Title: Spatial Empirical Dynamic Modeling
Description: Inferring causation from spatial cross-sectional data through empirical dynamic modeling (EDM), with methodological extensions including geographical convergent cross mapping from Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>, as well as the spatial causality test following the approach of Herrera et al. (2016) <doi:10.1111/pirs.12144>, together with geographical pattern causality proposed in Zhang et al. (2025) <doi:10.1080/13658816.2025.2581207>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.10 dated 2026-02-01 and 1.11 dated 2026-02-03
DESCRIPTION | 6 MD5 | 74 +++++----- NEWS.md | 8 + inst/CITATION | 2 inst/doc/main1_pkgintro.Rmd | 2 inst/doc/main1_pkgintro.html | 2 inst/doc/main2_ssr.Rmd | 2 inst/doc/main2_ssr.html | 2 inst/doc/main3_gccm.Rmd | 6 inst/doc/main3_gccm.html | 10 - inst/doc/main4_gpc.Rmd | 2 inst/doc/main4_gpc.html | 6 inst/doc/main5_gcmc.Rmd | 2 inst/doc/main5_gcmc.html | 6 inst/doc/main6_scpcm.Rmd | 3 inst/doc/main6_scpcm.html | 47 +++--- inst/doc/si1_slm.Rmd | 2 inst/doc/si1_slm.html | 2 inst/doc/si2_sct.Rmd | 318 +++++++++++++++++++++---------------------- inst/doc/si2_sct.html | 26 +-- man/figures/gccm/fig1-1.png |binary man/figures/gccm/fig2-1.png |binary man/figures/gcmc/fig1-1.png |binary man/figures/gcmc/fig2-1.png |binary man/figures/gpc/fig1-1.png |binary man/figures/gpc/fig2-1.png |binary src/GridExp.cpp | 123 ++++++++++------ src/LatticeExp.cpp | 32 ++++ src/SymbolicDynamics.cpp | 2 src/SymbolicDynamics.h | 2 vignettes/main1_pkgintro.Rmd | 2 vignettes/main2_ssr.Rmd | 2 vignettes/main3_gccm.Rmd | 6 vignettes/main4_gpc.Rmd | 2 vignettes/main5_gcmc.Rmd | 2 vignettes/main6_scpcm.Rmd | 3 vignettes/si1_slm.Rmd | 2 vignettes/si2_sct.Rmd | 318 +++++++++++++++++++++---------------------- 38 files changed, 549 insertions(+), 475 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 2.1.0 dated 2025-11-05 and 2.1.1 dated 2026-02-03
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nuggets-2.1.1/nuggets/tests/testthat/test-cluster_associations.R | 34 nuggets-2.1.1/nuggets/tests/testthat/test-dig.R | 1 nuggets-2.1.1/nuggets/tests/testthat/test-dig_associations.R | 194 - nuggets-2.1.1/nuggets/tests/testthat/test-dig_tautologies.R | 4 nuggets-2.1.1/nuggets/tests/testthat/test-partition.R | 8 nuggets-2.1.1/nuggets/tests/testthat/test-ui-aboutTable.R | 2 nuggets-2.1.1/nuggets/tests/testthat/test-ui-callDataTable.R | 2 nuggets-2.1.1/nuggets/tests/testthat/test-ui-callExtension.R | 14 nuggets-2.1.1/nuggets/tests/testthat/test-ui-conditionFilterModule.R | 16 nuggets-2.1.1/nuggets/tests/testthat/test-ui-creationParamsTable.R | 2 nuggets-2.1.1/nuggets/tests/testthat/test-ui-formatRulesForTable.R | 12 nuggets-2.1.1/nuggets/tests/testthat/test-ui-highlightCondition.R | 10 nuggets-2.1.1/nuggets/tests/testthat/test-ui-infoBox.R | 2 nuggets-2.1.1/nuggets/tests/testthat/test-ui-infoTable.R | 6 nuggets-2.1.1/nuggets/tests/testthat/test-ui-numericFilterModule.R | 11 nuggets-2.1.1/nuggets/tests/testthat/test-ui-rulebaseTable.R | 2 228 files changed, 10569 insertions(+), 5503 deletions(-)
Title: Testing Similarity Between Binary Datasets using
Jaccard/Tanimoto Coefficients
Description: Calculate statistical significance of Jaccard/Tanimoto similarity
coefficients.
Author: Neo Christopher Chung [aut, cre],
Blażej Miasojedow [aut],
Michal Startek [aut],
Anna Gambin [aut]
Maintainer: Neo Christopher Chung <nchchung@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2018-06-14
Diff between jaccard versions 0.1.0 dated 2018-06-14 and 0.1.2 dated 2026-02-03
DESCRIPTION | 43 ++++++++++++++++++++++++++++-------------- MD5 | 36 +++++++++++++++++++++-------------- NAMESPACE | 4 +++ R/RcppExports.R | 4 +-- R/jaccard.R | 8 +++++-- R/jaccard.rahman.R | 16 ++++++--------- R/jaccard.test.R | 14 ++++++------- R/runJaccardApp.R |only inst |only man/jaccard.Rd | 2 - man/jaccard.ev.Rd | 2 - man/jaccard.rahman.Rd | 14 +++++-------- man/jaccard.test.Rd | 7 ++---- man/jaccard.test.bootstrap.Rd | 12 +++++++++-- man/jaccard.test.mca.Rd | 11 ++++++++-- man/jaccard.test.pairwise.Rd | 11 +++++++--- man/runJaccardApp.Rd |only src/RcppExports.cpp | 5 ++++ 18 files changed, 120 insertions(+), 69 deletions(-)
Title: Transport Modeling: Network Processing, Route Enumeration, and
Traffic Assignment
Description: High-performance tools for transport modeling - network processing, route
enumeration, and traffic assignment in R. The package implements the Path-Sized Logit
model for traffic assignment - Ben-Akiva and Bierlaire (1999) <doi:10.1007/978-1-4615-5203-1_2> -
an efficient route enumeration algorithm, and provides powerful utility functions for (multimodal)
network generation, consolidation/contraction, and/or simplification. The user is expected to provide
a transport network (either a graph or collection of linestrings) and an origin-destination (OD)
matrix of trade/traffic flows. Maintained by transport consultants at CPCS (cpcs.ca).
