans/inst/doc/basics.html | 16 - emmeans-2.0.0/emmeans/inst/doc/comparisons.html | 18 - emmeans-2.0.0/emmeans/inst/doc/confidence-intervals.html | 12 - emmeans-2.0.0/emmeans/inst/doc/interactions.html | 28 +- emmeans-2.0.0/emmeans/inst/doc/messy-data.html | 14 - emmeans-2.0.0/emmeans/inst/doc/models.html | 4 emmeans-2.0.0/emmeans/inst/doc/predictions.html | 6 emmeans-2.0.0/emmeans/inst/doc/re-engineering-clds.html | 4 emmeans-2.0.0/emmeans/inst/doc/sophisticated.html | 8 emmeans-2.0.0/emmeans/inst/doc/transformations.html | 16 - emmeans-2.0.0/emmeans/inst/doc/utilities.html | 4 emmeans-2.0.0/emmeans/inst/doc/vignette-topics.Rmd | 6 emmeans-2.0.0/emmeans/inst/doc/vignette-topics.html | 15 + emmeans-2.0.0/emmeans/inst/doc/xplanations.html | 14 - emmeans-2.0.0/emmeans/inst/doc/xtending.R | 17 + emmeans-2.0.0/emmeans/inst/doc/xtending.Rmd | 62 +++++ emmeans-2.0.0/emmeans/inst/doc/xtending.html | 106 ++++++++-- emmeans-2.0.0/emmeans/man/emm_options.Rd | 28 ++ emmeans-2.0.0/emmeans/man/emmc-functions.Rd | 2 emmeans-2.0.0/emmeans/man/emmip.Rd | 35 ++- emmeans-2.0.0/emmeans/man/extending-emmeans.Rd | 6 emmeans-2.0.0/emmeans/man/figures/logo.png |binary emmeans-2.0.0/emmeans/man/hpd.summary.Rd | 5 emmeans-2.0.0/emmeans/man/mvregrid.Rd | 102 ++++----- emmeans-2.0.0/emmeans/man/plot.Rd | 30 +- emmeans-2.0.0/emmeans/man/qdrg.Rd | 44 ++-- emmeans-2.0.0/emmeans/man/summary.emmGrid.Rd | 11 - emmeans-2.0.0/emmeans/man/untidy.Rd | 62 ++--- emmeans-2.0.0/emmeans/vignettes/vignette-topics.Rmd | 6 emmeans-2.0.0/emmeans/vignettes/xtending.Rmd | 62 +++++ 52 files changed, 948 insertions(+), 473 deletions(-)
Title: Retrieve Records from the Urban Institute's Education Data
Portal API
Description: Allows R users to retrieve and parse data from the Urban
Institute's Education Data API <https://educationdata.urban.org/> into a
'data.frame' for analysis.
Author: Erika Tyagi [cre],
Kyle Ueyama [aut],
Andrew Martin [ctb] ,
The Urban Institute [cph]
Maintainer: Erika Tyagi <etyagi@urban.org>
Diff between educationdata versions 0.1.3 dated 2022-09-29 and 0.1.5 dated 2025-10-29
educationdata-0.1.3/educationdata/build |only educationdata-0.1.3/educationdata/inst |only educationdata-0.1.3/educationdata/vignettes |only educationdata-0.1.5/educationdata/DESCRIPTION | 12 educationdata-0.1.5/educationdata/MD5 | 24 educationdata-0.1.5/educationdata/NEWS.md | 11 educationdata-0.1.5/educationdata/R/download-csv.R | 10 educationdata-0.1.5/educationdata/R/get-page-data.R | 20 educationdata-0.1.5/educationdata/R/get_education_data.R | 23 educationdata-0.1.5/educationdata/R/validate-args.R | 1 educationdata-0.1.5/educationdata/README.md | 338 +++++----- educationdata-0.1.5/educationdata/man/figures |only educationdata-0.1.5/educationdata/man/get_education_data.Rd | 5 educationdata-0.1.5/educationdata/tests/testthat/test-validation.R | 15 14 files changed, 253 insertions(+), 206 deletions(-)
Title: Messages, Warnings, Strings with Ascii Animals
Description: Allows printing of character strings as messages/warnings/etc.
with ASCII animals, including cats, cows, frogs, chickens, ghosts,
and more.
Author: Scott Chamberlain [aut, cre],
Amanda Dobbyn [aut],
Tyler Rinker [ctb],
Thomas Leeper [ctb],
Noam Ross [ctb],
Rich FitzJohn [ctb],
Carson Sievert [ctb],
Kiyoko Gotanda [ctb],
Andy Teucher [ctb],
Karl Broman [ctb],
Franz-Sebastian Krah [ctb],
Lucy D'Ag [...truncated...]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between cowsay versions 1.2.0 dated 2025-03-28 and 1.2.2 dated 2025-10-29
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- NEWS.md | 5 +++ R/constants.R | 2 - R/say.R | 40 +++++++++++------------- README.md | 83 +++++++++++++++++++-------------------------------- build/vignette.rds |binary inst/doc/cowsay.html | 6 +-- man/say.Rd | 6 --- 9 files changed, 70 insertions(+), 96 deletions(-)
Title: R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Description: R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek [aut, cre, cph] ,
Jeffrey Horner [aut]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.6-5 dated 2025-08-20 and 1.7-0 dated 2025-10-29
DESCRIPTION | 8 - MD5 | 13 +- NEWS | 16 ++- configure.win | 2 src/cairogd.c | 10 - src/cairogd.h | 21 +++- src/cairotalk.c | 288 ++++++++++++++++++++++++++++++++++++++++---------------- src/coreutil.c |only 8 files changed, 256 insertions(+), 102 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.17-3 dated 2025-08-18 and 2.17-4 dated 2025-10-29
DESCRIPTION | 11 ++- MD5 | 8 +- R/ensemble.blockCV.R | 56 ++++++++++++++------ inst/ChangeLog | 8 ++ man/ensemble.blockCV.Rd | 133 +++++++++++++++++++++--------------------------- 5 files changed, 119 insertions(+), 97 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 1.1.1 dated 2025-08-22 and 1.2.0 dated 2025-10-29
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 14 ++++++++++++++ R/Object.R | 30 +++++++++++++++++++++++++----- R/Operations.R | 23 ++++++++++++++++++++--- inst/doc/UsingAndromeda.html | 6 +++--- man/flushAndromeda.Rd | 4 +++- tests/testthat/test-object.R | 2 +- 8 files changed, 79 insertions(+), 26 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download comprehensive datasets of local,
state, and federal election results in Germany from 1990 to 2025. The package
facilitates access to data on turnout, vote shares for major parties, and
demographic information across different levels of government (municipal, state,
and federal). It offers access to geographically harmonized datasets
that account for changes in municipal boundaries over time and incorporate
mail-in voting districts. Users can easily retrieve, clean, and standardize
German electoral data, making it ready for analysis. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.2.1 dated 2025-10-06 and 0.3.0 dated 2025-10-29
DESCRIPTION | 8 +-- MD5 | 22 +++++--- NAMESPACE | 3 + NEWS.md | 20 +++++++- R/gerda_covariates.R |only R/sysdata.rda |binary README.md | 44 +++++++++++++++++ inst/doc/gerda.R | 32 +++++++++++++ inst/doc/gerda.Rmd | 75 ++++++++++++++++++++++++++++++ inst/doc/gerda.html | 96 +++++++++++++++++++++++++++++++++++---- man/add_gerda_covariates.Rd |only man/gerda_covariates.Rd |only man/gerda_covariates_codebook.Rd |only vignettes/gerda.Rmd | 75 ++++++++++++++++++++++++++++++ 14 files changed, 352 insertions(+), 23 deletions(-)
Title: Fetch and Explore the Cornell Lab of Ornithology Open Tree of
Life Avian Phylogeny
Description: Fetches the Cornell Lab of Ornithology Open Tree of Life (clootl) tree in a specified taxonomy. Optionally prune it to a given set of study taxa. Provide a recommended citation list for the studies that informed the extracted tree. Tree generated as described in McTavish et al. (2024) <doi:10.1101/2024.05.20.595017>.
Author: Eliot Miller [aut, cre],
Emily Jane McTavish [aut],
Luna L. Sanchez Reyes [ctb, aut]
Maintainer: Eliot Miller <clootlmaintainers@gmail.com>
Diff between clootl versions 0.1.1 dated 2025-04-10 and 0.1.2 dated 2025-10-29
DESCRIPTION | 8 +-- MD5 | 40 ++++++++-------- NAMESPACE | 1 NEWS.md | 3 + R/data.R | 100 +++++++++++++++++++++++++++++++++--------- R/extractTree.R | 84 +++++++++++++++++++---------------- R/getCitations.R | 70 +++++++++++++++-------------- R/sampleTrees.R | 25 +++++++--- R/utils.R | 66 +++++++-------------------- R/zzz.R | 2 README.md | 9 +++ data/clootl_data.rda |binary man/clootl_data.Rd | 97 +++++++++++++++++++++++++++++++++------- man/extractTree.Rd | 44 ++++++++++-------- man/getCitations.Rd | 62 ++++++++++++++------------ man/get_avesdata_repo.Rd | 14 ++++- man/sampleTrees.Rd | 20 +++++--- man/set_avesdata_repo_path.Rd | 7 ++ man/taxonomyGet.Rd | 18 ++++--- man/treeGet.Rd | 27 +---------- tests/testthat/test_basics.R | 15 +++--- 21 files changed, 430 insertions(+), 282 deletions(-)
Title: A Library for using 'Pathling'
Description: R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.
Author: Australian e-Health Research Centre, CSIRO [cph, cre],
Piotr Szul [aut],
John Grimes [aut]
Maintainer: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>
Diff between pathling versions 8.1.0 dated 2025-09-22 and 9.0.0 dated 2025-10-28
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoglu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb] ,
Tuomas Borman [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.6.2 dated 2025-08-22 and 1.7.0 dated 2025-10-28
DESCRIPTION | 21 ++-- LICENSE | 2 MD5 | 80 ++++++++--------- NAMESPACE | 15 +++ NEWS.md | 14 ++- R/corr_feats.R | 5 - R/preprocess.R | 163 ++++++++++++++++++++++++++++++++---- R/run_ml.R | 133 ++++++++++++++++++++++------- README.md | 17 ++- inst/doc/introduction.html | 5 - man/calc_baseline_precision.Rd | 4 man/calc_perf_bootstrap_split.Rd | 21 +--- man/calc_perf_metrics.Rd | 7 - man/check_all.Rd | 33 +++---- man/check_dataset.Rd | 4 man/check_group_partitions.Rd | 4 man/check_groups.Rd | 4 man/check_kfold.Rd | 4 man/check_method.Rd | 7 - man/check_outcome_column.Rd | 4 man/check_outcome_value.Rd | 4 man/collapse_correlated_features.Rd | 14 ++- man/define_cv.Rd | 10 +- man/find_permuted_perf_metric.Rd | 14 +-- man/get_binary_corr_mat.Rd | 6 - man/get_corr_feats.Rd | 4 man/get_feature_importance.Rd | 27 ++--- man/get_hyperparams_list.Rd | 7 - man/get_performance_tbl.Rd | 21 +--- man/get_seeds_trainControl.Rd | 3 man/get_tuning_grid.Rd | 3 man/group_correlated_features.Rd | 6 - man/mikropml-package.Rd | 1 man/preprocess_data.Rd | 80 ++++++++++++++++- man/randomize_feature_order.Rd | 4 man/rm_missing_outcome.Rd | 4 man/run_ml.Rd | 101 +++++++++++++++------- man/split_outcome_features.Rd | 4 man/train_model.Rd | 16 +-- tests/testthat/test-preprocess.R | 87 ++++++++++++++++++- tests/testthat/test-run_ml.R | 26 +++++ 41 files changed, 730 insertions(+), 259 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.7.4 dated 2025-09-23 and 0.7.5 dated 2025-10-28
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 8 R/composition.R | 9 - R/reorder-graph.R | 6 R/structure-to-iupac.R | 274 +++++++++++++++++++------------ R/structure.R | 2 README.md | 8 build/vignette.rds |binary inst/doc/glycan-graph.html | 8 inst/doc/glyrepr.html | 34 +-- inst/doc/smap.html | 30 +-- tests/testthat/_snaps/structure.md | 7 tests/testthat/test-structure-to-iupac.R | 46 ++--- 14 files changed, 277 insertions(+), 189 deletions(-)
Title: Betas-Select in Structural Equation Models and Linear Models
Description: It computes betas-select, coefficients after standardization in
structural equation models and regression models, standardizing only selected
variables. Supports models with moderation, with product terms formed after
standardization. It also offers confidence intervals that account for
standardization, including bootstrap confidence intervals as proposed by
Cheung et al. (2022) <doi:10.1037/hea0001188>.
