Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 3.0.3 dated 2025-08-22 and 5.0.0 dated 2025-11-29
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics: locate and tag peaks and valleys; label plot with the
equation of a fitted polynomial or other types of models including major
axis, quantile and robust and resistant regression. Labels for P-value,
R^2 or adjusted R^2 or information criteria for fitted models; parametric
and non-parametric correlation; label with ANOVA table for fitted models;
label with summary table for fitted models; annotations for multiple
comparisons with adjusted P-values. Model fit classes for which suitable
methods are provided by package 'broom' and 'broom.mixed' are supported as
well as user-defined wrappers on model fit functions. Scales and stats to
build volcano and quadrant plots based on
outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Samer Mouksassi [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.6.2 dated 2025-07-08 and 0.6.3 dated 2025-11-29
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ggpmisc-0.6.3/ggpmisc/R/utilities-fm.R |only ggpmisc-0.6.3/ggpmisc/R/utilities-gg.R |only ggpmisc-0.6.3/ggpmisc/R/utilities-labels.R | 140 + ggpmisc-0.6.3/ggpmisc/README.md | 36 ggpmisc-0.6.3/ggpmisc/build/partial.rdb |binary ggpmisc-0.6.3/ggpmisc/build/vignette.rds |binary ggpmisc-0.6.3/ggpmisc/inst/doc/cheat-sheet.Rmd | 34 ggpmisc-0.6.3/ggpmisc/inst/doc/cheat-sheet.html | 119 - ggpmisc-0.6.3/ggpmisc/inst/doc/user-guide.R | 8 ggpmisc-0.6.3/ggpmisc/inst/doc/user-guide.Rmd | 56 ggpmisc-0.6.3/ggpmisc/inst/doc/user-guide.html | 1005 +++++----- ggpmisc-0.6.3/ggpmisc/man/check_poly_formula.Rd | 15 ggpmisc-0.6.3/ggpmisc/man/distrmix_helper_fun.Rd |only ggpmisc-0.6.3/ggpmisc/man/fail_safe_formula.Rd | 2 ggpmisc-0.6.3/ggpmisc/man/figures/README-readme-04-1.png |binary ggpmisc-0.6.3/ggpmisc/man/figures/README-unnamed-chunk-1-1.png |binary ggpmisc-0.6.3/ggpmisc/man/find_peaks.Rd | 46 ggpmisc-0.6.3/ggpmisc/man/ggpmisc-ggproto.Rd | 13 ggpmisc-0.6.3/ggpmisc/man/ggpmisc-package.Rd | 65 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ggpmisc-0.6.3/ggpmisc/man/stat_quant_line.Rd | 48 ggpmisc-0.6.3/ggpmisc/man/swap_xy.Rd | 2 ggpmisc-0.6.3/ggpmisc/man/use_label.Rd | 2 ggpmisc-0.6.3/ggpmisc/tests/testthat/_snaps/stat-distrmix-eq |only ggpmisc-0.6.3/ggpmisc/tests/testthat/_snaps/stat-distrmix-line |only ggpmisc-0.6.3/ggpmisc/tests/testthat/test-check-poly-formula.R | 10 ggpmisc-0.6.3/ggpmisc/tests/testthat/test-stat-distrmix-eq.R |only ggpmisc-0.6.3/ggpmisc/tests/testthat/test-stat-distrmix-line.R |only ggpmisc-0.6.3/ggpmisc/vignettes/cheat-sheet.Rmd | 34 ggpmisc-0.6.3/ggpmisc/vignettes/user-guide.Rmd | 56 344 files changed, 2702 insertions(+), 2528 deletions(-)
Title: Multivariate Birth-Death Processes
Description: Computationally efficient functions to provide direct likelihood-based
inference for partially-observed multivariate birth-death processes. Such processes
range from a simple Yule model to the complex susceptible-infectious-removed model
in disease dynamics. Efficient likelihood evaluation facilitates maximum likelihood
estimation and Bayesian inference.
Author: Lam S.T. Ho [aut],
Marc A. Suchard [aut, cre],
Forrest W. Crawford [aut],
Jason Xu [ctb],
Vladimir N. Minin [ctb]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between MultiBD versions 0.2.0 dated 2016-07-28 and 1.0.0 dated 2025-11-29
MultiBD-0.2.0/MultiBD/vignettes/SIR-MCMC.md |only MultiBD-1.0.0/MultiBD/DESCRIPTION | 26 - MultiBD-1.0.0/MultiBD/MD5 | 66 ++-- MultiBD-1.0.0/MultiBD/NAMESPACE | 1 MultiBD-1.0.0/MultiBD/R/MultiBD.R | 3 MultiBD-1.0.0/MultiBD/R/RcppExports.R | 20 - MultiBD-1.0.0/MultiBD/R/SEIR_prob.R |only MultiBD-1.0.0/MultiBD/R/SIR_prob.R | 49 ++ MultiBD-1.0.0/MultiBD/README.md | 34 +- MultiBD-1.0.0/MultiBD/build/vignette.rds |binary MultiBD-1.0.0/MultiBD/inst/doc/SIR-MCMC.R | 30 - MultiBD-1.0.0/MultiBD/inst/doc/SIR-MCMC.Rmd | 2 MultiBD-1.0.0/MultiBD/inst/doc/SIR-MCMC.pdf |binary MultiBD-1.0.0/MultiBD/inst/doc/SIRtrans.R | 394 +++++++++++++++++++++--- MultiBD-1.0.0/MultiBD/inst/doc/SIRtrans.Rnw | 204 ++++++++---- MultiBD-1.0.0/MultiBD/inst/doc/SIRtrans.pdf |binary MultiBD-1.0.0/MultiBD/man/Eyam.Rd | 7 MultiBD-1.0.0/MultiBD/man/MultiBD.Rd | 17 - MultiBD-1.0.0/MultiBD/man/SEIR_prob.Rd |only MultiBD-1.0.0/MultiBD/man/SIR_prob.Rd | 36 +- MultiBD-1.0.0/MultiBD/man/bbd_prob.Rd | 19 - MultiBD-1.0.0/MultiBD/man/dbd_prob.Rd | 19 - MultiBD-1.0.0/MultiBD/src/Makevars | 2 MultiBD-1.0.0/MultiBD/src/Makevars.win | 3 MultiBD-1.0.0/MultiBD/src/RcppExports.cpp | 121 +++++-- MultiBD-1.0.0/MultiBD/src/SEIR_Cpp.cpp |only MultiBD-1.0.0/MultiBD/src/SIR_Cpp.cpp | 19 - MultiBD-1.0.0/MultiBD/src/ThreadPool.h | 34 +- MultiBD-1.0.0/MultiBD/src/bb_lt_Cpp.cpp | 26 - MultiBD-1.0.0/MultiBD/src/bb_lt_invert_Cpp.cpp | 103 +++--- MultiBD-1.0.0/MultiBD/src/bbd.h | 310 +++++++++--------- MultiBD-1.0.0/MultiBD/src/bbd_lt_invert_Cpp.cpp | 100 +++--- MultiBD-1.0.0/MultiBD/src/prod_lambda2_Cpp.cpp | 14 MultiBD-1.0.0/MultiBD/src/prod_mu2_Cpp.cpp | 14 MultiBD-1.0.0/MultiBD/src/tb_lt_Cpp.cpp |only MultiBD-1.0.0/MultiBD/src/tb_lt_invert_Cpp.cpp |only MultiBD-1.0.0/MultiBD/tests/testthat/test_SIR.R | 57 ++- 37 files changed, 1185 insertions(+), 545 deletions(-)
Title: Correlation-Based and Model-Based Predictor Pruning
Description: Provides functions for predictor pruning using association-based and model-based approaches. Includes corrPrune() for fast correlation-based pruning, modelPrune() for VIF-based regression pruning, and exact graph-theoretic algorithms (Eppstein–Löffler–Strash, Bron–Kerbosch) for exhaustive subset enumeration. Supports linear models, GLMs, and mixed models ('lme4', 'glmmTMB').