Author: Sebastian Krantz [aut, cre],
Kamol Roy [ctb]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between flownet versions 0.1.1 dated 2026-01-27 and 0.1.2 dated 2026-02-03
DESCRIPTION | 6 +-- MD5 | 24 ++++++------- NEWS.md | 8 +++- R/assignment.R | 26 +++++++------- R/utils.R | 55 ++++++++++++++++-------------- README.md | 17 ++++++--- inst/doc/introduction.Rmd | 2 - inst/doc/introduction.html | 80 +++++++++------------------------------------ man/consolidate_graph.Rd | 24 ++++++------- man/flownet-package.Rd | 18 +++++----- man/run_assignment.Rd | 26 +++++++------- man/simplify_network.Rd | 4 +- vignettes/introduction.Rmd | 2 - 13 files changed, 134 insertions(+), 158 deletions(-)
Title: Cross-Validation for Linear and Ridge Regression Models
Description: Implements cross-validation methods for linear and ridge regression models. The package provides grid-based selection of the ridge penalty parameter using Singular Value Decomposition (SVD) and supports K-fold cross-validation, Leave-One-Out Cross-Validation (LOOCV), and Generalized Cross-Validation (GCV). Computations are implemented in C++ via 'RcppArmadillo' with optional parallelization using 'RcppParallel'. The methods are suitable for high-dimensional settings where the number of predictors exceeds the number of observations.
Author: Philip Nye [aut, cre]
Maintainer: Philip Nye <phipnye@proton.me>
Diff between cvLM versions 1.0.4 dated 2024-08-01 and 2.0.0 dated 2026-02-03
cvLM-1.0.4/cvLM/src/FUNScvLM.cpp |only cvLM-1.0.4/cvLM/src/FUNScvLM.h |only cvLM-1.0.4/cvLM/src/Main.cpp |only cvLM-1.0.4/cvLM/src/cvLM.cpp |only cvLM-1.0.4/cvLM/src/cvLM.h |only cvLM-1.0.4/cvLM/src/cvLMWorker.cpp |only cvLM-1.0.4/cvLM/src/cvLMWorker.h |only cvLM-1.0.4/cvLM/src/cvRidge.cpp |only cvLM-1.0.4/cvLM/src/cvRidge.h |only cvLM-1.0.4/cvLM/src/cvRidgeWorker.cpp |only cvLM-1.0.4/cvLM/src/cvRidgeWorker.h |only cvLM-2.0.0/cvLM/DESCRIPTION | 19 cvLM-2.0.0/cvLM/LICENSE | 4 cvLM-2.0.0/cvLM/MD5 | 71 ++- cvLM-2.0.0/cvLM/NAMESPACE | 7 cvLM-2.0.0/cvLM/NEWS.md |only cvLM-2.0.0/cvLM/R/RcppExports.R | 8 cvLM-2.0.0/cvLM/R/checks.R |only cvLM-2.0.0/cvLM/R/cvLM.R | 266 ++++++++---- cvLM-2.0.0/cvLM/R/data-utils.R |only cvLM-2.0.0/cvLM/R/grid.search.R | 145 ++++-- cvLM-2.0.0/cvLM/R/model-stats.R |only cvLM-2.0.0/cvLM/R/reg.table.R | 392 ++++++++---------- cvLM-2.0.0/cvLM/R/string-format.R |only cvLM-2.0.0/cvLM/README.md | 51 +- cvLM-2.0.0/cvLM/build/partial.rdb |binary cvLM-2.0.0/cvLM/man/cvLM-package.Rd | 167 +++++-- cvLM-2.0.0/cvLM/man/grid.search.Rd | 101 ++-- cvLM-2.0.0/cvLM/man/reg.table.Rd | 4 cvLM-2.0.0/cvLM/src/CV-Stochastic-Worker.h |only cvLM-2.0.0/cvLM/src/CV.h |only cvLM-2.0.0/cvLM/src/ClosedForm.cpp |only cvLM-2.0.0/cvLM/src/ClosedForm.h |only cvLM-2.0.0/cvLM/src/CompleteOrthogonalDecomposition.h |only cvLM-2.0.0/cvLM/src/ConstexprOptional.h |only cvLM-2.0.0/cvLM/src/DataLoader.cpp |only cvLM-2.0.0/cvLM/src/DataLoader.h |only cvLM-2.0.0/cvLM/src/Enums.h |only cvLM-2.0.0/cvLM/src/Grid-Deterministic-Worker.h |only cvLM-2.0.0/cvLM/src/Grid-Generator.cpp |only cvLM-2.0.0/cvLM/src/Grid-Generator.h |only cvLM-2.0.0/cvLM/src/Grid-LambdaCV.h |only cvLM-2.0.0/cvLM/src/Grid-Stochastic-Worker.h |only cvLM-2.0.0/cvLM/src/Grid.h |only cvLM-2.0.0/cvLM/src/Makevars | 11 cvLM-2.0.0/cvLM/src/Makevars.win | 10 cvLM-2.0.0/cvLM/src/RcppExports.cpp | 49 +- cvLM-2.0.0/cvLM/src/SingularValueDecomposition.h |only cvLM-2.0.0/cvLM/src/Utils-Data.h |only cvLM-2.0.0/cvLM/src/Utils-Decompositions.h |only cvLM-2.0.0/cvLM/src/Utils-Folds.cpp |only cvLM-2.0.0/cvLM/src/Utils-Folds.h |only cvLM-2.0.0/cvLM/src/Utils-Parallel.h |only cvLM-2.0.0/cvLM/src/main.cpp |only cvLM-2.0.0/cvLM/tests |only 55 files changed, 781 insertions(+), 524 deletions(-)
Title: Convert Gene IDs Between Each Other and Fetch Annotations from
Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but
that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function
in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the
'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes"
can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol()
attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre],
Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Diff between convertid versions 0.1.12 dated 2026-01-09 and 0.2.0 dated 2026-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/convertId2.R | 24 +++++++++++++++++++++--- man/todisp2.Rd | 28 +++++++++++++++++++++++++++- 4 files changed, 55 insertions(+), 11 deletions(-)
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-test, wilcox.test, ANOVA models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <mirzaghaderi@gmail.com>
Diff between rtpcr versions 2.1.2 dated 2026-01-23 and 2.1.3 dated 2026-02-03
rtpcr-2.1.2/rtpcr/R/ANCOVA_DDCt.R |only rtpcr-2.1.2/rtpcr/R/REPEATED_DDCt.R |only rtpcr-2.1.2/rtpcr/man/ANCOVA_DDCt.Rd |only rtpcr-2.1.2/rtpcr/man/REPEATED_DDCt.Rd |only rtpcr-2.1.3/rtpcr/DESCRIPTION | 15 rtpcr-2.1.3/rtpcr/MD5 | 52 - rtpcr-2.1.3/rtpcr/NAMESPACE | 2 rtpcr-2.1.3/rtpcr/NEWS.md | 20 rtpcr-2.1.3/rtpcr/R/ANOVA_DCt.R | 354 +++++++-- rtpcr-2.1.3/rtpcr/R/ANOVA_DDCt.R | 359 ++++++++-- rtpcr-2.1.3/rtpcr/R/TTEST_DDCt.R | 21 rtpcr-2.1.3/rtpcr/R/WILCOX_DDCt.R | 20 rtpcr-2.1.3/rtpcr/R/compute_wDCt.R | 64 + rtpcr-2.1.3/rtpcr/R/globalVariables.R | 2 rtpcr-2.1.3/rtpcr/R/meanTech.R | 11 rtpcr-2.1.3/rtpcr/R/plotFactor.R | 2 rtpcr-2.1.3/rtpcr/R/qpcrhlpr.R | 535 +-------------- rtpcr-2.1.3/rtpcr/inst/doc/Manual.R | 13 rtpcr-2.1.3/rtpcr/inst/doc/Manual.Rmd | 89 +- rtpcr-2.1.3/rtpcr/inst/doc/Manual.html | 183 +++-- rtpcr-2.1.3/rtpcr/inst/extdata/data_2factorBlock3ref.csv | 48 - rtpcr-2.1.3/rtpcr/man/ANOVA_DCt.Rd | 112 ++- rtpcr-2.1.3/rtpcr/man/ANOVA_DDCt.Rd | 54 + rtpcr-2.1.3/rtpcr/man/TTEST_DDCt.Rd | 5 rtpcr-2.1.3/rtpcr/man/WILCOX_DDCt.Rd | 5 rtpcr-2.1.3/rtpcr/man/compute_wDCt.Rd | 11 rtpcr-2.1.3/rtpcr/man/meanTech.Rd | 15 rtpcr-2.1.3/rtpcr/man/plotFactor.Rd | 2 rtpcr-2.1.3/rtpcr/vignettes/Manual.Rmd | 89 +- 29 files changed, 1150 insertions(+), 933 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 0.6.0 dated 2025-10-31 and 0.6.1 dated 2026-02-03