Author: Shu Fai Cheung [aut, cre] ,
Rong Wei Sun [aut] ,
Florbela Chang [aut] ,
Wendie Yang [aut] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between betaselectr versions 0.1.2 dated 2025-05-02 and 0.1.3 dated 2025-10-28
DESCRIPTION | 8 MD5 | 38 ++- NEWS.md | 39 +++ R/lav_betaselect.R | 48 +++- R/lav_betaselect_helpers.R | 144 +++++++++++++- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/betaselectr_lav.Rmd | 64 ++---- inst/doc/betaselectr_lav.html | 213 ++++++++++----------- man/lav_betaselect.Rd | 20 + tests/testthat/test-lav_betaselect_mg.R | 8 tests/testthat/test-lav_betaselect_mod.R | 9 tests/testthat/test-lav_betaselect_mod_Intercept.R |only tests/testthat/test-lav_betaselect_mod_colon.R |only tests/testthat/test-lav_betaselect_mod_mg.R |only tests/testthat/test-lav_betaselect_mod_no_center.R |only tests/testthat/test-lav_betaselect_user_boot_1.R | 1 vignettes/articles |only vignettes/betaselectr_lav.Rmd | 64 ++---- vignettes/betaselectr_lav.Rmd.original | 19 + 21 files changed, 443 insertions(+), 234 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.1.1 dated 2025-10-28 and 0.1.6 dated 2025-10-28
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 1 R/Ganttify.R | 936 ++++++++++++++++++++++++++++++++++++++++++++-------- R/data.R | 2 README.md | 192 ++++++++-- man/Ganttify.Rd | 222 +++++++++--- man/test_project.Rd | 2 8 files changed, 1132 insertions(+), 247 deletions(-)
Title: Dynamic Spectrogram Visualizations
Description: A set of tools to generate dynamic spectrogram visualizations in video format.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
This is a re-admission after prior archival of version 1.0.4 dated 2025-07-23
Diff between dynaSpec versions 1.0.4 dated 2025-07-23 and 1.0.5 dated 2025-10-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ data/canyon_wren.rda |binary 4 files changed, 11 insertions(+), 6 deletions(-)
Title: Parametrically Guided Kernel Density Estimator for Spherical
Data
Description: Nonparametric density estimation for (hyper)spherical data by means of a parametrically guided kernel estimator (Alonso-Pena et al. (2024) <doi:10.1111/sjos.12737>. The package also allows the data-driven selection of the smoothing parameter and the representation of the estimated density for circular and spherical data. Estimators of the density without guide can also be obtained.
Author: Maria Alonso-Pena [aut, cre],
Gerda Claeskens [aut],
Irene Gijbels [aut]
Maintainer: Maria Alonso-Pena <mariaalonso.pena@usc.es>
Diff between pgKDEsphere versions 1.0.1 dated 2024-02-07 and 1.0.2 dated 2025-10-28
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- R/pi.kappa.R | 4 ++-- R/sphkde.pg.R | 6 +++--- R/sphkde.plot.R | 6 +++--- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Healthcare Analysis Methods
Description: Conducts analyses for healthcare program evaluations or intervention
studies. Calculates regression analyses for standard ordinary least squares
(OLS or linear) or logistic models. Performs regression models used for
causal modeling such as differences-in-differences (DID) and interrupted
time series (ITS) models. Provides limited interpretations of model
results and a ranking of variable importance in models. Performs
propensity score models, top-coding of model outcome variables, and
can return new data with the newly formed variables. Also performs Cronbach's
alpha for various scale items (e.g., survey questions). See Github URL for
examples in the README file. For more details on the statistical methods, see
Allen & Yen (1979, ISBN:0-8185-0283-5),
Angrist & Pischke (2009, ISBN:9780691120355),
Harrell (2016, ISBN:978-3-319-19424-0),
Kline (1999, ISBN:9780415211581),
Linden (2015) <doi:10.1177/1536867X1501500208>,
Merlo (2006) <doi:10.1136/jech.2004.029454>
Muthen [...truncated...]
Author: Stephen Zuniga [aut, cre, cph]
Maintainer: Stephen Zuniga <rms.shiny@gmail.com>
Diff between ham versions 1.0.0 dated 2025-08-28 and 1.1.0 dated 2025-10-28
DESCRIPTION | 18 MD5 | 54 - NAMESPACE | 20 NEWS.md | 20 R/assess.R | 59 + R/group.R |only R/interpret.R | 50 - R/plot.assess.R | 1414 ++++++++++++++++++++++++++++++-- R/plot.group.R |only README.md | 441 ++++++--- build |only data/hosp1.rda |binary data/hosprog.rda |binary inst/CITATION | 32 inst/doc |only man/figures/README-plotAssess-1.png |binary man/figures/README-plotGroup1-1.png |only man/figures/README-plotGroup2-1.png |only man/figures/README-plotGroup3-1.png |only man/figures/README-plotImportance-1.png |binary man/figures/README-revDID0-1.png |only man/figures/README-revDID1-1.png |only man/figures/README-revDID2-1.png |only man/figures/README-revITS1-1.png |only man/figures/README-revITS2-1.png |only man/figures/README-revITS3-1.png |only man/figures/README-revITS4-1.png |only man/figures/logo.png |only man/group.Rd |only man/plot.assess.Rd | 98 ++ man/plot.group.Rd |only tests/testthat/test-assess.R | 14 tests/testthat/test-group.R |only tests/testthat/test-interpret.R | 2 tests/testthat/test-itsEffect.R | 2 vignettes |only 36 files changed, 1922 insertions(+), 302 deletions(-)
Title: Clinical Coding of Patients with Kidney Disease
Description: Clinical coding and diagnosis of patients with kidney using
clinical practice guidelines. The guidelines used are the evidence-based
KDIGO guidelines, see <https://kdigo.org/guidelines/> for more information.
This package covers acute kidney injury (AKI), anemia, and
chronic kidney disease (CKD).
Author: Alwin Wang [aut, cre] ,
Lisa Toh [aut] ,
Davis Vaughan [ctb],
Olivier Roy [ctb],
Inaki Ucar [ctb]
Maintainer: Alwin Wang <alwin.wang@austin.org.au>
Diff between epocakir versions 0.9.9 dated 2023-01-06 and 1.0.0 dated 2025-10-28
DESCRIPTION | 36 LICENSE | 2 MD5 | 120 +- NAMESPACE | 154 +-- NEWS.md | 344 ++++---- R/Txp-candidate.R | 2 R/Txp-recipient.R | 2 R/aki.R | 760 +++++++++--------- R/anemia.R | 150 +-- R/bp.R | 2 R/ckd.R | 1676 ++++++++++++++++++++--------------------- R/ckd_diabetes.R | 2 R/ckd_mbd.R | 2 R/data-aki.R | 14 R/data-anemia.R | 14 R/data-clinical_obs.R | 14 R/data-eGFR.R | 14 R/gn.R | 2 R/hep-c.R | 2 R/ld.R | 2 R/lipid.R | 4 R/utils.R | 724 ++++++++--------- build/vignette.rds |binary inst/doc/epocakir.R | 146 +-- inst/doc/epocakir.Rmd | 324 +++---- inst/doc/epocakir.html | 1246 +++++++++++++++--------------- man/Albuminuria_stages.Rd | 56 - man/Albuminuria_staging_ACR.Rd | 104 +- man/Albuminuria_staging_AER.Rd | 104 +- man/GFR_stages.Rd | 44 - man/GFR_staging.Rd | 110 +- man/aki_SCr.Rd | 108 +- man/aki_UO.Rd | 108 +- man/aki_bCr.Rd | 102 +- man/aki_pt_data.Rd | 38 man/aki_stages.Rd | 44 - man/aki_staging.Rd | 154 +-- man/anemia.Rd | 118 +- man/anemia_pt_data.Rd | 38 man/as_metric.Rd | 66 - man/binary2factor.Rd | 62 - man/clinical_obvs.Rd | 38 man/combine_date_time_cols.Rd | 60 - man/combn_changes.Rd | 82 +- man/conversion_factors.Rd | 56 - man/dob2age.Rd | 80 - man/eGFR.Rd | 230 ++--- man/eGFR_adult_SCr.Rd | 112 +- man/eGFR_adult_SCr_SCysC.Rd | 122 +- man/eGFR_adult_SCysC.Rd | 106 +- man/eGFR_child_SCr.Rd | 100 +- man/eGFR_child_SCr_BUN.Rd | 106 +- man/eGFR_child_SCysC.Rd | 94 +- man/eGFR_pt_data.Rd | 38 man/reexports.Rd | 38 tests/testthat.R | 16 tests/testthat/test-aki.R | 476 +++++------ tests/testthat/test-anemia.R | 136 +-- tests/testthat/test-ckd.R | 4 tests/testthat/test-utils.R | 600 +++++++------- vignettes/epocakir.Rmd | 324 +++---- 61 files changed, 4945 insertions(+), 4887 deletions(-)
Title: Quantify the Relationship Between Development Rate and
Temperature in Ectotherms
Description: A set of functions to quantify the relationship between development
rate and temperature and to build phenological models. The package comprises
a set of models and estimated parameters borrowed from a literature review
in ectotherms. The methods and literature review are described in Rebaudo
et al. (2018) <doi:10.1111/2041-210X.12935>, Rebaudo and Rabhi (2018)
<doi:10.1111/eea.12693>, and Regnier et al. (2021) <doi:10.1093/ee/nvab115>.
An example can be found in Rebaudo et al. (2017)
<doi:10.1007/s13355-017-0480-5>.
Author: Francois Rebaudo [aut, cre] ,
Baptiste Regnier [aut] ,
Camila Benavides [ctb] ,
Tanusson Selvarajah [ctb] ,
Nicolas Bonnal [ctb] ,
Badre Rabhi [ctb] ,
Quentin Struelens [ctb]
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>
This is a re-admission after prior archival of version 0.2.5 dated 2025-08-25
Diff between devRate versions 0.2.5 dated 2025-08-25 and 0.2.6 dated 2025-10-28
DESCRIPTION | 6 - MD5 | 96 ++++++++++++------------- NEWS.md | 3 README.md | 4 - data/analytis_77.RData |binary data/bayoh_03.RData |binary data/beta_16.RData |binary data/beta_95.RData |binary data/bieri1_83.RData |binary data/briere1_99.RData |binary data/briere2_99.RData |binary data/campbell_74.RData |binary data/damos_08.RData |binary data/damos_11.RData |binary data/davidson_44.RData |binary data/devRateEqList.RData |binary data/harcourtYee_82.RData |binary data/hilbertLogan_83.RData |binary data/janisch_32.RData |binary data/kontodimas_04.RData |binary data/lactin1_95.RData |binary data/lactin2_95.RData |binary data/lamb_92.RData |binary data/logan10_76.RData |binary data/logan6_76.RData |binary data/perf2_11.RData |binary data/poly2.RData |binary data/poly4.RData |binary data/ratkowsky_82.RData |binary data/ratkowsky_83.RData |binary data/regniere_12.RData |binary data/rootsq_82.RData |binary data/schoolfieldHigh_81.RData |binary data/schoolfieldLow_81.RData |binary data/schoolfield_81.RData |binary data/sharpeDeMichele_77.RData |binary data/shi_11.RData |binary data/stinner_74.RData |binary data/taylor_81.RData |binary data/wagner_88.RData |binary data/wang_82.RData |binary data/wangengel_98.RData |binary inst/doc/guiaDelUsuario.html | 138 ++++++++++++++++++------------------- inst/doc/helicoverpa_armigera.R | 1 inst/doc/helicoverpa_armigera.Rmd | 1 inst/doc/helicoverpa_armigera.html | 41 +++++----- inst/doc/modelEvaluation.html | 4 - inst/doc/quickUserGuide.html | 4 - vignettes/helicoverpa_armigera.Rmd | 1 49 files changed, 153 insertions(+), 146 deletions(-)
Title: Behavioral Insight Design: A Toolkit for Integrating Behavioral
Science in UI/UX Design
Description: Provides a framework and toolkit to guide 'shiny' developers in
implementing the Behavioral Insight Design (BID) framework. The package offers
functions for documenting each of the five stages (Interpret, Notice,
Anticipate, Structure, and Validate), along with a comprehensive concept
dictionary.