Author: Gilles Colling [aut, cre]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between corrselect versions 2.0.1 dated 2025-09-08 and 3.0.2 dated 2025-11-29
corrselect-2.0.1/corrselect/inst/doc/corrselect_upcoming.R |only corrselect-2.0.1/corrselect/inst/doc/corrselect_upcoming.Rmd |only corrselect-2.0.1/corrselect/inst/doc/corrselect_upcoming.html |only corrselect-2.0.1/corrselect/inst/doc/corrselect_vignette.R |only corrselect-2.0.1/corrselect/inst/doc/corrselect_vignette.Rmd |only corrselect-2.0.1/corrselect/inst/doc/corrselect_vignette.html |only corrselect-2.0.1/corrselect/vignettes/corrselect_upcoming.Rmd |only corrselect-2.0.1/corrselect/vignettes/corrselect_vignette.Rmd |only corrselect-3.0.2/corrselect/DESCRIPTION | 20 corrselect-3.0.2/corrselect/MD5 | 159 ++- corrselect-3.0.2/corrselect/NAMESPACE | 7 corrselect-3.0.2/corrselect/NEWS.md | 118 ++ corrselect-3.0.2/corrselect/R/CorrCombo.R | 51 corrselect-3.0.2/corrselect/R/MatSelect.R | 6 corrselect-3.0.2/corrselect/R/RcppExports.R | 4 corrselect-3.0.2/corrselect/R/assocSelect.R | 519 +++++----- corrselect-3.0.2/corrselect/R/cor_example.R |only corrselect-3.0.2/corrselect/R/corrPrune.R |only corrselect-3.0.2/corrselect/R/corrSelect.R | 460 ++++---- corrselect-3.0.2/corrselect/R/data.R |only corrselect-3.0.2/corrselect/R/modelPrune.R |only corrselect-3.0.2/corrselect/README.md | 349 ++++-- corrselect-3.0.2/corrselect/build/vignette.rds |binary corrselect-3.0.2/corrselect/data |only corrselect-3.0.2/corrselect/inst/doc/advanced.R |only corrselect-3.0.2/corrselect/inst/doc/advanced.Rmd |only corrselect-3.0.2/corrselect/inst/doc/advanced.html |only corrselect-3.0.2/corrselect/inst/doc/comparison.R |only corrselect-3.0.2/corrselect/inst/doc/comparison.Rmd |only corrselect-3.0.2/corrselect/inst/doc/comparison.html |only corrselect-3.0.2/corrselect/inst/doc/quickstart.R |only corrselect-3.0.2/corrselect/inst/doc/quickstart.Rmd |only corrselect-3.0.2/corrselect/inst/doc/quickstart.html |only corrselect-3.0.2/corrselect/inst/doc/theory.R |only corrselect-3.0.2/corrselect/inst/doc/theory.Rmd |only corrselect-3.0.2/corrselect/inst/doc/theory.html |only corrselect-3.0.2/corrselect/inst/doc/workflows.R |only corrselect-3.0.2/corrselect/inst/doc/workflows.Rmd |only corrselect-3.0.2/corrselect/inst/doc/workflows.html |only corrselect-3.0.2/corrselect/inst/extdata |only corrselect-3.0.2/corrselect/man/CorrCombo.Rd | 150 +- corrselect-3.0.2/corrselect/man/assocSelect.Rd | 233 ++-- corrselect-3.0.2/corrselect/man/bioclim_example.Rd |only corrselect-3.0.2/corrselect/man/cor_example.Rd |only corrselect-3.0.2/corrselect/man/corrPrune.Rd |only corrselect-3.0.2/corrselect/man/genes_example.Rd |only corrselect-3.0.2/corrselect/man/longitudinal_example.Rd |only corrselect-3.0.2/corrselect/man/modelPrune.Rd |only corrselect-3.0.2/corrselect/man/survey_example.Rd |only corrselect-3.0.2/corrselect/src/RcppExports.cpp | 14 corrselect-3.0.2/corrselect/src/method_greedy.cpp |only corrselect-3.0.2/corrselect/src/method_greedy.h |only corrselect-3.0.2/corrselect/tests/testthat.R |only corrselect-3.0.2/corrselect/tests/testthat/test-CorrCombo.R | 6 corrselect-3.0.2/corrselect/tests/testthat/test-assocSelect.R | 6 corrselect-3.0.2/corrselect/tests/testthat/test-corrMatSelect-bron-kerbosch.R | 5 corrselect-3.0.2/corrselect/tests/testthat/test-corrPrune.R |only corrselect-3.0.2/corrselect/tests/testthat/test-corrSelect.R | 32 corrselect-3.0.2/corrselect/tests/testthat/test-modelPrune.R |only corrselect-3.0.2/corrselect/vignettes/advanced.Rmd |only corrselect-3.0.2/corrselect/vignettes/benchmarks.R |only corrselect-3.0.2/corrselect/vignettes/comparison.Rmd |only corrselect-3.0.2/corrselect/vignettes/corrselect_vignette.R |only corrselect-3.0.2/corrselect/vignettes/quickstart.Rmd |only corrselect-3.0.2/corrselect/vignettes/theory.Rmd |only corrselect-3.0.2/corrselect/vignettes/workflows.Rmd |only corrselect-3.0.2/corrselect/vignettes/workflows_cache |only 67 files changed, 1196 insertions(+), 943 deletions(-)
Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD
intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512).