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-0.6.1/omock/DESCRIPTION | 6 omock-0.6.1/omock/MD5 | 84 +--- omock-0.6.1/omock/NEWS.md | 102 ++--- omock-0.6.1/omock/R/changeCdmVersion.R | 2 omock-0.6.1/omock/R/checkInputs.R | 17 omock-0.6.1/omock/R/checks.R | 108 ----- omock-0.6.1/omock/R/mockCdmFromTables.R | 4 omock-0.6.1/omock/R/mockCdmReference.R | 2 omock-0.6.1/omock/R/mockCohort.R | 5 omock-0.6.1/omock/R/mockConditionOccurrence.R | 17 omock-0.6.1/omock/R/mockDatasets.R | 143 ++++++- omock-0.6.1/omock/R/mockDeath.R | 4 omock-0.6.1/omock/R/mockDrugExposure.R | 7 omock-0.6.1/omock/R/mockMeasurement.R | 29 + omock-0.6.1/omock/R/mockObservation.R | 8 omock-0.6.1/omock/R/mockObservationPeriod.R | 5 omock-0.6.1/omock/R/mockPerson.R | 25 + omock-0.6.1/omock/R/mockProcedureOccurrence.R | 8 omock-0.6.1/omock/R/mockVisitOccurrence.R | 3 omock-0.6.1/omock/R/sysdata.rda |binary omock-0.6.1/omock/README.md | 12 omock-0.6.1/omock/build/vignette.rds |binary omock-0.6.1/omock/data/mockDatasets.rda |binary omock-0.6.1/omock/inst/doc/mock_from_tables.html | 49 +- omock-0.6.1/omock/inst/doc/synthetic_clinical_tables.html | 19 omock-0.6.1/omock/inst/doc/synthetic_cohorts.html | 5 omock-0.6.1/omock/inst/doc/synthetic_datasets.html | 196 +++++----- omock-0.6.1/omock/inst/doc/synthetic_vocabulary.html | 5 omock-0.6.1/omock/man/mockCdmFromTables.Rd | 4 omock-0.6.1/omock/man/mockCdmReference.Rd | 2 omock-0.6.1/omock/man/mockConditionOccurrence.Rd | 5 omock-0.6.1/omock/man/mockDeath.Rd | 4 omock-0.6.1/omock/man/mockDrugExposure.Rd | 4 omock-0.6.1/omock/man/mockMeasurement.Rd | 5 omock-0.6.1/omock/man/mockObservation.Rd | 4 omock-0.6.1/omock/man/mockObservationPeriod.Rd | 5 omock-0.6.1/omock/man/mockPerson.Rd | 4 omock-0.6.1/omock/man/mockProcedureOccurrence.Rd | 5 omock-0.6.1/omock/tests/testthat/test-mockMeasurement.R | 13 47 files changed, 478 insertions(+), 442 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.12.0-1 dated 2025-11-24 and 1.12.0-2 dated 2026-02-03
highs-1.12.0-1/highs/inst/HiGHS/extern/filereaderlp |only highs-1.12.0-1/highs/inst/HiGHS/extern/zstr/README |only highs-1.12.0-1/highs/inst/HiGHS/highs/highs_bindings.cpp |only highs-1.12.0-1/highs/inst/HiGHS/highs/interfaces |only highs-1.12.0-1/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/SymScaling.cpp |only highs-1.12.0-1/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/SymScaling.h |only highs-1.12.0-2/highs/DESCRIPTION | 6 highs-1.12.0-2/highs/MD5 | 346 +++-- highs-1.12.0-2/highs/inst/HiGHS/CMakeLists.txt | 139 +- highs-1.12.0-2/highs/inst/HiGHS/HiGHS.sln |only highs-1.12.0-2/highs/inst/HiGHS/MODULE.bazel | 24 highs-1.12.0-2/highs/inst/HiGHS/README.md | 38 highs-1.12.0-2/highs/inst/HiGHS/THIRD_PARTY_NOTICES.md |only highs-1.12.0-2/highs/inst/HiGHS/cmake/FindCUDAConf.cmake | 2 highs-1.12.0-2/highs/inst/HiGHS/cmake/FindHipoDeps.cmake | 300 ++-- highs-1.12.0-2/highs/inst/HiGHS/cmake/README.md | 34 highs-1.12.0-2/highs/inst/HiGHS/cmake/cpp-highs.cmake | 36 highs-1.12.0-2/highs/inst/HiGHS/cmake/set-version.cmake | 2 highs-1.12.0-2/highs/inst/HiGHS/cmake/sources-python.cmake | 16 highs-1.12.0-2/highs/inst/HiGHS/cmake/sources.cmake | 88 + highs-1.12.0-2/highs/inst/HiGHS/extern/CLI11.hpp |only highs-1.12.0-2/highs/inst/HiGHS/extern/amd |only highs-1.12.0-2/highs/inst/HiGHS/extern/metis |only highs-1.12.0-2/highs/inst/HiGHS/extern/rcm |only highs-1.12.0-2/highs/inst/HiGHS/extern/zstr/LICENSE |only highs-1.12.0-2/highs/inst/HiGHS/highs/CMakeLists.txt | 33 highs-1.12.0-2/highs/inst/HiGHS/highs/Highs.h | 30 highs-1.12.0-2/highs/inst/HiGHS/highs/HighsRun.md |only highs-1.12.0-2/highs/inst/HiGHS/highs/highspy/__init__.py | 1 highs-1.12.0-2/highs/inst/HiGHS/highs/highspy/highs.py | 9 highs-1.12.0-2/highs/inst/HiGHS/highs/io/FilereaderLp.cpp | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/io/HighsIO.cpp | 8 highs-1.12.0-2/highs/inst/HiGHS/highs/io/filereaderlp |only highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/IpxWrapper.cpp | 99 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/IpxWrapper.h | 3 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/Auxiliary.cpp | 23 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/Auxiliary.h | 29 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/IntConfig.h | 18 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/mycblas.h | 66 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Analyse.cpp | 438 +++--- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Analyse.h | 29 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/CallAndTimeBlas.cpp | 88 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/CallAndTimeBlas.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/CliqueStack.cpp |only highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/CliqueStack.h |only highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/DataCollector.cpp | 172 +- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/DataCollector.