Author: Jeremy Winget [aut, cre]
Maintainer: Jeremy Winget <contact@jrwinget.com>
Diff between bidux versions 0.3.1 dated 2025-09-07 and 0.3.2 dated 2025-10-28
bidux-0.3.1/bidux/R/bid-classes.R |only bidux-0.3.1/bidux/R/bid-concepts.R |only bidux-0.3.1/bidux/R/bidux-package.R |only bidux-0.3.1/bidux/R/structure_rank.R |only bidux-0.3.1/bidux/R/suggest-components.R |only bidux-0.3.1/bidux/R/telemetry.R |only bidux-0.3.1/bidux/R/utils.R |only bidux-0.3.2/bidux/DESCRIPTION | 16 bidux-0.3.2/bidux/MD5 | 291 - bidux-0.3.2/bidux/NAMESPACE | 13 bidux-0.3.2/bidux/NEWS.md | 82 bidux-0.3.2/bidux/R/bid_anticipate.R | 185 - bidux-0.3.2/bidux/R/bid_interpret.R | 536 +- bidux-0.3.2/bidux/R/bid_notice.R | 22 bidux-0.3.2/bidux/R/bid_package.R |only bidux-0.3.2/bidux/R/bid_report.R | 24 bidux-0.3.2/bidux/R/bid_structure.R | 37 bidux-0.3.2/bidux/R/bid_validate.R | 215 - bidux-0.3.2/bidux/R/data_classes.R |only bidux-0.3.2/bidux/R/data_concepts.R |only bidux-0.3.2/bidux/R/mappings.R | 23 bidux-0.3.2/bidux/R/s3_classes.R |only bidux-0.3.2/bidux/R/structure_components.R |only bidux-0.3.2/bidux/R/structure_suggest.R | 50 bidux-0.3.2/bidux/R/suggest_rules.R | 120 bidux-0.3.2/bidux/R/telemetry_analysis.R |only bidux-0.3.2/bidux/R/telemetry_ingest.R |only bidux-0.3.2/bidux/R/telemetry_notices.R |only bidux-0.3.2/bidux/R/telemetry_utils.R |only bidux-0.3.2/bidux/R/utils_core.R |only bidux-0.3.2/bidux/R/utils_domain.R |only bidux-0.3.2/bidux/R/utils_formatting.R |only bidux-0.3.2/bidux/R/utils_messaging.R |only bidux-0.3.2/bidux/R/utils_safe_access.R |only bidux-0.3.2/bidux/R/utils_stage.R |only bidux-0.3.2/bidux/R/utils_suggestions.R |only bidux-0.3.2/bidux/R/utils_validation.R |only bidux-0.3.2/bidux/README.md | 28 bidux-0.3.2/bidux/build/vignette.rds |binary bidux-0.3.2/bidux/inst/WORDLIST | 8 bidux-0.3.2/bidux/inst/doc/advanced-workflows.R | 457 ++ bidux-0.3.2/bidux/inst/doc/advanced-workflows.Rmd | 474 ++ bidux-0.3.2/bidux/inst/doc/advanced-workflows.html | 1847 ++++++---- bidux-0.3.2/bidux/inst/doc/api-modernization.R |only bidux-0.3.2/bidux/inst/doc/api-modernization.Rmd |only bidux-0.3.2/bidux/inst/doc/api-modernization.html |only bidux-0.3.2/bidux/inst/doc/getting-started.R | 204 - bidux-0.3.2/bidux/inst/doc/getting-started.Rmd | 267 + bidux-0.3.2/bidux/inst/doc/getting-started.html | 289 + bidux-0.3.2/bidux/inst/doc/practical-examples.R | 242 + bidux-0.3.2/bidux/inst/doc/practical-examples.Rmd | 273 + bidux-0.3.2/bidux/inst/doc/practical-examples.html | 949 +++-- bidux-0.3.2/bidux/inst/doc/telemetry-integration.R | 760 ++-- bidux-0.3.2/bidux/inst/doc/telemetry-integration.Rmd | 913 +++- bidux-0.3.2/bidux/inst/doc/telemetry-integration.html | 1466 +++++-- bidux-0.3.2/bidux/man/adjust_suggestion_score.Rd | 6 bidux-0.3.2/bidux/man/as_tibble.bid_issues.Rd | 2 bidux-0.3.2/bidux/man/as_tibble.bid_stage.Rd | 2 bidux-0.3.2/bidux/man/bid_address.Rd | 2 bidux-0.3.2/bidux/man/bid_anticipate.Rd | 6 bidux-0.3.2/bidux/man/bid_concept.Rd | 2 bidux-0.3.2/bidux/man/bid_concepts.Rd | 2 bidux-0.3.2/bidux/man/bid_flags.Rd | 2 bidux-0.3.2/bidux/man/bid_get_quiet.Rd |only bidux-0.3.2/bidux/man/bid_ingest_telemetry.Rd | 23 bidux-0.3.2/bidux/man/bid_interpret.Rd | 53 bidux-0.3.2/bidux/man/bid_notice.Rd | 12 bidux-0.3.2/bidux/man/bid_notice_issue.Rd | 4 bidux-0.3.2/bidux/man/bid_notices.Rd | 2 bidux-0.3.2/bidux/man/bid_pipeline.Rd | 2 bidux-0.3.2/bidux/man/bid_result.Rd | 2 bidux-0.3.2/bidux/man/bid_set_quiet.Rd |only bidux-0.3.2/bidux/man/bid_stage.Rd | 2 bidux-0.3.2/bidux/man/bid_structure.Rd | 15 bidux-0.3.2/bidux/man/bid_suggest_components.Rd | 2 bidux-0.3.2/bidux/man/bid_telemetry.Rd | 12 bidux-0.3.2/bidux/man/bid_telemetry_presets.Rd |only bidux-0.3.2/bidux/man/bid_validate.Rd | 28 bidux-0.3.2/bidux/man/bid_with_quiet.Rd |only bidux-0.3.2/bidux/man/bidux-package.Rd | 4 bidux-0.3.2/bidux/man/build_concept_group.Rd | 8 bidux-0.3.2/bidux/man/build_groups_with_suggestions.Rd | 8 bidux-0.3.2/bidux/man/create_confusion_notice.Rd | 2 bidux-0.3.2/bidux/man/create_delay_notice.Rd | 2 bidux-0.3.2/bidux/man/create_error_notice.Rd | 2 bidux-0.3.2/bidux/man/create_navigation_notice.Rd | 2 bidux-0.3.2/bidux/man/create_unused_input_notice.Rd | 2 bidux-0.3.2/bidux/man/detect_telemetry_format.Rd | 2 bidux-0.3.2/bidux/man/dot-calculate_severity_metrics.Rd | 6 bidux-0.3.2/bidux/man/dot-classify_issue_type.Rd | 2 bidux-0.3.2/bidux/man/dot-create_issues_tibble.Rd | 2 bidux-0.3.2/bidux/man/dot-flags_from_issues.Rd | 2 bidux-0.3.2/bidux/man/extract_stage.Rd | 2 bidux-0.3.2/bidux/man/extract_stage1_theory.Rd | 8 bidux-0.3.2/bidux/man/find_confusion_patterns.Rd | 8 bidux-0.3.2/bidux/man/find_delayed_sessions.Rd | 4 bidux-0.3.2/bidux/man/find_error_patterns.Rd | 4 bidux-0.3.2/bidux/man/find_navigation_dropoffs.Rd | 4 bidux-0.3.2/bidux/man/find_unused_inputs.Rd | 4 bidux-0.3.2/bidux/man/get_cognitive_load_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_concepts_data.Rd | 2 bidux-0.3.2/bidux/man/get_consolidated_suggestion_rules.Rd | 7 bidux-0.3.2/bidux/man/get_default_concepts_data.Rd | 9 bidux-0.3.2/bidux/man/get_dual_processing_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_fallback_concepts_data.Rd |only bidux-0.3.2/bidux/man/get_generic_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_information_scent_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_metadata.Rd | 2 bidux-0.3.2/bidux/man/get_onboarding_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_progressive_disclosure_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_proximity_suggestions.Rd | 6 bidux-0.3.2/bidux/man/get_stage.Rd | 2 bidux-0.3.2/bidux/man/get_visual_hierarchy_suggestions.Rd | 6 bidux-0.3.2/bidux/man/infer_concepts_from_story.Rd | 8 bidux-0.3.2/bidux/man/is_bid_stage.Rd | 2 bidux-0.3.2/bidux/man/is_complete.Rd | 2 bidux-0.3.2/bidux/man/load_concepts_data.Rd |only bidux-0.3.2/bidux/man/new_bias_mitigations.Rd |only bidux-0.3.2/bidux/man/new_bid_result.Rd | 2 bidux-0.3.2/bidux/man/new_bid_stage.Rd | 2 bidux-0.3.2/bidux/man/new_data_story.Rd |only bidux-0.3.2/bidux/man/new_user_personas.Rd |only bidux-0.3.2/bidux/man/normalize_telemetry_columns.Rd | 2 bidux-0.3.2/bidux/man/print.bid_bias_mitigations.Rd |only bidux-0.3.2/bidux/man/print.bid_data_story.Rd |only bidux-0.3.2/bidux/man/print.bid_issues.Rd | 2 bidux-0.3.2/bidux/man/print.bid_result.Rd | 2 bidux-0.3.2/bidux/man/print.bid_stage.Rd | 2 bidux-0.3.2/bidux/man/print.bid_user_personas.Rd |only bidux-0.3.2/bidux/man/rank_and_sort_suggestions.Rd | 8 bidux-0.3.2/bidux/man/read_telemetry_data.Rd | 6 bidux-0.3.2/bidux/man/read_telemetry_json.Rd | 2 bidux-0.3.2/bidux/man/read_telemetry_sqlite.Rd | 6 bidux-0.3.2/bidux/man/structure_suggestions.Rd | 26 bidux-0.3.2/bidux/man/summary.bid_result.Rd | 2 bidux-0.3.2/bidux/man/summary.bid_stage.Rd | 2 bidux-0.3.2/bidux/man/validate_bid_result.Rd | 2 bidux-0.3.2/bidux/man/validate_bid_stage.Rd | 2 bidux-0.3.2/bidux/man/validate_concepts_data_structure.Rd |only bidux-0.3.2/bidux/man/validate_param.Rd |only bidux-0.3.2/bidux/tests/testthat.R | 1 bidux-0.3.2/bidux/tests/testthat/helpers-for-tests.R |only bidux-0.3.2/bidux/tests/testthat/test-bid_anticipate.R | 1102 +---- bidux-0.3.2/bidux/tests/testthat/test-bid_classes.R | 183 bidux-0.3.2/bidux/tests/testthat/test-bid_concepts.R | 183 bidux-0.3.2/bidux/tests/testthat/test-bid_ingest_telemetry.R | 719 +-- bidux-0.3.2/bidux/tests/testthat/test-bid_interpret.R | 886 ++-- bidux-0.3.2/bidux/tests/testthat/test-bid_issues.R | 125 bidux-0.3.2/bidux/tests/testthat/test-bid_mappings.R | 816 ++-- bidux-0.3.2/bidux/tests/testthat/test-bid_notice.R | 108 bidux-0.3.2/bidux/tests/testthat/test-bid_report.R | 6 bidux-0.3.2/bidux/tests/testthat/test-bid_structure.R | 67 bidux-0.3.2/bidux/tests/testthat/test-bid_suggest_components.R | 440 ++ bidux-0.3.2/bidux/tests/testthat/test-bid_validate.R | 1141 +++--- bidux-0.3.2/bidux/tests/testthat/test-bridges.R | 118 bidux-0.3.2/bidux/tests/testthat/test-coverage-strategy.R |only bidux-0.3.2/bidux/tests/testthat/test-data_concepts.R |only bidux-0.3.2/bidux/tests/testthat/test-s3_classes.R |only bidux-0.3.2/bidux/tests/testthat/test-structure_suggest.R | 104 bidux-0.3.2/bidux/tests/testthat/test-suggest_rules.R | 220 - bidux-0.3.2/bidux/tests/testthat/test-telemetry_analysis.R |only bidux-0.3.2/bidux/tests/testthat/test-telemetry_helpers.R | 164 bidux-0.3.2/bidux/tests/testthat/test-telemetry_ingest.R |only bidux-0.3.2/bidux/tests/testthat/test-telemetry_notices.R |only bidux-0.3.2/bidux/tests/testthat/test-telemetry_utils.R |only bidux-0.3.2/bidux/tests/testthat/test-utils.R | 1156 +++--- bidux-0.3.2/bidux/tests/testthat/test-validation-utils.R |only bidux-0.3.2/bidux/vignettes/advanced-workflows.Rmd | 474 ++ bidux-0.3.2/bidux/vignettes/api-modernization.Rmd |only bidux-0.3.2/bidux/vignettes/getting-started.Rmd | 267 + bidux-0.3.2/bidux/vignettes/practical-examples.Rmd | 273 + bidux-0.3.2/bidux/vignettes/telemetry-integration.Rmd | 913 +++- 172 files changed, 11816 insertions(+), 7850 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark [aut, cre],
Daniel Taylor-Rodriquez [aut]