By placing this library in this package, we offer an efficient distribution system for
Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre],
Andrew J. Holbrook [aut],
Observational Health Data Sciences and Informatics [cph],
Johan Mabille [cph, ctb] ,
Sylvain Corlay [cph, ctb] ,
Alexander J. Lee [cph, ctb]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between RcppXsimd versions 7.1.6 dated 2021-01-21 and 7.1.6-1 dated 2025-11-29
RcppXsimd-7.1.6-1/RcppXsimd/DESCRIPTION | 10 ++-- RcppXsimd-7.1.6-1/RcppXsimd/MD5 | 20 +++----- RcppXsimd-7.1.6-1/RcppXsimd/NEWS.md | 6 ++ RcppXsimd-7.1.6-1/RcppXsimd/R/RcppXsimd.R | 3 - RcppXsimd-7.1.6-1/RcppXsimd/README.md | 8 +-- RcppXsimd-7.1.6-1/RcppXsimd/inst/CITATION | 23 ++++++---- RcppXsimd-7.1.6-1/RcppXsimd/man/RcppXsimd.Rd | 18 +++++++ RcppXsimd-7.1.6-1/RcppXsimd/src/Makevars | 2 RcppXsimd-7.1.6-1/RcppXsimd/src/Makevars.win | 5 -- RcppXsimd-7.1.6-1/RcppXsimd/src/RcppExports.cpp | 5 ++ RcppXsimd-7.1.6/RcppXsimd/src/FeatureDetector/cpu_aarch64.cpp |only RcppXsimd-7.1.6/RcppXsimd/src/FeatureDetector/cpu_aarch64.h |only 12 files changed, 63 insertions(+), 37 deletions(-)
Title: Local Political Actor Network Diachronic Analysis Tools
Description: Provides functions to prepare, visualize, and analyse diachronic
network data on local political actors, with a particular focus on
the development of local party systems and identification of actor groups.
Formalizes and automates a continuity diagram method that has been previously
applied in research on Czech local politics, e.g. Bubenicek and Kubalek (2010,
ISSN:1803-8220), Kubalek and Bubenicek (2012, ISSN:1803-8220), and Cmejrek,
Bubenicek, and Copik (2010, ISBN:978-80-247-3061-5). The package also
includes several example datasets derived from Czech municipal
elections, compiled from official election results, field research, and
previously published case studies on Czech local politics.
Author: Vaclav Bubenicek [aut, cre, cph] )
Maintainer: Vaclav Bubenicek <bubenicek@pef.czu.cz>
Diff between lpanda versions 0.1.1 dated 2025-09-01 and 0.2.0 dated 2025-11-29
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Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanes Bove et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [a [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
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Title: Tools and Infrastructure for Developing 'Scalable' 'HDF5'-Based
Methods
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, QR decomposition, and canonical correlation analysis) written
in C++ and R. These building blocks are designed not only for direct use,
but also as foundational components for developing new statistical methods
that must operate on datasets too large to fit in memory. The package
supports data provided either as 'HDF5' files or standard R objects, and is
intended for high-dimensional applications such as 'omics' and
precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
This is a re-admission after prior archival of version 0.99.32 dated 2022-03-29
Diff between BigDataStatMeth versions 0.99.32 dated 2022-03-29 and 1.0.2 dated 2025-11-29
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BigDataStatMeth-1.0.2/BigDataStatMeth/src/RcppExports.cpp | 1121 +- BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_CholeskyDec.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_QRDecomposition.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_SVD.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_SolveEqation.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_applyFunction.cpp | 701 - BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_bdPCA.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_bindDatasets.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blockCrossprod.cpp | 560 - BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blockNormalization.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blockSum.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blockmult.cpp | 351 BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blockmultSparse.cpp | 383 BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blocksubstract.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_blocktCrossprod.cpp | 586 - BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_createDiagonalDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_createEmptyDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_createGroup.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_createMatrix.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_diagonalOperations.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_eigenDecomposition.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_fileLocked.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_getDatasetDimensions.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_getDatasetList.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_getMatrixProperties.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_importFile.cpp | 625 - BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_imputation.cpp | 500 BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_invCholesky.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_matrixCorrelation.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_matrixDiagonals.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_matrixSdMean.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_moveDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_pseudoinverse.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_reduceDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_removeElement.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_removeLowData.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_removeMAF.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_sortDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_splitDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_subsetDataset.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_triangular.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_vectormatrix.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/hdf5_writeDimnames.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_blockmult.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_blocksubstract.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_blocksum.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_correlation.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_crossprod.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_scalarprod.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_tcrossprod.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/src/mem_weightprod.cpp |only BigDataStatMeth-1.0.2/BigDataStatMeth/vignettes/BigDataStatMeth.Rmd |only BigDataStatMeth-1.0.2/BigDataStatMeth/vignettes/references.bib | 103 223 files changed, 9047 insertions(+), 4229 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Create Upset Plots
Description: Create Upset plots using a combination of 'ggplot2' and 'patchwork'.