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/DenseFactHybrid.cpp | 44 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/DenseFactKernel.cpp | 32 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FactorHiGHS.cpp | 8 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FactorHiGHS.h | 15 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Factorise.cpp | 240 +-- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Factorise.h | 21 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FormatHandler.cpp | 7 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FormatHandler.h | 11 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridHybridFormatHandler.cpp | 66 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridHybridFormatHandler.h | 12 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridSolveHandler.cpp | 155 -- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridSolveHandler.h | 5 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Numeric.cpp | 46 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Numeric.h | 3 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/ReturnValues.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/SolveHandler.cpp | 7 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/SolveHandler.h | 7 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Swaps.cpp | 1 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Symbolic.cpp | 29 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Symbolic.h | 36 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Timing.h | 68 + highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/FactorHiGHSSolver.cpp | 602 +++++---- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/FactorHiGHSSolver.h | 35 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Iterate.cpp | 308 ++-- highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Iterate.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Model.cpp | 83 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Model.h | 27 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Options.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Parameters.h | 9 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Solver.cpp | 67 - highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Solver.h | 15 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Status.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/ipx/lp_solver.cc | 47 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/ipx/lp_solver.h | 6 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/ipx/lu_update.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/ipx/maxvolume.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/ipm/ipx/model.h | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HConst.h | 17 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HStruct.h | 17 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/Highs.cpp | 328 +---- highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsCallbackStruct.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsDeprecated.cpp | 51 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsIis.cpp | 27 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsIis.h | 8 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsInterface.cpp | 160 +- highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsLpUtils.cpp | 25 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsLpUtils.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsModelUtils.cpp | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsOptions.cpp | 10 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsOptions.h | 39 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolution.cpp | 48 highs-1.12.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolution.h | 3 highs-1.12.0-2/highs/inst/HiGHS/highs/meson.build | 35 highs-1.12.0-2/highs/inst/HiGHS/highs/mip/HighsCliqueTable.cpp | 356 ++--- highs-1.12.0-2/highs/inst/HiGHS/highs/mip/HighsCliqueTable.h | 3 highs-1.12.0-2/highs/inst/HiGHS/highs/mip/HighsDebugSol.cpp | 3 highs-1.12.0-2/highs/inst/HiGHS/highs/mip/HighsDomain.cpp | 88 - 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highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/HEkk.cpp | 60 highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/HEkk.h | 5 highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/HEkkDebug.cpp | 27 highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/HEkkDual.cpp | 2 highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/HEkkPrimal.cpp | 29 highs-1.12.0-2/highs/inst/HiGHS/highs/simplex/SimplexStruct.h | 4 highs-1.12.0-2/highs/inst/HiGHS/highs/util/HighsUtils.h | 54 highs-1.12.0-2/highs/inst/HiGHS/meson.build | 1 highs-1.12.0-2/highs/inst/HiGHS/nuget/README.md | 2 highs-1.12.0-2/highs/inst/HiGHS/nuget/arm-toolchain.cmake | 2 highs-1.12.0-2/highs/inst/HiGHS/pyproject.toml | 1 highs-1.12.0-2/highs/inst/HiGHS/tests/test_highspy.py | 56 143 files changed, 4105 insertions(+), 2962 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre] ,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 4.0.1 dated 2025-11-14 and 4.0.2 dated 2026-02-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ R/make-constructor.R | 7 +++++-- inst/doc/extending-ggplot2.html | 4 ++-- inst/doc/profiling.html | 6 +++--- 6 files changed, 27 insertions(+), 15 deletions(-)
Title: Evaluating Heterogeneous Treatment Effects
Description: Provides various statistical methods for evaluating heterogeneous treatment effects (HTE) in randomized experiments. The package includes tools to estimate uniform confidence bands for estimation of the group average treatment effect sorted by generic machine learning algorithms (GATES). It also provides the tools to identify a subgroup of individuals who are likely to benefit from a treatment the most "exceptional responders" or those who are harmed by it. Detailed reference in Imai and Li (2023) <doi:10.48550/arXiv.2310.07973>.