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.6.2 dated 2022-05-23 and 2.7 dated 2025-10-28
DESCRIPTION | 18 MD5 | 36 NAMESPACE | 3 R/gjamCensorY.r | 45 R/gjamHfunctions.R | 1311 +++++++-------- R/gjamSpec2Trait.r | 2 build/vignette.rds |binary inst/CITATION | 24 inst/doc/gjamVignette.R | 1308 +++++++------- inst/doc/gjamVignette.Rmd | 10 inst/doc/gjamVignette.html | 3401 +++++++++++++++++++++++++++------------ man/gjam-package.Rd | 40 man/gjam.Rd | 2 man/gjamCensorY.Rd | 2 man/gjamConditionalParameters.Rd | 2 man/gjamFillMissingTimes.Rd | 2 src/Makevars | 11 src/Makevars.win | 11 vignettes/gjamVignette.Rmd | 10 19 files changed, 3788 insertions(+), 2450 deletions(-)
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(-)
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(-)
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 lefko3-6.6.0/lefko3/vignettes/Ch2.37-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch5.19-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch5.20-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch5.21-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch5.25-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch5.26-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch5.29-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch6.16-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch8.16-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch8.17-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch8.20-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch8.21-1.png |only lefko3-6.6.0/lefko3/vignettes/Ch8.24-1.png |binary lefko3-6.6.0/lefko3/vignettes/Ch8.25-1.png |only lefko3-6.6.0/lefko3/vignettes/Chapter1.Rmd | 24 lefko3-6.6.0/lefko3/vignettes/Chapter2.Rmd | 61 lefko3-6.6.0/lefko3/vignettes/Chapter2.Rmd.orig | 57 lefko3-6.6.0/lefko3/vignettes/Chapter5.Rmd | 333 lefko3-6.6.0/lefko3/vignettes/Chapter5.Rmd.orig | 166 lefko3-6.6.0/lefko3/vignettes/Chapter6.Rmd | 8 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(-)
Title: Stability Assessment of Statistical Learning Methods
Description: Graphical and computational methods that can be used to assess the
stability of results from supervised statistical learning.
Author: Michel Philipp [aut],
Carolin Strobl [aut],
Achim Zeileis [aut, cre] ,
Thomas Rusch [aut],
Kurt Hornik [aut] ,
Lennart Schneider [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between stablelearner versions 0.1-6 dated 2025-07-24 and 0.1-7 dated 2025-10-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 11 +++++++++++ R/stablelearner.R | 14 ++++++++++++-- inst/doc/forests.html | 4 ++-- 5 files changed, 33 insertions(+), 12 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>
Diff between SEQTaRget versions 1.0.1 dated 2025-10-01 and 1.1.1 dated 2025-10-27
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/SEQopts.R | 3 +++ R/SEQuential.R | 20 ++++++++++++++++++++ tests/testthat/test_deviation.R |only 5 files changed, 30 insertions(+), 6 deletions(-)
Title: Product Plots for R
Description: Framework for visualising tables of counts, proportions
and probabilities. The framework is called product plots, alluding to
the computation of area as a product of height and width, and the
statistical concept of generating a joint distribution from the
product of conditional and marginal distributions. The framework,
with extensions, is sufficient to encompass over 20 visualisations
previously described in fields of statistical graphics and 'infovis',
including bar charts, mosaic plots, 'treemaps', equal area plots and
fluctuation diagrams.
Author: Hadley Wickham [aut, cre],
Heike Hofmann [aut]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between productplots versions 0.1.1 dated 2016-07-03 and 0.1.2 dated 2025-10-27
DESCRIPTION | 13 ++++--- MD5 | 65 +++++++++++++++++++-------------------- NEWS.md |only R/labels.r | 5 +-- R/templates.r | 10 +++--- README.md | 3 - man/col_labels.Rd | 1 man/colour_level.Rd | 1 man/colour_weight.Rd | 1 man/ddecker.Rd | 1 man/find_col_level.Rd | 1 man/find_row_level.Rd | 1 man/fluct.Rd | 1 man/flucts.Rd | 1 man/happy.Rd | 5 +-- man/hbar.Rd | 1 man/hspine.Rd | 1 man/mosaic.Rd | 1 man/nested.Rd | 1 man/parse_product_formula.Rd | 1 man/prodcalc.Rd | 11 ++++-- man/prodplot.Rd | 13 ++++++- man/row_labels.Rd | 1 man/scale_x_product.Rd | 1 man/scale_y_product.Rd | 1 man/spine.Rd | 1 man/stacked.Rd | 1 man/tile.Rd | 1 man/vbar.Rd | 1 man/vspine.Rd | 1 tests/testthat/helper-division.r | 4 -- tests/testthat/test-division.r | 2 - tests/testthat/test-labels.r | 34 ++++++++++---------- tests/testthat/test-plotting.r | 34 ++++++++++---------- 34 files changed, 104 insertions(+), 116 deletions(-)
Title: OCI Based Oracle Database Interface for R
Description: Oracle Database interface (DBI) driver for R.
This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin [aut],
David A. James [aut],
Jake Luciani [aut],
Rajendra S. Pingte [aut, cre]
Maintainer: Rajendra S. Pingte <rajendra.pingte@oracle.com>
Diff between ROracle versions 1.3-1.1 dated 2021-11-10 and 1.5-1 dated 2025-10-27
DESCRIPTION | 35 INSTALL | 769 +++-- MD5 | 201 - NAMESPACE | 2 NEWS | 44 R/dbi.R | 37 R/oci.R | 363 ++ configure | 974 ++++-- configure.ac | 144 configure.win | 94 inst/doc/man/de/Oracle.Rd | 262 + inst/doc/man/de/dbConnect-methods.Rd | 4 inst/doc/man/de/dbReadTable-methods.Rd | 4 inst/doc/man/de/dbSendQuery-methods.Rd | 2 inst/doc/man/de/oracleProc-methods.Rd |only inst/doc/man/en/Oracle.Rd | 542 +++ inst/doc/man/en/dbCommit-methods.Rd | 6 inst/doc/man/en/dbConnect-methods.Rd | 23 inst/doc/man/en/dbDriver-methods.Rd | 33 inst/doc/man/en/dbGetInfo-methods.Rd | 89 inst/doc/man/en/dbListConnections-methods.Rd | 8 inst/doc/man/en/dbReadTable-methods.Rd | 65 inst/doc/man/en/dbSendQuery-methods.Rd | 18 inst/doc/man/en/fetch-methods.Rd | 4 inst/doc/man/en/oracleProc-methods.Rd | 12 inst/doc/man/en/p.txt |only inst/doc/man/en/summary-methods.Rd | 2 inst/doc/man/es/Oracle.Rd | 260 + inst/doc/man/es/oracleProc-methods.Rd |only inst/doc/man/fr/Oracle.Rd | 260 + inst/doc/man/fr/dbCommit-methods.Rd | 2 inst/doc/man/fr/oracleProc-methods.Rd |only inst/doc/man/it/Oracle.Rd | 260 + inst/doc/man/it/oracleProc-methods.Rd |only inst/doc/man/ja/Oracle.Rd | 260 + inst/doc/man/ja/dbReadTable-methods.Rd | 2 inst/doc/man/ja/oracleProc-methods.Rd |only inst/doc/man/ko/ExtDriver-class.Rd | 2 inst/doc/man/ko/Oracle.Rd | 260 + inst/doc/man/ko/dbConnect-methods.Rd | 2 inst/doc/man/ko/dbGetInfo-methods.Rd | 2 inst/doc/man/ko/dbListConnections-methods.Rd | 2 inst/doc/man/ko/dbSendQuery-methods.Rd | 6 inst/doc/man/ko/fetch-methods.Rd | 2 inst/doc/man/ko/oracleProc-methods.Rd |only inst/doc/man/ko/summary-methods.Rd | 2 inst/doc/man/pt_BR/Oracle.Rd | 260 + inst/doc/man/pt_BR/dbGetInfo-methods.Rd | 2 inst/doc/man/pt_BR/oracleProc-methods.Rd |only inst/doc/man/zh_CN/Oracle.Rd | 260 + inst/doc/man/zh_CN/oracleProc-methods.Rd |only inst/doc/man/zh_TW/Oracle.Rd | 264 + inst/doc/man/zh_TW/dbCommit-methods.Rd | 4 inst/doc/man/zh_TW/dbDriver-methods.Rd | 4 inst/doc/man/zh_TW/dbGetInfo-methods.Rd | 2 inst/doc/man/zh_TW/dbReadTable-methods.Rd | 6 inst/doc/man/zh_TW/oracleProc-methods.Rd |only man/Oracle.Rd | 542 +++ man/dbCommit-methods.Rd | 6 man/dbConnect-methods.Rd | 23 man/dbDriver-methods.Rd | 33 man/dbGetInfo-methods.Rd | 89 man/dbListConnections-methods.Rd | 8 man/dbReadTable-methods.Rd | 65 man/dbSendQuery-methods.Rd | 18 man/fetch-methods.Rd | 4 man/summary-methods.Rd | 2 po/R-de.po | 12 po/R-es.po | 12 po/R-fr.po | 12 po/R-it.po | 12 po/R-ja.po | 14 po/R-ko.po | 12 po/R-pt_BR.po | 12 po/R-zh_CN.po | 12 po/R-zh_TW.po | 12 po/de.po | 12 po/es.po | 12 po/fr.po | 12 po/it.po | 12 po/ja.po | 12 po/ko.po | 12 po/pt_BR.po | 12 po/zh_CN.po | 12 po/zh_TW.po | 12 src/Makevars.win | 5 src/oci/nzerror.h |only src/oci/nzt.h |only src/oci/occi.h |only src/oci/occiAQ.h |only src/oci/occiCommon.h |only src/oci/occiControl.h |only src/oci/occiData.h |only src/oci/occiObjects.h |only src/oci/oci.h |only src/oci/oci1.h |only src/oci/oci8dp.h |only src/oci/ociap.h |only src/oci/ociapr.h |only src/oci/ocidef.h |only src/oci/ocidem.h |only src/oci/ocidfn.h |only src/oci/ociextp.h |only src/oci/ocijson.h |only src/oci/ocikpr.h |only src/oci/ociver.h |only src/oci/ocixmldb.h |only src/oci/ocixstream.h |only src/oci/odci.h |only src/oci/orastruc.h |only src/oci/ori.h |only src/oci/orid.h |only src/oci/orl.h |only src/oci/oro.h |only src/oci/ort.h |only src/p.sh |only src/packagename_init.c |only src/rodbi.c | 2588 +++++++++++++---- src/rodbi.h | 147 - src/rooci.c | 3937 ++++++++++++++++++++++++++- src/rooci.h | 217 + src/roociload.c |only src/roociload.h |only 123 files changed, 11818 insertions(+), 1945 deletions(-)
Title: Easily Install and Load Redistricting Software
Description: Easy installation, loading, and control of packages for redistricting
data downloading, spatial data processing, simulation, analysis, and
visualization. This package makes it easy to install and load multiple
'redistverse' packages at once. The 'redistverse' is developed and maintained
by the Algorithm-Assisted Redistricting Methodology (ALARM) Project.