Author: Stevie Pederson [aut, cre]
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>
Diff between SimpleUpset versions 0.1.3 dated 2025-10-22 and 0.1.4 dated 2025-11-29
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/simpleUpSet.R | 1 - README.md | 4 ++-- build/vignette.rds |binary inst/doc/introduction.R | 8 ++++---- inst/doc/introduction.Rmd | 8 ++++---- inst/doc/introduction.html | 32 ++++++++++++++++---------------- man/figures |only tests/testthat/test-simpleUpSet.R | 14 ++++++++++++++ vignettes/introduction.Rmd | 8 ++++---- 11 files changed, 57 insertions(+), 43 deletions(-)
Title: Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Description: Provides a mechanism to plot an interactive map using 'Mapbox GL'
(<https://docs.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps,
and 'Deck.gl' (<https://deck.gl/>), a javascript library which uses 'WebGL' for
visualising large data sets.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between mapdeck versions 0.3.5 dated 2024-01-29 and 0.3.6 dated 2025-11-29
DESCRIPTION | 27 ++++++------ MD5 | 44 ++++++++++---------- NAMESPACE | 5 ++ NEWS.md | 6 ++ R/map_layer_h3.R | 13 ++++-- R/map_layer_path.R | 2 R/map_layer_scatterplot.R | 1 R/map_layer_text.R | 5 +- R/map_legend.R |only R/mapdeck_map_utilities.R | 1 inst/doc/mapdeck.html | 6 +- inst/htmlwidgets/lib/h3/h3.js | 8 +-- inst/htmlwidgets/lib/view_state/view_state.js | 3 - inst/htmlwidgets/mapdeck.js | 39 ++++++++++-------- inst/htmlwidgets/mapdeck_location.js | 55 +++++++++++++++----------- man/add_legend.Rd |only man/add_text.Rd | 3 + man/clear.Rd | 5 +- man/clear_legend.Rd | 34 +++++++++++++++- src/Makevars | 2 src/Makevars.win | 2 src/point.cpp | 4 - src/text.cpp | 2 tests/testthat/test-layer_polygon.R | 3 - 24 files changed, 173 insertions(+), 97 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.3-2 dated 2025-09-24 and 3.4-0 dated 2025-11-29
DESCRIPTION | 14 - MD5 | 81 ++++++---- NAMESPACE | 78 +++++++++ NEWS | 91 +++++++++++ R/densitylppVoronoi.R | 38 +++- R/diaglppm.R |only R/eval.linim.R |only R/lindirichlet.R | 12 + R/linequad.R | 234 +++++++++++++++++++++-------- R/linfun.R | 36 ++-- R/linim.R | 319 +++++++++++++++++++++++----------------- R/linnet.R | 83 ++++++---- R/linnetsurgery.R | 2 R/lintess.R | 62 +++++++ R/lintessmakers.R | 55 +++++- R/lpp.R | 17 +- R/lppm.R | 120 +++++++++++++-- R/qqplotLppm.R |only R/quadratcountlpp.R |only R/quadrattestlpp.R |only R/roclpp.R | 79 +++++---- build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/affine.linnet.Rd | 5 man/affine.lpp.Rd | 5 man/as.linfun.Rd | 34 +++- man/as.linim.Rd | 39 +++- man/as.linnet.psp.Rd | 35 +++- man/auc.lpp.Rd | 4 man/bw.voronoi.Rd | 24 ++- man/densityVoronoi.lpp.Rd | 22 ++ man/diagnose.lppm.Rd |only man/eem.lppm.Rd |only man/harmonise.linim.Rd |only man/integral.linim.Rd | 5 man/lineardirichlet.Rd | 19 ++ man/linequad.Rd | 20 ++ man/linim.apply.Rd |only man/lurking.lppm.Rd |only man/macros/defns.Rd | 3 man/parres.lppm.Rd |only man/qqplot.lppm.Rd |only man/quadrat.test.lpp.Rd |only man/quadratcount.lpp.Rd |only man/residuals.lppm.Rd |only man/roc.lpp.Rd | 4 man/spatstat.linnet-internal.Rd | 51 ++++++ tests/testsL.R | 17 +- 49 files changed, 1205 insertions(+), 405 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-22 0.1.2
2025-05-20 0.1.1
2025-02-20 0.1.0
Title: Making "Deduplicated" Functions
Description: Contains one main function deduped() which speeds up slow,
vectorized functions by only performing computations on the unique values
of the input and expanding the results at the end.
Author: Or Gadish [aut, cre, cph]
Maintainer: Or Gadish <orgadish@gmail.com>
Diff between deduped versions 0.2.0 dated 2023-11-07 and 0.3.0 dated 2025-11-29
DESCRIPTION | 10 - LICENSE | 4 MD5 | 29 ++-- NAMESPACE | 9 - NEWS.md | 37 +++-- R/deduped.R | 111 ++++++++------- R/deduped_map.R | 54 +++---- R/with_deduped.R |only README.md | 260 ++++++++++++++----------------------- inst/WORDLIST | 12 - man/deduped.Rd | 86 ++++++------ man/deduped_map.Rd | 113 ++++++++-------- man/with_deduped.Rd |only tests/testthat.R | 24 +-- tests/testthat/test-deduped.R | 100 +++++++------- tests/testthat/test-deduped_map.R | 18 +- tests/testthat/test-with_deduped.R |only 17 files changed, 424 insertions(+), 443 deletions(-)
Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values.
Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith,
and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>.
Other palettes available in this library have been derived from
'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and
'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between colourvalues versions 0.3.9 dated 2023-04-10 and 0.3.11 dated 2025-11-29
colourvalues-0.3.11/colourvalues/DESCRIPTION | 14 ++--- colourvalues-0.3.11/colourvalues/MD5 | 25 ++++------ colourvalues-0.3.11/colourvalues/NEWS.md | 8 +++ colourvalues-0.3.11/colourvalues/R/colour_values_hex.R | 12 ++-- colourvalues-0.3.11/colourvalues/R/colour_values_rgb.R | 6 -- colourvalues-0.3.11/colourvalues/R/palettes.R | 14 ++--- colourvalues-0.3.11/colourvalues/inst/include/colourvalues/api/api_hex.hpp | 22 ++++---- colourvalues-0.3.11/colourvalues/inst/include/colourvalues/api/api_rgb.hpp | 3 - colourvalues-0.3.11/colourvalues/inst/include/colourvalues/api/api_rgb_interleaved.hpp | 3 - colourvalues-0.3.11/colourvalues/inst/include/colourvalues/colours/generate_colours.hpp | 5 -- colourvalues-0.3.11/colourvalues/man/colour_palettes.Rd | 13 ++--- colourvalues-0.3.11/colourvalues/man/colour_values.Rd | 21 ++++++-- colourvalues-0.3.11/colourvalues/man/colour_values_rgb.Rd | 8 +-- colourvalues-0.3.9/colourvalues/inst/include/cardinal_cubic_b_spline.hpp |only 14 files changed, 83 insertions(+), 71 deletions(-)
Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in
'Tidy Eval' code that calculates the predictions. It works with
several databases back-ends because it leverages 'dplyr' and 'dbplyr'
for the final 'SQL' translation of the algorithm. It currently
supports lm(), glm(), randomForest(), ranger(), earth(),
xgb.Booster.complete(), cubist(), and ctree() models.