Author: Michael Lingzhi Li [aut, cre],
Kosuke Imai [aut],
Jialu Li [ctb]
Maintainer: Michael Lingzhi Li <mili@hbs.edu>
Diff between evalHTE versions 0.1.0 dated 2026-01-28 and 0.1.1 dated 2026-02-03
DESCRIPTION | 6 LICENSE | 4 MD5 | 44 - NAMESPACE | 86 +- NEWS.md | 10 R/hte_helpers.R | 216 +++--- R/hte_qoi.R | 272 ++++---- R/main.r | 64 +- README.md | 4 build/vignette.rds |binary inst/doc/ACIC2016.R | 610 +++++++++---------- inst/doc/ACIC2016.html | 1344 +++++++++++++++++++++--------------------- man/URATE.Rd | 78 +- man/compute_qoi.Rd | 32 - man/compute_qoi_user.Rd | 48 - man/estimate_hte.Rd | 128 ++-- man/evaluate_hte.Rd | 38 - man/plot.hte.Rd | 38 - man/plot_CI.hte.Rd | 42 - man/print.summary.hte.Rd | 38 - man/print.summary.test_hte.Rd | 38 - man/summary.hte.Rd | 46 - man/test_itr.Rd | 42 - 23 files changed, 1629 insertions(+), 1599 deletions(-)
Title: Distributional Random Forests
Description: An implementation of distributional random forests as introduced in Cevid & Michel & Naf & Meinshausen & Buhlmann (2022) <doi:10.48550/arXiv.2005.14458>.
Author: Jeffrey Naf [cre],
Loris Michel [aut],
Domagoj Cevid [aut]
Maintainer: Jeffrey Naf <jeffrey.naf@unige.ch>
Diff between drf versions 1.3.0 dated 2026-01-21 and 1.3.1 dated 2026-02-03
DESCRIPTION | 9 ++++----- MD5 | 10 +++++----- R/drf.R | 6 +++--- R/predict.R | 22 ++++++++++++---------- man/drf.Rd | 6 +++--- man/predict.drf.Rd | 22 ++++++++++++---------- 6 files changed, 39 insertions(+), 36 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like
objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] ,
Romain Francois [aut] ,
Lionel Henry [aut],
Kirill Mueller [aut] ,
Davis Vaughan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between dplyr versions 1.1.4 dated 2023-11-17 and 1.2.0 dated 2026-02-03
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Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of heterogeneity-robust difference-in-differences estimators, with a binary, discrete, or continuous treatment, in designs where past treatments may affect the current outcome.
Author: Anzony Quispe [aut, cre],
Diego Ciccia [aut],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Anzony Quispe <anzony.quispe@gmail.com>
Diff between DIDmultiplegtDYN versions 2.2.0 dated 2025-12-03 and 2.3.0 dated 2026-02-03
DIDmultiplegtDYN-2.2.0/DIDmultiplegtDYN/NEWS.md |only DIDmultiplegtDYN-2.2.0/DIDmultiplegtDYN/README.md |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/DESCRIPTION | 18 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/MD5 | 35 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/NAMESPACE | 8 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/RcppExports.R |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/cpp_helpers.R |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_bootstrap.R | 112 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_by_path.R | 16 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn.R | 2 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn_by_check.R | 8 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn_core.R | 3178 +++++----- DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn_design.R | 59 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn_dfs.R | 16 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_dyn_normweights.R | 8 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_multiplegt_main.R | 2510 ++++--- DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/did_save_sample.R | 4 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/polars_helpers.R |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/R/zzz.R |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/inst |only DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/man/did_multiplegt_dyn.Rd | 2 DIDmultiplegtDYN-2.3.0/DIDmultiplegtDYN/src |only 22 files changed, 3378 insertions(+), 2598 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut],
Song Wu [aut],
Jie Yang [aut]
Maintainer: Junying Wang <junying.wang.dl@gmail.com>
Diff between crm12Comb versions 0.1.11 dated 2025-03-30 and 0.1.12 dated 2026-02-03
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- inst/CITATION |only inst/doc/crm12Comb.html | 4 ++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [ctb],
Denes Toth [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 2.3.3 dated 2025-08-18 and 2.3.4 dated 2026-02-03
DESCRIPTION | 8 - MD5 | 18 +-- NEWS.md | 3 README.md | 3 build/vignette.rds |binary inst/doc/checkmate.html | 237 ++++++++++++++++++++++++------------------------ inst/doc/tinytest.html | 4 src/checks.c | 3 src/helper.c | 13 ++ src/helper.h | 1 10 files changed, 157 insertions(+), 133 deletions(-)
Title: Estimate Brain Networks and Connectivity with Population-Derived
Priors
Description: Implements Bayesian brain mapping with population-derived priors,
including the original model described in Mejia et al. (2020)
<doi:10.1080/01621459.2019.1679638>, the model with spatial priors described
in Mejia et al. (2022) <doi:10.1080/10618600.2022.2104289>, and the model
with population-derived priors on functional connectivity described in Mejia
et al. (2025) <doi:10.1093/biostatistics/kxaf022>. Population-derived priors
are based on templates representing established brain network maps, for
example derived from independent component analysis (ICA), parcellations,
or other methods. Model estimation is based on expectation-maximization or
variational Bayes algorithms. Includes direct support for 'CIFTI', 'GIFTI',
and 'NIFTI' neuroimaging file formats.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Nohelia Da Silva [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between BayesBrainMap versions 0.1.3 dated 2025-07-04 and 0.2.0 dated 2026-02-03