For more details see <https://alarm-redist.org>.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [aut] ,
tidyverse contributors [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between redistverse versions 0.1.0 dated 2024-06-18 and 0.1.1 dated 2025-10-27
DESCRIPTION | 20 +++---- LICENSE | 4 - MD5 | 39 +++++++-------- NAMESPACE | 8 +-- NEWS.md |only R/attach.R | 6 +- R/banner.R | 48 +++++++++---------- R/cache.R | 96 +++++++++++++++++++------------------- R/redistverse-package.R | 1 R/universe.R | 34 ++++++------- R/utils.R | 22 ++++---- R/zzz.R | 8 +-- README.md | 90 +++++++++++++++++------------------ inst/WORDLIST | 22 ++++---- man/redistverse-package.Rd | 72 ++++++++++++++-------------- man/redistverse_logo.Rd | 34 ++++++------- man/use_redistverse_r_universe.Rd | 34 ++++++------- tests/spelling.R | 6 +- tests/testthat.R | 24 ++++----- tests/testthat/_snaps/attach.md | 20 +++---- tests/testthat/test-attach.R | 26 +++++----- 21 files changed, 308 insertions(+), 306 deletions(-)
Title: Read in a 'Praat' 'TextGrid' File
Description: 'Praat' <https://www.fon.hum.uva.nl/praat/> is a widely
used tool for manipulating, annotating and analyzing speech and
acoustic data. It stores annotation data in a format called a
'TextGrid'. This package provides a way to read these
files into R.
Author: Tristan Mahr [aut, cre] ,
Dan Villarreal [ctb],
Jonathan Washington [ctb],
Josef Fruehwald [aut]
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>
Diff between readtextgrid versions 0.1.2 dated 2024-03-07 and 0.2.0 dated 2025-10-27
DESCRIPTION | 39 - MD5 | 44 + NAMESPACE | 4 NEWS.md | 25 R/cpp11.R |only R/legacy.R |only R/pivot.R |only R/pure-r-parser.R |only R/readtextgrid-package.R |only R/readtextgrid.R | 344 +++++++---- README.md | 376 ++++++++++--- inst/nested-intervals.TextGrid |only man/example_textgrid.Rd | 5 man/pivot_textgrid_tiers.Rd |only man/read_textgrid.Rd | 26 man/readtextgrid-package.Rd |only src |only tests/testthat/test-data/comment.TextGrid |only tests/testthat/test-data/elan.TextGrid |only tests/testthat/test-data/hard-to-parse-normalized.TextGrid |only tests/testthat/test-data/hard-to-parse.TextGrid |only tests/testthat/test-data/nested-intervals.TextGrid |only tests/testthat/test-data/praat-test |only tests/testthat/test-data/quoted.TextGrid |only tests/testthat/test-data/short.TextGrid |only tests/testthat/test-read-textgrid.R | 174 ++++++ 26 files changed, 815 insertions(+), 222 deletions(-)
Title: Unified Principal Sufficient Dimension Reduction Package
Description: A unified and user-friendly framework for applying the principal sufficient dimension reduction methods for both linear and nonlinear cases. The package has an extendable power by varying loss functions for the support vector machine, even for an user-defined arbitrary function, unless those are convex and differentiable everywhere over the support (Li et al. (2011) <doi:10.1214/11-AOS932>). Also, it provides a real-time sufficient dimension reduction update procedure using the principal least squares support vector machine (Artemiou et al. (2021) <doi:10.1016/j.patcog.2020.107768>).
Author: Jungmin Shin [aut, cre],
Seung Jun Shin [aut],
Andreas Artemiou [aut]
Maintainer: Jungmin Shin <c16267@gmail.com>
Diff between psvmSDR versions 1.0.2 dated 2024-09-09 and 2.0.1 dated 2025-10-27
DESCRIPTION | 15 +++--- MD5 | 17 ++++-- R/fn_npsdr.R | 128 +++++++++++++++++++++++++++++++++++----------------- R/fn_plot_npsdr.R | 14 +++-- R/fn_psdr.R | 9 +-- R/psvmSDR-package.R | 2 man/psdr.Rd | 6 +- tests |only 8 files changed, 122 insertions(+), 69 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.15 dated 2025-08-18 and 0.0.16 dated 2025-10-27
smoothemplik-0.0.15/smoothemplik/man/interpTwo.Rd |only smoothemplik-0.0.15/smoothemplik/src/interpolate.cpp |only smoothemplik-0.0.15/smoothemplik/tests/testthat/test-interpTwo.R |only smoothemplik-0.0.16/smoothemplik/DESCRIPTION | 6 smoothemplik-0.0.16/smoothemplik/MD5 | 112 - smoothemplik-0.0.16/smoothemplik/NAMESPACE | 5 smoothemplik-0.0.16/smoothemplik/NEWS.md | 9 smoothemplik-0.0.16/smoothemplik/R/RcppExports.R | 20 smoothemplik-0.0.16/smoothemplik/R/bartlett.R |only smoothemplik-0.0.16/smoothemplik/R/brent.R | 12 smoothemplik-0.0.16/smoothemplik/R/elfunctions.R | 640 +++++----- smoothemplik-0.0.16/smoothemplik/R/extrapolation.R |only smoothemplik-0.0.16/smoothemplik/R/helpers.R | 102 - smoothemplik-0.0.16/smoothemplik/R/selfunctions.R | 144 +- smoothemplik-0.0.16/smoothemplik/R/smoothers.R | 2 smoothemplik-0.0.16/smoothemplik/R/zzz.R | 5 smoothemplik-0.0.16/smoothemplik/README.md | 4 smoothemplik-0.0.16/smoothemplik/build/partial.rdb |binary smoothemplik-0.0.16/smoothemplik/inst/CITATION | 8 smoothemplik-0.0.16/smoothemplik/inst/REFERENCES.bib | 2 smoothemplik-0.0.16/smoothemplik/inst/doc/choice-of-SEL-weights.R | 147 +- smoothemplik-0.0.16/smoothemplik/inst/doc/choice-of-SEL-weights.Rmd | 187 ++ smoothemplik-0.0.16/smoothemplik/inst/doc/choice-of-SEL-weights.html | 410 ++++-- smoothemplik-0.0.16/smoothemplik/inst/doc/non-parametric-rcpp.html | 22 smoothemplik-0.0.16/smoothemplik/inst/figures |only smoothemplik-0.0.16/smoothemplik/man/EL.Rd | 156 -- smoothemplik-0.0.16/smoothemplik/man/EL0.Rd | 94 - smoothemplik-0.0.16/smoothemplik/man/EL1.Rd |only smoothemplik-0.0.16/smoothemplik/man/EuL.Rd | 51 smoothemplik-0.0.16/smoothemplik/man/ExEL1.Rd |only smoothemplik-0.0.16/smoothemplik/man/bartlettFactor.Rd |only smoothemplik-0.0.16/smoothemplik/man/brentZero.Rd | 14 smoothemplik-0.0.16/smoothemplik/man/ctracelr.Rd | 25 smoothemplik-0.0.16/smoothemplik/man/logTaylor.Rd | 3 smoothemplik-0.0.16/smoothemplik/man/smoothEmplik.Rd | 43 smoothemplik-0.0.16/smoothemplik/src/EL.cpp | 114 + smoothemplik-0.0.16/smoothemplik/src/EuL.cpp | 28 smoothemplik-0.0.16/smoothemplik/src/RcppExports.cpp | 71 - smoothemplik-0.0.16/smoothemplik/src/brent.cpp | 436 +++++- smoothemplik-0.0.16/smoothemplik/src/dampedNewton.cpp | 76 - smoothemplik-0.0.16/smoothemplik/src/parabola.cpp | 16 smoothemplik-0.0.16/smoothemplik/src/svdlm.cpp | 78 + smoothemplik-0.0.16/smoothemplik/tests/testthat/test-EL.R | 31 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-EL0.R | 58 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-EL1.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-EuL.R | 9 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-ExEL1.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-ExEL2.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-bartlettFactor.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-brentMin.R | 3 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-brentZero.R | 71 - smoothemplik-0.0.16/smoothemplik/tests/testthat/test-bw.CV.R | 24 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-bw.rot.R | 5 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-ctracelr.R | 4 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-dampedNewton.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-kernelDensity.R | 6 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-kernelFun.R | 1 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-kernelSmooth.R | 6 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-kernelWeights.R | 7 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-logTaylor.R | 7 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-prepareKernel.R | 8 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-smoothEmplik.R | 50 smoothemplik-0.0.16/smoothemplik/tests/testthat/test-svdlm.R |only smoothemplik-0.0.16/smoothemplik/tests/testthat/test-trimmed.weighted.mean.R |only smoothemplik-0.0.16/smoothemplik/vignettes/choice-of-SEL-weights.Rmd | 187 ++ 65 files changed, 2261 insertions(+), 1258 deletions(-)
Title: Read Data from Relational Database Management Systems and Health
Information Systems
Description: Import Data from Relational Database Management Systems
(RDBMS) and Health Information Systems ('HIS'). The current version of the
package supports importing data from RDBMS including 'MS SQL', 'MySQL',
'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and
'SORMAS'.
Author: Karim Mane [aut, cre, cph] ,
Emmanuel Kabuga [ctb] ,
Bubacarr Bah [ctb] ,
Bankole Ahadzie [ctb],
Nuredin Mohammed [ctb],
Abdoelnaser Degoot [ctb],
Hugo Gruson [rev] ,
Pratik Gupte [rev] ,
Andree Valle-Campos [rev] ,
London School of Hygiene and Tropi [...truncated...]
Maintainer: Karim Mane <karim.mane@lshtm.ac.uk>
Diff between readepi versions 1.0.1 dated 2025-10-01 and 1.0.2 dated 2025-10-27
DESCRIPTION | 6 MD5 | 35 - NEWS.md | 12 R/read_sormas-helpers.R | 6 inst/doc/design_principle.Rmd | 4 inst/doc/design_principle.html | 482 +++++++++---- inst/doc/install_drivers.Rmd | 4 inst/doc/install_drivers.html | 651 ++++++++++-------- inst/doc/query_parameters.Rmd | 4 inst/doc/query_parameters.html | 623 +++++++++--------- inst/doc/readepi.R | 46 - inst/doc/readepi.Rmd | 20 inst/doc/readepi.html | 1349 +++++++++++++++++++++------------------ inst/extdata/server_data.RDS |only tests/testthat/test-read_dhis2.R | 4 vignettes/design_principle.Rmd | 4 vignettes/install_drivers.Rmd | 4 vignettes/query_parameters.Rmd | 4 vignettes/readepi.Rmd | 20 19 files changed, 1855 insertions(+), 1423 deletions(-)
Title: Preparer of Main Scientific References for Automatic Insertion
in Academic Papers
Description: Generates a file, containing the main scientific references, prepared to be automatically inserted into an academic paper.