Author: Emil Hvitfeldt [aut, cre],
Edgar Ruiz [aut],
Max Kuhn [aut]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidypredict versions 0.5.1 dated 2024-12-19 and 1.0.0 dated 2025-11-29
tidypredict-0.5.1/tidypredict/tests/testthat/test-list.R |only tidypredict-1.0.0/tidypredict/DESCRIPTION | 16 tidypredict-1.0.0/tidypredict/MD5 | 147 tidypredict-1.0.0/tidypredict/NAMESPACE | 5 tidypredict-1.0.0/tidypredict/NEWS.md | 38 tidypredict-1.0.0/tidypredict/R/acceptable.R | 50 tidypredict-1.0.0/tidypredict/R/misc.R |only tidypredict-1.0.0/tidypredict/R/model-cubist.R | 72 tidypredict-1.0.0/tidypredict/R/model-earth.R | 40 tidypredict-1.0.0/tidypredict/R/model-glm.R | 4 tidypredict-1.0.0/tidypredict/R/model-glmnet.R |only tidypredict-1.0.0/tidypredict/R/model-lm.R | 130 tidypredict-1.0.0/tidypredict/R/model-partykit.R | 116 tidypredict-1.0.0/tidypredict/R/model-ranger.R | 105 tidypredict-1.0.0/tidypredict/R/model-rf.R | 123 tidypredict-1.0.0/tidypredict/R/model-xgboost.R | 214 - tidypredict-1.0.0/tidypredict/R/predict-column.R | 24 tidypredict-1.0.0/tidypredict/R/predict-fit.R | 11 tidypredict-1.0.0/tidypredict/R/predict-interval.R | 14 tidypredict-1.0.0/tidypredict/R/tidymodels.R | 24 tidypredict-1.0.0/tidypredict/R/tidypredict-package.R | 14 tidypredict-1.0.0/tidypredict/R/tidypredict_test.R | 268 + tidypredict-1.0.0/tidypredict/R/tree.R |only tidypredict-1.0.0/tidypredict/README.md | 2 tidypredict-1.0.0/tidypredict/build/vignette.rds |binary tidypredict-1.0.0/tidypredict/inst/doc/cubist.R | 9 tidypredict-1.0.0/tidypredict/inst/doc/cubist.Rmd | 13 tidypredict-1.0.0/tidypredict/inst/doc/cubist.html | 143 tidypredict-1.0.0/tidypredict/inst/doc/glm.html | 5 tidypredict-1.0.0/tidypredict/inst/doc/glmnet.R |only tidypredict-1.0.0/tidypredict/inst/doc/glmnet.Rmd |only tidypredict-1.0.0/tidypredict/inst/doc/glmnet.html |only tidypredict-1.0.0/tidypredict/inst/doc/lm.Rmd | 2 tidypredict-1.0.0/tidypredict/inst/doc/lm.html | 8 tidypredict-1.0.0/tidypredict/inst/doc/mars.html | 5 tidypredict-1.0.0/tidypredict/inst/doc/non-r.html | 5 tidypredict-1.0.0/tidypredict/inst/doc/ranger.R | 12 tidypredict-1.0.0/tidypredict/inst/doc/ranger.Rmd | 19 tidypredict-1.0.0/tidypredict/inst/doc/ranger.html | 97 tidypredict-1.0.0/tidypredict/inst/doc/rf.R | 10 tidypredict-1.0.0/tidypredict/inst/doc/rf.Rmd | 15 tidypredict-1.0.0/tidypredict/inst/doc/rf.html | 164 - tidypredict-1.0.0/tidypredict/inst/doc/save.html | 5 tidypredict-1.0.0/tidypredict/inst/doc/sql.html | 11 tidypredict-1.0.0/tidypredict/inst/doc/xgboost.R | 3 tidypredict-1.0.0/tidypredict/inst/doc/xgboost.Rmd | 5 tidypredict-1.0.0/tidypredict/inst/doc/xgboost.html | 209 - tidypredict-1.0.0/tidypredict/man/figures/logo.png |binary tidypredict-1.0.0/tidypredict/man/generate_case_when_trees.Rd |only tidypredict-1.0.0/tidypredict/man/generate_tree_node.Rd |only tidypredict-1.0.0/tidypredict/man/path_formula.Rd |only tidypredict-1.0.0/tidypredict/man/path_formulas.Rd |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/1.7.11.1 |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/3.1.2.1 |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-cubist.md | 49 tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-earth.md | 230 + tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-glm.md | 87 tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-glmnet.md |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-lm.md | 80 tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-partykit.md | 48 tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-ranger.md |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-rf.md | 1638 ---------- tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/model-xgboost.md | 287 - tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/tidymodels.md |only tidypredict-1.0.0/tidypredict/tests/testthat/_snaps/tree.md |only tidypredict-1.0.0/tidypredict/tests/testthat/helper-printing.R |only tidypredict-1.0.0/tidypredict/tests/testthat/test-misc.R |only tidypredict-1.0.0/tidypredict/tests/testthat/test-model-cubist.R | 90 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-earth.R | 334 +- tidypredict-1.0.0/tidypredict/tests/testthat/test-model-glm.R | 119 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-glmnet.R |only tidypredict-1.0.0/tidypredict/tests/testthat/test-model-lm.R | 147 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-partykit.R | 91 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-ranger.R | 104 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-rf.R | 67 tidypredict-1.0.0/tidypredict/tests/testthat/test-model-xgboost.R | 404 +- tidypredict-1.0.0/tidypredict/tests/testthat/test-sql.R | 5 tidypredict-1.0.0/tidypredict/tests/testthat/test-tidymodels.R |only tidypredict-1.0.0/tidypredict/tests/testthat/test-tidypredict_test.R | 11 tidypredict-1.0.0/tidypredict/tests/testthat/test-tree.R |only tidypredict-1.0.0/tidypredict/vignettes/cubist.Rmd | 13 tidypredict-1.0.0/tidypredict/vignettes/glmnet.Rmd |only tidypredict-1.0.0/tidypredict/vignettes/lm.Rmd | 2 tidypredict-1.0.0/tidypredict/vignettes/ranger.Rmd | 19 tidypredict-1.0.0/tidypredict/vignettes/rf.Rmd | 15 tidypredict-1.0.0/tidypredict/vignettes/xgboost.Rmd | 5 86 files changed, 2898 insertions(+), 3104 deletions(-)
Title: Formats Spatial Data for Use in Htmlwidgets
Description: Many packages use 'htmlwidgets' <https://CRAN.R-project.org/package=htmlwidgets>
for interactive plotting of spatial data.