BayesBrainMap-0.1.3/BayesBrainMap/R/BrainMap.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/BrainMap.methods.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/EM_BrainMap.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/VB_FCBrainMap.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/engagements.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/engagements.methods.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/engagements_utils.R |only BayesBrainMap-0.1.3/BayesBrainMap/R/orthonorm.R |only BayesBrainMap-0.1.3/BayesBrainMap/man/EM_BrainMap.Rd |only BayesBrainMap-0.1.3/BayesBrainMap/man/UpdateThetaSQUAREM_BrainMap.Rd |only BayesBrainMap-0.1.3/BayesBrainMap/man/UpdateTheta_BrainMap.Rd |only BayesBrainMap-0.1.3/BayesBrainMap/man/VB_FCBrainMap.Rd |only BayesBrainMap-0.1.3/BayesBrainMap/man/estimate_prior_FC.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/DESCRIPTION | 49 - BayesBrainMap-0.2.0/BayesBrainMap/MD5 | 122 +- BayesBrainMap-0.2.0/BayesBrainMap/NAMESPACE | 2 BayesBrainMap-0.2.0/BayesBrainMap/NEWS.md | 112 -- BayesBrainMap-0.2.0/BayesBrainMap/R/EM_BBM.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/VB_FC_BBM.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/aliases.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/dual_reg2.R | 31 BayesBrainMap-0.2.0/BayesBrainMap/R/estimate_prior.R | 428 +++++---- BayesBrainMap-0.2.0/BayesBrainMap/R/estimate_prior.methods.R | 468 ++++++---- BayesBrainMap-0.2.0/BayesBrainMap/R/fit_BBM.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/fit_BBM.methods.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/id_engagements.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/id_engagements.methods.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/id_engagements_utils.R |only BayesBrainMap-0.2.0/BayesBrainMap/R/make_mesh.R | 4 BayesBrainMap-0.2.0/BayesBrainMap/R/utils.R | 2 BayesBrainMap-0.2.0/BayesBrainMap/README.md | 14 BayesBrainMap-0.2.0/BayesBrainMap/man/BrainMap.Rd | 248 ----- BayesBrainMap-0.2.0/BayesBrainMap/man/EM_BBM.spatial.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/LL2_kappa.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/LL_SQUAREM.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/UpdateThetaSQUAREM_BBM.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/UpdateTheta_BBM.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/VB_FC_BBM.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/add_str.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/bdiag_m.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/bdiag_m2.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/compute_LL_std.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/compute_R_inv.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/compute_mu_s.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/dual_reg2.Rd | 3 BayesBrainMap-0.2.0/BayesBrainMap/man/engagements.Rd | 66 - BayesBrainMap-0.2.0/BayesBrainMap/man/estimate.ESS.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/estimate_prior.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/estimate_prior_FC_Chol.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/estimate_prior_FC_IW.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/estimate_prior_FC_empirical.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/estimate_prior_from_DR.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/fit_BBM.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/format_engagement_name.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/id_engagements.Rd |only BayesBrainMap-0.2.0/BayesBrainMap/man/lik.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/loglik_kappa_est.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/make_Pmat.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/orthonorm.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.bMap.cifti.Rd | 26 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.bMap.matrix.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.bMap.nifti.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.bMap_eng.cifti.Rd | 17 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.prior.cifti.Rd | 24 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.prior.gifti.Rd | 28 BayesBrainMap-0.2.0/BayesBrainMap/man/plot.prior.nifti.Rd | 30 BayesBrainMap-0.2.0/BayesBrainMap/man/sqrt_XtX.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap.cifti.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap.matrix.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap.nifti.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap_eng.cifti.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap_eng.matrix.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/summary.bMap_eng.nifti.Rd | 4 BayesBrainMap-0.2.0/BayesBrainMap/man/update_A.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/update_A_Chol.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/update_S.Rd | 2 BayesBrainMap-0.2.0/BayesBrainMap/man/update_tau2.Rd | 2 77 files changed, 851 insertions(+), 899 deletions(-)
Title: Linear Models for Sequence Count Data
Description: Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data.
Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.
Author: Justin Silverman [aut, cre],
Greg Gloor [aut],
Kyle McGovern [aut, ctb]
Maintainer: Justin Silverman <JustinSilverman@psu.edu>
Diff between ALDEx3 versions 1.0.0 dated 2026-01-31 and 1.0.1 dated 2026-02-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/dirichlet.R | 2 -- tests/testthat/test-aldex-mem.R | 2 ++ 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Downloads and Organizes Financial Data from Yahoo Finance
Description: Facilitates download of financial data from Yahoo Finance <https://finance.yahoo.com/>,
a vast repository of stock price data across multiple financial exchanges. The package offers a local caching system
and support for parallel computation.