The articles present in the list are chosen from the main references generated, by function principal_lister(), of the package 'bibliorefer'.
The generated file contains the list of metadata of the principal references in 'BibTex' format.
Massimo Aria, Corrado Cuccurullo. (2017) <doi:10.1016/j.joi.2017.08.007>.
Caibo Zhou, Wenyan Song. (2021) <doi:10.1016/j.jclepro.2021.126943>.
Hamid Derviş. (2019) <doi:10.5530/jscires.8.3.32>.
Author: Marcio Eustaquio [cre],
Marcio Eustaquio [aut]
Maintainer: Marcio Eustaquio <marcioeustaquio@id.uff.br>
Diff between gerefer versions 0.1.2 dated 2025-06-21 and 0.1.3 dated 2025-10-27
DESCRIPTION | 6 +++--- MD5 | 12 +++++++++--- NAMESPACE | 2 ++ R/article_bibextra.R |only R/congresso_bib.R | 4 ++-- R/example_database2.R |only inst/extdata/database_articleextra.csv |only inst/extdata/example_database2.csv |only man/article_bibextra.Rd |only man/example_database2.Rd |only 10 files changed, 16 insertions(+), 8 deletions(-)
Title: Alpha, Beta and Gamma Proximity to Irreplaceability
Description: Functions to measure Alpha, Beta and Gamma Proximity to Irreplaceability.
The methods for Alpha and Beta irreplaceability were first described in:
Baisero D., Schuster R. & Plumptre A.J.
Redefining and Mapping Global Irreplaceability.
Conservation Biology 2021;1-11.
<doi:10.1111/cobi.13806>.
Author: Daniele Baisero [aut, cre, cph]
Maintainer: Daniele Baisero <daniele.baisero@gmail.com>
Diff between proxirr versions 0.4 dated 2024-01-26 and 0.5 dated 2025-10-27
DESCRIPTION | 18 - LICENSE | 4 MD5 | 34 +- NAMESPACE | 27 + R/alphabeta.R | 391 ++++++++++++++++------------ R/dot_alphabeta.R | 252 ++++++++++-------- R/marxan.R | 571 ++++++++++++++++++++++------------------- README.md | 60 ++-- build/partial.rdb |binary inst/CITATION | 32 +- man/dot-gamma.Rd |only man/gamma.Rd |only man/marxan_gammas.Rd |only man/marxan_run.Rd | 18 - tests/testthat.R | 24 - tests/testthat/test_alpha.R | 78 ++--- tests/testthat/test_beta.R | 82 ++--- tests/testthat/test_dotalpha.R | 102 +++---- tests/testthat/test_dotbeta.R | 66 ++-- tests/testthat/test_dotgamma.R |only 20 files changed, 964 insertions(+), 795 deletions(-)
Title: Check Threatened Plant Species Status Against Peru's DS
043-2006-AG
Description: Provides tools to match plant species names against the official
threatened species list of Peru (Supreme Decree DS 043-2006-AG, 2006).
Implements a hierarchical matching pipeline with exact, fuzzy, and suffix
matching algorithms to handle nomenclatural variations and taxonomic changes.
Supports both the original 2006 nomenclature and updated taxonomic names,
allowing users to check protection status regardless of nomenclatural changes
since the decree's publication. Threat categories follow IUCN standards
(CR, EN, VU, NT).
Author: Paul E. Santos Andrade [aut, cre]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between peruflorads43 versions 0.1.1 dated 2023-08-21 and 0.2.0 dated 2025-10-27
peruflorads43-0.1.1/peruflorads43/R/category_ds043_2006.R |only peruflorads43-0.1.1/peruflorads43/R/classify.R |only peruflorads43-0.1.1/peruflorads43/R/data_build.R |only peruflorads43-0.1.1/peruflorads43/R/data_ds4306_ag.R |only peruflorads43-0.1.1/peruflorads43/R/globals.R |only peruflorads43-0.1.1/peruflorads43/R/grammar_defensive.R |only peruflorads43-0.1.1/peruflorads43/R/matching_function.R |only peruflorads43-0.1.1/peruflorads43/R/search_ds043.R |only peruflorads43-0.1.1/peruflorads43/R/zzz.R |only peruflorads43-0.1.1/peruflorads43/data |only peruflorads43-0.1.1/peruflorads43/man/category_ds043_2006.Rd |only peruflorads43-0.1.1/peruflorads43/man/dot-match_algorithm.Rd |only peruflorads43-0.1.1/peruflorads43/man/ds43_2006_sps_class.Rd |only peruflorads43-0.1.1/peruflorads43/man/ds_043_2006_ag.Rd |only peruflorads43-0.1.1/peruflorads43/man/figures/README-pressure-1.png |only peruflorads43-0.1.1/peruflorads43/man/search_ds043.Rd |only peruflorads43-0.1.1/peruflorads43/man/tab_ds43_2006.Rd |only peruflorads43-0.1.1/peruflorads43/man/tab_ds43_2006_position.Rd |only peruflorads43-0.1.1/peruflorads43/tests/testthat/test-category_ds043_2006.R |only peruflorads43-0.1.1/peruflorads43/tests/testthat/test-search_ds043.R |only peruflorads43-0.2.0/peruflorads43/DESCRIPTION | 51 peruflorads43-0.2.0/peruflorads43/LICENSE | 2 peruflorads43-0.2.0/peruflorads43/MD5 | 88 - peruflorads43-0.2.0/peruflorads43/NAMESPACE | 10 peruflorads43-0.2.0/peruflorads43/R/api_match.R |only peruflorads43-0.2.0/peruflorads43/R/data-access.R |only peruflorads43-0.2.0/peruflorads43/R/direct_match.R |only peruflorads43-0.2.0/peruflorads43/R/fuzzy_match.R |only peruflorads43-0.2.0/peruflorads43/R/internal.R |only peruflorads43-0.2.0/peruflorads43/R/matching-pipeline.R |only peruflorads43-0.2.0/peruflorads43/R/sufijo_match.R |only peruflorads43-0.2.0/peruflorads43/R/sysdata.R |only peruflorads43-0.2.0/peruflorads43/R/sysdata.rda |only peruflorads43-0.2.0/peruflorads43/R/threated_match.R |only peruflorads43-0.2.0/peruflorads43/README.md | 611 +++++++--- peruflorads43-0.2.0/peruflorads43/build |only peruflorads43-0.2.0/peruflorads43/inst/CITATION | 6 peruflorads43-0.2.0/peruflorads43/inst/doc |only peruflorads43-0.2.0/peruflorads43/man/check_ds043.Rd |only peruflorads43-0.2.0/peruflorads43/man/comparison_table_ds043.Rd |only peruflorads43-0.2.0/peruflorads43/man/direct_match.Rd |only peruflorads43-0.2.0/peruflorads43/man/direct_match_infra_rank_within_species.Rd |only peruflorads43-0.2.0/peruflorads43/man/direct_match_infra_rank_within_species_helper.Rd |only peruflorads43-0.2.0/peruflorads43/man/direct_match_species_within_genus_helper.Rd |only peruflorads43-0.2.0/peruflorads43/man/dot-backup_ambiguous_attrs.Rd |only peruflorads43-0.2.0/peruflorads43/man/dot-consolidate_ambiguous_attrs.Rd |only peruflorads43-0.2.0/peruflorads43/man/dot-final_assertions.Rd |only peruflorads43-0.2.0/peruflorads43/man/dot-restore_ambiguous_attrs.Rd |only peruflorads43-0.2.0/peruflorads43/man/figures/logo.png |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_genus.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_infraspecies2_within_infraspecies.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_infraspecies2_within_infraspecies_helper.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_infraspecies_within_species.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_infraspecies_within_species_helper.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_species_within_genus.Rd |only peruflorads43-0.2.0/peruflorads43/man/fuzzy_match_species_within_genus_helper.Rd |only peruflorads43-0.2.0/peruflorads43/man/genus_match.Rd |only peruflorads43-0.2.0/peruflorads43/man/get_ambiguous_matches.Rd |only peruflorads43-0.2.0/peruflorads43/man/get_database_summary.Rd |only peruflorads43-0.2.0/peruflorads43/man/get_threatened_database.Rd |only peruflorads43-0.2.0/peruflorads43/man/is_ds043_2006_ag.Rd |only peruflorads43-0.2.0/peruflorads43/man/is_threatened_peru.Rd |only peruflorads43-0.2.0/peruflorads43/man/map_dfr_progress.Rd |only peruflorads43-0.2.0/peruflorads43/man/matching_threatenedperu.Rd |only peruflorads43-0.2.0/peruflorads43/man/suffix_match_species_within_genus_helper.Rd |only peruflorads43-0.2.0/peruflorads43/tests/testthat.R | 3 peruflorads43-0.2.0/peruflorads43/tests/testthat/test-ambiguous-matches.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-consolidated-matching.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-database-integrity.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-direct-matching.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-edge-cases.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-fuzzy-matching.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-infraspecies-matching.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-integration.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-rank-classification.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-test-name-standardization.R |only peruflorads43-0.2.0/peruflorads43/tests/testthat/test-threatenedperu_test.R |only peruflorads43-0.2.0/peruflorads43/vignettes |only 78 files changed, 567 insertions(+), 204 deletions(-)
Title: Multiple Time Series Scanner
Description: Generate interactive html reports that enable quick visual review of multiple related time series stored in a data frame. For static datasets, this can help to identify any temporal artefacts that may affect the validity of subsequent analyses. For live data feeds, regularly scheduled reports can help to pro-actively identify data feed problems or unexpected trends that may require action. The reports are self-contained and shareable without a web server.
Author: T. Phuong Quan [aut, cre] ,
University of Oxford [cph],
National Institute for Health Research [fnd],
Rodrigo Pires [rev],
Margaret Siple [rev]
Maintainer: T. Phuong Quan <phuongquan567@outlook.com>
Diff between mantis versions 0.4.3 dated 2025-08-01 and 1.0.0 dated 2025-10-27
DESCRIPTION | 25 MD5 | 66 NEWS.md | 17 R/alert.R | 142 R/construct.R | 56 R/plots-interactive.R | 37 R/plots-static.R | 13 R/prepare.R | 197 R/utilities.R | 8 README.md | 47 inst/doc/alert-rules.R | 248 inst/doc/alert-rules.Rmd | 15 inst/doc/alert-rules.html | 24 inst/doc/bespoke-reports.Rmd | 34 inst/doc/bespoke-reports.html | 42 inst/doc/mantis.R | 54 inst/doc/mantis.html | 5 man/alert_rule_types.Rd | 10 man/bespoke_rmd_alert_results.Rd | 152 man/bespoke_rmd_initialise_widgets.Rd | 72 man/bespoke_rmd_output.Rd | 228 man/mantis-package.Rd | 4 tests/testthat/_snaps/plots-static/example-data-empty-static.svg | 14 tests/testthat/_snaps/plots-static/example-data-heatmap-static.svg | 9785 ++++------ tests/testthat/_snaps/plots-static/example-data-multipanel-static.svg | 12 tests/testthat/test-alert.R | 83 tests/testthat/test-plots-interactive.R | 2 tests/testthat/test-prepare.R | 815 tests/testthat/test-report.R | 10 tests/testthat/test-utilities.R | 8 vignettes/alert-rules.Rmd | 15 vignettes/articles/example-report-static-heatmap.Rmd | 2 vignettes/articles/example-report-static-multipanel.Rmd | 2 vignettes/bespoke-reports.Rmd | 34 34 files changed, 6438 insertions(+), 5840 deletions(-)
Title: IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 2.1.2 dated 2025-01-13 and 2.1.3 dated 2025-10-27
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/imagine-intro.html | 7 ++++--- src/agenbag-gradients.cpp | 2 +- src/convolution-with-quantiles.cpp | 2 +- src/quantile-filter.cpp | 2 +- 9 files changed, 24 insertions(+), 19 deletions(-)
Title: Data Quality Reporting for Temporal Datasets
Description: Generate reports that enable quick visual review of
temporal shifts in record-level data. Time series plots showing aggregated
values are automatically created for each data field (column) depending on its
contents (e.g. min/max/mean values for numeric data, no. of distinct
values for categorical data), as well as overviews for missing values,
non-conformant values, and duplicated rows. The resulting reports are shareable
and can contribute to forming a transparent record of the entire analysis process.