This package provides functions for converting R objects, such as simple features,
into structures suitable for use in 'htmlwidgets' mapping libraries.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between spatialwidget versions 0.2.5 dated 2024-01-22 and 0.2.6 dated 2025-11-29
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- inst/doc/spatialwidget.html | 6 +++--- src/Makevars | 2 -- src/Makevars.win | 2 -- 5 files changed, 16 insertions(+), 20 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 3.0.2 dated 2025-02-17 and 5.0.0 dated 2025-11-29
DESCRIPTION | 17 +++++++++-------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/computingutil.R | 32 +++++++++++++++++++++++++++----- data/theoFitOde.rda |binary man/bootplot.Rd | 2 +- man/bootstrapFit.Rd | 14 +++++++++++++- 7 files changed, 60 insertions(+), 21 deletions(-)
Title: Kirill's Miscellaneous Functions
Description: A collection of useful functions not found anywhere else,
mainly for programming: Pretty intervals, generalized lagged
differences, checking containment in an interval, and an alternative
interface to assign().
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between kimisc versions 1.0.0 dated 2024-12-02 and 1.0.1 dated 2025-11-29
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 11 +++++++++++ R/thisfile.R | 10 +++++----- R/vswitch.R | 20 +------------------- tests/testthat/test-vswitch.R | 20 ++++++++++---------- 6 files changed, 38 insertions(+), 45 deletions(-)
Title: Categorical Scatter (Violin Point) Plots
Description: Provides two methods of plotting categorical scatter plots such
that the arrangement of points within a category reflects the density of
data at that region, and avoids over-plotting.
Author: Erik Clarke [aut, cre],
Scott Sherrill-Mix [aut],
Charlotte Dawson [aut]
Maintainer: Erik Clarke <erikclarke@gmail.com>
Diff between ggbeeswarm versions 0.7.2 dated 2023-04-29 and 0.7.3 dated 2025-11-29
ggbeeswarm-0.7.2/ggbeeswarm/build/partial.rdb |only ggbeeswarm-0.7.2/ggbeeswarm/vignettes/usage_examples.Rmd |only ggbeeswarm-0.7.3/ggbeeswarm/DESCRIPTION | 10 ggbeeswarm-0.7.3/ggbeeswarm/MD5 | 30 -- ggbeeswarm-0.7.3/ggbeeswarm/R/geom-beeswarm.R | 52 ++- ggbeeswarm-0.7.3/ggbeeswarm/R/geom-quasirandom.R | 31 +- ggbeeswarm-0.7.3/ggbeeswarm/R/ggbeeswarm-package.R | 5 ggbeeswarm-0.7.3/ggbeeswarm/R/position-beeswarm.R | 220 ++++++++------- ggbeeswarm-0.7.3/ggbeeswarm/R/position-quasirandom.R | 26 + ggbeeswarm-0.7.3/ggbeeswarm/build/vignette.rds |binary ggbeeswarm-0.7.3/ggbeeswarm/inst/doc/usageExamples.pdf |binary ggbeeswarm-0.7.3/ggbeeswarm/man/geom_beeswarm.Rd | 124 +++++--- ggbeeswarm-0.7.3/ggbeeswarm/man/geom_quasirandom.Rd | 72 +--- ggbeeswarm-0.7.3/ggbeeswarm/man/ggbeeswarm.Rd | 3 ggbeeswarm-0.7.3/ggbeeswarm/man/offset_beeswarm.Rd | 10 ggbeeswarm-0.7.3/ggbeeswarm/man/position_beeswarm.Rd | 35 +- ggbeeswarm-0.7.3/ggbeeswarm/man/position_quasirandom.Rd | 14 17 files changed, 371 insertions(+), 261 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Benoît Depaire [cre],
Gert Janssenswillen [aut],
Gerard van Hulzen [ctb],
Marijke Swennen [ctb],
Ivan Esin [ctb],
Felix Mannhardt [ctb],
Hasselt University [cph]
Maintainer: Benoît Depaire <benoit.depaire@uhasselt.be>
Diff between edeaR versions 0.9.5 dated 2025-07-09 and 1.0.0 dated 2025-11-29
DESCRIPTION | 26 - LICENSE | 2 MD5 | 403 ++++++++++++------------- NAMESPACE | 7 NEWS.md | 11 R/activity_frequency.R | 262 ++++++---------- R/activity_frequency_activity.R | 18 - R/activity_frequency_case.R | 34 +- R/activity_frequency_log.R | 12 R/activity_frequency_trace.R | 18 - R/activity_presence.R | 207 ++++++------ R/augment.R | 326 ++++++++++---------- R/calculate_queuing_length.R | 144 ++++---- R/calculate_queuing_times.R | 116 +++---- R/calculate_work_schedule_time.R | 222 ++++++------- R/contains_sequence.R | 100 +++--- R/create_minimal_activity_log.R | 16 R/create_precedence_df.R | 158 ++++----- R/edeaR.R | 71 ++-- R/end_activities.R | 270 +++++++--------- R/end_activities_activity.R | 32 - R/end_activities_case.R | 16 R/end_activities_log.R | 20 - R/end_activities_resource.R | 34 +- R/end_activities_resource_activity.R | 36 +- R/filter_activity.R | 164 ++++------ R/filter_activity_frequency.R | 332 +++++++++----------- R/filter_activity_instance.R | 157 ++++----- R/filter_activity_presence.R | 332 +++++++++----------- R/filter_case.R | 160 ++++----- R/filter_case_condition.R | 76 ++-- R/filter_endpoints.R | 256 +++++++-------- R/filter_endpoints_condition.R | 304 ++++++++---------- R/filter_endpoints_percentile.R | 54 +-- R/filter_endpoints_sets.R | 46 +- R/filter_flow_time.R | 79 ++++ R/filter_idle_time.R | 57 +++ R/filter_idle_time_percentage.R | 28 - R/filter_idle_time_threshold.R | 36 +- R/filter_infrequent_flows.R | 115 +++++-- R/filter_lifecycle.R | 180 ++++------- R/filter_lifecycle_presence.R | 298 ++++++++---------- R/filter_precedence.R | 410 ++++++++++++------------- R/filter_precedence_condition.R | 287 ++++++++--------- R/filter_precedence_resource.R | 399 +++++++++++++----------- R/filter_processing_time.R | 312 +++++++++---------- R/filter_processing_time_percentile.R | 22 - R/filter_processing_time_threshold.R | 28 - R/filter_resource.R | 157 ++++----- R/filter_resource_frequency.R | 321 +++++++++---------- R/filter_throughput_time.R | 258 +++++++--------- R/filter_throughput_time_percentile.R | 28 - R/filter_throughput_time_threshold.R | 42 +- R/filter_time_period.R | 441 ++++++++++++--------------- R/filter_trace.R | 55 ++- R/filter_trace_frequency.R | 254 +++++++-------- R/filter_trace_frequency_percentile.R | 84 ++--- R/filter_trace_frequency_threshold.R | 48 +- R/filter_trace_length.R | 270 +++++++--------- R/filter_trace_length_percentile.R | 26 - R/filter_trace_length_threshold.R | 42 +- R/filter_trim.R | 354 +++++++++------------- R/filter_trim_lifecycle.R | 308 ++++++++----------- R/generate_pattern_dummies.R | 88 ++--- R/groupby_helpers.R |only R/idle_time.R | 313 ++++++++----------- R/idle_time_case.R | 112 +++--- R/idle_time_flow.R | 128 +++---- R/idle_time_log.R | 30 - R/idle_time_resource.R | 111 +++--- R/idle_time_trace.R | 39 +- R/ifilter.R | 2 R/number_of_repetitions.R | 465 ++++++++++++---------------- R/number_of_selfloops.R | 466 ++++++++++++----------------- R/number_of_traces.R | 110 +++--- R/plot.activity_frequency.R | 106 +++--- R/plot.activity_presence.R | 40 +- R/plot.end_activity.R | 120 ++++--- R/plot.idle_time.R | 95 ++--- R/plot.number_of_repetitions.R | 186 +++++------ R/plot.number_of_selfloops.R | 185 +++++------ R/plot.processing_time.R | 132 ++++---- R/plot.r | 262 ++++++++-------- R/plot.referral_matrix.R | 38 +- R/plot.resource_frequency.R | 130 ++++---- R/plot.resource_involvement.R | 95 ++--- R/plot.resource_specialisation.R | 97 ++---- R/plot.start_activities.R | 118 ++++--- R/plot.throughput_time.R | 96 +++-- R/plot.trace_coverage.R | 104 +++--- R/plot.trace_length.R | 92 ++--- R/processing_time.R | 404 +++++++++++-------------- R/processing_time_activity.R | 56 +-- R/processing_time_activity_instance.R | 112 +++--- R/processing_time_case.R | 56 +-- R/processing_time_log.R | 32 - R/processing_time_resource.R | 56 +-- R/processing_time_resource_activity.R | 60 +-- R/processing_time_trace.R | 52 +-- R/redo_repetitions_referral_matrix.R | 114 +++---- R/redo_selfloops_referral_matrix.R | 108 ++---- R/repetitions_all.R | 430 +++++++++++++------------- R/repetitions_redo.R | 430 +++++++++++++------------- R/repetitions_repeat.R | 416 ++++++++++++------------- R/resource_frequency.R | 304 +++++++----------- R/resource_frequency_activity.R | 20 - R/resource_frequency_case.R | 26 - R/resource_frequency_log.R | 36 +- R/resource_frequency_resource.R | 24 - R/resource_frequency_resource_activity.R | 34 +- R/resource_involvement.R | 212 +++++-------- R/resource_involvement_case.R | 22 - R/resource_involvement_resource.R | 24 - R/resource_involvement_resource_activity.R | 30 - R/resource_specialisation.R | 234 ++++++-------- R/resource_specialisation_activity.R | 22 - R/resource_specialisation_case.R | 28 - R/resource_specialisation_log.R | 36 +- R/resource_specialisation_resource.R | 20 - R/rework_base.R | 76 ++-- R/selfloops_all.R | 428 +++++++++++++------------- R/selfloops_redo.R | 428 +++++++++++++------------- R/selfloops_repeat.R | 404 ++++++++++++------------- R/setdiff.R | 78 ++-- R/size_of_repetitions.R | 331 ++++++++------------ R/size_of_selfloops.R | 344 ++++++++------------- R/start_activities.R | 267 +++++++--------- R/start_activities_activity.R | 46 +- R/start_activities_case.R | 18 - R/start_activities_log.R | 20 - R/start_activities_resource.R | 38 +- R/start_activities_resource_activity.R | 40 +- R/throughput_time.R | 349 +++++++++------------ R/throughput_time_activity.R | 49 +-- R/throughput_time_activity_instance.R | 66 ++-- R/throughput_time_case.R | 66 ++-- R/throughput_time_log.R | 34 +- R/throughput_time_trace.R | 45 +- R/trace_coverage.R | 182 ++++------- R/trace_coverage_case.R | 30 - R/trace_coverage_log.R | 24 - R/trace_coverage_trace.R | 30 - R/trace_length.R | 271 ++++++---------- R/trace_length_case.R | 14 R/trace_length_log.R | 26 - R/trace_length_trace.R | 40 +- R/utils.R | 180 +++++------ R/work_schedule.R | 326 ++++++++++---------- README.md | 3 inst/doc/filters.R | 2 inst/doc/filters.Rmd | 2 inst/doc/filters.html | 28 - inst/doc/metrics.html | 21 - inst/doc/queue.html | 9 inst/doc/work_schedules.html | 9 man/activity_frequency.Rd | 34 -- man/activity_presence.Rd | 49 --- man/calculate_queuing_times.Rd | 11 man/edeaR.Rd | 8 man/end_activities.Rd | 34 -- man/filter_activity.Rd | 16 man/filter_activity_frequency.Rd | 19 - man/filter_activity_instance.Rd | 35 -- man/filter_activity_presence.Rd | 19 - man/filter_case.Rd | 16 man/filter_endpoints.Rd | 19 - man/filter_endpoints_condition.Rd | 17 - man/filter_flow_time.Rd | 8 man/filter_idle_time.Rd | 8 man/filter_infrequent_flows.Rd | 20 - man/filter_lifecycle.Rd | 40 -- man/filter_lifecycle_presence.Rd | 24 - man/filter_precedence.Rd | 19 - man/filter_precedence_condition.Rd | 11 man/filter_precedence_resource.Rd | 22 - man/filter_processing_time.Rd | 19 - man/filter_resource.Rd | 16 man/filter_resource_frequency.Rd | 19 - man/filter_throughput_time.Rd | 19 - man/filter_time_period.Rd | 25 - man/filter_trace.Rd | 16 man/filter_trace_frequency.Rd | 19 - man/filter_trace_length.Rd | 38 -- man/filter_trim.Rd | 25 - man/filter_trim_lifecycle.Rd | 29 - man/idle_time.Rd | 34 -- man/ifilter.Rd | 68 ---- man/number_of_repetitions.Rd | 34 -- man/number_of_selfloops.Rd | 34 -- man/number_of_traces.Rd | 8 man/processing_time.Rd | 34 -- man/redo_repetitions_referral_matrix.Rd | 8 man/redo_selfloops_referral_matrix.Rd | 8 man/resource_frequency.Rd | 34 -- man/resource_involvement.Rd | 24 - man/resource_specialisation.Rd | 29 - man/size_of_repetitions.Rd | 34 -- man/size_of_selfloops.Rd | 34 -- man/start_activities.Rd | 34 -- man/throughput_time.Rd | 34 -- man/trace_coverage.Rd | 36 -- man/trace_length.Rd | 62 --- vignettes/filters.Rmd | 2 203 files changed, 10377 insertions(+), 11691 deletions(-)
Title: Collection of Methods to Detect Dichotomous, Polytomous, and
Continuous Differential Item Functioning (DIF)
Description: Methods to detect differential item functioning (DIF) in dichotomous, polytomous,
and continuous items, using both classical and modern approaches. These include
Mantel-Haenszel procedures, logistic regression (including ordinal models), and
regularization-based methods such as LASSO. Uniform and non-uniform DIF effects
can be detected, and some methods support multiple focal groups. The package
also provides tools for anchor purification, rest score matching, effect size
estimation, and DIF simulation. See Magis, Beland, Tuerlinckx, and De Boeck
(2010, Behavior Research Methods, 42, 847–862, <doi:10.3758/BRM.42.3.847>) for
a general overview.