Author: Marcelo Perlin [aut, cre],
Nic Crane [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>),
Alexander Fischer [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>)
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between yfR versions 1.1.2 dated 2025-05-19 and 1.1.3 dated 2026-02-03
DESCRIPTION | 11 +-- MD5 | 24 +++---- NEWS.md | 6 + R/yf_get.R | 9 +- R/yf_get_index_components.R | 35 ++++------ inst/doc/diff-batchgetsymbols.html | 4 - inst/doc/getting-started.html | 61 +++++++++--------- inst/doc/using-collections.html | 9 +- inst/extdata/fallback-indices/DOW.rds |binary inst/extdata/fallback-indices/FTSE.rds |binary inst/extdata/fallback-indices/IBOV.rds |binary inst/extdata/fallback-indices/SP500.rds |binary inst/extdata/fallback-indices/testthat-collection.rds |binary 13 files changed, 84 insertions(+), 75 deletions(-)
Title: Extract and Tidy Canadian 'Hydrometric' Data
Description: Provides functions to access historical and real-time national 'hydrometric'
data from Water Survey of Canada data sources and then applies tidy data principles.
Author: Sam Albers [aut, cre, cph] ,
Province of British Columbia [cph] ,
Tula Foundation [cph] ,
David Hutchinson [ctb],
Dewey Dunnington [ctb],
Ryan Whaley [ctb],
Government of Canada [dtc],
Luke Winslow [rev] ,
Laura DeCicco [rev]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between tidyhydat versions 0.7.2 dated 2025-10-23 and 1.0.0 dated 2026-02-03
tidyhydat-0.7.2/tidyhydat/tests/testthat/_snaps |only tidyhydat-1.0.0/tidyhydat/DESCRIPTION | 56 ++ tidyhydat-1.0.0/tidyhydat/LICENSE | 4 tidyhydat-1.0.0/tidyhydat/MD5 | 193 +++++---- tidyhydat-1.0.0/tidyhydat/NAMESPACE | 6 tidyhydat-1.0.0/tidyhydat/NEWS.md | 8 tidyhydat-1.0.0/tidyhydat/R/available-classes.R |only tidyhydat-1.0.0/tidyhydat/R/available.R |only tidyhydat-1.0.0/tidyhydat/R/base_url.R |only tidyhydat-1.0.0/tidyhydat/R/data.R | 54 +- tidyhydat-1.0.0/tidyhydat/R/download.R | 2 tidyhydat-1.0.0/tidyhydat/R/historical-webservice.R |only tidyhydat-1.0.0/tidyhydat/R/hy.R | 86 +--- tidyhydat-1.0.0/tidyhydat/R/hy_annual_stats.R | 20 - tidyhydat-1.0.0/tidyhydat/R/hy_daily.R | 12 tidyhydat-1.0.0/tidyhydat/R/hy_daily_flows.R | 46 +- tidyhydat-1.0.0/tidyhydat/R/hy_daily_levels.R | 44 +- tidyhydat-1.0.0/tidyhydat/R/hy_db.R | 14 tidyhydat-1.0.0/tidyhydat/R/hy_monthly_flows.R | 20 - tidyhydat-1.0.0/tidyhydat/R/hy_monthly_levels.R | 20 - tidyhydat-1.0.0/tidyhydat/R/hy_plot.R | 6 tidyhydat-1.0.0/tidyhydat/R/hy_sed_daily_loads.R | 14 tidyhydat-1.0.0/tidyhydat/R/hy_sed_daily_suscon.R | 16 tidyhydat-1.0.0/tidyhydat/R/hy_sed_monthly_loads.R | 20 - tidyhydat-1.0.0/tidyhydat/R/hy_sed_monthly_suscon.R | 20 - tidyhydat-1.0.0/tidyhydat/R/hy_sed_samples.R | 36 - tidyhydat-1.0.0/tidyhydat/R/hy_sed_samples_psd.R | 12 tidyhydat-1.0.0/tidyhydat/R/hy_stations.R | 42 +- tidyhydat-1.0.0/tidyhydat/R/realtime-webservice.R | 134 +----- tidyhydat-1.0.0/tidyhydat/R/realtime.R | 43 -- tidyhydat-1.0.0/tidyhydat/R/realtime_plot.R | 6 tidyhydat-1.0.0/tidyhydat/R/utils.R | 80 +++- tidyhydat-1.0.0/tidyhydat/R/webservice-classes.R |only tidyhydat-1.0.0/tidyhydat/R/zzz.R | 2 tidyhydat-1.0.0/tidyhydat/README.md | 195 +++++++--- tidyhydat-1.0.0/tidyhydat/build/partial.rdb |binary tidyhydat-1.0.0/tidyhydat/build/vignette.rds |binary tidyhydat-1.0.0/tidyhydat/data/allstations.rda |binary tidyhydat-1.0.0/tidyhydat/data/hy_data_symbols.rda |binary tidyhydat-1.0.0/tidyhydat/data/hy_data_types.rda |binary tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_an_introduction.Rmd | 136 +++++- tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_an_introduction.html | 184 ++++++--- tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_example_analysis.Rmd | 12 tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_example_analysis.html | 36 + tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_hydat_db.Rmd | 16 tidyhydat-1.0.0/tidyhydat/inst/doc/tidyhydat_hydat_db.html | 18 tidyhydat-1.0.0/tidyhydat/man/allstations.Rd | 22 - 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Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the fu [...truncated...]