It is designed with Electronic Health Records in mind, but can be used for
any type of record-level temporal data (i.e. tabular data where each row represents
a single "event", one column contains the "event date", and other columns
contain any associated values for the event).
Author: T. Phuong Quan [aut, cre] ,
Jack Cregan [ctb],
University of Oxford [cph],
National Institute for Health Research [fnd],
Brad Cannell [rev]
Maintainer: T. Phuong Quan <phuongquan567@outlook.com>
Diff between daiquiri versions 1.2.0 dated 2025-06-24 and 1.2.1 dated 2025-10-27
DESCRIPTION | 15 MD5 | 28 NEWS.md | 5 R/aggregate_data.R | 2 R/reports.R | 21 inst/doc/daiquiri.html | 5 inst/extdata/example_prescriptions.csv |17994 ++++++++++++++-------------- man/daiquiri-package.Rd | 2 tests/testthat/_snaps/reports |only tests/testthat/test-reports.R | 301 tests/testthat/testdata/completetestset.csv | 2 11 files changed, 9343 insertions(+), 9032 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox& [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.4.2 dated 2025-10-22 and 1.4.3 dated 2025-10-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/extract.level.R | 18 ++++++++++-------- inst/WORDLIST | 1 + tests/testthat/test_extract.level.R | 12 ++++++++++++ 6 files changed, 35 insertions(+), 16 deletions(-)
Title: Simulate the Effect of Management Policies on Restoration
Efforts
Description: Simulation methods to study the effect of management policies on
efforts to restore populations back to their original genetic composition.
Allows for single-scenario simulation and for optimization of specific chosen
scenarios. Further information can be found in Hernandez, Janzen and Lavretsky
(2023) <doi:10.1111/1755-0998.13892>.
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between simRestore versions 1.1.4 dated 2023-11-17 and 1.1.5 dated 2025-10-27
DESCRIPTION | 8 MD5 | 16 - R/optimize_static.R | 12 - README.md | 2 build/vignette.rds |binary inst/doc/demonstration.html | 342 +++++++++++++++++----------------- src/main_functions.cpp | 1 src/organism.cpp | 2 tests/testthat/test-optimize_static.R | 4 9 files changed, 196 insertions(+), 191 deletions(-)
Title: Nonparametric Analysis of Multivariate Data in Factorial Designs
Description: Analysis of multivariate data with two-way completely randomized
factorial design. The analysis is based on fully nonparametric, rank-based
methods and uses test statistics based on the Dempster's ANOVA, Wilk's Lambda,
Lawley-Hotelling and Bartlett-Nanda-Pillai criteria. The multivariate
response is allowed to be ordinal, quantitative, binary or a mixture of the
different variable types. The package offers two functions performing the
analysis, one for small and the other for large sample sizes. The underlying methodology
is largely described in Bathke and Harrar (2016) <doi:10.1007/978-3-319-39065-9_7> and in
Munzel and Brunner (2000) <doi:10.1016/S0378-3758(99)00212-8> and in
Kiefel and Bathke (2022) <doi:10.1515/stat-2022-0112>.
Author: Maximilian Kiefel [cre, aut],
Arne C. Bathke [ctb]
Maintainer: Maximilian Kiefel <physik210@hotmail.com>
Diff between nparMD versions 0.2.1 dated 2022-03-09 and 0.2.3 dated 2025-10-27
DESCRIPTION | 19 ++++++--- MD5 | 10 ++--- R/nparml.R | 115 +++++++++++++++++++++++++++++----------------------------- R/nparms.R | 84 +++++++++++++++++++++++------------------- man/nparml.Rd | 10 +++++ man/nparms.Rd | 10 +++++ 6 files changed, 142 insertions(+), 106 deletions(-)
Title: Inferential Methods for Multimodal and Other Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate
conditional uniform graph and quadratic assignment procedure testing,
and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.5.2 dated 2025-09-12 and 1.5.3 dated 2025-10-27
DESCRIPTION | 8 +-- MD5 | 25 ++++++----- NEWS.md | 15 ++++++ R/data_mpn.R | 10 ++-- R/migraph-defunct.R | 4 + R/migraph-package.R | 6 ++ R/model_distrib.R |only R/model_tests.R | 74 --------------------------------- man/mpn_elite_mex.Rd | 17 ++++--- man/mpn_elite_usa.Rd | 2 man/test_distributions.Rd | 6 +- tests/testthat/test-measure_over.R |only tests/testthat/test-model_distrib.R |only tests/testthat/test-model_regression.R | 12 ++++- tests/testthat/test-model_tests.R | 15 ++++++ 15 files changed, 87 insertions(+), 107 deletions(-)
Title: Multi Variate Multi Response ADMM with Interaction Effects
Description: This system allows one to model a multi-variate, multi-response
problem with interaction effects. It combines the usual squared error loss
for the multi-response problem with some penalty terms to encourage
responses that correlate to form groups and also allow for modeling main and
interaction effects that exit within the covariates.
The optimization method employed is the Alternating Direction Method of
Multipliers (ADMM). The implementation is based on the methodology
presented on Quachie Asenso, T., & Zucknick, M. (2023)
<doi:10.48550/arXiv.2303.11155>.
Author: Theophilus Quachie Asenso [aut],
Manuela Zucknick [aut],
Waldir Leoncio [aut, cre] ,
Chi Zhang [aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between MADMMplasso versions 1.0.0 dated 2025-01-08 and 1.0.1 dated 2025-10-27
DESCRIPTION | 11 ++++++----- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/MADMMplasso-package.R | 2 +- R/admm_MADMMplasso.R | 6 +++--- R/objective.R | 2 +- R/predict.MADMMplasso.R | 2 +- build/partial.rdb |binary inst/examples/cv_MADMMplasso_example.R | 6 +++--- man/cv_MADMMplasso.Rd | 6 +++--- src/admm_MADMMplasso.cpp | 2 +- tests/testthat/Rplots.pdf |only tests/testthat/test-issue_53.R | 8 +++++--- tests/testthat/test-issue_62.R |only tests/testthat/test-parallel.R | 3 ++- 16 files changed, 48 insertions(+), 35 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 1.2.1 dated 2025-07-16 and 1.2.2 dated 2025-10-27
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/lpdaUsersGuide.R | 1 + inst/doc/lpdaUsersGuide.Rmd | 1 + inst/doc/lpdaUsersGuide.html | 38 ++++++++++++++++++++------------------ vignettes/lpdaUsersGuide.Rmd | 1 + 7 files changed, 36 insertions(+), 27 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, art]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.3.0 dated 2025-10-21 and 1.3.1 dated 2025-10-27
DESCRIPTION | 10 MD5 | 53 +-- NAMESPACE | 8 NEWS.md | 8 R/IssueTrackeR-package.R | 38 +- R/check.R | 10 R/finding-objects.R | 320 +++++++++++++------ R/print.R | 632 +++++++++++++++++++------------------- R/summary.R | 2 R/update_database.R | 4 R/wrangling_dataset_issues.R | 54 +-- R/wrangling_dataset_labels.R | 29 + R/wrangling_dataset_milestones.R | 83 ++++ R/wrangling_repo.R | 19 + inst/data_issues/generate-files.R | 10 man/IssueTrackeR-package.Rd | 2 man/author_last_comment.Rd |only man/format_issues.Rd | 2 man/format_labels.Rd | 2 man/format_milestones.Rd | 2 man/get.Rd | 3 man/get_all_repos.Rd | 67 ++-- man/get_nbr_comments.Rd |only man/update_database.Rd | 4 man/with_comments.Rd |only man/with_labels.Rd | 64 +-- man/with_text.Rd | 4 man/write.Rd | 6 tests/testthat/test-check.R | 162 ++++----- 29 files changed, 925 insertions(+), 673 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Antonio Castro [aut],
Antonio Mello [aut],
Diego Carvalho [ctb],
Eduardo Bezerra [ctb],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Luca [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.2.737 dated 2025-08-20 and 1.2.747 dated 2025-10-27
DESCRIPTION | 8 LICENSE | 4 MD5 | 198 ++++++++++++------------ NAMESPACE | 296 ++++++++++++++++++------------------ R/data.R | 75 +++++---- R/globals.R | 4 R/han_autoencoder.R | 180 ++++++++++++---------- R/hanc_ml.R | 131 +++++++++------- R/hanct_dtw.R | 144 +++++++++-------- R/hanct_kmeans.R | 123 ++++++++------- R/hanr_arima.R | 156 ++++++++++--------- R/hanr_emd.R | 131 ++++++++-------- R/hanr_fbiad.R | 90 ++++++----- R/hanr_fft.R | 120 ++++++++------ R/hanr_fft_amoc.R | 153 ++++++++++-------- R/hanr_fft_amoc_cusum.R | 190 +++++++++++------------ R/hanr_fft_binseg.R | 152 ++++++++++-------- R/hanr_fft_binseg_cusum.R | 169 +++++++++++--------- R/hanr_fft_sma.R | 184 +++++++++++----------- R/hanr_garch.R | 105 +++++++------ R/hanr_hist.R | 128 ++++++++------- R/hanr_ml.R | 113 ++++++++------ R/hanr_remd.R | 183 +++++++++++----------- R/hanr_rtad.R | 269 ++++++++++++++++----------------- R/hanr_wavelet.R | 82 +++++----- R/har_ensemble.R | 229 ++++++++++++++-------------- R/har_eval.R | 176 +++++++++++---------- R/har_eval_soft.R | 347 +++++++++++++++++++++---------------------- R/har_plot.R | 260 ++++++++++++++++---------------- R/harbinger.R | 112 ++++++++----- R/harbinger_utils.R | 183 +++++++++++++--------- R/hcp_amoc.R | 81 ++++++---- R/hcp_binseg.R | 83 ++++++---- R/hcp_cf_arima.R | 156 ++++++++++--------- R/hcp_cf_ets.R | 137 ++++++++-------- R/hcp_cf_lr.R | 122 ++++++++------- R/hcp_chow.R | 80 +++++---- R/hcp_garch.R | 141 +++++++++-------- R/hcp_gft.R | 110 +++++++------ R/hcp_pelt.R | 80 +++++---- R/hcp_scp.R | 158 ++++++++++--------- R/hdis_mp.R | 122 ++++++++------- R/hdis_sax.R | 232 ++++++++++++++-------------- R/hmo_mp.R | 122 ++++++++------- R/hmo_sax.R | 211 +++++++++++++------------- R/hmo_xsax.R | 216 ++++++++++++++------------ R/hmu_pca.R | 92 ++++++----- R/mas.R | 88 +++++----- R/trans_sax.R | 113 +++++++------- R/trans_xsax.R | 115 +++++++------- README.md | 218 +++++++++++++-------------- man/detect.Rd | 49 +++--- man/examples_anomalies.Rd | 78 +++++---- man/examples_changepoints.Rd | 73 ++++----- man/examples_harbinger.Rd | 75 ++++----- man/examples_motifs.Rd | 69 ++++---- man/han_autoencoder.Rd | 82 ++++++---- man/hanc_ml.Rd | 120 ++++++++------ man/hanct_dtw.Rd | 97 ++++++------ man/hanct_kmeans.Rd | 97 ++++++------ man/hanr_arima.Rd | 87 ++++++---- man/hanr_emd.Rd | 92 ++++++----- man/hanr_fbiad.Rd | 89 ++++++----- man/hanr_fft.Rd | 89 ++++++----- man/hanr_fft_amoc.Rd | 103 ++++++------ man/hanr_fft_amoc_cusum.Rd | 107 ++++++------- man/hanr_fft_binseg.Rd | 106 +++++++------ man/hanr_fft_binseg_cusum.Rd | 115 +++++++------- man/hanr_fft_sma.Rd | 103 ++++++------ man/hanr_garch.Rd | 88 ++++++---- man/hanr_histogram.Rd | 88 +++++----- man/hanr_ml.Rd | 101 ++++++------ man/hanr_remd.Rd | 95 ++++++----- man/hanr_rtad.Rd | 103 ++++++------ man/hanr_wavelet.Rd | 92 ++++++----- man/har_ensemble.Rd | 87 +++++----- man/har_eval.Rd | 96 ++++++----- man/har_eval_soft.Rd | 103 ++++++------ man/har_plot.Rd | 162 ++++++++++---------- man/harbinger.Rd | 56 ++++-- man/harutils.Rd | 68 ++++++-- man/hcp_amoc.Rd | 88 ++++++---- man/hcp_binseg.Rd | 93 ++++++----- man/hcp_cf_arima.Rd | 88 +++++----- man/hcp_cf_ets.Rd | 82 +++++----- man/hcp_cf_lr.Rd | 81 +++++----- man/hcp_chow.Rd | 76 ++++----- man/hcp_garch.Rd | 87 +++++----- man/hcp_gft.Rd | 84 +++++----- man/hcp_pelt.Rd | 87 ++++++---- man/hcp_scp.Rd | 85 +++++----- man/hdis_mp.Rd | 96 ++++++----- man/hdis_sax.Rd | 93 ++++++----- man/hmo_mp.Rd | 96 ++++++----- man/hmo_sax.Rd | 95 ++++++----- man/hmo_xsax.Rd | 94 ++++++----- man/hmu_pca.Rd | 91 ++++++----- man/mas.Rd | 98 ++++++------ man/trans_sax.Rd | 58 ++++--- man/trans_xsax.Rd | 61 ++++--- 100 files changed, 6386 insertions(+), 5389 deletions(-)
Title: Download Weather Station Data from GHCNd
Description: The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.