Author: David Magis [aut] ,
Sebastien Beland [aut, cre] ,
Carl F. Falk [aut] ,
Gilles Raiche [aut] ,
Adela Hladka [aut] ),
Josh Gilbert [aut]
Maintainer: Sebastien Beland <sebastien.beland@umontreal.ca>
Diff between difR versions 6.0.0 dated 2025-05-26 and 6.1.0 dated 2025-11-29
difR-6.0.0/difR/R/difMantel.poly.R |only difR-6.0.0/difR/man/difMantel.poly.Rd |only difR-6.1.0/difR/DESCRIPTION | 42 - difR-6.1.0/difR/MD5 | 50 - difR-6.1.0/difR/NAMESPACE | 15 difR-6.1.0/difR/NEWS | 12 difR-6.1.0/difR/R/Continuous.R |only difR-6.1.0/difR/R/ILHTEdif.R |only difR-6.1.0/difR/R/Logistik.R | 175 ++-- difR-6.1.0/difR/R/LogistikPoly.R | 60 - difR-6.1.0/difR/R/difContinuous.R |only difR-6.1.0/difR/R/difLogistic.R | 1115 ++++++++++++++++++------------ difR-6.1.0/difR/R/difMH.R | 1159 ++++++++++++++++++-------------- difR-6.1.0/difR/R/difMantelPoly.R |only difR-6.1.0/difR/R/difSIBTEST.R | 848 +++++++++++++---------- difR-6.1.0/difR/R/lassoDIF.ABWIC.R | 66 + difR-6.1.0/difR/R/liu_agresti_ccor.R | 187 +++-- difR-6.1.0/difR/R/mantelHaenszel.R | 177 ++-- difR-6.1.0/difR/R/private.R |only difR-6.1.0/difR/R/zzz-globals.R |only difR-6.1.0/difR/TODO | 8 difR-6.1.0/difR/man/Continuous.Rd |only difR-6.1.0/difR/man/ILHTEdif.Rd |only difR-6.1.0/difR/man/Logistik.Rd | 445 +++++++----- difR-6.1.0/difR/man/difContinuous.Rd |only difR-6.1.0/difR/man/difLogistic.Rd | 738 ++++++++++++-------- difR-6.1.0/difR/man/difMH.Rd | 611 ++++++++++------ difR-6.1.0/difR/man/difMantelPoly.Rd |only difR-6.1.0/difR/man/difR-package.Rd | 31 difR-6.1.0/difR/man/difSIBTEST.Rd | 466 ++++++++---- difR-6.1.0/difR/man/liu_agresti_ccor.Rd | 57 + difR-6.1.0/difR/man/plot_lasso_paths.Rd | 2 32 files changed, 3832 insertions(+), 2432 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 (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 al. [...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 0.8.12 dated 2025-10-31 and 0.8.13 dated 2025-11-29
DESCRIPTION | 10 - MD5 | 32 +-- R/Optimal_Dispersion.R | 17 + R/blocked_anticlustering.R |only R/categories_to_binary.R | 58 ++++-- R/input-validation.R | 34 +++ R/nn-centroid-clustering.R | 2 R/wrapper-anticlustering.R | 110 +++++++++--- build/vignette.rds |binary inst/doc/Anticlustering_in_2025.html | 230 +++++++++++++------------- inst/doc/Categorical_vars.R | 32 +++ inst/doc/Categorical_vars.Rmd | 55 +++++- inst/doc/Categorical_vars.html | 240 ++++++++++++++++++++++++---- inst/doc/Speeding_up_anticlustering.html | 26 +-- inst/tinytest/test-blocked-anticlustering.R |only man/anticlustering.Rd | 91 +++++++--- man/categories_to_binary.Rd | 44 +++-- vignettes/Categorical_vars.Rmd | 55 +++++- 18 files changed, 758 insertions(+), 278 deletions(-)
Title: Computing Log-Transformed Kernel Density Estimates for Positive
Data
Description: Computes log-transformed kernel density estimates for positive data using a variety of kernels. It follows the methods described in Jones, Nguyen and McLachlan (2018) <doi:10.21105/joss.00870>.
Author: Hien D. Nguyen [aut],
Andrew T. Jones [aut],
Geoffrey J. McLachlan [aut],
Andrew Thomas Jones [cre]
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between logKDE versions 0.3.2 dated 2018-08-09 and 0.3.3 dated 2025-11-29
DESCRIPTION | 32 +++++++++++++++++------- MD5 | 30 ++++++++++++---------- NEWS.md | 6 ++++ R/logKDE.R | 4 +-- README.md | 50 ++++++++++++++++++-------------------- build/vignette.rds |binary man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |binary man/figures/README-example2-1.png |binary man/figures/README-example3-1.png |binary man/figures/README-example4-1.png |binary man/logdensity.Rd | 16 +++++++++--- man/logdensity_fft.Rd | 16 +++++++++--- src/Makevars.txt |only src/Makevars.win |only src/RcppExports.cpp | 5 +++ src/logKDE.cpp | 1 17 files changed, 102 insertions(+), 58 deletions(-)