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.5.6 dated 2025-06-23 and 2.6.1 dated 2026-02-03
psych-2.5.6/psych/man/guttman.Rd |only psych-2.6.1/psych/DESCRIPTION | 8 - psych-2.6.1/psych/MD5 | 129 +++++++++++++----------- psych-2.6.1/psych/NAMESPACE | 17 ++- psych-2.6.1/psych/R/ED.r |only psych-2.6.1/psych/R/anova.psych.R | 146 ++++++++++++++++++---------- psych-2.6.1/psych/R/cfa.r |only psych-2.6.1/psych/R/cta.15.R | 2 psych-2.6.1/psych/R/cta.R | 2 psych-2.6.1/psych/R/diagram.R | 8 - psych-2.6.1/psych/R/error.bars.R | 5 psych-2.6.1/psych/R/error.bars.by.R | 14 +- psych-2.6.1/psych/R/fa.R | 61 ++++++++++- psych-2.6.1/psych/R/fa.parallel.R | 3 psych-2.6.1/psych/R/fa.pooled.r | 6 - psych-2.6.1/psych/R/fa.sort.R | 3 psych-2.6.1/psych/R/factor.congruence.R | 26 +++- psych-2.6.1/psych/R/factor.scores.R | 15 ++ psych-2.6.1/psych/R/factor.stats.R | 50 ++++++--- psych-2.6.1/psych/R/factor2cluster.R | 4 psych-2.6.1/psych/R/fsi.R |only psych-2.6.1/psych/R/lmCor.R | 24 +++- psych-2.6.1/psych/R/misc.R | 3 psych-2.6.1/psych/R/omega.R | 4 psych-2.6.1/psych/R/omega.diagram.R | 20 +++ psych-2.6.1/psych/R/omega.stats.r |only psych-2.6.1/psych/R/parse.R | 82 +++++++++++++++ psych-2.6.1/psych/R/principal.R | 2 psych-2.6.1/psych/R/print.psych.R | 13 +- psych-2.6.1/psych/R/print_psych.cfa.r |only psych-2.6.1/psych/R/residuals.psych.R | 3 psych-2.6.1/psych/R/scatter.hist.R | 23 ++++ psych-2.6.1/psych/R/score.alpha.r | 1 psych-2.6.1/psych/R/score.irt.r | 3 psych-2.6.1/psych/R/score.items.R | 3 psych-2.6.1/psych/R/score.multiple.choice.R | 6 - psych-2.6.1/psych/R/scoreOverlap.r | 8 + psych-2.6.1/psych/R/sim.circ.R | 1 psych-2.6.1/psych/R/sim.structural.R | 32 ++++-- psych-2.6.1/psych/R/summary.psych.R | 68 ++++++++++++- psych-2.6.1/psych/build/partial.rdb |binary psych-2.6.1/psych/build/vignette.rds |binary psych-2.6.1/psych/data/Harman_5.rda |only psych-2.6.1/psych/inst/CITATION | 4 psych-2.6.1/psych/inst/NEWS.Rd | 46 ++++++++ psych-2.6.1/psych/inst/doc/scoring.Rnw | 4 psych-2.6.1/psych/inst/doc/scoring.pdf |binary psych-2.6.1/psych/man/Harman.Rd | 15 +- psych-2.6.1/psych/man/Schmid.Leiman.Rd | 17 +++ psych-2.6.1/psych/man/bigCor.Rd | 25 ++++ psych-2.6.1/psych/man/cfa.Rd |only psych-2.6.1/psych/man/cluster.cor.Rd | 2 psych-2.6.1/psych/man/cta.Rd | 12 ++ psych-2.6.1/psych/man/error.bars.Rd | 7 + psych-2.6.1/psych/man/fa.Rd | 47 ++++++--- psych-2.6.1/psych/man/factor.scores.Rd | 23 ++-- psych-2.6.1/psych/man/factor.stats.Rd | 9 + psych-2.6.1/psych/man/fparse.Rd | 44 +++++++- psych-2.6.1/psych/man/fsi.Rd |only psych-2.6.1/psych/man/irt.responses.Rd | 4 psych-2.6.1/psych/man/lmCor.Rd | 37 ++++--- psych-2.6.1/psych/man/omegaStats.Rd |only psych-2.6.1/psych/man/scatter.hist.Rd | 2 psych-2.6.1/psych/man/schmid.Rd | 3 psych-2.6.1/psych/man/score.alpha.Rd | 4 psych-2.6.1/psych/man/score.irt.Rd | 21 ++-- psych-2.6.1/psych/man/score.items.Rd | 13 +- psych-2.6.1/psych/man/sim.Rd | 3 psych-2.6.1/psych/man/sim.irt.Rd | 8 + psych-2.6.1/psych/man/splitHalf.Rd |only psych-2.6.1/psych/vignettes/scoring.Rnw | 4 71 files changed, 856 insertions(+), 293 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.4.1 dated 2025-09-23 and 1.5.0 dated 2026-02-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/source.R | 27 +++++++++++++++++++++++++++ 4 files changed, 38 insertions(+), 6 deletions(-)
Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cph] ,
Diego Hernangomez [aut] ,
James Joseph Balamuta [ctb, cre, aut] ,
Scott Chamberlain [ctb] ,
Kurt Hornik [ctb] ,
Brian Ripley [ctb] ,
Michael Koohafkan [ctb],
Mathew W. McLean [ctb]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between bibtex versions 0.5.1 dated 2023-01-26 and 0.5.2 dated 2026-02-03
bibtex-0.5.1/bibtex/inst/NEWS.Rd |only bibtex-0.5.2/bibtex/DESCRIPTION | 37 +++++++------- bibtex-0.5.2/bibtex/MD5 | 26 +++++---- bibtex-0.5.2/bibtex/NEWS.md | 33 ++++++++++++ bibtex-0.5.2/bibtex/R/bibtex.R | 2 bibtex-0.5.2/bibtex/R/utils.R | 2 bibtex-0.5.2/bibtex/README.md | 2 bibtex-0.5.2/bibtex/inst/bib/issue_trailing_space.bib |only bibtex-0.5.2/bibtex/tests/testthat/_snaps/devel |only bibtex-0.5.2/bibtex/tests/testthat/_snaps/examples.md | 4 - bibtex-0.5.2/bibtex/tests/testthat/_snaps/full_xampl.md | 15 +++-- bibtex-0.5.2/bibtex/tests/testthat/_snaps/preamble.md | 4 - bibtex-0.5.2/bibtex/tests/testthat/test-examples.R | 8 ++- bibtex-0.5.2/bibtex/tests/testthat/test-full_xampl.R | 4 + bibtex-0.5.2/bibtex/tests/testthat/test-previous-issues.R | 14 +++++ 15 files changed, 103 insertions(+), 48 deletions(-)