Author: Emilio Berti [aut, cre]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between GHCNr versions 1.4.5 dated 2025-01-07 and 1.4.6 dated 2025-10-27
DESCRIPTION | 13 +-- MD5 | 34 ++++----- R/annual.R | 1 R/coverage.R | 12 +-- R/daily.R | 2 R/data.R | 6 + R/monthly.R | 1 R/utils.R | 4 - build/vignette.rds |binary data/CA003076680.rda |binary data/USC00010655.rda |binary inst/doc/daily.R | 128 +++++++++++++++++----------------- inst/doc/daily.Rmd | 11 +- inst/doc/daily.html | 162 +++++++++++++++++++------------------------- man/CA003076680.Rd | 3 man/daily.Rd | 7 + tests/testthat/test-utils.R | 4 - vignettes/daily.Rmd | 11 +- 18 files changed, 192 insertions(+), 207 deletions(-)
Title: Identification of Counterfactual Queries in Causal Models
Description: Facilitates the identification of counterfactual queries in
structural causal models via the ID* and IDC* algorithms
by Shpitser, I. and Pearl, J. (2007, 2008) <doi:10.48550/arXiv.1206.5294>,
<https://jmlr.org/papers/v9/shpitser08a.html>.
Provides a simple interface for defining causal diagrams and counterfactual
conjunctions. Construction of parallel worlds graphs and counterfactual graphs
is carried out automatically based on the counterfactual query and the causal
diagram. See Tikka, S. (2023) <doi:10.32614/RJ-2023-053> for a tutorial of
the package.
Author: Santtu Tikka [aut, cre]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between cfid versions 0.1.7 dated 2023-11-27 and 0.1.8 dated 2025-10-27
DESCRIPTION | 13 +++++++------ MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/algorithms.R | 11 +++++++---- R/cfid-package.R | 4 +--- R/graphs.R | 17 +++++++++++++---- R/probability.R | 7 ++++--- man/cfid-package.Rd | 12 ++++++++++++ tests/testthat/test-algorithms.R | 9 +++++++++ tests/testthat/test-graphs.R | 12 ++++++------ 10 files changed, 73 insertions(+), 35 deletions(-)
Title: Helpful Functions for Cleaning Surveillance Data
Description: Helpful functions for the cleaning and manipulation of surveillance data, especially with regards to the creation and validation of panel data from individual level surveillance data.
Author: Richard Aubrey White [aut, cre] ,
CSIDS [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between cstidy versions 2023.5.24 dated 2023-05-24 and 2025.10.27 dated 2025-10-27
cstidy-2023.5.24/cstidy/R/csdb_validator.R |only cstidy-2023.5.24/cstidy/inst/doc/csfmt_rts_data_v1.R |only cstidy-2023.5.24/cstidy/inst/doc/csfmt_rts_data_v1.Rmd |only cstidy-2023.5.24/cstidy/inst/doc/csfmt_rts_data_v1.html |only cstidy-2023.5.24/cstidy/man/csdb_validator_field_contents_csfmt_rts_data_v1.Rd |only cstidy-2023.5.24/cstidy/man/csdb_validator_field_types_csfmt_rts_data_v1.Rd |only cstidy-2023.5.24/cstidy/vignettes/csfmt_rts_data_v1.Rmd |only cstidy-2025.10.27/cstidy/DESCRIPTION | 10 cstidy-2025.10.27/cstidy/LICENSE | 2 cstidy-2025.10.27/cstidy/MD5 | 66 cstidy-2025.10.27/cstidy/NAMESPACE | 12 cstidy-2025.10.27/cstidy/NEWS.md | 12 cstidy-2025.10.27/cstidy/R/1_env.R |only cstidy-2025.10.27/cstidy/R/csfmt_rts_generics.R |only cstidy-2025.10.27/cstidy/R/csfmt_rts_v1.R | 466 ----- cstidy-2025.10.27/cstidy/R/csfmt_rts_v2.R |only cstidy-2025.10.27/cstidy/R/sysdata.rda |binary cstidy-2025.10.27/cstidy/README.md | 31 cstidy-2025.10.27/cstidy/build/vignette.rds |binary cstidy-2025.10.27/cstidy/inst/doc/benchmarks.Rmd | 3 cstidy-2025.10.27/cstidy/inst/doc/benchmarks.html | 7 cstidy-2025.10.27/cstidy/inst/doc/csfmt_rts_data_v2.R |only cstidy-2025.10.27/cstidy/inst/doc/csfmt_rts_data_v2.Rmd |only cstidy-2025.10.27/cstidy/inst/doc/csfmt_rts_data_v2.html |only cstidy-2025.10.27/cstidy/inst/doc/cstidy.R | 12 cstidy-2025.10.27/cstidy/inst/doc/cstidy.Rmd | 18 cstidy-2025.10.27/cstidy/inst/doc/cstidy.html | 818 +++++----- cstidy-2025.10.27/cstidy/man/expand_time_to.Rd | 7 cstidy-2025.10.27/cstidy/man/figures/logo.png |binary cstidy-2025.10.27/cstidy/man/generate_test_data.Rd | 10 cstidy-2025.10.27/cstidy/man/heal_time_csfmt_rts_data_v1.Rd | 4 cstidy-2025.10.27/cstidy/man/heal_time_csfmt_rts_data_v2.Rd |only cstidy-2025.10.27/cstidy/man/identify_data_structure.Rd | 11 cstidy-2025.10.27/cstidy/man/remove_class_csfmt_rts_data.Rd | 5 cstidy-2025.10.27/cstidy/man/set_csfmt_rts_data_v1.Rd | 37 cstidy-2025.10.27/cstidy/man/set_csfmt_rts_data_v2.Rd |only cstidy-2025.10.27/cstidy/man/unique_time_series.Rd | 7 cstidy-2025.10.27/cstidy/vignettes/benchmarks-csfmt_rts_data_v1.RDS |binary cstidy-2025.10.27/cstidy/vignettes/benchmarks-unnamed-chunk-1-1.png |binary cstidy-2025.10.27/cstidy/vignettes/benchmarks.Rmd | 3 cstidy-2025.10.27/cstidy/vignettes/csfmt_rts_data_v2.Rmd |only cstidy-2025.10.27/cstidy/vignettes/cstidy.Rmd | 18 42 files changed, 565 insertions(+), 994 deletions(-)
Title: Automated Topic Labeling with Language Models
Description: Leveraging (large) language models for automatic topic labeling. The main function converts a list of top terms into a label for each topic. Hence, it is complementary to any topic modeling package that produces a list of top terms for each topic. While human judgement is indispensable for topic validation (i.e., inspecting top terms and most representative documents), automatic topic labeling can be a valuable tool for researchers in various scenarios.
Author: Jonas Rieger [aut, cre] ,
Fritz Peters [aut] ,
Andreas Fischer [aut] ,
Tim Lauer [aut] ,
Andre Bittermann [aut]
Maintainer: Jonas Rieger <rieger@statistik.tu-dortmund.de>
Diff between topiclabels versions 0.2.0 dated 2024-10-21 and 0.3.0 dated 2025-10-27
topiclabels-0.2.0/topiclabels/man/figures/topiclabels.gif |only topiclabels-0.3.0/topiclabels/DESCRIPTION | 21 ++--- topiclabels-0.3.0/topiclabels/MD5 | 11 +- topiclabels-0.3.0/topiclabels/R/helpers.R | 5 - topiclabels-0.3.0/topiclabels/R/interact.R | 52 +++++++------- topiclabels-0.3.0/topiclabels/R/label_topics.R | 10 +- topiclabels-0.3.0/topiclabels/man/label_topics.Rd | 10 +- 7 files changed, 56 insertions(+), 53 deletions(-)
Title: Microeconometrics with R
Description: Functions, data sets and examples for the book: Yves Croissant (2025) "Microeconometrics with R", Chapman and Hall/CRC The R Series <doi:10.1201/9781003100263>. The package includes a set of estimators for models used in microeconometrics, especially for count data and limited dependent variables. Test functions include score test, Hausman test, Vuong test, Sargan test and conditional moment test. A small subset of the data set used in the book is also included.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between micsr versions 0.1-3 dated 2025-07-09 and 0.1-4 dated 2025-10-27
DESCRIPTION | 8 +-- MD5 | 46 +++++++++++--------- NAMESPACE | 2 NEWS.md | 13 +++++ R/methods.R | 12 +++-- R/test.R | 5 +- R/tools.R | 99 +++++++++++++++++++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/charitable.R | 10 ++-- inst/doc/charitable.pdf |binary inst/doc/charitable.qmd | 4 + inst/doc/escount.pdf |binary inst/doc/expreg.pdf |binary inst/doc/lm_function.pdf |binary inst/doc/micsr_objects.pdf |binary inst/doc/micsr_objects.qmd | 4 - inst/doc/misc_tools.R |only inst/doc/misc_tools.pdf |only inst/doc/misc_tools.qmd |only inst/doc/ndvuong.pdf |binary man/dummy.Rd |only man/maximize.Rd |only man/micsr.Rd | 2 vignettes/charitable.qmd | 4 + vignettes/micsr_objects.qmd | 4 - vignettes/misc_tools.qmd |only 27 files changed, 144 insertions(+), 69 deletions(-)
Title: Multiple Hurdle Tobit Models
Description: Estimation of models with dependent variable left-censored at zero.
Null values may be caused by a selection process
Cragg (1971) <doi:10.2307/1909582>, insufficient resources
Tobin (1958) <doi:10.2307/1907382>, or infrequency of purchase
Deaton and Irish (1984) <doi:10.1016/0047-2727(84)90067-7>.
Author: Yves Croissant [aut, cre] ,
Fabrizio Carlevaro [aut],
Stephane Hoareau [aut]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mhurdle versions 1.3-1 dated 2024-06-17 and 1.3-2 dated 2025-10-27
DESCRIPTION | 11 ++++---- MD5 | 18 +++++++------- NEWS.md | 2 + build/partial.rdb |binary build/vignette.rds |binary data/Interview.rda |binary inst/doc/mhurdle.R | 34 -------------------------- inst/doc/mhurdle.Rmd | 64 +++++++++++++++++++++++++------------------------- inst/doc/mhurdle.pdf |binary vignettes/mhurdle.Rmd | 64 +++++++++++++++++++++++++------------------------- 10 files changed, 82 insertions(+), 111 deletions(-)